Dynamical and Integrative Cell Signaling: Challenges for the New Biology

Biotechnology and Bioengineering

Volumn 84, Issue 7, 2003, Pages 773-782

  Levchenko, Andre ^a  

^a JOHNS HOPKINS UNIVERSITY   (United States)

Author keywords

Computational modeling; High throughput data; Signal transduction

Indexed keywords

CELLS; DIFFUSION; NEURAL NETWORKS; PROTEINS;

INTERCELLULAR NETWORKS;

BIOTECHNOLOGY;

CELL COMPARTMENTALIZATION; CELL FUNCTION; CHEMICAL INTERACTION; ENVIRONMENTAL FACTOR; GENETIC DATABASE; HIGH THROUGHPUT SCREENING; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; NONHUMAN; REVIEW; SIGNAL TRANSDUCTION;

CELL COMMUNICATION; METABOLISM; MODELS, BIOLOGICAL; RESEARCH; SIGNAL TRANSDUCTION;

EID: 0346502065     PISSN: 00063592     EISSN: None     Source Type: Journal    
DOI: 10.1002/bit.10854     Document Type: Review

References (74)

1. Albanese C, D'Amico M, Reutens AT, Fu M, Watanabe G, Lee RJ, Kitsis RN, Henglein B, Avantaggiati M, Somasundaram K, et al. 1999. Activation of the cyclin D1 gene by the E1A-associated protein p300 through AP-1 inhibits cellular apoptosis. J Biol Chem 274:34186-34195.
2. Ayscough KR, Drubin DG. 1998. A role for the yeast actin cytoskeleton in pheromone receptor clustering and signalling. Curr Biol 8:927-930.
3. Bakiri L, Matsuo K, Wisniewska M, Wagner EF, Yaniv M. 2002. Promoter specificity and biological activity of tethered AP-1 dimers. Mol Cell Biol 22:4952-4964.
4. Bauer A, Mikulits W, Lagger G, Stengl G, Brosch G, Beug H. 1998. The thyroid hormone receptor functions as a ligand-operated developmental switch between proliferation and differentiation of erythroid progenitors. EMBO J 17:4291-4303.
5. Bell B, Xing H, Yan K, Gautam N, Muslin AJ. 1999. KSR-1 binds to G-protein betagamma subunits and inhibits beta gamma-induced mitogen-activated protein kinase activation. J Biol Chem 274:7982-7986.
6. Ben-Jacob E, Schochet O, Tenenbaum A, Cohen I, Czirok A, Vicsek T. 1994. Generic modelling of cooperative growth patterns in bacterial colonies. Nature 368:46-49.
7. Bhalla US. 2002. The chemical organization of signaling interactions. Bioinformatics 18:855-863.
8. Bhalla US. 2003. Understanding complex signaling networks through models and metaphors. Progr Biophys Molec Biol 81:45-65.
9. Bhalla US, Ram PT, Iyengar R. 2002. MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 297:1018-1023.
10. Bhattacharya S, Eckner R, Grossman S, Oldread E, Arany Z, D'Andrea A, Livingston DM. 1996. Cooperation of Stat2 and p300/CBP in signalling induced by interferon-alpha. Nature 383:344-347.
11. Bronnikov GE, Zhang S-J, Cannon B, Nedergaard J. 1999. A dual component analysis explains the distinctive kinetics of cAMP accumulation in brown adipocytes. J Biol Chem 274:37770-37780.
12. Bruggeman FJ, Westerhoff HV, Hoek JB, Kholodenko BN. 2002. Modular response analysis of cellular regulatory networks. J Theor Biol 218:507-520.
13. Burack WR, Sturgill TW. 1997. The activating dual phosphorylation of MAPK by MEK is nonprocessive. Biochemistry 36:5929-5333.
14. Chan HM, La Thangue NB. 2001. p300/CBP proteins: HATs for transcriptional bridges and scaffolds. J Cell Sci 114:2363-2373.
15. Cherkasova V, Lyons DM, Elion EA. 1999. Fus3p and Kss1p control G1 arrest in Saccharomyces cerevisiae through a balance of distinct arrest and proliferative functions that operate in parallel with Far1p. Genetics 151:989-1004.
16. Dohlman HG, Thorner JW. 2001. Regulation of G protein-initiated signal transduction in yeast: Paradigms and principles. Annu Rev Biochem 70:703-754.
17. 2+ response amplitude and duration. Nature 386:855-858.
18. Elion EA. 2000. Pheromone response, mating and cell biology. Curr Opin Microbiol 3:573-581.
19. Ferrell JE Jr. 2002. Self-perpetuating states in signal transduction: Positive feedback, double-negative feedback and bistability. Curr Opin Cell Biol 14:140-148.
20. Feske S, Draeger R, Peter HH, Eichmann K, Rao A. 2000. The duration of nuclear residence of NFAT determines the pattern of cytokine expression in human SCID T cells. J Immunol 165:297-305.
21. Feske S, Gilmane J, Dolmetsch R, Staudt LM, Rao A. 2001. Gene regulation mediated by calcium signals in T lymphocytes. Nat Immunol 2:316-324.
