Metabolic control in integrated biochemical systems

European Journal of Biochemistry

Volumn 269, Issue 18, 2002, Pages 4399-4408

  De La Fuente, Alberto ^a   Snoep, Jacky L ^b   Westerhoff, Hans V ^c,d   Mendes, Pedro ^a  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^b STELLENBOSCH UNIVERSITY   (South Africa)

^c STELLENBOSCH INSTITUTE FOR ADVANCED STUDY   (South Africa)

^d BioCentrum Amsterdam   (Netherlands)

Author keywords

Gene expression; Hierarchical control; Metabolic control analysis; Metabolism

Indexed keywords

ACCURACY; ARTICLE; BIOCHEMISTRY; CHEMICAL PARAMETERS; COMPUTER SIMULATION; ENZYME ACTIVITY; INTERMETHOD COMPARISON; METABOLIC REGULATION; PRIORITY JOURNAL; PROCESS CONTROL; STEADY STATE;

ENZYMES; GENE EXPRESSION REGULATION; KINETICS; METABOLISM; MODELS, BIOLOGICAL; TRANSCRIPTION, GENETIC;

EID: 0036380802     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1432-1033.2002.03088.x     Document Type: Article

References (32)

1. Kacser, H. & Burns, J.A. (1973) The control of flux. Symp. Soc. Exp. Biol. 27, 65-104.
2. Heinrich, R. & Rapoport, T.A. (1974) A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur. J. Biochem. 42, 89-95.
3. Burns, J.A., Cornish-Bowden, A., Groen, A.K., Heinrich, R., Kacser, H., Porteous, J.W., Rapoport, S.M., Rapoport, T.A. & Tager, J.M. (1985) Can we agree on metabolic control? Trends Biochem. Sci. 10, 152.
4. Fell, D.A. & Sauro, H.M. (1985) Metabolic control and its analysis. Additional relationships between elasticities and control coefficients. Eur. J. Biochem. 148, 555-561.
5. Sauro, H.M., Small, J.R. & Fell, D.A. (1987) Metabolic control and its analysis. Extensions to the theory and matrix method. Eur. J. Biochem. 165, 215-221.
6. Westerhoff, H.V. & Kell, D.B. (1987) Matrix method for determining steps most rate-limiting to metabolic fluxes in biotechnological processes. Biotechnol. Bioeng. 30, 101-107.
7. Reder, C. (1988) Metabolic control theory. A structural approach. J. Theoret. Biol. 135, 175-201.
8. Westerhoff, H.V. & van Workum, M. (1990) Control of DNA structure and gene expression. Biomed. Biochim. Acta. 49, 839-853.
9. Kahn, D. & Westerhoff, H.V. (1991) Control theory of regulatory cascades. J. Theor. Biol. 153, 255-285.
10. Westerhoff, H.V. & Kahn, D. (1993) Control involving metabolism and gene expression: the square-matrix method for modular decomposition. Acta Biotheor. 41, 75-83.
11. Jensen, P.R., Van Der Weijden, C.C., Jensen, L.B., Westerhoff, H.V. & Snoep, J.L. (1999) Extensive regulation compromises the extent to which DNA gyrase controls DNA supercoiling and growth rate of Escherichia coli. Eur. J. Biochem. 266, 865-877.
12. Snoep, J.L., van de Weijden, C.C., Andersen, H.W., Westerhoff, H.V. & Jensen, P.R. (2000) Hierarchical control of DNA supercoiling in Escherichia coli: how to study homeostatically controlled sytems using control analysis. BTK2000: Animating the Cellular Map (Hofmeyr, J.-H.S., Rohwer, J.H. & Snoep, J.L., eds), Stellenbosch University Press, Stellenbosch.
13. Snoep, J.L., Van der Weijden, C.C., Andersen, H.W., Westerhoff, H.V. & Jensen, P.R. (2002) DNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving gene-expression and metabolic regulation of both topoisomerase I and DNA gyrase. Eur. J. Biochem. 269, 1662-1669.
