Proteome-wide analysis of protein lipidation using chemical probes: in-gel fluorescence visualization, identification and quantification ofN-myristoylation,N- andS-acylation,O-cholesterylation,S-farnesylation andS-geranylgeranylation

Wouter W. Kallemeijn, Thomas Lanyon-Hogg, Nattawadee Panyain, Andrea Goya Grocin, Paulina Ciepla, Julia Morales-Sanfrutos, Edward W. Tate

Published: 2021-10-26 DOI: 10.1038/s41596-021-00601-6

Protein lipidation

Chemical proteomics

Quantitative mass spectrometry

In-gel fluorescence

Lipid PTMs

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Protein lipidation is one of the most widespread post-translational modifications (PTMs) found in nature, regulating protein function, structure and subcellular localization. Lipid transferases and their substrate proteins are also attracting increasing i
Introduction
Materials
Procedure 1: in-gel fluorescence visualization of lipid probe–nobreaklabeled proteins
Procedure 2: identification and quantification of lipid PTMs by chemical proteomics
Troubleshooting
Anticipated results
References
ACKNOWLEDGMENTS

Chen, B., Sun, Y., Niu, J., Jarugumilli, G. K. & Wu, X. Protein lipidation in cell signaling and diseases: function, regulation, and therapeutic opportunities. Cell Chem. Biol. 25, 817–831 (2018).
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).
Hentschel, A., Zahedi, R. P. & Ahrends, R. Protein lipid modifications—more than just a greasy ballast. Proteomics 16, 759–782 (2016).
Garner, A. L. & Janda, K. D. cat-ELCCA: a robust method to monitor the fatty acid acyltransferase activity of ghrelin O-acyltransferase (GOAT). Angew. Chem. Int. Ed. Engl. 49, 9630–9634 (2010).
Goncalves, V. et al. A fluorescence-based assay for N-myristoyltransferase activity. Anal. Biochem. 421, 342–344 (2012).
Lanyon-Hogg, T. et al. Click chemistry armed enzyme-linked immunosorbent assay to measure palmitoylation by hedgehog acyltransferase. Anal. Biochem. 490, 66–72 (2015).
Lanyon-Hogg, T. et al. Microfluidic mobility shift assay for real-time analysis of peptide N-palmitoylation. SLAS Discov. 22, 418–424 (2017).
Lanyon-Hogg, T. et al. Acylation-coupled lipophilic induction of polarisation (Acyl-cLIP): a universal assay for lipid transferase and hydrolase enzymes. Chem. Sci. 10, 8995–9000 (2019).
Kakugawa, S. et al. Notum deacylates Wnt proteins to suppress signalling activity. Nature 519, 187–192 (2015).
Won, S. J. et al. Molecular mechanism for isoform-selective inhibition of acyl protein thioesterases 1 and 2 (APT1 and APT2). ACS Chem. Biol. 11, 3374–3382 (2016).
Ma, D. et al. Crystal structure of a membrane-bound O-acyltransferase. Nature 562, 286–290 (2018).
Rana, M. S. et al. Fatty acyl recognition and transfer by an integral membrane S-acyltransferase. Science 359, eaao6326 (2018).
Kuchay, S. et al. GGTase3 is a newly identified geranylgeranyltransferase targeting a ubiquitin ligase. Nat. Struct. Mol. Biol. 26, 628–636 (2019).
Dian, C. et al. High-resolution snapshots of human N-myristoyltransferase in action illuminate a mechanism promoting N-terminal Lys and Gly myristoylation. Nat. Commun. 11, 1132 (2020).
Jiang, Y., Benz, T. L. & Long, S. B. Substrate and product complexes reveal mechanisms of Hedgehog acylation by HHAT. Science 372, 1215–1219 (2021).
Tate, E. W., Kalesh, K. A., Lanyon-Hogg, T., Storck, E. M. & Thinon, E. Global profiling of protein lipidation using chemical proteomic technologies. Curr. Opin. Chem. Biol. 24, 48–57 (2015).
Thinon, E. et al. Global profiling of co- and post-translationally N-myristoylated proteomes in human cells. Nat. Commun. 5, 4919 (2014).
Daf Duluc, L. et al. Tipifarnib prevents development of hypoxia-induced pulmonary hypertension. Cardiovasc. Res. 113, 276–287 (2017).
