A plethora of novel information has emerged over the past decade regarding protein lipidation. The reversible attachment of palmitic acid to cysteine residues, termed S-palmitoylation, has focused a special attention. This is mainly due to the unique role of this modification in the regulation of protein trafficking and function. A large family of protein acyltransferases (PATs) containing a conserved aspartate–histidine–histidine–cysteine motif use ping-pong kinetic mechanism to catalyze S-palmitoylation of a substrate protein. Here, we discuss the topology of PAT proteins and their cellular localization. We will also give an overview of the mechanism of protein palmitoylation and how it is regulated. New information concerning the recent discovery of depalmitoylating enzymes belonging to the family of α/β-hydrolase domain-containing protein 17 (ABHD17A) is included. Considering the recent advances that have occurred in understanding the mechanisms underlying the interplay between palmitoylation and depalmitoylation, it is clear that we are beginning to understand the fundamental nature of how cellular signal-transduction mediates membrane-level organization in health and disease.
Impact statement
Protein palmitoylation is one of most important reversible post-translational modifications of protein function in cell-signaling systems. This review gathers the latest information on the molecular mechanism of protein palmitoyl transferase action. It also discusses the issue of substrate specificity of palmitoyl transferases. Another important question is the role of depalmitoylation enzymes. This review should help to formulate questions concerning the regulation of activity of particular PATs as well as of depalmitoylating enzymes (APT).
DeMarJCJr.AndersonRE. Identification and quantitation of the fatty acids composing the CoA ester pool of bovine retina, heart, and liver. J Biol Chem1997; 272: 31362–8.
2.
LiangXLuYNeubertTAReshMD. Mass spectrometric analysis of GAP-43/neuromodulin reveals the presence of a variety of fatty acylated species. J Biol Chem2002; 277: 33032–40.
3.
Valdez-TaubasJPelhamH. Swf1-dependent palmitoylation of the SNARE Tlg1 prevents its ubiquitination and degradation. EMBO J2005; 24: 2524–32.
4.
KongEPengSChandraGSarkarCZhangZBaghMBMukherjeeAB. Dynamic palmitoylation links cytosol-membrane shuttling of acyl-protein thioesterase-1 and acyl-protein thioesterase-2 with that of proto-oncogene H-ras product and growth-associated protein-43. J Biol Chem2013; 288: 9112–25.
5.
GreavesJChamberlainLH. Palmitoylation-dependent protein sorting. J Cell Biol2007; 176: 249–54.
6.
LeventalIGrzybekMSimonsK. Greasing their way: lipid modifications determine protein association with membrane rafts. Biochemistry2010; 49: 6305–16.
7.
LachAGrzybekMHegerEKoryckaJWolnyMKubiakJKolondraABoguslawskaDMAugoffKMajkowskiMPodkalickaJKaczorJStefankoAKuliczkowskiKSikorskiAF. Palmitoylation of MPP1 (membrane-palmitoylated protein 1)/p55 is crucial for lateral membrane organization in erythroid cells. J Biol Chem2012; 287: 18974–84.
8.
MilnerwoodAJParsonsMPYoungFBSingarajaRRFranciosiSVoltaMBergeronSHaydenMRRaymondLA. Memory and synaptic deficits in Hip14/DHHC17 knockout mice. Proc Natl Acad Sci U S A2013; 110: 20296–301.
9.
DunphyJTSchroederHLeventisRGreentreeWKKnudsenJKSilviusJRLinderME. Differential effects of acyl-CoA binding protein on enzymatic and non-enzymatic thioacylation of protein and peptide substrates. Biochim Biophys Acta2000; 1485: 185–98.
10.
KoryckaJLachAHegerEBoguslawskaDMWolnyMToporkiewiczMAugoffKKorzeniewskiJSikorskiAF. Human DHHC proteins: a spotlight on the hidden player of palmitoylation. Eur J Cell Biol2012; 91: 107–17.
11.
RothAFFengYChenLDavisNG. The yeast DHHC cysteine-rich domain protein Akr1p is a palmitoyl transferase. J Cell Biol2002; 159: 23–8.
12.
Gonzalez MontoroAChumpen RamirezSValdez TaubasJ. The canonical DHHC motif is not absolutely required for the activity of the yeast S-acyltransferases Swf1 and Pfa4. J Biol Chem2015; 290: 22448–59.
