Question

Compare and contrast Rho-dependent and Rhoindependent termination. What is a common feature in both mechanisms?

Short answer

Answer: A common feature shared by both Rho-dependent and Rho-independent termination mechanisms is that they ultimately result in the release of the newly synthesized RNA molecule and the RNA polymerase from the DNA template, marking the end of the transcription process.

Step-by-step solution

1. Rho-dependent Termination

Rho-dependent termination is a transcription termination process in bacteria that requires the Rho protein. This plays an essential role in recognizing specific sequences on the synthesized RNA, known as Rho utilization sites (rut). The Rho protein binds to the rut sequence and moves along the RNA until it reaches the RNA polymerase. At this point, it triggers termination by releasing the newly synthesized RNA and the RNA polymerase from the DNA template.

2. Rho-independent Termination

Rho-independent termination, also known as intrinsic termination, does not require the Rho protein. Instead, it relies on the formation of a GC-rich hairpin structure on the newly synthesized RNA molecule. This structure is formed due to the presence of self-complementary sequences followed by a stretch of Uracil (U) residues. When RNA polymerase transcribes these sequences, the hairpin forms, causing the RNA polymerase to pause. The weak AU bonds after the hairpin eventually give way, leading to the release of the RNA molecule and termination of transcription.

3. Comparing Rho-dependent and Rho-independent Termination

There are several differences between the two mechanisms: - Rho-dependent termination requires Rho protein, whereas Rho-independent termination does not. - Rho-dependent termination relies on the recognition of a rut site on the RNA, while Rho-independent termination occurs due to the formation of a hairpin structure. - Rho-dependent termination involves the Rho protein catching up to the RNA polymerase and causing its release, while in Rho-independent termination, the RNA polymerase releases itself due to weak AU bonds.

4. Common Feature

Despite their differences, both Rho-dependent and Rho-independent termination mechanisms ultimately result in the release of the newly synthesized RNA molecule and the RNA polymerase from the DNA template. This release marks the end of the transcription process, allowing the RNA molecule to move on to translation and the RNA polymerase to initiate transcription elsewhere on the DNA.