Mathematical modeling of complex regulatory networks

IEEE Transactions on Nanobioscience

Volumn 3, Issue 3, 2004, Pages 172-179

  Stelling, Jörg ^a   Gilles, Ernst Dieter ^a  

^a MAX PLANCK INSTITUTE FOR DYNAMICS OF COMPLEX TECHNICAL SYSTEMS   (Germany)

Author keywords

Cell cycle regulation; Mathematical modeling; Regulatory networks; Systems biology

Indexed keywords

CELLS; CHROMOSOMES; DATA REDUCTION; DNA; GENETIC ENGINEERING; INFORMATION SCIENCE; MATHEMATICAL MODELS; PROTEINS;

CELL CYCLE REGULATIONS; CHROMATIDS; REGULATORY NETWORKS; SYSTEMS BIOLOGY;

NEURAL NETWORKS;

SACCHAROMYCES CEREVISIAE PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; BIOLOGICAL MODEL; CELL CYCLE; COMPARATIVE STUDY; COMPUTER SIMULATION; CYTOLOGY; EVALUATION; FEEDBACK SYSTEM; GENE EXPRESSION REGULATION; HOMEOSTASIS; MATHEMATICAL COMPUTING; METABOLISM; PHYSIOLOGY; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; STATISTICAL MODEL;

CELL CYCLE; COMPUTER SIMULATION; FEEDBACK; GENE EXPRESSION REGULATION; HOMEOSTASIS; MODELS, BIOLOGICAL; MODELS, STATISTICAL; NUMERICAL ANALYSIS, COMPUTER-ASSISTED; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SIGNAL TRANSDUCTION; TRANSCRIPTION FACTORS;

EID: 4544260212     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2004.833688     Document Type: Article

References (54)

