Mass spectrometric analysis of GAP-43/neuromodulin reveals the presence of a variety of fatty acylated species

Dual acylation is required for trafficking of growth-associated protein-43 (GAP-43) to endosomal recycling compartment via an Arf6-associated endocytic vesicular pathway

GAP-43 (growth-associated protein-43) is a dually palmitoylated protein, at cysteine residues at positions 3 and 4, that mostly localizes in plasma membrane both in neural and non-neural cells. In the present study, we have examined membrane association, subcellular distribution and intracellular trafficking of GAP-43 in CHO (Chinese hamster ovary)-K1 cells. Using biochemical assays and confocal and video microscopy in living cells we demonstrated that GAP-43, at steady state, localizes at the recycling endosome in addition to the cytoplasmic leaflet of the plasma membrane and TGN (trans-Golgi network). Pharmacological inhibition of newly synthesized GAP-43 acylation or double mutation of Cys3 and Cys4 of GAP-43 completely disrupts TGN, plasma membrane and recycling endosome association. A combination of selective photobleaching techniques and time-lapse fluorescence microscopy reveals a dynamic association of GAP-43 with recycling endosomes in equilibrium with the plasma membrane pool. Newly synthesized GAP-43 is found mainly associated with the TGN, but not with the pericentriolar recycling endosome, and traffics to the plasma membrane by a brefeldin A-insensitive pathway. Impairment of plasma membrane fusion and internalization by treatment with tannic acid does affect the trafficking of GAP-43 from plasma membrane to recycling endosomes which reveals a vesicle-mediated retrograde trafficking of GAP-43. Here, we also show that internalization of GAP-43 is regulated by Arf (ADP-ribosylation factor) 6. Taken together, these results demonstrate that dual acylation is required for sorting of peripheral membrane-associated GAP-43 to recycling endosome via an Arf6-associated endocytic vesicular pathway.

Palmitoylation of the synaptic vesicle fusion machinery

The fusion of synaptic vesicles with the pre-synaptic plasma membrane mediates the secretion of neurotransmitters at nerve terminals. This pathway is regulated by an array of protein-protein interactions. Of central importance are the soluble NSF (N-ethylmaleimide-sensitive factor) attachment protein receptor (SNARE) proteins syntaxin 1 and SNAP25, which are associated with the pre-synaptic plasma membrane and vesicle-associated membrane protein (VAMP2), a synaptic vesicle SNARE. Syntaxin 1, SNAP25 and VAMP2 interact to form a tight complex bridging the vesicle and plasma membranes, which has been suggested to represent the minimal membrane fusion machinery. Synaptic vesicle fusion is stimulated by a rise in intraterminal Ca2+ levels, and a major Ca2+ sensor for vesicle fusion is synaptotagmin I. Synaptotagmin is likely to couple Ca2+ entry to vesicle fusion via Ca2+-dependent and independent interactions with membrane phospholipids and the SNARE proteins. Intriguingly, syntaxin 1, SNAP25, VAMP2 and synaptotagmin I have all been reported to be modified by palmitoylation in neurons. In this review, we discuss the mechanisms and dynamics of palmitoylation of these proteins and speculate on how palmitoylation might contribute to the regulation of synaptic vesicle fusion.

Regulation of GAP-43 at serine 41 acts as a switch to modulate both intrinsic and extrinsic behaviors of growing neurons, via altered membrane distribution

GAP-43 is the major neuronal substrate of protein kinase C (PKC). Its phosphorylation status dictates the severity of pathfinding errors by GAP-43 (+/-) growth cones in vivo, as well as its modulation of actin dynamics in vitro. These experiments show that stably overexpressing cDNAs mutant at its single PKC phosphorylation site at serine41 in retinoic acid treated SH-Sy5Y neuroblastoma cells regulates intrinsic and extrinsic behaviors of growing neurons. Intrinsically, only Wt and pseudophosphorylated GAP-43Ser41Asp precipitated with F-actin and potentiated F-actin - regulated filopodia formation. GAP-43Ser41Asp inhibited neurite outgrowth whereas only unphosphorylatable GAP-43Ser41Ala precipitated neurotubulin, potentiated neurotubulin accumulation in neurites and increased outgrowth. When PI3-kinase was inhibited GAP-43Ser41Asp-mediated filopodia formation was inhibited whereas GAP-43Ser41Ala-mediated neurite extension was potentiated. Extrinsically, only Wt and GAP-43Ser41Asp potentiated both homotypic adhesion and neurite outgrowth on NCAM-expressing monolayers and promoted NCAM stability. With respect to the underlying mechanism, more F-actin and NCAM colocalized with Wt and GAP-43Ser41Asp in detergent resistant membranes (DRMs) isolated from live cells and GAP-43Ser41Asp-mediated functions were insensitive to cholesterol depletion. In contrast, GAP-43Ser41Ala-mediated functions were sensitive to cholesterol depletion. Neither GAP-43Ser41Asp nor GAP-43Ser41Ala was able to protect against growth cone collapse mediated by PIP2 inhibitors. The results show that modification of GAP-43 at its PKC phosphorylation site directs its distribution to different membrane microdomains that have distinct roles in the regulation of intrinsic and extrinsic behaviors in growing neurons.

