title: 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: BACKGROUND
  Soluble 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.
  
  
  RESULTS
  Derepression 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.
  
  
  CONCLUSIONS
  We 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.
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia. b.jugder@unsw.edu.au.
authors.forename: Bat-Erdene
authors.initials: BE
authors.lastname: Jugder
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia. Zhiliang.chen@unsw.edu.au.|Systems Biology Initiative, University of New South Wales, Sydney, 2052, Australia. Zhiliang.chen@unsw.edu.au.
authors.forename: Zhiliang
authors.initials: Z
authors.lastname: Chen
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia. tantekping@hotmail.com.
authors.forename: Darren Tan Tek
authors.initials: DT
authors.lastname: Ping
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia. h.lebhar@unsw.edu.au.
authors.forename: Helene
authors.initials: H
authors.lastname: Lebhar
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia. j.welch@unsw.edu.au.
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Welch
authors.affiliation: School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, 2052, Australia. c.marquis@unsw.edu.au.
authors.forename: Christopher P
authors.initials: CP
authors.lastname: Marquis
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D001431:Bacteriological Techniques; D061249:Batch Cell Culture Techniques; D019149:Bioreactors / Q000382:microbiology; D020118:Cupriavidus necator / Q000201:enzymology / Q000235:genetics* / Q000254:growth & development; D004734:Energy Metabolism / Q000235:genetics; D005285:Fermentation; D005632:Fructose / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D005990:Glycerol / Q000378:metabolism; D052836:Heterotrophic Processes; D006864:Hydrogenase / Q000235:genetics* / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D059467:Transcriptome
chemical_list: D001426:Bacterial Proteins; D005632:Fructose; D006864:Hydrogenase; D005990:Glycerol