TY - JOUR
T1 - An infection-relevant transcriptomic compendium for salmonella enterica serovar typhimurium
AU - Kröger, Carsten
AU - Colgan, Aoife
AU - Srikumar, Shabarinath
AU - Händler, Kristian
AU - Sivasankaran, Sathesh K.
AU - Hammarlöf, Disa L.
AU - Canals, Rocío
AU - Grissom, Joe E.
AU - Conway, Tyrrell
AU - Hokamp, Karsten
AU - Hinton, Jay C.D.
N1 - Funding Information:
We are grateful to Jörg Vogel, Kai Papenfort, Konrad Förstner, Cynthia M. Sharma, and Yanjie Chao for sharing unpublished data and ideas; to Mark Stevens and Tim Wallis for discussions about strain 4/74; and to Jonathan Hardy, Ken Sanderson, and Susan Hoiseth for details of the construction of SL1344 in Bruce Stocker’s lab. We appreciate Katie Breen and Jane Twohig for technical support. The authors thank José L. Puente, Andrew D.S. Cameron, and Ian R. Monk for their insight and Stephen Fitzgerald for sharing primers. We also thank Fritz Thümmler (Vertis Biotechnologie AG) for excellent cDNA construction. The work was financially supported by Science Foundation Ireland (Grant 08/IN.1/B2104) and the University of Liverpool.
PY - 2013/12/11
Y1 - 2013/12/11
N2 - 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.
AB - 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.
UR - https://www.scopus.com/pages/publications/84890302568
UR - https://www.scopus.com/pages/publications/84890302568#tab=citedBy
U2 - 10.1016/j.chom.2013.11.010
DO - 10.1016/j.chom.2013.11.010
M3 - Article
C2 - 24331466
AN - SCOPUS:84890302568
SN - 1931-3128
VL - 14
SP - 683
EP - 695
JO - Cell Host and Microbe
JF - Cell Host and Microbe
IS - 6
ER -