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1.  Sequential Analysis of Trans-SNARE Formation in Intracellular Membrane Fusion 
PLoS Biology  2012;10(1):e1001243.
SM proteins stabilize cis-SNARE complexes leading to a specific preferred topology for trans-SNARE formation.
SNARE complexes are required for membrane fusion in the endomembrane system. They contain coiled-coil bundles of four helices, three (Qa, Qb, and Qc) from target (t)-SNAREs and one (R) from the vesicular (v)-SNARE. NSF/Sec18 disrupts these cis-SNARE complexes, allowing reassembly of their subunits into trans-SNARE complexes and subsequent fusion. Studying these reactions in native yeast vacuoles, we found that NSF/Sec18 activates the vacuolar cis-SNARE complex by selectively displacing the vacuolar Qa SNARE, leaving behind a QbcR subcomplex. This subcomplex serves as an acceptor for a Qa SNARE from the opposite membrane, leading to Qa-QbcR trans-complexes. Activity tests of vacuoles with diagnostic distributions of inactivating mutations over the two fusion partners confirm that this distribution accounts for a major share of the fusion activity. The persistence of the QbcR cis-complex and the formation of the Qa-QbcR trans-complex are both sensitive to the Rab-GTPase inhibitor, GDI, and to mutations in the vacuolar tether complex, HOPS (HOmotypic fusion and vacuolar Protein Sorting complex). This suggests that the vacuolar Rab-GTPase, Ypt7, and HOPS restrict cis-SNARE disassembly and thereby bias trans-SNARE assembly into a preferred topology.
Author Summary
Cellular components often travel between organelles in vesicular entities. This intracellular traffic usually involves production of a vesicle containing cargo from one organelle membrane, movement of the vesicle to its destination, and then fusion of the vesicle with the target organelle. Thus, membrane fusion is a fundamental process required for these intracellular trafficking events. SNARE proteins and SM proteins mediate this fusion process. SNAREs form complexes that are either located on the same membrane or vesicle (called cis-SNARE complexes) or bridge two membrane compartments or vesicles (trans-SNARE complexes). The cis-SNARE complexes must be activated before trans-SNARE complexes can form and allow the membranes to fuse. We investigated the mechanism of cis-SNARE activation and trans-SNARE formation by studying the fusion of highly purified yeast vacuoles. We found that cis-SNARE activation involves the selective removal of a single SNARE protein from a pre-existing cis-SNARE complex, which is replaced by a similar SNARE originating from the other fusion partner. The activated cis-SNARE complexes depended on SM proteins for their stability. Thus, we have shown that the preferred topology of trans-SNARE formation is determined by cis-SNARE–SM protein interactions.
PMCID: PMC3260307  PMID: 22272185
2.  Hierarchy of protein assembly at the vertex ring domain for yeast vacuole docking and fusion 
The Journal of Cell Biology  2003;160(3):365-374.
Vacuole tethering, docking, and fusion proteins assemble into a “vertex ring” around the apposed membranes of tethered vacuoles before catalyzing fusion. Inhibitors of the fusion reaction selectively interrupt protein assembly into the vertex ring, establishing a causal assembly hierarchy: (a) The Rab GTPase Ypt7p mediates vacuole tethering and forms the initial vertex ring, independent of t-SNAREs or actin; (b) F-actin disassembly and GTP-bound Ypt7p direct the localization of other fusion factors; (c) The t-SNAREs Vam3p and Vam7p regulate each other's vertex enrichment, but do not affect Ypt7p localization. The v-SNARE Vti1p is enriched at vertices by a distinct pathway that is independent of the t-SNAREs, whereas both t-SNAREs will localize to vertices when trans-pairing of SNAREs is blocked. Thus, trans-SNARE pairing is not required for SNARE vertex enrichment; and (d) The t-SNAREs regulate the vertex enrichment of both G-actin and the Ypt7p effector complex for homotypic fusion and vacuole protein sorting (HOPS). In accord with this hierarchy concept, the HOPS complex, at the end of the vertex assembly hierarchy, is most enriched at those vertices with abundant Ypt7p, which is at the start of the hierarchy. Our findings provide a unique view of the functional relationships between GTPases, SNAREs, and actin in membrane fusion.
PMCID: PMC2172665  PMID: 12566429
membrane fusion; SNAREs; yeast vacuoles; Rab GTPase; actin
3.  HOPS Initiates Vacuole Docking by Tethering Membranes before trans-SNARE Complex Assembly 
Molecular Biology of the Cell  2010;21(13):2297-2305.
Large oligomeric tethering complexes such as exocyst, TRAPP, and HOPS have been implicated in Rab- and SNARE-dependent membrane fusion. This paper shows that HOPS directly tethers liposomes that bear vacuolar lipids or the Rab Ypt7p and that tethering is the main mechanism by which HOPS stimulates trans-SNARE complex formation and fusion.
Vacuole homotypic fusion has been reconstituted with all purified components: vacuolar lipids, four soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins, Sec17p, Sec18p, the Rab Ypt7p, and the hexameric homotypic fusion and vacuole protein sorting complex (HOPS). HOPS is a Rab-effector with direct affinity for SNAREs (presumably via its Sec1-Munc18 homologous subunit Vps33p) and for certain vacuolar lipids. Each of these pure vacuolar proteins was required for optimal proteoliposome clustering, raising the question of which was most directly involved. We now present model subreactions of clustering and fusion that reveal that HOPS is the direct agent of tethering. The Rab and vacuole lipids contribute to tethering by supporting the membrane association of HOPS. HOPS indirectly facilitates trans-SNARE complex formation by tethering membranes, because the synthetic liposome tethering factor polyethylene glycol can also stimulate trans-SNARE complex formation and fusion. SNAREs further stabilize the associations of HOPS-tethered membranes. HOPS then protects newly formed trans-SNARE complexes from disassembly by Sec17p/Sec18p.
