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RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes.

Le Rhun A, Beer YY, Reimegård J, Chylinski K, Charpentier E - RNA Biol (2016)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Related in: MedlinePlus

Expression profiles of sRNAs regulated by RNases. Northern blot analysis of selected sRNAs showing a variation in expression or processing between WT (SF370), ΔRNase III (Δrnc) and ΔRNase Y (Δrny) strains grown to early logarithmic (EL), mid logarithmic (ML) and early stationary (ES) phases. 5S rRNA is used as a loading control. For each sRNA, the locus is depicted with the sRNA in green and the surrounding genes in gray. The prophage regions are indicated in purple. For a detailed set of Northern blots and sRNA sequencing expression patterns, refer to Figure S4.
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f0003: Expression profiles of sRNAs regulated by RNases. Northern blot analysis of selected sRNAs showing a variation in expression or processing between WT (SF370), ΔRNase III (Δrnc) and ΔRNase Y (Δrny) strains grown to early logarithmic (EL), mid logarithmic (ML) and early stationary (ES) phases. 5S rRNA is used as a loading control. For each sRNA, the locus is depicted with the sRNA in green and the surrounding genes in gray. The prophage regions are indicated in purple. For a detailed set of Northern blots and sRNA sequencing expression patterns, refer to Figure S4.

Mentions: Northern blot analysis shows that the expression of 2 novel sRNAs is regulated by RNase III (Spy_sRNA1222613 and Spy_sRNA1571135) and the expression of 4 novel sRNAs is regulated by RNase Y (Spy_sRNA1222613, Spy_sRNA1300419, Spy_sRNA1774740 and Spy_sRNA1775122) (Fig. 3 and Fig. S4).Figure 3.


RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes.

Le Rhun A, Beer YY, Reimegård J, Chylinski K, Charpentier E - RNA Biol (2016)

Expression profiles of sRNAs regulated by RNases. Northern blot analysis of selected sRNAs showing a variation in expression or processing between WT (SF370), ΔRNase III (Δrnc) and ΔRNase Y (Δrny) strains grown to early logarithmic (EL), mid logarithmic (ML) and early stationary (ES) phases. 5S rRNA is used as a loading control. For each sRNA, the locus is depicted with the sRNA in green and the surrounding genes in gray. The prophage regions are indicated in purple. For a detailed set of Northern blots and sRNA sequencing expression patterns, refer to Figure S4.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4829319&req=5

f0003: Expression profiles of sRNAs regulated by RNases. Northern blot analysis of selected sRNAs showing a variation in expression or processing between WT (SF370), ΔRNase III (Δrnc) and ΔRNase Y (Δrny) strains grown to early logarithmic (EL), mid logarithmic (ML) and early stationary (ES) phases. 5S rRNA is used as a loading control. For each sRNA, the locus is depicted with the sRNA in green and the surrounding genes in gray. The prophage regions are indicated in purple. For a detailed set of Northern blots and sRNA sequencing expression patterns, refer to Figure S4.
Mentions: Northern blot analysis shows that the expression of 2 novel sRNAs is regulated by RNase III (Spy_sRNA1222613 and Spy_sRNA1571135) and the expression of 4 novel sRNAs is regulated by RNase Y (Spy_sRNA1222613, Spy_sRNA1300419, Spy_sRNA1774740 and Spy_sRNA1775122) (Fig. 3 and Fig. S4).Figure 3.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

No MeSH data available.


Related in: MedlinePlus