Genetic Transformation

GENETIC
TRANSFORMATION
Edited by María Alejandra Alvarez

Genetic Transformation
Edited by María Alejandra Alvarez

Published by InTech
Janeza Trdine 9, 51000 Rijeka, Croatia
Copyright © 2011 InTech
All chapters are Open Access articles distributed under the Creative Commons
Non Commercial Share Alike Attribution 3.0 license, which permits to copy, distribute, transmit, and adapt the work in any medium, so long as the original work is properly cited. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source.
Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published articles. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book.
Publishing Process Manager Dragana Manestar
Technical Editor Teodora Smiljanic
Cover Designer Jan Hyrat
Image Copyright Sashkin, 2011. Used under license from Shutterstock.com
First published August, 2011
Printed in Croatia
A free online edition of this book is available at www.intechopen.com
Additional hard copies can be obtained from [e-mail]

Genetic Transformation, Edited by María Alejandra Alvarez
p. cm.
ISBN 978-953-307-364-4

free online editions of InTech
Books and Journals can be found at www.intechopen.com Contents
Preface IX
Part 1

Agrobacterium: New Insights into a Natural Engineer 1

Chapter 1

Agrobacterium-Mediated Genetic Transformation:
History and Progress 3
Minliang Guo, Xiaowei Bian, Xiao Wu and Meixia Wu

Chapter 2

Structure-Function Analysis of Transformation Events
Yuri N. Zhuravlev and Vladik A. Avetisov

Part 2

29

Plant Transformation: Improving Quality of Fruits,
Crops and Trees - Molecular Farming 53

Chapter 3

Genetic Transformation in Tomato: Novel Tools to Improve Fruit Quality and Pharmaceutical Production 55
Antonio Di Matteo, Maria Manuela Rigano,
Adriana Sacco, Luigi Frusciante and Amalia Barone

Chapter 4

Genetic Transformation Strategies in Fruit Crops
Humberto Prieto

Chapter 5

Citrus Transformation: Challenges and Prospects 101
Vicente Febres, Latanya Fisher, Abeer Khalaf and Gloria A. Moore

Chapter 6

Evaluation of Factors Affecting European Plum
(Prunus domestica L.) Genetic Transformation 123
Yuan Song, Fatih Ali Canli, Farida Meerja, Xinhua Wang,
Hugh A. L. Henry, Lizhe An and Lining Tian

Chapter 7

Genetic Transformation of Wheat:
Advances in the Transformation Method and Applications for Obtaining Lines with Improved Bread-Making Quality and Low Toxicity in Relation to Celiac Disease 135
Javier Gil-Humanes, Carmen Victoria Ozuna, Santiago Marín,
Elena León, Francisco Barro and Fernando Pistón

81

VI

Contents

Chapter 8

Maize Transformation to Obtain Plants
Tolerant to Viruses by RNAi Technology 151
Newton Portilho Carneiro and Andréa Almeida Carneiro

Chapter 9

Genetic Transformation of Triticeae Cereals for Molecular Farming 171
Goetz Hensel

Chapter 10

Genetic Transformation of Forest Trees 191
Osvaldo A. Castellanos-Hernández, Araceli Rodríguez-Sahagún,
Gustavo J. Acevedo-Hernández and Luis R. Herrera-Estrella

Chapter 11

Agrobacterium-Mediated Transformation of Indonesian Orchids for Micropropagation 215
Endang Semiarti, Ari Indrianto, Aziz Purwantoro,
Yasunori Machida and Chiyoko Machida

Chapter 12

Transient Transformation of Red Algal Cells:
Breakthrough Toward Genetic Transformation of Marine Crop Porphyra Species 241
Koji Mikami, Ryo Hirata, Megumu Takahashi,
Toshiki Uji and Naotsune Saga

Part 3

Plant Transformation as a Tool for Regulating Secondary Metabolism 259

Chapter 13

Application of Agrobacterium Rol Genes in Plant Biotechnology: A Natural Phenomenon of Secondary Metabolism Regulation 261
Victor P Bulgakov, Yuri N Shkryl, Galina N Veremeichik,
Tatiana Y Gorpenchenko and Yuliya V Inyushkina

Chapter 14

Transformed Root Cultures of Solanum dulcamara L.:
A Model for Studying Production of Secondary Metabolites 271
Amani M. Marzouk, Stanley G. Deans,
Robert J. Nash and Alexander I. Gray

Chapter 15

Genetic Transformation for Metabolic Engineering of Tropane Alkaloids
María Alejandra Alvarez and Patricia L. Marconi

Chapter 16

Transgenic Plants for Enhanced
Phytoremediation – Physiological Studies 305
Paulo Celso de Mello- Farias, Ana Lúcia Soares Chaves and Claiton Leoneti Lencina

291

Preface
It has been more than twenty five years now since the first transformed plant was reported. Plant transgenesis has evolved since those first attempts; the advances have led to the elucidation of numerous aspects of plant biology, physiology, and
Agrobacterium biology. Even more spectacular is the impact of plant transformation on crop improvement. To this date, transgenic crops represent a 10 % of the 1.5 billion hectares of cropland worldwide, and constitute one of the main sources of incomes for countries like the USA (66.8 million hectares), Brazil (25.4), Argentina (22.9), India
(9.4), Canada (8.8), China (3.5), Paraguay (2.6), Pakistan (2.4), South Africa (2.2) and
Uruguay with 1.1 million hectares. Also, plant transformation had influence on fruit and forest improvement and the development of desirable traits for ornamental plant breeders. Moreover, the significant advances made in the use of transformed plants for the production of recombinant proteins and for the engineering of secondary metabolism pathways have made a new easy-scalable and economical rendering platform available to the pharmaceutical industry.
Chapters in this book represent selected examples of the advances that are currently undergoing in this field. In the first section, the history and progress of Agrobacterium utilization as a transformation vector is presented along with a chapter dedicated to the analysis of the related events from a structure-functional analysis. Also the physiological and molecular background of phytoremediation is analyzed.
In the second section, the subject of plant improvement is widely covered in the chapters related to the amelioration of crops, fruits and flowers with a couple of chapters dedicated to the last advances in molecular farming and RNAi technology.
Finally, in the last section the paramount contribution that plant transformation has made on secondary metabolism is reviewed.
I would like to thank each of the authors for their great efforts in producing their articles. I am sure the readers will appreciate the contribution each of the researchers has made and will recognize the value of each chapter.

X

Preface

Finally, I would like to thank the staff of the InTech Open Access Publisher for their invaluable support along the process of publishing this book, particularly Ms. Dragana
Manestar and Ms. Natalia Reinic.

Dr. María Alejandra Alvarez
National Scientific and Technical Research Council (CONICET)
Buenos Aires
Argentina

Part 1
Agrobacterium:
New Insights into a Natural Engineer

1
Agrobacterium-Mediated Genetic
Transformation: History and Progress
Minliang Guo*, Xiaowei Bian, Xiao Wu and Meixia Wu

College of Bioscience and Biotechnology, Yangzhou University, Jiangsu,
P. R. China
1. Introduction
Agrobacterium tumefaciens is a Gram-negative soil phytopathogenic bacterium that causes the crown gall disease of dicotyledonous plants, which is characterized by a tumorous phenotype. It induces the tumor by transferring a segment of its Ti plasmid DNA
(transferred DNA, or T-DNA) into the host genome and genetically transforming the host.
One century has past after A. tumefaciens was firstly identified as the causal agent of crown gall disease (Smith & Townsend, 1907). However, A. tumefaciens is still central to diverse fields of biological and biotechnological research, ranging from its use in plant genetic engineering to representing a model system for studies of a wide variety of biological processes, including bacterial detection of host signaling chemicals, intercellular transfer of macromolecules, importing of nucleoprotein into plant nuclei, and interbacterial chemical signaling via autoinducer-type quorum sensing (McCullen & Binns, 2006; Newton & Fray,
2004; Pitzschke & Hirt, 2010). Therefore, the molecular mechanism underlying the genetic transformation has been the focus of research for a wide spectrum of biologists, from bacteriologists to molecular biologists to botanists.
1.1 History of Agrobacterium tumefaciens research
A. tumefaciens is capable of inducing tumors at wound sites of hundreds of dicotyledonous plants, and some monocots and gymnosperms (De Cleene and De Ley, 1976), which may happen on the stems, crowns and roots of the host. At the beginning of the last century, crown gall disease was considered a major problem in horticultural production. This disease caused significant loss of crop yield in many perennial horticultural crops (Kennedy, 1980), such as cherry (Lopatin, 1939), apple (Ricker et al., 1959), and grape (Schroth et al., 1988). All these horticultural crops are woody species and propagated by grafting scions onto rootstocks. The grafting wounds are usually covered by soil and thus provide an excellent infection point for the soil-borne A. tumefaciens. In 1941, it was proved that crown gall tumor tissue could be permanently transformed by only transient exposure to the pathogen of A. tumefaciens (White and Braun, 1941). Thereafter, a ‘tumor-inducing capacity’ was proposed to be transmitted from A. tumefaciens to plant tissue (Braun, 1947; Braun and Mandle, 1948).
Twenty years late, molecular techniques provided the first evidence that crown gall tumors,
*

corresponding author: [e-mail]

4

Genetic Transformation

cultured axenically, contained DNA of A. tumefaciens origin, which implied that host cells were genetically transformed by Agrobacterium (Schilperoort et al., 1967). In 1974, the tumorinducing (Ti) plasmid was identified to be essential for the crown gall-inducing ability (Van
Larebeke et al., 1974; Zaenen et al., 1974). Southern hybridization turned out to prove that the bacterial DNA transferred to host cells originates from the Ti plasmid and ultimately resulted in the discovery of T-DNA (transferred DNA), specific segments transferred from
A. tumefaciens to plant cells (Chilton et al., 1977; Chilton et al., 1978; Depicker et al., 1978).
The T-DNA is referred to as the T-region when located on the Ti-plasmid. The T-region is delimited by 25-bp directly repeated sequences, which are called T-DNA border sequences.
The T-DNAs, when transferred to plant cells, encode enzymes for the synthesis of (1) the plant hormones auxin and cytokinin and (2) strain-specific low molecular weight amino acid and sugar phosphate derivatives called opines. The massive accumulation of auxin and cytokinin in transformed plant cells causes uncontrolled cell proliferation and the synthesis of nutritive opines that can be metabolized specifically by the infecting A. tumefaciens strain.
Thus, the opine-producing tumor effectively creates an ecological niche specifically suited to the infecting A. tumefaciens strain (Escobar & Dandekar, 2003; Gelvin, 2003). Besides the TDNAs, Ti-plasmid also contains most of the genes that are required for the transfer of the TDNAs from A. tumefaciens to the plant cell.
Initial study of these plant tumors was intended to reveal the molecular mechanism that may be relevant to animal neoplasia. Although no relationship was found between animal and plant tumors, A. tumefaciens and plant tumor were proved to be of intrinsic interest because the tumorous growth was shown to result from the transfer of T-DNA from bacterial Ti-plasmid to the plant cell and the stable integration of the T-DNA to plant genome. The demonstration that wild-type T-DNA coding region can be replaced by any
DNA sequence without any effect on its transfer from A. tumefaciens to the plant inspired the promise that A. tumefaciens might be used as gene vector to deliver genetic material into plants. In the early of 1980’s, two events about A. tumefaciens mediated genetic transformation signaled the beginning of the era of plant genetic engineering. First, A. tumefaciens and its Ti-plasmid were used as a gene vector system to produce the first transgenic plant (Zambryski et al., 1983). The healthy transgenic plants had the ability to transmit the disarmed T-DNA, including the foreign genes, to their progeny. Second, nonplant antibiotic-resistance genes, for example, a bacterial kanamycin-resistance gene, could be instructed to function efficiently in plant cells by splicing a plant-active promoter to the coding region of the bacterial genes. This enabled accurate selection of transformed plant cells (Beven, 1984). The eventual success of using A. tumefaciens as a gene vector to create transgenic plants was viewed as a prospect and a “wish”. The future of A. tumefaciens as a gene vector for crop improvement began to look bright. During the 1990’s, maize, a monocot plant species that was thought to be outside the A. tumefaciens “normal host range”, was successfully transformed by A. tumefaciens (Chilton, 1993). Today, many agronomically and horticulturally important plant species are routinely transformed by A. tumefaciens, and the list of plant species that can be genetically transformed by A. tumefaciens seems to grow daily (Gelvin, 2003). At present, many economically important crops, such as corn, soybean, cotton, canola, potatoes, and tomatoes, were improved by A. tumefaciens–mediated genetic transformation and these transgenic varieties are growing worldwide (Valentine, 2003). By now, the species that are susceptible to A. tumefaciens–mediated transformation were broadened to yeast, fungi, and mammalian cells (Lacroix et al., 2006b).

Agrobacterium-Mediated Genetic Transformation: History and Progress

5

In the new century, intrests of most Agrobacterium community shifted to the transfer channel and host. Most recent important articles on Agrobacterium-mediated T-DNA transfer are to explore the molecular mechanism of T-complex targeting to plant nucleus. Recent progresses of these aspects of Agrobacterium-mediated genetic transformation will be the emphases of this chapter and be discussed in the following related sections.
1.2 Basic process of A. tumefaciens–mediated genetic transformation
The process of A. tumefaciens–mediated genetic transformation is a long journey. For the sake of description, many authors divided this process into several steps (Guo et al., 2009a;
Guo, 2010; McCullen & Binns, 2006; Pitzschke & Hirt, 2010). Here, we arbitrarily and simply split it into five steps: (1) Sensing of plant chemical signals and inducing of virulence (vir) proteins. The chemical signals released by wounded plant are perceived by a VirA/VirG two-component system of A. tumefaciens, which leads to the transcription of virulence (vir) gene promoters and thus the expression of vir proteins. (2) T-DNA processing. T-DNA is nicked by VirD2/VirD1 from the T-region of Ti plasmid and forms a single-stranded linear
T-strand with one VirD2 molecule covalently attached to the 5′end of the T-strand. (3)
Attaching of A. tumefaciens to plant and transferring of T-complex to plant cell. A. tumefaciens cell attaches to plant and transfers the T-complex from A. tumefaciens to plant cell by a
VirD4/B T4SS transport system. (4) Targeting of T-complex to plant cell nucleus and integrating of T-DNA into plant genome. The T-complex is transported into the nucleoplasm under the assistance of some host proteins and then integrated into plant genomic DNA. (5) Expressing of T-DNA in plant cell and inducing of plant tumor. The TDNA genes encode phytohormone synthases that lead to the uncontrolled proliferation of plant cell and opine synthases that provide nutritive compounds to infecting bacteria.

2. Events happening in Agrobacteriun
A. tumefaciens can perceive the signal molecules from plants and recognize the competent hosts. To fulfill the infection, Agrobacterium must respond to the signal molecules. The respondence occuring in Agrobacterium includes host recognition, virulence gene expression, and T-DNA processing.
2.1 Sensing of plant signal molecules and vir gene induction
Many genes are involved in A. tumefaciens-mediated T-DNA transfer, but most of the genes required for T-DNA transfer are found on the vir region of Ti plasmid. This vir region comprises at least six essential operons (virA, virB, virC, virD, virE, and virG,) and two nonessential operons (virF and virH) encoding approximate 25 proteins (Gelvin, 2000; Zhu et al.,
2000; Ziemienowicz, 2001). These proteins are termed virulence (vir) proteins and required for the sensing of plant signal molecules as well as the processing, transfer, and nuclear localization of T-DNA, and the integration of T-DNA into the plant genome. The protein number encoded by each operon differs; virA, virG and virF encode only one protein; virE, virC, and virH encode two proteins; virD encodes four proteins and virB encodes eleven proteins. Only virA and virG are constitutively transcripted. The transcription of all other vir operons in vir region is coordinately induced during infection by a family of host-released phenolic compounds in combination with some monosaccharides and extracellular acidity in the range of pH 5.0 to 5.8. Virtually all of the genes in the vir region are tightly regulated by two proteins VirA and VirG encoded by virA operon and virG operon (Lin et al., 2008).

6

Genetic Transformation

The inducible expression of vir operons was first found by using the cocultivation of A. tumerfaciens with mesophyll protoplasts, isolated plant cells or cultured tissues (Stachel et al., 1986). In vegetatively growing bacteria, only virA and virG are expressed at significant level. However, when Agrobacteria are cocultivated with the susceptible plant cells, the expression of virB, virC, virD, virE and virG are induced to high levels (Engstrom et al.,
1987). The partially purified extracts of conditioned media from root cultures can also induce the expression of vir operons, demonstrating that the vir-inducing factors are some diffusible plant cell metabolites. By screening 40 plant-derived chemicals, Bolton et al. (1986) identified seven simple plant phenolic compounds that possess the vir-inducing activity.
Most of these vir-inducing phenolic compounds are needed to make lignin, a plant cell wall polymer. The best characterized and most effective vir gene inducers are acetosyringone
(AS) and hydroxy-acetosyringone from tobacco cells or roots (Stachel et al., 1985). The specific composition of phenolic compounds secreted by wounded plants is thought to underlie the host specificity of some Agrobacterium strains. Besides phenolic compounds, other inducing factors include aldose monosaccharides, low pH, and low phosphate
(Brencic & Winans, 2005; McCullen & Binns, 2006; Palmer et al., 2004). However, phenols are indispensable for vir gene induction, whereas the other inducing factors sensitise
Agrobacteria to phenols.
2.2 Regulation of vir gene induction
The regulatory pathway for vir gene induction by phenolic compounds is mediated by the
VirA/VirG two-component system, which has structural and functional similarities to other already described for other cellular regulation mechanisms (Bourret et al., 1991; Nixon et al.,
1986). Two component regulatory systems comprise two core components, a sensor kinase and an intracellular response regulator. The sensor kinase responds to signal input and mediates the activation of the intracellular response regulator by controlling the latter’s phoshporylation status (Brencic & Winans, 2005; McCullen & Binns, 2006). For the
Agrobacterium VirA/VirG two-component system, VirA is a membrane-bound sensor kinase. The presence of acidic environment and phenolic compounds at a plant wound site may directly or indirectly induce autophosphorylation of VirA. The phosphorylated VirA can transfer its phosphate to the cytoplasmic VirG to activate VirG. The activated VirG binds to the specific 12bp DNA sequences called vir box enhancer elements that are found in the promoters of the virA, virB, virC, virD, virE and virG operons, and then upregulates the transcription of these operons (Winans, 1992).
Octopine-type Ti plasmid encoded VirA protein has 829 amino acids. VirA is a member of the histidine protein kinase class and able to autophosphorylate. When VirA autophosphorylates in vitro, the phosphate was found to bind to histidine residue 474, a histidine residue that is absolutely conserved among homologous proteins (Jin et al., 1990). VirA protein can be structurally divided into a number of domains. In an order from N-terminus to C-terminus, these domains are defined as transmembrane domain 1 (TM1), periplasmic domain, transmembrane domain 2 (TM2), linker domain, kinase domain and receiver domain (Lee et al., 1996). The periplasmic domain is required for the interaction with ChvE, the sugar-binding protein that responds to the vir-inducing sugars. The linker domain is located on the region of amino acid 280~414, which was supposed to interact with the vir gene inducing phenolic compounds (Chang & Winans 1992). A highly amphipathic helix sequence of 11 amino acids was identified in the region of amino acid 278-288. This amphipathic sequence is highly

Agrobacterium-Mediated Genetic Transformation: History and Progress

7

conserved in a large number of chemoreceptor proteins and thus was supposed to be the receptor site for phenolic inducers (Turk et al., 1994). However, it is unclear whether the phenolic inducers interact with VirA directly or indirectly. The kinase domain is a highly conserved domain that presents in the family of the sensor proteins and contains the conserved histidine residue 474 that is the autophosphorylation site. Site-directing mutation of this His 474 results in avirulence and the lost of vir gene inducing expression in the presence of plant signal molecules (Jin et al., 1990). The receiver domain shows an unusual feature that is homologous to a region of VirG. Similar receiver domains are present in a small number of homologous histidine protein kinases, but the function of this domain is unclear.
VirG is a transcriptional activator of 241 amino acid residues. It is composed of two main domains, N-terminal domain and C-terminal domain. The aspartic acid 52 in the N-terminal domain of VirG can be phosphorylated by the phosphorylated VirA (Jin et al, 1993). The phosphorylation of N-terminal domain is thought to induce the conformation change of Cterminal domain. The C-terminal domain of VirG possesses the DNA-binding function, resulting in VirG specifically binding to the vir box sequence that is found within 80 nucleotides upstream from the transcription initiation sites of vir genes. Phosphorylation is required for the transcriptional activation function of VirG, but how phosphorylation modulates the properties of VirG is unknown. Some models suggested that phosphorylation might increase the affinity of VirG to its binding sites or promote the ability of VirG to contact RNA polymerase (Lin et al., 2008; McCullen & Binns, 2006; Wang et al., 2002).
2.3 T-DNA processing
The activation of vir genes initiates a cascade of events. Following the expression of vir genes, some Vir proteins produce the transfer intermediate, a linear single stranded (ss)
DNA called T-DNA or T-strand that is derived from the bottom (coding) strand of the Tregion of the Ti plasmid. T-region is flanked by two 25 bp long imperfect direct repeats, termed border sequences. VirD2/VirD1 is able to recognize the border sequences and cleave the bottom strand of T-region at identical positions between bp 3 and 4 from the left end of each border (Sheng & Citovsky, 1996). Upon the cleavage of T-DNA border sequence, VirD2 remains covalently associated with the 5´-end of the ssT-strand via tyrosine residue 29
(Vogel & Das, 1992). The excised ssT-strand is removed, and the resulting single-stranded gap in the T-region is repaired, most likely replaced by a newly synthesizing DNA strand.
The association of VirD2 with the 5´-end of the ssT-strand is believed to prevent the exonucleolytic attack to the 5´-end of the ssT-strand (Durrenberger et al., 1989) and to distinguish the 5´-end as the leading end of the T-DNA complex during transfer.
One report indicated that VirD1 possesses a topoisomerase-like activity (Ghai and Das,
1989). VirD1 appears to be a type I DNA topoisomerase that do not require ATP for activity.
However, a late study (Scheiffele et al., 1995) contradicted this conclusion. The VirD1 protein purified by Scheiffele et al. (1995) never showed any topoisomerase activity. It was speculated that the topoisomerase activity observed by Ghai and Das (1989) might originate from VirD2. Mutational study of VirD1 showed that a region from amino acids 45~60 is important for VirD1 activity. Sequence comparison of this fragment with the functionally analogous proteins of conjugatable bacterial plasmids showed that this region is a potential
DNA-binding domain (Vogel & Das, 1994).
The nopaline Ti plasmid encoded VirD2 consists of 447 amino acids with a molecular weight of 49.7 kDa. Deletion analysis of VirD2 demonstrated that the C-terminal 50% of VirD2 could be deleted or replaced without affecting its endonuclease activity. Sequence

8

Genetic Transformation

comparison of VirD2 from different Agrobacterium species shows that the N-terminus is highly conserved with 90% homology, whereas only 26% homology is found in the Cterminus (Wang et al., 1990). A sequence comparison of VirD2 protein with its functionally homologous proteins in bacterial conjugation and in rolling circle replication revealed that a conserved 14-residue motif lies in the residues 126~139 of VirD2. This motif contains the consensus sequence HxDxD(H/N)uHuHuuuN (invariant residues in capital letters; x, any amino acid; u, hydrophobic residue) (Ilyina & Koonin, 1992). Mutational analysis indicated that all the invariant residues except for the last asparagine (N) in this motif are important for the endonuclease activity of VirD2. The second aspartic acid (D) and three nonconserved residues in this motif are also essential for the endonuclease activity of VirD2 (Vogel et al.,
1995). This motif is believed to coordinate the essential cofactor Mg2+ by the two histidines in the hydrophobic region of the motif (Ilyina & Koonin, 1992). The poorly conserved Cterminal halves of VirD2 from different Agrobacterium species displayed a very similar hydropathy profile (Wang et al., 1990). The C-terminal domain of VirD2 is thought to guide the T-complex to the plant nucleus. The sequence characterization and function of this region of VirD2 will be discussed in a late section of this chapter.

3. Contact of Agrobacterium with plant and transfer of Agrobacterial molecules to plant
3.1 Chemotaxis of A. tumefaciens
A. tumefaciens is a motile organism, with peritrichous flagellae, that possesses a highly sensitive chemotaxis system. It could respond to a range of sugars and amino acids and be attracted to these sugars and amino acids (Loake et al., 1988). A. tumefaciens mutants deficient in motility and in chemotaxis were fully virulent when inoculated directly.
However, when used to inoculate soil, which was air-dried and then used to grow plants, these mutants were completely avirulent. These results indicated that the motility and chemotaxis are critical to A. tumefaciens infection under natural conditions (Hawes & Smith,
1989). Wild-type A. tumefaciens strains both containing and lacking Ti plasmid exhibited chemotaxis toward excised root tips from all plant species tested and toward root cap cells of pea and maize, suggesting that the majority of chemotactic responses in A. tumefaciens appear to be chromosomally encoded (Loake et al., 1988; Parke et al., 1987). However, the chemotactic response to some phenolic compounds, for example acetosyringone, which were identified as strong vir gene inducers, is controversial. Some reports showed that chemotaxis toward acetosyringone requires the presence of a Ti plasmid, specifically the regulatory genes virA and virG, and occurs with a threshold sensitivity of < 10-8 M, some
1000-fold below the maximal vir-inducing concentration (Ashby et al., 1988; Shaw et al.,
1989). Whereas, reports from other groups indicated that acetosyringone did not elicit chemotaxis at any concentration (Hawes & Smith, 1989) and chemotaxis toward related compounds did not require the Ti plasmid (Park et al., 1987). So, it does seem difficult to rationalize a role for acetosyringone and the regulatory genes virA and virG in chemotaxis. 3.2 Attachment of A. tumefaciens to plant
It is reasonable that an intimate association between pathogen and host cells is required for the transfer of T-DNA and virulence proteins from A. tumefaciens to plant cells. A. tumefaciens can efficiently attach to both plant tissues and abiotic surfaces, and establish

Agrobacterium-Mediated Genetic Transformation: History and Progress

9

complex biofilms at colonization sites. Microscopic observation of bacteria interacting with the plant cells demonstrates a significant propensity to attach in a polar fashion (Smith &
Hindley, 1978; Tomlinson & Fuqua, 2009). All Agrobacterium mutants deficient in attachment to plant cells are either avirulent or extremely attenuated in virulence (Cangelosi et al., 1989;
Douglas et al., 1982, 1985; Matthysse & McMahan, 2001; O’Connell & Handelsman, 1989).
Although obviously critical, the attachment process is one of the least-characterized sets of cellular processes in the entire interaction. Little progress on this area was made in recent years (Tomlinson & Fuqua, 2009).
3.2.1 Bacterial genes involved in the attachment of A. tumefaciens to plant
The binding of A. tumefaciens to host plant cells seems to require the participation of specific receptors that may exist on the bacterial and plant cell surface because the binding of A. tumefaciens to host plant cells is saturable and unrelated bacteria fail to inhibit the binding of
A. tumefaciens to host plant cells (B.B. Lippincot & J.A. Lippincot, 1969). A number of A. tumefaciens mutants reported to affect the attachment of bacteria to plant cells have been isolated. Some related genes are identified and sequenced (Matthysse et al., 2000; Reuhs et al., 1997). However, it is surprising that a large number of genes are involved in the bacterial attachment to host cells and the actual functions of most genes are unclear (Matthysse et al.,
2000). All the genes reported to affect the bacterial attachment to host cells are chromosomal genes.The genes involved in the binding of bacteria to host plant cells are identified to mainly locate on two regions of the bacterial chromosome.
The binding of bacteria to host cells is thought to be a two-step process (Matthysse &
McMahan, 1998). The binding in the first step is loose and reversible because the bound bacteria are easy to being washed from the binding sites by shear forces, such as water washing or vortexing of tissue culture cells. Genes involved in this step are identified to locate on the att gene region (more than 20 kb in size) of the bacterial chromosome. Gene mutations in this region abolish virulence. The mutants in the att gene region can be divided into two groups. The first group can be restored to attachment and virulence by the addition of conditioned medium. This group appears to be altered in signal exchange between the bacterium and the host. Mutations in this group of mutants occur in the genes homologous to ABC transporters and transcriptional regulator as well as some closely linked downstream genes (Matthysse et al., 2000; Matthysse & McMahan, 1998; Reuhs et al., 1997).
The second group of mutants in the att gene region is not affected by the presence of conditioned medium. This mutant group appears to affect the synthesis of surface molecules, which may play a role in the bacterial attachment to the host. This group includes mutants in the genes homologous to transcriptional regulator and ATPase as well as a number of biosynthetic genes, which include the transacetylase required for the formation of an acetylated capsular polysaccharide. The acetylated capsular polysaccharide is required for the bacterial attachment to some plants because the production of the acetylated capsular polysaccharide is correlated to the attachment of wild-type strain C58 to the host cells and the purified acetylated capsular polysaccharide from wild-type strains blocks the binding of the bacteria to some host cells (Matthysse et al., 2000; Matthysse &
McMahan, 1998, 2001; Reuhs et al., 1997).
The second step in the bacterial attachment to the host results in tight binding of the bacteria to the plant cell surface because the bound bacteria can no longer be removed

10

Genetic Transformation

from the plant cell surface by shear forces. This step requires the synthesis of cellulose fibrils by the bacteria, which recruits larger numbers of bacteria to the wound sites.
Cellulose-minus bacterial mutants show reduced virulence (Minnemeyer et al., 1991). The genes required for the synthesis of bacterial cellulose fibrils (cel genes) are identified to locate on the bacterial chromosome near, but not contiguous with the att gene region
(Robertson et al., 1988).
Some other chromosomal virulence genes chvA, chvB, and pscA (exoC) are believed to be involved indirectly in bacterial attachment to host (Cangelosi et al., 1987; Douglas et al.,
1982; O’Connell & Handelsman, 1989). These genes are involved in the synthesis, processing, and export of a cyclic β-1,2-glucan, which has been implicated in the bacterial binding to plant cells. Mutations in chvA, chvB, and pscA (exoC) cause a 10-fold decrease in binding of bacteria to zinnea mesophyll cells and strongly attenuate virulence (Douglas et al., 1985; Kamoun et al., 1989; Thomashow et al., 1987). ChvB is believed to be involved in the synthesis of the cyclic β-1,2-glucan (Zorreguieta & Ugalde, 1986). ChvA is homologous to a family of membrane-bound ATPases and appears to be involved in the export of the cyclic β-1,2-glucan from the cytoplasm to the periplasm and extracellular fluid (Cangelosi et al., 1989; De Iannino & Ugalde, 1989). However, the virulence of chvB mutants is temperature sensitive (Banta et al., 1998). At lower temperature (16 ºC), chvB mutants became virulent and were able to attach to plant roots (Bash & Matthysse, 2002).
3.2.2 Plant factors involved in the attachment of A. tumefaciens to plant
In addition to bacterial factors, some plant factors are essential for the attachment of A. tumefaciens to plant cells. Two plant cell wall proteins: a vitronectin-like protein (Wagner &
Matthysse, 1992) and a rhicadhesin-binding protein (Swart et al., 1994) have been proposed to mediate the bacterial attachment to plant cells. Vitronectin is an animal receptor that is specifically utilized by different pathogenic bacteria (Burridge et al., 1988). A plant vitronectin-like protein is reported to occur in several A. tumefaciens host plant (Sanders et al., 1991). Human vitronectin and antivitronectin antibodies were shown to inhibit the binding of A. tumefaciens to plant tissues. Nonattaching A. tumefaciens mutants, such as chvB, pscA and att mutants, showed a reduction in the ability to bind vitronectin. Therefore, the plant vitronectin-like protein was proposed to play a role in A. tumefaciens attachment to its host cells (Wagner & Matthysse, 1992). However, a recent report argues against the role of the vitronectinlike protein in bacterial attachment and Agrobacterium-mediated transformation (Clauce-Coupel et al., 2008).
Genetic studies showed that additional plant cell-surface proteins might play a role in A. tumefaciens attachment. Two Arabidopsis ecotypes, B1-1 and Petergof, which are highly recalcitrant to Agrobacterium-mediated transformation, were proposed to be blocked at an early step of the binding (Nam et al., 1997). Two Arabidopsis T-DNA insertion mutants of the ecotype Ws, rat1 and rat3, which are resistant to Agrobacterium transformation (rat mutants), are deficient in A. tumefaciens binding to cut root surfaces (Nam et al., 1999). DNA sequence analysis indicated that rat1 and rat3 mutations affect an arabinogalactan protein (AGP) and a potential cell-wall protein, respectively. AGPs were confirmed to be involved in A. tumefaciens transformation (Nam et al., 1999). Interestingly, AGP17 (rat1 mutant) appears to be involved in host defense reactions and signaling (Gaspar et al., 2004; Gelvin, 2010a).
Other two rat mutans, ratT8 and ratT9, were identified to be mutated in the genes coding for receptor-like protein kinases (Zhu et al., 2003).

Agrobacterium-Mediated Genetic Transformation: History and Progress

11

3.3 Transfer of Agrobacterial molecules to plant
Following the production of T-DNA and attachment to the host cells, Agrobacterium transports T-DNA and virulence proteins into the host. The transportation must cross the bacterial cell membrane and wall, as well as host cell membrane and wall.
3.3.1 Transfer apparatus
A. tumefaciens uses type IV secretion system (T4SS) to transfer T-DNA and effector proteins to its host cells (Cascales & Christie, 2003, 2004). The T4SS was initially defined to be a class of DNA transporters whose components are highly homologous to the conjugal transfer
(tra) system of the conjugative IncN plasmid pKM101 and the A. tumefaciens T-DNA transfer system (Burns, 2003; Christie & Vogel, 2000). T4SS, also known as the mating pair formation
(Mpf) apparatus, is a cell envelope-spanning complex (composed of 11-13 core proteins) that is believed to form a pore or channel through which DNA and/or protein is delivered from the donor cell to the recipient cell. Recently the members of T4SS have steady increased, with the identification of additional systems involved in DNA and protein translocation
(Alvarez-Martinez & Christie, 2009; Cascales & Christie, 2003; Christie & Vogel, 2000;
Gillespie, 2010). However, the best-studied T4SS member is the VirB/D4 transporter of A. tumefaciens. In the past decade, much of the research on Agrobacterium-mediated T-DNA transfer focused on the vir-specific T4SS, the T-complex transporter. Therefore, the A. tumefaciens T-complex transporter has become a paradigm of T4SS (Alvarez-Martinez &
Christie, 2009; Cascales & Christie, 2003).
The VirB/D4 T4SS is assembled from 11 proteins (VirB1 to VirB11) encoded by the virB operon, and VirD4. At least 10 of the 11 VirB proteins are believed to be the structural subunits of the T-pilin and associated transport apparatus that spans from the cytoplasm of the cell, through the inner membrane, periplasmic space and outer membrane, to the outside of the cell. In the past few years, work in identifying the interactions among the VirB protein subunits and defining the steps in the transporter assembly pathway has extended our knowledge of the structure of the VirB transport apparatus. To demonstrate the architecture of the VirB/D4 transporter, a model that depicts the subcellular locations and interactions of the VirB and VirD4 subunits of the A. tumefaciens VirB/D4 T4SS was proposed (AlvarezMartinez & Christie, 2009; Cascales & Christie, 2004). Recently, VirB7, VirB9, and VirB10 homologs from the pKM101 T4SS were purified and the cryoEM structure of a core complex composed of pKM101 VirB7-like TraN, VirB9-like TraO, and VirB10-like TraF was revealed
(Fronzes et al., 2009).
Agrobacterium-mediated T-DNA transfer to plant shows striking similarities to the plasmid interbacterial conjugation (Ream, 1989; Stachel & Zambryski, 1986). Bacterial conjugation can be visualized as the merging of two ancient bacterial systems: the DNA rolling-circle replication system and type IV secretion system (T4SS) (Llosa et al., 2002). The DNA rollingcircle replication system in plasmid conjugation was also known as the DNA transfer and replication (Dtr) system. The Dtr system corresponds to the T-DNA relaxase nucleoprotein complex. The T4SS responding for the plasmid conjugation was initially called mating pair formation (Mpf) system. In order to recognize these two systems and link them, a protein is normally required for many conjugal plasmids to couple the Dtr to the Mpf. This protein was called coupling protein as its function (Gomis-Ruth et al., 2002).
VirD4 is a homologue of coupling protein family and is believed to be the coupling protein that links the transferred molecules and T4SS transporter. VirD4 is an inner membrane

12

Genetic Transformation

protein with potential DNA binding ability and ATPase activity. Membrane topology analysis of VirD4 revealed that VirD4 contains an N-terminal-proximal region, which includes two transmembrane helices and a small periplasmic domain, and a large Cterminal cytoplasmic domain (Cascales & Christie, 2003; Das & Xie, 1998). VirD4 localizes to the cell pole. The polar location of VirD4 was not dependent on T-DNA processing, the assembly of T4SS transporter and the expression of other Vir proteins. Both the small periplasmic domain and the cytoplasmic nucleotide-binding domain are required for the polar localization of VirD4 and essential for T-DNA transfer. VirD4 forms a large oligomeric complex (Kumar & Das, 2002). VirD4 can recruit VirE2 to the cell poles (Atmakuri et al.,
2003) and weakly interact with VirD2-T-strand complex (Cascales & Christie, 2004).
Although VirD4 is essential for coordinating the T4SS to drive T-DNA transfer, it has been unclear whether VirD4 physically/directly interacts with the T4SS transporter. However, the interaction between VirD4 homologues and the protein components of Dtr system exhibits specificity. It was supposed that VirD4 protein might recruit T-complex to the T4SS transporter through contacts with the T-complex protein and then through the contacts with
VirB10 coordinate the passage of T-complex through the T4SS channel (Cascales & Christie,
2003; Llosa et al., 2003). However, it should be pointed out that the recruitment of Tcomplex might be much more difficult than the recruitment of single VirE2 molecule due to the difference of molecular size between T-complex and VirE2. Recently, two cytoplasmic proteins, VBP (VirD2-binding protein) (Guo et al., 2007a, 2007b) and VirC1 (Atmakuri et al.,
2007) were reported to be involved in the recruitment of the T-complex to T4SS. Genomewide sequence analysis showed that A. tumefaciens contains three vbp homologous genes.
Reverse genetic study showed that mutatons of three vbp genes highly attenuated the bacterial ability to cause tumors on plants (Guo et al., 2007a, 2009b).
3.3.2 Agrobacterial molecules transported to plant
Agrobacterial molecules transported into host cells by VirB/D4 T4SS include the VirD2-Tstrand complex, VirE2, VirE3, VirF, and VirD5. VirD2 is covalently bound to the 5′end of the T-strand. The bound VirD2, probably in conjunction with other protein components, such as VBP (Guo et al., 2007a, 2007b) and VirC1 (Atmakuri et al., 2007), confers recognition of the VirD2-T-strand complex by the VirB/D4 T4SS. VirD2 also “pilots” the
T-strand through the translocation channel. It was supposed that the VirB/D4 T4SS is actually a protein transporter and the T-strand is the “hitchhiker” (Cascales & Christie,
2004).
VirE2 is a single-stranded DNA-binding protein (Christie et al., 1988; Citovsky et al., 1988) that can bind single-stranded DNA without sequence specificity, and is supposed to protect the T-strand from the nucleolytic degradation because single-stranded T-DNA is believed to be susceptible to nucleases. The binding of VirE2 to single-stranded DNA is strong and cooperative, suggesting that VirE2 coats the T-strand along its length (Citovsky et al., 1989).
Another possible function of VirE2 is to guide the nuclear import of T-DNA (Ziemienowicz et al., 1999, 2001). This will be discussed in the following section of this chapter. Induced
Agrobacterium cell can produce sufficient VirE2 to bind all intracellular single-stranded TDNA. When bound to single-stranded DNA, VirE2 can alter the ssDNA from a random-coil conformation to a telephone cord-like coiled structure and increases the relative rigidity
(Citovsky et al., 1997). Initial hypothesis is that the protective role of VirE2 is required to function in both bacteria and plant cells. So, the prevailing view on the T-DNA transfer is that a packaged nucleoprotein complex, the T-complex, composed of the T-strand DNA

Agrobacterium-Mediated Genetic Transformation: History and Progress

13

containing the 5´-associated VirD2 and coated with VirE2 along its length, is the transfer intermediate (Howard & Citovsky, 1990; Zupan & Zambryski, 1997). This T-complex structure model implies that both VirD2 and VirE2 together with the T-strand are transported into plant cell in the same time. This idea makes biological sense because it is likely that VirE2 with a high affinity to ssDNA may form a complex with the T-strand already inside Agrobacterium cell, especially if both VirE2 and the T-strand are transported through the same channel (Binns et al., 1995). Indeed, the T-complex, which contains Tstrand, VirD2 and VirE2, was observed in the crude extracts from vir-induced Agrobacterium by using anti-VirE2 antibodies to co-immunoprecipitate both T-strand and VirE2 (Christie et al., 1988).
However, two kinds of evidence argued against that the protective role of VirE2 is required to function inside bacterial cells. The first is the observation that a strain expressing virE2 but lacking T-DNA can complement a virE2 mutant in a tumor formation assay (Otten et al.,
1984) and the T-strand accumulates to wild-type levels in virE2 mutants (Stachel et al., 1987;
Veluthambi et al., 1988). The second kind of evidence is that virE2 expression in transgenic tobacco plants restores the infectivity of a VirE2-deficient Agrobacterium strain (Citovsky et al., 1992). In addition, the observation that virE2 mutants can transfer T-DNA into plant cells
(Yusibov et al., 1994) also proved that VirE2 is not essential for the export of T-DNA. All these data appear to support that T-DNA may not be packaged by VirE2 in the bacterial cells, at least, the packaging of T-DNA inside bacterial cells by VirE2 is not necessary for the tumor formation. VirE2 can be transported independently, but the transportation of VirE2 requires the activities of VirE1. VirE1 is a chaperone and is necessary for VirE2 translation and stability but not essential for the recognition of the translocation signal of ViE2 by the transport machinery and the subsequent translocation of VirE2 into plant cells, indicating that the role of VirE1 playing in the export process of VirE2 seems restricted to the stabilization of VirE2 by preventing VirE2 from the premature interactions in the bacterial cell before translocation into plant cells (Vergunst et al., 2003).
Like VirD2 and VirE2, agrobacterial protein VirF can also be exported to plant cell (Vergunst et al., 2000). virF gene is found only in the octopine-specific Ti plasmid. It is not essential for
T-DNA transfer. Initially, VirF is thought to be a host-range factor of Agrobacterium
(Regensburg-Tuink & Hooykaas, 1993). A more recent report showed that VirF interacts with an Arabidopsis Skp1 protein (Schrammeijer et al., 2001). Yeast Skp1 protein and its animal and plant homologs are subunits of the complexes involved in targeted proteolysis.
This targeted proteolysis can regulate the plant cell cycle. So, it was suggested that VirF may function in setting the plant cell cycle to effect better transformation (Gelvin, 2003; Tzfira &
Citovsky, 2002).
Protein truncation and fusion of T4SS substrates demonstrated that certain C-terminal motifs were required for the export of targeted substrates. The C-terminal 37 amino acids of VirF and the C-terminal 50 amino acids of VirE2 and VirE3 are sufficient to mediate transport of these fusion proteins to plants (Vergunst et al., 2000, 2003). The minimal size of VirF required to direct the translocation of VirF-fusion protein to plants is the Cterminal 10 amino acids. Site-directed mutations showed that several arginines within this region are required for transport (Vergunst et al. 2005). These export signals mediate the recognition of substrates by the VirB/D4 T4SS. A possible consensus sequence R-x(7)-R-xR-x-R (x, any amino acid) was identified in the C termini of substrates secreted by the
VirB/D4 T4SS.

14

Genetic Transformation

4. Events happening in host
Following the entry of agrobacterial molecules in plant cell cytoplasm, the VirD2-T-strand interacts with VirE2 and plant proteins, likely forming “super-T-complex”, which is responsible for subcellular travelling of T-strand from cytoplasm through nuclear membrame into nucleus, and to the chromatin, thus facilitating T-DNA integration into host genome. All these biological processes occurring in host cells require the involvement of many host factors.
4.1 Nuclear targeting of T-complex
The dense structure of the cytoplasm, which greatly restricts the free diffusion of macromolecules, and the size of the “super-T-complex”, which far exceeds the 60 kDa sizeexclusion limit of the nuclear pore (Lacroix et al., 2006a), indicate that active transport processes are required for the nuclear import of T-complex. As a rule, active nuclear import of proteins requires a specific nuclear localization signal (NLS). Typical nuclear localization signals are short regions rich in basic amino acids (Silver, 1991).
4.1.1 Nuclear localization signals in Agrobacterial molecules
Because T-strand is presumed to be completely coated with proteins inside plant cells it is impossible for T-strand itself to carry NLSs. Thus, the NLSs that guide T-complex nuclear import most likely reside in its associated proteins, VirD2 and VirE2. Sequence analysis reveals that both VirD2 and VirE2 contain NLSs. Two NLSs are found in VirD2. One is the typical bipartite NLS that resides in residues 396~413. The nuclear localizing function of this bipartite NLS was confirmed by the observation that VirD2-GUS fusion protein, when expressed in tobacco protoplasts, can target to plant cell nuclei (Howard et al., 1992; Tinland et al., 1992). However, mutations that destroy this bipartite NLS attenuate, and do not abolish tumorigenesis, indicating that although this NLS plays a role in T-DNA transfer, it is not essential (Rossi et al., 1993; Shurvinton et al., 1992). Another NLS in VirD2 is found in residues 32~35, adjacent to the active site in the endonuclease domain (Tinland et al., 1992).
This NLS is a monopartite NLS. GUS proteins fused with this NLS accumulate in plant nuclei, but this NLS does not play a role in T-DNA nuclear localization (Shurvinton et al.,
1992). The sequences of residues 419~423 at the C-terminus of VirD2, known as the ω domain, are important for tumorigenesis, but do not contribute to nuclear localization activity despite its proximity to the bipartite NLS. The ω domain was supposed to be involved in T-DNA integration (Mysore et al., 1998).
VirE2, the most abundant protein component of the T-complex, contains two bipartite NLSs in its central region (residues 205~221, and residues 273~287). When fused to GUS, each
VirE2 NLS is capable of directing the fusion protein to the nucleus of a plant cell, but the maximum accumulation in the nucleus requires both VirE2 NLSs (Citovsky et al., 1992).
Because these two NLSs overlap with the DNA binding domains, mutations of virE2 that abolish the activity of one of these NLSs will also eliminate the DNA binding activity. So, no genetic evidence can be provided to verify the function of these two VirE2 NLSs in Tcomplex nuclear localization. When VirE2 binds to T-strand, the NLSs of VirE2 may be occluded and inactive. It has been observed that for the nuclear import of short ssDNA,
VirD2 was sufficient, whereas import of long ssDNA additionally required VirE2
(Ziemienowicz et al., 2001). Although predominantly nuclear localization of VirE2 was

Agrobacterium-Mediated Genetic Transformation: History and Progress

15

observed in earlier studies, several recent reports demonstrated the cytoplasmic localization of VirE2 (Bhattacharjee et al., 2008; Grange et al., 2008). Indeed, results from different research groups indicate that VirE2 localizes to different subcellular compartments in different tissues (Gelvin, 2010b). All the evidence argued against the function of VirE2 in Tcomplex nuclear localization. RecA, a NLS-lacking ssDNA binding protein, could substitute for VirE2 in the nuclear import of T-strand, further demonstrating that VirE2 functions not in the nuclear localization, possibly in mediating the passage of T-strand through the nuclear pore (Ziemienowicz et al., 2001). VirE2 was assumed to shape the T-complex such that it is accepted for translocation into the nucleus.
4.1.2 Plant proteins involved in T-complex nuclear targeting
Besides the agrobacterial proteins VirD2 and VirE2, some plant proteins were supposed to be involved in the T-complex nuclear translocation. Early yeast two-hybrid screen identified an A. thaliana importin-α (AtKAP, now known as importin-α1) that interacts with VirD2
(Ballas & Citovsky, 1997). Importin-α proteins interact with NLS-containing proteins and guide the nuclear translocation of these proteins. Importin-α proteins constitute a protein family and Arabidopsis encodes at least nine of these proteins (Gelvin, 2003). Interaction between VirD2 and importin-α1 was verified to be VirD2 NLS dependent (Ballas &
Citovsky, 1997). The importance of importin-α proteins in the T-complex transfer process was confirmed by the genetic evidence that a T-DNA insertion into the importin-α7 gene, or antisense inhibition of expression of the importin-α1 gene, highly reduces the transformation efficiency (Gelvin, 2003). Importin-α1, as well as all other investigated importin-α family members, also interacts with VirE2 (Bhattacharjee et al., 2008) and VirE3
(Garcia-Rodriguez et al., 2006).
Other plant proteins that were identified to interact with VirD2 include several cyclophilins, a kinase CAK2M, and a protein phosphatase 2C (PP2C). Deng et al. (1998) showed that an
Arabdopsis cyclophilin interacted strongly with VirD2. They further characterized the interaction domain of VirD2 and found that a central domain of VirD2 (residues 274~337) was involved in the interaction with cyclophilin. No previous function of VirD2 had been ascribed to this central region. Cyclosporin A, an inhibitor of VirD2-cyclophilin interaction, inhibits Agrobacterium-mediated transformation of Arabidopsis and tobacco (Deng et al.,
1998). Cyclophilin were presumed to serve as a molecular chaperone to help in T-complex trafficking within the plant cell. Cyclin-dependent kinase-activating kinase CAK2M interacts with VirD2 and catalyzes the phosphorylation of VirD2 in vivo. CAK2M may target
VirD2 to the C-terminal regulatory domain of RNA polymerase II large subunit (RNApolII
CTD) (Pitzschke & Hirt, 2010). A tomato type 2C protein phosphatase (PP2C) that was identified to interact with VirD2 can catalyze the dephosphorylation of VirD2. This phosphatase was assumed to be involved in the phosphorylation and dephosphorylation of a serine residue near the C-terminal NLS in the VirD2. Overexpression of this phosphatase decreased the nuclear targeting of a GUS-VirD2-NLS fusion protein, suggesting that phosphorylation of the C-terminal NLS region may affect the nuclear targeting function of
VirD2 (Tao et al, 2004).
Two VirE2-interacting proteins were designated VIP1 and VIP2. VIP1 was showed to facilitate the VirE2 nuclear import in yeast and mammalian cells. Tobacco VIP1 antisense plants were highly resistant to A. tumefaciens infection (Tzfira et al., 2001), whereas,

16

Genetic Transformation

transgenic plants that overexpress VIP1 are hypersusceptible to A. tumefaciens transformation (Tzfira et al., 2002). VIP1 is a basic leucine zipper (bZIP) motif protein and shows no significant homology to known animal or yeast proteins (Tzfira et al., 2001). So, how VIP1 facilitates the nuclear import of VirE2 remains unclear. Unlike VIP1, VIP2 was unable to mediate VirE2 into the yeast cell nucleus. However, VIP1 and VIP2 interacted with each other. Thus, VIP1, VIP2 and VirE2 were assumed to function in a multiprotein complex
(Tzfira & Citovsky, 2000, 2002). A recent paper showed that VIP1 is phosphorylated by the mitogenactivated protein kinase MPK3 and the VIP1 phosphorylation affects both nuclear localization of VIP1 and Agrobacterium-mediated transformation, implying that VIP1 phosphorylation is important for super-T-complex nuclear targeting (Djamei et al., 2007).
4.2 Integration of T-DNA into plant genome
The integration of the incoming ssT-strand of the T-complex into plant genome is the final step of the Agrobacterium-mediated genetic transformation. Whether or not the host can be successfully transformed is highly dependent on whether the T-DNA could be integrated into the suitable sites of the host genome.
4.2.1 Integration site
The DNA sequence analysis of several T-DNA host DNA junctions revealed that these junctions, in general, appear more variable than the junctions created by insertions of transposons, retroviruses, or retrotransposons (Gheysen et al., 1987). A statistical analysis of
88,000 T-DNA genome-wild insertions of Arabidopsis revealed the existence of a large integration site bias at both the chromosome and gene levels (Alonso et al., 2003). At the chromosomal level, fewer T-DNA insertions were found at the centromeric region. At the gene level, insertions within promotor and coding exons make up nearly 50% of all insertion sites. However, these statistical results may be skewed by the antibiotic resistance selection of transformed plants (T1 plants) because only the T1 plants with transcriptionally active TDNA insertions can be selected (Alonso et al., 2003; Valentine, 2003). Recently, a genomewide analysis of T-DNA-integration sites in Arabidopsis performed under non-selective conditions showed that T-DNA integration occurs rather randomly (Kim et al., 2007).
Another statistical analysis of 9000 flanking sequence tags characterizing transferred DNA
(T-DNA) transformants in Arabidopsis showed that there are microsimilarities involved in the integration of both the right and left borders of the T-DNA insertions. These microsimilarities occur only in a stretch of 3 to 5 bp and can be between any T-DNA and genomic sequence. This mini-match of 3 to 5 bp basically allows T-DNA to integrate at any locus in the genome. It was also showed that T-DNA integration is favored in plant DNA regions with an A-T-rich content (Brunaud et al., 2002).
4.2.2 Integration mechanism
The observation of the random, as opposed to targeted, nature of T-DNA integration indicated that the integration occurs in illegitimate recombination. To date, it has not been possible to target T-DNA to any particular locus in the genome with any great efficiency. So, the T-DNA integration has been one of the motives of intense investigation of A. tumefaciens.
But, the molecular mechanism of the T-DNA integration remains largely unknown. Two major models for T-DNA integration have been proposed: single-strand-gap repair model

Agrobacterium-Mediated Genetic Transformation: History and Progress

17

and double-strand-break repair model (Gelvin, 2010a; Mayerhofer et al., 1991; Tzfira et al.,
2004).
In the single-strand-gap repair model, VirD2-T-strands invade regions of microhomology between T-DNA and plant DNA sequences and partially anneal to the microhomologous regions. VirD2 on the 5´-end of the T-strand causes a nick in one strand of plant DNA and ligates the T-strand to the nick. Following the ligation of the T-strand to the target DNA, a nick is introduced in the second strand of the target DNA and extended to a gap by exonucleases. During the gap repairing, the complementary strand of T-DNA is synthesized, resulting in incorporation of a double-strand copy of the T-strand into the plant genome. The double-strand-break repair model hypothesizes that single-strand T-strands are replicated in the plant nucleus to a double-strand form and then the double-strand TDNA is integrated into double-strand breaks in the target DNA. The double-strand-break repair model requires the T-DNA to be converted to a double-strand form before its integration into the double-strand breaks. However, there are more results that strongly support the double-strand-break repair model (Lacroix et al., 2006a). It seems that doublestranded T-DNA integration is the native model of T-DNA integration.
4.2.3 Plant proteins involved in the T-DNA integration
The plant proteins that may be involved in the T-DNA integration process are only now beginning to be defined. As mentioned before, CAK2M phosphorylates VirD2 and targets
VirD2 to the C-terminal regulatory domain of RNA polymerase II large subunit (RNApolII
CTD), a factor that is responsible for recruiting TATA-box binding proteins (TBP) to actively transcribed regions. CAK2M can also phosphorylate CTD. By associating with VirD2, TBP may guide T-strands to transcriptionally active regions of chromatin for integration. It was supposed that TBP or CAK2M may target VirD2 to the CTD, thereby controlling T-DNA integration (Bako et al., 2003). These nuclear VirD2-binding factors provide a link between
T-DNA integration and transcription-coupled repair, suggesting that transcription and transcription-coupled repair may play a role in T-DNA integration (Bako et al., 2003).
To integrate into plant chromosomal DNA, T-DNA must interact with chromatin. More than
109 chromatin genes of 15 gene families were identified to be related to the transformation susceptibility (Crane and Gelvin, 2007). As T-DNA integrates into the plant genome by illegitimate recombination (Mayerhofer et al, 1991), proteins involved in DNA repair and recombination should also be involved in T-DNA integration. Non-homologous end-joining proteins, including Ku70, Ku80, Rad50, Mre11, Xrs2, and Sir4, were identified to be required for T-DNA intigration (Gelvin, 2010a; Tzfira and Citovsky, 2006; Van Attikum et al., 2001).

5. Conclusions
Several decades of intensive studies on Agrobacterium make the transformation of many plant and non-plant species by Agrobacterium-mediated transformation protocols become routine. The ability of Agrobacterium to genetically transform a wide variety of plant and non-plant species has earned it an honour of “nature’s genetic engineer” and placed it at the forefront of future biotechnological applications (Rao et al., 2009). However, the
Agrobacterium-mediated genetic transformation is still an extremely inefficient process, in which only few of the host cells can be infected, and T-DNA integration and stable expression occur in an even smaller fraction of the infected cells. Out of question, a better understanding of the fundamental mechanisms of Agrobacterium-mediated genetic

18

Genetic Transformation

transformation is essential for improving the biotechnological applications of this bacterium as a gene vector for genetic transformation of plant and non-plant species. In addition,
Agrobacterium-mediated genetic transformation serves as an important model system for studying host-pathogen recognition and delivery of macromolecules into target cells and thus the in-depth study and molecular analysis of Agrobacterium-mediated transformation will also add to our understanding of all the biological processes involved in the
Agrobacterium-mediated genetic transformation.
Agrobacterium-mediated genetic transformation is a complex process that involves
Agrobacterium reactions to wounded plant, T-DNA transfer in both bacteria and host cells, host reactions to Agrobacterium infection, and genetic transformation of host cells. This complex process requires the concerted function of both Agrobacterium and host. The golden period of Agrobacterium research led us to understand many of the Agrobacterium’s biological processes and mechanisms, such as virulence protein inducing, T-DNA processing, and macromolecule exporting by T4SS. However, many key steps of Agrobacterium-mediated genetic transformation still remain poorly understood and require further investigation.
Particularly the events happening in the host infected by Agrobacterium are relatively more poorly understood.

6. Acknowledgement
We apologize to colleagues whose works have not been cited because of space limitations.
Work in our laboratory is supported by The National Natural Science Foundation of China
(30870054), The Funding Plan for the High-level Talents with Oversea Education to Work in
China from Ministry of Human Resources and Social Security of the People’s Republic of
China., and The Scientific Research Foundation for the Returned Overseas Chinese Scholars from Ministry of Education of the People’s Republic of China.

7. References
Alonso, J.M., Stepanova, A.N., Leisse, T.J., Kim, C.J., Chen, H., Shinn, P., Stevenson, D.K.,
Zimmerman, J., & Barajas, P. et al. (2003) Genome-wide insertional mutagenesis of
Arabidopsis thaliana. Science 301: 653-657.
Alvarez-Martinez, C.E., & Christie, P.J. (2009) Biological diversity of prokaryotic type IV secretion systems. Microbiol Mol Biol Rev 73(4): 775-808.
Ashby, A.M., Watson, M.D., Loake, G.Y. & Shaw, C.H. (1988) Ti plasmid-specified chemotaxis of Agrobacterium tumefaciens C58C1 toward vir-inducing phenolic compounds and soluble factors from monocotyledonous and dicotyledonous plants. J Bacteriol 170: 4181-4187.
Atmakuri, K., Cascales, E., Burton, O.T., Banta, L.M., & Christie, P.J. (2007) Agrobacterium
ParA/MinD-like VirC1 spatially coordinates early conjugative DNA transfer reactions. EMBO J. 26: 2540–2551.
Atmakuri, K., Ding, Z., & Christie, P.J. (2003) VirE2, a type IV secretion substrate, interacts with the VirD4 transfer protein at cell poles of Agrobacterium tumefaciens. Mol
Microbiol 49: 1699-1713.
Bako, L., Umeda, M., Tiburcio, A.F., Schell, J., & Koncz, C. (2003) The VirD2 pilot protein of
Agrobacterium-transferred DNA interacts with the TATA box-binding protein and a nuclear protein kinase in plants. Proc Natl Acad Sci USA 100: 10108-10113.

Agrobacterium-Mediated Genetic Transformation: History and Progress

19

Ballas, N., & Citovsky, V. (1997) Nuclear localization signal binding protein from Arabidopsis mediates nuclear import of Agrobacterium VirD2 protein. Proc Natl Acad Sci USA 94:
10723-10728.
Banta, L.M., Bohne, J., Lovejoy, S.D., & Dostal, K. (1998) Stability of the Agrobacterium tumefaciens VirB10 protein is modulated by growth temperature and periplasmic osmoadaption. J Bacteriol 180: 6597-6606.
Bash, R., & Matthysse, A.G. (2002) Attachment to roots and virulence of a chvB mutant of
Agrobacterium tumefaciens are temperature sensitive. Mol Plant-Microbe Interact 15:
160-163.
Bevan, M. (1984) Binary Agrobacterium vectors for plant transformation. Nucleic Acids Res 12:
8711-8721.
Bhattacharjee, S., Lee, L.-Y., Oltmanns, H., Cao, H., Veena, Cuperus, J. & Gelvin, SB. (2008)
AtImpa-4, an Arabidopsis importinαisoform, is preferentially involved in
Agrobacterium-mediated plant transformation. Plant Cell 20: 2661-2680.
Binns, A.N., Beaupre, C.E., & Dale, E.M. (1995) Inhibition of VirB-mediated transfer of diverse substrates from Agrobacterium tumefaciens by the InQ plasmid RSF1010. J
Bacteriol 177: 4890-4899.
Bolton, G.W., Nester, E.W., & Gordon, M.P. (1986) Plant phenolic compounds induce expression of the Agrobacterium tumefaciens loci needed for virulence. Science 232:
983-985.
Bourret, R., Borkovich, K., & Simon, M. (1991) Signal transduction pathways involving protein phosphorylation in prokaryotes. Annu Rev Biochem 60: 401-441.
Braun, A.C. (1947) Thermal studies on the factors responsible for the tumor initiation in crown gall. Am J Bot 34: 234-240.
Braun, A.C., & Mandle, R.J. (1948) Studies on the inactivation of the tumor-inducing principle in crown gall. Growth 12: 255-269.
Brencic A., & Winans S.C. (2005) Detection of and response to signals involved in hostmicrobe interactions by plant-associated bacteria. Microbiol Mol Biol Rev 69: 155–
194.
Brunaud, V., Balzeergue, S., Dubreucq, B., Aubourg, S., Samson, F., Chauvin, S., Bechtold,
N. Cruaud, C., & DeRose, R. et al. (2002) T-DNA integration into the Arabidopsis genome depends on sequences of pre-insertion sites. EMBO Rep 3: 1152-1157.
Burns, D.L. (2003) Type IV transporters of pathogenic bacteria. Current Opinion in
Microbiology 6: 29-34.
Burridge, K., Fath, K., Kelly, T., Nuckolls, G., & Turner, C. (1988) Focal adhesions: transmembrane junctions between the extracellular matrix and the cytoskeleton.
Annu Rev Cell Biol 4: 487-525.
Cangelosi, G.A., Hung, L., Puvanesarajah, V., Stacey, G., Ozga, D.A., Leigh, J.A., & Nester,
E.W. (1987) Common loci for Agrobacterium tumefaciens and Rhizobium meliloti exopolysaccharide synthesis and their roles in plant interactions. J Bacteriol 169:
2086-2091.
Cangelosi, G.A., Martinetti, A.G., Leigh, J.A., Lee, C.C., Theines, C., & Nester, E.W. (1989)
Role of Agrobacterium tumefaciens ChvA protein in export of β-1,2-glucan. J Bacteriol
171: 1609-1615.
Cascales, E., & Christie, P.J. (2003) The versatile bacterial type IV secretion system. Nature
Rev Microbiol 1: 137-149.

20

Genetic Transformation

Cascales, E., & Christie, P.J. (2004) Definition of a bacterial type IV secretion pathway for a
DNA substrate. Science 304: 1170-1173.
Chang, C.-H., & Winans, S.C. (1992) Functional roles assigned to the periplasmic, linker, and receiver domains of the Agrobacterium tumefaciens VirA protein. J Bacteriol 174: 70337039.
Chilton, M.-D. (1993) Agrobacterium gene transfer: Progress on a “poor man’s vector” for maize. Proc Natl Acad Sci USA 90: 3119-3120.
Chilton, M.-D., Drummond, M.H., Merlo, D.J., & Sciaky, D. (1978) Highly conserved DNA of
Ti plasmids overlaps T-DNA maintained in plant tumors. Nature 275: 147-149.
Chilton, M.-D., Drummond, M.H., Merlo, D.J., Sciaky, D., Montoya, A.L., Gordon, M.P., &
Nester, E.W. (1977) Stable incorporation of plasmid DNA into higher plant cells: the molecular basis of crown gall tumorigenesis. Cell 11: 263-271.
Christie, P.J., & Vogel, J.P. (2000) Bacterial type IV secretion: conjugation systems adapted to deliver effector molecules to host cells. Trends in Microbiology 8: 354-360.
Christie, P.J., Ward, J.E., Winans, S.C., & Nester, E.W. (1988) The Agrobacterium tumefaciens virE2 gene product is a single-stranded-DNA-binding protein that associates with
T-DNA. J Bacteriol 170: 2659-2667.
Citovsky, V., De Vos, G., & Zambryski, P. (1988) Single-stranded DNA binding protein encoded by the virE locus of Agrobacterium tumefaciens. Science 240: 501-504.
Citovsky, V., Guralnick, B., Simon, M.N., & Wall, J.S. (1997) The molecular structure of
Agrobacterium VirE2-single stranded DNA complexes involved in nuclear import. J
Mol Biol 271: 718-727.
Citovsky, V., Kozlovsky, S.V., Lacriox, B., Zaltsman, A., Dafny-Yelin, M., Vyas, S., Tovkach,
A. & Tzfira, T. (2007) Biological systems of the host cell involved in Agrobacterium infection. Cell Microbiol, 9: 9-20.
Citovsky, V., Wong, M.L., & Zambryski, P. (1989) Cooperative interaction of Agrobacterium
VirE2 protein with single stranded DNA: implications for the T-DNA transfer process. Proc Natl Acad Sci USA 86: 1193-1197.
Citovsky, V., Zupan, J., Warnick, D., & Zambryski, P. (1992) Nuclear localization of
Agrobacterium VirE2 protein in plant cells. Science 256: 1802-1805.
Clauce-Coupel, H., Chateau, S., Ducrocq, C., Niot, V. & Kaveri, S., et al. (2008) Role of vitronectin-like protein in Agrobacterium attachment and transformation of
Arabidopsis cells. Protoplasma 234: 65075
Crane, Y.M. & Gelvin, S.B. (2007) RNAi-mediated gene silencing reveals involvement of
Arabidopsis chromatin-related genes in Agrobacterium-mediated root transformation.
Proc Natl Acad Sci USA 104: 15156–15161.
Dafny-Yelin, M., Levy, A. & Tzfira, T. (2008) The ongoing saga of Agrobacterium–host interactions. Trends Plant Sci 13: 102-105.
Das, A. & Xie, Y.-H. (1998) Construction of transposon Tn3phoA: Its application in defining the membrane topology of the Agrobacterium tumefaciens DNA transfer proteins.
Mol Microbiol 27: 405-414.
De Cleene, M., & De Ley, J. (1976) The host range of crown gall. Bot Rev 42: 389-466.
De Iannino, N.I., & Ugalde, R.A. (1989) Biochemical characterization of avirulent
Agrobacterium tumefaciens chvA mutants: synthesis and excretion of β-(1,2)glucan. J
Bacteriol 171: 2842-2849.