22. Furthauer M, Lin W, Ang SL, Thisse B, Thisse C. 2002. Sef is a feedback-induced antagonist of Ras/MAPK-mediated FGF signalling. Nat Cell Biol 4:170-174.
23. Gagiano M, Bauer FF, Pretorius IS. 2002. The sensing of nutritional status and the relationship to filamentous growth in Saccharomyces cerevisiae. FEM Yeast Res 2:433-470.
24. Gawantka V, Pollet N, Delius H, Vingron M, Pfister R, Nitsch R, Blumenstock C, Niehrs C. 1998. Gene expression screening in Xenopus identifies molecular pathways, predicts gene function and provides a global view of embryonic patterning. Mech Dev 77:95-141.
25. Gong Q, Cheng AM, Akk AM, Alberola-Ila J, Gong G, Pawson T, Chan AC. 2001. Disruption of T cell signaling networks and development by Grb2 haploid insufficiency. Nat Immunol 2:29-36.
26. Grotewold L, Plum M, Dildrop R, Peters T, Ruther U. 2001. BAMBI is coexpressed with BMP-4 during mouse embryogenesis. Mech Dev 100:327-330.
27. Guo QM. 2003. DNA microarray and cancer. Curr Opin Oncol 15:36-43.
28. Hartwell LH, Hopfield JJ, Leibler S, Murray AW. 1999. From molecular to modular cell biology. Nature 402(suppl):C47-C52.
29. Hendriks BS, Opresko LK, Wiley HS, Lauffenburger D. 2003. Quantitative analysis of HER2-mediated effects on HER2 and epidermal growth factor receptor endocytosis: distribution of homo-and heterodimers depends on relative HER2 levels. J Biol Chem 278:23343-23351.
30. Hoffmann A, Levchenko A, Scott ML, Baltimore D. 2002. The IκB-NF-κB signaling module: Temporal control and selective gene activation. Science 298:1241-1245.
31. Holme P, Huss M, Jeong H. 2003. Subnetwork hierarchies of biochemical pathways. Bioinformatics 19:532-538.
32. Lacasta AM, Cantalapiedra IR, Auguet CE, Penaranda A, Ramirez-Piscina L. 1999. Modeling of spatiotemporal patterns in bacterial colonies. Phys Rev E Stat Phys Plasmas Fluids Rel Interdiscipl Topics 59:7036-7041.
33. Lahaye K, Kricha S, Bellefroid EJ. 2002. XNAP, a conserved ankyrin repeat-containing protein with a role in the Notch pathway during Xenopus primary neurogenesis. Mech Dev 110:113-124.
34. Lallemand D, Spyrou G, Yaniv M, Pfarr CM. 1997. Variations in Jun and Fos protein expression and AP-1 activity in cycling, resting and stimulated fibroblasts. Oncogene 14:819-830.
35. Lamar E, Deblandre G, Wettstein D, Gawantka V, Pollet N, Niehrs C, Kintner C. 2001. Nrarp is a novel intracellular component of the Notch signaling pathway. Genes Dev 15:1885-1899.
36. Lebel JM, Dussault JH, Puymirat J. 1994. Overexpression of the beta 1 thyroid receptor induces differentiation in neuro-2a cells. Proc Natl Acad Sci USA 91:2644-2648.
37. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GK, Hannett NM, Harbison CT, Thompson CM, Simon I, et al. 2002. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799-804.
38. Levchenko A, Bruck J, Sternberg PW. 2000. Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. Proc Natl Acad Sci USA 97:5818-5823.
39. Lim HW, New L, Han J, Molkentin JD. 2001. Calcineurin enhances MAPK phosphatase-1 expression and p38 MAPK inactivation in cardiac myocytes. J Biol Chem 276:15913-15919.
40. Lyons DM, Mahanty SK, Choi KY, Manandhar M, Elion EA. 1996. The SH3-domain protein Bem1 coordinates mitogen-activated protein kinase cascade activation with cell cycle control in Saccharomyces cerevisiae. Mol Cell Biol 16:4095-4106.
41. Marshall CJ. 1995. Specificity of receptor tyrosine kinase signaling: Transient versus sustained extracellular signal-regulated kinase activation. Cell 80:179-185.
42. Metzler B, Hu Y, Sturm G, Wick G, Xu Q. 1998. Induction of mitogen-activated protein kinase phosphatase-1 by arachidonic acid in vascular smooth muscle cells. J Biol Chem 273:33320-33326.
43. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U. 2002. Network motifs: Simple building blocks of complex networks. Science 298:824-827.
44. Mink S, Haenig B, Klempnauer KH. 1997. Interaction and functional collaboration of p300 and C/EBPbeta. Mol Cell Biol 17:6609-6617.
45. Miyamoto S, Schmitt MJ, Verma IM. 1994. Qualitative changes in the subunit composition of kappa B-binding complexes during murine B-cell differentiation. Proc Natl Acad Sci USA 91:5056-5060.
