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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}
}
  • In order to experimentally establish the criteria for designing gene-specific and group-specific oligonucleotide probes, an oligonucleotide array was constructed that contained perfect match (PM) and mismatch (MM) probes (50mers and 70mers) based upon 4 genes. The effects of probe-target identity, continuous stretch, mismatch position, and hybridization free energy on specificity were examined. Little hybridization was observed at a probe-target identity of <85% for both 50mer and 70mer probes........Based on the experimental results, a set of criteria are suggested for the design of gene-specific and group-specific oligonucleotide probes, and these criteria should provide valuable information for the development of new softwaremore » and algorithms for microarray-based studies.; Microarrays with oligonucleotides of different lengths were used to monitor gene expression at a wholegenome level. To determine what length of oligonucleotide is a better alternative to PCR-generated probes, the performance of oligonucleotide probes was systematically compared to that of their PCR-generated counterparts for 96 genes from Shewanella oneidensis MR-1 in terms of overall signal intensity, numbers of genes detected, specificity, sensitivity, and differential gene expression under experimental conditions. .......To evaluate differential gene expression under experimental conditions, S. oneidensis MR-1 cells were exposed to low- or high-pH conditions for 30 and 60 min, and the transcriptional profiles detected by oligonucleotide probes (50-mer, 60-mer, and 70-mer) were closely correlated with those detected by the PCR probes. The results demonstrated that 70-mer oligonucleotides can provide the performance most comparable to the performance obtained with PCR-generated probes.; Desulfovibrio vulgaris was cultivated in a defined medium, and biomass was sampled for approximately 70 h to characterize the shifts in gene expression as cells transitioned from the exponential to the stationary phase during electron donor depletion. In addition to temporal transcriptomics, total protein, carbohydrate, lactate, acetate, and sulfate levels were measured. The microarray data were examined for statistically significant expression changes, hierarchical cluster analysis, and promoter element prediction and were validated by quantitative PCR. ..... Our results indicated that in addition to expected changes (e.g., energy conversion, protein turnover, translation, transcription, and DNA replication and repair), genes related to phage, stress response, carbohydrate flux, the outer envelope, and iron homeostasis played important roles as D. vulgaris cells experienced electron donor depletion.« less
  • Dehalococcoides ethenogenes strain 195 (DE195) was grown in a sustainable syntrophic association with Desulfovibrio vulgaris Hildenborough (DVH) as a co-culture, as well as with DVH and the hydrogenotrophic methanogen Methanobacterium congolense (MC) as a tri-culture using lactate as the sole energy and carbon source. In the co- and tri-cultures, maximum dechlorination rates of DE195 were enhanced by approximately three times (11.0±0.01 lmol per day for the co-culture and 10.1±0.3 lmol per day for the tri-culture) compared with DE195 grown alone (3.8±0.1 lmol per day). Cell yield of DE195 was enhanced in the co-culture (9.0±0.5 x 107 cells per lmol Cl{supmore » -} released, compared with 6.8±0.9x 107 cells per lmol Cl{sup -} released for the pure culture), whereas no further enhancement was observed in the tri-culture (7.3±1.8x 107 cells per lmol Cl{sup -} released). The transcriptome of DE195 grown in the co-culture was analyzed using a whole-genome microarray targeting DE195, which detected 102 significantly up- or down-regulated genes compared with DE195 grown in isolation, whereas no significant transcriptomic difference was observed between co- and tri-cultures. Proteomic analysis showed that 120 proteins were differentially expressed in the co-culture compared with DE195 grown in isolation. Physiological, transcriptomic and proteomic results indicate that the robust growth of DE195 in co- and tri-cultures is because of the advantages associated with the capabilities of DVH to ferment lactate to provide H2 and acetate for growth, along with potential benefits from proton translocation, cobalamin-salvaging and amino acid biosynthesis, whereas MC in the tri-culture provided no significant additional benefits beyond those of DVH.« less
