title: Organization and evolution of the biological response to singlet oxygen stress.
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.
authors: Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA.
authors: Yann S
authors: YS
authors: Dufour
authors: Robert
authors: R
authors: Landick
authors: Timothy J
authors: TJ
authors: Donohue
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D005075:Biological Evolution; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis; D018384:Oxidative Stress; D010802:Phylogeny; D011401:Promoter Regions, Genetic; D018085:Regulon; D012242:Rhodobacter sphaeroides / Q000145:classification / Q000502:physiology*; D016415:Sequence Alignment; D012808:Sigma Factor / Q000235:genetics / Q000378:metabolism*; D026082:Singlet Oxygen / Q000378:metabolism*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; C093117:ChrR protein, Rhodobacter sphaeroides; D012808:Sigma Factor; D014157:Transcription Factors; C063202:sporulation-specific sigma factors; D026082:Singlet Oxygen