Journal article
The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium
Trinity College Dublin1
Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark2
University of Würzburg3
National Food Institute, Technical University of Denmark4
Division of Epidemiology and Microbial Genomics, National Food Institute, Technical University of Denmark5
Division of Microbiology and Risk Assessment, National Food Institute, Technical University of Denmark6
Wellcome Sanger Institute7
University College Dublin8
Quadram Institute9
Department of Systems Biology, Technical University of Denmark10
...and 0 moreMore 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
Language: | English |
---|---|
Publisher: | National Academy of Sciences |
Year: | 2012 |
Pages: | E1277-86 |
ISSN: | 10916490 and 00278424 |
Types: | Journal article |
DOI: | 10.1073/pnas.1201061109 |
ORCIDs: | Leekitcharoenphon, Pimlapas |
Genome sequence Noncoding RNA Pathogenicity Posttranscriptional regulation Transcriptional mapping
Base Sequence Biological Sciences Blotting, Northern Chromatin Immunoprecipitation Gene Expression Regulation, Bacterial Gene Library Microarray Analysis Microbiology Molecular Sequence Data Oligonucleotides PNAS Plus Promoter Regions, Genetic RNA, Small Untranslated Regulatory Sequences, Ribonucleic Acid Salmonella typhimurium Sequence Analysis, RNA Transcription Initiation Site Transcription, Genetic genome sequence noncoding RNA pathogenicity posttranscriptional regulation transcriptional mapping