Agrobacterium-Mediated Genetic Transformation: History and Progress

21

Deng, W., Chen, L., Peng, W.-T., Liang, X., Sekiguchi, S., Gordon, M.P., Comai, L., & Nester,
E.W. (1999) VirE1 is a specific molecular chaperone for the exported singlestranded-DNA-binding protein VirE2 in Agrobacterium. Mol Microbiol 31: 1795-1807.
Deng, W., Chen, L., Wood, D.W., Metcalfe, T., Liang, X., Gordon, M.P., Comai, L., & Nester,
E.W. (1998) Agrobacterium VirD2 protein interacts with plant host cyclophilins. Proc
Natl Acad Sci USA 95: 7040-7045.
Depicker, A., Van Montagu, M., & Schell, J. (1978) Homologous sequences in different Ti plasmids are essential for oncogenicity. Nature 275:150-152.
Djamei, A., Pitzschke, A., Nakagami, H., Rajh, I., & Hirt, H. (2007) Trojan horse strategy in
Agrobacterium transformation: abusing MAPK defense signaling. Science 318: 453456.
Douglas, C.J., Halperin, W., & Nester, E.W. (1982) Agrobacterium tumefaciens mutants affected in attachment to plant cells. J Bacteriol 152: 1265-1275.
Douglas, C.J., Staneloni, R.J., Rubin, R.A., & Nester, E.W. (1985) Identification and genetic analysis of an Agrobacterium tumefaciens chromosomal virulence gene. J Bacteriol
161: 850-860.
Durrenberger, F., Crameri, A., Hohn, B., & Koukolikova-Nicola, Z. (1989) Covalently bound
VirD2 protein of Agrobacterium tumefaciens protects the T-DNA from exonucleolytic degradation. Proc Natl Acad Sci USA 86: 9154-9158.
Engstrom, P., Zambryski, P., Montagu, M.V., & Stachel, S. (1987) Charaterization of
Agrobacterium tumefaciens virulence proteins induced by the plant factor acetosyringone. J Mol Biol 197: 635-645.
Escobar, M.A., & Dandekar, A.M. (2003) Agrobacterium tumefaciens as an agent of disease.
TRENDS in Plant Science 8: 380-386.
Fronzes, R., Schafer, E., Wang, L., Saibil, H. R., Orlova, E. V., & Waksman, G. (2009)
Structure of a type IV secretion system core complex. Science 323: 266–268.
Garcia-Rodriguez, F.M., Schrammeijer, B. & Hooykaas, P.J.J. (2006) The Agrobacterium VirE3 effector protein: a potential plant transcriptional activator. Nucl Acids Res 34: 6496–
504.
Gaspar, Y.M., Nam, J., Schultz, C.J., Lee, L.-Y. & Gilson, P.R., et al. (2004). Characterization of the Arabidopsis lysine-rich arabinogalactan-protein AtAGP17 mutant (rat1) that results in a decreased efficiency of Agrobacterium transformation. Plant Physiol. 135:
2162–2171.
Gelvin, S.B. (2000) Agrobacterium and plant genes involved in T-DNA transfer and integration. Annu Rev Plant Physiol Plant Mol Biol 51: 223-256.
Gelvin, S.B. (2003) Agrobacterium-mediated plant transformation: the biology behind the
“gene-jockeying” tool. Microbiol Mol Biol Rev 67: 16-37.
Gelvin, S. B. (2010a) Plant proteins involved in Agrobacterium-mediated genetic transformation. Annu Rev Phytopathol 48: 45–68.
Gelvin, S. B. (2010b) Finding a way to the nucleus. Current Opinion in Microbiology. 13: 53–58.
Ghai, J., & Das, A. (1989) The virD operon of Agrobacterium tumefaciens Ti plasmid encodes a
DNA-relaxing enzyme. Proc Natl Acad Sci USA 86: 3109-3113.
Gheysen, G., Van Montagu, M., & Zambryski, P. (1987). Integration of Agrobacterium tumefaciens transfer DNA (T-DNA) involves rearrangements of target plant DNA sequences. Proc Natl Acad Sci USA 84: 6169-6173.

22

Genetic Transformation

Gillespie, J.J., Brayton, K.A., Williams, K.P., Quevedo Diaz, M.A., Brown, W.C., Azad, A.F.,
& Sobral, B.W. (2010). Phylogenomics reveals a diverse Rickettsiales type IV secretion system. Infect Immun 78: 1809–1823.
Gomis-Ruth, F.X., Moncalian, G., de la Cruz, F., & Coll, M. (2002) Conjugative plasmid protein TrwB, an integral membrane type IV secretion system coupling protein.
Detailed structural features and mapping of the active site cleft. J Biol Chem 277:
7556-7566.
Grange, W., Duckely, M., Husale, S., Jacob, S., Engel, A. & Hegner, M. (2008) VirE2: a unique ssDNA-compacting molecular machine. PloS Biol, 6: 343-351.
Guo, M., Hou, Q., Hew, C. L., & Pan, S. Q. (2007a) Agrobacterium VirD2-binding protein is involved in tumorigenesis and redundantly encoded in conjugative transfer gene clusters. Mol Plant-Microbe Interact 20: 1201-1212.
Guo, M., Jin, S., Sun, D., Hew, C. L., & Pan, S. Q. (2007b) Recruitment of conjugative DNA transfer substrate to Agrobacterium type IV secretion apparatus. Proc Natl Acad Sci
USA 104: 20019-20024.
Guo, M., Gao, D., & Jin, Y. (2009a) Progress in the formation and transfer of Agrobacterium Tcomplex. Pro Biochem Biophys 36: 1408-1414.
Guo, M., Zhu, Q., & Gao, D. (2009b) Development and optimization of method for generating unmarked A. tumefaciens mutants. Pro Biochem Biophys 36: 556-565.
Guo, M. (2010) Discovery and biologocal function identification of Agrobacterium T-complex recruiting protein. Acta Agriculturea Universitatis Jiangxiensis 32: 992-996.
Hawes, M.C., & Smith, L.Y. (1989) Requirement for chemotaxis in pathogenicity of
Agrobacterium tumefaciens on roots of soil-grown pea plants. J Bacteriol 171: 56685671.
Howard, E., & Citovsky, V. (1990) The emerging structure of the Agrobacterium T-DNA tansfer complex. Bioessays 12: 103-108.
Howard, E.A., Zupan, J.R., Citovsky, V., & Zambryski, P.C. (1992) The VirD2 protein of
Agrobacterium tumefaciens contains a C-terminal bipartite nuclear localization signal:
Implications for nuclear uptake of DNA in plant cells. Cell 68: 109-118.
Ilyina, T., & Koonin, E. (1992) Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria. Nucleic Acids Res 20: 3279-3285.
Jasper, F., Koncz, C., Schell, J., & Steinbiss, H-H. (1994) Agrobacterium T-strand production in vitro: sequence-specific cleavage and 5’ protection of single-stranded DNA templates by purified VirD2 protein. Proc Natl Acad Sci USA 91: 694-698.
Jin, S., Roitsch, T., Ankenbauer, R.G., Gordon, M.P., & Nester, E.W. (1990) The VirA protein of Agrobacterium tumefaciens is autophosphorylated and essential for vir gene induction. J Bacteriol 172: 525-530.
Jin, S., Song, Y., Pan, S.Q., & Nester, N.W. (1993) Characterization of a virG mutation that confers constitutive virulence gene expression in Agrobacterium tumefaciens. Mol
Microbiol 7: 555-562.
Kamoun, S., Cooley, M.B., Rogowsky, U.M., & Kado, C.I. (1989) Two chromosomal loci involved in production of exopolysaccharide in Agrobacterium tumefaciens. J
Bacteriol 171: 1755-1759.
Kennedy, B.W. (1980) Estimates of U.S. crop losses to prokaryote plant pathogens. Plant Dis
64: 674-676.

Agrobacterium-Mediated Genetic Transformation: History and Progress

23

Kim, S.I., Veena, J.H. & Gelvin, S.B. (2007) Genome-wide analysis of Agrobacterium T-DNA integration sites in the Arabidopsis genome generated under non-selective conditions. Plant J. 51: 779–791.
Kumar, R.B. & Das, A. (2002) Polar location and functional domains of the Agrobacterium tumefaciens DNA transfer protein VirD4. Mol Microbiol 43: 1523-1532.
Lacroix, B., Li, J., Tzfira, T., & Citovsky, V. (2006a) Will you let me use your nucleus? How
Agrobacterium gets its T-DNA expressed in the host plant cell. Can J Physiol
Pharmacol 84: 333-345.
Lacroix, B., Tzfira, T., Vainstein, A., & Citovsky, V. (2006) A case of promiscuity:
Agrobacterium’s endless hunt for new partners. TRENDS in Genetics 22: 29-37.
Lee, Y., Jin, S., Sim, W., & Nester, E.W. (1996) The sensing of plant signal molecules by
Agrobacterium: genetic evidence for direct recognition of phenolic inducers by the
VirA protein. Gene 179: 83-88.
Lin, Yi-Han, Gao, R, Binns A.N. & Lynn D.G. (2008) Capturing the VirA/VirG TCS of
Agrobacterium tumefaciens. Adv Exp Med Biol 631: 161-177.
Lippincott, B.B., & Lippincott, J.A. (1969) Bacterial attachment to a specific wound site as an essential stage in tumor initiation by Agrobacterium tumefaciens. J Bacteriol 97: 620628.
Llosa, M., Gomis-Ruth, F.X., Coll, M., & Cruz, F. (2002) Bacterial conjugation: a two-step mechanism for DNA transport. Mol Microbiol 45: 1-8.
Llosa, M., Zunzunegui, S., & Cruz, F. (2003) Conjugative coupling proteins interact with cognate and heterologous VirB10-like proteins while exhibiting specificity for cognate relaxosomes. Proc Natl Acad Sci USA 100: 10465-10470.
Loake, G.J., Ashby, A.M., & Shaw, C.M. (1988) Attraction of Agrobacterium tumefaciens C58C1 towards sugars involves a highly sensitive chemotaxis system. J Gen Microbiol 134:
1427-1432.
Lopatin, M.I. (1939) Influence of bacterial root canter on the development of the cherry tree in the orchard. Plant Prot 18:167-173.
Matthysse, A.G., & McMahan, S. (1998) Root colonization by Agrobacterium tumefaciens is reduced in cel, attB, attD, and attR mutants. Appl Environ Microb 64: 2341-2345.
Matthysse, A.G., & McMahan, S. (2001) The effect of the Agrobacterium tumefaciens attR mutation on attachment and root colonization differs between legumes and other dicots. Appl Environ Microb 67: 1070-1075.
Matthysse, A.G., Yarnall, H., Boles, S.B., & McMahan, S. (2000) A region of the Agrobacterium tumefaciens chromosome containing genes required for virulence and attachment to host cells. Biochimica et Biophysica Acta 1490: 208-212.
Mayerhofer, R., Koncz-Kalman, Z., Nawrath, C., Bakkeren, G., Crameri, A., Angelis, K.,
Redei, G.P., Schell, J., Hohn, B., & Koncz, C. (1991) T-DNA integration: A model of illegitimate recombination in plants. EMBO J 10: 697-704.
McCullen C.A., & Binns A.N. Agrobacterium tumefaciens and plant cell interactions and activities required for interkingdom macromolecular transfer. Annu Rev Cell Dev
Biol, 2006, 22: 101-127.
Minnemeyer, S.L., Lightfoot, L.R., & Matthysse, A.G. (1991) A semi-quantitative bioassay for relative virulence of Agrobacterium tumefaciens strains on Bryophyllum daigremontiana. J Bacteriol. 173: 7723-7724.

24

Genetic Transformation

Mysore, K.S., Bassuner, B., Deng, X., Darbinian, N.S., Motchoulski, A., Ream, W., & Gelvin,
S.B. (1998) Role of the Agrobacterium tumefaciens VirD2 protein in T-DNA transfer and integration. Mol Plant-Microbe Interact 11: 668-683.
Nam, J., Matthysse, A.G., & Gelvin, S.B., (1997) Differences in susceptibility of Arabidopsis ecotypes to crown gall disease may result from a deficiency in T-DNA integration.
Plant Cell 9: 317-333.
Nam, J., Mysore, K.S., Zheng, C., Knue, M.K., & Matthysse, A.G., et al. (1999) Identification of T-DNA tagged Arabidopsis mutants that are resistant to transformation by
Agrobacterium. Mol Gen Genet 261: 429-438.
Newton, J.A., & Fray, R.G. (2004) Integration of environmental and host-derived signals with quorum sensing during plant-microbe interactions. Cellular Microbiology 6:
213-224.
Nixon, B.T., Ronson, C.W., & Ausubel, F.M. (1986) Two-component regulatory systems responsive to environmental stimuli share strongly conserved domains with the nitrogen assimilation regulatory genes ntrB and ntrC. Proc Nat Acad Sci USA 83:
7850-7854.
O’Connell, K.P., & Handelsman, J. (1989) chvA locus may be involved in export of neutral cyclic β-1,2 linked D-glucan from Agrobacterium tumefaciens. Mol Plant-Microbe
Interact 2: 11-16.
Otten, L., DeGreve, H., Leemans, J., Hain, R., Hooykass, P., & Schell, J. (1984) Restoration of virulence of vir region mutants of A. tumefaciens strain B6S3 by coinfection with normal and mutant Agrobacterium strains. Mol Gen Genet 195: 159-163.
Palmer, A.G., Gao, R., Maresh, J., Erbiol, W.K. & Lynn, D.G. 2004. Chemical biology of multihost/pathogen interactions: chemical perception and metabolic complementation. Annu Rev Phytopathol 42: 439–64.
Pansegrau, W., Schoumacher, F., Hohn, B., & Lanka, E. (1993) Site-specific cleavage and joining of single-stranded DNA by VirD2 protein of Agrobacterium tumefaciens Ti plasmids: analogy to bacterial conjugation. Proc Natl Acad Sci USA 90: 11538-11542.
Parke, D., Ornston, L.N., & Nester, E.W. (1987) Chemotaxis to plant phenolic inducers of virulence genes is constitutively expressed in the absence of the Ti plasmid in
Agrobacterium tumefaciens. J Bacteriol 169: 5336-5338.
Pitzschke1, A., & Hirt, H. (2010) New insights into an old story: Agrobacterium-induced tumour formation in plants by plant transformation. EMBO J 29: 1021-1032.
Rao, A. Q., Bakhsh, A., Kiani, S., Shahzad, K., Shahid, A. A., Husnain, T., & Riazuddin, S.
(2009). The myth of plant transformation. Biotechnology Advances. 27: 753-763.
Ream, W. (1989) Agrobacterium tumefaciens and interkingdom genetic exchange. Annu Rev
Phytopathol 27: 583-618.
Regensburg-Tuink, A.J., & Hooykaas, P.J. (1993) Transgenic N. glauca plants expressing bacterial virulence gene virF are converted into hosts for nopaline strains of A. tumefaciens. Nature 363: 69-71.
Reuhs, B.L., Kim, J.S., & Matthysse, A.G. (1997) Attachment of Agrobacterium tumefacins to carrot cells and Arabidopsis wound sites is correlated with the presence of a cellassociated, acidic polysaccharide. J Bacteriol 179: 5372-5379.
Ricker, A.J., Berbee, J.G., & Smalley, E.B. (1959) Effects of crown gall and hairy root on the growth of apple trees. Phytopathology 49: 88-90.

Agrobacterium-Mediated Genetic Transformation: History and Progress

25

Robertson, J.L., Holliday, T., & Matthysse, A.G. (1988) Mapping of Agrobacterium tumefaciens chromosomal genes affecting cellulose synthesis and bacterial attachment to host cells. J Bacteriol. 170: 1408-1411.
Rossi, L., Hohn, B., & Tinland, B. (1993) The VirD2 protein of Agrobacterium tumefaciens carries nuclear localization signals important for transfer of T-DNA to plants. Mol
Gen Genet 239: 345-353.
Salman, H., Abu-Arish, A., Oliel, S., Loyter, A., & Klafter, J., et al. (2005) Nuclear localization signal peptides induce molecular delivery along microtubules. Biophys. J. 89, 2134–
2145
Sanders, L., Wang, C.-O., Walling, L., & Lord, E. (1991) A homolog of the substrate adhesion molecule vitronectin occurs in four species of flowering plants. Plant Cell
3: 629-635.
Scheiffele, P., Pansegrau, W., & Lanka, E. (1995) Initiation of Agrobacterium tumefaciens TDNA processing: purified protein VirD1 and VirD2 catalyze site- and strandspecific cleavage of superhelical T-border DNA in vitro. J Biol Chem 270: 1269-1276.
Schilperoort, R.A., Veldstra, H., Warnaar, S.Q. Mulder, G., & Cohen, J.A. (1967) Formation of complexes between DNA isolated from tobacco crown gall tumours and complementary to Agrobacterium tumefaciens DNA. Biochim Biophys Acta 145: 523525.
Schrammeijer, B., Dulk-Ras, A., Vergunst, A.C., Jacome, E.J., & Hooykaas, P.J.J. (2003)
Analysis of Vir protein translocation from Agrobacterium tumefaciens using
Saccharomyces cerevisiae as a model: evidence for transport of a novel effector protein VirE3. Nucleic Acids Research 31: 860-868.
Schrammeijer, B., Risseeuw, E., Pansegrau, W., Regensburg-Tuink, T.J.G., Crosby, W.L., &
Hooykaas, P.J.J. (2001) Interaction of the virulence protein VirF of Agrobacterium tumefaciens with plant homologs of the yeast Skp1 protein. Curr Biol 11: 258-262.
Schroth, M.N., Mccain, A.H., Foott, J.H., & Huisman, O.C. (1988) Reduction in yield and vigor of grapevine caused by crown gall disease. Plant Dis 72: 241-246.
Shaw, C.H.J., Ashby, A.M., Brown, A., Royal, C., Loake, G.J., & Shaw, C.H. (1989) VirA and
G are necessary for acetosyringone chemotaxis in Agrobacterium tumefaciens. Mol
Microbiol 2: 413-417.
Sheng, J., & Citovsky, V. (1996) Agrobacterium-plant cell DNA transport: Have virulence proteins, will travel. The Plant Cell 8: 1699-1710.
Shurvinton, C.E., Hodge, L., & Ream, W. (1992) A nuclear localization signal and the Cterminal omega sequence in the Agrobacterium tumefaciens VirD2 endonuclease are important for tumor formation. Proc Natl Acad Sci USA 89: 11837-11841.
Silver, P.A. (1991) How proteins enter the nucleus. Cell 64: 489-497.
Smith, E.F., & Townsend, C.O. (1907) A plant-tumor of bacterial origin. Scince 24: 671-673.
Smith, V.A. & Hindley, J. (1978) Effect of agrocin 84 on attachment of Agrobacterium tumefaciens to cultured tobacco cells. Nature 276:498–500.
Stachel, S.E., Messens, E., Van Montagu, M., & Zambryski, P. (1985) Identification of the signal molecules produced by wounded plant cells that activate T-DNA transfer in
Agrobacterium tumefaciens. Nature 318: 624-629.
Stachel, S.E., Nester, E.W., & Zambryski, P.C. (1986) A plant cell factor induces
Agrobacterium tumefaciens vir gene expression. Proc Natl Acad Sci USA 83: 379-383.

26

Genetic Transformation

Stachel, S.E., Timmerman, B., & Zambryski, P. (1987) Activation of Agrobacterium tumefaciens vir gene expression generates multiple single-stranded T-strand molecules from the pTiA6 T-region: Requirement of 5’ virD gene products. EMBO J 6: 857-863.
Stachel, S.E., & Zambryski, P.C. (1986) Agrobacterium tumefaciens and the susceptible plant cell: a novel adaptation of extracellular recognition and DNA conjugation. Cell 47:
155-157.
Sundberg, C., Meek, L., Carroll, K., Das, A., & Ream, W. (1996) VirE1 protein mediates export of the single-stranded DNA binding protein VirE2 from Agrobacterium tumefaciens into plant cells. J Bacteriol 178: 1207-1212.
Sundberg, C.D., & Ream, W. (1999) The Agrobacterium tumefaciens chaperone-like protein,
VirE1, interacts with VirE2 at domains required for single-stranded DNA binding and cooperative interaction. J Bacteriol 181: 6850-6855.
Swart, S., Logman, T.J., Smit, G., Lugtenberg, B.J., & Kijne, J.W. (1994) Purification and partial characterization of a glycoprotein from pea (Pisum sativum) with receptor activity for rhicadhesin, an attachment protein of Rhizobiaceae. Plant Mol Biol 24:
171-183.
Tao, Y., Rao, P.K. Bhattacharjee, S. & Gelvin, S.B. (2004) Expression of plant protein phosphatase 2C interferes with nuclear import of the Agrobacterium T-complex protein VirD2. Proc Natl Acad Sci USA 101: 5164–5169.
Thomashow M.F., Karlinsey J.E., Marks J.R., & Hurlbert R.E. (1987) Identification of a new virulence locus in Agrobacterium tumefaciens that affects polysaccharide composition and plant cell attachment. J Bacteriol 169: 3209-3216.
Tinland, B., Koukolikova-Nicola, Z., Hall, M.N., & Hohn, B. (1992) The T-DNA-linked VirD2 protein contains two distinct functional nuclear localization signals. Proc Natl Acad
Sci USA 89: 7442-7446.
Tinland, B., Schoumacher, F., Gloeckler, V., Bravo-Angel, A.M., & Hohn, B. (1995) The
Agrobacterium tumefaciens virulence D2 protein is responsible for precise integration of T-DNA into the plant genome. EMBO J 14: 3585-3595.
Tomlinson, A.D. & Fuqua, C. (2009) Mechanisms and regulation of polar surface attachment in Agrobacterium tumefaciens. Curr Opin Microbiol. 12: 708–714.
Turk, S.C.H.J., Van Lange, R.P., Regensburg-Tuink, T.J.G., & Hooykaas, P.J.J. (1994)
Localization of the VirA domain involved in acetosyringone-mediated vir gene induction in Agrobacterium tumefaciens. Plant Mol Biol 25: 899-907.
Tzfira, T., & Citovsky, V. (2000) From host recognition to T-DNA integration: function of bacterial and plant genes in the Agrobacterium-plant cell interaction. Mol Plant
Pathol 1: 201-212.
Tzfira, T., & Citovsky, V. (2002) Partners-in-infection: host proteins involved in the transformation of plant cells by Agrobacterium. TRENDS in Cell Biology 12: 121-129.
Tzfira, T., & Citovsky, V. (2006) Agrobacterium-mediated genetic transformation of plants: biology and biotechnology. Curr Opin Biotechnol 17: 147-154.
Tzfira, T., Li, J., Lacroix, B. & Citovsky, V. (2004) Agrobacterium T-DNA integration: molecules and models. Trends Genet 20: 375–83.
Tzfira, T., Vaidya, M., & Citovsky, V. (2001) VIP1, an Arabidopsis protein that interacts with
Agrobacterium VirE2, is involved in VirE2 nuclear import and Agrobacterium infectivity. EMBO J 20: 3596-3607.

Agrobacterium-Mediated Genetic Transformation: History and Progress

27

Tzfira, T., Vaidya, M. & Citovsky, V. (2002) Increasing plant susceptibility to Agrobacterium infection by overexpression of the Arabidopsis nuclear protein VIP1. Proc Natl Acad
Sci USA 99: 10435–440
Van Attikum, H., Bundock, P. & Hooykaas, P.J.J. (2001) Non-homologous end-joining proteins are required for Agrobacterium T-DNA integration. EMBO J 20: 6550–58.
Van Larebeke, N., Enbler, G., Holsters, M., Van Den Elsacker, S., Zaenen, I., Schilperoort,
R.A., & Schell. J. (1974) Large plasmid in Agrobacterium tumefaciens essential for crown gall-inducing ability. Nature 252: 169-170.
Vanlentine, L. (2003) Agrobacterium tumefaciens and the plant: the David and Goliath of modern genetics. Plant Physiol 133: 948-955.
Veluthambi, K., Ream, W., & Gelvin, S.B. (1988) Virulence genes, borders, and overdrive generate single-stranded T-DNA molecules from the A6 Ti plasmid of
Agrobacterium tumefaciens. J Bacteriol 170: 1523-1532.
Vergunst, A.C., Lier, M.C.M., Dulk-Ras, A.D., & Hooykaas P.J.J. (2003) Recognition of the
Agrobacterium tumefaciens VirE2 translocation signal by the VirB/D4 transport system does not require VirE1. Plant Physiol 133: 978-988.
Vergunst, A.C., Lier, M.C.M., Dulk-Ras, A.D., Stuve, T.A.G., Ouwehand, A., & Hooykaas
P.J.J. (2005) Positive charge is an important feature of the C-terminal transport signal of the VirB/D4-translocated proteins of Agrobacterium. Proc Natl Acad Sci
USA 102: 832-837.
Vergunst, A.C., Schrammeijer, B., Dulk-Ras, A., Vlaam, C.M.T., Regensburg-Tuink, T.J.G., &
Hooykaas, P.J.J. (2000) VirB/D4-dependent protein translocation from
Agrobacterium into plant cells. Science 290: 979-982.
Vogel, A.M., & Das, A. (1992) Mutational analysis of Agrobacterium tumefaciens VirD2: tyrosine 29 is essential for endonuclease activity. J Bacteriol 174: 303-308.
Vogel, A.M., & Das, A. (1994) Mutational analysis of Agrobacterium tumefaciens pTiA6 virD1: identification of functionally important residues. Mol Microbiol 12: 811-817.
Vogel, A.M., Yoon, J., & Das, A. (1995) Mutational analysis of a conserved motif of
Agrobacterium tumefaciens VirD2. Nucleic Acids Res 23: 4087-4091.
Wagner, V.T., & Matthysse, A.G. (1992) Involvement of a vitronectin-like protein in attachment of Agrobacterium tumefaciens to carrot suspension culture cells. J Bacteriol
174: 5999-6003.
Wang, K., Herrera-Estrella, A., & Van Montagu, M. (1990) Overexpression of virD1 and virD2 genes in Agrobacterium tumefaciens enhances T-complex formation and plant transformation. J Bacteriol 172: 4432-4440.
Wang, Y., Gao, R. & Lynn, D.G. (2002) Ratcheting up vir gene expression in Agrobacterium tumefaciens: coiled-coil in histidine kinase signal transduction. Chembiochem 3: 311–
317.
White, P.R., & Braun, A.C. (1941) Crown gall production by bacteria-free tumor tissues.
Science 94: 239-241.
Winans, S.P. (1992) Two-way chemical signaling in Agrobacterium-plant interactions.
Microbiol Rev 56: 12-31.
Yusibov, V.M., Steck, T.R., Gupta, V., & Gelvin, S.B. (1994) Association of single-stranded transferred DNA from Agrobacterium tumefaciens with tobacco cells. Proc Natl Acad
Sci USA 91: 2994-2998.

28

Genetic Transformation

Zaenen, I., Van Larebeke, N., Teuchy, H., Van Montagu, M., & Schell, J. (1974) Supercoiled circular DNA in crown-gall inducing Agrobacterium strains. J Mol Biol 86: 109-127.
Zambryski, P., Joos, P.H., Genetello, C., Leemans, J., Van Montagu, M., & Schell, J. (1983) Ti plasmid vector for the intriduction of DNA into plant cells without alteration of their normal regeneration capacity. EMBO J 2: 2143-2150.
Zhu, J., Oger, P.M., Schrammeijer, B., Hooykaas, P.J.J., Farrand, S.K., & Winans, S.C. (2000)
The bases of crown gall tumorigenesis. J Bacteriol 182: 3885-3895.
Zhu, Y., Nam, J., Humara, J.M., Mysore, K.S., Lee, L.Y., Cao, H., Valentine, L., Li, J., Kaiser,
A.D., & Kopecky, A.L., et al. (2003) Identification of Arabidopsis rat mutants. Plant
Physiol 132: 494-505.
Ziemienowicz, A. (2001) Odyssey of Agrobacterium T-DNA. Acta Biochimica Polonica 48: 623635.
Ziemienowicz, A., Gorlich, D., Lanka, E., Hohn, B., & Rossi, L. (1999) Import of DNA into mammalian nuclei by proteins originating from a plant pathogenic bacterium. Proc
Natl Acad Sci USA 96: 3729-3733.
Ziemienowicz, A., Merkle, T., Schoumacher, F., Hohn, B., & Rossi, L. (2001) Import of
Agrobacterium T-DNA into plant nuclei: two distinct functions of VirD2 and VirE2 proteins. Plant Cell 13: 369-383.
Zorreguieta, A., & Ugalde, R.A. (1986) Formation in Rhizobium and Agrobacterium spp. of a
235-kilodalton protein intermediate in β-D-(1-2)glucan synthesis. J Bacteriol 167:
947-951.
Zupan, J., & Zambryski, P. (1997) The Agrobacterium DNA transfer complex. Critical Reviews in Plant Sciences 16: 279-295.

2
Structure-Function Analysis of Transformation Events
1Institute

Yuri N. Zhuravlev1 and Vladik A. Avetisov2

of Biology and Soil Science, Russian Academy of Sciences, Far Eastern Branch
2Semenov Institute of Chemical Physics, Russian Academy of Sciences
Russian Federation

1. Introduction
At the beginning of the twenty-first century, critical reforms were outlined in biology. This was due to the fact that the increase of information garnered from the sequences of informational molecules (DNA, RNA and proteins) and their perception by the scientific community were incompatible with the narrow horizons of the dogmas and paradigms that shaped the ideology of biological knowledge at the end of the last century. The clear linear representations that were invoked during the initial period of the development of molecular biology were at first encountered with numerous exceptions to these "clear" rules and then lost in the avalanche of new representations that were incompatible with the linear schemes.
As a result, new directions of study and even meta-directions (e.g., epigenetics, epigenomics and biosemiotics - for reviews, see Allis et al., 2007; Ferguson-Smith et al., 2009; Hoffmeyer,
2008) have arisen, and functionally oriented divisions of biological science have formed that are named as various “–omics” (including the extravagant “biblioma”- Abi-Haidar et al.,
2007), the RNA machine (Amaral et al., 2008), and the molecular mechanisms of cell cycle regulation and individual development. In turn, these disciplines have demanded new theoretical implementations involving novel approaches from the theory of networks and systems (Barabasi et al., 2000; West & Brown, 2005; Zaretzky & Letelier, 2002).
The last two decades have been particularly rich in discoveries concerning the mechanisms of the expression of biological information, such as new ways of alternative splicing
(Rodríguez-Trelles et al., 2006), a variety of functions for non-coding transcripts and the role of short RNAs as forward and reverse regulators (Mattick et al., 2009). Presently, we have a situation in biology in which it would be nearly impossible to publish a book with the title
“DNA Makes RNA Makes Protein” (Pentris et al., 1983). However, another book, with a title equally as concise and perfectly reflecting the new biological paradigm, has not yet been written. In other words, a revision of the old concepts has not been completed with a new and clear way of structuring the data from the quickly growing "body" of biological science.
Theoretical biology is also at a critical state, which is characterized by attempts to formulate or reformulate the basic concepts and axioms of the discipline. Signs of such attempts may be the revival of interest in the definition of life, the revision of “sets” and even “types”, signs that distinguish the living from the non-living and increased attention to the genotypephenotype relationship.

30

Genetic Transformation

This specific creative climate is generated in the interaction zone of theoretical biology and directions relating to the theory of artificial intelligence1, and it is packed with the new fundamental knowledge that artificial intelligence has absorbed from the different fields of mathematics, physics, and logic (see reviews in Bersini, 2009; Cárdenas et al., 2010; Longo,
2010). It is in this climate that a systems approach to the analysis of biological phenomena is the most productive, yet difficult, for biologists. In journals, the contents of which always gravitate toward theoretical biology, publications on autopoesis, autonomy and incompleteness, and the determinism and unpredictability of biological systems have become commonplace. Notable among these reports is a group of publications that explore the phenomenon of causal closure in living systems as one of the key events on the way to biological complexity (Cárdenas et al., 2010; Kauffmann et al., 2008; Longo, 2010).
Practical achievements of new biological technologies are also impressive. Transgenic plants with useful properties have spread across the globe, displacing more than half of the varieties generated by conventional breeding (Godfray et al., 2010). Information about
“cloned” mammals and “replacement components” of mammalian organisms has become standard (e.g., see Ficz et al., 2009; Morgan, et al., 2005). Nevertheless, the theoretical basis for even the most impressive achievements in biotechnology remains underdeveloped, and many promises remain unfulfilled or have been replaced with surrogate solutions.
There is a similar situation with regard to experiments on the genetic transformation of biological objects, where many publications use the terminology and views of the last century. Although many of these terms and concepts are still relevant, it seems appropriate to review the most common events of transformation from a position of a new system of knowledge. We believe that such an analysis will be able to correctly classify several important areas of transformation, to discuss the reasons for failures in some cases and to outline ways to achieve the assigned goals. Therefore, we do not advocate a quick alteration of the terminology and concepts or the creation of a new theoretical foundation of biological science. Personally, we cannot proceed without the concepts of gene, species and many other supposedly “outdated” terms. The task of this publication is to gain a deeper understanding of examples of genetic engineering, those acquired in biotechnology and often having analogs in the wild, with help of a structure-function analysis and to apply new knowledge for the planning of experiments and the prediction of their results. Likely, even this limited goal can scarcely be solved in one study. However, we hope that even the smallest success in this direction will soon be in demand.
We associate certain expectations with the operational presentation of a biological object, where, in the most general mode, the program elements (see below for content on the term
“program element” and other elements of the triad) are mapped into the observables.
Application of an operational definition of a biological object can help to distinguish (rather conditionally) the mappings associated with the transformation of structures (actual objects) from those associated with the transformation of functions (relations). Such a distinction plays an important role in the interpretation of the transformation events because the result of transformation can be involved primarily in the structural flow or, conversely, in the functional flow of the individual development of the transformed object.

1

Henceforth, terms and metaphors will be used, which may create the impression that the authors present an organism similar to a computer. In fact, it is not, and we do not know exactly to what extent the notion about the organism can be reduced to the notion about the machine.

Structure-Function Analysis of Transformation Events

31

In this work, we logically elaborate on the basic ideas of the entity-set representation of biological objects, which has been performed earlier in the framework of plant morphogenesis (Zhuravlev & Omelko, 2008), and show how they can be exploited to describe the individual development of transformed organisms. The chapter is organized as follows. In the first two sections, we determine which transformation events will be included in our analysis and what the relationship is with the individual development of the object. The next two sections present a description of the operational triad as a means of creating a biological object and as a target for transformation. The fifth and largest section provides an analysis of the changes of individual development, which are induced by transformation in the transgenic organisms. Some examples from experiments with producers of secondary metabolites and from experiments on the re-programming of the somatic cells of plants and animals are scrutinized. In the sixth section, the results of the performed analyses are summarized to allow some predictions and suggestions. Last, the conclusion section draws attention to the complex and convoluted character of the mappings between programmed and phenotypic characters that allows for deterministic and probabilistic manifestations.

2. What is a transformation event?
The problem specified in the title of this section is more complex than it seems. This is well illustrated by the example of attempts to define life itself (Luisi, 1998; Ruiz-Mirazo et al.,
2004; Zhuravlev & Avetisov, 2006), and defining transformation is equally as difficult. Of course, we can agree to interpret transformation as a particular biotechnological method, consisting of the construction of recombinant DNA and the subsequent introduction of the resulting structure into a living system, but this interpretation does not coincide with all of the similar phenomena in the wild. This idea relates to questions of whether we consider transformation as an exclusively human invention (i.e., as one of the techniques in the arsenal of our human exploration of reality) or an invention of nature, achieved long before the human mind and related to the arsenal of ‘becoming’ in the living world? The depth of our understanding of transformation events will depend greatly on what point of view is preferred. The phenomenon of transformation was discovered in the late 1920s, when F. Griffith established that pneumococcal cells could convert from a harmless form to a disease-causing type. This transformation was heritable, and its “transforming principle” was identified as
DNA. Since then, and until very recently, transformation events have been associated with
DNA. The Encyclopedia Britannica describes transformation in biology as2: ’one of several processes by which genetic material in the form of ‘naked’ deoxyribonucleic acid (DNA) is transferred between microbial cells. Its discovery and elucidation constitutes one of the significant cornerstones of molecular genetics. The term also refers to the change in an animal cell invaded by a tumour-inducing virus.’
In microbiology, transduction events are accepted as distinguishable and considered separately as a process very similar to transformation where genetic recombination in bacteria results from the incorporation of a fragment of bacterial DNA into the genome of a bacteriophage. Then, during infection, this fragment (together with bacteriophage DNA) is
2

http://www.britannica.com/EBchecked/topic/602613/transformation

32

Genetic Transformation

carried into another host cell; this process will be covered in more detail in Section 5.1.
The field of transformation is closely connected with genetic engineering, which assumes the development of approaches to manipulate the genetic material of a cell to produce new characteristics in an organism. Genes from plants, microbes, and animals can be recombined
(recombinant DNA) and introduced into the living cells of any of these organisms.
Organisms that have had genes from other species inserted into their genome (the full complement of an organism 's genes) are called transgenic.3
The abovementioned examples are positioned inside the scope of transformation, but they illustrate a trend toward a greater differentiation in the scope of transformation. For example, there is a tendency in the understanding of transgenic organisms to exclusively those obtained by so-called gene cloning. However, this differentiation gives rise to restrictions. In the specific case of transgenes, primary meaning is associated with the mechanism of the creation of the transgene, and the definition sets aside the result of that action: whether or not a transformed phenotype was created. We emphasize here that the first transformations were found at the phenotypic level, and therefore, the restriction of the notion of transformation strongly constricts the number of examples of transformation and narrows our outlook on this issue. Based on such a narrow view, it is impossible to determine what constitutes a "transformation event". Assume that we have transformed cells using recombinant DNA and have shown the presence of the inserted fragment in the
DNA of recipient cell. Can we consider the event of transformation accomplished? Of course, the appearance of the expected sign inclines us to a positive answer, but what can we say when the recombinant DNA is integrated successfully and the expected observable sign does not appear? Some specific cases of transgene silencing will be discussed below, but here, we note only that the transformation event can be viewed as the action itself: the transformation and its result, the manifestation of a new trait. This is a common situation where a function is identified with the result of its action, and this situation tells us that we are dealing with events that can be modeled as a function or as a map. This circumstance will be used in the next section.
It should be emphasized that to understand the mechanism of the expression of observable traits in the cell and to assess the results of an experimental intervention in the operation of this mechanism, we must take the broadest approach possible. To do this, we must replace the concept of the gene with the concept of a hereditary trait, thus referring to the events in transformation as whether the creation (or loss) of the trait is unusual (or usual) in the antecedent cycles of the development of the individual. A direct consequence of such a change will be that the terms of our consideration will include all of the operations that result in the transformation of an organism, whatever their origin may be. This situation will be complicated by the fact that all types of mutations, lateral transfer and hybridization may fall within such operations. We must, for example, classify in this way the phenomenon of the spread of unrelated traits in plants with pollen (in both experimental and natural conditions, equally). Strictly speaking, according to our viewpoint, all of these events must be considered in their relation to transformation in the wide sense. For example, viral diseases must be considered here because they induce heritable changes of phenotypic traits. This effect is especially interesting with regard to functional shifts in the host, and it is appropriate place to remember that RNA-directed DNA methylation was discovered in viroid-infected tobacco plants (Wassenegger et al., 1994).
3

http://www.britannica.com/EBchecked/topic/463327/plant-disease

Structure-Function Analysis of Transformation Events

33

However, it is clear that such a broad analysis cannot be the subject of merely a single chapter. Therefore, for our analysis, we have chosen only a few examples of the range of events that relate to the production of transgenic organisms, corresponding to the set {Pr,Pd}, where Pr and Pd denote the sets of recipient and donor characters, respectively. We will include constant reminders that we have consciously limited the scope of our research and that the events analyzed, in fact, can be assessed using scales of different dimensions. Of course, this is a fairly broad idea, but it is this breadth that allows us to make the necessary generalizations. 3. Schematic representation of the development of multicellular organisms
In describing the process of transformation, schemes and diagrams are a common means of representation, but only the structure of the recombinant DNA is usually represented on the schemes. The second participant (i.e., the object of transformation) is usually absent, apparently due to the complexity of its presentation with the same level of detail as for the recombinant DNA. However, to analyze transformation events in this manner, refinement is not required. We need a level of generalization (modeling) of individual development, which will illustrate the relationships of the host and transforming principle.
All of the possible alternatives for the development of an individual can be reduced to a single module, which is the transition (of cells, tissues, organisms, systems) from the less differentiated state to a more differentiated one. The transition itself can occur as a division, multiplication or death. Consequently, this versatile module can be represented as an expression (1):
{(G,Ph)s→(G,Ph)f},

(1)

where G indicates genotype, Ph indicates phenotype, and s and f indicate the initial (start) and final states, respectively.
A schematic representation of the plant organism in vitro has been published previously
(Zhuravlev & Omelko, 2008). Additionally, a rather similar schema, based on the conventional binate idea of genotype-phenotype interactions and also demonstrating
EVO:DEVO relationships, has been recently published (Andrade, 2010). Here, we present a modified scheme, which provides the relationship between genotype and phenotype as relationships between sets of inherited and observed properties (Fig. 1).
The scheme in Fig. 1 illustrates the relationship between genotype and phenotype in the rather classical representation, namely from the viewpoint that the genotype, G, is a preimage of the phenotype, Ph. However, the first attempt to differentially trace the relationships of these two moieties already meets with some difficulties. We cannot trace their transmutations as two parallel lines, where each previous state of G or Ph has been converted into the next state. Instead, every division induces changes in G between two states that correspond to the active and condensed state of chromatin. Only the active state of chromatin opens the possibility for G to be mapped into Ph. This type of mapping is dead-end in some sense.
An absence of direct connections between the states of phenotype is of importance in this schema because, for the external observer, the ontogeny of the object appears as a succession of observables. However, we cannot figure the continuous mapping, such as
Ph1→Ph2→Ph3..., as the appearance of every new state of Ph is a result of a rather long route of mappings, each starting from new state of G. The diagram (2) below is not commutative.

34

Genetic Transformation

Fig. 1. Scheme of genotype-phenotype interactions during the succession of events in one particular cell line. G0 corresponds to the compact chromatin state in the course of cell division, and Gd corresponds to the active chromatin state when the expression of the genes responsible for the phenotypic traits is permitted; Phi - the phenotypic character.
(2)
As we will demonstrate, this idea reflects and explains some of the difficulties of dedifferentiation in experiments on nuclear transfer. We can suppose that this also was a reason why G. Longo and P.-E. Tendero asserted that the existence of empirical correlations between genotypic and phenotypic modifications does not demonstrate the existence of a direct causal relationship between them (Longo, 2009; Longo & Tendero, 2007).
If we use the elaborated diagram (2) and scheme of the development of an individual cell line (Fig. 1) to determine the position of a foreign gene in the transformed genome, we will see that the only place for transgene incorporation is in the set of the oscillating states of G.
However, this set is inhomogeneous, and the dynamics of expressions in the transition from
G0 to Gd is not equal to that in the opposite direction because the composition of chromatin, its architecture and the ways of its decoding change in this way. Therefore, in some definite cases, the fate of a transgene will be dependent on its position and the direction of chromatin modeling.

4. Operational triad and individual development
For further analysis of transformation, we require a definition of a biological object. We hypothesized that the definition of a biological object is a task comparable with that for the definition of life itself. Insurmountable obstacles for the latter definition have been reviewed in many publications (Luisi, 1998; Ruiz-Mirazo et al., 2004; Zhuravlev & Avetisov, 2006).

Structure-Function Analysis of Transformation Events

35

Therefore, we will attempt to define a biological object operationally, in a rather narrow sense, which reflects the individual development of the object. We believe that it will be sufficient to restrict our analytical purpose to the scope of ontogeny. Moreover, we believe that the operational representation of a biological object can be reduced to the analysis of the relationships between the hereditary characteristics of an object and their manifestations; in other words, between the genotype and phenotype. However, the notions of genotype and phenotype have both been subjected to a recent radical revision (Costa, 2008; Fox Keller &
Harel, 2007; Gerstein et al., 2007; Snyder & Gerstein, 2003).
With the new molecular knowledge that was partially reviewed in the Introduction section and is partially presented below, it seems problematic to associate the content of an inherited character with a single DNA fragment. As a reflection of the problem, the publications in which the conventional concept of the gene was proposed should be replaced by a “more functional” concept, such as the genon (Scherrer & Jost, 2007) and the deme-bene concept (Fox Keller & Harel, 2007). Within these ideas, the notion of the irreducibility of the content of heritable characters of an organism to a single molecule of
DNA has been developed, causing researchers to suggest hereditary mechanisms "beyond the genes" (Amaral & Mattick, 2008; Fox Keller & Harel, 2007), whereas others have defined the genome as an RNA machine (Amaral et al., 2008).
In this context, it seems reasonable to interpret the informational content of DNA and other molecules possessing informational content as a databank or "polytypic library" that causes or begets (in an operational sense) the observable characteristics of the biological object.
With this interpretation, hereditary characteristics are not directly associated with certain nucleotide sequences but with a set of characters with respect to which the observable characteristics, such as phenotypic traits, are understood as an operational image of this set.
In other words, hereditary characteristics are understood as (remote or direct) operational pre-images of the observable characteristics. However, the cause-and-effect relationships between the pre-images and the observables, even in the case of "typical" transcription/translation, are not (unambiguously) determined. The observable characteristics of the same objects, such as observables of insects during metamorphosis, can vary greatly at different stages of development, while their DNA or other informational structures (pre-images) remains the same. To make the relationship between the pre-image and the image clearer, we must introduce the operational component, which can be attributed neither to pre-image characters nor to the observable characteristics. One can find one of the first rationales of the need for such a similarity of the operating system in
Hoffmeyer’s early publication, where he stated ’that the conversion of a one-dimensional sequence of symbols, e.g. “DNA inscription” … in a three-dimensional organism’ has to be deciphered (Hoffmeyer, 1996, p. 20).
To meet these requirements, we introduce the notion of a function in a broad sense, F. Thus, the biological object can be operationally represented by a short universal list:
O=(P,F,Ph)

(3)

The symbol G, used above in schemes (2) and (3), is replaced with P in expression (3). This may lead to confusion, meaning that we “extract” DNA from the complex image of chromatin to obtain a pure program. Indeed, for our task, we must separate the DNA moiety from the other content of chromatin. However, we interpret the program character more broadly. The programs, P, are understood as characteristics of an informational nature

36

Genetic Transformation

(e.g., instructions or directives) that present the informational content inherent in biological objects. In particular, the programs constitute the operational pre-images of the observables.
The most famous, but not the only possible carriers of instructive information, are fragments of DNA that encode proteins. The functions, F, are the operations per se that implement interrelationships between the programs, as well as the relationships between the programs and the observables. From the latter, it becomes clear that the part of chromatin released after “DNA extraction” can be considered as a property of F.
The observables are the structural and/or functional characteristics of a biological object that can be established by measurements of the object in its interaction with the environment. Phenotypic characteristics of an organism, Ph, as observables, are well known, but are not the only possible examples of such characteristics. Therefore, any current state of a biological object is referred to as the particular combination of P-, F-, and Ph-characters (a triad), i.e., the object itself and its current states can be represented by the composition of the following general notations:
F: P→Ph

(4)

Such organization allows the object to be represented as both a self-making entity and an element of a self-making entity of higher rank. Similarly, the cell in its operational representation can be considered as an individual entity and as an element of an entity of higher rank (e.g., a tissue or organ). In the biological world, before the appearance of mankind, a biological object was solely executor of any its representation. An object creates itself, displays itself in the surroundings as a successive representation of states of creation
(becoming) and interacts with its surroundings in nature.
The triad is understood by us as an operational unit that helps us to represent the individual development as a succession of directed mappings of operational units working in sequential and parallel modes, with cis- and trans-interactions between the units, their compositions, and nests. This can be implemented in the example of a promoter DNA fragment. This fragment can be considered as an argument for several different functions.
Particularly, in the course of DNA replication, it is a part of the DNA strand in a chromosome; it is a small part of the bigger argument. However, the promoter can be considered as an entirely independent argument when it is modified by a methyltransferase or other nuclear enzyme. Finally, when specific regulators of transcription, such as protein repressor complexes (Bantignies & Cavalli, 2006), bind to the chromatin, the promoter fragment of DNA can again be considered as part of the larger argument (of collective body of all repressed promoters).
Such manifold representation is characteristic of many informational molecules and their fragments in the cell. A more detailed analysis in this vein requires the assistance of relevant mathematical languages, as was validated in Mossio et al. (2009). To obtain a general image of the diversity of representations characteristic to elements of the triad, we confine ourselves to the following schematic representation (Fig. 2).
The scheme in Fig. 2 is based on the distributed representation of the existence of two functionally different types of cells (germ and somatic) in a multi-cellular organism.
Divisions of cells in the germ line are divisions where non-differentiated cells are obtained as a result of the division of pre-existing (meristem or stem) non-differentiated cells.
Landscapes of methylation and other labels distributions are very similar in generations of both germ cell lines and meristematic cells. The totipotency of these kinds of cells has been demonstrated in experiments with both plants and animals (Batygina, 2009; Nagy et al.,

Structure-Function Analysis of Transformation Events

37

1993; Takebe, 1968). Actually, every division in germ cells can be regarded as the identity map or the identity function.
Conversely, the mappings that lead to the creation of observables form a different class of maps, which is performed by different functions. To distinguish between these functions, we introduce the symbols φ and f (see Fig. 2). Both classes of functions can be divided into more-detailed subclasses in accordance with their role in the development of the individual.
Thus, the function of the substitution of histones with polyamines in developing sperm can be considered as a subclass of the function φ-class. In turn, functions f1, f2, f3... can be considered as subclasses of functions in different tissues and organs.
It must be emphasized that functional activities corresponding to symbols φ and f are often inconsistent with each other. It can be a consequence of the fact that chromatin expression activity is inconsistent with some stages of the cell cycle (Jacobs, 1995). In contrast to scheme
1 and diagram 2, the relationship between genotype and phenotype is not visible in Fig. 2.
This relationship is symbolized by the differential activity of genes in cells in different states
(note the different color of the dots in the nuclei). The attempt to represent the relationship in more detail leads to a catastrophic growth in the complexity of the representation, as can be seen in an article representing the genetic landscape of a cell (Costanzo et al., 2010).

Fig. 2. Scheme illustrating the interrelationships between the elements of the operational triad in two lines of cells in a developing organism. The set of P elements is roughly the same for both germ and somatic cells. However, two different types of functions are associated with these two main directions of cell division in the embryo. Thus, the symbols φ and f are assigned the divisions of the germ and somatic cells, respectively. S0, Si and Sf symbolize the initial, intermodal and final states of the object, respectively. The dots of different colors in the nuclei of the cells denote the differential activity of the chromatin.

38

Genetic Transformation

However, the relationships represented in Fig. 2 are sufficient to argue that these relationships cannot be interpreted as a one-to-one mapping in the majority of cases.
Moreover, most of the maps that precede the final (producing the observable) map cannot be expressed in terms of states. The latter entails a specific architecture of the biological object where the set of programs and data are “wrapped” in several shells of specifically arranged mappings. Only the outer shell of observables participates in the contact with surroundings, though many inner layers include the measurable structures that can be identified as observable.
4.1 How many units in dividing cell are portable?
In the beginning of this section, we will emphasize the complex design of chromatin. This complexity is specific to biology because this feature is not an invariant measure, but it develops in the course of the individual development of the object. Moreover, this complex body builds itself of its own accord. During this building, the different structures of chromatin may be interpreted as functions and, thereafter, can be applied to other structures of chromatin as to the arguments. Thus, the repressive complex PRC1 acts as a function for methylated promoter though both, the complex and promoter, are constituents of chromatin. Due to this activity, an inseparable complex of DNA and other chromatin structures carrying general function, F, are created.
The idea of the inseparability of DNA and other chromatin structures is not yet generally acknowledged. Researchers and philosophers, seeking to understand the role of DNA in a living organism, have considered the portability feature of DNA as an indication that it belongs to the world of software. For example, G. Longo (2009) writes ’…Ending with portability of software: even on different, but suitable environment, a fortiori over identical environments, programs may be repeated at will. And it works’. We contend that this argument is not universal. Any enzyme will work in a suitable environment. The idea of inseparability consists of the affirmation that no single, inseparable part of an object can be extracted from the object (or system) without the complete destruction of the object. In other words, the physical extraction of DNA from the object will destroy this object as an individual. Of course, naked DNA transferred to another suitable environment (hardware) can realize itself through the interaction with this new environment, but the probability that this realization will result in the creation of an initial object is negligible. Indeed, such is only the case with rather complex entities. We can take numerous examples of the transmission of infectious agents by the naked DNA of viruses and bacteriophages. However, these objects are devoid of individuality hereupon one cannot decide whether the initial object was reproduced or not.
In all cases, when the matter is the division or multiplication of cells, where we have to use the term chromatin, the individuality of the object is connected with the DNA-protein complex. At the current level of knowledge, we cannot exclude the fact that this complex is even more complicated and involves an RNA component (Amaral & Mattick, 2008; Yao,
2008). Of course, these two components (protein and RNA) possess a portable nature.
For example, what is observed in experiments on vegetative plant hybridization? We know that grafting to cold-resistant stock increases the cold resistance of the graft. The graft of a tall plant becomes stunted even if there is a small insertion of the dwarf plant between the root and stem. It is unlikely that we would have reason to believe that these changes in phenotype are associated with the transportability of DNA. The transfer of these properties

Structure-Function Analysis of Transformation Events

39

can be assumed to involve two other components of chromatin. There is experimental evidence that certain transcription factors (Kim et al., 2002) and short RNAs may be regarded as mobile signaling molecules (Dinger et al., 2008).
The examples of vegetative hybridization discussed here indicate that very distinct and specific phenotypic traits can be created by means of these signaling molecules. However, if this is so, we can no longer assert that all of the specific information is concentrated in the
DNA. Thus, we would need to accept the idea that the transportability of the other components of chromatin is relevant for the phenotypic manifestations of living organisms.
We hope that due to this short analysis of chromatin dynamics, we succeeded in the elaboration of the chromatin image as a supramolecular and complex (in chemical sense) body. This body, however, is an indispensible part of the cell and has multifold connections with the rest part of the cell (and organism). Nevertheless, chromatin, as a specific formation of living cell, possesses its own intrinsic topology and dynamics. DNA and some proteins are the regular constituents of chromatin whereas many others signal molecules can incorporate into the system, reactivate and remodel corresponding sites and leave the system. The aggregation of signal molecules with the meaning-bearing fragments of constituent parts can radically convert the functional meaning of these fragments as transmutation functions in arguments. As a result, composition and orientation of operational units in the chromatin body will change too. The individual development of a biological object is, to a large extent, offered by the dynamics of the functional part of chromatin body.

5. Operational triads as targets for transformation
From the operational definition of a biological object established in the previous section, it follows that the individual development can be understood as successions of continuous mappings that build the structure of the object as a complex web, with branchings and the interactions between the operational units. However, these branchings and interactions entangle the web. Even the task of finding one particular fragment of DNA that encodes a necessary protein, among 35,000 such fragments, which together make up scarcely more than 1.5% of the total DNA, cannot be solved by a simple search. This creates a problem that is characteristic of computing science, called data typing, which has some analogs in biology (e.g., blood typing and DNA fingerprinting). In large-scale typing in cell, transposons apparently take part (von Sternberg & Shapiro, 2005). However, in this specific case, DNA typing is a function-oriented process where the typing is performed from the viewpoint (and on behalf) of becoming an operating system. The typed data, P, can be properly treated with the corresponding functions, F, and the results of this processing are handled by other functions. Only after numerous iterations, recursions and destruction of intermediate states are a set of observables, Ph, corresponding to the current state of the object, created.
Only this moment of the creation of a set of observables is critical mapping, in the sense of the creation of Hoffmeyer’s three-dimensional organism. However, this critical mapping is preceded by a large and complex task for the proper organization of data and the creation of the necessary operating system. This work remains directly uncommitted in the final mapping, but its role in producing the final observable factor is determinative.
Due to this, any intervention in the structure and organization of the database or in the composition of functions can modify the result of transformation.

40

Genetic Transformation

5.1 Recombinant DNA carrying one to several genes of known function
The reports described below originated with a study of a phenomenon that Joshua
Lederberg and his student Norton D. Zinder termed transduction. In 1952, they revealed that certain bacteriophages were capable of carrying a bacterial gene from one strain of
Salmonella to another. Although the capacity of the bacteriophage genome is low and because most bacteriophages can only infect restricted variants of bacterial species, a number of microorganisms that produce important proteins were nonetheless obtained.
Worthy of mention are those proteins, hormones, interleukins and other enzymes whose genes are not complex structures and that presented no issues with folding or solubility in the microbe or in the laboratory. These transformations, though producing metabolites unusual for the microbes, ought to be classified as the simplest transformation events because the route from recombinant DNA fragment to observable product is relatively short and because the microbial set of DNA-regulating mechanisms is simple due to their unicellular nature.
Similar results have been obtained in the transformation of plant cells growing in a bioreactor as separated cells or small cell aggregates. However, these cells, their DNA, nucleus and the cell as a whole are equipped with more complex gene expression control mechanisms than bacteria. Furthermore, some intercellular effects can even be observed in thick cell suspensions.
Very often, plant cell transformation is directed at increasing the yield of secondary metabolites that are a characteristic of the plant species. In this case, some evolutionarily developed mechanisms may help the cell to avoid the over-expression of individual genes, including the transgene. A useful way to evade this controlling mechanism is to use viral promoters, which often are unresponsive to host control. This approach protects the transgene from the cis-control of the host and from individual trans-control, whereas the expression of the transgene can be blocked during the more general form of chromatin remodeling. However, the remodeling of chromatin by such a general transforming principle (e.g., a plant oncogene of a Ti-plasmid) can result in the over-expression of certain sets of host genes (Bulgakov et al., 2009; Zhuravlev et al., 1990). The slow cis-control of host
DNA (DNA reparation) can destroy the transgene because mutations seem to occur more often in the transgene that in the host DNA (Kiselev et al., 2009).
Several products can be obtained from plant cells through transformation (Godfray et al.,
2010). Thus, a certain resonance has been caused by the cultivation of transgenic crops that produce proteins of the human immune system, modified fragments of infectious agents, and other important products of a proteinaceous nature. Important industrial progress has been made in the field of plant protection against pests by the transformation of agricultural crops with the bacillotoxin gene, initially detected in Bacillus thuringensis.
The progress of this research was largely determined by the ability of plants to regenerate an entire plant from transformed cells, i.e., it depended on the implementation of the totipotency of plant somatic cells. In cases where the production of somaclones from transformed cells is a complex task, embryogenic culture, embryo or meristem cells are bombarded with microparticles loaded with the corresponding recombinant DNA. Less commonly, the transformation is accomplished by introducing the vector constructs in the course of the "normal" sexual process. This last method is one of few that are suitable for the transformation of multicellular animal species when examples of their somatic embryogenesis are unknown or rare.

