Model-based investigation of the transcriptional activity of p53 and its feedback loop regulation via 14-3-3σ

IET Systems Biology

Volumn 5, Issue 5, 2011, Pages 293-307

  Vera, J ^a   Nikolov, S ^b   Lai, X ^a   Singh, A ^a   Wolkenhauer, O ^a  

^a UNIVERSITY OF ROSTOCK   (Germany)

^b INSTITUTE OF MECHANICS   (Bulgaria)

Author keywords

[No Author keywords available]

Indexed keywords

BASIC PROPERTIES; BIFURCATION ANALYSIS; DNA DAMAGES; EXPRESSION PATTERNS; FEED-BACK LOOP; MATHEMATICAL MODELLING; OSCILLATORY SIGNALS; P53 INHIBITORS; PHYSIOLOGICAL CONDITION; STRESS SIGNALS; TRANSCRIPTIONAL ACTIVITY; TURNOVER RATE;

BIFURCATION (MATHEMATICS); GENES; NUCLEIC ACIDS; TRANSCRIPTION;

PROTEINS;

EXONUCLEASE; MDM2 PROTEIN, HUMAN; PROTEIN 14 3 3; PROTEIN MDM2; PROTEIN P53; SFN PROTEIN, HUMAN; TUMOR MARKER;

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; DNA DAMAGE; FEEDBACK SYSTEM; GENE EXPRESSION REGULATION; GENETICS; HUMAN; METABOLISM; METHODOLOGY; OSCILLOMETRY; SIGNAL TRANSDUCTION; STATISTICAL MODEL; THEORETICAL MODEL; TUMOR SUPPRESSOR GENE;

14-3-3 PROTEINS; ALGORITHMS; COMPUTATIONAL BIOLOGY; DNA DAMAGE; EXONUCLEASES; FEEDBACK, PHYSIOLOGICAL; GENE EXPRESSION REGULATION; GENES, P53; HUMANS; MODELS, BIOLOGICAL; MODELS, STATISTICAL; MODELS, THEORETICAL; OSCILLOMETRY; PROTO-ONCOGENE PROTEINS C-MDM2; SIGNAL TRANSDUCTION; TUMOR MARKERS, BIOLOGICAL; TUMOR SUPPRESSOR PROTEIN P53;

EID: 80054714867     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb.2010.0080     Document Type: Article

References (42)

