The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

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

  • Author: Kröger, Carsten, Ireland

    Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Ireland

  • Author: Dillon, Shane C., Ireland

    Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Ireland

  • Author: Cameron, Andrew D. S., Ireland

    Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Ireland

  • Author: Papenfort, Kai, Germany

    Institute for Molecular Infection Biology, University of Würzburg, Germany

  • Author: Sivasankaran, Sathesh K., Ireland

    Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Ireland

  • Author: Hokamp, Karsten, Ireland

    Department of Genetics, School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Ireland

  • Author: Chao, Yanjie, Germany

    Institute for Molecular Infection Biology, University of Würzburg, Germany

  • Author: Sittka, Alexandra

  • Author: Hébrard, Magali, Ireland

    Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Ireland

  • Author: Händler, Kristian, Ireland

    Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Ireland

  • Author: Colgan, Aoife, Ireland

    Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Ireland

  • Author: Leekitcharoenphon, Pimlapas

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

  • Author: Langridge, Gemma C., United Kingdom

    The Wellcome Trust Sanger Institute, United Kingdom

  • Author: Lohan, Amanda J., Ireland

    Conway Institute, University College Dublin, Ireland

  • Author: Loftus, Brendan, Ireland

    Conway Institute, University College Dublin, Ireland

  • Author: Lucchini, Sacha, Ireland

    Institute of Food Research, Ireland

  • Author: Ussery, David

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

  • Author: Dorman, Charles J., Ireland

    Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Ireland

  • Author: Thomson, Nicholas R., United Kingdom

    The Wellcome Trust Sanger Institute, United Kingdom

  • Author: Vogel, Jörg, Germany

    Institute for Molecular Infection Biology, University of Würzburg, Germany

  • Author: Hinton, Jay C. D., Ireland

    Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Ireland

View graph of relations

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
Publication date2012
Volume109
Journal number20
PagesE1277-E1286
Number of pages10
ISSN0027-8424
DOIs
StatePublished
CitationsWeb of Science® Times Cited: 41

Keywords

  • Transcriptional mapping, Noncoding RNA, Posttranscriptional regulation, Pathogenicity, Genome sequence
Download as:
Download as PDF
Select render style:
APAAuthorCBEHarvardMLAStandardVancouverShortLong
PDF
Download as HTML
Select render style:
APAAuthorCBEHarvardMLAStandardVancouverShortLong
HTML
Download as Word
Select render style:
APAAuthorCBEHarvardMLAStandardVancouverShortLong
Word

ID: 8072065