title: An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium.
abstract: Bacterial transcriptional networks consist of hundreds of transcription factors and thousands of promoters. However, the true complexity of transcription in a bacterial pathogen and the effect of the environments encountered during infection remain to be established. We present a simplified approach for global promoter identification in bacteria using RNA-seq-based transcriptomic analyses of 22 distinct infection-relevant environmental conditions. Individual RNA samples were combined to identify most of the 3,838 Salmonella enterica serovar Typhimurium promoters in just two RNA-seq runs. Individual in vitro conditions stimulated characteristic transcriptional signatures, and the suite of 22 conditions induced transcription of 86% of all S. Typhimurium genes. We highlight the environmental conditions that induce the Salmonella pathogenicity islands and present a small RNA expression landscape of 280 sRNAs. This publicly available compendium of environmentally controlled expression of every transcriptional feature of S. Typhimurium constitutes a useful resource for the bacterial research community.
authors: Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
authors: Carsten
authors: C
authors: Kröger
authors: Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
authors: Aoife
authors: A
authors: Colgan
authors: Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
authors: Shabarinath
authors: S
authors: Srikumar
authors: Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
authors: Kristian
authors: K
authors: Händler
authors: Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
authors: Sathesh K
authors: SK
authors: Sivasankaran
authors: Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
authors: Disa L
authors: DL
authors: Hammarlöf
authors: Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
authors: Rocío
authors: R
authors: Canals
authors: Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.
authors: Joe E
authors: JE
authors: Grissom
authors: Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.
authors: Tyrrell
authors: T
authors: Conway
authors: Department of Genetics, School of Genetics & Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
authors: Karsten
authors: K
authors: Hokamp
authors: Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland; Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK. Electronic address: jay.hinton@liverpool.ac.uk.
authors: Jay C D
authors: JC
authors: Hinton
mesh_terms: D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D011401:Promoter Regions, Genetic; D012480:Salmonella Infections / Q000382:microbiology*; D012486:Salmonella typhimurium / Q000235:genetics*