Question

Which protein(s) helps RNAP to recover from a stall caused by the temporary shortage of nucleotides, and how?

A. RNAP core active site; by scrunching more DNA template into the catalytic site.

B. GreA and NtrC; by pushing nascent RNA out of the exit pore, thus helping to convert scrunched RNA/DNA hybrid.

C. NtrC; using ATP, it provides the energy to continue elongation.

D. GreA and GreB; reposition Mg2+ ions in the active site, which makes RNAP cleave the trailing end off nascent RNA to align it correctly in the catalytic site.

Answer 1

The correct answer is option d. GreA and GreB assist in the recovery of stalled RNA polymerase by repositioning Mg2+ ions in the RNAP active site, leading to cleavage of the nascent RNA for realignment in the catalytic site.

Step-by-step explanation:

The proteins GreA and GreB help RNA polymerase (RNAP) to recover from a stall caused by a temporary shortage of nucleotides. This stalling can occur due to a variety of reasons such as encountering difficult-to-transcribe sequences or a damaged DNA template. When RNAP stalls, GreA and GreB assist by repositioning Mg2+ ions within the RNAP active site.

This repositioning prompts RNAP to cleave the nascent RNA thereby realigning it correctly within the catalytic site which allows transcription to resume. The answer, in this case, points to letter D. These proteins use an intrinsic nuclease activity of RNAP to remove the truncated RNA and permit the enzyme to retry transcription elongation. This process is an essential part of the transcriptional proofreading mechanism and ensures the fidelity and efficiency of RNA synthesis.