Transcriptomic analysis of aerobic respiratory and anaerobic photosynthetic states in Rhodobacter capsulatus and their modulation by global redox regulators RegA, FnrL and CrtJ

Abstract

Anoxygenicphotosynthetic prokaryotes have simplified photosystems that represent ancient lineages that predate the more complex oxygen evolving photosystems present in cyanobacteria and chloroplasts. These organisms thrive under illuminated anaerobic photosynthetic conditions, but also have the ability to grow under dark aerobic respiratory conditions. This study provides a detailed snapshot of transcription ground states of both dark aerobic and anaerobic photosynthetic growth modes in the purple photosynthetic bacterium Rhodobactercapsulatus. Using 18 biological replicates for aerobic and photosynthetic states, we observed that 1834 genes (53 % of the genome) exhibited altered expression between aerobic and anaerobic growth. In comparison with aerobically grown cells, photosynthetically grown anaerobic cells showed decreased transcription of genes for cobalamin biosynthesis (−45 %), iron transport and homeostasis (−42 %), motility (−32 %), and glycolysis (−34 %). Conversely and more intuitively, the expression of genes involved in carbon fixation (547 %), bacteriochlorophyll biosynthesis (162 %) and carotenogenesis (114 %) were induced. We also analysed the relative contributions of known global redox transcription factors RegA, FnrL and CrtJ in regulating aerobic and anaerobic growth. Approximately 50 % of differentially expressed genes (913 of 1834) were affected by a deletion of RegA, while 33 % (598 out of 1834) were affected by FnrL, and just 7 % (136 out of 1834) by CrtJ. Numerous genes were also shown to be controlled by more than one redox responding regulator.

Porphyrin Excretion Resulting From Mutation of a Gene Encoding a Class I Fructose 1,6-Bisphosphate Aldolase in Rhodobacter capsulatus

“…Therefore it appears that the FBA encoded by rcc01707 is a Class I enzyme that operates in glycolysis. This interpretation is supported by transcriptomic data obtained by Kumka et al (2017), presented in their Supplementary Material. The transcripts of rcc01707 did not change significantly between aerobic chemotrophic and anaerobic phototrophic growth (6,296 vs. 6,225 counts, respectively).…”

“…There are several reasons for this conclusion. Firstly, hemN1 and hemN2 , but not hemN3 , are induced in phototrophically grown (anaerobic) cells, and so hemN3 appears to encode an aerobic enzyme (Kumka et al, 2017). Secondly, the R. capsulatus HemN1 and the Escherichia coli anaerobic heme degradation enzyme ChuW are 41% identical in a BLAST alignment, and the R. capsulatus hemN1 is in an operon with a putative chuX , just as the E. coli chuW (LaMattina et al, 2016).…”

Interactions among Redox Regulators and the CtrA Phosphorelay in Dinoroseobacter shibae and Rhodobacter capsulatus

“…FnrL is the only Crp/Fnr regulator that has been studied in R. capsulatus [29]. Its loss did not result in any large changes in transcript levels for the examined traits under anaerobic phototrophic conditions ( Figure 5), and the same was observed for the loss of crtJ, which encodes a transcription factor that controls numerous photosynthesis and cytochrome genes [32] (Figure 5). RegA is the response regulator of the RegB/A two-component system that controls photosynthesis, nitrogen and carbon fixation, denitrification, and respiration genes in response to oxygen availability [26].…”

Disruption of poly (3-hydroxyalkanoate) depolymerase gene and overexpression of three poly (3-hydroxybutyrate) biosynthetic genes improve poly (3-hydroxybutyrate) production from nitrogen rich medium by Rhodobacter sphaeroides

“…Therefore, the cause of the suppression of PHB biosynthesis by nitrogen may be a posttranscriptional process. The gene expression vector pLP-1.2 used in this study has a puf promoter containing part of the bacteriochlorophyll biosynthetic and light harvesting machinery genes [22] and therefore, can highly express the gene of interest not only during anaerobic photosynthesis but also during aerobic respiration [23]. Indeed, successful production of each gene product was confirmed by assaying its activity (Table 1) even when the recombinant strains used for the enzyme assays were grown in AAY medium containing 10 mM AS.…”

“…The different derivatives of pLP-1.2 were introduced into R. sphaeroides HJ and HJΔ phaZ cells using conjugative DNA transfer via E. coli S17-1 [23]. Transformants harboring pLP-1.2 derivatives were selected using Km resistance.…”