Structure-Function Analysis of Transformation Events

41

The main problem in research of this type is not only the transformation itself but also the regeneration of the transgenic organism from a transformed cell. Until recently, such regeneration from somatic cells was known only in plant systems. Although numerous transformed plants have been obtained by means of somatic embryogenesis, many details of the induction mechanism remain unclear.
We are more interested in the fate of the gene in the context of its relationship with the process of the expression of genetic information of the host cell. A transgene integrated in
DNA, as would be assimilated by the database, is indistinguishable from "its own data" in most cases, which (as we shall see below) we cannot say about the transfer of a nucleus.
However, in mixed populations, the transformed cells and organisms may differ from untransformed ones by such factors as growth rate and sensitivity to abiotic factors (i.e., being subject to selection). The best results can be obtained when the selection scheme includes the production of cellular clones, such as in the following scheme: a cell suspension enriched with super-producers → single-cell suspension → the seeding on solid media of a highly diluted suspension → the selection of colonies originating from a single cell → receipt and comparison of clonal lines.
This means that the cell population must originate from a single cell. However, this choice is fraught with the unlikelihood that a uniform population will be obtained with the same resistance characteristics for all of the cells that may result in the decline of the population stability. 5.2 Transfer of the nucleus (nuclear transplantation)
As it is understood in biotechnology and classical genetics (i.e. offspring production of one and the same cell), cloning does not belong to the events of transformation. The term cloning, which is often used in the procedure for the reprogramming of a nucleus of the somatic cells of large animals, is used inappropriately, whereas the terms regeneration and hybridization are more adequate in most cases. However, some attempts toward the regeneration of adult animals from somatic cells, including a procedure of transformation with recombinant molecules or nucleus transfer, in the broadest sense, can also be viewed as a transformation. The first phase of experiments with somatic cells is represented by attempts to reprogram somatic cells as a result of a merger with an undifferentiated cell
(often an oocyte), enucleated or with an inactivated nucleus (Jaenisch & Gurdon, 2007).
In plant biotechnology, such manipulations are called somatic or parasexual hybridization.
Well before the end of the twentieth century, the problem of dedifferentiation
(reprogramming) was shown to be less acute in experiments with the cells of higher plants, so the studies were primarily conducted as examples of inter-specific hybridization (Gleba
& Sytnik, 1984). However, these experiments have only had a limited theoretical yield. As far as we know, the hybrid Brassica napus was constructed in this way.
In the biotechnology of vertebrates, The Encyclopedia Britannica (2011) cites experiments performed by the British molecular biologist J.B. Gurdon as one of the landmark studies in this direction. J.B. Gurdon transplanted a mature nucleus from an intestinal cell of a tadpole into an enucleated egg of a frog, which subsequently developed into a normal, adult frog.
’Gurdon thus demonstrated that a highly differentiated intestinal cell nucleus, with only intestinal cell genes functioning, could undifferentiate in the environment of the enucleated egg cell and could reactivate those genes necessary to create an entire frog. The frog that was produced was a "clone" in the sense that the entire genome of the donor tadpole was

42

Genetic Transformation

present in all the cells of the newly formed frog’4. For a more detailed history and the recent state of the field, see Jaenisch & Gurdon (2007).
Approximately 20 years later, reports began appearing about the successful development of transplanted mammalian nuclei. In these experiments, the acceptor cell usually originated from germ line cells; more often, it was an oocyte. After fusion, successfully induced embryos were transferred into a surrogate female to promote the full-term development of the new animal. Just as with frogs, the obtained organisms are incorrectly called clones (see, for example, Eggan et al. 2001, 2004).
From the view of knowledge obtained in experiments on plant cells, all of the experiments to obtain "clones" of large animals should be classified as a special case of intra-specific somatic hybridization, where hybridization with undifferentiated enucleated cells was used for the induction of totipotency of a differentiated donor nucleus. All of the examples where the nucleus was taken from one animal and an undifferentiated enucleated cell from another animal are essentially examples of the receipt of a chimeric genotype because cytoplasmic hereditary factors belong to the acceptor cell. For this reason, it is logical to expect that the hybrid offspring would not be an exact copy of the donor; just this has been observed in practice. The most significant differences of the phenotypic "somatic" descendant from the nucleusdonor phenotype can be assumed to be associated with cytoplasmic hereditary factors, chief of which are the mitochondria. In endothermal animals, mitochondria are inherited through the maternal line. Therefore, when the donor of a somatic nucleus is a male, genome mixing is inevitable because the oocyte can only be obtained through the female line.
However, this is only a design part of the problem, whereas a functional part also exists. It is important to remember the following details in the technique of cell hybridization (Egli et al., 2007): for the successful induction of embryogenic development of the hybrid cell, the phase of the cell-cycle in which the enucleation of acceptor cell was performed is important.
Notably, the state of the nuclear membrane and the level of compactness of chromatin are decisive. The authors believe that the ’removal of the pronuclei during enucleation would deplete these factors and prevent development. In contrast, removal of the condensed chromosomes from a metaphase II, meiotic egg would not do so‘ (Egli et al., 2007, p.683).
It suggests that some components of the cell-acceptor nucleus, which passed into the cytoplasm in this stage (see subsection 4.1) and, therefore, had the opportunity to interact with the transplanted nucleus, were needed for reprogramming the donor chromatin.
Among such important factors, methyltransferase Dnmt1 is suspected. This enzyme is present in the nucleus in the course of one cell cycle only and then is removed from it
(Surani & Reik, 2007). This, or some other, transferase can be crucial for the establishment of the specific architecture of donor chromatin as making it available for further control during embryogenesis. In one viewpoint, the post-nuclear transfer development of the hybrid cell can be understood as an interaction between the transplanted nucleus with a soluble part of the acceptor chromatin (i.e., as an interaction of the nucleus with the nucleus, which, of course, contradicts the intention of the experiment). It is also important to remember that many successful experiments with nuclear transfer in frogs were performed by the UV inactivation of the recipient nucleus, and such inactivation does not exclude the possibility that some low molecular weight chromatin structure of the recipient remained intact and played some role in reprogramming the donor nucleus.
4

http://www.britannica.com/EBchecked/topic/262934/heredity

Structure-Function Analysis of Transformation Events

43

The number of transcription factors required for the induction of embryonic development in mammals has recently been reduced to three (Ficz et al., 2009). However, we have no reason to believe that these transcription factors (and only these transcription factors) were released into the acceptor cytoplasm. Taking into account the possibility that their first "products" can be enzymes of DNA demethylation (Bhutani et al., 2010; Popp et al., 2010), we cannot exclude the possibility that these enzymes are themselves passed into the cytoplasm.
For the hybridization of animal somatic cells, it has been assumed that the donor DNA, as the database, remains intact. Therefore, the main problem is to create a new operating unit, which would start operating from scratch. However, operating from scratch is impossible because the chromatin of the transplanted nucleus is a complex combination of different structures (see above sections), and even the DNA in transplanted chromatin is quite different from that in a zygote. Using the language of artificial intelligence, the problem includes the following: i) a database state that is inappropriate to the initial one, and ii) the remnants of the previous operational structure that support the state available at the moment of nuclear transfer. There is reason to believe that the operating structure is presented mainly by the short-lived regulatory elements. In addition, continuous division, being the basis of development and differentiation, may lead to the rapid dilution of relatively stable regulatory elements. In this respect, experiments on secondary embryogenesis in some plants, rarely giving somaclonal variants, are very informative. For instance, for ginseng (Panax ginseng C.A. Meyer), it is relatively easy to obtain vegetative shoots in vitro, but they root poorly, presumably because the required level of dedifferentiation in somatic cells was not reached. We can suppose that these effects were associated with DNA demethylation, as demonstrated in other experiments (Bhutani et al.,
2010; Laurent et al., 2010; Popp et al., 2010). However, if the ginseng embryoids deficient in root formation were transplanted to a new medium, then after a short period of callus growth, the secondary embryos would develop into normal plants with roots. The molecular mechanism of root initiation was recently revealed to be connected with a movable agent (Schlereth et al., 2010). Thus, additional divisions can result in a decrease in the level of methylation of DNA or in the dilution of some hypothetic factor(s) blocking root initiation. In Arabidopsis embryogenesis, an extra-embryonic cell (of the suspensor) is specified to become the founder cell of the primary root meristem, the hypophysis, in response to signals from adjacent embryonic cells (Schlereth et al., 2010). In the course of somatic embryogenesis, no suspensor structure can usually be specified in the callus cells around the embryo (Batygina, 2009). Consequently, two competent cells have to occur in contact to give rise to the somatic embryo and the extra-embryonic root meristem. Of course, this contact is easier when a movable signal exists. Similar events may have taken place in the experiments with vertebrates, where the improvement of embryo formation was obtained due to a procedure known as ”serial cloning”.
5.3 Transformation instead of transplantation
It is known and was reviewed above that the induction of embryo development is a critical phase in experiments on nuclear transfer (Bhutani et al., 2010; Ficz et al., 2009). In this regard, the induction of embryogenesis in plants with phytohormones, antitubulin factors and abiotic factors seems to be more understandable (Zhuravlev & Omelko, 2008).
Nevertheless, the problem of induction of embryogenesis remains a major issue for biotechnology in both animal and plant cells. It is particularly urgent in cases that require the generation of a transformed organism in which all of the cells are modified. Currently,

44

Genetic Transformation

this can only be achieved through the induction of embryogenesis in a separate transformed cell. If the transformant is not a zygote, the difficulties of its induction to embryogenic development may become an insurmountable obstacle to obtaining a transgenic organism.
Even in the biotechnology of plant cells, we are faced with fundamental difficulties. For example, the possibility of somatic embryogenesis in such important cultivated plants as soybeans (for a review, see Dos Santos et al., 2006) is severely limited. However, many obstacles impede the application of somatic embryogenesis in the biotechnology of economically important animals. Above, we discussed the problems associated with this socalled cloning. Here, we focus on receiving the reprogrammed fibroblasts through their transformation. As we show below, this process can also be interpreted as applying an induction function, but it is a significantly more economical and accurate attempt than in nuclear transplantation.
The direction of this research came in 2006, after K. Takahashi and S. Yamanaka demonstrated that transformation with vectors carrying genes encoding the Oct4, Sox2, cMyc and Klf4 transcription factors induced the transformation of mouse fibroblasts into pluripotent stem cells (induced pluripotent stem [iPS] cells). These factors play an important role in the early stages of embryogenesis. Thus, the Oct3/4 and Sox2 genes encode regulatory proteins required for the maintenance of the properties of stem cells (induced in zygote and embryonic tissues). The c-Myc and Klf4 factors maintain the self-renewal of stem cells, and Klf4 also increases the level of Oct4. After the experiments by Takahashi and
Yamanaka (2006), similar experiments were performed (Okita et al., 2007; Wering et al.,
2007), which successfully demonstrated live-born chimeras using an injection of mixed iPS cells into blastocysts. It became clear that there was a new prospect for cloning, namely the replacement of the nuclear transfer procedure for the induction of somatic embryogenesis from minimally differentiated cells of the connective tissue of animals (i.e., fibroblasts). It should be noted that the wound tissue of plants, callus, is even less differentiated, and the use of this tissue in plant biotechnology has yielded progress in the attainment of somaclonal and gametoclonal variants. Therefore, we expect that this model (induced fibroblasts) will lead to comparable success, though the calli of plants and the connective tissue of animals should not be equated.
Nevertheless, the few achievements obtained with this model confirmed its promise. There is, however, one major difficulty. Transformation, causing an induction, can be considered as the creation of a certain intermediate operating unit, whose fate is not indifferent to the further development of the transformed cells. If it continues to function, it can become an obstacle to further development. We are faced with a similar problem when using the transformation of callus cells with the rolC gene to induce embryogenesis in ginseng. The transformed cells are successfully induced and form an embryo-like structure. However, without reaching the torpedo stage, the structures revert to embryogenesis, now secondary, and the cycle is repeated over many passages (Gorpenchenko et al., 2006). We understand the results of this experiment as follows. Under the influence of rolC, cells are exposed to dedifferentiation and take the form and properties of embryonic cells. The inductive effect is, however, permanent. With the development of the embryo, and in the course of differentiation, these cells are again faced with factors produced by the recombinant DNA causing the induction. As a result, they revert to an undifferentiated state and, thus, give rise to a new cycle of embryogenesis. In terms of programming, one can say that the operational structure causing the induction is extremely stable, and its function is performed whenever the cells reached a certain degree of differentiation.

Structure-Function Analysis of Transformation Events

45

Although the molecular mechanism of the induction of embryogenesis with the transformation by rol genes or transcription factors genes is still not clear, the fundamental aspect of the matter is plain enough. In addition, the significance of these results for planning experiments on morphogenesis is also obvious: when transformation is used for induction, the transformation must be temporary. How can we halt or dilute the inducing signal?
The number of induction (parental) factors in a "normal" zygote can be assumed to be limited and reduced with each division (perhaps by half). A rapid dilution eliminates the possibility of secondary induction. However, what about a situation where (at this stage of knowledge) transformation seems the only possibility for the implementation of an induction? We see the solution in the creation of short-lived vectors unable to integrate into the host DNA (Zhuravlev & Omelko, 2008). The creation of such structures in plants (e.g., the use of attenuated tobacco mosaic virus, containing the mRNA from transcription factors genes) can be used as a method in the induction of embryogenesis in crop plants, whose somaclonal variants are difficult to obtain.
A successful implementation has been achieved by K. Kaji et al. (2009) in their attempt to obtain the virus-free induction of pluripotency in mouse and human fibroblasts and a subsequent excision of reprogramming factors. A drug-inducible lentiviral reprogramming strategy has also been designed to achieve the tight control of transgene expression in iPS cells (Boland et al., 2009). In this work, the four original reprogramming factors (Oct4, Sox2,
Klf4 and c-Myc) were placed under the control of the tetO promoter, which is activated by the reverse tetracycline transactivator (rtTA) protein in the presence of the tetracycline analogue doxycycline (dox). This construct makes possible the control of the level of expression of reprogramming factors.
However, the task of managing the development of an individual is not always reduced to the necessity of the rapid dilution or direct removal of initiation factors; occasionally, the opposite is necessary. The low content of such factors in the zygote has apparently caused the failure of attempts to split the embryos of cattle. If this is predominantly due to the lack of transcription factors it is possible that their direct injection into blastomeres will be decisive in the embryo splitting technique for rapid breeding of cattle.

6. The problems of transformation and some routes to success
This section concerns the question of the unpredictability of the results of transformation and, in more general terms, the uncertainty and unpredictability of the individual development of any organism. This question in the aspect of embryogenesis in plants in vitro has been partially discussed in a previous publication (Zhuravlev & Omelko, 2008).
Those working in biotechnology are often faced with a problem when a transformation does not produce the desired result and the target product accumulates only in small amounts.
These phenomena are associated with the uncertainty of the location of transgene insertion, variations in the number of integrated copies and the active defense of the cell against the expression of foreign DNA fragments. The first two facts are usually clear and established by experiments. With regard to the protective measures, there are less data, and these data are more difficult to interpret. Indeed, the number of mutations in the DNA inserts from plasmids is significantly above the average mutation rate in the non-transformed DNA of ginseng (Kiselev et al., 2009).
Perhaps these considerations may have a more general nature, and the very unpredictable results of transformation may be associated with the uncertainty of the developmental paths

46

Genetic Transformation

of the transformed organism. Another basis for the unpredictability of the results of morphogenesis in vitro can often be the indeterminate number of induced cells. The point here is that when the induction covers not just one but a number of neighboring cells, each characterized by different states of chromatin activity, the overall result is difficult to predict. Simultaneous operation of many sources of signal molecules complicates the model and deprives its predictive power.
Another important condition that leads to unpredictability in plant morphogenesis is the low level of specificity of the signal that induces the start of the morphogenetic transformations. Such signals in plants may be various biotic and abiotic factors, such as stress, phytohormones, a shift of the ionic environment, or an electrical impulse. To induce morphogenesis in animal cells in vitro, most of these factors have proven to be ineffective, indicating the greater specificity of the primary signal in animal cells. The structural features of plant cells, especially the cytoskeleton, predispose the cell to the perception of external signals of an abiotic nature (see review in Rowat et al., 2008). This structural feature, among others, likely makes the induction of morphogenesis in plants easier but less selective in comparison with the systems of an animal nature. The induction of somatic embryogenesis in animals, with the many known limitations, requires more specific endogenous inducers.
In addition to transcription factors, which have already been mentioned, transcribed and non-transcribed RNAs of the mother organism may be such highly specific inducers, which are deposited in the egg and direct the early stages of development. Maternal RNA degrades during embryogenesis and is replaced by zygotic RNA as the transcription of zygotic genes is triggered. Before this, the zygotic genome in animals is transcriptionally inactive (Amaral & Mattick, 2008; Schier, 2007; Yao, 2008).
Taking these facts into consideration, it is logical to expect that the unpredictability of results of transformation is associated with the indirect mode of mapping the genotype on the phenotype, which was apparently a historical necessity because the organisms were placed in front of an intractable task to increase and diversify the phenotype without significantly increasing the genotype. In artificial intellect programs, this problem occurs very rapidly. One possible solution may be to use an indirect genetic encoding that takes the form of a developmental process (Nowacki et al., 2008; Roggen et al., 2007).
In this chapter, we developed a dual idea representing the organism as the following: i) an integral, indivisible entity, and ii) a complex construction in which three functionally entangled bodies can be abstracted, namely, the P, F and Ph sets. The task to describe the relationships of these sets resembles the Poincare’s three-body problem, which was recently analyzed by G. Longo (2009) in its relation to biological objects.

7. Conclusion
The current shift of paradigm in the science of complex systems has affected our view of biological object, its development and its transformation. Depending on the construct used, transformation can relate to different intracellular processes, which are characterized by non-linearity and self-referencing, self-construction and self-modification. The problem now is how long distance is between the introduced DNA fragment and the desirable phenotypic character and how many side effects will be induced on this route.
This route is short only in the simplest unicellular organisms. In more complex organisms and especially in those organisms that manifest individuality, the route includes numerous iterations and alternatives, which are incompatible with the idea of predictability of results

Structure-Function Analysis of Transformation Events

47

of transformation. In situation where the transformation aims for induction (of embryogenesis) only, the problem of eliminating the transforming agent after the execution of its signal function necessarily arises. However, recent publications have given us confidence that these problems can be solved in the biotechnology of both mammals and seed plants.
Transformation, with the aim to produce a specific product, has been more successful when the site of incorporation of the transforming agent is closer to the final map in observables.
In this case, however, there are some additional uncertainties. First, the introduction of one or two genes is not always sufficient to produce the final product. Second, the overaccumulation of the product may be harmful to the host (the conflict of phenotypes). Third, the conditions of the host may be inconsistent with the demands for correct labeling and folding of target product (usually of protein nature) and, therefore, inactivate it.
In addition to these features, there is another uncertainty of a more common nature, which is peculiar to the individual development of biological systems in general. It lies in the fact that there is not a strict determinism in the ways in which and in what order the information of a DNA fragment to its phenotypic embodiment will be realized. Nevertheless, there are apparently still some obscure channels that allow a biological object to successfully realize its individual development by the creation of the phenotype with properties similar to those expected. 8. Acknowledgment
Yu. Zhuravlev is very grateful to Dr. E.V. Sundukova for help with collecting literature and the manuscript preparation.
This work was partially supported by the Program of Presidium RAS “Biosphere
Origination and Evolution” (№: 09-1-П25 (I and II, 2011) and by the Leading Schools of
Thought from the President of the Russian Federation (NSh-1635-2008.4).

9. References
Abi-Haidar, A., Kaur, J., Maguitman, A., Radivojac, P., Retchsteiner, A., Verspoor, K., Wang,
Z. & Rocha, L.M. (2007). Uncovering Protein-Protein Interactions in the Bibliome.
Proceedings of the Second BioCreative Challenge Evaluation Workshop, pp. 247-255,
ISBN 84-933255-6-2, Madrid, Spain, April 23-25, 2007.
Adami, C. (2002). What is Complexity? BioEssays, Vol.24, N12, (December 2002), pp. 1085–
1094, ISSN 1521-1878.
Allis, C.D., Jenuwein, T. & Reinberg, D. (Eds.). (2007). Epigenetics, CSHL Press, ISBN
0879697245, New York, U.S.A.
Amaral, P., Dinger, M., Mercer, T. & Mattick, J. (2008). The Eukaryotic Genome as an RNA
Machine. Science, Vol.319, N.5871, (28 March 2008), pp. 1787-1789, ISSN 0036-8075.
Amaral, P. & Mattick, J. (2008). Noncoding RNA in Development. Mammalian Genome,
Vol.19, N.7-8, (August 2008), pp. 454-492, ISSN 0938-8990.
Andrade, E. (2005). The Interrelations between Genotype/Phenotype/Environment: A
Semiotic Contribution to the Evo:Devo Debate. S.E.E.D. Journal (Semiotics,
Evolution, Energy, and Development), Vol.5, N.2, (December 2005), pp. 27-65.

48

Genetic Transformation

Bantignies, F. & Cavalli, G. (2006). Cellular Memory and Dynamic Regulation of Polycomb
Group Proteins. Current Opinion in Cell Biology, Vol.18, N3, (June 2006), pp. 275-283,
ISSN 0955-0674.
Barabasi, A. L., Albert, R. & Jeong, H. (2000). Scale-Free Characteristics of Random
Networks: the Topology of the World-Wide Web. Physica A: Statistical Mechanics and its Applications, Vol.281, N1-4, (15 June 2000), pp. 69-77, ISSN 0378-4371.
Batygina, T.B. (Ed.) (2009). Embryology of Flowering Plants: Terminology and Concepts.
Reproductive Systems. Science Publisher Inc., ISBN 978-1-57808-265-0, U.S.A.
Bersini, H. (2009). How artificial life relates to theoretical biology, In: Origins of Life: SelfOrganization and/or Biological Evolution? M. Gérin and M.-C. Maurel (Eds.), 61–78,
EDP Sciences, ISBN: 978-2-7598-0476-4, Paris, France.
Bhutani, N., Brady, J., Damian, M., Sacco, A., Corbel, S. & Blau, H. (2010). Reprogramming
Towards Pluripotency Requires AID-dependent DNA Demethylation. Nature,
Vol.463 N7284, (25 February 2010), pp. 1042-1047, ISSN 0028-0836.
Boland, M., Hazen, J., Nazor, K., Rodriguez, A., Gifford, W., Martin, G., Kupriyanov, S. &
Baldwin, K. (2009). Adult Mice Generated from Induced Pluripotent Stem Cells.
Nature, Vol.461, N7260, (3 September 2009), pp. 91-94, ISSN 0028-0836.
Bulgakov, V.P., Inyushkina, Y.V., Gorpenchenko, T.Y., Koren, O.G., Shkryl, Y.N. &
Zhuravlev, Y.N. (2009). Emerging Roles of Agrobacterial Plant-Transforming
Oncogens in Plant Defence Reaction. AIP Conference Proceedings, Vol.1089, (12
January 2009), pp. 94-103, ISBN 978-0-7354-0622-3.
Cárdenas, M.L., Letelier, J.C., Gutierrez, C., Cornish-Bowden, A. & Soto-Andrade, J. (2010)
Closure to Efficient Causation, Computability and Artificial Life, Journal of
Theoretical Biology, Vol.263, N1, (March 2010), pp. 79-92, ISSN 0022-5193.
Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E.D., Sevier, C.S., Ding, H., Koh,
J.L.Y., Toufighi, K., Mostafavi, S., Prinz, J., St.Onge, R.P., VanderSluis, B.,
Makhnevych, T., Vizeacoumar, F.J., Alizadeh, S., Bahr, S., Brost, R.L., Chen, Y.,
Cokol, M., Deshpande, R., Li, Z., Lin, Z.Y., Liang, W., Marback, M., Paw, J., San
Luis, B.J., Shuteriqi, E., Tong, A.H.Y., van Dyk, N., Wallace, I.M., Whitney, J.A.,
Weirauch, M. T., Zhong, G., Zhu, H., Houry, W.A., Brudno, M., Ragibizadeh, S.,
Papp, B., C. Pal, C., Roth, F.P., Giaever, G., Nislow, C., Troyanskaya, O.G., Bussey,
H., Bader, G.D., Gingras, A.C., Morris, Q.D., Kim, P.M., Kaiser, C.A., Myers, C.L.,
Andrews, B.J. & Boone, C. (2010). The Genetic Landscape of a Cell. Science, Vol.327,
N5964, (22 January 2010), pp. 425-431, ISSN 0036-8075.
Costa, F.F. (2008) Non-coding RNAs, epigenetics and complexity, Gene, Vol.410, N1, (29
February 2008), pp. 9–17, ISSN 0378-1119. de Vries, S.C. (1998) Making Embryos in Plants. Trends in Plant Sciences, Vol.3, N12, (1
December 1998), pp. 451-452, ISSN 1360-1385.
Dinger, M.E., Mercer, T.R. & Mattick, J.S. (2008). RNAs as Extracellular Signaling Molecules.
Journal of Molecular Endocrinology, Vol.40, N4, (April 2008), pp. 151-159, ISSN 09525041.
Dos Santos, K.G.B., de Araujo, M.J.E., Moco, M.C.C. & Bodanese-Zanettini. M.H. (2006).
Somatic Embryogenesis from Immature Cotyledons of Soybean (Glycine max (L.)
Merr.): Ontogeny of Somatic Embryos. Brazilian Archivs of Biology and Technology, V.
49. N1, (January 2006), pp. 49–55, ISSN 1516-8913.

Structure-Function Analysis of Transformation Events

49

Eggan, K., Akutsu, H., Loring, J., Jackson-Grusby, L., Klemm, M., Rideout 3rd, W.M.,
Yanagimachi, R. & Jaenisch, R. (2001). Hybrid Vigor, Fetal Overgrowth, and
Viability of Mice Derived by Nuclear Cloning and Tetraploid Embryo
Complementation. Proceedings of the National Academy of Sciences U.S.A., Vol.98,
N11, (May 2001), pp. 6209-6214, ISSN 0027-8424.
Eggan, K., Baldwin, K., Tackett, M., Osborne, J., Gogos, J., Chess, A., Axel, R. & Jaenisch, R.
(2004) Mice Cloned from Olfactory Sensory Neurons. Nature, Vol.428, N6978, (4
March 2004), pp. 44 -49, ISSN 0028-0836.
Egli, D., Rosains, J., Birkhoff, G. & Eggan, K. (2007). Developmental Reprogramming After
Chromosome Transfer into Mitotic Mouse Zygotes. Nature, Vol.447, N7338, (7 June
2007), pp. 679-686, ISSN 0028-0836.
Ferguson-Smith, A.C., Greally, J.M., Martienssen, R.A. (Eds.). (2009). Epigenomics, Springer,
ISBN: 978-1-4020-9186-5.
Ficz, G., Farthing, C.R. & Reik, W. (2009). The Epigenomic Landscape of Reprogramming in
Mammals. In: Epigenomics, A.C. Ferguson-Smith, J.M. Greally, R.A. Martienssen
(Eds.), 259-282, Springer, ISBN: 978-1-4020-9186-5.
Fox Keller, E. & Harel, D, (2007). Beyond the Gene. PLoS ONE, Vol.2, N11, (28 November
2007), e1231, eISSN-1932-6203.
Gerstein, M.B., Bruce, C., Rozowsky, J.S., Zheng, D., Du, J., Korbel, J.O., Emanuelsson, O.,
Zhang, Z.D., Weissman, S. & Snyder, M. (2007). What is a Gene, Post-ENCODE?
History and Updated Definition. Genome Research, Vol.17, N6, (June 2007), pp. 669681, ISSN 1088-9051.
Gleba, Y.Y., Sytnik, K.M. (1984). Protoplast fusion: Genetic engineering in higher plants.
Springer-Verlag, ISBN 3540132848, Berlin-Heidelberg-New York-Tokyo.
Godfray, H.C., Beddington, J.R., Crute, I.R., Haddad, L., Lawrence, D., Muir, J.F., Pretty, J.,
Robinson, S., Thomas, S.M. & Toulmin, C. (2010). Food Security: The Challenge of
Feeding 9 Billion People. Science, Vol.327, N5967, (12 February 2010), pp. 812-818,
ISSN 0036-8075.
Gorpenchenko, T.Y., Kiselev, K.V., Bulgakov, V.P. Tchernoded, G.K., Bragina, E.A.,
Khodakovskaya, M.V., Koren, O.G., Batygina, T.B. & Zhuravlev, Yu.N. (2006). The
Agrobacterium rhizogenes rolC-Gene-Induced Somatic Embryogenesis and Shoot
Organogenesis in Panax ginseng Transformed Calluses. Planta, Vol.223, N 3,
(February 2006), pp. 457–467, ISSN 0032-0935.
Hoffmeyer, J. (1996). Signs of Meaning in the Universe. Indiana University Press, ISBN 0-25333233-8, Bloomington, U.S.A.
Hoffmeyer, J. (2008). Biosemiotics: An Examination into the Signs of Life and the Life of Signs.
University of Scranton Press, ISBN: 9781589661691, Scranton PA, U.S.A.
Jacobs, T. (1995). Cell Cycle Control. Annual Review of Plant Physiology and Plant Molecular
Biology, Vol.46, N, (June 1995), pp. 317–339, ISSN 1040-2519.
Jaenisch, R. & Gurdon, J. (2007). Nuclear Transplantation and and the Reprogramming of the Genome. In: Epigenetics, Allis, C.D., Jenuwein, T. & Reinberg, D. (Eds.). CSHL
Press, ISBN 0879697245, New York, U.S.A.
Kaji, K., Norrby, K., Paca, A., Mileikovsky, M., Mohseni, P. & Woltjen, K. (2009). Virus-free
Induction of Pluripotency and Subsequent Excision of Reprogramming Factors.
Nature, Vol.458, N7239, (9 April 2009), pp. 771-775, ISSN 0028-0836.

50

Genetic Transformation

Kauffman, S., Logan, R., Este, R., Goebel, R., Hobill, D. & Shmulevich, I. (2008) Propagating organization: an enquiry. Biology and Philosophy, Vol.23, N1, (January 2008), pp. 2745, ISSN 0169-3867.
Kim, J.Y., Yuan, Z., Cilia, M., Khalfan-Jagani, Z. & Jackson, D. (2002). Intercellular
Trafficking of A KNOTTED1 Green Fluorescent Protein Fusion in the Leaf and
Shoot Meristem of Arabidopsis. Proceedings of the National Academy of Sciences U.S.A.,
Vol.99, N6, (19 March 2002), pp. 4103–4108, ISSN 0027-8424.
Kiselev, K.V., Turlenko, A.V., Tchernoded, G.K. & Zhuravlev, Yu.N. (2009). Nucleotide
Substitutions in rolC and nptII Gene Sequences During Long-term Cultivation of
Panax ginseng Cell Cultures. Plant Cell Reports, Vol.28, N8, (August 2009), pp. 12731278, ISSN 0721-7714.
Laurent, L., Wong, E., Li, G., Huynh, T., Tsirigos, A., Ong, C., Low, H., Sung, K., Rigoutsos,
I., Loring, J. & Wei, C. (2010). Dynamic Changes in the Human Methylome During
Differentiation. Genome Research, Vol.20, N3, (March 2010), pp. 320–331, ISSN 10889051.
Longo, G. (2010). Incomputability in Physics and Biology. Extended and revised version of an Invited Lecture, 6th Conference on Computability in Europe, CiE 2010, Ponta
Delgada, Azores, Portugal, June 30 – July 4, 2010.
Longo, G. (2009). Randomness and Determination, from Physics and Computing towards
Biology. Lecture Notes in Computer Science, Vol. 5404, pp. 49-61, ISSN 0302-9743.
Longo, G. & Tendero, P.-E. (2007). The Differential Method and the Causal Incompleteness of Programming Theory in Molecular Biology. In Foundation of Science, Vol.12, N4,
(December 2007), pp. 337-366, ISSN 1233-1821.
Luisi, P. (1998). About Various Definitions of Life. Origins of Life and Evolution of Biospheres,
Vol.28, N4-6, (October 1998), pp. 613–622, ISSN 0169-6149.
Mattick, J., Amaral, P., Dinger, M., Mercer, T. & Mehler, M. (2009). RNA Regulation of
Epigenetic Processes. BioEssays, Vol.31, N1, (January 2009), pp. 51–59, ISSN 15211878.
Morgan, H.D., Santos, F., Green, K., Dean, W. & Reik, W. (2005). Epigenetic Reprogramming in Mammals. Human Molecular Genetics, Vol.14, Siuppl.1, (15 April 2005), R47–R58,
ISSN 0964-6906
Mossio, M., Longo, G. & Stewart, J. (2009). An Expression of Closure to Efficient Causation in Terms of Lambda-calculus. Journal of Theoretical Biology, Vol.257, N3, (7 April
2009), pp. 489-498, ISSN 0022-5193.
Nagy, A., Rossant, J., Nagy, R., Abramow-Newerly, W. & Roder, J.C. (1993). Derivation of
Completely Cell Culture-derived Mice from Early-passage Embryonic Stem Cells.
Proceedings of the National Academy of Sciences U.S.A., Vol.90, N 18, (15 September
1993), pp. 8424–8428, ISSN 0027-8424.
Okita, K., Ichisaka, T. & Yamanaka, S. (2007). Generation of Germline-competent Induced
Pluripotent Stem Cells. Nature, Vol.448, N7151, (19 July 2007), pp. 313–317, ISSN
0028-0836.
Pentris, S., Hunt, T. & Tooze, J. (Eds.) (1983). DNA Makes RNA Makes Protein. Elsevier, ISBN
0444804919, U.S.A.
Popp, C., Dean, W., Feng, S., Cokus, S.J., Andrews, S., Pellegrini, M., Jacobsen, S.E. & Reik,
W. (2010). Genome-wide Erasure of DNA Methylation in Mouse Primordial Germ

Structure-Function Analysis of Transformation Events

51

Cells Is Affected by AID Deficiency. Nature, Vol.463, N 7284, (22 January 2010), pp.
1101-1105, ISSN 0028-0836.
Rodríguez-Trelles, F., Tarrío, R. & Ayala, F.J. (2006). Origins and Evolution of Spliceosomal
Introns. Annual Review of Genetics, Vol.40, pp. 47-76, ISSN 0066-4197.
Roggen, D., Federici, D. & Floreano, D. (2007). Evolutionary Morphogenesis for Multicellular Systems. Genetic Programming and Evolvable Machines, Vol.8, N1, (March
2007), pp. 61–96, ISSN 1389-2576.
Rowat, A., Lammerding, J., Herrmann, H. & Aebi, U. (2008). Towards an Integrated
Understanding of the Structure and Mechanics of the Cell Nucleus. BioEssays,
Vol.30, N3, (March 2008), pp. 226–236, ISSN 1521-1878.
Ruiz-Mirazo, K., Peretó, J. & Moreno, A. (2004). A Universal Definition of Life: Autonomy and Open-Ended Evolution. Origins of Life and Evolution of Biospheres, Vol.34, N3,
(June 2004), pp. 323-346, ISSN 0169-6149.
Scherrer, K. & Jost, J. (2007). Gene and Genon Concept: Coding Versus Regulation. Theory in
Biosciences, Vol.126, N2-3, (October 2007), pp. 65-113, ISSN 1431-7613.
Schlereth, A., Möller, B., Liu, W., Kientz, M., Flipse, J., Rademacher, E.H., Schmid, M.,
Jürgens, G. & Weijers, D. (2010). MONOPTEROS Controls Embryonic Root
Initiation by Regulating a Mobile Transcription Factor. Nature, Vol.464, N 7290, (8
April 2010), pp. 913-917, ISSN 0028-0836.
Schier, A.F. (2007). The Maternal-Zygotic Transition: Death and Birth of RNAs. Science,
Vol.316, N 5823, (20 April 2007), pp. 406-407, ISSN 0036-8075.
Snyder, M. & Gerstein, M. (2003). Defining Genes in the Genomics Era. Science, Vol.300,
N5617, (11 April 2003), pp. 258–260, ISSN 0036-8075. von Sternberg, R. & Shapiro, J.A. (2005). How Repeated Retroelements Format Genome
Function. Cytogenetic and Genome Research, Vol.110, N1-4, (), pp. 108-116, ISBN 9783-8055-7964-3.
Takahashi, K. & Yamanaka, S. (2006). Induction of Pluripotent Stem Cells From Mouse
Embryonic and Adult Fibroblast Cultures by Defined Factors. Cell, Vol.126, N4, (25
August 2006), pp. 663-676, ISSN 0092-8674.
Takebe, I., Otsuki, Y. & Aoki, S. (1968). Isolation of Tobacco Mesophyll Cells in Intact and
Active State. Plant Cell Physiology, Vol.9, N1, pp. 115–124, ISSN 0032-0781.
Wassenegger, M., Heimes, S., Riedel, L. & Sänger, H.L. (1994) RNA-Directed de novo
Methylation of Genome Sequences in Plants. Cell, Vol.76, N3, (11 February 1994), pp. 567-576, ISSN 0092-8674.
Wernig, M., Meissner, A., Foreman, R., Brambrink, T., Ku, M., Hochedlinger, K., Bernstein,
B.E. & Jaenisch, R. (2007). In vitro Reprogramming of Fibroblasts into a Pluripotent
ES-cell-like State. Nature, Vol.448, N7151, (July 2007), pp. 318–324, ISSN 0028-0836.
West, G.B. & Brown, J.H. (2005). The Origin of Allometric Scaling Laws in Biology from
Genomes to Ecosystems: towards a Quantitative Unifying Theory of Biological
Structure and Organization. Journal of Experimental Biology, Vol.208, N9, (1 May
2005), pp. 1575-1592, ISSN 0022-0949.
Yao, M.C. (2008). RNA Rules. Nature, Vol.451, N7175, (10 January 2008), pp. 131-132, ISSN
0028-0836.
Zaretzky, A.N. & Letelier, J.C. (2002). Metabolic Networks from (M,R) Systems and
Autopoiesis Perspective. Journal of Biological Systems, Vol.10, N3, (September 2002), pp. 265-280, ISSN 0218-3390.

52

Genetic Transformation

Zhuravlev, Yu.N. & Avetisov, V.A. (2006). The Definition of Life in the Context of its Origin.
Biogeosciences, Vol.3, N3, (10 July 2006), pp. 281-291, ISSN 1726-4170.
Zhuravlev, Yu.N., Bulgakov, V.P., Moroz, L.A., Uvarova, N.I., Makhan’kov, V.V.,
Malinovskaya, G.V., Artyukov, A.A. & Elyakov, G.B. (1990). Accumulation of
Panaxosides in a Culture of Cells of Panax ginseng C. A. Mey Transformed with the
Aid of Agrobacterium rhizogenes. Doklady Akademii Nauk SSSR (Bot.Sci). New
York: Springer Consultants Bureau. Vol.311, pp. 22-23. NAL Call No.: 511-P444AE
Zhuravlev, Yu.N. & Omelko, A.M. (2008). Plant Morphogenesis in vitro. Russian Journal of
Plant Physiology, Vol.55, N5, (September 2008), pp. 579-596, ISSN 1021-4437.

Part 2
Plant Transformation: Improving Quality of Fruits, Crops and Trees - Molecular Farming

3
Genetic Transformation in Tomato:
Novel Tools to Improve Fruit Quality and
Pharmaceutical Production
Antonio Di Matteo, Maria Manuela Rigano, Adriana Sacco,
Luigi Frusciante and Amalia Barone

Department of Soil, Plant, Environmental and Animal Production Sciences
University of Naples “Federico II”, Naples,
Italy
1. Introduction
Tomato is one of the most important vegetable crop worldwide with a total production of around 141 million tons on a cultivated area of around 5 million hectares (FAOSTAT, 2009, http://faostato.fao.org). Among the most representative countries, Italy contributes with more than 6 million tons to the world production, on a cultivated area of around 117.000 hectares, both in open fields and greenhouses (FAOSTAT, 2009). This crop represents also one of the major products of the food industry worldwide and Italy ranks first for processing tomato production among Countries of the Mediterranean Region (World
Processing Tomato Council, 2009, www.wptc.to). Indeed, the high variability of tomato fruits, ranging from the cherry type to the big round or elongated berry, supplies both fresh market and processing products, such as paste, juice, sauce, powder or whole. In the last years, tomato consumption has further increased since it was demonstrated that tomato fruit could protect against diseases, such as cancer and cardiovascular disorders, due to its antioxidant properties (Rein et al., 2006). Tomato fruits are particularly rich of nutritional compounds such as lycopene and alfa-carotene, vitamin C, flavonoids and hydroxycinnamic acid derivatives whose intake would account for health benefits.
The cultivated tomato (Solanum lycopersicum) belongs to the Solanaceae family that includes more than 3.000 species, among which 12 represent tomato wild relatives. These species exhibit a wide variety of adaptation to diverse habitats, plant morphology, fruit size and colour, the latter varying from green to white, yellow, pink, red, brown, depending mainly on the metabolites fruit content. The wild related tomato species represent a potential reservoir of useful genes that have been greatly used in breeding programs (Bai & Lindhout,
2007; Gur & Zamir, 2004). Indeed, this vegetable is one of the most investigated crop both at genetic and genomic level not only because of its economic importance but also because it is one of the best characterized plant systems. It has diploid genetics (24 somatic chromosomes), a small genome size (950 Mb per haploid nucleus), is self-pollinated, has a short generation time, is easily reproduced by seed and vegetative propagation and is crosscompatible with many wild species. All these characteristics make it amenable to genetic analysis. 56

Genetic Transformation

The huge amount of researches focused on tomato allowed the development of new tools and platforms for genetics and genomics analyses (Barone et al., 2008). Since tomato is considered the model species among the Solanaceae, these novel techniques have been also exploited for other economically important crops, such as potato, pepper, and eggplant.
Moreover, due to the high sinteny existing among Solanaceae species, tomato was chosen as reference genome to be completely sequenced by the International Tomato Genome
Sequencing Consortium at the end of the year 2003 (Mueller et al., 2005). Molecular comparative mapping studies revealed a high level of conserved gene content and order within this family (Wu & Tanksley, 2010), as well as within other families (i.e grasses, crucifers, legumes). Indeed, a high level of microsinteny amongst the genomes of tomato, potato, pepper and eggplant was observed. Therefore, determination of the tomato genome sequence could allow extending information among species, thus creating a common mapbased framework of knowledge. This could allow inferring the sequence organization of other Solanaceae crops as basis for understanding how plants diversify and adapt to new and adverse environments.
The recent release of the tomato genome sequence (Mueller et al., 2009), together with the powerful genetic and genomic resources available today for this species, allowed plant biotechnologists to implement novel methods to obtain new genotypes that could answer to new consumer, producer and processor requirements. These resources, in fact, could help the transfer of useful genes among species and/or improved genotypes through assisted breeding programs as well as through genetic transformation technologies.
In the present review, after providing some information on tomato genetic and genomic resources, we will give an overview of genetic transformation techniques and biotechnology applications investigated in this species. Several recent review reported new studies on tomato genetic transformation as a tool for the improvement of resistance to pests and pathogens (Balaji & Smart, 2011; Khan et al., 2011; Panthee & Chen, 2010; Wu et al., 2011;
Zhang et al., 2010). Therefore, after a short description of main transformation techniques to which tomato is well adapted, herein we will focus on the use of genetic transformation for fruit quality engineering and pharmaceutical production.

2. Genetic and genomic resources
Among cultivated species, tomato is one of the richest in genetic and genomic resources
(Table 1 and Table 2), including information now available from the complete genome sequencing that was released in the last year in a preliminary version. All these tools, used together or separately, are having a great impact on tomato breeding and genetics (Barone et al., 2009; Foolad, 2007).
This cultivated species could count on a number of wild and related species, on a wide collection of naturally or induced mutants and on many well-characterized genetic stocks, such as cultivars and landraces, cytogenetic stocks and pre-bred lines. Today this germplasm is publicly available (Table 1). In the miscellaneous group, the Backcross
Recombinant Inbreds and Introgression Lines are particularly useful for the identification of genes and/or QTLs, since they constitute "immortal" population to be used for quantitative analyses (Grandillo et al., 2008). In addition, they also represent exotic libraries that allow to better exploit biodiversity exhibited by wild species. Indeed, the IL population is composed by many lines, each carrying a single homozygous genomic region from the wild species, altogether covering the whole wild genome (Eshed & Zamir, 1995; Fridman et al., 2004).

Genetic Transformation in Tomato:
Novel Tools to Improve Fruit Quality and Pharmaceutical Production

GENETIC
RESOURCE
Wild species
Monogenic mutants
Miscellaneous stock
Introgression lines
(IL)
Backcross
Recombinant
Inbreds (RIL)
Induced-mutant
stocks

NOTES

WEBSITE

More than 1.100 accessions More than 600 mutants
More than 1.500 accessions from S. pennellii, S. habrochaites, S. lycopersicoides 57

TGRC (http://tgrc.ucdavis.edu),
NPGS (www.ars-usda.gov)
TGRC

S. lycopersicum x S. pimpinellifolium More than 3.400 induced-mutants from cv M82
Around 1000 inducedmutants from MicroTom
More than 5.000 mutants from cv Red
Setter

TGRC, NPGS
TGRC

TGRC
SGN
(http://zamir.sgn.cornell.edu/mutants)
TOMATOMA
(http://tomatoma.nbrp.jp)
LycoTill
(www.agrobios.it/tilling/index.html)

Table 1. Tomato genetic resources publicly accessible via web
Currently, IL populations that derive from various wild species are available, even though others are being generated (Barone et al., 2009). The first population (from S. pennellii) has been so far widely used to localize QTLs (Lippman et al., 2007) and to clone them (Frary et al., 2000; Fridman et al., 2000).
In addition to a collection of natural mutants available at TGRC (Tomato Genetic Resource
Centre), wide collections of induced mutants were generated in different genetic backgrounds, by chemical or physical mutagenesis (Emmanuel & Levy, 2002; Menda et al.,
2004; Watanabe et al., 2007). These mutants were widely phenotyped for many traits and contributed to better understand some developmental processes, such as growth habit, flowering and fruit ripening (Giovannoni, 2007; Pineda et al., 2010; Saito et al., 2011). In addition, induced mutagenesis has often been implemented with gene-specific detection of single-nucleotide mutations to generate TILLING platforms. So far, TILLING was developed for the cv. M82 (Piron et al., 2010), Red Setter (Minoia et al., 2010), Tpaadasu
(Gady et al., 2009) and Micro-Tom (Saito et al., 2011) and its use has allowed the pinpointing of mutations in genes of interest.
The variability displayed by the different sources of germplasm available for tomato could be explored to search for new genes or favourable alleles to be transferred by conventional breeding and/or genetic transformation in selected genotypes to obtain new varieties.
In recent years, genetic resources combined with tomato specific genomic tools (Barone et al., 2009) allowed to successfully achieve various objectives, including the development of new varieties resistant to biotic and abiotic stresses and with improved fruit quality traits and yield. Most of these resources are also publicly available for the scientific community and are accessible via web (Table 2).

58
GENOMIC
RESOURCE
Molecular markers

Molecular maps

Genetic Transformation

NOTES
Thousands markers
(i.e RFLP, AFLP, SSR,
COS, CAPS, SNP)
10 genetic maps involving crosses among different species and varieties

WEBSITE
SGN (http://solgenomics.net)

SGN

Physical map

from S. lycopersicum

SGN

Complete genome sequence released version SL2.40
January 2011

SGN

EST collections

transcriptomic array Metabolomic platforms TILLING platforms
SNP array
Bioinformatic
platforms

Around 300.000 from various tissues and developmental stages

TOM1 (approx. 8000 unigenes) TOM2 (approx. 11.000 independent genes)
Affimetrix (approx.
10.000 genes)
Combimatrix
TomatoArray1.0 (more than 20.000 probes)
Metabolites from S. pennellii and S. habrochaites ILs , metabolomics of tomato fruit from 96 cultivars From cv. Red Setter,
M82
SolCAP approx. 8000
SNPs from 6 genotypes
Data mining and integration, genome annotation SOLESTdb
(http://biosrv.cab.unina/solestdb)
Tomato Gene Index
(http://compbio.dfci.harvard.edu/tgi),
plantGDB (http://www.plantgdb.org),
MiBASE
(http://www.kazusa.or.jp/jsol/microt om) Tomato Functional Genomics database
(http://ted.bti.cornell.edu)
TFGD
(http://www.affymetrix.com)
Functional Genomic Center
(http://ddlab.sci.univr.it)

TFGD, MoToDB
(http://appliedbioinformatics.wur.nl)
LycoTill, UTill
(http://urgv.evry.inra.fr/UTILLdb),
(http://tilling.ucdavis.edu/index.php/
TomatoTilling)
SolCAP (http://solcap.msu.edu)
SGN, TFGD

Table 2. Tomato genomic resources publicly accessible via web

Genetic Transformation in Tomato:
Novel Tools to Improve Fruit Quality and Pharmaceutical Production

59

Since the beginning of 1990s, the contribution of molecular markers and maps to tomato breeding and gene identification has been widely documented (Foolad, 2007; Frary et al.,
2005; Gupta et al., 2009), and more than 15.000 different markers are collected in the SGN database, where markers can be searched by name, chromosome position and mapping population. Moreover, cytological and cytogenetic maps are also available, as well as a detailed physical map, which was the foundation for the tomato genome sequencing project
(Mueller et al., 2005). Contemporarily, gene expression analyses performed on different tissues and developmental stages, as well as on genotypes that differ in their answer to environmental stimuli, have dramatically raised the number of ESTs available at various websites. Consequently, several microarray platforms have being designed and are being used for transcriptional profiling, thus contributing to the identification of novel genes
(Baxter et al., 2005b; Di Matteo et al., 2010). In addition bioinformatics resources aiming at integrating the forthcoming tomato genome sequence, wide collections of ESTs and data from transcriptomic, proteomic and metabolomic platforms available for tomato will enhance the design and management of genetic transformation approaches, such as those pointing at fruit quality engineering and production of pharmaceutical proteins.

3. Techniques for tomato genetic transformation
Since the 1980s several Agrobacterium-mediated transformation protocols have been developed in tomato, using cotyledons or leaves (Pino et al., 2010; Sharma et al.; 2009; Van Eck et al.,
2006). Transformation efficiencies obtained in various cultivars range from 10 to 41%. Many factors were believed to be crucial for tomato transformation using Agrobacterium tumefaciens, including the application of nurse cells or acetosyringone to the culture or pre-culture media, the type of explants, the Agrobacterium strain used and its concentration, co-cultivation period and the concentration of thiamine, 6-benzylamino purine (BAP), zeatin and indole acetic acid
(IAA). Also, new transformation procedures have been developed for tomato varieties with low in vitro regeneration capacity (Fuentes et al., 2008) and alternative transformation methods, such as floral dip, have been tested (Yasmeen et al., 2009). In addition, novel resources for temporal and tissue-specific manipulation of gene expression in tomato plants are now available for the scientific community. In this regard, it is noteworthy the work from
Fernandez et al. (2009) and Estornell et al. (2009) that created new Solanaceae genetic toolkit for targeted gene expression and silencing in tomato fruits.
Recently, as the information provided by the tomato genome sequencing become available, the demand for efficient functional genomics tools are increasing. Functional genomics studies of the tomato plant require the use of high-throughput methods for functional analysis of many genes including simple and easily reproducible plant transformation systems. The miniature tomato cultivar MicroTom is a rapid-cycling cherry tomato variety that differs from standard tomato cultivars primarily by two recessive genes that confer the dwarf genotype (Dan et al., 2006). MicroTom shares some traits with the model plant
Arabidopsis thaliana such as the small size, short life cycle (70-90 days from sowing to fruitripening) and small genome (950 Mb) and it is therefore considered a model cultivar for tomato genetics and functional genomics. Several studies investigated the production of improved protocols for Agrobacterium-mediated MicroTom transformation obtaining a transformation efficiencies ranging from 20 to 56% (Dan et al., 2006; Qiu et al., 2007; Sun et al., 2006). Recently, Pino et al. (2010) developed an efficient and inexpensive method for

60

Genetic Transformation

MicroTom transformation using a new tomato genotype harbouring the allele Rg1 that greatly improves tomato in vitro regeneration.
Another breakthrough in the field of tomato genetic transformation was the development of a system for stable genetic transformation of tomato plastids (Ruf et al., 2001). In comparison with conventional nuclear transformation, the integration of transgenes in the plastid genome presents several advantages: 1) high expression levels of recombinant proteins attainable owing to the high ploidy level of the plastid genome (up to 10,000 plastid genomes per cell); 2) efficient transgene integration since integration into the plastid genome relies on homologous recombination between the targeting regions of the transformation vector and the wild-type plastid DNA; 3) absence of epigenetic effects (gene silencing); 4) increased biosafety due to the biological containment of transgenes and recombinant products owing to maternal inheritance of plastid and plastid transgenes and absence of dispersal in the environment through the pollen; 5) possibility to express multiple transgenes from prokaryotic-like operons, thus simplifying engineering metabolic pathways
(Bock & Warzecha; Cardi et al., 2010; Ruf et al., 2001; Wurbs et al., 2007).
The availability of a technology for transgene expression from the tomato plastid genome opened up new possibilities for metabolic engineering and the use of plants as bioreactors for the production of pharmaceuticals (Ruf et al., 2001, Wurbs et al., 2007). The group of
Ralph Bock investigated the possibility to elevate the pro-vitamin A content of tomatoes using the chloroplast transformation technology (Apel & Bock, 2009; Wurbs et al., 2007).
Apel & Bock (2009) introduced the lycopene β-cyclase genes from the eubacterium Erwinia herbicola and the plant daffodil (Narcissus pseudonarcissus) into the tomato plastid genome in order to enhance carotenoid biosynthesis inducing lycopene-to-provitamin A conversion.
The expression of the enzyme from the higher plant daffodil in fruits of transplastomic tomato plants triggered efficient conversion of lycopene to β-carotene and resulted in a
>50% increase in total carotenoid accumulation. Zhou et al. (2008) studied the feasibility of producing human immunodeficiency virus (HIV) antigen in transplastomic plant and demonstrated that the HIV antigens p24 and Nef in the plastid could be expressed in plastid of tomato plants.
Today, the technology of stable plant transformation is successful in tomato; however, the lack of an efficient, simple and reliable protocol and the length of time required to produce transgenic lines complicate the analysis of gene function. In alternative, transient assays could provide a rapid tool for the functional analysis of transgenes and have been often used as an alternative to the analysis of stably transformed lines (Wroblewsky et al., 2005). A powerful tool for fast reverse genetics is the virus-induced gene silencing (VIGS) technology
(Orzaez & Granell, 2009). Using this method, recombinant virus vectors carrying hostderived sequences are used to infect the plant; systemic spreading of this recombinant virus causes specific degradation of the endogenous gene transcripts by PTGS (posttranscriptional gene silencing) (Dinesh-Kumar et al., 2003; Liu et al., 2002). In 2002, Liu and colleagues demonstrated that a tobacco rattle virus (TRV)-based VIGS vector could be used in tomato to silence genes efficiently. To shorten the time and simplify the functional analysis in fruits, Orzaez et al. (2006) developed a methodology that allowed transient expression of transgenes directly in fruit tissues. However, the identification and quantification of non-visual phenotypes could be hampered by the irregular distribution of fruit VIGS. In a recent paper Orzaez et al. (2009) developed an anthocyanin-guided VIGS in order to overcome the limitations of this technique such as its irregular distribution and efficiency. To develop a visually traceable system the authors developed a method

Genetic Transformation in Tomato:
Novel Tools to Improve Fruit Quality and Pharmaceutical Production

61

comprising: 1) a tomato line expressing Rosea1 and Delila transcription factors under the control of the E8 promoter that showed a purple-fruited phenotype and 2) a modified TRV
VIGS vector incorporating partial Rosea1 and Delila sequences agro-injected in the transformed lines and that was able to restore the red-fruited phenotype.

4. Biotechnology applications
4.1 Fruit quality engineering
Tomato fruit quality includes several aspects that may be grouped into two categories: organoleptic properties and nutritious contents. Organoleptic quality involves color and texture of the fruit, but also taste and aroma, whereas nutritional quality refers to the content of metabolites contributing to the intake of nutritious such as sugars, carotenoids, flavonoids, ascorbic acid and folate.
Most of the quality traits show a continuous variation, are attributed to the joint action of many genes and are strongly induced by environmental conditions. Beside their complex inheritance, fruit quality traits have often been engineered in tomato through approaches of reverse genetics, such as genetic transformation and mutagenesis, pointing at controlling the expression of single major genes involved in the regulation of a desirable phenotype. In addition, genetic transformation has often been successful in enhancing fruit quality-related traits in tomato investigating simultaneously the role of candidate genes in specific biological processes in the fruit.
In general, there are three main goals of engineering strategies in plants (Verpoorte et al.,
2000): the enhancement of a desired trait, the decrease in the expression of a specific unwanted trait, and the development of a novel trait (i.e. a molecule that is produced in nature but not usually in the host plant, or a completely novel compound). Strategies aimed at inducing changes in the expression of a trait changing the synthesis of a specific metabolite are referred to as metabolic engineering. Approaches for achieving the redirection of metabolic fluxes include the engineering of single steps in a pathway to increase or decrease metabolic flux to target compounds, to block competitive pathways or to introduce short cuts that divert metabolic flux in a particular way. However, this strategy has only limited value because the effects of modulating single enzymatic steps are often absorbed by the system in an attempt to restore homeostasis. Recently, strategies aimed at targeting multiple steps in the same pathway are gaining increasing interest because they help to control metabolic flux in a more predictable manner. This might involve up-regulating several consecutive enzymes in a pathway; up-regulating enzymes in one pathway while suppressing those in another competing pathway; or using regulatory genes such as transcription factors (TF) to establish multipoint control over one or more pathways in the cell. Since technical hurdles limits the number of genes that can be transferred to plants and pyramiding of transgenes by crossing transformants for single targets is a highly time-consuming approach, researchers developed new transformation methods to introduce multiple transgenes into plants and express them in a coordinated manner (Navqvi et al., 2009). In addition, controlling the expression of a single
TF or a combination of TFs provides attractive tools for overcoming flux bottlenecks involving multiple enzymatic steps, or for deploying pathway genes in specific organs, cell types or even plants where they normally do not express.
A schematic description of successful metabolic engineering for enhancement of fruit quality in tomato is provided in Table 3 and Table 4. Genetic transformation targeting a single TF has been used to successfully engineer tomato for inducing development of parthenocarpic and

62

Genetic Transformation

seedless fruit. Parthenocarpy enables fruit set and growth to be independent from pollination, fertilization and seed development circumventing the environmental constraints on fruit production and ensuring yield stability. Seedless fruits enhance consumer appeal and could also be a valuable trait for industrial tomatoes because parthenocarpy increases the content of soluble solids, improves yield and flavour of paste and reduces processing costs. Reported applications involved the overexpression of an auxin response factor 8 (ARF8) from Arabidopsis
(Goetz et al., 2007) and downregulation of Aux/IAA9 transcription factor (Wang et al., 2005) to promote fruit parthenocarpic development.
Modifications of fruit softening and of the overall firmness have been achieved mostly by engineering genes controlling single enzymatic steps in cell wall-associated pathways. In particular, polygalacturonase (Kramer et al., 1992; Langley et al. 1994; Smith et al., 1990), pectin methylesterase (Tieman & Handa, 1994), expansin (Brummell et al., 1999) and βgalactosidase (Smith et al., 2002) genes showed effectiveness in controlling fruit firmness and softening in transgenic tomato plants. A dosage series of the gene fw2.2, a negative regulator of cell division (Frary et al., 2000) was generated in tomato by genetic transformation allowing to modulate fruit weight in tomato without affecting cell size in pericarp and placenta tissues (Liu et al., 2003).
Two examples of successful metabolic engineering modifying tomato fruit flavour relayed on heterologous single-gene expression to introduce in tomato untypical traits. In the first example, a biologically active thaumatin, a sweet-tasting, flavour-enhancing protein from the African plant Thaumatococcus daniellii Benth was expressed in transgenic tomatoes that produced sweeter fruits with a specific aftertaste (Bartoszewski et al., 2003). In the second example, the lemon basil geraniol synthase (GES) gene was overexpressed under the control of the strong fruit-ripening-specific tomato polygalacturonase promoter (PG). GES encodes the enzyme responsible for the production of geraniol from GDP and its expression caused the plastidial terpenoid biosynthetic flux to divert, leading to a reduced lycopene accumulation and to dramatic changes in the aroma and overall flavour of the transgenic fruits (Davidovich-Rikanati et al., 2007).
In another study, the overexpression of either LeAADC1A or LeAADC2, encoding for phenylalanine decarboxylases that are involved in the synthesis of 2-phenylethanol from phenylalanine, resulted in fruits with up to 10-fold increased emissions of the products of the pathway, including 2-phenylacetaldehyde, 2-phenylethanol, and 1-nitro-2-phenylethane.
On the other hand, antisense reduction of LeAADC2 significantly reduced emissions of these volatiles (Tieman et al., 2006).
In addition to organoleptic fruit quality, nutritional attributes of tomato fruit have recently received increasing attention by molecular biologists. For instance, the fruit soluble solid content was engineered by using an RNAi approach to generate transgenic plants that were exclusively altered in the expression of a specific isoform of the cell wall invertase LIN5
(Baxter et al., 2005a; Fridman et al., 2000, 2004; Schauer et al., 2006; Zanor et al., 2009).
Several attempts have been made also to engineer higher carotenoid contents in tomato fruit and a number of tomato lines have been generated with enhanced levels of lycopene, βcarotene and xanthophylls (mainly zeaxanthin and lutein) and low levels of nonendogenous carotenoids such as ketocarotenoids (Fraser et al., 2009). One of the most interesting achievements is the HighCaro (HC) tomato plant (D’Ambrosio et al. 2004), a transgenic line carrying the tomato lycopene β-cyclase (tLcy-b) cDNA. Carotenoid biosynthetic pathway is a highly regulated, interconnected, compartmentalized, membrane bound pathway that can be successfully engineered to enhance carotenoids in crop plants

Genetic Transformation in Tomato:
Novel Tools to Improve Fruit Quality and Pharmaceutical Production

63

circumventing homeostasis. Carotenoids are biosynthetically related to gibberellins via geranyl-geranyl pyrophosphate and isopentenyl pyrophosphate and this often caused in transgenic plants unpredictable phenotypes. For example, in transgenic lines overexpressing the endogenous gene Psy-1, besides an effect on gibberellins formation, the levels of other isoprenoid derived phytohormones were altered in vegetative tissues as well as chlorophyll and tocopherol contents in fruit (Fray et al., 1995). In order to minimize these detrimental effects, engineering approaches to enhance carotenoids in tomato have recently focused on the use of tissue-specific promoters. The use of tomato ripening enhanced promoters allowed a controlled expression at this stage facilitating co-ordination with endogenous carotenoid formation and reducing competition with other branches of the isoprenoid pathway. On the other hand, transcriptional up-regulation of a gene does not always correlate to increased protein or enzyme activity and forward-feed regulation mechanisms could operate within the pathway to maintain homeostasis. For example, in tomato lines expressing a bacterial derived phytoene synthase (CrtB) the subsequent desaturation step in the pathway was reduced (Fraser et al., 2002). Moreover, transgenic lines expressing a bacterial desaturase had a reduced phytoene synthase transcription and enzyme activity. In addition, tomato lines overexpressing deoxy-D-xylulose 5-phosphate synthase (Dxs) showed elevated phytoene formation in ripe fruit, however desaturation limited progression through the pathway (Enfissi et al., 2005). Finally in tomato lines overexpressing Psy-1 a lycopene cyclase (CYC-B) is induced resulting in increased enzyme activity generating βcarotene as an unintended end-product (Fraser et al., 2007). By contrast, feedback inhibition could also limit accumulation of end-products as was the case of tomato lines expressing the
CrtI enzyme where the elevated β-carotene levels reduced phytoene synthase (Romer et al.,
2000). In contrast with results obtained in rice and potato, multiple step engineering strategies in the carotenoid and isoprenoid precursor pathways in tomato were only partially successful (Diretto et al., 2007). Finally, the simultaneous expression of an
Arabidopsis LCY-B gene and a pepper CHY-B gene resulted in the production of xanthophylls, while the expression of CrtW and CrtZ from Paracoccus spp. leaded to the formation of low fruit levels of ketocarotenoids (Dharmapuri et al., 2002; Ralley et al., 2004).
Innovative strategies for carotenoid engineering in tomato fruit consist in alteration of cryptochromes and components of the light signal transduction pathway. These approaches have the advantages of elevating the carotenoid content of the fruit and also other important health related phytochemicals such as phenylpropanoids and flavonoids (Davuluri et al.,
2005).
Due to their presumed health benefits, there is growing interest in the development of food crops with tailor-made levels and composition of flavonoids. The repertoire of case studies aimed at increasing the levels of flavonoids in tomato fruit also offers the wider range of examples of successful engineering strategies ever realized. Herein we will list some of the results recently obtained.
The first strategy is related to engineering single structural genes controlling key steps in the pathway, such as a chalcone isomerase (CHI) (Muir et al., 2001) and a chalcone synthase
(CHS) (Colliver et al., 2002). More encouraging results were obtained targeting multiple constitutive genes within the flavonoid pathway. For instance, the concomitant ectopic expression of Petunia CHS, CHI, F3H (flavanone hydroxylase) and FLS (flavonol synthase) in tomato fruit led to increased levels of flavonols in both peel (primarily quercetin glycosides) and flesh (primarily kaempferol glycosides). In another case, the concomitant expression of both CHS and FLS had a synergistic effect resulting in a significant accumulation of both

64

Genetic Transformation

naringenin- and kaempferol-glycosides in tomato flesh (Colliver et al., 2002). Secondly, in order to increase the range of flavonoids produced in tomato fruit, a different strategy was taken that consisted in introducing branches to the pathway leading to the synthesis of atypical flavonoids. The overexpression of a grape stylbene synthase (STS) resulted in the accumulation of resveratrol aglycon and its glucoside in tomato fruit peel, while the level of naringenine chalcone was negatively affected because of a competition effect with the main pathway (Schijlen et al., 2006). Similarly, the concomitant overexpression of a petunia CHS and an alfalfa chalcone reductase (CHR) allowed deoxychalcones to accumulate in the tomato peel. When a gerbera FNS-II gene and a Petunia CHI gene were simultaneous overexpressed in tomato, flavones (mainly as luteolin aglycon) accumulated in their peel
(Schijlen et al., 2006). The third strategy involved engineering of transcription factors to enhance a wider range of flavonoid compounds. Besides the increased level of flavonoids induced in tomato fruit by silencing DET1, the expression in tomato of the transcription regulator AtMYB12 activated flavonol biosynthesis as well as the caffeoylquinic acid biosynthetic pathway (Adato et al., 2009). Also, a 60-fold increase in kaempferol glycosides has been achieved in tomato flesh tissue by simultaneous ectopic expression of the two maize transcription factors Lc and C1 (Bovy et al., 2002). Most surprisingly, the expression of the Delila (Del) and Rosea1 (Ros1) genes, two transcription factors from the snapdragon
Antirrhinum majus, in the fruit of transgenic tomatoes induced the accumulation of high levels of anthocyanins in tomato (Butelli et al., 2008) through the activation of a broad range of flavonoid biosynthetic pathway related genes.
In contrast with flavonoid metabolism, so far a reduced number of efforts have been placed into genetic transformation-mediated metabolic engineering of tomato fruit for enhanced ascorbic acid levels. Only few of them succeeded in effectively affect ascorbic acid content and only for a limited number of structural genes within the ascorbic acid pathway. In a fruit systems biological approach, transgenic tomato lines silenced for a mitochondrial ascorbic acid synthesizing enzyme L-galactono-1,4-lactone dehydrogenase performed an increased fruit ascorbic acid level (Garcia et al., 2009) whereas the silencing of an GDP-Dmannose-3’,5’-epimerase resulted in a reduced fruit ascorbic acid accumulation (Gilbert et al., 2009). On the other hand, overexpression of GDP-D-mannose-3’,5’-epimerase genes resulted in enhances ascorbic acid accumulation in tomato fruit (Zhang et al., 2011).
Similarly to ascorbic acid, the opportunity of engineering folate accumulation in tomato fruit has been mostly overlooked and only a few attempts gave rise to successful outcomes. In order to increase pteridines, which act as folate precursors and are synthesized from paminobenzoate, a GTP cyclohydrolase I was overexpressed and a 2-fold increase in folate level in tomato fruit was gained (de la Garza et al., 2004). A higher folate accumulation (up to 25-fold increase) was achieved in tomato fruit by combining in the same plant the overexpression of an aminodeoxychorismate synthase, the p-aminobenzoate-forming enzyme, and the GTP cyclohydrolase I (de la Garza et al., 2007).
Comprehensively, within genetic engineering strategies for crop improvements, the most striking advances so far have involved plants engineered to produce missing nutrients or increase the level of nutrients that are already synthesized. An important trend is to move away from plants engineered to produce single nutritional compounds towards those simultaneously engineered to produce multiple nutrients, a development made possible by the increasing use of multigene engineering or regulative genetic element with pleiotropic effects.

