The Major Role of the Rab Ypt7p in Vacuole Fusion Is Supporting HOPS Membrane Association

Yeast vacuole fusion requires soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs), the Rab GTPase Ypt7p, vacuolar lipids, Sec17p and Sec18p, and the homotypic fusion and vacuole protein sorting complex (HOPS). HOPS is a multisubunit protein with direct affinities for SNAREs, vacuolar lipids, and the GTP-bound form of Ypt7p; each of these affinities contributes to HOPS association with the organelle. Using all-purified components, we have reconstituted fusion, but the Rab Ypt7p was not required. We now report that phosphorylation of HOPS by the vacuolar kinase Yck3p blocks HOPS binding to vacuolar lipids, making HOPS membrane association and the ensuing fusion depend on the presence of Ypt7p. In accord with this finding in the reconstituted fusion reaction, the inactivation of Ypt7p by the GTPase-activating protein Gyp1–46p only blocks the fusion of purified vacuoles when Yck3p is present and active. Thus, although Ypt7p may contribute to other fusion functions, its central role is to bind HOPS to the membrane.Rab proteins are small GTP-binding proteins involved in multiple steps of membrane traffic, including protein sorting, vesicle transport, and SNARE³-dependent membrane fusion (1). Rabs in their GTP-bound state bind proteins that are essential for mediating Rab function, which are therefore termed “effectors.” These effectors are diverse and perform various biochemical functions. For membrane fusion, Rabs and their effectors support tethering, the initial membrane contact that is needed for the subsequent assembly of trans-SNARE complexes between membranes (1, 2). A central question in organelle trafficking, which we now address, is whether Rabs are only required for binding their effectors to the membrane or whether they also activate the bound effector or provide some additional essential function for membrane fusion.We study membrane fusion using isolated yeast vacuoles (3). Yeast vacuole fusion requires the Rab GTPase Ypt7p, the heterohexameric HOPS complex, four vacuolar SNAREs, the SNARE disassembly chaperones Sec17p and Sec18p, and chemically minor yet functionally essential lipids, termed “regulatory” lipids. The HOPS complex is an effector of Ypt7p (4) and belongs to a group of functionally conserved large multisubunit tethering complexes, many of which are Rab effectors (5). The Vps39p subunit of HOPS is a nucleotide exchange factor for Ypt7p (6). HOPS is also a SNARE chaperone; its Vps33p subunit is a Sec1p/Munc18-1 family (SM) protein, HOPS binds multiple vacuolar SNAREs (7–9), and it proofreads SNARE complex structure (10). HOPS also binds to specific phosphoinositides (8), and these are among the regulatory lipids that are important for fusion (11–13).We have recently reconstituted membrane fusion using proteoliposomes of pure vacuolar proteins and lipids (13). HOPS and the regulatory lipids are crucial for rapid fusion of proteoliposome pairs bearing the three Q-SNAREs on one proteoliposome and the R-SNARE on the other and are absolutely required when all four SNAREs are present on each proteoliposome and Sec17p and Sec18p are present. Ypt7p is not required, showing that HOPS can stimulate SNARE-dependent fusion in vitro even in the absence of its Rab, although Ypt7p stimulates the fusion of these proteoliposomes.4Yeast vacuole fusion can be negatively regulated either by GTPase-activating proteins (GAPs) (14, 15) that promote GTP hydrolysis by Ypt7p or by the kinase Yck3p, which phosphorylates the Vps41p subunit of HOPS (16) and the vacuolar SNARE Vam3p (15). Yck3p is a palmitoylated (17), vacuole-localized kinase of the casein kinase I family (18). The complete fragmentation of vacuoles in vivo, indicating a block of fusion, requires both Ypt7p inactivation by a RabGAP and the presence of Yck3p (15). Yck3p is necessary for efficient vacuole inheritance (16) and normal vacuole morphology (19), suggesting that its function is part of the normal mechanism of vacuole segregation during the cell cycle. Although Yck3p clearly regulates vacuole fusion through phosphorylation of HOPS, it remains unclear which activities of HOPS are inhibited by Yck3p phosphorylation and whether Yck3p must also phosphorylate other vacuole fusion proteins such as Vam3p to block fusion.We now show that phosphorylation of the Vps41p subunit of HOPS by purified Yck3p reduces HOPS binding to membrane lipids, thereby making HOPS association with the membrane and the ensuing fusion of reconstituted proteoliposomes dependent on active Ypt7p. These data with proteoliposomes are supported by assays with purified vacuoles; the RabGAP Gyp1–46p only inhibits the in vitro fusion of yck3Δ vacuoles when purified Yck3p is added. As for Ypt7p and HOPS, the major function of other Rabs may also be to act as membrane receptors for their effectors.     

