The yeast DHHC cysteine-rich domain protein Akr1p is a palmitoyl transferase

Regulation of GABAA receptor trafficking, channel activity, and functional plasticity of inhibitory synapses

Neural inhibition in the brain is mainly mediated by ionotropic gamma-aminobutyric acid type A (GABA(A)) receptors. Different subtypes of these receptors, distinguished by their subunit composition, are either concentrated at postsynaptic sites where they mediate phasic inhibition or found at perisynaptic and extrasynaptic locations where they prolong phasic inhibition and mediate tonic inhibition, respectively. Of special interest are mechanisms that modulate the stability and function of postsynaptic GABA(A) receptor subtypes and that are implicated in functional plasticity of inhibitory transmission in the brain. We will summarize recent progress on the classification of synaptic versus extrasynaptic receptors, the molecular composition of the postsynaptic cytoskeleton, the function of receptor-associated proteins in trafficking of GABA(A) receptors to and from synapses, and their role in post-translational signaling mechanisms that modulate the stability, density, and function of GABA(A) receptors in the postsynaptic membrane.

Exocytic pathway-independent plasma membrane targeting of heterotrimeric G proteins

Heterotrimeric G proteins are lipid-modified, peripheral membrane proteins that function at the inner surface of the plasma membrane (PM) to relay signals from cell-surface receptors to downstream effectors. Cellular trafficking pathways that direct nascent G proteins to the PM are poorly defined. In this report, we test the proposal that G proteins utilize the classical exocytic pathway for PM targeting. PM localization of the G protein heterotrimers alpha s beta 1 gamma 2 and alpha q beta 1 gamma 2 occurred independently of treatment of cells with Brefeldin A, which disrupts the Golgi, or expression of Sar1 mutants, which prevent the formation of endoplasmic reticulum to Golgi transport vesicles. Moreover, the palmitoylation of alpha q was unaffected by Brefeldin A treatment, even though the palmitoylation of SNAP25 was blocked by Brefeldin A. Non-palmitoylated mutants of alpha s and alpha q failed to stably bind to beta gamma and displayed a dispersed cytoplasmic localization when co-expressed with beta gamma. These findings support a refined model of the PM trafficking pathway of G proteins, involving assembly of the heterotrimer at the endoplasmic reticulum and transport to the PM independently of the Golgi.

Localization and activity of the SNARE Ykt6 determined by its regulatory domain and palmitoylation

Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) catalyze compartment-specific membrane fusion. Whereas most SNAREs are bona fide type II membrane proteins, Ykt6 lacks a proteinaceous membrane anchor but contains a prenylation consensus motif (CAAX box) and exists in an inactive cytosolic and an active membrane-bound form. We demonstrate that both forms are farnesylated at the carboxyl-terminal cysteine of the CCAIM sequence. Farnesylation is the prerequisite for subsequent palmitoylation of the upstream cysteine, which permits stable membrane association of Ykt6. The double-lipid modification and membrane association is crucial for intra-Golgi transport in vitro and cell homeostasis/survival in vivo. The membrane recruitment and palmitoylation is controlled by the N-terminal domain of Ykt6, which interacts with the SNARE motif, keeping it in an inactive closed conformation. Together, these results suggest that conformational changes control the lipid modification and function of Ykt6. Considering the essential and central role of Ykt6 in the secretory pathway, this spatial and functional cycle might provide a mechanism to regulate the rate of intracellular membrane flow.

The palmitoyltransferase of the cation-dependent mannose 6-phosphate receptor cycles between the plasma membrane and endosomes