Mousnier, A. et al. Fragment-derived inhibitors of human N-myristoyltransferase block capsid assembly and replication of the common cold virus. Nat. Chem. 10, 599–606 (2018).
Heal, W. P., Wickramasinghe, S. R., Leatherbarrow, R. J. & Tate, E. W. N-Myristoyl transferase-mediated protein labeling in vivo. Org. Biomol. Chem. 6, 2308–2315 (2008).
Wright, M. H., Heal, W. P., Mann, D. J. & Tate, E. W. Protein myristoylation in health and disease. J. Chem. Biol. 3, 19–35 (2010).
Chamberlain, L. H. & Shipston, M. J. The physiology of protein S-acylation. Physiol. Rev. 95, 341–376 (2015).
Rodgers, U. R. et al. Characterization of hedgehog acyltransferase inhibitors identifies a small molecule probe for hedgehog signaling by cancer cells. ACS Chem. Biol. 11, 3256–3262 (2016).
Storck, E. M. et al. Dual chemical probes enable quantitative system-wide analysis of protein prenylation and prenylation dynamics. Nat. Chem. 11, 552–561 (2019).
Ciepla, P. et al. New chemical probes targeting cholesterylation of Sonic Hedgehog in human cells and zebrafish. Chem. Sci. 5, 4249–4259 (2014).
Rioux, V. et al. Exogenous myristic acid acylates proteins in cultured rat hepatocytes. J. Nutr. Biochem. 13, 66–74 (2002).
Taguchi, Y. & Schätzl, H. M. Small-scale Triton X-114 extraction of hydrophobic proteins. Bio Protoc. 4, e1139 (2014).
Drisdel, R. C. & Green, W. N. Labeling and quantifying sites of protein palmitoylation. Biotechniques 36, 276–285 (2004).
Forrester, M. T. et al. Site-specific analysis of protein S-acylation by resin-assisted capture. J. Lipid Res. 52, 393–398 (2011).
Blanc, M. et al. SwissPalm: protein palmitoylation database. F1000Res 4, 261 (2015).
Devabhaktuni, A. et al. TagGraph reveals vast protein modification landscapes from large tandem mass spectrometry datasets. Nat. Biotechnol. 37, 469–479 (2019).
Heal, W. P., Wright, M. H., Thinon, E. & Tate, E. W. Multifunctional protein labeling via enzymatic N-terminal tagging and elaboration by click chemistry. Nat. Protoc. 7, 105–117 (2011).
Charron, G. et al. Robust fluorescent detection of protein fatty-acylation with chemical reporters. J. Am. Chem. Soc. 131, 4967–4975 (2009).
Thinon, E., Morales-Sanfrutos, J., Mann, D. J. & Tate, E. W. N-Myristoyltransferase inhibition induces ER-stress, cell cycle arrest, and apoptosis in cancer cells. ACS Chem. Biol. 11, 2165–2176 (2016).
Kallemeijn, W. W. et al. Validation and invalidation of chemical probes for the human N-myristoyltransferases. Cell Chem. Biol. 26, 892–900.e4 (2019).
Demetriadou, A. et al. Mouse Stbd1 is N-myristoylated and affects ER-mitochondria association and mitochondrial morphology. J. Cell Sci. 130, 903–915 (2017).
Schlott, A. C. et al. Structure-guided identification of resistance breaking antimalarial N-myristoyltransferase inhibitors. Cell Chem. Biol. 26, 991–1000.e7 (2019).
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).
Tapodi, A. et al. BFSP1 C-terminal domains released by post-translational processing events can alter significantly the calcium regulation of AQP0 water permeability. Exp. Eye Res. 185, 107585 (2019).
Wright, M. H. et al. Validation of N-myristoyltransferase as an antimalarial drug target using an integrated chemical biology approach. Nat. Chem. 6, 112–121 (2014).
Wright, M. H. et al. Global analysis of protein N-myristoylation and exploration of N-myristoyltransferase as a drug target in the neglected human pathogen Leishmania donovani. Chem. Biol. 22, 342–354 (2015).
Wright, M. H., Paape, D., Price, H. P., Smith, D. F. & Tate, E. W. Global profiling and inhibition of protein lipidation in vector and host stages of the sleeping sickness parasite Trypanosoma brucei. ACS Infect. Dis. 2, 427–441 (2016).