1. H. Kitano, "Systems biology: A brief overview," Science, vol. 295, pp. 1662-1664, 2002.
2. D. Endy and R. Brent, "Modeling cellular behavior," Nature, vol. 409, pp. 391-395, 2001.
3. A. Gilman and A. Arkin, "Genetic "code": Representations and dynamical models of genetic components and networks," Annu. Rev. Genomics Hum. Genet., vol. 3, pp. 341-369, 2002.
4. U. Bhalla and R. Iyengar, "Emergent properties of networks of biological signaling pathways," Science, vol. 283, pp. 381-387, 1999.
5. B. Schoeberl, C. Eichler-Jonsson, E. Gilles, and G. Müller, "Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors," Nature Biotechnol., vol. 20, pp. 370-375, 2002.
6. R. Heinrich, B. Neel, and T. Rapoport, "Mathematical models of protein kinase signal transduction," Mol. Cell, vol. 9, pp. 957-970, 2002.
7. E. Lee, A. Salic, R. Kruger, R. Heinrich, and M. Kirschner, "The roles of APC and axin derived from experimental and theoretical analysis of the Wnt pathway," PLoS Biol., vol. 1, p. E10, 2003.
8. K. Chen, A. Csikasz-Nagy, B. Gyorffy, J. Val, B. Novak, and J. Tyson, "Kinetic analysis of a molecular model of the budding yeast cell cycle," Mol. Biol. Cell, vol. 11, pp. 369-391, 2000.
9. J. Hasty, D. McMillen, and J. Collins, "Computational studies of gene regulatory networks: In numero molecular biology," Nature Rev. Genet., vol. 2, pp. 268-279, 2001.
10. A. Goldbeter, "Computational approaches to cellular rhythms," Nature, vol. 420, pp. 238-245, 2002.
11. P. Spellman, G. Sherlock, M. Zhang, V. Iyer, K. Anders, M. Eisen, P. Brown, D. Botstein, and B. Futcher, "Comprehensive identification of cell-cycle regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization," Mol. Biol. Cell, vol. 9, pp. 3273-3297, 1998.
12. M. Miller and F. Cross, "Cyclin specificity: How many wheels do you need on a unicycle?," J. Cell Sci., vol. 114, pp. 1811-1820, 2001.
13. F. Cross, V. Archambault, M. Miller, and M. Klovstad, "Testing a mathematical model of the yeast cell cycle," Mol. Biol. Cell, vol. 13, pp. 52-70, 2002.
14. M. Mendenhall and A. Hodge, "Regulation of Cdc28 cyclin-dependent protein kinase activity during the cell cycle of the yeast Saccharomyces cerevisiae," Microbiol. Mol. Biol. Rev., vol. 62, no. 4, pp. 1191-1243, 1998.
15. L. Breeden, "Periodic transcription: A cycle within a cycle," Curr. Biol., vol. 13, pp. R31-R38, 2003.
16. A. Hershko, "Roles of ubiquitin-mediated proteolysis in cell cycle control," Curr. Opin. Cell Biol., vol. 9, pp. 788-799, 1997.
17. I. Simon, J. Barnett, N. Hannett, C. Harbison, N. Rinaldi, T. Volkert, J. Wyrick, J. Zeitlinger, D. Gifford, T. Jaakkola, and R. Young, "Serial regulation of transcriptional regulators in the yeast cell cycle," Cell, vol. 106, pp. 697-708, 2001.
18. D. Reynolds, B. Shi, C. McLean, F. Katsis, B. Kemp, and S. Dalton, "Recruitment of Thr-319 phosphorylated Ndd1p to the FHA domain of Fkh2p requires Clb kinase activity: A mechanism for CLB cluster gene activation," Genes Develop., vol. 17, pp. 1789-1802, 2003.
19. Z. Darieva, A. Pic-Taylor, J. Boros, A. Spanos, M. Geymonat, R. Reece, S. Sedgwick, A. Sharrocks, and B. Morgan, "Cell cycle-regulated transcription through the FHA domain of Fkh2p and the coactivator Ndd1p," Curr. Biol., vol. 13, pp. 1740-1745, 2003.
20. P. Jorgensen and M. Tyers, "The fork' ed path to mitosis," Genome Biol., vol. 1, no. 3, pp. 1022.1-1022.4, 2000.
21. M. Schwab, M. Neutzner, D. Mocker, and W. Seufert, "Yeast Hct1 recognizes the mitotic cyclin Clb2 and other substrates of the ubiquitin ligase APC," EMBO J., vol. 20, no. 18, pp. 5165-5175, 2001.
22. H. Yu, "Regulation of APC-Cdc20 by the spindle checkpoint," Curr. Opin. Cell Biol., vol. 14, pp. 706-714, 2002.
23. R. Feldman, C. Correll, K. Kaplan, and R. Deshaies, "A complex of Cdc4p, Skplp and Cdc53p/Cullin catalyzes ubiquitination of the phosphorylated CDK inhibitor Sic1p," Cell, vol. 91, pp. 221-230, 1997.
24. 1 arrested yeast cells to inhibit B-type cyclin accumulation and to prevent uncontrolled entry into S-phase," J. Cell Sci., vol. 110, no. 13, pp. 1523-1531, 1997.
25. SIC1," Mol. Cell. Biol., vol. 16, no. 10, pp. 5701-5707, 1996.
26. S. Elsasser, F. Lou, B. Wang, J. Campell, and A. Jong, "Interaction between yeast Cdc6 protein and B-type cyclin/Cdc28 kinases," Mol. Biol. Cell, vol. 7, pp. 1723-1735, 1996.
27. A. Calzada, M. Sancristán, E. Sánchez, and A. Bueno, "Cdc6 cooperates with Sic1 and Hct1 to inactivate mitotic cyclin-dependent kinases," Nature, vol. 412, pp. 355-358, 2001.
28. O. Cohen-Fix, J.-M. Kirschner, and D. Koshland, "Anaphase initiation in Saccharomyces cerevisiae is controlled by the APC-dependent degradation of the anaphase inhibitor Pds1p," Genes Develop., vol. 10, pp. 3081-3093, 1996.
29. F. Yeong, H. Lim, C. Padmashree, and U. Surana, "Exit from mitosis in budding yeast: Biphasic inactivation of the Cdc28-Clb2 mitotic kinase and the role of Cdc20," Mol. Cell, vol. 5, pp. 501-511, 2000.
