The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium

Carsten Kröger, Shane C. Dillon, Andrew D. S. Cameron, Kai Papenfort, Sathesh K. Sivasankaran, Karsten Hokamp, Yanjie Chao, Alexandra Sittka, Magali Hébrard, Kristian Händler, Aoife Colgan, Pimlapas Leekitcharoenphon, Gemma C. Langridge, Amanda J. Lohan, Brendan Loftus, Sacha Lucchini, David Ussery, Charles J. Dorman, Nicholas R. Thomson, Jörg VogelJay C. D. Hinton

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

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
JournalProceedings of the National Academy of Sciences of the United States of America
Volume109
Issue number20
Pages (from-to)E1277-E1286
Number of pages10
ISSN0027-8424
DOIs
Publication statusPublished - 2012

Keywords

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

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