Abstract
The RegB/RegA two-component system from Rhodobacter capsulatus regulates global changes in gene expression in response to alterations in oxygen levels. Studies have shown that RegB/RegA controls many energy-generating and energy-utilizing systems such as photosynthesis, nitrogen fixation, carbon fixation, hydrogen utilization, respiration, electron transport and denitrification. In this report, we utilized RNA-seq and ChIP-seq to analyse the breadth of genes indirectly and directly regulated by RegA. A comparison of mRNA transcript levels in wild type cells relative to a RegA deletion strain shows that there are 257 differentially expressed genes under photosynthetic defined minimal growth medium conditions and 591 differentially expressed genes when grown photosynthetically in a complex rich medium. ChIP-seq analysis also identified 61 unique RegA binding sites with a well-conserved recognition sequence, 33 of which exhibit changes in neighbouring gene expression. These transcriptome results define new members of the RegA regulon including genes involved in iron transport and motility. These results also reveal that the set of genes that are regulated by RegA are growth medium specific. Similar analyses under dark aerobic conditions where RegA is thought not to be phosphorylated by RegB reveal 40 genes that are differentially expressed in minimal medium and 20 in rich medium. Finally, a comparison of the R. capsulatus RegA regulon with the orthologous PrrA regulon in Rhodobacter sphaeroides shows that the number of photosystem genes regulated by RegA and PrrA are similar but that the identity of genes regulated by RegA and PrrA beyond those involved in photosynthesis are quite distinct.
Highlights
The survival of bacteria in a variety of different environments requires that they constantly assess and adapt to Received 9 June 2016; Accepted 21 July 2016 their surroundings
Genes directly and indirectly regulated by RegA were identified by performing RNA-seq analyses of both aerobically and anaerobically grown WT cells as well as cells deleted for RegA (DregA)
We undertook an analysis of WT–DregA changes in gene expression under both dark aerobic and illuminated anaerobic growth conditions in cells grown in rich growth medium (PY) and in cells grown in defined minimal malate medium (RCV) (Tables 1, S1 and S2)
Summary
The survival of bacteria in a variety of different environments requires that they constantly assess and adapt to Received 9 June 2016; Accepted 21 July 2016 their surroundings. One of the many signals that two-component systems sense is the presence or absence of environmental oxygen, which is critical for regulating a switch between aerobic respiratory and anaerobic growth modes (Wu et al, 2012). This is true for metabolically diverse anoxygenic purple photosynthetic bacteria that engage in dark aerobic respiration in the presence of oxygen or photosynthetic growth under light anaerobic conditions (Bauer et al, 2009).
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