13.
PolitisEGRothAFDavisNG. Transmembrane topology of the protein palmitoyl transferase Akr1. J Biol Chem2005; 280: 10156–63.
14.
OhnoYKiharaASanoTIgarashiY. Intracellular localization and tissue-specific distribution of human and yeast DHHC cysteine-rich domain-containing proteins. Biochim Biophys Acta2006; 1761: 474–83.
15.
GottliebCDZhangSLinderME. The cysteine-rich domain of the DHHC3 palmitoyltransferase is palmitoylated and contains tightly bound zinc. J Biol Chem2015; 290: 29259–69.
16.
SmotrysJESchoenfishMJStutzMALinderME. The vacuolar DHHC-CRD protein Pfa3p is a protein acyltransferase for Vac8p. J Cell Biol2005; 170: 1091–9.
17.
HemsleyPAGriersonCS. The ankyrin repeats and DHHC S-acyl transferase domain of AKR1 act independently to regulate switching from vegetative to mating states in yeast. PLoS One2011; 6: e28799–e28799.
18.
YangWDi VizioDKirchnerMSteenHFreemanMR. Proteome scale characterization of human S-acylated proteins in lipid raft-enriched and non-raft membranes. Mol Cell Proteomics2010; 9: 54–70.
19.
MitchellDAVasudevanALinderMEDeschenesRJ. Protein palmitoylation by a family of DHHC protein S-acyltransferases. J Lipid Res2006; 47: 1118–27.
20.
Gonzalez MontoroAQuirogaRMaccioniHJValdez TaubasJ. A novel motif at the C-terminus of palmitoyltransferases is essential for Swf1 and Pfa3 function in vivo. Biochem J2009; 419: 301–8.
LemonidisKWernoMWGreavesJDiez-ArdanuyCSanchez-PerezMCSalaunCThomsonDMChamberlainLH. The zDHHC family of S-acyltransferases. Biochem Soc Trans2015; 43: 217–21.
23.
IwanagaTTsutsumiRNoritakeJFukataYFukataM. Dynamic protein palmitoylation in cellular signaling. Prog Lipid Res2009; 48: 117–27.
24.
RocksOGerauerMVartakNKochSHuangZPPechlivanisMKuhlmannJBrunsveldLChandraAEllingerBWaldmannHBastiaensPI. The palmitoylation machinery is a spatially organizing system for peripheral membrane proteins. Cell2010; 141: 458–71.
25.
PutilinaTWongPGentlemanS. The DHHC domain: a new highly conserved cysteine-rich motif. Mol Cell Biochem1999; 195: 219–26.
26.
Bohm S, Frishman D, Mewes HW. Variations of the C2H2 zinc finger motif in the yeast genome and classification of yeast zinc finger proteins. Nucleic Acids Res 1997;25:2464–2469.
27.
Gonzalez MontoroAQuirogaRValdez TaubasJ. Zinc co-ordination by the DHHC cysteine-rich domain of the palmitoyltransferase Swf1. Biochem J2013; 454: 427–35.
28.
Fernandez-HernandoCFukataMBernatchezPNFukataYLinMIBredtDSSessaWC. Identification of Golgi-localized acyl transferases that palmitoylate and regulate endothelial nitric oxide synthase. J Cell Biol2006; 174: 369–77.
29.
LemonidisKGorlekuOASanchez-PerezMCGrefenCChamberlainLH. The Golgi S-acylation machinery comprises zDHHC enzymes with major differences in substrate affinity and S-acylation activity. Mol Biol Cell2014; 25: 3870–83.
30.
GreavesJCarmichaelJAChamberlainLH. The palmitoyl transferase DHHC2 targets a dynamic membrane cycling pathway: regulation by a C-terminal domain. Mol Biol Cell2011; 22: 1887–95.
31.
GorlekuOABarnsAMPrescottGRGreavesJChamberlainLH. Endoplasmic reticulum localization of DHHC palmitoyltransferases mediated by lysine-based sorting signals. J Biol Chem2011; 286: 39573–84.