The fat controller: roles of palmitoylation in intracellular protein trafficking and targeting to membrane microdomains (Review)

The attachment of palmitic acid to the amino acid cysteine via thioester linkage (S-palmitoylation) is a common post-translational modification of eukaryotic proteins. In this review, we discuss the role of palmitoylation as a versatile protein sorting signal, regulating protein trafficking between distinct intracellular compartments and the micro-localization of proteins within membranes.

Palmitoylation modification of Galpha(o) depresses its susceptibility to GAP-43 activation

Interaction between GAP-43 (growth associated protein-43) and Galpha(o) (alpha subunit of Go protein) influences the signal transduction pathways leading to differentiation of neural cells. GAP-43 is known to increase guanine nucleotide exchange by Galpha(o), which is a major component of neuronal growth cone membranes. However, it is not clear whether GAP-43 stimulation is related to the Galpha(o) palmitoylation or the conversion of Galpha(o) from oligmers to monomers, which was shown to be a necessary regulatory factor in GDP/GTP exchange of Galpha(o). Here we expressed and purified GAP-43, GST-GAP-43 and Galpha(o) proteins, detected their stimulatory effect on [(35)S]-GTPgammaS binding of Galpha(o). It was found that the EC(50) of both GAP-43 and GST-GAP-43 activation were tenfold lower in case of depalmitoylated Galpha(o) than palmitoylated Galpha(o). Non-denaturing gel electrophoresis and p-PDM cross-linking analysis revealed that addition of GST-GAP-43 induced disassociation of depalmitoylated Galpha(o) from oligomers to monomers, but did not influence the oligomeric state of palmitoylated Galpha(o), which suggests that palmitoylation is a key regulatory factor in GAP-43 stimulation on Galpha(o). These results indicated the interaction of GAP-43 and Galpha(o) could accelerate conversion of depalmitoylated Galpha(o) but not palmitoylated Galpha(o) from oligomers to monomers, so as to increase the GTPgammaS binding activity of Galpha(o). Results here provide new evidence about how signaling protein palmitoylation is involved in the G-protein-coupled signal transduction cascade, and give a useful clue on the participation of GAP-43 in G-protein cycle by its preferential activation of depalmitoylated Galpha(o).

A crosslinking analysis of GAP-43 interactions with other proteins in differentiated N1E-115 cells

It has been suggested that GAP-43 (growth-associated protein) binds to various proteins in growing neurons as part of its mechanism of action. To test this hypothesis in vivo, differentiated N1E-115 neuroblastoma cells were labeled with [³⁵S]-amino acids and were treated with a cleavable crosslinking reagent. The cells were lysed in detergent and the lysates were centrifuged at 100,000 × g to isolate crosslinked complexes. Following cleavage of the crosslinks and analysis by two-dimensional gel electrophoresis, it was found that the crosslinker increased the level of various proteins, and particularly actin, in this pellet fraction. However, GAP-43 was not present, suggesting that GAP-43 was not extensively crosslinked to proteins of the cytoskeleton and membrane skeleton and did not sediment with them. GAP-43 also did not sediment with the membrane skeleton following nonionic detergent lysis. Calmodulin, but not actin or other proposed interaction partners, co-immunoprecipitated with GAP-43 from the 100,000 × g supernatant following crosslinker addition to cells or cell lysates. Faint spots at 34 kDa and 60 kDa were also present. Additional GAP-43 was recovered from GAP-43 immunoprecipitation supernatants with anti-calmodulin but not with anti-actin. The results suggest that GAP-43 is not present in complexes with actin or other membrane skeletal or cytoskeletal proteins in these cells, but it is nevertheless possible that a small fraction of the total GAP-43 may interact with other proteins.

Identification of CKAP4/p63 as a major substrate of the palmitoyl acyltransferase DHHC2, a putative tumor suppressor, using a novel proteomics method

Protein palmitoylation is the post-translational addition of the 16-carbon fatty acid palmitate to specific cysteine residues by a labile thioester linkage. Palmitoylation is mediated by a family of at least 23 palmitoyl acyltransferases (PATs) characterized by an Asp-His-His-Cys (DHHC) motif. Many palmitoylated proteins have been identified, but PAT-substrate relationships are mostly unknown. Here we present a method called palmitoyl-cysteine isolation capture and analysis (or PICA) to identify PAT-substrate relationships in a living vertebrate system and demonstrate its effectiveness by identifying CKAP4/p63 as a substrate of DHHC2, a putative tumor suppressor.

