Potential and flux landscapes quantify the stability and robustness of budding yeast cell cycle network

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 18, 2010, Pages 8195-8200

  Wang, Jin ^a,b   Li, Chunhe ^a,c   Wang, Erkang ^a  

^a CHANGCHUN INSTITUTE OF APPLIED CHEMISTRY   (China)

^b STONY BROOK UNIVERSITY   (United States)

^c UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

Barrier height; Entropy production and dissipation; Global stability; Oscillation; Sensitivity

Indexed keywords

ARTICLE; CELL BUDDING; CELL CYCLE; CELL CYCLE PHASE; MITOSIS; NONHUMAN; OSCILLATION; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; TOPOGRAPHY; YEAST CELL;

CELL CYCLE; CELL CYCLE PROTEINS; DIFFUSION; ENTROPY; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCETALES;

EID: 77952334362     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0910331107     Document Type: Article

References (35)

1. Swain PS, Elowitz MB, Siggia ED (2002) Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci USA 99:12795-12800.
2. Thattai M, Oudenaarden A (2001) Intrinsic noise in gene regulatory networks. Proc Natl Acad Sci USA 98:8614-8619. (Pubitemid 32678076)
3. Davidson EH, et al. (2002) A genomic regulatory network for development. Science 295:1669-1678.
4. Huang CY, Ferrell JE (1996) Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc Natl Acad Sci USA 93:10078-10082.
5. Hu G (1994) Stochastic Forces and Nonlinear Systems, ed BL Hao (Shanghai Scientific and Technological Education Press, Shanghai), pp 68-74.
6. Hatano T, Sasa S (2001) Steady state themodynamics of langevin systems. Phys Rev Lett 86:3463-3466.
7. Sasai M, Wolynes PG (2003) Stochastic gene expression as a many-body problem. Proc Natl Acad Sci USA 100:2374-2379. (Pubitemid 36297506)
8. Ao P (2004) Potential in stochastic differential equations: Novel construction. J Phys A Math Gen 37:L25-L30. (Pubitemid 38148924)
9. Hornos JEM, et al. (2005) Self-regulating gene: An exact solution. Phys Rev E 72:051907.
10. Qian H, Reluga TC (2005) Nonequilibrium thermodynamics and nonlinear kinetics in a cellular signaling switch. Phys Rev Lett 94:028101. (Pubitemid 40620187)
11. Han B, Wang J (2007) Quantifying robustness and dissipation cost of yeast cell cycle network: The funneled energy landscape perspectives. Biophys J 92:3755-3763. (Pubitemid 46910564)
12. Kim K, Wang J (2007) Potential energy landscape and robustness of a gene regulatory network: Toggle switch. PLOS Comput Biol 3:0565-0577. (Pubitemid 46535748)
13. Lapidus S, Han B, Wang J (2008) Intrinsic noise, dissipation cost, and robustness of cellular networks: The underlying energy landscape of MAPK signal transduction. Proc Natl Acad Sci USA 105:6039-6044. (Pubitemid 351758395)
14. Wang J, Xu L, Wang EK (2008) Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation and coherence of biochemical oscillations. Proc Natl Acad Sci USA 105:12271-12276.
15. Prost J, Joanny JF, Parrondo JMR (2009) Generalized fluctuation- dissipation theorem for steady-state systems. Phys Rev Lett 103:090601.
16. Novak B, et al. (1998) Mathematical model of the fission yeast cell cycle with checkpoint controls at the G1/S, G2/M and metaphase/anaphase transitions. Biophys Chem 72:185-200.
17. Tyson JJ, Novak B (2001) Regulation of the eukaryotic cell cycle: Molecular antagonism, hysteresis, and irreversible transitions. J Theor Biol 210:249-263.
18. Kar S, Baumann WT, Paul MR, Tyson JJ (2009) Exploring the roles of noise in the eukaryotic cell cycle. Proc Natl Acad Sci USA 106:6471-6476.
19. Chen KC, et al. (2000) Kinetic analysis of a molecular model of the budding yeast cell cycle. Mol Biol Cell 11:369-391.
20. Chen KC, et al. (2004) Integrative analysis of cell cycle control in budding yeast. Mol Biol Cell 15:3841-3862. (Pubitemid 38989719)
21. Battogtokh D, Tyson JJ (2004) Bifurcation analysis of a model of the budding yeast cell cycle. Chaos 14:653-661. (Pubitemid 39443298)
22. Csikasz-Nagy A, et al. (2006) Analysis of a generic model of eukaryotic cell cycle regulation. Biophys J 90:4361-4379. (Pubitemid 43830884)
23. Tyson JJ, Novak B (2008) Temporal organization of the cell cycle. Curr Biol 18: R759-R768.
24. Qian H (2001) Mesoscopic nonequilibrium thermodynamics of single macromolecules and dynamic entropy-energy compensation. Phys Rev E 65:016102.
25. Yoda M, Ushikubo T, Inoue W, Sasai M (2007) Roles of noise in single and coupled multiple genetic oscillators. J Chem Phys 126:115101-115111. (Pubitemid 46516377)
26. Skotheim JM, Di Talia S, Siggia ED, Cross FR (2008) Positive feedback of G1 cyclins ensures coherent cell cycle entry. Nature 454:291-296. (Pubitemid 352009994)
27. Di Talia S, Skotheim JM, Bean JM, Siggia ED, Cross FR (2007) The effects of molecular noise and size control on variability in the budding yeast cell cycle. Nature 448:947-951.
28. Tyers M, Tokiwa G, Futcher B (1993) Comparison of the Saccharomyces cerevisiae G1 cyclins: Cln3 may be an upstream activator of Cln1, Cln2 and other cyclins. EMBO J 12:1955-1968.
29. Wijnen H, Landman A, Futcher B (2002) The G(1) cyclin Cln3 promotes cell cycle entry via the transcription factor Swi6. Mol Cell Biol 22:4402-4418. (Pubitemid 34556607)
30. Dirick L, Bohm T, Nasmyth K (1995) Roles and regulation of Cln/Cdc28 kinases at the start of the cell cycle of Saccharomyces cerevisiae. EMBO J 14:4803-4813.
31. Surana U, et al. (1991) The role of CDC28 and cyclins during mitosis in the budding yeast S. cerevisiae. Cell 65:145-161. (Pubitemid 121001222)
32. Lim HH, Goh PY, Surana U (1998) Cdc20 is essential for the cyclosome-mediated proteolysis of both Pds1 and Clb2 during M phase in budding yeast. Curr Biol 8:231-234.
33. Tsai TY, et al. (2008) Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science 321:126-129.
34. Santos SD, Ferrell JE, Jr (2008) On the cell cycle and its switches. Nature 454:288-289.
35. Van Kampen NG (1992) Stochastic Processes in Physics and Chemistry (North-Holland, Amsterdam), pp 120-127.