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Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida

Post-transcriptional regulation is an important step in the control of bacterial gene expression in response to environmental and cellular signals. Pseudomonas putida KT2440 harbors three known members of the CsrA/RsmA family of post-transcriptional regulators: RsmA, RsmE and RsmI. We have carried o...

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Autores principales: Huertas-Rosales, Óscar, Romero, Manuel, Chan, Kok-Gan, Hong, Kar-Wai, Cámara, Miguel, Heeb, Stephan, Barrientos-Moreno, Laura, Molina-Henares, María Antonia, Travieso, María L., Ramos-González, María Isabel, Espinosa-Urgel, Manuel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7937890/
https://www.ncbi.nlm.nih.gov/pubmed/33693029
http://dx.doi.org/10.3389/fmolb.2021.624061
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author Huertas-Rosales, Óscar
Romero, Manuel
Chan, Kok-Gan
Hong, Kar-Wai
Cámara, Miguel
Heeb, Stephan
Barrientos-Moreno, Laura
Molina-Henares, María Antonia
Travieso, María L.
Ramos-González, María Isabel
Espinosa-Urgel, Manuel
author_facet Huertas-Rosales, Óscar
Romero, Manuel
Chan, Kok-Gan
Hong, Kar-Wai
Cámara, Miguel
Heeb, Stephan
Barrientos-Moreno, Laura
Molina-Henares, María Antonia
Travieso, María L.
Ramos-González, María Isabel
Espinosa-Urgel, Manuel
author_sort Huertas-Rosales, Óscar
collection PubMed
description Post-transcriptional regulation is an important step in the control of bacterial gene expression in response to environmental and cellular signals. Pseudomonas putida KT2440 harbors three known members of the CsrA/RsmA family of post-transcriptional regulators: RsmA, RsmE and RsmI. We have carried out a global analysis to identify RNA sequences bound in vivo by each of these proteins. Affinity purification and sequencing of RNA molecules associated with Rsm proteins were used to discover direct binding targets, corresponding to 437 unique RNA molecules, 75 of them being common to the three proteins. Relevant targets include genes encoding proteins involved in signal transduction and regulation, metabolism, transport and secretion, stress responses, and the turnover of the intracellular second messenger c-di-GMP. To our knowledge, this is the first combined global analysis in a bacterium harboring three Rsm homologs. It offers a broad overview of the network of processes subjected to this type of regulation and opens the way to define what are the sequence and structure determinants that define common or differential recognition of specific RNA molecules by these proteins.
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spelling pubmed-79378902021-03-09 Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida Huertas-Rosales, Óscar Romero, Manuel Chan, Kok-Gan Hong, Kar-Wai Cámara, Miguel Heeb, Stephan Barrientos-Moreno, Laura Molina-Henares, María Antonia Travieso, María L. Ramos-González, María Isabel Espinosa-Urgel, Manuel Front Mol Biosci Molecular Biosciences Post-transcriptional regulation is an important step in the control of bacterial gene expression in response to environmental and cellular signals. Pseudomonas putida KT2440 harbors three known members of the CsrA/RsmA family of post-transcriptional regulators: RsmA, RsmE and RsmI. We have carried out a global analysis to identify RNA sequences bound in vivo by each of these proteins. Affinity purification and sequencing of RNA molecules associated with Rsm proteins were used to discover direct binding targets, corresponding to 437 unique RNA molecules, 75 of them being common to the three proteins. Relevant targets include genes encoding proteins involved in signal transduction and regulation, metabolism, transport and secretion, stress responses, and the turnover of the intracellular second messenger c-di-GMP. To our knowledge, this is the first combined global analysis in a bacterium harboring three Rsm homologs. It offers a broad overview of the network of processes subjected to this type of regulation and opens the way to define what are the sequence and structure determinants that define common or differential recognition of specific RNA molecules by these proteins. Frontiers Media S.A. 2021-02-22 /pmc/articles/PMC7937890/ /pubmed/33693029 http://dx.doi.org/10.3389/fmolb.2021.624061 Text en Copyright © 2021 Huertas-Rosales, Romero, Chan, Hong, Cámara, Heeb, Barrientos-Moreno, Molina-Henares, Travieso, Ramos-González and Espinosa-Urgel. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Huertas-Rosales, Óscar
Romero, Manuel
Chan, Kok-Gan
Hong, Kar-Wai
Cámara, Miguel
Heeb, Stephan
Barrientos-Moreno, Laura
Molina-Henares, María Antonia
Travieso, María L.
Ramos-González, María Isabel
Espinosa-Urgel, Manuel
Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida
title Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida
title_full Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida
title_fullStr Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida
title_full_unstemmed Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida
title_short Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida
title_sort genome-wide analysis of targets for post-transcriptional regulation by rsm proteins in pseudomonas putida
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7937890/
https://www.ncbi.nlm.nih.gov/pubmed/33693029
http://dx.doi.org/10.3389/fmolb.2021.624061
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