Metabolic response of Geobacter sulfurreducens towards electron donor/acceptor variation

Microbial Cell Factories

Volumn 9, Issue , 2010, Pages

  Yang, Tae Hoon ^a   Coppi, Maddalena V ^b   Lovley, Derek R ^b   Sun, Jun ^a  

^a GENOMATICA INC   (United States)

^b UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACETIC ACID; ACETIC ACID C 13; ACETYL COENZYME A; AMINO ACID; CARBON; CARBON 13; FERRIC ION; FUMARIC ACID; HYDROGEN; PHOSPHOENOLPYRUVATE CARBOXYKINASE (GTP); PYRUVIC ACID; RADIOPHARMACEUTICAL AGENT; TRICARBOXYLIC ACID; UNCLASSIFIED DRUG; FUMARIC ACID DERIVATIVE; PYRUVIC ACID DERIVATIVE;

AMINO ACID METABOLISM; AMINO ACID SYNTHESIS; ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; BACTERIAL GROWTH; BACTERIUM CULTURE; BIOREMEDIATION; BIOTRANSFORMATION; CARBON SOURCE; CELL CULTURE; CITRIC ACID CYCLE; CONTROLLED STUDY; ELECTRON; ELECTRON TRANSPORT; GEOBACTER SULFURREDUCENS; GLUCONEOGENESIS; ISOTOPE LABELING; METABOLIC REGULATION; MICROBIAL BIOMASS; NONHUMAN; OXIDATIVE STRESS; BIOSYNTHESIS; CHEMISTRY; GEOBACTER; GROWTH, DEVELOPMENT AND AGING; METABOLISM; OXIDATION REDUCTION REACTION;

GEOBACTER SULFURREDUCENS;

ACETIC ACID; ACETYL COENZYME A; AMINO ACIDS; CARBON ISOTOPES; CITRIC ACID CYCLE; ELECTRONS; FERRIC COMPOUNDS; FUMARATES; GEOBACTER; GLUCONEOGENESIS; OXIDATION-REDUCTION; PHOSPHOENOLPYRUVATE CARBOXYKINASE (GTP); PYRUVATES;

EID: 78549269463     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-9-90     Document Type: Article

References (52)