Mapping of Vps21 and HOPS Binding Sites in Vps8 and Effect of Binding Site Mutants on Endocytic Trafficking

Vps8 is a subunit of the CORVET tethering complex, which is involved in early-to-late endosome fusion. Here, we examine the role of Vps8 in membrane fusion at late endosomes in Saccharomyces cerevisiae. We demonstrate that Vps8 associates with membranes and that this association is independent of the class C/HOPS core complex and, contrary to a previous report, also independent of the Rab GTPase Vps21. Our data indicate that Vps8 makes multiple contacts with membranes. One of these membrane binding regions could be mapped to the N-terminal part of the protein. By two-hybrid analysis, we obtained evidence for a physical interaction between Vps8 and the Rab5 homologue Vps21. In addition, the interaction with the HOPS core complex was confirmed by immunoprecipitation experiments. By deletion analysis, the Vps21 and HOPS binding sites were mapped in Vps8. Deletions that abrogated HOPS core complex binding had a strong effect on the turnover of the endocytic cargo protein Ste6 and on vacuolar sorting of carboxypeptidase Y. In contrast, deletions that abolished Vps21 binding showed only a modest effect. This suggests that the Vps21 interaction is not essential for endosomal trafficking but may be important for some other aspect of Vps8 function.The compartments of the exocytic/endocytic membrane system are dynamic structures that continuously exchange materials by budding and fusion of transport vesicles. Despite this continuous exchange, the compartments maintain their specific identities. A basic machinery consisting of tethering factors, Rab GTPases, SNARE proteins, and Sec1/Munc18 (SM) proteins accomplishes membrane targeting and fusion. For each individual membrane fusion event, a characteristic set of proteins is used.We are interested in a particular membrane fusion step, the fusion of early endosome-derived vesicles with late endosomes. Screening for vps (vacuolar protein sorting) mutants in Saccharomyces cerevisiae identified factors involved in this fusion step (3). Mutants defective in the early-to-late endosome trafficking step belong to the class D group of vps mutants, whose hallmark is an enlarged vacuole (21). Among the class D functions, representatives of the main groups of targeting and fusion factors can be found. The Q-SNARE protein Pep12, for instance, a member of the syntaxin family, serves as a marker for late endosomal membranes (2). Together with the Q-SNAREs Vti1 and Syn8 or Tlg1, it forms two alternative t-SNARE complexes on late endosomal membranes (17). These t-SNAREs combine with the v-SNARES Snc1/Snc2 or Ykt6 to form functional trans-SNARE complexes. Pep12 functionally interacts with another class D protein, the SM protein Vps45 (4). Another component of the basic fusion machinery at late endosomes is the class D protein Vps21, a member of the Rab GTPase family and the yeast homologue of mammalian Rab5 (8, 12, 30). Rab proteins are key regulators of membrane fusion (9). They are involved in the recruitment of tethering and docking factors, and by their interplay with Rab effectors they contribute to the establishment of specific membrane domains. Another class D protein connected to Rab function is Vps9, a guanidine nucleotide exchange factor (GEF) for Vps21 (11).Additional class D proteins are involved in vesicle tethering at late endosomes. Basically, there are two kinds of tethers, proteins containing extensive coiled-coil domains and large multisubunit complexes (33). The prototype of the coiled-coil tethers is p115, with its yeast homologue Uso1, involved in tethering of vesicles to Golgi apparatus membranes (25). Another member of this class is EEA1, which is involved in tethering of vesicles to endosomes. The yeast class D protein Vps19/Pep7/Vac1 could be functionally similar to EEA1 (16). Two further class D proteins, Vps3 and Vps8, are part of the multisubunit (class C core vacuole/endosome tethering) CORVET tethering complex (20, 32). This complex shares core components with the HOPS (homotypic fusion and vacuole protein sorting) tethering complex involved in homotypic vacuolar fusion (28). This core complex, the class C Vps complex, consists of Vps11/Pep5, Vps16, Vps18/Pep3, and the SM protein Vps33 (26). Instead of Vps3 and Vps8, HOPS contains two additional subunits, Vps39/Vam6 and Vps41 (35), which appear to be functionally equivalent to Vps3 and Vps8 (20). In addition to bridging donor and acceptor membranes, tethers appear to be involved in coordinating Rab and SNARE functions. This was suggested by the finding that the equivalent CORVET/HOPS subunits Vps3 and Vps39/Vam6 both display GEF activity toward their respective Rab proteins, Vps21 and Ypt7 (20, 35). In addition, whole tethering complexes act as Rab effectors by binding to activated Rab-GTP and interact with the corresponding SNARE complexes (6, 20, 31).How exactly the tethers coordinate Rab and SNARE functions during membrane fusion is at present unclear. Here, we examine the function of the CORVET subunit Vps8 (5, 13) in membrane fusion at late endosomes in yeast. We demonstrate that Vps8 directly associates with membranes. Contrary to a previous report (13), we show that this membrane association is not dependent on Vps21. We further investigate the functional relationship between Vps8 and Vps21. We found that Vps21 physically interacts with Vps8 but that this interaction does not appear to be absolutely required for endosomal trafficking. Finally, we speculate that Vps8 could be part of a higher-order structure.     

