title: RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes.
abstract: Streptococcus pyogenes is a human pathogen responsible for a wide spectrum of diseases ranging from mild to life-threatening infections. During the infectious process, the temporal and spatial expression of pathogenicity factors is tightly controlled by a complex network of protein and RNA regulators acting in response to various environmental signals. Here, we focus on the class of small RNA regulators (sRNAs) and present the first complete analysis of sRNA sequencing data in S. pyogenes. In the SF370 clinical isolate (M1 serotype), we identified 197 and 428 putative regulatory RNAs by visual inspection and bioinformatics screening of the sequencing data, respectively. Only 35 from the 197 candidates identified by visual screening were assigned a predicted function (T-boxes, ribosomal protein leaders, characterized riboswitches or sRNAs), indicating how little is known about sRNA regulation in S. pyogenes. By comparing our list of predicted sRNAs with previous S. pyogenes sRNA screens using bioinformatics or microarrays, 92 novel sRNAs were revealed, including antisense RNAs that are for the first time shown to be expressed in this pathogen. We experimentally validated the expression of 30 novel sRNAs and antisense RNAs. We show that the expression profile of 9 sRNAs including 2 predicted regulatory elements is affected by the endoribonucleases RNase III and/or RNase Y, highlighting the critical role of these enzymes in sRNA regulation.
authors.affiliation: a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.|b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany.
authors.forename: Anaïs
authors.initials: A
authors.lastname: Le Rhun
authors.affiliation: b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany.
authors.forename: Yan Yan
authors.initials: YY
authors.lastname: Beer
authors.affiliation: c Science for Life Laboratory , Department of Cell and Molecular Biology, Uppsala University, S-75003 , Uppsala , Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Reimegård
authors.affiliation: a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.|d Max F. Perutz Laboratories (MFPL), University of Vienna, A-1030 , Vienna , Austria.
authors.forename: Krzysztof
authors.initials: K
authors.lastname: Chylinski
authors.affiliation: a The Laboratory for Molecular Infection Sweden (MIMS), Umeå Center for Microbial Research (UCMR), Department of Molecular Biology; Umeå University, S-90187 , Umeå , Sweden.|b Helmholtz Centre for Infection Research (HZI), Department of Regulation in Infection Biology, D-38124 , Braunschweig , Germany.|e Hannover Medical School (MHH), D-30625 , Hannover , Germany.|f Max Planck Institute for Infection Biology , Department of Regulation in Infection Biology, D-10117 , Berlin , Germany.
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Charpentier
mesh_terms: D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016372:RNA, Antisense / Q000235:genetics*; D058727:RNA, Small Untranslated / Q000235:genetics*; D058928:Riboswitch / Q000235:genetics*; D017423:Sequence Analysis, RNA; D013297:Streptococcus pyogenes / Q000235:genetics* / Q000472:pathogenicity
chemical_list: D016372:RNA, Antisense; D058727:RNA, Small Untranslated; D058928:Riboswitch
keywords: Antisense RNAs; RNA sequencing; Streptococcus pyogenes; T-boxes; gene expression regulation; leader RNAs; riboswitches; small RNAs