Rigor of cell fate decision by variable p53 pulses and roles of cooperative gene expression by p53

Biophysics

Volumn 8, Issue , 2012, Pages 41-50

  Murakami, Yohei ^a   Takada, Shoji ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Apoptosis; Cell death; Computational biology; Systems biology

Indexed keywords

EID: 84857066223     PISSN: None     EISSN: 13492942     Source Type: Journal    
DOI: 10.2142/biophysics.8.41     Document Type: Article

References (38)

1. Aylon, Y. & Oren, M. Living with p53, dying of p53. Cell 130, 597-600 (2007).
2. Batchelor, E., Loewer, A. & Lahav, G. The ups and downs of p53: understanding protein dynamics in single cells. Nat. Rev. Cancer 9, 371-377 (2009).
3. Vousden, K. H. & Lane, D. P. p53 in health and disease. Nat. Rev. Mol. Cell Biol. 8, 275-283 (2007).
4. Adams, J.M. & Cory, S. The Bcl-2 apoptotic switch in cancer development and therapy. Oncogene 26, 1324-1337 (2007).
5. Cotter, T.G. Apoptosis and cancer: the genesis of a research field. Nat. Rev. Cancer 9, 501-507 (2009).
6. Mattson, M. P. Apoptosis in neurodegenerative disorders. Nat. Rev. Mol. Cell Biol. 1, 120-129 (2000).
7. Vogelstein, B., Lane, D. & Levine, A. J. Surfing the p53 network. Nature 408, 307-310 (2000).
8. Batchelor, E., Mock, C. S., Bhan, I., Loewer, A. & Lahav, G. Recurrent initiation: a mechanism for triggering p53 pulses in response to DNA damage. Mol. Cell 30, 277-289 (2008).
9. Geva-Zatorsky, N., Rosenfeld, N., Itzkovitz, S., Milo, R., Sigal, A., Dekel, E., Yarnitzky, T., Liron, Y., Polak, P., Lahav, G. & Alon, U. Oscillations and variability in the p53 system. Mol. Syst. Biol. 2, 0033 (2006).
10. Lahav, G., Rosenfeld, N., Sigal, A., Geva-Zatorsky, N., Levine, A. J., Elowitz, M. B. & Alon, U. Dynamics of the p53-Mdm2 feedback loop in individual cells. Nat. Genet. 36, 147-150 (2004).
11. Loewer, A., Batchelor, E., Gaglia, G. & Lahav, G. Basal dynamics of p53 reveal transcriptionally attenuated pulses in cycling cells. Cell 142, 89-100 (2010).
12. Ramalingam, S., Honkanen, P., Young, L., Shimura, T., Austin, J., Steeg, P. S. & Nishizuka, S. Quantitative assessment of the p53-Mdm2 feedback loop using protein lysate microarrays. Cancer Res. 67, 6247-6252 (2007).
13. Tyson, J. J. Monitoring p53's pulse. Nat. Genet. 36, 113-114 (2004).
14. Hamada, H., Tashima, Y., Kisaka, Y., Iwamoto, K., Hanai, T., Eguchi, Y. & Okamoto, M. Sophisticated framework between cell cycle arrest and apoptosis induction based on p53 dynamics. PLoS One 4, e4795 (2009).
15. Iwamoto, K., Hamada, H., Eguchi, Y. & Okamoto, M. Mathematical modeling of cell cycle regulation in response to DNA damage: exploring mechanisms of cell-fate determination. Biosystems 103, 384-391 (2011).
16. Sun, T., Chen, C., Wu, Y., Zhang, S., Cui, J. & Shen, P. Modeling the role of p53 pulses in DNA damage-induced cell death decision. BMC Bioinformatics 10, 190 (2009).
17. Wee, K. B., Surana, U. & Aguda, B. D. Oscillations of the p53-Akt network: implications on cell survival and death. PLoS One 4, e4407 (2009).
18. Zhang, T., Brazhnik, P. & Tyson, J. J. Exploring mechanisms of the DNA-damage response: p53 pulses and their possible relevance to apoptosis. Cell Cycle 6, 85-94 (2007).
