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Global profiling of dynamic protein palmitoylation

Nature Methods volume 9, pages 84–89 (2012)Cite this article

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Abstract

The reversible thioester linkage of palmitic acid on cysteines, known as protein S-palmitoylation, facilitates the membrane association and proper subcellular localization of proteins. Here we report the metabolic incorporation of the palmitic acid analog 17-octadecynoic acid (17-ODYA) in combination with stable-isotope labeling with amino acids in cell culture (SILAC) and pulse-chase methods to generate a global quantitative map of dynamic protein palmitoylation events in cells. We distinguished stably palmitoylated proteins from those that turn over rapidly. Treatment with a serine lipase–selective inhibitor identified a pool of dynamically palmitoylated proteins regulated by palmitoyl-protein thioesterases. This subset was enriched in oncoproteins and other proteins linked to aberrant cell growth, migration and cancer. Our method provides a straightforward way to characterize global palmitoylation dynamics in cells and confirms enzyme-mediated depalmitoylation as a critical regulatory mechanism for a specific subset of rapidly cycling palmitoylated proteins.

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Figure 1: Quantitative analysis of protein palmitoylation.
Figure 2: Enhanced assignment of palmitoylated proteins using SILAC 17-ODYA proteomics.
Figure 3: HDFP is a lipase-selective inhibitor.
Figure 4: Lipase inhibition by HDFP enhances 17-ODYA labeling and prevents palmitoylation turnover.
Figure 5: Enzymatically regulated, dynamically cycling palmitoylated proteins.

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References

  1. Schmidt, M.F.G. & Schlesinger, M.J. Fatty acid binding to vesicular stomatitis virus glycoprotein: a new type of post-translational modification of the viral glycoprotein. Cell 17, 813–819 (1979).

    Article  CAS  Google Scholar 

  2. Schlesinger, M., Magee, A. & Schmidt, M. Fatty acid acylation of proteins in cultured cells. J. Biol. Chem. 255, 10021–10024 (1980).

    CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  4. Wan, J., Roth, A.F., Bailey, A.O. & Davis, N.G. Palmitoylated proteins: purification and identification. Nat. Protoc. 2, 1573–1584 (2007).

    Article  CAS  Google Scholar 

  5. Yang, W., Di Vizio, D., Kirchner, M., Steen, H. & Freeman, M.R. Proteome scale characterization of human S-acylated proteins in lipid raft-enriched and non-raft membranes. Mol. Cell. Proteomics 9, 54–70 (2010).

    Article  CAS  Google Scholar 

  6. Kang, R. et al. Neural palmitoyl-proteomics reveals dynamic synaptic palmitoylation. Nature 456, 904–909 (2008).

    Article  CAS  Google Scholar 

  7. Hang, H.C. et al. Chemical probes for the rapid detection of fatty-acylated proteins in mammalian cells. J. Am. Chem. Soc. 129, 2744–2745 (2007).

    Article  CAS  Google Scholar 

  8. Martin, B.R. & Cravatt, B.F. Large-scale profiling of protein palmitoylation in mammalian cells. Nat. Methods 6, 135–138 (2009).

    Article  CAS  Google Scholar 

  9. Speers, A.E. & Cravatt, B.F. Profiling enzyme activities in vivo using click chemistry methods. Chem. Biol. 11, 535–546 (2004).

    Article  CAS  Google Scholar 

  10. Zhang, M.M., Tsou, L.K., Charron, G., Raghavan, A.S. & Hang, H.C. Tandem fluorescence imaging of dynamic S-acylation and protein turnover. Proc. Natl. Acad. Sci. USA 107, 8627–8632 (2010).

    Article  CAS  Google Scholar 

  11. Ong, S.-E. et al. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376–386 (2002).

    Article  CAS  Google Scholar 

  12. Weerapana, E. et al. Quantitative reactivity profiling predicts functional cysteines in proteomes. Nature 468, 790–795 (2010).

