Structural bistability of the GAL regulatory network and characterization of its domains of attraction

Journal of Computational Biology

Volumn 19, Issue 2, 2012, Pages 148-162

  Cosentino, Carlo ^a   Salerno, Luca ^a   Passanti, Antonio ^a   Merola, Alessio ^a   Bates, Declan G ^b   Amato, Francesco ^a  

^a UNIVERSITY MAGNA GRAECIA OF CATANZARO   (Italy)

^b UNIVERSITY OF EXETER   (United Kingdom)

Author keywords

bistability; chemical reaction network theory (CRNT); domains of attraction (DA); GAL regulatory network

Indexed keywords

GALACTOSE; SACCHAROMYCES CEREVISIAE PROTEIN;

ALGORITHM; BIOLOGICAL MODEL; COMPUTER SIMULATION; CONFERENCE PAPER; FEEDBACK SYSTEM; GENE EXPRESSION REGULATION; GENETICS; KINETICS; METABOLISM; SACCHAROMYCES CEREVISIAE;

ALGORITHMS; COMPUTER SIMULATION; FEEDBACK; GALACTOSE; GENE EXPRESSION REGULATION, FUNGAL; KINETICS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS;

SACCHAROMYCES CEREVISIAE;

EID: 84856732719     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0251     Document Type: Conference Paper

References (32)

1. Acar, M., Becskei, A., and van Oudenaarden, A. 2005. Enhancement of cellular memory by reducing stochastic transitions. Nature 435, 228-232. (Pubitemid 40685951)
2. Amato, F. 2006. Robust Control of Linear Systems Subject to Uncertain Time-Varying Parameters. Springer Verlag, Berlin.
3. Amato, F., Cosentino, C., and Merola, A. 2007. On the region of attraction of nonlinear quadratic systems. Automatica 43, 2119-2123. (Pubitemid 350137266)
4. Angeli, D., Ferrel, J.E., and Sontag, E.D. 2004. Detection of multistability, bifurcation, and hysteresis in a large class of biological positive-feedback systems. Proc. Natl. Acad. Sci. USA 101, 1822-1827. (Pubitemid 38228975)
5. Bagowski, C.P., and Ferrell, J.E. 2001. Bistability in the JNK cascade. Curr. Biol. 11, 1176-1182. (Pubitemid 32722570)
6. Balázsi, G., Van Oudernaarden, A., and Collins, J.J. 2011. Cellular decision making and biological noise: from microbes to mammals. Cell 144, 910-925.
7. Bhat, P.J. 2008. Galactose Regulon of Yeast: From Genetics to Systems Biology. Springer-Verlag, Berlin.
8. Boyd, S.P., El Ghaoui, L., Feron, E., et al. 1994. Linear Matrix Inequalities in System and Control Theory. SIAM Press, Philadelphia.
9. Chickarmane, V., Troein, C., Nuber, U.A., et al. 2006. Transcriptional dynamics of the embryonic stem cell switch. PLoS Comput. Biol. 2, e123.
10. Cosentino, C., and Bates, D.G. 2011. Feedback Control in Systems Biology. CRC Press, Boca Raton, FL.
11. Craciun, G., and Feinberg, M. 2005. Multiple equilibria in complex chemical reaction networks. I. The injectivity property. SIAM J. Appl. Math. 65, 1526-1546. (Pubitemid 41639786)
12. de Atauri P., Orrell D., Ramsey S., et al. 2004. Evolution of design principles in biochemical networks. IEEE Proc. Syst. Biol. 1, 28-40.
13. Ellison, P. 1998. The advanced deficiency algorithm and its applications to mechanism discrimination [Ph.D. dissertation]. University of Rochester, Rochester, NY.
14. Feinberg, M. 1988. Chemical reaction network structure and the stabiliyt of complex isothermal reactors. II. Multiple steady states for network of deficiency one. Chem. Eng. Sci. 43, 1-25. (Pubitemid 18549697)
15. Feinberg, M. 1987. Chemical reaction network structure and the stability of complex isothermal reactors. I. The deficiency zero and deficiency one theorems. Chem. Eng. Sci. 42, 2229-2268. (Pubitemid 18529434)
16. Ferrell, J.E., Jr., and Machleder, E.M. 1998. The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 280, 895-898. (Pubitemid 28215598)
17. Gardner, T.S., Cantor C.R., and Collins, J.J. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339-342. (Pubitemid 30062394)
18. Johnston, M. 1987. A model fungal gene regulatory mechanism: the GAL genes of Saccharomyces cereviasiae. Microbiol. Rev. 51, 458-476.
19. Khalil, M.K. 1991. Nonlinear Systems. Macmillan, New York.
20. Klein, C.J.L., Olsson, L., and Nielsen, J. 1998. Glucose control in Saccharomyces cerevisiae: the role of MIG1 in metabolic functions. Microbiology 144, 13-24. (Pubitemid 28045209)
21. Kulkarni, V.V., Kareenhalli, V., Malakar, P., et al. 2010. Stability analysis of the GAL regulatory network in Saccharomyces cerevisiae and Kluyveromyces lactis. BMC Bioinform. 11, S43.
22. La Salle, J.P. 1960. Some extensions of Lyapunov's second method. IRE Trans. Circuit Theor. CT-7, 520-527.
23. Lohr, D., Venkov, P., and Zlatanova, J. 1995. Transcriptional regulation in the yeast GAL gene family: a complex genetic network. FASEB J. 9, 777-786.
24. MathWorks, 2011. MATLAB Robust Control Toolbox. MathWorks, Inc., Natick, MA.
25. Melcher, K., and Xu, H.E. 2001. Gal80-Gal80 interaction on adjacent Gal4p binding sites is required for complete GAL gene repression. EMBO J. 20, 841-851. (Pubitemid 32167648)
26. Murray, J.D. 2001. Mathematical Biology: I. An Introduction. Springer, New York.
27. Pannala, V.R., Bhat, P.J., Bhartiya, S., et al. 2010. System biology of GAL regulon in Saccharomyces cerevisiae. WIREs Syst. Biol. Med. 2, 98-106.
28. Peng, G., and Hopper, J.E. 2002. Gene activation by interaction of an inhibitor with a cytoplasmic signaling protein. Proc. Natl. Acad. Sci. USA 99, 8548-8553. (Pubitemid 34693599)
29. Pomenering, J.R., Sontag, E.D., and Ferrell, J.E., Jr. 2003. Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2. Nat. Cell Biol. 5, 346-351. (Pubitemid 36432300)
30. Sha, W., Moore, J., Chen, K., et al. 2003. Hysteresis drives cell-cycle transitions in Xenopous laevis egg extracts. Proc. Natl. Acad. Sci. USA. 100, 975-980. (Pubitemid 36183940)
31. Smidtas, S., Schachter, V. and Képès, F. 2006. The adaptive filter of the yeast galactose pathway. J. Theor. Biol. 242, 372-381. (Pubitemid 44251119)
32. Timson, D.J., Ross, H.C., and Reece, R.J. 2002. Gal3p and Gal1p interact with the transcriptional repressor Gal80p to form a complex of 1:1 stoichiometry. Biochem. J. 363, 515-520. (Pubitemid 34526371)