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The ratcheted and ratchetable structural states of RNA polymerase underlie multiple transcriptional functions.

Sekine S, Murayama Y, Svetlov V, Nudler E, Yokoyama S
Mol Cell 57 408-21 (2015)
Cited: 59 times
EuropePMC logo PMID: 25601758

Abstract

DNA-dependent RNA polymerase (RNAP) accomplishes multiple tasks during transcription by assuming different structural forms. Reportedly, the "tight" form performs nucleotide addition to nascent RNA, while the "ratcheted" form is adopted for transcription inhibition. In this study, we performed Cys-pair crosslinking (CPX) analyses of various transcription complexes of a bacterial RNAP and crystallographic analyses of its backtracked and Gre-factor-bound states to clarify which of the two forms is adopted. The ratcheted form was revealed to support GreA-dependent transcript cleavage, long backtracking, hairpin-dependent pausing, and termination. In contrast, the tight form correlated with nucleotide addition, mismatch-dependent pausing, one-nucleotide backtracking, and factor-independent transcript cleavage. RNAP in the paused/backtracked state, but not the nucleotide-addition state, readily transitions to the ratcheted form ("ratchetable"), indicating that the tight form represents two distinct regulatory states. The 3' end and the hairpin structure of the nascent RNA promote the ratchetable nature by modulating the trigger-loop conformation.

Reviews - 4wqt mentioned but not cited (1)

  1. Structural biology of bacterial RNA polymerase. Murakami KS. Biomolecules 5 848-864 (2015)

Articles - 4wqt mentioned but not cited (4)

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Reviews citing this publication (10)

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Articles citing this publication (44)

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  6. Structural basis of transcription arrest by coliphage HK022 Nun in an Escherichia coli RNA polymerase elongation complex. Kang JY, Olinares PD, Chen J, Campbell EA, Mustaev A, Chait BT, Gottesman ME, Darst SA. Elife 6 e25478 (2017)
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  11. Dynamic turnover of paused Pol II complexes at human promoters. Erickson B, Sheridan RM, Cortazar M, Bentley DL. Genes Dev 32 1215-1225 (2018)
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  13. Biochemical Analysis of Yeast Suppressor of Ty 4/5 (Spt4/5) Reveals the Importance of Nucleic Acid Interactions in the Prevention of RNA Polymerase II Arrest. Crickard JB, Fu J, Reese JC. J Biol Chem 291 9853-9870 (2016)
  14. NusG inhibits RNA polymerase backtracking by stabilizing the minimal transcription bubble. Turtola M, Belogurov GA. Elife 5 e18096 (2016)
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  26. High intrinsic hydrolytic activity of cyanobacterial RNA polymerase compensates for the absence of transcription proofreading factors. Riaz-Bradley A, James K, Yuzenkova Y. Nucleic Acids Res 48 1341-1352 (2020)
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