Spatially distributed cell signalling

FEBS Letters

Volumn 583, Issue 24, 2009, Pages 4006-4012

  Kholodenko, Boris N ^a,b  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

^b THOMAS JEFFERSON UNIVERSITY   (United States)

Author keywords

Protein modification cycle; Signal transduction; Spatial gradient; Spatiotemporal dynamic

Indexed keywords

PHOSPHOPROTEIN;

CELL METABOLISM; CELL POLARITY; CELL SHAPE; CELL SIZE; CELLULAR DISTRIBUTION; DIFFUSION; ENZYME ACTIVATION; FEEDBACK SYSTEM; HUMAN; MATHEMATICAL MODEL; MICROSCOPY; MOLECULAR IMAGING; NONHUMAN; PRIORITY JOURNAL; PROTEIN PROCESSING; PROTEIN TRANSPORT; REVIEW; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

BIOLOGICAL TRANSPORT; CELL POLARITY; CELL SIZE; FEEDBACK, PHYSIOLOGICAL; MAP KINASE SIGNALING SYSTEM; PHOSPHOPROTEINS; PROTEIN PROCESSING, POST-TRANSLATIONAL;

EID: 71149087930     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2009.09.045     Document Type: Review

References (50)

1. Kholodenko B.N., and Westerhoff H.V. The macroworld versus the microworld of biochemical regulation and control. Trends Biochem. Sci. 20 (1995) 52-54
2. Agius, L., Sheratt, H.S.A. (1997) Channeling in Intermediary Metabolism. Portland Press.
3. Srere P.A. Macromolecular interactions: tracing the roots. Trends Biochem. Sci. 25 (2000) 150-153
4. Bastiaens P., Caudron M., Niethammer P., and Karsenti E. Gradients in the self-organization of the mitotic spindle. Trends Cell Biol. 16 (2006) 125-134
5. Mori Y., Jilkine A., and Edelstein-Keshet L. Wave-pinning and cell polarity from a bistable reaction-diffusion system. Biophys. J. 94 (2008) 3684-3697
6. Kholodenko B.N., and Kolch W. Giving space to cell signaling. Cell 133 (2008) 566-567
7. Turing A.M. The chemical basis of morphogenesis. Phil. Trans. R. Soc. Lond. B Biol. Sci. 237 (1952) 37-72
8. Asai R., Taguchi E., Kume Y., Saito M., and Kondo S. Zebrafish leopard gene as a component of the putative reaction-diffusion system. Mech. Dev. 89 (1999) 87-92
9. Brown G.C., and Kholodenko B.N. Spatial gradients of cellular phospho-proteins. FEBS Lett. 457 (1999) 452-454
10. Seet B.T., Dikic I., Zhou M.M., and Pawson T. Reading protein modifications with interaction domains. Nat. Rev. Mol. Cell Biol. 7 (2006) 473-483
11. Sauro H.M., and Kholodenko B.N. Quantitative analysis of signaling networks. Prog. Biophys. Mol. Biol. 86 (2004) 5-43
12. Goldbeter A., and Koshland Jr. D.E. Ultrasensitivity in biochemical systems controlled by covalent modification. Interplay between zero-order and multistep effects. J. Biol. Chem. 259 (1984) 14441-14447
13. Bluthgen N., Bruggeman F.J., Legewie S., Herzel H., Westerhoff H.V., and Kholodenko B.N. Effects of sequestration on signal transduction cascades. FEBS J. 273 (2006) 895-906
14. van Albada S.B., and ten Wolde P.R. Enzyme localization can drastically affect signal amplification in signal transduction pathways. PLoS Comput. Biol. 3 (2007) 1925-1934
15. Kalab P., Weis K., and Heald R. Visualization of a Ran-GTP gradient in interphase and mitotic Xenopus egg extracts. Science 295 (2002) 2452-2456
16. Niethammer P., Bastiaens P., and Karsenti E. Stathmin-tubulin interaction gradients in motile and mitotic cells. Science 303 (2004) 1862-1866
17. Maeder C.I., Hink M.A., Kinkhabwala A., Mayr R., Bastiaens P.I., and Knop M. Spatial regulation of Fus3 MAP kinase activity through a reaction-diffusion mechanism in yeast pheromone signalling. Nat. Cell Biol. 9 (2007) 1319-1326
18. Fuller B.G., et al. Midzone activation of aurora B in anaphase produces an intracellular phosphorylation gradient. Nature 453 (2008) 1132-1136
19. Slepchenko B.M., and Terasaki M. Cyclin aggregation and robustness of bio-switching. Mol. Biol. Cell 14 (2003) 4695-4706
20. 2+ oscillations. Biophys. J. 67 (1994) 447-456
21. Stelling, J. and Kholodenko, B.N. (2008) Signaling cascades as cellular devices for spatial computations. J. Math. Biol.
22. Kusumi A., et al. Paradigm shift of the plasma membrane concept from the two-dimensional continuum fluid to the partitioned fluid: high-speed single-molecule tracking of membrane molecules. Annu. Rev. Biophys. Biomol. Struct. 34 (2005) 351-378
23. Singer S.J., and Nicolson G.L. The fluid mosaic model of the structure of cell membranes. Science 175 (1972) 720-731
24. Ritchie K., Shan X.Y., Kondo J., Iwasawa K., Fujiwara T., and Kusumi A. Detection of non-Brownian diffusion in the cell membrane in single molecule tracking. Biophys. J. 88 (2005) 2266-2277
