Promoter clearance of RNA polymerase involves an inherent problem, in that the e
ID: 59217 • Letter: P
Question
Promoter clearance of RNA polymerase involves an inherent problem, in that the energetic forces that attract the polymerase to the promoter in the first place will tend to hold it there, at the promoter, thereby preventing transcription. How can the transcription machinery overcome this problem and enable the polymerase to clear the promoter? Be Sure to explain both prokaryotic and eukaryotic mechanisms. Promoter clearance of RNA polymerase involves an inherent problem, in that the energetic forces that attract the polymerase to the promoter in the first place will tend to hold it there, at the promoter, thereby preventing transcription. How can the transcription machinery overcome this problem and enable the polymerase to clear the promoter? Be Sure to explain both prokaryotic and eukaryotic mechanisms. Promoter clearance of RNA polymerase involves an inherent problem, in that the energetic forces that attract the polymerase to the promoter in the first place will tend to hold it there, at the promoter, thereby preventing transcription. How can the transcription machinery overcome this problem and enable the polymerase to clear the promoter? Be Sure to explain both prokaryotic and eukaryotic mechanisms.Explanation / Answer
RNA polymerase alone does not bind to the promotor region. Instead, it is an assenblage of a group of transcription factors, which forms a preinitiation complex (PIC) at the polymerase binding site. The polymerase PIC formation required at least five general transcription factors (not mentioned here). These transcription factors form several interactions with the polymerase.
After assembly of PIC, the polymerase cannot initiate transcription until the template strands are separated. To open the double stranded DNA and form open complex, ATP is required, and opening is mediated by XPB subunit of TFIIH (one of the transcription factors of PIC complex). TFIIH acts by rotating downstream DNA while retaining the fixed position of upstream contact within the PIC. The initiation bubble extends about -9 to -2 positions relative to transcription start site.
The position of the open bubble is fixed of its upstream edge relative to the TATA box, and not to transcription start site. During initiation of RNA synthesis, the RNA-DNA hybrid is very short and cannot be stable. Thus, the short transcript can be released out and the two DNA strands may reanneal. However, TFIIH prevents this reannealing of DNA strands, and takes help of helicase enzyme to do so.
As the RNA is extended, the bubble extends further. Once the bubble reaches a length of 17-18 bases, collapse of the bubble occurs and leaves only about 10 bases unpaired. However, the transcription machinery now becomes stable as an elongation complex. Changes occur in PIC complex that accompany bubble collapse (independent of helicase, complex stability, fall-off of slippage). Bubble collapse marks the loss of contacts between polymerase and PIC. TFIIB transcription factor is released and the polymerase starts adding futher nucleotides.
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