title: Pathway confirmation and flux analysis of central metabolic pathways in Desulfovibrio vulgaris hildenborough using gas chromatography-mass spectrometry and Fourier transform-ion cyclotron resonance mass spectrometry.
abstract: Flux distribution in central metabolic pathways of Desulfovibrio vulgaris Hildenborough was examined using 13C tracer experiments. Consistent with the current genome annotation and independent evidence from enzyme activity assays, the isotopomer results from both gas chromatography-mass spectrometry (GC-MS) and Fourier transform-ion cyclotron resonance mass spectrometry (FT-ICR MS) indicate the lack of an oxidatively functional tricarboxylic acid (TCA) cycle and an incomplete pentose phosphate pathway. Results from this study suggest that fluxes through both pathways are limited to biosynthesis. The data also indicate that >80% of the lactate was converted to acetate and that the reactions involved are the primary route of energy production [NAD(P)H and ATP production]. Independently of the TCA cycle, direct cleavage of acetyl coenzyme A to CO and 5,10-methyl tetrahydrofuran also leads to production of NADH and ATP. Although the genome annotation implicates a ferredoxin-dependent oxoglutarate synthase, isotopic evidence does not support flux through this reaction in either the oxidative or the reductive mode; therefore, the TCA cycle is incomplete. FT-ICR MS was used to locate the labeled carbon distribution in aspartate and glutamate and confirmed the presence of an atypical enzyme for citrate formation suggested in previous reports [the citrate synthesized by this enzyme is the isotopic antipode of the citrate synthesized by the (S)-citrate synthase]. These findings enable a better understanding of the relation between genome annotation and actual metabolic pathways in D. vulgaris and also demonstrate that FT-ICR MS is a powerful tool for isotopomer analysis, overcoming the problems with both GC-MS and nuclear magnetic resonance spectroscopy.
authors.affiliation: Virtual Institute of Microbial Stress and Survival, Department of Chemical Engineering and Bioengineering, University of California, Berkeley, California, USA.
authors.forename: Yinjie
authors.initials: Y
authors.lastname: Tang
authors.forename: Francesco
authors.initials: F
authors.lastname: Pingitore
authors.forename: Aindrila
authors.initials: A
authors.lastname: Mukhopadhyay
authors.forename: Richard
authors.initials: R
authors.lastname: Phan
authors.forename: Terry C
authors.initials: TC
authors.lastname: Hazen
authors.forename: Jay D
authors.initials: JD
authors.lastname: Keasling
mesh_terms: D000105:Acetyl Coenzyme A / Q000378:metabolism; D002247:Carbon Isotopes; D002952:Citric Acid Cycle / Q000502:physiology; D017357:Cyclotrons; D016969:Desulfovibrio vulgaris / Q000254:growth & development / Q000378:metabolism*; D005583:Fourier Analysis; D008401:Gas Chromatography-Mass Spectrometry / Q000379:methods*; D007700:Kinetics; D013058:Mass Spectrometry / Q000295:instrumentation / Q000379:methods*; D053858:Metabolic Networks and Pathways; D015394:Molecular Structure; D021241:Spectrometry, Mass, Electrospray Ionization / Q000295:instrumentation / Q000379:methods
chemical_list: D002247:Carbon Isotopes; D000105:Acetyl Coenzyme A