19. Zhang, T., Brazhnik, P. & Tyson, J. J. Computational analysis of dynamical responses to the intrinsic pathway of programmed cell death. Biophys. J. 97, 415-434 (2009).
20. Zhang, X. P., Liu, F., Cheng, Z. & Wang, W. Cell fate decision mediated by p53 pulses. Proc. Natl. Acad. Sci. USA 106, 12245-12250 (2009).
21. Zhang, X. P., Liu, F. & Wang, W. Coordination between cell cycle progression and cell fate decision by the p53 and E2F1 pathways in response to DNA damage. J. Biol. Chem. 285, 31571-31580 (2010).
22. Haupt, S., Berger, M., Goldberg, Z. & Haupt, Y. Apoptosis-the p53 network. J. Cell Sci. 116, 4077-4085 (2003).
23. Brenner, D. & Mak, T.W. Mitochondrial cell death effectors. Curr. Opin. Cell Biol. 21, 871-877 (2009).
24. Youle, R. J. & Strasser, A. The BCL-2 protein family: opposing activities that mediate cell death. Nat. Rev. Mol. Cell Biol. 9, 47-59 (2008).
25. Yu, J. & Zhang, L. The transcriptional targets of p53 in apoptosis control. Biochem. Biophys. Res. Commun. 331, 851-858 (2005).
26. Nakano, K. & Vousden, K.H. PUMA, a novel proapoptotic gene, is induced by p53. Mol. Cell 7, 683-694 (2001).
27. Villunger, A., Michalak, E.M., Coultas, L., Mullauer, F., Bock, G., Ausserlechner, M. J., Adams, J. M. & Strasser, A. p53-and drug-induced apoptotic responses mediated by BH3-only proteins puma and noxa. Science 302, 1036-1038 (2003).
28. Yu, J., Zhang, L., Hwang, P.M., Kinzler, K.W. & Vogelstein, B. PUMA induces the rapid apoptosis of colorectal cancer cells. Mol. Cell 7, 673-682 (2001).
29. Balagurumoorthy, P., Sakamoto, H., Lewis, M. S., Zambrano, N., Clore, G.M., Gronenborn, A. M., Appella, E. & Harrington, R. E. Four p53 DNA-binding domain peptides bind natural p53-response elements and bend the DNA. Proc. Natl. Acad. Sci. USA 92, 8591-8595 (1995).
30. Weinberg, R.L., Veprintsev, D. B. & Fersht, A.R. Cooperative binding of tetrameric p53 to DNA. J. Mol. Biol. 341, 1145-1159 (2004).
31. Chen, C., Cui, J., Lu H., Wang R., Zhang, S. & Shen, P. Modeling of the role of a Bax-activation switch in the mitochondrial apoptosis decision. Biophys. J. 92, 4304-4315 (2007).
32. Cui, J., Chen, C., Lu, H., Sun, T. & Shen, P. Two independent positive feedbacks and bistability in the Bcl-2 apoptotic switch. PLoS One 3, e1469 (2008).
33. Sun, T., Lin, X., Wei, Y., Xu, Y. & Shen, P. Evaluating bistability of Bax activation switch. FEBS Lett. 584, 954-960 (2010).
34. Albeck, J.G., Burke, J. M., Aldridge, B. B., Zhang, M., Lauffenburger, D. A. & Sorger, P. K. Quantitative analysis of pathways controlling extrinsic apoptosis in single cells. Mol. Cell 30, 11-25 (2008).
35. Vaughan, A. T., Betti, C. J. & Villalobos, M. J. Surviving apoptosis. Apoptosis 7, 173-177 (2002).
36. Tyson, J. J. Another turn for p53. Mol. Syst. Biol. 2, 0032 (2006).
37. Slee, E. A., Harte, M. T., Kluck, R. M., Wolf, B. B., Casiano, C.A., Newmeyer, D. D., Wang, H.G., Reed, J. C., Nicholson, D.W., Alnemri, E. S., Green, D. R. & Martin, S. J. Ordering the cytochrome c-initiated caspase cascade: hierarchical activation of caspases-2,-3,-6,-7,-8, and-10 in a caspase-9-dependent manner. J. Cell Biol. 144, 281-292 (1999).
38. Legewie, S., Bluthgen, N. & Herzel, H. Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability. PLoS Comput. Biol. 2, e120 (2006).