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.