ERK as a model for systems biology of enzyme kinetics in cells

Current Biology

Volumn 23, Issue 21, 2013, Pages

  Futran, Alan S ^a   Link, A James ^a,b   Seger, Rony ^c   Shvartsman, Stanislav Y ^a,b  

^a Princeton University   (United States)

^b PRINCETON UNIVERSITY   (United States)

^c WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

MITOGEN ACTIVATED PROTEIN KINASE;

ANIMAL; BIOLOGICAL MODEL; CATALYSIS; CHEMICAL MODEL; CHEMISTRY; HUMAN; KINETICS; REVIEW; SYSTEMS BIOLOGY;

ANIMALS; CATALYSIS; EXTRACELLULAR SIGNAL-REGULATED MAP KINASES; HUMANS; KINETICS; MODELS, BIOLOGICAL; MODELS, CHEMICAL; SYSTEMS BIOLOGY;

EID: 84887165987     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2013.09.033     Document Type: Review

References (79)

1. M.A. Sainz-Polo, M. Ramirez-Escudero, A. Lafraya, B. Gonzalez, J. Marin-Navarro, J. Polaina, and J. Sanz-Aparicio Three-dimensional structure of Saccharomyces invertase: role of a non-catalytic domain in oligomerization and substrate specificity J. Biol. Chem. 288 2013 9755 9766
2. K.A. Johnson, and R.S. Goody The original Michaelis constant: translation of the 1913 Michaelis-Menten paper Biochemistry 50 2011 8264 8269
3. L. Michaelis, and M.L. Menten Die kinetik der invertinwirkung Biochem. Z 49 1913 333 369
4. J.S. Fruton Proteins, Enzymes, Genes: The Interplay of Chemistry and Biology 1999 Yale University Press
5. A. Cornish-Bowden The origins of enzyme kinetics FEBS Lett. 587 2013 2725 2730
6. K.A. Johnson A century of enzyme kinetic analysis, 1913 to 2013 FEBS Lett. 587 2013 2753 2766
7. B. Chance The kinetics of the enzyme-substrate compound of peroxidase J. Biol. Chem. 151 1943 553 577
8. J. Gunawardena Some lessons about models from Michaelis and Menten Mol. Biol. Cell 23 2012 517 519
9. J. Avruch MAP kinase pathways: The first twenty years Biochim. Biophys. Acta 1773 2007 1150 1160
10. R. Seger, and E.G. Krebs The MAPK signaling cascade FASEB J. 9 1995 726 735
11. T.W. Sturgill, L.B. Ray, E. Erikson, and J.L. Maller Insulin-stimulated MAP-2 kinase phosphorylates and activates ribosomal protein S6 kinase II Nature 334 1988 715 718
12. T.G. Boulton, G.D. Yancopoulos, J.S. Gregory, C. Slaughter, C. Moomaw, J. Hsu, and M.H. Cobb An insulin-stimulated protein kinase similar to yeast kinases involved in cell cycle control Science 249 1990 64 67
13. T.G. Boulton, S.H. Nye, D.J. Robbins, N.Y. Ip, E. Radziejewska, S.D. Morgenbesser, R.A. DePinho, N. Panayotatos, M.H. Cobb, and G.D. Yancopoulos ERK's: a family of protein-serine/threonine kinases that are activated and tyrosine phosphorylated in response to insulin and NGF Cell 65 1991 663 675
14. Y. Keshet, and R. Seger The MAP kinase signaling cascades: a system of hundreds of components regulates a diverse array of physiological functions Methods Mol. Biol. 661 2010 3 38
15. N.G. Anderson, J.L. Maller, N.K. Tonks, and T.W. Sturgill Requirement for integration of signals from two distinct phosphorylation pathways for activation of MAP kinase Nature 143 1990 651 653
