Cargando…
Dynamic insights on transcription initiation and RNA processing during bacterial adaptation
Transcription initiation and RNA processing govern gene expression and enable bacterial adaptation by reshaping the RNA landscape. The aim of this study was to simultaneously observe these two fundamental processes in a transcriptome responding to an environmental signal. A controlled σ(E) system in...
Autores principales: | , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cold Spring Harbor Laboratory Press
2020
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7075262/ https://www.ncbi.nlm.nih.gov/pubmed/31992590 http://dx.doi.org/10.1261/rna.073288.119 |
_version_ | 1783507006894637056 |
---|---|
author | Lacoux, Caroline Fouquier d'Hérouël, Aymeric Wessner-Le Bohec, Françoise Innocenti, Nicolas Bohn, Chantal Kennedy, Sean P. Rochat, Tatiana Bonnin, Rémy A. Serror, Pascale Aurell, Erik Bouloc, Philippe Repoila, Francis |
author_facet | Lacoux, Caroline Fouquier d'Hérouël, Aymeric Wessner-Le Bohec, Françoise Innocenti, Nicolas Bohn, Chantal Kennedy, Sean P. Rochat, Tatiana Bonnin, Rémy A. Serror, Pascale Aurell, Erik Bouloc, Philippe Repoila, Francis |
author_sort | Lacoux, Caroline |
collection | PubMed |
description | Transcription initiation and RNA processing govern gene expression and enable bacterial adaptation by reshaping the RNA landscape. The aim of this study was to simultaneously observe these two fundamental processes in a transcriptome responding to an environmental signal. A controlled σ(E) system in E. coli was coupled to our previously described tagRNA-seq method to yield process kinetics information. Changes in transcription initiation frequencies (TIF) and RNA processing frequencies (PF) were followed using 5′ RNA tags. Changes in TIF showed a binary increased/decreased pattern that alternated between transcriptionally activated and repressed promoters, providing the bacterial population with transcriptional oscillation. PF variation fell into three categories of cleavage activity: (i) constant and independent of RNA levels, (ii) increased once RNA has accumulated, and (iii) positively correlated to changes in TIF. This work provides a comprehensive and dynamic view of major events leading to transcriptomic reshaping during bacterial adaptation. It unveils an interplay between transcription initiation and the activity of specific RNA cleavage sites. This study utilized a well-known genetic system to analyze fundamental processes and can serve as a blueprint for comprehensive studies that exploit the RNA metabolism to decipher and understand bacterial gene expression control. |
format | Online Article Text |
id | pubmed-7075262 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Cold Spring Harbor Laboratory Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-70752622021-04-01 Dynamic insights on transcription initiation and RNA processing during bacterial adaptation Lacoux, Caroline Fouquier d'Hérouël, Aymeric Wessner-Le Bohec, Françoise Innocenti, Nicolas Bohn, Chantal Kennedy, Sean P. Rochat, Tatiana Bonnin, Rémy A. Serror, Pascale Aurell, Erik Bouloc, Philippe Repoila, Francis RNA Report Transcription initiation and RNA processing govern gene expression and enable bacterial adaptation by reshaping the RNA landscape. The aim of this study was to simultaneously observe these two fundamental processes in a transcriptome responding to an environmental signal. A controlled σ(E) system in E. coli was coupled to our previously described tagRNA-seq method to yield process kinetics information. Changes in transcription initiation frequencies (TIF) and RNA processing frequencies (PF) were followed using 5′ RNA tags. Changes in TIF showed a binary increased/decreased pattern that alternated between transcriptionally activated and repressed promoters, providing the bacterial population with transcriptional oscillation. PF variation fell into three categories of cleavage activity: (i) constant and independent of RNA levels, (ii) increased once RNA has accumulated, and (iii) positively correlated to changes in TIF. This work provides a comprehensive and dynamic view of major events leading to transcriptomic reshaping during bacterial adaptation. It unveils an interplay between transcription initiation and the activity of specific RNA cleavage sites. This study utilized a well-known genetic system to analyze fundamental processes and can serve as a blueprint for comprehensive studies that exploit the RNA metabolism to decipher and understand bacterial gene expression control. Cold Spring Harbor Laboratory Press 2020-04 /pmc/articles/PMC7075262/ /pubmed/31992590 http://dx.doi.org/10.1261/rna.073288.119 Text en © 2020 Lacoux et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society http://creativecommons.org/licenses/by-nc/4.0/ This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/. |
spellingShingle | Report Lacoux, Caroline Fouquier d'Hérouël, Aymeric Wessner-Le Bohec, Françoise Innocenti, Nicolas Bohn, Chantal Kennedy, Sean P. Rochat, Tatiana Bonnin, Rémy A. Serror, Pascale Aurell, Erik Bouloc, Philippe Repoila, Francis Dynamic insights on transcription initiation and RNA processing during bacterial adaptation |
title | Dynamic insights on transcription initiation and RNA processing during bacterial adaptation |
title_full | Dynamic insights on transcription initiation and RNA processing during bacterial adaptation |
title_fullStr | Dynamic insights on transcription initiation and RNA processing during bacterial adaptation |
title_full_unstemmed | Dynamic insights on transcription initiation and RNA processing during bacterial adaptation |
title_short | Dynamic insights on transcription initiation and RNA processing during bacterial adaptation |
title_sort | dynamic insights on transcription initiation and rna processing during bacterial adaptation |
topic | Report |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7075262/ https://www.ncbi.nlm.nih.gov/pubmed/31992590 http://dx.doi.org/10.1261/rna.073288.119 |
work_keys_str_mv | AT lacouxcaroline dynamicinsightsontranscriptioninitiationandrnaprocessingduringbacterialadaptation AT fouquierdherouelaymeric dynamicinsightsontranscriptioninitiationandrnaprocessingduringbacterialadaptation AT wessnerlebohecfrancoise dynamicinsightsontranscriptioninitiationandrnaprocessingduringbacterialadaptation AT innocentinicolas dynamicinsightsontranscriptioninitiationandrnaprocessingduringbacterialadaptation AT bohnchantal dynamicinsightsontranscriptioninitiationandrnaprocessingduringbacterialadaptation AT kennedyseanp dynamicinsightsontranscriptioninitiationandrnaprocessingduringbacterialadaptation AT rochattatiana dynamicinsightsontranscriptioninitiationandrnaprocessingduringbacterialadaptation AT bonninremya dynamicinsightsontranscriptioninitiationandrnaprocessingduringbacterialadaptation AT serrorpascale dynamicinsightsontranscriptioninitiationandrnaprocessingduringbacterialadaptation AT aurellerik dynamicinsightsontranscriptioninitiationandrnaprocessingduringbacterialadaptation AT boulocphilippe dynamicinsightsontranscriptioninitiationandrnaprocessingduringbacterialadaptation AT repoilafrancis dynamicinsightsontranscriptioninitiationandrnaprocessingduringbacterialadaptation |