Genetic Transformation in Tomato:
Novel Tools to Improve Fruit Quality and Pharmaceutical Production

65

Trait

Engineering strategy Inserted target Fruit phenotype

Parthenocarpy

single TF

Arf8
IAA9

induced parthenocarpy PG

reduced softening

PME

reduced shelf-life

EXP1A

reduced firmness

βgalactosidase

increased firmness

fw2.2

increased size

Frary et al.,
2000

thaumatin

enhanced flavour

Bartoszewski et al., 2003

GES

changes in flavor
aroma

DavidovichRikanati et al.,
2007

LeAADC1A,
LeAADC2

Increased/ decreased 2phenylacetaldehyd,
2-phenylethanol,
and 1-nitro-2phenylethane

Firmness

Size
Flavour

Flavour and aroma single biosynthetic key gene

dosage series of a single gene heterologous single gene heterologous single gene for diverting biosynthetic flux single biosynthetic key gene

Reference
Goetz et al.,
2007; Wang et al., 2005
Langley et al.
1994
Tieman and
Handa, 1994
Brummell et al., 1999
Smith et al.,
2002

Tieman et al.,
2006

Table 3. Examples of successful fruit engineering for organoleptic quality trait in tomato.
Abbreviations: TF, transcription factor; SG, silencing; SI, serial increase of gene dosage

66

Genetic Transformation

Soluble solids content

Engineering strategy Inserted target Fruit phenotype

Reference

single biosynthetic key gene

Lin5

reduced sugars accumulation Zanor et al., 2009

Dxs

Trait

increased phytoene
& carotenoids

Enfissi et al., 2005

CrtB, CrtI,
CrtY

increased carotenoids Fraser et al., 2002,
2007; Wurbs et al.,
2007

single biosynthetic key gene

PSY-1
CYC-B,
LCY-B

Carotenoid content genes targeting biosynthetic steps LCY-B,
CHY-B
CRY-2

single regulative gene

DET-1,
COP1LIKE,
CUL4
FIBRILLIN

Flavonoid content single biosynthetic key gene single biosynthetic key gene genes targeting biosynthetic steps heterologous gene/genes for diverting flux increased carotenoids increased lycopene & carotene

Rosati et al., 2000
D’Ambrosio et al.,
2004; Ronen et al., 2000

β-cryptoxanthin
& zeaxanthin

Dharmapuri et al.,
2002

increased carotenoid increased carotenoid and flavonoid increased carotenoids and volatiles Römer et al., 2000

Giliberto et al., 2005
Liu et al., 2004;
Wang et al., 2008;
Davuluri et al., 2005
Smikin et al., 2007

spermidine synthase increased lycopene

Neily et al., 2011

CHI

increased fruit peel flavonol Muir et al., 2001

CHS, CHI,
F3H, FLS

increased flavonols

Colliver et al., 2002

STS, CHS,
CHR, FNSII, CHI

single TF

MYB12

Multiple TFs

Del, Ros1

accumulation of resveratrol, deoxychalcones,
& flavones accumulation of flavonols high levels of anthocyanins Schijlen et al., 2006
Adato et al., 2009
Butelli et al., 2008

Genetic Transformation in Tomato:
Novel Tools to Improve Fruit Quality and Pharmaceutical Production

Trait

Ascorbic acid content

Engineering strategy single biosynthetic key gene genes targeting consecutive biosynthetic steps 67

Inserted target Fruit phenotype

Reference

GalLDH,
GME

increased/ decreased fruit ascorbic acid

Garcia et al., 2009;
Gilbert et al., 2011;
Zhang et al., 2011

GCHI and/or ADCS

increased fruit folate Diaz de la Garza et al., 2004; 2007

Table 4. Examples of successful fruit engineering for nutritional quality traits in tomato.
Abbreviations: TF, transcription factor; SG, silencing; IPP, isopenthenilpyrophosphate
4.2 Production of pharmaceutical proteins
Genetically modified plants are currently being evaluated as promising alternative for the production of recombinant proteins and antigens. Major advantages of plant-made pharmaceuticals include low cost of production, higher scale-up capacity and lack of risk of contamination with mammalian pathogens. Several antigenic proteins have been produced in plant, examples are plant-made vaccines against smallpox, HIV and HPV (Human
Papilloma Virus) (Lenzi et al., 2008; Rigano et al., 2009; Scotti et al., 2009). In addition, transgenic plants can represent a suitable vehicle for oral delivery of pharmaceuticals since the plant cell wall protects the recombinant antigen in the harsh condition of stomach and intestine (Sharma et al., 2008a). The delivery of vaccines to mucosal surface makes immunization practise safe and acceptable and is capable of inducing both humoral and cell-mediated immune responses (Salyaev et al., 2010). The production of plant-made mucosal vaccines eliminates needle-associated risks and downstream processing of traditional vaccines such as purification, sterilization and refrigeration. Recently, in addition to other systems, tomato plants have been used as vehicles for the expression and oral delivery of vaccines since tomato is edible, generates abundant biomass at low cost, has flexible growth conditions and contains the natural adjuvant -tomatine (Salyaev et al.,
2010; Soria-Guerra et al., 2011). In this regards, it is noteworthy the work from Zhang and colleagues (2006) that expressed the recombinant Norwalk virus capsid protein in tomato and potato and demonstrated that, although in mice oral immunization with both dried tomato fruit and potato tuber elicited systemic and mucosal antibody responses, the recombinant vaccine in transgenic tomato fruit, especially in air-dried material, was a more potent oral immunogen than potato. The authors speculated that the robust immunogenicity of tomato-derived vaccines was due to natural bioencapsulation by the plant cell matrix and membrane systems, larger amount of smaller 23 nm Virus-like particles and the presence of the natural adjuvant -tomatine. In this paragraph, we will describe several examples of pharmaceuticals produced in tomato plants focusing on the most recently reported studies.
Several studies reported the production of transgenic tomato plants for the expression of viral antigens. In 2008, Perea Arango and colleagues reported high-level expression of the entire coding region of the nucleoprotein (N) gene of rabies virus in transgenic tomato plants. When mice were immunized both intraperitoneally (i.p.) and orally with the tomatomade N protein, the antibody titer of mice immunized i.p. was at least four times higher

68

Genetic Transformation

than that of mice immunized orally. In addition, only mice immunized i.p. were partially protected against a peripheral virus challenge. In the same year, Pan et al. (2008) described the production of genetically modified tomato plants that expressed the structural polyprotein, P1-2A, and protease, 3C, from foot-and-mouth disease virus (FMDV). Guinea pigs vaccinated intramuscularly with foliar extracts from the transgenic material developed a virus-specific antibody response and were protected against a challenge infection.
Recently, in order to develop a vaccine against HPV Paz De la Rosa et al. (2009) expressed in tomato plants chimeric particles containing the HPV 16 L1 sequence fused to a string of Tcell epitopes from HPV 16 E6 and E7 proteins. L1 fused to the string of epitopes was able to assemble into chimeric VLPs (Virus-like particles); in addition, intraperitoneal administration in mice of the transgenic material was able to induce both neutralizing antibodies against the viral particle and a cytotoxic T-lymphocytes activity against the epitopes. Up to date, several groups investigated the production of a mucosal vaccine against HIV and HBV (Hepatitis B virus) in genetically modified tomato plants (Lou et al.,
2007; Salyaev et al., 2010; Zhou et al., 2008). For instance, Shchelkunov et al. (2006) investigated the production of transgenic plants expressing a synthetic chimeric gene, TBIHBS, encoding the immunogenic ENV and GAG epitopes of HIV-1 and the surface protein antigen (HBsAg) of HBV and investigated the immunogenicity of the transgenic material fed to experimental mice. Peña Ramirez and colleagues (2007) investigated the possibility of expressing the HIV-1 Tat protein in fruits of tomato plants. In mice, oral feeding with the tomato-based vaccine was able to raise mucosal IgAs and induce serum IgGs with neutralizing activity. More recently, Cueno at al. (2010) expressed the HIV-1 protein Tat in tomato plants reaching up to 4 μg of recombinant protein per milligram plant protein. In addition, tomato extracts intradermally inoculated into mice were found to induce both humoral and cellular immune responses.
Bacterial antigens have also been expressed in transgenic tomato plants. Alvarez and colleagues (2006) expressed in transgenic tomato plants the FI-V antigen fusion protein for the production of a vaccine against pneumonic and bubonic plague. The authors tested the immunogenicity of the tomato-made vaccine in mice which were primed subcutaneously with bacterially produced F1-V and boosted orally with freeze-dried, powdered transgenic tomato fruit and demonstrated that the vaccine elicited IgG1 in serum and mucosal IgA in fecal pellets. In 2007, Soria-Guerra and collegues expressed in tomato a plant-optimized synthetic gene encoding the recombinant polypeptide sDTP (diphtheria-pertussis-tetanus), containing six DTP immunoprotective exotoxin epitopes and two adjuvants in order to develop an edible multicomponent DPT vaccine. Recently, the same group examined whether immunization of mice fed with freeze-dried tomato material elicited specific antibody responses. Sera of immunized mice tested for IgG antibody response to pertussis, tetanus and diphtheria toxin showed responses to the foreign antigens; in addition, high response of IgA against tetanus toxin was evident in gut (Soria-Guerra et al., 2011). In addition, several studies investigated the feasibility of production of a safe, inexpensive plant-based mucosal vaccine against cholera. For instance, Jang et al. (2007) expressed the
Cholera toxin B subunit (CTB) in transgenic tomato fruits and demonstrated the immunogenicity of the tomato-made vaccine in mice. In alternative, Sharma and colleagues
(2008b) produced the toxin co-regulated pilus subunit A (TCPA) of Vibrio cholerae and its immunogenic epitopes P4 or P6 fused to cholera toxin B subunit (CTB) in tomato plants. In the same year, the same research group reported the production of genetically modified

Genetic Transformation in Tomato:
Novel Tools to Improve Fruit Quality and Pharmaceutical Production

69

tomato plants for the expression of accessory colonization factor subunit A (ACFA) of Vibrio cholerae and ACFA fused to CTB (Sharma et al., 2008a).
Another advantage of using transgenic plants for the production of recombinant protein of biopharmaceutical and industrial importance is that plant cells are able to perform complex post-translational modification, including glycosylation (Agarwal et al., 2008). In this regard, the feasibility of expression of glycosylated and biologically active recombinant human -1antitrypsin (AAT) protein in transgenic tomato plants was demonstrated. In this study, in order to achieve high-level expression of recombinant protein in transgenic plant cells, the gene encoding human AAT protein was optimized by codon adjustment and elimination of mRNA destabilizing sequences. In addition, the synthetic gene was expressed with different signal sequences, translation initiation context sequence, Alfalfa mosaic virus UTR
(untranslated region) at 5’ end and ER (endoplasmic reticulum) retention signal sequence
(KDEL) at 3’ end. The modified gene driven by CaMV35S duplicated enhancer promoter resulted in high-level expression (up to 1.55% of TSP) of recombinant protein in transgenic tomato plants. Elias-Lopez et al. (2008) described the production of transgenic tomato plants expressing interleukin-12. BALB/c mice were infected with either Mycobacterium tuberculosis
H37Rv strain or multi-drug-resistant clinical isolate (MDR) and treated with a daily oral dose of transgenic fruit extracts. Oral administration of the transgenic plant material improved protective immunity and induced higher resistance to mycobacterial infection, when administered the day before infection or during late progressive disease induced by virulent mycobacteria. Other therapeutic proteins produced in transgenic tomato plants include the analgesic-antitumor peptide (AGAP) from the venom of Buthus martensii Karsch
(Lai et al., 2009) and human beta-amyloid for the production of a vaccine against
Alzheimer`s disease (Youm et al., 2008).
Another alternative for the production of recombinant antigens in plant cells is transgene expression from the plastid genome. Chloroplast transformation offers a number of advantages, including the potential to accumulate enormous amounts of recombinant protein, uniform transgene expression rates, no gene silencing and transgene containment.
Recently, Zhou et al. (2008) expressed HIV antigens p24 and Nef from tomato`s plastid genome. In tomato, antigen accumulation reached values of approximately 40% of total leaf protein. When the authors determined p24-Nef accumulation in fruits they found that although green tomatoes accumulated the HIV antigens to approximately 2.5% of the TSP, there was no expression in ripe fruits. The authors speculated that this was due to the presence in red-fruited tomatoes of chromoplasts that, compared to chloroplasts, are usually less active in plastid gene expression.
Up to date, several studies demonstrated the feasibility of using tomato plants as vehicles for the production of pharmaceuticals. One drawback of a tomato-made vaccine could be the short shelf-life of fresh fruits. To provide antigen stability during storage, foodprocessing techniques, such as freeze-drying, could be applied to transgenic tomato fruits expressing recombinant proteins. Freeze-dried plant material could be stored for long time and consumed without cooking; in addition, this technique could allow to standardize and concentrate the plant-made vaccine. Several studies applied this technique to vaccine produced in transgenic tomato and demonstrated that freeze-dried produced stable formulations for oral delivery (Alvarez et al., 2006; Salyaev et al., 2010; Shchelkunov et al.,
2006; Soria-Guerra et al., 2011; Zhang et al., 2006).

70

Genetic Transformation

5. Conclusion
In the present review, we underlined the role of genetic transformation as method to improve fruit quality and pharmaceutical production. In addition, we highlighted the double role of genetic transformation as tool for biotechnology applications and functional analyses of genes of interest (Figure 1). For tomato, these approaches are feasible following strategies of gene/QTL identification based on the use of genetic and genomic resources today available for this species.
Nowadays, European politicians often debate about perceived risks of genetically modified crops, while ignoring potential benefits; therefore, it is highly unlikely that engineered crops will be adopted in the short-to-medium term.
Considering these constraints, mutants could be envisaged as valid alternative to engineer tomato plants for enhanced fruit quality (Figure 1). Mutants could be selected from natural variation or generated using different approaches. In addition, if the mutant exhibits superior alleles, it could be used as improved genotypes or as donor parent in backcrossing breeding schemes to deliver the desirable trait. The isogenic mutant resources available today for tomato are useful for dissecting the mechanisms underlying mutant phenotypes, and such mutagenized populations are also being used to develop targeting induced local lesions in genomes (TILLING) platforms, which represent a high-throughput genetic strategy to screen for point mutations in specific regions of targeted genes, and to validate gene function (McCallum et al., 2000).

Fig. 1. Flow-Chart of steps from the screening of genetic and genomic resources to improved tomato lines

Genetic Transformation in Tomato:
Novel Tools to Improve Fruit Quality and Pharmaceutical Production

71

Another alternative approach to obtain tomato with desirable traits is to discover gene markers that discriminate contrasting alleles in genes or QTLs that control the trait(s) of interest (Figure 1). Following their identification, useful genes or QTLs can be introgressed into desirable genetic backgrounds via Marker Assisted Selection (MAS), where the selection for a trait is based on the genotype rather that the trait itself (Foolad, 2007). The knowledge of the tomato genome sequence dramatically enhances identification of novel molecular markers. Indeed we can envisage that, notwithstanding the implementation of recently developed Next Generation Sequencing technologies, the routine application of markers in tomato breeding will increase (Varshney et al., 2009).
In conclusion, the use of different approaches, such as tomato genetic transformation, exploiting of mutants and identification of allele-specific markers, could not only speed up the process of gene transfer, but it could also allow pyramiding of desirable genes and QTLs from different genetic backgrounds. The rapid integration of new alleles in elite tomato lines will allow new cultivars with desirable traits to enter the market in a shorter time compared to cultivar obtained through traditional breeding.

6. Acknowledgment
Contribution no.Book 007 from the DISSPAPA

7. References
Adato, A.; Mandel, T.; Mintz-Oron, S.; Venger, I.; Levy, D.; Yativ, M.; Dominguez, E.; Wang,
Z.; De Vos, R. C.; Jetter, R.; Schreiber, L.; Heredia, A.; Rogachev, I. & Aharoni, A.
(2009). Fruit-surface flavonoid accumulation in tomato is controlled by a SlMYB12regulated transcriptional network. PLoS Genetics, Vol.5, No.12, e1000777
Agarwal, S.; Singh, R.; Sanyal, I. & Amla, D.V. (2008) Expression of modified gene encoding functional human α-1-antitrypsin protein in transgenic tomato plants. Transgenic
Research, Vol.17, pp. 881-896
Alvarez, M.L.; Pinyeard, H.L.; Crisantes, J.D.; Rigano, M.M; Pinkhasov J.; Walsmley, A.M.;
Mason, H.S. & Cardineau, G.A. (2006) Plant-made subunit vaccine against pneumonic and bubonic plague is orally immunogenic in mice. Vaccine, Vol.24, pp.2477-2490 Apel, W. & Bock, R. (2009) Enhancement of carotenoid biosynthesis in transplastomic tomatoes by induced lycopene-to-provitamin A conversion. Plant Physiology,
Vol.151, pp.59-66
Bai, Y. & Lindhout, P. (2007). Domestication and Breeding of Tomatoes: What have We
Gained and What Can We Gain in the Future? Annals of Botany, Vol.100, pp. 1085–
1094
Balaji, V. & Smart, C.D. (2011). Over-expression of snakin-2 and extensin-like protein genes restricts pathogen invasiveness and enhances tolerance to Clavibacter michiganensis subsp. michiganensis in transgenic tomato (Solanum lycopersicum).
Transgenic Research, doi:10.1007/s11248-011-9506-x
Barone, A.; Chiusano, M. L.; Ercolano, M.R.; Giuliano, G.; Grandillo, S. & Frusciante, L.
(2008). Structural and functional genomics of tomato. International Journal Plant
Genomics, doi:10.1155/2008/820274

72

Genetic Transformation

Barone, A.; Di Matteo, A.; Carputo, D. & Frusciante, L. (2009). High-throughput genomics enhances tomato breeding efficiency. Current Genomics, Vol.10, No.1, pp. 1-9
Bartoszewski, G.; Niedziela, A.; Szwacka, M. & Niemirowicz-Szczytt, K. (2003).
Modification of tomato taste in transgenic plants carrying a thaumatin gene from Thaumatococcus daniellii Benth. Plant Breeding, Vol.122, No.4, pp.347–351
Baxter, C. J.; Carrari, F.; Bauke, A.; Overy, S.; Hill, S. A.; Quick, P. W.; Fernie, A. R. &
Sweetlove, L. J. (2005a). Fruit carbohydrate metabolism in an introgression line of tomato with increased fruit soluble solids. Plant Cell Physiology, Vol.46, pp.425-437
Baxter, C.J.; Sabar, M.; Quick, W.P.& Sweetlove, L.J. (2005b). Comparison of changes in fruit gene expression in tomato introgression lines provides evidence of genome-wide transcriptional changes and reveals links to mapped QTLs and described traits.
Journal of Experimental Botany, Vol.56, pp. 1591–1604
Bock, R. & Warzecha H. (2010) Solar-powered factories for new vaccines and antibiotics.
Trends in Biotechnology, Vol. 28, Issue No 5, pp.246-252.
Bovy, A.; de Vos, R.; Kemper, M.; Schijlen, E.; Pertejo, M.A.; Muir, S.; Collins, G.; Robinson,
S.; Verhoeyen, M.; Hughes, S.; Santos-Buelga, C. & van Tunen, A. (2002). High flavonol tomatoes resulting from the heterologous expression of the maize transcription factor genes Lc and C1. Plant Cell, Vol.14, pp. 2509-2526
Brummell, D. A.; Harpster, M. H.; Civello, P. M.; Palys, J. M., Bennett, A. B. & Dunsmuir P.
(1999). Modification of Expansin Protein Abundance in Tomato Fruit Alters
Softening and Cell Wall Polymer Metabolism during Ripening. The Plant Cell, Vol.
11, pp.2203–2216
Butelli, E.; Titta, L.; Giorgio, M.; Mock, H.P.; Matros, A.; Peterek, S.; Schijlen, E.G.; Hall, R.D.;
Bovy, A.G.; Luo, J. & Martin, C. (2008). Enrichment of tomato fruit with healthpromoting anthocyanins by expression of select transcription factors. Nature
Biotechnology,Vol.26, pp. 1301-1308
Cardi, T.; Lenzi, P. & Maliga, P. (2010). Chloroplasts as expression platforms for plantproduced vaccines. Expert Review of Vaccines, Vol.9, Issue No 8, pp.893-911
Chen, H.; Chang, M.; Chiang, B. & Jeng, S. (2006). Oral immunization of mice using transgenic tomato fruit expressing VP1 protein from enterovirus 71. Vaccine, Vol.24, pp.2944-2951 Colliver, S.; Bovy,A.; Collins, G.; Muir, S.; Robinson, S.; de Vos,C.H.R. & Verhoeyen, M.E.
(2002). Improving the nutritional content of tomatoes through reprogramming their flavonoid biosynthetic pathway. Phytochemistry Reviews, Vol.1, pp. 113-123
Cueno, M.E.; Hibi, Y.; Karamatsu, K.; Yasutomi, Y.; Imai, K.; Laurena, A.C. & Okamoto, T.
(2010). Preferential expression and immunogenicity of HIV-1 Tat fusion protein expressed in tomato plant. Transgenic Research,Vol.19, pp.889-895
D’Ambrosio, C.; Giorio, G.; Marino, I.; Merendino, A.; Petrozza, A.; Salfi, L.; Stigliani, A. L.
& Cellini, F. (2004). Virtually complete conversion of lycopene into β-carotene in fruits of tomato plants transformed with the tomato lycopene β-cyclase (tlcy-b) cDNA. Plant Science, Vol.166, pp.207–214
Dan, Y.; Yan, H.; Munyikw, T.; Dong, J.; Zhang, Y. & Armstrong, C.L. (2006) MicroTom - a high-throughput model transformation system for functional genomics. Plant Cell
Reports, Vol.25, pp.432 – 441
Davidovich-Rikanati, R.; Sitrit, Y.; Tadmor, Y.; Iijima, Y.; Bilenko, N.; Bar, E.; Carmona, B.;
Fallik, E.; Dudai, N.; Simon, J. E.; Pichersky, E. & Lewinsohn E. (2007). Enrichment

Genetic Transformation in Tomato:
Novel Tools to Improve Fruit Quality and Pharmaceutical Production

73

of tomato flavor by diversion of the early plastidial terpenoid pathway. Nature
Biotechnology, Vol.25, pp.899-901
Davuluri, G. R.; van Tuinen, A.; Fraser, P. D.; Manfredonia, A.; Newman, R.; Burgess, D.;
Brummell, D. A.; King, S. R.; Palys, J.; Uhlig, J.; Bramley, P. M.; Pennings, H. M. &
Bowler, C. (2005). Fruit-specific RNAi-mediated suppression of DET1 enhances carotenoid and flavonoid content in tomatoes. Nature Biotechnology, Vol.23, pp.890895 de la Garza, R. I. D.; Gregory, J.F. & Hanson, A.D. (2007). Folate biofortification of tomato fruit. Proceedings of the National Academy of Sciences of the United States of America,
Vol.104 No.10, pp. 4218-4222 de la Garza, R. I. D.; Quinlivan, R.; Klaus, E.P.; Basset, S.M.; Gregory, G.J.; & Hanson, A.D.
(2004). Folate biofortification in tomatoes by engineering the pteridine branch of folate synthesis. Proceedings of the National Academy of Sciences of the United States of
America, Vol.101, pp 13720-13725
Dharmapuri, S.; Rosati, C.; Pallara, P.; Aquilani, R.; Bouvier, F.; Camara, B. & Giuliano, G.
(2002). Metabolic engineering of xanthophyll content in tomato fruits. FEBS Letters,
Vol.519, pp.30-34
Di Matteo, A.; Sacco, A.; Anacleria, M.; Pezzotti, M.; Delledonne, M.; Ferrarini, A.;
Frusciante, L. & Barone, A. (2010). The ascorbic acid content of tomato fruits is associated with the expression of genes involved in pectin degradation. BMC Plant
Biology, Vol.10, pp. 163-173
Dinesh-Kumar, S.P.; Anandalakshmi, R.; Marathe, R.; Schiff, M. & Liu, Y. (2003). VirusInduced gene silencing. Methods in Molecular Biology, Vol.236, pp.287-94
Diretto, G.; Al-Babili, S.; Tavazza, R.; Papacchioli, V.; Beyer, P. & Giuliano, G. (2007).
Metabolic engineering of potato carotenoid content through tuber-specific overexpression of a bacterial mini-pathway. PLoS ONE, Vol.2, e350
Elías-López, A.L.; Marquina, B.; Gutiérrez-Ortega, A.; Aguilar, D.; Gomez-Lim, M. &
Hernández-Pando, R. (2008). Transgenic tomato expressing interleukin-12 has a therapeutic effect in a murine model of progressive pulmonary tuberculosis.
Clinical and Experimental Immunology, Vol.154, pp.123-133
Emmanuel, E. & Levy, A.A. (2002). Tomato mutants as tools for functional genomics.
Current Opinion in Plant Biology, Vol.5, pp. 112-117
Enfissi, E. M. A.; Fraser, P. D.; Lois, L. M.; Boronat, A.; Schuch, W. & Bramley; P. M. (2005).
Metabolic engineering of the mevalonate and non-mevalonate isopentenyl diphosphate-forming pathways for the production of health-promoting isoprenoids. Plant Biotechnology Journal, Vol.3, pp.17–27
Eshed, Y. & Zamir, D. (1995). An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yieldassociated QTL. Genetics, Vol.141, pp. 1147-1162
Estornell, L.H.; Orzaez, D.; Lopez-Pena, L.; Pineda, B.; Anton, M.T.; Moreno, V. & Granell,
A. (2009) A multisite gateway-based toolkit for targeted gene expression and hairpin RNA silencing in tomato fruits. Plant Biotechnology Journal, Vol.7, pp. 298309
Fernandez, A.I.; Viron, N.; Alhagdow, M.; Karimi, M.; Jones, M.; Amsellem, Z.; Sicard, A.;
Czerednik, A.; Angenent, G.; Grierson, D.; May, S.; Seymour, G.; Eshed, Y.;

74

Genetic Transformation

Lemaire-Chamkey, M.; Rothan, C. & Hilson P. (2009). Flexible tools for gene expression and silencing in tomato. Plant Physiology, Vol. 151, pp. 1729-1740
Foolad, M.R. (2007). Genome Mapping and Molecular Breeding of Tomato. International
Journal of Plant Genomics, doi:10.1155/2007/64358
Frary, A.; Nesbitt, T.C.; Grandillo, S.; van der Knaap, E.; Cong, B.; Liu, J.; Meller, J.; Elber, R.;
Alpert, K.B. & Tanksley, S.D. (2000). fw2.2: A Quantitative Trait Locus Key to the
Evolution of Tomato Fruit Size. Science, Vol.289, No.5476, pp. 85-88
Frary, A.; Xu, Y.; Liu, J.; et al. (2005). Development of a set of PCR-based anchor markers encompassing the tomato genome and evaluation of their usefulness for genetics and breeding experiments. Theoretical and Applied Genetics, Vol.111, No.2, pp. 291312
Fraser, P. D.; Enfissi, E. M. & Bramley, P. M. (2009). Genetic engineering of carotenoid formation in tomato fruit and the potential application of systems and synthetic biology approaches. Archives of Biochemistry and Biophysics, Vol.483, pp.196-204
Fraser, P. D.; Enfissi, E. M.; Halket, J. M.; Truesdale, M. R.; Yu, D.; Gerrish, C. & Bramley, P.
M. (2007). Manipulation of phytoene levels in tomato fruit: effects on isoprenoids, plastids, and intermediary metabolism. Plant Cell, Vol.19, pp.3194-3211
Fraser, P.D., Roemer, S., Shipton, C.A., Mills, P.B., Kiano, J.W., Misawa, N., Drake, R.G.,
Schuch, W. & Bramley, P. M. (2002). Evaluation of transgenic tomato plants expressing an additional phytoene synthase in a fruit-specific manner. Proceedings of the National Academy of Sciences of the United States of America, Vol.99, pp.1092–
1097
Fray, R. G.; Wallace, A.; Fraser, P. D.; Valero, D.; Hedden, P.; Bramley, P. M. & Grierson, D.
(1995). Constitutive expression of a fruit phytoene synthase gene in transgenic tomatoes causes dwarfism by redirecting metabolites from the gibberellin pathway. Plant Journal, Vol.8, pp.693–701
Fridman, E.; Carrari, F.; Liu, Y. S.; Fernie, A. R. & Zamir, D. (2004). Zooming in on a quantitative trait for tomato yield using interspecific introgressions. Science,
Vol.305, pp.1786-1789
Fridman, E.; Pleban, T. & Zamir, D. (2000). A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene.
Proceedings of the National Academy of Sciences of the United States of America, Vol.97, pp.4718-4723 Fuentes, A. D.; Ramos, P. L.; Sanchez, Y.; Callard, D.; Ferreira, A.; Tiel, K.; Cobas, K.;
Rodriguez, R.; Borroto, C.; Doreste, V. & Pujol, M. (2008). A transformation procedure for recalcitrant tomato by addressing transgenic plant-recovery limiting factors. Biotechnology Journal, Vol.3, pp. 1088-1093
Gady, A. L. F.; Hermans, F. W. K.; Van de Wal M. H. B. J.; van Loo, E. N.; Visser, R. G. F. &
Bachem, C. W. B. (2009). Implementation of two high through-put tech- niques in a novel application: detecting point mutations in large EMS mutated plant populations. Plant Methods, Vol.5, pp. 1-14
Garcia, V.; Stevens, R.; Gil, L.; Gilbert, L.; Gest, N.; Petit, J.; Faurobert, M.; Maucourt, M.;
Deborde, C.; Moing, A.; Poessel, J.L.; Jacob, D.; Bouchet, J.P.; Giraudel, J.L.; Gouble,
B.; Page, D.; Alhagdow, M.; Massot, C.; Gautier, H.; Lemaire-Chamley, M.; Rolin,
D.; Usadel, B.; Lahaye, M.; Causse, M.; Baldet, P. & Rothan, C. (2009). An integrative genomics approach for deciphering the complex interactions between

Genetic Transformation in Tomato:
Novel Tools to Improve Fruit Quality and Pharmaceutical Production

75

ascorbate metabolism and fruit growth and composition in tomato. Comptes Rendus
Biologies, Vol.332, pp. 1007-1021
Gilbert, L.; Alhagdow, M.; Nunes-Nesi, A.; Quemener, B.; Guillon, F.; Bouchet, B.; Faurobert,
M.; Gouble, B.; Page, D.; Garcia, V.; Petit, J.; Stevens, R.; Causse, M.; Fernie, A.R.;
Lahaye, M.; Rothan, C. & Baldet, P. (2009). GDP-D-mannose 3,5-epimerase (GME) plays a key role at the intersection of ascorbate and non-cellulosic cell-wall biosynthesis in tomato. The Plant Journal, Vol.60, pp. 499-508
Giliberto, L.; Perrotta, G.; Pallara, P.; Weller, J. L.; Fraser, P. D.; Bramley, P. M.; Fiore, A.,
Tavazza, M. & Giuliano, G. (2005). Manipulation of the Blue Light Photoreceptor
Cryptochrome 2 in Tomato Affects Vegetative Development, Flowering Time, and
Fruit Antioxidant Content. Plant Physiology, Vol.137, pp.199–208
Giovannoni, J.J. (2007). Fruit ripening mutants yield insights into ripening control. Current
Opinion in Plant Biology, Vol.10, No.3, pp. 283-289
Goetz, M.; Hooper, L. C.; Johnson, S. D.; Rodrigues, J.C.; Vivian-Smith, A. & Koltunow, A.
M. (2007). Expression of aberrant forms of AUXIN RESPONSE FACTOR8 stimulates parthenocarpy in Arabidopsis and tomato. Plant Physiology, Vol.145, pp.351-366 Grandillo, S.; Tanksley, S.D. & Zamir, D. (2008). Exploitation of natural biodiversity through genomics, In Genomics Assisted Crop Improvement: Vol I Genomics Approaches and
Platforms (R.K. Varshney & R. Tuberosa Ed.) Springer, The Netherlands: pp 121-150
Gupta, V.; Mathur, S.; Solanke, A.U.; Sharma, M.K.; Kumar, R.; Vyas, S.; Khurana, P.;
Khurana, J.P.; Tyagi, A.K. & Sharma, A.K. (2009). Genome analysis and genetic enhancement of tomato. Critical Reviews in Biotechnology, Vol.29, No.2, pp 152-181
Gur, A. & Zamir D. (2004). Unused natural variation can lift yield barriers in plant breeding.
PLoS Biology,Vol.2, No.10, e245
Jang, X.; He, Z.; Peng, Z.; Qi, Y.; Chen, Q. & Yu, S. (2007). Cholera toxin B protein in transgenic tomato fruit induces systemic immune response in mice. Transgenic
Research, Vol.16, pp.169- 175
Khan, R. S.; Nakamura, I. & Mii, M. (2011). Development of disease-resistant marker-free tomato by R/RS site-specific recombination. Plant Cell Reports, doi:10.1007/s00299011-1011-4
Kramer, M.; Sanders, R.; Bolkan, H.; Waters, C., Sheeny, R. E. & Hiatt W. R. (1992).
Postharvest evaluation of transgenic tomatoes with reduced levels of polygalacturonase: processing, firmness and disease resistance. Postharvest Biology and Technology, Vol.1, No.3, pp.241-255
Lai, L.; Huang, T.; Wang, Y.; Liu, Y.; Zhang, J. & Song, Y. (2009). The expression of analgesicantitumor peptide (AGAP) from Chinese Buthus martensii Karsch in transgenic tobacco and tomato. Molecular Biology Reports, Vol.36, pp.1033-1039
Langley, K. R., Martin, A., Stenning, R.; Murray, A. J.; Hobson, G. E.; Schuch, W. W. &
Bird, C. R. (1994). Mechanical and optical assessment of the ripening of tomato fruit with reduced polygalacturonase activity. Journal of the Science of Food and
Agriculture, Vol.66, No.4, pp.547–554
Lenzi, P.; Scotti, N.; Alagna, F.; Tornesello, M.L.; Pompa, A.; Vitale, A.; De Stradis, A.; Monti,
L.; Grillo, S.; Buonaguro, F.M.; Maliga, P. & Cardi T. (2008). Translational fusion of chloroplast-expressed human papillomavirus type 16 L1 capsid protein enhances

76

Genetic Transformation

antigen accumulation in transplastomic tobacco. Transgenic Research, Vol.17, Issue
No 6, pp.1091-102
Lippman, Z.B.; Semel, Y. & Zamir, D. (2007). An integrated view of quantitative trait variation using tomato interspecific introgression lines. Current Opinion in Genetics
& Development, Vol.17, pp. 545-552
Liu, J.; Cong, B. & Tanksley, S. D. (2003). Generation and analysis of an artificial gene dosage series in tomato to study the mechanisms by which the cloned quantitative trait locus fw2.2 controls fruit size. Plant Physiology, Vol.132, pp.292-299
Liu, Y.; Roof, S.; Ye, Z.; Barry, C.; van Tuinen, A.; Vrebalov, J.; Bowler, C. & Giovannoni, J.
(2004). Manipulation of light signal transduction as a means of modifying fruit nutritional quality in tomato. Proceedings of the National Academy of Sciences of the
United States of America, Vol.101, pp.9897-9902
Liu, Y.; Schiff, M. & Dinesh-Kumar, S. P. (2002). Virus-Induced gene silencing in tomato. The
Plant Journal, Vol.31, Issue No 6, pp. 777-786
Lou, X.; Yao, Q.; Zhang, Z.; Peng, R.; Xiong, A. & Wang, H. (2007). Expression of the human hepatitis B virus large surface antigen gene in transgenic tomato plants. Clinical and
Vaccine Immunology, Vol.14, Issue No.4, pp. 464-469
McCallum, C. M.; Comai L.; Greene, E. A. & Henikoff, S. (2000). Targeting induced local lesions in genomes (TILLING) for plant functional genomics. Plant Physiology,
Vol.123, pp.439-442.
Menda, N.; Semel, Y.; Peled, D.; Eshed, Y. & Zamir, D. (2004). In silico screening of a saturated mutation library of tomato. Plant Journal, Vol.38, No.5, pp. 861-872
Minoia, S.; Petrozza, A.; D’Onofrio, O.; Piron, F.; Mosca, G.; Sozio, G.; Cellini, F.;
Bendahmane, A. & Carriero, F. (2010). A new mutant genetic resource for tomato crop improvement by TILLING technology. BMC Research Notes, Vol.3, pp. 69
Mueller, L.A.; Lankhorst, R.K.; Tanksley, S.D. et al. (2009). A Snapshot of the Emerging
Tomato Genome Sequence. The Plant Genome, Vol.2, No.1, pp. 78-92
Mueller, L.A.; Tanksley, S.D.; Giovannoni, J.J. et al. (2005). The Tomato Sequencing Project, the first cornerstone of the International Solanaceae Project (SOL). Comparative and
Functional Genomics, Vol.6, No.3, pp. 153-158
Muir, S. R.; Collins, G. J.; Robinson, S.; Hughes, S. G.; Bovy, A. G.; de Vos, C. H.; van Tunen,
A. J. & Verhoeyen, M. E. (2001). Overexpression of petunia chalcone isomerase in tomato results in fruit containing dramatically increased levels of flavonols. Nature
Biotechnology, Vol.19, pp.470–474
Naqvi, S.; Farré, G.; Sanahuja, G.; Capell, T.; Zhu C. & Christou, P. (2009). When more is better: multigene engineering in plants. Trends in Plant Science, Vol. 15, No. 1, pp.
48-56
Neily, M. H.; Matsukura, C.; Maucourt, M.; Bernillon, S.; Deborde, C.; Moing, A., Yin, Y.-G.;
Saito, T.; Mori, K., Asamizu, E.; Rolin, D.; Moriguchi, T. & Ezura, H. (2011).
Enhanced polyamine accumulation alters carotenoid metabolism at the transcriptional level in tomato fruit over-expressing spermidine synthase. Journal of
Plant Physiology, Vol.168, No.3, pp.242-252
Orzaez, D. & Granell, A. (2009). Reverse genetics and transient gene expression in fleshy fruits. Plant Signaling and Behaviour, Vol.4, Issue No 9, pp.864- 86
Orzaez, D.; Medina, A.; Torre, S.; Fernandez-Moreno, J.P.; Rambla, J.L., Fernandez-delCarmen, A.; Butelli, E.; Martin, C. & Granell, A. (2009). A visual-reporter system for

Genetic Transformation in Tomato:
Novel Tools to Improve Fruit Quality and Pharmaceutical Production

77

virus-induced gene silencing in tomato fruit based on anthocyanin accumulation.
Plant Physiology, Vol.150, pp. 1122.1134
Orzaez, D.; Mirabel, S.; Wieland, W.H & Granell, A. (2006). Agroinjection of tomato fruits. A tool for rapid functional analysis of transgenes directly in fruit. Plant Physiology,
Vol.140, pp.3-11
Pan, L.; Zhang, Y.; Wang, Y.; Wang, B.; Wang, W.; Fang, Y.; Jiang, S.; Lv, J.; Wang, W.; Sun,
Y. & Xie, Q. (2008). Foliar extracts from transgenic tomato plants expressing the structural polyprotein, P1-2A, and protease, 3C, from foot-and-mouth disease virus elicit a protective response in guinea pigs. Veterinary Immunology and
Immunopathology, Vol.121, pp.83-90
Panthee, D.R. & Chen, F. (2010). Genomics of Fungal Disease Resistance in Tomato. Current
Genomics, Vol.31, No.1, pp. 30, ISSN: 1389-2029
Paz De la Rosa, G.; Monroy-Garcia, A.; de Lourdes Mora-Garcia, M.; Reynaga Peña, C.G.;
Hernández-Montes, J.; Weiss-Steider, B. & Gómez Lim, A.M. (2009). An HPV 16 L1based chimeric human papilloma virus-like particles containing a string of epitopes produced in plants is able to elicit humoral and cytotoxic T-cell activity in mice.
Virology Journal, Vol.6, pp.2
Peña Ramírez, Y.J.; Tasciotti, E.; Gutierrez-Ortega, A.; Donayre Torres, A.J.; Olivera Flores,
M.T.; Giacca, M. & Gómez Lim, M.A. (2007). Fruit-specific expression of the human immunodeficiency virus type 1 tat gene in tomato plants and its immunogenic potential in mice. Clinical and Vaccine Immunology, Vol.14, pp.685-692
Perea Arango, I.; Loza Rubio, E.; Rojas Anaya, E.; Olivera Flores, T.; Gonzalez de la Vara, L.
& Gomez Lim, M.A. (2008). Expression of the rabies virus nucleoprotein in plants at high-levels and evaluation of immune responses in mice. Plant Cell Reports, Vol.27, pp.677-685 Pineda, B.; Gimenez-Caminero, E.; Garcia-Sogo, B.; Anton, M.T.; Atares, A.; Capel, J. et al.
(2010). Genetic and physiological charac- terization of the arlequin insertional mutant reveals a key regulator of reproductive development in tomato. Plant Cell
Physiology, Vol.51, pp. 435–447
Pino, L.E.; Lombardi-Crestana, S.; Azevedo, M.S.; Scotton, D.C.; Borgo, L.; Quecini, V.;
Figueira, A. & Peres, L.E.P. (2010). The Rg1 allele as a valuable tool for genetic transformation of the tomato “Micro-Tom” model system. Plant Methods, Vol.6, pp.23 Piron, F.; Nicolai, M.; Minoia, S.; Piednoir, E.; Moretti, A.; Salgues, A.; Zamir, D.; Caranta, C.
& Bendahmane, A. (2010). An induced mutation in tomato eIF4E leads to immunity to two potyviruses. PLoS One, Vol.5, No.6, pp. e11313
Qiu, D.; Diretto, G.; Tavarza, R.& Giuliano, G. (2007). Improved protocol for Agrobacterium mediated transformation of tomato and production of transgenic plants containing carotenoid biosynthetic gene CsZCD. Scientia Horticulturae, Vol.112, pp.172-175
Ralley, L., Enfissi, E.M.; Misawa, N.; Schuch, W.; Bramley, P. M. & Fraser, P. D. (2004).
Metabolic engineering of ketocarotenoid formation in higher plants. Plant Journal,
Vol.39, pp.477-486
Rein, D.; Schijlen, E.; Kooistra, T.; Herbers, K.; Verschuren, L.; Hall, R.; Sonnewald, U.; Bovy,
A. & Kleemann, R. (2006). Transgenic flavonoid tomato intake reduces C- reactive protein in human C-reactive protein transgenic mice more than wild-type tomato.
Jouirnal of Nutrition, Vol.136, pp. 2331-2337

78

Genetic Transformation

Rigano, M.M.; Manna, C.; Giulini, A.; Pedrazzini, E.; Capobianchi, M.; Castilletti, C.; Di
Caro, A.; Ippolito, G.; Beggio, P.; De Giuli Morghen, C.; Monti, L.; Vitale, A. &
Cardi, T (2009).Transgenic chloroplasts are efficient sites for high-yield production of the vaccinia virus envelope protein A27L in plant cells. Plant Biotechnology
Journal, Vol.7, Issue No 6, pp. 577–591
Römer, S.; Fraser, P. D.; Kiano, J. W.; Shipton, C. A.; Mills, P. B.; Drake, R.; Schuch, W. &
Bramley, P. M. (2000). Elevation of the provitamin A content of transgenic tomato plants. Nature Biotechnology, Vol.18, pp.666–669
Ronen, G.; Carmel-Goren, L.; Zamir, D. & Hirschberg, J. (2000). An alternative pathway to βcarotene formation in plant chromoplasts discovered by map-based cloning of beta and old-gold color mutations in tomato. Proceedings of the National Academy of
Sciences of the United States of America, Vol.97, pp.11102–11107
Rosati, C.; Aquilani, R.; Dharmapuri, S.; Pallara, P.; Marusic, C.; Tavazza, R.; Bouvier, F.;
Camara, B. & Giuliano, G. (2000). Metabolic engineering of β-carotene and lycopene content in tomato fruit. Plant Journal, Vol.24, pp.413–420
Ruf, S.; Hermann, M.; Berger, I.J.; Carrer, H. & Bock, R. (2001). Stable genetic transformation of tomato plastids and expression of a foreign protein in fruit. Nature Biotechnology,
Vol.19, pp.870- 875
Saito, T.; Ariizumi, T.; Okabe, Y.; Asamizu, E.; Hiwasa-Tanase, K. Fukuda, N.; Mizoguchi,
T.; Yamazaki, Y.; Aoki, K. & Ezura, H. (2011). TOMATOMA: A Novel Tomato
Mutant Database Distributing Micro-Tom Mutant Collections. Plant and Cell
Physiology, Vol.52, No.2, pp. 283-296
Salyaev, R.K.; Rigano, M.M. & Rekoslavskaya, N.I. (2010) Development of plant-based mucosal vaccines against widespread infectious diseases. Expert Reviews of Vaccines,
Vol.9, Issue No 8, pp.937-46
Schauer, N.; Semel, Y.; Roessner, U.; Gur, A.; Balbo, I.; Carrari, F.; Pleban, T.; Perez-Melis, A.;
Bruedigam, C.; Kopka, J.; Willmitzer, L.; Zamir, D. & Fernie, A. R. (2006).
Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nature Biotechnology, Vol.24, pp.447-454
Schijlen, E.; de Vos C.H.R; Jonker, H.; van den Broeck, H.; Molthoff, J.; van Tunen, A.;
Martens, S. & Bovy,A. (2006). Pathway engineering for healthy phytochemicals leading to the production of novel flavonoids in tomato fruit. Plant Biotechnology
Journal, Vol.4, pp. 433-444
Scotti, N.; Alagna, F.; Ferraiolo, E.; Formisano, G.; Sannino, L.; Buonaguro, L.; De Stradis, A.;
Vitale, A.; Monti, L.; Grillo, S.; Buonaguro, F.M. & Cardi, T. (2009). High-level expression of the HIV-1 Pr55gag polyprotein in transgenic tobacco chloroplasts.
Planta, Vol.229, Issue No 5, pp.1109-22
Sharma, M.K.; Jani, D.; Thungapathra, M.; Gautam, J.K.; Meena, L.S.; Singh, Y.; Ghosh, A.;
Tyagi, A.K.; Sharma, A.K. (2008a). Expression of accessory colonization factor subunit A (ACFA) of Vibrio cholerae and ACFA fused to cholera toxin B subunit in transgenic tomato (Solanum lycopersicum). Journal of Biotechnology, Vol.135, pp.22-27
Sharma, M.K.; Singh, N.K.; Jani, D.; Sisodia, R.; Thungapathra, M.; Gautam, J.K.; Meena,
L.S.; Singh, Y.; Ghosh, A.; Tyagi, A.K.; Sharma, A.K. (2008b). Expression of toxin coregulated pilus subunit A (TCPA) of Vibrio cholerae and its immunogenic epitopes fused to cholera toxin B subunit in transgenic tomato (Solanum lycopersicum). Plant
Cell Reports, Vol.27, pp.307-318

Genetic Transformation in Tomato:
Novel Tools to Improve Fruit Quality and Pharmaceutical Production

79

Sharma, M.K.; Solanke, A.U.; Jani, D.; Singh, Y.; Sharma, A.K. (2009). A simple and efficient
Agrobacterium-mediated procedure for transformation of tomato. Journal of
Biosciences, Vol.34, Issue No 3, pp.423-433
Shchelkunov, S.N.; Salyaev, R.K.; Posdnyakov, S.G.; Rekoslavskaya, N.I.; Nesterov, A.E.;
Ryzhova, T.S.; Sumtsova, V.M.; Pakova, N.V.; Mishutina, U.O.; Kopytina, T.V. &
Hammond, R.W. (2006). Immunogenicity of a novel, bivalent, plant-based oral vaccine against hepatitis B and human immunodeficiency viruses. Biotechnology
Letters, Vol.28, pp.959-967
Simkin, A. J.; Gaffé, J.; Alcaraz, J. P.; Carde, J. P.; Bramley, P. M.; Fraser, P. D. & Kuntz, M.
(2007). Fibrillin influence on plastid ultrastructure and pigment content in tomato fruit. Phytochemistry, Vol.68, No.11, pp.1545-1556
Smith, C. J. S.; Watson, C. F.; Bird, C. R.; Ray, J.; Schuch, W. & Grierson, D. (1990).
Expression of a truncated tomato polygalacturonase gene inhibits expression of the endogenous gene in transgenic plants. Molecular and General Genetics, Vol.224,
No.3, pp.477-481
Smith, D. L.; Abbott, J. A. & Gross, K. C. (2002). Down-regulation of tomato betagalactosidase 4 results in decreased fruit softening. Plant Physiology, Vol.129, pp.1755-1762 Soria-Guerra, R.E.; Rosales-Mendoza, S.; Márquez-Mercado, C.; López-Revilla, R.; CastilliCollazo, R. & Alpuche-Solís, AG. (2007). Transgenic tomatoes express an antigenic polypeptide containing epitopes of the diphtheria, pertussis and tetanus exotoxins, encoded by a synthetic gene. Plant Cell Reports, Vol.26, pp.961-968
Soria-Guerra, R.E.; Rosales-Mendoza, S.; Moreno-Fierros, L.; López-Revilla, R. & AlpucheSolís, A.G. (2011). Oral immunogenicity of tomato derived sDPT polypeptide containing Corynebacterium diphteriae, Bordetella pertussis and Clostridium tetani exotoxin epitopes. Plant Cell Reports, Vol.30, pp.417-424
Sun, H.; Uchii, S.; Watanabe, S. & Ezura, H. (2006). A highly efficient transformation protocol for Micro-Tom, a model cultivar for tomato functional genomics. Plant and
Cell Physiology, Vol.47, Issue No 3, pp.426-431
Tieman, D. M.; Handa, A. K. (1994). Reduction in pectin methyltransferase activity modifies tissue integrity and cation levels in ripening tomato (Lycopersicon esculentum
Mill.) fruits. Plant Physiology, Vol.106, pp.429-436
Tieman, D. M.; Zeigler, M.; Schmelz, E. A.; Taylor, M. G.; Bliss, P.; M.Kirst & Klee H. J.
(2006). Identification of loci affecting flavour volatile emissions in tomato fruits.
Journal of Experimental Botany, Vol.57, pp.887-896
Van Eck, J.; Kirk, D.D. & Walsmley, A.M. (2006). Tomato (Lycopersicum esculentum). Methods in Molecular Biology, Vol.343, pp.459-4773
Varshney, R. K.; Nayak, S. N.; May, G. D. & Jackson, S. A. (2009). Next-generation sequencing technologies and their implications for crop genetics and breeding.
Trends in Biotechnology, Vol.27, No.9, pp.522-530
Verpoorte, R.; van der Heijdenvan, R. & Memelink, J. (2000). Engineering the plant cell factory for secondary metabolite production. Transgenic Research, Vol.9, pp. 323-343
Wang, H.; Jones, B.; Li, Z.; Frasse, P.; Delalande, C.; Regad, F.; Chaabouni, S.; Latche, A.;
Pech, J. C. & Bouzayen, M. (2005). The tomato Aux/IAA transcription factor IAA9 is involved in fruit development and leaf morphogenesis. Plant Cell, Vol.17, pp.2676-2692 80

Genetic Transformation

Wang, S.; Liu, J.; Feng, Y.; Niu, X.; Giovannoni, J. & Liu, Y. (2008). Altered plastid levels and potential for improved fruit nutrient content by downregulation of the tomato
DDB1-interacting protein CUL4. The Plant Journal, Vol.55, No.1, pp.89–103
Watanabe, S.; Mizoguchi, T.; Aoki, K.; Kubo, Y.; Mori, H.; Imanishi, S.; Yamazaki, Y.;
Shibata, D.; Ezura, H. (2007). Ethylmethanesulfonate (EMS) mutagenesis of
Solanum lycopersicum cv. Micro-Tom for large-scale mutant screens. Plant
Biotechnology, Vol.24, pp. 33–38
Wroblewski, T.; Tomczak, A. & Michelmore, R. (2005). Optimization of Agrobacteriummediated transient assays of gene expression in lettuce, tomato and Arabidopsis.
Plant Biotechnology Journal, Vol. 3, pp.259-273
Wu, F. & Tanksley, S.D. (2010). Chromosomal evolution in the plant family Solanaceae. BMC
Genomics, Vol.17, No.11, pp. 182
Wu, Y.; He, Y. & Ge, X. (2011). Functional characterization of the recombinant antimicrobial peptide Trx-Ace-AMP1 and its application on the control of tomato early blight disease. Applied Microbiology and Biotechnology, doi:10.1007/s00253-011-3166-x
Wurbs, D.; Ruf, S. & Bock, B. (2007). Contained metabolic engineering in tomatoes by expression of carotenoid biosynthesis genes from the plastid genome. The Plant
Journal, Vol.49, pp.276-288
Yasmeen, A.; Mirza, B.; Inayatullah, S.; Safdar, N.; Jamil, M.; Ali, S. & Choudhry, M.F.
(2009). In planta transformation of tomato. Plant Molecular Biology Reporter, Vol.27, pp.20–28 Youm, J.W.; Jeon, J.H.; Kim, H.; Kim, Y.H.; Ko, K.; Joung, H. & Kim, H. (2008). Transgenic tomatoes expressing human beta-amyloid for use as a vaccine against Alzheimer`s disease. Biotechnology Letters, Vol.30, pp.1839 – 1845
Zanor, M. I.; Osorio, S.; Nunes-Nesi, A.; Carrari, F.; Lohse, M.; Usadel, B.; Kuhn, C.; Bleiss,
W.; Giavalisco, P.; Willmitzer, L.; Sulpice, R.; Zhou, Y. H. & Fernie, A. R. (2009).
RNA interference of LIN5 in tomato confirms its role in controlling Brix content, uncovers the influence of sugars on the levels of fruit hormones, and demonstrates the importance of sucrose cleavage for normal fruit development and fertility. Plant
Physiology, Vol.150, pp.1204-1218
Zhang, C.; Liu, J.; Zhang, Y.; Cai, X.; Gong, P., Zhang, J.; Wang, T.; Li, H. & Ye, Z. (2011).
Overexpression of SlGMEs leads to ascorbate accumulation with enhanced oxidative stress, cold, and salt tolerance in tomato. Plant Cell Reports, Vol.30, pp.
389-398
Zhang, X.; Buehner, N.A.; Hutson, A.M.; Estes, M.L. & Mason, H.S. (2006). Tomato is a highly effective vehicle for expression and oral immunization with Norwalk virus capsid protein. Plant Biotechnology Journal, Vol.4, pp.419-432
Zhang, X.; Li, H.; Zhang, J.; Zhang, C.; Gong, P.; Ziaf, K.; Xiao, F. & Ye, Z. (2010). Expression of artificial microRNAs in tomato confers efficient and stable virus resistance in a cell-autonomous manner. Transgenic Research, doi:10.1007/s11248-010-9440-3
Zhou, F.; Badillo-Corona, J.A.; Karcher, D.; Gonzalez-Rabade, N.; Piepenburg, K.; Borchers,
A.M. Maloney, A.P.; Kavanagh, T.A.; Gray, J.C. & Bock, R. (2008). High-level expression of human immunodeficiency virus antigens from the tobacco and tomato plastid genomes. Plant Biotechnology Journal, Vol.6, pp.897-913.

4
Genetic Transformation Strategies in Fruit Crops
Humberto Prieto
La Platina Research Station /
National Institute of Agriculture (INIA)
Chile
1. Introduction
Genetic transformation provides the means for adding single horticultural traits in existing cultivars without modify their commercial characteristics. This capability is particularly valuable for perennial plants and fruit tree species, in which conventional breeding is hampered by their long generation time and juvenile periods, complex reproductive biology, high levels of heterozygosity, limited genetic sources and linkage drag of undesirable traits from wild relatives. In addition, gene transfer technologies for fruit tree species take the inherent advantage of vegetative propagation used for their reproduction, which allowed for the application of a high scale production of the desired transgenic line starting from one successful transformed line. Despite this opportunity, final setting of transformation protocols in this type of species, endures major limiting factors preventing the development of new varieties: a) explants recalcitrance to regenerate adventitious transformed shoots and b) a limited regeneration capability, usually extended to just few genotypes (i.e. cultivar dependence).
This chapter illustrates the road between the establishment of transformation methodologies on particular species of Vitis spp. and Prunus spp. and their use as technical baselines for achievement of transformation procedures in new, eventually more recalcitrant, cultivars or genus members.
1.1 Genetic transformation of fruits in the current research era
Genetic improvement of fruit trees is essential for increasing fruit production. For most of these species, the desired new varieties contemplate the presence of agronomic and horticultural traits related to propagation, yield, appearance, quality, disease and pest control, abiotic stress and shelf-life. Incorporation of these traits into the genetic backgrounds of species by conventional breeding needs overcome some major disadvantages, including long juvenile periods and reduced possibility of introgression of the suitable traits (when available) into commercially relevant cultivars. Although currently the use of new technologies based on high throughput platforms for sequencing and genotyping has deeply contributed to accelerate the association of molecular markers and major genes to these relevant traits, there exists a bottle neck in this strategy when

82

Genetic Transformation

phenotyping must be carried out. In addition, breeding by controlled crosses is hampered due to factors specifically related to complex characteristics belonging to these species, such as delayed flowering, unsuccessful fruit setting due to abortive embryos, massive fruit drop, and self-incompatibility barriers found in many of them.
Genetic transformation represents inherent advantages for fruit tree improvement, although in fruit trees this area of research is not a routine procedure. The transversal negative perception about the “transgenic technology” is added to an additional degree of difficulty for setting up adequate technical systems in fruit tree species. Eventually, if a proper regenerative system has been established, any DNA construct designed for either a major gene over-expression or gene silencing (i.e. interfering RNA´s in vivo generation) can be introduced into a desired genome. Consequently, the feasibility of genetic modification relies on adequate technical systems which allowed for results in a reasonable time frame.
Regardless the final objectives of transformed events (a product or fundamental research), highly regenerative systems for explants production and whole plants regeneration are key steps of fruit tree genetic transformation. In addition, the relevance of these procedures is even higher when an era of candidate genes evaluation has begun as a result of the current knowledge about genomes.

2. Use of grapevine systems as a model in fruit species
2.1 Grapevine somatic embryogenesis and genetic transformation of somatic embryos Since its first report in 1976 (Mullins and Srinivasan, 1976), somatic embryogenesis (SE) in
Vitis vinifera L. has been described in different cultivars and their hybrids (Martinelli and
Gribaudo, 2001, 2009), becoming the most efficient procedure for the generation of in vitro cultures prone to genetic transformation (Stamp and Meredith, 1988; Scorza et al., 1996;
Martinelli et al., 2001a; Iocco et al., 2001; Torregrosa et al., 2002; Hinrichsen et al., 2005, Li et al., 2008). As described by Ammirato (1983), SE is understood as the initiation of embryos from plant somatic tissues closely resembling their zygotic counterparts. As a fruit species, grapevine SE is not a routine procedure that can be easily and efficiently reproduced among different cultivars (Martinelli et al., 2001; Araya et al., 2008). Grapevine SE has been successfully reached using as source explants stamens and pistils (Rajasekaran and Mullins,
1983; Martinelli et al., 2001a, Araya et al., 2008), unfertilized ovules (Mullins and Srinivasan,
1976), ovaries (Martinelli et al., 2001), leaves (Martinelli et al., 1993), petioles (Martinelli et al.,
1993), and tendrils (Salunkhe et al., 1997). In the conventional approach, grapevine SE is induced to the generation of pro-embryogenic (PE) and embryogenic (E) cell masses by cultivation of these explants in solid X6 medium using TC agar Petri dishes for 30 days (Li et al., 2001). X6 corresponds to a modified MS (Murashige and Skoog, 1962) medium lacking glycine and supplemented with KNO3 and NH4Cl as the sole nitrogen source, in addition to sucrose, myo-inositol, and activated charcoal. For transformation, cells are pre-conditioned by a seven days treatment in DM (Driver and Kuniyuki, 1984) solid medium and then infected with Agrobacterium tumefaciens by immersion of explants in liquid DM medium containing the bacteria. After two days in co-cultivation, an early selection is applied using solid DMcck (DM medium supplemented with carbenicillin, cefotaxime, and kanamycin) medium for 21 days. Transformed cells are, again, induced to generate E cells in solid X6

83

Genetic Transformation Strategies in Fruit Crops

medium up to appearance of mature structures and fully developed somatic embryos, which are picked up and harvested as putative transgenic lines (Figure 1).
SE process based on the use of Petri dishes is illustrated for both leaves and inflorescences as source explants. This process leads to somatic embryo generation (embryogenic masses) prone for Agrobacterium infection. After co-cultivation, a selection step is applied by 21 days.
Afterwards, embryo development leading to the regeneration of whole plants, acclimatization and field trial of the obtained individuals are carried out. The field trial shown in Figure 1 corresponds to an assay of genetically modified plants generated to introduce tolerance to the fungus Botrytis cinerea carried out since 2004 at La Platina Station in the National Institute of Agriculture, Santiago, Chile.
Field material

Floral buds cultivation A. tumefaciens infection Embryogenic masses Selection

In vitro material

Embryo germination

Field trial

Plant development

Plantlet selection

Fig. 1. Conventional work flow involved in somatic embryogenesis (SE) and Agrobacteriummediated genetic transformation of grapevine ´Thompson Seedless´.
2.2 Current requirements in grapevine genetic transformation
The convergence of genome sequencing studies on V. vinifera cv. ´Pinot Noir´ (Jaillon et al.,
2007; Velasco et al., 2007) and a high through-put transformation pipeline to carry out the evaluation of candidate genes, seem a current major priority. The SE-mediated transformation process of grapevine has not been directed to the massive generation of transformable explants. Improvements to the technology have recently showed up by maintenance of embryogenic cultures using suspension cultures in flasks. These efforts did not report major morphological or anatomical differences in the generated E and PE masses when compared to the above described procedures using solid media (Jayasankar et al.,

84

Genetic Transformation

2003). Recently, Li et al. (2008) improved this fundamental methodology by introduction of a flask-based calli processing before starting the second round of sub-culturing in solid X6 medium. This additional step consisted of four consecutive sub-cultures using agitated flasks containing DMcck; i.e. under a permanent selection by increasing the kanamycin working concentrations (in grapevines this is referred as concentrations from 20 to 50 mg/L). A final selective pressure is applied (for instance 100 mg/L) by addition of kanamycin to solid DMcck Petri dishes. The processed calli were reinserted into the second round of culturing in solid X6 medium dishes, until embryo harvesting and development for evaluation.
In general terms, the whole process requires a total time of 24 to 25 weeks and leads to the generation of candidate genetically modified plantlets ready for a primary, PCR-based, screening. Regardless the strategy (solid media Petri dishes or solid media plus the inclusion of a flasks’ step), both routes share a critical and consistent problem referred to the massive generation of adequate amounts of E or PE masses supporting routine transformation experiments. 2.3 Optimizing somatic embryogenesis platforms. Different strategies
It is accepted that the developmental stage of source explants is of great importance in grapevine SE setting (Martinelli and Gribaudo, 2009). Commonly, SE systems in grapes are initiated from stamens and pistils and responses are variety-dependent. The best developmental stages to initiate embryogenic cultures have been deduced for some genotypes using the basis of phenological stages of inflorescences (Dhekney et al., 2009); whereas stamens and pistils from some cultivars such as ´Pinot Gris´ must be collected at early developmental stages; other genotypes such as ´Merlot´, ´Sauvignon Blanc´ and
´Freedom´ must be induced using explants at more advanced maturity stages.
In vitro leaves have been also proposed as source explants for SE induction in grapevines.
Although lower efficiencies than stamens and pistils have been obtained, the use of unopened leaves (i.e. between 1.5 to 5.0 mm long) placed abaxial side down on Petri dishes supplemented with solid NB2 medium leads to the generation of PE masses that later will regenerate into whole plants in ´Superior Seedless´, ´Thompson Seedless´ and ´Freedom´ genotypes (Dhekney et al., 2009). Alternatively, convenient procedures to introduce material from the field have been reached by proper cultivation of grapevine sterile buds in solid
C2D4B medium (Araya et al., 2008; Gray, 1995) by one to four months and then culturing the processed tissues into NB2 solid medium.
The use of induction media based on modified MS or Nitsch (described by Li et al., 2008), established the basis for additional improvements in grapevine SE. This time, authors were focused on the yield of the system. Solid cultures are heterogeneous and diffusion-limited; on the other hand, agitated liquid cultures, involve mainly faster, more uniform, efficient, and controllable mass transfer processes. It is accepted that use of liquid cultures offers numerous technical advantages over solid cultures (Archambault et al., 1994). However, the actual evaluation of embryogenic protocols must be carried out on the basis of volumetric productions, true plant organ (i.e. torpedo shape, Jayasankar et al., 2003), system homogeneity, and finally, conversion of embryo cells into whole plants (Archambault et al.,
1994). In ´Thompson Seedless´, application of an induction period by six weeks using Li´s

85

Genetic Transformation Strategies in Fruit Crops

modifications generated PE masses that are transferred into maintenance liquid media based on B5 major salts (Gamborg et al., 1968) and vitamins from MS. These flask assays have been the basis for the generation of an air-lift bioreactor as recently described Tapia et al. (2009). The system was designed to improve biomass production of ´Thompson Seedless´ somatic embryos and, at the same time, enabled a preliminary characterization of cell´s behavior during the grapevine SE time-course. The very first improvement derived from the use of liquid systems was that biomass multiplication rate decreased from 60 to about 40 days due to the use of agitated flasks (Figure 2a). Even better, the use of an air-lift bioreactor improved this rate to seven days (Tapia et al., 2009). In addition, a lower than expected sugar consumption was observed during the SE process, suggesting side roles for this substrate during culturing. Li´s procedures described that flasks culturing leaded to the generation of up to 400 mg of biomass, obtaining PE and E cells; in those experiments, bigger inocula leaded to explants’ oxidation. On the contrary, the 2 L vessel’s reactor (Figure 2b) regularly admitted 2 g inocula without affecting the process, including explants viability and duplication of this biomass at the seventh day of batching. Genetic transformation procedures of somatic embryos obtained from this system did not show any difference compared to explants produced by the regular solid media-based system (depicted in Figure
1), generating fully regenerated transgenic plants (Tapia et al., 2009).

A)

B)
Iniciation

Maintenance

Culturing

medium

medium

into solid dishes

Selection

Germinating

Regeneration

embryos

into whole plants

Fig. 2. Improved pipeline for somatic embryogenesis and Agrobacterium-mediated genetic transformation of grapevine ´Thompson Seedless´ and ´Princess´ using liquid media (A) and an air-lift bioreactor (B). Main steps are indicated.
2.4 Inducing somatic embryogenesis in recalcitrant germplasms. New strategies
Embryogenic competence can be considered as an exception more than a rule. Several genotypes have shown low or null responses to protocols that have been successfully evaluated in certain varieties. An optimized SE procedure for ´Thompson Seedless´ (Figure
3a) is not as efficient as applied on ´Red Globe´ (Figure 3b). Analyses of factors affecting competence have been recently reported (Dhekney et al., 2009) by exploring changes in the induction phase. The use of MS and Nitsch macro- and micro-elements supplemented with

86

Genetic Transformation

6-bencyl aminopurine (BAP) at 4.5 and 8.9 µM plus 2,4-dichlorophenoxy acetic acid (2,4-D) at 8.9 and 4.5 µM, respectively, leaded to most of the 18 evaluated cultivars and eight Vitis hybrids, to produce SE to some degree in that work. In that line, from the learning process to design and build an air-lift system, the use of liquid media offered important data about the effect of different nutrients applied in closer contact with grapevine PE cells. These findings have leaded to the use of mixed (i.e. having solid and liquid steps) protocols on diverse lowcompetence backgrounds such as ´Freedom´ or ´Red Globe´.