1. Lovley DR, Giovannoni SJ, White DC, Champine JE, Phillips EJ, Gorby YA, Goodwin S. Geobacter metallireducens gen. nov. sp. nov., a microorganism capable of coupling the complete oxidation of organic compounds to the reduction of iron and other metals. ArchMicrobiol 1993, 159:336-344.
2. Mahadevan R, Bond DR, Butler JE, Esteve-Nunez A, Coppi MV, Palsson BO, Schilling CH, Lovley DR. Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling. Appl Environ Microbiol 2006, 72:1558-1568. 10.1128/AEM.72.2.1558-1568.2006, 1392927, 16461711.
3. Risso C, Van Dien SJ, Orloff A, Lovley DR, Coppi MV. Elucidation of an alternate isoleucine biosynthesis pathway in Geobacter sulfurreducens. JBacteriol 2008, 190:2266-2274.
4. Sun J, Sayyar B, Butler JE, Pharkya P, Fahland TR, Famili I, Schilling CH, Lovley DR, Mahadevan R. Genome-scale constraint-based modeling of Geobacter metallireducens. BMC Syst Biol 2009, 3:15. 10.1186/1752-0509-3-15, 2640342, 19175927.
5. Reguera G, McCarthy KD, Mehta T, Nicoll JS, Tuominen MT, Lovley DR. Extracellular electron transfer via microbial nanowires. Nature 2005, 435:1098-1101. 10.1038/nature03661, 15973408.
6. Reguera G, Nevin KP, Nicoll JS, Covalla SF, Woodard TL, Lovley DR. Biofilm and nanowire production leads to increased current in Geobacter sulfurreducens fuel cells. Appl Environ Microbiol 2006, 72:7345-7348. 10.1128/AEM.01444-06, 1636155, 16936064.
7. Bond DR, Holmes DE, Tender LM, Lovley DR. Electrode-reducing microorganisms that harvest energy from marine sediments. Science 2002, 295:483-485. 10.1126/science.1066771, 11799240.
8. Holmes DE, Bond DR, O'Neil RA, Reimers CE, Tender LR, Lovley DR. Microbial communities associated with electrodes harvesting electricity from a variety of aquatic sediments. Microb Ecol 2004, 48:178-190. 10.1007/s00248-003-0004-4, 15546038.
9. Lovley DR. Bug juice: harvesting electricity with microorganisms. Nat Rev Microbiol 2006, 4:497-508. 10.1038/nrmicro1442, 16778836.
10. Lovley DR. Microbial fuel cells: novel microbial physiologies and engineering approaches. Curr Opin Biotechnol 2006, 17:327-332. 10.1016/j.copbio.2006.04.006, 16679010.
11. Lovley DR. Cleaning up with genomics: applying molecular biology to bioremediation. NatRevMicrobiol 2003, 1:35-44.
12. Methe BA, Nelson KE, Eisen JA, Paulsen IT, Nelson W, Heidelberg JF, Wu D, Wu M, Ward N, Beanan MJ, et al. Genome of Geobacter sulfurreducens: metal reduction in subsurface environments. Science 2003, 302:1967-1969. 10.1126/science.1088727, 14671304.
13. Segura D, Mahadevan R, Juarez K, Lovley DR. Computational and experimental analysis of redundancy in the central metabolism of Geobacter sulfurreducens. PLoS Comput Biol 2008, 4:e36. 10.1371/journal.pcbi.0040036, 2233667, 18266464.
14. Schuetz R, Kuepfer L, Sauer U. Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli. MolSystBiol 2007, 3:119.
15. Antoniewicz MR, Kelleher JK, Stephanopoulos G. Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab Eng 2007, 9:68-86. 10.1016/j.ymben.2006.09.001, 1994654, 17088092.
16. Wiechert W. 13C metabolic flux analysis. MetabEng 2001, 195-206.
17. Wittmann C, Heinzle E. Mass spectrometry for metabolic flux analysis. Biotechnol Bioeng 1999, 62:739-750. 10.1002/(SICI)1097-0290(19990320)62:6<739::AID-BIT13>3.0.CO;2-E, 10099575.
18. Yang TH, Frick O, Heinzle E. Hybrid optimization for 13C metabolic flux analysis using systems parametrized by compactification. BMC Syst Biol 2008, 2:29. 10.1186/1752-0509-2-29, 2333969, 18366780.
19. Antoniewicz MR, Kelleher JK, Stephanopoulos G. Accurate assessment of amino acid mass isotopomer distributions for metabolic flux analysis. AnalChem 2007, 79:7554-7559.
20. Blank LM, Kuepfer L, Sauer U. Large-scale 13C-flux analysis reveals mechanistic principles of metabolic network robustness to null mutations in yeast. Genome Biol 2005, 6:R49. 10.1186/gb-2005-6-6-r49, 1175969, 15960801.
21. Dauner M, Sauer U. GC-MS analysis of amino acids rapidly provides rich information for isotopomer balancing. Biotechnol Prog 2000, 16:642-649. 10.1021/bp000058h, 10933840.
22. Krömer JO, Sorgenfrei O, Klopprogge K, Heinzle E, Wittmann C. In-depth profiling of lysine-producing Corynebacterium glutamicum by combined analysis of the transcriptome, metabolome, and fluxome. J Bacteriol 2004, 186:1769-1784. 10.1128/JB.186.6.1769-1784.2004, 355958, 14996808.
23. Sauer U. High-throughput phenomics: experimental methods for mapping fluxomes. Curr Opin Biotechnol 2004, 15:58-63. 10.1016/j.copbio.2003.11.001, 15102468.
24. Sauer U. Metabolic networks in motion: 13C-based flux analysis. MolSystBiol 2006, 2:62.
25. Wahl SA, Dauner M, Wiechert W. New tools for mass isotopomer data evaluation in 13C flux analysis: mass isotope correction, data consistency checking, and precursor relationships. Biotechnol Bioeng 2004, 85:259-268. 10.1002/bit.10909, 14748080.
26. Wiechert W, Mollney M, Petersen S, de Graaf AA. A universal framework for 13C metabolic flux analysis. Metab Eng 2001, 3:265-283. 10.1006/mben.2001.0188, 11461148.
27. Yang TH, Bolten CJ, Coppi MV, Sun J, Heinzle E. Numerical bias estimation for mass spectrometric mass isotopomer analysis. Anal Biochem 2009, 388:192-203. 10.1016/j.ab.2009.03.005, 19275875.