16. N.G. Ahn, R. Seger, R.L. Bratlien, C.D. Diltz, N.K. Tonks, and E.G. Krebs Multiple components in an epidermal growth factor-stimulated protein kinase cascade. In vitro activation of myelin basic protein/microtubule-associated protein-2 kinase J. Biol. Chem. 266 1991 4220 4227
17. N. Gomez, and P. Cohen Dissection of the protein kinase cascade by which nerve growth factor activates MAP kinases Nature 353 1991 170 173
18. C.M. Crews, A. Alessandrini, and R.L. Erikson The primary structure of MEK, a protein kinase that phosphorylates the ERK gene product Science 258 1992 478 480
19. R. Seger, D. Seger, F.J. Lozeman, N.G. Ahn, L.M. Graves, J.S. Campbell, L. Ericsson, M. Harrylock, A.M. Jensen, and E.G. Krebs Human T-cell Map kinase kinases are related to yeast signal transduction kinases J. Biol. Chem. 267 1992 25628 25631
20. D.R. Alessi, N. Gomez, G. Moorhead, T. Lewis, S.M. Keyse, and P. Cohen Inactivation of p42 MAP kinase by protein phosphatase 2A and a protein tyrosine phosphatase, but not CL100, in various cell lines Curr. Biol. 5 1995 283 295
21. H. Sun, C.H. Charles, L.F. Lau, and N.K. Tonks MKP-1 (3CH134), an immediate early gene product, is a dual specificity phosphatase that dephosphorylates MAP kinase in vivo Cell 75 1993 487 493
22. W.H.d. Biggs, and S.L. Zipursky Primary structure, expression, and signal-dependent tyrosine phosphorylation of a Drosophila homolog of extracellular signal-regulated kinase Proc. Natl. Acad. Sci. USA 89 1992 6295 6299
23. E.M. O'Neill, I. Rebay, R. Tjian, and G.M. Rubin The activities of two Ets-related transcription factors required for Drosophila eye development are modulated by the Ras/MAPK pathway Cell 78 1994 137 147
24. L. Gabay, R. Seger, and B.Z. Shilo In situ activation pattern of Drosophila EGF receptor pathway during development Science 277 1997 1103 1106
25. L. Gabay, R. Seger, and B.Z. Shilo MAP kinase in situ activation atlas during Drosophila embryogenesis Development 124 1997 3535 3541
26. S. Arur, M. Ohmachi, S. Nayak, M. Hayes, A. Miranda, A. Hay, A. Golden, and T. Schedl Multiple ERK substrates execute single biological processes in Caenorhabditis elegans germ-line development Proc. Natl. Acad. Sci. USA 106 2009 4776 4781
27. M.-C. Delfini, J. Dubrulle, P. Malapert, J. Chal, and O. Pourquié Control of the segmentation process by graded MAPK/ERK activation in the chick embryo Proc. Natl. Acad. Sci. USA 102 2005 11343 11348
28. H. Gille, A.D. Sharrocks, and P.E. Shaw Phosphorylation of transcription factor p62TCF by MAP kinase stimulates ternary complex formation at c-fos promoter Nature 358 1992 414 417
29. A. Seth, E. Alvarez, S. Gupta, and R.J. Davis A phosphorylation site located in the NH2-terminal domain of c-Myc increases transactivation of gene expression J. Biol. Chem. 266 1991 23521 23524
30. B.J. Pulverer, J.M. Kyriakis, J. Avruch, E. Nikolakaki, and J.R. Woodgett Phosphorylation of c-jun mediated by MAP kinases Nature 353 1991 670 674
31. A.D. Sharrocks, S.H. Yang, and A. Galanis Docking domains and substrate-specificity determination for MAP kinases Trends Biochem. Sci. 25 2000 448 453