14. Hofmeyr, J.H. & Westerhoff, H.V. (2001) Building the cellular puzzle: control in multi-level reaction networks. J. Theoret. Biol. 208, 261-285.
15. Raamsdonk, L.M., Teusink, B., Broadhurst, D., Zhang, N., Hayes, A., Walsh, M.C., Berden, J.A., Brindle, K.M., Kell, D.B., Rowland, J.J., Westerhoff, H.V., van Dam, K. & Oliver, S.G. (2001) A functional genomics strategy that uses metabolome data to reveal the phenotype of silent mutations. Nat. Biotechnol. 19, 45-50.
16. Mendes, P. (1993) GEPASI: a software package for modelling the dynamics, steady-states and control of biochemical and other systems. Comput. Appl. Biosci. 9, 563-571.
17. Mendes, P. (1997) Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci. 22, 361-363.
18. Mendes, P. & Kell, D.B. (1998) Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14, 869-883.
19. de la Fuente van Bentem, A., Mendes, P., Westerhoff, H.V. & Snoep, J.L. (2000) Can metabolic control analysis be applied to hierarchical regulated metabolism? MCA versis HCA. BTK2000: Animating the Cellular Map (Hofmeyr, J.-H.S., Rohwer, J.H. & Snoep, J.L., eds), pp. 191-198. Stellenbosch University Press, Stellenbosch.
20. Liao, J.C. & Delgado, J. (1992) Dynamic metabolic control theory - a methodology for investigating metabolic regulation using transient metabolic data. Ann. NY Acad. Sci. 165, 27-38.
21. Sorribas, A., Samitier, S., Canela, E.I. & Cascante, M. (1993) Metabolic pathway characterization from transient response data obtained in-situ. Parameter estimation in S-system models. J. Theoret. Biol. 162, 81-102.
22. Jensen, P.R., Westerhoff, H.V. & Michelsen, O. (1993) The use of lac-type promoters in control analysis. Eur. J. Biochem. 211, 181-191.
23. ter Kuile, B.H. & Westerhoff, H.V. (2001) Transcriptome meets metabolome: hierarchical and metabolic regulation of the glycolytic pathway. FEBS Lett. 500, 169-171.
24. Westerhoff, H.V., Jensen, P.R., Egger, L., Van Heeswijk, W.C., Van Spanning, R.J.M., Kholodenko, B.N. & Snoep, J.L. (1998) Hierarchical control of electron-transfer. paper presented at the NATO/ESF Workshop Bioelectron-Transfer Chains. NATO/ESF, Tomar, Portugal.
25. Kholodenko, B.N., Demin, O.V., Moehren, G. & Hoek, J.B. (1999) Quantification of short term signaling by the epidermal growth factor receptor. J. Biol. Chem. 274, 30169-30181.
26. Kholodenko, B.N., Hoek, J.B. & Westerhoff, H.V. (2000) Why cytoplasmic signalling proteins should be recruited to cell membranes. Trends Cell Biol. 10, 173-178.
27. Stucki, J.W. (1978) Stability analysis of biochemical systems. A practical guide. Progr. Biophys. Mol. Biol. 33, 99-187.
28. Easterby, J.S. (1981) A generalized theory of the transition time for sequential enzyme reactions. Biochem. J. 199, 155-161.
29. Acerenza, L., Sauro, H.M. & Kacser, H. (1989) Control analysis of time dependent metabolic systems. J. Theoret. Biol. 137, 423-444.
30. Heinrich, R. & Reder, C. (1991) Metabolic control analysis of relaxation processes. J. Theoret. Biol. 151, 343-350.
31. Schena, M., Shalon, D., Davis, R.W. & Brown, P.O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 270, 467-470.
32. Mann, M., Hendrickson, R.C. & Pandey, A. (2001) Analysis of proteins and proteomes by mass spectrometry. Ann. Rev. Biochem. 70, 437-473.