Abrogating Munc18-1-SNARE Complex Interaction Has Limited Impact on Exocytosis in PC12 Cells

Neuronal communication relies on the fusion of neurotransmitter-containing vesicles with the plasma membrane. The soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor (SNARE) proteins initiate membrane fusion through the formation of the SNARE complex, a process tightly regulated by Sec1/Munc18-1 (SM) proteins. The emerging trend is that SM proteins promote SNARE-mediated membrane fusion by binding to a Syntaxin N-terminal motif. Here we report that mutations in the hydrophobic pocket of Munc18-1 (F115E and E132A), predicted to disrupt the N-terminal Sx1a interaction have a modest effect on binding to Sx1a in its free state, but abolish binding to the SNARE complex. Overexpression of the Munc18-1 mutant in PC12 cells lacking Munc18-1 rescues both neuroexocytosis and the plasma membrane localization of Syntaxin. However, total internal reflection fluorescence microscopy analysis reveals that expression of a Munc18-1 double mutant reduces the rate of vesicle fusion, an effect only detectable at the onset of stimulation. The Munc18-1 hydrophobic pocket is therefore critical for SNARE complex binding. However, mutations abrogating this interaction have a limited impact on Ca²⁺-dependent exocytosis in PC12 cells.Following stimulation of neurons, a number of well orchestrated protein/protein (1) and protein/lipid (2) interactions underpin the fusion of secretory vesicles with the presynaptic plasma membrane. In this sequence of interactions, vesicles approach the plasma membrane (tethering and docking), undergo priming and, upon Ca²⁺ influx, fuse with the plasma membrane, thereby releasing neurotransmitter into the synaptic cleft (1). Vesicular exocytosis relies on the function of soluble N-ethylmaleimide-sensitive fusion protein attachment protein receptor (SNARE)² proteins as demonstrated by the blockade of neuroexocytosis following SNARE protein cleavage by clostridial neurotoxins (3). One of the key players in SNARE regulation is the cytosolic regulatory protein, Munc18-1 (Munc18a, nsec-1) (4–7). Although the function of SNARE proteins in mediating exocytosis is well established (2, 8), the precise role of Munc18-1 in exocytosis is still a subject of heated debate (6, 7, 9, 10).Munc18-1 belongs to the Sec1/Munc18 (SM) family of proteins that are involved in mediating membrane trafficking events (11–13). Mutations in these proteins have recently been associated with infantile epileptic encephalopathy (14). Although the function of Munc18-1 and its interaction with SNAREs have been studied for over 10 years, the molecular mechanism of Munc18-1 regulation of membrane fusion is still not clear. Munc18-1 was originally characterized as a negative regulator of exocytosis as it binds to the target membrane SNARE, Syntaxin 1a (Sx1a) (5) in a conformation that sequesters the Sx1a SNARE helix and inhibits SNARE complex formation (7, 15). Other SM proteins have been shown to bind to their cognate syntaxins via an N-terminal motif (16–19), allowing interactions that are associated with a positive role for SM proteins in SNARE-mediated membrane fusion (20). Despite biochemical evidence supporting a negative regulatory role for Munc18-1, there is strong genetic evidence for a critical positive role for Munc18-1 in exocytosis, as demonstrated by a Munc18-1 knock-out mouse that exhibits a complete blockage of neurotransmission (21).Recently, a short N-terminal peptide from Sx1a was also shown to bind to Munc18-1 via a novel interaction that promotes SNARE-mediated fusion of liposomes in vitro (6). Moreover, the N-terminal truncation of Sx1a only affects the binding of the open conformation of Sx1a to Munc18-1 occurring near the plasma membrane (10). Oddly, the Munc18-1-Sx1a interaction in solution predominantly involves the closed conformation (10), which raises the question of the relative contribution of the Sx1a N terminus to the overall Munc18-1-Sx1a interaction.To address the functional significance of the N-terminal interaction, we took a reverse strategy and investigated the molecular nature of the binding of Munc18-1 to the Sx1a N terminus and to the SNARE complex. We mutated Munc18-1:Phe¹¹⁵ and Glu¹³², which are located in an evolutionarily conserved surface pocket of Munc18-1 (17, 22). We found that whereas these mutations have only a mild effect on the binding of Munc18-1 to Sx1a in its free state, they completely abrogate Munc18-1 binding to the SNARE complex. Expression of these mutants in PC12 cells lacking Munc18-1 rescues exocytosis to a similar extent to that obtained with Munc18-1-WT. Total internal reflection fluorescence (TIRF) microscopy of vesicle docking at the cell surface reveals that these mutations support exocytosis. However, the rate of vesicle fusion is markedly reduced at the onset of stimulation, arguing for a role of Munc18-1 in regulating the dynamics of SNARE-mediated vesicle fusion during exocytosis.     

