What bioechnologists knew all along...?

Journal of Theoretical Biology

Volumn 182, Issue 3, 1996, Pages 411-420

  Westerhoff, Hans V ^a,b   Kell, Douglas B ^c  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

^b VU UNIVERSITY AMSTERDAM   (Netherlands)

^c ABERYSTWYTH UNIVERSITY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOTECHNOLOGY; CONCENTRATION RESPONSE; METABOLIC REGULATION; METABOLITE; PRIORITY JOURNAL; REVIEW; SITE DIRECTED MUTAGENESIS; ANIMAL; ARTICLE; BIOLOGY; METABOLISM;

ANIMALS; BIOTECHNOLOGY; COMPUTATIONAL BIOLOGY; METABOLISM; MUTAGENESIS, SITE-DIRECTED;

EID: 0030573816     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1006/jtbi.1996.0181     Document Type: Article

References (86)

1. ACERENZA, L., SAURO, H. M. & KACSER, H. (1989). Control analysis of time-dependent metabolic systems. J. theor. Biol. 137, 423-444.
2. ACERENZA, L. (1993). Metabolic control design. J. theor. Biol. 165, 63-85.
3. BAILEY, J. E. (1991). Toward a science of metabolic engineering. Science 252, 1668-1675.
4. BAILEY, J. E., BIRNBAUM, S., GALAZZO, J. L., KHOSLA, C. & SHANKS, J. V. (1990). Strategies and challenges in metabolic engineering. Ann. N.Y. Acad. Sci. 589, 1-15.
5. BARTHELMESS, I. B., CURTIS, C. F. & KACSER, H. (1974). Control of flux to arginine in Neurospora crassa de-repression of the last three enzymes of the arginine pathway. J. Mol. Biol. 87, 303-316.
6. BURNS, J. A., CORNISH-BOWDEN, A., GROEN, A. K., HEINRICH, R., KACSER, H., PORTEOUS, J. W., RAPOPORT, S. M., RAPOPORT, T. A., STUCKI, J. W., TAGER, J. M., WANDERS, R. J. A. & WESTERHOFF, H. V. (1985). Control analysis of metabolic systems. Trends Biochem. Sci. 10, 16.
7. CAMERON, D. C. & TONG, I. (1993) Cellular and metabolic engineering: an overview. Appl. Biochem. Biotechnol. 38, 105-140.
8. CLEGG, J. S. (1984). Properties and metabolism of the aqueous cytoplasm and its boundaries. Am. J. Physiol. 246, R133-R151.
9. DAVEY, H. M. & KELL, D. B. (1996). Flow cytometry and cell sorting of heterogeneous microbial populations: the unimportance of single-cell analyses. Microbiol. Rev., (in press).
10. GROEN, A. K., WANDERS, R. J. A., WESTERHOFF, H. V., VAN DER MEER, R. & TAGER, J. M. (1982). Quantification of the contribution of various steps to the control of mitochondrial respiration. J. Biol. Chem. 257, 2754-2757.
11. HAFNER, R. P., BROWN G. C. & BRAND, M. D. (1990). Analysis of the control of respiration rate, phosphorylation rate, proton leak rate and protonmotive force in isolated mitochondria using the 'top-down' approach of metabolic control theory. Eur. J. Biochem. 188, 313-319.
12. HEINRICH, R., RAPOPORT, S. M. & RAPOPORT, T. A. (1977). Metabolic regulation and mathematical models. Progr. Biophys. Mol. Biol. 32, 1-83.
13. HEINRICH, R. & RAPOPORT, T. A. (1973). Linear theory of enzymatic chains: its application for the analysis of the crossover theorem and of the glycolysis of human erythrocytes. Acta Biol. Med. Germ. 31, 479-494.
14. HEINRICH, R. & REDER, C. (1991). Metabolic control analysis of relaxation processes. J. theor. Biol. 151, 343-350.
15. HIGGINS, J. J. (1965). Dynamics and control in cellular reactions. In: Control of Energy Metabolism (Chance, B., Estabrook, R. W. & Higgins, J. J., eds.), pp. 13-46. New York: Academic Press.
16. HLAVACEK, W. S. & SAVAGEAU, M. A. (1995). Subunit structure of regulator proteins influences the design of gene circuitry: Analysis of perfectly coupled and completely uncoupled circuits. J. Mol. Biol. 248, 739-755.
17. HÖFER, T. & HEINRICH, R. (1993). A second-order approach to metabolic control analysis. J. theor. Biol. 164, 85-102.
18. HOFMEYR, J.-H. S. & CORNISH-BOWDEN, A. (1991). Quantitative assessment of regulation in metabolic systems. Eur. J. Biochem. 200, 223-236.
