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Cited by 56Click Chemistry and ApplicationsLipid metabolism and biosynthesisSphingolipid Metabolism and Signaling

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A palmitoyl transferase chemical–genetic system to map ZDHHC-specific S-acylation

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Ocasio, Cory A., Baggelaar, Marc P., Sipthorp, James, Losada de la Lastra, Ana, Tavares, Manuel, Volarić, Jana, Soudy, Christelle, Storck, Elisabeth M., Houghton, Jack W., Palma-Duran, Susana A., MacRae, James I., Tomić, Goran, Carr, Lotte, Downward, Julian, Eggert, Ulrike S., Tate, Edward W.·2024·Nature Biotechnology
DOI 10.1038/s41587-023-02030-0PMC PMC11471619

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Abstract

The 23 human zinc finger Asp-His-His-Cys motif-containing (ZDHHC) S -acyltransferases catalyze long-chain S -acylation at cysteine residues across an extensive network of hundreds of proteins important for normal physiology or dysregulated in disease. Here we present a technology to directly map the protein substrates of a specific ZDHHC at the whole-proteome level, in intact cells. Structure-guided engineering of paired ZDHHC ‘hole’ mutants and ‘bumped’ chemically tagged fatty acid probes enabled probe transfer to specific protein substrates with excellent selectivity over wild-type ZDHHCs. Chemical–genetic systems were exemplified for five human ZDHHCs (3, 7, 11, 15 and 20) and applied to generate de novo ZDHHC substrate profiles, identifying >300 substrates and S -acylation sites for new functionally diverse proteins across multiple cell lines. We expect that this platform will elucidate S -acylation biology for a wide range of models and organisms.

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Research works printed but not linked: 64

