title: RNase J depletion leads to massive changes in mRNA abundance in Helicobacter pylori.
abstract: Degradation of RNA as an intermediate message between genes and corresponding proteins is important for rapid attenuation of gene expression and maintenance of cellular homeostasis. This process is controlled by ribonucleases that have different target specificities. In the bacterial pathogen Helicobacter pylori, an exo- and endoribonuclease RNase J is essential for growth. To explore the role of RNase J in H. pylori, we identified its putative targets at a global scale using next generation RNA sequencing. We found that strong depletion for RNase J led to a massive increase in the steady-state levels of non-rRNAs. mRNAs and RNAs antisense to open reading frames were most affected with over 80% increased more than 2-fold. Non-coding RNAs expressed in the intergenic regions were much less affected by RNase J depletion. Northern blotting of selected messenger and non-coding RNAs validated these results. Globally, our data suggest that RNase J of H. pylori is a major RNase involved in degradation of most cellular RNAs.
authors.affiliation: a Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter , ERL CNRS 3526.
authors.forename: Yulia
authors.initials: Y
authors.lastname: Redko
authors.affiliation: a Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter , ERL CNRS 3526.
authors.forename: Eloïse
authors.initials: E
authors.lastname: Galtier
authors.affiliation: b INSERM U869, University of Bordeaux , 146 rue Léo Saignat, 33076 Bordeaux , France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Arnion
authors.affiliation: b INSERM U869, University of Bordeaux , 146 rue Léo Saignat, 33076 Bordeaux , France.
authors.forename: Fabien
authors.initials: F
authors.lastname: Darfeuille
authors.affiliation: c Institut Pasteur, Plate-Forme 2 - Transcriptome et Epigénome.
authors.forename: Odile
authors.initials: O
authors.lastname: Sismeiro
authors.affiliation: c Institut Pasteur, Plate-Forme 2 - Transcriptome et Epigénome.
authors.forename: Jean-Yves
authors.initials: JY
authors.lastname: Coppée
authors.affiliation: d CNRS-UMR 8030 and Commissariat à l'Energie Atomique et aux Energies Alternatives CEA/DSV/IG/Genoscope LABGeM , Evry , France.
authors.forename: Claudine
authors.initials: C
authors.lastname: Médigue
authors.affiliation: d CNRS-UMR 8030 and Commissariat à l'Energie Atomique et aux Energies Alternatives CEA/DSV/IG/Genoscope LABGeM , Evry , France.
authors.forename: Marion
authors.initials: M
authors.lastname: Weiman
authors.affiliation: d CNRS-UMR 8030 and Commissariat à l'Energie Atomique et aux Energies Alternatives CEA/DSV/IG/Genoscope LABGeM , Evry , France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Cruveiller
authors.affiliation: a Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter , ERL CNRS 3526.
authors.forename: Hilde
authors.initials: H
authors.lastname: De Reuse
mesh_terms: D005786:Gene Expression Regulation; D016480:Helicobacter pylori / Q000201:enzymology* / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D020871:RNA Stability / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics*; D012335:RNA, Ribosomal / Q000235:genetics; D012260:Ribonucleases / Q000235:genetics*
chemical_list: D012333:RNA, Messenger; D012335:RNA, Ribosomal; D012260:Ribonucleases
keywords: H. pylori; RNA metabolism; RNA sequencing; RNase J; post-transcriptional regulation; ribonuclease; transcriptome