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Cell fate decisions are specified by the dynamic ERK interactome

Nature Cell Biology volume 11, pages 1458–1464 (2009)Cite this article

An Author Correction to this article was published on 18 February 2022

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Abstract

Extracellular signal-regulated kinase (ERK) controls fundamental cellular functions, including cell fate decisions1,2. In PC12, cells shifting ERK activation from transient to sustained induces neuronal differentiation3. As ERK associates with both regulators and effectors4, we hypothesized that the mechanisms underlying the switch could be revealed by assessing the dynamic changes in ERK-interacting proteins that specifically occur under differentiation conditions. Using quantitative proteomics, we identified 284 ERK-interacting proteins. Upon induction of differentiation, 60 proteins changed their binding to ERK, including many proteins that were not known to participate in differentiation. We functionally characterized a subset, showing that they regulate the pathway at several levels and by different mechanisms, including signal duration, ERK localization, feedback, crosstalk with the Akt pathway and differential interaction and phosphorylation of transcription factors. Integrating these data with a mathematical model confirmed that ERK dynamics and differentiation are regulated by distributed control mechanisms rather than by a single master switch.

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Figure 1: Identification of dynamic ERK1 interactions.
Figure 2: NF1 controls Ras activity and signal duration.
Figure 3: Regulation of ERK localization in PC12 cells by PEA-15.
Figure 4: Differential regulation of transcriptional repressors by EGF and NGF in PC12 cells.
Figure 5: Kinetic mathematical model of the ERK pathway in PC12 cells.

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References

  1. Shaul, Y. D. & Seger, R. The MEK/ERK cascade: from signaling specificity to diverse functions. Biochim. Biophys. Acta 1773, 1213–1226 (2007).

    Article  CAS  Google Scholar 

  2. Galabova-Kovacs, G. et al. ERK and beyond: insights from B-Raf and Raf-1 conditional knockouts. Cell Cycle 5, 1514–1518 (2006).

    Article  CAS  Google Scholar 

  3. Marshall, C. J. Specificity of receptor tyrosine kinase signaling: transient versus sustained extracellular signal-regulated kinase activation. Cell 80, 179–185 (1995).

    Article  CAS  Google Scholar 

  4. Yoon, S. & Seger, R. The extracellular signal-regulated kinase: multiple substrates regulate diverse cellular functions. Growth Factors 24, 21–44 (2006).

    Article  CAS  Google Scholar 

  5. Leicht, D. T. et al. Raf kinases: function, regulation and role in human cancer. Biochim. Biophys. Acta 1773, 1196–1212 (2007).

    Article  CAS  Google Scholar 

  6. Clark-Lewis, I., Sanghera, J. S. & Pelech, S. L. Definition of a consensus sequence for peptide substrate recognition by p44mpk, the meiosis-activated myelin basic protein kinase. J. Biol. Chem. 266, 15180–15184 (1991).

    Article  CAS  Google Scholar 

  7. Akella, R., Moon, T. M. & Goldsmith, E. J. Unique MAP Kinase binding sites. Biochim. Biophys. Acta 1784, 48–55 (2008).

    Article  CAS  Google Scholar 

  8. Sasagawa, S., Ozaki, Y., Fujita, K. & Kuroda, S. Prediction and validation of the distinct dynamics of transient and sustained ERK activation. Nature Cell Biol. 7, 365–373 (2005).

    Article  CAS  Google Scholar 

  9. Santos, S. D., Verveer, P. J. & Bastiaens, P. I. Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate. Nature Cell Biol. 9, 324–330 (2007).

    Article  CAS  Google Scholar 

  10. Niihori, T. et al. Germline KRAS and BRAF mutations in cardio-facio-cutaneous syndrome. Nature Genet. 38, 294–296 (2006).

