Systems theory of Smad signalling

IEE Proceedings: Systems Biology

Volumn 153, Issue 6, 2006, Pages 412-424

  Clarke, D C ^a   Betterton, M D ^a   Liu, X ^a  

^a UNIVERSITY OF COLORADO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CELL CULTURE; GENES; GROWTH KINETICS; MATHEMATICAL MODELS; PROTEINS; STATISTICAL METHODS;

DEPHOSPHORYLATION; PHOSPHORYLATION; SMAD NUCLEAR ACCUMULATION; SMAD SIGNALLING;

CYTOLOGY;

ISOPROTEIN; SMAD PROTEIN; SMAD2 PROTEIN; SMAD3 PROTEIN; SMAD4 PROTEIN; TRANSFORMING GROWTH FACTOR BETA;

ANIMAL CELL; ARTICLE; BIOACCUMULATION; CANONICAL ANALYSIS; CELL LEVEL; CELL NUCLEUS; COMPLEX FORMATION; CONTROLLED STUDY; DISSOCIATION; EPITHELIUM CELL; GENE TARGETING; LUNG ALVEOLUS EPITHELIUM; MATHEMATICAL MODEL; MATHEMATICAL PARAMETERS; MINK; NONHUMAN; PROTEIN BINDING; PROTEIN DEPHOSPHORYLATION; PROTEIN LOCALIZATION; PROTEIN PHOSPHORYLATION; REGULATORY MECHANISM; SIGNAL TRANSDUCTION; STATISTICAL ANALYSIS;

ANIMALS; COMPUTER SIMULATION; EPITHELIAL CELLS; MINK; MODELS, BIOLOGICAL; PHOSPHORYLATION; SIGNAL TRANSDUCTION; SMAD PROTEINS; SYSTEMS THEORY; TRANSFORMING GROWTH FACTOR BETA;

MUSTELA VISON;

EID: 33750845118     PISSN: 17412471     EISSN: None     Source Type: Journal    
DOI: 10.1049/ip-syb:20050055     Document Type: Article

References (69)

