An investigation of spatial signal transduction in cellular networks

BMC Systems Biology

Volumn 6, Issue , 2012, Pages

  Alam Nazki, Aiman ^a   Krishnan, J ^a,b  

^a Centre for Process Systems Engineering   (United Kingdom)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

Cellular signal processing; Diffusion; Global regulation; Networks; Non linear dynamics; Signalling motifs; Spatial signalling

Indexed keywords

EUKARYOTA;

ARTICLE; BIOLOGICAL MODEL; CELLS; CYTOLOGY; DIFFUSION; FEEDBACK SYSTEM; METHODOLOGY; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

CELLS; DIFFUSION; FEEDBACK, PHYSIOLOGICAL; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

MLCS; MLOWN;

EID: 84863459584     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-6-83     Document Type: Article

References (60)

1. Gomperts BD, Kramer IM, Tatham PER. Signal Transduction 2009, London: Academic Press.
2. Kholodenko BN, Hancock JF, Kolch W. Signalling ballet in space and time. Nat Rev Mol Cell Biol 2010, 11:414-426. 10.1038/nrm2901, 2977972, 20495582.
3. Stelling J, Kholodenko BN. Signaling cascades as cellular devices for spatial computations. J Math Biol 2009, 58:35-55. 10.1007/s00285-008-0162-6, 2574718, 18283462.
4. Sturrock M, Terry AJ, Xirodimas DP, Thompson AM, Chaplain MAJ. Spatio-temporal modelling of the Hes1 and p53-Mdm2 intracellular signalling pathways. J Theor Biol 2011, 9:11352-11357.
5. Rappaport R. Cytokinesis in animal cells. Int Rev Cytol 1971, 31:169-213.
6. Nelson WJ. Adaptation of core mechanisms to generate cell polarity. Nature 2003, 422:766-774. 10.1038/nature01602, 3373010, 12700771.
7. Eisenbach M. Chemotaxis 2004, London: Imperial College Press.
8. Berridge MJ, Lipp P, Bootman MD. The versatility and universality of calcium signalling. Nat Rev Mol Cell Biol 2000, 1:11-21.
9. Shapiro L, McAdams HH, Losick R. Why and how bacteria localize proteins. Science 2009, 326:1225-1228. 10.1126/science.1175685, 19965466.
10. Loose M, Fischer-Friedrich E, Ries J, Kruse K, Schwille P. Spatial regulators for bacterial cell division self-organize into surface waves in vitro. Science 2008, 320:789-792. 10.1126/science.1154413, 18467587.
11. Schwarz-Romond T, Gorski SA. Focus on the Spatial Organization of Signalling. THE EMBO Journal 2010, 29:2675-2676. 10.1038/emboj.2010.185, 2924656, 20717137.
12. Hurtley S. Location, Location, Location. Science 2009, 326:1205. 10.1126/science.326.5957.1205, 19965460.
13. Kholodenko BN. Cell-signalling dynamics in time and space. Nat Rev Mol Cell Biol 2006, 7:165-176. 10.1038/nrm1838, 1679905, 16482094.
14. Ma L, Janetopoulos C, Yang L, Devreotes PN, Iglesias PA. Two complementary, local excitation, global inhibition mechanisms acting in parallel can explain the chemoattractant-induced regulation of PI(3,4,5)P3 response in dictyostelium cells. Biophys J 2004, 87(6):3764-3774. [http://dx.doi.org/10.1529/biophysj.104.045484], 10.1529/biophysj.104.045484, 1304889, 15465874.
15. Alam-Nazki A, Krishnan J. A Mathematical Modelling Framework for Understanding Chemorepulsive Signal Transduction in Dictyostelium. J Theor Biol 2010, [http://dx.doi.org/10.1016/j.jtbi.2010.05.017].
16. Moore TI, Chou CS, Nie Q, Jeon NL, Yi TM. Robust spatial sensing of mating pheromone gradients by yeast cells. PLoS One 2008, 3(12):e3865. [http://dx.doi.org/10.1371/journal.pone.0003865], 10.1371/journal.pone.0003865, 2586657, 19052645.
17. Dawes AT, Edelstein-Keshet L. Phosphoinositides and Rho proteins spatially regulate actin polymerization to initiate and maintain directed movement in a one-dimensional model of a motile cell. Biophys J 2007, 92:744-768. 10.1529/biophysj.106.090514, 1779977, 17098793.
18. Maly IV, Wiley HS, A LD. Self-organization of polarized cell signaling via autocrine circuits: computational model analysis. Biophys J 2004, 86:10-22. 10.1016/S0006-3495(04)74079-5, 1303773, 14695245.
