The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

Publication: Research - peer-reviewJournal article – Annual report year: 2012

  • Author: Kröger, Carsten

    Trinity College Dublin, Ireland

  • Author: Dillon, Shane C.

    Trinity College Dublin, Ireland

  • Author: Cameron, Andrew D. S.

    Trinity College Dublin, Ireland

  • Author: Papenfort, Kai

    University of Würzburg, Germany

  • Author: Sivasankaran, Sathesh K.

    Trinity College Dublin, Ireland

  • Author: Hokamp, Karsten

    Trinity College Dublin, Ireland

  • Author: Chao, Yanjie

    University of Würzburg, Germany

  • Author: Sittka, Alexandra

  • Author: Hébrard, Magali

    Trinity College Dublin, Ireland

  • Author: Händler, Kristian

    Trinity College Dublin, Ireland

  • Author: Colgan, Aoife

    Trinity College Dublin, Ireland

  • Author: Leekitcharoenphon, Pimlapas

    Division of Microbiology and Risk Assessment, Division of Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark, Søltofts Plads, 2800, Kgs. Lyngby, Denmark

  • Author: Langridge, Gemma C.

    Wellcome Trust Sanger Institute, United Kingdom

  • Author: Lohan, Amanda J.

    University College Dublin, Ireland

  • Author: Loftus, Brendan

    University College Dublin, Ireland

  • Author: Lucchini, Sacha

    Institute of Food Research, Ireland

  • Author: Ussery, David

    Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kemitorvet, 2800, Kgs. Lyngby, Denmark

  • Author: Dorman, Charles J.

    Trinity College Dublin, Ireland

  • Author: Thomson, Nicholas R.

    Wellcome Trust Sanger Institute, United Kingdom

  • Author: Vogel, Jörg

    University of Würzburg, Germany

  • Author: Hinton, Jay C. D.

    Trinity College Dublin, Ireland

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More than 50 y of research have provided great insight into the physiology, metabolism, and molecular biology of Salmonella enterica serovar Typhimurium (S. Typhimurium), but important gaps in our knowledge remain. It is clear that a precise choreography of gene expression is required for Salmonella infection, but basic genetic information such as the global locations of transcription start sites (TSSs) has been lacking. We combined three RNA-sequencing techniques and two sequencing platforms to generate a robust picture of transcription in S. Typhimurium. Differential RNA sequencing identified 1,873 TSSs on the chromosome of S. Typhimurium SL1344 and 13% of these TSSs initiated antisense transcripts. Unique findings include the TSSs of the virulence regulators phoP, slyA, and invF. Chromatin immunoprecipitation revealed that RNA polymerase was bound to 70% of the TSSs, and two-thirds of these TSSs were associated with σ70 (including phoP, slyA, and invF) from which we identified the −10 and −35 motifs of σ70-dependent S. Typhimurium gene promoters. Overall, we corrected the location of important genes and discovered 18 times more promoters than identified previously. S. Typhimurium expresses 140 small regulatory RNAs (sRNAs) at early stationary phase, including 60 newly identified sRNAs. Almost half of the experimentally verified sRNAs were found to be unique to the Salmonella genus, and
Original languageEnglish
JournalNational Academy of Sciences. Proceedings
Volume109
Issue number20
Pages (from-to)E1277-E1286
Number of pages10
ISSN0027-8424
DOIs
StatePublished - 2012
Peer-reviewedYes
CitationsWeb of Science® Times Cited: 91

Keywords

  • Transcriptional mapping, Noncoding RNA, Posttranscriptional regulation, Pathogenicity, Genome sequence
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