32. D. Jacobs, D. Glossip, H. Xing, A.J. Muslin, and K. Kornfeld Multiple docking sites on substrate proteins form a modular system that mediates recognition by ERK MAP kinase Genes Dev. 13 1999 163 175
33. F. Zhang, A. Strand, D. Robbins, M.H. Cobb, and J.G. Goldsmith Atomic structure of the MAP kinase ERK2 at 2.3 Å resolution Nature 367 1994 704 711
34. B.J. Canagarajah, A. Khokhlatchev, M.H. Cobb, and E.J. Goldsmith Activation mechanism of the MAP kinase ERK2 by dual phosphorylation Cell 90 1997 859 869
35. S.J. Mansour, W.T. Matten, A.S. Hermann, J.M. Candia, S. Rong, K. Fukasawa, G.F. Wounde-Vande, and N.G. Ahn Transformation of mammalian cells by constitutively active MAP kinase kinase Science 265 1994 966 970
36. A. Plotnikov, E. Zehorai, S. Procaccia, and R. Seger The MAPK cascades: Signaling components, nuclear roles and mechanisms of nuclear translocation Biochim. Biophys. Acta 1813 2011 1619 1633
37. W. Kolch Coordinating ERK/MAPK signalling through scaffolds and inhibitors Nat. Rev. Mol. Cell Biol. 6 2005 827 837
38. J.E. Ferrell Jr. Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs Trends Biochem. Sci. 21 1996 460 466
39. C.Y. Huang, and J.E. Ferrell Jr. Ultrasensitivity in the mitogen-activated protein kinase cascade Proc. Natl. Acad. Sci. USA 93 1996 10078 10083
40. N. Bluthgen, and S. Legewie Systems analysis of MAPK signal transduction Essays Biochem. 45 2008 95 107
41. R. Fritsche-Guenther, F. Witzel, A. Sieber, R. Herr, N. Schmidt, S. Braun, T. Brummer, C. Sers, and N. Bluthgen Strong negative feedback from Erk to Raf confers robustness to MAPK signalling Mol. Syst. Biol. 7 2011 489
42. S.M. Carlson, C.R. Chouinard, A. Labadorf, C.J. Lam, K. Schmelzle, E. Fraenkel, and F.M. White Large-scale discovery of ERK2 substrates identifies ERK-mediated transcriptional regulation by ETV3 Sci. Signal. 4 2011 rs11
43. H. Kosako, N. Yamaguchi, C. Aranami, M. Ushiyama, S. Kose, N. Imamoto, H. Taniguchi, E. Nishida, and S. Hattori Phosphoproteomics reveals new ERK MAP kinase targets and links ERK to nucleoporin-mediated nuclear transport Nat. Struct. Mol. Biol. 16 2009 1026 1035
44. S. Yoon, and R. Seger The extracellular signal-regulated kinase: multiple substrates regulate diverse cellular functions Growth Factors 24 2006 21 44
45. L. Bardwell Mechanisms of MAPK signalling specificity Biochem. Soc. Trans. 34 2006 837 841
46. S.-H. Yang, P.R. Yates, A.J. Whitmarsh, R.J. Davis, and A.D. Sharrocks The Elk-1 ETS-domain transcription factor contains a mitogen-activated protein kinase targeting motif Mol. Cell. Biol. 18 1998 710 720
47. T. Lee, A.N. Hoofnagle, Y. Kabuyama, J. Stroud, X. Min, E.J. Goldsmith, L. Chen, K.A. Resing, and N.G. Ahn Docking motif interactions in MAP kinases revealed by hydrogen exchange mass spectrometry Mol. Cell 14 2004 43 55
48. T. Tanoue, R. Maeda, M. Adachi, and E. Nishida Identification of a docking groove on ERK and p38 MAP kinases that regulates the specificity of docking interactions EMBO J. 20 2001 466 479
49. T. Tanoue, M. Adachi, T. Moriguchi, and E. Nishida A conserved docking motif in MAP kinases common to substrates, activators and regulators Nat. Cell Biol. 2 2000 110 116