1. Riley, T., Sontag, E., Chen, P., and Levine, A.: 'Transcriptional control of human p53-regulated genes', Nat. Rev. Mol. Cell Biol., 2008, 9, p. 402-41210.1038/nrm2395
2. Vousden, K.H., and Prives, C.: 'Blinded by the light: the growing complexity of p53', Cell, 2009, 137, p. 413-43110.1016/j.cell.2009.04.037
3. Lev Bar-Or, R., Maya, R., and Segel, L.A.: et al. 'Generation of oscillations by the p53-Mdm2 feedback loop: a theoretical and experimental study', Proc. Natl. Acad. Sci. U.S.A., 2000, 97, p. 11250-1125510.1073/pnas.210171597 0027-8424
4. Lahav, G., Rosenfeld, N., and Sigal, A.: et al. 'Dynamics of the p53-Mdm2 feedback loop in individual cells', Nat. Genet., 2004, 36, p. 147-15010.1038/ng1293
5. Geva-Zatorsky, N., Rosenfeld, N., and Sigal, A.: et al. 'Oscillations and variability in the p53 system', Mol. Syst. Biol., 2006, 2, p. 003310.1038/msb4100068
6. Hamstra, D.A., Bhojani, M.S., and Griffin, L.B.: et al. 'Real-time evaluation of p53 oscillatory behavior in vivo using bioluminescent imaging', Cancer Res., 2006, 66, p. 7482-748910.1158/0008-5472.CAN-06-1405
7. Novák, B., and Tyson, J.J.: 'Design principles of biochemical oscillators', Nat. Rev. Mol. Cell. Biol., 2008, 9, p. 981-99110.1038/nrm2530
8. Ma, L., Wagner, J., and Rice, J.J.: et al. 'A plausible model for the digital response of p53 to DNA damage', Proc. Natl. Acad. Sci. USA, 2005, 102, p. 14266-1427110.1073/pnas.0501352102 0027-8424
9. Puszyński, K., Hat, B., and Lipniacki, T.: 'Oscillations and bistability in the stochastic model of p53 regulation', J. Theor. Biol., 2008, 254, p. 452-46510.1016/j.jtbi.2008.05.039
10. Hunziker, A., Jensen, M.H., and Krishna, S.: 'Stress-specific response of the p53-Mdm2 feedback loop', BMC Syst. Biol., 2010, 4, p. 94
11. Zhang, T., Brazhnik, P., and Tyson, J.J.: 'Exploring mechanisms of the DNA-damage response: p53 pulses and their possible relevance to apoptosis', Cell. Cycle, 2007, 6, p. 85-9410.4161/cc.6.1.3705
12. Zhang, X.-P., Liu, F., Cheng, Z., and Wang, W.: 'Cell fate decision mediated by p53 pulses', Proc. Natl. Acad. Sci. USA, 2009, 106, p. 12245-1225010.1073/pnas.0813088106 0027-8424
13. Vera, J., Schultz, J., and Ibrahim, S.: et al. 'Dynamical effects of epigenetic silencing of 14-3-3sigma expression', Mol. Biosyst., 2010, 6, p. 264-27310.1039/b907863k
14. Lane, D.P., Midgley, C.A., and Hupp, T.R.: et al. 'On the regulation of the p53 tumour suppressor, and its role in the cellular response to DNA damage', Philos. Trans. R. Soc. Lond. B, Biol. Sci., 1995, 347, p. 83-8710.1098/rstb.1995.0013
15. Brooks, C.L., and Gu, W.: 'p53 ubiquitination: Mdm2 and beyond', Mol. Cell, 2006, 21, p. 307-31510.1016/j.molcel.2006.01.020
16. Inoue, T., Geyer, R.K., Howard, D., Yu, Z.K., and Maki, C.G.: 'MDM2 can promote the ubiquitination, nuclear export, and degradation of p53 in the absence of direct binding', J. Biol. Chem., 2001, 276, p. 45255-4526010.1074/jbc.M107477200
17. Barak, Y., Juven, T., Haffner, R., and Oren, M.: 'mdm2 expression is induced by wild type p53 activity', EMBO J, 1993, 12, p. 461-468
18. Freedman, D.A., Wu, L., and Levine, A.J.: 'Functions of the MDM2 oncoprotein', Cell. Mol. Life Sci. (CMLS), 1999, 55, p. 96-10710.1007/s000180050273
19. Legewie, S., Herzel, H., Westerhoff, H.V., and Blüthgen, N.: 'Recurrent design patterns in the feedback regulation of the mammalian signalling network', Mol. Syst. Biol., 2008, 4, p. 19010.1038/msb.2008.29
20. Schmidt, H., and Jacobsen, E.W.: 'Linear systems approach to analysis of complex dynamic behaviours in biochemical networks', Syst. Biol. (Stevenage), 2004, 1, p. 149-15810.1049/sb:20045015
21. Geva-Zatorsky, N., Dekel, E., Batchelor, E., Lahav, G., and Alon, U.: 'Fourier analysis and systems identification of the p53 feedback loop', Proc. Natl. Acad. Sci. USA, 2010, 107, p. 13550-1355510.1073/pnas.1001107107 0027-8424