PMCID: PMC2893992  PMID: 20462954
4.  A distinct tethering step is vital for vacuole membrane fusion 
eLife  2014;3:e03251.
Past experiments with reconstituted proteoliposomes, employing assays that infer membrane fusion from fluorescent lipid dequenching, have suggested that vacuolar SNAREs alone suffice to catalyze membrane fusion in vitro. While we could replicate these results, we detected very little fusion with the more rigorous assay of lumenal compartment mixing. Exploring the discrepancies between lipid-dequenching and content-mixing assays, we surprisingly found that the disposition of the fluorescent lipids with respect to SNAREs had a striking effect. Without other proteins, the association of SNAREs in trans causes lipid dequenching that cannot be ascribed to fusion or hemifusion. Tethering of the SNARE-bearing proteoliposomes was required for efficient lumenal compartment mixing. While the physiological HOPS tethering complex caused a few-fold increase of trans-SNARE association, the rate of content mixing increased more than 100-fold. Thus tethering has a role in promoting membrane fusion that extends beyond simply increasing the amount of total trans-SNARE complex.
eLife digest
Cells of higher organisms contain compartments called organelles and structures called vesicles that transfer molecules and proteins between these organelles. Each organelle and each vesicle is enclosed within a membrane, and these membranes must fuse together to allow these transfers to take place. A certain group of proteins, called SNAREs, have a central role in these fusion events.
Since membrane fusion is difficult to observe directly, many researchers have used a method called ‘fluorescent lipid dequenching’ to study it indirectly. In this approach, one fraction of vesicles is labeled with two fluorescent molecules, with one of these molecules quenching the fluorescence of the other. However, when a labeled vesicle fuses with an unlabeled vesicle, the surface concentrations of the fluorescent molecules are diluted. This reduces the amount of quenching and the resulting increase in fluorescence can be measured.
Experiments utilizing this technique had suggested that SNARE proteins are sufficient for fusion to take place, and that no other protein complexes need to be present. However, when a different assay method called ‘lumenal compartment mixing’ was used, little fusion was seen when the only proteins present were the SNAREs. The lumenal compartment mixing approach relies on measuring the degree of mixing between the contents of two vesicles.
To address these conflicting results, Zick and Wickner used both methods to study fusion in a yeast-based system. The lumenal compartment mixing approach, which is the more reliable method, revealed that rapid and efficient membrane fusion in fact requires another protein complex, called HOPS, to hold the two membrane vesicles together.
Zick and Wickner found that the HOPS complex does not enable fusion by just increasing the amount of interactions between the SNARE proteins. Rather, it seems to facilitate the formation of a particular quality of SNARE interactions. Future work is needed to work out how the SNARE complexes become ‘fusion-competent’, and to explore the mechanism that allows the HOPS complex to assist in the formation of fusion-competent SNARE complexes.
PMCID: PMC4200421  PMID: 25255215
membrane; fusion; SNARE; tethering; assay; S. cerevisiae
5.  HOPS Proofreads the trans-SNARE Complex for Yeast Vacuole Fusion 
Molecular Biology of the Cell  2008;19(6):2500-2508.
The fusion of yeast vacuoles, like other organelles, requires a Rab-family guanosine triphosphatase (Ypt7p), a Rab effector and Sec1/Munc18 (SM) complex termed HOPS (homotypic fusion and vacuole protein sorting), and soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs). The central 0-layer of the four bundled vacuolar SNAREs requires the wild-type three glutaminyl (Q) and one arginyl (R) residues for optimal fusion. Alterations of this layer dramatically increase the Km value for SNAREs to assemble trans-SNARE complexes and to fuse. We now find that added purified HOPS complex strongly suppresses the fusion of vacuoles bearing 0-layer alterations, but it has little effect on the fusion of vacuoles with wild-type SNAREs. HOPS proofreads at two levels, inhibiting the formation of trans-SNARE complexes with altered 0-layers and suppressing the ability of these mismatched 0-layer trans-SNARE complexes to support membrane fusion. HOPS proofreading also extends to other parts of the SNARE complex, because it suppresses the fusion of trans-SNARE complexes formed without the N-terminal Phox homology domain of Vam7p (Qc). Unlike some other SM proteins, HOPS proofreading does not require the Vam3p (Qa) N-terminal domain. HOPS thus proofreads SNARE domain and N-terminal domain structures and regulates the fusion capacity of trans-SNARE complexes, only allowing full function for wild-type SNARE configurations. This is the most direct evidence to date that HOPS is directly involved in the fusion event.
PMCID: PMC2397298  PMID: 18385512
6.  The tethering complex HOPS catalyzes assembly of the soluble SNARE Vam7 into fusogenic trans-SNARE complexes 
Molecular Biology of the Cell  2013;24(23):3746-3753.
Large tethering complexes play an essential role in many intracellular membrane fusion events, yet their mode of action is poorly understood. A new function of the HOPS complex is uncovered in facilitating vacuolar fusion, the specific recruitment of the soluble SNARE Vam7 for the formation of fusogenic trans-SNARE complexes.
The fusion of yeast vacuolar membranes depends on the disassembly of cis–soluble N-ethylmaleimide–sensitive factor attachment protein receptor (SNARE) complexes and the subsequent reassembly of new SNARE complexes in trans. The disassembly of cis-SNARE complexes by Sec17/Sec18p releases the soluble SNARE Vam7p from vacuolar membranes. Consequently, Vam7p needs to be recruited to the membrane at future sites of fusion to allow the formation of trans-SNARE complexes. The multisubunit tethering homotypic fusion and vacuole protein sorting (HOPS) complex, which is essential for the fusion of vacuolar membranes, was previously shown to have direct affinity for Vam7p. The functional significance of this interaction, however, has been unclear. Using a fully reconstituted in vitro fusion reaction, we now show that HOPS facilitates membrane fusion by recruiting Vam7p for fusion. In the presence of HOPS, unlike with other tethering agents, very low levels of added Vam7p suffice to induce vigorous fusion. This is a specific recruitment of Vam7p rather than an indirect stimulation of SNARE complex formation through tethering, as HOPS does not facilitate fusion with a low amount of a soluble form of another vacuolar SNARE, Vti1p. Our findings establish yet another function among the multiple tasks that HOPS performs to catalyze the fusion of yeast vacuoles.
