title: RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium.
abstract: Salmonella enterica serovar Typhimurium is arguably the world's best-understood bacterial pathogen. However, crucial details about the genetic programs used by the bacterium to survive and replicate in macrophages have remained obscure because of the challenge of studying gene expression of intracellular pathogens during infection. Here, we report the use of deep sequencing (RNA-seq) to reveal the transcriptional architecture and gene activity of Salmonella during infection of murine macrophages, providing new insights into the strategies used by the pathogen to survive in a bactericidal immune cell. We characterized 3583 transcriptional start sites that are active within macrophages, and highlight 11 of these as candidates for the delivery of heterologous antigens from Salmonella vaccine strains. A majority (88%) of the 280 S. Typhimurium sRNAs were expressed inside macrophages, and SPI13 and SPI2 were the most highly expressed pathogenicity islands. We identified 31 S. Typhimurium genes that were strongly up-regulated inside macrophages but expressed at very low levels during in vitro growth. The SalComMac online resource allows the visualisation of every transcript expressed during bacterial replication within mammalian cells. This primary transcriptome of intra-macrophage S.-Typhimurium describes the transcriptional start sites and the transcripts responsible for virulence traits, and catalogues the sRNAs that may play a role in the regulation of gene expression during infection.
authors.affiliation: Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland.|Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
authors.forename: Shabarinath
authors.initials: S
authors.lastname: Srikumar
authors.affiliation: Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland.|Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
authors.forename: Carsten
authors.initials: C
authors.lastname: Kröger
authors.affiliation: Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland.
authors.forename: Magali
authors.initials: M
authors.lastname: Hébrard
authors.affiliation: Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland.
authors.forename: Aoife
authors.initials: A
authors.lastname: Colgan
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
authors.forename: Siân V
authors.initials: SV
authors.lastname: Owen
authors.affiliation: Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland.
authors.forename: Sathesh K
authors.initials: SK
authors.lastname: Sivasankaran
authors.affiliation: Department of Biology, University of Regina, Regina, Saskatchewan, Canada.
authors.forename: Andrew D S
authors.initials: AD
authors.lastname: Cameron
authors.affiliation: Department of Genetics, School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College, Dublin, Ireland.
authors.forename: Karsten
authors.initials: K
authors.lastname: Hokamp
authors.affiliation: Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland.|Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom.
authors.forename: Jay C D
authors.initials: JC
authors.lastname: Hinton
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics*; D005798:Genes, Bacterial / Q000235:genetics; D044404:Genomic Islands / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D008264:Macrophages / Q000378:metabolism*; D012329:RNA, Bacterial / Q000235:genetics*; D022562:Salmonella Vaccines / Q000235:genetics; D012486:Salmonella typhimurium / Q000235:genetics*; D059467:Transcriptome / Q000235:genetics*; D014774:Virulence / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D012329:RNA, Bacterial; D022562:Salmonella Vaccines