A)

B)

Fig. 3. Differential results of SE procedures in ´Thompson Seedless´ and ´Red Globe´.
A, An efficient SE system in ´Thompson Seedless´ generating PE and E cells (right picture, whitest cells); B, the same system applied on ´Red Globe´ showing an inefficient result.
The new strategies include the above referred use of in vitro leaf explants as a source of starting material for SE. Multiple in vitro buds are obtained from in vitro leaves using C2D4B
(Araya et al., 2008; Gray, 1995) by at least 30 days of cultivation. When these buds are transferred to solid NB2 media supplemented with 2,4-D (4.5 µM) and BAP (1 µM) by additional 120 days, PE masses are generated. These masses are the pivot for a new branch of procedures in which solid and liquid cultures are used. In ´Thompson Seedless´ or
´Princess´, bud production by culturing of leaves in C2D4B media prepare cells that will produce as many somatic embryos as required during the phase of cultivation in NB2 medium; these cultivars describe high yield enough to accomplish considerable number of transformation experiments (Dhekney et al., 2009) (Figure 3a). However, such yield is not observed when the strategy is applied on ´Harmony´, ´Freedom´ or ´Red Globe´ genotypes
(Figure 4a). Although very few somatic embryos are prone for transformation purposes from these materials (see whitest cells in the right picture on Figure 3b), the strategy leads to the production of a considerable remaining material, which in our hands was formerly discarded for transformation assays (Figure 4a). After several trials for recovering these masses and re-convert them into SE competent cells, a highly productive cycle was observed by culturing them solid X6 media and the addition of a liquid pulse of MS modified medium supplemented with glutamine (400 mg/L) and kinetin (4.6 µM). Under such treatments, cells are propagated, disintegrated into minimal groups of cells and leaded to

87

Genetic Transformation Strategies in Fruit Crops

new developmental stages; as a result, the generation of an extremely high amount of somatic embryos after 30 days of treatment is achieved (Figure 4b). Although these procedures have fixed the competence for SE in these genotypes, it remains to be evaluated if such combined treatments could help this process in other grape genotypes. In the meantime, genetic transformation of grapevine rootstocks is now plausible and efforts evaluating genes related to root-linked disorders can be now evaluated.
A)

-Embryo development
-Material maintenance

-Visual inspection of proper material for transformation -Reutilization of discarded material B)
Secondary round of embryogenesis -Liquid medium pulse -Biomass multiplication MS* RG

• Dedifferenciation
• Proembryogenic calli formation X6* RG

Fig. 4. Improved procedures to induce somatic embryogenesis in ´Red Globe ´. The low efficiency protocol to induce and transform embryos (black arrows, A) leads to the formation of remaining cells that can be incorporated into a new round of SE based on the use of glutamine and kinetin (red circle in the diagram, B) for yield improvement.

3. Genetic transformation of plums in the waiting for a peach transformation system It has already been almost 20 years since the generation of the most highlighted event in the field of stone fruits genetic transformation: the Plum Pox Virus (PPV) Prunus domestica resistant line named C5. Obtained by transformation of ´Bluebyrd´ explants, C5 was derived from transformation events using A. tumefaciens strain C58/Z707 containing a binary plasmid with the coat protein (CP) PPV gene plus the 3’ non-translated region of the viral genome (EMBL Accession No X16415, Teycheney et al., 1989). The high degree of resistance observed has been stable in more than 10 years of evaluations in greenhouses and in the field (Hily et al., 2004; Malinowski et al., 2006; Polák et al.; 2008). In C5, the clone has exhibited resistance associated to RNA interference (RNAi), i.e. a high level of transgene transcription in the nucleus associated to a low level of mRNA in the cytoplasm, whereas the genetic analysis has revealed multicopy transgene insertions with repeated sequences in the presence of additional one or more aberrant copies (Scorza et al. 2001). RNAi in C5 was

88

Genetic Transformation

later confirmed by detection of small interfering RNAs (siRNAs) homologous to PPV sequences (Hily et al., 2005); siRNAs of 22 and 25-26 nucleotides in length were found in challenged C5 plants, whereas short siRNAs were found exclusively in wild type infected P. domestica controls. Results suggested that the high level virus resistance in C5 is connected with the production of this long-sized class of siRNAs (Hily et al., 2005). Recently, multicopy arrangements of T-DNA fragments from the transformation plasmid in the C5´s genome have been determined, showing the occurrence of an in planta hairpin structure of the introduced CP gene (Kundu et al., 2008; Scorza et al., 2010) and explaining the possible source for RNAi in C5.
Multiple tissues have been used for plant regeneration in the Prunus genus, including leaves
(Gentile et al., 2002; Yancheva, 2002; Dolgov et al., 2005), cotyledons (Mante et al., 1989), embryos (Pérez-Clemene et al., 2004), and hypocotyls (Mante et al., 1991; Gonzalez-Padilla et al., 2003). As a system, generation of C5 represents to date the more successful and reproducible procedure for plant regeneration in this genus, obtained by the use of medial hypocotyl segments (Mante et al., 1991). To get this procedure, 1-phenyl-3-(1,2,3-thidiazol-5il) urea (thidiazuron, TDZ) at 7.5 µM and indole-3-butyric acid (IBA) at 0.25 µM were applied to the explants in order to regenerate Agrobacterium-mediated transformed hypocotyl segments. The hypocotyls based system was later improved by González-Padilla et al. (2003); these authors described a reduction in the total number of regenerated shoots without affecting the transformation rate by application of early selection (80 mg/L of kanamycin and 300 mg/L of Timentin) during shoot regeneration in a medium consisting on half-strength MS salts and vitamins supplemented with 5 mM α-naphthaleneacetic acid
(NAA) and 0.01 mM kinetin.
From these works, new improvement was made in the diploid species Prunus salicina. The regeneration and genetic transformation of Japanese plum using the approach of hypocotyl segments described in P. domestica was described by Urtubia et al. in 2008 (Figure 5).
Previously, Tian et al. (2007) used a constant concentration of TDZ (7.5 µM) that eventually was combined with variable amounts of BAP (2.5 or 12.5 µM) or kinetin (12.5 µM) to induce shoot formation in ´Shiro´ and ´Early Golden´; additional evaluation of ´Redheart´ hypocotyl segments did not generate plantlets by this protocol. In successful genotypes, results demonstrated that the use either of TDZ or of TDZ plus BAP have allowed the establishment of whole plants acclimatized at greenhouse level. For transformation setting up of this species, Urtubia et al. (2008) described the use of different TDZ/IBA ratios (6:1 to
10:1) to regenerate Agrobacterium transformed ´Angeleno´ and ´Larry Ann´ hypocotyl segments. The shooting on average on 12% of the total cultured explants and the establishment of whole plants expressing the green fluorescent protein in the greenhouse concluded this research and established Japanese plum as a model diploid species in Prunus transformation. Despite this, the observed varietal dependence of results and the low number of confirmed positive transgenic lines ratified the difficulty to obtain genetic transformation systems in stone fruit species. Authors also described the effect of using different Agrobacterium strains on the co-cultivated P. salicina explants; whereas the use of
LBA4404 strain leaded to significant oxidation in the treated explants, infections with EHA or GV strains led to the production of whole plants with no major disadvantages throughout the protocol.

89

Genetic Transformation Strategies in Fruit Crops
Unique / multiple buds

Hypocotils

Transient GFP expression Selection

Infection

Greenhouse
Conditioning

Elongation

Rooting

Fig. 5. ´Angeleno´ Japanese plum genetic transformation procedures. The complete pipeline for Agrobacterium-mediated genetic transformation of P. salicina is showed.
3.1 A new example: RNAi-based PPV resistance in Japanese plums
Holding the research focus on PPV, new strategies against the virus can be evaluated with improved expectations, including new technology development obtained for gene silencing.
As mentioned, an additive effect of multicopy T-DNA fragments arranged in C5´s genome and the occurrence of an in planta hairpin structure for the introduced CP gene (Kundu et al., 2008;
Scorza et al., 2010) onset an adequate silencing scenario in the plant. Hairpin RNA inducing
DNAs have been described as an important activator of RNAi in transgenic plants (Watson et al., 2005). Artificial in vivo generation of siRNA was soon published by introduction of hairpin
RNA inducing plasmids into target cells (Wesley et al., 2001); since then, multiple findings have been focused on the development of optimal constructs to generate siRNAs in transgenic plants (Watson et al., 2005; Qu et al., 2007), and making gene silencing through RNAi one of the most promissory strategies to boost plant immunity nowadays (Pennisi, 2010).
Recently, Dolgov et al. (2010) developed and used a coat protein gene-based hairpin inducing plasmid to generate RNAi transgenic P. domestica L. ‘Startovaya’ plants. This group had previously generated a transformation protocol for European plum using adult tissue-derived explants by use of 5-12 days old leaves (Mikhaylov and Dolgov, 2007). This alternate transformation strategy involves slight wounding of explants and the application of a five hours auxin shock in liquid MS medium supplemented with indole-3-acetic acid (28 µM).
After co-cultivation procedures, regeneration is induced by culturing in MS modified salts including BAP (22 µM) and IBA (1.96 µM) and the presence of convenient selection antibiotics
(hygromycin) plus cefotaxime to keep A. tumefaciens AGL0 used in the process under control.
Elongation of treated explants is obtained by use of the same growth regulators in lower quantities than used for regeneration (BAP 8.8 µM, IBA 0.5 µM) and the inclusion of a 16 h photoperiod. As preliminary results of transformed individuals challenged by grafting experiments, these authors have indicated the potential development of five candidate lines that challenged by grafting on PPV-infected rootstocks demonstrated successfully disease resistance with no virus accumulation as suggested the use of Western blotting experiments.

90

Genetic Transformation

Considering that genome annotation for peach is expected in the very near future, the advantage of transforming a diploid species in the Prunus genus opened space for candidate gene evaluation in this type of fruit trees, making very attractive the use of Japanese plums as a closer model. The approach of silencing PPV sequences has been under development in
P. salicina; an arrangement of “hot-spot” target sequences from the coat protein gene and predicted as highly sensitive to gene silencing, have been located in tandem in a construct designed to generate in vivo RNA hairpin. The use of this construct for genetic transformation of Japanese plum hypocotyls leaded to the generation of six transgenic lines that putatively could silence the PPV coat protein gene. Acclimatized and rooted transgenic plants harboring this construct were used has a source of scions for grafting experiments on
PPV-infected Prunus insititia rootstocks that previously had been used for a confined evaluation of C5 scions (Wong et al., 2010). Symptomatology (Figure 6) and ELISA data from the first season of evaluations for these lines have indicated the existence of two transgenic lines showing the recovery and resistant phenotypes, respectively (Figure 6). Massive sequencing data is under development for these lines in order to corroborate small RNAs populations generated in these challenged ´Angeleno´ scions.
Adesoto
infected with
PPV-D isolate #

112

116

114

12

Symptoms on:
Adesoto
(rootstock)
Nov´10

Adesoto
(rootstock)
Mar´11

P. tomentosa

Prunus salicina

PPViRNA624
(scion)
Nov´10
PPV infected P. insititia

PPViRNA624
(scion)
Mar´11

PPViRNA600
(scion)
Nov´10

Fig. 6. Genetically modified ´Angeleno´ plants challenged by micro-grafting onto previously infected ‘Adesoto’ rootstocks. Four different PPV-D Chilean isolates (numbers) have been evaluated. These assays are carried out in a biosafety greenhouse at La Platina Station of the National
Institute of Agriculture, Santiago, Chile.

Genetic Transformation Strategies in Fruit Crops

91

4. Towards peach genetic transformation
In parallel to the systems developed for plum, the race for a Prunus persica genetic transformation procedure has been run with not such a clear achievement. Peach highlights as one of the more recalcitrant species regarding the in vitro organogenesis process. First attempts for tissue culture in peach were focused on propagation (Hammerschlag, 1982).
From these studies, some factors affecting the establishment of apical buds were identified, such as disinfection procedures for introduced material from the field, plant growth regulators applied and temperature of culturing. Also, as observed in grapevines, genotypedependent responses were obtained mainly in the rooting and acclimatization steps during in vitro establishment. Authors suggested that endogenous hormone variations were responsible for these differential responses obtained at culturing (Hammerschlag et al.,
1987). In 1989, da Câmara Machado et al. gave patterns for bud generation using leaf discs and micro-sticks from some apple, pear and peach cultivars to address Agrobacteriummediated genetic transformation of these species. Results from such studies showed just slight callusing leading to rare budding in the cutting edges of the explants with no regeneration. In the same period, other works reported poor bud generation from P. persica explants such as immature endosperms (Meng and Zou, 1981), zygotic embryo-derived calli
(Hammerschlag et al., 1985; Bhansali et al., 1990; Scorza et al., 1990a), immature (Mante et al.,
1989) and mature (Pooler and Scorza, 1995) cotyledons.
Most of the studies describing genetic transformation in peach have described the use of A. tumefaciens infection in either immature or mature explants (Hammerschlag et al., 1989;
Scorza and Sherman, 1996; Pérez-Clemente et al., 2004; Padilla et al., 2006); in general, targeting on immature tissues leads over the use of mature explants in woody species (da
Câmara Machado et al., 1992; Ye et al., 1994). In those experiments, the use of cytokinines
(BAP, kinetin, zeatin or isopentyladenine) has been reported in order to induce regeneration of immature cotyledons, although the number of produced buds has been extremely low.
Pérez-Clemente et al. (2004) reported the use of mature cotyledons with a very low adventitius budding efficiency. No whole plants or stable foreign DNA incorporation into the tissues were described from these reports. In addition, Pérez-Clemente et al. (2004) proposed the use of longitudinal embryo segments as a reliable method for regeneration and plant genetic transformation, however, massiveness and reproducibility of this methodology has not been really achieved.
Transversal stem segments isolated from mature plants were infected with the shooty
Agrobacterium mutant (tms328::Tn5; Hammerschlag et al., 1989), which commonly induces budding in tobacco calli. A cytokinine-independent growth was observed in the treated tissues, although no budding was finally observed. In a similar strategy, in which stems were replaced by immature embryos, Smigocki and Hammerschlag (1991) reached regeneration of a few buds from calli generated from embryos; however, a marked trend to rooting of the treated explants and no transgenic status of the obtained buds was reported by the authors. Recently, Padilla et al. (2006) described optimal conditions for gene transfer using Agrobacterium in different explants types (hypocotyls cylinders, cotyledons, embryonic axis from no germinated seeds, internodal segments isolated from epicotyls obtained from non germinated seeds). Initially, authors established transient expression rates for different
DNA constructs and Agrobacterium strains, determining that cotyledons and nodal segments were the explants showing the highest β-glucuronidase and green fluorescent protein (GFP)

92

Genetic Transformation

transient expression. These observed responses were variety dependent and none of these explants leaded to fully regenerated plants.
4.1 Combining trials to obtain genetically modified peaches
As depicted, explants from P. persica excepting a couple of examples referred to embryo longitudinal segments and mature cotyledons, the species can be considered as recalcitrant to in vitro regeneration. In addition, these successful responses do not represent a reliable process applicable to several other varieties or hybrids.
In our hands, the use of leaves as starting explants in the transformation pipeline for
´O´Henry´ did not produce a consistent number of buds, on the contrary to the reported by
Gentile et al. (2002). Despite this and after several years of evaluations, the use of immature cotyledons leaded us to propose a combined procedure based on these procedures for regeneration and transformation of this and other commercial cultivars. ´O´Henry´ and
´Rich Lady´ immature cotyledons have been cultivated in LP modified medium (Gentile et al., 2002) generating viable explants that can produce either direct budding in MP modified medium (Gentile et al., 2002) supplemented with BAP (5 µM) and NAA (concentrations between 3 and 5 µM) or lead to formation of white structures (as shown in Figure 7) that, in presence of LP medium and 2,4-D (1 µM), will become into green buds after 60-90 days of culturing. Fig. 7. Prunus persica regeneration system. A brief and summarized scheme of the system for peach regeneration using immature cotyledons.
These results are quite similar to those obtained using mature cotyledons from Prunus avium and the technical approach is the same (Canli and Tian, 2008). Activated tissues can be then cultured in LP medium supplemented with 2,4-D (1 µM) and BAP (3 µM) for additional 90 days and then transferred into LP salts with no growth regulators to obtain gradually green buds which can be transferred into a LP derivative medium supplemented with BAP (0.5 µM), IBA (0.01 µM) and glutamine (0.2 g/L). Shoots start to appear after eight months of total treatments and generation of plantlets can be reached after 8-12 months. Up to date, in the most responsive cultivars (i.e. ‘O’Henry’ and ‘Rich Lady’), regeneration rates are close to
20% and transformation efficiencies in the regenerated plantlets are close to 2%.

93

Genetic Transformation Strategies in Fruit Crops

By this methodology, trees expressing GFP have been generated (Figures 8 and 9); interestingly, the behavior of a 35S RNA Cauliflower Mosaic Virus promoter driving the gfp gene expression could be analyzed (observed) in peaches by epifluorescence microscopy in leaves, fruit tissues (mesocarps), and radicles (Figure 8). The same qualitative analysis carried out in flowers from these trees (Figure 9), have shown clear differences in the fluorescence obtained when transformed tissues are compared to the corresponding non transgenic controls.

leaf + UV

Wild type + UV mesocarp mesocarp + UV

Radicle + UV

Wild type + UV cotyledon cotyledon + UV

Fig. 8. Genetically modified peach tree expressing GFP.
Epifluorescence microscopy in different tissues from a genetically modified peach tree. Red fonts indicate view of transgenic tissues under UV light (+UV); black fonts show views of the corresponding tissues from non transformed trees used as a control.

94

Genetic Transformation

WT flower

GFP 104.4 flower

Fig. 9. Schematic representation of different floral organs from a genetically modified peach flower expressing GFP (right, GFP 104.4 flower) compared to wild type tissues (left, WT flower). 5. Conclusions
A compact view about different strategies to reach successful genetic transformation experiments in grapes and stone fruits (plums and peach) has been presented using results from our close experimentation. This time, the focus has been on mixing different ideas from procedures used in both genera and their corresponding results. Vitis spp. genetic transformation has mainly relied on the use and availability of SE procedures. Early in the
´70s, regeneration of whole Gloryvine (V. vinifera x V. rupestris) plants was achieved from somatic embryos previously obtained in this hybrid by anthers tissue culture cultivation.
Since then, successful procedures have made possible SE establishment in V. vinifera, V. labruscana and V. rotundifolia. Recently, mixing of solid and liquid media-based procedures, grapevine SE has leaded to the design, characterization and scaled-up production of
´Thompson Seedless´ embryogenesis using an air-lift bioreactor. The system can be expanded to other genotypes. The accumulated information derived from this scaling-up process fused to the characterization of some of the kinetic parameters involved in grapevine SE, have enabled design of new experimentation focused on the development of
SE protocols for genotypes such as rootstocks (´Harmony´, ´Freedom´ or ´Salt Creek´) and more recalcitrant cultivars such as ´Red Globe´. The results indicate that grape genetic transformation can be considered as a model system in which efficiency is not necessarily an issue and the possibility for high through-put candidate gene evaluation is plausible.

Genetic Transformation Strategies in Fruit Crops

95

In case of Prunus spp., European and Japanese plums have been the more successful rosaceous fruit models to be regenerated and transformed in our hands (plums and peach).
Under the trade name HoneySweet and deregulated in 2009, the PPV-resistant C5 event established a baseline for regeneration protocols using seed-derived tissue explants; these were successfully dissected and evaluated on P. salicina using four relatively close media.
The regenerative responses, with shooting on about 12% on the total cultured explants in two varieties (´Larry Ann´ and ´Angeleno), leaded to the generation of stable genetically modified lines. The research “baseline” in plums transformation has later conducted to improving regeneration and transformation efficiencies in both species, from which new
PPV-resistant plant materials have been produced. Hairpin dsRNA inducing constructs are currently under evaluation for silencing different PPV genes, from which CP has been here illustrated. Finally, these achievements have been recently optimized, reaching the successful transformation of European plum leaf explants in some genotypes. Plum can be considered as an attainable model system for candidate gene evaluation in stone fruits, with hexaploid and diploid versions for such studies. At the same time, plum genetic transformation can be judged as a proof of concept for peaches.
For P. persica, genetic transformation seems attainable although not reproducible. Several protocols have worked just in the place when they were generated. In our hands, the use of immature cotyledons subjected to modifications in the workflow described for leaves regeneration has allowed for generation of GFP expressing peaches. Consistently, this platform has leaded to the production of new transgenic lines and constructs already evaluated in Japanese plum (i.e. PPV silencing), are now used for this species. The peach case reinforces the concept that one previous development is a necessary step leading to the next one. 6. Acknowledgments
The author gratefully acknowledges to all colleagues and students joined since 2001 to the genetic transformation and molecular biology group at La Platina Station in Santiago de
Chile. Special thanks to the current group members: Grapevine genetic transformation team:
Catalina Álvarez, Hayron Canchignia, Álvaro Castro, María de los Ángeles Miccono,
Christian Montes, Marisol Muñoz, Blanca Olmedo, Luis Ortega, Eduardo Tapia, and Evelyn
Sánchez. Stone fruits transformation team: Manuel Acuña, Paola Barba, Daniel Espinoza,
Julia Rubio, Catalina Toro, and Wendy Wong. Thanks to all of you!
All the Figures´ composition was made by team´s members using original results. Special thanks to compositions made by Manuel Acuña (plum and peach work), Álvaro Castro (SE work) and Eduardo Tapia (bioreactor work).
Local advances presented in this chapter are funded by joint-venture programs between the governmental agencies FONDEF-Chile, PBCT-Chile, CONICYT-Chile, and INNOVA-Chile and the Fruit Technology Consortium “Biofrutales” S.A. This publication is funded by the
INIA-CSIC Grant 501646-70.

7. References
Ammirato, P. (1983). Embryogenesis. In: Handbook of Plant Cell Cultures, Techniques for
Propagation and Breeding. D.A. Evans, W.R. Sharp, P.V. Ammirato, & Y. Yamada
(Eds.), McMillan, ISBN 0-02-949230-0, New York, USA.

96

Genetic Transformation

Araya, S., Prieto, H. & Hinrichsen, P. (2008). An efficient buds culture method for the regeneration via somatic embryogenesis of table grapes cvs. Red Globe and Flame
Seedless. Vitis, Vol. 47, No. 4, 251-252, ISSN 00427500.
Archambault, J., Williams, R., Lavoie, L., Pepin, M. & Chavarie, C. (1994). Production of somatic embryos in a helical ribbon impeller bioreactor. Biotechnology and
Bioengineering, Vol. 44, No. 8, 930–943, ISSN 0006-3592.
Bhansali, R., Drive, J. & Durzan, D. (1990). Rapid multiplication of adventitious somatic embryos in peach and nectarine by secondary embryogenesis. Plant Cell Reports,
Vol. 9, No. 5, 280-284, ISSN 0721-7714.
Canli, F. & Tian, L. (2008). In vitro shoot regeneration from stored mature cotyledons of sweet cherry (Prunus avium L.) cultivars. Scientia Horticulturae, Vol. 116, No. 1, 34–
40, ISSN 0304-4238.
Da Câmara Machado, M., Da Câmara Machado, A., Hanzer, V., Mattanovich, D., Himier, G.
& Katinger, H. (1989). Regeneration of shoots from leaf discs and stem microcuttings of fruit trees as a tool for transformation. Proceedings of the XIV International
Symposium on Fruit Tree Virus Diseases - Acta Horticulturae 235, 85-92, ISBN 978-9066053-33-5, Thessaloniki, Greece, June 12-18, 1988.
Da Câmara Machado, M., Da Câmara Machado, A., Hanzer, V., Weiss, H., Regner, F.,
Steinkeliner, H., Mattanovich, D., Plail, R., Knapp, E., Kalthoff, B. & Katinger, H.
(1992). Regeneration of transgenic plants of Prunus armeniaca containing the coat protein gene of Plum Pox Virus. Plant Cell Reports, Vol. 11, No. 1, 25-29, ISSN 07217714.
Dhekney, S., Li, Z., Compton, M. & Gray, D. (2009). Optimizing initiation and maintenance of Vitis embryogenic cultures. HortScience 44, 5, 1400–1406, ISSN 0018-5345.
Dolgov, S., Mikhailov, R. & Shulga, O. (2005). Genetic engineering approach in stone fruits breeding. Proceedings of the International Symposium on Biotechnology of Temperate
Fruit Crops and Tropical Species, ISSN 0567-7572, Daytona Beach, Florida, USA,
October 10-14, 2005.
Dolgov, S., Mikhaylov, R., Serova, T., Shulga, O. & Firsov, A. (2010). Pathogen-derived methods for improving resistance of transgenic plums (Prunus domestica L.) for
Plum pox virus infection. Proceedings of the 21st International Conference on Virus and other Graft Transmissible Diseases of Fruit Crops - Julius-Kühn-Archiv, 133-140, ISBN
978-3-930037-67-4, Neustadt, Germany, July 5-10, 2009.
Driver, J. & Kuniyuki, A. (1984). In vitro propagation of Paradox walnut rootstock.
HortScience, Vol. 19, No. 4, 507–509, ISSN 0018-5345.
Gamborg, O., Miller, R. & Ojima, K. (1968). Nutrient requirements of suspension cultures of soybean root cells. Experimental Cell Research, Vol. 50, No. 1, 151–158, 0014-4827.
Gentile, A., Monticelli, S. & Damiano, C. (2002). Adventitious shoot regeneration in peach
(Prunus persica (L.) Batsch). Plant Cell Reports, Vol. 20, No. 11, 1011-1016, ISSN 07217714.
González-Padilla, I., Webb, K. & Scorza, R. (2003). Early antibiotic selection and efficient rooting and acclimatization improved the production of transgenic plum plants
(Prunus domestica L.). Plant Cell Reports, Vol. 22, No. 1, 38-45, ISSN 0721-7714.
Gray, D. (1995). Somatic embryogenesis in grape. In: Somatic embryogenesis in woody plants – vol 2, P. Gupta, S. Jain, & R. Newton (Eds.), 191-217, Kluwer Academic, ISBN 07923-3070-6, Dordrecht, The Netherlands.
Hammerschlag, F. (1982). Factors affecting establishment and growth of peach shoots in vitro. HortScience, Vol. 17, No. 1, 85-86, ISSN 0018-5345.

Genetic Transformation Strategies in Fruit Crops

97

Hammerschlag, F., Bauchan, G. & Scorza, R. (1985). Regeneration of peach plants from callus derived from immature embryos. Theoretical and Applied Genetics, Vol. 70, No.
3, 248-251, ISSN 0040-5752.
Hammerschlag, F., Bauchan, G. & Scorza, R. (1987). Factors influencing in vitro multiplication and rooting of peach cultivars. Plant Cell Tissue Organ Culture, Vol. 8,
No. 3, 235-242, ISSN 0167-6857.
Hammerschlag, F., Oowns, L. & Smigocki, A. (1989). Agrobacterium mediated transformation of Peach cells derived from mature plants that were propagated in vitro. Journal of the American Society for Horticultural Science, Vol. 114, No. 3, 508-510, ISSN 003-1062.
Hily, J., Scorza, R., Malinowski, T., Zawadzka, B. & Ravelonandro, M. (2004). Stability of gene silencing-based resistance to Plum pox virus in transgenic plum (Prunus domestica L.) under field conditions. Transgenic Research, Vol. 13, No. 5, 427-436,
ISSN 0962-8819.
Hily, J., Scorza, R., Webb, K. & Ravelonandro, M. (2005). Accumulation of the long class of siRNA is associated with resistance to Plum pox virus in a transgenic woody perennial plum tree. Molecular Plant Microbe Interaction, Vol. 18, No. 8, 794-799,
ISSN 0894-0282.
Hinrichsen, P., Reyes, M., Castro, A., Blanchard, E., Araya, S., Garnier, M., Reyes, F.,
Dell’Orto, P., Moynihan, M., Prieto, H. & Muñoz, C. (2005). Genetic transformation of grapevines with Trichoderma harzianum and antimicrobial peptide genes for improvement of fungal tolerance. Proceddings of the VII International Symposium on
Grapevine Physiology and Biotechnology - Acta Horticulturae, Vol. 689, 469-474, ISBN
978-90-66057-18-0, Davis, California, USA, June 21-25, 2004.
Iocco, O., Franks, T. & Thomas, M. (2001). Genetic transformation of major wine grape cultivars of Vitis vinifera L. Transgenic Research, Vol. 10, No. 2, 105-112, ISSN 09628819.
Jaillon, O., Aury, J., Noel, B., Policriti, A., Clepet, C., Casagrande, A., Choisne, N., Aubourg,
S., Vitulo, N., Jubin, C., Vezzi, A., Legeai, F., Hugueney, P., Dasilva, C., Horner, D.,
Mica, E., Jublot, D., Poulain, J., Bruyère, C., Billault, A., Segurens, B., Gouyvenoux,
M., Ugarte, E., Cattonaro, F., Anthouard, V., Vico, V., Del Fabbro, C., Alaux, M., Di
Gaspero, G., Dumas, V., Felice, N., Paillard, S., Juman, I., Moroldo, M., Scalabrin, S.,
Canaguier, A., Le Clainche, I., Malacrida, G., Durand, E., Pesole, G., Laucou, V.,
Chatelet, P., Merdinoglu, D., Delledonne, M., Pezzotti, M., Lecharny, A., Scarpelli,
C., Artiguenave, F., Pè, M.E., Valle, G., Morgante, M., Caboche, M., Adam-Blondon,
A.F., Weissenbach, J., Quétier, F. & Wincker, P. (2007). French-Italian Public
Consortium for Grapevine Genome Characterization. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature,
Vol. 449, No. 7161, 463-467, 0028-0836.
Jayasankar, S., Bondada, B., Li, Z. & Gray, D. (2003). Comparative anatomy and morphology of Vitis vinifera (Vitaceae) somatic embryos from solid- and liquid-culture-derived proembryogenic masses. American Journal of Botany, Vol. 90, No. 90,973–979, ISSN
0002-9122.
Kundu, J., P. Briard, J. Hily, M. Ravelonandro & Scorza, R. (2008). Role of the 25–26 nt siRNA in the resistance of transgenic Prunus domestica graft inoculated with Plum pox virus. Virus Genes¸Vol. 36, No. 1, 215-220, ISSN 0920-8569.
Li, A., Jayasankar, S. & Gray, D. (2001). Expression of a bifunctional green fluorescent protein (GFP) fusion marker under the control of three constitutive promoters and enhanced derivatives in transgenic grape (Vitis vinifera). Plant Science, Vol. 160, No.
5, 877-887, ISSN 0168-9452.

98

Genetic Transformation

Li, Z., Dhekney, S., Dutt, M. & Gray, D. (2008). An improved protocol for Agrobacteriummediated transformation of grapevine (Vitis vinifera L.). Plant Cell Tissue and Organ
Culture, Vol. 93, No. 3, 311–321, ISSN 0167-6857.
Malinowski, T., Cambra, M., Capote, N., Zawadzka, B., Gorris, M., Scorza, R. &
Ravelonandro, M. (2006). Field trials of plum clones transformed with the Plum Pox
Virus coat protein (PPV-CP) gene. Plant Disease, Vol. 90, No. 8, 1012-1018, ISSN
0191-2917.
Mante, S., Scorza, R. & Cordts, J. (1989). Plant regeneration from cotyledons of Prunus persica, Prunus domestica, and Prunus cerasus. Plant Cell Tissue and Organ Culture,
Vol. 19, No. 1, 1-11, ISSN 0167-6857.
Mante, S., Morgens, P., Scorza, R., Cordts, J. & Callahan, A. (1991). Agrobacterium-mediated transformation of plum (Prunus domestica) hypocotyls slices and regeneration of transgenic plants. Nature Biotechnology, Vol. 9, No. 9, 853-857, ISSN 1087-0156.
Martinelli, L., Bragagna, P., Poletti, V. & Scienza, A. (1993). Somatic embryogenesis from leaf- and petiole-derived callus of Vitis rupestris. Plant Cell Reports, Vol. 12, No. 4,
207–210. ISSN 0721-7714
Martinelli, L. & Gribaudo, I. (2001). Somatic embryogenesis in grapevine. In: Molecular
Biology and Biotechnology of the Grapevine. K.A. Roubelakis-Angelakis (Ed.), 393-410,
Kluwer Academic Publishers, ISBN 0792369491, Dordrecht, The Netherlands.
Martinelli, L., Candioli, E., Costa, D. & Poletti, V. (2001). Morphogenic competence of Vitis rupestris secondary somatic embryos with a long culture history. Plant Cell Reports,
Vol. 20, No. 4, 279-284, ISSN 0721-7714.
Martinelli, L., Gribaudo, I., Bertoldi, D., Candioli, E. & Poletti, V. (2001a). High efficiency somatic embryogenesis and plant germination in grapevine cultivars Chardonnay and Brachetto a grappolo lungo. Vitis, Vol. 40, No. 3, 111-115, ISSN 0042-7500.
Martinelli, L. & Gribaudo, I. (2009). Strategies for effective somatic embryogenesis in grapevine: an appraisal. In: Grapevine molecular physiology and biotechnology, Second
Edition, K. A. Roubelakis-Angelakis (Ed.), 461-494, Springer, ISBN, 978-90-481-23049, Dordrecht, The Netherlands.
Meng, X. & Zhou, W. (1981). Induction of embroid and production of plantlets in vitro from endosperm of peach. Acta Agriculturae Universitatis Pekinensis, Vol. 7, 95-98, ISSN
0479-8007.
Mikhaylov, R. & Dolgov, S.V. (2007). Transgenic plum (Prunus domestica L.) plants obtained by Agrobacterium-mediated transformation of leaf explants with various selective agents. Proceedings of the International Symposium on Biotechnology of Temperate Fruit
Crops and Tropical Species - Acta Horticulturae, Vol. 738, 613-623, ISBN 978-90-6605219-2, Daytona Beach, Florida, USA, October 10-14, 2005.
Mullins, M. & Srinivasan, C. (1976). Somatic embryos and plantlets from an ancient clone of grapevine (cv. Cabernet-Sauvignon) by apomixes in vitro. Journal of Experimental
Botany, Vol. 27, No. 100, 1022–1030, ISSN 0022-0957.
Murashige, T. & Skoog, F. (1962). A revised medium for rapid growth and bioassay with tobacco tissue culture. Physiologia Plantarum, Vol. 15, No. 43, 473-497, ISSN 00319317.
Padilla, I., Golis, A., Gentile, A., Damiano, C. & Scorza, R. (2006). Evaluation of transformation in peach Prunus persica explants using green fluorescent protein
(GFP) and beta-glucuronidase (GUS) reporter genes. Plant Cell, Tissue and Organ
Culture, Vol. 84, No. 3, 309-314, ISSN 0167-6857.
Pennisi, E. (2010). Sowing the seeds for the ideal crop. Science, Vol. 327, No. 5967, 802-803,
ISSN 0036-8075.

Genetic Transformation Strategies in Fruit Crops

99

Pérez-Clemente, R., Pérez-Sanjuán, A., García-Férriz, L., Beltrán, J. & Cañas, L. (2004).
Transgenic peach plants (Prunus persica L.) produced by genetic transformation of embryo sections using the green fluorescent protein (GFP) as an in vivo marker.
Molecular Breeding, Vol. 14, No. 4,419–427, ISSN 1380-3743.
Polák, J., Pívalová, J., Kundu, M., Jokes, M., Scorza, R. & Ravelonandro, M. (2008). Behaviour of transgenic Plum pox virus-resistant Prunus domestica L. Clone C5 grown in the open field under a high and permanent infection pressure of the PPV-rec strain.
Journal of Plant Patholology, Vol. 90, No 1-Supplement, S1.33-S1.36, ISSN 1125-4653.
Pooler, M. & Scorza, R. (1995). Regeneration of peach (Prunus persica (L.) Batsch) rootstock cultivars from cotyledons of mature stored seed. HortScience, Vol. 30, No 2, 355-356,
ISSN 0018-5345.
Qu, J., Ye, J. & Fang, R., (2007). Artificial microRNA-mediated virus resistance in plants.
Journal of Virology, Vol. 81, No 12, 6690-6699, ISSN 0022-538X.
Rajasekaran, K. & Mullins, M., (1983). Influence of genotype and sex-expression on formation of plantlets by cultured anthers of grapevines. Agronomie, Vol. 3, No. 3,
233–238, ISSN 0249-5627.
Salunkhe, C., Rao, P. & Mhatre, M. (1997). Induction of somatic embryogenesis and plantlets in tendrils of Vitis vinifera L. Plant Cell Reports, Vol. 17, No. 1, 65-67. ISSN 0721-7714
Scorza, R., Cordts, J. & Mante, S. (1990). Long-Term somatic embryo production and regeneration from embryo-derived peach callus. Proceeding of the I International
Symposium on In Vitro Culture and Horticultural Breeding - Acta Horticulturae, Vol.
280, 183-190, ISBN 978-90-66052-14-7, Bologna, Cesena, Italy, May 30-June 3, 1989.
Scorza, R., Cordts, J., Gray, D., Emershad, R. & Ramming, D. (1996). Producing transgenic
´Thompson Seedless´ grape (Vitis vinifera L.) plants. Journal of American Society for
Horticultural Science, Vol. 121, No. 4, 616-619, ISSN 0003-1062.
Scorza, R., A. Callahan, L. Levy, V. Damsteegt, K. Webb & M. Ravelonandro (2001). Posttranscriptional gene silencing in Plum pox virus resistant transgenic European plum containing the Plum pox potyvirus coat protein gene. Transgenic Research, Vol. 10,
No. 3, 201-209, ISSN 0962-8819.
Scorza, R., Georgi, L., Callahan, A., Petri, C., Hily, J., Dardick, C., Damsteegt, V. &
Ravelonandro, M. (2010). Hairpin Plum Pox Virus coat protein (hpPPV-CP) structure in ‘HoneySweet’ C5 plum provides PPV resistance when genetically engineered into plum (Prunus domestica) seedlings. Proceeding of the 21st
International Conference on Virus and Other Graft Transmissible Diseases of Fruit Crops Julius-Kühn-Archiv Vol. 427, 141-146, ISSN 1868-9892, Neustadt, Germany July 5 10, 2009.
Scorza, R. & Sherman, W. (1996). Peaches. In: Fruit Breeding vol. I: Tree and Tropical Fruits. J.
Wiley & J. Moore (Eds.), Wiley, 047131014X, New York, USA.
Smigocki, A. & Hammerschlag, F. (1991). Regeneration of plants from peach embryo cells infected with a shooty mutant strain of Agrobacterium. Journal of the American Society for Horticultural Science, Vol. 116, No. 6, 1092-1097, ISSN 0003-1062.
Stamp, J. & Meredith, C. (1988). Somatic embryogenesis from leaves and anthers of grapevine. Scientia Horticulturae, Vol. 35, Nos. 3-4, 235-250, ISSN 0304-4238.
Tapia, E., Sequeida, A., Castro, A, Montes, C., Zamora, P. & Prieto, P. (2009). Development of grapevine somatic embryogenesis using an air-lift bioreactor as an efficient tool in the generation of transgenic plants. Journal of Biotechnology, Vol. 139, No 1, 95101, ISSN 0168-1656.

100

Genetic Transformation

Teycheney, P.Y., G. Tavert, R. Delbos, M. Ravelonandro & J. Dunez (1989). The complete nucleotide sequence of Plum Pox Virus RNA (strain D). Nucleic Acids Research, Vol.
17, No. 23, 10115-10116, ISSN 0305-1048.
Tian, L., Wen, Y., Jayasankar, S. & Sibbald, S. (2007). Regeneration of Prunus salicina Lindl
(Japanese plum) from hypocotyls of mature seeds. In Vitro Cellular and
Developmental Biology – Plant, Vol. 43, No. 4, 343-347, ISSN 1054-5476.
Torregrosa, L., Iocco, P. & Thomas, M. (2002). Influence of Agrobacterium strain, culture medium, and cultivar on the transformation efficiency of Vitis vinifera L. American
Journal of Enology and Viticulture, Vol. 53, No. 3, 183-190, ISSN 0002-9254.
Urtubia, C., Devia, J., Castro, A., Zamora, P., Aguirre, C., Tapia, E., Barba, P., Dell`Orto, P.,
Moynihan, M., Petri, C., Scorza, R. & Prieto, H. (2008). Agrobacterium-mediated genetic transformation of Prunus salicina. Plant Cell Reports, Vol. 27, No. 9, 13331340, ISSN 0721-7714.
Velasco, R., Zharkikh, A., Troggio, M., Cartwright, D., Cestaro, A., Pruss, D., Pindo, M.,
Fitzgerald, L., Vezzulli, S., Reid, J., Malacarne, G., Iliev, D., Coppola, G., Wardell,
B., Micheletti, D., Macalma, T., Facci, M., Mitchell, J., Perazzolli, M., Eldredge, G.,
Gatto, P., Oyzerski, R., Moretto, M., Gutin, N., Stefanini, M., Chen, Y., Segala, C.,
Davenport, C., Demattè, L., Mraz, A., Battilana, J., Stormo, K., Costa, F., Tao, Q., SiAmmour, A., Harkins, T., Lackey, A., Perbost, C., Taillon, B., Stella, A., Solovyev,
V., Fawcett, J.A., Sterck, L., Vandepoele, K., Grando, S.M., Toppo, S., Moser, C.,
Lanchbury, J., Bogden, R., Skolnick, M., Sgaramella, V., Bhatnagar, S.K., Fontana,
P., Gutin, A., Van de Peer, Y., Salamini, F. & Viola, R., (2007). A high quality draft consensus sequence of the genome of a heterozygous grapevine variety. PLoS ONE,
Vol. 2, No. 12, e1326, ISSN 1932-6203.
Watson, J., Fusaro, A., Wang, M. & Waterhouse, P. (2005). RNA silencing platforms in plants. FEBS Letters, Vol. 579, No. 26, 5982–5987, ISSN 0014-5793.
Wesley, S., Helliwell, C., Smith, N., Wang, M., Rouse, D., Liu, Q., Gooding, P., Singh, S.,
Abbott, D., Stoutjesdijk, P., Robinson, S., Gleave, A., Green, A. & Waterhouse, P.
(2001). Construct design for efficient, effective and high-throughput gene silencing in plants. The Plant Journal, Vol. 27, No. 6,581-590, ISSN 0960-7412.
Wong W., Barba P., Álvarez C., Castro A., Acuña M., Zamora P., Rosales M., Dell 'Orto P.,
Moynihan M., Scorza, R. & Prieto H. (2010) Evaluation of the resistance of transgenic C5 plum (Prunus domestica l.) Against four Chilean Plum pox virus isolates through micro-grafting. Chilean Journal of Agricultural Research, Vol. 70, No.
3, 372 – 380, ISSN 0365-2807.
Yancheva, S., Druart, Ph. & Watillon, B. (2002). Agrobacterium-mediated transformation of plum (Prunus domestica L.). Proceeding of the VII International Symposium on Plum and
Prune Genetics, Breeding and Pomology - Acta Horticulturae, Vol. 577, 215-217, ISBN
978-90-66058-95-8, Plovdiv, Bulgaria, August 20-24, 2001.
Ye, X., Brown, S. & Scorza, R. (1994). Genetic transformation of peach tissue by particle bombardment. Journal of the American Society for Horticultural Science, Vol. 119, No.
2, 367-373, ISSN 0003-1062.

5
Citrus Transformation:
Challenges and Prospects
Vicente Febres, Latanya Fisher, Abeer Khalaf and Gloria A. Moore

Horticultural Sciences Department, Plant Molecular and
Cellular Biology Program, University of Florida
USA

1. Introduction
Citrus is an important commodity worldwide and is produced in tropical and subtropical regions around the world. Annually, the total citrus fruit production is estimated to be more than 124.5 million tonnes worldwide, with China, Brazil, the United States, Mexico and India the main producers (FAO, 2011). Oranges, lemons, tangerines and grapefruits are among the most commonly grown citrus types and they are traded as fresh fruit, juice, or as concentrate.
Growers, however, face important challenges for maintaining or improving yield: disease, drought, cold and soil salinity are some of the factors that can limit production and can have an important economic impact on growers. Traditional breeding methods have been used successfully over the years to improve citrus; however this is done with difficulty due to the slow growth and maturation of this crop, incompatibility, polyembryony, parthenocarpy, etc.
Because traditional breeding takes such a long time the fast incorporation of desirable traits is not possible. In other instances, certain desirable traits are not present in cultivated citrus types. This has been made more evident in the battle against diseases. Diseases can appear in a region and within a few years spread and become limiting factors for production and have a major economical impact because of yield reduction and/or increased production costs.
Therefore, genetic engineering via citrus transformation is an alternative method used to incorporate desirable traits into citrus genotypes.

2. Citrus transformation: generalities
The genetic transformation procedure involves two major processes. The first is the incorporation of the foreign gene of interest into the plant genome while the second entails the regeneration of the transformed cells into whole transgenic plants (Singh & Rajam,
2009). The success of the genetic transformation technique depends on an effective and reliable procedure as efficiencies are often low. Several techniques such as polyethylene glycol (PEG)-mediated direct uptake of DNA by protoplast (Kobayashi & Uchimaya, 1989), particle bombardment (Yao et al., 1996) and Agrobacterium-mediated transformations
(Hidaka & Omura, 1993) have been developed and used with various Citrus spp. However, the latter transformation system is now the most commonly used method because it has been proven most successful with higher transformation efficiencies resulting in the production of transgenic plants (Peña et al., 2007; Singh & Rajam, 2009; Yu et al., 2002).

102

Genetic Transformation

2.1 Protoplast transformation
Although, Agrobacterium-mediated transformation is considered the best overall method, direct uptake of DNA by protoplasts and particle bombardment have their advantages over the former method. Protoplast transformation is mostly used with commercially important citrus genotypes that are either seedless or contain very few seeds, which is required in most
Agrobacterium-mediated transformation procedures (Fleming et al., 2000). Here, the citrus plant is regenerated from the protoplast via somatic embryogenesis and additionally it can eliminate the need for the use of antibiotics either for plant selection or bacterial inhibition
(Fleming et al., 2000). This method also allows the improvement of citrus genotypes that are sexually incompatible by producing superior scion or rootstock somatic hybrids (Fleming et al., 2000; Grosser et al., 1998a; Grosser et al., 1998b). Regeneration using this system has been used with many citrus species, including lemons [C. limon (L.) Burm. F.], limes [C. aurantifolia (Cristm.) Swingle], mandarins (C. reticulata Blanco), grapefruits (C. paradisi
Macf.), sweet orange (C. sinensis Osbeck) and sour orange (C. aurantium L.). Although, limited success has previously been reported using protoplast transformation with sweet orange, rough lemon (C. jambhiri Lush.) and ‘Ponkan’ mandarin (Hidaka & Omura, 1993;
Kobayashi & Uchimaya, 1989; Vardi et al., 1990). Fleming et al. (2000) have reported success in recovering transgenic sweet orange plantlets by an optimized version of this method.
2.2 Particle bombardment
Particle bombardment involves the direct delivery of DNA coated onto microprojectiles into intact cells or organized tissue via a gene gun or a biolistic particle delivery system (Yao et al., 1996). This method is used alternatively in cases where citrus genotypes are recalcitrant to Agrobacterium infection. A reason for this is that citrus is not a natural host for the bacteria
(Khan, 2007). A problem that arises from this method is the low regeneration frequency of stably transformed cells from calli as was observed with tangelo (C. reticulata x C. paradisi)
(Yao et al., 1996). Nevertheless, transformation efficiencies of 93%, based on transient expression experiments, have been reported with citrange (C. sinensis x P. trifoliata) when particle bombardment is carried out using thin epicotyl segments (Bespalhok et al., 2003).
2.3 Agrobacterium-mediated transformation
This system uses the ability of the Agrobacterium-plant interaction to transfer and integrate genetic information into the plant’s genome. The bacteria, depending on the species, contain either a rhizogenic (Ri) or a tumor-inducing (Ti) plasmid which includes a T-region or transferred DNA region (T-DNA). This T-DNA region is manipulated by genetic engineering to include the gene of interest for transfer in the transformation process. The TDNA movement from Agrobacterium occurs only onto wounded plant cells (Gelvin, 2003;
Messens et al., 1990). The initiation of this transfer depends on the induction of the virulence
(vir) region located in the Ti plasmid. There are 6 vir genes virA-virE and virG that make up this 35 kilobase pairs (kb) region between the left and right borders of the T-DNA. Wounded plant cells produce vir inducing compounds such as acetosyringone and αhydroxyacetosyringone that induce the expression of these vir genes initiating the T-DNA transfer and thus transformation of the plant cells (Gelvin, 2003; Messens et al., 1990).
Agrobacterium-mediated transformation experiments have been carried out with numerous hybrids and species of citrus, such as grapefruit, sour orange, sweet orange, trifoliate orange
(Poncirus trifoliata Raf.), ‘Carrizo’ citrange, ‘Mexican’ lime, ‘Swingle’ citrumelo (C. paradisi x
P. trifoliata), ‘Cleopatra’ mandarin, and alemow (C. macrophylla Wester) (Dominguez et al.,

Citrus Transformation: Challenges and Prospects

103

2000; Ghorbel et al., 2000; Gutierrez-E et al., 1997; Luth & Moore, 1999; Molinari et al., 2004;
Moore et al., 1992; Peña et al., 2004, 2007). Transformation of other economically important citrus cultivars with the existing protocols has not yet been successful.
Generally, transformation efficiencies obtained by using Agrobacterium with most citrus cultivars can range from 0 to 45%. This is due to a number of limiting factors that can affect the transformation process. These include: species or cultivar specificity, age and type of explant used, competence of the citrus cells or tissues, Agrobacterium strains used and inoculation procedure, co-cultivation and pre-culturing conditions, adequate selection conditions and recovery of transgenic shoots (Bond & Roose, 1998; Costa et al., 2002; Peña et al., 2007; Yu et al., 2002).
2.3.1 Species or cultivar specificity
Data from early studies indicated that the type of citrus species and cultivar used in transformation experiments affect transformation efficiencies. Bond & Roose (1998) showed that when 7 citrus cultivars, ‘Washington navel’ and ‘Olinda Valencia’ oranges, ‘Lisbon’ lemon, ‘Rio Red’ grapefruit, ‘Carrizo’ citrange, mandarin and ‘Mexican’ lime were transformed with Agrobacterium only ‘Washington navel’ and ‘Carrizo’, resulted in GUSpositive shoots. These results were indicative of the receptiveness of these cultivars to this type of transformation protocol compared to the others. Although very little diversity exists between the sweet orange cultivars, ‘Washington navel’ and ‘Olinda Valencia’, the difference that exists was sufficient to affect the transformation efficiency. As a result, different protocols have been developed for different citrus species and cultivars (Bond &
Roose, 1998; Costa et al., 2002; Peña et al., 1997).
2.3.2 Age and type of explant used
Studies have also shown that lower transformation efficiencies are obtained with older segments (Moore et al., 1992; Peña et al., 1995a). Transformations of three week old
‘Washington navel’ orange epicotyl segments resulted in efficiencies of up to 87%, while 5 to
8 week old epicotyl segments gave lower efficiencies of 5 to 40% (Bond & Roose, 1998). This reduction in transformation efficiency is presumed to be the result of older epicotyl segments having a lower number of actively dividing cells and consequently less susceptible to T-DNA integration and the regeneration of shoots (Bond & Roose, 1998; Villemont et al.,
1997). In addition, it is regarded that older epicotyl segments have different wound exudates or cell wall components that result in a reduction in bacterial binding or the activation of the virulence genes (Bond & Roose, 1998).
Various types of explants such as, callus, leaf sections, seeds, epicotyl nodal and inter-nodal stem segments are often used, with varying results (Hidaka & Omura, 1993; Kaneyoshi et al., 1994; Moore et al., 1992). For instance, higher transformation efficiencies are obtained from citrus callus of ‘Ponkan’ mandarin. The advantages of using callus as explants are that a larger number of transgenic plants are produced, there is rapid proliferation and chimeras are rarely observed during the regeneration process (Li et al., 2002). However, drawbacks to using this system are that some citrus varieties do not possess embryogenic potential and the regenerated plants are juvenile, resulting in a long waiting period for the evaluation of the traits of interest and, additionally, it increases the risk of somaclonal variation which results in abnormal plant morphologies (Cervera et al., 2000; Li et al., 2002). Agrobacteriummediated transformation involving epicotyl and internodal stem segments are the

104

Genetic Transformation

predominantly used explants for regeneration of transgenic citrus plants. These types of explant are the most widely used in citrus transformation experiments and appear to be the most responsive. The disadvantage of using these types of explants is that the process is very laborious and takes a long time. Alternatively, another efficient system uses cotyledons from ungerminated mature seeds, followed by shoot regeneration via direct organogenesis
(Khawale et al., 2006; de Oliveira, Fisher and Moore unpublished). The advantage of this method is that it is less time consuming and laborious. It involves the use of mature seeds that are sterilized, subsequently the seed coat is removed and the cotyledons are directly inoculated with the Agrobacterium suspension and later transferred to the appropriate selection media. The use of this type of explant eliminates the time required for germination of seedlings to produce epicotyl segments and we have obtained higher transformation and regeneration frequencies with grapefruit and sweet orange. Although GUS expression was observed, we have not yet carried out the evaluation for stable integration of the transgene in the putative transgenic plants generated by this method. However, Khawale et al. (2006) proved the stability of this transformation method in ‘Nagpur’ mandarin.
2.3.3 Competence of the citrus cells or tissues
Cell division and dedifferentiation of plant cells are responsible for the explants’ competent state and result in callus proliferation (Peña et al., 1997, 2004). Observations of transformed citrus inter-nodal and epicotyl segments showed that resulting transgenic cells were localized in callus tissue and are of cambial origin. It is also suggested that certain treatments such as the inclusion of auxins, which promote active cell division and dedifferentiation of plant cells, correlated with higher transformation efficiencies (Peña et al., 2004).
2.3.4 Agrobacterium strains used and inoculation procedure
A study involving the use of three different strains of Agrobacterium (C58 C1, EHA101-5 and
LB4404) to transform seven citrus cultivars showed varying transformation efficiencies
(Bond & Roose, 1998). In four separate experiments, strain C58 C1 had the highest transformation efficiency of 45%, while strains EHA101-5 and LB4404 resulted in transformation efficiencies of 29% and 0%, respectively (Bond & Roose, 1998).
The inoculation of the citrus explants with the Agrobacterium culture typically requires incubation periods of 1 to 30 minutes (Bond & Roose, 1998; Costa et al., 2002; Luth & Moore,
1999; Peña et al., 1997). However, incubation periods greater than 10 minutes have led to the increase in regeneration of escape shoots and a reduction in transformation efficiency (Costa et al., 2002).
The optimal Agrobacterium culture concentrations that have been determined for the effective inoculation and transformation of citrus are 5x108 and 4x107 cfu/ml, and are dependent on the citrus cultivar being transformed (Bond & Roose, 1998; Cervera et al.,
1998b; Costa et al., 2002; Dominguez et al., 2000; Luth & Moore, 1999; Peña et al., 1995a; Yu et al., 2002). A limited source of bacterial cells reduces the frequency of T-DNA transfer while excess bacteria stress the plant cells (Costa et al., 2002; Yu et al., 2002).
2.3.5 Co-cultivation and pre-culturing conditions
Co-cultivation involves incubating both the explants and Agrobacterium on media containing no selective agent for the transformed cells or against the bacteria, for a period of time. An increase in the co-cultivation period has been associated with a higher number of

Citrus Transformation: Challenges and Prospects

105

regenerated and transformed shoots (Costa et al., 2002). Transformation frequency increased when the co-cultivation period was increased from 1 to 5 days at which it reached a maximum (Cervera et al., 1998a). However, prolonged co-cultivation periods often lead to an overgrowth of Agrobacterium which reduces the regeneration frequency of transformed shoots (Cervera et al., 1998b; Costa et al., 2002). As a result, most transformation protocols routinely use a 2 to 3 days co-cultivation period (Cervera et al., 1998b; Costa et al., 2002;
Luth & Moore, 1999; Peña et al., 1997).
The composition of the co-cultivation medium also affects the transformation process. The presence of auxins such as 2,4 dichlorophenoxyacetic acid (2,4-D), in co-cultivation medium has resulted in higher transformation frequencies in comparison to co-cultivation medium containing a filter paper layer, tomato cell suspension or a cell feed layer alone (Cervera et al., 1998b; Costa et al., 2002). The use of tomato cell feeder layers with high auxin concentrations has also improved citrus transformation (Costa et al., 2002).
The principle of pre-culturing the explants on co-cultivation medium before inoculation with Agrobacterium is to promote the production of vir-inducing cell components by metabolically active cells, which enhances the transformation process (Costa et al., 2002;
Spencer & Towers, 1991). However, some studies have shown that pre-culturing citrus explants has a negative effect on the transformation efficiency (Cervera et al., 1998b; Costa et al., 2002). Explants without pre-culture gave a reported 8.4-fold higher level in transformation efficiency compared to those that were pre-cultured (Costa et al., 2002). Most transformation experiments have bypassed this pre-culturing stage and have instead used acetosyringone (Cervera et al., 1998b). In nature, this phenolic compound is produced in wounded plant cells and is responsible for the activation of the vir genes. This has been shown to increase transformation efficiencies when added to the Agrobacterium inoculum and the co-cultivation medium by promoting transcription of A. tumefaciens virulence genes
(Cervera et al., 1998b; Kaneyoshi et al., 1994); however, in our personal experience working with grapefruit the addition of acetosyringone does not have much of an effect on the transformation efficiencies.
2.3.6 Adequate selection conditions
Finding suitable selective agents to recover transformed cells is critical in citrus transformation in order to eliminate the high numbers of chimeras and escapes that can be obtained during the process (Gutierrez-E et al., 1997; Moore et al., 1992; Peña et al., 1995a).
Hence, an effective selective agent is required to improve transformation recovery. Selection is usually based on antibiotic or herbicide resistance. Kanamycin is one of the most widely used selective antibiotics in transformation processes and is most effective when used in concentrations of up to 100 mg/L. However, shoot regeneration may be inhibited at this concentration. Other antibiotics such as geneticin and hygromycin have also been used, but are not as effective as kanamycin (Costa et al., 2002; Peña et al., 1997). The selective antibiotic can be ineffective in situations where residual Agrobacterium cells are present or neighboring transformed cells result in the break down or neutralization of the antibiotic. Invariably, non-transformed plant cells, i.e. escapes, strive in the absence of selective pressure (Cervera et al., 1998b). Other non-toxic selective genes, for instance manA, which encodes for the enzyme phosphomannose-isomerase (PMI), have been successfully used in the transformation of sweet orange (Boscariol et al., 2003). The principle is based on the ability of the transformed cells to metabolize mannose as a carbon source present in the selective

106

Genetic Transformation

medium. Additionally, the use of non-metabolizable genes instead of antibiotic and herbicide resistance genes as selective agents provides a suitable alternative and would satisfy public concerns about their dissemination into the environment and potential effect to consumers. This PMI positive selection system has been shown to be more effective than using kanamycin in many plant transformation protocols (Sundar & Sakthivel, 2008) but this did not seem to be the case in citrus.
2.3.7 Recovery of transgenic shoots
Recovering whole transgenic plants from transformation experiments is often difficult.
Typically, most regenerated transformed shoots are either placed directly in soil containing rooting hormone or on rooting media containing varying levels (0 to 1.0 mg/l) of the auxin naphthaleneacetic acid (NAA) which promotes root development (de Oliveira et al., 2009;
Gutierrez-E et al., 1997; Luth & Moore, 1999; Moore et al., 1992). Some researchers have gotten better results by first transferring the shoots to hormone-free media to eliminate the cytokinin benzyl aminopurine (BA) from the regeneration media before placing on NAA containing media. Different combinations of BA, NAA and another auxin, indole 3-butyric acid (IBA), NAA and IBA only or just IBA and BA in the rooting medium have been tested so as to improve rooting efficiency in citrus cultivars such as mandarin, lemon, ‘Troyer’ citrange and lime (Al-Bahrany, 2002; Jajoo, 2010; Moreira-Dias et al., 2000; Singh et al., 1994).
Again, the concentrations of these phytohormones vary depending on the citrus genotype.
High rooting efficiencies of transgenic shoots have been obtained with citrus types, such as grapefruit, ‘Carrizo’ citrange and P. trifoliata (Peña et al., 2007), but with other citrus types, the rooting efficiency is very low. This problem is overcome by shoot-tip micrografting the transgenic shoot onto a decapitated rootstock seedling (Peña et al., 1995a, 1995b).

3. Genetic engineering and disease control in citrus
Recent advances in genomics, both in citrus and other species, have made available an abundance of genes that can be easily cloned and used in transformation. This is particularly useful in the genetic engineering process as characterized gene(s) derived from known sources can be incorporated into the genome of a recipient plant to obtain desirable traits.
Because of its economic impact, disease control is often the objective of plant improvement programs. Hence, resistance and defense genes isolated from well studied plant species have been successfully incorporated into other species to generate pathogen-resistant plants.
Another successful strategy in the control of diseases has been the transformation of genes derived from pathogens which can also result in resistant plants.
According to the USDA economic research service, genetically engineered (GE) crops have been widely adopted since their introduction in 1996 (USDA, 2010). Herbicidetolerant genetically engineered soybeans and cotton have been the most extensively and rapidly adopted GE crops in the U.S., followed by insect-resistant cotton and corn (Cao et al., 2010). The positive impact of these GE crops was due to lower labor and production costs, and gains in profitability, in addition to their increased environmental benefits. In the particular case of citrus, although a variety of transgenic types have been reported in the literature, none has reached commercialization. However, field trials, including our own, are underway. Below we describe some recent and relevant cases of transgenics in citrus. Citrus Transformation: Challenges and Prospects

107

3.1 Pathogen-derived genes
Some of the earliest success stories in the control of diseases by genetic engineering were using pathogen-derived genes from viruses (Abel et al., 1986). When certain viral genes, particularly the capsid protein (CP), were transformed into plants they showed resistance or immunity against closely related viral strains. A well-known case in a perennial species is the control of Papaya ringspot virus by the insertion of its CP into the papaya genome. This effort virtually saved this industry in Hawaii (Gonsalves, 1998). The control mechanism that prevents viral replication in the transgenic plants was initially denominated co-suppression but it is currently referred to as RNA interference or RNA silencing.
Several studies have transformed sequences from a variety of economically important viruses into different citrus types to attempt to produce resistant plants. One of such viral diseases is caused by Citrus tristeza virus (CTV). Severe strains of CTV can dramatically reduce production and in some instances lead to tree death in a relatively short period of time (Moreno et al., 2008). In some areas of the world CTV is an important or the most important limiting factor in citrus production and incorporation of resistance by traditional breeding techniques is not possible. For this reason many laboratories have tried to genetically engineer different CTV sequences into citrus as a way to control this important pathogen. However, these attempts have never been completely successful. For example, transforming the major CP (p25) into ‘Mexican‘ lime had two types of response to viral challenge. In replicate plants, propagated from the same line (i.e. genetically identical), 10 to
33% were resistant to CTV while the rest developed typical symptoms, despite a significant delay in virus accumulation (Domínguez et al., 2002). Similar results were obtained in
‘Duncan‘ grapefruit when translatable and untranslatable versions of the major CP were transformed (Febres et al., 2003, 2008). Various forms (full length, hairpins) of the p23 gene, located in the 3‘ end of the viral genome, have also been transformed into citrus genotypes.
In ‘Mexican‘ lime expression of the p23 protein produced viral symptoms in some plants
(Fagoaga et al., 2005). Lines with normal phenotype (no symptoms) were further propagated and tested for CTV resistance and again the results were mixed with some plants completely immune to the virus while others from the same line had delayed symptom development and virus accumulation (Fagoaga et al., 2006; López et al., 2010). The use of the 3‘ region of the p23 and the contiguous 3‘-untranslated region (UTR), either as a hairpin or as single copy, has also been transformed into 'Duncan ', 'Flame ', 'Marsh ', and 'Ruby Red ' grapefruit and alemow plants with similar results as described above in which some plants derived from a particular line were fully resistant and others were not (Ananthakrishnan et al., 2007;
Batuman et al., 2006; Febres et al., 2008). Only in one line full resistance was observed
(Febres et al., 2008). This line is currently being evaluated in the field for its horticultural value and durability of the resistance under natural conditions. Other CTV genes have been used but either no transgenic plants were regenerated (p20 and minor CP/p27) or they did not show resistance (RdRp gene) (Febres et al., 2003, 2008).
Resistance to another important viral disease, Citrus psorosis virus (CPsV), has been reported in transgenic sweet orange plants transformed with intron-hairpin constructs (ihp) corresponding to the viral CP, the 54K or the 24K genes (Reyes et al., 2011). After challenge with the virus, the CP transgenic plants were more effective in controlling the CPsV and consistently showed lower virus levels and no symptom development compared to 54K and
24K transgenic plants. The study reported that the observed CPsV resistance was due to preactivated RNA silencing rather than the siRNA accumulation levels in the ihp-CP transgenic sweet orange plants prior to virus challenge (Reyes et al., 2011).