19. Howell AS, Savage NS, Johnson SA, Bose I, Wagner AW, Zyla TR, Nijhout HF, Reed MC, Goryachev AB, Lew DJ. Singularity in polarization: rewiring yeast cells to make two buds. Cell 2009, 139(4):731-743. [http://dx.doi.org/10.1016/j.cell.2009.10.024], 10.1016/j.cell.2009.10.024, 2783644, 19914166.
20. Altschuler SJ, Angenent SB, Wang Y, Wu LF. On the spontaneous emergence of cell polarity. Nature 2008, 454(7206):886-889. [http://dx.doi.org/10.1038/nature07119], 10.1038/nature07119, 2562338, 18704086.
21. Zhao Q, Yi M, Liu Y. Spatial distribution and dose-response relationship for different operation modes in a reaction-diffusion model of the MAPK cascade. Phys Biol 2011, 8(5):055004. [http://dx.doi.org/10.1088/1478-3975/8/5/055004], 10.1088/1478-3975/8/5/055004, 21832801.
22. Vilela M, Morgan JJ, Lindahl PA. Mathematical model of a cell size checkpoint. PLoS Comput Biol 2010, 6(12):e1001036. [http://dx.doi.org/10.1371/journal.pcbi.1001036], 10.1371/journal.pcbi.1001036, 3002998, 21187911.
23. Padte NN, Martin SG, Howard M, Chang F. The cell-end factor pom1p inhibits mid1p in specification of the cell division plane in fission yeast. Curr Biol 2006, 16(24):2480-2487. [http://dx.doi.org/10.1016/j.cub.2006.11.024], 10.1016/j.cub.2006.11.024, 17140794.
24. Caudron M, Bunt G, Bastiaens P, Karsenti E. Spatial coordination of spindle assembly by chromosome-mediated signaling gradients. Science 2005, 309(5739):1373-1376. [http://dx.doi.org/10.1126/science.1115964], 10.1126/science.1115964, 16123300.
25. Karsenti E. Self-organization in cell biology: a brief history. Nat Rev Mol Cell Biol 2008, 9:255-262.
26. Turing AM. The chemical basis of morphogenesis. Phil Trans Roy Soc 1952, 237:37-72.
27. Gierer A, Meinhardt H. A theory of biological pattern formation. Kybernetik 1972, 12:30-39. 10.1007/BF00289234, 4663624.
28. Tyson JJ, Chen KC, Novak B. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 2003, 15:221-231. 10.1016/S0955-0674(03)00017-6, 12648679.
29. Alon U. An Introduction to Systems Biology: Design Principles of Biological Circuits 2006, Boca Raton, Florida: Chapman and Hall/CRC.
30. Krishnan J. Signal processing through a generalized module of adaptation and spatial sensing. J Theor Biol 2009, 259:31-43. 10.1016/j.jtbi.2009.02.015, 19254728.
31. Krishnan J. Effects of saturation and enzyme limitation in feedforward adaptive signal transduction. IET Syst Biol 2011, 5:208. 10.1049/iet-syb.2010.0048, 21639593.
32. Ferrell JE. Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs. Trends Biochem Sci 1996, 21:460-466. 10.1016/S0968-0004(96)20026-X, 9009826.
33. Goldbeter A, Koshland DE. An amplified sensitivity arising from covalent modification in biological systems. Proc Natl Acad Sci U S A 1981, 78:6840-6844. 10.1073/pnas.78.11.6840, 349147, 6947258.
34. Ferrell JE, Xiong W. Bistability in cell signaling: How to make continuous processes discontinuous, and reversible processes irreversible. Chaos 2001, 11:227-236. 10.1063/1.1349894, 12779456.
35. Tyson JJ, Novák B. Functional motifs in biochemical reaction networks. Annu Rev Phys Chem 2010, 61:219-240. [http://dx.doi.org/10.1146/annurev.physchem.012809.103457], 10.1146/annurev.physchem.012809.103457, 20055671.
36. Park CS, Schneider IC, Haugh JM. Kinetic Analysis of Platelet-derived Growth Factor Receptor/Phosphoinositide 3-Kinase/Akt Signaling in Fibroblasts. Journ Biol Chem 2003, 278:37064-37072.
37. Krauss G. Biochemistry of Signal Transduction and Regulation 2008, Weinheim: Wiley.
38. Levchenko A, Iglesias PA. Models of eukaryotic gradient sensing: application to chemotaxis of amoebae and neutrophils. Biophys J 2002, 82:50-63. 10.1016/S0006-3495(02)75373-3, 1302448, 11751295.
39. Krishnan J, Alam-Nazki A. An investigation of design principles underlying repulsive and attractive gradient sensing and their switching. J Theor Biol 2011, 273:80-99. [http://dx.doi.org/10.1016/j.jtbi.2010.11.046], 10.1016/j.jtbi.2010.11.046, 21167180.