Targeting Synaptic Pathology with a Novel Affinity Mass Spectrometry Approach

We report a novel strategy for studying synaptic pathology by concurrently measuring levels of four SNARE complex proteins from individual brain tissue samples. This method combines affinity purification and mass spectrometry and can be applied directly for studies of SNARE complex proteins in multiple species or modified to target other key elements in neuronal function. We use the technique to demonstrate altered levels of presynaptic proteins in Alzheimer disease patients and prion-infected mice.One prominent pathological feature of neuropsychiatric disorders such as Alzheimer disease (AD)¹ is severe synaptic loss (1–3). Previous reports of AD patients have shown that presynaptic dysfunction might occur early in the disease process (1, 4). Cortical synapse pathology has also been shown to correlate to the severity of dementia more closely than other pathological hallmarks of AD such as plaques and neurofibrillary tangles (5, 6). The SNARE proteins are essential components for the regulation of neurotransmitter exocytosis at the presynaptic site (7). Animal models suggest that changed expression or modification of SNARE complex proteins (synaptosomal-associated protein 25 (SNAP-25), syntaxin-1, and vesicle-associated membrane protein (VAMP)) alters synaptic function and is an interesting target for the development of therapeutics for neuropsychiatric illness (8, 9). The constituents of the SNARE complex are either localized in synaptic vesicles (VAMPs) or anchored at the presynaptic plasma membrane (SNAP-25 and syntaxin). The SNARE proteins are tightly assembled, and subsequent neurotransmitter release of the complex is quickly dissociated by N-ethylmaleimide-sensitive factor (7, 10–12). Because they are both strongly associated into complexes and membrane associated, the SNARE proteins are difficult to analyze via mass spectrometry, which is incompatible with most detergents necessary for the solubilization of proteins. Each SNARE complex protein exists in several isoforms that are differently distributed within the central nervous system (13–18). Post-translational modifications and truncated variants of the SNARE proteins make investigation of the protein expression even more complicated.In this study we developed an approach for the characterization and concurrent quantification of SNARE complex proteins that combines affinity purification by immunoprecipitation and mass spectrometry (IP-MS). We used precipitation with monoclonal antibodies against SNAP-25 to target the SNARE complex proteins and nanoflow LC–tandem mass spectrometry (LC-MS/MS) to characterize the co-immunoprecipitated interaction partners. Selected reaction monitoring (SRM) on a triple quadrupole mass spectrometer coupled to a microflow LC system was used for quantification of the SNARE proteins. To demonstrate the usability of the IP-MS method, we performed a comparison of SNARE complex protein levels in brain tissue from AD patients and age-matched controls, as well as a study of SNARE complex protein levels in brain tissue from prion-infected mice.     

