Bidirectional reaction steps in metabolic networks: I. Modeling and simulation of carbon isotope labeling experiments

Biotechnology and Bioengineering

Volumn 55, Issue 1, 1997, Pages 101-117

  Wiechert, Wolfgang ^a,b   De Graaf, Albert A ^a  

^a FORSCHUNGSZENTRUM JÜLICH   (Germany)

^b UNIVERSITY OF SIEGEN   (Germany)

Author keywords

13C isotope labeling experiments; Metabolic engineering; Metabolite flux balancing; NMR; Stationary flux analysis

Indexed keywords

ALGORITHMS; CARBON; COMPUTER SIMULATION; COMPUTER SOFTWARE; CONVERGENCE OF NUMERICAL METHODS; ISOTOPES; MATHEMATICAL MODELS; MATHEMATICAL TRANSFORMATIONS; NONLINEAR EQUATIONS; NUCLEAR MAGNETIC RESONANCE; PROBLEM SOLVING;

CARBON ISOTOPE LABELING; METABOLITE FLUX BALANCING; STATIONARY FLUX ANALYSIS;

METABOLISM;

CARBON 13;

ARTICLE; BIOENGINEERING; ISOTOPE LABELING; MATHEMATICAL MODEL; METABOLISM; METABOLITE; NUCLEAR MAGNETIC RESONANCE; SIMULATION;

EID: 0031554635     PISSN: 00063592     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0290(19970705)55:1<101::AID-BIT12>3.0.CO;2-P     Document Type: Article

References (55)

