The effects of alternate optimal solutions in constraint-based genome-scale metabolic models

Metabolic Engineering

Volumn 5, Issue 4, 2003, Pages 264-276

  Mahadevan, R ^a   Schilling, C H ^a  

^a GENOMATICA INC   (United States)

Author keywords

Alternate optima; Escherichia coli; Flux variability; In silico model; Spectrum analysis

Indexed keywords

ESCHERICHIA COLI;

EID: 1642457253     PISSN: 10967176     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ymben.2003.09.002     Document Type: Article

References (35)

1. Bailey, J.E., 2001. Complex biology with no parameters. Nat. Biotechnol. 19, 503-504.
2. Beard, D.A., Liang, S.C., Qian, H., 2002. Energy balance for analysis of complex metabolic networks. Biophys. J. 83, 79-86.
3. Berg, C.M., Whalen, W.A., Archambault, L.B., 1983. Role of alanine-valilne transaminase in Salmonella typhimurium and analysis of an avtA:: tn5 mutant. J Bacteriol. 155, 1009-1014.
4. Bonarius, H.P.J., Schmid, G., Tramper, J., 1997. Flux analysis of underdetermined metabolic networks: The quest for the missing constraints. Trends Biotechnol. 15, 308-314.
5. Burgard, A.P., Vaidyaraman, S., Maranas, C.D., 2001. Minimal reaction sets for E. coli metabolism under different growth requirements and uptake environments. Biotechnol. Prog. 17, 791-797.
6. Edwards, J.S., Palsson, B.O., 1999. Systems properties of the Haemophilus influenzae Rd metabolic genotype. J. Biol. Chem. 274, 17410-17416.
7. Edwards, J.S., Palsson, B.O., 2000. The E. coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc. Natl. Acad. Sci. USA 97, 5528-5533.
8. Edwards, J.S., Ibarra, R.U., Palsson, B.O., 2001. In silico predictions of E. coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol. 19, 125-130.
9. Edwards, J.S., Covert, M., Palsson, B.O., 2002. Metabolic modeling of microbes: the flux balance approach. Environ. Microbiol. 4 (3), 133-140 (Ref Type: Generic).
10. Endy, D., Brent, R., 2001. Modelling cellular behaviour. Nature 409 (Suppl.), 391-395.
11. Fell, D.A., 1996. Understanding the Control of Metabolism. Portland Press, London.
12. Flores, S., Gosset, G., Flores, N., de Graaf, A.A., Bolivar, F., 2002. Analysis of carbon metabolism in E. coli strains with an inactive phosphotransferase system by (13)C labeling and NMR spectroscopy. Metab. Eng. 4, 124-137.
13. Fong, S.S., Marciniak, J.Y., Palsson, B., 2003. Description and Interpretation of Adaptive Evolution of E. coli K12 MG1655 Using a Genome-scale in silico Metabolic Model. Journal of Bacteriology, accepted for publication.
14. Hatzimanikatis, V., Floudas, C.A., Bailey, J.E., 1996. Optimization of regulatory architectures in metabolic reaction networks. Biotechnol. Bioeng. 52, 485-500.
15. Heinrich, R., Schuster, S., 1996. The Regulation of Cellular Systems. Kluwer Academic Publishers, Hingham, MA.
16. Ibarra, R.U., Edwards, J.S., Palsson, B.O., 2002. E. coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420, 186-189.
17. Jordan, A., Aragall, E., Gibert, I., Barbe, J., 1996. Promoter identification and expression analysis of Salmonella typhimurium and E. coli nrdEF operons encoding one of two class I ribonucleotide reductases present in both bacteria. Mol. Microbiol. 19, 777-790.
18. Kitano, H., 2002. Computational systems biology. Nature 420, 206-210.
19. Lee, S., Phalakornkule, C., Domach, M.M., Grossmann, I.E., 2000. Recursive MILP model for finding all the alternate optima in LP models for metabolic networks. Comput. Chem. Eng. 24, 711-716.
20. Mahadevan, R., Edwards, J.S., Doyle, F.J., 2002. Dynamic flux balance analysis of diauxic growth in E. coli. Biophys. J. 83, 1331-1340.
21. Palsson, B., 2000. The challenges of in silico biology. Nat. Biotechnol. 18, 1147-1150.
22. Phalakornkule, C., Lee, S., Zhu, T., Koepsel, R., Ataai, M.M., Grossmann, I.E., Domach, M.M., 2001. A MILP-based flux alternative generation and NMR experimental design strategy for metabolic engineering. Metab. Eng. 3, 124-137.
23. Price, N.D., Famili, I., Beard, D.A., Palsson, B.O., 2002a. Extreme pathways and Kirchhoff's second law. Biophys. J. 83, 2879-2882.
24. Price, N.D., Papin, J.A., Palsson, B.O., 2002b. Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Res. 12, 760-769.
25. Price, N.D., Papin, J.A., Schilling, C.H., Palsson, B., 2003. Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol. 21, 162-169.
26. Reed, J.L., Vo, T.D., Schilling, C.H., Palsson, B., 2003. E. coli IJR904: an expanded genome-scale model of E coli k-12. Genome Biol. 4, R54.1.
27. Reich, J.G., Selkov, E.E., 1981. Energy Metabolism of the Cell: A Theoretical Treatise. Acad. Press, New York, NY.
28. Schilling, C.H., Schuster, S., Palsson, B.O., Heinrich, R., 1999. Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era. Biotechnol. Prog. 15, 296-303.
29. Schilling, C.H., Letscher, D., Palsson, B.O., 2000. Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J. Theor. Biol. 203, 229-248.
30. Schilling, C.H., Covert, M.W., Famili, I., Church, G.M., Edwards, J.S., Palsson, B.O., 2002. Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol. 184, 4582-4593.
31. Segre, D., Vitkup, D., Church, G.M., 2002. Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. USA 99, 15112-15117.
32. Stephanopoulos, G.N., Aristidou, A.A., Nielsen, J., 1998. Metabolic Engineering: Principles and Methodologies. Academic Press, San Diego, CA.
33. Umbarger, H.E., 1996. Biosynthesis of branched-chain amino acids. In: Neidhardt, F. (Ed.), E. coli and Salmonella: Cellular and Molecular Biology. ASM Press, Washington, DC.
34. Varma, A., Palsson, B., 1994. Metabolic flux balancing: basic concepts, scientific and practical use. Bio/Technology 12, 994-12998.
35. Varner, J., Ramkrishna, D., 1999. Metabolic engineering from a cybernetic perspective. 1. Theoretical preliminaries. Biotechnol. Prog. 15, 407-425.