PMCID: PMC3843000  PMID: 24088569
7.  HOPS drives vacuole fusion by binding the vacuolar SNARE complex and the Vam7 PX domain via two distinct sites 
Molecular Biology of the Cell  2011;22(14):2601-2611.
The homotypic fusion and protein sorting (HOPS) tethering complex of the yeast vacuole is involved in multiple fusion reactions. We demonstrate that HOPS has two binding sites for SNAREs and that binding to the minimal SNARE complex is necessary for HOPS-stimulated fusion. Our data highlight the dual role of HOPS in Rab-mediated tethering and SNARE-driven fusion.
Membrane fusion within the endomembrane system follows a defined order of events: membrane tethering, mediated by Rabs and tethers, assembly of soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein receptor (SNARE) complexes, and lipid bilayer mixing. Here we present evidence that the vacuolar HOPS tethering complex controls fusion through specific interactions with the vacuolar SNARE complex (consisting of Vam3, Vam7, Vti1, and Nyv1) and the N-terminal domains of Vam7 and Vam3. We show that homotypic fusion and protein sorting (HOPS) binds Vam7 via its subunits Vps16 and Vps18. In addition, we observed that Vps16, Vps18, and the Sec1/Munc18 protein Vps33, which is also part of the HOPS complex, bind to the Q-SNARE complex. In agreement with this observation, HOPS-stimulated fusion was inhibited if HOPS was preincubated with the minimal Q-SNARE complex. Importantly, artificial targeting of Vam7 without its PX domain to membranes rescued vacuole morphology in vivo, but resulted in a cytokinesis defect if the N-terminal domain of Vam3 was also removed. Our data thus support a model of HOPS-controlled membrane fusion by recognizing different elements of the SNARE complex.
PMCID: PMC3135484  PMID: 21613544
8.  Membranes linked by trans-SNARE complexes require lipids prone to non-bilayer structure for progression to fusion 
eLife  null;3:e01879.
Like other intracellular fusion events, the homotypic fusion of yeast vacuoles requires a Rab GTPase, a large Rab effector complex, SNARE proteins which can form a 4-helical bundle, and the SNARE disassembly chaperones Sec17p and Sec18p. In addition to these proteins, specific vacuole lipids are required for efficient fusion in vivo and with the purified organelle. Reconstitution of vacuole fusion with all purified components reveals that high SNARE levels can mask the requirement for a complex mixture of vacuole lipids. At lower, more physiological SNARE levels, neutral lipids with small headgroups that tend to form non-bilayer structures (phosphatidylethanolamine, diacylglycerol, and ergosterol) are essential. Membranes without these three lipids can dock and complete trans-SNARE pairing but cannot rearrange their lipids for fusion.
eLife digest
All cells are enclosed with a membrane that is made of phospholipid molecules, and many of the structures found inside cells—such as the vacuoles in plant and fungal cells—are also enclosed with a phospholipid membrane. To form a membrane, the phospholipid molecules—which have a phosphate head and two fatty acid tails—arrange themselves in two layers, with the fatty acid tails pointing into the membrane, and the phosphate heads pointing outwards. This structure is known as a phospholipid bilayer.
Vacuoles are filled with water that contains various proteins and molecules in solution, and adjust their volume to keep the concentrations of substances in the cell in balance. To do this, the vacuoles fuse with each other. This fusion process requires dramatic spatial rearrangements of the phospholipid molecules.
The SNARE family of proteins plays a key role in membrane fusion. As the two membranes come together, SNARE proteins located on each membrane form a complex known as a trans-SNARE complex. This docks the vacuole in place beside another vacuole while the phospholipid molecules in the two membranes rearrange. However, much less is known about the phospholipid molecules that are involved in the fusion process.
Now, Zick et al. have shown that three types of phospholipid molecules must be present for membrane fusion to be completed. These have in common that their phosphate ‘headgroups’ are small and they do not tend to form bilayers. The vacuoles can dock beside each other if these small headgroup phospholipid molecules are not present, but the bilayer lipids in the vacuole membranes cannot rearrange themselves in the absence of these particular lipids.
The importance of these nonbilayer lipid molecules had not previously been established, as the majority of experiments investigating membrane fusion used concentrations of SNARE proteins that were much higher than those found physiologically. At such high concentrations, fusion can go ahead without the nonbilayer lipid molecules being present.
PMCID: PMC3937803  PMID: 24596153
membrane fusion; SNAREs; ergosterol; diacylglycerol; phosphatidylethanolamine; S. cerevisiae
9.  LegC3, an Effector Protein from Legionella pneumophila, Inhibits Homotypic Yeast Vacuole Fusion In Vivo and In Vitro 
PLoS ONE  2013;8(2):e56798.