    Article  CAS  Google Scholar 

  13. Bachovchin, D.A. et al. Superfamily-wide portrait of serine hydrolase inhibition achieved by library-versus-library screening. Proc. Natl. Acad. Sci. USA 107, 20941–20946 (2010).

    Article  CAS  Google Scholar 

  14. Leung, D., Hardouin, C., Boger, D.L. & Cravatt, B.F. Discovering potent and selective reversible inhibitors of enzymes in complex proteomes. Nat. Biotechnol. 21, 687–691 (2003).

    Article  CAS  Google Scholar 

  15. Tully, S.E. & Cravatt, B.F. Activity-based probes that target functional subclasses of phospholipases in proteomes. J. Am. Chem. Soc. 132, 3264–3265 (2010).

    Article  CAS  Google Scholar 

  16. Adibekian, A. et al. Click-generated triazole ureas as ultrapotent in vivo–active serine hydrolase inhibitors. Nat. Chem. Biol. 7, 469–478 (2011).

    Article  CAS  Google Scholar 

  17. Yoo, B.K. et al. Astrocyte elevated gene-1 (AEG-1): A multifunctional regulator of normal and abnormal physiology. Pharmacol. Ther. 130, 1–8 (2011).

    Article  CAS  Google Scholar 

  18. Fukata, Y. & Fukata, M. Protein palmitoylation in neuronal development and synaptic plasticity. Nat. Rev. Neurosci. 11, 161–175 (2010).

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  20. Wedegaertner, P.B. & Bourne, H.R. Activation and depalmitoylation of Gs alpha. Cell 77, 1063–1070 (1994).

    Article  CAS  Google Scholar 

  21. Baker, T.L., Zheng, H., Walker, J., Coloff, J.L. & Buss, J.E. Distinct rates of palmitate turnover on membrane-bound cellular and oncogenic H-Ras. J. Biol. Chem. 278, 19292–19300 (2003).

    Article  CAS  Google Scholar 

  22. Duncan, J.A. & Gilman, A.G. A cytoplasmic acyl-protein thioesterase that removes palmitate from G protein alpha subunits and p21RAS. J. Biol. Chem. 273, 15830–15837 (1998).

    Article  CAS  Google Scholar 

  23. Camp, L. & Hofmann, S. Purification and properties of a palmitoyl-protein thioesterase that cleaves palmitate from H-Ras. J. Biol. Chem. 268, 22566–22574 (1993).

    CAS  PubMed  Google Scholar 

  24. Dekker, F.J. et al. Small-molecule inhibition of APT1 affects Ras localization and signaling. Nat. Chem. Biol. 6, 449–456 (2010).

    Article  CAS  Google Scholar 

  25. Ahearn, I.M. et al. FKBP12 binds to acylated H-Ras and promotes depalmitoylation. Mol. Cell 41, 173–185 (2011).

    Article  CAS  Google Scholar 

  26. Quinn, B.J. et al. Erythrocyte scaffolding protein p55/MPP1 functions as an essential regulator of neutrophil polarity. Proc. Natl. Acad. Sci. USA 106, 19842–19847 (2009).

    Article  CAS  Google Scholar 

  27. Wennerberg, K., Rossman, K.L. & Der, C.J. The Ras superfamily at a glance. J. Cell Sci. 118, 843–846 (2005).

    Article  CAS  Google Scholar 

  28. Konstantinopoulos, P.A., Karamouzis, M.V. & Papavassiliou, A.G. Post-translational modifications and regulation of the RAS superfamily of GTPases as anticancer targets. Nat. Rev. Drug Discov. 6, 541–555 (2007).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank S. Hofmann (University of Texas Southwestern Medical School) for providing purified PPT1 enzyme, A. Spears and M. Dix for mass spectrometry assistance, and members of the Cravatt laboratory for helpful discussions. Funding was provided by US National Institutes of Health (CA087660), F32NS060559 (B.R.M.), K99CA151460 (B.R.M.), DRG1978-08 (S.E.T.), Deutscher Akademischer Austausch Dienst (A.A.) and The Skaggs Institute for Chemical Biology.

