In silico geobacter sulfurreducens metabolism and its representation in reactive transport models

Applied and Environmental Microbiology

Volumn 75, Issue 1, 2009, Pages 83-92

  King, E L ^a   Tuncay, K ^b   Ortoleva, P ^c   Meile, C ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b MIDDLE EAST TECHNICAL UNIVERSITY   (Turkey)

^c INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AQUEOUS ENVIRONMENTS; CELL METABOLISMS; CELL MODELS; ENVIRONMENTAL CONDITIONS; EXTRACELLULAR CONDITIONS; EXTRACELLULAR SUBSTRATES; FLUX BALANCE MODELS; GEOBACTER SULFURREDUCENS; GROWTH EFFICIENCIES; IN SILICO; KEY COMPONENTS; MICROBIAL ACTIVITIES; MICROBIAL DYNAMICS; MICROBIAL GROWTH DYNAMICS; MICROBIAL POPULATIONS; PARAMETERIZING; POROUS MEDIUMS; REACTIVE TRANSPORT MODELS; REACTIVE TRANSPORTS; SIMPLIFIED MODELS; SPATIAL DISTRIBUTION OF; SUBSTRATE UPTAKES;

AQUIFERS; BIOCHEMISTRY; CELL GROWTH; DYNAMICS; GROWTH (MATERIALS); METABOLISM; POROUS MATERIALS; SIZE DISTRIBUTION;

SUBSTRATES;

ANTHROPOGENIC SOURCE; AQUIFER; BACTERIUM; KINETICS; METABOLISM; MICROBIAL ACTIVITY; MODELING; PARAMETERIZATION;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; GEOBACTER; METABOLIC NETWORKS AND PATHWAYS; POPULATION DYNAMICS; WATER MICROBIOLOGY;

GEOBACTER SULFURREDUCENS;

EID: 58149347795     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01799-08     Document Type: Article

References (51)