30. M. Bäumer, G. Braus, and S. Irniger, "Two different modes of cyclin Clb2 proteolysis during mitosis in Saccharomyces cerevisiae" FEBS Lett., vol. 468, pp. 142-148, 2000.
31. R. Visintin, K. Craig, E. Hwang, S. Prinz, M. Tyers, and A. Amon, "The phosphatase Cdc14 triggers mitotic exit by reversal of Cdk-dependent phosphorylation," Mol. Cell, vol. 2, pp. 709-718, 1998.
32. S. Jaspersen, J. Charles, and D. Morgan, "Inhibitory phosphorylation of the APC regulator Hct1 is controlled by the kinase Cdc28 and the phosphatase Cdc14," Curr. Biol., vol. 9, pp. 227-236, 1999.
33. W. Shou, J. Seol, A. Shevchenko, C. Baskerville, D. Moazed, Z. Chen, J. Jang, A. Shevchenko, H. Charbonneau, and R. Deshaies, "Exit from mitosis is triggered by Tem 1-dependent release of the protein phosphatase Cdc14 from the nucleolar RENT complex," Cell, vol. 97, pp. 233-244, 1999.
34. E. Traverse, C. Baskerville, H. Liu, W. Shou, P. James, R. Deshaies, and H. Charbonneau, "Characterization of the Netl cell-cycle dependent regulator of the Cdc14 phosphatase from budding yeast," J. Biol. Chem., vol. 276, no. 24, pp. 21924-21931, 2001.
35. D. McCollum and K. Gould, "Timing is everything: Regulation of mitotic exit and cytokinesis by the MEN and SIN," Trends Cell Biol., vol. 11, no. 2, pp. 89-95, 2001.
36. M. Geymonat, S. Jensen, and L. Johnston, "Mitotic exit: The Cdc14 double cross," Curr. Biol., vol. 12, pp. R482-R484, 2002.
37. D. Lauffenburger, "Cell signaling pathways as control modules: Complexity for simplicity?," Proc. Nat. Acad. Sci., vol. 97, no. 10, pp. 5031-5033, 2000.
38. E. Ravasz, A. Somera, D. Mongru, Z. Oltvai, and A.-L. Barabási, "Hierarchical organization of modularity in metabolic networks," Science, vol. 297, pp. 1551-1555, 2002.
39. A. Kremling, K. Jahreis, J. Lengeler, and E. Gilles, "The organization of metabolic reaction networks: A signal-oriented approach to cellular models," Metabolic Eng., vol. 2, no. 3, pp. 190-200, 2000.
40. A. Kremling and E. Gilles, "The organization of metabolic reaction networks: II. Signal processing in hierarchical structured functional units," Metabolic Eng., vol. 3, no. 2, pp. 138-150, 2001.
41. J. Stelling, A. Kremling, M. Ginkel, K. Bettenbrock, and E. Gilles, "Toward a virtual biological laboratory," in Foundations of Systems Biology, H. Kitano, Ed. Cambridge, MA: MIT Press, 2001, pp. 189-212.
42. M. Ginkel, A. Kremling, T. Nutsch, R. Rehner, and E. Gilles, "Modular modeling of cellular systems with ProMoT/Diva," Bioinformatics, vol. 19, pp. 1169-1176, 2003.
43. H. Kitano, "A graphical notation for biochemical networks," BioSilico, vol. 1, pp. 169-176, 2003.
44. R. Heinrich and S. Schuster, The Regulation of Cellular Systems. New York: Chapman & Hall, 1996.
45. B. Shapiro, A. Levchenko, and E. Mjolsness, "Automatic model generation for signal transduction with applications to MAP-kinase pathways," in Proc. 1st Int. Conf. Systems Biology, 2000, pp. 64-74.
46. B. Futcher, G. Latter, P. Monardo, C. McLaughlin, and J. Garrels, "A sampling of the yeast proteome," Mol. Cell. Biol., vol. 19, no. 11, pp. 7357-7368, 1999.
47. F. Holstege, E. Jennings, J. Wyrick, T. Lee, C. Hengartner, M. Green, T. Golub, E. Lander, and R. Young, "Dissecting the regulatory circuitry of a eukaryotic genome," Cell, vol. 95, pp. 717-728, 1998.
48. J. Stelling and E. Gilles et al., "Robustness vs. identiflabilily of regulatory modules? The case of mitotic control in budding yeast cell cycle regulation," in Proc. 2nd Int. Conf. Systems Biology, T. Yi et al., Eds., 2001, pp. 181-190.
49. D. Fesquet, P. Fitzpatrick, A. Johnson, K. Kramer, and K. Johnston, "A Bub2p-dependent spindle checkpoint pathway regulates the Dbf2p kinase in budding yeast," EMBO J., vol. 18, no. 9, pp. 2424-2434, 1999.
50. U. Surana, A. Amon, C. Dowzer, J. McGrew, B. Byers, and K. Nasmyth, "Destruction of the CDC28/CLB mitotic kinase is not required for the metaphase to anaphase transition in budding yeast," EMBO J., vol. 12, no. 5, pp. 1969-1978, 1993.
51. F. Yeong, J. Lim, Y. Wang, and U. Surana, "Early expressed Clb proteins allow accumulation of mitotic cyclin by inactivating proteolytic machinery during S phase," Mol. Cell. Biol., vol.21, no. 15, pp. 5071-5081, 2001.
52. G. Alexandra, W. Zachariae, A. Schleiffer, and K. Nasmyth, "Sister chromatid separation and chromosome re-duplication are regulated by different mechanisms in response to spindle damage," EMBO J., vol. 18, no. 10, pp. 2707-2721, 1999.
53. S. Ghaemmaghami, W.-K. Huh, K. Bower, R. Howson, A. Belle, N. Dephoure, E. O'Shea, and J. Weissman, "Global analysis of protein expression in yeast," Nature, vol. 425, pp. 737-741, 2003.
54. J. Hood, W. Hwang, and P. Silver, "The Saccharmoyces cerevisiae cyclin Clb2p is targeted to multiple subcellular locations by cis- and trans-ecting determinants," J. Cell Sci., vol. 114, pp. 589-597, 2001.