During infection, the intracellular pathogenic bacterium Legionella pneumophila causes an extensive remodeling of host membrane trafficking pathways, both in the construction of a replication-competent vacuole comprised of ER-derived vesicles and plasma membrane components, and in the inhibition of normal phagosome:endosome/lysosome fusion pathways. Here, we identify the LegC3 secreted effector protein from L. pneumophila as able to inhibit a SNARE- and Rab GTPase-dependent membrane fusion pathway in vitro, the homotypic fusion of yeast vacuoles (lysosomes). This vacuole fusion inhibition appeared to be specific, as similar secreted coiled-coiled domain containing proteins from L. pneumophila, LegC7/YlfA and LegC2/YlfB, did not inhibit vacuole fusion. The LegC3-mediated fusion inhibition was reversible by a yeast cytosolic extract, as well as by a purified soluble SNARE, Vam7p. LegC3 blocked the formation of trans-SNARE complexes during vacuole fusion, although we did not detect a direct interaction of LegC3 with the vacuolar SNARE protein complexes required for fusion. Additionally, LegC3 was incapable of inhibiting a defined synthetic model of vacuolar SNARE-driven membrane fusion, further suggesting that LegC3 does not directly inhibit the activity of vacuolar SNAREs, HOPS complex, or Sec17p/18p during membrane fusion. LegC3 is likely utilized by Legionella to modulate eukaryotic membrane fusion events during pathogenesis.
PMCID: PMC3577674  PMID: 23437241
10.  Sec1/Munc18 protein Vps33 binds to SNARE domains and the quaternary SNARE complex 
Molecular Biology of the Cell  2012;23(23):4611-4622.
Vps33, a member of the Sec1/Munc18 family of soluble N-ethylmaleimide–sensitive factor attachment protein receptor (SNARE) chaperones, is a subunit of the homotypic fusion and protein sorting and class C core vacuole/endosome tethering complexes and essential for endolysosomal transport. In this study, Vps33 interactions with SNARE proteins are investigated using genetic and biochemical approaches.
Soluble N-ethylmaleimide–sensitive factor attachment protein receptor (SNARE) proteins catalyze membrane fusion events in the secretory and endolysosomal systems, and all SNARE-mediated fusion processes require cofactors of the Sec1/Munc18 (SM) family. Vps33 is an SM protein and subunit of the Vps-C complexes HOPS (homotypic fusion and protein sorting) and CORVET (class C core vacuole/endosome tethering), which are central regulators of endocytic traffic. Here we present biochemical studies of interactions between Saccharomyces cerevisiae vacuolar SNAREs and the HOPS holocomplex or Vps33 alone. HOPS binds the N-terminal Habc domain of the Qa-family SNARE Vam3, but Vps33 is not required for this interaction. Instead, Vps33 binds the SNARE domains of Vam3, Vam7, and Nyv1. Vps33 directly binds vacuolar quaternary SNARE complexes, and the affinity of Vps33 for SNARE complexes is greater than for individual SNAREs. Through targeted mutational analyses, we identify missense mutations of Vps33 that produce a novel set of defects, including cargo missorting and the loss of Vps33-HOPS association. Together these data suggest a working model for membrane docking: HOPS associates with N-terminal domains of Vam3 and Vam7 through Vps33-independent interactions, which are followed by binding of Vps33, the HOPS SM protein, to SNARE domains and finally to the quaternary SNARE complex. Our results also strengthen the hypothesis that SNARE complex binding is a core attribute of SM protein function.
PMCID: PMC3510022  PMID: 23051737
11.  Topological arrangement of the intracellular membrane fusion machinery 
Molecular Biology of the Cell  2011;22(14):2612-2619.
The topology of the SNARE complex is strictly restricted: of all the possible topological combinations, only one is fusogenic—the topology compatible with both the basal fusion and the SM activation. A fusogenic SNARE complex must contain a complete set of the QabcR SNARE helices.
Soluble N-ethylmaleimide–sensitive factor attachment protein receptors (SNAREs) form a four-helix coiled-coil bundle that juxtaposes two bilayers and drives a basal level of membrane fusion. The Sec1/Munc18 (SM) protein binds to its cognate SNARE bundle and accelerates the basal fusion reaction. The question of how the topological arrangement of the SNARE helices affects the reactivity of the fusion proteins remains unanswered. Here we address the problem for the first time in a reconstituted system containing both SNAREs and SM proteins. We find that to be fusogenic a SNARE topology must support both basal fusion and SM stimulation. Certain topological combinations of exocytic SNAREs result in basal fusion but cannot support SM stimulation, whereas other topologies support SM stimulation without inducing basal fusion. It is striking that of all the possible topological combinations of exocytic SNARE helices, only one induces efficient fusion. Our results suggest that the intracellular membrane fusion complex is designed to fuse bilayers according to one genetically programmed topology.
PMCID: PMC3135485  PMID: 21633111
12.  The Lipid Composition and Physical Properties of the Yeast Vacuole Affect the Hemifusion-Fusion Transition 
Traffic (Copenhagen, Denmark)  2013;14(6):650-662.
Yeast vacuole fusion requires the formation of SNARE bundles between membranes. Although the function of vacuolar SNAREs is controlled in part by regulatory lipids, the exact role of the membrane in regulating fusion remains unclear. Because SNAREs are membrane-anchored and transmit the force required for fusion to the bilayer, we hypothesized that the lipid composition and curvature of the membrane aid in controlling fusion. Here, we examined the effect of altering membrane fluidity and curvature on the functionality of fusion-incompetent SNARE mutants that are thought to generate insufficient force to trigger the hemifusion-fusion transition. The hemifusion-fusion transition was inhibited by disrupting the 3Q:1R stoichiometry of SNARE bundles with the mutant SNARE Vam7pQ283R. Similarly, replacing the transmembrane domain of the syntaxin homolog Vam3p with a lipid anchor allowed hemifusion, but not content mixing. Hemifusion-stalled reactions containing either of the SNARE mutants were stimulated to fuse with chlorpromazine, an amphipathic molecule that alters membrane fluidity and curvature. The activity of mutant SNAREs was also rescued by the overexpression of SNAREs, thus multiplying the force transferred to the membrane. Thus, we conclude that either increasing membrane fluidity, or multiplying SNARE-generated energy restored the fusogenicity of mutant SNAREs that are stalled at hemifusion. We also found that regulatory lipids differentially modulated the complex formation of wild-type SNAREs. Together, these data indicate that the physical properties and the lipid composition of the membrane affect the function of SNAREs in promoting the hemifusion-fusion transition.
