Simplified modelling of metabolic pathways for flux prediction and optimization: Lessons from an in vitro reconstruction of the upper part of glycolysis

Biochemical Journal

Volumn 396, Issue 2, 2006, Pages 317-326

  Fiévet, Julie B ^a,b   Dillman, Christine ^a   Curien, Gilles ^b   De Vienne, Dominique ^a  

^a INRA Institut National de la Recherche Agronomique   (France)

^b UNIV GRENOBLE ALPES   (France)

Author keywords

Biochemical pathway; Flux computation; Glycolysis; Hyperbolic fitting; Optimal enzyme concentration; Systemic enzyme parameter

Indexed keywords

BIOMEDICAL ENGINEERING; CONCENTRATION (PROCESS); ENZYMES; MATHEMATICAL TECHNIQUES; OPTIMIZATION; PARAMETER ESTIMATION;

BIOCHEMICAL PATHWAY; FLUX COMPUTATION; GLYCOLYSIS; HYPERBOLIC FITTING; OPTIMAL ENZYME CONCENTRATION; SYSTEMIC ENZYME PARAMETER;

METABOLISM;

GLYCEROL 3 PHOSPHATE DEHYDROGENASE; HEXOKINASE;

ARTICLE; ENZYME ACTIVITY; ENZYME KINETICS; GLYCOLYSIS; IN VITRO STUDY; MATHEMATICAL COMPUTING; METABOLIC ENGINEERING; METABOLIC REGULATION; PRIORITY JOURNAL; TITRIMETRY;

EID: 33744806334     PISSN: 02646021     EISSN: None     Source Type: Journal    
DOI: 10.1042/BJ20051520     Document Type: Article

References (47)