1. Massague, J.: 'The transforming growth factor-beta family', Annu. Rev. Cell Biol., 1990, 6, p. 597-641
2. Shi, Y., and Massague, J.: 'Mechanisms of TGF-beta signaling from cell membrane to the nucleus', Cell, 2003, 113, p. 685-700
3. Massague, J., Blain, S.W., and Lo, R.S.: ' TGFβ signaling in growth control, cancer, and heritable disorders', Cell, 2000, 103, p. 295-309
4. Pasche, B.: 'Role of transforming growth factor beta in cancer', J. Cell Physiol., 2001, 186, p. 153-168
5. Flanders, K.C., and Roberts, A.B.: 'TGF-β' Oppenheim, J.J., Feldmann, M., Durum, S.K., Cytokine reference: A compendium of cytokines and other mediators of host defense, (Academic Press, San Diego, CA 2001)
6. Massague, J., Cheifetz, S., Boyd, F.T., and Andres, J.L.: 'TGF-beta receptors and TGF-beta binding proteoglycans: Recent progress in identifying their functional properties', Ann. N Y Acad. Sci., 1990, 593, p. 59-72
7. Derynck, R., and Zhang, Y.E.: 'Smad-dependent and Smad-independent pathways in TGF-beta family signalling' Nature, 2003, 425, p. 577-584 0028-0836
8. Liu, F.: 'Receptor-regulated Smads in TGF-beta signaling', Front. Biosci., 2003, 8, p. 1280-1303
9. Nakao, A., Imamura, T., Souchelnytskyi, S., Kawabata, M., Ishisaki, A., Oeda, E., Tamaki, K., Hanai, J., Heldin, C.H., Miyazono, K., and ten Dijke, P.: 'TGF-beta receptor-mediated signalling through Smad2, Smad3 and Smad4', Embo J., 1997, 16, p. 5353-5362
10. ten Dijke, P., and Hill, C.S.: 'New insights into TGF-beta-Smad signalling', Trends Biochem. Sci., 2004, 29, p. 265-273
11. Xu, L., Chen, Y.G., and Massague, J.: 'The nuclear import function of Smad2 is masked by SARA and unmasked by TGFbeta-dependent phosphorylation', Nat. Cell Biol., 2000, 2, p. 559-562
12. Tsukazaki, T., Chiang, T.A., Davison, A.F., Attisano, L., and Wrana, J.L.: 'SARA, a FYVE domain protein that recruits Smad2 to the TGFbeta receptor', Cell, 1998, 95, p. 779-791
13. Dong, C., Li, Z., Alvarez, R., Feng, X.H., and Goldschmidt-Clermont, P.J.: 'Microtubule binding to Smads may regulate TGF beta activity', Mol. Cell, 2000, 5, p. 27-34
14. Xu, L., Chen, Y.G., and Massague, J.: 'The nuclear import function of Smad2 is masked by SARA and unmasked by TGFß-dependent phosphorylation', Nat. Cell. Biol., 2000, 2, p. 559-562
15. Chen, H.B., Rud, J.G., Lin, K., and Xu, L.: 'Nuclear targeting of transforming growth factor-β-activated Smad complexes', J. Biol. Chem., 2005, 280, p. 21329-21336
16. Pierreux, C.E., Nicolas, F.J., and Hill, C.S.: 'Transforming growth factor beta-independent shuttling of Smad4 between the cytoplasm and nucleus', Mol. Cell Biol., 2000, 20, p. 9041-9054
17. Subramanian, G., Schwarz, R.E., Higgins, L., McEnroe, G., Chakravarty, S., Dugar, S., and Reiss, M.: 'Targeting endogenous transforming growth factor beta receptor signaling in SMAD4-deficient human pancreatic carcinoma cells inhibits their invasive phenotype1', Cancer Res., 2004, 64, p. 5200-5211
18. Inman, G.J., Nicolas, F.J., and Hill, C.S.: 'Nucleocytoplasmic shuttling of Smads 2, 3, and 4 permits sensing of TGF-beta receptor activity', Mol. Cell, 2002, 10, p. 283-294
19. Kholodenko, B.N., Demin, O.V., Moehren, G., and Hoek, J.B.: 'Quantification of short term signaling by the epidermal growth factor receptor', J. Biol. Chem., 1999, 274, p. 30169-30181
20. Schoeberl, B., Eichler-Jonsson, C., Gilles, E.D., and Muller, G.:'Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors', Nat. Biotechnol., 2002, 20, p. 370-375
21. Haugh, J.M., Wells, A., and Lauffenburger, D.A.: 'Mathematical modeling of epidermal growth factor receptor signaling through the phospholipase C pathway: Mechanistic insights and predictions for molecular interventions', Biotechnol. Bioeng., 2000, 70, p. 225-238
22. Park, C.S., Schneider, I.C., and Haugh, J.M.: 'Kinetic analysis of platelet-derived growth factor receptor/phosphoinositide 3-kinase/Akt signaling in fibroblasts', J. Biol. Chem., 2003, 278, p. 37064-37072
23. Sedaghat, A.R., Sherman, A., and Quon, M.J.: 'A mathematical model of metabolic insulin signaling pathways', Am. J. Physiol. Endocrinol. Metab., 2002, 283, p. E1084-E1101
24. Zi, Z., Cho, K.H., Sung, M.H., Xia, X., Zheng, J., and Sun, Z.: 'In silico identification of the key components and steps in IFN-gamma induced JAK-STAT signaling pathway', FEBS Lett., 2005, 579, p. 1101-1108
