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Reference set of regulons in Desulfovibrionales inferred by comparative genomics approach

Description: in this study, we carried out large-scale comparative genomics analysis of regulatory interactions in Desulfovibrio vulgaris and 12 related genomes from Desulfovibrionales order using our recently developed web server RegPredict (http://regpredict.lbl.gov). An overall reference collection of 26 Desulfovibrionales regulogs can be accessed through RegPrecise database (http://regpredict.lbl.gov).
Date: November 15, 2010
Creator: Kazakov, A.E.; Rodionov, D.A.; Price, M.N.; Arkin, A.P.; Dubchak, I. & Novichkov, P.S.
Partner: UNT Libraries Government Documents Department

Global Analysis of Heat Shock Response in Desulfovibrio vulgaris Hildenborough.

Description: Desulfovibrio vulgaris Hildenborough belongs to a class ofsulfate-reducing bacteria (SRB) and is found ubiquitously in nature.Given the importance of SRB-mediated reduction for bioremediation ofmetal ion contaminants, ongoing research on D. vulgaris has been in thedirection of elucidating regulatory mechanisms for this organism under avariety of stress conditions. This work presents a global view of thisorganism's response to elevated growth temperature using whole-celltranscriptomics and proteomics tools. Transcriptional response (1.7-foldchange or greater; Z>1.5) ranged from 1,135 genes at 15 min to 1,463genes at 120 min for a temperature up-shift of 13oC from a growthtemperature of 37oC for this organism and suggested both direct andindirect modes of heat sensing. Clusters of orthologous group categoriesthat were significantly affected included posttranslationalmodifications; protein turnover and chaperones (up-regulated); energyproduction and conversion (down-regulated), nucleotide transport,metabolism (down-regulated), and translation; ribosomal structure; andbiogenesis (down-regulated). Analysis of the genome sequence revealed thepresence of features of both negative and positive regulation whichincluded the CIRCE element and promoter sequences corresponding to thealternate sigma factors ?32 and ?54. While mechanisms of heat shockcontrol for some genes appeared to coincide with those established forEscherichia coli and Bacillus subtilis, the presence of unique controlschemes for several other genes was also evident. Analysis of proteinexpression levels using differential in-gel electrophoresis suggestedgood agreement with transcriptional profiles of several heat shockproteins, including DnaK (DVU0811), HtpG (DVU2643), HtrA (DVU1468), andAhpC (DVU2247). The proteomics study also suggested the possibility ofposttranslational modifications in the chaperones DnaK, AhpC, GroES(DVU1977), and GroEL (DVU1976) and also several periplasmic ABCtransporters.
Date: September 16, 2005
Creator: Chhabra, S.R.; He, Q.; Huang, K.H.; Gaucher, S.P.; Alm, E.J.; He,Z. et al.
Partner: UNT Libraries Government Documents Department

Response of Desulfovibrio vulgaris to Alkaline Stress

Description: The response of exponentially growing Desulfovibrio vulgarisHildenborough to pH 10 stress was studied using oligonucleotidemicroarrays and a study set of mutants with genes suggested by microarraydata to be involved in the alkaline stress response deleted. The datashowed that the response of D. vulgaris to increased pH is generallysimilar to that of Escherichia coli but is apparently controlled byunique regulatory circuits since the alternative sigma factors (sigma Sand sigma E) contributing to this stress response in E. coli appear to beabsent in D. vulgaris. Genes previously reported to be up-regulated in E.coli were up-regulated in D. vulgaris; these genes included three ATPasegenes and a tryptophan synthase gene. Transcription of chaperone andprotease genes (encoding ATP-dependent Clp and La proteases and DnaK) wasalso elevated in D. vulgaris. As in E. coli, genes involved in flagellumsynthesis were down-regulated. The transcriptional data also identifiedregulators, distinct from sigma S and sigma E, that are likely part of aD. vulgaris Hildenborough-specific stress response system.Characterization of a study set of mutants with genes implicated inalkaline stress response deleted confirmed that there was protectiveinvolvement of the sodium/proton antiporter NhaC-2, tryptophanase A, andtwo putative regulators/histidine kinases (DVU0331 andDVU2580).
Date: November 30, 2007
Creator: Stolyar, S.; He, Q.; He, Z.; Yang, Z.; Borglin, S.E.; Joyner, D. et al.
Partner: UNT Libraries Government Documents Department