Cab45b, a Munc18b-interacting Partner, Regulates Exocytosis in Pancreatic ��-Cells

Cab45b is a cytosolic Ca²⁺-binding protein reported to regulate zymogen secretion in pancreatic acini. We now show that Cab45b is also expressed in pancreatic islet β-cells and interacts there with the Sec1-Munc18 protein Munc18b. We employed patch clamp cell capacitance measurements to show that antibodies against Cab45b inhibited depolarization-evoked membrane capacitance increments, suggesting an impact on β-cell granule exocytosis, both the readily releasable granule pool and refilling of this pool. Site-specific mutants in the Cab45b EF-hands were used to dissect the molecular interactions involved in Cab45b function. Mutants in EF-hands 2 and 3 had no detectable effects on interaction of Cab45b with Munc18b and did not affect the depolarization-evoked calcium currents, but remarkably, they facilitated the complex formation of Munc18b with syntaxin-2 and -3. As a result, these two EF-hand mutants inhibited β-cell membrane capacitance increments. This inhibition is mediated via Munc18b because Munc18b silencing with small interfering RNA abolished the effects of these two mutants. The results suggest a mechanism for Cab45b action that involves regulating the dynamic association of Munc18b with SNAREs to impact β-cell granule exocytosis.It is well established that the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE)² proteins form the core machinery responsible for the fusion of transport vesicles, including secretory granules, with their target membranes. A number of accessory factors regulate SNARE function in membrane fusion (1). The Sec1-Munc18 (SM) proteins constitute a family of central SNARE regulators that bind syntaxins to influence secretory vesicle docking and fusion directly (2, 3). In mammals, there are seven SM proteins, of which the Munc18 isoforms a, b, and c are involved in exocytosis at the plasma membrane (4, 5). The Munc18 proteins were initially proposed to function as negative regulators of membrane fusion by inhibiting the assembly of trans-SNARE complexes. However, recent studies suggest that the Munc18 proteins regulate the transition of syntaxin from closed to open conformation, thereby facilitating SNARE complex assembly (6, 7).A number of non-syntaxin-binding partners of the SM proteins have been identified and are suggested to modulate the SM protein-syntaxin interactions (8–11). Recently, we reported a novel SM-binding protein, a cytosolic splice variant of the EF-hand Ca²⁺-binding protein Cab45 (designated Cab45b) expressed in pancreatic acini. Cab45b binds to Munc18b in complex with syntaxin-2 (Syn-2) and -3 (Syn-3) and directly influences amylase release from acini (12). Munc18b is thought to control secretory functions in non-neuronal cells, such as epithelial cells (13–15), pancreatic acinar cells (12), mast cells (16), and kidney medullary cells (17), whereas no function in neuronal or neuroendocrine cells has been assigned to this protein. In this study, we demonstrate that Cab45b is expressed in the neuroendocrine pancreatic islet β-cells and is associated with Munc18b-Syn-2 and Munc18b-Syn-3 complexes. Using cell membrane capacitance measurement, a well established technique for monitoring exocytosis in neurons and neuroendocrine cells (18, 19), we further dissect the functional domains within Cab45b (EF-hands 2 and 3) that impact the association of Munc18b with syntaxins to influence insulin granule exocytosis.     

Sec35p,a Novel Peripheral Membrane Protein,Is Required for ER to Golgi Vesicle Docking

