Responses of the Rhodobacter sphaeroides transcriptome to blue light under semiaerobic conditions

Abstract

Exposure to blue light of the facultative phototrophic proteobacterium Rhodobacter sphaeroides grown semiaerobically results in repression of the puc and puf operons involved in photosystem formation. To reveal the genome-wide effects of blue light on gene expression and the underlying photosensory mechanisms, transcriptome profiles of R. sphaeroides during blue-light irradiation (for 5 to 135 min) were analyzed. Expression of most photosystem genes was repressed upon irradiation. Downregulation of photosystem development may be used to prevent photooxidative damage occurring when the photosystem, oxygen, and high-intensity light are present simultaneously. The photoreceptor of the BLUF-domain family, AppA, which belongs to the AppA-PpsR antirepressor-repressor system, is essential for maintenance of repression upon prolonged irradiation (S. Braatsch et al., Mol. Microbiol. 45:827-836, 2002). Transcriptome data suggest that the onset of repression is also mediated by the AppA-PpsR system, albeit via an apparently different sensory mechanism. Expression of several genes, whose products may participate in photooxidative damage defense, including deoxypyrimidine photolyase, glutathione peroxidase, and quinol oxidoreductases, was increased. Among the genes upregulated were genes encoding two sigma factors: sigmaE and sigma38. The consensus promoter sequences for these sigma factors were predicted in the upstream sequences of numerous upregulated genes, suggesting that coordinated action of sigmaE and sigma38 is responsible for the upregulation. Based on the dynamics of upregulation, the anti-sigmaE factor ChrR or its putative upstream partner is proposed to be the primary sensor. The identified transcriptome responses provided a framework for deciphering blue-light-dependent signal transduction pathways in R. sphaeroides.

FIG. 1.

Major expression patterns of the downregulated genes in R. sphaeroides in response to blue light. Clusters were derived by using GeneSpring software. (A) Cluster 1 represents genes whose expression was downregulated at 5 min of irradiation and remained low during irradiation. (B) Cluster 2 represents genes whose expression was significantly downregulated at 45 min but not at 5 min of irradiation. (C) PS gene cluster and puc operons. PpsR-binding sites are shown as red vertical arrows. Putative transcripts are shown as black horizontal arrows. Colors: green, bacteriochlorophyll biosynthesis genes; red, carotenoid biosynthesis genes; blue, genes encoding structural polypeptides of photocomplexes; gray, genes encoding assembly factors or proteins of unknown function; orange, genes encoding regulatory factors; pink, genes encoding enzymes common to bacteriochlorophyll and ubiquinone biosynthesis. Circled genes were directly repressed by PpsR (Moskvin et al., submitted). (D) Relative expression of the PS genes in the ΔappA mutant APP11 and the wild type expressing higher levels of PpsR, 2.4.1(pPNs), compared to the wild-type strain. The expression of every gene in the wild type (not shown) was assigned to 1. The expression levels in APP11 and 2.4.1(pPNs) are according to the color scheme shown.

FIG. 2.

Major expression patterns of the upregulated genes in R. sphaeroides in response to blue light. (A) Cluster 3 represents genes whose expression was severalfold upregulated at 5 min of irradiation and remained upregulated at the attenuated levels upon prolonged irradiation. (B) Cluster 4 represents genes whose expression was upregulated ≤2.5-fold at 45 min of irradiation and did not change drastically at other time points.

FIG. 3.

Deduced consensus sites presented as sequence logos (52). (A) Putative σ^E promoter; (B) putative σ³⁸ promoter.