The cation-dependent mannose 6-phosphate receptor (CD-MPR) mediates the transport of lysosomal enzymes from the trans-Golgi network to endosomes. Evasion of lysosomal degradation of the CD-MPR requires reversible palmitoylation of a cysteine residue in its cytoplasmic tail. Because palmitoylation is reversible and essential for correct trafficking, it presents a potential regulatory mechanism for the sorting signals within the cytoplasmic domain of the CD-MPR. Characterization of the palmitoylation performing an in vitro palmitoylation assay by using purified full-length CD-MPR revealed that palmitoylation of the CD-MPR occurs enzymatically by a membrane-bound palmitoyltransferase. In addition, analysis of the localization revealed that the palmitoyltransferase cycles between endosomes and the plasma membrane. This was identified by testing fractions from HeLa cell homogenate separated on a density gradient in the in vitro palmitoylation assay and further confirmed by in vivo labeling experiments by using different treatments to block specific protein trafficking steps within the cell. We identified a novel palmitoyltransferase activity in the endocytic pathway responsible for palmitoylation of the CD-MPR. The localization of the palmitoyltransferase not only fulfills the requirement of our hypothesis to be a regulator of the intracellular trafficking of the CD-MPR but also may affect the sorting/activity of other receptors cycling through endosomes.

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.

Characterization and partial purification of protein fatty acyltransferase activity from rat liver

The acylation of proteins through the addition of palmitate to cysteine residues is a common posttranslational modification for a variety of proteins, but the enzymology of this reversible modification has resisted elucidation. We developed a strategy to purify protein fatty acyltransferase (PAT) activity from rat livers that took advantage of recent knowledge on the cellular location and inhibition of PAT activity. We determined that three different thiolases have PAT activity in the presence of imidazole and therefore started the purification with a plasma membrane fraction to minimize the contamination with these enzymes. After detergent extraction of the plasma membrane fraction, the PAT activity was enriched about 90-fold by sequential chromatography including affinity chromatography to a cerulenin-based inhibitor of palmitoylation. The partially purified PAT activity (1) was lost with treatments to degrade or denature proteins, (2) could acylate tubulin, Galpha(i) and RGS16 and (3) showed a preference for palmitate and to a lesser degree other long-chain fatty acids. This purification procedure is a significant advance over previous efforts at PAT purification and a starting point for a proteomic approach for identification of mammalian PAT.

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.

The SNARE Ykt6 mediates protein palmitoylation during an early stage of homotypic vacuole fusion

The NSF homolog Sec18 initiates fusion of yeast vacuoles by disassembling cis-SNARE complexes during priming. Sec18 is also required for palmitoylation of the fusion factor Vac8, although the acylation machinery has not been identified. Here we show that the SNARE Ykt6 mediates Vac8 palmitoylation and acts during a novel subreaction of vacuole fusion. This subreaction is controlled by a Sec17-independent function of Sec18. Our data indicate that Ykt6 presents Pal-CoA via its N-terminal longin domain to Vac8, while transfer to Vac8's SH4 domain occurs spontaneously and not enzymatically. The conservation of Ykt6 and its localization to several organelles suggest that its acyltransferase activity may also be required in other intracellular fusion events.

The yeast casein kinase Yck3p is palmitoylated, then sorted to the vacuolar membrane with AP-3-dependent recognition of a YXXPhi adaptin sorting signal

Our previous work found the two yeast plasma membrane-localized casein kinases Yck1p and Yck2p to be palmitoylated on C-terminal Cys-Cys sequences by the palmitoyl transferase Akr1p. The present work examines a third casein kinase, Yck3p, which ends with the C-terminal sequence Cys-Cys-Cys-Cys-Phe-Cys-Cys-Cys. Yck3p is palmitoylated and localized to the vacuolar membrane. While the C-terminal cysteines are required for this palmitoylation, Akr1p is not. Palmitoylation requires the C-terminal Yck3p residues 463-524, whereas information for vacuolar sorting maps to the 409-462 interval. Vacuolar sorting is disrupted in cis through deletion of the 409-462 sequences and in trans through mutation of the AP-3 adaptin complex; both cis- and trans-mutations result in Yck3p missorting to the plasma membrane. This missorted Yck3p restores 37 degrees C viability to yck1Delta yck2-ts cells. yck1Delta yck2-ts suppressor mutations isolated within the YCK3 gene identify the Yck3p vacuolar sorting signal-the tetrapeptide YDSI, a perfect fit to the YXXPhi adaptin-binding consensus. Although YXXPhi signals have a well-appreciated role in the adaptin-mediated sorting of mammalian cells, this is the first signal of this class to be identified in yeast.