Biosynthesis of the tunicamycins: a review

Tunicamycins are nucleotide sugar analogs produced by several Streptomyces species. In eukaryotes, tunicamycins inhibit UDP-N-acetylglucosamine: dolichol phosphate GlcNAc-1-P transferase (GPT) that catalyzes the first step in protein glycosylation. In bacteria they inhibit UDP-N-acetylmuramoyl-pentapeptide: undecaprenol phosphate MurNAc-pentapeptide-1-P transtransferase (MraY) that catalyzes an early stage in peptidoglycan cell wall assembly. Tunicamycins are substrate analog of GPT and MraY, such that the alphabeta-1'',11'-linked GlcNAc residue of the tunicamycins mimics the transferred GlcNAc-1-phosphate. The unusual structure of tunicamycins, particularly the unique 11-carbon sugar, tunicamine, and the alphabeta-1'',11'-O-glycosidic linkage, suggest its biosynthesis to be unique. This review discusses potential biosyntheses for tunicamycins via the synthesis and conjugation of uridine-5'-aldehyde and UDP-4-keto-N-acetylgalactosamine-5,6-ene and the subsequent formation of the alpha,beta-1'',11' glycosidic linkage.

The Importance of N-terminal Polycysteine and Polybasic Sequences for G14α and G16α Palmitoylation, Plasma Membrane Localization, and Signaling Function

Plasma membrane targeting of G protein alpha (Galpha) subunits is essential for competent receptor-to-G protein signaling. Many Galpha are tethered to the plasma membrane by covalent lipid modifications at their N terminus. Additionally, it is hypothesized that Gq family members (Gqalpha,G11alpha,G14alpha, and G16alpha) in particular utilize a polybasic sequence of amino acids in their N terminus to promote membrane attachment and protein palmitoylation. However, this hypothesis has not been tested, and nothing is known about other mechanisms that control subcellular localization and signaling properties of G14alpha and G16alpha. Here we report critical biochemical factors that mediate membrane attachment and signaling function of G14alpha and G16alpha. We find that G14alpha and G16alpha are palmitoylated at distinct polycysteine sequences in their N termini and that the polycysteine sequence along with the adjacent polybasic region are both important for G16alpha-mediated signaling at the plasma membrane. Surprisingly, the isolated N termini of G14alpha and G16alpha expressed as peptides fused to enhanced green fluorescent protein each exhibit differential requirements for palmitoylation and membrane targeting; individual cysteine residues, but not the polybasic regions, determine lipid modification and subcellular localization. However, full-length G16alpha, more so than G14alpha, displays a functional dependence on single cysteines for membrane localization and activity, and its full signaling potential depends on the integrity of the polybasic sequence. Together, these findings indicate that G14alpha and G16alpha are palmitoylated at distinct polycysteine sequences, and that the adjacent polybasic domain is not required for Galpha palmitoylation but is important for localization and functional activity of heterotrimeric G proteins.

S-acylation regulates Kv1.5 channel surface expression

The number of ion channels expressed on the cell surface shapes the complex electrical response of excitable cells. An imbalance in the ratio of inward and outward conducting channels is unfavorable and often detrimental. For example, over- or underexpression of voltage-gated K(+) (Kv) channels can be cytotoxic and in some cases lead to disease. In this study, we demonstrated a novel role for S-acylation in Kv1.5 cell surface expression. In transfected fibroblasts, biochemical evidence showed that Kv1.5 is posttranslationally modified on both the NH(2) and COOH termini via hydroxylamine-sensitive thioester bonds. Pharmacological inhibition of S-acylation, but not myristoylation, significantly decreased Kv1.5 expression and resulted in accumulation of channel protein in intracellular compartments and targeting for degradation. Channel protein degradation was rescued by treatment with proteasome inhibitors. Time course experiments revealed that S-acylation occurred in the biosynthetic pathway of nascent channel protein and showed that newly synthesized Kv1.5 protein, but not protein expressed on the cell surface, is sensitive to inhibitors of thioacylation. Sensitivity to inhibitors of S-acylation was governed by COOH-terminal, but not NH(2)-terminal, cysteines. Surprisingly, although intracellular cysteines were required for S-acylation, mutation of these residues resulted in an increase in Kv1.5 cell surface channel expression, suggesting that screening of free cysteines by fatty acylation is an important regulatory step in the quality control pathway. Together, these results show that S-acylation can regulate steady-state expression of Kv1.5.

Trafficking and signaling by fatty-acylated and prenylated proteins

A wide variety of signaling proteins are modified by covalently linked fatty acids and/or prenyl groups. These hydrophobic moieties, which include myristate, palmitate, farnesyl and geranylgeranyl, are more than just fat: they provide distinct information that modulates the specificity and efficiency of signal transduction. Recent studies show that lipid modification influences the movement of a signaling protein within the cell and its final destination. Protein lipidation can also confer reversible association with membranes and other signaling proteins. These findings provide new insights into the biochemical and biophysical mechanisms that regulate membrane targeting, trafficking and signaling by lipid-modified proteins.

