Principles behind the multifarious control of signal transduction: ERK phosphorylation and kinase/phosphatase control

FEBS Journal

Volumn 272, Issue 1, 2005, Pages 244-258

  Hornberg, Jorrit J ^a   Bruggeman, Frank J ^a   Binder, Bernd ^b   Geest, Christian R ^a   Bij De Vaate, A J Marjolein ^a   Lankelma, Jan ^a,c   Heinrich, Reinhart ^b   Westerhoff, Hans V ^a,d  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

^b HUMBOLDT UNIVERSITY   (Germany)

^c VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^d UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

Control analysis; Kinase; MAPK pathway; Phosphatase; Systems biology

Indexed keywords

MITOGEN ACTIVATED PROTEIN KINASE; PHOSPHATASE; PHOSPHOTRANSFERASE;

ANIMAL CELL; ARTICLE; CELL DIFFERENTIATION; CELL GROWTH; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME PHOSPHORYLATION; NONHUMAN; PRIORITY JOURNAL; RAT; SIGNAL TRANSDUCTION; VALIDATION PROCESS;

BLOTTING, WESTERN; MITOGEN-ACTIVATED PROTEIN KINASES; PHOSPHORIC MONOESTER HYDROLASES; PHOSPHORYLATION; SIGNAL TRANSDUCTION;

ANIMALIA;

EID: 11444260258     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1432-1033.2004.04404.x     Document Type: Article

References (47)

