title: Global transcriptomic analysis of Desulfovibrio vulgaris on different electron donors.
abstract: Whole-genome microarrays of Desulfovibrio vulgaris were used to determine relative transcript levels in cells grown to exponential or stationary phase on a medium containing either lactate or formate as electron donor. The results showed that 158 and 477 genes were differentially expressed when comparing exponential to stationary phase in lactate- or formate-based media, respectively; and 505 and 355 genes were responsive to the electron donor used at exponential or stationary phase, respectively. Functional analyses suggested that the differentially regulated genes were involved in almost every aspect of cellular metabolism, with genes involved in protein synthesis, carbon, and energy metabolism being the most regulated. The results suggested that HynBA-1 might function as a primary periplasmic hydrogenase responsible for oxidation of H2 linked to the proton gradient in lactate-based medium, while several periplasmic hydrogenases including HynBA-1 and Hyd might carry out this role in formate-based medium. The results also indicated that the alcohol dehydrogenase and heterodisulfide reductase catalyzed pathway for proton gradient formation might be actively functioning for ATP synthesis in D. vulgaris. In addition, hierarchical clustering analysis using expression data across different electron donors and growth phases allowed the identification of the common electron donor independent changes in gene expression specifically associated with the exponential to stationary phase transition, and those specifically associated with the different electron donors independent of growth phase. The study provides the first global description and functional interpretation of transcriptomic response to growth phase and electron donor in D. vulgaris.
authors.affiliation: Department of Microbiology, Pacific Northwest National Laboratory, 902 Battelle Boulevard, 999, Richland, WA 99352, USA. Weiwen.Zhang@pnl.gov
authors.forename: Weiwen
authors.initials: W
authors.lastname: Zhang
authors.forename: David E
authors.initials: DE
authors.lastname: Culley
authors.forename: Johannes C M
authors.initials: JC
authors.lastname: Scholten
authors.forename: Mike
authors.initials: M
authors.lastname: Hogan
authors.forename: Luigi
authors.initials: L
authors.lastname: Vitiritti
authors.forename: Fred J
authors.initials: FJ
authors.lastname: Brockman
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D003470:Culture Media; D016969:Desulfovibrio vulgaris / Q000254:growth & development* / Q000378:metabolism; D005561:Formates / Q000378:metabolism*; D020869:Gene Expression Profiling; D015964:Gene Expression Regulation, Bacterial; D006859:Hydrogen / Q000378:metabolism; D006864:Hydrogenase / Q000378:metabolism; D007773:Lactates / Q000378:metabolism*; D020411:Oligonucleotide Array Sequence Analysis; D020543:Proteome; D014158:Transcription, Genetic
chemical_list: D001426:Bacterial Proteins; D003470:Culture Media; D005561:Formates; D007773:Lactates; D020543:Proteome; D006859:Hydrogen; D006864:Hydrogenase