1. An Infection-Relevant Transcriptomic Compendium for Salmonella enterica Serovar Typhimurium
- Author
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Karsten Hokamp, Tyrrell Conway, Joe E. Grissom, Rocío Canals, Sathesh K. Sivasankaran, Aoife Colgan, Shabarinath Srikumar, Carsten Kröger, Jay C. D. Hinton, Disa L. Hammarlöf, and Kristian Händler
- Subjects
Salmonella typhimurium ,Small RNA ,Salmonella ,Cancer Research ,Molecular Sequence Data ,medicine.disease_cause ,Microbiology ,03 medical and health sciences ,Transcription (biology) ,Virology ,Immunology and Microbiology(all) ,medicine ,Gene Regulatory Networks ,Promoter Regions, Genetic ,Gene ,Transcription factor ,Molecular Biology ,030304 developmental biology ,Genetics ,0303 health sciences ,biology ,030306 microbiology ,Gene Expression Profiling ,High-Throughput Nucleotide Sequencing ,Promoter ,biology.organism_classification ,Pathogenicity island ,Salmonella enterica ,Salmonella Infections ,Parasitology - Abstract
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.
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