RpoE regulon in Rhodobacter sphaeroides

In Rhodobacter sphaeroides a transcriptional response to the reactive oxygen species singlet oxygen is controlled by the group IV sigma factor RpoE and the anti-sigma factor ChrR. In this study, we integrated various large datasets to identify genes within the singlet oxygen stress response that contain RpoE-dependent promoters within R. sphaeroides. Transcript pattern clustering and a RpoE-binding sequence model were used to predict candidate promoters that respond to singlet oxygen stress in R. sphaeroides. These candidate promoters were experimentally validated to nine R. sphaeroides RpoE-dependent promoters that control the transcription of 15 genes activated by singlet oxygen. DNA immunoprecipitated with polyclonal antibodies against RpoE or the Beta' subunit of RNA polymerase was labelled with Cy5 and hybridized on two-color tilling arrays (triplicates for each) with genomic DNA as an input control labelled with Cy3.