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  1. Brent R Martin

    Present address: Present address: Department of Chemistry, University of Michigan, Ann Arbor, Michigan, USA.,

Authors and Affiliations

  1. The Department of Chemical Physiology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California, USA

    Brent R Martin, Chu Wang, Alexander Adibekian, Sarah E Tully & Benjamin F Cravatt

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  1. Brent R Martin
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Contributions

B.R.M. and B.F.C. designed research. B.R.M. performed research. A.A., B.R.M., S.E.T. and C.W. contributed new analytical tools. B.R.M. and B.F.C. analyzed data and wrote the manuscript.

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Correspondence to Brent R Martin or Benjamin F Cravatt.

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Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–2, Supplementary Note (PDF 4660 kb)

Supplementary Table 1

Palmitoylated protein validation by SILAC 17-ODYA proteomics. Heavy and light isotope–labeled cells were prepared in two groups. In group 1 (runs 1–5), heavy and light isotope–labeled cells were treated overnight with 20 μM palmitic acid or 20 μM 17-ODYA, respectively, overnight in their standard growth media. In group 2 (runs 6–10), the order of labeling is inversed (heavy, palmitic acid and light, 17-ODYA). Ratio values are given as 17-ODYA/palmitic acid data. MS1 peaks present only in light or only in heavy samples that pass additional criteria (Online Methods) were assigned an upper-limit ratio of 20. Only proteins that were identified in both groups with median ratios greater than 1.5 are listed. Peptides that did not meet the stringent quantification criteria are listed with a ratio of zero. (XLS 1643 kb)

Supplementary Table 2

Hydroxylamine (NH2OH) sensitivity of putative palmitoylated proteins. Heavy and light isotope–labeled cells were both labeled for 8 h with 20 μM 17-ODYA. In run 1, 'heavy' membrane lysates were treated with 1 M hydroxylamine, precipitated and mixed with 17-ODYA–labeled 'light' membrane lysates. In runs 2–3, light membrane lysates were treated with 1 M hydroxylamine, precipitated and mixed with 17-ODYA–labeled heavy membrane lysates. Mixtures were then reacted with biotin-azide, enriched and digested for proteomics analysis. Ratios are displayed as 17-ODYA/NH2OH data. Data were filtered by putative palmitoylated proteins identified in Supplementary Table 1. (XLS 843 kb)

Supplementary Table 3

Palmitoylated protein validation by spectral counting. Spectral counts were grouped to assigned proteins and filtered to have an average across all replicates equal or greater than 2. The ratio of average spectral counts comparing 17-ODYA and palmitic acid (PA) groups was calculated and filtered to exclude ratios less than 5. Proteins with spectral count averages of 2–5 were defined as 'medium confidence', and those with spectral count averages greater than 5 are classified as 'high confidence'. Proteins in red font contain a consensus myristoylation motif (Met-Gly) at the N terminus, and those assigned by SILAC proteomics are noted. (XLS 71 kb)

Supplementary Table 4

ABPP-SILAC profiling of serine hydrolases inhibited by HDFP. Ratio values are given as DMSO/HDFP data, and all quantified serine hydrolases are listed. Four separate experiments were performed. Runs 1–2 ('light' cells treated with HDFP) and runs 3–4 ('heavy' cells treated with HDFP) are from different cell preparations. Runs 1 and 3 are from soluble proteomes, and runs 2 and 4 are from membrane proteomes. Individual MS1 spectra were manually analyzed to include the additional hydrolases PPT1, PGAP1 and ABHD13 as valid HDFP targets. Peptides that did not meet the stringent quantification criteria are listed with a ratio of zero. (XLS 231 kb)

