Constraint-based modelling captures the metabolic versatility of Desulfovibrio vulgaris
Jason J. Flowers
Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
Search for more papers by this authorMatthew A. Richards
Institute for Systems Biology, Seattle, WA, USA
Search for more papers by this authorBirte Meyer
Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
Search for more papers by this authorCorresponding Author
David A. Stahl
Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
For correspondence. Email: [email protected]; Tel. (206) 685-8502; Fax (206) 685-9185.Search for more papers by this authorJason J. Flowers
Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
Search for more papers by this authorMatthew A. Richards
Institute for Systems Biology, Seattle, WA, USA
Search for more papers by this authorBirte Meyer
Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
Search for more papers by this authorCorresponding Author
David A. Stahl
Department of Civil and Environmental Engineering, University of Washington, Seattle, WA, USA
For correspondence. Email: [email protected]; Tel. (206) 685-8502; Fax (206) 685-9185.Search for more papers by this authorSummary
A refined Desulfovibrio vulgaris Hildenborough flux balance analysis (FBA) model (iJF744) was developed, incorporating 1016 reactions that include 744 genes and 951 metabolites. A draft model was first developed through automatic model reconstruction using the ModelSeed Server and then curated based on existing literature. The curated model was further refined by incorporating three recently proposed redox reactions involving the Hdr-Flx and Qmo complexes and a lactate dehydrogenase (LdhAB, DVU 3027-3028) indicated by mutation and transcript analyses to serve electron transfer reactions central to syntrophic and respiratory growth. Eight different variations of this model were evaluated by comparing model predictions to experimental data determined for four different growth conditions - three for sulfate respiration (with lactate, pyruvate or H2/CO2-acetate) and one for fermentation in syntrophic coculture. The final general model supports (i) a role for Hdr-Flx in the oxidation of DsrC and ferredoxin, and reduction of NAD+ in a flavin-based electron confurcating reaction sequence, (ii) a function of the Qmo complex in receiving electrons from the menaquinone pool and potentially from ferredoxin to reduce APS and (iii) a reduction of the soluble DsrC by LdhAB and a function of DsrC in electron transfer reactions other than sulfite reduction.
Supporting Information
Additional Supporting Information may be found in the online version of this article at the publisher's web-site:
Filename | Description |
---|---|
emi412619-sup-0001-suppinfo1.docx18.3 KB |
Table S1. Model media formulation. |
emi412619-sup-0002-suppinfo2.docx27.9 KB |
Table S2. Predicted growth rate, NGAM, GAM and key metabolic ratio for model variants under four tested growth conditions. |
emi412619-sup-0003-suppinfo3.docx22.3 KB |
Table S3. Predicted FVA results for key electron transfer reactions for iJF744 under the four tested growth conditions. |
emi412619-sup-0004-suppinfo4.docx16.3 KB |
Table S4. Results from essential reaction analysis. |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
References
- Badziong, W., and Thauer, R.K. (1978) Growth yields and growth rates of Desulfovibrio vulgaris (Marburg) growing on hydrogen plus sulfate and hydrogen plus thiosulfate as the sole energy sources. Arch Microbiol 117: 209–214.
- Burgard, A.P., Pharkya, P., and Maranas, C.D. (2003) Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 84: 647–657.
- Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C.A., et al. (2014) The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res 42: D459–D471.
- Czechowski, M.H., and Rossmoore, H.W. (1990) Purification and partial characterization of ad(−)-lactate dehydrogenase fromDesulfovibrio desulfuricans (ATCC 7757). J Ind Microbiol 6: 117–122.
- da Silva, S.M., Voordouw, J., Leitão, C., Martins, M., Voordouw, G., and Pereira, I.A.C. (2013) Function of formate dehydrogenases in Desulfovibrio vulgaris Hildenborough energy metabolism. Microbiol Read Engl 159: 1760–1769.
- Dehal, P.S., Joachimiak, M.P., Price, M.N., Bates, J.T., Baumohl, J.K., Chivian, D., et al. (2010) MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res 38: D396–D400.
