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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doaj-cf475173b3a9498b94b1775a7b39c5142021-02-22T05:18:36ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2021-02-01810.3389/fmolb.2021.624061624061Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putidaÓscar Huertas-Rosales0Manuel Romero1Kok-Gan Chan2Kok-Gan Chan3Kar-Wai Hong4Kar-Wai Hong5Miguel Cámara6Stephan Heeb7Laura Barrientos-Moreno8Laura Barrientos-Moreno9María Antonia Molina-Henares10María L. Travieso11María Isabel Ramos-González12Manuel Espinosa-Urgel13Department of Environmental Protection, Estación Experimental del Zaidín, CSIC, Granada, SpainNational Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United KingdomDivision of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, MalaysiaInternational Genome Centre, Jiangsu University, Zhenjiang, ChinaDivision of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, MalaysiaInternational Genome Centre, Jiangsu University, Zhenjiang, ChinaNational Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United KingdomNational Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United KingdomDepartment of Environmental Protection, Estación Experimental del Zaidín, CSIC, Granada, SpainNational Biofilms Innovation Centre, Biodiscovery Institute and School of Life Sciences, University of Nottingham, Nottingham, United KingdomDepartment of Environmental Protection, Estación Experimental del Zaidín, CSIC, Granada, SpainDepartment of Environmental Protection, Estación Experimental del Zaidín, CSIC, Granada, SpainDepartment of Environmental Protection, Estación Experimental del Zaidín, CSIC, Granada, SpainDepartment of Environmental Protection, Estación Experimental del Zaidín, CSIC, Granada, SpainPost-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.https://www.frontiersin.org/articles/10.3389/fmolb.2021.624061/fullRNA-binding proteinsglobal regulationbiofilmrhizosphereamino acid metabolismc-di-GMP signaling |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Óscar Huertas-Rosales Manuel Romero Kok-Gan Chan Kok-Gan Chan Kar-Wai Hong Kar-Wai Hong Miguel Cámara Stephan Heeb Laura Barrientos-Moreno Laura Barrientos-Moreno María Antonia Molina-Henares María L. Travieso María Isabel Ramos-González Manuel Espinosa-Urgel |
spellingShingle |
Óscar Huertas-Rosales Manuel Romero Kok-Gan Chan Kok-Gan Chan Kar-Wai Hong Kar-Wai Hong Miguel Cámara Stephan Heeb Laura Barrientos-Moreno Laura Barrientos-Moreno María Antonia Molina-Henares María L. Travieso María Isabel Ramos-González Manuel Espinosa-Urgel Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida Frontiers in Molecular Biosciences RNA-binding proteins global regulation biofilm rhizosphere amino acid metabolism c-di-GMP signaling |
author_facet |
Óscar Huertas-Rosales Manuel Romero Kok-Gan Chan Kok-Gan Chan Kar-Wai Hong Kar-Wai Hong Miguel Cámara Stephan Heeb Laura Barrientos-Moreno Laura Barrientos-Moreno María Antonia Molina-Henares María L. Travieso María Isabel Ramos-González Manuel Espinosa-Urgel |
author_sort |
Óscar Huertas-Rosales |
title |
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_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_sort |
genome-wide analysis of targets for post-transcriptional regulation by rsm proteins in pseudomonas putida |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Molecular Biosciences |
issn |
2296-889X |
publishDate |
2021-02-01 |
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. |
topic |
RNA-binding proteins global regulation biofilm rhizosphere amino acid metabolism c-di-GMP signaling |
url |
https://www.frontiersin.org/articles/10.3389/fmolb.2021.624061/full |
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