Computational approaches in metabolic engineering

Journal of Biomedicine and Biotechnology

Volumn 2010, Issue , 2010, Pages

  Reed, Jennifer L ^a   Senger, Ryan S ^b   Antoniewicz, MacIek R ^c   Young, Jamey D ^d  

^a Wisconsin Electric Machines and Power Electronics Consortium   (United States)

^b Virginia Polytechnic Institute and State University   (United States)

^c University of Delaware   (United States)

^d VANDERBILT UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; CELL METABOLISM; ELEMENTARY METABOLITE UNIT; ESCHERICHIA COLI; GENE EXPRESSION; GENETIC ALGORITHM; ISOTOPE LABELING; ISOTOPICALLY NONSTATIONARY METABOLIC FLUX ANALYSIS; KINETIC MODELING APPROACH; METABOLIC ENGINEERING; METABOLIC FLUX ANALYSIS; METABOLITE; NONHUMAN; OPTIMIZATION BASED APPROACH; PHENOTYPE; PROTEIN EXPRESSION; REVIEW; TECHNIQUE; THERMODYNAMICS; BIOLOGICAL MODEL; BIOLOGY; EDITORIAL; GENETIC ENGINEERING; METABOLOMICS;

COMPUTATIONAL BIOLOGY; GENETIC ENGINEERING; METABOLOMICS; MODELS, BIOLOGICAL;

EID: 79959483555     PISSN: 11107243     EISSN: 11107251     Source Type: Journal    
DOI: 10.1155/2010/207414     Document Type: Review

References (70)

