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Cell Host Microbe. 2013 Dec 11;14(6):683-95. doi: 10.1016/j.chom.2013.11.010.

An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium.

Author information

1
Department of Microbiology, School of Genetics & Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
2
Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
3
Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019, USA.
4
Department of Genetics, School of Genetics & Microbiology, Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
5
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.

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.

PMID:
24331466
DOI:
10.1016/j.chom.2013.11.010
[Indexed for MEDLINE]
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