1. Theobald, U., Mailinger, W., Baltes, M., Rizzi, M. and Reuss, M. (1997) In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II. Experimental observations. Biotechnol. Bioeng. 55, 305-316
2. Teusink, B., Passarge, J., Reijenga, C. A., Esgalhado, E., van der Weijden, C. C., Schepper, M., Walsh, M. C., Bakker, B. M., van Dam, K., Westerhoff, H. V. and Snoep, J. L. (2000) Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur. J. Biochem. 267, 5313-5329
3. Bakker, B. M., Michels, P. A., Opperdoes, F. R. and Westerhoff, H. V. (1997) Glycolysis in bloodstream form Trypanosoma brucei can be understood in terms of the kinetics of the glycolytic enzymes. J. Biol. Chem. 272, 3207-3215
4. Bali, M. and Thomas, S. R. (2001) A modelling study of feedforward activation in human erythrocyte glycolysis. C.R. Acad. Sci. III 324, 185-199
5. Mulquiney, P. J. and Kuchel, P. W. (1999) Model of 2,3- bisphosphoglycerate metabolism in the human erythrocyte based on detailed enzyme kinetic equations: equations and parameter refinement. Biochem. J. 342, 581-596
6. Mulquiney, P J. and Kuchel, P. W. (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
7. Lambeth, M. J. and Kushmerick, M. J. (2002) A computational model for glycogenolysis in skeletal muscle. Ann. Biomed. Eng. 30, 808-827
8. Fiévet, J., Dillmann, C., Lagniel, G., Davanture, M., Negroni, L., Labarre, J. and de Vienne, D. (2004) Assessing factors for reliable quantitative proteomics based on two-dimensional electrophoresis. Proteomics 4, 1939-1949
9. Gibon, Y., Blaesing, O. E., Hannemann, J., Carillo, P., Hohne, M., Hendriks, J. H., Palacios, N., Cross, J., Setbig, J. and Stitt, M. (2004) A robot-based platform to measure multiple enzyme activities in ArabirJopsis using a set of cycling assays: comparison of changes of enzyme activities and transcript levels during diurnal cycles and in prolonged darkness. Plant Cell 16, 3304-3325
10. Rizzi, M., Baltes, M., Theobald, U. and Reuss, M. (1997) In vivo analysis of metabolic dynamics in Saccharomyces cerevisiae: II. Mathematical model. Biotechnol. Bioeng. 55, 592-608
11. Visser, D. and Heijnen, J. J. (2003) Dynamic simulation and metabolic re-design of a branched pathway using linlog kinetics. Metab. Eng. 5, 164-176
12. Poolman, M. G., Fell, D. A. and Thomas, S. (2000) Modelling photosynthesis and its control. J. Exp. Bot. 51, 319-328
13. Edwards, J. S., Covert, M. and Palsson, B. (2002) Metabolic modelling of microbes: the flux-balance approach. Environ. Microbiol. 4, 133-140
14. Kacser, H. and Burns, J. A. (1973) The control of flux. Symp. Soc. Exp. Biol, 27, 65-104
15. Heinrich, R. and Rapoport, T. A. (1974) A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur. J. Biochem. 42, 89-95
16. Savageau, M. A. (1971) Concepts relating the behavior of biochemical systems to their underlying molecular properties. Arch. Biochem. Biophys. 145, 612-621
17. Torres, N. V., Voit, E. O., Glez-Alcon, C. and Rodriguez, F. (1997) An indirect optimisation method for biochemical systems: description of method and application to the maximization of the rate of ethanol, glycerol, and carbohydrate production in Saccharomyces cerevisiae. Biotechnol. Bioeng. 55, 758-772
18. Hatzimanikatis, V. and Bailey, J. E. (1997) Effects of spatiotemporal variations on metabolic control: approximate analysis using (log)linear kinetic models, Biotechnol. Bioeng. 54, 91-104
19. Visser, D., van der Heijden, R., Mauch, K., Reuss, M. and Heijnen, S. (2000) Tendency modeling: a new approach to obtain simplified kinetic models of metabolism applied to Saccharomyces cerevisiae. Metab. Eng. 2, 252-275
20. Giersch, C. (1995) Determining elasticities from multiple measurements of flux rates and metabolite concentrations. Application of the multiple modulation method to a reconstituted pathway. Eur. J. Biochem. 227, 194-201
21. Torres, N. V., Souto, R. and Melendez-Hevia, E. (1989) Study of the flux and transition time control coefficient profiles in a metabolic system in vitro and the effect of an external stimulator. Biochem. J. 260, 763-769
22. Saavedra, E., Encalada, R., Pineda, E., Jasso-Chavez, R. and Moreno-Sanchez, R. (2005) Glycolysis in Entamoeba histolytica. Biochemical characterization of recombinant glycolytic enzymes and flux control analysis. FEBS J. 272, 1767-1783
23. Schellenberger, W., Eschrich, K. and Hofmann, E. (1980) Selforganization of a glycolytic reconstituted enzyme system: alternate stable stationary states, hysteretic transitions and stabilization of the energy charge. Adv. Enzyme Regul. 19, 257-284
