Final answer:
Rho-dependent termination in bacteria involves the rho protein binding to a run of G nucleotides on the DNA template, which causes RNA polymerase to stall and subsequently leads to termination of transcription as rho unwinds the RNA-DNA hybrid.
Step-by-step explanation:
The cis element that Rho protein binds to in Rho-dependent termination is known as a rut site (Rho utilization site). This site is characterized by a run of G nucleotides on the DNA template. During transcription, the rho protein, which functions as an ATP-dependent helicase, follows the RNA polymerase on the nascent RNA strand. As RNA polymerase transcribes towards the end of a gene, it encounters this run of G nucleotides and stalls. This pause allows the rho protein to catch up and interact with the RNA polymerase. Subsequently, Rho unravels the RNA-DNA hybrid within the transcription bubble, leading to the release of the newly synthesized mRNA molecule and the termination of transcription.
Rho-independent termination, on the other hand, does not involve the rho protein but rather depends on the formation of a stable hairpin loop in the mRNA followed by a string of A-T nucleotides which causes the RNA polymerase to stall and then dissociate from the DNA template.