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Publication Abstract from PubMed

In sigma-dependent transcriptional pausing, the transcription initiation factor sigma, translocating with RNA polymerase (RNAP), makes sequence-specific protein-DNA interactions with a promoter-like sequence element in the transcribed region, inducing pausing. It has been proposed that, in sigma-dependent pausing, the RNAP active center can access off-pathway "backtracked" states that are substrates for the transcript-cleavage factors of the Gre family and on-pathway "scrunched" states that mediate pause escape. Here, using site-specific protein-DNA photocrosslinking to define positions of the RNAP trailing and leading edges and of sigma relative to DNA at the lambdaPR' promoter, we show directly that sigma-dependent pausing in the absence of GreB in vitro predominantly involves a state backtracked by 2-4 bp, and sigma-dependent pausing in the presence of GreB in vitro and in vivo predominantly involves a state scrunched by 2-3 bp. Analogous experiments with a library of 47 ( approximately 16,000) transcribed-region sequences show that the state scrunched by 2-3 bp-and only that state-is associated with the consensus sequence, T-3N-2Y-1G+1, (where -1 corresponds to the position of the RNA 3' end), which is identical to the consensus for pausing in initial transcription and which is related to the consensus for pausing in transcription elongation. Experiments with heteroduplex templates show that sequence information at position T-3 resides in the DNA nontemplate strand. A cryoelectron microscopy structure of a complex engaged in sigma-dependent pausing reveals positions of DNA scrunching on the DNA nontemplate and template strands and suggests that position T-3 of the consensus sequence exerts its effects by facilitating scrunching.

Structural and mechanistic basis of sigma-dependent transcriptional pausing.,Pukhrambam C, Molodtsov V, Kooshkbaghi M, Tareen A, Vu H, Skalenko KS, Su M, Yin Z, Winkelman JT, Kinney JB, Ebright RH, Nickels BE Proc Natl Acad Sci U S A. 2022 Jun 7;119(23):e2201301119. doi: , 10.1073/pnas.2201301119. Epub 2022 Jun 2. PMID:35653571^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.