PMCID: PMC3660517  PMID: 23438067
SNARE; Diacylglycerol; Lysophosphatidylcholine; Phosphoinositides; Vam7p; chlorpromazine; ergosterol; hemifusion
13.  Importance of the N-Terminal Domain of the Qb-SNARE Vti1p for Different Membrane Transport Steps in the Yeast Endosomal System 
PLoS ONE  2013;8(6):e66304.
SNAREs (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) on transport vesicles and target membranes are crucial for vesicle targeting and fusion. They form SNARE complexes, which contain four α-helical SNARE motifs contributed by three or four different SNAREs. Most SNAREs function only in a single transport step. The yeast SNARE Vti1p participates in four distinct SNARE complexes in transport from the trans Golgi network to late endosomes, in transport to the vacuole, in retrograde transport from endosomes to the trans Golgi network and in retrograde transport within the Golgi. So far, all vti1 mutants investigated had mutations within the SNARE motif. Little is known about the function of the N-terminal domain of Vti1p, which forms a three helix bundle called Habc domain. Here we generated a temperature-sensitive mutant of this domain to study the effects on different transport steps. The secondary structure of wild type and vti1-3 Habc domain was analyzed by circular dichroism spectroscopy. The amino acid exchanges identified in the temperature-sensitive vti1-3 mutant caused unfolding of the Habc domain. Transport pathways were investigated by immunoprecipitation of newly synthesized proteins after pulse-chase labeling and by fluorescence microscopy of a GFP-tagged protein cycling between plasma membrane, early endosomes and Golgi. In vti1-3 cells transport to the late endosome and assembly of the late endosomal SNARE complex was blocked at 37°C. Retrograde transport to the trans Golgi network was affected while fusion with the vacuole was possible but slower. Steady state levels of SNARE complexes mediating these steps were less affected than that of the late endosomal SNARE complex. As different transport steps were affected our data demonstrate the importance of a folded Vti1p Habc domain for transport.
PMCID: PMC3680383  PMID: 23776654
14.  Multiple and distinct strategies of yeast SNAREs to confer the specificity of membrane fusion 
Scientific Reports  2014;4:4277.
Trans-QabcR-SNARE pairing on opposing membranes is crucial for eukaryotic membrane fusion, but how selective pairs of Qabc- and R-SNARE proteins regulate membrane fusion specificity remains elusive. Here, we studied 14 purified full-length SNAREs that function in yeast endoplasmic reticulum (ER)-Golgi, intra-Golgi, endosomal, and vacuolar transport by comprehensively testing cis-QabcR-SNARE assembly and fusogenicity of reconstituted SNARE proteoliposomes. Strikingly, the cognate ER-Golgi and intra-Golgi SNARE-complex assemblies were highly stringent, whereas endosomal and vacuolar SNAREs assembled rather promiscuously into the non-cognate mixed complexes. However, these patterns of cis-SNARE assemblies cannot solely explain their potency to be fusogenic via trans-SNARE pairing: Only the vacuolar 3Q-SNARE combination is fusogenic in the absence of additional components; endosomal SNARE-dependent fusogenicity requires membrane-tethering factors; and ER-Golgi SNAREs can be fusogenic by synergistic actions of tethering factors and the cognate Sec1/Munc18-family protein Sly1p. Thus, our findings uncover multiple and distinct strategies of SNAREs to directly mediate fusion specificity.
PMCID: PMC3940976  PMID: 24589832
15.  The N-terminal Domain of the t-SNARE Vam3p Coordinates Priming and Docking in Yeast Vacuole Fusion 
Molecular Biology of the Cell  2001;12(11):3375-3385.
Homotypic fusion of yeast vacuoles requires a regulated sequence of events. During priming, Sec18p disassembles cis-SNARE complexes. The HOPS complex, which is initially associated with the cis-SNARE complex, then mediates tethering. Finally, SNAREs assemble into trans-complexes before the membranes fuse. The t-SNARE of the vacuole, Vam3p, plays a central role in the coordination of these processes. We deleted the N-terminal region of Vam3p to analyze the role of this domain in membrane fusion. The truncated protein (Vam3ΔN) is sorted normally to the vacuole and is functional, because the vacuolar morphology is unaltered in this strain. However, in vitro vacuole fusion is strongly reduced due to the following reasons: Assembly, as well as disassembly of the cis-SNARE complex is more efficient on Vam3ΔN vacuoles; however, the HOPS complex is not associated well with the Vam3ΔN cis-complex. Thus, primed SNAREs from Vam3ΔN vacuoles cannot participate efficiently in the reaction because trans-SNARE pairing is substantially reduced. We conclude that the N-terminus of Vam3p is required for coordination of priming and docking during homotypic vacuole fusion.
PMCID: PMC60262  PMID: 11694574
16.  Crystal structure of the Habc domain of neuronal syntaxin from the squid Loligo pealei reveals conformational plasticity at its C-terminus 
Intracellular membrane fusion processes are mediated by the spatial and temporal control of SNARE complex assembly that results in the formation of a four-helical bundle, composed of one vesicle SNARE and three target membrane SNARE polypeptide chains. Syntaxins are essential t-SNAREs and are characterized by an N-terminal Habc domain, a flexible linker region, a coiled-coil or SNARE motif and a membrane anchor. The N-terminal Habc domain fulfills important regulatory functions while the coiled-coil motif, present in all SNAREs, is sufficient for SNARE complex formation, which is thought to drive membrane fusion.
Here we report the crystal structure of the Habc domain of neuronal syntaxin from the squid Loligo pealei, s-syntaxin. Squid Habc crystallizes as a dimer and the monomer structure consists of a three-helical bundle. One molecule is strikingly similar to mammalian syntaxin 1A while the second one shows a structural deviation from the common fold in that the C-terminal part of helix C unwinds and adopts an extended conformation.