  1. Adhikari, S. et al. A high-stringency blueprint of the human proteome. Nat. Commun. 11, 5301 (2020). · DOI · Paper page
  2. Rana, M. S. et al. Fatty acyl recognition and transfer by an integral membrane S-acyltransferase. Science 359, eaao6326 (2018). · DOI
  3. Sanders, S. S. et al. Curation of the mammalian palmitoylome indicates a pivotal role for palmitoylation in diseases and disorders of the nervous system and cancers. PLoS Comput. Biol. 11, e1004405 (2015). · DOI
  4. Lanyon-Hogg, T., Faronato, M., Serwa, R. A. & Tate, E. W. Dynamic protein acylation: new substrates, mechanisms, and drug targets. Trends Biochem. Sci. 42, 566–581 (2017). · DOI
  5. Blanc, M., David, F. P. A. & van der Goot, F. G. SwissPalm 2: protein S-palmitoylation database. Methods Mol. Biol. 2009, 203–214 (2019). · DOI
  6. Rana, M. S., Lee, C.-J. & Banerjee, A. The molecular mechanism of DHHC protein acyltransferases. Biochem. Soc. Trans. 47, 157–167 (2019). · DOI
  7. Greaves, J. et al. Molecular basis of fatty acid selectivity in the zDHHC family of S-acyltransferases revealed by click chemistry. Proc. Natl Acad. Sci. USA 114, E1365–E1374 (2017). · DOI
  8. Jennings, B. C. & Linder, M. E. DHHC protein S-acyltransferases use similar ping-pong kinetic mechanisms but display different acyl-CoA specificities. J. Biol. Chem. 287, 7236–7245 (2012). · DOI
  9. Rodenburg, R. N. P. et al. Stochastic palmitoylation of accessible cysteines in membrane proteins revealed by native mass spectrometry. Nat. Commun. 8, 1280 (2017). · DOI
  10. Malgapo, M. I. P. & Linder, M. E. Substrate recruitment by zDHHC protein acyltransferases. Open Biol. 11, 210026 (2021). · DOI
  11. Philippe, J. M. & Jenkins, P. M. Spatial organization of palmitoyl acyl transferases governs substrate localization and function. Mol. Membr. Biol. 35, 60–75 (2019). · DOI
  12. Howie, J. et al. Substrate recognition by the cell surface palmitoyl transferase DHHC5. Proc. Natl Acad. Sci. USA 111, 17534–17539 (2014). · DOI
  13. Chamberlain, L. H., Shipston, M. J. & Gould, G. W. Regulatory effects of protein S-acylation on insulin secretion and insulin action. Open Biol. 11, 210017 (2021). · DOI
  14. Lin, H. Protein cysteine palmitoylation in immunity and inflammation. FEBS J. 288, 7043–7059 (2021). · DOI
  15. Losada de la Lastra, A., Hassan, S. & Tate, E. W. Deconvoluting the biology and druggability of protein lipidation using chemical proteomics. Curr. Opin. Chem. Biol. 60, 97–112 (2021). · DOI
  16. Won, S. J., Cheung See Kit, M. & Martin, B. R. Protein depalmitoylases. Crit. Rev. Biochem. Mol. Biol. 53, 83–98 (2018). · DOI
  17. Runkle, K. B. et al. Inhibition of DHHC20-mediated EGFR palmitoylation creates a dependence on EGFR signaling. Mol. Cell 62, 385–396 (2016). · DOI
  18. Yao, H. et al. Inhibiting PD-L1 palmitoylation enhances T-cell immune responses against tumours. Nat. Biomed. Eng. 3, 306–317 (2019). · DOI
  19. Zhang, M. et al. A STAT3 palmitoylation cycle promotes TH17 differentiation and colitis. Nature 586, 434–439 (2020). · DOI
  20. McMichael, T. M. et al. The palmitoyltransferase ZDHHC20 enhances interferon-induced transmembrane protein 3 (IFITM3) palmitoylation and antiviral activity. J. Biol. Chem. 292, 21517–21526 (2017). · DOI
  21. Virlogeux, A. et al. Increasing brain palmitoylation rescues behavior and neuropathology in Huntington disease mice. Sci. Adv. 7, eabb0799 (2021). · DOI
  22. Peng, T., Thinon, E. & Hang, H. C. Proteomic analysis of fatty-acylated proteins. Curr. Opin. Chem. Biol. 30, 77–86 (2016). · DOI
  23. Kallemeijn, W. W. et al. Proteome-wide analysis of protein lipidation using chemical probes: in-gel fluorescence visualization, identification and quantification of N-myristoylation, N- and S-acylation, O-cholesterylation, S-farnesylation and S-geranylgeranylation. Nat. Protoc. 16, 5083–5122 (2021). · DOI
  24. Davda, D. et al. Profiling targets of the irreversible palmitoylation inhibitor 2-bromopalmitate. ACS Chem. Biol. 8, 1912–1917 (2013). · DOI
  25. Azizi, S.-A. et al. Development of an acrylamide-based inhibitor of protein S-acylation. ACS Chem. Biol. 16, 1546–1556 (2021). · DOI
  26. Tian, L., McClafferty, H., Knaus, H.-G., Ruth, P. & Shipston, M. J. Distinct acyl protein transferases and thioesterases control surface expression of calcium-activated potassium channels. J. Biol. Chem. 287, 14718–14725 (2012). · DOI
  27. Kilpatrick, C. L. et al. Dissociation of Golgi-associated DHHC-type zinc finger protein (GODZ)- and Sertoli cell gene with a zinc finger domain-β (SERZ-β)-mediated palmitoylation by loss of function analyses in knock-out mice. J. Biol. Chem. 291, 27371–27386 (2016). · DOI
  28. Roth, A. F. et al. Global analysis of protein palmitoylation in yeast. Cell 125, 1003–1013 (2006). · DOI
  29. Swarthout, J. T. et al. DHHC9 and GCP16 constitute a human protein fatty acyltransferase with specificity for H- and N-Ras. J. Biol. Chem. 280, 31141–31148 (2005). · DOI
  30. Bishop, A. C. et al. A chemical switch for inhibitor-sensitive alleles of any protein kinase. Nature 407, 395–401 (2000). · DOI
  31. Gibson, B. A. et al. Chemical genetic discovery of PARP targets reveals a role for PARP-1 in transcription elongation. Science 353, 45–50 (2016). · DOI
  32. Islam, K. The bump-and-hole tactic: expanding the scope of chemical genetics. Cell Chem. Biol. 25, 1171–1184 (2018). · DOI
