title: Novel regulatory small RNAs in Streptococcus pyogenes.
abstract: Streptococcus pyogenes (Group A Streptococcus or GAS) is a Gram-positive bacterial pathogen that has shown complex modes of regulation of its virulence factors to cause diverse diseases. Bacterial small RNAs are regarded as novel widespread regulators of gene expression in response to environmental signals. Recent studies have revealed that several small RNAs (sRNAs) have an important role in S. pyogenes physiology and pathogenesis by regulating gene expression at the translational level. To search for new sRNAs in S. pyogenes, we performed a genomewide analysis through computational prediction followed by experimental verification. To overcome the limitation of low accuracy in computational prediction, we employed a combination of three different computational algorithms (sRNAPredict, eQRNA and RNAz). A total of 45 candidates were chosen based on the computational analysis, and their transcription was analyzed by reverse-transcriptase PCR and Northern blot. Through this process, we discovered 7 putative novel trans-acting sRNAs. Their abundance varied between different growth phases, suggesting that their expression is influenced by environmental or internal signals. Further, to screen target mRNAs of an sRNA, we employed differential RNA sequencing analysis. This study provides a significant resource for future study of small RNAs and their roles in physiology and pathogenesis of S. pyogenes.
authors.affiliation: Department of Microbiology, Southern Illinois University, Carbondale, Illinois, United States of America.
authors.forename: Rafael A
authors.initials: RA
authors.lastname: Tesorero
authors.forename: Ning
authors.initials: N
authors.lastname: Yu
authors.forename: Jordan O
authors.initials: JO
authors.lastname: Wright
authors.forename: Juan P
authors.initials: JP
authors.lastname: Svencionis
authors.forename: Qiang
authors.initials: Q
authors.lastname: Cheng
authors.forename: Jeong-Ho
authors.initials: JH
authors.lastname: Kim
authors.forename: Kyu Hong
authors.initials: KH
authors.lastname: Cho
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D012329:RNA, Bacterial / Q000235:genetics* / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000235:genetics* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012984:Software; D013297:Streptococcus pyogenes / Q000235:genetics* / Q000378:metabolism
chemical_list: D012329:RNA, Bacterial; D058727:RNA, Small Untranslated