Abstract

The appearance of atmospheric oxygen from photosynthetic activity led to the evolution of aerobic respiration and responses to the resulting reactive oxygen species. In Rhodobacter sphaeroides, a photosynthetic alpha-proteobacterium, a transcriptional response to the reactive oxygen species singlet oxygen ((1)O(2)) is controlled by the group IV sigma factor sigma(E) and the anti-sigma factor ChrR. In this study, we integrated various large datasets to identify genes within the (1)O(2) stress response that contain sigma(E)-dependent promoters both within R. sphaeroides and across the bacterial phylogeny. Transcript pattern clustering and a sigma(E)-binding sequence model were used to predict candidate promoters that respond to (1)O(2) stress in R. sphaeroides. These candidate promoters were experimentally validated to nine R. sphaeroides sigma(E)-dependent promoters that control the transcription of 15 (1)O(2)-activated genes. Knowledge of the R. sphaeroides response to (1)O(2) and its regulator sigma(E)-ChrR was combined with large-scale phylogenetic and sequence analyses to predict the existence of a core set of approximately eight conserved sigma(E)-dependent genes in alpha-proteobacteria and gamma-proteobacteria. The bacteria predicted to contain this conserved response to (1)O(2) include photosynthetic species, as well as free-living and symbiotic/pathogenic nonphotosynthetic species. Our analysis also predicts that the response to (1)O(2) evolved within the time frame of the accumulation of atmospheric molecular oxygen on this planet.