GreavesJGorlekuOASalaunCChamberlainLH. Palmitoylation of the SNAP25 protein family: specificity and regulation by DHHC palmitoyl transferases. J Biol Chem2010; 285: 24629–38.
36.
LemonidisKSanchez-PerezMCChamberlainLH. Identification of a novel sequence motif recognized by the ankyrin repeat domain of zDHHC17/13 S-Acyltransferases. J Biol Chem2015; 290: 21939–50.
37.
ThomasGMHayashiTChiuSLChenCMHuganirRL. Palmitoylation by DHHC5/8 targets GRIP1 to dendritic endosomes to regulate AMPA-R trafficking. Neuron2012; 73: 482–96.
38.
LiYHuJHoferKWongAMCooperJDBirnbaumSGHammerREHofmannSL. DHHC5 interacts with PDZ domain 3 of post-synaptic density-95 (PSD-95) protein and plays a role in learning and memory. J Biol Chem2010; 285: 13022–31.
39.
BrigidiGSSantyrBShimellJJovellarBBamjiSX. Activity-regulated trafficking of the palmitoyl-acyl transferase DHHC5. Nat Commun2015; 6: 8200–8200.
40.
FredericksGJHoffmannFWRoseAHOsterheldHJHessFMMercierFHoffmannPR. Stable expression and function of the inositol 1,4,5-triphosphate receptor requires palmitoylation by a DHHC6/selenoprotein K complex. Proc Natl Acad Sci U S A2014; 111: 16478–83.
41.
MitchellDAMitchellGLingYBuddeCDeschenesRJ. Mutational analysis of Saccharomyces cerevisiae Erf2 reveals a two-step reaction mechanism for protein palmitoylation by DHHC enzymes. J Biol Chem2010; 285: 38104–14.
42.
JenningsBCLinderME. DHHC protein S-acyltransferases use similar ping-pong kinetic mechanisms but display different acyl-CoA specificities. J Biol Chem2012; 287: 7236–45.
43.
MadzelanPLabunskaTWilsonMA. Influence of peptide dipoles and hydrogen bonds on reactive cysteine pKa values in fission yeast DJ-1. FEBS J2012; 279: 4111–20.
44.
DysonHJJengMFTennantLLSlabyILindellMCuiDSKuprinSHolmgrenA. Effects of buried charged groups on cysteine thiol ionization and reactivity in Escherichia coli thioredoxin: structural and functional characterization of mutants of Asp 26 and Lys 57. Biochemistry1997; 36: 2622–36.
45.
HuangKSandersSSKangRCarrollJBSuttonLWanJSingarajaRYoungFBLiuLEl-HusseiniADavisNGHaydenMR. Wild-type HTT modulates the enzymatic activity of the neuronal palmitoyl transferase HIP14. Hum Mol Genet2011; 20: 3356–65.
46.
RenWSunYDuK. DHHC17 palmitoylates ClipR-59 and modulates ClipR-59 association with the plasma membrane. Mol Cell Biol2013; 33: 4255–65.
47.
DuncanJAGilmanAG. Autoacylation of G protein alpha subunits. J Biol Chem1996; 271: 23594–600.
48.
VeitM. Palmitoylation of the 25-kDa synaptosomal protein (SNAP-25) in vitro occurs in the absence of an enzyme, but is stimulated by binding to syntaxin. Biochem J2000; 345 Pt 1: 145–51.
49.
SwarthoutJTLoboSFarhLCrokeMRGreentreeWKDeschenesRJLinderME. DHHC9 and GCP16 constitute a human protein fatty acyltransferase with specificity for H- and N-Ras. J Biol Chem2005; 280: 31141–8.
50.
GuidottiAForchettiCMCordaMGKonkelDBennettCDCostaE. Isolation, characterization, and purification to homogeneity of an endogenous polypeptide with agonistic action on benzodiazepine receptors. Proc Natl Acad Sci U S A1983; 80: 3531–5.
51.
FaergemanNJKnudsenJ. Role of long-chain fatty acyl-CoA esters in the regulation of metabolism and in cell signalling. Biochem J1997; 323: 1–12.
52.
RasmussenJTBorchersTKnudsenJ. Comparison of the binding affinities of acyl-CoA-binding protein and fatty-acid-binding protein for long-chain acyl-CoA esters. Biochem J1990; 265: 849–55.
