title: Decay-Initiating Endoribonucleolytic Cleavage by RNase Y Is Kept under Tight Control via Sequence Preference and Sub-cellular Localisation.
abstract: Bacteria depend on efficient RNA turnover, both during homeostasis and when rapidly altering gene expression in response to changes. Nevertheless, remarkably few details are known about the rate-limiting steps in targeting and decay of RNA. The membrane-anchored endoribonuclease RNase Y is a virulence factor in Gram-positive pathogens. We have obtained a global picture of Staphylococcus aureus RNase Y sequence specificity using RNA-seq and the novel transcriptome-wide EMOTE method. Ninety-nine endoribonucleolytic sites produced in vivo were precisely mapped, notably inside six out of seven genes whose half-lives increase the most in an RNase Y deletion mutant, and additionally in three separate transcripts encoding degradation ribonucleases, including RNase Y itself, suggesting a regulatory network. We show that RNase Y is required to initiate the major degradation pathway of about a hundred transcripts that are inaccessible to other ribonucleases, but is prevented from promiscuous activity by membrane confinement and sequence preference for guanosines.
authors.affiliation: Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Khemici
authors.affiliation: Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland.
authors.forename: Julien
authors.initials: J
authors.lastname: Prados
authors.affiliation: Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland.
authors.forename: Patrick
authors.initials: P
authors.lastname: Linder
authors.affiliation: Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland.
authors.forename: Peter
authors.initials: P
authors.lastname: Redder
mesh_terms: D015964:Gene Expression Regulation, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D012313:RNA / Q000235:genetics; D020871:RNA Stability / Q000235:genetics*; D012260:Ribonucleases / Q000096:biosynthesis / Q000235:genetics*; D017384:Sequence Deletion; D013203:Staphylococcal Infections / Q000235:genetics* / Q000382:microbiology; D013211:Staphylococcus aureus / Q000235:genetics* / Q000472:pathogenicity; D059467:Transcriptome / Q000235:genetics
chemical_list: D012313:RNA; D012260:Ribonucleases