Mathematical model of NF- κB regulatory module

Journal of Theoretical Biology

Volumn 228, Issue 2, 2004, Pages 195-215

  Lipniacki, Tomasz ^a,b,c   Paszek, Pawel ^b   Brasier, Allan R ^d   Luxon, Bruce ^c   Kimmel, Marek ^b,e  

^a INSTITUTE OF FUNDAMENTAL TECHNOLOGICAL RESEARCH   (Poland)

^b Rice University   (United States)

^c UNIVERSITY OF TEXAS MEDICAL BRANCH   (United States)

^d University of Texas Medical Branch School of Medicine   (United States)

^e SILESIAN UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

A20; I B ; NF B; Ordinary differential equations; Signaling pathways

Indexed keywords

I KAPPA B ALPHA; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN;

BIOLOGY; MODEL;

ARTICLE; CATALYSIS; MATHEMATICAL MODEL; PHOSPHORYLATION; PRIORITY JOURNAL; PROTEIN DEGRADATION; REGULATORY MECHANISM; SIGNAL TRANSDUCTION;

ANIMALS; BIOLOGICAL TRANSPORT; CELL NUCLEUS; CELLS; CYTOPLASM; I-KAPPA B PROTEINS; MODELS, BIOLOGICAL; NF-KAPPA B; PHOSPHORYLATION; PROTEINS; SIGNAL TRANSDUCTION;

EID: 1942421298     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jtbi.2004.01.001     Document Type: Article

References (40)

