Skip to main content
SpringerLink
Log in

Subtleties in control by metabolic channelling and enzyme organization

  • Published:
Molecular and Cellular Biochemistry Aims and scope Submit manuscript

Abstract

Because of its importance to cell function, the free-energy metabolism of the living cell is subtly and homeostatically controlled. Metabolic control analysis enables a quantitative determination of what controls the relevant fluxes. However, the original metabolic control analysis was developed for idealized metabolic systems, which were assumed to lack enzyme-enzyme association and direct metabolite transfer between enzymes (channelling). We here review the recently developed molecular control analysis, which makes it possible to study non-ideal (channelled, organized) systems quantitatively in terms of what controls the fluxes, concentrations, and transit times. We show that in real, non-ideal pathways, the central control laws, such as the summation theorem for flux control, are richer than in ideal systems: the sum of the control of the enzymes participating in a non-ideal pathway may well exceed one (the number expected in the ideal pathways), but may also drop to values below one. Precise expressions indicate how total control is determined by non-ideal phenomena such as ternary complex formation (two enzymes, one metabolite), and enzyme sequestration. The bacterial phosphotransferase system (PTS), which catalyses the uptake and concomitant phosphorylation of glucose (and also regulates catabolite repression) is analyzed as an experimental example of a non-ideal pathway. Here, the phosphoryl group is channelled between enzymes, which could increase the sum of the enzyme control coefficients to two, whereas the formation of ternary complexes could decrease the sum of the enzyme control coefficients to below one. Experimental studies have recently confirmed this identification, as well as theoretically predicted values for the total control. Macromolecular crowding was shown to be a major candidate for the factor that modulates the non-ideal behaviour of the PTS pathway and the sum of the enzyme control coefficients.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Ovadi J, Srere PA: Channel your energies. Trends Biochem Sci 17: 445–447, 1992

    Google Scholar 

  2. Welch GR, Easterby JS: Metabolic channelling versus free diffusion: Transition time analysis. Trends Biochem Sci 19: 193–197, 1994

    Google Scholar 

  3. Ovadi J: Physiological significance of metabolite channelling. J Theor Biol 152: 1–22, 1991

    Google Scholar 

  4. Keizer J, Smolen P: Mechanisms of metabolite transfer between enzymes: diffusional versus direct transfer. Curr Top Cell Regul 33: 391–405, 1992

    Google Scholar 

  5. Westerhoff HV, Welch GR: Enzyme organization and the direction of metabolic flow: Physicochemical considerations. Curr Top Cell Regul 33: 361–390, 1992

    Google Scholar 

  6. Kell DB, Westerhoff HV: Catalytic facilitation and membrane bioenergetics. In: GR Welch (ed). Organized Multienzyme Systems. Academic Press, New York, 1985, pp 63–138

    Google Scholar 

  7. Minton AP: A molecular model for the dependence of the osmotic pressure of bovine serum albumin upon concentration and pH. Biophys Chem 57: 65–70, 1995

    Google Scholar 

  8. Garner M: The consequences of macromolecular crowding for metabolic channelling. In: L Agius, HSA Sherratt (eds). Channelling in Intermediary Metabolism. Portland Press, London, 1997, pp 41–52

    Google Scholar 

  9. Kholodenko BN, Westerhoff HV: The macroworld versus the microworld of biochemical regulation and control. Trends Biochem Sci 20: 52–54, 1995

    Google Scholar 

  10. Easterby JS: Pathway dynamics and the analysis of metabolite channelling. In: L Agius, HSA Sherratt (eds). Channelling in Intermediary Metabolism. Portland Press, London, 1997, pp 71–90

    Google Scholar 

  11. Kacser H, Burns JA: The control of flux. In: DD Davies (ed). Rate Control of Biological Processes. Cambridge University Press, London, 1973, pp 65–104

    Google Scholar 

  12. Heinrich R, Rapoport TA: A linear steady-state treatment of enzymatic chains. General properties, control and effector strength. Eur J Biochem 42: 89–95, 1974

    Google Scholar 

  13. Kholodenko BN, Molenaar D, Schuster S, Heinrich R, Westerhoff HV: Defining control coefficients in non-ideal metabolic pathways. Biophys Chem 56: 215–226, 1995

    Google Scholar 

  14. Westerhoff HV, Arents JC: Two completely rate-limiting steps in one metabolic pathway? The resolution of a paradox using control theory and bacteriorhodopsin liposomes. Biosci Rep 4: 23–31, 1984

    Google Scholar 

  15. Jensen PR, Michelsen O, Westerhoff HV: Control analysis of the dependence of E. coli physiology on the H+-ATPase. Proc Natl Acad Sci USA 90: 8068–8072, 1993