Use of analogs and inhibitors to study the functional significance of protein palmitoylation

Covalent attachment of palmitate to proteins is a post-translational modification that exerts diverse effects on protein localization and function. The three key technical approaches required for an investigator to determine the role of palmitoylation of your favorite palmitoylated protein (YFPP) are methods to: (1) detect YFPP palmitoylation; (2) alter or inhibit palmitoylation of YFPP; (3) determine the functional significance of altered YFPP palmitoylation. Here, I describe experimental methods to address these three issues. Both radioactive (radiolabeling with [(3)H]palmitate or (125)I-IC16 palmitate) and non-radioactive (chemical labeling and mass spectrometry) methods to detect palmitoylated proteins are presented. Next, techniques to inhibit protein palmitoylation are described. These include site specific mutagenesis, and treatment of cells with inhibitors of protein palmitoylation, including 2-bromopalmitate, cerulenin, and tunicamycin. Alternative methods to replace palmitate with other fatty acids are also presented. Finally, general approaches to determining the effect of altered palmitoylation status on YFPP association with membranes and lipid rafts, as well as signal transduction, are described.

Assays of protein palmitoylation

Protein palmitoylation plays an important role in the structure and function of a wide array of proteins. Unlike other lipid modifications, protein palmitoylation is highly dynamic and cycles of palmitoylation and depalmitoylation can regulate protein function and localization. The dynamic nature of palmitoylation is poorly resolved because of limitations in assay methods. Here, we discuss various methods that can be used to measure protein palmitoylation and identify sites of palmitoylation. We describe new methodology based on "fatty acyl exchange labeling" in which palmitate is removed via hydroxylamine-mediated cleavage of the palmitoyl-thioester bond and then exchanged with a sulfhydryl-specific labeling compound. The techniques are highly sensitive and allow for quantitative estimates of palmitoylation. Unlike other techniques used to assay posttranslational modifications, the techniques we have developed can label all sites of modification with a variety of probes, radiolabeled or non-radioactive, and can be used to assay the palmitoylation of proteins from tissue samples.

Palmitoylation of ligands, receptors, and intracellular signaling molecules

Palmitate, a 16-carbon saturated fatty acid, is attached to more than 100 proteins. Modification of proteins by palmitate has pleiotropic effects on protein function. Palmitoylation can influence membrane binding and membrane targeting of the modified proteins. In particular, many palmitoylated proteins concentrate in lipid rafts, and enrichment in rafts is required for efficient signal transduction. This Review focuses on the multiple effects of palmitoylation on the localization and function of ligands, receptors, and intracellular signaling proteins. Palmitoylation regulates the trafficking and function of transmembrane proteins such as ion channels, neurotransmitter receptors, heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptors, and integrins. In addition, immune receptor signaling relies on protein palmitoylation at many levels, including palmitoylated co-receptors, Src family kinases, and adaptor or scaffolding proteins. The localization and signaling capacities of Ras and G proteins are modulated by dynamic protein palmitoylation. Cycles of palmitoylation and depalmitoylation allow H-Ras and G protein alpha subunits to reversibly bind to and signal from different intracellular cell membranes. Moreover, secreted ligands such as Hedgehog, Wingless, and Spitz use palmitoylation to regulate the extent of long- or short-range signaling. Finally, palmitoylation can alter signaling protein function by direct effects on enzymatic activity and substrate specificity. The identification of the palmitoyl acyltransferases has provided new insights into the biochemistry of this posttranslational process and permitted new substrates to be identified.

Localization of retinaldehyde dehydrogenases and retinoid binding proteins to sustentacular cells, glia, Bowman's gland cells, and stroma: potential sites of retinoic acid synthesis in the postnatal rat olfactory organ

Work from our laboratory suggests that retinoic acid (RA) influences neuron development in the postnatal olfactory epithelium (OE). The studies reported here were carried out to identify and localize retinaldehyde dehydrogenase (RALDH) expression in postnatal rat OE to gain a better understanding of potential in vivo RA synthesis sites in this continuously regenerating tissue. RALDH 1, 2, and 3 mRNAs were detected in postnatal rat olfactory tissue by RT-PCR analysis, but RALDH 1 and 2 transcripts were predominant. RALDH 1 immunoreactivity was localized to sustentacular cells in the OE and to Bowman's gland cells, and GFAP(+)/p75(-) olfactory ensheathing cells (OECs) in the underlying lamina propria (LP). RALDH 2 did not colocalize with RALDH 1, but appeared to be expressed in GFAP(-)/RALDH 1(-) OECs as well as in unidentified structures in the LP. Cellular RA binding protein (CRABP II) colocalized with RALDH 1. Cellular retinol/retinaldehyde binding protein (CRBP I) was localized to RALDH 1(+) sites in the OE and LP and RALDH 2(+) sites, primarily surrounding nerve fiber bundles in the LP. Vitamin A deficiency altered RALDH 1, but not RALDH 2 protein expression. The isozymes and binding proteins exhibited random variability in levels and areas of expression both within and between animals. These findings support the hypothesis that RA is synthesized in the postnatal OE (catalyzed by RALDH 1) and underlying LP (differentially catalyzed by RALDH 1 and RALDH 2) at sites that could influence the development, maturation, targeting, and/or turnover of olfactory receptor neurons throughout the olfactory organ.

