PNNL

Abstract

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