    Article  CAS  Google Scholar 

  11. Harrisingh, M. C. & Lloyd, A. C. Ras/Raf/ERK signalling and NF1. Cell Cycle 3, 1255–1258 (2004).

    Article  CAS  Google Scholar 

  12. Ahmadian, M. R., Hoffmann, U., Goody, R. S. & Wittinghofer, A. Individual rate constants for the interaction of Ras proteins with GTPase-activating proteins determined by fluorescence spectroscopy. Biochemistry 36, 4535–4541 (1997).

    Article  CAS  Google Scholar 

  13. York, R. D. et al. Rap1 mediates sustained MAP kinase activation induced by nerve growth factor. Nature 392, 622–626 (1998).

    Article  CAS  Google Scholar 

  14. Formstecher, E. et al. PEA-15 mediates cytoplasmic sequestration of ERK MAP kinase. Dev. Cell 1, 239–250 (2001).

    Article  CAS  Google Scholar 

  15. Traverse, S., Gomez, N., Paterson, H., Marshall, C. & Cohen, P. Sustained activation of the mitogen-activated protein (MAP) kinase cascade may be required for differentiation of PC12 cells. Comparison of the effects of nerve growth factor and epidermal growth factor. Biochem. J. 288 (Pt 2), 351–355 (1992).

    Article  CAS  Google Scholar 

  16. Krueger, J., Chou, F. L., Glading, A., Schaefer, E. & Ginsberg, M. H. Phosphorylation of phosphoprotein enriched in astrocytes (PEA-15) regulates extracellular signal-regulated kinase-dependent transcription and cell proliferation. Mol. Biol. Cell 16, 3552–3561 (2005).

    Article  CAS  Google Scholar 

  17. Trencia, A. et al. Protein kinase B/Akt binds and phosphorylates PED/PEA-15, stabilizing its antiapoptotic action. Mol. Cell Biol. 23, 4511–4521 (2003).

    Article  CAS  Google Scholar 

  18. Araujo, H., Danziger, N., Cordier, J., Glowinski, J. & Chneiweiss, H. Characterization of PEA-15, a major substrate for protein kinase C in astrocytes. J. Biol. Chem. 268, 5911–5920 (1993).

    Article  CAS  Google Scholar 

  19. Le Gallic, L., Virgilio, L., Cohen, P., Biteau, B. & Mavrothalassitis, G. ERF nuclear shuttling, a continuous monitor of Erk activity that links it to cell cycle progression. Mol. Cell Biol. 24, 1206–1218 (2004).

    Article  CAS  Google Scholar 

  20. Ando, R., Mizuno, H. & Miyawaki, A. Regulated fast nucleocytoplasmic shuttling observed by reversible protein highlighting. Science 306, 1370–1373 (2004).

    Article  CAS  Google Scholar 

  21. Volmat, V., Camps, M., Arkinstall, S., Pouyssegur, J. & Lenormand, P. The nucleus, a site for signal termination by sequestration and inactivation of p42/p44 MAP kinases. J. Cell Sci. 114, 3433–3443 (2001).

    Article  CAS  Google Scholar 

  22. Malik, T. H. et al. Transcriptional repression and developmental functions of the atypical vertebrate GATA protein TRPS1. EMBO J. 20, 1715–1725 (2001).

    Article  CAS  Google Scholar 

  23. Cantor, A. B. GATA transcription factors in hematologic disease. Int. J. Hematol. 81, 378–384 (2005).

    Article  CAS  Google Scholar 

  24. Brewer, A. & Pizzey, J. GATA factors in vertebrate heart development and disease. Expert Rev. Mol. Med. 8, 1–20 (2006).

    Article  Google Scholar 

  25. Kaiser, F. J. et al. Novel missense mutations in the TRPS1 transcription factor define the nuclear localization signal. Eur. J. Hum. Genet. 12, 121–126 (2004).

