Description and Interpretation of Adaptive Evolution of Escherichia coli K-12 MG1655 by Using a Genome-Scale In Silico Metabolic Model

Journal of Bacteriology

Volumn 185, Issue 21, 2003, Pages 6400-6408

  Fong, Stephen S ^a   Marciniak, Jennifer Y ^a   Palsson, Bernhard Ø ^a,b  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

2 OXOGLUTARIC ACID; LACTIC ACID; PYRUVIC ACID;

ADAPTATION; ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; BIOMASS; COMPUTER MODEL; ESCHERICHIA COLI; EVOLUTION; GENOME; GROWTH RATE; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL;

ADAPTATION, PHYSIOLOGICAL; COMPUTATIONAL BIOLOGY; CULTURE MEDIA; ESCHERICHIA COLI; EVOLUTION; GENOME, BACTERIAL; HEAT; KETOGLUTARIC ACIDS; LACTIC ACID; MODELS, BIOLOGICAL; PHENOTYPE; PYRUVIC ACID;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; ESCHERICHIA COLI K12; NEGIBACTERIA; PROKARYOTA;

EID: 0142152457     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.185.21.6400-6408.2003     Document Type: Article

References (36)

1. Bailey, J. E. 2001. Complex biology with no parameters. Nat. Biotechnol. 19:503-504.
2. Blattner, F. R., G. Plunkett 3rd, C. A. Bloch, N. T. Perna, V. Burland, M. Riley, J. Collado-Vides, J. D. Glasner, C. K. Rode, G. F. Mayhew, J. Gregor, N. W. Davis, H. A. Kirkpatrick, M. A. Goeden, D. J. Rose, B. Mau, and Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453-1474.
3. Bouche, N., and D. Bouchez. 2001. Arabidopsis gene knockout: phenotypes wanted. Curr. Opin. Plant Biol. 4:111-117.
4. Carlson, R., D. Fell, and F. Srienc. 2002. Metabolic pathway analysis of a recombinant yeast for rational strain development. Biotechnol. Bioeng. 79:121-134.
5. Covert, M.W., C. H. Schilling, I. Famili, J. S. Edwards, I. I. Goryanin, E. Selkov, and B. O. Palsson. 2001. Metabolic modeling of microbial strains in silico. Trends Biochem. Sci. 26:179-186.
6. Covert, M. W., B. O. Palsson, and C. H. Schilling. 2002. A more-palatable Helicobacter pylori: iterative model building through the peer review process. ASM News 68:529-530.
7. Drell, D. 2002. The Department of Energy Microbial Cell Project: a 180° paradigm shift for biology. Omics A J. Integr. Biol. 6:3-9.
8. 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.
9. 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.
10. Edwards, J. S., R. Ramakrishna, and B. O. Palsson. 2002. Characterizing the metabolic phenotype: a phenotype phase plane analysis. Biotechnol. Bioeng. 77:27-36.
11. Fell, D. 1996. Understanding the control of metabolism. Frontiers in metabolism, vol. 2. Portland Press, London, UK.
12. Gombert, A. K., and J. Nielsen. 2000. Mathematical modelling of metabolism. Curr. Opin. Biotechnol. 11:180-186.
13. 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.
14. Ideker, T., and L. Hood. 2001. A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2:343-372.
15. Karp, P. D., M. Riley, M. Saier, I. T. Paulsen, J. Collado-Vides, S. M. Paley, A. Pellegrini-Toole, C. Bonavides, and S. Gama-Castro. 2002. The EcoCyc Database. Nucleic Acids Res. 30:56-58.
16. Liao, J. C., and J. Delgado. 1993. Advances in metabolic control analysis. Biotechnol. Prog. 9:221-233.
17. Liao, J. C., S. Y. Hou, and Y. P. Chao. 1996. Pathway analysis, engineering and physiological considerations for redirecting central metabolism. Biotechnol. Bioeng. 52:129-140.
18. Mahadevan, R., J. S. Edwards, and F. J. Doyle. 2002. Dynamic flux balance analysis of diauxic growth in Escherichia coli. Biophys. J. 83:1331-1340.
19. Overbeek, R., N. Larsen, G. D. Pusch, M. D'Souza, E. Selkov, Jr., N. Kyrpides, M. Fonstein, N. Maltsev, and E. Selkov. 2000. WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. Nucleic Acids Res. 28:123-125.
20. Palsson, B. O. 2000. The challenges of in silico biology. Nat. Biotechnol. 18:1147-1150.
21. Price, N. D., J. A. Papin, and B. O. Palsson. 2002. Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Res. 12:760-769.
22. Raamsdonk, L. M., B. Teusink, D. Broadhurst, N. Zhang, A. Hayes, M. C. Walsh, J. A. Berden, K. M. Brindle, D. B. Kell, J. J. Rowland, H. V. Westerhoff, K. van Dam, and S. G. Oliver. 2001. A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat. Biotechnol. 19:45-50.
23. Raghunathan, A., and B. O. Palsson. 2003. Scalable method to determine mutations that occur during adaptive evolution of Escherichia coli. Biotechnol. Lett. 25:435-441.
24. Savinell, J. M., and B. O. Palsson. 1992. Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism. J. Theor. Biol. 154:421-454.
25. 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.
26. Schilling, C. H., J. S. Edwards, D. Letscher, and B. O. Palsson. 2000. Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems. Biotechnol. Bioeng. 71:286-306.
27. Schuster, S., D. A. Fell, and T. Dandekar. 2000. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol. 18:326-332.
28. Schuster, S., and C. Hilgetag. 1994. On elementary flux modes in biochemical reaction systems at steady state. J. Biol. Systems 2:165-182.
29. Selkov, E., N. Maltsev, G. J. Olsen, R. Overbeek, and W. B. Whitman. 1997. A reconstruction of the metabolism of Methanococcus jannaschii from sequence data. Gene 197:GC11-GC26.
30. Thorneycroft, D., S. M. Sherson, and S. M. Smith. 2001. Using gene knock-outs to investigate plant metabolism. J. Exp. Bot. 52:1593-1601.
31. Tomita, M., K. Hashimoto, K. Takahashi, T. S. Shimizu, Y. Matsuzaki, F. Miyoshi, K. Saito, S. Tanida, K. Yugi, J. C. Venter, and C. A. Hutchison 3rd. 1999. E-CELL: software environment for whole-cell simulation. Bioinformatics 15:72-84.
32. Vallino, J., and G. Stephanopoulos. 1993. Metabolic flux distributions in Cotynebacterium glutamicum during growth and lysine overproduction. Biotechnol. Bioeng. 41:633-646.
33. Van Dien, S. J., and M. E. Lidstrom. 2002. Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph Methylobacterium extorquens AM1, with application to reconstruction of C(3) and C(4) metabolism. Biotechnol. Bioeng. 78:296-312.
34. Varma, A., and B. O. Palsson. 1994. Metabolic flux balancing: basic concepts, scientific and practical use. Bio/Technology 12:994-998.
35. 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.
36. Voit, E. S. 2000. Computational analysis of biochemical systems. Cambridge University Press, Cambridge, UK.