  • Dehalococcoides ethenogenes strain 195 (DE195) was grown in a sustainable syntrophic association with Desulfovibrio vulgaris Hildenborough (DVH) as a co-culture, as well as with DVH and the hydrogenotrophic methanogen Methanobacterium congolense (MC) as a tri-culture using lactate as the sole energy and carbon source. In the co- and tri-cultures, maximum dechlorination rates of DE195 were enhanced by approximately three times (11.0 0.01 lmol per day for the co-culture and 10.1 0.3 lmol per day for the tri-culture) compared with DE195 grown alone (3.8 0.1 lmol per day). Cell yield of DE195 was enhanced in the co-culture (9.0 0.5107 cells permore » lmol Cl released, compared with 6.8 0.9107 cells per lmol Cl released for the pure culture), whereas no further enhancement was observed in the tri-culture (7.3 1.8107 cells per lmol Cl released). The transcriptome of DE195 grown in the co-culture was analyzed using a wholegenome microarray targeting DE195, which detected 102 significantly up- or down-regulated genes compared with DE195 grown in isolation, whereas no significant transcriptomic difference was observed between co- and tri-cultures. Proteomic analysis showed that 120 proteins were differentially expressed in the co-culture compared with DE195 grown in isolation. Physiological, transcriptomic and proteomic results indicate that the robust growth of DE195 in co- and tri-cultures is because of the advantages associated with the capabilities of DVH to ferment lactate to provide H2 and acetate for growth, along with potential benefits from proton translocation, cobalamin-salvaging and amino acid biosynthesis, whereas MC in the tri-culture provided no significant additional benefits beyond those of DVH.« less
  • Dehalococcoides ethenogenes strain 195 (DE195) was grown in a sustainable syntrophic association with Desulfovibrio vulgaris Hildenborough (DVH) as a co-culture, as well as with DVH and the hydrogenotrophic methanogen Methanobacterium congolense (MC) as a tri-culture using lactate as the sole energy and carbon source. In the co- and tri-cultures, maximum dechlorination rates of DE195 were enhanced by approximately three times (11.0 0.01 lmol per day for the co-culture and 10.1 0.3 lmol per day for the tri-culture) compared with DE195 grown alone (3.8 0.1 lmol per day). Cell yield of DE195 was enhanced in the co-culture (9.0 0.5107 cells permore » lmol Cl released, compared with 6.8 0.9107 cells per lmol Cl released for the pure culture), whereas no further enhancement was observed in the tri-culture (7.3 1.8107 cells per lmol Cl released). The transcriptome of DE195 grown in the co-culture was analyzed using a wholegenome microarray targeting DE195, which detected 102 significantly up- or down-regulated genes compared with DE195 grown in isolation, whereas no significant transcriptomic difference was observed between co- and tri-cultures. Proteomic analysis showed that 120 proteins were differentially expressed in the co-culture compared with DE195 grown in isolation. Physiological, transcriptomic and proteomic results indicate that the robust growth of DE195 in co- and tri-cultures is because of the advantages associated with the capabilities of DVH to ferment lactate to provide H2 and acetate for growth, along with potential benefits from proton translocation, cobalamin-salvaging and amino acid biosynthesis, whereas MC in the tri-culture provided no significant additional benefits beyond those of DVH.« less
  • Abstract Advances in DNA microarray and proteomics technologies have enabled high-throughput measurement of mRNA expression and protein abundance. Parallel profiling of mRNA and protein on a global scale and integrative analysis of these two data types could provide additional insight into the metabolic mechanisms underlying complex biological systems. However, because protein abundance and mRNA expression are affected by many cellular and physical processes, there have been conflicting results on the correlation of these two measurements. In addition, as current proteomic methods can detect only a small fraction of proteins present in cells, no correlation study of these two data typesmore » has been done thus far at the whole-genome level. In this study, we describe a novel data-driven statistical model to integrate whole-genome microarray and proteomic data collected from Desulfovibrio vulgaris grown under three different conditions. Based on the Poisson distribution pattern of proteomic data and the fact that a large number of proteins were undetected (excess zeros), Zero-inflated Poisson models were used to define the correlation pattern of mRNA and protein abundance. The models assumed that there is a probability mass at zero representing some of the undetected proteins because of technical limitations. The models thus use abundance measurements of transcripts and proteins experimentally detected as input to generate predictions of protein abundances as output for all genes in the genome. We demonstrated the statistical models by comparatively analyzing D. vulgaris grown on lactate-based versus formate-based media. The increased expressions of Ech hydrogenase and alcohol dehydrogenase (Adh)-periplasmic Fe-only hydrogenase (Hyd) pathway for ATP synthesis were predicted for D. vulgaris grown on formate.« less