Do Most Operons Have Rho-Independent Termination?

Termination of transcription is an extremely controlled process. As termination progresses, the production of phosphodiester bonds ceases, the DNA/RNA hybrid helices are unwound, DNA recombines to form a double helix once again, and DNA is freed from RNA polymerase. RNA synthesis will continue along the DNA template until the polymerase encounters a signal that tells it to stop. In prokaryotes, this signal can take one of two forms: ρ – dependent and ρ- independent. ρ – Independent termination (also known as intrinsic termination) does not use ρ factor protein to carry out termination. Sequencing of the entire E. coli genome has shown that most operons have Rho-independent termination sites. A hairpin loop forms from a palindrome
This momentary pause is brought about either by the nusA protein, a protein that binds to the RNA polymerase so tightly it causes the polymerase to stall [1], or by a run of G nucleotides on the template strand near the end of the gene[2] . Next, the DNA/RNA helix formed in the Oligo (U) tail becomes unstable due the rU/dA bond only containing 2 hydrogen bonds. The G/C rich region of the hairpin gives the structure extra strength and stability due to the 3 hydrogen bonds between cytosine and guanine. The interruption in transcription allows the newly formed and weakly bound RNA to dissociate from the DNA template, thereby terminating transcription. The transcription bubble is then closed as the single strand of DNA reanneals to form the double
In E. coli it is a ~274.6 kD hexamer of identical subunits, each subunit containing an RNA-binding site and an ATP- hydrolysis domain.
The ρ factor protein travels along the RNA strand in the 5' to 3' direction until it encounters RNA polymerase which causes the RNA to be ripped from RNA Pol and pries the RNA from it's DNA template, in turn breaking the RNA/DNA hybrid helices and stopping transcription.

Whether or not termination takes place relies upon Rho's ability to 'catch up' to RNA Pol paused at the termination site.
Therefore, it has become known that this pause in RNA Pol during elongation is essential for both ρ-dependent and ρ-independent termination.[5]
Rho-dependent termination was first recognized during in vitro studies of transcription of λ-phage DNA (DNA from a bacterial virus that infects E. coli) [6]
Unlike in the case of rho-independent termination, there seems to be no apparent correlation between the binding sites of rho- dependent termination therefore they cannot be easily predicted by sequence analysis, but each sequence is highly specific and complex as even minute changes to the sequence disrupt its