50. A.J. Waskiewicz, A. Flynn, C.G. Proud, and J.A. Cooper Mitogen-activated protein kinases activate the serine/threonine kinases Mnk1 and Mnk2 EMBO J. 16 1997 1909 1920
51. M.A. Rainey, K. Callaway, R. Barnes, B. Wilson, and K.N. Dalby Proximity-Induced Catalysis by the Protein Kinase ERK2 J. Am. Chem. Soc. 127 2005 10494 10495
52. S. Bandyopadhyay, C.-y. Chiang, J. Srivastava, M. Gersten, S. White, R. Bell, C. Kurschner, C.H. Martin, M. Smoot, and S. Sahasrabudhe A human MAP kinase interactome Nat. Methods 7 2010 801 805
53. T.S. Lewis, J.B. Hunt, L.D. Aveline, K.R. Jonscher, D.F. Louie, J.M. Yeh, T.S. Nahreini, K.A. Resing, and N.G. Ahn Identification of novel MAP kinase pathway signaling targets by functional proteomics and mass spectrometry Mol. Cell 6 2000 1343 1354
54. J. Lovrić, S. Dammeier, A. Kieser, H. Mischak, and W. Kolch Activated Raf induces the hyperphosphorylation of Stathmin and the reorganization of the microtubule network J. Biol. Chem. 273 1998 22848 22855
55. A. Vinayagam, U. Stelzl, R. Foulle, S. Plassmann, M. Zenkner, J. Timm, H.E. Assmus, M.A. Andrade-Navarro, and E.E. Wanker A directed protein interaction network for investigating intracellular signal transduction Sci. Signal. 4 2011 rs8
56. A. von Kriegsheim, D. Baiocchi, M. Birtwistle, D. Sumpton, W. Bienvenut, N. Morrice, K. Yamada, A. Lamond, G. Kalna, and R. Orton Cell fate decisions are specified by the dynamic ERK interactome Nat. Cell Biol. 11 2009 1458 1464
57. T.C. Whisenant, D.T. Ho, R.W. Benz, J.S. Rogers, R.M. Kaake, E.A. Gordon, L. Huang, P. Baldi, and L. Bardwell Computational prediction and experimental verification of new MAP kinase docking sites and substrates including Gli transcription factors PLoS Comput. Biol. 6 2010 e1000908
58. A.A. Friedman, G. Tucker, R. Singh, D. Yan, A. Vinayagam, Y. Hu, R. Binari, P. Hong, X. Sun, and M. Porto Proteomic and functional genomic landscape of receptor tyrosine kinase and Ras to extracellular signal-regulated kinase signaling Sci. Signal. 4 2011 rs10-
59. Y. Kim, M. Coppey, R. Grossman, L. Ajuria, G. JimÈnez, Z.e. Paroush, and S.Y. Shvartsman MAPK substrate competition integrates patterning signals in the Drosophila embryo Curr. Biol. 20 2010 446 451
60. O. Grimm, V.S. Zini, Y. Kim, J. Casanova, S.Y. Shvartsman, and E. Wieschaus Torso RTK controls Capicua degradation by changing its subcellular localization Development 139 2012 3962 3968
61. Y. Kim, M.J. Andreu, B. Lim, K. Chung, M. Terayama, G. JimÈnez, C.A. Berg, H. Lu, and S.Y. Shvartsman Gene regulation by MAPK substrate competition Dev. Cell 20 2011 880 887
62. D.J. Robbins, E. Zhen, H. Owaki, C.A. Vanderbilt, D. Ebert, T.D. Geppert, and M.H. Cobb Regulation and properties of extracellular signal-regulated protein kinases 1 and 2 in vitro J. Biol. Chem. 268 1993 5097 5106
63. D.M. Payne, A.J. Rossomando, P. Martino, A.K. Erickson, J.H. Her, J. Shabanowitz, D.F. Hunt, M.J. Weber, and T.W. Sturgill Identification of the regulatory phosphorylation sites in pp42/mitogen-activated protein kinase (MAP kinase) EMBO J. 10 1991 885 892
