Convergence of the Transcriptional Responses to Heat Shock and Singlet Oxygen Stresses

Abstract

Cells often mount transcriptional responses and activate specific sets of genes in response to stress-inducing signals such as heat or reactive oxygen species. Transcription factors in the RpoH family of bacterial alternative σ factors usually control gene expression during a heat shock response. Interestingly, several α-proteobacteria possess two or more paralogs of RpoH, suggesting some functional distinction. We investigated the target promoters of Rhodobacter sphaeroides RpoHI and RpoHII using genome-scale data derived from gene expression profiling and the direct interactions of each protein with DNA in vivo. We found that the RpoHI and RpoHII regulons have both distinct and overlapping gene sets. We predicted DNA sequence elements that dictate promoter recognition specificity by each RpoH paralog. We found that several bases in the highly conserved TTG in the −35 element are important for activity with both RpoH homologs; that the T-9 position, which is over-represented in the RpoHI promoter sequence logo, is critical for RpoHI–dependent transcription; and that several bases in the predicted −10 element were important for activity with either RpoHII or both RpoH homologs. Genes that are transcribed by both RpoHI and RpoHII are predicted to encode for functions involved in general cell maintenance. The functions specific to the RpoHI regulon are associated with a classic heat shock response, while those specific to RpoHII are associated with the response to the reactive oxygen species, singlet oxygen. We propose that a gene duplication event followed by changes in promoter recognition by RpoHI and RpoHII allowed convergence of the transcriptional responses to heat and singlet oxygen stress in R. sphaeroides and possibly other bacteria.

Oxygen-Dependent Regulation of Bacterial Lipid Production

“…The AppA-PpsR regulatory system is composed of a DNA-binding repressor, PpsR, and the light-and redox-sensitive antirepressor AppA (18). FnrL, a member of the FNR (fumarate and nitrate reductase) family of transcription factors, is a global regulator of anaerobic gene expression that is directly inhibited by the presence of O 2 (19,20). These three pathways each contribute to increased expression of photosynthesis genes at low O 2 tension, including those in the puf and puc operons (encoding polypeptides of the RC, LH1, and LH2 complexes), biosynthetic enzymes for bacteriochlorophyll (BChl) and carotenoid (Crt) pigments, and electron transport chain components (12,13,16,(21)(22)(23).…”

An RpoHI-Dependent Response Promotes Outgrowth after Extended Stationary Phase in the Alphaproteobacterium Rhodobacter sphaeroides

“…For example, the genes of one of the nuo operons (RSP_0100 to RSP_0112) are regulated by RpoHI and RpoHII, and binding of the sigma factors upstream of the first gene of the operon was demonstrated (15), but these nuo genes mostly showed decreased expression in outgrowth phase, which was also strongly dependent on RpoHI in our transcriptome analysis. The facts that not all promoters induced in outgrowth following late stationary phase in R. sphaeroides have RpoH recognition motifs and, further, that genes preceded by RpoH binding sites show different growthphase-dependent expression suggest that additional factors are responsible for the differential expression patterns of some genes.…”

“…3) or by an RpoHII-or RpoHI/RpoHII-dependent promoter (Table S1) (15,16). Since a role of the alternative RpoHI/RpoHII sigma factors in the response to singlet oxygen was observed in previous studies (12,16,25,28), we also tested for a correlation of genes induced during outgrowth (following prolonged stationary phase of 72 h after inoculation) (this study) and genes induced by singlet oxygen, as determined in the study by Berghoff et al (25) (Fig.…”

“…Among the 265 genes which showed at least 2-fold higher expression after 20 min of outgrowth than in exponential phase (following late stationary phase), 105 genes were known or predicted to be transcribed by the alternative sigma factor RpoHI, RpoHII, or both (Table S1) (12,15,16). Members of the RpoH family of sigma factors often control genes during a heat shock response.…”

“…The alternative sigma factor RpoE activates the rpoHII gene in response to singlet oxygen, and RpoHII consequently activates many genes with functions in the detoxification of peroxides or methylglyoxal, singlet oxygen scavenging, and iron and redox homeostasis (12). RpoHI also has an important role in the singlet oxygen response, and there is a big overlap of the RpoHI and RpoHII regulons (15,16). More recently, it was demonstrated that several stress factors besides heat and singlet oxygen, like organic peroxides, hydrogen peroxide, superoxide, and CdCl 2 , can activate RpoHI/RpoHIIdependent promoters (17).…”