title: The target spectrum of SdsR small RNA in Salmonella.
abstract: Model enteric bacteria such as Escherichia coli and Salmonella enterica express hundreds of small non-coding RNAs (sRNAs), targets for most of which are yet unknown. Some sRNAs are remarkably well conserved, indicating that they serve cellular functions that go beyond the necessities of a single species. One of these 'core sRNAs' of largely unknown function is the abundant ∼100-nucleotide SdsR sRNA which is transcribed by the general stress σ-factor, σSand accumulates in stationary phase. In Salmonella, SdsR was known to inhibit the synthesis of the species-specific porin, OmpD. However, sdsR genes are present in almost all enterobacterial genomes, suggesting that additional, conserved targets of this sRNA must exist. Here, we have combined SdsR pulse-expression with whole genome transcriptomics to discover 20 previously unknown candidate targets of SdsR which include mRNAs coding for physiologically important regulators such as the carbon utilization regulator, CRP, the nucleoid-associated chaperone, StpA and the antibiotic resistance transporter, TolC. Processing of SdsR by RNase E results in two cellular SdsR variants with distinct target spectra. While the overall physiological role of this orphan core sRNA remains to be fully understood, the new SdsR targets present valuable leads to determine sRNA functions in resting bacteria.
authors.affiliation: RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, D-97080 Würzburg, Germany.|Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, D-82152 Martinsried, Germany.
authors.forename: Kathrin S
authors.initials: KS
authors.lastname: Fröhlich
authors.affiliation: RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, D-97080 Würzburg, Germany.
authors.forename: Katharina
authors.initials: K
authors.lastname: Haneke
authors.affiliation: Department of Biology I, Microbiology, Ludwig-Maximilians-University Munich, D-82152 Martinsried, Germany kai.papenfort@lmu.de.
authors.forename: Kai
authors.initials: K
authors.lastname: Papenfort
authors.affiliation: RNA Biology Group, Institute for Molecular Infection Biology, University of Würzburg, Josef-Schneider-Straße 2, D-97080 Würzburg, Germany joerg.vogel@uni-wuerzburg.de.
authors.forename: Jörg
authors.initials: J
authors.lastname: Vogel
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D015870:Gene Expression; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D017930:Genes, Reporter; D009690:Nucleic Acid Conformation; D034622:RNA Interference; D012329:RNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics*; D015203:Reproducibility of Results; D012475:Salmonella / Q000235:genetics*
chemical_list: D012329:RNA, Bacterial; D012333:RNA, Messenger; D058727:RNA, Small Untranslated