1. Albe, K. R., M. H. Butler, and B. E, Wright. 1990. Cellular concentrations of enzymes and their substrates. J. Theor. Biol. 143:163-195.
2. Bakker, B. M., P. A. M. Michels, F. R. Opperdoes, and H. V. Westerhoff. 1997. Glycolysis in bloodstream from Trypanosoma brucei can be understood in terms of the kinetics of the glycolytic enzymes. J. Biol. Chem. 272: 3207-3215.
3. Bear, J. 1972. Dynamics of fluids in porous media. American Elsevier Publishing Company, Inc., New York, NY.
4. Behrends, T., and P. Van Cappellen. 2005. Competition between enzymatic and abiotic reduction of uranium(VI) under iron reducing conditions. Chem. Geol. 220:315-327.
5. Bond, D. R., T. Mester, C. L. Nesbo, A. V. Izquierdo-Lopez, F. L. Collart, and D, R. Lovley. 2005. Characterization of citrate synthase from Geobacter sulfurreducens and evidence for a family of citrate synthases similar to those of eukaryotes throughout the Geobacteraceae. Appl. Environ. Microbiol. 71: 3858-3865.
6. Bradley, P, M., and F, H. Chapelle. 1996. Anaerobic mineralization of vinyl chloride in Fe(II)-reducing aquifer sediments. Environ. Sci. Techno]. 30: 2084-2086.
7. Brun, A., P. Engesgaard, T. H, Christensen, and D. Rosbjerg. 2002. Modeling of transport and biogeochemical processes in pollution plumes: Vejen landfill, Denmark. J. Hydrol. 256:228-247.
8. Caccavo, F. J., D. Lonergan, D. R. Lovley, M. Davis, J. F. Stolz, and M. J, McInerney. 1994. Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. Appl. Environ. Microbiol. 60:3752-3759.
9. Canfield, D. E., E. Kristensen, and B. Thamdrup. 2005. Aquatic geomicrobiology. Elsevier Academic Press, New York, NY.
10. Champine, J, E., and S. Goodwin. 1991. Acetate catabolism in the dissimilatory iron-reducing isolate GS-15. J. Bacteriol. 173: 2704-2706.
11. Chohnan, S., T. Nagata, and Y. Midorikawa. 1994. Purification and characterization of a novel bifunctional enzyme, cyclic-ribonucleotide phospho-mutase-5'-phosphodiesterase, from Aspergillus niger. Biosci. Biotechnol. Biochem. 58:250-255.
12. Esteve-Núñez, A., M. Rothermich, M, Sharma, and D. R. Lovley. 2005. Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture. Environ. Microbiol. 7:641-648.
13. Forster, J., I. Famili, P. Fu, B. O. Palsson, and J. Nielsen. 2003. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 13:244-253.
14. 2 with elemental sulfur in Desulfuromonas acetoxidans. Arch. Microbiol. 141: 392-398.
15. Goldberg, R. N., Y. B. Tewari, and T. N. Bhat. 2004. Thermodynamics of enzyme-catalyzed reactions-a database for quantitative biochemistry. Bioinformatics 20: 2874-2877.
16. Gunten, U. V., and J. Zobrist. 1993. Biogeochemical changes in groundwater-infiltration systems: column studies. Geochim. Cosmochim. Acta 57: 3895-3906.
17. Herbel, M., and S. Fendorf. 2006. Biogeochemical processes controlling the speciation and transport of arsenic within iron coated sands. Chem. Geol. 228:16-32.
18. Hunter, K. S., Y. Wang, and P. Van Cappellen. 1998. Kinetic modeling of microbially-driven redox chemistry in subsurface environments: coupling transport, microbial metabolism and geochemistry. J. Hydrol. 209: 53-58.
19. Jackowski, S., and C. O. Rock. 1986. Consequences of reduced intracellular coenzyme-a content in Escherichia coli. J. Bacteriol. 166:866-871.
20. Jeong, H., B. Tombor, R. Albert, Z. N. Oltavai, and A.-L. Barbasi. 2000. The large-scale organization of metabolic networks. Nature 407:651-654.
21. Leang, C., M. V. Coppi, and D. R. Lovley.2003. OmcB, a c-type polyheme cytochrome, involved in Fe(III) reduction in Geobacter sulfurreducens. J. Bacteriol. 185:2096-2103.
22. Lovley, D. R. 2003. Cleaning up with genomics: applying molecular biology to bioremediation. Nat. Rev. Microbiol. 1:35-44.
23. Lovley, D. R. 1993. Dissimilatory metal reduction. Annu. Rev. Microbiol. 47:263-290.
24. Lovley, D. R., D. E. Holmes, and K. P. Nevin. 2004. Dissimilatory Fe(III) and Mn(IV) reduction. Adv. Microb. Physiol. 49:219-286.
25. Lovley, D. R., E. J. P. Phillips, Y. A. Gorby, and E. R. Landa. 1991. Microbial reduction of uranium. Nature 350:413-416.
26. Mahadevan, R., D. R. Bond, J. E. Butler, A. Esteve-Nunez, M. V. Coppi, B. O. Palsson, C. H. Schulling, and D. R, Lovley. 2006. Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling. Appl. Environ. Microbiol. 72:1558-1568.
27. Mauclaire, L., O. Pelz, M. Thullner, W. R. Abraham, and J. Zeyer. 2003. Assimilation of toluene carbon along a bacteria-protist food chain determined by C-13-enrichment of biomarker fatty acids. J. Microbiol. Methods 55:635-649.
28. McCleary, W. R., and J. B. Stock. 1994. Acetyl phosphate and the activation of 2-component response regulators. J. Biol. Chem. 269: 31567-31572.