19. HOFMEYR, J. H. S., CORNISH-BOWDEN, A. & ROHWER, J. M. (1993). Taking enzyme kinetics out of control - putting control into regulation. Eur. J. Biochem. 212, 833-837.
20. HOFMEYR, J.-H. S., KACSER, H. & VAN DER MERWE, K. J. (1986). Metabolic control analysis of moiety-conserved cycles. Eur. J. Biochem. 155, 631-641.
21. JENSEN, P. R., WESTERHOFF, H. V. & MICHELSEN, O. (1993a). The use of lac-type promoters in control analysis. Eur. J. Biochem. 211, 181-191.
22. +-ATPase and inverse respiratory control in Escherichia coli. EMBO J. 12, 1277-1282.
23. JENSEN, P. R., SNOEP, J. L., MOLENAAR, D., VAN HEESWIJK, W. C., KHOLODENKO, B. N., VAN DER GUGTEN, A. A. & WESTERHOFF, H. V. (1995). Molecular biology for flux control. Biochem. Soc. Trans., 23, 367-370.
24. KACSER, H. (1995). Recent developments beyond metabolic control analysis. Biochem. Soc. Trans. 23, 387-391.
25. KACSER, H. & BURNS, J. A. (1973). The control of flux. Symp. Soc. Exp. Biol. 27, 65-104.
26. KACSER, H. & BURNS, J. A. (1981). The molecular basis of dominance. Genetics 97, 639-666.
27. KACSER, H. & ACERENZA, L. (1993). A universal method for achieving increases in metabolite production. Eur. J. Biochem. 216, 361-367.
28. KAHN, D. & WESTERHOFF, H. V. (1991). Control theory of regulatory cascades. J. theor. Biol. 153, 255-285.
29. KAHN, D. & WESTERHOFF, H. V. (1993). The regulatory strength: How to be precise about regulation and homeostasis. Acta Biotheor. 41, 85-96.
30. KATCHALSKY, A. & CURRAN, P. F. (1967) Non Equilibrium Thermodynamics in Biophysics. Cambridge, MA: Harvard University Press.
31. KATSUMATA, R. & IKEDA, M. (1993) Hyperproduction of tryptophan in Corynebacterium glutamicum by pathway engineering. Bio/Technology 11, 921-925.
32. KELL, D. B. & WESTERHOFF, H. V. (1985). Catalytic facilitation and membrane bioenergetics. In: Organized Multienzyme Systems. Catalytic Properties (Welch G. R., ed.) pp. 63-138. New York: Academic Press.
33. KELL, D. B. & WESTERHOFF, H. V. (1986a). Metabolic control theory: Its role in microbiology and biotechnology. FEMS Microbiol. Rev. 39, 305-320.
34. KELL, D. B. & WESTERHOFF, H. V. (1986b). Towards a rational approach to the optimisation of flux in microbial biotransformations. Trends Biotechnol. 4, 137-142.
35. KELL, D. B., VAN DAM, K. & WESTERHOFF, H. V. (1989). Control analysis of microbial growth and productivity. In: Microbial Products: New Approaches (Banmberg S., Hunter I. & Rhodes M., eds), (Soc. Gen. Microbiol. Symp. 44), pp. 61-93. Cambridge: Cambridge University Press.
36. KELL, D. B. & WESTERHOFF, H. V. (1990). Control analysis of organised multienzyme systems. In: Structural and Organizational Aspects of Metabolic Regulation (Srere, P., Jones, M. E. & Mathews, C., eds), pp. 273-289. New York: Alan R. Liss.
37. KELL, D. B., RYDER, H. M., KAPRELYANTS, A. S. & WESTERHOFF, H. V. (1991). Quantifying heterogenity: Flow cytometry of bacterial cultures. Antonie van Leeuwenhoek 60, 145-158.
38. KELL, D. B., KAPRELYANTS, A. S. & GRAFEN, A. (1995). On pheromones, social behaviour and the functions of secondary metabolism in bacteria. Trends Ecol. Evolution 10, 126-129.
39. KELL, D. B. & SONNLEITNER, B. (1995). GMP - Good Modelling Practice: an essential component of good manufacturing practice. Trends Biotechnol. 13, 481-492.
40. KHOLODENKO, B. N. & WESTERHOFF, H. V. (1993). Metabolic channelling and control of flux. FEBS Lett. 320, 71-74.
41. KHOLODENKO, B. N. & WESTERHOFF, H. V. (1995a). Control theory of group-transfer pathways. Biochim. Biophys. Acta 1229, 256-274.
42. KHOLODENKO, B. N. & WESTERHOFF, H. V. (1995b). The macroworld versus the microworld of biochemical regulation and control. Trends Biochem. Sci. 20, 52-54.
43. KHOLODENKO, B. N., CASCANTE, M. & WESTERHOFF, H. V. (1995a). Control theory of metabolic channelling. Mol. Cellul. Biochem. 143, 151-168.
