title: The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium.
abstract: 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 σ(70) (including phoP, slyA, and invF) from which we identified the -10 and -35 motifs of σ(70)-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 <20% were found throughout the Enterobacteriaceae. This description of the transcriptional map of SL1344 advances our understanding of S. Typhimurium, arguably the most important bacterial infection model.
authors.affiliation: Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland.
authors.forename: Carsten
authors.initials: C
authors.lastname: Kröger
authors.forename: Shane C
authors.initials: SC
authors.lastname: Dillon
authors.forename: Andrew D S
authors.initials: AD
authors.lastname: Cameron
authors.forename: Kai
authors.initials: K
authors.lastname: Papenfort
authors.forename: Sathesh K
authors.initials: SK
authors.lastname: Sivasankaran
authors.forename: Karsten
authors.initials: K
authors.lastname: Hokamp
authors.forename: Yanjie
authors.initials: Y
authors.lastname: Chao
authors.forename: Alexandra
authors.initials: A
authors.lastname: Sittka
authors.forename: Magali
authors.initials: M
authors.lastname: Hébrard
authors.forename: Kristian
authors.initials: K
authors.lastname: Händler
authors.forename: Aoife
authors.initials: A
authors.lastname: Colgan
authors.forename: Pimlapas
authors.initials: P
authors.lastname: Leekitcharoenphon
authors.forename: Gemma C
authors.initials: GC
authors.lastname: Langridge
authors.forename: Amanda J
authors.initials: AJ
authors.lastname: Lohan
authors.forename: Brendan
authors.initials: B
authors.lastname: Loftus
authors.forename: Sacha
authors.initials: S
authors.lastname: Lucchini
authors.forename: David W
authors.initials: DW
authors.lastname: Ussery
authors.forename: Charles J
authors.initials: CJ
authors.lastname: Dorman
authors.forename: Nicholas R
authors.initials: NR
authors.lastname: Thomson
authors.forename: Jörg
authors.initials: J
authors.lastname: Vogel
authors.forename: Jay C D
authors.initials: JC
authors.lastname: Hinton
mesh_terms: D001483:Base Sequence; D015152:Blotting, Northern; D047369:Chromatin Immunoprecipitation; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics*; D015723:Gene Library; D046228:Microarray Analysis; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D058727:RNA, Small Untranslated / Q000235:genetics*; D038621:Regulatory Sequences, Ribonucleic Acid / Q000235:genetics*; D012486:Salmonella typhimurium / Q000235:genetics*; D017423:Sequence Analysis, RNA / Q000379:methods; D024363:Transcription Initiation Site; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D009841:Oligonucleotides; D058727:RNA, Small Untranslated; D038621:Regulatory Sequences, Ribonucleic Acid