1. Anest V., Hanson J.L., Cogswell P.C., Steinbrecher K.A., Strahl B.D., Baldwin A.S. A nucleosomal function for. Iκ B kinase- α in NF - κ B -dependent gene expression Nature. 423:2003;659-663.
2. Arvelo M.B., Cooper J.T., Longo C., Soizic D., Grey S.T., Mahiou J., Czismadia E., Abu-Jawdeh G., Ferran C. A20 protects mice from D-galactosamine/lipopolysaccharide acute toxic lethal hepatitis. Hepatology. 35:2002;535-543.
3. Beyaert R., Heyninck K., Van Huffel S. A20 and A20-binding proteins as cellular inhibitors of nuclear factor-kappa B-dependent gene expression and apoptosis. Biochem. Pharmacol. 60:2000;1143-1151.
4. Blattner C., Kannouche P., Litfin M., Bender K., Rahmsdorf H.J., Angulo J.F., Herrlich P. UV-induced stabilization of c-fos and other short-lived mRNAs. Mol. Cell. Biol. 20:2000;3616-3625.
5. Caamano J., Hunter C.A. NF - κ B family of transcription factors central regulators of innate and adaptive immune functions Clin. Microbiol. Rev. 15:2002;414-429.
6. Carlotti F., Dower S.K., Qwarnstrom E.E. Dynamic shuttling of nuclear factor kappa B between the nucleus and cytoplasm as a consequence of inhibitor dissociation. J. Biol. Chem. 275:2000;41028-41034.
7. Carter R.S., Geyer B.C., Xie M., Acevedo-Suarez C.A., Ballard D.W. Persistent activation of. NF - κ B by the tax transforming protein involves chronic phosphorylation of Iκ B kinase subunits IKKβ and IKKγ J. Biol. Chem. 276:2001;24445-24448.
8. Chen F.E., Huang D., Chen Y., Ghosh G. Crystal structure of p50/p65 heterodimer of transcription factor NF-. κ B bound to DNA Nature. 391:1998;410-413.
9. Delhase M., Hayakawa M., Chen Y., Karin M. Positive and negative regulation of. Iκ B kinase activity through IKKβ subunit phosphorylation Science. 284:1999;309-313.
10. Gerondakis S., Grossmann M., Nakamura Y., Pohl T., Grumont R. Genetic approaches in mice to understand. Rel/NF - κ B and Iκ B function transgenics and knockouts Oncogene. 18:1999;6888-6895.
11. Ghosh S., Karin M. Missing pieces in the. NF - κB puzzle Cell. 109:2002;S81-S96.
12. Ghosh S., May M.J., Kopp E.B. NF - κ B and Rel Proteins evolutionary conserved mediators of immune responses Annu. Rev. Immunol. 16:1998;225-260.
13. He K.-L., Ting A.T. A20 Inhibits tumor necrosis factor (TNF) alpha-induced apoptosis by disrupting recruitment of TRADD and RIP to the TNF receptor 1 complex in jurkat T cells. Mol. Cell. Biol. 22:2002;6034-6045.
14. Heilker R., Freuler F., Vanek M., Pulfer R., Kobel T., Peter J., Zerwes H.G., Hofstetter H., Eder J. The kinetics of association and phosphorylation of. Iκ B isoforms by Iκ B kinase 2 correlate with their cellular regulation in human endothelial cells Biochemistry. 38:1999;6231-6238.
15. Heyninck K., Kreike M.M., Beyaert R. Structure-function analysis of the A20-binding inhibitor of. NF - κ B activation, ABIN-1 FEBS Lett. 536:2003;135-140.
16. Hoffmann A., Levchenko A., Scott M.L., Baltimore D. The. Iκ B - NF - κ B signaling module temporal control and selective gene activation Science. 298:2002;1241-1245.
17. Karin M. The beginning of the end. Iκ B kinase (IKK) and NF - κ B activation J. Biol. Chem. 274:1999;27339-27342.
18. Krikos A., Laherty C.D., Dixit V.M. Transcriptional activation of the tumor necrosis factor alpha-inducible zinc finger protein, A20, is mediated by kappa B elements. J. Biol. Chem. 267:1992;17971-17976.
19. Kunsch C., Ruben S.M., Rosen C.A. Selection of optimal kappa B/Rel DNA-binding motifs. interaction of both subunits of NF-kappa B with DNA is required for transcriptional activation Mol. Cell. Biol. 12:1992;4412-4421.
20. Lee E.G., Boone D.L., Chai S., Libby S.L., Chien M., Lodolce J.P., Ma A. Failure to regulate TNF-induced. NF - κ B and cell death responses in A20-deficient mice Science. 289:2000;2350-2354.
21. Levin, B., 2000. Genes, Vol. VII. Oxford University Press, Oxford.
22. Li T., Narhi L.O., Wen J., Philo J.S., Sitney K., Inoue J., Yamamoto T., Arakawa T. Interactions between. NF - κ B and its inhibitor Iκ B biophysical characterization of NF - κ B Iκ Bα complex Journal of Protein Chemistry. 17(8):1998;757-763.
23. MacKichan M.L., Logeat F., Israel A. Phosphorylation of p105 PEST sequence via a redox-insensitive pathway upregulates processing of p50. NF - κ B J. Biol. Chem. 271:1996;6084-6091.
24. Malek S., Huxford T., Ghosh G. Iκ Bα functions through direct contacts with the nuclear localization signals and the DNA binding sequences of NF - κ B J. Biol. Chem. 273:1998;25427-25435.
25. Pando M.P., Verma I.M. Signal-dependent and -independent degradation of free and. NF - κ B -bound Iκ Bα J. Biol. Chem. 275:2000;21278-21286.
26. Rice N.R., Ernst M.K. In vivo control of. NF - κ B activation by Iκ Bα EMBO. 12:1993;4685-4695.
27. Rodriguez M.S., Thompson J., Hay R.T., Dargemont C. Nuclear retention of. Iκ Bα protects it from signal-induced degradation and inhibits nuclear factor κ B transcriptional activation J. Biol. Chem. 274:1999;9108-9115.
28. Song H.Y., Rothe M., Goeddel D.V. The tumor necrosis factor-inducible zinc finger protein A20 interacts with TRAF1/TRAF2 and inhibits. NF - κ B activation Proc. Natl Acad. Sci. USA. 93:1996;6721-6725.
29. Sun S.-C., Ganchi P.A., Ballard D.W., Greene W.C. NF - κ B Controls expression of inhibitor Iκ Bα evidence for an inducible autoregulatory pathway Science. 259:1993;1912-1915.
30. Tangethoff S., Behlke J., Scheidereit C. Tetrameric oligomerization of. Iκ B kinase γ ( IKKγ ) is obligatory for IKK complex activity and NF - κ B activation Mol. Cell. Biol. 23:2003;2029-2041.
31. Tian B., Brasier A.R. Identification of a nuclear factor kappa B-dependent gene network. Recent Prog. Horm. Res. 58:2003;95-130.
32. Tian B., Zhang Y., Luxon B.A., Garofalo P.G., Casola A., Sinha M., Brasier A.R. Identification of. NF - κ B -dependent gene networks in respiratory syncytial virus-infected cells J. Virol. 76:2002;6800-6814.
33. Tyson J.J., Chen K.C., Novak B. Sniffers, buzzers, toggles and blinkers. dynamics of regulatory and signaling pathway in the cell Curr. Opin. Cell Biol. 15:2003;221-231.
34. Wajant H., Pfiizenmaier K., Scheurich P. Tumor necrosis factor signaling. Cell Death Differ. 10:2003;45-65.
35. Yamamoto Y., Verma U.N., Prajapati S., Kwak Y., Gaynor R.B. Histone H3 phosphorylation by. IKKα is critical for cytokine-induced gene expression Nature. 423:2003;655-659.
36. Yamaoka S., Courtois G., Bessia C., Whiteside S.T., Weil R., Agou F., Kirk H.E., Kay R.J., Israël A. Complementation cloning of NEMO, a component of the. Iκ B kinase complex essential for NF - κ B activation Cell. 93:1998;1231-1240.
37. Yang L., Chen H., Qwarnstrom E.E. Degradation of. Iκ Bα is limited by a phosphorylation/ubiquitination event Biochem. Biophys. Res. Commun. 285:2001;603-608.
38. Yang L., Ross K., Qwarnstrom E.E. RelA control of. Iκ Bα phosphorylation J. Biol. Chem. 278:2003;30881-30888.
39. Zandi E., Chen Y., Karin M. Direct phosphorylation of. Iκ B by IKKα and IKKβ discrimination between free and NF - κ B -bound substrate Science. 281:1998;1360-1363.
40. Zhang S.Q., Kovalenko A., Cantarella G., Wallach D. Recruitment of the IKK Signalosome to the p55 TNF receptor. RIP and A20 bind to Nemo ( IKKγ ) upon receptor stimulation Immunity. 12:2000;301-311.