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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.

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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

Author notes

    • Rujun Kang
    • , Junmei Wan
    • , Nicholas G. Davis
    •  & Alaa El-Husseini

    These authors contributed equally to this work.

    • Alaa El-Husseini

    Deceased.

Affiliations

  1. Department of Psychiatry, Brain Research Centre, University of British Columbia, Vancouver V6T 1Z3, British Columbia, Canada

    • Rujun Kang
    • , Pamela Arstikaitis
    • , Hideto Takahashi
    • , Kun Huang
    •  & Alaa El-Husseini
  2. Department of Pharmacology, Wayne State University School of Medicine, Detroit, Michigan 48201, USA

    • Junmei Wan
    • , Amy F. Roth
    •  & Nicholas G. Davis
  3. Department of Cell Biology, The Scripps Research Institute, La Jolla, California 10550, USA

    • Aaron O. Bailey
    • , James X. Thompson
    •  & John R. Yates III
  4. Department of Neurobiology, University of Chicago, Chicago, Illinois 60637, USA

    • Renaldo C. Drisdel
    • , Ryan Mastro
    •  & William N. Green

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Correspondence to Rujun Kang or Nicholas G. Davis.

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    Supplementary Information

    This file contains Supplementary Figures 1-12 with Legends, Supplementary Methods, Supplementary Discussions and Supplementary References.

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https://doi.org/10.1038/nature07605

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