46. Muller D, Exler S, Aguilera-Vazquez L, Guerrero-Martin E, Reuss M. 2003. Cyclic AMP mediates the cell cycle dynamics of energy metabolism in Saccharomyces cerevisiae. Yeast 20:351-367.
47. Niehrs C, Pollet N. 1999. Synexpression groups in eukaryotes. Nature 402:483-487.
48. O'Rourke SM, Herskowitz I. 1998. The Hog1 MAPK prevents cross talk between the HOG and pheromone response MAPK pathways in Saccharomyces cerevisiae. Genes Dev 12:2874-2886.
49. Pan X, Harashima T, Heitman J. 2000. Signal transduction cascades regulating pseudohyphal differentiation of Saccharomyces cerevisiae. Curr Opin Microbiol 3:567-572.
50. Pan X, Heitman J. 2002. Protein kinase A operates a molecular switch that governs yeast pseudohyphal differentiation. Mol Cell Biol 22:3981-3993.
51. Peter M, Gartner A, Horecka J, Ammerer G, Herskowitz I. 1993. FARI links the signal transduction pathway to the cell cycle machinery in yeast. Cell 73:747-460.
52. Posas F, Takekawa M, Saito H. 1998. Signal transduction by MAP kinase cascades in budding yeast. Curr Opin Microbiol 1:175-182.
53. Pribyl M, Muratov CB, Shvartsman SY. 2003. Discrete models of autocrine cell communication in epithelial layers. Biophys J 84:3624-3635.
54. Rao CV, Arkin AP. 2001. Control motifs for intracellular regulatory networks. Annu Rev Biomed Eng 3:391-419.
55. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi A-L. 2002. Hierarchical organization of modularity in metabolic networks. Science 297:1551-1555.
56. Ravi R, Mookerjee B, van Hensbergen Y, Bedi GC, Giordano A, El-Deiry WS, Fuchs EJ, Bedi A. 1998. p53-mediated repression of nuclear factor-kappaB RelA via the transcriptional integrator p300. Cancer Res 58:4531-4536.
57. Reynolds TB, Fink GR. 2001. Bakers' yeast, a model for fungal biofilm formation. Science 291:878-881.
58. Rives AW, Galitski T. 2003. Modular organization of cellular networks. Proc Natl Acad Sci USA 100:1128-1133.
59. Rolland F, Winderickx J, Thevelein JM. 2002. Glucose-sensing and -signalling mechanisms in yeast. FEM Yeast Res 2:183-201.
60. Sabbagh W Jr., Flatauer LJ, Bardwell AJ, Bardwell L. 2001. Specificity of MAP kinase signaling in yeast differentiation involves transient versus sustained MAPK activation. Mol Cell 8:683-691.
61. Sams TSK, Jensen MH, Ellegaard C, Christensen BE, Thrane U. 1997. Morphological instabilities in a growing yeast colony: Experiment and theory. Phys Rev Lett 79:313-316.
62. Sellers LA, Alderton F, Carruthers AM, Schindler M, Humphrey PP. 2000. Receptor isoforms mediate opposing proliferative effects through gbe tagamma-activated p38 or Akt pathways. Mol Cell Biol 20:5974-5985.
63. Steffen M, Petti A, Aach J, D'Haeseleer P, Church G. 2002. Automated modelling of signal transduction networks. BMC Bioinformatics 3:34.
64. Sugiura R, Toda T, Dhut S, Shuntoh H, Kuno T. 1999. The MAPK kinase Pek1 acts as a phosphorylation-dependent molecular switch. Nature 399:479-483.
65. Thieffry D, Romero D. 1999. The modularity of biological regulatory networks. Biosystems 50:49-59.
66. Tsang M, Friesel R, Kudoh T, Dawid IB. 2002. Identification of Sef, a novel modulator of FGF signalling. Nat Cell Biol 4:165-169.
67. Tyson JJ, Chen K, Novak B. 2001. Network dynamics and cell physiology. Nat Rev Mol Cell Biol 2:908-916.
68. Tyson JJ, Chen KC, Novak B. 2003. Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15:221-231.
69. Weng G, Bhalla US, Iyengar R. 1999. Complexity in biological signaling systems. Science 284:92-96.
70. Wennstrom S, Downward J. 1999. Role of phosphoinositide 3-kinase in activation of Ras and mitogen-activated protein kinase by epidermal growth factor. Mol Cell Biol 19:4279-4288.
71. Wiley SH, Shvartsman SY, Lauffenburger DA. 2003. Computational modeling of the EGF-receptor system: A paradigm for systems biology. Trends Cell Biol 13:43-50.
72. Wolfram S. 2002. A new kind of science. Champaign, IL: Wolfram Media.
73. Yang C, Shapiro LH, Rivera M, Kumar A, Brindle PK. 1998. A role for CREB binding protein and p300 transcriptional coactivators in Ets-1 transactivation functions. Mol Cell Biol 18:2218-2229.
74. Yuan W, Condorelli G, Caruso M, Felsani A, Giordano A. 1996. Human p300 protein is a coactivator for the transcription factor MyoD. J Biol Chem 271:9009-9013.