SEC35 was identified in a novel screen for temperature-sensitive mutants in the secretory pathway of the yeast Saccharomyces cerevisiae (Wuestehube et al., 1996. Genetics. 142:393–406). At the restrictive temperature, the sec35-1 strain exhibits a transport block between the ER and the Golgi apparatus and accumulates numerous vesicles. SEC35 encodes a novel cytosolic protein of 32 kD, peripherally associated with membranes. The temperature-sensitive phenotype of sec35-1 is efficiently suppressed by YPT1, which encodes the rab-like GTPase required early in the secretory pathway, or by SLY1-20, which encodes a dominant form of the ER to Golgi target -SNARE–associated protein Sly1p. Weaker suppression is evident upon overexpression of genes encoding the vesicle-SNAREs SEC22, BET1, or YKT6. The cold-sensitive lethality that results from deleting SEC35 is suppressed by YPT1 or SLY1-20. These genetic relationships suggest that Sec35p acts upstream of, or in conjunction with, Ypt1p and Sly1p as was previously found for Uso1p. Using a cell-free assay that measures distinct steps in vesicle transport from the ER to the Golgi, we find Sec35p is required for a vesicle docking stage catalyzed by Uso1p. These genetic and biochemical results suggest Sec35p acts with Uso1p to dock ER-derived vesicles to the Golgi complex.Protein transport through the secretory pathway occurs via transport vesicles under the direction of a large set of protein components (Rothman, 1994). The process can be divided into three stages: (a) vesicle budding, (b) vesicle docking, and (c) membrane fusion, with distinct sets of proteins mediating each phase. The budding step involves recruitment of coat proteins to the membrane and culminates with the release of coated vesicles (Schekman and Orci, 1996). The docking reaction is likely to require a set of integral membrane proteins on the vesicle and target membranes, termed v-SNAREs¹ and t-SNAREs (vesicle- and target membrane-soluble N-ethylmaleimide–sensitive fusion protein [NSF] attachment protein [SNAP] receptors, respectively), that are thought to confer specificity through their pair-wise interactions (Söllner et al., 1993b ). Small GTP-binding proteins of the rab family also assist in the docking process (Ferro-Novick and Novick, 1993), but their precise function is not known. The fusion step ensues after docking and results in the delivery of the vesicular cargo to the next compartment in the secretory pathway.Vesicular transport from the ER to the Golgi apparatus in the yeast Saccharomyces cerevisiae has been extensively characterized. Transport vesicle budding involves the assembly of the COPII coat, composed of the Sec13p/Sec31p (Pryer et al., 1993; Salama et al., 1993; Barlowe et al., 1994) and Sec23p/Sec24p heterodimers (Hicke and Schekman, 1989; Hicke et al., 1992), under the direction of an integral membrane protein, Sec12p (Nakano et al., 1988; Barlowe and Schekman, 1993), a small GTPase, Sar1p (Nakano and Muramatsu, 1989), and a multidomain protein, Sec16p (Espenshade et al., 1995; Shaywitz et al., 1997). Docking is thought to require a tethering event mediated by Uso1p (Cao et al., 1998), the yeast homologue of mammalian p115 (Barroso et al., 1995; Sapperstein et al., 1995), followed by or concurrent with the interaction of a set of ER to Golgi v-SNAREs, Bet1p, Bos1p, Sec22p (Newman and Ferro-Novick, 1987; Newman et al., 1990; Ossig et al., 1991; Shim et al., 1991; Søgaard et al., 1994) and perhaps Ykt6p (Søgaard et al., 1994; McNew et al., 1997), with the cognate t-SNARE on the Golgi, Sed5p (Hardwick and Pelham, 1992). For some time it was thought that fusion may be initiated by disassembly of the v/t-SNARE complex (Söllner et al., 1993a ) by yeast SNAP, Sec17p, (Griff et al., 1992) and NSF, Sec18p (Eakle et al., 1988; Wilson et al., 1989). However, this concept has been challenged by studies with a yeast system that reconstitutes homotypic vacuolar fusion, which suggests the action of Sec18p is before vesicle docking (Mayer et al., 1996; Mayer and Wickner, 1997). In addition, a prefusion role for NSF has been supported by the recent finding that liposomes bearing SNAREs alone can fuse in the absence of NSF (Weber et al., 1998).Several proteins involved in the regulation of yeast ER to Golgi v/t-SNARE complex assembly have been identified, including Ypt1p, Uso1p, and Sly1p. Ypt1p is a member of the rab family of small GTP-binding proteins that have been identified as important components of almost every stage in the secretory pathway (Ferro-Novick and Novick, 1993). Hydrolysis of GTP by rab-like proteins has been hypothesized to provide the regulatory switch that controls the fidelity of vesicular transport (Bourne, 1988). A second protein, Uso1p (Nakajima et al., 1991), appears to function in the same pathway as Ypt1p (Sapperstein et al., 1996), and both proteins have been demonstrated to be essential for SNARE complex assembly (Søgaard et al., 1994; Sapperstein et al., 1996; Lupashin and Waters, 1997). The third protein, Sly1p, is associated with the t-SNARE Sed5p (Søgaard et al., 1994). SLY1 is an essential gene in yeast (Dascher et al., 1991; Ossig et al., 1991), and Sly1p is required for ER to Golgi transport in vitro (Lupashin et al., 1996) and in vivo (Ossig et al., 1991). However, several lines of evidence, particularly from Sly1p homologues in other organisms, indicate that Sly1p may also function as a negative regulator of v/t-SNARE complex assembly, perhaps by preventing the association of the v- and t-SNAREs (Hosono et al., 1992; Pevsner et al., 1994; Schulze et al., 1994). A dominant allele of SLY1, termed SLY1-20, is capable of suppressing mutations in YPT1 and USO1, including complete deletions (Dascher et al., 1991; Sapperstein et al., 1996). Thus, in the presence of Sly1-20p, two components required for SNARE complex assembly are no longer essential. We have proposed a model (Sapperstein et al., 1996; Lupashin and Waters, 1997) in which Ypt1p and Uso1p function to relieve the inhibitory action of Sly1p on SNARE complex assembly. In this model Sly1-20p can be thought of as a noninhibitory form of SLY1 that renders Ypt1p and Uso1p superfluous.We believe that the ability of SLY1-20 to suppress defects in upstream docking regulators can be used to identify additional components involved in the regulation of vesicular docking. We have undertaken a genetic screen (to be presented elsewhere) to isolate novel components in this pathway which, when mutated, depend upon Sly1-20p for viability. In the course of this work, we discovered that two recently identified mutants, sec34 and sec35, can be suppressed by SLY1-20 and thus satisfy the criterion of our screen. These mutants were isolated in a novel screen to identify components involved in transport at any step between the ER and the trans-Golgi network (i.e., the Kex2p compartment) in yeast (Wuestehube et al., 1996). Both sec34 and sec35 accumulate the core-glycosylated form of secretory proteins at the nonpermissive temperature, indicating a block in ER to Golgi transport. Furthermore, electron microscopy indicated that both sec34 and sec35 accumulate numerous vesicles upon shift to the restrictive temperature (Wuestehube et al., 1996), a hallmark of genes whose protein products are involved in the docking or fusion phase of transport (Kaiser and Schekman, 1990). In this report we describe the cloning of SEC35 and analysis of its genetic interactions with other secretory genes. Strong genetic interaction between SEC35 and SLY1, YPT1, and USO1 suggests that Sec35p may function in vesicle docking. To test this possibility, we devised an in vitro transport assay that depends on the addition of purified Sec35p and Uso1p. Vesicles synthesized in the absence of functional Sec35p do not fuse with the Golgi compartment and remain as freely diffusible intermediates. Upon addition of Sec35p and Uso1p, vesicles dock to the Golgi and proceed to membrane fusion. Requirements for Sec35p at the vesicle docking step correlates our genetic experiments with the biochemically distinguishable steps of vesicle docking and membrane fusion.     