  33. Grammel, M. & Hang, H. C. Chemical reporters for biological discovery. Nat. Chem. Biol. 9, 475–484 (2013). · DOI
  34. Lee, C.J. et al. Bivalent recognition of fatty acyl-CoA by a human integral membrane palmitoyltransferase. Proc. Natl Acad. Sci. USA 119, e2022050119 (2022). · DOI
  35. Collins, M. O., Woodley, K. T. & Choudhary, J. S. Global, site-specific analysis of neuronal protein S-acylation. Sci. Rep. 7, 4683 (2017). · DOI
  36. Benfield, C. T. et al. Bat IFITM3 restriction depends on S-palmitoylation and a polymorphic site within the CD225 domain. Life Sci. Alliance 3, e201900542 (2020). · DOI
  37. Hamel, L. D., Deschenes, R. J. & Mitchell, D. A. A fluorescence-based assay to monitor autopalmitoylation of zDHHC proteins applicable to high-throughput screening. Anal. Biochem. 460, 1–8 (2014). · DOI
  38. Mesquita, F. S. et al. S-acylation controls SARS-CoV-2 membrane lipid organization and enhances infectivity. Dev. Cell 56, 2790–2807 (2021). · DOI
  39. Ohno, Y., Kihara, A., Sano, T. & Igarashi, Y. Intracellular localization and tissue-specific distribution of human and yeast DHHC cysteine-rich domain-containing proteins. Biochim. Biophys. Acta 1761, 474–483 (2006). · DOI
  40. Thinon, E., Fernandez, J. P., Molina, H. & Hang, H. C. Selective enrichment and direct analysis of protein S-palmitoylation sites. J. Proteome. Res. 17, 1907–1922 (2018). · DOI
  41. Yang, X. et al. Palmitoylation of tetraspanin proteins: modulation of CD151 lateral interactions, subcellular distribution, and integrin-dependent cell morphology. Mol. Biol. Cell. 13, 767–781 (2002). · DOI
  42. Percher, A. et al. Mass-tag labeling reveals site-specific and endogenous levels of protein S-fatty acylation. Proc. Natl Acad. Sci. USA 113, 4302–4307 (2016). · DOI
  43. Barylko, B. et al. Palmitoylation controls the catalytic activity and subcellular distribution of phosphatidylinositol 4-kinase IIα. J. Biol. Chem. 284, 9994–10003 (2009). · DOI
  44. Branon, T. C. et al. Efficient proximity labeling in living cells and organisms with TurboID. Nat. Biotechnol. 36, 880–887 (2018). · DOI · Paper page
  45. Buljan, M. et al. Kinase interaction network expands functional and disease roles of human kinases. Mol. Cell 79, 504–520 (2020). · DOI
  46. Lee, S. et al. Distinct structural mechanisms determine substrate affinity and kinase activity of protein kinase Cα. J. Biol. Chem. 292, 16300–16309 (2017). · DOI
  47. Taylor, S. S. & Kornev, A. P. Protein kinases: evolution of dynamic regulatory proteins. Trends Biochem. Sci. 36, 65–77 (2011). · DOI
  48. Hou, H., John Peter, A. T., Meiringer, C., Subramanian, K. & Ungermann, C. Analysis of DHHC acyltransferases implies overlapping substrate specificity and a two-step reaction mechanism. Traffic 10, 1061–1073 (2009). · DOI
  49. McClafferty, H. & Shipston, M. J. siRNA knockdown of mammalian zDHHCs and validation of mRNA expression by RT–qPCR. Methods Mol. Biol. 2009, 151–168 (2019). · DOI
  50. Thiele, C., Wunderling, K. & Leyendecker, P. Multiplexed and single cell tracing of lipid metabolism. Nat. Methods 16, 1123–1130 (2019). · DOI
  51. Debets, M. F. et al. Metabolic precision labeling enables selective probing of O-linked N-acetylgalactosamine glycosylation. Proc. Natl Acad. Sci. USA 117, 25293–25301 (2020). · DOI
  52. Abrami, L. et al. Identification and dynamics of the human ZDHHC16-ZDHHC6 palmitoylation cascade. eLife 6, e27826 (2017). · DOI
  53. Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N. & Sternberg, M. J. E. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 10, 845–858 (2015). · DOI · Paper page
  54. Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012). · DOI · Paper page
  55. Yang, X., Ma, Y., Li, N., Cai, H. & Bartlett, M. G. Development of a method for the determination of acyl-CoA compounds by liquid chromatography mass spectrometry to probe the metabolism of fatty acids. Anal. Chem. 89, 813–821 (2017). · DOI
  56. Matyash, V., Liebisch, G., Kurzchalia, T. V., Shevchenko, A. & Schwudke, D. Lipid extraction by methyl-tert-butyl ether for high-throughput lipidomics. J. Lipid Res. 49, 1137–1146 (2008). · DOI
  57. Cajka, T. & Fiehn, O. Increasing lipidomic coverage by selecting optimal mobile-phase modifiers in LC–MS of blood plasma. Metabolomics 12, 34 (2016). · DOI
  58. Tsugawa, H. et al. MS-DIAL: data-independent MS/MS deconvolution for comprehensive metabolome analysis. Nat. Methods 12, 523–526 (2015). · DOI
  59. Koelmel, J. P. et al. LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data. BMC Bioinformatics 18, 331 (2017). · DOI
  60. Kessner, D., Chambers, M., Burke, R., Agus, D. & Mallick, P. ProteoWizard: open source software for rapid proteomics tools development. Bioinformatics 24, 2534–2536 (2008). · DOI · Paper page
  61. Rappsilber, J., Ishihama, Y. & Mann, M. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 75, 663–670 (2003). · DOI
  62. Goya Grocin, A., Serwa, R. A., Morales Sanfrutos, J., Ritzefeld, M. & Tate, E. W. Whole proteome profiling of N-myristoyltransferase activity and inhibition using sortase A. Mol. Cell Proteomics 18, 115–126 (2019). · DOI
  63. Labun, K. et al. CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. Nucleic Acids Res. 47, W171–W174 (2019). · DOI
  64. Mi, H. et al. PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. Nucleic Acids Res. 49, D394–D403 (2021). · DOI · Paper page