108

Genetic Transformation

Pathogen-derived genes have also been used to control bacterial diseases. Citrus canker, caused by Xanthomonas axonopodis pv. citri is an economically important disease, especially for the fresh fruit market. The pthA protein is involved in the pathogenesis and symptom development of this bacterial pathogen and the C-terminus contains three nuclear localizing signals (NLS) critical for the interaction with a host protein, translocation to the nucleus and function (Yang et al., 2011). By using a truncated version of the pthA gene, coding only for the C-terminus portion of the protein, it was theorized that the resulting protein would interrupt binding and function of the native bacterial pthA during infection and prevent symptom development and pathogen growth. Indeed transgenic sweet orange plants that expressed the truncated protein showed lower disease incidence and symptom development compared to wild type plants, demonstrating a certain degree of resistance
(Yang et al., 2011). The authors are currently conducting field experiments to determine the effectiveness of this strategy under natural conditions.
In another strategy, also to control citrus canker, a hrpN gene derived from Erwinia amylovora was transformed into ‘Hamlin’ sweet orange plants. The hrpN encodes a harpin protein that elicits the hypersensitive response (HR) and systemic acquired resistance (SAR) in plants.
The hrpN gene was inserted in a construct made up of gst1, a pathogen-inducible promoter
(so the gene would not be expressed constitutively and hence the SAR response would only be induced in the presence of the pathogen), a signal peptide for protein secretion to the apoplast (the canker bacterium does not penetrate the cell and remains apoplastic). Several of the hrpN transgenic lines showed reduction in their susceptibility to citrus canker as compared to wild type plants, and one line in particular displayed very high resistance to the pathogen (up to 79% reduction in disease severity) (Barbosa-Mendes et al., 2009).
Fungal pathogens also affect citrus production. In particular, Phytophthora spp can cause root rot and gummosis in mature trees and damping-off in seedlings. For the control of
Phytophthora nicotianae Azevedo et al (2006) used a bacterio-opsin (bO) gene to transform
‘Rangpur’ lime. The bO gene is derived from Halobacteria halobium and can spontaneously activate programmed cell death and enhance broad-spectrum disease resistance accompanied by pathogenesis-related (PR) protein accumulation. In two of the transgenic lines, higher levels of tolerance to this pathogen with significantly smaller lesions were observed; however, these lines also exhibited HR-like lesions in the absence of pathogen
(Azevedo et al., 2006). It remains to be seen if this strategy will work under field conditions given the fact that the transgenic plants develop spontaneous lesions.
3.2 Plant defense genes
Upon recognition of a potential pathogen plants naturally respond by triggering defense mechanisms that can, in some instances, halt pathogen colonization. One such defense mechanism is SAR, a form of inducible defense in which infection by a pathogen leads to an enhanced defense state that is durable and provides resistance or tolerance to a wide range of pathogens in subsequent challenges (Durrant & Dong, 2004).
A gene that has been identified as critical in the establishment of SAR is the NONEXPRESSOR OF PATHOGENESIS RELATED 1 (NPR1). NPR1 is a transcription co-activator and plays a key role in regulating defense gene transcription and signal transduction pathways that lead to SAR (Despres et al., 2000; Zhang et al., 1999). Under normal conditions the NPR1 protein does not induce SAR, however in the presence of a pathogen and increased levels of salicylic acid (SA) NPR1 is translocated to the nucleus where it

Citrus Transformation: Challenges and Prospects

109

interacts with transcription factors that ultimately induce the expression of SAR-associated genes (Kinkema et al., 2000).
A number of studies have demonstrated that the over-expression of the Arabidopsis NPR1 provides a broad-spectrum enhanced resistance to various pathogens (Cao et al., 1998; Lin et al., 2004). Our laboratory and others have invested a considerable amount of time and effort investigating the nature of SAR in citrus and the full length sequences of five citrus NPR1like genes has been cloned and sequenced. Their expression levels are differentially affected by pathogen and other treatments (Febres and Khalaf, unpublished results).
Zhang et al. (2010) reported transforming the Arabidopsis NPR1 gene into ‘Duncan’ grapefruit and ‘Hamlin’ sweet orange. The over-expression of this gene increased resistance to citrus canker and the observed resistance correlated with the expression levels of the transgene. Our results of transgenic ‘Carrizo’ citrange plants, also transformed with the
Arabidopsis NPR1 gene indicated that the transgenic lines were as well more tolerant to citrus canker (slower lesion development) and had higher levels of pathogenesis-related
(PR) genes than wild type plants (Febres, unpublished).
3.3 Additional strategies
As mentioned above, attempts to use pathogen-derived sequences for the control of CTV have not rendered consistent results. A different approach has recently been tested (Cervera et al., 2010) by using single-chain variable fragments (scFv) from two monoclonal antibodies that in combination seem to detect the major CP from most CTV isolates. ‘Mexican’ lime plants were transformed with each scFv either individually or in combination. Essentially all constructs conferred some level of protection when the plants were challenged with a severe strain of CTV. Between 40 to 60% of the plants tested did not get infected, compared to 95% infection in control plants. In addition a delay and attenuation in symptom development was also observed. Although complete resistance was not observed in this case either it is still a promising approach that needs further investigation.

4. Emerging technologies
The production of new varieties via transformation in citrus and many other woody perennials poses a challenge not found in the breeding of annuals and other fast-growing plants. Due to combinations of long juvenile periods, biological barriers to crossing, and the difficulty of reconstituting favored types, such as the complex hybrids sweet orange and grapefruit in citrus, new cultivars will probably have to be selected from T0 transformants.
There are several implications to this, discussed below.
One of the greatest challenges of producing and testing transgenic Citrus plants is the long juvenile periods observed in this genus. As discussed above, most citrus transformation techniques utilize explants derived from juvenile tissue, and the transgenic plants must be grown for many years, in most cases, for their horticultural attributes to be evaluated. Two approaches are being investigated to overcome this problem. The first is efforts to decrease the juvenile periods of transgenic plants. There are both historical work and ongoing efforts to use horticultural methods to bring citrus plants into bearing earlier. Another alternative for shortening the juvenile period is to produce transgenic plants that over-express a flower meristem identity gene that causes them to flower earlier. The Arabidopsis LEAFY and
APETALA1 genes have been over-expressed in ‘Carrizo’ citrange (Peña et al., 2001) and transgenic Poncirus plants over-expressing a citrus orthologue of Arabidopsis FLOWERING

110

Genetic Transformation

LOCUS T (FT) have been produced (Endo et al., 2005; Nishikawa et al., 2010). However, in most cases, the expression of these genes, while dramatically reducing time to flowering, also conferred deleterious morphological phenotypes to the transgenic plants. Thus this approach may benefit citrus breeding efforts and early testing of traits designed to be evinced in fruit, it may not produce T0 transgenic plants that could directly be used in production. However, all possibilities of this approach have not been explored. For instance, citrus genomes contain at least three orthologues of FT that produce quite different phenotypes when overexpressed in transgenic tobacco (Kamps and Moore, unpublished).
Also, Carrizo plants transformed with APETALA1 displayed normal morphology (Peña &
Séguin, 2001).
The second approach for overcoming juvenility is to use explants from mature plants for transformation. However, taking explants directly from mature trees is not likely to be successful due to the low regeneration potential of such explants and perhaps also of lower competence for transformation. Success has been achieved by reinvigorating mature citrus types by grafting mature buds on vigorous juvenile rootstocks and using the first flushes for
Agrobacterium-mediated transformation (Cervera et al., 1998a, 2005). However, this is a technically demanding approach. The plant material must be in excellent condition, which is particularly difficult to achieve in humid climates, where the pathogen load on tissue, even when grown under greenhouse conditions, may make disinfection of explants difficult.
Even then, only a relatively small number of explants can be obtained from the first flush or two of the grafted plant. In some genotypes, a lack of bud uniformity in sprouting and morphology is problematic (Cervera et al., 2008). In other cases, culture requirements for regeneration may be quite different for even closely related citrus types (Almeida et al.,
2003; Rodríguez et al., 2008). Kobayashi (2003) circumvented some of these problems by using already grafted ‘Pera’ sweet orange nursery plants for harvest of explants and by thin segments (1 to 2 mm) of stems as explants. In all cases, transgenic plants in the greenhouse began to flower after 14 months or less after micrografting the transgenic scions on rootstock. Experiments are underway in several laboratories to improve still further on the production of transgenic plants from mature tissue. The importance of the cambium in producing transgenic tissue in many of the above reports and the recent description of the cambium cells of several plants as analogous to vascular stem cells (Lee et al., 2010) suggest that one research direction could be exploration of other types of explants where the cambium cells are maximally exposed to Agrobacterium and subsequent growth hormones in the culture medium.
Another problem with using T0 plants is that the gene insertion site(s) is unknown. This can affect the expression of the transgene and could lead to altered morphology that was not intended. However, genomic changes that are not selected for also may happen during conventional breeding due to, for instance, transposon activity or irradiation and mutation breeding. Of course there are also advantages to utilizing T0 transformants in perennials. With the explosion in genomic information, the functions of more and more genes are being elucidated (Talon & Gmitter Jr, 2008), so choosing a transgene that will impart a particular trait should be more targeted in the future. It has also been found in both conventional and molecular breeding that valuable genes or alleles are found in plant relatives or wild species.
In such cases using T0 transgenics circumvents the problem of linkage drag that may result from the transfer of unknown and undesirable genes that are linked to the desirable gene or allele from the donor parent. It might also be possible to “stack” valuable genes or alleles in

Citrus Transformation: Challenges and Prospects

111

a desirable citrus type via multiple transformations or multiple genes inserted in a single transformation. Another important area of research has been to increasing the cold hardiness of citrus. This could potentially extend production areas to new regions where pathogens or other limiting factors are not present. As in the case with disease resistance there are some citrus relatives that can endure freezing temperatures. While most commercially important citrus varieties are susceptible to freezing, P. trifoliata for instance can tolerate temperatures well bellow freezing if cold acclimated prior to the exposure (Talon & Gmitter Jr, 2008).
Genes associated with cold acclimation have been identified in citrus as an initial milestone in a multistep approach to ultimately incorporate some of these genes in the genome of selected citrus varieties that are naturally susceptible to freezing. Our laboratory and others have studied the effect of cold stress or freezing on gene expression. For instance, in an attempt to minimize the chilling injury during citrus fruits storage, a genome-wide transcriptional profiling analysis was performed (Maul et al., 2008). Grapefruit flavedo RNA was used to study the responses of citrus fruit to low temperatures. The study applied a prestorage conditioning treatment of 16°C for 7 days and utilized an Affymetrix Citrus
GeneChip microarray. While the applied treatment seemed to have halted the expression of general cellular metabolic activity, it induced changes in the expression of transcripts related to membranes, lipid, sterol and carbohydrate metabolism, stress stimuli, hormone biosynthesis, and modifications in DNA binding and transcription factors.
Our laboratory provided the first evidence of an association in citrus between C-repeat binding factors (CBF) expression levels and the extent of cold tolerance (Champ et al., 2007).
CBFs have been identified in many species and they function as transcriptional activators regulating the expression levels of a number of genes that impart cold and stress tolerance.
P. trifoliata, a Citrus relative, can survive freezes of -20°C when fully cold acclimated. On the other hand, grapefruit cannot withstand temperatures lower than 0°C. In P. trifoliata transcripts of CBF1 and CORc115 (a cold-induced group II LEA gene, and a likely target of
CBF1) accumulate both earlier and to higher levels than in grapefruit when exposed to cold temperatures. Additionally, using subtractive hybridization we identified a number of new, differentially cold-regulated genes from P. trifoliata (Sahin-Cevik & Moore, 2006). Although several of the genes identified were unique sequences, many were homologous to cold and environmental stress-induced genes from other species. Taken together, our results indicate that similar pathways are present and activated during cold acclimation in diverse plant species. In a more recent study (Crifo et al., 2011) performed a transcriptome analysis based on subtractive hybridization to study cold stress response of pigmented sweet oranges (blood oranges) in order to study the overall induction in gene expression after the exposure to low temperatures. On the whole, the expression of transcripts related to defense, oxidative damage, osmo-regulation, lipid desaturation and primary and secondary metabolism were induced. In addition, cold stress induced flavonoid biosynthesis, including those reactions involved in anthocyanin biosynthesis and metabolic pathways supplying it. Several transcription factors were identified for the first time as cold responsive genes in plants.
In summary, cold stress has been linked to signaling pathways where gene expression can further interrelate with additional stress related pathways. The entire signaling network throughout the plant affects its response(s) to biotic or abiotic stress. Along with the mentioned gene annotations, additional functional analyses are crucial to study the nature of the expected phenotype before we can introduce new genes into the Citrus genome using transformation techniques.

112

Genetic Transformation

Antimicrobial peptides (AMPs) are currently the subject of intense research for the control of diseases in citrus, particularly canker and huanglongbing (HLB) or citrus greening. There is no known resistance in Citrus to HLB (caused by Candidatus Liberibacter spp); however, it can have devastating effects by reducing overall production. Infected trees have smaller fruits with less juice, the flavor of the juice is changed and it eventually leads to micronutrient deficiencies, defoliation and tree death. It has been known for years that
AMPs play a vital role in plant defense. Plant AMPs are monomer or oligomer building units that have mostly three-dimensional or tertiary structures of either amphipathic or amphiphylic nature (Sitaram & Nagaraj, 1999, 2002). The latter characteristic and folding are essential for the peptides antibacterial activity (Epand & Vogel, 1999). Different scenarios for their function have been suggested but they all agree on the fact that these AMPs operate by the formation of membrane pores that ultimately cause the disruption of the membrane and subsequently cell death through ion and metabolite leakage (Yeamn & Yount, 2003). A number of studies have confirmed the inhibitory effect of these peptides to fungal and bacterial pathogens when expressed in different plant species such as rice, wheat, and tomato fruits (Jha & Chattoo, 2010; Jha et al., 2009; Ramamoorthy et al., 2007). In a recent study, two AMP genes, Shiva A and Cecropin B, were transformed into ‘Jincheng’ and
‘Newhall’ sweet orange. Subsequently, the transgenic plants were challenged with
Xanthomonas axonopodis pv. citri, the causal agent of citrus canker. In both greenhouse and field experiments with artificial or natural inoculation, respectively, some transgenic lines were highly resistant to canker and either did not develop canker lesions or the number of lesions was significantly reduced compared to wild types. The plants were also phenotypically normal, flowered after two years (grafted on Poncirus), borne fruit and the juice was no different in solid and sugar content and acidity from non-transgenic plants (He et al., 2011).
4.1 Transformation vs. transient expression
Transient expression systems are beneficial for some purposes, such as rapidly and easily assaying promoter function or gene expression under some conditions. Although it has been surprisingly difficult to implement transient expression in citrus leaves it has been possible to transiently express genes in the fruit, particularly young fruit (Ahmad & Mirza, 2005;
Spolaore et al., 2001).
Finally, a vector based on CTV has been developed (Folimonov et al., 2007). Such vectors have been used in herbaceous plants to study gene function, expression, and silencing, but have not been available for woody plants. This can be seen as a hybrid strategy between transient expression and stable transformation. Although the virus vector nucleic acid is not incorporated into the genome of the citrus host, Folimonov et al. (2007) reported that expression of GFP continued for up to four years after introduction of the scorable marker into CTV vectors.

5. Conclusions: The future of citrus transformation
Ultimately the use of genetic engineering is just another tool in the improvement of citrus.
Genetic transformation has the advantage of potentially reducing breeding time, particularly important in the case of a perennial crop such as citrus with a long juvenile period, and also facilitating the introduction of traits not readily available in the particular species. Breeding programs take into consideration the needs of both farmers and

Citrus Transformation: Challenges and Prospects

113

consumers. Production of genetically modified citrus should also take into consideration the needs of both; however, genetically modified organisms (GMOs) tend to be more controversial and subjected to more public scrutiny than traditionally produced varieties.
For instance, a recent European survey indicated that among respondents GMOs were considered unnatural (70%), made them feel uneasy (61%), harmed the environment (59%) and were unsafe for people 's health (59%) (European Comission, 2010). Regardless of whether these concerns are just perceived or real they will have to be addressed in order to fully implement the benefits of genetic engineering in solving real and important problems for citrus farmers and at the same time delivering desirable products to consumers.
Two major concerns regarding GMOs are: 1) impact to the environment, in the form of the transgene 'escaping ' and transferring to wild species and thus eroding the biodiversity of wild relatives of the crop or, on the other hand, creating 'super weeds ' of species that acquire the transgene and become better fitted and difficult to control (Azevedo & Araujo, 2003;
Parrott, 2010; Sweet, 2009); and 2) impact to human health by a potentially toxic or allergenic transgenic protein (Domingo & Gine Bordonaba, 2011).
In the particular case of citrus there are ways to mitigate these concerns. Essentially all presently grown GMOs are transgenic in nature, with “trans” referring to genetic sequences that come from organisms that are not crossable with the plant in question, such as sequences from viruses or bacteria or even from a plant species that is not crossable, for instance the insertion of an Arabidopsis gene into a citrus plant. This has led to many countries and groups being resistant to the growth and consumption of GMOs. Thus, there are proponents of producing GMOs that are cisgenic, where all of the inserted genetic material comes from the original plant or a crossable type (Jacobsen & Schouten, 2008). Such genes could be perceived by the public as more “natural” and could potentially be less likely to be toxic or allergenic (although this would have to be tested experimentally on a case by case basis). Plants transformed this way do not appear to raise the fear and ethical concerns that the production of transgenic plants inspires (Conner et al., 2006; Rommens et al., 2007).
However, this approach would rule out the use of most commonly used selectable and scorable marker genes, as well as the most commonly used promoters and termination sequences and the necessary T-DNA borders for Agrobacterium-mediated transformation. A cisgene consists of a native gene with its native promoter and termination. In these discussions, there is also mention of intragenes in which gene parts can originate from different genes as long as the donor is a crossable type (Jacobsen & Schouten, 2008). Many laboratories are now looking for plant DNA sequences that are homologous to the bacterial sequences present in T-DNA borders and for methods to produce genetically modified plants where selectable and scorable genes can be either removed after transformation or are of plant origin (Rommens et al., 2007).
There has been a small amount of research of this kind in citrus. Fleming et al. (2000) transformed sweet orange protoplasts with a construct containing the GFP scorable gene using a PEG method. Transformed regenerating somatic embryos were identified by their
GFP expression and physically separated from nontransformed tissues, resulting in transgenic plants. No Agrobacterium was involved and there was no selective agent applied.
Ballester et al. (2008) compared the most common citrus transformation and selection system, using kanamycin selection and scorable GUS staining to three methods that did not utilize antibiotic selection, in ‘Carrizo’ citrange and ‘Pineapple’ sweet orange. The alternative methods included scoring for GUS staining without applying selection, transforming explants with a multi-autotransformation (MAT) vector, combining an

114

Genetic Transformation

inducible recombinase-specific recombination system (R/RS) with transgenic-shoot selection through expression of isopentenyl transferase (ipt) and indoleacetamide hydrolase/tryptophan monooxygenase (iaaM/H) marker genes, and selection with the
PMI/mannose conditional positive selection system (Boscariol et al., 2003). Transgenic plants were obtained from all treatments, but selection for nptII expression was by far the most efficient. The authors preferred the MAT vector, because with it they could obtain transformed plants where the selectable marker would recombine out (Ballester et al., 2007).
However, all of the transgenic plants still contained some sequences of bacterial origin.
Another approach is the use of promoters that do not express the transgene in the edible parts (fruits). Again this would potentially reduce the possibility of becoming harmful to human health. Several groups are actively searching for such promoters in citrus, including inducible promoters that would be turned on at will by chemical application, etc. As explained before the genomic information currently available should facilitate this endeavor. A third strategy we are exploring is the use of transgenic rootstocks that could confer the desired trait to the wild type (non transgenic) scion, without the need of incorporating and expressing transgenes in the scion and edible parts of the plant. This would prevent or at least reduce the chances of spreading transgenic pollen into the wild.
There is evidence for the transfer of genetic material between rootstock and scion but this seems to be limited to the graft union region (Stegemann & Bock, 2009). However, it is unlikely that this grafting approach would work with all transgenes since not all expressed proteins are translocated and/or have a systemic effect. One case in which it could work in citrus is the reduction of juvenility using the FT protein. Transgenic FT is capable of inducing flowering through graft unions (Notaguchi et al., 2008; Notaguchi et al., 2009).
Induction of pathogen defense could potentially be tackled this way as well since some of the proteins activate systemic signaling (Xia et al., 2004).
These approaches take into consideration consumer’s perception about GMOs, educated concerns about the release of GMOs and the needs of citrus farmers for better, disease resistant crops. Citrus production faces important challenges due to climate change and disease and genetic engineering has the potential, as has been the case in other crops, of becoming an important weapon in the arsenal against these major challenges.

6. Acknowledgment
Research in our laboratory is funded in part by the Citrus Research & Development
Foundation of Florida and a USDA Special Grant.

7. References
Abel P. P.; Nelson R. S.; De B.; Hoffmann N.; Rogers S. G.; Fraley R. T. & Beachy R. N.
(1986). Delay of Disease Development in Transgenic Plants That Express the
Tobacco Mosaic Virus Coat Protein Gene. Science,Vol.232, No.4751, pp 738-743
Ahmad M. & Mirza B. (2005). An Efficient Protocol for Transient Transformation of Intact
Fruit and Transgene Expression in Citrus. Plant Molecular Biology Reporter,Vol.23,
No.4, pp 419-420
Al-Bahrany A. M. (2002). Effect of Phytohormones on in Vitro Shoot Multiplication and
Rooting of Lime Citrus aurantifolia (Christm.) Swing. Scientia Horticulturae,Vol.95,
No.4, pp 285-295

Citrus Transformation: Challenges and Prospects

115

Almeida W. A. B.; Mourao F. A. A.; Pino L. E.; Boscariol R. L.; Rodriguez A. P. M. & Mendes
B. M. J. (2003). Genetic Transformation and Plant Recovery from Mature Tissues of
Citrus sinensis L. Osbeck. Plant Science,Vol.164, No.2, pp 203-211
Ananthakrishnan G.; Orbovic V.; Pasquali G.; Calovic M. & Grosser J. W. (2007). Transfer of
Citrus Tristeza Virus (CTV)-Derived Resistance Candidate Sequences to Four
Grapefruit Cultivars through Agrobacterium-Mediated Genetic Transformation. In
Vitro Cellular & Developmental Biology-Plant,Vol.43, No.6, pp 593-601
Azevedo F. A.; Mourao F. A. A.; Mendes B. M. J.; Almeida W. A. B.; Schinor E. H.; Pio R.;
Barbosa J. M.; Guidetti-Gonzalez S.; Carrer H. & Lam E. (2006). Genetic
Transformation of Rangpur Lime (Citrus limonia Osbeck) with the B0 (BacterioOpsin) Gene and Its Initial Evaluation for Phytophthora nicotianae Resistance. Plant
Molecular Biology Reporter,Vol.24, No.2, pp 185-196
Azevedo J. L. & Araujo W. L. (2003). Genetically Modified Crops: Environmental and
Human Health Concerns. Mutation research,Vol.544, No.2-3, pp 223-233
Ballester A.; Cervera M. & Pena L. (2008). Evaluation of Selection Strategies Alternative to
NPTII in Genetic Transformation of Citrus. Plant Cell Reports,Vol.27, No.6, pp 10051015
Ballester A.; Cervera M. & Peña L. (2007). Efficient Production of Transgenic Citrus Plants
Using Isopentenyl Transferase Positive Selection and Removal of the Marker Gene by Site-Specific Recombination. Plant Cell Reports,Vol.26, No.1, pp 39-45
Barbosa-Mendes J. M.; Mourao F. D. A.; Bergamin A.; Harakava R.; Beer S. V. & Mendes B.
M. J. (2009). Genetic Transformation of Citrus sinensis cv. Hamlin with Hrpn Gene from Erwinia amylovora and Evaluation of the Transgenic Lines for Resistance to
Citrus Canker. Scientia Horticulturae,Vol.122, No.1, pp 109-115
Batuman O.; Mawassi M. & Bar-Joseph M. (2006). Transgenes Consisting of a dsRNA of an
RNAi Suppressor Plus the 3 ' UTR Provide Resistance to Citrus Tristeza Virus
Sequences in Nicotiana benthamiana but Not in Citrus. Virus genes,Vol.33, No.3, pp
319-327
Bespalhok F. J. C.; Kobayashi A. K.; Pereira L. F. P.; Galvao R. M. & Vieira L. G. E. (2003).
Transient Gene Expression of β-Glucuronidase in Citrus Thin Epicotyl Transversal
Sections Using Particle Bombardment. Brazilian Archives of Biology and
Technology,Vol.46, No.1, pp 1-6
Bond J. E. & Roose M. L. (1998). Agrobacterium-Mediated Transformation of the
Commercially Important Citrus Cultivar Washington Navel Orange. Plant Cell
Reports,Vol.18, No.3-4, pp 229-234
Boscariol R. L.; Almeida W. A. B.; Derbyshire M. T. V. C.; Mourão Filho F. A. A. & Mendes
B. M. J. (2003). The Use of the PMI/Mannose Selection System to Recover
Transgenic Sweet Orange Plants (Citrus Sinensis L. Osbeck). Plant Cell
Reports,Vol.22, No.2, pp 122-128
Cao H.; Li X. & Dong X. N. (1998). Generation of Broad-Spectrum Disease Resistance by
Overexpression of an Essential Regulatory Gene in Systemic Acquired Resistance.
Proceedings of the National Academy of Sciences of the United States of America,Vol.95,
No.11, pp 6531-6536

116

Genetic Transformation

Cao M.; Sato S. J.; Behrens M.; Jiang W. Z.; Clemente T. E. & Weeks D. P. (2010). Genetic
Engineering of Maize (Zea mays) for High-Level Tolerance to Treatment with the
Herbicide Dicamba. Journal of Agricultural and Food Chemistry. 10.1021/jf104233h
Cervera M.; Esteban O.; Gil M.; Gorris M. T.; Martinez M. C.; Pena L. & Cambra M. (2010).
Transgenic Expression in Citrus of Single-Chain Antibody Fragments Specific to
Citrus Tristeza Virus Confers Virus Resistance. Transgenic Research,Vol.19, No.6, pp
1001-1015
Cervera M.; Juarez J.; Navarro A.; Pina J. A.; Duran-Vila N.; Navarro L. & Peña L. (1998a).
Genetic Transformation and Regeneration of Mature Tissues of Woody Fruit Plants
Bypassing the Juvenile Stage. in Transgenic Research (Springer Netherlands), pp 5159
Cervera M.; Juarez J.; Navarro L. & Pena L. (2005). Genetic Transformation of Mature Citrus
Plants. Methods in Molecular Biology,Vol.286, No.III, pp 177-188
Cervera M.; Navarro A.; Navarro L. & Peña L. (2008). Production of Transgenic Adult Plants from Clementine Mandarin by Enhancing Cell Competence for Transformation and
Regeneration. Tree Physiology,Vol.28, No.1, pp 55-66
Cervera M.; Pina J. A.; Juarez J.; Navarro L. & Pena L. (2000). A Broad Exploration of a
Transgenic Population of Citrus: Stability of Gene Expression and Phenotype.
Theoretical and Applied Genetics,Vol.100, No.5, pp 670-677
Cervera M.; Pina J. A.; Juarez J.; Navarro L. & Peña L. (1998b). Agrobacterium-Mediated
Transformation of Citrange: Factors Affecting Transformation and Regeneration.
Plant Cell Reports,Vol.18, No.3-4, pp 271-278
Champ K. I.; Febres V. J. & Moore G. A. (2007). The Role of CBF Transcriptional Activators in Two Citrus Species (Poncirus and Citrus) with Contrasting Levels of Freezing
Tolerance. Physiologia Plantarum,Vol.129, No.3, pp 529-541
Conner A. J.; Barrell P. J.; Baldwin S. J.; Lokerse A. S.; Cooper P. a.; Erasmuson A. K.; Nap J.P. & Jacobs J. M. E. (2006). Intragenic Vectors for Gene Transfer without Foreign
DNA. Euphytica,Vol.154, No.3, pp 341-353
Costa M. G. C.; Otoni W. C. & Moore G. A. (2002). An Evaluation of Factors Affecting the
Efficiency of Agrobacterium-Mediated Transformation of Citrus paradisi (Macf.) and
Production of Transgenic Plants Containing Carotenoid Biosynthetic Genes. Plant
Cell Reports,Vol.21, No.4, pp 365-373
Crifo T.; Puglisi I.; Petrone G.; Recupero G. R. & Lo Piero A. R. (2011). Expression Analysis in Response to Low Temperature Stress in Blood Oranges: Implication of the
Flavonoid Biosynthetic Pathway. Gene,Vol.476, No.1-2, pp 1-9 de Oliveira M. L.; Febres V. J.; Costa M. G.; Moore G. A. & Otoni W. C. (2009). HighEfficiency Agrobacterium-Mediated Transformation of Citrus Via Sonication and
Vacuum Infiltration. Plant Cell Reports,Vol.28, No.3, pp 387-395
Despres C.; DeLong C.; Glaze S.; Liu E. & Fobert P. R. (2000). The Arabidopsis NPR1/NIM1
Protein Enhances the DNA Binding Activity of a Subgroup of the TGA Family of
Bzip Transcription Factors. The Plant Cell,Vol.12, No.2, pp 279-290
Domingo J. L. & Gine Bordonaba J. (2011). A Literature Review on the Safety Assessment of
Genetically Modified Plants. Environment International, Vol. 37, No. 4, pp 734-742
Domínguez A.; de Mendoza A. H.; Guerri J.; Cambra M.; Navarro L.; Moreno P. & Peña L.
(2002). Pathogen-Derived Resistance to Citrus Tristeza Virus (CTV) in Transgenic

Citrus Transformation: Challenges and Prospects

117

Mexican Lime (Citrus aurantifolia (Christ.) Swing.) Plants Expressing Its P25; Coat
Protein Gene. Molecular Breeding,Vol.10, No.1, pp 1-10
Dominguez A.; Guerri J.; Cambra M.; Navarro L.; Moreno P. & Peña L. (2000). Efficient
Production of Transgenic Citrus Plants Expressing the Coat Protein Gene of Citrus
Tristeza Virus. Plant Cell Reports,Vol.19, No.4, pp 427-433
Durrant W. E. & Dong X. (2004). Systemic Acquired Resistance. Annual Review of
Phytopathology,Vol.42, pp 185-209
Endo T.; Shimada T.; Fujii H.; Kobayashi Y.; Araki T. & Omura M. (2005). Ectopic Expression of an FT Homolog from Citrus Confers an Early Flowering Phenotype on Trifoliate
Orange (Poncirus trifoliata L. Raf.). Transgenic Research,Vol.14, No.5, pp 703-712
Epand R. M. & Vogel H. J. (1999). Diversity of Antimicrobial Peptides and Their
Mechanisms of Action. Biochimica et Biophysica Acta (BBA) - Biomembranes,Vol.1462,
No.1-2, pp 11-28
European Comission (2010). Special Eurobarometer-Biotechnology. Eurobarometer. 341
(Wave 73.1): pp 385. http://ec.europa.eu/public_opinion/archives/ebs/ebs_341_en.pdf Fagoaga C.; Lopez C.; de Mendoza A. H.; Moreno P.; Navarro L.; Flores R. & Pena L. (2006).
Post-Transcriptional Gene Silencing of the P23 Silencing Suppressor of Citrus
Tristeza Virus Confers Resistance to the Virus in Transgenic Mexican Lime. Plant
Molecular Biology,Vol.60, No.2, pp 153-165
Fagoaga C.; Lopez C.; Moreno P.; Navarro L.; Flores R. & Pena L. (2005). Viral-Like
Symptoms Induced by the Ectopic Expression of the P23 Gene of Citrus Tristeza
Virus Are Citrus Specific and Do Not Correlate with the Pathogenicity of the Virus
Strain. Molecular Plant-Microbe Interactions,Vol.18, No.5, pp 435-445
FAO (2011). Citrus Fruit Production. Food And Agriculture Organization (FAO) Of The United
Nations, FAOSTAT. 2009. http://faostat.fao.org
Febres V. J.; Lee R. F. & Moore G. A. (2008). Transgenic Resistance to Citrus Tristeza Virus in
Grapefruit. Plant Cell Reports,Vol.27, No.1, pp 93-104
Febres V. J.; Niblett C. L.; Lee R. F. & Moore G. A. (2003). Characterization of Grapefruit
Plants (Citrus paradisi Macf.) Transformed with Citrus Tristeza Closterovirus Genes.
Plant Cell Reports,Vol.21, No.5, pp 421-428
Fleming G. H.; Olivares-Fuster O.; Del-Bosco S. F. & Grosser J. W. (2000). An Alternative
Method for the Genetic Transformation of Sweet Orange. In Vitro Cellular &
Developmental Biology - Plant,Vol.36, No.6, pp 450-455
Folimonov A. S.; Folimonova S. Y.; Bar-Joseph M. & Dawson W. O. (2007). A Stable RNA
Virus-Based Vector for Citrus Trees. Virology,Vol.368, No.1, pp 205-216
Gelvin S. B. (2003). Agrobacterium-Mediated Plant Transformation: The Biology Behind the
"Gene-Jockeying" Tool. Microbiology and Molecular Biology Reviews,Vol.67, No.1, pp
16-37
Ghorbel R.; Domínguez A.; Navarro L. & Peña L. (2000). High Efficiency Genetic
Transformation of Sour Orange (Citrus aurantium) and Production of Transgenic
Trees Containing the Coat Protein Gene of Citrus Tristeza Virus. Tree
Physiology,Vol.20, No.17, pp 1183-1189
Gonsalves D. (1998). Control of Papaya Ringspot Virus in Papaya: A Case Study. Annual
Review of Phytopathology,Vol.36, pp 415-437

118

Genetic Transformation

Grosser J. W.; Jiang J.; Louzada E. S.; Chandler J. L. & Gmitter F. G. (1998a). Somatic
Hybridization, an Integral Component of Citrus Cultivar Improvement: II.
Rootstock Improvement. Hortscience,Vol.33, No.6, pp 1060-1061
Grosser J. W.; Jiang J.; Mourao F. D. A.; Louzada E. S.; Baergen K.; Chandler J. L. & Gmitter
F. G. (1998b). Somatic Hybridization, an Integral Component of Citrus Cultivar
Improvement: I. Scion Improvement. Hortscience,Vol.33, No.6, pp 1057-1059
Gutierrez-E M. A.; Luth D. & Moore G. A. (1997). Factors Affecting Agrobacterium-Mediated
Transformation in Citrus and Production of Sour Orange (Citrus aurantium L.)
Plants Expressing the Coat Protein Gene of Citrus Tristeza Virus. Plant Cell
Reports,Vol.16, No.11, pp 745-753
He Y. R.; Chen S. C.; Peng A. H.; Zou X. P.; Xu L. Z.; Lei T. G.; Liu X. F. & Yao L. X. (2011).
Production and Evaluation of Transgenic Sweet Orange (Citrus sinensis Osbeck)
Containing Bivalent Antibacterial Peptide Genes (Shiva A and Cecropin B) Via a
Novel Agrobacterium-Mediated Transformation of Mature Axillary Buds. Scientia
Horticulturae,Vol.128, No.2, pp 99-107
Hidaka T. & Omura M. (1993). Agrobacterium-Mediated Transformation and Regeneration of
Citrus Spp. From Suspension Cells. Journal of the Japanese Society for Horticultural
Science,Vol.62, No.2, pp 371-376
Jacobsen E. & Schouten H. J. (2008). Cisgenesis, a New Tool for Traditional Plant Breeding,
Should Be Exempted from the Regulation on Genetically Modified Organisms in a
Step by Step Approach. Potato Research,Vol.51, No.1, pp 75-88
Jajoo A. (2010). In Vitro Propagation of Citrus limonia Osbeck through Nucellar Embryo
Culture. Current Research Journal of Biological Sciences,Vol.2 No.1, pp 6-8
Jha S. & Chattoo B. (2010). Expression of a Plant Defensin in Rice Confers Resistance to
Fungal Phytopathogens. Transgenic Research,Vol.19, No.3, pp 373-384
Jha S.; Tank H.; Prasad B. & Chattoo B. (2009). Expression of Dm-Amp1 in Rice Confers
Resistance to Magnaporthe oryzae and Rhizoctonia solani. Transgenic Research,Vol.18,
No.1, pp 59-69
Kaneyoshi J.; Kobayashi S.; Nakamura Y.; Shigemoto N. & Doi Y. (1994). A Simple and
Efficient Gene-Transfer System of Trifoliate Orange (Poncirus trifoliata Raf). Plant
Cell Reports,Vol.13, No.10, pp 541-545
Khan I. A. (2007). Citrus Genetics, Breeding and Biotechnology (CABI, Wallingford, UK ;
Cambridge, MA) 370 p.
Khawale R. N.; Singh S. K.; Garg G.; Baranwal V. K. & Ajirlo S. A. (2006). AgrobacteriumMediated Genetic Transformation of Nagpur Mandarin (Citrus reticulata Blanco).
Current Science,Vol.91, No.12, pp 1700-1705
Kinkema M.; Fan W. & Dong X. (2000). Nuclear Localization of NPR1 Is Required for
Activation of PR Gene Expression. The Plant Cell,Vol.12, No.12, pp 2339-2350
Kobayashi A. K. (2003). Plant Regeneration of Sweet Orange (Citrus sinensis) from Thin
Sections of Mature Stem Segments. In Vitro,Vol.74, No.1, pp 99-102
Kobayashi S. & Uchimaya H. (1989). Expression and Integration of a Foreign Gene in
Orange (Citrus sinensis Osb.) Protoplasts by Direct DNA Transfer. Japanese Journal of
Genetics,Vol.64, No.2, pp 91-97
Lee E. K.; Jin Y. W.; Park J. H.; Yoo Y. M.; Hong S. M.; Amir R.; Yan Z.; Kwon E.; Elfick A.;
Tomlinson S.; Halbritter F.; Waibel T.; Yun B. W. & Loake G. J. (2010). Cultured

Citrus Transformation: Challenges and Prospects

119

Cambial Meristematic Cells as a Source of Plant Natural Products. Nature
Biotechnology,Vol.28, No.11, pp 1213-1217
Li D. D.; Shi W. & Deng X. X. (2002). Agrobacterium-Mediated Transformation of
Embryogenic Calluses of Ponkan Mandarin and the Regeneration of Plants
Containing the Chimeric Ribonuclease Gene. Plant Cell Reports,Vol.21, No.2, pp 153156
Lin W. C.; Lu C. F.; Wu J. W.; Cheng M. L.; Lin Y. M.; Yang N. S.; Black L.; Green S. K.; Wang
J. F. & Cheng C. P. (2004). Transgenic Tomato Plants Expressing the Arabidopsis
NPR1 Gene Display Enhanced Resistance to a Spectrum of Fungal and Bacterial
Diseases. Transgenic Research,Vol.13, No.6, pp 567-581
López C.; Cervera M.; Fagoaga C.; Moreno P.; Navarro L.; Flores R. & Peña L. (2010).
Accumulation of Transgene-Derived Sirnas Is Not Sufficient for RNAi-Mediated
Protection against Citrus Tristeza Virus in Transgenic Mexican Lime. Molecular plant pathology,Vol.11, No.1, pp 33-41
Luth D. & Moore G. A. (1999). Transgenic Grapefruit Plants Obtained by Agrobacterium tumefaciens-Mediated Transformation. Plant Cell, Tissue and Organ Culture,Vol.57,
No.3, pp 219-222
Maul P.; McCollum G. T.; Popp M.; Guy C. L. & Porat R. (2008). Transcriptome Profiling of
Grapefruit Flavedo Following Exposure to Low Temperature and Conditioning
Treatments Uncovers Principal Molecular Components Involved in Chilling
Tolerance and Susceptibility. Plant Cell Environ,Vol.31, No.6, pp 752-768
Messens E.; Dekeyser R. & Stachel S. E. (1990). A Nontransformable Triticum monococcum
Monocotyledonous Culture Produces the Potent Agrobacterium Vir-Inducing
Compound Ethyl Ferulate. Proceedings of the National Academy of Sciences of the
United States of America,Vol.87, pp 4368-4372
Molinari H.; Bespalhok J. C.; Kobayashi A. K.; Pereira L. F. P. & Vieira L. G. E. (2004).
Agrobacterium Tumefaciens-Mediated Transformation of Swingle Citrumelo
(Citrus paradisi Macf.× Poncirus trifoliata L. Raf.) Using Thin Epicotyl Sections.
Scientia Horticulturae,Vol.99, No.3-4, pp 379-385
Moore G. A.; Jacono C. C.; Neidigh J. L.; Lawrence S. D. & Cline K. (1992). AgrobacteriumMediated Transformation of Citrus Stem Segments and Regeneration of Transgenic
Plants. Plant Cell Reports,Vol.11, No.5-6, pp 238-242
Moreira-Dias J. M.; Molina R. V.; Bordón Y.; Guardiola J. L. & García-Luis A. (2000). Direct and Indirect Shoot Organogenic Pathways in Epicotyl Cuttings of Troyer Citrange
Differ in Hormone Requirements and in Their Response to Light. Annals of
Botany,Vol.85, No.1, pp 103-110
Moreno P.; Ambros S.; Albiach-Marti M. R.; Guerri J. & Pena L. (2008). Citrus Tristeza Virus:
A Pathogen That Changed the Course of the Citrus Industry. Molecular Plant
Pathology,Vol.9, No.2, pp 251-268
Nishikawa F.; Endo T.; Shimada T.; Fujii H.; Shimizu T.; Kobayashi Y.; Araki T. & Omura M.
(2010). Transcriptional Changes in Cift-Introduced Transgenic Trifoliate Orange
(Poncirus trifoliata L. Raf.). Tree Physiology,Vol.30, No.3, pp 431-439
Notaguchi M.; Abe M.; Kimura T.; Daimon Y.; Kobayashi T.; Yamaguchi A.; Tomita Y.; Dohi
K.; Mori M. & Araki T. (2008). Long-Distance, Graft-Transmissible Action of

120

Genetic Transformation

Arabidopsis Flowering Locus T Protein to Promote Flowering. Plant & Cell
Physiology,Vol.49, No.11, pp 1645-1658
Notaguchi M.; Daimon Y.; Abe M. & Araki T. (2009). Graft-Transmissible Action of
Arabidopsis Flowering Locus T Protein to Promote Flowering. Plant Signaling &
Behavior,Vol.4, No.2, pp 123-125
Parrott W. (2010). Genetically Modified Myths and Realities. New Biotechnology,Vol.27, No.5, pp 545-551
Peña L.; Cervera M.; Fagoaga C.; Romero J.; Juárez J.; Pina J. A. & Navarro L. (2007). Citrus.
Biotechnology in Agriculture and Forrestry Vol.60, pp 35-50.
Peña L.; Cervera M.; Juarez J.; Navarro A.; Pina J. A.; Duranvila N. & Navarro L. (1995a).
Agrobacterium-Mediated Transformation of Sweet Orange and Regeneration of
Transgenic Plants. Plant Cell Reports,Vol.14, No.10, pp 616-619
Peña L.; Cervera M.; Juarez J.; Navarro A.; Pina J. A. & Navarro L. (1997). Genetic
Transformation of Lime (Citrus aurantifolia Swing): Factors Affecting
Transformation and Regeneration. Plant Cell Reports,Vol.16, No.11, pp 731-737
Peña L.; Cervera M.; Juarez J.; Ortega C.; Pina J. A.; Duran-Vila N. & Navarro L. (1995b).
High Efficiency Agrobacterium-Mediated Transformation and Regeneration of
Citrus. Plant Science,Vol.104, No.2, pp 183-191
Peña L.; Martin-Trillo M.; Juarez J.; Pina J. A.; Navarro L. & Martinez-Zapater J. M. (2001).
Constitutive Expression of Arabidopsis Leafy or Apetala1 Genes in Citrus Reduces
Their Generation Time. Nature Biotechnology,Vol.19, No.3, pp 263-267
Peña L.; Perez R. M.; Cervera M.; Juarez J. A. & Navarro L. (2004). Early Events in
Agrobacterium-Mediated Genetic Transformation of Citrus Explants. Annals of
Botany,Vol.94, No.1, pp 67-74
Peña L. & Séguin a. (2001). Recent Advances in the Genetic Transformation of Trees. Trends in Biotechnology,Vol.19, No.12, pp 500-506
Ramamoorthy V.; Cahoon E. B.; Li J.; Thokala M.; Minto R. E. & Shah D. M. (2007).
Glucosylceramide Synthase Is Essential for Alfalfa Defensin-Mediated Growth
Inhibition but Not for Pathogenicity of Fusarium graminearum. Molecular
Microbiology,Vol.66, No.3, pp 771-786
Reyes C. A.; De Francesco A.; Pena E. J.; Costa N.; Plata M. I.; Sendin L.; Castagnaro A. P. &
Garcia M. L. (2011). Resistance to Citrus Psorosis Virus in Transgenic Sweet Orange
Plants Is Triggered by Coat Protein-Rna Silencing. Journal of Biotechnology,Vol.151,
No.1, pp 151-158
Rodríguez A.; Cervera M.; Peris J. E. & Peña L. (2008). The Same Treatment for Transgenic
Shoot Regeneration Elicits the Opposite Effect in Mature Explants from Two
Closely Related Sweet Orange (Citrus sinensis (L.) Osb.) Genotypes. Plant Cell,
Tissue and Organ Culture,Vol.93, No.1, pp 97-106
Rommens C. M.; Haring M. A.; Swords K.; Davies H. V. & Belknap W. R. (2007). The
Intragenic Approach as a New Extension to Traditional Plant Breeding. Trends in
Plant Science,Vol.12, No.9, pp 397-403
Sahin-Cevik M. & Moore G. A. (2006). Identification and Expression Analysis of ColdRegulated Genes from the Cold-Hardy Citrus Relative Poncirus trifoliate (L.) Raf.
Plant Molecular Biology,Vol.62, No.1-2, pp 83-97

Citrus Transformation: Challenges and Prospects

121

Singh S. & Rajam M. V. (2009). Citrus Biotechnology: Achievements, Limitations and Future
Directions. Physiology and Molecular Biology of Plants,Vol.15, No.1, pp 3-22
Singh S.; Ray B. K.; Bhattacharyya S. & Deka P. C. (1994). In Vitro Propagation of Citrus reticulata Blanco and Citrus limon Burm.F. Hortscience,Vol.29, No.3 pp 214-216
Sitaram N. & Nagaraj R. (1999). Interaction of Antimicrobial Peptides with Biological and
Model Membranes: Structural and Charge Requirements for Activity. Biochimica et
Biophysica Acta (BBA) - Biomembranes,Vol.1462, No.1-2, pp 29-54
Sitaram N. & Nagaraj R. (2002). Host-Defense Antimicrobial Peptides: Importance of
Structure for Activity. Current Pharmaceutical Design,Vol.8, No.9, pp 1381-6128
Spencer P. A. & Towers G. H. N. (1991). Restricted Occurrence of Acetophenone Signal
Compounds. Phytochemistry,Vol.30, No.9, pp 2933-2937
Spolaore S.; Trainotti L. & Casadoro G. (2001). A Simple Protocol for Transient Gene
Expression in Ripe Fleshy Fruit Mediated by Agrobacterium. Journal of experimental botany,Vol.52, No.357, pp 845-850
Stegemann S. & Bock R. (2009). Exchange of Genetic Material between Cells in Plant Tissue
Grafts. Science,Vol.324, No.5927, pp 649-651
Sundar I. K. & Sakthivel N. (2008). Advances in Selectable Marker Genes for Plant
Transformation. Journal of Plant Physiology,Vol.165, No.16, pp 1698-1716
Sweet J. (2009). The 10th International Symposium on the Biosafety of Genetically Modified
Organisms (Isbgmo), Wellington, New Zealand, November 2008. Environmental
Biosafety Research,Vol.8, No.3, pp 161-181
Talon M. & Gmitter Jr F. G. (2008). Citrus Genomics. International Journal of Plant
Genomics,Vol.2008, pp Article ID 528361
USDA (2010). Adoption of Genetically Engineered Crops in the U.S. Economic Research
Service, Data Set. http://www.ers.usda.gov/Data/BiotechCrops/
Vardi A.; Bleichman S. & Aviv D. (1990). Genetic Transformation of Citrus Protoplasts and
Regeneration of Transgenic Plants. Plant Science,Vol.69, No.2, pp 199-206
Villemont E.; Dubois F.; Sangwan R. S.; Vasseur G.; Bourgeois Y. & SangwanNorreel B. S.
(1997). Role of the Host Cell Cycle in the Agrobacterium-Mediated Genetic
Transformation of Petunia: Evidence of an S-Phase Control Mechanism for T-DNA
Transfer. Planta,Vol.201, No.2, pp 160-172
Xia Y.; Suzuki H.; Borevitz J.; Blount J.; Guo Z.; Patel K.; Dixon R. A. & Lamb C. (2004). An
Extracellular Aspartic Protease Functions in Arabidopsis Disease Resistance
Signaling. The EMBO journal,Vol.23, No.4, pp 980-988
Yang L.; Hu C.; Li N.; Zhang J.; Yan J. & Deng Z. (2011). Transformation of Sweet Orange
[Citrus sinensis (L.) Osbeck] with PthA-nls for Acquiring Resistance to Citrus
Canker Disease. Plant Molecular Biology,Vol.75, No.1-2, pp 11-23
Yao J. L.; Wu J. H.; Gleave A. P. & Morris B. A. M. (1996). Transformation of Citrus
Embryogenic Cells Using Particle Bombardment and Production of Transgenic
Embryos. Plant Science,Vol.113, No.2, pp 175-183
Yeamn M. R. & Yount N. Y. (2003). Mechanisms of Atnimicrobial Peptide Action and
Resistance. Pharmacoloy Reviews,Vol.55, No.1, pp 27-55
Yu C. H.; Huang S.; Chen C. X.; Deng Z. N.; Ling P. & Gmitter F. G. (2002). Factors Affecting
Agrobacterium-Mediated Transformation and Regeneration of Sweet Orange and
Citrange. Plant Cell Tissue and Organ Culture,Vol.71, No.2, pp 147-155

122

Genetic Transformation

Zhang X. D.; Francis M. I.; Dawson W. O.; Graham J. H.; Orbovic V.; Triplett E. W. & Mou Z.
L. (2010). Over-Expression of the Arabidopsis NPR1 Gene in Citrus Increases
Resistance to Citrus Canker. European Journal of Plant Pathology,Vol.128, No.1, pp
91-100
Zhang Y. L.; Fan W. H.; Kinkema M.; Li X. & Dong X. N. (1999). Interaction of NPR1 with
Basic Leucine Zipper Protein Transcription Factors That Bind Sequences Required for Salicylic Acid Induction of the PR-1 Gene. Proceedings of the National Academy of
Sciences of the United States of America,Vol.96, No.11, pp 6523-6528

6
Evaluation of Factors Affecting European Plum
(Prunus domestica L.) Genetic Transformation
Yuan Song1,4, Fatih Ali Canli2, Farida Meerja3,4, Xinhua Wang3,4,
Hugh A. L. Henry3, Lizhe An1 and Lining Tian4
1School

of Life Sciences, Lanzhou University, Lanzhou, Gansu
2Department of Horticulture, Faculty of Agriculture,
Suleyman Demirel University, Cunur/Isparta
3Department of Biology, University of Western Ontario,
4Southern Crop Protection and Food Research Centre
Agriculture and Agri-Food Canada
1China
2Turkey
3,4Canada

1. Introduction
With the advancement of genomics research, many genes have been identified and cloned from various plants. Transfer of these genes into plants for gene function studies and for plant improvement is important in the post-genomics era. At this time, the lack of efficient, effective, and high throughput genetic transformation systems in many crops and varieties is a major barrier and a challenge in functional genomics research and for plant trait improvement via biotechnology (Petri and Burgos 2005). Studies and understanding of different aspects and factors in plant transformation are important and are a prerequisite in the development of effective and efficient transformation technologies for various crops and varieties (Gill et al. 2004; Petri and Burgos 2005).
European plum (Prunus domestica L.) is an economically important fruit crop and is widely grown across the world (Hartmann 1994; Okie and Ramming 1999; Kaufmane et al. 2002).
There have been a number of technology reports of European plum genetic transformation via Agrobacterium tumefaciens using hypocotyls as explants (Mante et al. 1991; Padilla et al.
2003; Petri et al. 2008). These studies were actually all conducted in a single research laboratory. Several studies have reported use of transgenic plum for disease resistance
(Scorza et al. 1994; 2001; Ravelonandro et al. 2000; Hily et al. 2004; Malimowski et al. 1998,
2006; Capote et al. 2008), however, transgenic plum plants used in these studies were apparently generated in the same research laboratory indicated before. Several other laboratories have reported plum transformation but only putative transformants were reported and Southern blot and other related analyses, which were essential for confirmation of transformation, were not provided (Da Camara-Machado et al. 1994;
Yancheva et al. 2002). Use of leaves as explants for plum transformation was described recently but again Southern blot analysis was not provided to confirm transformation

124

Genetic Transformation

(Kikhailov et al., 2008). Indeed, European plum genetic transformation has only been successful in a few laboratories. Tian et al. (2006) evaluated in vitro regeneration of
European plum germplasms and varieties adapted to high latitude and developed genetic transformation technology for these types of plum plants via hopcotyl regeneration (Tian et al. 2009). Nevertheless, at this time, wide and practical use of plum genetic transformation technology in many other laboratories and studies is still not feasible and is difficult. In addition, transformation of European plum has been reported in only a few varieties and the efficiency is low. Development of transformation technologies for many commercial plum varieties and improvement of transformation technology for high efficiency are still major tasks and also important for the germplasm improvement of European plum via biotechnology. Plant transformation is a complicated process which involves various factors, such as plant genotype and variety, regeneration efficiency, culture medium and condition, selectable marker, infection condition, gene construct and Agrobacterium strain. Any of these factors can be important in the success of transformation. Studying, understanding and optimizing various factors are important for the development of transformation technologies for different germplasms and varieties and for technology improvement (Gill et al. 2004; Petri and Burgos 2005).
The objective of this research was to study important aspects of Agrobacterium-mediated genetic transformation in European plum via hypocotyl regeneration system. The research results contribute to the knowledge advancement of plum transformation and are useful for the development and improvement of transformation technologies for different varieties for
European plum improvement, especially for the genotypes and germplasms adapted to high latitude. 2. Materials and methods
2.1 Plant materials
Plum (Prunus domestica L.) plants adapted to high latitude were used in this study. These types of plum germplasms and varieties have been developed by Canadian Prunus breeding program over the past years. These genotypes and varieties are more resistant to cold weather, the fruit development and maturation of these genotypes are relative slow, and the fruit ripening is also relatively late in the season (Dr. J. Submaranian, Prunus tree breeding program, person. communication). Our previous studies indicate that these plums have low response to in vitro regeneration (Tian et al. 2006) and the genetic transformation efficiency is also low (Tian et al. 2009).
Plum fruits, two weeks prior to maturation, were collected from plum trees in Vineland,
Ontario, Canada. Endocarps were cracked open and the seeds were sterilized in 10% commercial bleach solution. The seeds were then rinsed three times with sterile distilled water in the laminar flow hood and were imbibed in final rinsing water overnight. After a removal of the seed coat, the embryonic axis was excised from the cotyledons. Embryonic axis was cut into five sections with one radicle, three hypocotyls and one epicotyl.
Hypocotyl and epicotyl segments were employed in transient gene expression studies while the radicle was discarded. For stable transformation studies, only hypocotyl slices were used in the experiments. Transformation was conducted using hypocotyls as explants as described by Mante et al. (1991) and Padilla et al. (2003) with modifications by Tian et al.
(2009) and in this study.

Evaluation of Factors Affecting European Plum (Prunus domestica L.) Genetic Transformation

125

2.2 Agrobacterium and vectors
Three Agrobacterium tumefaciens strains, namely EHA105 (Hood et al.1993), LBA4404
(Hoekema et al. 1983) and GV3101 (Holster et al. 1980) and five vectors were included in the research. The vector pCAMBIA2301 (pC2301) has the GUS (uidA) reporter gene coding for β-glucuronidase and the nptII gene coding for neomycin phosphotransferase under the control of the 35S promoters in the following order: 35S- uidA -35S-nptII. The plasmid pCAMBIA1301 (pC1301) carries the GUS reporter gene and the hpt gene coding for hygromycin B phosphotransferase under the control of the 35S promoters in the following order: 35S- uidA -35S-hpt. The two vectors are the same except for the selectable marker. The
GUS gene in these pCAMBIA vectors contains a plant specific intron which can only be recognized in plant cells and thus cannot express in Agrobacterium. The constructs pPV1, pPV2, and pPV3 carry the genes of interest (not shown, unpublished constructs) other than the nptII marker gene. These genes were cloned using proper restriction enzymes into the pCaMter X vector and the constructs were introduced in Agrobacterium strains LBA4404 and
GV3101, respectively.
2.3 Agrobacterium infection and plant transformation
Agrobacterium was grown in LB medium with appropriate antibiotics to optimal OD600 reading. Explants were immersed in Agrobacterium solution for 30 minutes and were blotted dry on sterile Whatman filter paper. The explants were then transferred on co-culture MS medium. The co-culture medium consisted of MS salts (Murashige and Skoog 1962) supplemented with 2.5 µM indolebutyric acid (IBA), 555 µM myo-inositol, 1.2 µM thiamine
HCl, 1.4 µM nicotinic acid, 2.4 µM pyridoxine HCl, 25 g L-1 sucrose, and 7 g L-1 Bactogar. The pH of the medium was adjusted to 5.9 prior to autoclaving. Thidiazuron (TDZ, 7.5 µM) was added to the medium after autoclaving. Different antibiotics and other chemicals were added to the culture medium as needed. The culture was maintained at 25±1°C with 16 hour photoperiod supplied by fluorescent Sylvania “Cool White” light with a Photosynthetic
Photon Flux of about 50µmol.m-2.s-1. The explants were collected five days after the infection for transient expression studies. For stable transformation, explants were maintained on cocultivation MS medium for one week. After co-cultivation, the explants were transferred onto the shoot induction medium. Shoot induction media was the same as the co-cultivation medium but contained 75 mg L-1 kanamycin or 5 mg L-1 hygromycin depending on the transformation vector used and 300 mg L-1 timentin was added to the media. The explants were sub-cultured on fresh induction medium every three weeks. For evaluation of medium type on transformation, B5 medium (Gamborg et al. 1968) was included in the research and other chemicals were added in to B5 medium as in MS medium.
Regenerated shoots at about 0.5 -1 cm in length from antibiotic selections were excised from the explants and transferred to fresh shoot induction medium containing the same antibiotics as well as timetin. After another 2-3 subcultures, well established and developed shoots in antibiotic-containing medium were placed in Magenta boxes containing rooting medium. The rooting medium consisted of 1/2-strength MS salts (Murashige and Skoog
1962), 5 µM naphthalene acetic acid (NAA), 0.01 µM kinetin, vitamins (555 µM myo-inositol,
1.2 µM thiamine HCl, 1.4 µM nicotinic acid, 2.4 µM pyridoxine HCl), 10 g L-1 sucrose, and 7 g L-1 Bactoagar. Plants developed in magenta containers were transferred to soil and plants were established in a greenhouse. Plants were analyzed for transformation using different approaches as described in previous studies (Tian et al. 2009).

126

Genetic Transformation

2.4 Histochemical and Fluorogenic GUS expression assay
Five days after Agrobacterium infection, explants were collected from co-cultivation media and incubated in 5-bromo-4-chloro-indolyl β-D-glucuronide (X-Glu) in 100 mM sodium phosphate buffer, pH 7.0 overnight at 37oC. Histochemical GUS analysis followed the procedure described in Jefferson et al. (1987). The GUS expression was scaled from 1 - 3 depending on the intensity of GUS staining, with 1 the minimum and 3 the maximum.
For fluorometric GUS expression, plant tissues five days after Agrobacterium infection were ground in liquid nitrogen with a pestle and a mortar. A volume of 50 µL of the crude extract was incubated at 37°C with 1 mM 4-methylumbelliferyl glucuronide (MUG) in 0.3 mL of
GUS assay buffer (50 mM NaPO4, pH 7.0, 10 mM EDTA, 0.1% [v/v] Triton X-100, 10 mM βmercaptoethanol). At different time periods of incubation, 0.1 mL aliquot was removed and added to 1.9 ml of 0.2 M Na2CO3 to terminate the reaction. Protein standard curve was made by Bradford protein assay and GUS activity was expressed as picomoles of 4methylumbelliferone (MU) per milligram of protein per hour.

3. Results and discussion
Efficient infection of Agrobacterium to plant cells and the subsequent transfer of T-DNA from
Agrobacterium into plant cells are the first and also essential steps in the stable transformation process. Transient reporter gene expression can be used to evaluate
Agrobacterium infection and gene transfer into plants cells. The relationship between transient and stable transformation is complicated and varies among species. Studies must be conducted for a particular species to understand how these two aspects are related. If a positive relation can be found and established for a plant species, study of transient reporter gene expression can be very useful for evaluation of various factors for development and optimization of genetic transformation technologies (Chen et al. 1998; Petri et al. 2004).
The plum explants were infected with different Agrobacterium strains containing construct pC2301 or pC1301. These constructs carry the GUS-intron design and GUS expression is only activated in plant cells and the GUS expression cannot be due to the presence of
Agrobacterium cells. Histochemical assay was first conducted to evaluate transient GUS expression in explants infected by different Agrobacterium strains and plum varieties Stanley and Vanette were used in the experiments. Results showed that GUS expression was significantly higher when Agrobacterium strains LBA4404 and EHA105 were used (Fig. 1,
Fig. 2). Enzymatic assay was then conducted in plum Stanley and the results showed that
GUS expression in explants was significantly higher using Agrobacterium strains LBA4404 and EHA105 than using GV3101 (Fig.3). Research was also conducted to evaluate transient
GUS expression using some additional plum varieties including V72511, Veeblue, and
Italian. Results showed that explants infected with Agrobacterium strains LBA4404 and
EHA105 in overall exhibited higher levels of GUS enzyme activities than GV3101 (not shown). Stable transformation were conducted with either kanamycin selection or hygromycin selection depending on the vectors used. It appeared that transient reporter gene expression was well related to the effectiveness of stable transformation in plum (Table 1, Fig. 2&3).
Specifically, higher levels of transient GUS expression after EHA105 and LBA4404 infection led to the effectiveness of stable transformation and consistently generated transgenic lines
(Table 1). On the other hand, lower transient GUS expression using strain GV3101 resulted in ineffectiveness of stable transformation (Table 1, Fig. 2&3). Such relation is consistent

Evaluation of Factors Affecting European Plum (Prunus domestica L.) Genetic Transformation

127

using different constructs and with either the kanamycin selection or the hygromycin selection (Table 1).

Fig. 1. Transient GUS expression in European plum (Prunus domestica L.) after infection by
Agrobacterium strains LBA4404, EHA105 and GV3101 containing either pCAMBIA2301 or pCAMBIA1301 plasmids.

Fig. 2. Histochemical analysis of GUS gene expression in Stanley and Vanette varieties infected by different Agrobacterium strains containing either pCAMBIA2301 or pCAMBIA1301 vector.

128

Genetic Transformation

Fig. 3. GUS gene expression via fluorometric assay with Stanley after infection by different
Agrobacterium strains containing either pCAMBIA2301 or pCAMBIA1301 vector.

Vector pC2301 pC1301

Agrobacterium
Strain
EHA105
LBA4404
GV3101
EHA105
LBA4404
GV3101

Selection scheme Kanamycin
Kanamycin
Kanamycin
Hygromycin
Hygromycin
Hygromycin

No of
Explants
272
270
272
272
271
272

No. of
Transformants
6
2
0
3
2
0

Transformation
Efficiency
2.2%
0.7%
0%
1.1%
0.7%
0%

Table 1. Stable transformation of European plum using and Agrobacterium strains
LBA4404, EHA105 and GV3101 containing either pCAMBIA2301 or pCAMBIA1301 vector. L-cysteine
(mg/L)

Number of explants 0
900

78
78

% of explants transiently expressing GUS gene 80.0
22.7

Number of transgenic line

Transformation efficiency 2
0

2.6%
0

Table 2. Transient GUS expression and stable transformation of European plum using Lcysteine in culture medium.

Evaluation of Factors Affecting European Plum (Prunus domestica L.) Genetic Transformation

129

Our previous studies have indicated that use of culture medium including L-cysteine, which was used in media for transformation improvement (Olhoft et al. 2001), could affect transient GUS gene expression in plum (non-published results). We conducted research to study how transient gene expression was related to stable transformation using medium containing L-cysteine. The results showed that explants cultured in medium with L-cysteine resulted in significantly low levels of transient GUS gene expression (Table 2) as found in previous studies. No transformation was obtained from the explants cultured in the presence of L-cysteine. On the other hand, high level of transient GUS expression was observed in explants without L-cysteine treatment and stable transformation was routinely recovered (Table 2). This study further indicated that transient reporter gene expression was related to stable transformation in European plum. The positive relationship between transient reporter gene expression and stable transformation in plum could be important for studying and evaluating various factors and conditions for transformation, which can be useful in the development and improvement of stable transformation technologies in different plum varieties.

