SwissPalm: Protein Palmitoylation database

F1000Research

Volumn 4, Issue , 2015, Pages

  Blanc, Mathieu ^a   David, Fabrice ^a   Abrami, Laurence ^a   Migliozzi, Daniel ^a   Armand, Florence ^a   Bürgi, Jérôme ^a   van der Goot, Françoise Gisou ^a  

^a EPFL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

CYSTEINE; PROTEOME;

ARTICLE; CONTENT ANALYSIS; INTERNET; PALMITOYLATION; PROTEIN DATABASE; PROTEIN DETERMINATION; PROTEIN LOCALIZATION; PROTEIN MOTIF; PROTEIN PROCESSING; PROTEOMICS; SWISSPALM DATABASE;

EID: 84940973446     PISSN: 20461402     EISSN: 1759796X     Source Type: Journal    
DOI: 10.12688/f1000research.6464.1     Document Type: Article

References (88)

1. Salaun C Greaves J Chamberlain LH: The intracellular dynamic of protein palmitoylation. J Cell Biol. 2010;191(7):1229-38. 21187327 10.1083/jcb.201008160 3010063
2. Blaskovic S Blanc M van der Goot FG: What does S-palmitoylation do to membrane proteins? FEBS J. 2013;280(12):2766-74. 23551889 10.1111/febs.12263
3. Levental I Lingwood D Grzybek M: Palmitoylation regulates raft affinity for the majority of integral raft proteins. Proc Natl Acad Sci U S A. 2010;107(51):22050-4. 21131568 10.1073/pnas.1016184107 3009825
4. Abrami L Kunz B Deuquet J: Functional interactions between anthrax toxin receptors and the WNT signalling protein LRP6. Cell Microbiol. 2008;10(12):2509-19. 18717822 10.1111/j.1462-5822.2008.01226.x
5. Fukata Y Fukata M: Protein palmitoylation in neuronal development and synaptic plasticity. Nat Rev Neurosci. 2010;11(3):161-75. 20168314 10.1038/nrn2788
6. Lakkaraju AK Abrami L Lemmin T: Palmitoylated calnexin is a key component of the ribosome-translocon complex. EMBO J. 2012;31(7):1823-35. 22314232 10.1038/emboj.2012.15 3321195
7. Gauthier-Kemper A Igaev M Sündermann F: Interplay between phosphorylation and palmitoylation mediates plasma membrane targeting and sorting of GAP43. Mol Biol Cell. 2014;25(21):3284-99. 25165142 10.1091/mbc.E13-12-0737 4214776
8. Rossin A Durivault J Chakhtoura-Feghali T: Fas palmitoylation by the palmitoyl acyltransferase DHHC7 regulates Fas stability. Cell Death Differ. 2015;22(4):643-53. 25301068 10.1038/cdd.2014.153 4356335
9. Kong C Lange JJ Samovski D: Ubiquitination and degradation of the hominoid-specific oncoprotein TBC1D3 is regulated by protein palmitoylation. Biochem Biophys Res Commun. 2013;434(2):388-93. 23578663 10.1016/j.bbrc.2013.04.001 3646999
10. Zhu YC Li D Wang L: Palmitoylation-dependent CDKL5-PSD-95 interaction regulates synaptic targeting of CDKL5 and dendritic spine development. Proc Natl Acad Sci U S A. 2013;110(22):9118-23. 23671101 10.1073/pnas.1300003110 3670390
11. Linder ME Deschenes RJ: Palmitoylation: policing protein stability and traffic. Nat Rev Mol Cell Biol. 2007;8(1):74-84. 17183362 10.1038/nrm2084
12. Abrami L Kunz B Iacovache I: Palmitoylation and ubiquitination regulate exit of the Wnt signaling protein LRP6 from the endoplasmic reticulum. Proc Natl Acad Sci U S A. 2008;105(14):5384-9. 18378904 10.1073/pnas.0710389105 2291096
13. Resh MD: Covalent lipid modifications of proteins. Curr Biol. 2013;23(10):R431-5. 23701681 10.1016/j.cub.2013.04.024 3712495
14. Rocks O Peyker A Kahms M: An acylation cycle regulates localization and activity of palmitoylated Ras isoforms. Science. 2005;307(5716):1746-52. 15705808 10.1126/science.1105654
15. Lynch SJ Snitkin H Gumper I: The differential palmitoylation states of N-Ras and H-Ras determine their distinct Golgi subcompartment localizations. J Cell Physiol. 2015;230(3):610-9. 25158650 10.1002/jcp.24779 4269384
