An analysis of the changes in soluble hydrogenase and global gene expression in Cupriavidus necator (Ralstonia eutropha) H16 grown in heterotrophic diauxic batch culture

Abstract

BackgroundSoluble hydrogenases (SH) are enzymes that catalyse the oxidation of molecular hydrogen. The SH enzyme from Cupriavidus necator H16 is relatively oxygen tolerant and makes an attractive target for potential application in biochemical hydrogen fuel cells. Expression of the enzyme can be mediated by derepression of the hox promoter system under heterotrophic conditions. However, the overall impact of hox derepression, from a transcriptomic perspective, has never been previously reported.ResultsDerepression of hydrogenase gene expression upon fructose depletion was confirmed in replicate experiments. Using qRT-PCR, hoxF was 4.6-fold up-regulated, hypF2 was up-regulated in the cells grown 2.2-fold and the regulatory gene hoxA was up-regulated by a mean factor of 4.5. A full transcriptomic evaluation revealed a substantial shift in the global pattern of gene expression. In addition to up-regulation of genes associated with hydrogenase expression, significant changes were observed in genes associated with energy transduction, amino acid metabolism, transcription and translation (and regulation thereof), genes associated with cell stress, lipid and cell wall biogenesis and other functions, including cell motility.ConclusionsWe report the first full transcriptome analysis of C. necator H16 grown heterotrophically on fructose and glycerol in diauxic batch culture, which permits expression of soluble hydrogenase under heterotrophic conditions. The data presented deepens our understanding of the changes in global gene expression patterns that occur during the switch to growth on glycerol and suggests that energy deficit is a key driver for induction of hydrogenase expression in this organism.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-015-0226-4) contains supplementary material, which is available to authorized users.

Genomic, transcriptomic and proteomic analyses of Dehalobacter UNSWDHB in response to chloroform

“…Additionally, all subunits of another trimeric cytoplasmic Fe‐Fe hydrogenase (HymABC; UNSWDHB_RS08115‐08125) were detected. This enzyme is homologous to a NADP‐reducing HndABCD hydrogenase found in Desulfovibrio fructosovorans (Nouailler et al ., ) and also shares sequence similarity with other similar bidirectional soluble hydrogenases, such as HoxFUYHWI and the HydABC complex (Jugder et al ., ; Jugder et al ., ) (Supporting Information Table S4). In the same cluster, the gene encoding a redox‐sensing transcriptional repressor (Rex, UNSWDHB_RS08130) is situated downstream of the hymABC genes.…”

Protein Activity Sensing in Bacteria in Regulating Metabolism and Motility

“…The HoxBC complex converts hydrogen into protons and electrons and acts as a cytoplasmic hydrogen sensor in connection with the histidine kinase HoxJ and the regulator protein HoxA. HoxA acts as the main DNA-binding transcriptional activator of hydrogenase genes found within several operons present in R. eutropha ( Figure 3C) (Buhrke et al, 2004;Jugder et al, 2015). The exact sensory mechanism is still under investigation, but likely involves enzyme activity changes under conditions of oxidative stress.…”

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“…Bacterial strains, growth conditions, plasmids and oligonucleotides C. necator H16 (Cupriavidus necator, DSM 428) was routinely cultivated heterotrophically in minimal medium FGN as described in our previous work (Jugder et al, 2015, Jugder et al, 2016…”

“…necator H16 is induced on poorly utilised carbon sources (e.g., glycerol). Culture of this organism in minimal medium FGN (fructose-glycerol-nitrogen) is characterized by initial growth on the preferred fructose carbon source with hydrogenase expression repressed, followed by derepression of hydrogenase expression as the organism switches to growth on the less-preferred substrate glycerol upon fructose exhaustion (Jugder et al, 2015, Jugder et al, 2016.…”

“…Under the first condition, H 2 must be available in the growth media and typically a mixture of H 2 , CO 2 and O 2 with a volume ratio of 8:1:1 (autotrophic growth) has been employed widely to achieve induction in defined media. The second alternate inducing condition is achieved by the absence of preferentially utilized carbon and energy sources, such as fructose, in the medium which is conveniently achieved by using FGN medium whereby substrate shift occurs from fructose to glycerol under heterotrophic conditions (Friedrich et al, 1981, Schlegel et al, 1961, Jugder et al, 2015. The use of reporter genes fused to a gene of interest has been widely reported for studying gene expression and promoter activity in a diverse array of living organisms.…”