Applications of metabolic modeling to drive bioprocess development for the production of value-added chemicals

Biotechnology and Bioprocess Engineering

Volumn 10, Issue 5, 2005, Pages 408-417

  Mahadevan, Radhakrishnan ^a   Burgard, Anthony P ^a   Famili, Iman ^a   Van Dien, Steve ^a   Schilling, Christophe H ^a  

^a GENOMATICA INC   (United States)

Author keywords

Biopress development; Constraint based modeling; Metabolic engineering; SimPheny

Indexed keywords

CHEMICAL COMPOUND;

BIOPROCESS; BIOTRANSFORMATION; DATA ANALYSIS; FERMENTATION; FERMENTATION OPTIMIZATION; GENOME; HIGH THROUGHPUT SCREENING; INDUSTRY; METABOLIC ENGINEERING; MICROBIAL METABOLISM; MICROORGANISM; NONHUMAN; PREDICTION; PROCESS DEVELOPMENT; REVIEW; SIMULATION; STATISTICAL MODEL; SYNTHESIS; TECHNOLOGY;

EID: 27744488443     PISSN: 12268372     EISSN: None     Source Type: Journal    
DOI: 10.1007/BF02989823     Document Type: Review

References (86)

1. Price, N. D., J. L. Reed, and B. O. Palsson (2004) Genome-scale models of microbial cells: Evaluating the consequences of constraints. Nat. Rev. Microbiol. 2: 886-897.
2. Edwards, J. S. and B. O. Palsson (2000) The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. USA 97: 5528-5533.
3. Reed, J. L., T. D. Vo, C. H. Schilling, and B. Palsson (2003) Escherichia coli iJR904: An expanded genome-scale model of E. coli K12. Genome Biol. 4: R54.1-R54.12.
4. Famili, I., J. Forster, J. Nielsen, and B. O. Palsson (2003) Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network. Proc. Natl. Acad. Sci. USA 100: 13134-13139.
5. Dauner, M. and U. Sauer (2001) Stoichiometric growth model for riboflavin-producing Bacillus subtilis. Biotechnol. Bioeng. 76: 132-143.
6. Hong, S. H., J. S. Kim, S. Y. Lee, Y. H. In, S. S. Choi, J. K. Rih, C. H. Kim, H. Jeong, C. G. Hur, and J. J. Kim (2004) The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens. Nat. Biotechnol. 22: 1275-1281.
7. Covert, M. W., E. M. Knight, J. L. Reed, M. J. Herrgard, and B. O. Palsson (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429: 92-96.
8. Ciaramella, M., A. Napoli, and M. Rossi (2005) Another extreme genome: How to live at pH 0. Trends Microbiol. 13: 49-51.
9. 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.
10. Schilling, C. H., M. W. Covert, I. Famili, G. M. Church, J. S. Edwards, and B. O. Palsson (2002) Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol. 184: 4582-4593.
11. Varma, A., B. W. Boesch, and B. O. Palsson (1993) Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates. Appl. Environ. Microbiol. 59: 2465-2473.
12. Varma, A. and B. O. Palsson (1994) Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl. Environ. Microbiol. 60: 3724-3731.
13. Edwards, J. S., R. U. Ibarra, and B. O. Palsson (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19: 125-130.
14. Ibarra, R. U., J. S. Edwards, and B. O. Palsson (2002) Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420: 186-189.
15. Varma, A., B. W. Boesch, and B. O. Palsson (1993) Biochemical production capabilities of Escherichia coli. Biotechnol. Bioeng. 42: 59-73.
16. Edwards, J. S. and B. O. Palsson (2000) Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions. BMC Bioinformatics 1:1.
17. Segre, D., D. Vitkup, and G. M. Church (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA 99: 15112-15117.
18. Shlomi, T., O. Berkman, and E. Ruppin (2005) Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc. Natl. Acad. Sci. USA 102: 7695-7700.
19. Papp, B., C. Pal, and L. D. Hurst (2004) Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 429: 661-664.
20. Segre, D., A. Deluna, G. M. Church, and R. Kishony (2005) Modular epistasis in yeast metabolism. Nat. Genet. 37: 77-83.
