Quantitative analysis of the human T cell palmitome

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Morrison, Eliot ^a   Kuropka, Benno ^a,b   Kliche, Stefanie ^c   Brügger, Britta ^d   Krause, Eberhard ^b   Freund, Christian ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b LEIBNIZ INSTITUT FÜR MOLEKULARE PHARMAKOLOGIE   (Germany)

^c OTTO VON GUERICKE UNIVERSITY   (Germany)

^d UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME;

CELL CULTURE; HUMAN; JURKAT CELL LINE; LIPOYLATION; LIQUID CHROMATOGRAPHY; METABOLISM; PROCEDURES; PROTEIN PROCESSING; PROTEOMICS; T LYMPHOCYTE; TANDEM MASS SPECTROMETRY; WESTERN BLOTTING;

BLOTTING, WESTERN; CELLS, CULTURED; CHROMATOGRAPHY, LIQUID; HUMANS; JURKAT CELLS; LIPOYLATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOME; PROTEOMICS; T-LYMPHOCYTES; TANDEM MASS SPECTROMETRY;

EID: 84933054770     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep11598     Document Type: Article

References (34)

1. Roth, A. F., Feng, Y., Chen, L. & Davis, N. G. The yeast DHHC cysteine-rich domain protein Akr1p is a palmitoyl transferase. J. Cell Biol. 159, 23-28, doi: 10.1083/jcb.200206120 (2002).
2. Tsutsumi, R., Fukata, Y. & Fukata, M. Discovery of protein-palmitoylating enzymes. Pflugers Arch., EJP 456, 1199-1206, doi: 10.1007/s00424-008-0465-x (2008).
3. Rocks, O. et al. The palmitoylation machinery is a spatially organizing system for peripheral membrane proteins. Cell 141, 458-471, doi: 10.1016/j.cell.2010.04.007 (2010).
4. Lobo, S., Greentree, W. K., Linder, M. E. & Deschenes, R. J. Identification of a Ras palmitoyltransferase in Saccharomyces cerevisiae. J. Biol. Chem. 277, 41268-41273, doi: 10.1074/jbc.M206573200 (2002).
5. Ladygina, N., Martin, B. R. & Altman, A. Dynamic palmitoylation and the role of DHHC proteins in T cell activation and anergy. Adv. Immunol. 109, 1-44, doi: 10.1016/B978-0-12-387664-5.00001-7 (2011).
6. Mansilla, F. et al. Differential expression of DHHC9 in microsatellite stable and instable human colorectal cancer subgroups. Br. J. Cancer 96, 1896-1903, doi: 10.1038/sj.bjc.6603818 (2007).
7. Young, F. B., Butland, S. L., Sanders, S. S., Sutton, L. M. & Hayden, M. R. Putting proteins in their place: palmitoylation in Huntington disease and other neuropsychiatric diseases. Prog. Neurobiol. 97, 220-238, doi: 10.1016/j.pneurobio.2011.11.002 (2012).
8. Vesa, J. et al. Mutations in the palmitoyl protein thioesterase gene causing infantile neuronal ceroid lipofuscinosis. Nature 376, 584-587, doi: 10.1038/376584a0 (1995).
9. Mukai, J. et al. Evidence that the gene encoding ZDHHC8 contributes to the risk of schizophrenia. Nat. Genet. 36, 725-731, doi: 10.1038/ng1375 (2004).
10. Yanai, A. et al. Palmitoylation of huntingtin by HIP14 is essential for its trafficking and function. Nat. Neurosci. 9, 824-831, doi: 10.1038/nn1702 (2006).
11. 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, doi: 10.1074/mcp.M800448-MCP200 (2010).
12. Wan, J., Roth, A. F., Bailey, A. O. & Davis, N. G. Palmitoylated proteins: purification and identification. Nat. Protoc. 2, 1573-1584, doi: 10.1038/nprot.2007.225 (2007).
13. Martin, B. R. & Cravatt, B. F. Large-scale profiling of protein palmitoylation in mammalian cells. Nat. Meth. 6, 135-138, doi: 10.1038/nmeth.1293 (2009).
14. 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, doi: 10.1021/ja0685001 (2007).
15. Martin, B. R., Wang, C., Adibekian, A., Tully, S. E. & Cravatt, B. F. Global profiling of dynamic protein palmitoylation. Nat. Meth. 9, 84-89, doi: 10.1038/nmeth.1769 (2012).
16. Jones, M. L., Collins, M. O., Goulding, D., Choudhary, J. S. & Rayner, J. C. Analysis of protein palmitoylation reveals a pervasive role in Plasmodium development and pathogenesis. Cell Host Microbe 12, 246-258 (2012).
