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RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons

DNA transcription initiates after an RNA polymerase (RNAP) molecule binds to the promoter of a gene. In bacteria, the canonical picture is that RNAP comes from the cytoplasmic pool of freely diffusing RNAP molecules. Recent experiments suggest the possible existence of a separate pool of polymerases...

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Autores principales: Tenenbaum, Debora, Inlow, Koe, Friedman, Larry, Cai, Anthony, Gelles, Jeff, Kondev, Jane
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9934669/
https://www.ncbi.nlm.nih.gov/pubmed/36798213
http://dx.doi.org/10.1101/2023.02.10.528045
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author Tenenbaum, Debora
Inlow, Koe
Friedman, Larry
Cai, Anthony
Gelles, Jeff
Kondev, Jane
author_facet Tenenbaum, Debora
Inlow, Koe
Friedman, Larry
Cai, Anthony
Gelles, Jeff
Kondev, Jane
author_sort Tenenbaum, Debora
collection PubMed
description DNA transcription initiates after an RNA polymerase (RNAP) molecule binds to the promoter of a gene. In bacteria, the canonical picture is that RNAP comes from the cytoplasmic pool of freely diffusing RNAP molecules. Recent experiments suggest the possible existence of a separate pool of polymerases, competent for initiation, which freely slide on the DNA after having terminated one round of transcription. Promoter-dependent transcription reinitiation from this pool of post-termination RNAP may lead to coupled initiation at nearby operons, but it is unclear whether this can occur over the distance- and time-scales needed for it to function widely on a bacterial genome in vivo. Here, we mathematically model the hypothesized reinitiation mechanism as a diffusion-to-capture process and compute the distances over which significant inter-operon coupling can occur and the time required. These quantities depend on previously uncharacterized molecular association and dissociation rate constants between DNA, RNAP and the transcription initiation factor σ(70); we measure these rate constants using single-molecule experiments in vitro. Our combined theory/experimental results demonstrate that efficient coupling can occur at physiologically relevant σ(70) concentrations and on timescales appropriate for transcript synthesis. Coupling is efficient over terminator-promoter distances up to ∼ 1, 000 bp, which includes the majority of terminator-promoter nearest neighbor pairs in the E. coli genome. The results suggest a generalized mechanism that couples the transcription of nearby operons and breaks the paradigm that each binding of RNAP to DNA can produce at most one messenger RNA.
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spelling pubmed-99346692023-02-17 RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons Tenenbaum, Debora Inlow, Koe Friedman, Larry Cai, Anthony Gelles, Jeff Kondev, Jane bioRxiv Article DNA transcription initiates after an RNA polymerase (RNAP) molecule binds to the promoter of a gene. In bacteria, the canonical picture is that RNAP comes from the cytoplasmic pool of freely diffusing RNAP molecules. Recent experiments suggest the possible existence of a separate pool of polymerases, competent for initiation, which freely slide on the DNA after having terminated one round of transcription. Promoter-dependent transcription reinitiation from this pool of post-termination RNAP may lead to coupled initiation at nearby operons, but it is unclear whether this can occur over the distance- and time-scales needed for it to function widely on a bacterial genome in vivo. Here, we mathematically model the hypothesized reinitiation mechanism as a diffusion-to-capture process and compute the distances over which significant inter-operon coupling can occur and the time required. These quantities depend on previously uncharacterized molecular association and dissociation rate constants between DNA, RNAP and the transcription initiation factor σ(70); we measure these rate constants using single-molecule experiments in vitro. Our combined theory/experimental results demonstrate that efficient coupling can occur at physiologically relevant σ(70) concentrations and on timescales appropriate for transcript synthesis. Coupling is efficient over terminator-promoter distances up to ∼ 1, 000 bp, which includes the majority of terminator-promoter nearest neighbor pairs in the E. coli genome. The results suggest a generalized mechanism that couples the transcription of nearby operons and breaks the paradigm that each binding of RNAP to DNA can produce at most one messenger RNA. Cold Spring Harbor Laboratory 2023-02-10 /pmc/articles/PMC9934669/ /pubmed/36798213 http://dx.doi.org/10.1101/2023.02.10.528045 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
Tenenbaum, Debora
Inlow, Koe
Friedman, Larry
Cai, Anthony
Gelles, Jeff
Kondev, Jane
RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons
title RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons
title_full RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons
title_fullStr RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons
title_full_unstemmed RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons
title_short RNA polymerase sliding on DNA can couple the transcription of nearby bacterial operons
title_sort rna polymerase sliding on dna can couple the transcription of nearby bacterial operons
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9934669/
https://www.ncbi.nlm.nih.gov/pubmed/36798213
http://dx.doi.org/10.1101/2023.02.10.528045
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