Transcriptomics

Dataset Information

2

RpoE regulon in Rhodobacter sphaeroides


ABSTRACT: 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.

ORGANISM(S): Rhodobacter sphaeroides 2.4.1  

SUBMITTER: Robert Landick   Timothy J Donohue  Yann S Dufour 

PROVIDER: E-GEOD-22576 | ArrayExpress | 2010-06-30

SECONDARY ACCESSION(S): GSE22576PRJNA128415

REPOSITORIES: GEO, ArrayExpress

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Publications

Organization and evolution of the biological response to singlet oxygen stress.

Dufour Yann S YS   Landick Robert R   Donohue Timothy J TJ  

Journal of molecular biology 20080813 3


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 res  ...[more]

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