title: Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq-dependent small RNA.
abstract: The small RNA, ArcZ (previously RyhA/SraH), was discovered in several genome-wide screens in Escherichia coli and Salmonella. Its high degree of genomic conservation, its frequent recovery by shotgun sequencing, and its association with the RNA chaperone, Hfq, identified ArcZ as an abundant enterobacterial 'core' small RNA, yet its function remained unknown. Here, we report that ArcZ acts as a post-transcriptional regulator in Salmonella, repressing the mRNAs of the widely distributed sdaCB (serine uptake) and tpx (oxidative stress) genes, and of STM3216, a horizontally acquired methyl-accepting chemotaxis protein (MCP). Both sdaCB and STM3216 are regulated by sequestration of the ribosome binding site. In contrast, the tpx mRNA is targeted in the coding sequence (CDS), arguing that CDS targeting is more common than appreciated. Transcriptomic analysis of an arcZ deletion strain further argued for the existence of a distinct set of Salmonella loci specifically regulated by ArcZ. In contrast, increased expression of the sRNA altered the steady-state levels of > 16% (> 750) of all Salmonella mRNAs, and rendered the bacteria non-motile. Deep sequencing detected a dramatically changed profile of Hfq-bound sRNAs and mRNAs, suggesting that the unprecedented pleiotropic effects by a single sRNA might in part be caused by altered post-transcriptional regulation.
authors.affiliation: Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland.
authors.forename: Kai
authors.initials: K
authors.lastname: Papenfort
authors.affiliation: Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland.
authors.forename: Nelly
authors.initials: N
authors.lastname: Said
authors.affiliation: Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland.
authors.forename: Tim
authors.initials: T
authors.lastname: Welsink
authors.affiliation: Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland.
authors.forename: Sacha
authors.initials: S
authors.lastname: Lucchini
authors.affiliation: Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland.
authors.forename: Jay C D
authors.initials: JCD
authors.lastname: Hinton
authors.affiliation: Max Planck Institute for Infection Biology, RNA Biology Group, Charitéplatz 1, 10117 Berlin, Germany.Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK.Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin 2, Ireland.
authors.forename: Jörg
authors.initials: J
authors.lastname: Vogel
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D017124:Conserved Sequence; D015964:Gene Expression Regulation, Bacterial; D035001:Host Factor 1 Protein / Q000235:genetics / Q000378:metabolism; D008969:Molecular Sequence Data; D012323:RNA Processing, Post-Transcriptional; D012329:RNA, Bacterial / Q000378:metabolism*; D012333:RNA, Messenger / Q000378:metabolism*; D012486:Salmonella typhimurium / Q000235:genetics* / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D001426:Bacterial Proteins; D035001:Host Factor 1 Protein; D012329:RNA, Bacterial; D012333:RNA, Messenger