title: ChIP-Seq Analysis of the σE Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response.
abstract: The alternative sigma factor σE functions to maintain bacterial homeostasis and membrane integrity in response to extracytoplasmic stress by regulating thousands of genes both directly and indirectly. The transcriptional regulatory network governed by σE in Salmonella and E. coli has been examined using microarray, however a genome-wide analysis of σE-binding sites in Salmonella has not yet been reported. We infected macrophages with Salmonella Typhimurium over a select time course. Using chromatin immunoprecipitation followed by high-throughput DNA sequencing (ChIP-seq), 31 σE-binding sites were identified. Seventeen sites were new, which included outer membrane proteins, a quorum-sensing protein, a cell division factor, and a signal transduction modulator. The consensus sequence identified for σE in vivo binding was similar to the one previously reported, except for a conserved G and A between the -35 and -10 regions. One third of the σE-binding sites did not contain the consensus sequence, suggesting there may be alternative mechanisms by which σE modulates transcription. By dissecting direct and indirect modes of σE-mediated regulation, we found that σE activates gene expression through recognition of both canonical and reversed consensus sequence. New σE regulated genes (greA, luxS, ompA and ompX) are shown to be involved in heat shock and oxidative stress responses.
authors.affiliation: Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, United States of America.
authors.forename: Jie
authors.initials: J
authors.lastname: Li
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America.
authors.forename: Christopher C
authors.initials: CC
authors.lastname: Overall
authors.affiliation: Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, United States of America.
authors.forename: Rudd C
authors.initials: RC
authors.lastname: Johnson
authors.affiliation: Department of Infectious Diseases, J. Craig Venter Institute, Rockville, Maryland, United States of America.
authors.forename: Marcus B
authors.initials: MB
authors.lastname: Jones
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America.
authors.forename: Jason E
authors.initials: JE
authors.lastname: McDermott
authors.affiliation: Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, United States of America.
authors.forename: Fred
authors.initials: F
authors.lastname: Heffron
authors.affiliation: Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, United States of America.
authors.forename: Joshua N
authors.initials: JN
authors.lastname: Adkins
authors.affiliation: Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, United States of America.
authors.forename: Eric D
authors.initials: ED
authors.lastname: Cambronne
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D001483:Base Sequence; D016384:Consensus Sequence; D015964:Gene Expression Regulation, Bacterial; D018869:Heat-Shock Response; D006801:Humans; D008969:Molecular Sequence Data; D018384:Oxidative Stress; D018085:Regulon; D012480:Salmonella Infections / Q000382:microbiology; D012486:Salmonella typhimurium / Q000235:genetics* / Q000378:metabolism; D012808:Sigma Factor / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D012808:Sigma Factor; C063202:sporulation-specific sigma factors