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

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.