Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Neural palmitoyl-proteomics reveals dynamic synaptic palmitoylation

Abstract

Palmitoylation regulates diverse aspects of neuronal protein trafficking and function. Here a global characterization of rat neural palmitoyl-proteomes identifies most of the known neural palmitoyl proteins—68 in total, plus more than 200 new palmitoyl-protein candidates, with further testing confirming palmitoylation for 21 of these candidates. The new palmitoyl proteins include neurotransmitter receptors, transporters, adhesion molecules, scaffolding proteins, as well as SNAREs and other vesicular trafficking proteins. Of particular interest is the finding of palmitoylation for a brain-specific Cdc42 splice variant. The palmitoylated Cdc42 isoform (Cdc42-palm) differs from the canonical, prenylated form (Cdc42-prenyl), both with regard to localization and function: Cdc42-palm concentrates in dendritic spines and has a special role in inducing these post-synaptic structures. Furthermore, assessing palmitoylation dynamics in drug-induced activity models identifies rapidly induced changes for Cdc42 as well as for other synaptic palmitoyl proteins, suggesting that palmitoylation may participate broadly in the activity-driven changes that shape synapse morphology and function.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Global analysis of neuronal protein palmitoylation.
Figure 2: Palmitylation of a brain-specific Cdc42 splice variant.
Figure 3: Role of Cdc42-palm in dendritic spine induction.
Figure 4: Broad modulation of palmitoylation levels in neuronal activity models.

Similar content being viewed by others

References

  1. Huang, K. & El-Husseini, A. Modulation of neuronal protein trafficking and function by palmitoylation. Curr. Opin. Neurobiol. 15, 527–535 (2005)

    Article  CAS  Google Scholar 

  2. Resh, M. D. Palmitoylation of ligands, receptors, and intracellular signaling molecules. Sci. STKE 2006, re14 (2006)

    Article  Google Scholar 

  3. Smotrys, J. E. & Linder, M. E. Palmitoylation of intracellular signaling proteins: regulation and function. Annu. Rev. Biochem. 73, 559–587 (2004)

    Article  CAS  Google Scholar 

  4. Linder, M. E. & Deschenes, R. J. Palmitoylation: policing protein stability and traffic. Nature Rev. Mol. Cell Biol. 8, 74–84 (2007)

    Article  CAS  Google Scholar 

  5. El-Husseini, A. E.-D. et al. Synaptic strength regulated by palmitate cycling on PSD-95. Cell 108, 849–863 (2002)

    Article  CAS  Google Scholar 

  6. Roth, A. F. et al. Global analysis of protein palmitoylation in yeast. Cell 125, 1003–1013 (2006)

    Article  CAS  Google Scholar 

  7. Drisdel, R. C. & Green, W. N. Labeling and quantifying sites of protein palmitoylation. Biotechniques 36, 276–285 (2004)

    Article  CAS  Google Scholar 

  8. Link, A. J. et al. Direct analysis of protein complexes using mass spectrometry. Nature Biotechnol. 17, 676–682 (1999)

    Article  CAS  Google Scholar 

  9. Liu, H., Sadygov, R. G. & Yates, J. R. A model for random sampling and estimation of relative protein abundance in shotgun proteomics. Anal. Chem. 76, 4193–4201 (2004)

    Article  CAS  Google Scholar 

  10. Wan, J. et al. Palmitoylated proteins: purification and identification. Nature Protoc. 2, 1573–1584 (2007)

    Article  CAS  Google Scholar 

  11. Hayashi, T., Rumbaugh, G. & Huganir, R. L. Differential regulation of AMPA receptor subunit trafficking by palmitoylation of two distinct sites. Neuron 47, 709–723 (2005)

    Article  CAS  Google Scholar 

  12. Nishimura, T. et al. Role of numb in dendritic spine development with a Cdc42 GEF intersectin and EphB2. Mol. Biol. Cell 17, 1273–1285 (2006)

    Article  CAS  Google Scholar 

  13. Negishi, M. & Katoh, H. Rho family GTPases and dendrite plasticity. Neuroscientist 11, 187–191 (2005)

    Article  CAS  Google Scholar 

  14. Choi, J. et al. Regulation of dendritic spine morphogenesis by insulin receptor substrate 53, a downstream effector of Rac1 and Cdc42 small GTPases. J. Neurosci. 25, 869–879 (2005)

    Article  CAS  Google Scholar 

  15. Scott, E. K., Reuter, J. E. & Luo, L. Small GTPase Cdc42 is required for multiple aspects of dendritic morphogenesis. J. Neurosci. 23, 3118–3123 (2003)

    Article  CAS  Google Scholar 

  16. Nakazawa, T. et al. p250GAP, a novel brain-enriched GTPase-activating protein for Rho family GTPases, is involved in the N-methyl-d-aspartate receptor signaling. Mol. Biol. Cell 14, 2921–2934 (2003)

    Article  CAS  Google Scholar 

  17. Wilson, A. L. et al. Prenylation of Rab8 GTPase by type I and type II geranylgeranyl transferases. Biochem. J. 333, 497–504 (1998)

    Article  CAS  Google Scholar 

  18. Marks, P. W. & Kwiatkowski, D. J. Genomic organization and chromosomal location of murine Cdc42. Genomics 38, 13–18 (1996)

    Article  CAS  Google Scholar 

  19. Kreis, P. et al. The p21-activated kinase 3 implicated in mental retardation regulates spine morphogenesis through a Cdc42-dependent pathway. J. Biol. Chem. 282, 21497–21506 (2007)