24. Schellenberger, W. and Hervagault, J. F. (1991) Irreversible transitions in the 6-phosphofructokinase/fructose 1,6-bisphosphatase cycle. Eur. J. Bioctiem. 195, 109-113
25. Curien, G., Ravanel, S. and Dumas, R. (2003) A kinetic model of the branch-point between the methionine and threonine biosynthesis pathways in Arabidopsis thaliana. Eur. J. Biochem. 270, 4615-4627
26. Kuchel, P. W. (1985) Kinetic analysis of multienzyme systems in homogeneous solution. In Organized Multienzyme Systems (Welch, G. R., ed.), pp. 303-380, Academic Press, New York
27. Heinrich, R., Schuster, S. and Holzhutter, H. G. (1991) Mathematical analysis of enzymic reaction systems using optimization principles. Eur. J. Biochem. 201, 1-21
28. Scopes, R. K. (1974) Measurement of protein by spectrophotometry at 205 nm. Anal. Biochem. 59, 277-282
29. Cornish-Bowden, A. (1995) Fundamentals of Enzyme Kinetics, Portland Press, London
30. van Kempen, G. M. and van Vliet, L. J. (2000) Mean and variance of ratio estimators used in fluorescence ratio imaging. Cytometry 39, 300-305
31. Kacser, H. and Burns, J. A. (1981) The molecular basis of dominance. Genetics 97, 639-666
32. Niederberger, P., Prasad, R., Miozzari, G. and Kacser, H. (1992) A strategy for increasing an In vivo flux by genetic manipulations. The tryptophan system of yeast. Biochem. J. 287, 473-479
33. Rossignol, R., Faustin, B., Rocher, C., Malgat, M., Mazat, J.-P. and Letellier, T. (2003) Mitochondrial threshold effects. Biochem. J. 370, 751-762
34. Sen, A. K. (1996) On the sign pattern of metabolic control coefficients. J. Theor. Biol. 182, 269-275
35. Jung, G. Y. and Stephanopoulos, G. (2004) A functional protein chip for pathway optimization and in vitro metabolic engineering. Science 304, 428-431
36. Aiston, S., Trinh, K. Y., Lange, A. J., Newgard, C. B. and Agius, L. (1999) Glucose-6-phosphatase overexpression lowers glucose 6-phosphate and inhibits glycogen synthesis and glycolysis in hepatocytes without affecting glucokinase translocation. Evidence against feedback inhibition of glucokinase. J. Biol. Chem. 274, 24559-24566
37. Cohen, P. (1985) The coordinated control of metabolic pathways by broad-specificity protein kinases and phosphatases. Curr. Top. Cell. Regul. 27, 23-37
38. Alston, S., Hampson, L., Gomez-Foix, A. M., Guinovart, J. J. and Agius, L. (2001) Hepatic glycogen synthesis is highly sensitive to phosphorylase activity: evidence from metabolic control analysis. J. Biol. Chem. 276, 23858-23866
39. LaPorte, D. C., Walsh, K. and Koshland, Jr, D. E. (1984) The branch point effect. Ultrasensitivity and subsensitivity to metabolic control. J. Biol. Chem. 259, 14068-14075
40. Kruckeberg, A. L., Neuhaus, H. E., Feil, R., Gottlieb, L. D. and Stitt, M. (1989) Decreased-activity mutants of phosphoglucose isomerase in the cytosol and chloroplast of Clarkia xaritiana. Impact on mass-action ratios and fluxes to sucrose and starch, and estimation of flux control coefficients and elasticity coefficients. Biochem. J. 261, 457-467
41. Peter Smits, H., Hauf, J., Muller, S., Hobley, T. J., Zimmermann, F. K., Hahn-Hagerdal, B., Nielsen, J. and Olsson, L. (2000) Simultaneous overexpression of enzymes of the lower part of glycolysis can enhance the fermentative capacity of Sacchammyces cerevisiae. Yeast 16, 1325-1334
42. Snoep, J. L., Yomano, L. P., Westerhoff, H. V. and Ingram, L. O. (1995) Protein burden in Zymomonas mobilis: negative flux and growth control due to overproduction of glycolytic enzymes. Microbiology 141, 2329-2337
43. Lion, S., Gabriel, F., Bost, B., Fievet, J., Dillmann, C. and de Vienne, D. (2004) An extension to the metabolic control theory taking into account correlations between enzyme concentrations. Eur. J. Biochem. 271, 4375-4391
44. Banta, S., Boston, M., Jarnagin, A. and Anderson, S. (2002) Mathematical modeling of in vitro enzymatic production of 2-keto-L-gulonic acid using NAD(H) or NADP(H) as cofactors. Metab. Eng. 4, 273-284
45. Puigjaner, J., Rais, B., Burgos, M., Comin, B., Ovadi, J. and Cascante, M. (1997) Comparison of control analysis data using different approaches: modelling and experiments with muscle extract. FEBS Lett. 418, 47-52
46. Torres, N. V., Mateo, F., Melendez-Hevia, E. and Kacser, H. (1986) Kinetics of metabolic pathways. A system in vitro to study the control of flux. Biochem. J. 234, 169-174
47. Pierre, J. N., Prieto, J. L., Gadal, P. and Vidal, J. (2004) In situ C4 phosphoenolpyruvate carboxylase activity and kinetic properties in isolated Digitariasanguinalis mesophyll cells. Photosynth. Res. 79, 349-355