title: Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools.
abstract: Inactivation of the Pseudomonas aeruginosa (PAO1) hfq gene, encoding the Sm-like Hfq protein, resulted in pleiotropic effects that included an attenuated virulence. As regulation by Hfq often involves the action of small regulatory RNAs (sRNAs), we have used a shotgun cloning approach (RNomics) and bioinformatic tools to identify sRNAs in strain PAO1. For cDNA library construction, total RNA was extracted from PAO1 cultures either grown to stationary phase or exposed to human serum. The cDNA libraries were generated from small-sized RNAs of PAO1 after co-immunoprecipitation with Hfq. Of 400 sequenced cDNA clones, 11 mapped to intergenic regions. Band-shift assays and Northern blot analyses performed with two selected sRNAs confirmed that Hfq binds to and affects the steady-state levels of these RNAs. A proteome study performed upon overproduction of one sRNA, PhrS, implicated it in riboregulation. PhrS contains an ORF, and evidence for its translation is presented. In addition, based on surveys with structure-based bioinformatic tools, we provide an electronic compilation of putative sRNA and non-coding RNA genes of PAO1 based on their evolutionarily conserved structure.
authors.affiliation: Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Sonnleitner
authors.affiliation: Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria.
authors.forename: Theresa
authors.initials: T
authors.lastname: Sorger-Domenigg
authors.affiliation: Innsbruck Biocenter, Division of Genomics and RNomics, Medical University Innsbruck, Fritz-Pregl Str. 3, A-6020 Innsbruck, Austria.
authors.forename: Monika J
authors.initials: MJ
authors.lastname: Madej
authors.affiliation: Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.
authors.forename: Sven
authors.initials: S
authors.lastname: Findeiss
authors.affiliation: Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.
authors.forename: Jörg
authors.initials: J
authors.lastname: Hackermüller
authors.affiliation: Innsbruck Biocenter, Division of Genomics and RNomics, Medical University Innsbruck, Fritz-Pregl Str. 3, A-6020 Innsbruck, Austria.
authors.forename: Alexander
authors.initials: A
authors.lastname: Hüttenhofer
authors.affiliation: Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.affiliation: Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria.
authors.forename: Udo
authors.initials: U
authors.lastname: Bläsi
authors.affiliation: Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, University of Vienna, Dr. Bohrgasse 9, A-1030 Vienna, Austria.
authors.forename: Isabella
authors.initials: I
authors.lastname: Moll
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics; D001483:Base Sequence; D015152:Blotting, Northern; D019295:Computational Biology / Q000379:methods; D024202:Electrophoretic Mobility Shift Assay; D015723:Gene Library; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D035001:Host Factor 1 Protein / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D010957:Plasmids; D011485:Protein Binding; D020543:Proteome / Q000235:genetics; D011550:Pseudomonas aeruginosa / Q000235:genetics*; D012329:RNA, Bacterial / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins; D035001:Host Factor 1 Protein; D020543:Proteome; D012329:RNA, Bacterial; D022661:RNA, Untranslated