28. Yang TH, Heinzle E, Wittmann C. Theoretical aspects of 13C metabolic flux analysis with sole quantification of carbon dioxide labeling. Comput Biol Chem 2005, 29:121-133. 10.1016/j.compbiolchem.2005.02.005, 15833440.
29. Zamboni N, Fischer E, Sauer U. FiatFlux--a software for metabolic flux analysis from 13C-glucose experiments. BMC Bioinformatics 2005, 6:209. 10.1186/1471-2105-6-209, 1199586, 16122385.
30. Quek LE, Wittmann C, Nielsen LK, Kromer JO. OpenFLUX: efficient modelling software for 13C-based metabolic flux analysis. Microb Cell Fact 2009, 8:25. 10.1186/1475-2859-8-25, 2689189, 19409084.
31. Tang YJ, Chakraborty R, Martin HG, Chu J, Hazen TC, Keasling JD. Flux analysis of central metabolic pathways in Geobacter metallireducens during reduction of soluble Fe(III)-nitrilotriacetic acid. Appl Environ Microbiol 2007, 73:3859-3864. 10.1128/AEM.02986-06, 1932749, 17468285.
32. Butler JE, Glaven RH, Esteve-Nunez A, Nunez C, Shelobolina ES, Bond DR, Lovley DR. Genetic characterization of a single bifunctional enzyme for fumarate reduction and succinate oxidation in Geobacter sulfurreducens and engineering of fumarate reduction in Geobacter metallireducens. J Bacteriol 2006, 188:450-455. 10.1128/JB.188.2.450-455.2006, 1347312, 16385034.
33. Caccavo F, Lonergan DJ, Lovley DR, Davis M, Stolz JF, McInerney MJ. Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. Appl Environ Microbiol 1994, 60:3752-3759. 201883, 7527204.
34. Coppi MV, O'Neil RA, Lovley DR. Identification of an uptake hydrogenase required for hydrogen-dependent reduction of Fe(III) and other electron acceptors by Geobacter sulfurreducens. J Bacteriol 2004, 186:3022-3028. 10.1128/JB.186.10.3022-3028.2004, 15126463.
35. Galushko AS, Schink B. Oxidation of acetate through reactions of the citric acid cycle by Geobacter sulfurreducens in pure culture and in syntrophic coculture. ArchMicrobiol 2000, 174:314-321.
36. Esteve-Nunez A, Rothermich A, Sharma M, Lovley DR. Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture. Environmental Microbiology 2005, 7:641-648. 10.1111/j.1462-2920.2005.00731.x, 15819846.
37. Coppi MV, Leang C, Kaufmann F, O'Neil RA, Bond DR, Lovley DR. Genetic analysis of a putative soluble Fe(III) reductase from Geobacter sulfurreducens. J Bacteriol 2005, In Preparation, 1151787, 15968061.
38. Massart DL. Handbook of chemometrics and qualimetrics. 1997, Amsterdam; New York: Elsevier.
39. Qian H, Beard DA. Metabolic futile cycles and their functions: a systems analysis of energy and control. Syst Biol (Stevenage) 2006, 153:192-200.
40. Dauner M, Storni T, Sauer U. Bacillus subtilis metabolism and energetics in carbon-limited and excess-carbon chemostat culture. J Bacteriol 2001, 183:7308-7317. 10.1128/JB.183.24.7308-7317.2001, 95580, 11717290.
41. Coppi MV. The hydrogenases of Geobacter sulfurreducens: a comparative genomic perspective. Microbiology 2005, 151:1239-1254. 10.1099/mic.0.27535-0, 15817791.
42. Coppi MV, O'Neil RA, Lovley DR. Identification of an uptake hydrogenase required for hydrogen-dependent reduction of Fe(III) and other electron acceptors by Geobacter sulfurreducens. J Bacteriol 2004, 186:3022-3028. 10.1128/JB.186.10.3022-3028.2004, 400607, 15126463.
43. Coppi MV, O'Neil RA, Leang C, Kaufmann F, Methe BA, Nevin KP, Woodard TL, Liu A, Lovley DR. Involvement of Geobacter sulfurreducens SfrAB in acetate metabolism rather than intracellular, respiration-linked Fe(III) citrate reduction. Microbiology 2007, 153:3572-3585. 10.1099/mic.0.2007/006478-0, 17906154.
44. Galushko AS, Schink B. Oxidation of acetate through reactions of the citric acid cycle by Geobacter sulfurreducens in pure culture and in syntrophic coculture. Arch Microbiol 2000, 174:314-321. 10.1007/s002030000208, 11131021.
45. Lovley DR, Phillips EJP, Gorby YA, Landa ER. Microbial reduction of uranium. Nature 1991, 350:413-416.
46. Esteve-Nunez A, Nunez C, Lovley DR. Preferential reduction of Fe(III) over fumarate by Geobacter sulfurreducens. J Bacteriol 2004, 186:2897-2899. 10.1128/JB.186.9.2897-2899.2004, 387788, 15090532.
47. Lovley DR, Lonergan DJ. Anaerobic oxidation of toluene, phenol, and p-cresol by the dissimilatory Iron-reducing organism, GS-15. Appl Environ Microbiol 1990, 56:1858-1864. 184522, 16348226.
48. Lovley DR, Coates JD. Bioremediation of metal contamination. CurrOpinBiotechnol 1997, 8:285-289.
49. Lovley DR, Dworkin SFERKHSM, Stackebrandt E. Fe(III)- and Mn(IV)-reducing prokaryotes. The Prokaryotes 2000, New York: Springer-Verlag, Inc., http://www.prokaryotes.com.;
50. Lovley DR, Phillips EJ. Novel mode of microbial energy metabolism: organic carbon oxidation coupled to dissimilatory reduction of iron or manganese. Appl Environ Microbiol 1988, 54:1472-1480. 202682, 16347658.
51. Smith PK, Krohn RI, Hermanson GT, Mallia AK, Gartner FH, Provenzano MD, Fujimoto EK, Goeke NM, Olson BJ, Klenk DC. Measurement of protein using bicinchoninic acid. AnalBiochem 1985, 150:76-85.
52. Antoniewicz MR, Kelleher JK, Stephanopoulos G. Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements. Metab Eng 2006, 8:324-337. 10.1016/j.ymben.2006.01.004, 16631402.