Temporal transcriptomic analysis of Desulfovibrio vulgaris Hildenborough transition into stationary phase growth during electrondonor depletion

Description: 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. As the cells transitioned from the exponential phase to the stationary phase, a majority of the down-expressed genes were involved in translation and transcription, and this trend continued at the remaining times. There were general increases in relative expression for intracellular trafficking and secretion, ion transport, and coenzyme metabolism as the cells entered the stationary phase. As expected, the DNA replication machinery was down-expressed, and the expression of genes involved in DNA repair increased during the stationary phase. Genes involved in amino acid acquisition, carbohydrate metabolism, energy production, and cell envelope biogenesis did not exhibit uniform transcriptional responses. Interestingly, most phage-related genes were up-expressed at the onset of the stationary phase. This result suggested that nutrient depletion may affect community dynamics and DNA transfer mechanisms of sulfate-reducing bacteria via the phage cycle. The putative feoAB system (in addition to other presumptive iron metabolism genes) was significantly up-expressed, and this suggested the possible importance of Fe{sup 2+} acquisition under metal-reducing conditions. The expression of a large subset of carbohydrate-related genes was altered, and the total cellular carbohydrate levels declined during the growth phase transition. Interestingly, the D. vulgaris genome does not contain a putative rpoS gene, a common attribute of the {delta}-Proteobacteria genomes sequenced to date, and the transcription profiles of other putative rpo genes were not significantly altered. Our results indicated that in addition to ...
Date: August 1, 2006
Creator: Clark, M.E.; He, Q.; He, Z.; Huang, K.H.; Alm, E.J.; Wan, X.-F. et al.
Partner: UNT Libraries Government Documents Department

How sulphate-reducing microorganisms cope with stress: Lessons from systems biology

Description: Sulphate-reducing microorganisms (SRMs) are a phylogenetically diverse group of anaerobes encompassing distinct physiologies with a broad ecological distribution. As SRMs have important roles in the biogeochemical cycling of carbon, nitrogen, sulphur and various metals, an understanding of how these organisms respond to environmental stresses is of fundamental and practical importance. In this Review, we highlight recent applications of systems biology tools in studying the stress responses of SRMs, particularly Desulfovibrio spp., at the cell, population, community and ecosystem levels. The syntrophic lifestyle of SRMs is also discussed, with a focus on system-level analyses of adaptive mechanisms. Such information is important for understanding the microbiology of the global sulphur cycle and for developing biotechnological applications of SRMs for environmental remediation, energy production, biocorrosion control, wastewater treatment and mineral recovery.
Date: April 1, 2011
Creator: Zhou, J.; He, Q.; Hemme, C.L.; Mukhopadhyay, A.; Hillesland, K.; Zhou, A. et al.
Partner: UNT Libraries Government Documents Department

The electron transfer system of syntrophically grown Desulfovibrio vulgaris

Description: Interspecies hydrogen transfer between organisms producing and consuming hydrogen promotes the decomposition of organic matter in most anoxic environments. Although syntrophic couplings between hydrogen producers and consumers are a major feature of the carbon cycle, mechanisms for energy recovery at the extremely low free energies of reactions typical of these anaerobic communities have not been established. In this study, comparative transcriptional analysis of a model sulfate-reducing microbe, Desulfovibrio vulgaris Hildenborough, suggested the use of alternative electron transfer systems dependent upon growth modality. During syntrophic growth on lactate with a hydrogenotrophic methanogen, D. vulgaris up-regulated numerous genes involved in electron transfer and energy generation when compared with sulfate-limited monocultures. In particular, genes coding for the putative membrane-bound Coo hydrogenase, two periplasmic hydrogenases (Hyd and Hyn) and the well-characterized high-molecular weight cytochrome (Hmc) were among the most highly expressed and up-regulated. Additionally, a predicted operon coding for genes involved in lactate transport and oxidation exhibited up-regulation, further suggesting an alternative pathway for electrons derived from lactate oxidation during syntrophic growth. Mutations in a subset of genes coding for Coo, Hmc, Hyd and Hyn impaired or severely limited syntrophic growth but had little affect on growth via sulfate-respiration. These results demonstrate that syntrophic growth and sulfate-respiration use largely independent energy generation pathways and imply that understanding of microbial processes sustaining nutrient cycling must consider lifestyles not captured in pure culture.
Date: May 1, 2009
Creator: Walker, C. B.; He, Z.; Yang, Z.K.; Ringbauer, J. A., Jr.; He, Q.; Zhou, J. et al.
Partner: UNT Libraries Government Documents Department

