Bistability, stochasticity, and oscillations in the mitogen-activated protein kinase cascade

Biophysical Journal

Volumn 90, Issue 6, 2006, Pages 1961-1978

  Wang, Xiao ^a   Hao, Nan ^b   Dohlman, Henrik G ^b   Elston, Timothy C ^b  

^a The University of North Carolina at Chapel Hill   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MITOGEN ACTIVATED PROTEIN KINASE; PHEROMONE; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; CELL ACTIVITY; CHEMICAL ANALYSIS; CONCENTRATION (PARAMETERS); ENZYME ACTIVATION; ENZYME REGULATION; FUNGAL STRAIN; GENETIC ANALYSIS; MATHEMATICAL MODEL; MOLECULAR STABILITY; NONHUMAN; OSCILLATION; PROTEIN EXPRESSION; PROTEIN STABILITY; SACCHAROMYCES CEREVISIAE; SIGNAL TRANSDUCTION; STOCHASTIC MODEL; TRANSCRIPTION INITIATION; VALIDATION STUDY; BIOLOGICAL MODEL; BIOLOGICAL RHYTHM; COMPUTER SIMULATION; DRUG EFFECT; GENE EXPRESSION REGULATION; METABOLISM; PHYSIOLOGY; STATISTICAL MODEL;

SACCHAROMYCES CEREVISIAE;

BIOLOGICAL CLOCKS; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; MAP KINASE SIGNALING SYSTEM; MODELS, BIOLOGICAL; MODELS, STATISTICAL; PHEROMONES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 33645979394     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.073874     Document Type: Article

References (33)