1. U. Sauer, "Metabolic networks in motion: 13C-based flux analysis," Molecular Systems Biology, vol. 2, article 62, 2006.
2. J. Nielsen, "It is all about metabolic fluxes," Journal of Bacteriology, vol. 185, no. 24, pp. 7031-7035, 2003.
3. W. Wiechert, "C metabolic flux analysis," Metabolic Engineering, vol. 3, no. 3, pp. 195-206, 2001.
4. W. Wiechert, M. Möllney, N. Isermann, M. Wurzel, and A. A. De Graaf, "Bidirectional reaction steps in metabolic networks-III. Explicit solution and analysis of isotopomer labeling systems," Biotechnology and Bioengineering, vol. 66, no. 2, pp. 69-85, 1999.
5. J. F. Moxley, M. C. Jewett, M. R. Antoniewicz et al., "Linking high-resolution metabolic flux phenotypes and transcriptional regulation in yeast modulated by the global regulator Gcn4p," Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 16, pp. 6477-6482, 2009.
6. M. R. Antoniewicz, J. K. Kelleher, and G. Stephanopoulos, "Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions," Metabolic Engineering, vol. 9, no. 1, pp. 68-86, 2007.
7. P. F. Suthers, Y. J.Chang, andC.D.Maranas, "Improved computational performance of MFA using elementary metabolite units and flux coupling," Metabolic Engineering, vol. 12, no. 2, pp. 123-128, 2010.
8. M. R. Antoniewicz, D. F. Kraynie, L. A. Laffend, J. González- Lergier, J. K. Kelleher, and G. Stephanopoulos, "Metabolic flux analysis in a nonstationary systemml: fed-batch fermentation of a high yielding strain of E. coli producing 1,3-propanediol," Metabolic Engineering, vol. 9, no. 3, pp. 277-292, 2007.
9. Y. Noguchi, J. D. Young, J. O. Aleman, M. E. Hansen, J. K. Kelleher, and G. Stephanopoulos, "Effect of anaplerotic fluxes and amino acid availability on hepatic lipoapoptosis," Journal of Biological Chemistry, vol. 284, no. 48, pp. 33425-33436, 2009.
10. K. Nöh, K. Grönke, B. Luo, R. Takors, M. Oldiges, and W. Wiechert, "Metabolic flux analysis at ultra short time scale: isotopically non-stationary 13C labeling experiments," Journal of Biotechnology, vol. 129, no. 2, pp. 249-267, 2007.
11. S. A. Wahl, K. Nöh, and W. Wiechert, "13C labeling experiments at metabolic nonstationary conditions: an exploratory study," BMC Bioinformatics, vol. 9, article 152, 2008.
12. K. Schmidt, A. Marx, A. A. De Graaf et al., "13C tracer experiments and metabolite balancing for metabolic flux analysis: comparing two approaches," Biotechnology and Bioengineering, vol. 58, no. 2-3, pp. 254-257, 1998.
13. J. D. Young, J. L. Walther, M. R. Antoniewicz, H. Yoo, and G. Stephanopoulos, "An elementary metabolite unit (EMU) based method of isotopically nonstationary flux analysis," Biotechnology and Bioengineering, vol. 99, no. 3, pp. 686-699, 2008.
14. Z. Zhao, K. Kuijvenhoven, C. Ras et al., "Isotopic nonstationary 13C gluconate tracer method for accurate determination of the pentose phosphate pathway split-ratio in Penicillium chrysogenum," Metabolic Engineering, vol. 10, no. 3-4, pp. 178-186, 2008.
15. K. Maier, U. Hofmann, M. Reuss, and K. Mauch, "Identification of metabolic fluxes in hepatic cells from transient Clabeling experiments-part II. Flux estimation," Biotechnology and Bioengineering, vol. 100, no. 2, pp. 355-370, 2008.
16. J. Munger, B. D. Bennett, A. Parikh et al., "Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for antiviral therapy," Nature Biotechnology, vol. 26, no. 10, pp. 1179-1186, 2008.
17. K. Maier, U. Hofmann, A. Bauer et al., "Quantification of statin effects on hepatic cholesterol synthesis by transient 13Cflux analysis," Metabolic Engineering, vol. 11, no. 4-5, pp. 292-309, 2009.
18. S. Iwatani, Y. Yamada, and Y. Usuda, "Metabolic flux analysis in biotechnology processes," Biotechnology Letters, vol. 30, no. 5, pp. 791-799, 2008.
19. A. A. Shastri and J. A. Morgan, "A transient isotopic labeling methodology for C metabolic flux analysis of photoautotrophicmicroorganisms, " Phytochemistry, vol. 68, no. 16-18, pp. 2302-2312, 2007.
20. W. Wiechert and K. Nöh, "From stationary to instationary metabolic flux analysis," Advances in Biochemical Engineering/ Biotechnology, vol. 92, pp. 145-172, 2005.
21. J. Schwender, "Metabolic flux analysis as a tool in metabolic engineering of plants," Current Opinion in Biotechnology, vol. 19, no. 2, pp. 131-137, 2008.
22. C. Yang, Q. Hua, and K. Shimizu, "Metabolic flux analysis in Synechocystis using isotope distribution from C-labeled glucose," Metabolic Engineering, vol. 4, no. 3, pp. 202-216, 2002.
23. B. D. Bennett, E. H. Kimball, M. Gao, R. Osterhout, S. J. Van Dien, and J. D. Rabinowitz, "Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli," Nature Chemical Biology, vol. 5, no. 8, pp. 593-599, 2009.
