Modeling oscillatory control in NF-κB, p53 and Wnt signaling

Current Opinion in Genetics and Development

Volumn 20, Issue 6, 2010, Pages 656-664

  Mengel, Benedicte ^a   Hunziker, Alexander ^a   Pedersen, Lykke ^a   Trusina, Ala ^a   Jensen, Mogens H ^a   Krishna, Sandeep ^a,b  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b TATA INSTITUTE OF FUNDAMENTAL RESEARCH   (India)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; PROTEIN P53; WNT PROTEIN;

CALCIUM SIGNALING; CELL DEATH; CELL FUNCTION; CELL GROWTH; CIRCADIAN RHYTHM; EMBRYO DEVELOPMENT; GENETIC TRANSCRIPTION; HUMAN; IMMUNE SYSTEM; MOLECULAR MECHANICS; NEGATIVE FEEDBACK; NONHUMAN; OSCILLATION; PRIORITY JOURNAL; PROTEIN DEGRADATION; REVIEW; SIGNAL TRANSDUCTION; STEADY STATE;

ANIMALS; CIRCADIAN RHYTHM; HUMANS; MODELS, BIOLOGICAL; NF-KAPPA B; SIGNAL TRANSDUCTION; TUMOR SUPPRESSOR PROTEIN P53; WNT PROTEINS;

EID: 78349311201     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.gde.2010.08.008     Document Type: Review

References (71)