21. Mahadevan, R. and B. O. Palsson (2005) Properties of metabolic networks: Structure versus function. Biophys. J. 88: L07-L09.
22. DeRisi, J. L., V. R. Iyer, and P. O. Brown (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278: 680-686.
23. Patterson, S. D. and R. H. Aebersold (2003) Proteomics: The first decade and beyond. Nat. Genet. 33 Suppl: 311-323.
24. Kell, D. B (2004) Metabolomics and systems biology: making sense of the soup. Curr. Opin. Microbiol. 7: 296-307.
25. Churchill, G. A. (2004) Using ANOVA to analyze microarray data. Biotechniques 37: 173-177.
26. Sharan, R., R. Elkon, and R. Shamir (2002) Cluster analysis and its applications to gene expression data. Ernst. Schering. Res Found. Workshop 83-108.
27. Ideker, T., V. Thorsson, J. A. Ranish, R. Christmas, J. Buhler, J. K. Eng, R. Bumgarner, D. R. Goodlett, R. Aebersold, and L. Hood (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292: 929-934.
28. Burgard, A. P., E. V. Nikolaev, C. H. Schilling, and C. D. Maranas (2004) Flux coupling analysis of genome-scale metabolic network reconstructions. Genome Res. 14: 301-312.
29. Oh, M. K. and J. C. Liao (2000) Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli. Biotechnol. Prog. 16: 278-286.
30. Tao, H., R. Gonzalez, A. Martinez, M. Rodriguez, L. O. Ingram, J. F. Preston, and K. T. Shanmugam (2001) Engineering a homo-ethanol pathway in Escherichia coli: Increased glycolytic flux and levels of expression of glycolytic genes during xylose fermentation. J. Bacteriol. 183: 2979-2988.
31. Akesson, M., J. Forster, and J. Nielsen (2004) Integration of gene expression data into genome-scale metabolic models. Metab. Eng. 6: 285-293.
32. Patil, K. R. and J. Nielsen (2005) Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc. Natl. Acad. Sci. USA 102: 2685-2689.
33. Covert, M. W., C. H. Schilling, and B. Palsson (2001) Regulation of gene expression in flux balance models of metabolism. J. Theor. Biol. 213: 73-88.
34. van der Heijden, R. T. J. M., J. J. Heijnen, C. Hellinga, B. Romein, and K. C. A. M. Luyben (1994) Linear constraint relations in biochemical reaction systems: II. Diagnosis and estimation of gross measurement errors. Biotechnol. Bioeng. 43: 11-20.
35. Raghunathan, A. U., J. R. Perez-Correa, and L. T. Biegler (2003) Data reconciliation and parameter estimation in flux-balance analysis. Biotechnol. Bioeng. 84: 700-708.
36. Mahadevan, R. and C. H. Schilling (2003) The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab. Eng. 5: 264-276.
37. Vallino, J. J. and G. Stephanopoulos (1993) Metabolic fluc distributions in Corynebacterium glutamicum during growth and lysine overproduction. Biotechnol. Bioeng. 41: 633-646.
38. van Gulik, W. M., W. T. de Laat, J. L. Vinke, and J. J. Heijnen (2000) Application of metabolic flux analysis for the identification of metabolic bottlenecks in the biosynthesis of penicillin-G. Biotechnol. Bioeng. 68: 602-618.
39. Schilling, C. H., J. S. Edwards, and B. O. Palsson (1999) Toward metabolic phenomics: Analysis of genomic data using flux balances. Biotechnol. Prog. 15: 288-295.
40. Shimizu, H., N. Takiguchi, H. Tanaka, and S. Shioya (1999) A maximum production strategy of lysine based on a simplified model derived from a metabolic reaction network. Metab. Eng. 1: 299-308.
41. 13C metabolic flux analysis. Metab. Eng. 195-206.
42. Marx, A., A. A. de Graaf, W. Wiechert, L. Eggeling, and H. Sahm (1996) Determination of the fluxes in central metabolism of Corynebacterium glutamicum by NMR spectroscopy combined with metabolite balancing. Biotechnol. Bioeng. 49: 111-129.
