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-Structure paper
タイトル | Structural and mechanistic basis of σ-dependent transcriptional pausing. |
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ジャーナル・号・ページ | Proc Natl Acad Sci U S A, Vol. 119, Issue 23, Page e2201301119, Year 2022 |
掲載日 | 2022年6月7日 |
著者 | Chirangini Pukhrambam / Vadim Molodtsov / Mahdi Kooshkbaghi / Ammar Tareen / Hoa Vu / Kyle S Skalenko / Min Su / Zhou Yin / Jared T Winkelman / Justin B Kinney / Richard H Ebright / Bryce E Nickels / |
PubMed 要旨 | In σ-dependent transcriptional pausing, the transcription initiation factor σ, translocating with RNA polymerase (RNAP), makes sequence-specific protein–DNA interactions with a promoter-like ...In σ-dependent transcriptional pausing, the transcription initiation factor σ, 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 σ-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 σ relative to DNA at the λPR′ promoter, we show directly that σ-dependent pausing in the absence of GreB in vitro predominantly involves a state backtracked by 2–4 bp, and σ-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 (∼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 σ-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. |
リンク | Proc Natl Acad Sci U S A / PubMed:35653571 / PubMed Central |
手法 | EM (単粒子) |
解像度 | 3.8 Å |
構造データ | EMDB-24148, PDB-7n4e: |
化合物 | ChemComp-ZN: ChemComp-MG: |
由来 |
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キーワード | TRANSFERASE/DNA/RNA / elongation / pausing / sigma 70 / transcription complex / DNA scrunching / TRANSFERASE-DNA-RNA complex |