16. Greaves J Chamberlain LH: DHHC palmitoyl transferases: substrate interactions and (patho)physiology. Trends Biochem Sci. 2011;36(5):245-53. 21388813 10.1016/j.tibs.2011.01.003
17. Fukata Y Iwanaga T Fukata M: Systematic screening for palmitoyl transferase activity of the DHHC protein family in mammalian cells. Methods. 2006;40(2):177-82. 17012030 10.1016/j.ymeth.2006.05.015
18. El-Husseini AE Craven SE Chetkovich DM: Dual palmitoylation of PSD-95 mediates its vesiculotubular sorting, postsynaptic targeting, and ion channel clustering. J Cell Biol. 2000;148(1):159-72. 10629226 10.1083/jcb.148.1.159 2156213
19. Misra C Restituito S Ferreira J: Regulation of synaptic structure and function by palmitoylated AMPA receptor binding protein. Mol Cell Neurosci. 2010;43(4):341-52. 20083202 10.1016/j.mcn.2010.01.001 3061853
20. Hayashi T Thomas GM Huganir RL: Dual palmitoylation of NR2 subunits regulates NMDA receptor trafficking. Neuron. 2009;64(2):213-26. 19874789 10.1016/j.neuron.2009.08.017 2788208
21. Singaraja RR Huang K Sanders SS: Altered palmitoylation and neuropathological deficits in mice lacking HIP14. Hum Mol Genet. 2011;20(20):3899-909. 21775500 10.1093/hmg/ddr308 3177655
22. Liu H Abecasis GR Heath SC: Genetic variation in the 22q11 locus and susceptibility to schizophrenia. Proc Natl Acad Sci U S A. 2002;99(26):16859-64. 12477929 10.1073/pnas.232186099 139234
23. Mizumaru C Saito Y Ishikawa T: Suppression of APP-containing vesicle trafficking and production of beta-amyloid by AID/DHHC-12 protein. J Neurochem. 2009;111(5):1213-24. 19780898 10.1111/j.1471-4159.2009.06399.x
24. Iwabuchi M Sheng H Thompson JW: Characterization of the ubiquitin-modified proteome regulated by transient forebrain ischemia. J Cereb Blood Flow Metab. 2014;34(3):425-32. 24301296 10.1038/jcbfm.2013.210 3948117
25. Yamamoto Y Chochi Y Matsuyama H: Gain of 5p15.33 is associated with progression of bladder cancer. Oncology. 2007;72(1-2):132-8. 18025801 10.1159/000111132
26. Kang R Wan J Arstikaitis P: Neural palmitoyl-proteomics reveals dynamic synaptic palmitoylation. Nature. 2008;456(7224):904-9. 19092927 10.1038/nature07605 2610860
27. Oyama T Miyoshi Y Koyama K: Isolation of a novel gene on 8p21.3-22 whose expression is reduced significantly in human colorectal cancers with liver metastasis. Genes Chromosomes Cancer. 2000;29(1):9-15. 10918388 10.1002/1098-2264(2000)9999:9999<::AID-GCC1001>3.0.CO;2-#
28. Birkenkamp-Demtroder K Christensen LL Olesen SH: Gene expression in colorectal cancer. Cancer Res. 2002;62(15):4352-63. 12154040
29. Yeste-Velasco M Mao X Grose R: Identification of ZDHHC14 as a novel human tumour suppressor gene. J Pathol. 2014;232(5):566-77. 24407904 10.1002/path.4327
30. Blanc M Blaskovic S van der Goot FG: Palmitoylation, pathogens and their host. Biochem Soc Trans. 2013;41(1):84-8. 23356263 10.1042/BST20120337
31. Roth AF Wan J Bailey AO: Global analysis of protein palmitoylation in yeast. Cell. 2006;125(5):1003-13. 16751107 10.1016/j.cell.2006.03.042 2246083
32. Wan J Roth AF Bailey AO: Palmitoylated proteins: purification and identification. Nat Protoc. 2007;2(7):1573-84. 17585299 10.1038/nprot.2007.225
33. Forrester MT Hess DT Thompson JW: Site-specific analysis of protein S-acylation by resin-assisted capture. J Lipid Res. 2011;52(2):393-8. 21044946 10.1194/jlr.D011106 3023561
34. Martin BR Cravatt BF: Large-scale profiling of protein palmitoylation in mammalian cells. Nat Methods. 2009;6(2):135-8. 19137006 10.1038/nmeth.1293 2775068
