Data-driven Modeling Reconciles Kinetics of ERK Phosphorylation, Localization, and Activity States

Overview

Journal Mol Syst Biol

Specialty Molecular Biology

Date 2014 Feb 4

PMID 24489118

Citations 38

Authors

Shoeb Ahmed

Kyle G Grant

Laura E Edwards

Anisur Rahman

Murat Cirit

Michael B Goshe

Jason M Haugh

Affiliations

Soon will be listed here.

Abstract

The extracellular signal-regulated kinase (ERK) signaling pathway controls cell proliferation and differentiation in metazoans. Two hallmarks of its dynamics are adaptation of ERK phosphorylation, which has been linked to negative feedback, and nucleocytoplasmic shuttling, which allows active ERK to phosphorylate protein substrates in the nucleus and cytosol. To integrate these complex features, we acquired quantitative biochemical and live-cell microscopy data to reconcile phosphorylation, localization, and activity states of ERK. While maximal growth factor stimulation elicits transient ERK phosphorylation and nuclear translocation responses, ERK activities available to phosphorylate substrates in the cytosol and nuclei show relatively little or no adaptation. Free ERK activity in the nucleus temporally lags the peak in nuclear translocation, indicating a slow process. Additional experiments, guided by kinetic modeling, show that this process is consistent with ERK's modification of and release from nuclear substrate anchors. Thus, adaptation of whole-cell ERK phosphorylation is a by-product of transient protection from phosphatases. Consistent with this interpretation, predictions concerning the dose-dependence of the pathway response and its interruption by inhibition of MEK were experimentally confirmed.

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References

Shankaran H, Ippolito D, Chrisler W, Resat H, Bollinger N, Opresko L . Rapid and sustained nuclear-cytoplasmic ERK oscillations induced by epidermal growth factor. Mol Syst Biol. 2009; 5:332. PMC: 2824491. DOI: 10.1038/msb.2009.90. View

Park C, Schneider I, Haugh J . Kinetic analysis of platelet-derived growth factor receptor/phosphoinositide 3-kinase/Akt signaling in fibroblasts. J Biol Chem. 2003; 278(39):37064-72. DOI: 10.1074/jbc.M304968200. View

Yoon S, Seger R . The extracellular signal-regulated kinase: multiple substrates regulate diverse cellular functions. Growth Factors. 2006; 24(1):21-44. DOI: 10.1080/02699050500284218. View

Lidke D, Huang F, Post J, Rieger B, Wilsbacher J, Thomas J . ERK nuclear translocation is dimerization-independent but controlled by the rate of phosphorylation. J Biol Chem. 2009; 285(5):3092-102. PMC: 2823437. DOI: 10.1074/jbc.M109.064972. View

Herbst K, Allen M, Zhang J . Spatiotemporally regulated protein kinase A activity is a critical regulator of growth factor-stimulated extracellular signal-regulated kinase signaling in PC12 cells. Mol Cell Biol. 2011; 31(19):4063-75. PMC: 3187359. DOI: 10.1128/MCB.05459-11. View

Rowland M, Fontana W, Deeds E . Crosstalk and competition in signaling networks. Biophys J. 2013; 103(11):2389-98. PMC: 3514525. DOI: 10.1016/j.bpj.2012.10.006. View

Chen W, Schoeberl B, Jasper P, Niepel M, Nielsen U, Lauffenburger D . Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data. Mol Syst Biol. 2009; 5:239. PMC: 2644173. DOI: 10.1038/msb.2008.74. View

Burack W, Shaw A . Live Cell Imaging of ERK and MEK: simple binding equilibrium explains the regulated nucleocytoplasmic distribution of ERK. J Biol Chem. 2004; 280(5):3832-7. DOI: 10.1074/jbc.M410031200. View

Haugh J . Live-cell fluorescence microscopy with molecular biosensors: what are we really measuring?. Biophys J. 2012; 102(9):2003-11. PMC: 3341566. DOI: 10.1016/j.bpj.2012.03.055. View

10.

Bardwell A, Abdollahi M, Bardwell L . Docking sites on mitogen-activated protein kinase (MAPK) kinases, MAPK phosphatases and the Elk-1 transcription factor compete for MAPK binding and are crucial for enzymic activity. Biochem J. 2003; 370(Pt 3):1077-85. PMC: 1223246. DOI: 10.1042/BJ20021806. View

11.

Schoeberl B, Eichler-Jonsson C, Gilles E, Muller G . Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat Biotechnol. 2002; 20(4):370-5. DOI: 10.1038/nbt0402-370. View

12.

Ahmed S, Grant K, Edwards L, Rahman A, Cirit M, Goshe M . Data-driven modeling reconciles kinetics of ERK phosphorylation, localization, and activity states. Mol Syst Biol. 2014; 10:718. PMC: 4023404. DOI: 10.1002/msb.134708. View

13.

Harvey C, Ehrhardt A, Cellurale C, Zhong H, Yasuda R, Davis R . A genetically encoded fluorescent sensor of ERK activity. Proc Natl Acad Sci U S A. 2008; 105(49):19264-9. PMC: 2614750. DOI: 10.1073/pnas.0804598105. View

14.

Birtwistle M, Hatakeyama M, Yumoto N, Ogunnaike B, Hoek J, Kholodenko B . Ligand-dependent responses of the ErbB signaling network: experimental and modeling analyses. Mol Syst Biol. 2007; 3:144. PMC: 2132449. DOI: 10.1038/msb4100188. View

15.

Kim Y, Andreu M, Lim B, Chung K, Terayama M, Jimenez G . Gene regulation by MAPK substrate competition. Dev Cell. 2011; 20(6):880-7. PMC: 3580161. DOI: 10.1016/j.devcel.2011.05.009. View

16.

Bhalla U, Ram P, Iyengar R . MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science. 2002; 297(5583):1018-23. DOI: 10.1126/science.1068873. View

17.

Horgan A, Stork P . Examining the mechanism of Erk nuclear translocation using green fluorescent protein. Exp Cell Res. 2003; 285(2):208-20. DOI: 10.1016/s0014-4827(03)00037-5. View

18.

Hao N, Yildirim N, Nagiec M, Parnell S, Errede B, Dohlman H . Combined computational and experimental analysis reveals mitogen-activated protein kinase-mediated feedback phosphorylation as a mechanism for signaling specificity. Mol Biol Cell. 2012; 23(19):3899-910. PMC: 3459865. DOI: 10.1091/mbc.E12-04-0333. View

19.

Xu B, Wilsbacher J, Collisson T, Cobb M . The N-terminal ERK-binding site of MEK1 is required for efficient feedback phosphorylation by ERK2 in vitro and ERK activation in vivo. J Biol Chem. 1999; 274(48):34029-35. DOI: 10.1074/jbc.274.48.34029. View

20.

Joslin E, Shankaran H, Opresko L, Bollinger N, Lauffenburger D, Wiley H . Structure of the EGF receptor transactivation circuit integrates multiple signals with cell context. Mol Biosyst. 2010; 6(7):1293-306. PMC: 3306786. DOI: 10.1039/c003921g. View