Characterizing the metabolic phenotype: A phenotype phase plane analysis

Biotechnology and bioengineering

Volumn 77, Issue 1, 2002, Pages 27-36

  Edwards, Jeremy S ^a   Ramakrishna, Ramprasad ^b   Palsson, Bernhard O ^c  

^a University of Delaware   (United States)

^b Physiome Sciences Inc   (United States)

^c UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENOME; BIOLOGICAL MODEL; BIOLOGY; ESCHERICHIA COLI; GENETICS; METABOLISM; METHODOLOGY; PHENOTYPE; STATISTICAL ANALYSIS;

COMPUTATIONAL BIOLOGY; DATA INTERPRETATION, STATISTICAL; ESCHERICHIA COLI; GENOME, BACTERIAL; MODELS, BIOLOGICAL; PHENOTYPE; SUPPORT, U.S. GOV'T, NON-P.H.S.; SUPPORT, U.S. GOV'T, P.H.S.;

EID: 0037021804     PISSN: 00063592     EISSN: None     Source Type: Journal    
DOI: 10.1002/bit.10047     Document Type: Article

References (39)

1. Blattner FR, et al. 1997. The complete genome sequence of Escherichia coli K‐12. Science 277: 1453–1474.
2. Bonarius HPJ, et al. 1996. Metabolic flux analysis of hybridoma cells in different culture media using mass balances. Biotechnol Bioeng 50: 299–318.
3. Bonarius HPJ, Schmid G, Tramper J. 1997. Flux analysis of underdetermined metabolic networks: The quest for the missing constraints. Trends Biotechnol 15: 308–314.
4. Brown PO, Botstein D. 1999. Exploring the new world of the genome with DNA microarrays. Nat Genet 21: 33–37.
5. Edwards JS. 1990. PhD thesis, University of California, San Diego, San Diego CA, USA.
6. Edwards JS, Ibarra RU, Palsson BO. 2001. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 19: 125–130.
7. Edwards JS, Palsson BO. 1999. Systems properties of the Haemophilus influenzae Rd metabolic genotype. J Biol Chem 274: 17410–17416.
8. Edwards JS, Palsson BO. 2000. The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 97: 5528–5533.
9. Edwards JS, Ramakrishna R, Schilling CH, Palsson BO. 1999. In: Lee SY, Papoutsakis ET, editors. Metabolic engineering. New York: Marcel Dekker. p 13–57.
10. Fell D. 1996. Understanding the control of metabolism. London: Portland Press.
11. Gygsi SP, et al. 1999. Quantitative analysis of complex protein mixtures using isotope‐coded affinity tags. Nat Biotechnol 17: 994–999.
12. Jensen PR, Michelson O. 1992. Carbon and energy metabolism of atp mutants of Escherichia coli. J Bacteriol 174: 7635–7641.
13. Joshi A, Palsson BO. 1989. Metabolic dynamics in the human red cell. Part I–A comprehensive kinetic model. J Theor Biol 141: 515–528.
14. Kacser H, Burns JA. 1973. The control of flux. Symp Soc Biol 27: 65–104.
15. Karp PD, Krummenacker M, Paley S, Wagg J. 1999. Integrated pathway‐genome databases and their role in drug discovery. Trends Biotechnol 17: 275–281.
16. Karp PD, Ouzounis C, Paley S. 1996. HinCyc: A knowledge base of the complete genome and metabolic pathways of H. influenzae. Intelligent Systems for Molecular Biology 4: 116–124.
17. Karp PD, et al. 2000. The EcoCyc and MetaCyc databases. Nucl Acids Res 28: 56–59.
18. Kompala DS, Ramkrishna D, Jansen NB, Tsao GT. 1986. Investigation of bacterial growth on mixed substrates. Experimental evaluation of cybernetic models. Biotechnol Bioeng 28: 1044–1056.
19. Liao JC, Hou SY, Chao YP. 1996. Pathway analysis, engineering and physiological considerations for redirecting central metabolism. Biotechnol Bioeng 52: 129–140.
20. Mavrovouniotis M, Stephanopoulos G. 1992. Synthesis of biochemical production routes. Comput Chem Eng 16: 605–619.
21. Mulquiney PJ, Kuchel PW. 1999. Model of 2,3‐bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: computer simulation and metabolic control analysis. Biochem J 342: 597–604.
22. Neidhardt FC, editor. 1996a. Escherichia coli and Salmonella: Cellular and molecular biology. Washington, DC: ASM Press.
23. Neidhardt FC, Umbarger HE, 1996b. Escherichia coli and Salmonella: Cellular and molecular biology. Vol. 1. Washington, DC: ASM Press. p 13–16.
24. Ogata H, Goto S, Fujibuchi W, Kanehisa M. 1998. Computation with the KEGG pathway database. Biosystems 47: 119–128.
25. Overbeek R, et al. 2000. WIT: Integrated system for high‐throughput genome sequence analysis and metabolic reconstruction. Nucl Acids Res 28: 123–125.
26. Palsson BO, Joshi A, Ozturk SS. 1987. Reducing complexity in metabolic networks: Making metabolic meshes manageable. Fed Proc 46: 2485–2489.
27. Pramanik J, Keasling JD. 1997. Stoichiometric model of Escherichia coli metabolism: Incorporation of growth‐rate dependent biomass composition and mechanistic energy requirements. Biotechnol Bioeng 56: 398–421.
28. Savageau MA. 1969. Biochemical systems analysis. II. The steady‐state solutions for an n‐pool system using a power‐law approximation. J Theor Biol 25: 370–379.
29. Schilling CH, Schuster S, Palsson BO, Heinrich R. 1999. Metabolic pathway analysis: Basic concepts and scientific applications in the post‐genomic era. Biotechnol Prog 15: 296–303.
30. Schuster S, Dandekar T, Fell DA. 1999. Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering. Trends Biotechnol 17: 53–60.
31. Selkov E, Jr., Grenchkin Y, Mikhailova N, Selkov E. 1998. MPW: The metabolic pathways database. Nucl Acids Res 26: 43–45.
32. Shu J, Shuler ML. 1989. A mathematical model for the growth of a single cell of Escherichia coli on a glucose/glutamine/ammonium medium. Biotechnol Bioeng 33: 1117–1126.
33. Tatusov RL, et al. 1996. Metabolism and evolution of Haemophilus influenzae deduced from a whole‐genome comparison with Escherichia coli. Curr Biol 6: 279–291.
34. Varma A, Boesch BW, Palsson BO. 1993. Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates. Appl Environ Microbiol 59: 2465–2473.
35. Varma A, Palsson BO. 1993. Metabolic capabilities of Escherichia coli: II. Optimal growth patterns. J Theor Biol 165: 503–522.
36. Varma A, Palsson BO 1994a. Metabolic flux balancing: Basic concepts, scientific and practical use. Bio/Technology 12: 994–998.
37. Varma A, Palsson BO. 1994b. Stoichiometric flux balance models quantitatively predict growth and metabolic by‐product secretion in wild‐type Escherichia coli W3110. Appl Environ Microbiol 60: 3724–3731.
38. Varner J, Ramkrishna D. 1998. Application of cybernetic models to metabolic engineering: Investigation of storage pathways. Biotechnol Bioeng 58: 282–291.
39. Weikert C, Sauer U, Bailey JE. 1997. Use of a glycerol‐limited, long‐term chemostat for isolation of Escherichia coli mutants with improved physiological properties. Microbiology 143: 1567–1574.