A Novel Function of Heparan Sulfate in the Regulation of Cell-Cell Fusion

Despite the important contribution of cell-cell fusion in the development and physiology of eukaryotes, little is known about the mechanisms that regulate this process. Our study shows that glycosaminoglycans and more specifically heparan sulfate (HS) expressed on the cell surface and extracellular matrix may act as negative regulator of cell-cell fusion. Using herpes simplex virus type-1 as a tool to enhance cell-cell fusion, we demonstrate that the absence of HS expression on the cell surface results in a significant increase in cell-cell fusion. An identical phenomenon was observed when other viruses or polyethylene glycol was used as fusion enhancer. Cells deficient in HS biosynthesis showed increased activity of two Rho GTPases, RhoA and Cdc42, both of which showed a correlation between increased activity and increased cell-cell fusion. This could serve as a possible explanation as to why HS-deficient cells showed significantly enhanced cell-cell fusion and suggests that HS could regulate fusion via fine tuning of RhoA and Cdc42 activities.Cell-cell fusion is an important physiological process widespread in organisms ranging from yeast to humans (1). It is critical for several biological phenomena including fertilization, placenta formation, skeletal muscle and bone development, tumorigenesis, immune response, and stem cell differentiation (1–9). Defects in cell-cell fusion can lead to serious diseases, such as myotonic dystrophy, centronuclear myopathy, preeclampsia, and osteopetrosis (10–13). Defects in sperm-egg fusion are a major cause of infertility (5). Cell-cell fusion has also been utilized for therapeutic applications, including the generation of monoclonal antibody-producing hybridomas (14) as well as new agents for cancer immunotherapy (15–17).Because of its critical nature, many studies have looked at the mechanism by which cell-cell fusion occurs. Although it can occur in a variety of different biological processes, many of the fusion events share common characteristics (8). For example, tetraspanin proteins function in gamete-, myoblast-, macrophage-, and virus-mediated fusion events (18–21). Although many mediators of cell-cell fusion are known, little is known about the fine-tuning mechanisms that may regulate the membrane fusion process.Viruses have been a useful tool for studying cell-cell fusion since the discovery that they could induce the fusion of somatic cells in vitro (22). Enveloped viruses, like herpes simplex virus type-1 (HSV-1),² use transmembrane viral proteins to mediate fusion with the host cell during entry and spread (23–25). For HSV-1, fusion occurs after the virus has attached to host cells by binding to heparan sulfate (HS) using glycoproteins gB and gC (26). Fusion of the virus envelope with the plasma membrane requires that an additional glycoprotein, gD, binds to one of its receptors, a process that also requires HSV-1 gB, gH, and gL (27–29). During HSV-1-mediated cell-cell fusion, gB, gD, gH, and gL are expressed on the surface of infected cells, allowing them to bind and fuse with surrounding uninfected cells, forming syncytia.Heparan sulfate proteoglycans are ubiquitously expressed cell surface molecules composed of a protein core, commonly syndecan, covalently attached to one or more HS glycosaminoglycan (GAG) side chains via a linker region (30). HS polysaccharide chains are composed of alternating hexuronic acid and d-glucosamine units (30, 31). HS chains undergo extensive modifications during their biosynthesis, including sulfation and epimerization, resulting in a variety of structurally diverse HS chains (30, 32–33). This diversity allows HS to interact with an array of functionally unrelated proteins and participate in various processes, such as the regulation of embryonic development, angiogenesis, blood coagulation, growth factor/cytokine interactions, cell adhesion, and lipid metabolism (30).Much remains to be learned about the cell-cell fusion mechanism and regulation of this phenomenon. The purpose of our study was to examine the effect of HS on cell-cell fusion and how it may function in the fusion mechanism. Using HSV-1 as a tool, we discovered that the absence of HS from the cell surface significantly enhanced the ability of cells to fuse with each other. This effect was also seen independently of HSV-1 in cells that neither expressed HSV-1 glycoproteins nor their receptors. This suggests a novel role for HS as a negative regulator and a fine-tuner of cell-cell fusion events.     