53.
RosendalJErtbjergPKnudsenJ. Characterization of ligand binding to acyl-CoA-binding protein. Biochem J1993; 290: 321–6.
54.
RasmussenJTFaergemanNJKristiansenKKnudsenJ. Acyl-CoA-binding protein (ACBP) can mediate intermembrane acyl-CoA transport and donate acyl-CoA for beta-oxidation and glycerolipid synthesis. Biochem J1994; 299: 165–70.
55.
LeventisRJuelGKnudsenJKSilviusJR. Acyl-CoA binding proteins inhibit the nonenzymic S-acylation of cysteinyl-containing peptide sequences by long-chain acyl-CoAs. Biochemistry1997; 36: 5546–53.
56.
AugoffKKolondraAChorzalskaALachAGrabowskiKSikorskiAF. Expression, purification and functional characterization of recombinant human acyl-CoA-binding protein (ACBP) from erythroid cells. Acta Biochim Pol2010; 57: 533–40.
57.
BachovchinDAJiTLiWSimonGMBlankmanJLAdibekianAHooverHNiessenSCravattBF. Superfamily-wide portrait of serine hydrolase inhibition achieved by library-versus-library screening. Proc Natl Acad Sci U S A2010; 107: 20941–6.
58.
DuncanJAGilmanAG. A cytoplasmic acyl-protein thioesterase that removes palmitate from G protein alpha subunits and p21(RAS). J Biol Chem1998; 273: 15830–7.
59.
YehDCDuncanJAYamashitaSMichelT. Depalmitoylation of endothelial nitric-oxide synthase by acyl-protein thioesterase 1 is potentiated by Ca(2+)-calmodulin. J Biol Chem1999; 274: 33148–54.
60.
TomatisVMTrenchiAGomezGADaniottiJL. Acyl-protein thioesterase 2 catalyzes the deacylation of peripheral membrane-associated GAP-43. PLoS One2010; 5: e15045–e15045.
61.
MartinBRWangCAdibekianATullySECravattBF. Global profiling of dynamic protein palmitoylation. Nat Methods2011; 9: 84–9.
62.
DekkerFJRocksOVartakNMenningerSHedbergCBalamuruganRWetzelSRennerSGerauerMScholermannBRuschMKramerJWRauhDCoatesGWBrunsveldLBastiaensPIWaldmannH. Small-molecule inhibition of APT1 affects Ras localization and signaling. Nat Chem Biol2010; 6: 449–56.
63.
RuschMZimmermannTJBurgerMDekkerFJGormerKTriolaGBrockmeyerAJanningPBottcherTSieberSAVetterIRHedbergCWaldmannH. Identification of acyl protein thioesterases 1 and 2 as the cellular targets of the Ras-signaling modulators palmostatin B and M. Angew Chem Int Ed Engl2011; 50: 9838–42.
64.
TianLMcClaffertyHKnausHGRuthPShipstonMJ. Distinct acyl protein transferases and thioesterases control surface expression of calcium-activated potassium channels. J Biol Chem2012; 287: 14718–25.
65.
BurgerMZimmermannTJKondohYStegePWatanabeNOsadaHWaldmannHVetterIR. Crystal structure of the predicted phospholipase LYPLAL1 reveals unexpected functional plasticity despite close relationship to acyl protein thioesterases. J Lipid Res2012; 53: 43–50.
66.
JiaLChisariMMaktabiMHSobieskiCZhouHKonopkoAMMartinBRMennerickSJBlumerKJ. A mechanism regulating G protein-coupled receptor signaling that requires cycles of protein palmitoylation and depalmitoylation. J Biol Chem2014; 289: 6249–57.
67.
YokoiNFukataYSekiyaAMurakamiTKobayashiKFukataM. Identification of PSD-95 depalmitoylating enzymes. J Neurosci2016; 36: 6431–44.
68.
LinDTConibearE. ABHD17 proteins are novel protein depalmitoylases that regulate N-Ras palmitate turnover and subcellular localization. Elife2015; 4: e11306–e11306.
69.
NotredameCHigginsDGHeringaJ. T-Coffee: a novel method for fast and accurate multiple sequence alignment. J Mol Biol2000; 302: 205–17.