    Article  CAS  Google Scholar 

  26. Kobayashi, H. et al. Missense mutation of TRPS1 in a family of tricho-rhino-phalangeal syndrome type III. Am. J. Med. Genet. 107, 26–29 (2002).

    Article  Google Scholar 

  27. Rodriguez-Viciana, P. et al. Germline mutations in genes within the MAPK pathway cause cardio-facio-cutaneous syndrome. Science 311, 1287–1290 (2006).

    Article  CAS  Google Scholar 

  28. Kholodenko, B. N. Cell-signalling dynamics in time and space. Nature Rev. Mol. Cell Biol. 7, 165–176 (2006).

    Article  CAS  Google Scholar 

  29. George, A. J., Stark, J. & Chan, C. Understanding specificity and sensitivity of T-cell recognition. Trends Immunol. 26, 653–659 (2005).

    Article  CAS  Google Scholar 

  30. Trinkle-Mulcahy, L. et al. Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. J. Cell Biol. 183, 223–239 (2008).

    Article  CAS  Google Scholar 

  31. de Rooij, J. & Bos, J. L. Minimal Ras-binding domain of Raf1 can be used as an activation-specific probe for Ras. Oncogene 14, 623–625 (1997).

    Article  CAS  Google Scholar 

  32. Obenauer, J. C., Cantley, L. C. & Yaffe, M. B. Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res. 31, 3635–3641 (2003).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank P. Mortensen for help with MSQuant, A. Pitt and C. Ward for help with MS, O.Rath for the design of primers and G. Cesareni and A. Chatraryamontri for help with submission of the interaction data to the IMEx consortium through MINT. The work was supported by the European Union Interaction Proteome project (LSHG-CT-2003-505520), the RASOR project (BBSRC and EPSRC) and Cancer Research UK.

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Author notes

  1. Daniela Baiocchi

    Present address: Current address: Experimental Pathology, University of Bologna, 40126 Bologna, Italy.,

  2. David Gilbert

    Present address: Current address: School of Information Systems, Computing & Mathematics, Brunel University, Uxbridge, Middlesex, UB8 3PH, UK.,

  3. Marc Birtwistle & Walter Kolch

    Present address: Current address: Systems Biology Ireland, University College Dublin, Dublin 4, Ireland.,

  4. Daniela Baiocchi and Marc Birtwistle: These authors contributed equally to this work.

Authors and Affiliations

  1. Signalling and Proteomics Laboratory, The Beatson Institute for Cancer Research, G61 1BD, Glasgow, UK

    Alex von Kriegsheim, Daniela Baiocchi, Marc Birtwistle, David Sumpton, Willy Bienvenut, Gabriella Kalna & Walter Kolch

  2. MRC Protein Phosphorylation Unit, University of Dundee, Scotland, DD1 5EH, Dundee, UK

    Nicholas Morrice

  3. Wellcome Trust Centre for Gene Regulation and Expression, University of Dundee, Scotland, DD1 5EH, Dundee, UK

    Kayo Yamada & Angus Lamond

  4. Department of Computing Science, Bioinformatics Research Centre, University of Glasgow, G12 8QQ, Glasgow, UK

    David Gilbert

  5. Sir Henry Wellcome Functional Genomics Facility, University of Glasgow, G12 8QQ, Glasgow, UK

    Richard Orton & Walter Kolch

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Contributions

A.v.K. performed most of the experiments, analysed the data and wrote the paper; D.B. performed the PEA-15 experiments; M.B., R.O. and D.G. generated the mathematical model; D.S., W.B., A.v.K., N.M., K.Y., and A.L. generated and analysed MS data; G.K. performed bioinformatic analysis; W.K. conceived the study and edited the paper.

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Correspondence to Walter Kolch.

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von Kriegsheim, A., Baiocchi, D., Birtwistle, M. et al. Cell fate decisions are specified by the dynamic ERK interactome. Nat Cell Biol 11, 1458–1464 (2009). https://doi.org/10.1038/ncb1994

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