TY - JOUR
T1 - Genome-Wide Analysis of Targets for Post-Transcriptional Regulation by Rsm Proteins in Pseudomonas putida
AU - Huertas-Rosales, Óscar
AU - Romero, Manuel
AU - Chan, Kok Gan
AU - Hong, Kar Wai
AU - Cámara, Miguel
AU - Heeb, Stephan
AU - Barrientos-Moreno, Laura
AU - Molina-Henares, María Antonia
AU - Travieso, María L.
AU - Ramos-González, María Isabel
AU - Espinosa-Urgel, Manuel
N1 - Funding Information:
This work was supported by grants BFU2013-43469-P, BFU2016-80122-P and PID2019-109372GB-I00 from the Plan Estatal de I+D+I (Agencia Estatal de Investigación, Spanish Ministry of Science and Innovation and FEDER funds). Funding from the Biotechnology and Biological Sciences Research Council, United Kingdom (BB/R012415/1), and the University of Malaya (FRGS grant FP022-2018A and HIR grant H-50001-00-A000027) are also gratefully acknowledged.
Publisher Copyright:
© Copyright © 2021 Huertas-Rosales, Romero, Chan, Hong, Cámara, Heeb, Barrientos-Moreno, Molina-Henares, Travieso, Ramos-González and Espinosa-Urgel.
PY - 2021/2/22
Y1 - 2021/2/22
N2 - 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.
AB - 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.
KW - amino acid metabolism
KW - biofilm
KW - c-di-GMP signaling
KW - global regulation
KW - rhizosphere
KW - RNA-binding proteins
UR - http://www.scopus.com/inward/record.url?scp=85102270092&partnerID=8YFLogxK
U2 - 10.3389/fmolb.2021.624061
DO - 10.3389/fmolb.2021.624061
M3 - Article
AN - SCOPUS:85102270092
SN - 2296-889X
VL - 8
JO - Frontiers in Molecular Biosciences
JF - Frontiers in Molecular Biosciences
M1 - 624061
ER -