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Title: A Proteomic View of Desulfovibrio Vulgaris Metabolim as Determined by Liquid Chromatography Coupled with Tandem Mass Spectrometry

Abstract

Direct liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to examine the proteins from Desulfovibrio vulgaris grown at exponential or stationary phase on a minimal medium containing either lactate or formate as the primary carbon source, with the goal of an initial characterization of the diversity of proteins synthesized under these conditions. 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. Among these, fifty-two out of 55 predicted ribosomal proteins (~95%) were identified with high confidence. Functional 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 open reading frames (ORFs) originally annotated as hypothetical proteins were found to encode expressed proteins, which provided verification for the authenticity of these hypothetical proteins. Proteomic analysis showed that members of the proton gradient pathway, catalyzed by alcohol dehydrogenases and heterodisulfide reductases, and [NiFe] hydrogenase (HynAB-1) of the hydrogen cycling pathway 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 involvedmore » in substrate-level phosphorylation were also detected in all tested conditions. However, no enzyme involved in CO cycling or formate cycling was detected, suggesting these are not the primary pathways for ATP biosynthesis under the tested conditions. This study provides the first proteomic overview of the cellular metabolism of D. vulgaris.« less

Authors:
; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
891112
Report Number(s):
PNNL-SA-45506
15891; TRN: US200621%%58
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Journal Name:
Proteomics, 6(15):4286-4299
Additional Journal Information:
Journal Name: Proteomics, 6(15):4286-4299
Country of Publication:
United States
Language:
English
Subject:
08 HYDROGEN; ALCOHOL DEHYDROGENASE; BIOSYNTHESIS; CARBON SOURCES; CHROMATOGRAPHY; DESULFOVIBRIO; ENZYMES; FORMATES; FUNCTIONAL ANALYSIS; FUNCTIONALS; GENES; HYDROGEN; HYDROGENASES; LACTATES; MASS SPECTROSCOPY; METABOLISM; OXIDOREDUCTASES; PHOSPHORYLATION; PROTEINS; PROTONS; SYNTHESIS; VERIFICATION; Environmental Molecular Sciences Laboratory

Citation Formats

Zhang, Weiwen, Gritsenko, Marina A, Moore, Ronald J, Culley, David E, Nie, Lei, Petritis, Konstantinos, Strittmatter, Eric F, Camp, David G, Smith, Richard D, and Brockman, Fred J. A Proteomic View of Desulfovibrio Vulgaris Metabolim as Determined by Liquid Chromatography Coupled with Tandem Mass Spectrometry. United States: N. p., 2006. Web. doi:10.1002/pmic.200500930.
Zhang, Weiwen, Gritsenko, Marina A, Moore, Ronald J, Culley, David E, Nie, Lei, Petritis, Konstantinos, Strittmatter, Eric F, Camp, David G, Smith, Richard D, & Brockman, Fred J. A Proteomic View of Desulfovibrio Vulgaris Metabolim as Determined by Liquid Chromatography Coupled with Tandem Mass Spectrometry. United States. doi:10.1002/pmic.200500930.
Zhang, Weiwen, Gritsenko, Marina A, Moore, Ronald J, Culley, David E, Nie, Lei, Petritis, Konstantinos, Strittmatter, Eric F, Camp, David G, Smith, Richard D, and Brockman, Fred J. Tue . "A Proteomic View of Desulfovibrio Vulgaris Metabolim as Determined by Liquid Chromatography Coupled with Tandem Mass Spectrometry". United States. doi:10.1002/pmic.200500930.
@article{osti_891112,
title = {A Proteomic View of Desulfovibrio Vulgaris Metabolim as Determined by Liquid Chromatography Coupled with Tandem Mass Spectrometry},
author = {Zhang, Weiwen and Gritsenko, Marina A and Moore, Ronald J and Culley, David E and Nie, Lei and Petritis, Konstantinos and Strittmatter, Eric F and Camp, David G and Smith, Richard D and Brockman, Fred J},
abstractNote = {Direct liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to examine the proteins from Desulfovibrio vulgaris grown at exponential or stationary phase on a minimal medium containing either lactate or formate as the primary carbon source, with the goal of an initial characterization of the diversity of proteins synthesized under these conditions. 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. Among these, fifty-two out of 55 predicted ribosomal proteins (~95%) were identified with high confidence. Functional 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 open reading frames (ORFs) originally annotated as hypothetical proteins were found to encode expressed proteins, which provided verification for the authenticity of these hypothetical proteins. Proteomic analysis showed that members of the proton gradient pathway, catalyzed by alcohol dehydrogenases and heterodisulfide reductases, and [NiFe] hydrogenase (HynAB-1) of the hydrogen cycling pathway 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 these are not the primary pathways for ATP biosynthesis under the tested conditions. This study provides the first proteomic overview of the cellular metabolism of D. vulgaris.},
doi = {10.1002/pmic.200500930},
journal = {Proteomics, 6(15):4286-4299},
number = ,
volume = ,
place = {United States},
year = {2006},
month = {8}
}