1. Dohlman, H. G., and J. W. Thorner. 2001. Regulation of G-protein-initiated signal transduction in yeast: paradigms and principles. Annu. Rev. Biochem. 70:703-754.
2. Wang, Y., and H. G. Dohlman. 2004. Pheromone signaling mechanisms in yeast: a prototypical sex machine. Science. 306:1508-1509.
3. Hume, D. A. 2000. Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression. Blood. 96:2323-2328.
4. Ferrell, J. E., Jr. 2002. Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr. Opin. Cell Biol. 14:140-148.
5. Kaern, M., T. C. Elston, W. J. Blake, and J. J. Collins. 2005. Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 6:451-464.
6. Tyson, J. J., K. C. Chen, and B. Novak. 2003. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell Biol. 15:221-231.
7. Markevich, N. I., J. B. Hoek, and B. N. Kholodenko. 2004. Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J. Cell Biol. 164:353-359.
8. Hicke, L. 1999. Gettin' down with ubiquitin: turning off cell-surface receptors, transporters and channels. Trends Cell Biol. 9:107-112.
9. Wang, Y., and H. G. Dohlman. 2002. Pheromone-dependent ubiquitination of the mitogen-activated protein kinase kinase Ste7. J. Biol. Chem. 277:15766-15772.
10. Esch, R. K., and B. Errede. 2002. Pheromone induction promotes Ste11 degradation through a MAPK feedback and ubiquitin-dependent mechanism. Proc. Natl. Acad. Sci. USA. 99:9160-9165.
11. Wang, Y., Q. Ge, D. Houston, J. Thorner, B. Errede, and H. G. Dohlman. 2003. Regulation of Ste7 ubiquitination by Ste11 phosphorylation and the Skp1-Cullin-F-box complex. J. Biol. Chem. 278:22284-22289.
12. Nelson, C., S. Goto, K. Lund, W. Hung, and I. Sadowski. 2003. Srb 10/Cdk8 regulates yeast filamentous growth by phosphorylating the transcription factor Ste12. Nature. 421:187-190.
13. Ferrell, J. E., Jr., and R. R. Bhatt. 1997. Mechanistic studies of the dual phosphorylation of mitogen-activated protein kinase. J. Biol. Chem. 272:19008-19016.
14. Gillespie, D. 1977. Exact stochastic simulation of coupled chemical reactions. J. Chem. Phys. 81:2340-2361.
15. Adalsteinsson, D., D. McMillen, and T. C. Elston. 2004. Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks. BMC Bioinformatics. 5:24.
16. Ermentrout, B. 2002. Simulating, Analyzing, and Animating Dynamical Systems: A Guide to XPPAUT for Researchers and Students. Society for Industrial and Applied Mathematics, Philadelphia, PA.
17. Zhao, Y., and Z. Y. Zhang. 2001. The mechanism of dephosphorylation of extracellular signal-regulated kinase 2 by mitogen-activated protein kinase phosphatase 3. J. Biol. Chem. 276:32382-32391.
18. Ghaemmaghami, S., W. K. Huh, K. Bower, R. W. Howson, A. Belle, N. Dephoure, E. K. O'Shea, and J. S. Weissman. 2003. Global analysis of protein expression in yeast. Nature. 425:737-741.
19. Hao, N., N. Yildirim, Y. Wang, T. C. Elston, and H. G. Dohlman. 2003. Regulators of G-protein signaling and transient activation of signaling: experimental and computational analysis reveals negative and positive feedback controls on G-protein activity. J. Biol. Chem. 278:46506-46515.
20. Siekhaus, D. E., and D. G. Drubin. 2003. Spontaneous receptor-independent heterotrimeric G-protein signalling in an RGS mutant. Nat. Cell Biol. 5:231-235.
21. Poritz, M. A., S. Malmstrom, M. K. Kim, P. J. Rossmeissl, and A. Kamb. 2001. Graded mode of transcriptional induction in yeast pheromone signalling revealed by single-cell analysis. Yeast. 18:1331-1338.
22. Bardwell, L., J. G. Cook, E. C. Chang, B. R. Cairns, and J. Thorner. 1996. Signaling in the yeast pheromone response pathway: specific and high-affinity interaction of the mitogen-activated protein (MAP) kinases Kss1 and Fus3 with the upstream MAP kinase kinase Ste7. Mol. Cell. Biol. 16:3637-3650.
23. Strogatz, S. H. 1994. Nonlinear Dynamics and Chaos: With Applications to Physics, Biology, Chemistry, and Engineering. Addison-Wesley, Reading, MA.
24. Dietzel, C., and J. Kurjan. 1987. Pheromonal regulation and sequence of the Saccharomyces cerevisiae SST2 gene: a model for desensitization to pheromone. Mol. Cell. Biol. 7:4169-4177.
25. Elion, E. A., B. Satterberg, and J. E. Kranz. 1993. FUS3 phosphorylates multiple components of the mating signal transduction cascade: evidence for STE12 and FAR1. Mol. Biol. Cell. 4:495-510.
26. Blake, W. J., M. Kaern, C. R. Cantor, and J. J. Collins. 2003. Noise in eukaryotic gene expression. Nature. 422:633-637.
27. Heinrich, R., B. G. Neel, and T. A. Rapoport. 2002. Mathematical models of protein kinase signal transduction. Mol. Cell. 9:957-970.
28. Huang, C. Y., and J. E. Ferrell, Jr. 1996. Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc. Natl. Acad. Sci. USA. 93:10078-10083.
29. Shvartsman, S. Y., M. P. Hagan, A. Yacoub, P. Dent, H. S. Wiley, and D. A. Lauffenburger. 2002. Autocrine loops with positive feedback enable context-dependent cell signaling. Am. J. Physiol. Cell Physiol. 282:C545-C559.
30. Bhalla, U. S., P. T. Ram, and R. Iyengar. 2002. MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science. 297:1018-1023.
31. Kholodenko, B. N. 2000. Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur. J. Biochem. 267:1583-1588.
32. Lewis, T. S., P. S. Shapiro, and N. G. Ahn. 1998. Signal transduction through MAP kinase cascades. Adv. Cancer Res. 74:49-139.
33. Yang, L., W. R. MacLellan, Z. Han, J. N. Weiss, and Z. Qu. 2004. Multisite phosphorylation and network dynamics of cyclin-dependent kinase signaling in the eukaryotic cell cycle. Biophys. J. 86:3432-3443.