Plasmodium Biology

The highly A+T rich genomes of human and rodent malarial parasites offer unprecedented glimpses of a lineage that is distinct from other model organisms. Plasmodium is distinguished by the presence of numerous low complexity inserts within globular domains of proteins. It displays several peculiarities in its transcription apparatus, and its DNA repair system appears to favor a certain innate level of mutability. Plasmodium possesses many cell surface molecules with "animal-like" adhesion modules. Potential genetic footprints of the ancestral eukaryotic algal precursor of the apicoplast are also detectable in its genome.

Exploratory and confirmatory gene expression profiling of mac1Delta

Exploratory outlier identification methods and confirmatory gene expression studies showed induction of the iron regulon in Saccharomyces cerevisiae lacking Mac1p, a copper-responsive transcription factor. The Aft1p/Aft2p binding motif was the most discriminating motif between up- and down-regulated genes, and we identified new genes potentially regulated by Aft1p/Aft2p. In addition, multiple genes encoding proteins containing Fe-S clusters were down-regulated suggesting metabolic reorganization to conserve iron in mac1Delta. Null mutants of each of the differentially expressed genes were characterized for copper- or iron-related phenotypes. New or additional support for a role in copper and iron homeostasis is provided in this study for the gene products of AKR1, MRS4, PCA1, SSU1, TIS11, YBR047W, YHL035C, YHR045W, YLR047C, YLR126C, and YTP1.

Palmitoylation and plasma membrane localization of Ras2p by a nonclassical trafficking pathway in Saccharomyces cerevisiae

Subcellular localization of Ras proteins to the plasma membrane is accomplished in part by covalent attachment of a farnesyl moiety to the conserved CaaX box cysteine. Farnesylation targets Ras to the endoplasmic reticulum (ER), where additional processing steps occur, resulting in translocation of Ras to the plasma membrane. The mechanism(s) by which this occurs is not well understood. In this report, we show that plasma membrane localization of Ras2p in Saccharomyces cerevisiae does not require the classical secretory pathway or a functional Golgi apparatus. However, when the classical secretory pathway is disrupted, plasma membrane localization requires Erf2p, a protein that resides in the ER membrane and is required for efficient palmitoylation of Ras2p. Deletion of ERF2 results in a Ras2p steady-state localization defect that is more severe when combined with sec-ts mutants or brefeldin A treatment. The Erf2p-dependent localization of Ras2p correlates with the palmitoylation of Cys-318. An Erf2p-Erf4p complex has recently been shown to be an ER-associated palmitoyltransferase that can palmitoylate Cys-318 of Ras2p (S. Lobo, W. K. Greentree, M. E. Linder, and R. J. Deschenes, J. Biol. Chem. 277:41268-41273, 2002). Erf2-dependent palmitoylation as well as localization of Ras2p requires a region of the hypervariable domain adjacent to the CaaX box. These results provide evidence for the existence of a palmitoylation-dependent, nonclassical endomembrane trafficking system for the plasma membrane localization of Ras proteins.

Intracellular trafficking of a palmitoylated membrane-associated protein component of enveloped vaccinia virus

The F13L protein of vaccinia virus, an essential and abundant palmitoylated peripheral membrane component of intra- and extracellular enveloped virions, associates with Golgi, endosomal, and plasma membranes in the presence or absence of other viral proteins. In the present study, the trafficking of a fully functional F13L-green fluorescent protein (GFP) chimera in transfected and productively infected cells was analyzed using specific markers and inhibitors. We found that Sar1(H79G), a trans-dominant-negative protein inhibitor of cargo transport from the endoplasmic reticulum, had no apparent effect on the intracellular distribution of F13L-GFP, suggesting that the initial membrane localization occurs at a downstream compartment of the secretory pathway. Recycling of F13L-GFP from the plasma membrane was demonstrated by partial colocalization with FM4-64, a fluorescent membrane marker of endocytosis. Punctate F13L-GFP fluorescence overlapped with clathrin and Texas red-conjugated transferrin, suggesting that endocytosis occurred via clathrin-coated pits. The inhibitory effects of chlorpromazine and trans-dominant-negative forms of dynamin and Eps15 protein on the recycling of F13L-GFP provided further evidence for clathrin-mediated endocytosis. In addition, the F13L protein was specifically coimmunoprecipitated with alpha-adaptin, a component of the AP-2 complex that interacts with Eps15. Nocodazole and wortmannin perturbed the intracellular trafficking of F13L-GFP, consistent with its entry into late and early endosomes through the secretory and endocytic pathways, respectively. The recycling pathway described here provides a mechanism for the reutilization of the F13L protein following its deposition in the plasma membrane during the exocytosis of enveloped virions.