44. KHOLODENKO, B. N., SCHUSTER, S., ROHWER, J. M., CASCANTE, M. & WESTERHOFF, H. V. (1995b). Composite control of cell function: metabolic pathways behaving as a single control unit. FEBS Lett. 368, 1-4.
45. KHOLODENKO, B. N., SAURO, H. M. & WESTERHOFF, H. V. (1994). Control by enzymes, coenzymes and conserved moieties: a generalisation of the connectivity theorem of metabolic control analysis. Eur. J. Biochem. 225, 179-186.
46. LIAO, J. C. & DELGADO, J. (1993). Advances in metabolic control analysis. Biotechnol. Progr. 9, 221-233.
47. LIPSHUTZ, R. J., MORRIS, D., CHEE, M., HUBBELL, E., KOZAL, M. J., SHAH, N., SHEN, N., YANG, R. & FODOR, S. P. A. (1995). Using Oligonucleotide Probe Arrays to Access Genetic Diversity. Biotechniques 19, 442-447.
48. MADDOX, J. (1994) Towards more measurement in biology. Nature 368, 95.
49. MARKUS M. & HESS B. (1990) Control of Metabolic Oscillations: Unpredictability, Critical Slowing Down, Optimal Stability and Hysteresis. In: Control of Metabolic Processes (Cornish-Bowden, A. & Cárdenas M. L., eds), pp. 303-313. New York: Plenum Press.
50. MENDES, P. (1993). GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Computer Appl. Biosci. 9, 563-571.
51. MENDES, P. (1996). Gepasi 3: a 32-bit Microsoft Windows computer program for simulating biochemical dynamics. In: Bio Thermokinetics of the Living Cell (Westerhoff, M. U., Snoep, J. L., Sluse, F. E. Wijker, J. E. & Kholodenko, B. N., eds), pp. 258-261. Amsterdam: Bio Thermokinetics Press.
52. MENDES, P., KELL, D. B. & WESTERHOFF, H. V. (1996) Why and when channelling can decrease pool size at constant net flux in a simple dynamic channel. Biochim. Biophys. Acta, 1289, 175-186.
53. MERMELSTEIN, L. D., WELKER, N. E., PETERSEN, D. J., BENNETT, G. N. & PAPOUTSAKIS, E. T. (1994). Genetic and Metabolic Engineering of Clostridium-Acetobutylicum ATCC-824. Ann. N.Y. Acad. Sci. 721, 54-68.
54. RUIJTER, G., POSTMA, P. W. & VAN DAM, K. (1991). Control of glucose metabolism by enzyme Hglc of the phosphoenolpyruvate-dependent phosphotransferase system in Escherichia coli. J. Bacteriol. 173, 6184-6191.
55. RUTGERS, M., VAN DAM, K. & WESTERHOFF, H. V. (1991). Control and thermodynamics of microbial growth. Rational tools for bioengineering. CRC Crit. Rev. Biotechnol. 11, 367-395.
56. SAURO, H. M. (1990). Regulatory responses and control analysis: assessment of the relative importance of internal effectors. In: Control of Metabolic Processes. (Cornish-Bowden, A. & Cárdenas, M. L., eds), pp. 225-230. New York Plenum Press.
57. SAURO, H. M. & KACSER, H. (1990). Enzyme-enzyme interactions and control analysis 2. The case of nonindependence-heterologous associations. Eur. J. Biochem. 187, 493-500.
58. 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.
59. SAVAGEAU, M. A. (1976) Biochemical Systems Analysis. Reading, MA: Addison-Wesley.
60. SCHUSTER, S. & HEINRICH, R. (1992). The definitions of metabolic control analysis revisited. BioSystems 27, 1-15.
61. SCHUSTER, S., KAHN, D. & WESTERHOFF, H. V. (1993). Modular analysis of the control of complex metabolic pathways. Biophys. Chem. 48, 1-17.
62. SENN, H., LENDENMANN, U., SNOZZI, M., HAMER, G. & EGLI, T. (1994). The growth of Escherichia coli in glucose-limited chemostat cultures: A re-examination of the kinetics. Biochim. Biophys. Acta 1202, 424-436.
63. SIMPSON, T. W., COLON, G. E. & STEPHANOPOULOS, G. (1995). 2 Paradigms of Metabolic Engineering Applied to Amino-Acid Biosynthesis. Biochemical Society Transactions 23, 381-387.
64. SKATRUD, P. L., TIETZ, A. J., INGOLIA, T. D., CANTWELL, C. A., FISHER, D. L., CHAPMAN, J. L. & QUEENER, S. W. (1989). Use of recombinant DNA to improve production of cephalosporin C by Cephalosporium acremonium. Bio/Technology 7, 477-485.
65. SMALL, J. R. (1994). Design and analysis of chemostat experiments using Metabolic Control Analysis: A top-down approach. Microbiol. 140, 2439-2449.
