title: A proteomic view of Desulfovibrio vulgaris metabolism as determined by liquid chromatography coupled with tandem mass spectrometry.
abstract: Direct LC-MS/MS was used to examine the proteins extracted from exponential or stationary phase Desulfovibrio vulgaris cells that had been grown on a minimal medium containing either lactate or formate as the primary carbon source. Across all four growth conditions, 976 gene products were identified with high confidence, which is equal to approximately 28% of all predicted proteins in the D. vulgaris genome. Bioinformatic analysis showed that the proteins identified were distributed among almost all functional classes, with the energy metabolism category containing the greatest number of identified proteins. At least 154 ORFs originally annotated as hypothetical proteins were found to encode the expressed proteins, which provided verification for the authenticity of these hypothetical proteins. Proteomic analysis showed that proteins potentially involved in ATP biosynthesis using the proton gradient across membrane, such as ATPase, alcohol dehydrogenases, heterodisulfide reductases, and [NiFe] hydrogenase (HynAB-1) of the hydrogen cycling were highly expressed in all four growth conditions, suggesting they may be the primary pathways for ATP synthesis in D. vulgaris. Most of the enzymes involved in substrate-level phosphorylation were also detected in all tested conditions. However, no enzyme involved in CO cycling or formate cycling was detected, suggesting that they are not the primary ATP-biosynthesis pathways under the tested conditions. This study provides the first proteomic overview of the cellular metabolism of D. vulgaris. The complete list of proteins identified in this study and their abundances (peptide hits) is provided in Supplementary Table 1.
authors.affiliation: Microbiology Group, Pacific Northwest National Laboratory, Richland, WA, USA. Weiwen.Zhang@pnl.gov
authors.forename: Weiwen
authors.initials: W
authors.lastname: Zhang
authors.forename: Marina A
authors.initials: MA
authors.lastname: Gritsenko
authors.forename: Ronald J
authors.initials: RJ
authors.lastname: Moore
authors.forename: David E
authors.initials: DE
authors.lastname: Culley
authors.forename: Lei
authors.initials: L
authors.lastname: Nie
authors.forename: Konstantinos
authors.initials: K
authors.lastname: Petritis
authors.forename: Eric F
authors.initials: EF
authors.lastname: Strittmatter
authors.forename: David G
authors.initials: DG
authors.lastname: Camp
authors.forename: Richard D
authors.initials: RD
authors.lastname: Smith
authors.forename: Fred J
authors.initials: FJ
authors.lastname: Brockman
mesh_terms: D000426:Alcohol Dehydrogenase / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism*; D002851:Chromatography, High Pressure Liquid / Q000379:methods*; D016969:Desulfovibrio vulgaris / Q000235:genetics / Q000254:growth & development / Q000378:metabolism*; D015180:Electrophoresis, Gel, Two-Dimensional; D004734:Energy Metabolism / Q000235:genetics / Q000502:physiology; D005561:Formates / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D006864:Hydrogenase / Q000235:genetics / Q000378:metabolism; D019344:Lactic Acid / Q000378:metabolism; D013058:Mass Spectrometry / Q000379:methods*; D008954:Models, Biological; D016366:Open Reading Frames / Q000235:genetics; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D013431:Sulfates / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D005561:Formates; D012333:RNA, Messenger; D013431:Sulfates; C030544:formic acid; D019344:Lactic Acid; D010088:Oxidoreductases; D000426:Alcohol Dehydrogenase; C043296:nickel-iron hydrogenase; D006864:Hydrogenase; C087171:heterodisulfide reductase