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The alternative sigma factor σ E  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 σ E  in  Salmonella  and  E .  coli  has been examined using microarray, however a genome-wide analysis of σ E –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 σ E –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 σ E   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 σ E –binding sites did not contain the consensus sequence, suggesting there may be alternative mechanisms by which σ E  modulates transcription. By dissecting direct and indirect modes of σ E -mediated regulation, we found that σ E  activates gene expression through recognition of both canonical and reversed consensus sequence. New σ E  regulated genes ( greA ,  luxS ,  ompA  and  ompX ) are shown to be involved in heat shock and oxidative stress responses.

plos one

ChIP-Seq Analysis of the σE Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response