TY - JOUR
T1 - The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium
AU - Kröger, Carsten
AU - Dillon, Shane C.
AU - Cameron, Andrew D. S.
AU - Papenfort, Kai
AU - Sivasankaran, Sathesh K.
AU - Hokamp, Karsten
AU - Chao, Yanjie
AU - Sittka, Alexandra
AU - Hébrard, Magali
AU - Händler, Kristian
AU - Colgan, Aoife
AU - Leekitcharoenphon, Pimlapas
AU - Langridge, Gemma C.
AU - Lohan, Amanda J.
AU - Loftus, Brendan
AU - Lucchini, Sacha
AU - Ussery, David
AU - Dorman, Charles J.
AU - Thomson, Nicholas R.
AU - Vogel, Jörg
AU - Hinton, Jay C. D.
PY - 2012
Y1 - 2012
N2 - More than 50 y of research have provided great insight into the physiology, metabolism, and molecular biology of Salmonella enterica serovar Typhimurium (S. Typhimurium), but important gaps in our knowledge remain. It is clear that a precise choreography of gene expression is required for Salmonella infection, but basic genetic information such as the global locations of transcription start sites (TSSs) has been lacking. We combined three RNA-sequencing techniques and two sequencing platforms to generate a robust picture of transcription in S. Typhimurium. Differential RNA sequencing identified 1,873 TSSs on the chromosome of S. Typhimurium SL1344 and 13% of these TSSs initiated antisense transcripts. Unique findings include the TSSs of the virulence regulators phoP, slyA, and invF. Chromatin immunoprecipitation revealed that RNA polymerase was bound to 70% of the TSSs, and two-thirds of these TSSs were associated with σ70 (including phoP, slyA, and invF) from which we identified the −10 and −35 motifs of σ70-dependent S. Typhimurium gene promoters. Overall, we corrected the location of important genes and discovered 18 times more promoters than identified previously. S. Typhimurium expresses 140 small regulatory RNAs (sRNAs) at early stationary phase, including 60 newly identified sRNAs. Almost half of the experimentally verified sRNAs were found to be unique to the Salmonella genus, and
AB - More than 50 y of research have provided great insight into the physiology, metabolism, and molecular biology of Salmonella enterica serovar Typhimurium (S. Typhimurium), but important gaps in our knowledge remain. It is clear that a precise choreography of gene expression is required for Salmonella infection, but basic genetic information such as the global locations of transcription start sites (TSSs) has been lacking. We combined three RNA-sequencing techniques and two sequencing platforms to generate a robust picture of transcription in S. Typhimurium. Differential RNA sequencing identified 1,873 TSSs on the chromosome of S. Typhimurium SL1344 and 13% of these TSSs initiated antisense transcripts. Unique findings include the TSSs of the virulence regulators phoP, slyA, and invF. Chromatin immunoprecipitation revealed that RNA polymerase was bound to 70% of the TSSs, and two-thirds of these TSSs were associated with σ70 (including phoP, slyA, and invF) from which we identified the −10 and −35 motifs of σ70-dependent S. Typhimurium gene promoters. Overall, we corrected the location of important genes and discovered 18 times more promoters than identified previously. S. Typhimurium expresses 140 small regulatory RNAs (sRNAs) at early stationary phase, including 60 newly identified sRNAs. Almost half of the experimentally verified sRNAs were found to be unique to the Salmonella genus, and
KW - Transcriptional mapping
KW - Noncoding RNA
KW - Posttranscriptional regulation
KW - Pathogenicity
KW - Genome sequence
U2 - 10.1073/pnas.1201061109
DO - 10.1073/pnas.1201061109
M3 - Journal article
SN - 0027-8424
VL - 109
SP - E1277-E1286
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 20
ER -