Supplementary Table 5

Pulse-chase analysis of HDFP-stabilized protein palmitoylation. A summary of three experiments are shown in a single table. Each experiment contains an equal number of biological replicates where either 'heavy' cells or 'light' cells were perturbed. For each experiment, four columns are listed, including the median ratio, the mean ratio, the standard error and the number (N) of quantitated peptides. In experiment 1 (N = 6 biological replicates), cells were labeled with 17-ODYA (2 h) and collected or placed in 'chase' medium for an additional 4 h. In experiment 2 (N = 8 biological replicates), cells were labeled for 2 h with 17-ODYA, then placed in 'chase' medium for 4 h with DMSO or HDFP. In experiment 3 (N = 2 biological replicates), lysates from experiment 1 were directly mixed and digested without enrichment for proteomic analysis of relative protein abundance. Data were filtered to display assigned palmitoylated proteins (Supplementary Table 1). Singleton peptides (defined in Online Methods) were assigned an arbitrary ratio of 20 but were not included in any of the listed calculations (mean, median and others), except when they were the only representative peptides. (XLS 127 kb)

Supplementary Table 6

Protein and peptide ratios for experiment 1 (pulse-chase analysis of t = 0 /t = 4). Quantitative proteomics analysis of proteins undergoing dynamic depalmitoylation. In experiment 1 (N = 6 biological replicates), cells were labeled with 17-ODYA (2 h) and collected or placed in 'chase' medium for an additional 4 h. Calculated peptide ratios are displayed in the column titled 'median', and the median ratio is listed in the first line for each protein. The 'run' column lists the replicate where the given peptide was quantified. In runs 1–3, the heavy isotope–labeled sample was frozen immediately after the 2-h pulse, and the light isotope–labeled cells were placed in chase medium for 4 h. In runs 4–6, the light isotope–labeled cells were immediately frozen after the pulse labeling, and the heavy isotope–labeled cells were placed in chase medium for 4 h. After inverting the ratios for runs 1–3, the data from all experiments were combined and listed. Peptides classified as singletons were assigned a ratio of 20. Peptides listed with a ratio of 0 were assigned a sequence by Sequest, but the MS1 data did not meet the stringent criteria for ratio assignment. (XLS 785 kb)

Supplementary Table 7

Protein and peptide ratios for experiment 3 (unenriched analysis). Samples prepared as described in Supplementary Table 6 were prepared without click chemistry or enrichment and are identified as experiment 3. Unenriched lysates were mixed and digested for direct assessment of protein abundance. Again, the order of isotopic labeling was inverted in the two biological replicates. After inverting the ratios for run 1, the data from all experiments were combined and listed. Peptides classified as singletons are assigned a ratio of 20. Peptides listed with a ratio of 0 were assigned a sequence by Sequest, but the MS1 data did not meet the stringent criteria for ratio assignment. (XLS 320 kb)

Supplementary Table 8

Protein and peptide ratios for experiment 2 (pulse-chase analysis of HDFP/DMSO data). Quantitative proteomics analysis of palmitoylated proteins protected from turnover by addition of HDFP. In experiment 2 (N = 8 biological replicates), cells were labeled with 17-ODYA (2 h) and placed in 'chase' medium for an additional 4 h with or without the addition of HDFP. Calculated peptide ratios are displayed in the column titled 'median', and the median ratio is listed in the first line for each protein. The 'run' column lists the replicate where the given peptide was quantified. In runs 1–4, the heavy isotope–labeled cells were treated with HDFP and the light isotope–labeled cells were treated with DMSO for 4 h in chase medium containing excess palmitic acid. In runs 5–8, the light isotope–labeled cells were treated with HDFP and the heavy isotope–labeled cells were treated with DMSO for 4 h in chase medium containing excess palmitic acid. After inverting the ratios for runs 1–4, the data from all experiments were combined and listed. Peptides classified as singletons are assigned a ratio of 20. Peptides listed with a ratio of 0 were assigned a sequence by Sequest, but the MS1 data did not meet the stringent criteria for ratio assignment. (XLS 995 kb)

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Martin, B., Wang, C., Adibekian, A. et al. Global profiling of dynamic protein palmitoylation. Nat Methods 9, 84–89 (2012). https://doi.org/10.1038/nmeth.1769

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