1. Widmann C, Gibson S, Jarpe MB & Johnson GL (1999) Mitogen-activated protein kinase: conservation of a three-kinase module from yeast to human. Physiol Rev 79, 143-180.
2. Cobb MH (1999) MAP kinase pathways. Prog Biophys Mol Biol 71, 479-500.
3. Sun H & Tonks NK (1994) The coordinated action of protein tyrosine phosphatases and kinases in cell signaling. Trends Biochem Sci 19, 480-485.
4. Hoshino R, Chatani Y, Yamori T, Tsuruo T, Oka H, Yoshida O, Shimada Y, Ari-i S, Wada H, Fujimoto J & Kohno M (1999) Constitutive activation of the 41-/43-kDa mitogen-activated protein kinase signaling pathway in human tumors. Oncogene 18, 813-822.
5. Bos JL (1989) ras Oncogenes in human cancer: a review. Cancer Res 49, 4682-4689.
6. Davies H, Bignell GR, Cox C, Stephens P, Edkins S, Clegg S, Teague J, Woffendin H, Garnett MJ, Bottomley W et al. (2002) Mutations of the BRAF gene in human cancer. Nature 417, 949-954.
7. Marshall CJ (1995) Specificity of receptor tyrosine kinase signaling: transient versus sustained extracellular signal-regulated kinase activation. Cell 80, 179-185.
8. Tombes RM, Auer KL, Mikkelsen R, Valerie K, Wymann MP, Marshall CJ, McMahon M & Dent P (1998) The mitogen-activated protein (MAP) kinase cascade can either stimulate or inhibit DNA synthesis in primary cultures of rat hepatocytes depending upon whether its activation is acute/phasic or chronic. Biochem J 330, 1451-1460.
9. Cook SJ, Aziz N & McMahon M (1999) The repertoire of fos and jun proteins expressed during the G1 phase of the cell cycle is determined by the duration of mitogen-activated protein kinase activation. Mol Cell Biol 19, 330-341.
10. Kahn D & Westerhoff HV (1991) Control theory of regulatory cascades. J Theo Biol 153, 255-285.
11. Bakker BM, Michels PA, Opperdoes FR & Westerhoff HV (1999) What controls glycolysis in bloodstream form Trypanosoma brucei? J Biol Chem 274, 14551-14559.
12. Bhalla US, Ram PT & Iyengar R (2002) MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 297, 1018-1023.
13. Kitano H (2002) Systems biology: a brief overview. Science 295, 1662-1664.
14. Huang CY & Ferrell JE Jr (1996) Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc Natl Acad Sci USA 93, 10078-10083.
15. Kholodenko BN, Demin OV, Moehren G & Hoek JB (1999) Quantification of short term signaling by the epidermal growth factor receptor. J Biol Chem 274, 30169-30181.
16. Bhalla US & Iyengar R (1999) Emergent properties of networks of biological signaling pathways. Science 283, 381-387.
17. Asthagiri AR & Lauffenburger DA (2001) A computational study of feedback effects on signal dynamics in a mitogen-activated protein kinase (MAPK) pathway model. Biotechnol Prog 17, 227-239.
18. Schoeberl B, Eichler-Jonsson C, Gilles ED & Muller G (2002) Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat Biotechnol 20, 370-375.
19. Lee E, Salic A, Kruger R, Heinrich R & Kirschner MW (2003) The roles of APC and axin derived from experimental and theoretical analysis of the Wnt pathway. PLoS Biology 1, e10.
20. Swameye I, Muller TG, Timmer J, Sandra O & Klingmuller U (2003) Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by data-based modeling. Proc Natl Acad Sci USA 100, 1028-1033.
21. Brown GC & Kholodenko BN (1999) Spatial gradients of cellular phospho-proteins. FEBS Lett 457, 452-454.
22. Heinrich R, Neel BG & Rapoport TA (2002) Mathematical models of protein kinase signal transduction. Mol Cell 9, 957-970.
23. Peletier MA, Westerhoff HV & Kholodenko BN (2003) Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law. J Theor Biol 225, 477-487.
24. van Zoelen EJ (1991) Phenotypic transformation of normal rat kidney cells: a model for studying cellular alterations in oncogenesis. Crit Rev Oncog 2, 311-333.
25. Pages G, Lenormand P, L'Allemain G, Chambard JC, Meloche S & Pouyssegur J (1993) Mitogen-activated protein kinases p42mapk and p44mapk are required for fibroblast proliferation. Proc Natl Acad Sci USA 90, 8319-8323.
26. Alessi DR, Cuenda A, Cohen P, Dudley DT & Saltiel AR (1995) PD098059 is a specific inhibitor of the activation of mitogen-activated protein kinase kinase in vitro and in vivo. J Biol Chem 270, 27489-27494.
27. Lahav G, Rosenfeld N, Sigal A, Geva-Zatorsky N, Levine AJ, Elowitz MB & Alon U (2004) Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat Genet 36, 147-150.
28. Burns JA, Cornish-Bowden A, Groen AK, Heinrich R, Kacser H, Porteous JW, Rapoport SM, Rapoport TA, Stucki JW, Tager JM et al (1985) Control analysis of metabolic systems, Trends in Biochem Sci 10, 16.
29. Westerhoff HV & Van Dam K (1987) Thermodynamics and Control of Biological Free-Energy Transduction. Elsevier, Amsterdam.
30. Fell DA (1992) Metabolic control analysis: a survey of its theoretical and experimental development. Biochem J 286, 313-330.
31. Heinrich R & Schuster S (1996) The Regulation of Cellular Systems. Chapman & Hall, New York.
32. Lahaye DH, Camps MG, Erp PE, Peters PH & Zoelen EJ (1998) Epidermal growth factor (EGF) receptor density controls mitogenic activation of normal rat kidney (NRK) cells by EGF. J Cell Physiol 174, 9-17.
33. Cascante M, Boros LG, Comin-Anduix B, de Atauri P, Centelles JJ & Lee PW (2002) Metabolic control analysis in drug discovery and disease. Nat Biotechnol 20, 243-249.
34. Kacser H & Burns JA (1973) The control of flux. Symp Soc Exp Biol 27, 65-104.
35. Fell DA (1997) Understanding the Control of Metabolism. Portland Press, London.
36. Heinrich R & Rapoport TA (1975) Mathematical analysis of multienzyme systems. II. Steady state and transient control. Biosystems 7, 130-136.
37. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D & Alon U (2002) Network motifs: simple building blocks of complex networks. Science 298, 824-827.
38. Shen-Orr SS, Milo R, Mangan S & Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31, 64-68.
39. Sebolt-Leopold JS (2000) Development of anticancer drugs targeting the MAP kinase pathway. Oncogene 19, 6594-6599.
40. Shawver LK, Slamon D & Ullrich A (2002) Smart drugs: Tyrosine kinase inhibitors in cancer therapy. Cancer Cell 1, 117-123.
41. Mendes P (1997) Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem Sci 22, 361-363.
42. Mendes P & Kell D (1998) Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14, 869-883.
43. Huyer G, Liu S, Kelly J, Moffat J, Payette P, Kennedy B, Tsaprailis G, Gresser MJ & Ramachandran C (1997) Mechanism of inhibition of protein-tyrosine phosphatases by vanadate and pervanadate. J Biol Chem 272, 843-851.
44. Acerenza L, Sauro HM & Kacser H (1989) Control analysis of time-dependent metabolic systems. J Theor Biol 137, 423-444.
45. Kholodenko BN, Demin OV & Westerhoff HV (1997) Control analysis of periodic phenomena in biological systems. J Physical Chem B. 101, 2070-2081.
46. Ingalls BP & Sauro HM (2003) Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories. J Theor Biol 222, 23-36.
47. Westerhoff HV & Chen YD (1984) How do enzyme activities control metabolite concentrations? An additional theorem in the theory of metabolic control. Eur J Biochem 142, 425-430.