1. Kitayama Y., Nishiwaki T., Terauchi K., Kondo T. Dual kaic-based oscillations constitute the circadian system of cyanobacteria. Genes Dev 2008, 22:1513-1521.
2. Dong G., Golden S.S. How a cyanobacterium tells time. Curr Opin Microbiol 2008, 11:541-546.
3. Lu Y., Cross F.R. Periodic cyclin-cdk activity entrains an autonomous cdc14 release oscillator. Cell 2010, 141:268-279.
4. 2+ oscillation frequency regulates agonist-stimulated gene expression in vascular endothelial cells. J Cell Sci 2008, 121:2511-2518.
5. Ciccone N.A., Xu S., Lacza C.T., Carroll R.S., Kaiser U.B. Frequency-dependent regulation of follicle-stimulating hormone beta by pulsatile gonadotropin-releasing hormone is mediated by functional antagonism of bzip transcription factors. Mol Cell Biol 2010, 30:1028-1040.
6. Hoffmann A., Levchenko A., Scott M.L., Baltimore D. The IκB-NF-κB signaling module: temporal control and selective gene activation. Science 2002, 298:1241-1245.
7. Nelson D.E., Ihekwaba A.E.C., Elliott M., Johnson J.R., Gibney C.A., Foreman B.E., Nelson G., See V., Horton C.A., Spiller D.G., et al. Oscillations in NF-κB signaling control the dynamics of gene expression. Science 2004, 306:704-708.
8. Lee T.K., Denny E.M., Sanghvi J.C., Gaston J.E., Maynard N.D., Hughey J.J., Covert M.W. A noisy paracrine signal determines the cellular NF-kappaB response to lipopolysaccharide. Sci Signal 2009, 2:ra65.
9. Bartfeld S., Hess S., Bauer B., Machuy N., Ogilvie L.A., Schuchhardt J., Meyer T.F. High-throughput and single-cell imaging of NF-κB oscillations using monoclonal cell lines. BMC Cell Biol 2010, 11:21.
10. Geva-Zatorsky N., Rosenfeld N., Itzkovitz S., Milo R., Sigal A., Dekel E., Yarnithky T., Polak P., Liron Y., Kam Z., et al. Oscillations and variability in the p53 system. Mol Syst Biol 2006, 2006.0033.
11. Hamstra D.A., Bhojani M.S., Griffin L.B., Laxman B., Ross B.D., Rehemtulla A. Real-time evaluation of p53 oscillatory behavior in vivo using bioluminescent imaging. Cancer Res 2006, 66:7482-7489.
12. Aulehla A., Herrmann B.G. Segmentation in vertebrates: clock and gradient finally joined. Genes Dev 2004, 18:2060-2067.
13. Dequeant M.L., Glynn E., Gaudenz K., Wahl M., Chen J., Mushegian A., Pourquie O. A complex oscillating network of signaling genes underlies the mouse segmentation clock. Science 2006, 314:1595-1598.
14. Aulehla A., Wiegraebe W., Baubet V., Wahl M.B., Deng C., Taketo M., Kewandoski M., Pourquie O. A beta-catenin gradient links the clock and wavefront systems in mouse embryo segmentation. Nat Cell Biol 2008, 10:168-210.
15. Ingolia N.T., Murray A.W. The ups and downs of modeling the cell cycle. Curr Biol 2004, 14:R771-R777.
16. Ferrell J.E., Pomerening J.R., Kim S.Y., Trunnell N.B., Xiong W., Huang C.Y., Machleder E.M. Simple, realistic models of complex biological processes: positive feedback and bistability in a cell fate switch and a cell cycle oscillator. FEBS Lett 2009, 583:3999-4005.
17. Sneppen K., Krishna S., Semsey S. Simplified models of biological networks. Annu Rev Biophys 2010, 39:43-59.
18. Tiana G., Krishna S., Pigolotti S., Jensen M.H., Sneppen K. Oscillations and temporal signalling in cells. Phys Biol 2007, 4:R1-R17.
19. Jensen M.H., Sneppen K., Tiana G. Sustained oscillations and time delays in gene expression of protein hes1. FEBS Lett 2003, 541:176-177.
20. Monk N.A.M. Oscillatory expression of hes1, p53, and NF-κB driven by transcriptional time delays. Curr Biol 2003, 13:1409-1413.
21. Mackey M.C., Glass L. Oscillation and chaos in physiological control systems. Science 1977, 197:287-289.
22. Tiana G., Sneppen K., Jensen M.H. Time delay as a key to apoptosis induction in the p53 network. Europhys J B 2002, 29:135-140.
23. Lewis J. Autoinhibition with transcriptional delay: a simple mechanism for the zebrafish somitogenesis oscillator. Curr Biol 2003, 13:1398-1408.
24. Li J., Kuang Y., Mason C.C. Modeling the glucose-insulin regulatory system and ultradian insulin secretory oscillations with two explicit time delays. J Theor Biol 2006, 242:722-735.
25. Walker J.J., Terry J.R., Lightman S.L. Origin of ultradian pulsatility in the hypothalamic-pituitary-adrenal axis. Proc Biol Sci 2010, 277:1627-1633.
26. Elowitz M.B., Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403:335-338.
27. Stricker J., Cookson S., Bennett M.R., Mather W.H., Tsimring L.S., Hasty J. A fast, robust and tunable synthetic gene oscillator. Nature 2008, 456:516-519.
28. Goodwin B.C. Oscillatory behavior in enzymatic control processes. Adv Enzym Regul 1965, 3:425-438.
29. Tsai T.Y., Choi Y.S., Ma W., Pomerening J.R., Tang C., Ferrell J.E. Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science 2008, 321:126-129.
30. Krishna S., Semsey S., Jensen M.H. Frustrated bistability as a means to engineer oscillations in biological systems. Phys Biol 2009, 6:1-8.
31. Pomerening J.R., Kim S.Y., Ferrell J.E. Systems-level dissection of the cell-cycle oscillator: bypassing positive feedback produces damped oscillations. Cell 2005, 122:565-578.
32. Gerard C., Goldbeter A. Temporal self-organization of the cyclin/cdk network driving the mammalian cell cycle. Proc Natl Acad Sci (USA) 2009, 106:21643-21648.
33. Cookson N.A., Tsimring L.S., Hasty J. The pedestrian watchmaker: genetic clocks from engineered oscillators. FEBS Lett 2009, 583:3931-3937.
34. Howard M., Kruse K. Cellular organization by self-organization: mechanisms and models for min protein dynamics. J Cell Biol 2005, 168:533-536.