Serwa, R. A., Abaitua, F., Krause, E., Tate, E. W. & O'Hare, P. Systems analysis of protein fatty acylation in herpes simplex virus-infected cells using chemical proteomics. Chem. Biol. 22, 1008–1017 (2015).
Schlott, A. C., Holder, A. A. & Tate, E. W. N-Myristoylation as a drug target in malaria: exploring the role of N-myristoyltransferase substrates in the inhibitor mode of action. ACS Infect. Dis. 4, 449–457 (2018).
Broncel, M. et al. Myristoylation profiling in human cells and zebrafish. Data Brief 4, 379–383 (2015).
Broncel, M. et al. Multifunctional reagents for quantitative proteome-wide analysis of protein modification in human cells and dynamic profiling of protein lipidation during vertebrate development. Angew. Chem. Int. Ed. Engl. 54, 5948–5951 (2015).
Rangan, K. J., Yang, Y. Y., Charron, G. & Hang, H. C. Rapid visualization and large-scale profiling of bacterial lipoproteins with chemical reporters. J. Am. Chem. Soc. 132, 10628–10629 (2010).
Charlton, T. M., Kovacs-Simon, A., Michell, S. L., Fairweather, N. F. & Tate, E. W. Quantitative lipoproteomics in Clostridium difficile reveals a role for lipoproteins in sporulation. Chem. Biol. 22, 1562–1573 (2015).
Martin, B. R., Wang, C., Adibekian, A., Tully, S. E. & Cravatt, B. F. Global profiling of dynamic protein palmitoylation. Nat. Methods 9, 84–89 (2011).
Won, S. J. & Martin, B. R. Temporal profiling establishes a dynamic S-palmitoylation cycle. ACS Chem. Biol. 13, 1560–1568 (2018).
Schroeder, G. N. et al. Legionella pneumophila effector LpdA is a palmitoylated phospholipase D virulence factor. Infect. Immun. 83, 3989–4002 (2015).
Kalinin, A. et al. Expression of mammalian geranylgeranyltransferase type-II in Escherichia coli and its application for in vitro prenylation of Rab proteins. Protein Expr. Purif. 22, 84–91 (2001).
Nguyen, U. T. et al. Analysis of the eukaryotic prenylome by isoprenoid affinity tagging. Nat. Chem. Biol. 5, 227–235 (2009).
Suazo, K. F. et al. Metabolic labeling of prenylated proteins using alkyne-modified isoprenoid analogues. Curr. Protoc. Chem. Biol. 10, e46 (2018).
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).
Martin, B. R. Chemical approaches for profiling dynamic palmitoylation. Biochem. Soc. Trans. 41, 43–49 (2013).
Yang, Y., Yang, X. & Verhelst, S. H. Comparative analysis of click chemistry mediated activity-based protein profiling in cell lysates. Molecules 18, 12599–12608 (2013).
Werner, T. et al. Ion coalescence of neutron encoded TMT 10-plex reporter ions. Anal. Chem. 86, 3594–3601 (2014).
End, D. W. et al. Characterization of the antitumor effects of the selective farnesyl protein transferase inhibitor R115777 in vivo and in vitro. Cancer Res. 61, 131–137 (2001).
Lanyon-Hogg, T. et al. Photochemical probe identification of a small-molecule inhibitor binding site in hedgehog acyltransferase (HHAT)*. Angew. Chem. Int. Ed. Engl. 60, 13542–13547 (2021).
Rafiee, M. R. et al. Protease-resistant streptavidin for interaction proteomics. Mol. Syst. Biol. 16, e9370 (2020).
Ran, F. A. et al. Genome engineering using the CRISPR-Cas9 system. Nat. Protoc. 8, 2281–2308 (2013).
Percher, A., Thinon, E. & Hang, H. Mass-tag labeling using acyl-PEG exchange for the determination of endogenous protein S-fatty acylation. Curr. Protoc. Protein Sci. 89, 14.17.1–14.17.11 (2017).
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).
Lynes, E. M. et al. Palmitoylation is the switch that assigns calnexin to quality control or ER Ca2+ signaling. J. Cell Sci. 126, 3893–3903 (2013).

Proteome-wide analysis of protein lipidation using chemical probes: in-gel fluorescence visualization, identification and quantification ofN-myristoylation,N- andS-acylation,O-cholesterylation,S-farnesylation andS-geranylgeranylation

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