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Title: Global Transcriptomic Analysis of Desulfovibrio vulgaris Grown on Different Carbon Sources

Abstract

Abstract Whole-genome microarrays of Desulfovibrio vulgaris were used to determine relative transcript levels in cells grown to exponential or stationary phase on a minimal 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 genes differentially regulated were involved in almost every aspect of cellular metabolism, with the genes involved in protein synthesis, carbon, and energy metabolism being the most regulated. The results suggested that hynAB-1 might function as a primary periplasmic hydrogenase responsible for oxidation of H2 inked to the proton gradient in lactate-based medium, while several periplasmic hydrogenases including hynAB-1 and hyd might carry out this role in formate-based medium. The results also indicated the proton gradient pathway catalyzed by alcohol dehydrogenase and heterodisulfide reductase might be actively functioning for ATP synthesis in D. vulgaris. The possible pathways for ethanol generation from lactate and formate metabolism were also discussed. In addition, hierarchical clustering analysis using expression data across carbon sources and growth phases allowedmore » the identification of the common change specifically associated with the exponential to stationary phase transition, and that specifically associated with the carbon source change from lactate to formate. The study provides the first global description and a functional interpretation of transcriptomic response to growth phase and carbon source in D. vulgaris.« less

Authors:
; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
886713
Report Number(s):
PNNL-SA-45424
Journal ID: ISSN 0003-6072; ALJMAO; TRN: US0604005
DOE Contract Number:  
AC05-76RL01830
Resource Type:
Journal Article
Resource Relation:
Journal Name: Antonie Van Leeuwenhoek, 89(2):221-237; Journal Volume: 89; Journal Issue: 2
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS; ALCOHOL DEHYDROGENASE; BINDING ENERGY; CARBON; CARBON SOURCES; DESULFOVIBRIO; ELECTRONS; ETHANOL; FORMATES; FUNCTIONALS; GENES; HYDROGENASES; LACTATES; METABOLISM; OXIDATION; OXIDOREDUCTASES; PROTEINS; PROTONS; SYNTHESIS; VALENCE

Citation Formats

Zhang, Weiwen, Culley, David E., Scholten, Johannes C., Hogan, Mike, Vitiritti, Luigi, and Brockman, Fred J. Global Transcriptomic Analysis of Desulfovibrio vulgaris Grown on Different Carbon Sources. United States: N. p., 2006. Web. doi:10.1007/s10482-005-9024-z.
Zhang, Weiwen, Culley, David E., Scholten, Johannes C., Hogan, Mike, Vitiritti, Luigi, & Brockman, Fred J. Global Transcriptomic Analysis of Desulfovibrio vulgaris Grown on Different Carbon Sources. United States. doi:10.1007/s10482-005-9024-z.
Zhang, Weiwen, Culley, David E., Scholten, Johannes C., Hogan, Mike, Vitiritti, Luigi, and Brockman, Fred J. Wed . "Global Transcriptomic Analysis of Desulfovibrio vulgaris Grown on Different Carbon Sources". United States. doi:10.1007/s10482-005-9024-z.
@article{osti_886713,
title = {Global Transcriptomic Analysis of Desulfovibrio vulgaris Grown on Different Carbon Sources},
author = {Zhang, Weiwen and Culley, David E. and Scholten, Johannes C. and Hogan, Mike and Vitiritti, Luigi and Brockman, Fred J.},
abstractNote = {Abstract Whole-genome microarrays of Desulfovibrio vulgaris were used to determine relative transcript levels in cells grown to exponential or stationary phase on a minimal 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 genes differentially regulated were involved in almost every aspect of cellular metabolism, with the genes involved in protein synthesis, carbon, and energy metabolism being the most regulated. The results suggested that hynAB-1 might function as a primary periplasmic hydrogenase responsible for oxidation of H2 inked to the proton gradient in lactate-based medium, while several periplasmic hydrogenases including hynAB-1 and hyd might carry out this role in formate-based medium. The results also indicated the proton gradient pathway catalyzed by alcohol dehydrogenase and heterodisulfide reductase might be actively functioning for ATP synthesis in D. vulgaris. The possible pathways for ethanol generation from lactate and formate metabolism were also discussed. In addition, hierarchical clustering analysis using expression data across carbon sources and growth phases allowed the identification of the common change specifically associated with the exponential to stationary phase transition, and that specifically associated with the carbon source change from lactate to formate. The study provides the first global description and a functional interpretation of transcriptomic response to growth phase and carbon source in D. vulgaris.},
doi = {10.1007/s10482-005-9024-z},
journal = {Antonie Van Leeuwenhoek, 89(2):221-237},
number = 2,
volume = 89,
place = {United States},
year = {Wed Feb 01 00:00:00 EST 2006},
month = {Wed Feb 01 00:00:00 EST 2006}
}