Toward a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough

Description: Protein–protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study E. coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio 5 vulgaris Hildenborough, a model anaerobe and sulfate reducer. In this paper we present the first attempt to identify protein-protein interactions in an obligate anaerobic bacterium. We used suicide vector-assisted chromosomal modification of 12 open reading frames encoded by this sulfate reducer to append an eight amino acid affinity tag to the carboxy-terminus of the chosen proteins. Three biological replicates of the 10 ‘pulled-down’ proteins were separated and analyzed using liquid chromatography-mass spectrometry. Replicate agreement ranged between 35% and 69%. An interaction network among 12 bait and 90 prey proteins was reconstructed based on 134 bait-prey interactions computationally identified to be of high confidence. We discuss the biological significance of several unique metabolic features of D. vulgaris revealed by this protein-protein interaction data 15 and protein modifications that were observed. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.
Date: May 1, 2011
Creator: Chhabra, S.R.; Joachimiak, M.P.; Petzold, C.J.; Zane, G.M.; Price, M.N.; Gaucher, S. et al.
Partner: UNT Libraries Government Documents Department

Impact of elevated nitrate on sulfate-reducing bacteria: A comparative study of Desulfovibrio vulgaris

Description: Sulfate-reducing bacteria have been extensively studied for their potential in heavy-metal bioremediation. However, the occurrence of elevated nitrate in contaminated environments has been shown to inhibit sulfate reduction activity. Although the inhibition has been suggested to result from the competition with nitrate-reducing bacteria, the possibility of direct inhibition of sulfate reducers by elevated nitrate needs to be explored. Using Desulfovibrio vulgaris as a model sulfate-reducing bacterium, functional genomics analysis reveals that osmotic stress contributed to growth inhibition by nitrate as shown by the upregulation of the glycine/betaine transporter genes and the relief of nitrate inhibition by osmoprotectants. The observation that significant growth inhibition was effected by 70 mM NaNO{sub 3} but not by 70 mM NaCl suggests the presence of inhibitory mechanisms in addition to osmotic stress. The differential expression of genes characteristic of nitrite stress responses, such as the hybrid cluster protein gene, under nitrate stress condition further indicates that nitrate stress response by D. vulgaris was linked to components of both osmotic and nitrite stress responses. The involvement of the oxidative stress response pathway, however, might be the result of a more general stress response. Given the low similarities between the response profiles to nitrate and other stresses, less-defined stress response pathways could also be important in nitrate stress, which might involve the shift in energy metabolism. The involvement of nitrite stress response upon exposure to nitrate may provide detoxification mechanisms for nitrite, which is inhibitory to sulfate-reducing bacteria, produced by microbial nitrate reduction as a metabolic intermediate and may enhance the survival of sulfate-reducing bacteria in environments with elevated nitrate level.
Date: July 15, 2010
Creator: He, Q.; He, Z.; Joyner, D.C.; Joachimiak, M.; Price, M.N.; Yang, Z.K. et al.
Partner: UNT Libraries Government Documents Department

Hydrogen-peroxide-induced oxidative stress responses in Desulfovibrio vulgaris Hildenborough