Characterization of human palmitoyl-acyl transferase activity using peptides that mimic distinct palmitoylation motifs

The covalent attachment of palmitate to proteins commonly occurs on cysteine residues near either N-myristoylated glycine residues or C-terminal farnesylated cysteine residues. It therefore seems likely that multiple palmitoyl-acyl transferase (PAT) activities exist to recognize and modify these distinct palmitoylation motifs. To evaluate this possibility, two synthetic peptides representing these palmitoylation motifs, termed MyrGCK(NBD) and FarnCNRas(NBD), were used to characterize PAT activity under a variety of conditions. The human tumour cell lines MCF-7 and Hep-G2 each demonstrated high levels of PAT activity towards both peptides. In contrast, normal mouse fibroblasts (NIH/3T3 cells) demonstrated PAT activity towards the myristoylated substrate peptide but not the farnesylated peptide, while ras -transformed NIH/3T3 cells were able to palmitoylate the FarnCNRas(NBD) peptide. The kinetic parameters for PAT activity were determined using membranes from MCF-7 cells, and indicated that the K (m) values for palmitoyl-CoA were identical for PAT activity towards the two substrate peptides; however, the K (m) for MyrGCK(NBD) was 5-fold lower than the K (m) for FarnCNRas(NBD). PAT activity towards the two substrate peptides was dose-dependently inhibited by 2-bromopalmitate and 3-(1-oxo-hexadecyl)oxiranecarboxamide (16C; IC(50) values of approx. 4 and 1.3 microM, respectively); however, 2-bromopalmitate was found to be uncompetitive with respect to palmitoyl-CoA, whereas 16C was competitive. To seek additional evidence for multiple PATs, the effects of altering the assay conditions on the palmitoylation of MyrGCK(NBD) and FarnCNRas(NBD) were compared. PAT activity towards the two peptide substrates was modulated similarly by changing the ionic strength or incubation temperature, or by the addition of dithiothreitol. In contrast, the enzymic palmitoylation of the two peptides was differentially affected by N -ethylmaleimide and thermal denaturation. Overall, these data demonstrate that the enzymic palmitoylation of farnesyl- and myristoyl-containing peptide substrates can be differentiated, suggesting that multiple motif-specific PATs exist.

AKRL1 and AKRL2 activate the JNK pathway

BACKGROUND

c-Jun N-terminal kinase (JNK), a member of the mitogen-activated protein kinase (MAPK) family, is activated by specific cytokines and various environmental stresses. MKK4 and MKK7 are shown to be direct activators of JNK. Although several upstream components of the JNK pathway, including members of the MAPKKK family have been described, the components lying between the receptors or sensors and JNK have not been fully characterized.

RESULTS

We have identified AKRL1 and AKRL2 (Akr1p-like 1 and 2) as novel activators of the JNK pathway. AKRL1 and AKRL2 proteins have a considerable sequence similarity to Akr1p, a protein essential for endocytosis in Saccharomyces cerevisiae. Expression of AKRL1 or AKRL2 activates JNK and its activators MKK4 and MKK7. This AKRL1/2-induced JNK activation is significantly suppressed by the expression of a kinase-negative mutant of TAK1, a member of the MAPKKK family. AKRL1 and AKRL2 localize to the Golgi. Both the N-terminal half and the C-terminal transmembrane domain of AKRL1/2 are required for the JNK activation. The C-terminal transmembrane domain of AKRL1/2 is required for localization to the Golgi.

CONCLUSION

AKRL1 and AKRL2 are localized to Golgi and the novel activators of the JNK pathway.