22. Ouattara, D.A., Abou-Jaoudé, W., and Kaufman, M.: 'From structure to dynamics: frequency tuning in the p53-Mdm2 network. II Differential and stochastic approaches', J. Theor. Biol., 2010, 264, p. 1177-118910.1016/j.jtbi.2010.03.031
23. Abou-Jaoudé, W., Chaves, M., and Gouzé, J.-L.: 'A theoretical exploration of birhythmicity in the p53-Mdm2 network', PLoS ONE 2011, 6, p. e1707510.1371/journal.pone.0017075
24. Jiang, C., Xuan, Z., Zhao, F., and Zhang, M.Q.: 'TRED: a transcriptional regulatory element database, new entries and other development', Nucleic Acids Res., 2007, 35, p. D137-14010.1093/nar/gkl1041
25. Ashall, L., Horton, C.A., and Nelson, D.E.: et al. 'Pulsatile stimulation determines timing and specificity of NF-kappaB-dependent transcription', Science, 2009, 324, p. 242-24610.1126/science.1164860 0036-8075
26. Marcello, M., and White, M.R.H.: 'Spatial and temporal information coding and noise in the NF-κB system', Biochem. Soc. Trans., 2010, 38, p. 1247-125010.1042/BST0381247
27. Ciliberto, A., Novak, B., and Tyson, J.J.: 'Steady states and oscillations in the p53/Mdm2 network', Cell. Cycle, 2005, 4, p. 488-49310.4161/cc.4.3.1548
28. Abou-Jaoudé, W., Ouattara, D.A., and Kaufman, M.: 'From structure to dynamics: frequency tuning in the p53-Mdm2 network I. Logical approach', J. Theor. Biol., 2009, 258, p. 561-57710.1016/j.jtbi.2009.02.005
29. Yang, H.-Y., Wen, Y.Y., and Lin, Y.I.: et al. 'Roles for negative cell regulator 14-3-3sigma in control of MDM2 activities', Oncogene, 2007, 26, p. 7355-736210.1038/sj.onc.1210540
30. Schultz, J., Ibrahim, S.M., Vera, J., and Kunz, M.: '14-3-3sigma gene silencing during melanoma progression and its role in cell cycle control and cellular senescence', Mol. Cancer, 2009, 8, p. 5310.1186/1476-4598-8-53
31. Lodygin, D., and Hermeking, H.: 'The role of epigenetic inactivation of 14-3-3sigma in human cancer', Cell. Res., 2005, 15, p. 237-24610.1038/sj.cr.7290292
32. Aguda, B.D., and Clarke, B.L.: 'Bistability in chemical reaction networks: theory and application to the peroxidase-oxidase reaction', J. Chem. Phys., 1987, 87, p. 346110.1063/1.452991 0021-9606
33. Nikolov, S.: 'Estimating of bifurcations and chaotic behaviour in a four-dimensional system', J. Calcutta Math. Soc., 2006, 2, p. 17-28
34. Domijan, M., and Kirkilionis, M.: 'Bistability and oscillations in chemical reaction networks', J. Math Biol., 2009, 59, (4), p. 467-501, Epub 200810.1007/s00285-008-0234-7 0303-6812
35. Bautin, N.: 'Behaviour of dynamical systems near the boundary of stability', (Nauka, Moscow 1984)
36. Andronov, A.A., Vitt, A.A., and Khaikin, S.E.: 'Theory of Oscillators', (Dover Publications 1987)
37. Nikolov, S., Lai, X., Liebal, U.W., Wolkenhauer, O., and Vera, J.: 'Integration of sensitivity and bifurcation analysis to detect critical processes in a model combining signalling and cell population dynamics', Int. J. Syst. Sci., 2010, 41, p. pp. 1, 81-10510.1080/00207720903147746 0020-7721
38. Shilnikov, L., Shilnikov, A., Turaev, D., and Chua, L.: 'Methods of qualitative theory in nonlinear dynamics', (World Scientific, London 2001), part II
39. Nemytskii, V.V., and Stepanov, V.V.: 'Qualitative theory of differential equations', (Courier Dover Publications 1989)
40. Pomerening, J.: 'Uncovering mechanisms of bistability in biological systems', Curr. Opin. Biotechnol., 2008, 19, (4), p. 381-38810.1016/j.copbio.2008.06.009
41. Neimark, Y.I., and Landa, P.S.: 'Stochastic and chaotic oscillations', (Springer 1992)
42. Urano, T., Saito, T., and Tsukui, T.: et al. 'Efp targets 14-3-3 sigma for proteolysis and promotes breast tumour growth', Nature, 2002, 417, (6891), p. 871-87510.1038/nature00826 0028-0836