    Article  CAS  Google Scholar 

  20. Node-Langlois, R., Muller, D. & Boda, B. Sequential implication of the mental retardation proteins ARHGEF6 and PAK3 in spine morphogenesis. J. Cell Sci. 119, 4986–4993 (2006)

    Article  CAS  Google Scholar 

  21. Wegner, A. M. et al. N-wasp and the arp2/3 complex are critical regulators of actin in the development of dendritic spines and synapses. J. Biol. Chem. 283, 15912–15920 (2008)

    Article  CAS  Google Scholar 

  22. Ethell, I. M. & Pasquale, E. B. Molecular mechanisms of dendritic spine development and remodeling. Prog. Neurobiol. 75, 161–205 (2005)

    Article  CAS  Google Scholar 

  23. Hering, H., Lin, C. C. & Sheng, M. Lipid rafts in the maintenance of synapses, dendritic spines, and surface AMPA receptor stability. J. Neurosci. 23, 3262–3271 (2003)

    Article  CAS  Google Scholar 

  24. Fischer, M. et al. Rapid actin-based plasticity in dendritic spines. Neuron 20, 847–854 (1998)

    Article  CAS  Google Scholar 

  25. Ehlers, M. D. Activity level controls postsynaptic composition and signaling via the ubiquitin-proteasome system. Nature Neurosci. 6, 231–242 (2003)

    Article  CAS  Google Scholar 

  26. Kirov, S. A. & Harris, K. M. Dendrites are more spiny on mature hippocampal neurons when synapses are inactivated. Nature Neurosci. 2, 878–883 (1999)

    Article  CAS  Google Scholar 

  27. McKinney, R. A. et al. Miniature synaptic events maintain dendritic spines via AMPA receptor activation. Nature Neurosci. 2, 44–49 (1999)

    Article  CAS  Google Scholar 

  28. Soriano, F. X. et al. Preconditioning doses of NMDA promote neuroprotection by enhancing neuronal excitability. J. Neurosci. 26, 4509–4518 (2006)

    Article  CAS  Google Scholar 

  29. Halpain, S., Hipolito, A. & Saffer, L. Regulation of F-actin stability in dendritic spines by glutamate receptors and calcineurin. J. Neurosci. 18, 9835–9844 (1998)

    Article  CAS  Google Scholar 

  30. Fannjiang, Y. et al. BAK alters neuronal excitability and can switch from anti- to pro-death function during postnatal development. Dev. Cell 4, 575–585 (2003)

    Article  CAS  Google Scholar 

  31. Chen, L. & Toth, M. Fragile X mice develop sensory hyperreactivity to auditory stimuli. Neuroscience 103, 1043–1050 (2001)

    Article  CAS  Google Scholar 

  32. Mollner, S., Beck, K. & Pfeuffer, T. Acylation of adenylyl cyclase catalyst is important for enzymic activity. FEBS Lett. 371, 241–244 (1995)

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This paper is dedicated to the memory of our friend and colleague, Alaa El-Husseini, whose ideas about palmitoylation and plasticity inspired this work (deceased 23 Dec 2007). We thank J. Levinson, M.-F. Lise, C. Jiang and E. Yu for technical assistance. This work was supported by grants to A.E.-H. from the Canadian Institutes for Health Research (CIHR) (A.E.-H., 20R90479 and 20R91909), the Michael Smith foundation for Health Research (A.E.-H., 20R52464), the EJLB Foundation and Neuroscience Canada (A.E.-H., 20R61933), as well as from grants from the National Institutes of Health to N.G.D. (GM65525), J.R.Y. (RR011823) and W.N.G. (NS043782, DA13602 and DA019695), and the Peter F. McManus Trust. H.T. was supported by a research fellowship from the Uehara Memorial Foundation. We thank L. Raymond, Y. T. Wang, K. Gerrow, R. Hines, M. Prior and I. Papanayotou for comments on manuscript.

Author Contributions R.K. and J.W. are co-first authors. R.K. was responsible for assessing candidate palmitoyl-protein palmitoylation, siRNA knockdown effects in neurons, and activity-dependent palmitoylation changes. J.W. was responsible for the ABE purifications of samples used for western blotting and mass spectrometry analysis, and for the quantitative northern analysis. P.A. and H.T. analysed filopodia and spine changes in transfected neurons. K.H. analysed palmitoylated proteins using an ABE assay. A.O.B., J.X.T. and J.R.Y. performed the mass spectrometry. N.G.D. analysed, assembled and interpreted the mass spectral data. R.C.D., R.M. and W.N.G. contributed to analysis of some of the palmitoylated proteins. A.F.R. constructed plasmids, particularly those used for the siRNA analysis and rescue. The original co-corresponding authors, A.E.-H. and N.G.D., provided hypothesis development, experimental design input, data interpretation and co-wrote the manuscript. With the passing of A.E.-H., N.G.D. supervised the experimental analyses and rewriting required for the revised manuscript.

Author information

Authors and Affiliations

Authors

Corresponding authors

Correspondence to Rujun Kang or Nicholas G. Davis.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-12 with Legends, Supplementary Methods, Supplementary Discussions and Supplementary References. (PDF 8348 kb)

Supplementary Tables

This file contains Supplementary Tables 1-6 with Supplementary Data. (PDF 1726 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Kang, R., Wan, J., Arstikaitis, P. et al. Neural palmitoyl-proteomics reveals dynamic synaptic palmitoylation. Nature 456, 904–909 (2008). https://doi.org/10.1038/nature07605

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature07605

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing