Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in Candida albicans

Journal of Theoretical Biology

Volumn 258, Issue 1, 2009, Pages 71-88

  Sriram, K ^a   Soliman, Sylvain ^a   Fages, François ^a  

^a INRIA ROCQUENCOURT   (France)

Author keywords

Bifurcation analysis; Candida albicans; Interlocked positive feedback loop; Stochastic simulation

Indexed keywords

BIFURCATION; CELL ORGANELLE; CHROMOSOME; EUKARYOTE; FUNGUS; MUTATION; PATHOGEN; PHENOTYPE; SIMULATION;

ARTICLE; BIOLOGY; CANDIDA ALBICANS; CELL CYCLE; CELL DIVISION; CELL TYPE; CONTROLLED STUDY; DYNAMICS; EPIGENETICS; EUKARYOTE; FEEDBACK SYSTEM; GENE MUTATION; NONHUMAN; PHENOTYPE; POSITIVE FEEDBACK; PRIORITY JOURNAL; SIMULATION; STOCHASTIC MODEL; THYMUS; TRANSCRIPTION REGULATION;

CANDIDA ALBICANS; COMPUTER SIMULATION; EPIGENESIS, GENETIC; FEEDBACK, BIOCHEMICAL; GENE EXPRESSION REGULATION, FUNGAL; GENES, SWITCH; MODELS, GENETIC; STOCHASTIC PROCESSES;

CANDIDA ALBICANS; EUKARYOTA;

EID: 63549128842     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2009.01.008     Document Type: Article

References (54)