25. Yamada, S., Shiono, S., Joo, A., and Yoshimura, A.: 'Control mechanism of JAK/STAT signal transduction pathway', FEBS Lett., 2003, 534, p. 190-196
26. Lee, E., Salic, A., Kruger, R., Heinrich, R., and Kirschner, M.W.: 'The roles of APC and Axin derived from experimental and theoretical analysis of the Wnt pathway', PLoS Biol., 2003, 1, p. E10
27. Hoffmann, A., Levchenko, A., Scott, M.L., and Baltimore, D.: 'The IkappaB-NF-kappaB signaling module: Temporal control and selective gene activation', Science, 2002, 298, p. 1241-1245 0036-8075
28. Vilar, J.M., Jansen, R., and Sander, C.: 'Signal processing in the TGF-beta superfamily ligand-receptor network', PLoS Comput. Biol., 2006, 2, p. e3
29. Lander, A.D., Nie, Q., and Wan, F.Y.: 'Do morphogen gradients arise by diffusion?', Dev. Cell, 2002, 2, p. 785-796
30. Huang, C.Y., and Ferrell, J.E.: 'Ultrasensitivity in the mitogen-activated protein kinase cascade', Proc. Natl. Acad. Sci. USA, 1996, 93, p. 10078-10083 0027-8424
31. Brightman, F.A., and Fell, D.A.: 'Differential feedback regulation of the MAPK cascade underlies the quantitative differences in EGF and NGF signalling in PC12 cells', FEBS Lett., 2000, 482, p. 169-174
32. Barkai, N., and Leibler, S.: 'Robustness in simple biochemical networks', Nature, 1997, 387, p. 913-917 0028-0836
33. von Dassow, G., Meir, E., Munro, E.M., and Odell, G.M.: 'The segment polarity network is a robust developmental module', Nature, 2000, 406, p. 188-192 0028-0836
34. Bhalla, U.S., and Iyengar, R.: 'Emergent properties of networks of biological signaling pathways', Science, 1999, 283, p. 381-387 10.1126/ science.283.5400.381 0036-8075
35. Ferrell, J.E., and Xiong, H.: 'Bistability in cell signaling: how to make continuous processes discontinuous, and reversible processes irreversible', Chaos, 2001, 11, p. 227-236 10.1063/1.1349894 1054-1500
36. Gardner, T.S., Cantor, C.R., and Collins, J.J.: 'Construction of a genetic toggle switch in Escherichia coli', Nature, 2000, 403, p. 339-342 0028-0836
37. Fung, E., Wong, W.W., Suen, J.K., Bulter, T., Lee, S.G., and Liao, J.C.: 'A synthetic gene-metabolic oscillator', Nature, 2005, 435, p. 118-122 0028-0836
38. Remy, I., Montmarquette, A., and Michnick, S.W.: 'PKB/Akt modulates TGF-beta signalling through a direct interaction with Smad3', Nat. Cell Biol., 2004, 6, p. 358-365
39. Conery, A.R., Cao, Y., Thompson, E.A., Townsend, C.M., Ko, T.C., and Luo, K.: 'Akt interacts directly with Smad3 to regulate the sensitivity to TGF-beta induced apoptosis', Nat. Cell Biol., 2004, 6, p. 366-372
40. Colland, F., Jacq, X., Trouplin, V., Mougin, C., Groizeleau, C., Hamburger, A., Meil, A., Wojcik, J., Legrain, P., and Gauthier, J.M.: 'Functional proteomics mapping of a human signaling pathway', Genome Res., 2004, 14, p. 1324-1332
41. Tewari, M., Hu, P.J., Ahn, J.S., Ayivi-Guedehoussou, N., Vidalain, P.O., Li, S., Milstein, S., Armstrong, C.M., Boxem, M., Butler, M.D., Busiguina, S., Rual, J.F., Ibarrola, N., Chaklos, S.T., Bertin, N., Vaglio, P., Edgley, M.L., King, K.V., Albert, P.S., Vandenhaute, J., Pandey, A., Riddle, D.L., Ruvkun, G., and Vidal, M.: 'Systematic interactome mapping and genetic perturbation analysis of a C. elegans TGF-beta signaling network', Mol. Cell, 2004, 13, p. 469-482
42. Fogler, H.S.: 'Elements of chemical reaction engineering', (Prentice - Hall PTR, Upper Saddle River, NJ 1999)
43. Nicolas, F.J., and Hill, C.S.: 'Attenuation of the TGF-beta- Smad signaling pathway in pancreatic tumor cells confers resistance to TGF-beta-induced growth arrest', Oncogene, 2003, 22, p. 3698-3711
44. Nakao, A., Roijer, E., Imamura, T., Souchelnytskyi, S., Stenman, G., Heldin, C.H., and ten Dijke, P.: 'Identification of Smad2, a human Mad-related protein in the transforming growth factor beta signaling pathway', J. Biol. Chem., 1997, 272, p. 2896-2900
45. Tian, F., DaCosta Byfield, S., Parks, W.T., Yoo, S., Felici, A., Tang, B., Piek, E., Wakefield, L.M., and Roberts, A.B.: 'Reduction in Smad2/3 signaling enhances tumorigenesis but suppresses metastasis of breast cancer cell lines', Cancer Res., 2003, 63, p. 8284-8292
46. Poncelet, A.C., de Caestecker, M.P., and Schnaper, H.W.: 'The transforming growth factor-beta/SMAD signaling pathway is present and functional in human mesangial cells', Kidney Int., 1999, 56, p. 1354-1365