24. C. S. Henry, M. D. Jankowski, L. J. Broadbelt, and V. Hatzimanikatis, "Genome-scale thermodynamic analysis of Escherichia coli metabolism," Biophysical Journal, vol. 90, no. 4, pp. 1453-1461, 2006.
25. A. Kümmel, S. Panke, and M. Heinemann, "Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data," Molecular Systems Biology, vol. 2, article 2006.0034, 2006.
26. M. Klimacek, S. Krahulec, U. Sauer, and B. Nidetzky, "Limitations in xylose-fermenting saccharomyces cerevisiae, made evident through comprehensive metabolite profiling and thermodynamic analysis," Applied and Environmental Microbiology, vol. 76, no. 22, pp. 7566-7574, 2010.
27. S. A. Becker and B. O. Palsson, "Context-specific metabolic networks are consistent with experiments," PLoS Computational Biology, vol. 4, no. 5, Article ID e1000082, 2008.
28. C. Colijn, A. Brandes, J. Zucker et al., "Interpreting expression data with metabolic flux models: predicting Mycobacterium tuberculosis mycolic acid production," PLoS Computational Biology, vol. 5, no. 8, article e1000489, 2009.
29. T. Shlomi, M. N. Cabili, M. J. Herrgård, B. Ø. Palsson, and E. Ruppin, "Network-based prediction of human tissue-specific metabolism," Nature Biotechnology, vol. 26, no. 9, pp. 1003-1010, 2008.
30. A. von Kamp and S. Schuster, "Metatool 5.0: fast and flexible elementary modes analysis," Bioinformatics, vol. 22, no. 15, pp. 1930-1931, 2006.
31. S. Klamt, J. Gagneur, and A. von Kamp, "Algorithmic approaches for computing elementary modes in large biochemical reaction networks," IEE Proceedings Systems Biology, vol. 152, no. 4, pp. 249-255, 2005.
32. S. Klamt, J. Stelling, M. Ginkel, and E. D. Gilles, "FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps," Bioinformatics, vol. 19, no. 2, pp. 261-269, 2003.
33. I. Rocha, P. Maia, P. Evangelista et al., "OptFlux: an opensource software platform for in silico metabolic engineering," BMC Systems Biology, vol. 4, article 45, 2010.
34. S. Klamt and J. Stelling, "Combinatorial complexity of pathway analysis in metabolic networks," Molecular Biology Reports, vol. 29, no. 1-2, pp. 233-236, 2002.
35. S. Pérès, F. Vallée, M. Beurton-Aimar, and J. P. Mazat, "AComml: a classification method for elementary flux modes based on motif finding," BioSystems, vol. 103, no. 3, pp. 410-419, 2011.
36. B. A. Boghigian, H. Shi, K. Lee, and B. A. Pfeifer, "Utilizing elementary mode analysis, pathway thermodynamics, and a genetic algorithm for metabolic flux determination and optimalmetabolic network design," BMC Systems Biology, vol.4, article 49, 2010.
37. C. T. Trinh, P. Unrean, and F. Srienc, "Minimal Eschenchia coli cell for the most efficient production of ethanol from hexoses and pentoses," Applied and Environmental Microbiology, vol. 74, no. 12, pp. 3634-3643, 2008.
38. C. T. Trinh and F. Srienc, "Metabolic engineering of Escherichia coli for efficient conversion of glycerol to ethanol," Applied and Environmental Microbiology, vol. 75, no. 21, pp. 6696-6705, 2009.
39. P. Unrean, C. T. Trinh, and F. Srienc, "Rational design and construction of an efficient E. coli for production of diapolycopendioic acid," Metabolic Engineering, vol. 12, no. 2, pp. 112-122, 2010.
40. E. Almaas, B. Kovács, T. Vicsek, Z. N. Oltvai, and A. L. Barabási, "Global organization of metabolic fluxes in the bacterium Escherichia coli," Nature, vol. 427, no. 6977, pp. 839-843, 2004.
41. I. Thiele, N. D. Price, T. D. Vo, and B. Ø. Palsson, "Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet," Journal of Biological Chemistry, vol. 280, no. 12, pp. 11683-11695, 2005.
42. N. D. Price, J. L. Reed, and B. Ø. Palsson, "Genome-scale models of microbial cells: evaluating the consequences of constraints," Nature Reviews Microbiology, vol. 2, no. 11, pp. 886-897, 2004.
43. D. Segrè, D. Vitkup, and G.M. Church, "Analysis of optimality in natural and perturbed metabolic networks," Proceedings of the National Academy of Sciences of the United States of America, vol. 99, no. 23, pp. 15112-15117, 2002.
44. T. Shlomi, O. Berkman, and E. Ruppin, "Regulatory on/off minimization of metabolic flux changes after genetic perturbations," Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 21, pp. 7695-7700, 2005.
45. M. W. Covert and B. Ø. Palsson, "Transcriptional regulation in constraints-based metabolic models of Escherichia coli," Journal of Biological Chemistry, vol. 277, no. 31, pp. 28058-28064, 2002.
46. T. Shlomi, Y. Eisenberg, R. Sharan, and E. Ruppin, "A genome-scale computational study of the interplay between transcriptional regulation and metabolism,"Molecular Systems Biology, vol. 3, article 101, 2007.