66. SMALL, J. R. & FELL, D. A. (1990). Covalent modification and metabolic control analysis. Modification to the theorems and their application to metabolic systems containing covalently modifiable enzymes. Eur. J. Biochem. 191, 405-411.
67. SMALL, J. R. & KACSER, H. (1993). Responses of metabolic systems to large changes in enzyme activities and effectors. 1. The linear treatment of unbranched chains. Eur. J. Biochem. 213, 625-640.
68. SMALL, J. R. & KACSER, H. (1994). A method for increasing the concentration of a specific internal metabolite in steady-state systems. Eur. J. Biochem. 226, 649-657.
69. SNOEP, J. L., JENSEN, P. R., GROENEVELD, P., MOLENAAR, D., KHOLODENKO, B. N., & WESTERHOFF, H. V. (1994). How to determine control of growth rate in a chemostat using metabolic control analysis to resolve the paradox. Biochem. Mol. Biol. Inten. 33, 1023-1032.
70. STEMMER, W. P. C. (1994a). DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. USA 91, 10747-10751.
71. STEMMER, W. P. C. (1994b). Rapid evolution of a protein in vivo by DNA shuffling. Nature 370, 389-391.
72. STEPHANOPOULOS, G. & SINSKEY, A. J. (1993). Metabolic Engineering - Methodologies and Future-Prospects. Trends Biotechnology 11, 392-396.
73. STEPHANOPOULOS, G. & VALLINO, J. J. (1991). Network rigidity and metabolic engineering in metabolite overproduction. Science 252, 1675-1681.
74. VAN DAM, K., JANSEN, N., POSTMA, P., RICHARD, P., RUIJTER, G., RUTGERS, M. et al. (1993). Control and regulation of metabolic fluxes in microbes by substrates and enzymes. Antonie van Leeuwenhoek 63, 315-321.
75. WESTERHOFF, H. V. (1995). Subtlety in control - Metabolic pathway engineering. Trends Biotechnology 13, 242-244.
76. WESTERHOFF, H. V. & CHEN Y. (1984). How do enzyme activities control metabolite concentration? The resolution of a paradox using control theory and bacteriorhodopsin liposomes. Eur. J. Biochem. 142, 425-430.
77. WESTERHOFF, H. V. & KELL D. B. (1987). Matrix method for determining steps most rate-limiting to metabolic fluxes in biotechnological processes. Biotechnol. Bioengin. 30, 101-107.
78. WESTERHOFF, H. V. & KELL D. B. (1988). A control theoretical analysis of inhibitor titration assays of metabolic channelling. Comm. Molec. Cellul. Biophys. 5, 57-107.
79. WESTERHOFF, H. V., MELANDRI, B. A., VENTUROLI, G., AZZONE, G. F. & KELL, D. B. (1985). A minimal hypothesis for membrane-linked free-energy transduction: the role of independent, small coupling units. Biochim. Biophys. Acta 768, 257-292.
80. WESTERHOFF, H. V., SNOEP, J. L., SLUSE, F. E., WIJKER, J. E. & KHOLODENKO, B. N. (eds.) (1996). Bio Thermokinetics of the Living Cell, Amsterdam: BioThermokinetics Press.
81. WESTERHOFF, H. V. & VAN DAM, K. (1987) Thermodynamics and Control of Biological Free Energy Transduction. Amsterdam: Elsevier.
82. WESTERHOFF, H. V. & VAN WORKUM, M. (1990). Control of DNA structure and gene expression. Biomed. Biochim. Acta 49, 839-853.
83. WESTERHOFF, H. V., PLOMP, P. J. A. M., GROEN, A. K., WANDERS, R. J. A., BODE, J. A. & VAN DAM, K. (1987). On the origin of the limited control of mitochondrial respiration by the adenine nucleotide translocator. Arch. Biochem. Biophys. 257, 154-169.
84. WESTERHOFF, H. V., AON, M. A., VAN DAM, K., CORTASSA, S., KAHN, D. & VAN WORKUM, M. (1990). Dynamic and hierarchical coupling. Biochim. Biophys. Acta 1018, 142-146.
85. WESTERHOFF, H. V., VAN HEESWIJK, W., KAHN, D. & KELL, D. B. (1991). Quantitative approaches to the analysis of the control and regulation of microbial growth. Antonie van Leeuwenhoek 60, 193-207.
86. WESTERHOFF, H. V., HOFMEYR, J. H. S. & KHOLODENKO, B. N. (1994). Inverse control analysis: Getting to the inside using metabolic control analysis. Biophys. Chem. 50, 273-283.