- Feist, A.M., Henry, C.S., Reed, J.L., Krummenacker, M., Joyce, A.R., Karp, P.D., et al. (2007) A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3: 121.
- Fels, S.R., Zane, G.M., Blake, S.M., and Wall, J.D. (2013) Rapid transposon liquid enrichment sequencing (TnLE-seq) for gene fitness evaluation in underdeveloped bacterial systems. Appl Environ Microbiol 79: 7510–7517.
- Henry, C.S., DeJongh, M., Best, A.A., Frybarger, P.M., Linsay, B., and Stevens, R.L. (2010) High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol 28: 977–982.
- Kanehisa, M., and Goto, S. (2000) KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 28: 27–30.
- Keller, K.L., and Wall, J.D. (2011) Genetics and molecular biology of the electron flow for sulfate respiration in desulfovibrio. Front Microbiol 2: 135.
- Keller, K.L., Rapp-Giles, B.J., Semkiw, E.S., Porat, I., Brown, S.D., and Wall, J.D. (2014) New model for electron flow for sulfate reduction in Desulfovibrio alaskensis G20. Appl Environ Microbiol 80: 855–868.
- Kostromins, A., and Stalidzans, E. (2012) Paint4Net: COBRA toolbox extension for visualization of stoichiometric models of metabolism. Biosystems 109: 233–239.
- Kuehl, J.V., Price, M.N., Ray, J., Wetmore, K.M., Esquivel, Z., Kazakov, A.E., et al. (2014) Functional genomics with a comprehensive library of transposon mutants for the sulfate-reducing bacterium Desulfovibrio alaskensis G20. mBio 5: e01041–e01014.
- Lewis, N.E., Hixson, K.K., Conrad, T.M., Lerman, J.A., Charusanti, P., Polpitiya, A.D., et al. (2010) Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models. Mol Syst Biol 6: 390.
- Li, C., Donizelli, M., Rodriguez, N., Dharuri, H., Endler, L., Chelliah, V., et al. (2010) BioModels database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 4: 92.
- Meyer, B., Kuehl, J.V., Deutschbauer, A.M., Arkin, A.P., and Stahl, D.A. (2013a) Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes. J Bacteriol 195: 4900–4914.
- Meyer, B., Kuehl, J., Deutschbauer, A.M., Price, M.N., Arkin, A.P., and Stahl, D.A. (2013b) Variation among Desulfovibrio species in electron transfer systems used for syntrophic growth. J Bacteriol 195: 990–1004.
- Meyer, B., Kuehl, J.V., Price, M.N., Ray, J., Deutschbauer, A.M., Arkin, A.P., and Stahl, D.A. (2014) The energy-conserving electron transfer system used by Desulfovibrio alaskensis strain G20 during pyruvate fermentation involves reduction of endogenously formed fumarate and cytoplasmic and membrane-bound complexes, Hdr-Flox and Rnf. Environ Microbiol 16: 3463–3486.
- Neidhardt, F. (1987). Chemical Composition of Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. Washington, DC: American Society for Microbiology.
- Odom, J.M, and Peck, H.D. (1981) Hydrogen cycling as a general mechanism for energy coupling in the sulfate-reducing bacteria, Desulfovibrio sp. FEMS Microbiol Lett 12: 47–50.
- Pereira, I.A.C., Ramos, A.R., Grein, F., Marques, M.C., Silva, D., Marques, S., and Venceslau, S.S. (2011) A comparative genomic analysis of energy metabolism in sulfate reducing bacteria and archaea. Front Microbiol 2: 69.
- Pereira, P.M., He, Q., Valente, F.M.A., Xavier, A.V., Zhou, J., Pereira, I.A.C., and Louro, R.O. (2008) Energy metabolism in Desulfovibrio vulgaris Hildenborough: insights from transcriptome analysis. Antonie Van Leeuwenhoek 93: 347–362.