35. Yang W Di Vizio D Kirchner M: Proteome scale characterization of human S-acylated proteins in lipid raft-enriched and non-raft membranes. Mol Cell Proteomics. 2010;9(1):54-70. 19801377 10.1074/mcp.M800448-MCP200 2808267
36. Dowal L Yang W Freeman MR: Proteomic analysis of palmitoylated platelet proteins. Blood. 2011;118(13):e62-73. 21813449 10.1182/blood-2011-05-353078 3186346
37. Ivaldi C Martin BR Kieffer-Jaquinod S: Proteomic analysis of S-acylated proteins in human B cells reveals palmitoylation of the immune regulators CD20 and CD23. PLoS One. 2012;7(5):e37187. 22615937 10.1371/journal.pone.0037187 3355122
38. Marin EP Derakhshan B Lam TT: Endothelial cell palmitoylproteomic identifies novel lipid-modified targets and potential substrates for protein acyl transferases. Circ Res. 2012;110(10):1336-44. 22496122 10.1161/CIRCRESAHA.112.269514 3428238
39. Wilson JP Raghavan AS Yang YY: Proteomic analysis of fatty-acylated proteins in mammalian cells with chemical reporters reveals S-acylation of histone H3 variants. Mol Cell Proteomics. 2011;10(3):M110.001198. 21076176 10.1074/mcp.M110.001198 3047146
40. Merrick BA Dhungana S Williams JG: Proteomic profiling of S-acylated macrophage proteins identifies a role for palmitoylation in mitochondrial targeting of phospholipid scramblase 3. Mol Cell Proteomics. 2011;10(10):M110.006007. 21785166 10.1074/mcp.M110.006007 3205854
41. Ren W Jhala US Du K: Proteomic analysis of protein palmitoylation in adipocytes. Adipocyte. 2013;2(1):17-28. 23599907 10.4161/adip.22117 3627377
42. Yount JS Moltedo B Yang YY: Palmitoylome profiling reveals S-palmitoylation-dependent antiviral activity of IFITM3. Nat Chem Biol. 2010;6(8):610-4. 20601941 10.1038/nchembio.405 2928251
43. Li Y Martin BR Cravatt BF: DHHC5 protein palmitoylates flotillin-2 and is rapidly degraded on induction of neuronal differentiation in cultured cells. J Biol Chem. 2012;287(1):523-30. 22081607 10.1074/jbc.M111.306183 3249106
44. Martin BR Wang C Adibekian A: Global profiling of dynamic protein palmitoylation. Nat Methods. 2011;9(1):84-9. 22056678 10.1038/nmeth.1769 3248616
45. Hemsley PA Weimar T Lilley KS: A proteomic approach identifies many novel palmitoylated proteins in Arabidopsis. New Phytol. 2013;197(3):805-14. 23252521 10.1111/nph.12077
46. Wan J Savas JN Roth AF: Tracking brain palmitoylation change: predominance of glial change in a mouse model of Huntington's disease. Chem Biol. 2013;20(11):1421-34. 24211138 10.1016/j.chembiol.2013.09.018 3880188
47. Zhang MM Wu PY Kelly FD: Quantitative control of protein S-palmitoylation regulates meiotic entry in fission yeast. PLoS Biol. 2013;11(7):e1001597. 23843742 10.1371/journal.pbio.1001597 3699447
48. Jones ML Collins MO Goulding D: Analysis of protein palmitoylation reveals a pervasive role in Plasmodium development and pathogenesis. Cell Host Microbe. 2012;12(2):246-58. 22901544 10.1016/j.chom.2012.06.005 3501726
49. Wei X Song H Semenkovich CF: Insulin-regulated protein palmitoylation impacts endothelial cell function. Arterioscler Thromb Vasc Biol. 2014;34(2):346-54. 24357059 10.1161/ATVBAHA.113.302848 3953448
50. Hornbeck PV Kornhauser JM Tkachev S: PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 2012;40(Database issue):D261-70. 22135298 10.1093/nar/gkr1122 3245126
51. Altenhoff AM Schneider A Gonnet GH: OMA 2011: orthology inference among 1000 complete genomes. Nucleic Acids Res. 2011;39(Database issue):D289-94. 21113020 10.1093/nar/gkq1238 3013747
52. Kriventseva EV Tegenfeldt F Petty TJ: OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software. Nucleic Acids Res. 2015;43(Database issue):D250-6. 25428351 10.1093/nar/gku1220 4383991
