Question

Explain how the Rho protein terminates transcription.

Answer 1

Rho-dependent transcriptional termination takes place with help of a protein known as Rho factor (? factor). It is a critical prokaryotic protein (hexamer in E.coli ) with each subunit having an RNA- binding domain and an ATP hydrolysis domain. Being a hexameric helicase, it functions by wrapping nucleic acids around a single cleft extending around the entire hexamer. Rho functions as an ancillary factor for RNA polymerase. It binds to the transcription terminator pause site (recognizing the terminator sequence), an exposed region of single stranded RNA (a stretch of 72 nucleotides) after the open reading frame at C-rich/G-poor sequences (rho utilisation site (rut sites).

Rho factor binds to the rut site and starts "climbing" up the transcript towards RNA polymerase. Upon reaching the RNA Polymerase (ATPase activity to provide the energy to translocate along the RNA until it reaches the RNA–DNA helical region), it unwinds the hybrid duplex structure. RNA polymerase then pauses at the termination sequence. Since there is a specific site around 100 nt away from the Rho binding site called the Rho-sensitive pause site, the Rho factor is still able to catch up with the RNA polymerase inspite of the RNA polymerase moving about 40 nt per second faster than Rho. Thus, Rho factor acts as an ATP-dependent unwinding helicase enzyme, moving along the newly forming RNA molecule towards its 3? end and unwinding it from the DNA template as it proceeds.

Finally, when the Rho factor catches up with the polymerase at the transcription bubble, it pulls the RNA transcript and the template DNA strand apart, releasing the RNA molecule and thus terminating transcription.