17. Mirgorodskaya, O. A. et al. Quantitation of peptides and proteins by matrix-assisted laser desorption/ionization mass spectrometry using 18O-labeled internal standards. Rapid Commun. Mass Spectrom. 14, 1226-1232, doi: 10.1002/1097-0231(20000730)14: 14< 1226::AID-RCM14> 3.0.CO;2-V (2000).
18. Lange, S., Sylvester, M., Schümann, M., Freund, C. & Krause, E. Identification of Phosphorylation-Dependent Interaction Partners of the Adapter Protein ADAP using Quantitative Mass Spectrometry: SILAC vs 18O-Labeling. J. Proteome Res., doi: 10.1021/pr1003054 (2010).
19. Mirza, S. P., Greene, A. S. & Olivier, M. 18O labeling over a coffee break: a rapid strategy for quantitative proteomics. J. Proteome Res. 7, 3042-3048 (2008).
20. Wilson, J. P., Raghavan, A. S., Yang, Y.-Y., Charron, G. & Hang, H. C. Proteomic analysis of fatty-acylated proteins in mammalian cells with chemical reporters reveals S-acylation of histone H3 variants. Mol. Cell. Proteomics 10, M110.001198, doi: 10.1074/ mcp.M110.001198 (2011).
21. Heng, T. S. P. et al. The Immunological Genome Project: networks of gene expression in immune cells. Nat. Immunol. 9, 1091-1094, doi: 10.1038/ni1008-1091 (2008).
22. Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E. L. L. Predicting transmembrane protein topology with a hidden markov model: application to complete genomes. J. Mol. Biol. 305, 567-580, doi:10.1006/jmbi.2000.4315 (2001).
23. Ren, J. et al. CSS-Palm 2.0: an updated software for palmitoylation sites prediction. Protein Eng. Des. Sel. 21, 639-644, doi: 10.1093/protein/gzn039 (2008).
24. Marin, E. P., Derakhshan, B., Lam, T. T., Davalos, A. & Sessa, W. C. Endothelial cell palmitoylproteomic identifies novel lipidmodified targets and potential substrates for protein acyl transferases. Circ. Res. 110, 1336-1344, doi: 10.1161/ CIRCRESAHA.112.269514 (2012).
25. Merrick, B. A. et al. Proteomic profiling of S-acylated macrophage proteins identifies a role for palmitoylation in mitochondrial targeting of phospholipid scramblase 3. Mol. Cell. Proteomics 10, M110.006007 (2011).
26. Dowal, L., Yang, W., Freeman, M. R., Steen, H. & Flaumenhaft, R. Proteomic analysis of palmitoylated platelet proteins. Blood 118, e62-73, doi: 10.1182/blood-2011-05-353078 (2011).
27. Forrester, M. T. et al. Site-specific analysis of protein S-acylation by resin-assisted capture. J. Lipid Res. 52, 393-398, doi: 10.1194/ jlr.D011106 (2011).
28. Kang, R. et al. Neural palmitoyl-proteomics reveals dynamic synaptic palmitoylation. Nature 456, 904-909, doi: 10.1038/ nature07605 (2008).
29. Brdickova, N. et al. LIME: a new membrane Raft-associated adaptor protein involved in CD4 and CD8 coreceptor signaling. J. Exp. Med. 198, 1453-1462, doi: 10.1084/jem.20031484 (2003).
30. Charrin, S. et al. Differential stability of tetraspanin/tetraspanin interactions: role of palmitoylation. FEBS Lett. 516, 139-144, doi: 10.1016/S0014-5793(02)02522-X (2002).
31. Tsutsumi, K., Tomomura, M., Furuichi, T. & Hisanaga, S. Palmitoylation-dependent endosomal localization of AATYK1A and its interaction with Src. Genes Cells 13, 949-964, doi: 10.1111/j.1365-2443.2008.01219x (2008).
32. Zhang, W., Trible, R. P. & Samelson, L. E. LAT palmitoylation: its essential role in membrane microdomain targeting and tyrosine phosphorylation during T cell activation. Immunity 9, 239-246, doi: 10.1016/S1074-7613(00)80606-8 (1998).
33. Wirth, A. et al. Dual lipidation of the brain-specific Cdc42 isoform regulates its functional properties. Biochem. J. 456, 311-322, doi: 10.1042/BJ20130788 (2013).
34. Zhang, W., Sloan-Lancaster, J., Kitchen, J., Trible, R. P. & Samelson, L. E. LAT: the ZAP-70 tyrosine kinase substrate that links T cell receptor to cellular activation. Cell 92, 83-92, doi: 10.1016/S0092-8674(00)80901-0 (1998).