Protein palmitoylation by a family of DHHC protein S-acyltransferases

Protein palmitoylation refers to the posttranslational addition of a 16 carbon fatty acid to the side chain of cysteine, forming a thioester linkage. This acyl modification is readily reversible, providing a potential regulatory mechanism to mediate protein-membrane interactions and subcellular trafficking of proteins. The mechanism that underlies the transfer of palmitate or other long-chain fatty acids to protein was uncovered through genetic screens in yeast. Two related S-palmitoyltransferases were discovered. Erf2 palmitoylates yeast Ras proteins, whereas Akr1 modifies the yeast casein kinase, Yck2. Erf2 and Akr1 share a common sequence referred to as a DHHC (aspartate-histidine-histidine-cysteine) domain. Numerous genes encoding DHHC domain proteins are found in all eukaryotic genome databases. Mounting evidence is consistent with this signature motif playing a direct role in protein acyltransferase (PAT) reactions, although many questions remain. This review presents the genetic and biochemical evidence for the PAT activity of DHHC proteins and discusses the mechanism of protein-mediated palmitoylation.

A live cell, image-based approach to understanding the enzymology and pharmacology of 2-bromopalmitate and palmitoylation

The addition of a lipid moiety to a protein increases its hydrophobicity and subsequently its attraction to lipophilic environments like membranes. Indeed most lipid-modified proteins are localized to membranes where they associate with multiprotein signaling complexes. Acylation and prenylation are the two common categories of lipidation. The enzymology and pharmacology of prenylation are well understood but relatively very little is known about palmitoylation, the most common form of acylation. One distinguishing characteristic of palmitoylation is that it is a dynamic modification. To understand more about how palmitoylation is regulated, we fused palmitoylation substrates to fluorescent proteins and reported their subcellular distribution and trafficking. We used automated high-throughput fluorescence microscopy and a specialized computer algorithm to image and measure the fraction of palmitoylation reporter on the plasma membrane versus the cytoplasm. Using this system we determined the residence half-life of palmitate on the dipalmitoyl substrate peptide from GAP43 as well as the EC(50) for 2-bromopalmitate, a common inhibitor of palmitoylation.

Mass spectrometric sequencing and acylation character analysis of C-terminal anchoring segment from Influenza A hemagglutinin

Influenza A virus hemagglutinin (HA) is a major envelope glycoprotein mediating viral and cell membrane fusion. HA is anchored in the viral envelope by a light HA(2) chain containing one transmembrane domain and a cytoplasmic tail. Three cysteine residues in the C-terminal region, one in the transmembrane domain and two in the cytoplasmic tail, are highly conserved and potentially palmitoylated in all HA subtypes. The HA(2) C- terminal anchoring segments were extracted to organic phase from the bromelain-digested viruses (subviral particles) of three strains: A/X-31 (H3 subtype), A/Puerto Rico/8/34 (H1 subtype) and A/FPV/Weybridge/34 (H7 subtype). Their primary structures were assessed by matrix-assisted laser desorption/ionization time-of-flight time-of- flight mass spectrometry (MALDI-ToF-ToF MS). Trypsin-type protease-cleaved peptides prevailed over bromelain- cleaved ones in the peptide mixtures. All of them included transmembrane domains. Several distinctive features of the C-terminal HA(2) peptides acylation character were discovered by MALDI-ToF MS: 1) the peptides isolated from the viruses, which were digested by bromelain in the absence of beta-mercaptoethanol, were predominantly triply acylated; 2) the peptides were acylated not only by palmitic, but also by stearic acid residues; 3) the palmitate/stearate ratio was different for the three strains studied; 4) the A/FPV/Weybridge/34 strain has a priority to stearate binding. This fatty acid residue was discovered at the first of three conservative cysteine residues located in the transmembrane domain. It was found that presence of thiol reagent during preparation of subviral particles led to the appearence of the C-terminal HA(2) peptides acylated to different degrees. Triply, doubly, mono- and even unacylated peptides were detected. It was demonstrated that the thioester bond in the isolated acylpeptides was extremely sensitive to thiol reagents.