Conservation of surface residues indicates that the cytosolic part of s-syntaxin can adopt an auto-inhibitory closed conformation that may bind squid neuronal Sec1, s-Sec1, in the same manner as observed in structure of the rat nSec1/syntaxin 1A complex. Furthermore, despite the overall structural similarity, the observed changes at the C-terminus of one molecule indicate structural plasticity in neuronal syntaxin. Implications of the structural conservation and the changes are discussed with respect to potential Habc domain binding partners such as Munc13, which facilitates the transition from the closed to the open conformation.
PMCID: PMC415556  PMID: 15113421
17.  Phosphorylation of the effector complex HOPS by the vacuolar kinase Yck3p confers Rab nucleotide specificity for vacuole docking and fusion 
Molecular Biology of the Cell  2012;23(17):3429-3437.
The Rab GTPase Ypt7p and its effector complex HOPS participate in catalyzing the fusion of yeast vacuoles. The role of the vacuolar kinase Yck3p in this relation is examined. It is shown how the regulatory ability of the Rab GTPase cycle is enforced only by posttranslational modification of the effector complex HOPS.
The homotypic fusion of yeast vacuoles requires the Rab-family GTPase Ypt7p and its effector complex, homotypic fusion and vacuole protein sorting complex (HOPS). Although the vacuolar kinase Yck3p is required for the sensitivity of vacuole fusion to proteins that regulate the Rab GTPase cycle—Gdi1p (GDP-dissociation inhibitor [GDI]) or Gyp1p/Gyp7p (GTPase-activating protein)—this kinase phosphorylates HOPS rather than Ypt7p. We addressed this puzzle in reconstituted proteoliposome fusion reactions with all-purified components. In the presence of HOPS and Sec17p/Sec18p, there is comparable fusion of 4-SNARE (soluble N-ethylmaleimide–sensitive factor attachment protein receptor) proteoliposomes when they have Ypt7p bearing either GDP or GTP, a striking exception to the rule that only GTP-bound forms of Ras-superfamily GTPases have active conformations. However, the phosphorylation of HOPS by recombinant Yck3p confers a strict requirement for GTP-bound Ypt7p for binding phosphorylated HOPS, for optimal membrane tethering, and for proteoliposome fusion. Added GTPase-activating protein promotes GTP hydrolysis by Ypt7p, and added GDI captures Ypt7p in its GDP-bound state during nucleotide cycling. In either case, the net conversion of Ypt7:GTP to Ypt7:GDP has no effect on HOPS binding or activity but blocks fusion mediated by phosphorylated HOPS. Thus guanine nucleotide specificity of the vacuolar fusion Rab Ypt7p is conferred through downstream posttranslational modification of its effector complex.
PMCID: PMC3431944  PMID: 22787280
18.  Pulling force generated by interacting SNAREs facilitates membrane hemifusion 
In biological systems, membrane fusion is mediated by specialized proteins. Although soluble N-ethylmaleimide-sensitive factor attachment protein (SNAP) receptors (SNAREs) provide the minimal molecular machinery required to drive membrane fusion, the precise mechanism for SNARE-mediated fusion remains to be established. Here, we used atomic force microscope (AFM) spectroscopy to determine whether the pulling force generated by interacting SNAREs is directly coupled to membrane fusion. The mechanical strength of the SNARE binding interaction was determined by single molecule force measurements. It was revealed that the forced unbinding of the SNARE complex formed between opposing (trans) bilayers involves two activation barriers; where the steep inner barrier governs the transition from the bound to an intermediate state and the outer barrier governs the transition between the intermediate and the unbound state. Moreover, truncation of either SNAP-25 or VAMP 2 reduced the slope of the inner barrier significantly and, consequently, reduced the pulling strength of the SNARE complex; thus, suggesting that the inner barrier determines the binding strength of the SNARE complex. In parallel, AFM compression force measurements revealed that truncated SNAREs were less efficient than native SNAREs in facilitating hemifusion of the apposed bilayers. Together, these findings reveal a mechanism by which a pulling force generated by interacting trans-SNAREs reduces the slope of the hemifusion barrier and, subsequently, facilitates hemifusion and makes the membranes more prone to fusion.
PMCID: PMC2865556  PMID: 20023730
19.  Yeast homotypic vacuole fusion requires the Ccz1–Mon1 complex during the tethering/docking stage 
The Journal of Cell Biology  2003;163(5):973-985.
The function of the yeast lysosome/vacuole is critically linked with the morphology of the organelle. Accordingly, highly regulated processes control vacuolar fission and fusion events. Analysis of homotypic vacuole fusion demonstrated that vacuoles from strains defective in the CCZ1 and MON1 genes could not fuse. Morphological evidence suggested that these mutant vacuoles could not proceed to the tethering/docking stage. Ccz1 and Mon1 form a stable protein complex that binds the vacuole membrane. In the absence of the Ccz1–Mon1 complex, the integrity of vacuole SNARE pairing and the unpaired SNARE class C Vps/HOPS complex interaction were both impaired. The Ccz1–Mon1 complex colocalized with other fusion components on the vacuole as part of the cis-SNARE complex, and the association of the Ccz1–Mon1 complex with the vacuole appeared to be regulated by the class C Vps/HOPS complex proteins. Accordingly, we propose that the Ccz1–Mon1 complex is critical for the Ypt7-dependent tethering/docking stage leading to the formation of a trans-SNARE complex and subsequent vacuole fusion.
PMCID: PMC1705953  PMID: 14662743
class C Vps; HOPS; membrane fusion; Rab; SNAREs
20.  Yeast homotypic vacuole fusion requires the Ccz1–Mon1 complex during the tethering/docking stage 
The Journal of cell biology  2003;163(5):973-985.