35. Ciliberto A., Novak B., Tyson J.J. Steady states and oscillations in the p53/mdm2 network. Cell Cycle 2005, 4:488-493.
36. Puszynski K., Hat B., Lipniacki T. Oscillations and bistability in the stochastic model of p53 regulation. J Theor Biol 2008, 254:452-465.
37. Atkinson M.R., Savageau M.A., Myers J.T., Ninfa A.J. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 2003, 113:597-607.
38. Fung E., Wong W.W., Suen J.K., Bulter T., gu Lee S., Liao J.C. A synthetic gene-metabolic oscillator. Nature 2005, 435:118-122.
39. Krishna S., Jensen M.H., Sneppen K. Minimal model of spiky oscillations in NF-κB signaling. Proc Natl Acad Sci (USA) 2006, 103:10840-10845.
40. Mathes E., O'Dea E.L., Hoffmann A., Ghosh G. NF-kappaB dictates the degradation pathway of IkappaBalpha. EMBO J 2008, 27:1357.
41. O'Dea E.L., Barken D., Peralta R.Q., Tran K.T., Werner S.L., Kearns J.D., Levchenko A., Hoffmann A. A homeostatic model of IκB metabolism to control constitutive NF-κB activity. Mol Syst Biol 2007, 3:111.
42. Hunziker A, Jensen MH, Krishna S: Stress-specific response of the p53-mdm2 feedback loop. BMC Syst Biol.
43. Goldbeter A., Pourquie O. Modeling the segmentation clock as a network of coupled oscillations in the Notch, Wnt and FGF signaling pathways. J Theor Biol 2008, 252:574-585.
44. Jensen P.B., Pedersen L., Krishna S., Jensen M.H. A wnt oscillator model for somitogenesis. Biophys J 2010, 98:943-950.
45. Dunty W.C., Biris K.K., Chalamalasetty R.B., Taketo M.M., Lewandoski M., Yamaguchi T.P. Wnt3a/β-catenin signaling controls posterior body development by coordinating mesoderm formation and segmentation. Development 2008, 135:85-94.
46. Bliss R.D., Painter P.R., Marr A.G. Role of feedback inhibition in stabilizing the classical operon. J Theor Biol 1982, 97:177-193.
47. 2+ oscillations and for their frequency encoding through protein phosphorylation. Proc Natl Acad Sci (USA) 1990, 87:1461-1465.
48. Gerard C., Gonze D., Goldbeter A. Dependence of the period on the rate of protein degradation in minimal models for circadian oscillations. Phil Trans R Soc A 2009, 367:4665-4683.
49. Sneppen K., Lizana L., Jensen M.H., Pigolotti S., Otzen D. Modeling proteasome dynamics in parkinsons disease. Phys Biol 2009, 6:036005.
50. Cooke J., Zeeman E.C. A clock and wavefront model for control of the number of repeated structures during animal morphogenesis. J Theor Biol 1976, 58:455-476.
51. Pourquie O. The segmentation clock: converting embryonic time into spatial pattern. Science 2003, 301:328-330.
52. Yang Q., Pando B.F., Dong G., Golden S.S., van Oudenaarden A. Circadian gating of the cell cycle revealed in single cyanobacterial cells. Science 2010, 327:1522-1526.
53. Batchelor E., Loewer A., Lahav G. The ups and downs of p53: understanding protein dynamics in single cells. Nat Rev Cancer 2009, 9:371-377.
54. Kobayashi T., Kageyama R. Dynamic advances in NF-κB signaling analysis. Cell Biol 2009, 2:1-2.
55. Werner S.L., Barken D., Hoffmann A. Stimulus specificity of gene expression programs determined by temporal control of ikk activity. Science 2005, 309:1857-1861.
56. Werner S.L., Kearns J.D., Zadorozhnaya V., Lynch C., O'Dea E., Boldin M.P., Ma A., Baltimore D., Hoffmann A. Encoding NF-κB temporal control in response to tnf: distinct roles for the negative regulators ikbα and a20. Genes Dev 2008, 22:2093-2101.
57. Ashall L., Horton C.A., Nelson D.E., Paszek P., Harper C.V., Sillitoe K., Ryan S., Spiller D.G., Unitt J.F., Broomhead D.S., et al. Pulsatile stimulation determines timing and specificity of NF-κB-dependent transcription. Science 2009, 324:242-246.
58. Barken D., Wang C.J., Kearns J., Cheong R., Hoffmann A., Levchenko A. Comment on 'oscillations in NF-κB signaling control the dynamics of gene expression'. Science 2005, 308:52a.
59. Cheong R., Levchenko A. Wires in the soup: quantitative models of cell signaling. Trend Cell Biol 2008, 18:112-118.
60. Ankers J.M., Spiller D.G., White MRH C.V., Harper Spatio-temporal protein dynamics in single living cells. Curr Opin Biotechnol 2008, 19:375-380.
61. Harris S.L., Levine A.J. The p53 pathway: positive and negative feedback loops. Oncogene 2005, 24:2899.
62. Tyson J.J. Another turn for p53. Mol Sys Biol 2006, 2:0032.
63. Aulehla A., Pourquie O. Oscillating signaling pathways during embryonic development. Curr Opin Cell biol 2008, 20:632-637.
64. Ozbudak E.M., Pouriquie O. The vertebrate segmentation clock: the tip of the iceberg. Curr Opin Genet Dev 2008, 18:317-323.
65. Lipniacki T., Paszek P., Brasier A.R., Luxon B., Kimmel M. Mathematical model of NF-κB regulatory module. J Theor Biol 2004, 228:195-215.
66. Cheong R., Hoffmann A., Levchenko A. Understanding NF-κB signaling via mathematical modeling. Mol Sys Biol 2008, 4:1-11.
67. Ma L., Wagner J., Rice J.J., Hu W., Levine A.J., Stolovitzky G. A plausible model for the digital response of p53 to dna damage. Proc Natl Acad Sci (USA) 2005, 102:14266-14271.
68. 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 2008, 30:277-289.
69. Lee E., Salic A., Kruger R., Heinrich R., Kirschner M.W. The roles of apc and axin derived from experimental and theoretical analysis of the wnt pathway. PLoS Biol 2003, 1:10.
70. Rodriguez-Gonzalez J.G., Santillian M., Fowler A.C., Mackey M.C. The segmentation clock in mice: interaction between the Wnt and Notch signalling pathways. J Theor Biol 2007, 248:37-47.
71. Smolen P., Baxter D.A., Byrne J.H. Frequency selectivity, multistability and oscillations emerge from models of genetic regulatory systems. Am J Physiol Cell Physiol 1998, 274:531-542.