期刊
RNA BIOLOGY
卷 18, 期 11, 页码 1931-1952出版社
TAYLOR & FRANCIS INC
DOI: 10.1080/15476286.2021.1882180
关键词
Hfq RNA chaperone protein; small noncoding RNA; toxin-antitoxin; cis-antisense RNA; riboswitch; CRISPR; sporulation
资金
- Agence Nationale de la Recherche [ANR-13-JSV3-0005-01]
- Institut Universitaire de France
- University Paris-Saclay
- Institute for Integrative Biology of the Cell
- Pasteur Institute
- DIM-1HEALTH regional Ile-de-France program (LSP grant) [173403]
- CNRS-RFBR PRC 2019 [288426, 19-54-15003]
- Plateforme eBio I2BC, Institut Francais de Bioinformatique (IFB) [ANR-11-INSB-0013]
- Biomics Platform, C2RT, Institut Pasteur, Paris, France - France Genomique [ANR-10-INBS -09-09]
- IBISA
- Centre National de la Recherche Scientifique
- Universite de Paris
- 'Initiative d'Excellence' program from the French State (Grant 'DYNAMO') [ANR-11-LABX-0011]
- Agence Nationale de la Recherche (ANR) [ANR-13-JSV3-0005] Funding Source: Agence Nationale de la Recherche (ANR)
High-throughput sequencing of RNA immunoprecipitation revealed a diverse set of mRNAs and ncRNAs interacting with the RNA chaperone protein Hfq in C. difficile, shedding light on the post-transcriptional regulatory network of this pathogen.
Noncoding RNAs (ncRNA) have emerged as important components of regulatory networks governing bacterial physiology and virulence. Previous deep-sequencing analysis identified a large diversity of ncRNAs in the human enteropathogen Clostridioides (Clostridium) difficile. Some of them are trans-encoded RNAs that could require the RNA chaperone protein Hfq for their action. Recent analysis suggested a pleiotropic role of Hfq in C. difficile with the most pronounced effect on sporulation, a key process during the infectious cycle of this pathogen. However, a global view of RNAs interacting with C. difficile Hfq is missing. In the present study, we performed RNA immunoprecipitation high-throughput sequencing (RIP-Seq) to identify Hfq-associated RNAs in C. difficile. Our work revealed a large set of Hfq-interacting mRNAs and ncRNAs, including mRNA leaders and coding regions, known and potential new ncRNAs. In addition to trans-encoded RNAs, new categories of Hfq ligands were found including cis-antisense RNAs, riboswitches and CRISPR RNAs. ncRNA-mRNA and ncRNA-ncRNA pairings were postulated through computational predictions. Investigation of one of the Hfq-associated ncRNAs, RCd1, suggests that this RNA contributes to the control of late stages of sporulation in C. difficile. Altogether, these data provide essential molecular basis for further studies of post-transcriptional regulatory network in this enteropathogen.
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