title: The Impact of 18 Ancestral and Horizontally-Acquired Regulatory Proteins upon the Transcriptome and sRNA Landscape of Salmonella enterica serovar Typhimurium.
abstract: We know a great deal about the genes used by the model pathogen Salmonella enterica serovar Typhimurium to cause disease, but less about global gene regulation. New tools for studying transcripts at the single nucleotide level now offer an unparalleled opportunity to understand the bacterial transcriptome, and expression of the small RNAs (sRNA) and coding genes responsible for the establishment of infection. Here, we define the transcriptomes of 18 mutants lacking virulence-related global regulatory systems that modulate the expression of the SPI1 and SPI2 Type 3 secretion systems of S. Typhimurium strain 4/74. Using infection-relevant growth conditions, we identified a total of 1257 coding genes that are controlled by one or more regulatory system, including a sub-class of genes that reflect a new level of cross-talk between SPI1 and SPI2. We directly compared the roles played by the major transcriptional regulators in the expression of sRNAs, and discovered that the RpoS (σ38) sigma factor modulates the expression of 23% of sRNAs, many more than other regulatory systems. The impact of the RNA chaperone Hfq upon the steady state levels of 280 sRNA transcripts is described, and we found 13 sRNAs that are co-regulated with SPI1 and SPI2 virulence genes. We report the first example of an sRNA, STnc1480, that is subject to silencing by H-NS and subsequent counter-silencing by PhoP and SlyA. The data for these 18 regulatory systems is now available to the bacterial research community in a user-friendly online resource, SalComRegulon.
authors: Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland.
authors: Aoife M
authors: AM
authors: Colgan
authors: Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland.
authors: Carsten
authors: 0000-0003-0461-1530
authors: C
authors: Kröger
authors: Institute of Microbiology, ETH Zürich, Zürich, Switzerland.
authors: Médéric
authors: M
authors: Diard
authors: Institute of Microbiology, ETH Zürich, Zürich, Switzerland.
authors: Wolf-Dietrich
authors: WD
authors: Hardt
authors: Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, Mexico.
authors: José L
authors: JL
authors: Puente
authors: Department of Microbiology, School of Genetics and Microbiology, Moyne Institute of Preventive Medicine, Trinity College, Dublin, Ireland.
authors: Sathesh K
authors: SK
authors: Sivasankaran
authors: Department of Genetics, School of Genetics and Microbiology, Smurfit Institute of Genetics, Trinity College, Dublin, Ireland.
authors: Karsten
authors: K
authors: Hokamp
authors: 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: Jay C D
authors: JC
authors: Hinton
mesh_terms: D001426:Bacterial Proteins / Q000096:biosynthesis* / Q000235:genetics; D015964:Gene Expression Regulation, Bacterial; D035001:Host Factor 1 Protein / Q000096:biosynthesis / Q000235:genetics; D008565:Membrane Proteins / Q000096:biosynthesis* / Q000235:genetics; D058727:RNA, Small Untranslated / Q000235:genetics*; D012486:Salmonella typhimurium / Q000235:genetics* / Q000254:growth & development / Q000472:pathogenicity; D065288:Serogroup; D012808:Sigma Factor / Q000096:biosynthesis / Q000235:genetics; D059467:Transcriptome / Q000235:genetics; D014774:Virulence
chemical_list: D001426:Bacterial Proteins; D035001:Host Factor 1 Protein; D008565:Membrane Proteins; D058727:RNA, Small Untranslated; C440638:SPI-2 protein, Salmonella; D012808:Sigma Factor; C419942:Spi1 protein, Salmonella; C069567:sigma factor KatF protein, Bacteria