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Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA

Free-living bacteria have regulatory systems that can quickly reprogram gene transcription in response to changes in cellular environment. The RapA ATPase, a prokaryotic homolog of the eukaryote Swi2/Snf2 chromatin remodeling complex, may facilitate such reprogramming, but the mechanisms by which it...

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Autores principales: Inlow, Koe, Tenenbaum, Debora, Friedman, Larry J., Kondev, Jane, Gelles, Jeff
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10055430/
https://www.ncbi.nlm.nih.gov/pubmed/36993374
http://dx.doi.org/10.1101/2023.03.22.533849
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author Inlow, Koe
Tenenbaum, Debora
Friedman, Larry J.
Kondev, Jane
Gelles, Jeff
author_facet Inlow, Koe
Tenenbaum, Debora
Friedman, Larry J.
Kondev, Jane
Gelles, Jeff
author_sort Inlow, Koe
collection PubMed
description Free-living bacteria have regulatory systems that can quickly reprogram gene transcription in response to changes in cellular environment. The RapA ATPase, a prokaryotic homolog of the eukaryote Swi2/Snf2 chromatin remodeling complex, may facilitate such reprogramming, but the mechanisms by which it does so is unclear. We used multi-wavelength single-molecule fluorescence microscopy in vitro to examine RapA function in the E. coli transcription cycle. In our experiments, RapA at < 5 nM concentration did not appear to alter transcription initiation, elongation, or intrinsic termination. Instead, we directly observed a single RapA molecule bind specifically to the kinetically stable post-termination complex (PTC) -- consisting of core RNA polymerase (RNAP) bound to dsDNA -- and efficiently remove RNAP from DNA within seconds in an ATP-hydrolysis-dependent reaction. Kinetic analysis elucidates the process through which RapA locates the PTC and the key mechanistic intermediates that bind and hydrolyze ATP. This study defines how RapA participates in the transcription cycle between termination and initiation and suggests that RapA helps set the balance between global RNAP recycling and local transcription re-initiation in proteobacterial genomes.
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spelling pubmed-100554302023-03-30 Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA Inlow, Koe Tenenbaum, Debora Friedman, Larry J. Kondev, Jane Gelles, Jeff bioRxiv Article Free-living bacteria have regulatory systems that can quickly reprogram gene transcription in response to changes in cellular environment. The RapA ATPase, a prokaryotic homolog of the eukaryote Swi2/Snf2 chromatin remodeling complex, may facilitate such reprogramming, but the mechanisms by which it does so is unclear. We used multi-wavelength single-molecule fluorescence microscopy in vitro to examine RapA function in the E. coli transcription cycle. In our experiments, RapA at < 5 nM concentration did not appear to alter transcription initiation, elongation, or intrinsic termination. Instead, we directly observed a single RapA molecule bind specifically to the kinetically stable post-termination complex (PTC) -- consisting of core RNA polymerase (RNAP) bound to dsDNA -- and efficiently remove RNAP from DNA within seconds in an ATP-hydrolysis-dependent reaction. Kinetic analysis elucidates the process through which RapA locates the PTC and the key mechanistic intermediates that bind and hydrolyze ATP. This study defines how RapA participates in the transcription cycle between termination and initiation and suggests that RapA helps set the balance between global RNAP recycling and local transcription re-initiation in proteobacterial genomes. Cold Spring Harbor Laboratory 2023-03-24 /pmc/articles/PMC10055430/ /pubmed/36993374 http://dx.doi.org/10.1101/2023.03.22.533849 Text en https://creativecommons.org/licenses/by-nc-nd/4.0/This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nc-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
spellingShingle Article
Inlow, Koe
Tenenbaum, Debora
Friedman, Larry J.
Kondev, Jane
Gelles, Jeff
Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA
title Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA
title_full Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA
title_fullStr Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA
title_full_unstemmed Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA
title_short Recycling of Bacterial RNA Polymerase by the Swi2/Snf2 ATPase RapA
title_sort recycling of bacterial rna polymerase by the swi2/snf2 atpase rapa
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10055430/
https://www.ncbi.nlm.nih.gov/pubmed/36993374
http://dx.doi.org/10.1101/2023.03.22.533849
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