Understanding the choreography of Salmonella transcription with RNA-seq

Jay Photo 2015 Option 2 250Thursday 12 May, 15:00

MIMS-UCMR Seminar by Invited Speaker:
Professor Jay C.D Hinton
Institute of Integrative Biology, University of Liverpool, UK

Understanding the choreography of Salmonella transcription with RNA-seq

Mikael Rhen & Bernt Eric Uhlin

Thymine, Department of Molecular Biology, 2nd floor

Bacterial transcriptional networks typically consist of hundreds of transcription factors and thousands of promoters. However, the true complexity of transcription in a bacterial pathogen remains to be established. We devised a suite of 22 different environmental conditions that reflect the pathogenic lifestyle of Salmonella enterica serovar typhimurium strain 4/74 during infection of a host, and used RNA-seq to generate a compendium of Salmonella gene expression. Individual in vitro conditions stimulated characteristic transcriptional signatures, and the suite of 22 conditions induced expression of 86% of all S. typhimurium genes 1. Recently, we compared these in vitro conditions with the intra-macrophage gene expression profiles of S. typhimurium 2. All the data can be accessed at http://tinyurl.com/SalComMac. We hope that this database of environmentally-controlled expression of every transcriptional feature of S. typhimurium will be a useful resource for the bacterial research community, and the results explain the environmental signals that stimulate S. typhimurium promoters during infection.

We found that the transcription of the majority of the 3825 S. typhimurium promoters is environmentally-responsive. Our global approach has identified 280 small RNAs in S. typhimurium; these sRNAs were analysed in the context of chromosome localisation and Hfq-association.

I will discuss the environmental conditions that stimulate expression of the Salmonella pathogenicity islands, will present a comprehensive expression landscape of sRNAs and discuss our approach for defining the relative strength of S. Typhimurium promoters during macrophage infection.

1 Srikumar S, Kröger C, Hébrard M, Colgan A, Owen SV, Sivasankaran SK, Cameron ADS, Hokamp K, Hinton JCD: RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium. PLOS Pathogens 2015, 11:e1005262.

2 Kröger C, Colgan A, Srikumar S, Handler K, Sivasankaran SK, Hammarlof DL, Canals R, Grissom JE, Conway T, Hokamp K, Hinton JC: An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium. Cell Host Microbe 2013, 14:683-695.