Description: To understand how sulphate-reducing bacteria respond to oxidative stresses, the responses of Desulfovibrio vulgaris Hildenborough to H{sub 2}O{sub 2}-induced stresses were investigated with transcriptomic, proteomic and genetic approaches. H{sub 2}O{sub 2} and induced chemical species (e.g. polysulfide, ROS) and redox potential shift increased the expressions of the genes involved in detoxification, thioredoxin-dependent reduction system, protein and DNA repair, and decreased those involved in sulfate reduction, lactate oxidation and protein synthesis. A gene coexpression network analysis revealed complicated network interactions among differentially expressed genes, and suggested possible importance of several hypothetical genes in H{sub 2}O{sub 2} stress. Also, most of the genes in PerR and Fur regulons were highly induced, and the abundance of a Fur regulon protein increased. Mutant analysis suggested that PerR and Fur are functionally overlapped in response to stresses induced by H{sub 2}O{sub 2} and reaction products, and the upregulation of thioredoxin-dependent reduction genes was independent of PerR or Fur. It appears that induction of those stress response genes could contribute to the increased resistance of deletion mutants to H{sub 2}O{sub 2}-induced stresses. In addition, a conceptual cellular model of D. vulgaris responses to H{sub 2}O{sub 2} stress was constructed to illustrate that this bacterium may employ a complicated molecular mechanism to defend against the H{sub 2}O{sub 2}-induced stresses.
Date: July 1, 2010
Creator: Zhou, A.; He, Z.; Redding-Johanson, A.M.; Mukhopadhyay, A.; Hemme, C.L.; Joachimiak, M.P. et al.
Partner: UNT Libraries Government Documents Department

Global transcriptional, physiological and metabolite analyses of Desulfovibrio vulgaris Hildenborough responses to salt adaptation

Description: The response of Desulfovibrio vulgaris Hildenborough to salt adaptation (long-term NaCl exposure) was examined by physiological, global transcriptional, and metabolite analyses. The growth of D. vulgaris was inhibited by high levels of NaCl, and the growth inhibition could be relieved by the addition of exogenous amino acids (e.g., glutamate, alanine, tryptophan) or yeast extract. Salt adaptation induced the expression of genes involved in amino acid biosynthesis and transport, electron transfer, hydrogen oxidation, and general stress responses (e.g., heat shock proteins, phage shock proteins, and oxidative stress response proteins). Genes involved in carbon metabolism, cell motility, and phage structures were repressed. Comparison of transcriptomic profiles of D. vulgaris responses to salt adaptation with those of salt shock (short-term NaCl exposure) showed some similarity as well as a significant difference. Metabolite assays showed that glutamate and alanine were accumulated under salt adaptation, suggesting that they may be used as osmoprotectants in D. vulgaris. A conceptual model is proposed to link the observed results to currently available knowledge for further understanding the mechanisms of D. vulgaris adaptation to elevated NaCl.
Date: December 1, 2009
Creator: He, Z.; Zhou, A.; Baidoo, E.; He, Q.; Joachimiak, M. P.; Benke, P. et al.
Partner: UNT Libraries Government Documents Department

Comparison of multiple ecogenomics methods for determining ecosystem function in uranium-contaminated environments

Description: Background: Bioremediation may offer the only feasiblestrategy for the nearly intractable problem of metal and radionuclidecontamination of soil and groundwater. To understand bioremediation incontaminated environments, it is critical to determine the organismspresent in these environments, analyze their responses to stressconditions, and elucidate functional position in the environment.Methods: We used multiple molecular techniques on both sediment andgroundwater to develop a better understanding of the functionalcapability and stress level within the microbial community inrelationship to over one hundred geochemical parameters. Due to the lowpH (3.5-4.5) and high contaminant levels (e.g., uranium) microbialdensities and activities were low. We used a phage polymeraseamplification system to construct large and small insert DNA libraries,performed metagenome sequencing, constructed clonal libraries of selectfunctional genes (SSU rRNA gene, nirK, nirS, amoA, pmoA, and dsrAB), useda SSU rDNA Phylochip microarray (9,000 taxa), and a functional gene array(23K genes). A complete comparison for community differences andsimilarities between the different techniques was assessed using severalbioinformatics techniques. Results: SSU rDNA analysis revealed thepresence of distinct bacterial phyla, including proteobacteria,acidobacteria, and planctomycetes along the contaminant gradient.Metagenome analysis identified many of the same organisms, and diversitywas lower in water than sediment. Analysis with functional gene arrays,phylochip, and specific probes for genes and organisms involved inbiogeochemical cycling of C, N, and S, metal resistance, stress response,and contaminant degradation suggested that the dominant species could bebiostimulated during in situ uranium reduction. Several other findings ofdifference and similarities between methods are presented. Conclusion:These systems biology field studies could be enabling for strategies toattenuate nletal and radionuclide contamination.
Date: January 10, 2007
Creator: Hazen, T.C.; Dehal, P.; Arkin, A.P.; Fields, M.W.; Keller, M.; Zhou, J. et al.
Partner: UNT Libraries Government Documents Department