1. Ahlfors, L. V. 1979. Complex analysis. 3rd edition. McGraw Hill, New York.
2. Anderson, D. H. 1983. Compartmental modelling and tracer kinetics, vol. 50. In: Lecture notes in biomathematics. Springer, New York.
3. Bailey, J. E. 1991. Towards a science of metabolic engineering. Science 252: 1668-1674.
4. Blum, J. J., Stein, R. B. 1982. On the analysis of metabolic networks, pp. 99-124. In: R. F. Goldberger (eds.), Biological regulation and development, vol. 3A. Plenum, Press, New York.
5. 13C NMR spectroscopy and nonlinear least squares analysis. J. Biol. Chem. 270: 7999-8008.
6. Chatterjee, S., Hadi, A. S. 1988. Sensitivity analysis in linear regression. John Wiley & Sons, New York.
7. Crawford, J. M., Blum, J. J. 1983. Quantitative analysis of flux along the gluconeogenic, glycolytic and pentose phosphate pathways under reducing conditions in hepatocytes isolated from fed rats. Biochem. J. 212: 595-598.
8. Eisenreich, W., Strauss, G., Werz, U., Fuchs, G., Bacher, A. 1993. Retrobiosynthetic analysis of carbon fixation in the phototrophic eubacterium Chloroflexus aurantiacus. Eur. J. Biochem. 215: 619-632.
9. 13C nuclear magnetic resonance. J. Bacteriol. 156: 316-326.
10. Goel, A., Ferrance, J., Jeong, J., Ataai, M. M. 1993. Analysis of metabolic fluxes in batch and continuous cultures of Bacillus subtilis. Biotechnol. Bioeng. 42: 686-696.
11. van Heijden, R. T. J. M., Heijnen, J. J., Hellinga, C., Romein, B., Luyben, K. C. A. M. 1994a. Linear constraint relations in biochemical reaction systems: I. Classification of the calculability and the balanceability of conversion rates. Biotechnol. Bioeng. 43: 3-10.
12. van Heijden, R. T. J. M., Romein, B., Heijnen, J. J., Hellinga, C., Luyben, K. C. A. M. 1994b. Linear constraint relations in biochemical reaction systems: II. Diagnosis and estimation of gross errors. Biotechnol. Bioeng. 43: 11-20.
13. Hofmeyr, J. H. S. 1986. Steady-state modelling of metabolic pathways: a guide for the prospective simulator. Comp. Appl. Biosci. 2: 5-11.
14. Holzhütter, H. G. 1985. Compartmental analysis: theoretical aspects and applications. Biomed. Biochim. Acta 44: 863-873.
15. Jorgensen, H. 1995. Metabolic flux distributions in Penicillium chrysogenum during fed-batch cultivations. Biotechnol. Bioeng. 46: 117-131.
16. Lambrecht, R. M., Rescigno, A. (eds.) 1983. Tracer kinetics and physiological modelling. In: Lecture notes in biomathematics (no. 48). Springer, New York.
17. O'Leary, M. H. 1982. Heavy-atom isotope effects on enzyme-catalyzed reactions, pp. 67-75. In: H. L. Schmidt, H. Förstel, and K. Heinzinger (eds.), Analytical chemistry symposia series, vol. 11. Elsevier, Amsterdam.
18. 13C] xylose metabolism in Pichia stipitis under aerobic and anaerobic conditions. Appl. Microbiol. Biotechnol. 28: 293-296.
19. Marx, A., de Graaf, A. A., Wiechert, W., Eggeling, L., Sahm, H. 1996. Determination of the fluxes in central metabolism of Corynebacterium glutamicum by NMR spectroscopy combined with metabolite balancing. Biotechnol. Bioeng. 49: 111-129.
20. Mavrovouniotis, M. L. 1991. Estimation of standard Gibbs energy changes of biotransformations. J. Biol. Chem. 266: 14440-14445.
21. 13C] glucose incubation. Eur. J. Biochem. 217: 457-468.
22. Rabkin, M., Blum, J. J. 1985. Quantitative analysis of intermediary metabolism in hepatocytes incubated in the presence and absence of glucagon with a substrate mixture containing glucose, ribose, fructose, alanine and acetate. Biochem. J. 225: 761-786.
23. Reder, C. 1988. Metabolic control theory: a structural approach. J. Theor. Biol. 135: 175-201.
24. Rizzi, M., Theobald, U., Querfurth, E., Rohrhirsch, T., Baltes, M., Reuss, M. 1996. In vivo investigations of glucose transport in Saccharomyces cerevisiae. Biotechnol. Bioeng. 49: 316-327.
25. Roels, J. A. 1983. Energetics and kinetics in biotechnology. Elsevier, Amsterdam.
26. Schmidt, H.-L., Förstel, H., Heinzinger, K. (eds.) 1982. Stable isotopes. Analytical chemistry symposia series, vol. 11. Elsevier, Amsterdam.
27. Schügerl, K. (ed.) 1991. Biotechnology. Measuring, modelling and control, vol. 4. 2nd edition. Verlag Chemie, Weinheim.
28. Schuster, R., Schuster, S., Holzhütter, H.-G. 1992. Simplification of complex kinetic models used for the quantitative analysis of nuclear magnetic resonance or radioactive tracer studies. J. Chem. Soc. Faraday Trans. 88: 2837-2844.