53. Kumari B Kumar R Kumar M: PalmPred: an SVM based palmitoylation prediction method using sequence profile information. PLoS One. 2014;9(2):e89246. 24586628 10.1371/journal.pone.0089246 3929663
54. Ren J Wen L Gao X: CSS-Palm 2.0: an updated software for palmitoylation sites prediction. Protein Eng Des Sel. 2008;21(11):639-44. 18753194 10.1093/protein/gzn039 2569006
55. Fresno C Fernandez EA: RDAVIDWebService: a versatile R interface to DAVID. Bioinformatics. 2013;29(21):2810-1. 23958726 10.1093/bioinformatics/btt487
56. Huang da W Sherman BT Lempicki RA: Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009;4(1):44-57. 19131956 10.1038/nprot.2008.211
57. Shannon PT Grimes M Kutlu B: RCytoscape: tools for exploratory network analysis. BMC Bioinformatics. 2013;14:217. 23837656 10.1186/1471-2105-14-217 3751905
58. Smoot ME Ono K Ruscheinski J: Cytoscape 2.8: new features for data integration and network visualization. Bioinformatics. 2011;27(3):431-2. 21149340 10.1093/bioinformatics/btq675 3031041
59. Franceschini A Szklarczyk D Frankild S: STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res. 2013;41(Database issue):D808-15. 23203871 10.1093/nar/gks1094 3531103
60. Ruepp A Waegele B Lechner M: CORUM: the comprehensive resource of mammalian protein complexes--2009. Nucleic Acids Res. 2010;38(Database issue):D497-501. 19884131 10.1093/nar/gkp914 2808912
61. Vacic V Iakoucheva LM Radivojac P: Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments. Bioinformatics. 2006;22(12):1536-7. 16632492 10.1093/bioinformatics/btl151
62. Greaves J Gorleku OA Salaun C: Palmitoylation of the SNAP25 protein family: specificity and regulation by DHHC palmitoyl transferases. J Biol Chem. 2010;285(32):24629-38. 20519516 10.1074/jbc.M110.119289 2915699
63. Wurtzel JG Kumar P Goldfinger LE: Palmitoylation regulates vesicular trafficking of R-Ras to membrane ruffles and effects on ruffling and cell spreading. Small GTPases. 2012;3(3):139-53. 22751447 10.4161/sgtp.21084 3442799
64. Alvarez E Girones N Davis RJ: Inhibition of the receptor-mediated endocytosis of diferric transferrin is associated with the covalent modification of the transferrin receptor with palmitic acid. J Biol Chem. 1990;265(27):16644-55. 2398066
65. Lynes EM Bui M Yap MC: Palmitoylated TMX and calnexin target to the mitochondria-associated membrane. EMBO J. 2012;31(2):457-70. 22045338 10.1038/emboj.2011.384 3261551
66. Linder ME Middleton P Hepler JR: Lipid modifications of G proteins: alpha subunits are palmitoylated. Proc Natl Acad Sci U S A. 1993;90(8):3675-9. 8475115 10.1073/pnas.90.8.3675 46364
67. Lu D Sun HQ Wang H: Phosphatidylinositol 4-kinase IIalpha is palmitoylated by Golgi-localized palmitoyltransferases in cholesterol-dependent manner. J Biol Chem. 2012;287(26):21856-65. 22535966 10.1074/jbc.M112.348094 3381148
68. Ohno Y Kashio A Ogata R: Analysis of substrate specificity of human DHHC protein acyltransferases using a yeast expression system. Mol Biol Cell. 2012;23(23):4543-51. 23034182 10.1091/mbc.E12-05-0336 3510016
69. Park S Patterson EE Cobb J: Palmitoylation controls the dynamics of budding-yeast heterochromatin via the telomere-binding protein Rif1. Proc Natl Acad Sci U S A. 2011;108(35):14572-7. 21844336 10.1073/pnas.1105262108 3167557
70. Resh MD: Fatty acylation of proteins: new insights into membrane targeting of myristoylated and palmitoylated proteins. Biochim Biophys Acta. 1999;1451(1):1-16. 10446384 10.1016/S0167-4889(99)00075-0