Construct pPV-1 pPV-2

pPV-3

Summary

Agro strain

No. of total explants Lines recovered Efficiency

GV3101

444

0

0.0%

LBA4404

1019

17

1.7%

GV3101

330

1

0.3%

LBA4404

601

11

1.8%

GV3101

283

0

0.0%

LBA4404

769

20

2.6%

GV3101

1057

1

0.09%

LBA4404

2389

48

2.0%

Table 3. Stable genetic transformation of European plum using Agrobacterium strains
LBA4404 and GV3101 containing different transformation vectors with the genes of interest

Medium

Number of explants Number of transgenic lines

Transformation efficiency (%)

MS

300

6

2.0

B5

310

19

6.1

Table 4. Plum genetic transformation using B5 and MS co-cultivation and shoot induction media. 130

Genetic Transformation

Agrobacterium strain is a major factor in plant transformation. Numerous studies have indicated that the effectiveness of transformation via different strains of Agrobacterium can be significantly different (e.g., De Bondt et al. 1994; Le Gall et al. 1994; Bond and Rose 1998;
Cervera et al. 1998; Gill et al. 2004; Petri et al. 2004; Joyce et al. 2010). Several Agrobacterium strains, including LBA4404, EHA101, EHA105, GV3101, have been used in plum transformation previously (Mante et al. 1991; Padilla et al. 2003; Petri et al. 2008). No transformation efficiency difference was found using EHA105 and LBA4404 (Padilla et al
2003). Petri et al. (2008) conducted plum transformation using EHA105 and GV3101. The study showed that use of the same Agrobacterium strains carrying different transformation constructs resulted in significant difference of transformation efficiency (Petri et al. 2008).
This difference in the transformation efficiency could be due to the presence of the different constructs. Till date, the effect of Agrobacterium strains on plum transformation is still not well understood. In this research we studied two Agrobacterium strains, LBA4404 and
GV3101, which have never been directly compared in plum transformation. These two strains, in contrast to the study by Petri et al (2008), carried the identical constructs and transformation was conducted using a large number of explants. No stable transformation was achieved with constructs pPV-1 and pPV-3 when the strain GV3101 was used, whereas with strain LBA4404, the transformation efficiencies with these constructs were 1.7% and
2.6%, respectively (Table 3). Of the three constructs, only one transformant was recovered using GV3101 (Table 3). Combining the results of all three constructs and all experiments, the transformation efficiency with LAB4401 was 22 times higher than that using GV3101
(Table 3). The different transformation efficiencies of Agrobacterium strains can also be observed in the study of transient gene expression and stable transformation described before (Fig. 2,3; Table 1). The results showed that Agrobacterium strain LBA4404 was much more effective and was more suitable than GV3101 in plum transformation. The study suggests that Agrobacterium strains can be an important factor in plum transformation and should be carefully considered for various studies and for transformation of different plum varieties. Effective plum transformation using Agrobacterium strain LBA4404 is illustrated in
Fig. 4.
Plant genetic transformation is usually conducted via tissue culture systems. The culture medium is the platform and the fundamental base of transformation. Medium can be an important factor for plant transformation (Joyce et al. 2010). There is not report regarding the effect of different culture media on plum genetic transformation. We conducted research on this aspect. Two commonly used culture media, B5 medium and MS medium, and construct pCAMBIA2301 were used in the research. Explants, after Agrobacterium infection, were cultured on MS and B5 co-cultivation media as well as regeneration media respectively. The transformation efficiency using MS medium was 2.0% and the efficiency with B5 medium was 6.1% (Table 4). Use of B5 medium was three times more efficient in plum transformation. Use of different media apparently had a major impact on plum transformation. The B5 medium might have promoted more transformed cells to develop and regenerate into plants, resulting in higher transformation efficiency. A recent study has showed that adding 2, 4-D to culture medium can significantly increase plum transformation efficiency (Petri et al. 2008). This addition of a plant growth regulator probably increased recovery of more transformed cells as discussed in this study. We would conduct experiments to evaluate the effect of 2, 4-D on the transformation of plum genotypes adapted to high latitude.

Evaluation of Factors Affecting European Plum (Prunus domestica L.) Genetic Transformation

131

Fig. 4. European plum using Agrobacterium LBA4404. (A) Development of transgenic shoots on selection medium containing 75 mg·L-1 kanamycin. (B) Shoots excised from explants grew vigorously upon subculturing to the same selection medium. (C) Development of transgenic plants on rooting medium in Magenta boxes. (D) GUS expression in leaves of transgenic plum plants. (E) Transgenic plants in the greenhouse.

132

Genetic Transformation

4. Conclusion
Genetic transformation efficiency in Prunus crops is significantly lower and the technology is much less developed compared to some other fruit crops. We have studied some aspects of plum transformation which have not been explored before. The study shows that the transient gene expression is in general well related to stable transformation in plum. This is important for studying and optimizing various conditions and factors for stable transformation of plum varieties. The study also shows that certain Agrobacterium strains strongly affect European plum genetic transformation. While Agrobacterium strains LBA4404 can lead to successful plum transformation, the strain GV3101 is ineffective in generating transgenic lines. Moreover, use of different types of media can significantly affect stable transformation. The results obtained from this research would contribute to the knowledge advancement and to the development of more efficient and effective transformation technologies for plum fruit crop, especially for germplasms and varieties adapted to high latitude. 5. Acknowledgements
The authors would like to thank Dr. Jay Subramanian for providing plum research materials and for research discussion and Dr. A. Wang for providing some transformation constructs.
We also thank Dr. Ralph Scorza for providing some Agrobacterium strains and for transformation research discussion. We thank Susan Sibbald, Janny Lac and Kaalak Reddy for technical assistance.

6. References
Bond, J. E. and Roose, M. L. 1998. Agrobacterium-mediated transformation of the commercially important citrus cultivar Washington navel orange. Plant Cell Rep.
18:229-234.
Capote, N., Pérez-Panadés, J., Monzó, C., Carbonell, E., Urbaneja, A., Scorza, R.,
Ravelonandro, M. and Cambra, M. 2008. Assessment of the diversity and dynamics of Plum pox virus and aphid populations in transgenic European plums under
Mediterranean conditions. Transgenic Res. 17:367-377.
Cervera, M., Lopez, M. M., Navarro, L. and Pena, L. 1998. Virulence and supervirulence of
Agrobacterium Tumefaciens in woody fruit plants. Physiological and Molecular Plant
Pathology 52:67-78.
Chen, L., Zhang, S., Beachy, R. N. and Fauquet, C. M. 1998. A protocol for consistent, largescale production of fertile transgenic rice plants. Plant Cell Rep. 18:25-31. da Câmara Machado, A., Katinger, H. and Laimer da Câmara Machado, M. 1994. Coat protein-mediated protection against plum pox virus in herbaceous model plants and transformation of apricot and plum. Euphytica 77:129-134.
De Bondt, A., Eggermont, K., Druart, P., De Vil, M., Goderis, I., Vanderleyden, J. and
Broekaert, W. F. 1994. Agrobacterium-mediated transformation of apple (Malus x domestica Borkh.): An assessment of factors affecting gene transfer efficiency during early transformation steps. Plant Cell Rep. 13:587-593.
Gamborg, O. L., Miller, R. A. and Ojima, K. 1968. Nutrient requirements of suspension cultures of soybean root cell. Exp. Cell Research 50:151-158.

Evaluation of Factors Affecting European Plum (Prunus domestica L.) Genetic Transformation

133

Gill, M. I. S., Zora, S. and Agrez, V. 2004. Factors affecting Agrobacterium-mediated genetic transformation in fruit and nut crops - an overview. J. Food, Agriculture &
Environment 2:327-347.
Hartmann, W. 1994. Plum production in Germany. Acta Hort 359:17-25.
Hily, J. M., Scorza, R., Malinowski, T., Zawadzka, B. and Ravelonandro, M. 2004. Stability of gene silencing-based resistance to Plum pox virus in transgenic plum (Prunus domestica L.) under field conditions. Transgenic Res. 13:427-436.
Hoekema, A., Hirsch, P. R., Hooykaas, P. J. J. and Schilperoort, R. A. 1983. A binary plant vector strategy based on separation of vir- and T-region of the Agrobacterium tumefaciens Ti-plasmid. Nature 303:179-180.
Holsters, M., Silva, B., Van Vliet, F., Genetello, C., De Block, M., Dhaese, P., Depicker, A.,
Inzé, D., Engler, G., Villarroel, R. and others. 1980. The functional organization of the nopaline A. tumefaciens plasmid pTiC58. Plasmid 3:212-230.
Hood, E. E., Gelvin, S. B., Melchers, L. S. and Hoekema, A. 1993. New Agrobacterium helper plasmids for gene transfer to plants. Transgenic Res. 2:208-218.
Jefferson, R. A., Kavanaugh, T. A. and Bevan, M. W. 1987. GUS fusions: ß-glucuronidase as a sensitive and versatile gene fusion marker in higher plants. EMBO J. 6:3901-3907.
Joyce, P., Kuwahata, M., Turner, N. and Lakshmanan, P. 2010. Selection system and cocultivation medium are important determinants of Agrobacterium-mediated transformation of sugarcane. Plant Cell Rep. 29:173-183.
Kaufmane, E., Ikase, L., Trajkovski, V. and Lacis, G. 2002. Evaluation and characterization of plum genetic resources in Sweden and Latvia. Acta Hort. 577:207-213.
Kikhailov R.V,Shuga O.A., and Dolgov, S. V. 2008. Genetic transformation os somatic tissues and molecular biology approach for improving resistance to sharka disease of plum
(Prunuc domestica L.) varieties. First International Symposium on Biotechnology of
Fruit Species. September 1-5, 2008. Dreston, Germany.
Le Gall, O., Torregrosa, L., Danglot, Y., Candresse, T. and Bouquet, A. 1994. Agrobacteriummediated genetic transformation of grapevine somatic embryos and regeneration of transgenic plants expressing the coat protein of grapevine chrome mosaic nepovirus (GCMV). Plant Sci. 102:161-170.
Malinowski, T., Zawadzka, B, Ravelonandro, M. and Scorza, R. 1998 Preliminary report on the apparent breaking of resistance of a transgenic plum by chip bud inoculation of
Plum pox virus PPV-S. Acta Virol. 42:241–243
Malinowski, T., Cambra, M., Capote, N., Zawadzka, B, Gorris, M. T., Scorza, R. and
Ravelonandro, M. 2006. Field trials of plum clones transformed with the Plum pox virus coat protein (PPV-CT) gene. Planr Disease 90: 1012-1018.
Mante, S., Morgens, P. H., Scorza, R., Cordts, J. M. and Callahan, A. M. 1991. Agrobacteriummediated transformation of plum (Prunus domestica L.) hypocotyl slices and regeneration of transgenic plants. Bio/Technol 9:853-857.
Murashige, T. and Skoog, F. 1962. A revised medium for rapid growth and bioassay with tobacco tissue cultures. Physiol. Plant. 15:473-497.
Okie, W. R. and Ramming, D. W. 1999. Plum breeding worldwide. HortTechnology 9:162176.
Olhoft, P. M. and Somers, D. A. 2001. L-Cysteine increases Agrobacterium-mediated T-DNA delivery into soybean cotyledonary-node cells. Plant Cell Rep. 20:706-711.

134

Genetic Transformation

Padilla, I. M. G., Webb, K. and Scorza, R. 2003. Early antibiotic selection and efficient rooting and acclimatization improve the production of transgenic plum plants (Prunus
Domestica L.). Plant Cell Rep. 22:38-45.
Petri, C., Alburquerque, N., GarcÃa-Castillo, S., Egea, J. and Burgos, L. 2004. Factors affecting gene transfer efficiency to apricot leaves during early Agrobacteriummediated transformation steps. Journal of Hort. Sci. Biotech. 79:704-712.
Petri, C. and Burgos, L. 2005. Transformation of fruit trees. Useful breeding tool or continued future prospect? Transgenic Res. 14:15-26.
Petri, C., Webb, K., Hily, J. M., Dardick, C. and Scorza, R. 2008. High transformation efficiency in plum (Prunus domestica L.): A new tool for functional genomics studies in Prunus spp. Mole. Breed. 22:581-591.
Ravelonandro, M., Scorza, R., Callahan, A., Levy, L., Jacquet, C., Monsion, M. and
Damsteegt, V. 2000. The Use of Transgenic Fruit Trees as a Resistance Strategy for
Virus Epidemics: the Plum Pox (Sharka) Model. Virus Res. 71:63-69.
Scorza, R., Ravelonandro, M., Callahan, A. M., Cordts, J. M., Fuchs, M., Dunez, J. and
Gonsalves, D. 1994. Transgenic plums (Prunus domestica L.) express the plum pox virus coat protein gene. Plant Cell Rep. 14:18-22.
Scorza R, Callahan A, Levy L, Damsteegt V, Webb K, Ravelonandro M 2001 Posttranscriptional gene silencing in Plum pox virus resistant transgenic European plum containing the Plum pox potyvirus coat protein gene. Transgenic Res.10:201–
209.
Tian, L., Sibbald, S., Subramanian, J and Svircev, S. 2006. Characterization of Prunus domestica L. in vitro regeneration via hypocotyls. Sci. Hort.. 112:462-466.
Tian, L., Canli, F. A., Wang, X. and Sibbald, S. 2009. Genetic transformation of Prunus domestica L. using the hpt gene coding for hygromycin resistance as the selectable marker. Sci. Hort. 119:339-343.
Yancheva, S. D., Druart, P. and Watillon, B. 2002. Agrobacterium - nediated transformation of plum (Prunus domestica L.). Acta Hort. 577:215-217.

7
Genetic Transformation of Wheat:
Advances in the Transformation Method and
Applications for Obtaining Lines with
Improved Bread-Making Quality and
Low Toxicity in Relation to Celiac Disease
Javier Gil-Humanes, Carmen Victoria Ozuna, Santiago Marín,
Elena León, Francisco Barro and Fernando Pistón

Instituto de Agricultura Sostenible,
Agencia Estatal Consejo Superior de Investigaciones Científicas (CSIC),
Spain

1. Introduction
Wheat is one of the most important crops and is counted among the “big three” cereal crops
(rice, wheat and maize), with an annual world production of around 680 million tonnes in
2009. Wheat is also one of the main sources of calories and proteins in the human diet.
However, in spite of its global importance, wheat has been one of the last crops being transformed and it was not until 1992 when Vasil et al. (1992) obtained the first fertile transgenic plant of wheat. Nowadays, wheat transformation still presents more difficulties than transformation of other cereals, such as rice and maize, with lower transformation efficiencies and greater genotype dependence (Shewry & Jones, 2005). Particle bombardment is the most widely used method for genetic transformation of wheat, presenting higher transformation efficiencies than Agrobacterium-mediated transformation
(Lazzeri & Jones, 2009). However, particle bombardment causes physical damage to the scutellar tissues used for transformation, negatively affecting the embryogenesis, in vitro regeneration of the explants and therefore the transformation efficiency. Osmotic treatment is thought to offer protection to bombarded material by minimising cytoplasm leakage from target cells (Vain et al., 1993), so it is of great importance to optimise the duration and moment of application of the osmotic treatment to the explants.
Among the applications of genetic transformation, gene over-expression and posttranscriptional gene silencing (PTGS) are two strategies successfully used to enhance the wheat quality. In particular, the baking quality of wheat, largely determined by the high molecular weight glutenin subunits (HMW-GS), is one of the most important targets for genetic transformation. Transgenic wheat lines expressing additional copies of the 1Ax1,
1Dx5, 1Dy10 HMW-GS genes were obtained by particle bombardment by León et al.
(2009) (Fig. 1 A). In addition, new lines combining the three transgenic events were obtained by conventional crossing (León et al., 2010) (Fig. 1 B). Therefore, a set of

136

Genetic Transformation

transgenic wheat lines expressing one or two extra HMW-GS was generated. These lines were analysed and changes in the protein and starch composition were studied. In addition, the rheological and pasting properties of dough were substantially improved or altered by expressing those HMW-GS genes as described in León et al. (2009, 2010a,
2010b).
The transgenic line T619, which presents down-regulation of all the HMW-GS, was obtained when aimed to over-express a D hordein from Hordeum chilense in Triticum aestivum cv
Perico. D hordeins from H. chilense have a very similar structure and amino acid sequence to the HMW-GS from wheat as reported by Pistón et al. (2007). The result was the specific down-regulation of all the HMW-GS (Fig. 1 C), probably due to a transgene-induced silencing at the transcriptional or post-transcriptional level. These silencing phenomena presumably involve homology-dependent gene silencing (Meyer & Saedler, 1996) and resemble co-suppression in which mutual inactivation of transgenes and homologous genes occurs. Similar silencing effects in the HMW-GS were previously reported by Alvarez et al.
(2000) when expressing the 1Ax1 subunit transgene and over-expressing the 1Dx5 gene in wheat. PTGS by RNA interference (RNAi) is based on sequence-dependent RNA degradation that is triggered by the formation of double-stranded RNA (dsRNA) homologous in sequence to the targeted gene (Baulcombe, 2004). In contrast to other gene silencing methods such as insertional mutagenesis or TILLING (Targeting Induced Local Lesions in
Genomes) approaches, RNAi allows silencing of one gene or all members from a multigene family by targeting sequences that are specific or shared by several genes (Miki et al., 2005).
Wheat gliadins account for about 50% of total gluten proteins. Gliadins are divided into three or four groups named α/β-, γ- and ω-gliadins, based on their mobility in an acid polyacrylamide gel electrophoresis (A-PAGE) system. Gliadins are also considered the main factor triggering celiac disease (CD), a common enteropathy induced by ingestion of wheat gluten proteins and related prolamins from oat, rye, and barley in genetically susceptible individuals. When CD patients consume foods containing gluten, their immune systems react by damaging the small intestine, with severe consequences. The only available treatment for the disease is a lifelong gluten-exclusion diet. Therefore, another priority aspect regarding the improvement of wheat quality is the reduction of gluten toxicity for CD patients. Gil-Humanes et al. (2010) reported a high efficiency RNAi hairpin vector that was used in combination with genetic transformation to down-regulate the expression of genes from the three gliadin fractions at the same time in bread wheat. The RNAi approach was very effective in the shutdown of CD-related wheat gliadin T-cell epitopes. Although the suppression of gliadins had a high impact on protein fractions such as gliadins, glutenins, albumins and globulins, it did not affect significantly to the total protein content (GilHumanes et al., 2011).
In this work we have optimised the osmotic treatment for wheat transformation using particle bombardment. Immature scutella were exposed to 0.4 M mannitol treatment during
4h or 16h pre- or post-bombardment, and the results obtained have positively contributed to the optimization of the transformation method in wheat, increasing significantly the transformation efficiency. These osmotic treatments are now routinely used in the generation of transgenic plants at high efficiency. We also report the effects of HMW-GS over-expression and silencing, as well as the silencing of all the groups of gliadins, on the content and proportions of protein, starch and carbohydrates in transgenic wheat.

Genetic Transformation of Wheat: Advances in the Transformation Method and Applications for Obtaining Lines with Improved Bread-Making Quality and Low …

137

2. Materials and methods
2.1 Plant material and genetic transformation
Three cultivars of bread wheat (T. aestivum) were used in this study for genetic transformation: cv Bobwhite, supplied by the CIMMYT1, was used for the osmotic treatment study and gliadin down-regulation; cv Anza was used for HMW over-expression; and cv Perico was used for HMW-GS down-regulation (Fig. 1).
Transgenic lines of T. aestivum cv Anza expressing one or two extra HMW-GS genes were described by León et al. (2009, 2010a, 2010b) and are: line T580, line T581 and line T590, which express the subunits 1Ax1, 1Dx5, 1Dy10, respectively (Fig. 1 A); and the lines obtained by conventional crossing of the previous lines: line T606, line T616 and line T617, which express the pairs of subunits 1Ax1+1Dx5, 1Ax1+1Dy10 and 1Dx5+1Dy10, respectively (León et al., 2010b)(Fig. 1 B). Transgenic line T619, with down-regulation of all the HMW-GS, was obtained by transformation of T. aestivum cv Perico with a D hordein gene from H. chilense (Fig. 1 C). The down-regulation of all the groups of gliadins in T. aestivum cv Bobwhite was reported by Gil-Humanes et al. (2010) and for the present work we have used the following lines: D793, D894, E42 and E82. All the transgenic plants were self-pollinated for two to three generations to obtain homozygous lines.
The transformation method used to produce all the lines described in this work was the following: donor plants for genetic transformation were grown in the greenhouse under controlled conditions with supplementary lights providing a day/night regime of 16/8h and 23-25/18-19°C. Sixteen days after anthesis immature caryopses were isolated and sterilised by rinsing in 70% (v/v) aqueous ethanol for 5 min and soaking for 15-20 min in a
1% (v/v) sodium hypochlorite solution. Then, caryopses were washed three times with sterile distilled water. Embryos of approximately 0.5-1.5 mm length were used, since they have been demonstrated to be the most responsive in our conditions. To avoid the precocious germination, immature scutella were isolated from the seed embryos by removing the embryo axis and placed with the scutellum exposed in the induction medium
MP4 consisting in MS medium (Murashige & Skoog, 1962) supplemented with 30 gl-1 sucrose and 4 mgl-1 picloram. Explants were cultured in the dark at 25 ºC for 4 days prior bombardment (see Fig. 2). Osmotic treatment is thought to offer protection to bombarded material by minimising cytoplasm leakage from target cells (Vain et al., 1993), so in the
HMW-GS over-expression and gliadins silencing experiments, explants were subjected to a
4h osmotic treatment, before and/or after bombardment. In addition, in order to optimise the transformation conditions, different osmotic treatments (4h and 16h before bombardment and 4h and 16h after bombardment) were evaluated by placing the explants in medium MP40.4M consisting in MP4 solid medium supplemented with 0.4M mannitol
(for more details see Table 1). In the transformation experiments for down-regulation of the
HMW-GS genes, only 4h osmotic treatment post-bombardment was applied. Particle bombardment and selection of the transformed explants in the in vitro culture were as described by León et al. (2009). Modifications in the protocol were introduced in the experiments for optimization of the osmotic treatment as described below.

1

International maize and wheat improvement center

138

Genetic Transformation

Fig. 1. SDS-PAGE gels of wild type lines and transgenic lines with over-expression of (A) one HMW-GS gene, and (B) two HMW-GS genes; and (C) down-regulation of all the HMWGS. (D) A-PAGE of wild type and transgenic line D793 with down-regulation of all the gliadin fractions.
2.2 Osmotic treatment
Four different osmotic treatments were evaluated to increase the transformation efficiency of wheat (see Fig. 2). For each treatment, 1500 scutella distributed in 60 Petri dishes (25 scutella per dish) were isolated: 250 scutella were used as non transformed controls and did not receive the osmotic treatment (control-S); explants were transformed with the pAHC25 plasmid (Christensen & Quail, 1996) containing the uidA and bar genes, and subjected to one of the following osmotic treatments at a ratio of 250 scutella per treatment: 1) no osmotic treatment (control-B), 2) osmotic treatment of 4h prior bombardment, 3) 16h prior bombardment, 4) 4h after bombardment, and 5) 16h after bombardment (Fig. 2).

Genetic Transformation of Wheat: Advances in the Transformation Method and Applications for Obtaining Lines with Improved Bread-Making Quality and Low …

139

Fig. 2. Scheme of genetic transformation of wheat via particle bombardment. (A) Pictures of
(1) the explants used for transformation, (2) callus formation after 3 weeks of cultivation, (3) explants after 8 weeks of cultivation and (4) plantlets after transfer to soil. (B) Time sequence for genetic transformation of wheat: scutella isolation, particle bombardment, selections and transfer to soil.
After the bombardment and the respective osmotic treatments, the explants were cultured in the MP4 induction medium for 3 weeks in the dark at 20-25ºC. Then, the percentage of embryogenesis (% of scutellum surface presenting embryogenic response) was calculated.
Embryogenic calluses were transferred for shoot induction to the regeneration medium
RZPPT2, consisting in RZ medium, supplemented with 2,4-dichlorophenoxyacetic acid (2,4D), 5 mgl-1 zeatin and 2 mgl-1 L-phosphinothricin (L-PPT, the active ingredient of the herbicide BASTA) as described previously by Barro et al. (1998), except the untransformed explants (control-S) that were transferred to the same medium without the selective L-PPT.
After 3 weeks of culture in the regeneration medium at 25 ºC in the light, the percentage of regeneration (% of explants presenting shoots) was measured, and shoots were transferred to RPPT2 (R medium supplemented with 2 mgl-1 L-PPT) (Barro et al. 1998), where they were cultured for another 3 weeks. Plantlets surviving were sub-cultured for another 3 weeks in
RPPT2 medium, and then transferred to soil. Transgenic plants were determined by 1) the histochemical GUS assay and 2) by PCR amplification of a fragment of the bar gene. The

140

Genetic Transformation

transformation efficiency of each treatment was determined as % of transgenic plants transferred to soil over the total number of scutella isolated for each treatment.
2.3 Seed composition and statistical analysis
Six lines over-expressing the HMW-GS (T580, T581, T590, T606, T616 and T617), one line with down-regulation of HMW-GS (T619) and 4 lines with down-regulation of all the groups of gliadins (D793, D894, E42 and E82) were obtained and grown as described above.
Mature seeds from all the lines as well as the untransformed controls were collected and crushed into a fine powder. Three independent replicates were made for the determination of each of the following components: total protein, starch, water soluble carbohydrates, fructose, glucose, sucrose and maltose. Total protein was calculated from the Kjeldahl nitrogen content (%N x 5.7). Starch content was determined by polarimetry. Water soluble carbohydrates, as well as fructose, glucose, sucrose and maltose were quantified by HPLC with refractive index detection. Results obtained for all transgenic lines over-expressing one subunit of HMW, two subunits of HMW, and transgenic lines with down-regulation of all the gliadins, were grouped for statistical analysis and named ‘HMW1’, ‘HMW2’ and ‘–Gli’, respectively. Line T619 with down-regulation of all the HMW-GS was named ‘–HMW’
(Table 1).
Data were analysed with the statistical software R version 2.12.1 using the Graphical User
Interface (GUI) R Commander, and the SPSS version 11.0 statistical software package (SPSS
Inc., Somers, NY). Major assumptions of analysis of variance (ANOVA) were confirmed by the Kolmogorov-Smirnov’s test for normal distribution and by the Levene’s test for homogeneity of variances. ANOVA and two-tailed Dunnett’s test for median multiple comparisons were used to analyse the results and compare between transgenic and wild type lines. P values lower than 0.05 were considered significant, and lower than 0.01 were considered highly significant.

3. Results and discussion
The effect of the different osmotic treatments (prior and after particle bombardment) on the embryogenesis as well as on the efficiencies of regeneration and transformation has been studied. The results obtained can help to improve the transformation protocols in cereals.
In addition, the application of the transformation techniques to produce over-expression and silencing of genes encoding HMW-GS and gliadins, as well as the effects on the protein, starch and carbohydrates contents are discussed below.
3.1 Transformation method improvement: osmotic treatment
The ability of the particle bombardment to consistently transform wheat has been previously reported (Lonsdale et al., 1998, Vasil et al., 1992, Witrzens et al., 1998) . However, cereal transformation is still difficult due to the number of parameters involved in the technique, and many research works have been focused on the bombardment conditions such as amount of DNA, amount and size of gold particles, acceleration pressure, bombardment distance or the osmotic condition of tissues (Altpeter et al., 1996, Becker et al.,
1994, Li et al., 2003, Rasco Gaunt & Barcelo, 1998). An osmotic treatment of target tissues for stable transformation results in plasmolysis of cells and restricts damages by preventing extrusion of the protoplasm from bombarded cells (Vain et al., 1993). Osmotic treatment

Genetic Transformation of Wheat: Advances in the Transformation Method and Applications for Obtaining Lines with Improved Bread-Making Quality and Low …

141

both prior and after particle bombardment has been used in wheat transformation (Altpeter et al., 1996, Brinch-Pedersen et al., 2000, Jordan, 2000, Ortiz et al., 1996, Stoger et al., 1999). In this work we have studied the effect of the osmotic treatment with 0.4 M mannitol prior and after particle bombardment (4 h and 16 h) on the somatic embryogenesis, regeneration capacity and transformation efficiency (Table 1). The highest percentages of embryogenesis,
68.2% and 78.2%, were obtained with the 4 h pre-treatment (4h-pre) and 16 h post-treatment
(16h-post), respectively (Table 1). No significant differences were found between these treatments and the not bombarded control (control-S), and the embryogenesis was much higher than the obtained with the bombarded control (control-B). These data indicate that particle bombardment has a negative effect on somatic embryogeneis but the osmotic treatment prevents the damages caused by the particle bombardment. The 16h pretreatment showed the lowest level of embryogenesis, with only 38.0% of embryogenesis
(Table 1).

Treatment

Embryogenesis
(%)

Regeneration
(%)

Plants recovered Transgenic plants Pre-4h
Post-4h
Pre-16h
Post-16h
Control-Ba
Control-Sb

68,1 ab
57,3 abc
38,0 c
78,2 a
41,3 bc
73,1 a

78,4 ab
49,2 b
68,3 ab
64,1 ab
63,2 ab
93,4 a

64
38
7
36
19
N/A

3
17
2
4
0
N/A

Transformation efficiency (%)
1,2
6,8
0,8
1,6
0
N/A

Table 1. Effect of the osmotic treatment with 0.4 M mannitol before and after particle bombardment. aControl-B: same conditions of bombardment and herbicide selection, but with no mannitol treatment; bControl-S: no bombardment, no mannitol treatment and no herbicide selection.Values within the same column followed by the same letter are not significantly different (P80%). A strategy used is to introduce in lowproducing scopolamine species numerous copies of their own H6H gene. All the protocols have several common steps. First, the h6h cDNA is cloned into the binary vector and amplified in Escherichia coli. Then, A. rhizogenes is transformed with the binary vector obtained and used for re-introducing, by agrotransformation, that h6h cDNA into the genome of the same species from which it was isolated. However, the results were not successful because the H6H overexpressing clones obtained did not have a significant increase on alkaloid production. Those results could be attributed to an upstream regulation of alkaloid biosynthesis, to a rate limiting speed of H6H or to a deficiency of precursors.
Another strategy focus on the lack of substrates in the tropane alkaloid pathway. Thus, the carbon flux is redirect from the primary to the secondary metabolism, being PMT the key and pivot enzyme between both metabolisms. There is a strong expression of the pmt gene in the pericycle of Atropa belladona roots that is suppressed by the addition of exogenous auxins (Suzuki et al., 1999, Hibi et al., 1994, Palazón et al., 1995). There are several protocols describing the establishment of PMT overexpressing hairy roots. Nevertheless the results obtained are as disappointing as those obtained overexpressing H6H. The first report of
PMT overexpression in hairy roots was with Hyoscyamus albus (Hashimoto et al., 1989).
Tracer-feeding studies with radioactive aminoacids demonstrated that putrescine is the precursor of tropane alkaloids. Sato et al. (2000) have reported the overexpression of PMT in
Atropa belladonna hairy roots revealing an increase in polyamines pools. However, the alkaloid profile remained unchangeable. On the other hand, the overexpression of PMT from Nicotiana tabacum in Duboisia hybrid hairy roots (yielding scopolamine) produced an increase of pmt gene expression that is not reflected in the alkaloid production (Moyano et al. 2000). Also, there are reports of heterologous tests with non-tropane alkaloid producing species such as Solanum tuberosum (Stenzel et al., 2006) and Nicotiana sylvestris (Sato et al.,
2001). The overexpression of PMT in N. sylvestris increasead the nicotine concentration, probably for a higher metabolic flux towards the tropane and pyridinic alkaloid pathways.
However, when the pmt gene was overexpressed in the tropane alkaloid producer A. belladonna (Sato el al., 2001) and the Duboisia hybrid (Moyano et al., 2002), no significant increase in scopolamine was observed suggesting that methylputrescine is not the rate limiting substrate in the tropane alkaloid pathway.
The overexpression of only one enzyme in a complex metabolic net could not be sufficient to increase some secondary metabolite expression. Particularly, there are several works about the overexpression of more than one of the enzymes involved in the alkaloid tropane pathway (Zhang et al., 2004, Liu et al., 2010, Chunxian et al., 2011). However, not significant scopolamine yields were attained. The unsuccessful results could be attributed to the transgenic transformation processes itself. The mechanism of integration of transgenes into plant DNA is poorly understood, the integration of many genes at one or a few loci could not happen by chance. Also, multiple copies of one or more transgenes can result in postranscriptional gene silencing and turn unstable and reduce gene expression (Matzke &
Matzke; 1998; Palazón et al., 1998; Bulgakov et al., 2004; Kutty et al., 2011). Evidently, h6h played a more important role in stimulating scopolamine accumulation than pmt.
Nevertheless, when pmt redirects the carbon flux to the tropane pathway and h6h is overexpressed there is an accumulation of scopolamine (Zhang et al. 2004).
The genetic transformation with numerous in-tandem genes could be troublesome. For hairy root induction and pmt and h6h cDNA insertion, at least three tandem transformations

298

Genetic Transformation

Fig. 4. Scheme of the site-specific recombination between the PCR product harboring pmt or h6h cDNA and the binary vector. During the first PCR round (PCR 1st Reaction), the H6H
(or PMT) cDNA is isolated and purified from an agarose gel electrophoresis (A). The PCR fragment is inserted between the specific attachment sites sequences (att sites) into the Entry pCR8/FW/TOPO vector producing the plasmid pCR+H6H (B). The second round of PCR
(PCR 2nd Reaction) is carried out with the M13 forward and reverse primers in order to amplify a cDNA fragment encoding the sequence of interest flanked by the att left and right recombination sequences. These sequences permit the site-specific recombination between the extended PCR fragments and a Destination binary plasmid (pK7WG2.00) following the
Gateway protocol. LR Clonase II enzyme MIX is used to catalyze the site specific recombination reaction which is performed according to the manufacturer’s protocol
(Invitrogen). The final product is the binary destination vector pK7+H6H (C).

Genetic Transformation for Metabolic Engineering of Tropane Alkaloids

299

are needed. New and simple DNA transfer methods simplify the process as, for example, the Gateway system, based on bacteriophague Lambda site-specific recombination system
(Karimi et al., 2002; Attanasov et al., 2009; Dubin et al., 2008, Xu & Quinn, 2008). Figure 4 shows a protocol designed in our lab for the production of a PCR fragment for h6h cDNA ready to recombine into the destination vector independently of the antibiotic gene resistance. 4. New approaches
In this chapter, we have reviewed some of the most relevant strategies for improving tropane alkaloid biosynthesis such as the establishment of scopolamine overproducing organ cultures, the elicitation and the genetic transformation with homologous genes.
Nevertheless, the knowledge generated and the strategies in use have demonstrated that the tropane alkaloid metabolism is immersed into a complex net of metabolic pathways with a delicate equilibrium quite difficult to be manipulated. Modern system biology tools, like elicitation and overexpression, allow the carbon flux redirection with some limitations.
These margins cannot be overcome and decelerate the development of a competitive and sustainable production platform. Those troubles and limitations have fostered new strategies based on functional genomics (Goossens et al., 2002; Goossens & Rischer, 2007,
Oksman-Caldentey & Inzé, 2004) such as biotransformation.
Biotransformation is one of those new strategies. The production of scopolamine and other alkaloids was studied in engineered N. tabacum hairy roots overexpressing the h6h cDNA after feeding the cultures with exogenous hyoscyamine (Hakkinen et al., 2005). The results obtained have shown an efficient uptake of hyoscyamine from the culture medium and a higher rate of bioconversion of hyoscyamine to scopolamine (up to 85% of the total scopolamine being released to the culture medium). Moreover, it was also evident an enhanced production of various nicotine alkaloids suggesting that the regulation of the alkaloid production is probably more complex than presently known.
Another approach was the bioconversion of hyoscyamine to scopolamine using recombinant Saccharomyces cerevisiae that expresses the h6h cDNA isolated from B. candida as a biocatalyzer. Transformed S. cerevisiae CEM PK2 expressing H6H as heterologous protein was able to grow into yeast base medium supplemented with hyoscyamine. However, the results have shown a low ability of hyoscyamine conversion to scopolamine (Cardillo et al.,
2005 and 2008).

5. Conclusions
In the last two decades plant biotechnology has made considerable advances in the quest of a scopolamine and other tropane alkaloids productive process. Several groups have explored a wide spectrum of strategies that have led to the exhaustive knowledge of the tropane alkaloid pathway, its limiting steps and some of the regulation pathways. It is evident that genetic transformation is a promissory tool for engineering tropane alkaloid biosynthetic metabolism in order to produce high amounts of scopolamine. Combining genetic transformation and metabolic engineering would be a powerful strategy to re-direct the metabolic flux towards that biosynthetic pathway. It became clear, from the results already published, that the overexpression of pmt gene and/or h6h gene not only stimulated the conversion of hyoscyamine to scopolamine, but also the capacity of these hairy root lines

300

Genetic Transformation

to synthesize both tropane alkaloids. However, the yields obtained up to now did not reach those of the current scopolamine productive process. Future research could be done considering the higher structural diversity of tropane alkaloids that could be functional to create new metabolic pathways and biological active products. A possible strategy would be cloning and engineering those new metabolic pathways in heterologous organism to produce a chemical structure diversity for generating new compounds with scopolaminelike activity (Harvey, 2000, Butler, 2004, Potterat & Hamburger, 2008).

6. Acknowledgment
This work was supported by Consejo Nacional de Investigaciones Científicas y Técnicas
(CONICET) and the Agencia Nacional de Producción Científica y Tecnológica (ANPCyT)
(PICT2007 0552).

7. References
Ajungla, L., Patil, P.P., Barmukh, R.B. Nikam, T D (2009) Influence of biotic and abiotic elicitors on accumulation of hyoscyamine and scopolamine in root cultures of
Datura metel L. Indian J Biotechnol 9: 317-322.
Angelova, Z., Georgiev, S. & Ross, W. (2006) Elicitation in plants. Biotechnol Eq J 20: 72-83.
Attanassov, I.I., Etchells, J.P. & Turner, S.R. (2009) A simple, flexible & efficient PCRfusion/Gateway cloning procedure for gene fusion, site-direct mutagenesis, short sequence insertion & domain deletions and swaps. Plant Methods 4: 1-11.
Benhamou, N. (1996) Elicitor-induced plant defence pathways. Trends in Plant Sc 1:233-240.
Bulgakov, V.P., Tchernoded, G.K., Mischenko, N.P., Shkryl, Y.N., Fedoreyev, S.A. &
Zhuravlev, Y.N. (2004). The rolB and rolC genes activate synthesis of anthraquinones in Rubia cordifolia cells by mechanism independent of octadecanoid signaling pathway. Plant Sc 166:1069- 1075.
Butler, M.S. (2004) The role of natural product chemistry in drug discovery. J Nat Prod 67:
2141-2153
Canter, P.; Howard, T. & Edzard, E. (2005) Bringing medicinal plants into cultivation: opportunities and challenges for biotechnology. Trends in Biotechnol 23:180-185.
Cardillo, A.B., Silberstein, S., Giulietti, A.M. & Marconi, P.L. (2005) Biotransformation of hyoscyamine by a recombinant Saccharomyces cereviciae strain. 2nd Mercosur
Congress on Chemical Engineering 4th Mercosur Congress on Process Systems
Engineering, Brasil.
Cardillo, A.B., Rodriguez Talou, J. & Giulietti, A.M. (2008) Expression of Brugmansia candida Hyoscyamine 6beta-Hydroxylase gene in Saccharomyces cerevisiae and its potential use as biocatalyst. Microbial Cell Factories 7: 1-7.
Chunxian, Y., Min, Ch, Lingjiang, Z., Lei, Z., Xiaoqiang, L., Xiaozhong, L., Kexuan, T. &
Zhihua, L. (2011) Improvement of tropane alkaloids production in hairy root cultures of Atropa belladonna by overexpressing pmt and h6h genes. Plant Omics J 4:
29-33.
Dubin, M.J., Bowler, C. & Benvenuto, G. (2008) A modified gateway cloning strategy for overexpressing tagged proteins in plants. Plant Methods 4: 1-11.
Hamill J.D., Parr A.J., Rhodes H.J.C., Robbins R.J., Walton N.J. (1987) New routes to plant secondary products. Biotechnology, p. 800-804.

Genetic Transformation for Metabolic Engineering of Tropane Alkaloids

301

Guo, Z. J., Lamb, C. & Dixon, R. (1997) Release and biological activity of diffusible signal compounds from elicited plant cells. J Plant Physiol 151: 699-710.
Goossens, A., Ha, S.T., Into, L. K. , Seppa, T., nen-Laakso, S.B., De Sutter, V., Lammertyn, F.,
Nuutila, A.M., So derlund, S., Zabeau, M., Inze, D. & Oksman-Caldentey, K-M
(2002) A functional genomics approach toward the understanding of secondary metabolism in plant cells. Proc Natl Acad Sc 14: 8595-8600.
Goossens, A. & Rischer, H. (2007) Implementation of functional genomics for gene discovery in alkaloid producing plants. Phytochem Reviews 6: 35-49.
Hakkinen, S.T., Moyano, E., Cusido, M.R., Palazon, J., Teresa Pinol, M. & OksmanCaldentey, K-M (2005) Enhanced secretion of tropane alkaloids in Nicotiana tabacum hairy roots expressing heterologous hyoscyamine-6b-hydroxylase. J Experimental
Botany 56: 2611–2618.
Harvey, A. (2000) Strategies for discovering drugs from previously unexplored natural products. Drug Discov Technol 5: 294-300.
Hashimoto, T. & Yamada, Y. (1986) Hyoscyamnine6- hydroxylase, a 2 oxaglutarate – dependent oxygenase, in alkaloid production root cultures. Plan Physiol 81: 619-625.
Hashimoto, T. & Yamada, Y. (1987) Purification and characterization of hyoscyamine 6 βhydroxylase from root culture of Hyoscyamus niger L. Eur J Biochem 194: 277 – 285.
Hashimoto, T, Yukumine, Y. & Yamda, Y (1989) Putrescine and putrescine Nmethylransferase in the biosynthesis of tropane alkaloids in culture roots of
Hyoscyamus albus. Planta 178: 131-137
Hashimoto, T., Hayashi, A., Amano, Y., Kohno, J., Iwanari, H., Usuda, S. &, Yamada, Y.
(1991) Hyoscyamine 6 beta-hydroxylase, an enzyme involved in tropane alkaloid biosynthesis, is localized at the pericycle of the root. J Biol Chem 5: 4648-53.
Hashimoto, T., Yun, D.J. & Yamada, Y. (1993) Production of tropane alkaloids in genetically engineered root cultures. Phytochem 32 713–718.
Hashimoto, T., Matsuda, J. & Yamada, Y. (1993) Two-step epoxidation of hyoscyamine to scopolamine is catalyzed by bifunctional hyoscyamine 6-hydroxylase. FEBS Lett
329: 35–39.
Hibi, N., Higashiguchi, S., Hashimoto, T. &, Yamada, Y. (1994) Gene expression in tobacco low-nicotine mutants. Plant Cell 6: 723-735.
Jouhikainen, K., Lindgren, L., Jokelainen, T., Hiltunen, R., Teeri, T.H. & Oksman-Caldentey,
K-M. (1999) Enhancement of scopolamine production in Hyoscyamus muticus L. hairy root cultures by genetic engineering. Planta 208, 545-551.
Jung, H, Kang, S, Kang, M., Bahn, J, Yang, J. & Choi M. (2003) Enhanced production of scopolamine by bacterial elicitors in adventitious hairy root cultures of Scopolia parviflora. Enzyme Microb Technol 33: 987-900.
Karimi, M., Inzé, D. & Depicker, A. (2002) GATEWAY-vectors for Agrobacterium-mediated plant transformation. Trends Plant Sc 7: 193-195.
Kinghorn, A. D. & Seo, E. K. (1996) Plants as sources of drugs. Agricultural Materials as
Renewable Resources 647: 179−193.
Kutty, P.C., Parveez, G.K.A. & Huyop, F. (2011) Agrobacterium tumefaciens infection strategies for greater transgenic recovery in Nicotiana tabacum cv. TAPM26. I. J
Agricultural Research 6: 119-133.
Lawrence, C.B., Singh, N.P., Giu, J.S., Gardener, R.G. & Tuzun, S. (2000) Constitutive hydrolytic enzymes are associated with polygenic resistance of tomato to Alternaria

302

Genetic Transformation

solani and may function as an elicitor release mechanism. Physiol Molec Plant Pathol
57: 211-220.
Liu, X., Yang, C., Chen, M., Li, M., Liao, Z. & Tang, K. (2010) Promoting scopolamine accumulation in transgenic plants of Atropa belladonna generated from hairy roots with over expression of pmt and h6h gene. J Medicinal Plants Res 4: 1708–1713.
Marconi, P.L., Alvarez, M.A., & Pitta-Alvarez, S.I. (2006) How polyamine synthesis inhibitors and cinnamic acid affect tropane alkaloid production. Applied Biochem
Biotechnol 136: 63-76.
Marconi, P.L., Setten, L., Cálcena, E., Alvarez, M.A. & Pitta Alvarez, S.I. (2008) Changes in growth and tropane alkaloid production in long-term culture of hairy roots of
Brugmansia candida. J Integrative Biosc 3: 38-44.
Matsuda, J., Okabe, S., Hashimoto, T., & Yamada, Y. (1991) Molecular cloning of hyoscyamine 6B-hydroxylase, a 2-Oxoglutarate-dependent dioxygenase, from
Cultured Roots of Hyoscyamus niger. J Biol Chem 266: 9460-9464.
Matzke, A.J.M. & Matzke, M.A. (1998) Position effects and epigenetic silencing of plant transgenes. Current Opinion in Plant Biol 1 :142-l 48
Mizusaki, S., Tanabe, Y., Noguchi, M. & Tamaki, E. (1973) Changes in the activities of ornithine decarboxylase, putrescine N-methyltransferase and N-methylputrescine oxidase in tobacco roots in relation to nicotine biosynthesis. Plant Cell Physiol 14:
103-110.
Moyano E, Fornale A.S., Palazon J., Cusido R.M., Bonoll M, Morales C. & Piñol M.T. (1999)
Effect of Agrobacterium rhizogenes T-DNA on alkaloid production in Solanaceae plants. Phytochem 52, 1287-1292.
Moyano, E, Fornale, A.S., Palazón, J., Cusido, R.M., Bagni, N. & Piñol, M.T. (2002) Alkaloid production in Duboisia hybrid hairy root cultures overexpressing the pmt gene.Phytochem 59, 697-702.
Moyano, E., Jouhikainen, K., Tammela, P., Palazón, J., Cusido, R.M., Piñol, M.T., Teeri H.T.
& Oksman-Caldentey K-M. (2003) Effect of pmt gene overexpression on tropane alkaloid production in transformed root cultures of Datura metel and Hyoscyamus muticus. J Exp Botany 54: 203–211.
Oksman-Caldentey, K-M. & Strauss, A. (1986) Somaclonal variation of scopolamine content in protoplast-derived cell culture clones of Hyoscyamus muticus. Planta Medica 52, 612.
Oksman-Caldentey, K-M., Vuorela, H, Strauss, A. & Hiltunen, R. (1987) Variation in the tropane alkaloid content of Hyoscyamus muticus plants and cell culture clones.
Planta Medica 53, 349-354.
Oksman-Caldentey, K-M., KivelaÈ, O. & Hiltunen, R. (1991) Spontaneous shoot organogenesis and plant regeneration from hairy root cultures of Hyoscyamus muticus. Plant Science 78,129-136.
Oksman-Caldentey, K-.M. & Arroo, R. (2000) Regulation of tropane alkaloid metabolism in plants and plant cell cultures, in: R. Verpoorte, A.W. Alfermann (Eds.), Metabolic
Engineering of Plant Secondary Metabolism, Kluwer Academic Publishers,
Dordrecht, 2000, pp. 253–281.
Oksman-Caldentey, K.M. & Inze, D. (2004) Plant cell factories in the post-genomic era: new ways to produce designer secondary metabolites. Trends Plant Sc 9: 433-440.

Genetic Transformation for Metabolic Engineering of Tropane Alkaloids

303

Oksman-Caldentey, K.M., Häkkinen, S.T. & Rischer, H. (2007) Chapter 4: Metabolic
Engineering of the Alkaloid Biosynthesis in Plants: Functional Genomics
Approaches in: Applications of Plant Metabolic Engineering. Veerporte R.,
Alfermann, A.W., Johnson, T.S. Eds. Springer Netherlands, pp. 109-124.
Palazón, J., Altabella, T., Cusido, R.M., Ribo, M. & Piñol, M.T. (1995) Growth and tropane alkaloid production in Agrobacterium transformed roots and derived callus of
Datura. Biologia Plantarum 37, 161-168.
Palazón, J., Cusidó, R.M., Roig, C. & Piñol, M.T. (1998) Expression of the rolC gene and nicotine production in transgenic roots and their regenerated plants. Plant Cell Rep
17: 384-390.
Palazón, J., Moyano, E, Cusidó, R.M., Bonfill, M., Oksman-Caldentey, K-M & Piñol, M.T.
(2003) Alkaloid production in Duboisia hybrid hairy roots and plants overexpressing the h6h gene. Plant Sc 165: 1289–1295.
Palazón, J, Navarro-Ocaña, A., Hernandez-Vazquez, L. & Hossein Mirjalili, M. (2008)
Application of metabolic engineering to the production of scopolamine. Molecules
13: 1722-1742.
Pitta Alvarez, S.I. & Giulietti, A.M. (1997) Effect of gibberellin GA7 on kinetics of growth and tropane alkaloid accumulation in hairy roots of Brugmansia candida. In VitroPlant. , 33:147 – 153.
Pitta Alvarez, S.I., Spollansky, T.C. & Giulietti, A.M. (2000) Scpolamine and hyoscyamine production by hairy root cultures of Brugmansia candida: influence of calcium chloride, hemicelullase and theophylline. Biotechnol Lett 22: 1653-1656.
Pitta Alvarez, S.I., Marconi, P.L. & Giulietti, A. (2003) Comparison of the influence of different elicitors of hyosciamine and scopolamine content in hairy roots cultures of
Brugmansia candida. In Vitro-Plant, 36: 640-644.
Potterat, O. & Hamburger, M. (2008) Drug discovery and development with plant-derived compounds. In: progress in drug research, Vol. 65. Eds: F. Petersen & R. Amstutz.
Birkhauser Verlag, Basel, Switzerland. pp. 45-118.
Prakash Rout, S., Choudary, K.A., Kar, D.M., Das. L. & Jain, A. (2009) Plants in traditional medical system- future source of new drugs. I J Pharmacy Pharmac Sc 1: 1-23.
Qurishi, Y., Hamid, A., Zargar, M.A., Singh, S.K. & Saxena, A.K. (2010) Potential role of natural molecules in health and disease: Importance of boswellic acid. J Medicinal
Plants Res 4: 2778-2785.
Sato, F., Hashimoto, T., Hachiya, A., Tamura, K., Choi, K., Morishige, T., Fujimoto, H. &
Yamada, Y. (2001) Metabolic engineering of plant alkaloid biosynthesis. Proc Natl
Acad Sci 98: 367-372.
Shinjiro, O.; Uefuji, H., Masayki, M. & Hiroshi, S. (2005) Metabolic engineering of caffeine production. Plant Biotechnol 22: 461-468.
Stenzel, O., Teuber, M. & Drager, B. (2006) Putrescine N-methyltransferase in Solanum tuberosum L., a calystegine-forming plant. Planta 223: 200-212.
Suzuki, K.; Yun, D.-J.; Chen, X.Y.; Yamada, Y. & Hashimoto, T. (1999) An Atropa belladona hyoscyamine 6 β-hydroxylase gene is differentially expressed in the root pericycle and anthers. Plant Mol Biol 40: 141-152.
Theiss, C., Bohley, P. & Voigt, J. (2002) Regulation by polyamines of ornithine decarboxylase activity and cell division in the unicellular green alga Chlamydomonas reinhardtii.
Plant Physiol 128: 1470.

304

Genetic Transformation

Tytgat, G.L. (2007) Hyoscine Butylbromide: A Review of its Use in the Treatment of
Abdominal Cramping and Pain. Drugs 67: 1343-1357
Xu, R. & Quinn, Q.Q. (2008) Protocol: Streamline cloning of genes into binary vectors in
Agrobacterium via the Gateway® TOPO vector system. Plant Methods 8: 1-7.
Zabetakis, I., Edwards, R. & O´Hagan, D. (1998) Elicitation of tropane alkaloid biosynthesis in transformed root cultures of Datura stramonium. Phytochem 50:53-56.
Zhang, L., Ding, R., Chai, Y., Bonfill, M., Moyano, E., Oksman-Caldentey, K-M., Xu, T., Pi,
Y., Wang, Z., Zhang, H., Kai, G., Liao, Z., Sun, X., & Tang, K. (2004) Engineering tropane biosynthetic pathway in Hyoscyamus niger hairy root cultures. Proc Natl
Acad Sci 101: 6786–6791.

16
Transgenic Plants for Enhanced
Phytoremediation – Physiological Studies
Paulo Celso de Mello- Farias1, Ana Lúcia Soares Chaves2 and Claiton Leoneti Lencina2
1Federal

University of Rio Grande
University of Pelotas
Brazil

2Federal

1. Introduction
Natural processes such as volcanic eruptions, continental dusts and anthropogenic activities like mining, combustion of fossil fuel phosphate fertilizers, military activities and metal working industries lead to emission of heavy metals and accumulation of these chemicals in ecosystem. So, the metals found in our environment come from natural weathering process of earth’s crust, soil erosion, mining, industrial discharge, urban runoff, sewage effluents, air pollution fall out, pest or disease control agents. The concentrations of the contaminants can vary from highly toxic concentrations from an accidental spill to barely detectable concentrations that, after long-term exposure, can be detrimental to human health
(Alexander, 1999; Doty, 2008). Particularly, heavy metals are toxic because they cause DNA damage and their carcinogenic effects in animals and humans are probably caused by their mutagenic ability (Knasmuller et al., 1998; Baudouin et al., 2002; Hooda, 2007). Potential threat is that heavy metals are not degradable and without intervention stay in soil for centuries. The cleanup of most of the contaminated sites is mandatory in order to reclaim the area and to minimize the entry of toxic elements into the food chain. Various engineering – based methods such as soil excavation, soil washing or burning or pump and treat systems are already being used to remediate metal contaminated soils ((Hooda, 2007).
As a result over recent decades an annual worldwide release of heavy metals reached 22,000 t (metric ton) for cadmium, 939,000 t for copper, 783,000 t for lead and 1,350,000 t for zinc
(Singh et al., 2003).
The cost of cleaning up contaminated sites is extremely high. In the USA alone, U$ 6–8 billion is annually spent in remediation efforts, with global costs in the range of U$ 25–50 billion (Glass, 1999; Tsao, 2003). Engineering methods for the remediation of contaminated sites include excavation, transport, soil washing, extraction, pumping and treating of contaminated water, addition of reactants such as hydrogen peroxide or potassium permanganate, and incineration. A serious consequence of the high cost of remediation technologies is that polluted commercial properties are often abandoned rather than cleaned up. There are over 500,000 of these so-called brownfields in the USA.
Elemental pollutants are particularly difficult to remediate from soil, water, and air because, unlike organic pollutants that can be degraded to harmless small molecules, toxic elements

306

Genetic Transformation

such as mercury, arsenic, cadmium, lead, copper, and zinc, are immutable by all biochemical reactions and hence remain in the ecosystem (Kramer & Chardonnens, 2001). The heavy metals remainings in various ecosystems would seep into surface water, groundwater or even channel into the food chain by crops growing on such a soil (Lin et al., 1998). These heavy metals may adversely affect the soil ecosystem safety, not only agricultural product and water quality, but also the human health (Zhou et al., 2004).
Another popular clean-up method involves augmented bioremediation with the addition of specific microbial strains known to degrade the pollutant. Bacteria and fungi collectively can utilize a vast range of organic molecules. But for bioremediation using microbes at a particular site to be successful, many conditions must be met. These include the ability of the microbes with the desired metabolic activity to survive in that environment, the accessibility or bioavailability of the chemical, and the presence of inducers to activate expression of the necessary enzymes. Many organic pollutants are recalcitrant to degradation and cannot be used as sole carbon source (Doty, 2008). The pollutants are sometimes metabolized by enzymes with other natural substrates; therefore, these substrates sometimes need to be present in order for the genes to be expressed. This requirement is problematic if the inducing chemical is itself a harmful pollutant, such as phenol. Bioremediation also depends on the presence of sufficient carbon and energy sources. Often, thousands of gallons of a food source such as molasses must be pumped down into the site to allow bacterial growth
(Doty, 2008).
The use of microorganisms in engineered bioremediation systems has had mixed success. A review of this broad and active field is beyond the scope of this review; a recent book provides an excellent overview of bioremediation of xenobiotics, petroleum, BTEX (benzene, toluene, ethylbenzene, and xylene), explosives, and heavy metals (Fingerman &
Nagabhushanum, 2005; Doty, 2008).
Plants are autotrophic organisms capable of using sunlight and carbon dioxide as sources of energy and carbon. However, plants rely on the root system to take up water and other nutrients, such as nitrogen and minerals, from soil and groundwater. As a side effect, plants also absorb a diversity of natural and man-made toxic compounds for which they have developed diverse detoxification mechanisms (Eapen et al., 2007; Van Aken, 2008).
Pollutant-degrading enzymes in plants probably originate from natural defense systems against the variety of allelochemicals released by competing organisms, including microbes, insects and other plants (Singer, 2006; Van Aken, 2008). From this viewpoint, plants can be seen as natural, solar-powered pump-and-treat systems for cleaning up contaminated environments, leading to the concept of phytoremediation (Pilon-Smits, 2005; Van Aken,
2008).
First developed for the removal of heavy metals from soil, the technology has since proven to be efficient for the treatment of organic compounds, including chlorinated solvents, polyaromatic hydrocarbons and explosives (Pilon-Smits, 2005; Salt et al., 1998; Van Aken,
2008). Beyond the removal of contaminants from soil, phytoremediation involves different processes, such as enzymatic degradation, that potentially lead to contaminant detoxification (Pilon-Smits, 2005; Dietz & Schnoor, 2001; Van Aken, 2008). However, despite great promise, rather slow removal rates and potential accumulation of toxic compounds within plants might have limited the application of phytoremediation (Eapen et al., 2007;
Van Aken, 2008).
Unlike organic contaminants, metals cannot be degraded. Instead, phytoremediation strategies for metals are based on stabilization, accumulation, and in some cases on

Transgenic Plants for Enhanced Phytoremediation – Physiological Studies

307

volatilization. The phytostabilization of metals may simply involve the prevention of leaching through the upward water flow created by plant transpiration, reduced runoff due to above-ground vegetation, and reduced soil erosion via the stabilization of soil by plant roots (Vassilev et al., 2004; Martínez et al., 2006).
Phytoremediation, as a cost-effective and environmentally friendly method, is an emerging technology based on the use of plants to remove, transform, clean up or stabilize contaminants including organic pollutants located in water, sediments, or soils
(Cunningham et al., 1997; Cherian & Oliveira, 2005; Mello-Farias & Chaves, 2008). This method has attracted growing attention because of its distinctive potential and advantages compared with conventional technologies, such as soil replacement, solidification, and washing strategies (Yang et al., 2005; Mello-Farias & Chaves, 2008). The advantages of phytoremediation over usual bioremediation by microorganisms are that plants, as autotrophic systems with large biomass, require only modest nutrient input and they prevent the spreading of contaminants through water and wind erosion (Pulford & Watson,
2003; Cherian & Oliveira, 2005; Mello-Farias & Chaves, 2008). Plants also supply nutrients for rhizosphere bacteria, allowing the growth and maintenance of a microbial community for further contaminant detoxification (Cherian & Oliveira, 2005; Mello-Farias & Chaves,
2008). Phytoremediation takes advantage of the unique, selective and naturally occurring uptake capabilities of plant root systems, together with the translocation, bioaccumulation and pollutant storage/degradation abilities of the entire plant body. Besides being aesthetically pleasing, phytoremediation is on average tenfold cheaper than other physical, chemical or thermal remediation methods since it is performed in situ, is solar driven and can function with minimal maintenance once established (Hooda, 2007).
According to Sarma (2011), there are different strategies of phytoremediation, each having a different mechanism of action for remediating metal-polluted soil, sediment or water, like:
1) Phytoextraction: plants absorb metals from soil through the root system and translocate them to harvestable shoots where they accumulate. Hyperaccumulators mostly used this process to extract metals from contaminated site. The recoveries of extracted metals are also possible through harvesting the plants appropriately; 2) Phytovolatilization: plants used to extract certain metals from soil and then release them into the atmosphere by volatilization;
3) Phytostabilization: plant root microbial interaction can immobilize organic and some inorganic contaminants by binding them to soil particles and as a result reduce migration contaminants to grown water; 4) Phytofiltration: plant roots (rhizofiltration) or seedlings
(blastofiltration) absorb or adsorb pollutants, mainly metals from water and aqueous waste streams (Prasad & Freitas, 2003)
Many genes are involved in metal uptake, translocation and sequestration; the transfer of any of these genes into candidate plants is a possible strategy for genetic engineering of plants to improve phytoremediation traits. Depending on the strategy, transgenic plants can be engineered to accumulate high concentrations of metals in harvestable parts. Transfer or overexpression of genes will lead to enhanced metal uptake, translocation, sequestration or intracellular targeting. Genetic engineering of plants for synthesis of metal chelators will improve the capability of plant for metal uptake (Karenlampi et al., 2000; Pilon-Smits &
Pilon, 2002; Clemens et al., 2002; Eapen & D´Souza, 2005).
The application of powerful genetic and molecular techniques may surely identify a range of gene families that are likely to be involved in transition metal transport. Considerable progress has been made recently in identifying plant genes encoding metal ion transporters

308

Genetic Transformation

and their homologous in hyperaccumulator plants. Therefore, it is hoped that genetic engineering may offer a powerful new means by which to improve the capacity of plants to remediate environmental pollutants (Yang et al., 2005, Mello-Farias & Chaves, 2008).

2. Types of pollutants
There is a variety of different pollutants, originated, in most cases, by human action. To facilitate the development of studies on decontamination techniques and also according the different physical and chemical characteristics they present, the different types of contaminants were divided into two major classes: organic and inorganic. These two groups are further subdivided. Organic pollutants include various compounds such as polychlorinatedbiphenyls (PCB’s), polycyclicaromatichydrocarbons (PAH’s), nitroaromatic
(explosives), halogenated hydrocarbons, chlorinated solvents. When compared to inorganic, the organic pollutants are relatively less toxic to plants because they are less reactive and do not accumulate readly. Many of these compounds are not only toxic or teratogenic, but also carcinogenic. The inorganic contaminants include heavy metals, such as mercury, lead, cadmium, among others; and non-metallic compounds like arsenic and radionuclides like uranium, cesium, chromium, strontium, technetium, tritium, etc. Many metals are essential to growth and development of living forms. However, when in high concentrations, they become extremely toxic, leading the organism to oxidative stress with great production of harmful free radicals, highly dangerous to cells and tissues. Some particularly reactive metals interfere in the structure and function of proteins, and also cause the substitution of other essential nutrients (Garbisuet al. 2002; Pulfort; Watson, 2003; Taiz & Zeiger, 2002).
Many elemental pollutants penetrate the plant through regular systems of nutrient absorption. The plants protect themselves from these xenobiotics through degradation of endogenous toxic organic or sequestering them in the vacuoles (Meagher, 2000).
Different technologies of phytoremediation are compatible with a great number of pollutants. Constructed wetlands have been applied for many inorganics, including metals, nitrates, phosphates, cyanides, as well as organics such as explosives and herbicides (Horne
2000; Schnoor et al., 1995; Jacobson et al, 2003).
There is a special category of plants called hyperaccumulators (described later), for they accumulate a considerable amount of toxic metals and radionucleides in their tissues
(phytoextraction), keeping these compounds above the ground surface. This is the main goal of phytoremediation.
2.1 Inorganics
The absorption of any metal by plants depends on the metal relative bioavailability in the contaminated array. Changes in the soil chemistry, such as decreased pH, may increase the availability of many metals for the absorption by the roots. Many plants can absorb significant levels of metals in some soil conditions. Changes in rhizosphere microbial status
(e.g.: presence of mycorrhizae) can also have profound effects (positive or negative) on the uptake of metals by the roots (Smith, 1996). The general consensus of researchers in this area, however, is that phytoremediation, especially for heavy metals, will only be economically viable through the use of hyperaccumulators. The research in the past two decades has shown that certain specialized plants have the ability to accumulate more than
3% (dry weight) of heavy metals and over 25% (dry weight) in sap / latex with no apparent

Transgenic Plants for Enhanced Phytoremediation – Physiological Studies

309

damage to the plant (Baker & Brooks, 1989, Baker et al. 1994; Huang & Cunningham, 1996).
The mechanisms that govern this tolerance and absorption of excessive concentrations of metals in leaves were the subject of active research and vary according to the element
(Cunningham & Lee, 1995; Huang & Cunningham, 1996). The mechanisms of tolerance include the accumulation of Zn in cell walls; Ni associated with the pectin in large cells; Ni,
Co and Zn being chelated by malic acid; phytochelatin associated to Zn, Ni chelation by citrate; and Co associated with oxalate crystals calcium in plant tissues. Knowledge of the mechanisms of tolerance will aid in identifying the genetic characteristics necessary for the transfer of metal tolerance of plants capable of producing greater biomass with deeper rooting. It was suggested that in some cases, the resulting biomass rich in metals
(biominery) could be incinerated and have metals economically recycled. This
“biomineration” of metals can also be applied as a mining technique for metals with significant economic value (Robinson et al., 1998).
Another type of inorganic compounds that may be susceptible to phytoremediation are radionucleides. The presence of radionucleides in soil and water poses serious risk to human health. These contaminants come from the explosion of atomic bombs or nuclear power plant accidents such as Chernobyl, Ukraine and, more recently in Fukushima, Japan.
The selection of an appropriate cleaning technology of these contaminated areas is based on the environmental chemistry of each element, character of deposition and rate of radioactive decay. A variety of physicochemical methods are available, like soil washing, ion exchange, leaching with chelating agents, flocculation and osmosis-ultrafiltration. Recently there has been increasing interest in the use of biological methods to remove radionucleides
(Duschenkov, 2003). Negri and Hinchman (2000) reported data in the use of plants for the treatment of 3H, U, Pu, 137Cs and 90Sr.
2.2 Organics
More recently, with the development of the pesticide industry, the metabolic capacity of the plant system began to be assessed. The most modern herbicides are based on the selectivity of crops due to metabolic differences between species of plants. This capability, often created by man, is the cornerstone of the highly profitable market of herbicides. “Desirable” plants rapidly metabolize the herbicide compound in a nontoxic one, while “undesirable” herbs do not, and are therefore dead. This mechanism developed by the natural selection of plants, proves to be potentially exploitable in the remediation of contaminated soils.
This ability of plants to detoxify xenobiotics is widely recognized and with current utility.
Besides, plants generally have a metabolic system with differences in the efficiency of degradation of toxic compounds when compared to microorganisms, what makes the union of these two distinct systems in the rhizosphere, an ideal situation for a more efficient phytoremediation. Recent research includes plant selection, alternative patterns of rooting, the composition of exudates produced by the plant and its effect on microbial communities, exudation of specific compounds inducing specific metabolic pathways and, inoculation with rhizosphere microorganisms capable of degrading xenobiotics efficiently (Langenbach,
1994). The plants and their roots can create an environment in the soil which is rich in microbial activity, able to change the availability of organic contaminants or increase the degradation of certain organic compounds, such as hydrocarbons derived from Petroleum.
Siciliano et al. (2003) evaluated the impact of microbial remediation on soil mass and the capacity of microbial community to degrade hydrocarbons in order to determine whether phytoremediation treatments increase the metabolic potential of microbial community by

310

Genetic Transformation

altering its taxonomic structure. It was found that the best remediation system to reduce hydrocarbons in the soil was obtained by increasing the population of bacteria containing genes for the catabolism of hydrocarbons in the rhizosphere community, thus demonstrating the importance of using microorganisms in phytoremediation. However, it is necessary to identify the species of suitable plants that can beneficially alter microbial diversity for soil remediation. According to Pires et al. (2003), the absorption of herbicides by plants is affected by the compound 's chemical properties, environmental conditions and the characteristics of plant species. Actually, the probability of a plant being phytoremediator depends on the type of pollutant; plants should be tested to detect that one with the greater resistance to a specific pollutant. Esteve-Nunez et al. (2001) evaluated trinitrotoluene (TNT), and found that its chemical structure influences its biodegradability. According to these authors, the oxygenated metabolism for aromatic compounds by bacteria does not occur in TNT because of its chemical properties generating compounds not metabolized by microorganisms. However, anaerobic processes have advantages because of the absence of oxygen. Therefore the use of fungi for the bioremediation of TNT has generated considerable interest. Esteve-Nunez et al.
(2001) concluded that the remediation of TNT by these organisms is a very valid process; and the rhizoremediation by microbes able to colonize the rhizosphere of plants, will provide a fast and efficient mechanism for the removal of this pollutant. Figure 1 shows some types of organic pollutants.
There are other types of contaminants called Persistent Organic Pollutants (POPs) that resist long in the soil. Some examples are Dichlorodiphenyltrichloroethane (DDT),
Polychlorinated biphenyls (PCB), Dioxins, etc. Research has shown that a variety of plants can remove persistent compounds, transporting them to aerial plant tissues (Coutinho &
Barbosa, 2007). It is important to highlight that, due to variety of contaminants, the study of pollutant is very important to generate an effective phytoremediation.
Most current methods of cleaning metals and volatile organic compounds not on the soil surface are coarse, expensive and physically destructive (Baker et al., 1994). The remediation by conventional methods of engineering often costs 50 to 500 dollars per ton of soil, and certain specialized techniques can cost up to US$ 1000 (Cunningham & Ow, 1996).
Phytoremediation associated with biotechnology is an emerging technology that promises a viable remediation when pollutants: a) are close to the surface, b) are relatively nonleachable, and c) have little immediate risk to the environment (Cunningham & Lee, 1995).
The results are more effective in slightly or moderately polluted areas. For heavy contamination, the decontamination time is too long (Robinson et al., 1998). The combination of metal hyperaccumulation and degradation or, increased sequestration of organic compounds with greater biomass and deeper rooting systems can result in a powerful technology of phytoremediation that will provide cheaper, permanent and intrusive remediation. Table 1 shows a summary of the techniques applied to the different types of phytoremediated compounds.

