title: A conserved RpoS-dependent small RNA controls the synthesis of major porin OmpD.
abstract: A remarkable feature of many small non-coding RNAs (sRNAs) of Escherichia coli and Salmonella is their accumulation in the stationary phase of bacterial growth. Several stress response regulators and sigma factors have been reported to direct the transcription of stationary phase-specific sRNAs, but a widely conserved sRNA gene that is controlled by the major stationary phase and stress sigma factor, σ(S) (RpoS), has remained elusive. We have studied in Salmonella the conserved SdsR sRNA, previously known as RyeB, one of the most abundant stationary phase-specific sRNAs in E. coli. Alignments of the sdsR promoter region and genetic analysis strongly suggest that this sRNA gene is selectively transcribed by σ(S). We show that SdsR down-regulates the synthesis of the major Salmonella porin OmpD by Hfq-dependent base pairing; SdsR thus represents the fourth sRNA to regulate this major outer membrane porin. Similar to the InvR, MicC and RybB sRNAs, SdsR recognizes the ompD mRNA in the coding sequence, suggesting that this mRNA may be primarily targeted downstream of the start codon. The SdsR-binding site in ompD was localized by 3'-RACE, an experimental approach that promises to be of use in predicting other sRNA-target interactions in bacteria.
authors.affiliation: RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Strasse 2, D-97080 Würzburg, Germany.
authors.forename: Kathrin S
authors.initials: KS
authors.lastname: Fröhlich
authors.forename: Kai
authors.initials: K
authors.lastname: Papenfort
authors.forename: Allison A
authors.initials: AA
authors.lastname: Berger
authors.forename: Jörg
authors.initials: J
authors.lastname: Vogel
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D017124:Conserved Sequence; D004722:Endoribonucleases / Q000378:metabolism; D004755:Enterobacteriaceae / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D008969:Molecular Sequence Data; D018272:Porins / Q000096:biosynthesis* / Q000235:genetics; D012323:RNA Processing, Post-Transcriptional; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D058727:RNA, Small Untranslated / Q000096:biosynthesis / Q000235:genetics / Q000378:metabolism*; D012475:Salmonella / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment; D012808:Sigma Factor / Q000378:metabolism*; D013312:Stress, Physiological / Q000235:genetics; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; C470933:OmpD protein, Salmonella typhimurium; D018272:Porins; D012333:RNA, Messenger; D058727:RNA, Small Untranslated; D012808:Sigma Factor; C069567:sigma factor KatF protein, Bacteria; D004722:Endoribonucleases; C022537:ribonuclease E