64. N.G. Anderson, J.L. Maller, N.K. Tonks, and T.W. Sturgill Requirement for integration of signals from two distinct phosphorylation pathways for activation of MAP kinase Nature 343 1990 651 653
65. C. Kiel, and L. Serrano Cell type-specific importance of Ras-c-Raf complex association rate constants for MAPK signaling Sci. Signal. 2 2009 ra38
66. Y. Kim, Z. Paroush, K. Nairz, E. Hafen, G. Jimenez, and S.Y. Shvartsman Substrate-dependent control of MAPK phosphorylation in vivo Mol. Syst. Biol. 7 2011 467
67. D. Brunner, N. Oellers, J. Szabad, W.H. Biggs 3rd, S.L. Zipursky, and E. Hafen A gain-of-function mutation in Drosophila MAP kinase activates multiple receptor tyrosine kinase signaling pathways Cell 76 1994 875 888
68. N. Oellers, and E. Hafen Biochemical characterization of rolledSem, an activated form of Drosophila mitogen-activated protein kinase J. Biol. Chem. 271 1996 24939 24944
69. Y. Chu, P.A. Solski, R. Khosravi-Far, C.J. Der, and K. Kelly The mitogen-activated protein kinase phosphatases PAC1, MKP-1, and MKP-2 have unique substrate specificities and reduced activity in vivo toward the ERK2 sevenmaker mutation J. Biol. Chem. 271 1996 6497 6501
70. K. Aoki, M. Yamada, K. Kunida, S. Yasuda, and M. Matsuda Processive phosphorylation of ERK MAP kinase in mammalian cells Proc. Natl. Acad. Sci. USA 108 2011 12675 12680
71. N.I. Markevich, J.B. Hoek, and B.N. Kholodenko Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades J. Cell Biol. 164 2004 353 359
72. K. Takahashi, S. Tanase-Nicola, and P.R. ten Wolde Spatio-temporal correlations can drastically change the response of a MAPK pathway Proc. Natl. Acad. Sci. USA 107 2010 2473 2478
73. S. Prabakaran, R.A. Everley, I. Landrieu, J.M. Wieruszeski, G. Lippens, H. Steen, and J. Gunawardena Comparative analysis of Erk phosphorylation suggests a mixed strategy for measuring phospho-form distributions Mol. Syst. Biol. 7 2011 482
74. A. Friedman, and N. Perrimon A functional RNAi screen for regulators of receptor tyrosine kinase and ERK signalling Nature 444 2006 230 234
75. A. Fujioka, K. Terai, R.E. Itoh, K. Aoki, T. Nakamura, S. Kuroda, E. Nishida, and M. Matsuda Dynamics of the Ras/ERK MAPK cascade as monitored by fluorescent probes J. Biol. Chem. 281 2006 8917 8926
76. R.D. Fritz, M. Letzelter, A. Reimann, K. Martin, L. Fusco, L. Ritsma, B. Ponsioen, E. Fluri, S. Schulte-Merker, and J. van Rheenen A Versatile toolkit to produce sensitive FRET biosensors to visualize signaling in time and space Sci. Signal. 6 2013 rs12
77. T. Tomida, S. Oda, M. Takekawa, Y. Iino, and H. Saito The temporal pattern of stimulation determines the extent and duration of MAPK activation in a Caenorhabditis elegans sensory neuron Sci. Signal. 5 2012 ra76
78. C.D. Harvey, A.G. Ehrhardt, C. Cellurale, H. Zhong, R. Yasuda, R.J. Davis, and K. Svoboda A genetically encoded fluorescent sensor of ERK activity Proc. Natl. Acad. Sci. USA 105 2008 19264 19269
79. C. Kiel, and L. Serrano Challenges ahead in signal transduction: MAPK as an example Curr. Opin. Biotechnol. 23 2012 305 314