29. Schuster, R., Schuster, S. 1993. Refined algorithm and computer program for calculating all non-negative fluxes admissible in steady state of biochemical reaction systems with or without some flux rates fixed. Comp. Appl. Biosci. 9: 79-85.
30. Sharfstein, S. T., Tucker, S. N., Mancuso, A., Blanch, H. W., Clark, D. S. 1994. Quantitative in vivo nuclear magnetic resonance studies of hybridoma metabolism. Biotechnol. Bioeng. 43: 1059-1074.
31. Stein, R. B., Blum, J. J. 1979. Quantitative analysis of intermediary metabolism in Tetrahymena - cells grown in proteose-peptone and resuspended in a defined nutrient-rich medium. J. Biol. Chem. 254: 10385-10395.
32. Stephanopoulos, G., Vallino, J. J. 1991. Network rigidity and metabolic engineering in metabolite overproduction. Science 252: 1675-1681.
33. Stephanopoulos, G., Sinskey, A. J. 1993. Metabolic engineering -methodologies and future prospects. Tib Tech 11: 392-396.
34. Stryer, L. 1988. Biochemistry. 3rd edition. W. H. Freeman Co., New York.
35. 13C NMR studies. Biochemistry 32: 12725-12729.
36. 13C-labeling of proteinogenic amino acids - an efficient analytical tool to investigate intermediary metabolism. Eur. J. Biochem. 232: 433-448.
37. Vallino, J. J. 1991. Identification of branch-point restrictions in microbial metabolism through metabolic flux analysis and local network perturbations, Ph.D. thesis, Massachusetts Institute of Technology, Cambridge, MA, USA.
38. Vallino, J. J., Stephanopoulos, G. 1993. Metabolic flux distribution in Corynebacterium glutamicum durng growth and lysine overproduction. Biotechnol. Bioeng. 41: 633-646.
39. Varma, A., Palsson, B. O. 1994. Metabolic flux balancing: basic concepts scientific and practical use. Bio/Technol. 12: 994-998.
40. Westerhoff, H. V., van Dam, K. 1987. Mosaic nonequilibrium thermodynamics and control of biological free-energy transduction. Elsevier, Amsterdam.
41. Weuster-Botz, D., de Graaf, A. A. 1996. Reaction engineering methods to study intracellular metabolite concentrations. Adv. Biochem. Eng. Biotechnol. 54: 76-108.
42. 13C NMR isotope labelling experiments, pp. 305-310. In: E. Gnaiger, F. N. Gellerich, and M. Wyss (eds.), What is controlling life? Modern trends in biothermokinetics, vol. 3. Innsbruck University Press, Innsbruck, Austria.
43. 13C labelling systems, pp. 169-184. In: D. Schomburg and U. Lessel (eds.), Bioinformatics; from nucleic acids and proteins to cell metabolism. Verlag Chemie, Weinheim.
44. Wiechert, W. 1996a. Metabolische Kohlenstoff-Markierungssysteme - Modellierung, Simulation, Analyse, Datenauswertung. Habilitationsschrift, University of Bonn, Bonn, Germany.
45. 13C tracer experiments: analysis of sensitivity, identifiability and redundancy, pp. 128-135. In: J. Dolezal and J. Fidler (eds.), System modelling and optimization. Chapman & Hall, London.
46. 13C labelling in metabolic pathways for in vivo flux analysis using NMR, pp. 19-24. In: V. Bales (ed.), Modelling for improved bioreactor performance. Malé Centrum, Bratislava.
47. 13C NMR isotope labelling experiments. In: A. Munack and K. Schügerl (eds.), Computer applications in biotechnology. Pergamon Press, New York.
48. 13C labelling experiments. Adv. Biochem. Eng. Biotechnol. 54: 109-154.
49. Wiechert, W., Siefke, C., de Graaf, A. A., Marx, A. 1997. Bidirectional reaction steps in metabolic networks: II. Flux estimation and statistical analysis. Biotechnol. Bioeng. 55: 118-135.
50. 2 discrimination of the ribulose-1,5-bis-phosphate carboxylase reaction, pp. 83-89. In: H.-L. Schmidt, H. Förstel, and K. Heinzinger (eds.), Analytical chemistry symposia series, vol. 11. Elsevier, Amsterdam.
51. Wood, T. 1985. The pentose phosphate pathway. Academic Press, New York.
52. Zhang, M., Eddy, C., Deanda, K., Finkelstein, M., Picataggio, S. 1995. Metabolic engineering of a pentose metabolism pathway in ethanologenic Zymomonas mobilis. Science 267: 240-243.
53. Zoutendijk, G. 1991. Mathematical programming methods. North Holland, Amsterdam.
54. Zupke, C., Stephanopoulos, G. 1994. Modeling of isotope distributions and intracellular fluxes in metabolic networks using atom mapping matrices. Biotechnol. Prog. 10: 489-498.
55. 13C NMR. Biotechnol. Bioeng. 45: 292-303.