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RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes
Umea Univ, Lab Mol Infect Sweden MIMS, UCMR, Dept Mol Biol, S-90187 Umea, Sweden.;Helmholtz Ctr Infect Res HZI, Dept Regulat Infect Biol, D-38124 Braunschweig, Germany..
Helmholtz Ctr Infect Res HZI, Dept Regulat Infect Biol, D-38124 Braunschweig, Germany..
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
Umea Univ, Lab Mol Infect Sweden MIMS, UCMR, Dept Mol Biol, S-90187 Umea, Sweden.;Univ Vienna, MFPL, A-1030 Vienna, Austria..
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2016 (English)In: RNA Biology, ISSN 1547-6286, E-ISSN 1555-8584, Vol. 13, no 2, 177-195 p.Article in journal (Refereed) Published
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Abstract [en]

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.

Place, publisher, year, edition, pages
2016. Vol. 13, no 2, 177-195 p.
Keyword [en]
Antisense RNAs, gene expression regulation, leader RNAs, RNA sequencing, riboswitches, Streptococcus pyogenes, small RNAs, T-boxes
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-283674DOI: 10.1080/15476286.2015.1110674ISI: 000371745100010PubMedID: 26580233OAI: oai:DiVA.org:uu-283674DiVA: diva2:919502
Funder
Swedish Research CouncilSwedish National Infrastructure for Computing (SNIC), b20133265
Available from: 2016-04-14 Created: 2016-04-14 Last updated: 2017-11-30Bibliographically approved

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Reimegård, Johan

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