    Google Scholar 

  16. Cornish-Bowden A: Fundamentals of Enzyme Kinetics. Portland Press, London, 1995

    Google Scholar 

  17. Fell DA, Sauro HM: Metabolic control analysis. The effects of high enzyme concentrations. Eur J Biochem 192: 183–187, 1990

    Google Scholar 

  18. Kacser H, Sauro HM, Acerenza L: Enzyme-enzyme interactions and control analysis. 1. The case of non-additivity: Monomer-oligomer associations. Eur J Biochem 187: 481–491, 1990

    Google Scholar 

  19. Sauro HM, Kacser H: Enzyme-enzyme interactions and control analysis. 2. The case of non-independence: Heterologous associations. Eur J Biochem 187: 493–500, 1990

    Google Scholar 

  20. Kholodenko BN, Lyubarev AK, Kurganov BI: Control of metabolic flux in a system with high enzyme concentrations and moietyconserved cycles. The sum of the flux control coefficients can drop significantly below unity. Eur J Biochem 210: 147–153, 1992

    Google Scholar 

  21. Kholodenko BN, Westerhoff HV: Metabolic channelling and control of the flux. FEBS Lett 320: 71–74, 1993

    Google Scholar 

  22. Kholodenko BN, Cascante M, Westerhoff HV: Control and regulation of channelled versus ideal pathways. In: L Agius, HSA Sherratt (eds). Channelling in Intermediary Metabolism. Portland Press, London, 1997, pp 91–114

    Google Scholar 

  23. Kholodenko BN, Sauro HM, Westerhoff HV: Control by enzymes, coenzymes and conserved moieties: A generalization of the connectivity theorem of metabolic control analysis. Eur J Biochem 225: 179–186, 1994

    Google Scholar 

  24. Sauro HM: Moiety-conserved cycles and metabolic control analysis: Problems in sequestration and metabolic channelling. BioSystems 33: 55–67, 1994

    Google Scholar 

  25. Cori CF, Velick SF, Cori GT: Combination of diphosphopyridine nucleotide with glyceraldehyde phosphate debydrogenase. Biochim Biophys Acta 4: 160–169, 1950

    Google Scholar 

  26. Friedrich P: Dynamic compartmentation in soluble enzyme systems. Acta Biochim Biophys Acad Sci Hung 9: 159–173, 1974

    Google Scholar 

  27. Srivastava DK, Bernhard SA: Biophysical chemistry of metabolic reaction sequences in concentrated enzyme solution and in the cell. Annu Rev Biophys Biophys Chem 16: 175–204, 1987

    Google Scholar 

  28. Ushiroyama T, Fukushima T, Styre JD, Spivey HO: Substrate channelling of NADH in mitochondrial redox processes. Curr Top Cell Regul 33: 291–307, 1992

    Google Scholar 

  29. Kholodenko BN, Demin OV, Westerhoff HV: Channelled pathways can be more sensitive to specific regulatory signals. FEBS Lett 320: 75–78, 1993

    Google Scholar 

  30. Kholodenko BN, Cascante M, Westerhoff HV: Dramatic changes in control properties that accompany channelling and metabolite sequestration. FEBS Lett 336: 381–384, 1993

    Google Scholar 

  31. Kholodenko BN, Westerhoff HV, Puigjaner J, Cascante M: Control in channelled pathways. A matrix method calculating the enzyme control coefficients. Biophys Chem 53: 247–258, 1995

    Google Scholar 

  32. Kholodenko BN, Westerhoff HV, Brown GC: Rate limitation within a single enzyme is directly related to enzyme intermediate levels. FEBS Lett 349: 131–134, 1994

    Google Scholar 

  33. Brown GC, Westerhoff HV, Kholodenko BN: Molecular control analysis. Control within proteins and molecular processes. J Theor Biol 182: 389–396, 1996

    Google Scholar 

  34. Brown GC, Cooper CE: Control analysis applied to single enzymes: Can an isolated enzyme have a unique rate-limiting step? Biochem J 294: 87–94, 1993

    Google Scholar 

  35. Kholodenko BN, Westerhoff HV: Control theory of one enzyme. Biochim Biophys Acta 1208: 294–305, 1994

    Google Scholar 

  36. Van Dam K, Van der Vlag J, Kholodenko BN, Westerhoff HV: The sum of the flux control coefficients of all enzymes on the flux through a group-transfer pathway can be as high as two. Eur J Biochem 212: 791–799, 1993

    Google Scholar 

  37. Kholodenko BN, Westerhoff HV: Control theory of group-transfer pathways. Biochim Biophys Acta 1229: 256–274, 1995

    Google Scholar 

  38. Kholodenko BN, Westerhoff HV: How to reveal various aspects of regulation in group-transfer pathways. Biochim Biophys Acta 1229: 275–289, 1995