47. Lagna, G., Hata, A., Hemmati-Brivanlou, A., and Massague, J.: 'Partnership between DPC4 and SMAD proteins in TGF-beta signalling pathways', Nature, 1996, 383, p. 832-836 0028-0836
48. Zhang, Y., Feng, X., We, R., and Derynck, R.: 'Receptor-associated Mad homologues synergize as effectors of the TGF-beta response', Nature, 1996, 383, p. 168-172 0028-0836
49. Kim, S.G., Kim, H.A., Jong, H.S., Park, J.H., Kim, N.K., Hong, S.H., Kim, T.Y., and Bang, Y.J.: 'The endogenous ratio of Smad2 and Smad3 influences the cytostatic function of Smad3', Mol. Biol. Cell, 2005, 16, p. 4672-4683
50. Voet, D., and Voet, J.G.: 'Biochemistry', (John Wiley & Sons, New York 1996)
51. Funaba, M., and Mathews, L.S.: 'Identification and characterization of constitutively active Smad2 mutants: Evaluation of formation of Smad complex and subcellular distribution', Mol. Endocrinol., 2000, 14, p. 1583-1591
52. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., and Walter, P.: 'Molecular biology of the cell', (Garland Science, New York 2002)
53. Montgomery, D.C.: 'Design and analysis of experiments', (John Wiley and Sons, New York, New York, USA 2001)
54. Inman, G.J.: 'Linking Smads and transcriptional activation', Biochem. J, 2005, 386, p. e1-e3
55. Fink, S.P., Mikkola, D., Willson, J.K., and Markowitz, S.: 'TGF-beta-induced nuclear localization of Smad2 and Smad3 in Smad4 null cancer cell lines', Oncogene, 2003, 22, p. 1317-323
56. Nicolas, F.J., De Bosscher, K., Schmierer, B., and Hill, C.S.: 'Analysis of Smad nucleocytoplasmic shuttling in living cells', J.Cell Sci., 2004, 117, p. 4113-4125
57. Shi, Y., Wang, Y.F., Jayaraman, L., Yang, H., Massague, J., and Pavletich, N.P.: 'Crystal structure of a Smad MH1 domain bound to DNA: insights on DNA binding in TGF-beta signaling', Cell, 1998, 94, p. 585-594
58. Lodish, H.F., Baltimore, D., Berk, A., Zipursky, L., Matsudaira, P., and Darnell, J.E.: 'Molecular cell biology', (Scientific American Books: Distributed by W.H. Freeman and Co., New York 1995)
59. Brown, K.S., Hill, C.C., Calero, G.A., Myers, C.R., Lee, K.H., Sethna, J.P., and Cerione, R.A.: 'The statistical mechanics of complex signaling networks: Nerve growth factor signaling', Phys. Biol., 2004, 1, p. 184-95 1478-3967
60. Brown, K.S., and Sethna, J.P.: 'Statistical mechanical approaches to models with many poorly known parameters', Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 2003, 68, p. 021904
61. Battogtokh, D., Asch, D.K., Case, M.E., Arnold, J., and Schuttler, H.B.: 'An ensemble method for identifying regulatory circuits with special reference to the qa gene cluster of Neurospora crassa', Proc. Natl. Acad. Sci. USA, 2002, 99, p. 16904-16909 0027-8424
62. Alves, R., and Savageau, M.A.: 'Comparing systemic properties of ensembles of biological networks by graphical and statistical methods' Bioinformatics, 2000, 16, p. 527-533
63. Alves, R., and Savageau, M.A.: 'Systemic properties of ensembles of metabolic networks: Application of graphical and statistical methods to simple unbranched pathways', Bioinformatics, 2000, 16, p. 534-547
64. Schmierer, B., and Hill, C.S.: 'Kinetic analysis of Smad nucleocytoplasmic shuttling reveals a mechanism for transforming growth factor ß-dependent nuclear accumulation of smads', Mol. Cell Biol., 2005, 25, p. 9845-9858
65. Jayaraman, L., and Massague, J.: 'Distinct oligomeric states of SMAD proteins in the transforming growth factor-beta pathway', J. Biol. Chem., 2000, 275, p. 40710-40717
66. Wu, J.W., Fairman, R., Penry, J., and Shi, Y.: 'Formation of a stable heterodimer between Smad2 and Smad4', J. Biol. Chem., 2001, 276, p. 20688-20694
67. Kawabata, M., Inoue, H., Hanyu, A., Imamura, T., and Miyazono, K.: 'Smad proteins exist as monomers in vivo and undergo homo-and hetero-oligomerization upon activation by serine/threonine kinase receptors', EMBO J, 1998, 17, p. 4056-4065
68. Chacko, B.M., Qin, B.Y., Tiwari, A., Shi, G., Lam, S., Hayward, L.J., De Caestecker, M., and Lin, K.: 'Structural basis of heteromeric smad protein assembly in TGF-β signaling', Mol. Cell, 2004, 15, p. 813-823
69. Hager, G.L., Elbi, C., and Becker, M.: 'Protein dynamics in the nuclear compartment', Curr. Opin. Genet. Dev., 2002, 12, p. 137-141