New insights into the mechanisms of protein palmitoylation

Since its discovery more than 30 years ago, protein palmitoylation has been shown to have a role in protein-membrane interactions, protein trafficking, and enzyme activity. Until recently, however, the molecular machinery that carries out reversible palmitoylation of proteins has been elusive. In fact, both enzymatic and nonenzymatic S-acylation reaction mechanisms have been proposed. Recent reports of protein palmitoyltransferases in Saccharomyces cerevisiae and Drosophila provide the first glimpse of enzymes that carry out protein palmitoylation. Equally important is the mechanism of depalmitoylation. Two major classes of protein palmitoylthioesterases have been described. One family is lysosomal and is involved in protein degradation. The second is cytosolic and removes palmitoyl moieties preferentially from proteins associated with membranes. This review discusses recent advances in the understanding of mechanisms of addition of palmitate to proteins and removal of palmitate from proteins.

Biochemical characterization of the vacuolar palmitoyl acyltransferase

Vacuole fusion requires Sec18p-dependent acylation of the armadillo-repeat protein Vac8p that has been isolated with cis-SNARE complexes. To gain more insight into the mechanism of acylation, we analyzed the palmitoylation reaction on isolated vacuoles or in vacuolar detergent extracts. Recombinant Vac8p is palmitoylated when added to vacuoles and is anchored to membranes after modification. The palmitoyl acyltransferase (PAT) extracted from vacuolar membranes is functional in detergent extracts and shows all characteristics of an enzymatic activity: It modifies exogenous Vac8p in a temperature-, dose- and time-dependent manner, and is sensitive to bromo-palmitate, a known inhibitor of protein palmitoylation in vivo. Importantly, PAT is specific for palmitoyl-CoA, since myristoyl- and stearyl-CoA can compete with labeled Pal-CoA only at 10-fold higher amounts.

Erf4p and Erf2p form an endoplasmic reticulum-associated complex involved in the plasma membrane localization of yeast Ras proteins

Ras oncogene proteins are plasma membrane-associated signal transducers that are found in all eukaryotes. Posttranslational addition of lipid to a carboxyl-terminal CaaX box (where "C" represents a cysteine, "a" is generally an aliphatic residue, and X can be any amino acid) is required to target Ras proteins to the cytosolic surface of the plasma membrane. The pathway by which Ras translocates from the endoplasmic reticulum to the plasma membrane is currently not clear. We have performed a genetic screen to identify components of the Ras plasma membrane localization pathway. Mutations in two genes, ERF2 and ERF4/SHR5, have been shown to affect the palmitoylation and subcellular localization of Ras proteins. In this report, we show that Erf4p is localized on the endoplasmic reticulum as a peripheral membrane protein in a complex with Erf2p, an integral membrane protein that was identified from the same genetic screen. Erf2p has been shown to be required for the plasma membrane localization of GFP-Ras2p via a pathway distinct from the classical secretory pathway (X. Dong and R. J. Deschenes, manuscript in preparation). We show here that Erf4p, like Erf2p, is involved in the plasma membrane localization of Ras2p. Erf2p and Erf4p represent components of a previously uncharacterized subcellular transport pathway involved in the plasma membrane targeting of Ras proteins.

Plasma membrane localization of the Yck2p yeast casein kinase 1 isoform requires the C-terminal extension and secretory pathway function

The S. cerevisiae Yck2 protein is a plasma membrane-associated member of the casein kinase 1 protein kinase family that, with its homolog Yck1p, is required for bud morphogenesis, cytokinesis, endocytosis and other cellular processes. Membrane localization of Yckp is critical for its function, since soluble mutants do not provide sufficient biological activity to sustain normal growth. Yck2p has neither a predicted signal sequence nor obvious transmembrane domain to achieve its plasma membrane localization, but has a C-terminal -Cys-Cys sequence that is likely to be palmitoylated. We demonstrate here that Yck2p is targeted through association with vesicular intermediates of the classical secretory pathway. Yck2p lacking C-terminal Cys residues fails to associate with any membrane, whereas substitution of these residues with a farnesyl transferase signal sequence allows sec-dependent plasma membrane targeting and biological function, suggesting that modification is required for interaction with early secretory membranes but that targeting does not require a particular modification. Deletion analysis within the 185 residue C-terminus indicates that the final 28 residues are critical for membrane association, and additional sequences just upstream are required for proper plasma membrane targeting.