- Price, M.N., Deutschbauer, A.M., Kuehl, J.V., Liu, H., Witkowska, H.E., and Arkin, A.P. (2011) Evidence-based annotation of transcripts and proteins in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. J Bacteriol 193: 5716–5727.
- Price, M.N., Ray, J., Wetmore, K.M., Kuehl, J.V., Bauer, S., Deutschbauer, A.M., and Arkin, A.P. (2014) The genetic basis of energy conservation in the sulfate-reducing bacterium Desulfovibrio alaskensis G20. Frontiers of Microbiology 31 Oct 2014.
- Ramos, A.R., Grein, F., Oliveira, G.P., Venceslau, S.S., Keller, K.L., Wall, J.D., and Pereira, I.A.C. (2015) The FlxABCD-HdrABC proteins correspond to a novel NADH dehydrogenase/heterodisulfide reductase widespread in anaerobic bacteria and involved in ethanol metabolism in Desulfovibrio vulgaris Hildenborough. Environ Microbiol 17: 2288–2305.
- Ramos, A.R., Keller, K.L., Wall, J.D., and Pereira, I.A.C. (2012) The membrane QmoABC complex interacts directly with the dissimilatory Adenosine 5’-phosphosulfate reductase in sulfate reducing bacteria. Front Microbiol 3: 137.
- Santos, A.A., Venceslau, S.S., Grein, F., Leavitt, W.D., Dahl, C., Johnston, D.T., and Pereira, I.A.C. (2015) A protein trisulfide couples dissimilatory sulfate reduction to energy conservation. Science 350: 1541–1545.
- Schellenberger, J., Park, J.O., Conrad, T.M., and Palsson, B.Ø. (2010) BiGG: a biochemical genetic and genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinformatics 11: 213.
- Schellenberger, J., Lewis, N.E., and Palsson, B.Ø. (2011a) Elimination of thermodynamically infeasible loops in steady-state metabolic models. Biophys J 100: 544–553.
- Schellenberger, J., Que, R., Fleming, R.M.T., Thiele, I., Orth, J.D., Feist, A.M., et al. (2011b) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6: 1290–1307.
- Stolyar, S., Van Dien, S., Hillesland, K.L., Pinel, N., Lie, T.J., Leigh, J.A., and Stahl, D.A. (2007) Metabolic modeling of a mutualistic microbial community. Mol Syst Biol 3: 92.
- Traore, A.S., Gaudin, C., Hatchikian, C.E., Gall, J.L., and Belaich, J.P. (1983) Energetics of growth of a defined mixed culture of Desulfovibrio vulgaris and Methanosarcina barkeri: maintenance energy coefficient of the sulfate-reducing organism in the absence and presence of its partner. J Bacteriol 155: 1260–1264.
- Venceslau, S.S., Lino, R.R., and Pereira, I.A.C. (2010) The Qrc membrane complex, related to the alternative Complex III, is a menaquinone reductase involved in sulfate respiration. J Biol Chem 285: 22774–22783.
- Villanueva, L., Haveman, S.A., Summers, Z.M., and Lovley, D.R. (2008) Quantification of Desulfovibrio vulgaris dissimilatory sulfite reductase gene expression during electron donor- and electron acceptor-limited growth. Appl Environ Microbiol 74: 5850–5853.
- Vita, N., Valette, O., Brasseur, G., Lignon, S., Denis, Y., Ansaldi, M., et al. (2015) The primary pathway for lactate oxidation in Desulfovibrio vulgaris. Front Microbiol 6: 606.
- Voordouw, G. (1995) The genus Desulfovibrio: the centennial. Appl Environ Microbiol 61: 2813–2819.
- Walker, C.B., He, Z., Yang, Z.K., Ringbauer, J.A., He, Q., Zhou, J., et al. (2009) The electron transfer system of syntrophically grown Desulfovibrio vulgaris. J Bacteriol 191: 5793–5801.