29. Methé, B. A., K. E. Nelson, J. A. Eisen, I. T. Paulsen, W. Nelson, J. F. Heidelberg, D. Wu, M. Wu, N. Ward, M. J. Beanan, R. J. Dodson, R. Madupu, L. M. Brinkac, S. C. Daugherty, T. R. De Boy, A. S. Durkin, M. Gwinn, J. F. Dolonay, S. A. Sullivan, D. H. Haft, J. Selengut, T. M. Davidsen, N. Zafar, O. White, B. Tran, C. Romerio, H. A. Forberger, J. Weidman, H. Khouri, T. V. Feldblyum, T. R. Utterback, S. E. Van Aken, D. R. Lovley, and C. M. Fraser. 2003. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science 302: 1967-1969.
30. Navid, A., and P. J. Ortoleva. 2004. Simulated complex dynamics of glycolysis in the protozoan parasite Trypanosoma brucei. J. Theor. Biol. 228: 449-458.
31. Ortoleva, P., E. Berry, Y. Brun, J. Fan, M. Fontus, K. Hubbard, K. Jaqaman, L. Jarymowycz, A. Navid, A. Sayyed-Ahmad, Z. Shreif, F. Stanley, K. Tuncay, E. Weitzke, and L.-C. Wu. 2003. The Karyote physico-chemical genomic, proteomic metabolomic cell modeling system. OMICS 7:269-283.
32. Purich, D. L., and R. D, Allison. 1999. Handbook of biochemical kinetics. Academic Press, San Diego, CA.
33. Reed, J. L., T. D. Vo, C. H. Schilling, and B. O. Palsson. 2003. An expanded genome-scale model of Escherichia coli K-12 (UR904 GSM/GPR). Genome Biol. 4:R54.
34. Rockhold, M. L., R. R. Yarwood, and J. S. Selker. 2004. Coupled microbial and transport processes in soils. Vadose Zone J. 3:368-383.
35. Schaefer, U., W. Boos, R. Takors, and D. Weuster-Botz. 1999. Automated sampling device for monitoring intracellular metabolite dynamics. Anal. Biochem. 270:88-96.
36. Scheidegger, A. E. 1961. General theory of dispersion in porous media. J. Geophys. Res. 66: 3273-3278.
37. Seeliger, S., R. Cord-Ruwisch, and B. Schink. 1998. A periplasmic and extracellular c-type cytochrome of Geobacter sulfurreducens acts as a ferric iron reductase and as an electron carrier to other acceptors or to partner bacteria. J. Bacteriol. 180:3686-3691.
38. Seki, K., M. Thullner, and P. Baveye. 2004. Nutrient uptake kinetics of filamentous microorganisms: comparison of cubic, exponential, and Monod models. Ann. Microbiol. 54:181-188.
39. Snoeyenbos-West, O. L., K. P. Nevin, R. T. Anderson, and D. R. Lovley. 2000. Enrichment of Geobacter species in response to stimulation of Fe(III) reduction in sandy aquifer sediments. Microb. Ecol. 39: 153-167.
40. Spiteri, C., C. Slomp, K. Tuncay, and C. Meile. 2008. Modeling biogeochemical processes in subterranean estuaries: the effect of How dynamics and redox conditions on submarine groundwater discharge of nutrients. Water Resour. Res. doi:10.1029/2007WR006071.
41. Stelling, J. 2004. Mathematical models in microbial systems biology. Curr. Opin. Microbiol. 7:513-518.
42. Stelling, J., S. Klamt, K. Bettenbrock, S. Schuster, and E. D. Gilles.2002. Metabolic network structure determines key aspects of functionality and regulation. Nature 420:190-193.
43. Tang, Y. J., R. Chakraborty, H. Garcia Martin, J, Chu, T. C. Hazen, and J. D. Keasling. 2007. Flux analysis of central metabolic pathways in Geobacter metallireducens during reduction of soluble Fe(III)-nitrilotriacetic acid. Appl. Environ. Microbiol. 73:3859-3864.
44. Thullner, M., P. Regnier, and P. Van Cappellen. 2007. Modeling microbially induced carbon degradation in redox-stratified subsurface environments: concepts and open questions. Geomicrobiol. J. 24:139-155.
45. Tung, A. H. Y., G. Lesage, G. D. Bader, H. M. Ding, H. Xu, X. F. Xin, J. Young, G. F. Berriz, R. L. Brost, M. Chang, Y. Q. Chen, X. Cheng, G. Chua, H. Friesen, D. S. Goldberg, J. Haynes, C. Humphries, G. He, S. Hussein, L. Z. Ke, N. Krogan, Z. J. Li, J. N. Levinson, H. Lu, P. Menard, C. Munyana, A. B. Parsons, O. Ryan, R. Tonikian, T. Roberts, A. M. Sdicu, J. Shapiro, B. Sheikh, B. Suter, S. L. Wong, L. V. Zhang, H. W. Zhu, C. G. Burd, S. Munro, C. Sander, J. Rine, J. Greenblatt, M. Peter, A. Bretscher, G. Bell, F. P. Roth, G. W. Brown, B. Andrews, H. Bussey, and C. Boone, 2004. Global mapping of the yeast genetic interaction network. Science 303: 808-813.
46. Vandevivere, P., and P. Baveye. 1992. Saturated hydraulic conductivity reduction caused by aerobic-bacteria in sand columns. Soil Sci. Soc. Am. J. 56:1-13.
47. Walsh, K., and D. E. Koshland. 1984. Determination of flux through the branch point of 2 metabolic cycles-the tricarboxylic-acid cycle and the glyoxylate shunt. J. Biol. Chem. 259:9646-9654.
48. Watson, I. A., S. E. Oswald, K. U. Mayer, W. Youxian, and S. A. Banwart. 2003. Modeling kinetic processes controlling hydrogen and acetate concentrations in an aquifer-derived microcosm. Environ. Sci. Technol. 37:3910-3919.
49. Weiss, J. V., and I. M. Cozzarelli.2008. Biodegradation in contaminated aquifers: incorporating microbial/molecular methods. Ground Water 46:305-322.
50. Weitzke, E. L., and P. J. Ortoleva. 2003. Simulating cellular dynamics through a coupled transcription, translation, metabolic model. Comput. Biol. Chem. 27:469-481.
51. Wilkins, M. J., F. R. Livens, D. J, Vaughan, and J. R. Lloyd. 2006. The impact of Fe(III)-reducing bacteria on uranium mobility. Biogeochemistry 78: 125-150.