    Google Scholar 

  39. Westerhoff HV, Van Dam K: Thermodynamics and Control of Biological Free Energy Transduction. Elsevier, Amsterdam, 1987

    Google Scholar 

  40. Kholodenko BN: Control of molecular transformations in multienzyme systems: quantitative theory of metabolic regulation. Mol Biol (USSR) 22: 1238–1256, 1988. Engl transl 22: 990–1005, 1989

    Google Scholar 

  41. Giersch C: Control analysis of metabolic networks. Homogeneous functions and the summation theorems for control coefficients. Eur J Biochem 174: 509–513, 1988

    Google Scholar 

  42. Kholodenko BN: Modern Theory of Metabolic Control. Viniti Press, Moscow (in Russian), 1991

    Google Scholar 

  43. Garner MM, Burg MB: Macromolecular crowding and confinement in cells exposed to hypertonicity. Am J Physiol 266: C877–C892, 1994

    Google Scholar 

  44. Adair G: A theory of partial osmotic pressure and membrane equilibria with special reference to application of Dalton's Law to hemoglobine solutions in the presence of salts. Proc R Soc Lond A120: 573–603, 1928

    Google Scholar 

  45. Brand MD, Vallis, BPS, Kesseler A: The sum of the flux control coefficients in the electron-transport chain of mitochondria. Eur J Biochem 226: 819–829, 1994

    Google Scholar 

  46. Kholodenko BN, Westerhoff HV, Cascante M: Channelling and the concentration of bulk phase intermediates as cytosolic proteins get more concentrated. Biochem J 313: 921–926, 1996

    Google Scholar 

  47. Mendes P, Kell DB, Westerhoff HV: Channelling can decrease pool size. Eur J Biochem 204: 257–266, 1992

    Google Scholar 

  48. Mendes P, Kell DB, Westerhoff HV: Why and when channelling can decrease pool size at constant net flux in a simple dynamic channel. Biochim Biophys Acta 1289: 175–186, 1996

    Google Scholar 

  49. Easterby JS: A generalized theory of the transition time for sequential enzyme reactions. Biochem J 199: 155–161, 1981

    Google Scholar 

  50. Melendez-Hevia E, Torres NV, Sicilia J, Kacser H: Control analysis of transition times in metabolic systems. Biochem J 265: 195–202, 1990.

    Google Scholar 

  51. Easterby JS: Temporal analysis of the transition between steady states. In: A Cornish-Bowden and ML Cardenas (eds). Control of Metabolic Processes. Plenum Press, New York, 1990, pp 281–290

    Google Scholar 

  52. Cascante M, Melendez-Hevia E, Kholodenko BN, Sicilia J, Kacser H: Control analysis of transit time for free and enzyme-bound metabolites. Biochem J 308: 895–899, 1995

    Google Scholar 

  53. Kholodenko BN, Cascante M, Westerhoff HV: (1995b) Control theory of metabolic channelling. Mol Cell Biochem 143: 151–168, 1995

    Google Scholar 

  54. Snoep JL, Yomana LP, Westerhoff HV, Ingram LO: Protein burden in Zymomonas mobilis: Negative flux and growth control due to overproduction of glycolytic enzymes. Microbiology 141: 2329–2337, 1995

    Google Scholar 

  55. Rohwer JM: Interaction of functional units of metabolism. Control and regulation of the bacterial phoshoenolpyruvate-dependent phosphotransferase system. Ph.D. thesis, University of Amsterdam, 1997

Download references

Author information

Authors and Affiliations

  1. A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119899, Moscow, Russia

    Boris N. Kholodenko

  2. Departmento de Bioquímica i Biología Molecular, Universitat de Barcelona, Martí i Franquès 1, E-08028, Barcelona, Spain

    Boris N. Kholodenko & Marta Cascante

  3. E.C. Slater Institute, BioCentrum, University of Amsterdam, Plantage Muidergracht 12, NL-1018 TV, Amsterdam, The Netherlands

    Johann M. Rohwer & Hans V. Westerhoff

  4. Department of Microbial Physiology, BioCentrum, Faculty of Biology, Free University, De Boelelaan 1087, NL-1081 HV, Amsterdam, The Netherlands

    Hans V. Westerhoff

Authors
  1. Boris N. Kholodenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Johann M. Rohwer
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Marta Cascante
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Hans V. Westerhoff
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kholodenko, B.N., Rohwer, J.M., Cascante, M. et al. Subtleties in control by metabolic channelling and enzyme organization. Mol Cell Biochem 184, 311–320 (1998). https://doi.org/10.1023/A:1006809028612

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1006809028612

Search

Navigation