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An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options
Transcriptional pausing underpins the regulation of cellular RNA synthesis, but its mechanism remains incompletely understood. Sequence-specific interactions of DNA and RNA with the dynamic, multidomain RNA polymerase (RNAP) trigger reversible conformational changes at pause sites that temporarily i...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
National Academy of Sciences
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9974457/ https://www.ncbi.nlm.nih.gov/pubmed/36795753 http://dx.doi.org/10.1073/pnas.2215945120 |
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author | Kang, Jin Young Mishanina, Tatiana V. Bao, Yu Chen, James Llewellyn, Eliza Liu, James Darst, Seth A. Landick, Robert |
author_facet | Kang, Jin Young Mishanina, Tatiana V. Bao, Yu Chen, James Llewellyn, Eliza Liu, James Darst, Seth A. Landick, Robert |
author_sort | Kang, Jin Young |
collection | PubMed |
description | Transcriptional pausing underpins the regulation of cellular RNA synthesis, but its mechanism remains incompletely understood. Sequence-specific interactions of DNA and RNA with the dynamic, multidomain RNA polymerase (RNAP) trigger reversible conformational changes at pause sites that temporarily interrupt the nucleotide addition cycle. These interactions initially rearrange the elongation complex (EC) into an elemental paused EC (ePEC). ePECs can form longer-lived PECs by further rearrangements or interactions of diffusible regulators. For both bacterial and mammalian RNAPs, a half-translocated state in which the next DNA template base fails to load into the active site appears central to the ePEC. Some RNAPs also swivel interconnected modules that may stabilize the ePEC. However, it is unclear whether swiveling and half-translocation are requisite features of a single ePEC state or if multiple ePEC states exist. Here, we use cryo-electron microscopy (cryo-EM) analysis of ePECs with different RNA–DNA sequences combined with biochemical probes of ePEC structure to define an interconverting ensemble of ePEC states. ePECs occupy either pre- or half-translocated states but do not always swivel, indicating that difficulty in forming the posttranslocated state at certain RNA–DNA sequences may be the essence of the ePEC. The existence of multiple ePEC conformations has broad implications for transcriptional regulation. |
format | Online Article Text |
id | pubmed-9974457 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | National Academy of Sciences |
record_format | MEDLINE/PubMed |
spelling | pubmed-99744572023-08-16 An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options Kang, Jin Young Mishanina, Tatiana V. Bao, Yu Chen, James Llewellyn, Eliza Liu, James Darst, Seth A. Landick, Robert Proc Natl Acad Sci U S A Biological Sciences Transcriptional pausing underpins the regulation of cellular RNA synthesis, but its mechanism remains incompletely understood. Sequence-specific interactions of DNA and RNA with the dynamic, multidomain RNA polymerase (RNAP) trigger reversible conformational changes at pause sites that temporarily interrupt the nucleotide addition cycle. These interactions initially rearrange the elongation complex (EC) into an elemental paused EC (ePEC). ePECs can form longer-lived PECs by further rearrangements or interactions of diffusible regulators. For both bacterial and mammalian RNAPs, a half-translocated state in which the next DNA template base fails to load into the active site appears central to the ePEC. Some RNAPs also swivel interconnected modules that may stabilize the ePEC. However, it is unclear whether swiveling and half-translocation are requisite features of a single ePEC state or if multiple ePEC states exist. Here, we use cryo-electron microscopy (cryo-EM) analysis of ePECs with different RNA–DNA sequences combined with biochemical probes of ePEC structure to define an interconverting ensemble of ePEC states. ePECs occupy either pre- or half-translocated states but do not always swivel, indicating that difficulty in forming the posttranslocated state at certain RNA–DNA sequences may be the essence of the ePEC. The existence of multiple ePEC conformations has broad implications for transcriptional regulation. National Academy of Sciences 2023-02-16 2023-02-21 /pmc/articles/PMC9974457/ /pubmed/36795753 http://dx.doi.org/10.1073/pnas.2215945120 Text en Copyright © 2023 the Author(s). Published by PNAS. https://creativecommons.org/licenses/by-nc-nd/4.0/This article is distributed under Creative Commons Attribution-NonCommercial-NoDerivatives License 4.0 (CC BY-NC-ND) (https://creativecommons.org/licenses/by-nc-nd/4.0/) . |
spellingShingle | Biological Sciences Kang, Jin Young Mishanina, Tatiana V. Bao, Yu Chen, James Llewellyn, Eliza Liu, James Darst, Seth A. Landick, Robert An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options |
title | An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options |
title_full | An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options |
title_fullStr | An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options |
title_full_unstemmed | An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options |
title_short | An ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options |
title_sort | ensemble of interconverting conformations of the elemental paused transcription complex creates regulatory options |
topic | Biological Sciences |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9974457/ https://www.ncbi.nlm.nih.gov/pubmed/36795753 http://dx.doi.org/10.1073/pnas.2215945120 |
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