The function of the yeast lysosome/vacuole is critically linked with the morphology of the organelle. Accordingly, highly regulated processes control vacuolar fission and fusion events. Analysis of homotypic vacuole fusion demonstrated that vacuoles from strains defective in the CCZ1 and MON1 genes could not fuse. Morphological evidence suggested that these mutant vacuoles could not proceed to the tethering/docking stage. Ccz1 and Mon1 form a stable protein complex that binds the vacuole membrane. In the absence of the Ccz1–Mon1 complex, the integrity of vacuole SNARE pairing and the unpaired SNARE class C Vps/HOPS complex interaction were both impaired. The Ccz1–Mon1 complex colocalized with other fusion components on the vacuole as part of the cis-SNARE complex, and the association of the Ccz1–Mon1 complex with the vacuole appeared to be regulated by the class C Vps/HOPS complex proteins. Accordingly, we propose that the Ccz1– Mon1 complex is critical for the Ypt7-dependent tethering/ docking stage leading to the formation of a trans-SNARE complex and subsequent vacuole fusion.
PMCID: PMC1705953  PMID: 14662743
class C Vps; HOPS; membrane fusion; Rab; SNAREs
21.  Processive ATP-driven Substrate Disassembly by the N-Ethylmaleimide-sensitive Factor (NSF) Molecular Machine*♦ 
The Journal of Biological Chemistry  2013;288(32):23436-23445.
Background: NSF is an AAA+ protein that recycles the post-fusion SNARE complex during the membrane fusion cycle.
Results: NSF disassembles the SNARE complex processively in vitro and consumes dozens of ATP molecules per SNARE.
Conclusion: NSF is a processive motor that progressively unwinds the SNARE complex.
Significance: The physical mechanism of this poorly understood machine is illuminated using new assays and new measurements of ATP coupling ratios and processivity.
SNARE proteins promote membrane fusion by forming a four-stranded parallel helical bundle that brings the membranes into close proximity. Post-fusion, the complex is disassembled by an AAA+ ATPase called N-ethylmaleimide-sensitive factor (NSF). We present evidence that NSF uses a processive unwinding mechanism to disassemble SNARE proteins. Using a real-time disassembly assay based on fluorescence dequenching, we correlate NSF-driven disassembly rates with the SNARE-activated ATPase activity of NSF. Neuronal SNAREs activate the ATPase rate of NSF by ∼26-fold. One SNARE complex takes an average of ∼5 s to disassemble in a process that consumes ∼50 ATP. Investigations of substrate requirements show that NSF is capable of disassembling a truncated SNARE substrate consisting of only the core SNARE domain, but not an unrelated four-stranded coiled-coil. NSF can also disassemble an engineered double-length SNARE complex, suggesting a processive unwinding mechanism. We further investigated processivity using single-turnover experiments, which show that SNAREs can be unwound in a single encounter with NSF. We propose a processive helicase-like mechanism for NSF in which ∼1 residue is unwound for every hydrolyzed ATP molecule.
PMCID: PMC4520572  PMID: 23775070
ATPases; Exocytosis; Fluorescence; Membrane Fusion; Molecular Motors; AAA+ ATPase; Mechanochemical Coupling; Remodeling; Translocase; Unfoldase
22.  SM proteins Sly1 and Vps33 co-assemble with Sec17 and SNARE complexes to oppose SNARE disassembly by Sec18 
eLife  2014;3:e02272.
Secretory and endolysosomal fusion events are driven by SNAREs and cofactors, including Sec17/α-SNAP, Sec18/NSF, and Sec1/Munc18 (SM) proteins. SMs are essential for fusion in vivo, but the basis of this requirement is enigmatic. We now report that, in addition to their established roles as fusion accelerators, SM proteins Sly1 and Vps33 directly shield SNARE complexes from Sec17- and Sec18-mediated disassembly. In vivo, wild-type Sly1 and Vps33 function are required to withstand overproduction of Sec17. In vitro, Sly1 and Vps33 impede SNARE complex disassembly by Sec18 and ATP. Unexpectedly, Sec17 directly promotes selective loading of Sly1 and Vps33 onto cognate SNARE complexes. A large thermodynamic barrier limits SM binding, implying that significant conformational rearrangements are involved. In a working model, Sec17 and SMs accelerate fusion mediated by cognate SNARE complexes and protect them from NSF-mediated disassembly, while mis-assembled or non-cognate SNARE complexes are eliminated through kinetic proofreading by Sec18.
eLife digest
Eukaryotic organisms, from single-celled yeast to humans, divide their cells into membrane-bound compartments (organelles) of distinct function. To move from one compartment to another, or to enter or exit a cell, large molecules like proteins are packaged into small membrane sacs called vesicles.
To release its cargo, the membrane of a vesicle must fuse with the membrane of the correct destination compartment. The SNARE family of proteins plays a key role in this fusion process. As the membranes of a vesicle and target compartment come close, SNARE proteins located on each membrane form a SNARE complex that tethers the vesicle in place and causes the two membranes fuse. SNARE proteins do not act alone in this process: the SM family of proteins also plays an essential role in SNARE-mediated membrane fusion. However, it is still not clear exactly why the SM proteins are needed.
Lobingier et al. used the yeast model organism and biochemical studies with purified proteins to show that SM proteins help SNARE complexes form at the right time by regulating the delicate balance between SNARE complex formation and disassembly. This is achieved through the interplay of SM proteins and two other proteins (Sec17 and Sec18). Sec17 is known to load Sec18 onto SNARE complexes to break them apart. Lobingier et al. showed that Sec17 can also load SM proteins on SNARE complexes. This hinders Sec18 action, and so helps to keep the SNARE complexes intact. Because each SM protein tested only binds to the SNARE complex that should function at the membrane where the SM protein resides, these findings suggest SM proteins perform quality control at potential sites of membrane fusion.