Plasma membrane phosphoinositide organization by protein electrostatics

Phosphatidylinositol 4,5-bisphosphate (PIP2), which comprises only about 1% of the phospholipids in the cytoplasmic leaflet of the plasma membrane, is the source of three second messengers, activates many ion channels and enzymes, is involved in both endocytosis and exocytosis, anchors proteins to the membrane through several structured domains and has other roles. How can a single lipid in a fluid bilayer regulate so many distinct physiological processes? Spatial organization might be the key to this. Recent studies suggest that membrane proteins concentrate PIP2 and, in response to local increases in intracellular calcium concentration, release it to interact with other biologically important molecules.

Lipid-modified proteins as biomarkers for cardiovascular disease: a review

Lipid-modified proteins are classified based on the identity of the attached lipid, a post- or co-translational modification required for their biological function. At least five different lipid modifications of cysteines, glycines and other residues on the COOH- and NH(2)-terminal domains have been described. Cysteine residues may be modified by the addition of a 16-carbon saturated fatty acyl group by a labile thioester bond (palmitoylation) or by prenylation processes that catalyze the formation of thioether bond with mevalonate derived isoprenoids, farnesol and geranylgeraniol. The NH(2)-terminal glycine residues may undergo a quite distinct process involving the formation of an amide bond with a 14-carbon saturated acyl group (myristoylation), while glycine residues in the COOH-terminal may be covalently attached with a cholesterol moiety by an ester bond. Finally, cell surface proteins can be anchored to the membrane through the addition of glycosylphosphatidylinositol moiety. Several lines of evidence suggest that lipid-modified proteins are directly involved in different steps of the development of lesions of atherosclerosis, from leukocyte recruitment to plaque rupture, and their expression or lipid modification are likely altered during atherogenesis. This review will briefly summarize the different enzymatic pathways of lipid modification and propose a series of lipid-modified proteins that can be used as biomarkers for cardiovascular disease.

On the mechanism of protein palmitoylation

Protein palmitoylation or, more specifically, S-acylation is a reversible post-translational lipid modification. Despite the identification of several proteins that are altered in this way, our understanding of the enzymology of this process has been hampered by the lack of well-characterized acyltransferases. We now know of three proteins in Saccharomyces cerevisiae that promote palmitoylation: effector of Ras function (Erf2), ankyrin-repeat-containing protein (Akr1) and the SNARE protein Ykt6. Erf2 and Akr1 are integral membrane proteins that contain a cysteine-rich domain and an Asp-His-His-Cys motif, both of which catalyse acylation at the carboxyl terminus of their target proteins. Recently, we discovered that Ykt6 mediates the amino-terminal acylation of the fusion protein Vac8. Even though these three proteins differ in sequence, topology, size and substrate specificity, they might function in a similar manner. In this review, we discuss these observations in the context of a potential general mechanism of acylation.

Nerve Ending “Signal” Proteins GAP‐43, MARCKS, and BASP1

Mechanisms of growth cone pathfinding in the course of neuronal net formation as well as mechanisms of learning and memory have been under intense investigation for the past 20 years, but many aspects of these phenomena remain unresolved and even mysterious. "Signal" proteins accumulated mainly in the axon endings (growth cones and the presynaptic area of synapses) participate in the main brain processes. These proteins are similar in several essential structural and functional properties. The most prominent similarities are N-terminal fatty acylation and the presence of an "effector domain" (ED) that dynamically binds to the plasma membrane, to calmodulin, and to actin fibrils. Reversible phosphorylation of ED by protein kinase C modulates these interactions. However, together with similarities, there are significant differences among the proteins, such as different conditions (Ca2+ contents) for calmodulin binding and different modes of interaction with the actin cytoskeleton. In light of these facts, we consider GAP-43, MARCKS, and BASP1 both separately and in conjunction. Special attention is devoted to a discussion of apparent inconsistencies in results and opinions of different authors concerning specific questions about the structure of proteins and their interactions.

Signaling via a novel integral plasma membrane pool of a serine/threonine protein kinase PRK1 in mammalian cells

Mammalian serine/threonine protein kinases, except for TGF-beta receptor kinase family, are intracellular proteins. PRK1/PKN is a member of the protein kinase C superfamily of serine/threonine kinases and is one of the first identified effectors for RhoA GTPase. However, the role of PRK1 in mediating signaling downstream of activated RhoA is largely unknown. Here, we present evidence that identifies a novel plasma membrane pool of PRK1. This integral membrane form of PRK1 is catalytically active. The phosphorylation of serine377 of PRK1 is required for its integration into membranes. This integration is essential for PRK1 to function as a Rho effector as only the integral plasma membrane PRK1 is able to initiate RhoA-mediated and ligand-dependent transcriptional activation of the androgen receptor in human epithelial cells and to mediate RhoA-induced neurite retraction in mouse neuronal cells. These results indicate that RhoA signals via the integral membrane pool of its effectors in its immediate vicinity at the plasma membrane, thus establishing a new paradigm in mammalian cell signaling.