43. Dauner, M. and U. Sauer (2000) GC-MS analysis of amino acids rapidly provides rich information for isotopomer balancing. Biotechnol. Prog. 16: 642-649.
44. Schmidt, K., M. Carlsen, J. Nielsen, and J. Villadsen (1997) Modeling isotopomer distributions in biochemical networks using isotopomer mapping matrices. Biotechnol. Bioeng. 55: 831-840.
45. 13C-label tracing and mass spectrometry. Biotechnol. Bioeng. 84: 45-55.
46. Wiechert, W., C. Siefke, A. A. de Graaf, and A. Marx (1997) Bidirectional reaction steps in metabolic networks: II. Flux estimation and statistical analysis. Biotechnol. Bioeng. 55: 118-135.
47. Wiechert, W. and A. A. de Graaf (1997) Bidirectional reaction steps in metabolic networks: I. Modeling and simulation of carbon isotope labeling experiments. Biotechnol. Bioeng. 55: 101-117.
48. Wittmann, C. and E. Heinzle (1999) Mass spectrometry for metabolic flux analysis. Biotechnol. Bioeng. 62: 739-750.
49. Walsh, K. and D. E. Jr. Koshland (1984) Determination of flux through the branch point of two metabolic cycles. The tricarboxylic acid cycle and the glyoxylate shunt. J. Biol. Chem. 259: 9646-9654.
50. Park, S. M., M. I. Klapa, A. J. Sinskey, and G. N. Stephanopoulos (1999) Metabolite and isotopomer balancing in the analysis of metabolic cycles: II. Applications. Biotechnol. Bioeng. 62: 392-401.
51. Wendisch, V. F., A. A. de Graaf, H. Sahm, and B. J. Eikmanns (2000) Quantitative determination of metabolic fluxes during coutilization of two carbon sources: Comparative analyses with Corynebacterium glutamicum during growth on acetate and/or glucose. J. Bacteriol. 182: 3088-3096.
52. Petersen, S., A. A. de Graaf, L. Eggeling, M. Mollney, W. Wiechert, and H. Sahm (2000) In vivo quantification of parallel and bidirectional fluxes in the anaplerosis of Corynebacterium glutamicum. Metab. Eng. 3: 195-206.
53. Wittmann, C., H. M. Kim, and E. Heinzle (2004) Metabolic network analysis of lysine producing Corynebacterium glutamicum at a miniaturized scale. Biotechnol. Bioeng. 87: 1-6.
54. Sauer, U., D. R. Lasko, J. Fiaux, M. Hochuli, R. Glaser, T. Szyperski, K. Wuthrich, and J. E. Bailey (1999) Metabolic flux ratio analysis of genetic and environmental modulations of Escherichia coli central carbon metabolism. J. Bacteriol. 181: 6679-6688.
55. 13C-based flux analysis of an L-phenylalanine-producing E. coli strain using a sensor reactor. Biotechnol. Prog. 20: 706-714.
56. Sauer, U., V. Hatzimanikatis, J. E. Bailey, M. Hochuli, T. Szyperski, and K. Wuthrich (1997) Metabolic fluxes in riboflavin-producing Bacillus subtilis. Nat. Biotechnol. 15: 448-452.
57. Gombert, A. K., S. M. Moreira dos, B. Christensen, and J. Nielsen (2001) Network identification and flux quantification in the central metabolism of Saccharomyces cerevisiae under different conditions of glucose repression. J. Bacteriol. 183: 1441-1451.
58. 13C-labeled glucose. Biotechnol. Bioeng. 68: 652-659.
59. 13C-labeling experiments. Biotechnol. Bioeng. 78: 11-16.
60. Burgard, A. P. and C. D. Maranas (2001) Probing the performance limits of the Escherichia coli metabolic network subject to gene additions or deletions. Biotechnol. Bioeng. 74: 364-375.
61. Carlson, R., D. Fell, and F. Srienc (2002) Metabolic pathway analysis of a recombinant yeast for rational strain development. Biotechnol. Bioeng. 79: 121-34.
62. Fong, S. S. and B. O. Palsson (2004) Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat. Genet. 36: 1056-1058.
63. Burgard, A. P., P. Pharkya, and C. D. Maranas (2003) OptKnock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 84: 647-657.
64. Pharkya, P., A. P. Burgard, and C. D. Maranas (2003) Exploring the overproduction of amino acids using the bilevel optimization framework OptKnock. Biotechnol. Bioeng. 84: 887-899.