PMCID: PMC4060006  PMID: 24837546
membrane; SNARE; docking; HOPS; lysosome; Golgi; S. cerevisiae
23.  Membrane fusion catalyzed by a Rab, SNAREs, and SNARE chaperones is accompanied by enhanced permeability to small molecules and by lysis 
Molecular Biology of the Cell  2011;22(23):4635-4646.
The fusion of biological membranes entails a drastic rearrangement of the lipid bilayer. New assays that distinguish fusion from lysis were developed to study an in vitro reconstitution of the yeast vacuolar fusion machinery. These assays revealed that true fusion is accompanied by strongly enhanced membrane permeability to small molecules and by lysis.
The fusion of sealed biological membranes joins their enclosed aqueous compartments while mixing their membrane bilayers. Reconstituted fusion reactions are commonly assayed by lipid mixing, which can result from either true fusion or from lysis and its attendant reannealing of membranes. Fusion is also frequently assayed by the mixing of lumenal aqueous compartments, using probes of low molecular weight. With several probes (biotin, methylumbelliferyl-N-acetyl-α-d-neuraminic acid, and dithionite), we find that yeast vacuolar SNAREs (SNAP [Soluble NSF attachment protein] Receptors) increase the permeability of membranes to small molecules and that this permeabilization is enhanced by homotypic fusion and vacuole protein sorting complex (HOPS) and Sec17p/Sec18p, the vacuolar tethering and SNARE chaperone proteins. We now report the development of a novel assay that allows the parallel assessment of lipid mixing, the mixing of intact lumenal compartments, any lysis that occurs, and the membrane permeation of small molecules. Applying this assay to an all-purified reconstituted system consisting of vacuolar lipids, the four vacuolar SNAREs, the SNARE disassembly chaperones Sec17p and Sec18p, the Rab Ypt7p, and the Rab effector/SM protein complex HOPS, we show that true fusion is accompanied by strongly enhanced membrane permeability to small molecules and a measurable rate of lysis.
PMCID: PMC3226480  PMID: 21976702
24.  Modification of a Hydrophobic Layer by a Point Mutation in Syntaxin 1A Regulates the Rate of Synaptic Vesicle Fusion  
PLoS Biology  2007;5(4):e72.
Both constitutive secretion and Ca2+-regulated exocytosis require the assembly of the soluble N-ethylmaleimide–sensitive factor attachment protein receptor (SNARE) complexes. At present, little is known about how the SNARE complexes mediating these two distinct pathways differ in structure. Using the Drosophila neuromuscular synapse as a model, we show that a mutation modifying a hydrophobic layer in syntaxin 1A regulates the rate of vesicle fusion. Syntaxin 1A molecules share a highly conserved threonine in the C-terminal +7 layer near the transmembrane domain. Mutation of this threonine to isoleucine results in a structural change that more closely resembles those found in syntaxins ascribed to the constitutive secretory pathway. Flies carrying the I254 mutant protein have increased levels of SNARE complexes and dramatically enhanced rate of both constitutive and evoked vesicle fusion. In contrast, overexpression of the T254 wild-type protein in neurons reduces vesicle fusion only in the I254 mutant background. These results are consistent with molecular dynamics simulations of the SNARE core complex, suggesting that T254 serves as an internal brake to dampen SNARE zippering and impede vesicle fusion, whereas I254 favors fusion by enhancing intermolecular interaction within the SNARE core complex.
Author Summary
Most living cells constantly renew their membrane compositions and frequently communicate with neighboring cells by delivering cargo molecules from small vesicles. A key step in cargo delivery requires the fusion of the vesicle membrane with the target membrane mediated by SNARE proteins. In most cellular compartments, fusion occurs constitutively, requiring little participation of other molecules. In other cellular compartments, such as synapses in the nervous system, vesicle fusion is predominantly triggered by intracellular calcium ions. At present, constitutive and regulated fusion modes are not well understood.
In this study, we found that a mutant SNARE protein, syntaxin at the synapse, contained a building block commonly conserved for syntaxins functioning along constitutive secretory pathways. Further, our modeling predicted that the mutant syntaxin could form a tightly packed SNARE bundle closely resembling that found in the endosome, but differing from the relatively loosely packed bundle found at the wild-type synapse. Our experimental data support the hypothesis that the mutant syntaxin lowered the energy barrier for vesicle fusion by tightening the SNARE bundle. These findings reveal a novel, intrinsic structural feature of the SNARE complex that regulates vesicle fusion rate at different cellular compartments.
A syntaxin 1A threonine to isoleucine mutation is found to enhance SNARE complex formation and vesicle fusion. This structural change results in a syntaxin that resembles those in constitutive secretory pathways.
PMCID: PMC1808484  PMID: 17341138
25.  Tethering factor P115 
Bioarchitecture  2012;2(5):175-180.
The membrane tethering factor p115 has been shown to have important functions in ER to Golgi traffic and Golgi biogenesis. The multidomain structure of p115 allows for interactions with a diverse array of proteins that govern cargo movement at the ER-Golgi interface. Within its C-terminal region p115 contains four coiled-coil domains (CC1-CC4). Of the four coiled-coils, only CC1 has been shown to be required for p115 function, presumably by its ability to bind numerous SNARE proteins as well as the small GTPase Rab1. Recently, we showed that CC4 also interacts with SNARE proteins and that CC4 is required for p115 function in Golgi homeostasis and the trafficking of transmembrane but not soluble cargo. Here, we propose a novel model wherein p115 facilitates membrane tethering and fusion by simultaneously engaging its CC1 and CC4 domains with distinct SNARE proteins to promote formation of SNARE complexes.
PMCID: PMC3696062  PMID: 22992751
p115; SNARE; tethering; Golgi; coiled-coil domain

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