An Infection-Relevant Transcriptomic Compendium for Salmonella enterica Serovar Typhimurium

•RNA-seq analysis of S. Typhimurium performed under 22 infection-relevant conditions•The 22 conditions induce transcription of 86% of all S. Typhimurium genes•S. Typhimurium pathogenicity islands display characteristic transcriptional signatures•The expression landscape of 280 S. Typhimurium sRNAs is described

SummaryBacterial 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.