ChIP-Seq Analysis of the [sigma].sup.E Regulon of Salmonella enterica Serovar Typhimurium Reveals New Genes Implicated in Heat Shock and Oxidative Stress Response

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