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

Huertas-Rosales, �scar; Romero, Manuel; Chan, Kok Gan; Hong, Kar-Wai; Camara, Miguel; Heeb, Stephan; Barrientos-Moreno, Laura; Molina-Henares, Antonia Mar�a; Travieso, Mar�a L; Ramos, Maribel; Espinosa-Urgel, Manuel

doi:10.3389/fmolb.2021.624061

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

Huertas-Rosales, �scar; Romero, Manuel; Chan, Kok Gan; Hong, Kar-Wai; Camara, Miguel; Heeb, Stephan; Barrientos-Moreno, Laura; Molina-Henares, Antonia Mar�a; Travieso, Mar�a L; Ramos, Maribel; Espinosa-Urgel, Manuel

Authors

�scar Huertas-Rosales

Manuel Romero

Kok Gan Chan

Kar-Wai Hong

MIGUEL CAMARA MIGUEL.CAMARA@NOTTINGHAM.AC.UK
Professor of Molecular Microbiology

Dr STEPHAN HEEB stephan.heeb@nottingham.ac.uk
Assistant Professor

Laura Barrientos-Moreno

Antonia Mar�a Molina-Henares

Mar�a L Travieso

Maribel Ramos

Manuel Espinosa-Urgel

Abstract

© Copyright © 2021 Huertas-Rosales, Romero, Chan, Hong, Cámara, Heeb, Barrientos-Moreno, Molina-Henares, Travieso, Ramos-González and Espinosa-Urgel. 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.

Citation

Huertas-Rosales, Ó., Romero, M., Chan, K. G., Hong, K.-W., Camara, M., Heeb, S., …Espinosa-Urgel, M. (2021). Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida. Frontiers in Molecular Biosciences, 8, Article 624061. https://doi.org/10.3389/fmolb.2021.624061

Journal Article Type	Article
Acceptance Date	Jan 21, 2021
Online Publication Date	Feb 22, 2021
Publication Date	Feb 22, 2021
Deposit Date	Jan 22, 2021
Publicly Available Date	Feb 22, 2021
Journal	Frontiers in Molecular Biosciences
Electronic ISSN	2296-889X
Publisher	Frontiers Media
Peer Reviewed	Peer Reviewed
Volume	8
Article Number	624061
DOI	https://doi.org/10.3389/fmolb.2021.624061
Keywords	RNA-binding proteins, Global regulation, Biofilm, Rhizosphere, Amino acid metabolism, c-di-GMP signaling
Public URL	https://nottingham-repository.worktribe.com/output/5250242
Publisher URL	https://www.frontiersin.org/articles/10.3389/fmolb.2021.624061/abstract
Additional Information	First publication by Frontiers Media. Copyright © 2021 Huertas-Rosales, Romero, Chan, Hong, Cámara, Heeb, Barrientos-Moreno, Molina-Henares, Travieso, Ramos-González and Espinosa-Urgel. 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.