71. Ashburner M Ball CA Blake JA: Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25(1):25-9. 10802651 10.1038/75556 3037419
72. Caron JM Vega LR Fleming J: Single site alpha-tubulin mutation affects astral microtubules and nuclear positioning during anaphase in Saccharomyces cerevisiae: possible role for palmitoylation of alpha-tubulin. Mol Biol Cell. 2001;12(9):2672-87. 11553707 10.1091/mbc.12.9.2672 59703
73. George J Soares C Montersino A: Palmitoylation of LIM Kinase-1 ensures spine-specific actin polymerization and morphological plasticity. Elife. 2015;4:e06327. 25884247 10.7554/eLife.06327 4429338
74. Sha Z Brill LM Cabrera R: The eIF3 interactome reveals the translasome, a supercomplex linking protein synthesis and degradation machineries. Mol Cell. 2009;36(1):141-52. 19818717 10.1016/j.molcel.2009.09.026 2789680
75. Kabir MA Uddin W Narayanan A: Functional Subunits of Eukaryotic Chaperonin CCT/TRiC in Protein Folding. J Amino Acids. 2011;2011:843206. 22312474 10.4061/2011/843206 3268035
76. Roobol A Carden MJ: Subunits of the eukaryotic cytosolic chaperonin CCT do not always behave as components of a uniform hetero-oligomeric particle. Eur J Cell Biol. 1999;78(1):21-32. 10082421 10.1016/S0171-9335(99)80004-1
77. Ho GP Selvakumar B Mukai J: S-nitrosylation and S-palmitoylation reciprocally regulate synaptic targeting of PSD-95. Neuron. 2011;71(1):131-41. 21745643 10.1016/j.neuron.2011.05.033 3181141
78. Hess DT Stamler JS: Regulation by S-nitrosylation of protein post-translational modification. J Biol Chem. 2012;287(7):4411-8. 22147701 10.1074/jbc.R111.285742 3281651
79. Lee TY Chen YJ Lu CT: dbSNO: a database of cysteine S-nitrosylation. Bioinformatics. 2012;28(17):2293-5. 22782549 10.1093/bioinformatics/bts436
80. Chen YJ Lu CT Lee TY: dbGSH: a database of S-glutathionylation. Bioinformatics. 2014;30(16):2386-8. 24790154 10.1093/bioinformatics/btu301
81. Charych EI Jiang LX Lo F: Interplay of palmitoylation and phosphorylation in the trafficking and localization of phosphodiesterase 10A: implications for the treatment of schizophrenia. J Neurosci. 2010;30(27):9027-37. 20610737 10.1523/JNEUROSCI.1635-10.2010
82. Tian L Jeffries O McClafferty H: Palmitoylation gates phosphorylation-dependent regulation of BK potassium channels. Proc Natl Acad Sci U S A. 2008;105(52):21006-11. 19098106 10.1073/pnas.0806700106 2605631
83. Dorfleutner A Ruf W: Regulation of tissue factor cytoplasmic domain phosphorylation by palmitoylation. Blood. 2003;102(12):3998-4005. 12920028 10.1182/blood-2003-04-1149
84. Soskic V Nyakatura E Roos M: Correlations in palmitoylation and multiple phosphorylation of rat bradykinin B 2 receptor in Chinese hamster ovary cells. J Biol Chem. 1999;274(13):8539-45. 10085087 10.1074/jbc.274.13.8539
85. Yount JS Karssemeijer RA Hang HC: S-palmitoylation and ubiquitination differentially regulate interferon-induced transmembrane protein 3 (IFITM3)-mediated resistance to influenza virus. J Biol Chem. 2012;287(23):19631-41. 22511783 10.1074/jbc.M112.362095 3365998
86. Abrami L Leppla SH van der Goot FG: Receptor palmitoylation and ubiquitination regulate anthrax toxin endocytosis. J Cell Biol. 2006;172(2):309-20. 16401723 10.1083/jcb.200507067 2063559
87. Fairbank M Huang K El-Husseini A: RING finger palmitoylation of the endoplasmic reticulum Gp78 E3 ubiquitin ligase. FEBS Lett. 2012;586(16):2488-93. 22728137 10.1016/j.febslet.2012.06.011
88. Valdez-Taubas J Pelham H: Swf1-dependent palmitoylation of the SNARE Tlg1 prevents its ubiquitination and degradation. EMBO J. 2005;24(14):2524-32. 15973437 10.1038/sj.emboj.7600724 1176453