25. Mayawala K., Vlachos D.G., and Edwards J.S. Spatial modeling of dimerization reaction dynamics in the plasma membrane: Monte Carlo vs. Continuum differential equations. Biophys. Chem. 121 (2006) 194-208
26. Brinkerhoff C.J., Choi J.S., and Linderman J.J. Diffusion-limited reactions in G-protein activation: unexpected consequences of antagonist and agonist competition. J. Theor. Biol. 251 (2008) 561-569
27. Niehaus A.M., Vlachos D.G., Edwards J.S., Plechac P., and Tribe R. Microscopic simulation of membrane molecule diffusion on corralled membrane surfaces. Biophys. J. 94 (2008) 1551-1564
28. Costa M.N., Radhakrishnan K., Wilson B.S., Vlachos D.G., and Edwards J.S. Coupled stochastic spatial and non-spatial simulations of ErbB1 signaling pathways demonstrate the importance of spatial organization in signal transduction. PLoS One 4 (2009) e6316
29. Berezhkovskii A.M., Coppey M., and Shvartsman S.Y. Signaling gradients in cascades of two-state reaction-diffusion systems. Proc. Natl. Acad. Sci. USA 106 (2009) 1087-1092
30. Kholodenko B.N. MAP kinase cascade signaling and endocytic trafficking: a marriage of convenience?. Trends Cell Biol. 12 (2002) 173-177
31. Munoz-Garcia J., Neufeld Z., and Kholodenko B.N. Positional information generated by spatially distributed signaling cascades. PLoS Comput. Biol. 5 (2009) e1000330
32. Kholodenko B.N. Cell-signalling dynamics in time and space. Nat. Rev. Mol. Cell. Biol. 7 (2006) 165-176
33. Jilkine A., Maree A.F., and Edelstein-Keshet L. Mathematical model for spatial segregation of the Rho-family GTPases based on inhibitory crosstalk. Bull. Math. Biol. 69 (2007) 1943-1978
34. Athale C.A., Dinarina A., Mora-Coral M., Pugieux C., Nedelec F., and Karsenti E. Regulation of microtubule dynamics by reaction cascades around chromosomes. Science 322 (2008) 1243-1247
35. Meyers J., Craig J., and Odde D.J. Potential for Control of Signaling Pathways via Cell Size and Shape. Curr. Biol. 16 (2006) 1685-1693
36. Nalbant P., Hodgson L., Kraynov V., Toutchkine A., and Hahn K.M. Activation of endogenous Cdc42 visualized in living cells. Science 305 (2004) 1615-1619
37. Neves S.R., et al. Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks. Cell 133 (2008) 666-680
38. Fell D.A. Theoretical analyses of the functioning of the high- and low-Km cyclic nucleotide phosphodiesterases in the regulation of the concentration of adenosine 3′,5′-cyclic monophosphate in animal cells. J. Theor. Biol. 84 (1980) 361-385
39. Zaccolo M., and Pozzan T. Discrete microdomains with high concentration of cAMP in stimulated rat neonatal cardiac myocytes. Science 295 (2002) 1711-1715
40. Parent C.A., and Devreotes P.N. A cell's sense of direction. Science 284 (1999) 765-770
41. Iglesias P.A., and Devreotes P.N. Navigating through models of chemotaxis. Curr. Opin. Cell Biol. 20 (2008) 35-40
42. Ginty D.D., and Segal R.A. Retrograde neurotrophin signaling: Trk-ing along the axon. Curr. Opin. Neurobiol. 12 (2002) 268-274
43. Campenot R.B., and MacInnis B.L. Retrograde transport of neurotrophins: fact and function. J. Neurobiol. 58 (2004) 217-229
44. Perlson E., Hanz S., Ben-Yaakov K., Segal-Ruder Y., Seger R., and Fainzilber M. Vimentin-dependent spatial translocation of an activated MAP kinase in injured nerve. Neuron 45 (2005) 715-726
45. Perlson E., Michaelevski I., Kowalsman N., Ben-Yaakov K., Shaked M., Seger R., Eisenstein M., and Fainzilber M. Vimentin binding to phosphorylated Erk sterically hinders enzymatic dephosphorylation of the kinase. J. Mol. Biol. 364 (2006) 938-944
46. Reynolds A.R., Tischer C., Verveer P.J., Rocks O., and Bastiaens P.I. EGFR activation coupled to inhibition of tyrosine phosphatases causes lateral signal propagation. Nat. Cell. Biol. 5 (2003) 447-453
47. MacInnis B.L., Senger D.L., and Campenot R.B. Spatial requirements for TrkA kinase activity in the support of neuronal survival and axon growth in rat sympathetic neurons. Neuropharmacology 45 (2003) 995-1010
48. Markevich N.I., Tsyganov M.A., Hoek J.B., and Kholodenko B.N. Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades. Mol. Syst. Biol. 2 (2006) 61
49. Brown G.C., Westerhoff H.V., and Kholodenko B.N. Molecular control analysis: control within proteins and molecular processes. J. Theor. Biol. 182 (1996) 389-396
50. Peletier M.A., Westerhoff H.V., and Kholodenko B.N. Control of spatially heterogeneous and time-varying cellular reaction networks: a new summation law. J. Theor. Biol. 225 (2003) 477-487