3. Hyperaccumulators
Over recent years a special interest has emerged in the phenomenon of heavy-metal hyperaccumulation since this property may be exploited in the remediation of heavy-metalpolluted soils through phytoextraction and phytomining (Robinson et al., 1997; Martínez et al., 2006).

311

Transgenic Plants for Enhanced Phytoremediation – Physiological Studies
O

(Cl)n

(Cl)n

n = 1 to 10

(Cl)n

(Cl)n

O n = 1 to 4

PCB 's

Dioxines

Benzo[a]pyrene
PAH 's
-

O

Cl

Cl

TCE

Cl

Cl

Cl

+

N

N

O

Cl

O

+

Cl

-

O

Cl
+

-

O

N

Cl

O

Cl

DDT

Cl

Cl
DDE

TNT

F

F

Cl

Cl

Cl

F

O

Cl

R

O
N
O

N

O
NH

O
NH

Cl
S

Cl

N

NH

Cl

O

N

Hexachlorocyclohexane

N
N

NH

R = H - simazine
CH3 - atrazine

trifloxysulfuron sodium

fluorene

naphtalene

toluene

PH 's

Fig. 1. Different types of organic pollutants
Type of phytoremediation
Phytoaccumulation/extraction

Phytodegradation/transformation
Phytostabilization
Phytostimulation
Phytovolatilization
Phytofiltration

Chemicals Treated
Cd, Cr, Pb, Ni, Zn, radionuclides, BTEX*, penachlorophenol, short chained aliphatic compounds
Nitrobenzene, nitroethane, nitrotoluene, atrazine, chlorinated solvents
(chloroform, carbon tetrachloride, etc)
Heavy metals in ponds, phenols and chlorinated solvents
Polycyclicaromatic hydrocarbon, BTEX,
PCB#, tetrachloroethane
Chlorinated solvents, Hg, Se.
Heavy metals, organics and radionucleides. *BTEX = benzene, toluene, ethyl benzene, xylenes;
#PCB = Polychlorinated biphenyl

Table 1. Outline of phytoremediated chemicals (Nwoko, 2010).

312

Genetic Transformation

The concept of hyperaccumulation was originally introduced to plants containing more than
0.1% (1000 mg.kg-1) of Ni in dried plant tissues (Jaffré et al., 1976). At present, the criteria used for hyperaccumulation vary per metal, ranging from 100 mg.kg-1 dry mass for Cd, to
1000 mg.kg-1 for Cu, Co, Cr, and Pb, to 10000 mg.kg-1 for Zn and Mn. These values exhibit a shoot-to-soil metal concentration ratio, the so-called bioaccumulation factor that is higher than 1 (Baker et al., 1994).
An ideal plant for environmental cleanup should have a high biomass production, combined with superior capacity for pollutant tolerance, accumulation, and degradation, depending on the type of pollutant and the phytoremediation technology of choice.
Hyperaccumulators are good candidates in phytoremediation, particularly for the removal of heavy metals. Phytoremediation efficiency of plants can be substantially improved using genetic engineering technologies (Cherian & Oliveira, 2005; Mello-Farias & Chaves, 2008).
Transferring the genes responsible for the hyperaccumulating phenotype to higher shootbiomass-producing plants has been suggested as a potential avenue for enhancing phytoremediation as a viable commercial technology (Pilon-Smits & Pilon, 2002; Martínez et al., 2006).
Some of the plants belonging to Brassicaceae such as Alyssum species, Thlaspi species and
Brassica juncea, Violaceae such as Viola calaminaria, Leguminosae such as Astragalus racemosus are known to take up high concentrations of heavy metals and radionucleides (Reeves &
Baker, 2000; Negri & Hinchman, 2000, Eapen & D´Souza, 2005).
To date, there are approximately 400 known hyperaccumulators metal in the world (Reeves
& Baker, 2000; Eapen & D´Souza, 2005) and the number is increasing. However, the remediation potential of many of these plants is limited because of their slow growth and low biomass (Chaney et al., 2000; Lasat, 2002; McGrath et al., 2002; Eapen & D´Souza, 2005).

4. Cellular and molecular mechanisms involved in phytoremediation
Exposure to pollutants may cause a series of symptoms in plants. Pollutant action can result in inhibition of cellular activity or rupture of cell structure, due to possible damages of essential components (Coutinho & Barbosa, 2005). Plants show some potential cellular and molecular mechanisms and strategies, which can be involved in detoxification of organic and inorganic pollutants such as herbicides, explosives and heavy metals. These mechanisms can be related to the cell wall composition and root environment, plasma membrane properties and integrity, enzymatic transformation, complexation with ligands and vacuolar compartmentalization
(Hall, 2002; Cherian & Oliveira, 2005). Depending on the nature of pollutant (organic or inorganic) plant cells can use one or some of these systems of remediation (Coutinho &
Barbosa, 2005; Cherian & Oliveira, 2005; Mello-Farias & Chaves, 2008).
4.1 Cell wall composition and rhizosphere
Organic contaminants, when in contact with roots, may be sorbed to the root structure. The hydrophobic or hydrophilic nature of the organic compounds also determines their possible uptake. Hemicellulose in the cell wall and the lipid bilayer of plant membranes can bind hydrophobic organic pollutants effectively (Pilon-Smits, 2005). In addition, the root uptake of chemicals depends on many factors as plant’s uptake efficiency, the transpiration rate, and the chemical concentration in soil water. Further, organic pollutants can be degraded or mineralized by plants, either independently or in association with microorganisms. For example, organics like polycyclic aromatic hydrocarbons (PAHs), polychlorinated

Transgenic Plants for Enhanced Phytoremediation – Physiological Studies

313

biphenyls, and petroleum hydrocarbons are sufficiently degraded by rhizospheric microbial activity (Olson et al., 2003). Plants have significant metabolic activity in both roots and shoots, and some of the enzymes involved in these metabolic processes (e. g. nitroreductases, dehalogenases, laccases, peroxidases, etc.) are useful in the remediation process (Schnoor et al. 1995; Wolfe & Hoehamer, 2003).
Even though mycorrhizas and ectomycorrhizas are not considered in general reviews of plant metal tolerance mechanisms, they can ameliorate the effects of metal toxicity on the host plant. However, the mechanism involved in conferring this increase of tolerance is not yet well explained; they may be quite diverse and show considerable species and metal specificity since large differences in response to metals have been observed, both between fungal species and to different metals (specially Zn, Cu and Cd) within species (Hall, 2002).
Finally, cell walls may play an important role in detoxifying metals in plant cells of the Ni and Zn/Cd hyperaccumulating plant species. About 60–70% of Ni and/or Zn accumulated is distributed in the apoplast cell walls (Krämer et al., 2000; Li et al., 2005; Yang et al., 2005b).
However, molecular bases of metal detoxification by cell walls are not well understood
(Yang et al., 2005b).
4.2 Plasma membrane properties and integrity
Although there is no direct evidence for a role for plasma membrane efflux transporters in heavy metal tolerance in plants, recent research has revealed that plants possess several classes of metal transporters that must be involved in metal uptake and homeostasis in general and, thus, could play a key role in tolerance (Yang et al., 2005a). Transport proteins and intracellular high-affinity binding sites mediate the uptake of metals across the plasma membrane. A comprehensive understanding of the metal transport processes in plants is essential for formulating effective strategies to develop genetically engineered plants that can accumulate specific metals (Yang et al., 2005b).
Several classes of proteins have been implicated in heavy metal transport in plants. These include the heavy metal (or CPx-type) ATPases that are involved in the overall metal-ion homeostasis and tolerance in plants, the natural resistance-associated macrophage protein
(Nramp) family of proteins, and the cation diffusion facilitator (CDF) family proteins
(Williams et al., 2000), zinc–iron permease (ZIP) family proteins, etc. (Yang et al., 2005a; 2005b).
CPx-type heavy metal ATPases have been identified in a wide range of organisms and have been implicated in the transport of essential as well as potentially toxic metals like Cu, Zn, Cd, Pb across cell membranes (Williams et al.,
2000; Yang et al., 2005a; 2005b). These transporters use ATP to pump a variety of charged substrates across cell membranes and are distinguished by the formation of a charged intermediate during the reaction cycle (Yang et al., 2005a; 2005b).
Transport of metals and alkali cations across plant plasma membrane and organellar membranes is essential for plant growth, development, signal transduction, and toxic metal phytoremediation (Cherian and Oliveira, 2005).
Another factor concerning plasma membrane seems to be the maintenance of its physical integrity in presence of heavy metals, in order to prevent or reduce their entry in the cell, besides the efflux mechanisms described above (Hall, 2002; Coutinho & Barbosa, 2005).
4.3 Enzimatic transformation
Enzimatic transformation in plants concerns mainly organic pollutants and it can be considered a case of phytotransformation. In this process plants uptake organic pollutants and, subsequently, metabolize or transform them into less toxic metabolites. Once taken up

314

Genetic Transformation

and translocated the organic chemicals generally undergo three transformation stages: (a) chemical modification (oxidations, reductions, hydrolysis); (b) conjugation (with glutathione, sugars, amino acids); and (c) sequestration or compartmentalization
(conjugants are converted to other conjugates and deposited in plant vacuoles or bound to the cell wall and lignin) (Ohkawa et al., 1999; Cherian and Oliveira, 2005).
Plant enzymes that typically catalyze the first phase of the reactions are P450 monoxygenases and carboxylesterases (Coleman et al., 1997; Burken, 2003). The second phase involves conjugation to glutathione (GSH), glucose, or amino acids, resulting in soluble, polar compounds (Marrs, 1996). For instance, detoxification of herbicides in plants is attributed to conjugation with glutathione catalyzed by glutathione S-transferase (GST)
(Lamoureux et al., 1991). It was also reported that a group of GSTs mediate conjugation of organics to GSH in the cytosol (Kreuz et al., 1996; Neuefeind et al., 1997). Sometimes organic pollutants, such as atrazine and TNT, are partially degraded and stored in vacuoles as bound residues (Burken & Schnoor, 1997). The third phase of plant metabolism is compartmentalization and storage of soluble metabolites either in vacuoles or in the cell wall matrix. The glutathione S-conjugates are actively transported to the vacuole or apoplast by ATP-dependent membrane pumps (Martinoia et al., 1993). Also, an alternate conjugation-sequestration mechanism for organics exists in plants and involves coupling of a glucose or malonyl group to the organic compound, followed by the transport of the conjugate to the vacuole or the apoplast (Coleman et al., 1997).
Mechanisms as complexation whit ligands and vacuolar compartmentalization are described below.
4.4 Complexation with ligands
Complexation with ligands is a process associated to heavy metal pollutants, and it can be an extracellular or an intracellular molecular event. These ligands can be chelators as organic acids or peptides such phytochelatins (PCs), methallothioneins (MTs) or glutathione
(GSH) (Mello-Farias & Chaves, 2008).
Plant tolerance to heavy metals depends largely on plant efficiency in the uptake, translocation, and further sequestration of heavy metals in specialized tissues or in trichomes and organelles such as vacuoles. The uptake of metals depends on their bioavailability, and plants have evolved mechanisms to make micronutrients bioavailable
(Cherian and Oliveira, 2005). Chelators such as siderophores, organic acids, and phenolics can help release metal cations from soil particles, increasing their bioavailability. For example, organic acids (malate, citrate) excreted by plants act as metal chelators. By lowering the pH around the root, organic acids increase the bioavailability of metal cations
(Ross, 1994). However, organic acids may also inhibit metal uptake by forming a complex with the metal outside the root. Citrate inhibition of Al uptake resulting in aluminum tolerance in several plant species is an example of this mechanism (De la Fuente et al., 1997;
Pineros & Kochian, 2001; Papernik et al. 2001). Copper tolerance in Arabidopsis is also the result of a similar mechanism (Murphy et al., 1999).
Intracellular complexation involves peptide ligands, such as metallothioneins (MTs) and phytochelatins (PCs) (Yang et al., 2005b). Chelation of metals in the cytosol by high-affinity ligands is potentially a very important mechanism of heavy-metal detoxification and tolerance (Hall, 2002).
Metallothioneins (MTs) are cysteine-rich proteins that have high affinity to cations such as
Cd, Cu, and Zn (Cobbet & Goldsbrough, 2002; Singh et al., 2003; Cherian & Oliveira, 2005).

Transgenic Plants for Enhanced Phytoremediation – Physiological Studies

315

They confer heavy-metal tolerance and accumulation in yeast. Overexpression of genes involved in the synthesis of metal chelators may lead to enhanced or reduced metal uptake and enhanced metal translocation or sequestration, depending on the type of chelator and on its role and location (Cherian & Oliveira, 2005; Pilon-Smits, 2005). MT proteins were originally isolated as Cu, Cd and Zn binding proteins in mammals. There is now good evidence that four categories of these proteins occur in plants, which are encoded by at least seven genes in Arabidopsis thaliana (Cobbett & Goldsbrough, 2002; Hall, 2002; Gratão et al.,
2005).
The biosynthesis of MTs is regulated at the transcriptional level and is induced by several factors, such as hormones, cytotoxic agents, and metals, including Cd, Zn, Hg, Cu, Au, Ag,
Co, Ni, and Bi (Yang et al., 2005a).
Phytochelatins are a class of post-translationally synthesized (cysteine-rich metal-chelating) peptides that play a pivotal role in heavy-metal tolerance in plants and fungi by chelating these substances and decreasing their free concentrations (Vatamaniuk et al., 1999). PCs have been most widely studied in plants, particularly in relation to Cd tolerance (Cobbett,
2000; Goldsbrough, 2000). PCs consist of only three amino acids, glutamine (Glu), cysteine
(Cys), and glycine (Gly). They are structurally related to the tripeptide glutathione (GSH), and are enzymatically synthesized from GSH. PCs form a family of structures with increasing repetitions of the -Glu-Cys dipeptide followed by a terminal Gly, (-Glu-Cys)nGly, where n is generally in the range of 2–5, but can be as high as 11 (Cobbett, 2000; Yang et al., 2005b).
Many plants cope with the higher levels of heavy metals by binding them to PCs and sequestering the complexes inside their cells (Yang et al., 2005a). As mentioned above, PCs are synthesized non-translationally, using glutathione as a substrate by PC synthase, an enzyme that is activated in the presence of metal ions (Cobbett, 2000). So, PCs are structurally related to glutathione (GSH; γ-GluCysGly), and numerous physiological, biochemical, and genetic studies have confirmed that GSH (or, in some cases, related compounds) is the substrate for PC biosynthesis (Cobbett, 2000; Cobbett and Goldsbrough,
2002).
Although PCs clearly can have an important role in metal detoxification, alternative primary roles of PCs in plant physiology have also been proposed. These have included roles in essential metal ion homeostasis and in Fe or sulphur metabolism (Sanita di Toppi &
Gabbrielli, 1999; Cobbett and Goldsbrough, 2002). However, there is currently no direct evidence that PCs have functions outside of metal detoxification.
Because of MTs and PCs peptidic nature and because they bind metals in thiolate complexes, these peptide molecules demand a greater input of amino acids (especially cysteine), sulfur and nitrogen from the plant as the level of accumulated metals rise. Their synthesis is energy expensive and requires significant amounts of the growth limiting elements sulfur and nitrogen. Increased synthesis might thus at some point affect plant growth and therefore limit their use as phytoremediators (Tong et al., 2004).
4.5 Vacuolar compartmentalization
The vacuole is generally considered to be the main storage site for metals in yeast and plant cells and there is evidence that phytochelatin–metal complexes are pumped into the vacuole in fission yeast (Schizosaccharomyces pombe) and in plants (Tong et al., 2004; Yang et al.,
2005b). Compartmentalization of metals in the vacuole is also part of the tolerance mechanism of some metal hyperaccumulators. The Ni hyperaccumulator Thlaspi goesingense

316

Genetic Transformation

enhances its Ni tolerance by compartmentalizing most of the intracellular leaf Ni into the vacuole (Krämer et al., 2000; Tong et al., 2004). High-level expression of a vacuolar metal ion transporter TgMTP1 in T. goesingense was proposed to account for the enhanced ability to accumulate metal ions within shoot vacuoles (Persans et al., 2001; Tong et al., 2004; Yang et al., 2005b).

5. Genetically engineered plants for phytoremediation
The genetic and biochemical basis is becoming an interesting target for genetic engineering, because the knowledge of molecular genetics model organisms can enhance the understanding of the essencial metal metabolism components in plants.A fundamental understanding of both uptake and translocation processes in normal plants and metal hyperaccumulators, the regulatory control of these activities, and the use of tissue specific promoters offer great promise that the use of molecular biology tools can give scientists the ability to develop effective and economic phytoremediation plants for soil metals (Chaney et al., 1997; Fulekar et al., 2008). Plants such as Populus angustifolia, Nicotiana tabacum or Silene cucubalis have been genetically engineered to overexpress glutamylcysteine syntlietase, and thereby provide enhanced heavy metal accumulation as compared with a corresponding wild type plant (Fulekar et al., 2008).
Candidate plants for genetic engineering for phytoremediation should be a high biomass plant with either short or long duration (trees), which should have inherent capability for phytoremediation. The candidate plants should be amicable for genetic transformation.
Some of high biomass hyperaccumulators for which regeneration protocols are already developed include Indian mustard (Brassica juncea), sunflower (Helianthus annuus), tomato
(Lycopersicon esculentum) and yellow poplar (Liriodendron tulipifera) (Eapen & D’Souza, 2005;
Mello-Farias & Chaves, 2008).
The application of powerful genetic and molecular techniques may surely identify a range of gene families that are likely to be involved in transition metal transport. Considerable progress has been made recently in identifying plant genes encoding metal ion transporters and their homologous in hyperaccumulator plants. Therefore, it is hoped that genetic engineering may offer a powerful new means by which to improve the capacity of plants to remediate environmental pollutants (Yang et al., 2005a; Mello-Farias & Chaves, 2008).
Brassica juncea was genetically engineered to investigate rate-limiting factors for glutathione and phytochelatin production. To achieve this, Escherichia coli gshl gene was introduced. The γ-ECS transgenic seedlings showed increased tolerance to cadmium and had higher concentrations of phytochelatins, γ-GluCys, glutathione, and total nonprotein thiols compared to wild type seedlings (Ow, 1996; Fulekar et al., 2008). Study showed that cglutamylcysteine synthetase inhibitor, L-buthionine-[S,R]-sulphoximine (BSO), dramatically increases As sensitivity, both in non-adapted and As-hypertolerant plants, showing that phytochelatin-based sequestration is essential for both normal constitutive tolerance and adaptative hypertolerance to this metalloid (Schat et al., 2002; Fulekar et al., 2008).
Some genes have been isolated and introduced into plants with increased heavy metal (Cd) resistance and uptake, like AtNramps (Thomine et al., 2000), AtPcrs (Song et al., 2004), and
CAD1 (Ha et al., 1999) from Arabidopsis thaliana, library enriched in Cd-induced cDNAs from
Datura innoxia (Louie et al., 2003), gshI, gshII (Zhu et al., 1999a) and PCS cDNA clone (Heiss et al., 2003) from Brassica juncea.
There are some examples of transgenic plants for metal tolerance/phytoremediation, as tobacco with accumulation of Cd, Ca and Mn transformed with gene CAX-2 (vacuolar

Transgenic Plants for Enhanced Phytoremediation – Physiological Studies

317

transporters) from A. thaliana (Hirschi et al., 2000); A. thaliana tolerant to Al, Cu, and Na with gene Glutathione-S-transferase from tobacco (Ezaki et al., 2000); tobacco with Ni tolerance and
Pb accumulation with gene Nt CBP4 from tobacco (Arazi et al., 1999); tobacco (Goto et al.,
1998) and rice (Goto et al., 1998; 1999) with increased iron accumulation with gene Ferretin from soybean; A. thaliana and tobacco resistant to Hg with gene merA from bacteria (Rugh et al., 2000; Bizily et al., 2000; Eapen & D’Souza, 2005); indian mustard tolerant to Se transformed with a bacterial glutathione reductase in the cytoplasm and also in the chloroplast (D´Souza et al., 2000); transgenic A. thaliana plants expressing SRSIp/ArsC and
ACT 2p/γ-ECS together showed high tolerance to As, these plants accumulated 4- to 17-fold greater fresh shoot weight and accumulated 2- to 3-fold more arsenic per gram of tissue than wild plants or transgenic plants expressing γ-ECS or ArsC alone (Dhankher et al., 2002;
Mello-Farias & Chaves, 2008).
Even though there is a variety of different metal tolerance mechanisms, and there are many reports of transgenic plants with increased metal tolerance and accumulation, most, if not all, transgenic plants created to date rely on overexpressing genes involved in the biosynthesis pathways of metal-binding proteins and peptides (Zhu et al., 1999b; Mejäre &
Bülow, 2001; Bennett et al., 2003; Gisbert et al., 2003), genes that can convert a toxic ion into a less toxic or easier to handle form, or a combination of both (Dhankher et al., 2002; Yang et al., 2005b; Mello-Farias & Chaves, 2008).
At least three different engineering approaches to enhanced metal uptake can be envisioned
(Clemens et al., 2002), which include enhancing the number of uptake sites, alteration of specificity of uptake system to reduce competition by unwanted cations and increasing intracellular binding sites. Each metal has specific molecular mechanism for uptake, transport and sequestration (Eapen & D’Souza, 2005; Mello-Farias & Chaves, 2008).
New metabolic pathways can be introduced into plants for hyperaccumulation or phytovolatilization as in case of MerA and MerB genes which were introduced into plants which resulted in plants being several fold tolerant to Hg and volatilized elemental mercury
(Bizily et al., 2000; Dhankher et al., 2002; Eapen & D’Souza, 2005) developed transgenic
Arabidopsis plants which could transport oxyanion arsenate to aboveground, reduce to arsenite and sequester it to thiol peptide complexes by transfer of Escherichia coli ars C and γECS genes (Eapen & D’Souza, 2005).
Alteration of oxidative stress related enzymes may also result in altered metal tolerance as in the case of enhanced Al tolerance by overexpression of glutathione-S-transferase and peroxidase (Ezaki et al., 2000; Eapen & D’Souza, 2004). Overexpression of 1aminocyclopropane-1-carboxylic acid (ACC) deaminase led to an enhanced accumulation of a variety of metals (Grichko et al., 2000; Eapen & D’Souza, 2005).
According to Eapen & D’Souza (2005), it is essential to have plants with highly branched root systems with large surface area for efficient uptake of toxic metals. Experiments had shown that Agrobacterium rhizogenes could enhance the root biomass in some hyperaccumulator plants (Eapen, unpublished work). The hairy roots induced in some of the hyperaccumulators were shown to have high efficiency for rhizofiltration of radionuclide (Eapen et al., 2003) and heavy metals (Nedelkoska and Doran, 2000; Eapen et al., unpublished work).
Nowadays there are many different examples of genes that have been used for the development of transgenic plants for metal tolerance and/or phytoremediation, as shown on Table 2.

318

Genetic Transformation

6. Advantages and disadvantages of phytoremediation
Admittedly, phytoremediation has benefits to restore balance to a stressed environment, but it is important to proceed with caution. Plants enjoy enormous reduction in energy cost and utilization by virtue of deriving energy from solar radiation. The plant tolerates a wide range of environmental conditions.

Gene transferred

Origin

Target plant species

Effect

MT2 gene
MT1 gene
MTA gene
CUP-1 gene
CUP-1 gene γ-Glutamylcysteine synthetase
Glutathione
synthetase
Cysteine synthetase
CAX-2 (vacuolar transporters) Human
Mouse
Pea
Yeast
Yeast

Tobacco, oil seed rape
Tobacco
Arabidopsis
Cauliflower
Tobacco

Cd tolerance
Cd tolerance
Cu accumulation
Cd accumulation
Cu accumulation

E. coli

Indian mustard

Cd tolerance

Rice

Indian mustard

Cd tolerance

Rice

Tobacco

Arabidopsis

Tobacco

At MHX

Arabidopsis

Tobacco

Nt CBP4

Tobacco

Tobacco

FRE-1 and FRE-2
Glutathione-sTransferase
Citrate synthase
Nicotinamine amino transferase (NAAT)

Yeast

Tobacco

Cd tolerance
Accumulation of
Cd, Ca and Mn
Mg and Zn tolerance Ni tolerance and Pb accumulation More Fe content

Tobacco

Arabidopsis

Al, Cu, Na tolerance

Bacteria

Arabidopsis

Barley

Rice

Ferretin

Soybean

Tobacco

Ferretin

Soybean

Rice

Al tolerance
Grew in iron deficient soils
Increased iron accumulation Increased iron accumulation Arabidopsis

Arabidopsis

Zn accumulation

Bacteria

Indian mustard

As tolerance

E. coli

Arabidopsis

A. bisculatus

A. thaliana

Zn transporters ZAT
(At MTPI)
Arsenate reductase γ- glutamylcysteine synthetase Znt A-heavy metal transporters Selenocysteine methyl transferase
ATP sulfurylase
CAPS

Indian mustard

Cd and Pb resistance Resistance to selenite Se tolerance

319

Transgenic Plants for Enhanced Phytoremediation – Physiological Studies

Gene transferred

Origin

Cystathione-gamma synthase (CGS)
Glutathione-Stransferase,
peroxidase
Glutathione
reductase

Target plant species

Effect

Indian mustard

Se volatilization

Arabidopsis

Al tolerance

B. juncea

Cd accumulator
Many metal tolerance Cd and Pb tolerance
Se tolerance and accumulation ACC-deaminase

Bacteria

YCF1

Yeast

Arabidopsis

Se-cys lyase

Mouse

Arabidopsis

Phytochelatin synthase (Ta PCS)

Wheat

Nicotiana glauca

Pb accumulation

Table 2. Selected examples of transgenic plants for metal tolerance/phytoremediation (from
Eapen & D’Souza, 2005)
The molecular composition of plants, mainly related to their enzyme and protein profiles, is of great interest to phytoremediation, because this technology can exploit plant molecular and cellular mechanisms of detoxification, through the use of genetic engineering tools.
The nature of plants is still an advantage because they are able to develop, over time, complex mechanisms to absorb nutrients, detoxify pollutants and control the local geochemical conditions. The plants play an important role in regulation water contant in soil avoiding the penetration of liquids by infiltration, which is the main mechanism of entry of contaminants. Plant roots supplement microbial nutrients and provide aeration to the soil, increasing consequently microbial population compared to non-vegetated area. Above all, phytoremediation gives better aesthetic appeal than other physical means of remediation.
On the other hand, phytoremediation has several limitations that require further intensive research on plants and soil conditions. A major disadvantage is that this method of detoxification is too slow or only seasonally effective. Regulatory agencies often require significant progress in remediation to be made in only a few years, making most phytoremediation unsuitable. In many cases, like trichloroethylene and carbon tetrachloride, the concentration of pollutant is not reduced satisfactorily. Besides, in some contaminated sites, the pollutants can reach phytotoxic concentration, making the plant ineffective. For this reason, recent studies have been conducted with the aim of increasing the phytoremediation potential of plants using genetic engineering (Danh et al. 2009). In phytoremediation technology, multiple metal contaminated soil and water require specific metal hyperaccumulator species and therefore, a wide range of research prior to the application. Other factors are also tied to the success of phytoremediation such as the existence of a pollutant in a bio-available form. If the metal is strongly linked to the organic soil it will not be available to the plant. Moreover, the plants are quite specific to certain pollutants. Hyperaccumulators of Cd and Zn (Thlaspi caerulescens) can be sensitive to other metals, such as Cu, not allowing the detoxification of polluted areas with different pollutants (Mijovilovich et al., 2009). Despite the current limitations, present day phytoremediation technology is used worldwide and several researchers are working to

320

Genetic Transformation

overcome these limitations. Table 3 resumes advantages and limitations of some of the subprocess of phytoremediation.

7. Perspectives on biotechnology - based phytoremediation
The environmental contamination by pollutants, organic or inorganic, has great importance due to its impacts on human and animal health. Thus, the most effective and inexpensive technologies to promote detoxification are necessary in the recovery of affected biomes.
Great efforts have been made in identifying plant species and their detoxification mechanisms more efficient on those places. The mechanisms of pollutant uptake, accumulation, exclusion, among others, vary according to each plant species and are very important, for they will determine its specific role in phytoremediation.
Plants can have their detoxification capabilities significantly enhanced through the identification of specific genes in certain promising species and the transmission of these to other species, using genetic engineering tools. This can play a significant role in the more effective detoxification of contaminated sites by improving the cost-benefit.
Advantage

Limitation
Phytoextraction
Metal hyperaccumulators are generally
The plant must be able to produce abundant slow-growing and bioproductivity is biomass in short time. e. g.: in a greenhouse rather small and shallow root systems. experiment, gold was harvested from plants.
Phytomass after process must be disposed off properly
Phytostabilization
Often requires extensive fertilization or
It circumvents the removal of soil, low cost soil modification using amendments; and is less disruptive and enhances long-term maintenance is needed to ecosystem restoration/re-vegetation prevent leaching.
Phytovolatilization
The contaminant or a hazardous
Contaminant/Pollutant will be transformed metabolite might accumulate in plants into less-toxic forms. e. g.: elemental mercury and be passed on in later products such and dimethyl selenite gas. Atmospheric as fruit or lumber. Low levels of processes such as photochemical degradation metabolites have been found in plant for rapid decontamination/transformation. tissue. Phytofiltration/rhizofiltration pH of the medium to be monitored continually for optimizing uptake of
It can be either in situ (floating rafts on metals; chemical speciation and ponds) or ex situ (an engineered tanks interactions of all species in the influent system); terrestrial or aquatic. need be understood; functions like a bioreactor and intensive maintenance is needed. Table 3. Advantages and limitations of some of the phytoremediation sub-processes (Prasad,
2004; Gratão et al. 2005)

Transgenic Plants for Enhanced Phytoremediation – Physiological Studies

321

Studies on phytoremediation are developed in order to benefit the environment. Several pollutants are bringing some kind of harm to all habitats. Thus, the use of specific techniques already represents hope. The necessary mechanisms are different, however, the organisms, especially plants, have specific ways for the removal, detention or conversion of specific pollutants. The study and subsequent evaluation of the interaction between the soil and its microorganisms, plant and pollutant is very necessary and guiding.
All things considered, more studies must be carried out in this area to better know the phytoremediation capacity of living organisms and their possible use in combating pollution through plant transformation technology.

8. References
Alexander, M. (1999). Biodegradation and bioremediation. Ithaca, NY, USA: Academic Press.
Arazi, T.; Sunkar, R.; Kaplan, B. & Fromm, H.A. (1999). Tobacco plasma membrane calmodulin binding transporter confers Ni+ tolerance and Pb2+ hypersensitivity in transgenic plants. Plant Journal, Vol.20, pp. 171-182.
Baker, A.J.M. & Brooks, R.R. (1989). Terrestrial higher plants which hyperaccumulate metallic elements – a review of their distribution, ecology and phytochemistry.
Biorecovery, Vol.1, pp. 81-126.
Baker, A.J.M.; McGrath, S.P.; Sidoli, C.M.D. & Reeves, R.D. (1994). The possibility of in situ heavy metal decontamination of polluted soils using crops of metal accumulating plants. Resources, Conservation and Recycling, Vol.11, pp. 42-49.
Baudouin, C.; Charveron, M.; Tarrouse, R. & Gall, Y. (2002). Environmental pollutants and skin cancer. Cell Biology and Toxicology, Vol.18, pp. 341-348.
Bennett, L.E.; Burkhead, J.L.; Hale, K.L.; Terry, N.; Pilon, M. & Pilon-Smits, E.A.H. (2003).
Analysis of transgenic Indian mustard plants for phytoremediation of metalcontaminated mine tailings. Journal of Environmental Quality, Vol.32, pp. 432440.
Bizily, S.P.; Rugh, C.L. & Meagher, R.B. (2000). Phytodetoxification of hazardous organomercurials by genetically engineered plants. Nature Biotechnology, Vol.18, pp.
213-217.
Burken, J.G. & Schnoor, J.L. (1997). Uptake and metabolism of atrazine by poplar trees.
Enviromental Science and Technology, Vol.31, pp. 1399-1406.
Burken, J.G. (2003). Uptake and metabolism of organic compounds: green-liver models. In:
Phytoremediation: Transformation and Control of Contaminants, McCutcheon, S.C. &
Schnoor, J. L. (Ed.), 59-84, Wiley: New York.
Chaney, R.L.; Malik, M.; Li, Y.M.; Brown, S.L.; Angle, J.S. & Baker, A.J.M. (1997).
Phytoremediation of soil metals. Current Opinion in Biotechnology, Vol.8, pp. 279284.
Chaney R.L.; Li, Y.M.; Brown, S.L.; Homer, F.A.; Malik, M.; Angle, J.S.; Baker, A.J.M.;
Reeves, R.D. & Chin, M. (2000) Improving metal hyperaccumulator wild plants to develop phytoextraction systems: approaches and progress. In: Phytoremediation of contaminated soil and water, Terry, N. & Banuelos, G. (Ed.) 129-158, Boca: Lewis
Publishers.
Cherian, S. & Oliveira, M.M. (2005). Transgenic Plants in Phytoremediation: Recent
Advances and New Possibilities. Environmental Science & Technology, Vol.39, No.24, pp. 9377-9390.

322

Genetic Transformation

Clemens, S.; Palmgren, M.G. & Krämer, U. (2002). A long way ahead: understanding and engineering plant metal accumulation. Trends in Plant Science, Vol.7, pp. 309– 314.
Cobbett, C.S. (2000). Phytochelatin biosynthesis and function in heavy-metal detoxification.
Current Opinion in Plant Biology, Vol.3, pp. 211-216.
Cobbett, C. & Goldsbrough, P. (2002). Phytochelatins and Metallothioneins: Roles in Heavy
Metal Detoxification and Homeosteasis. Annual Review of Plant Biology, Vol.53, pp.
159-182.
Coleman, J.O.D.; Blake-Kalff, M.M.A. & Davies, T.G.E. (1997). Detoxification of xenobiotics by plants: chemical modification and vacuolar compartmentation. Trends in Plant
Science, Vol.2, pp. 144-151.
Coutinho, D.H. & Barbosa, A.R. (2007). Fitorremediação: Considerações Gerais e
Características de Utilização. Silva Lusitana, Vol.15, No.1, pp. 103 - 117, Portugal.
Cunningham, S.D. & Lee, C.R. (1995). Phytoremediation: Plant-based remediation of contaminated soils and sediments. In: Bioremediation: Science and Applications,
Skipper, H.D. & Turco, R.F. (Ed.), 145-156, SSSA Special Publication 43, Soil Science
Society of America, Madison, WI.
Cunningham, S.D. & Ow, D.W. (1996). Promises and prospects of phytoremediation. Plant
Physiology, Vol.110, No.3, pp. 715-719.
Cunningham, S.D.; Shann, J.R.; Crowley, D.E. & Anderson, T.A. (1997). Phytoremediation of contaminated water and soil: Phytoremediation of soil and water contaminations.
ACS Symposium Series, Vol.664, pp. 2-17.
Danh, L.T.; Truong, P.; Mammucari, R.; Tran, T. & Foster, N. (2009). Vetiver grass, Vetiveria zizanioides: A choice plant for phytoremediation of heavy metals and organic wastes. International Journal of Phytoremediation, Vol.11, pp. 664-691.
De la Fuente, J.M.; Ramirez-Rodriguez, V.; Cabrera-Ponce, J.L. & Herrera-Estrella, L. (1997).
Aluminium tolerance in transgenic plants by alteration of citrate synthesis. Science,
Vol.276, pp. 1566-1568.
Dhankher, O.P.; Li, Y.; Rosen, B.P.; Shi, J.; Salt, D.; Senecoff, J.F.; Sashti, N.A. & Meagher,
R.B. (2002). Engineering tolerance and hyperaccumulation of arsenic in plants by combining arsenate reductase and g-glutamylcysteine synthetase expression.
Nature Biotechnology, Vol.20, pp. 1140-1145.
Dietz, A.C. & Schnoor, J.L. (2001). Advances in phytoremediation. Environmental Health
Perspectives, Vol.109, pp. 163–168.
Doty, S.L. Enhancing phytoremediation through the use of transgenics and endophytes.
(2008). New Phytologist, Vol.179, pp. 318–333.
D´Souza, M.P.; Pilon-Smits, E.A.H. & Terry, N. (2000). The physiology and biochemistry of selenium volatilization by plants. In: Phytoremediation of toxic metals: using plants to clean up the environment, Raskin, I. & Ensley, B.D. (Ed.) 171- 188.
Dushenkov, S. (2003). Trend in phytoremediation of radionuclides. Plant and Soil, Vol.249, pp. 167-175.
Eapen, S.; Suseelan, K.; Tivarekar, S.; Kotwal, S. & Mitra, R. (2003). Potential for rhizofiltration of uranium using hairy root cultures of Brassica juncea and
Chenopodium amaranticolor. Environmental Research, Vol.91, pp. 127–33.
Eapen, S. & D’Souza, S.F. (2005). Prospects of genetic engineering of plants for phytoremediation of toxic metals. Biotechnology Advances, Vol.23, pp. 97– 114.

Transgenic Plants for Enhanced Phytoremediation – Physiological Studies

323

Eapen, S.; Singh, S. & D´Souza, S.F. (2007). Advances in development of transgenic plants for remediation of xenobiotic pollutants. Biotechnology Advances, Vol.25, pp. 442–
451.
Estevez-Núnez, A.; Caballero, A. & Ramos, J.L. (2001). Biological degradation of 2,4,6trinitrotoluene. Microbiology and Molecular Biology Reviews, Vol.65, No.3, pp. 335352.
Ezaki, B.; Gardner, R.C.; Ezaki, Y. & Matsumoto, H. (2000). Expression of aluminium induced genes in transgenic Arabidopsis plants can ameliorate aluminium stress and/or oxidative stress. Plant Physiology, Vol.122, pp. 657-665.
Fingerman, M. & Nagabhushanum, R. (2005). Bioremediation of aquatic and terrestrial ecosystems. Enfield, NH, USA: Science Publishers.
Fulekar, M.H.; Singh, A. & Bhaduri, A.M. (2008). Genetic engineering strategies for enhancing phytoremediation of heavy metals. African Journal of Biotechnology, Vol.8,
No.4, pp. 529-535.
Garbisu, C.; Hernandez, A.J.; Barrutia, O. Alkorta, J. & Bacerril, J.M. (2002).
Phytoremediation: a technology using green plants to remove contaminants from pollutes areas. Reviews of Environmental Health, Vol.17, No.3, pp. 173-188.
Gisbert, C.; Ros, R.; De Haro, A.; Walker, D.J.; Bernal, M.P.; Serrano, R. & Navarro-Avino, J.
(2003). A plant genetically modified that accumulates Pb is especially promising for phytoremediation. Biochemical and Biophysiscal Research Communities, Vol.303, pp.
440-445.
Glass, D. (1999). U.S. and International Markets for Phytoremediation, 1999–2000. Needham,
MA, USA: D. Glass Associates, Inc.
Goldsbrough, P. (2000). Metal tolerance in plants: the role of phytochelatins and metallothioneins. In: Phytoremediation of contaminated soil and water, Terry N. &
Bañuelos G. (Ed.), 221-233, CRC Press LLC.
Goto, F.; Yoshihara, T. & Saiki, H. (1998). Iron accumulation in tobacco plants expressing soybean ferritin gene. Transgenic Research, Vol.7, pp. 173-80.
Goto, F.; Yoshihara, T.; Shigemoto, N.; Toki, S. & Takaiwa, F. (1999). Iron accumulation in rice seed by soybean ferritin gene. Nature Biotechnology, Vol.17, pp. 282-286.
Gratão, P.L.; Prassad, M.N.V.; Cardoso, P.F.; Lea, P.J. & Azevedo, R.A. (2005).
Phytoremediation: green technology for the clean up of toxic metals in the environment. Brazilian Journal of Plant Physiology, Vol.17, No.1, pp. 53-64.
Grichko, V.P.; Filby, B. & Glick, B,R. (2000). Increased ability of transgenic plants expressing the bacterial enzyme ACC deaminase to accumulate Cd, Co, Cu, Ni, Pb and zinc.
Journal of Biotechnology, Vol.81, pp. 45– 53.
Ha, S.B.; Smith, A.P.; Howden, R.; Dietrich, W.M.; Bugg, S.; O 'Connell, M.J.; Goldsbrough,
P.B. & Cobbett, C.S. (1999). Phytochelatin synthase genes from Arabidopsis and the yeast Schizosaccharomyces pombe. Plant Cell, Vol.11, pp. 1153-1163.
Hall, J.L. (2002). Cellular mechanisms for heavy metal detoxification and tolerance. Journal of
Experimental Botany, Vol.53, pp. 1-11.
Heiss, S.; Wachter, A.; Bogs, J.; Cobbett, C. & Rausch, T. (2003). Phytochelatin synthase (PCS) protein is induced in Brassica juncea leaves after prolonged Cd exposure. Journal of
Experimental Botany, Vol.54, pp. 1833-1839.

324

Genetic Transformation

Hirschi, K.D.; Korenkov, V.D.; Wilganowski, N.L. & Wagner, G.J. (2000). Expression of
Arabidopsis CAX2 in tobacco altered metal accumulation and increased manganese tolerance. Plant Physiology, Vol.124, pp. 125-33.
Hooda, V. (2007). Phytoremediation of toxic metals from soil and waste water. Journal of
Environmental Biology, Vol.28, No.2, pp. 367-376.
Horne, A.J. (2000). Phytoremediation by constructed wetlands: In: Phytoremediation of contaminated soil and water, Terry, N. & Bañuelos, G. (Ed.), 13-40, Boca Raton: Lewis.
Huang, J.W. & Cunningham, S.D. (1996). Lead phytoextraction: species variation in lead uptake and translocation. New Phytologist, Vol.134, No.1, pp. 75-84.
Jaffré, T.; Brooks, R.R.; Lee, J. & Reeves, R.D. (1976). Sebertia acuminata: a hyperaccumulator of nickel from New Caledonia. Science, Vol.193, pp. 579–580.
Jacobson, M.E.; Chiang, S.Y.; Gueriguian, L.; Weshtholm, L.R. & Pierson, J. (2003).
Transformation kinetics of trinitrotoluene conversion in aquatic plants. In:
Phytoremediation: Transformation and control of contaminants, McCutcheon, S.C. &
Schnoor, J.L. (Ed.), 409-427,Wiley, NY.
Karenlampi, S.; Schat, H.; Vangronsveld, J.; Verkleij, J.A.C.; Van der Lelie, D.; Mergeay, M. &
Tervahauta, A.L. (2000). Genetic engineering in the improvement of plants for phytoremediation of metal polluted soils. Environmental Pollution, Vol.107, pp. 225–
31.
Knasmuller, S.; Gottmann, E.; Steinkellner, H.; Fomin, A.; Pickl, C.; Paschke, A.; God, R. &
Kundi, M. (1998). Detection of genotoxic effects of heavy metal contaminated soils with plant bioassays. Mutation Research, Vol.420, pp. 37-48.
Krämer, U.; Pickering, I.J.; Prince, R.C.; Raskin, I. & Salt, D.E. (2000). Subcellular localization and speculation of nickel in hyperaccumulator and non-accumulator Thlaspi species. Plant Physiology, Vol.122, pp. 1343-53.
Krämer, U. & Chardonnens, A.N. (2001). The use of transgenic plants in the bioremediation of soils contaminated with trace elements. Applied Microbiology and Biotechnology,
Vol.55, pp. 661-672.
Kreuz, K.; Tommasini, R. & Martinoia, E. (1996). Old enzymes for a new job: herbicide detoxification in plants. Plant Physiology, Vol.111, pp. 349-353.
Lamoureux, G.L.; Rusness, D.G.; Schroder, P. & Rennenberg, H. (1991). Diphenyl ether herbicide metabolism in a spruce cell suspension culture: the identification of two novel metabolites derived from glutathione conjugation. Pesticide Biochemistry and
Physiology, Vol.39, pp. 291-301.
Langenbach, T. (1994). Degradação de xenobiontes: potencialidades e limites. In:
Microrganismos de importância agrícola, Araújo, R.S. & Hungia, M. (Ed.), 218-236,
Brasília: EMBRAPA-SPI.
Lasat, M.M. (2002). Phytoextraction of toxic metals: a review of biological mechanisms.
Journal of Environmental Quality, Vol.31, pp. 109– 20.
Li, T.Q.; Yang, X.E.; He, Z.L.; Yang, J.Y. & Long, X.X. (2005). Zn accumulation and subcellular distribution in leaves of Zn hyperaccumulator species of Sedum alfredii
Hance. Pedosphere, Vol.16, No.5, pp. 616-623.
Lin, C.F.; Lo, S.S.; Lin, H.Y. & Lee, Y.C. (1998). Stabilization of cadmium contaminated soils using synthesized zeolite. Journal of Hazardous Material, Vol.60, pp. 217-226.

Transgenic Plants for Enhanced Phytoremediation – Physiological Studies

325

Louie, M.; Kondor, N. & Witt, J.G. (2003). Gene expression in cadmium-tolerant Datura innoxia: Detection and characterization of cDNAs induced in response to Cd2+.
Plant Molecular Biology, Vol.52, pp. 81-89.
Marrs, K.A. (1996). The functions and regulation of glutathione S-transferase in plants.
Annual Review of Plant Physioogy and Plant Molecular Biology, Vol.47, pp. 127-158.
Martínez, M.; Bernal, P.; Almela, C.; Vélez, D.; García-Agustín, P.; Serrano, R. & NavarroAviñó, J. (2006). An engineered plant that accumulates higher levels of heavy metals than Thlaspi caerulescens, with yields of 100 times more biomass in mine soils. Chemosphere, Vol.64, pp. 478–485.
Martinoia, E.; Grill, E.; Tomasini, R.; Kreuz, K. & Amrehin, N. (1993). ATP-dependent glutathione S-conjugate ‘export’ pump in the vacuolar membrane of plants. Nature,
Vol.364, pp. 247-249.
McGrath, S.P.; Zhao, F.J. & Lombi, E. (2002). Phytoremediation of metals, metalloids and radionuclides. Advances in Agronomy, Vol.75, pp.1–56.
Meagher, R.B. (2000). Phytoremediation of toxic elemental and organic pollutants. Current
Opinion of Plant Biology, Vol.3, pp. 153–162.
Mejäre, M. & Bülow, L. (2001). Metal-binding proteins and peptides in bioremediation and phytoremediation of heavy metals. Trends in Biotechnology, Vol.19, pp. 67-73.
Mello-Farias, P.C. & Chaves, A.L.S. (2008). Biochemical and molecular aspects of toxic metals phytoremediation using transgenic plants. In: Transgenic Approach in Plant
Biochemistry and Physiology, Tiznado-Hernandez, M.E.; Troncoso-Rojas, R. & RiveraDomínguez, M. A. (Ed.) 253-266, Research Signpost, Kerala, India.
Mijoviloch, A.B.; Leitenmaier, W.; Meyer-Klauche, P.M.; Kroneck, B.; Götz, B. & Kupper, H.
(2009). Complexation and toxicity of copper in higher plants. II. Differents mechanisms for copper versus cadmium detoxification in the cooper-sensitive cadmium/zinc hyperaccumulator Thlaspi caerulescens (Ganges Ecotype). Plant
Physiolology, Vol.151, pp. 715-731.
Murphy, A.S.; Eisenger, W.R.; Shaff, J.E.; Kochian, L.V. & Taiz, L. (1999). Early copperinduced leakage of K+ from Arabidopsis seedlings is mediated by ion channels and coupled to citrate efflux. Plant Physiology, Vol.121, pp. 1375-1382.
Nedelkoska, T.J. & Doran, P.M. (2000). Hyperaccumulation of cadmium by hairy roots of
Thlaspi caerulescens. Biotechnology Bioengineering, Vol.67, No.5, pp. 607– 15.
Negri, M.C. & Hinchman, R.R. (2000). The use of plants for the treatment of radionuclides.
In: Phytoremediation Of Toxic Metals: Using Plants to Clean Up the Environment,
Raskin, I. & Ensley, E.D. (Ed.), 107-132, New York: Wiley.
Neuefeind, T.; Reinemer, P. & Bieseler, B. (1997). Plant glutathione S-transferases and herbicide detoxification. Biological Chemistry, Vol.378, pp. 199-205.
Nwoko, C.O. (2010). Trends in phytoremediation of toxic elemental and organic pollutants.
African Journal of Biotechnology, Vol.9, No.37, pp. 6010-6016.
Ohkawa, H.; Imaishi, H. & Shiota, N. (1999). In: Pesticide Chemistry and Biosciences: The FoodEnvironment Challenge, Brooks, J.T. & Roberts, T.R. (Ed.), 259-264, Royal Society of
Chemistry, Cambridge, UK.
Olson, P.E.; Reardon, K.F. & Pilon-Smits, E.A.H. (2003). Ecology of rhizosphere bioremediation. In: Phytoremediation: Transformation and Control of Contaminants,
McCutcheon, S.C. & Schnoor, J.L. (Ed.), 317-354, Wiley: New York.

326

Genetic Transformation

Ow, D.W. (1996). Heavy metal tolerance genes-prospective tools for bioremediation.
Resources, Conservation and Recycling, Vol.18, pp. 135-149.
Papernik, L.A.; Bethea, A.S.; Singleton, T.E.; Magalhaes, J.V.; Garvin, D.F. & Kochian, L.V.
(2001). Physiological basis of reduced Al tolerance in ditelosomic lines of Chinese
Spring wheat. Planta, Vol.212, pp. 829-834.
Persans, M.W., Nieman, K. & Salt, D.E. (2001). Functional activity and role of cationefflux family members in Ni hyperaccumulation in Thlaspi goesingense. The Proceedings of the National Academy of Sciences USA, Vol.98, pp. 9995-1000.
Pilon-Smits, E. Phytoremediation. (2005). Annual Review of Plant Biology, Vol. 56, pp. 15-39.
Pilon-Smits, E. & Pilon, M. (2002). Phytoremediation of metals using transgenic plants.
Critical Reviews in Plant Science, Vol.21, pp. 439–456.
Pilon-Smits, E. (2005). Phytoremediation. Annual Reviews of Plant Biology, Vol.56, pp. 15–39.
Pineros, M.A. & Kochian, L.V. (2001). A patch-clamp study on the physiology of aluminium toxicity and aluminium tolerance in maize. Identification and characterization of
Al3+ induced anion channels. Plant Physiology, Vol.125, pp. 292-305.
Pires, F.R.; Souza, C.M.; Silva, A.A.; Procópio, S.O. & Ferreira, L.R. (2003). Fitorremediação de solos contaminados com herbicidas. Planta Daninha, Vol.21, No.2, pp. 335-341.
Prasad, M.N.V. (2004) Phytoremediation of metals in the environment for sustainable development. Proceedings of the Indian National Science Academy, Vol.70, pp. 71-98.
Prasad, M.N.V. & Freitas, H. (2003). Metal hyperaccumulation in plants: Biodiversity prospecting for phytoremediation technology. Electronic Journal of Biotechnology,
Vol.6, pp. 275-321.
Pulford, I.D. & Watson, C. (2003). Phytoremediation of heavy metal-contaminated land by trees - a review. Environment International, Vol.29, pp. 529-540.
Robinson, B.H.; Brooks, R.R.; Howes, A.W.; Kirkman, J.H. & Gregg, P.E.H. (1997). The potential of the high biomass nickel hyperaccumulator Berkheya coddii for phytoremediation and phytomining. Journal of Geochemical Exploration, Vol.60, pp.
115–126.
Robinson, B.H.; Leblanc, M.; Petit, D.; Brooks R.R.; Kirkman J.H. & Gregg P.E.H. (1998). The potential of Thlaspi caerulescens for phytoremediation of contaminated soils. Plant and Soil, Vol.203, pp. 47–56.
Reeves, R.D. & Baker, A.J.M. (2000). Metal-accumulating plants. In: Phytoremediation of toxic metals using plants to clean up the environment, Raskin, I. & Ensley, B.D. (Ed.) 193-230,
John Wiley and Sons, New York.
Rugh, C.L.; Bizily, S.P. & Meagher, R.B. (2000). Phytoremediation of environmental mercury pollution. In: Phytoremediation of toxic metals using plants to clean up the environment,
Raskin, I. & Ensley, B.D. (Ed.) 151-171, New York Wiley and Sons, New York.
Sanita di Toppi, L. & Gabbrielli, R. (1999). Response to cadmium in higher plants.
Environmental and Experimental Botany, Vol.41, pp. 105-30.
Schnoor, J.L.; Licht, L.A.; McCutcheon, S.C.; Wolf, N.L. & Carreira, L.H. (1995).
Phytoremediation of organic and nutrient contaminants. Environmental Science and
Technology, Vol.29, pp. 318-323.
Siciliano, S.D.; Germida, J.J.; Banks, K. & Green, C.W. (2003). Changes in Microbial
Communit
Composition and during a polyaromatic hydrocarbon phytoremediation field trial. Applied and Environmental Microbiology, Vol.69, No.1, pp. 483-489.

Transgenic Plants for Enhanced Phytoremediation – Physiological Studies

327

Siqueira, J.O. (1996). Avanços em fundamentos e aplicações de micorrizas. (edition) Lavras:
UFLA, 290p.
Ross, S.M. (1994). Toxic Metals in Soil-Plant Systems, Wiley & Sons: Chichester, UK.
Salt, D.E.; Smith, R.D. & Raskin, I. (1998) Phytoremediation. Annual Review of Plant
Physiology and Plant Molecular Biology, Vol.49, pp. 643–668.
Sarma, H. (2011). Metal hyperaccumulation in Plants: A Review Focusing on
Phytoremediation Technology. Journal of Environmental Science and Technology,
Vol.4, No.2, pp. 118-138.
Schat, H.; Llugany, M.; Voojis, R.; Harley-Whitaker, J. & Bleeker, P.M. (2002). The role of
Phytochelatin in constitutive and adaptive heavy metal tolerances in hyperaccumulator and non-hyperaccumulator metallophytes. Journal of
Experimental Botany, Vol.53, pp. 2381-2392.
Schnoor, J.L.; Licht, L.A.; McCutcheon, S.C.; Wolfe, N.L. & Carreira, L.H. (1995).
Phytoremediation of contaminated soils and sediments. Environmental Science and
Technology, Vol.29, 318-323.
Singer, A. (2006). The chemical ecology of pollutants biodegradation. In: Phytoremediation and Rhizoremediation: Theoretical Background, Mackova, M.; Dowling, D. & Macek, K.
(Ed.), 5–21, Springer.
Singh, O.V.; Labana, S.; Pandey, G.; Budhiraja, R. & Jain, R.K. (2003). Phytoremediation: an overview of metallic ion decontamination from soil. Applied Microbiology and
Biotechnology, Vol.61, pp. 405-412.
Song, W.Y.; Martinoia, E.; Lee, J.; Kim, D.; Kim, D.Y.; Vogt, E.; Shim, D.; Choi, K.S.; Hwang,
I. & Lee, Y. (2004). A novel family of cys-rich membrane proteins mediates cadmium resistance in Arabidopsis. Plant Physiology, Vol.135, pp. 1027-1039.
Taiz, L. & Zeiger, E. (2002). Plant Physiology; Sinauer: Sanderland, M.A., pp. 1-690.
Thomine, S.; Wang, R.; Ward, J.M.; Crawford, N.M. & Schroeder, J.I. (2000). Cadmium and iron transport by members of a plant metal transporter family in Arabidopsis with homology to Nramp genes. Proceedings of the National Academy of Sciences USA,
Vol.97, pp. 4991-4996.
Tsao, D.T. (2003). Overview of phytotechnologies. Advances in Biochemical Engineering and
Biotechnology, Vol.78, pp. 1–50.
Tong, Y.P.; Kneer, R. & Zhu, Y.G. (2004). Vacuolar compartimentalization: a second generation approach to engineering plants for phytoremediation. Trends in Plant
Science, Vol.9, No.1, pp. 7-9.
Van Aken, B. (2008). Transgenic plants for phytoremediation: helping nature to clean up environmental pollution. Trends in Biotechnology, Vol.26, No.5, pp. 225-227.
Vassilev, A.; Schwitzguebel, J.P.; Thewys, T.; Van der Lelie, D. & Vangronsveld, J. (2004).
The use of plants for remediation of metal-contaminated soils. The Scientific World
Journal, Vol.4, pp. 9–34.
Vatamaniuk, O.K.; Mari, S.; Lu, Y.P. & Rea, P.A. (1999). At PCS1, a phytochelatin synthase from Arabidopsis: isolation and in vitro reconstitution. The Proceedings of the National
Academy of Sciences USA, Vol. 96, No.12, pp. 7110- 7115.
Williams, L.E.; Pittman, J.K. & Hall, J.L. (2000). Emerging mechanisms for heavy metal transport in plants. Biochimica et Biophysica Acta, Vol.1465, pp. 104-26.

328

Genetic Transformation

Wolfe, N.L. & Hoehamer, C.F. (2003). Enzymes used by plants and microorganisms to detoxify organic compounds. In: Phytoremediation: Transformation and control of contaminants, Mc-Cutcheon, S.C. & Schnoor, J.L. (Ed.), 158-187, Wiley: New York.
Yang, X.; Jin, X.F.; Feng, Y. & Islam, E. (2005a). Molecular Mechanisms and Genetic bases of
Heavy Metal Tolerance/Hyperaccumulation in Plants. Journal of Integrative Plant
Biology, Vol.47, No.9, pp. 1025-1035.
Yang, X.; Feng, Y.; He, Z. & Stoffella, P. (2005b). Molecular mechanisms of heavy metal hiperaccumulation and phytoremediation. Journal of Trace Elements in Medicine and
Biology, Vol.18, pp. 339-353.
Zhou, Q.X.; Kong, F.X. & Zhu, L. (2004). Ecotoxicology. Science Press, p. 454, Beijing, China.
Zhu, Y.L.; Pilon-Smits, E.A.H.; Jouanin, L. & Terry, N. (1999a). Overexpression of glutathione synthetase in Indian mustard enhances cadmium accumulation and tolerance. Plant Physiology, Vol.119, pp. 73-79.
Zhu, Y.L.; Pilon-Smits, E.A.H.; Tarun, A.S.; Weber, S.U.; Jouanin, L. & Terry, N. (1999b).
Cadmium tolerance and accumulation in Indian mustard is enhanced by overexpressing g-glutamylcysteine synthetase. Plant Physiology, Vol.121, pp. 116977.

References: Alexander, M. (1999). Biodegradation and bioremediation. Ithaca, NY, USA: Academic Press. Arazi, T.; Sunkar, R.; Kaplan, B. & Fromm, H.A. (1999). Tobacco plasma membrane calmodulin binding transporter confers Ni+ tolerance and Pb2+ hypersensitivity in Baker, A.J.M. & Brooks, R.R. (1989). Terrestrial higher plants which hyperaccumulate metallic elements – a review of their distribution, ecology and phytochemistry. Baker, A.J.M.; McGrath, S.P.; Sidoli, C.M.D. & Reeves, R.D. (1994). The possibility of in situ heavy metal decontamination of polluted soils using crops of metal accumulating Baudouin, C.; Charveron, M.; Tarrouse, R. & Gall, Y. (2002). Environmental pollutants and skin cancer Bennett, L.E.; Burkhead, J.L.; Hale, K.L.; Terry, N.; Pilon, M. & Pilon-Smits, E.A.H. (2003). Bizily, S.P.; Rugh, C.L. & Meagher, R.B. (2000). Phytodetoxification of hazardous organomercurials by genetically engineered plants Burken, J.G. & Schnoor, J.L. (1997). Uptake and metabolism of atrazine by poplar trees. Enviromental Science and Technology, Vol.31, pp. 1399-1406. Burken, J.G. (2003). Uptake and metabolism of organic compounds: green-liver models. In: Phytoremediation: Transformation and Control of Contaminants, McCutcheon, S.C Chaney, R.L.; Malik, M.; Li, Y.M.; Brown, S.L.; Angle, J.S. & Baker, A.J.M. (1997). Phytoremediation of soil metals. Current Opinion in Biotechnology, Vol.8, pp. 279284. Cherian, S. & Oliveira, M.M. (2005). Transgenic Plants in Phytoremediation: Recent Advances and New Possibilities pp. 9377-9390. Clemens, S.; Palmgren, M.G. & Krämer, U. (2002). A long way ahead: understanding and engineering plant metal accumulation Cobbett, C.S. (2000). Phytochelatin biosynthesis and function in heavy-metal detoxification. Cobbett, C. & Goldsbrough, P. (2002). Phytochelatins and Metallothioneins: Roles in Heavy Metal Detoxification and Homeosteasis Coleman, J.O.D.; Blake-Kalff, M.M.A. & Davies, T.G.E. (1997). Detoxification of xenobiotics by plants: chemical modification and vacuolar compartmentation Coutinho, D.H. & Barbosa, A.R. (2007). Fitorremediação: Considerações Gerais e Características de Utilização Cunningham, S.D. & Lee, C.R. (1995). Phytoremediation: Plant-based remediation of contaminated soils and sediments Cunningham, S.D. & Ow, D.W. (1996). Promises and prospects of phytoremediation. Plant Physiology, Vol.110, No.3, pp Cunningham, S.D.; Shann, J.R.; Crowley, D.E. & Anderson, T.A. (1997). Phytoremediation of contaminated water and soil: Phytoremediation of soil and water contaminations. Danh, L.T.; Truong, P.; Mammucari, R.; Tran, T. & Foster, N. (2009). Vetiver grass, Vetiveria zizanioides: A choice plant for phytoremediation of heavy metals and organic De la Fuente, J.M.; Ramirez-Rodriguez, V.; Cabrera-Ponce, J.L. & Herrera-Estrella, L. (1997). Nature Biotechnology, Vol.20, pp. 1140-1145. Dietz, A.C. & Schnoor, J.L. (2001). Advances in phytoremediation. Environmental Health Perspectives, Vol.109, pp (2008). New Phytologist, Vol.179, pp. 318–333. D´Souza, M.P.; Pilon-Smits, E.A.H. & Terry, N. (2000). The physiology and biochemistry of selenium volatilization by plants Dushenkov, S. (2003). Trend in phytoremediation of radionuclides. Plant and Soil, Vol.249, pp Eapen, S.; Suseelan, K.; Tivarekar, S.; Kotwal, S. & Mitra, R. (2003). Potential for rhizofiltration of uranium using hairy root cultures of Brassica juncea and Eapen, S. & D’Souza, S.F. (2005). Prospects of genetic engineering of plants for phytoremediation of toxic metals Eapen, S.; Singh, S. & D´Souza, S.F. (2007). Advances in development of transgenic plants for remediation of xenobiotic pollutants Estevez-Núnez, A.; Caballero, A. & Ramos, J.L. (2001). Biological degradation of 2,4,6trinitrotoluene. Microbiology and Molecular Biology Reviews, Vol.65, No.3, pp. 335352. Ezaki, B.; Gardner, R.C.; Ezaki, Y. & Matsumoto, H. (2000). Expression of aluminium induced genes in transgenic Arabidopsis plants can ameliorate aluminium stress Fingerman, M. & Nagabhushanum, R. (2005). Bioremediation of aquatic and terrestrial ecosystems