65. Alper, H., Y. S. Jin, J. F. Moxley, and G. Stephanopoulos (2005) Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab. Eng. 7: 155-164.
66. Wilson, E. K. (2005) Engineering cell-based factories. Chem. Eng. News 83: 41-44.
67. Broadbelt, L. J., S. M. Stark, and M. T. Klein (1994) Computer-generated pyrolysis modeling-on-the-fly generation of species, reactions, and rates. Ind. Eng. Chem. Res. 33: 790-799.
68. Broadbelt, L. J., S. M. Stark, and M. T. Klein (1995) Termination of computer-generated reaction-mechanisms-species rank-based convergence criterion. Ind. Eng. Chem. Res. 34: 2566-2573.
69. Broadbelt, L. J., S. M. Stark, and M. T. Klein (1996) Computer generated reaction modelling: Decomposition and encoding algorithms for determining species uniqueness. Comput. Chem. Eng. 20: 113-129.
70. Hatzimanikatis, V., C. Li, J. A. Ionita, and L. J. Broadbelt (2004) Metabolic networks: Enzyme function and metabolite structure. Curr. Opin. Struct. Biol. 14: 300-306.
71. Kanehisa, M., S. Goto, S. Kawashima, Y. Okuno, and M. Hattori (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res. 32 Database issue: D277-D280.
72. Karp, P. D., M. Riley, M. Saier, I. T. Paulson, S. M. Paley, and A. Pellegrini-Toole (2000) The EcoCyc and MetaCyc databases. Nucleic Acids Res. 28: 56-59.
73. Krieger, C. J., P. Zhang, L. A. Mueller, A. Wang, S. Paley, M. Arnaud, J. Pick, S. Y. Rhee, and P. D. Karp (2004) MetaCyc: A multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 32 Database issue: D438-D442.
74. Li, C., C. S. Henry, M. D. Jankowski, J. A. Ionita, V. Hatzimanikatis, and L. J. Broadbelt (2004) Computational discovery of biochemical routes to specialty chemicals. Chem. Eng. Sci. 59: 5051-5060.
75. Hatzimanikatis, V., C. Li, J. A. Ionita, C. S. Henry, M. D. Jankowski, and L. J. Broadbelt (2005) Exploring the diversity of complex metabolic networks. Bioinformatics 21: 1603-1609.
76. Pharkya, P., A. P. Burgard, and C. D. Maranas (2004) OptStrain: A computational framework for redesign of microbial production systems. Genome Res. 14: 2367-2376.
77. Komives, C. and R. S. Parker (2003) Bioreactor state estimation and control. Curr. Opin. Biotechnol. 14: 468-474.
78. Covert, M. W. and B. O. Palsson (2002) Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J. Biol. Chem. 277: 28058-28064.
79. Mahadevan, R., J. S. Edwards, and F. J. Doyle (2002) Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophysical J. 83: 1331-1340.
80. Gadkar, K. G., F. J. Doyle, III, T. J. Crowley, and J. D. Varner (2003) Cybernetic model predictive control of a continuous bioreactor with cell recycle. Biotechnol Prog. 19: 1487-1497.
81. Mahadevan, R. and F. J. Doyle (2003) On-line optimization of recombinant product in a fed-batch bioreactor. Biotechnol. Prog. 19: 639-646.
82. Parekh, S., V. A. Vinci, and R. J. Strobel (2000) Improvement of microbial strains and fermentation processes. Appl. Microbiol. Biotechnol. 54: 287-301.
83. Zhang, S., J. Chu, and Y. Zhuang (2004) A multi-scale study of industrial fermentation processes and their optimization. Adv. Biochem. Eng. Biotechnol. 87: 97-150.
84. Gadkar, K. G., F. J. Doyle, J. S. Edwards, and R. Mahadevan (2005) Estimating optimal profiles of genetic alterations using constraint-based models. Biotechnol. Bioeng. 89: 243-251.
85. Lovley, D. R. (2003) Cleaning up with genomics: Applying molecular biology to bioremediation. Nat. Rev. Microbiol. 1: 35-44.
86. Beard, D. A. and H. Qian (2005) Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism. Am. J. Physiol. Endocrinol. Metab. 288: E633-E644.