1. Becksei A., and Serrano L. Engineering stability in gene networks by autoregulation. Nature 405 (2000) 590-593
2. Becksei A., Seraphin B., and Serrano L. Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J. 20 (2001) 2528-2535
3. Brandman O., Ferrell Jr. J.E., Li R., and Meyer T. Interlinked fast and slow positive feedback loops drive reliable cell decisions. Science 310 (2005) 496-498
4. Bundshuh R., Hayot F., and Jayaprakash C. The role of dimerization in noise reduction of simple genetic networks. J. Theor. Biol. 220 (2003) 261-269
5. Cherry J.L., and Adler F.R. How to make a biological switch. J. Theor. Bio. 203 (2003) 117-133
6. Ciliberto A., Novak B., and Tyson J.J. Mathematical model of the morphogenesis check point in budding yeast. J. Cell. Bio. 163 (2003) 1243-1254
7. Edwards J.E., Lehrer R.I., Stiehm E.R., Fischer T.J., and Young L.S. Severe Candidal infections: clinical perspective, immune defense mechanisms, and current concepts of therapy. Ann. Inter. Med. 89 (1978) 91-106
8. Ermentrout, B., 1996. XPPAUT-4.0, The differential equation tool. Available from 〈http://www.pitt.edu/∼bard/xpp/xpp.html〉.
9. Fages F., and Soliman S. Formal cell biology in BIOCHEM. In: Bernardo M., Degano P., and Zavattaro G. (Eds). Formal Methods for Computational System Biology, Lecture Notes in Computer Science 5016 (2008), Springer, Berlin 54-80
10. Ferrell Jr. J.E. Self-Perpetuating states un signal transduction: positive feedback, double-negative feedback and bistability. Curr. Opi. Cell Bio. 6 (2002) 140-148
11. Ferrell Jr. J.E., and Machleder E.M. The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 280 (1998) 895-898
12. Ferrell Jr. J.E., and Xiong W. Bistability in cell signalling: how to make continuous process discontinuous, and reversible process irreversible. Chaos 11 (2001) 227-236
13. Freeman M. Feedback control of intercellular signalling development. Nature 408 (2000) 313-319
14. Gammaitoni L., Hanngi P., Jung P., and Marchesoni F. Stochastic resonance. Rev. Mod. Phys. 70 (1998) 223-287
15. Gardner T.S., Cantor C.R., and Collins J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 403 (2000) 339-342
16. Guckenheimer J., and Holmes P. Nonlinear Oscillations, Dynamical Systems and Bifurcation of Vector Fields (1983), Springer, Berlin p. 1983
17. Hayer A., and Bhalla U.S. Molecular switches at the synapse emerge from receptor and kinase traffic. PLoS Comput. Biol. 1 2 (2005) e20
18. Hornung, G., Barkai, N., 2007. Noise propagation and signal sensitivity in biological networks: a role for positive feedback loop, PLoS Comput. Biol., doi:10.1371/journal.pcbi.0040008.eor.
19. Huang G., Wang H., Chou S., Nie X., Chen J., and Liu H. Bistable expression of WOR1, a master regulator of white-opaque switching in Candida albicans. Proc. Nat. Acad. Sci. USA 103 (2006) 12813-12818
20. Iglesias P.A., and Levechenko A. Modeling the cell's guidance system. Sci. STKE RE12 148 (2002) 1-10
21. Kaern M., Elston T.C., Blake W.J., and Collins J.J. Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 6 (2005) 451-464
22. Keller A.D. Specifying Epigenetic states with autoregulatory transcription factors. J. Theor. Bio. 170 (1994) 175-181
23. Kim D., Kwon Y., and Cho K. Coupled positive and negative feedback circuits form an essential building block of cellular signalling pathways. BioEssays 29 (2006) 85-90
24. Kim T.H., Jung S.H., and Cho K.H. Interlinked mutual inhibitory positive feedbacks induce robust cellular memory effects. FEBS Lett. 581 (2007) 4899-4904
25. Kim J.R., Yoon Y., and Cho K.W. Coupled feedback loops form dynamic motifs of cellular networks. Biophysical Journal 94 2 (2008) 359-365
26. Kolotila M.P., and Diamond R.D. Effects of neutrophils and invitro oxidants on the survival and phenotypic switching of Candida albicans WO-1. Infect. Immun. 58 (1990) 1174-1179
27. Laurent M., and Kellershon N. Multistability: a major means of cellular differentiation and evolution in biological systems. Trends Biochem. Sci. 24 (1999) 418-422
28. Levine K., Tinkelenberg A.H., and Cross F. The CLN family: central regulators of cell cycle start in budding yeast. Prog. Cell Cycle 1 (1995) 101-104
29. Maamar H., and Dubnau D. Bistability in the Bacillus subtillis K-state (competence) system requires a positive feedback loop. Mol. Microbiol. 56 (2005) 604-615
30. Miller M.G., and Johnson A.D. White-opaque switching in Candida albicans is controlled by the mating-type locus homeodomain proteins and allows efficient mating. Cell 110 (2002) 293-302
31. Novak B., Tyson J.J., Gyoffry B., and Csikasz-Nagy A. Irreversible cell cycle transitions are due to system-level feedback. Nat. Cell Biol. 9 (2007) 7244-7728
32. Pomerening J.R., Kim S.Y., and Ferrell Jr. J.E. Systems-level dissection of the cell cycle oscillator: bypassing positive feedback produces damped oscillations. Cell 122 (2005) 565-578
33. Rao C.V., Wolf D.M., and Arkin A.P. Control, exploitation and tolerance of intracellular noise. Nature 420 (2002) 231-237
34. Rikkernik E.H., Magee B.B., and Magee P.T. Opaque-white phenotype transition: a programmed morphological transition in C. albicans. J. Bacteriol. 170 (1988) 895-899
35. Robinson D.S. Th-2 cytokines in allergic disease. Br. Med. Bull. 56 (2000) 956-968
36. Robinson D.S., and Lloyd C.M. Asthma: T-bet-a master controller. Curr. Biol. 12 (2002) R322-324
37. Slutsky B., Staebell M., Anderson J., Risen L., Pfaller M., and Soll D.R. "White-Opaque transition": a second high frequency switching system in C. albicans. J. Bacteriol. 169 (1987) 189-197
38. Smits W.K., Kuipers O.P., and Veenig J.W. Phenotypic variation in bacteria: the role of feedback regulation. Nat. Rev. Microbiol. 4 (2006) 259-271
39. Smolen P., Baxter D.A., and Byrne J.H. Modeling transcriptional control in gene networks-methods, recent results, and future directions. Bull. Math. Biol. 62 (2000) 247-292
40. Soll D.R., Lockhard S.R., and Zhao R. Relationship between switching and mating in Candida albicans. Eukaryot. Cell 2 (2003) 387-390
41. Solomon M.J. Hysteresis meet cell cycle. Proc. Nat. Acad. Sci. USA 100 (2003) 771-772
42. Soule C. Graphical requirements for multistationarity. ComplexUS 1 (2003) 122-133
43. Srikantha T., Borneman A.R., Daniels K.J., Pujol C., Wu W., Seringhaus M.R., Gerstein M., Yi S., and Soll D.R. TOS9 regulates white-opaque switching in Candida albicans. Eukaryot. Cell 5 (2006) 1674-1687
44. Swain P.S., Elowitz M.B., and Siggia E. Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl. Acad. Sci. USA 99 (2002) 12795-12800
45. Swat M., Kel A., and Herzel H. Bifurcation analysis of regulatory modules of the G1/S transition. Bioinformatics 1 (2003) 1-5
46. Thomas, R., 1981. On the relation between the logical structure of systems and their ability to generate multiple steady states or oscillations. In: Springer Series in Synergestics, vol. 9, pp. 180-193.
47. Thomas R. Laws for the dynamics of regulatory networks. Int. J. Dev. Biol. 42 (1998) 479-485
48. Tyson J.J., Chen K.C., and Novak B. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Opi. Cell Biol. 15 (2003) 221-231
49. Wang J., Zhang J., Yuan Z., and Zhou T. Noise induced switches in network systems of the genetic toggle switch. BMC Syst. Biol. 1 (2007) 50 doi:10.1186/1752-0509-1-50
50. Yates A., Callard R., and Stark J. Combining cytokine signalling with T-bet and GATA3 regulation in the Th1 and Th2 differentiation: a model for cellular decision making. J. Theor. Biol. 231 (2004) 181-196
51. Yi T.M., Huang Y., Simon M.I., and Doyle J. Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc. Natl. Acad. Sci. USA 97 (2000) 4649-4653
52. Zordan R.E., Galgoczy D.J., and Johnson A.D. Epigenetic properties of white to opaque switching in C. albicans are based on transcriptional feedback loops. Proc. Natl. Acad. Sci. USA 103 (2006) 12807-12812
53. Zordan R.E., Miller M.G., Galgoczy D.J., Tuch B.B., and Johnson A.D. Interlocking transcriptional feedback loops control white-opaque switching in Candida albicans. PLoS Comput. Bio. 5 (2007) 2166-2176
54. 〈http://partsregistry.org/Main_Page〉.