B cell signaling is regulated by induced palmitoylation of CD81

Signaling through the B cell antigen receptor (BCR) is amplified and prolonged by coligation of the BCR to the CD19/CD21/CD81 coreceptor complex. Coligation is induced during immune responses by the simultaneous binding of complement-tagged antigens to the complement receptor, CD21, and to the BCR. Enhanced signaling is due in part to the ability of the CD19/CD21/CD81 complex to stabilize the BCR in sphingolipid- and cholesterol-rich membrane microdomains termed lipid rafts. The tetraspanin CD81 is essential for the raft-stabilizing function of the coreceptor. Here we show that coligation of the BCR and the CD19/CD21/CD81 complex leads to selective, rapid, and reversible palmitoylation of CD81 and that palmitoylation is necessary for the raft stabilizing function of the CD19/CD21/CD81 complex. Inducible palmitoylation may represent a novel mechanism by which tetraspanins function to facilitate lipid raft-dependent receptor signaling.

Labeling and quantifying sites of protein palmitoylation

As a reversible posttranslational modification, protein palmitoylation has the potential to regulate the trafficking and function of a variety of proteins. However, the extent, function, and dynamic nature of palmitoylation are poorly resolved because of limitations in assay methods. Here, we introduce methods where hydroxylamine-mediated cleavage of the palmitoyl-thioester bond generates a free sulfhydryl, which can then be specifically labeled with sulfhydryl-reactive reagents. This methodology is more sensitive and allows for quantitative estimates of palmitoylation. Unlike other techniques used to assay posttranslational modifications, the techniques we have developed can label all sites of modification with a variety of probes, radiolabeled or nonradioactive, and can be used to assay the palmitoylation of proteins expressed in vivo in brain or other tissues.

Rafts, little caves and large potholes: how lipid structure interacts with membrane proteins to create functionally diverse membrane environments

This chapter reviews how diverse lipid microdomains form in the membrane and partition proteins into different functional units that regulate cell trafficking, signalling and movement. We will concentrate upon five major issues: 1. the diversity of lipid structure that produces diverse microenvironments into which different subsets of proteins partition; 2. why ordered lipid domains exclude proteins, and the conditions required for select subsets of proteins to enter these domains; 3. the coupling of the inner and outer leaflets within ordered microdomains; 4. the effect of ordered lipid domains upon membrane properties including curvature and hydrophobicity that affect membrane fission, fusion and extension of filopodia; 5. the biological effects of these structural constraints; in particular how the properties of these domains combine to provide a very different signalling, trafficking and membrane fusion environment to that found in disordered (fluid mosaic) membrane. In addressing these problems, the review draws upon studies ranging from molecular dynamic modelling of lipid interactions, through physical studies of model membrane systems to structural and biological studies of whole cells, examining in the process problems inherent in visualising and purifying these microdomains. While the diversity of structure and function of ordered lipid microdomains is emphasised, some general roles emerge. In particular, the basis for having quite different, non-interacting ordered lipid domains on the same membrane is evident in the diversity of lipid structure and plays a key role in sorting signalling systems. The exclusion of ordered membrane from coated pits, and hence rapid endocytosis, is suggested to underlie the ability of highly ordered domains to establish stable secondary signalling systems required, for instance, in T cell receptor, insulin and neurotrophin signalling.

Membrane targeting of lipid modified signal transduction proteins

Covalent attachment of lipophilic moieties to proteins influences interaction with membranes and membrane microdomains, as well as signal transduction. The most common forms of fatty acylation include modification of the N-terminal glycine of proteins by N-myristoylation and/or attachment of palmitate to internal cysteine residues. Protein prenylation involves attachment of farnesyl or geranylgeranyl moieties via thio-ether linkage to cysteine residues at or near the C-terminus. Attachment of each of these lipophilic groups is catalyzed by a distinct enzyme or set of enzymes: N-myristoyl transferase for N-myristoylation, palmitoyl acyl transferases for palmitoylation, and farnesyl or geranylgeranyl transferases for prenylation. The distinct nature of the lipid modification determines the strength of membrane interaction of the modified protein as well as the specificity of membrane targeting. Clusters of basic residues can also synergize with the lipophilic group to promote membrane binding and targeting. The final destination of the modified protein is influenced by multiple factors, including the localization of the modifying enzymes, protein/protein interactions, and the lipid composition of the acceptor membrane. In particular, much interest has been focused on the ability of fatty acylated proteins to preferentially partition into membrane rafts, subdomains of the plasma membrane that are enriched in cholesterol and glycosphingolipids. Lipid raft localization is necessary for efficient signal transduction in a wide variety of systems, including signaling by T and B cell receptors, Ras, and growth factor receptors. However, certain membrane subdomains, such as caveolae, can serve as reservoirs for inactive signaling proteins. Heterogeneity in the types of membrane subdomains, as well as in the types of lipophilic groups that are attached to proteins, provide an additional level of complexity in the regulation of signaling by membrane bound proteins.