Metadata

Authors
Ocasio, C. A., Baggelaar, M. P., Sipthorp, J., Losada de la Lastra, A., Tavares, M., Volarić, J., Soudy, C., Storck, E. M., Houghton, J. W., Palma-Duran, S. A., MacRae, J. I., Tomić, G., Carr, L., Downward, J., Eggert, U. S., & Tate, E. W.
Affiliations
  • The Francis Crick Institute (GB)
  • Utrecht University (NL)
  • Imperial College London (GB)
  • King's College London (GB)
Corresponding author
Tate, Edward W.
ORCID
Venue
Nature Biotechnology
Publisher
Springer Science and Business Media LLC
Published
2024-01-08
Volume
42
Issue
10
Pages
1548-1558
ISSN
  • 0733-222X (ISSN-L)
  • 1087-0156
  • 1546-1696
DOI
10.1038/s41587-023-02030-0
PMC
PMC11471619
OpenAlex
W4390669556
Cited by
56
References
2
Citations by year
2026: 18 · 2025: 22 · 2024: 15
FWCI
7.94
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Biotechnology (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
  • Figshare (submittedVersion, cc-by)
  • Research Portal (King's College London) (submittedVersion, other-oa)
  • Spiral (Imperial College London) (submittedVersion, other-oa)
  • The Francis Crick Institute (cc-by)
Funders
  • Cancer Research UK (C29637/A27506, NS/A000078/1, C29637/A20183, DRCNPG-Nov21\100001, C24523/A27435)
  • Wellcome Trust (103799/Z/14/Z, 110060/Z/15/Z)
  • European Research Council Advanced Grant RASImmune
  • RCUK | Engineering and Physical Sciences Research Council (NS/A000078/1)
Topics
  • Physical Sciences › Chemistry › Organic Chemistry › Click Chemistry and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Biochemistry › Lipid metabolism and biosynthesis
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Sphingolipid Metabolism and Signaling
Keywords
S-acylation, palmitoylation, chemical genetics, structure-guided mutagenesis, cysteine palmitoylation
MeSH terms
Acylation, Acyltransferases, Humans, Substrate Specificity

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