47. S. Chandrasekaran and N. D. Price, "Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis," Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 41, pp. 17845-17850, 2010.
48. S. S. Fong and B. Ø. Palsson, "Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes," Nature Genetics, vol. 36, no. 10, pp. 1056-1058, 2004.
49. H. Alper, Y. S. Jin, J. F.Moxley, and G. Stephanopoulos, "Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli," Metabolic Engineering, vol. 7, no. 3, pp. 155-164, 2005.
50. H. Alper, K. Miyaoku, and G. Stephanopoulos, "Construction of lycopene-overproducing E. coli strains by combining systematic and combinatorial gene knockout targets," Nature Biotechnology, vol. 23, no. 5, pp. 612-616, 2005.
51. J. H. Park, K. H. Lee, T. Y. Kim, and S. Y. Lee, "Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation," Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 19, pp. 7797-7802, 2007.
52. K. H. Lee, J. H. Park, T. Y. Kim, H. U. Kim, and S. Y. Lee, "Systems metabolic engineering of Escherichia coli for L-threonine production," Molecular Systems Biology, vol. 3, article 149, 2007.
53. Y. K. Jung, T. Y. Kim, S. J. Park, and S. Y. Lee, "Metabolic engineering of Escherichia coli for the production of polylactic acid and its copolymers," Biotechnology and Bioengineering, vol. 105, no. 1, pp. 161-171, 2010.
54. A. P. Burgard, P. Pharkya, and C. D. Maranas, "OptKnock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization," Biotechnology and Bioengineering, vol. 84, no. 6, pp. 647-657, 2003.
55. J. A. Chemler, Z. L. Fowler, K. P. McHugh, and M. A. G. Koffas, "Improving NADPH availability for natural product biosynthesis in Escherichia coli by metabolic engineering," Metabolic Engineering, vol. 12, no. 2, pp. 96-104, 2010.
56. K. R. Patil, I. Rocha, J. Förster, and J. Nielsen, "Evolutionary programming as a platform for in silico metabolic engineering," BMC Bioinformatics, vol. 6, article 308, 2005.
57. D. S. Lun, G. Rockwell, N. J. Guido et al., "Large-scale identification of genetic design strategies using local search," Molecular Systems Biology, vol. 5, article 296, 2009.
58. P. Pharkya, A. P. Burgard, and C. D. Maranas, "OptStrain: a computational framework for redesign of microbial production systems," Genome Research, vol. 14, no. 11, pp. 2367-2376, 2004.
59. P. Pharkya and C. D. Maranas, "An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems," Metabolic Engineering, vol. 8, no. 1, pp. 1-13, 2006.
60. S. Ranganathan, P. F. Suthers, and C. D. Maranas, "Opt-Force: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions," PLoS Computational Biology, vol. 6, no. 4, article e1000744, 2010.
61. J. Kim and J. L. Reed, "OptORF: optimal metabolic and regulatory perturbations for metabolic engineering of microbial strains," BMC Systems Biology, vol. 4, article 53, 2010.
62. M. A. Asadollahi, J. Maury, K. R. Patil, M. Schalk, A. Clark, and J. Nielsen, "Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering," Metabolic Engineering, vol. 11, no. 6, pp. 328-334, 2009.
63. S. S. Fong, A. P. Burgard, C. D. Herring et al., "In silico design and adaptive evolution of Escherichia coli for production of lactic acid," Biotechnology and Bioengineering, vol. 91, no. 5, pp. 643-648, 2005.
64. A. R. Brochado, C. Matos, B. L. Møller, J. Hansen, U. H. Mortensen, and K. R. Patil, "Improved vanillin production in baker's yeast through in silico design,"Microbial Cell Factories, vol. 9, article 84, 2010.
65. H. Kacser and J. A. Burns, "The control of flux," Symposia of the Society for Experimental Biology, vol. 27, pp. 65-104, 1973.
66. R. Heinrich and T. A. Rapoport, "A linear steady-state treatment of enzymatic chains. General properties, control and effector strength," European Journal of Biochemistry, vol. 42, no. 1, pp. 89-95, 1974.
67. D. Visser and J. J. Heijnen, "Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics," Metabolic Engineering, vol. 5, no. 3, pp. 164-176,2003.
68. D. Visser, J.W. Schmid, K. Mauch,M. Reuss, and J. J. Heijnen, "Optimal re-design of primary metabolism in Escherichia coli using linlog kinetics," Metabolic Engineering, vol. 6, no. 4, pp. 378-390, 2004.
69. J. D. Young, K. L. Henne, J. A. Morgan, A. E. Konopka, and D. Ramkrishna, "Integrating cybernetic modeling with pathway analysis provides a dynamic, systems-level description of metabolic control," Biotechnology and Bioengineering, vol. 100, no. 3, pp. 542-559, 2008.
70. D. Ramkrishna, "A cybernetic perspective of microbial growth," in Foundations of Biochemical Engineering: Kinetics and Thermodynamics in Biological Systems, pp. 161-178, American Chemical Society, Washington, DC, USA, 1982.