Membrane/cytoskeleton communication

Accumulations of particular lipids in ordered arrays in the membrane (termed microdomains or lipid rafts) can attract proteins with specific targeting domains. Both the lipid and protein components of rafts communicate with the cytoskeleton directly thereby regulating cellular responses. Recent evidence implicating phosphoinositide 1,5 bisphosphate (PIP2) in cytoskeletal regulation shows that agonist sensitive regulation of PIP2 homoeostasis occurs specifically rafts, which appear to provide a major structural substrate for its function. The crucial role of PIP2 in generating cytoskeletal responses is chiefly achieved by regulating proteins that control actin dynamics directly. Many of these regulatory proteins are also specifically enriched in rafts either directly (by insertion into the lipid bilayer via acetylation motifs), or indirectly via interactions with other raft components. The notion that rafts form membrane platforms or modules that mediate signaling responses has been most extensively demonstrated in the immune synapse (IS) of T cells, a complex assemblage of rafts that integrates signaling cascades originating from the simultaneous activation of a wide variety of receptors. The IS is essential for both the amplification and maintenance of T-cell activation, and its assembly at the antigen presenting site depends on the interactions between rafts and the actin cytoskeleton that regulates coalescence of smaller raft components into the larger IS complex. Likewise the neuron, which represents the most highly polarized cell in the body, utilizes the regulation of actin dynamics in response to a plethora of extracellular signals to control axon pathfinding thereby sculpting nervous system cytoarchitecture with utmost precision. It is now becoming clear, that as in the T-cell, lipid rafts in the growing axon can assemble into highly specific, yet malleable and dynamic, signaling modules that regulate actin dynamics in a fashion that is also PIP2-dependent and that utilizes both familiar and novel regulatory mechanisms. It seems clear that raft mediated cytoskeletal regulation represents a highly conserved mechanism to integrate cellular responses to diverse signals.

The N-terminal SH4 region of the Src family kinase Fyn is modified by methylation and heterogeneous fatty acylation: role in membrane targeting, cell adhesion, and spreading

The N-terminal SH4 domain of Src family kinases is responsible for promoting membrane binding and plasma membrane targeting. Most Src family kinases contain an N-terminal Met-Gly-Cys consensus sequence that undergoes dual acylation with myristate and palmitate after removal of methionine. Previous studies of Src family kinase fatty acylation have relied on radiolabeling of cells with radioactive fatty acids. Although this method is useful for verifying that a given fatty acid is attached to a protein, it does not reveal whether other fatty acids or other modifying groups are attached to the protein. Here we use matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry to identify fatty acylated species of the Src family kinase Fyn. Our results reveal that Fyn is efficiently myristoylated and that some of the myristoylated proteins are also heterogeneously S-acylated with palmitate, palmitoleate, stearate, or oleate. Furthermore, we show for the first time that Fyn is trimethylated at lysine residues 7 and/or 9 within its N-terminal region. Both myristoylation and palmitoylation were required for methylation of Fyn. However, a general methylation inhibitor had no inhibitory effect on myristoylation and palmitoylation of Fyn, suggesting that methylation occurs after myristoylation and palmitoylation. Lysine mutants of Fyn that could not be methylated failed to promote cell adhesion and spreading, suggesting that methylation is important for Fyn function.

Active transport of the survival motor neuron protein and the role of exon-7 in cytoplasmic localization

Spinal muscular atrophy (SMA) is a neurodegenerative disease caused by deletion and/or mutation of the survival motor neuron protein Gene (SMN1) that results in the expression of a truncated protein lacking the C terminal exon-7. Whereas SMN has been shown to be an important component of diverse ribonucleoprotein (RNP) complexes, its function in neurons is unknown. We hypothesize that the active transport of SMN may be important for neurite outgrowth and that disruption of exon-7 could impair its normal intracellular trafficking. SMN was localized in granules that were associated with cytoskeletal filament systems and distributed throughout neurites and growth cones. Live cell imaging of enhanced green fluorescent protein (EGFP)-SMN granules revealed rapid, bidirectional and cytoskeletal-dependent movements. Exon-7 was necessary for localization of SMN into the cytoplasm but was not sufficient for granule formation and transport. A cytoplasmic targeting signal within exon-7 was identified that could completely redistribute the nuclear protein D-box binding factor 1 into the cytoplasm. Neurons transfected with SMN lacking exon-7 had significantly shorter neurites, a defect that could be rescued by redirecting the exon-7 deletion mutant into neurites by a targeting sequence from growth-associated protein-43. These findings provide the first demonstration of cytoskeletal-based active transport of SMN in neuronal processes and the function of exon-7 in cytoplasmic localization. Such observations provide motivation to investigate possible transport defects or inefficiency of SMN associated RNPs in motor neuron axons in SMA.