40. Calabrese EJ. Cell Migration/Chemotaxis: Biphasic Dose Responses. Crit Rev Toxicol 2001, 31:615-624. 10.1080/20014091111875, 11504186.
41. Nishiyama M, Hoshino A, Tsai L, Henley JR, Goshima Y, Tessier-Lavigne M, Poo M, Hong K. Cyclic AMP/GMP-dependent modulation of Ca2+ channels sets the polarity of nerve growth-cone turning. Nature 2003, 423(6943):990-995. [http://dx.doi.org/10.1038/nature01751], 10.1038/nature01751, 12827203.
42. Ferrell JE, Machleder ME. The Biochemical Basis of an All-or-None Cell Fate Switch in Xenopus Oocytes. Science 1998, 280:895-898. 10.1126/science.280.5365.895, 9572732.
43. Meyer T, Stryer L. Molecular model for receptor-stimulated calcium spiking. Proc Natl Acad Sci U S A 1988, 85(14):5051-5055. 10.1073/pnas.85.14.5051, 281685, 2455890.
44. Behar M, Hao N, Dohlman HG, Elston TC. Mathematical and computational analysis of adaptation via feedback inhibition in signal transduction pathways. Biophys J 2007, 93:806-821. 10.1529/biophysj.107.107516, 1913166, 17513354.
45. Marks F, Müller-Decker K, Klingmüller U. Cellular Signal Processing: An Introduction to the Molecular Mechanisms of Signal Transduction 2008, New York: Garland Science.
46. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Molecular Biology of the Cell 2008, New York: Garland Science, [http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=mboc4].
47. Mori A, Jilkine Y, Edelstein-Keshet L. Wave-pinning and cell polarity from a bistable reaction-diffusion system. Biophys J 2008, 94:3684-3697. 10.1529/biophysj.107.120824, 2292363, 18212014.
48. Murray JD. Mathematical Biology 2008, New York: Springer.
49. Markevich NI, Tsyganov MA, Hoek BJ, Kholodenko BN. Long-range signaling by phosphoprotein waves arising from bistability in protein kinase cascades. Mol Sys Biol 2006, 2:61.
50. Moseley JB, Mayeux A, Paoletti A, Nurse P. A spatial gradient coordinates cell size and mitotic entry in fission yeast. Nature 2009, 459:857-860. 10.1038/nature08074, 19474789.
51. Rosse C, Linch M, Kermorgant S, Cameron AJM, Boeckeler K, Parker PJ. PKC and the control of localized signal dynamics. Nat Rev Mol Cell Biol 2010, 11:103-112. 10.1038/nrm2847, 20094051.
52. Saini DK, Chisari M, Gautam N. Shuttling and translocation of heterotrimeric G proteins and Ras. Trends Pharmacol Sci 2009, 30:278-286. 10.1016/j.tips.2009.04.001, 3097116, 19427041.
53. Lipshtat A, Jayaraman G, He JC, Iyengar R. Design of versatile biochemical switches that respond to amplitude, duration, and spatial cues. Proc Natl Acad Sci U S A 2010, 107:1247-1252. 10.1073/pnas.0908647107, 2824311, 20080566.
54. Othmer H, Schaap P. Oscillatory cAMP signaling in the development of Dictyostelium discoideum. Comments on Theoretical Biology 1998, 5:175-282.
55. Narang A. Spontaneous polarization in eukaryotic gradient sensing: a mathematical model based on mutual inhibition of frontness and backness pathways. J Theor Biol 2006, 240:538-553. 10.1016/j.jtbi.2005.10.022, 16343548.
56. Levskaya A, Weiner OD, Lim WA, Voigt CA. Spatiotemporal control of cell signalling using a light-switchable protein interaction. Nature 2009, 461:997-1001. 10.1038/nature08446, 2989900, 19749742.
57. Good MC, Zalatan JG, Lim WA. Scaffold proteins: hubs for controlling the flow of cellular information. Science 2011, 332:680-686. 10.1126/science.1198701, 3117218, 21551057.
58. Liu AP, Fletcher DA. Biology under construction: in vitro reconstitution of cellular function. Nat Rev Mol Cell Biol 2009, 10(9):644-650. [http://dx.doi.org/10.1038/nrm2746], 10.1038/nrm2746, 2937256, 19672276.
59. Aguda BD. A quantitative analysis of the kinetics of the G(2) DNA damage checkpoint system. Proc Natl Acad Sci U S A 1999, 9:11352-11357.
60. Albeck J. Modeling a snap-action, variable-delay switch controlling extrinsic cell death. PLoS Biol 2008, 6:2831-2852. 2592357, 19053173.