The Clavesin Family, Neuron-specific Lipid- and Clathrin-binding Sec14 Proteins Regulating Lysosomal Morphology

Clathrin-coated vesicles (CCVs) originating from the trans-Golgi network (TGN) provide a major transport pathway from the secretory system to endosomes/lysosomes. Herein we describe paralogous Sec14 domain-bearing proteins, clavesin 1/CRALBPL and clavesin 2, identified through a proteomic analysis of CCVs. Clavesins are enriched on CCVs and form a complex with clathrin heavy chain (CHC) and adaptor protein-1, major coat components of TGN-derived CCVs. The proteins co-localize with markers of endosomes and the TGN as well as with CHC and adaptor protein-1. A membrane mimic assay using the Sec14 domain of clavesin 1 reveals phosphatidylinositol 3,5-bisphosphate as a specific lipid partner. Phosphatidylinositol 3,5-bisphosphate is localized to late endosomes/lysosomes, and interestingly, isoform-specific knockdown of clavesins in neurons using lentiviral delivery of interfering RNA leads to enlargement of a lysosome-associated membrane protein 1-positive membrane compartment with no obvious influence on the CCV machinery at the TGN. Since clavesins are expressed exclusively in neurons, this new protein family appears to provide a unique neuron-specific regulation of late endosome/lysosome morphology.Proteins entering the secretory pathway move through the Golgi apparatus to the trans-Golgi network (TGN)⁴ where they are sorted and packaged into carrier vesicles, including clathrin-coated vesicles (CCVs) for transport to their final destination (1). Adaptor protein-1 (AP-1), which is recruited to the TGN through dual interactions with Arf1 and phosphatidylinositol 4-phosphate (2), recruits clathrin to initiate CCV formation. AP-1 and clathrin form the membrane coat that shapes the vesicle and recruits an array of regulatory/accessory proteins, which control numerous aspects of CCV formation and function (3). Interactions with the clathrin·AP-1 coat complex also serve to recruit both transmembrane and cytosolic cargo to CCVs, allowing for their transport from the TGN to the endosomal network.The specificity and function of intracellular compartments depends in part on the presence of distinct PtdIns species. For example, phosphatidylinositol 4-phosphate is found predominantly at the TGN and contributes to AP-1 recruitment, whereas phosphatidylinositol 3-phosphate recruits effectors, such as EEA1 (early endosome antigen 1), to early endosomes to mediate membrane fusion (4–9). Early endosomes subsequently transition into late endosomes/lysosomes, and during this process, phosphatidylinositol 3-phosphate is converted to PtdIns(3,5)P₂ via the action of a phosphatidylinositol 3-phosphate 5-kinase named Fab1p in yeast and PIKfyve in mammals (10). PIKfyve is part of a protein complex nucleated by Vac14 (11, 12), and disruption of this complex leads to decreased PtdIns(3,5)P₂ levels and the formation of enlarged cytoplasmic vacuoles of endosomal/lysosomal origin (10, 13, 14). Intriguingly, despite the fact that Vac14 is found in all tissues (15) and regulates a ubiquitous trafficking process (10), decreases in PtdIns(3,5)P₂ levels resulting from Vac14 knock-out show massive neurodegeneration with little effect on other tissues (16). This neuron-specific effect has remained mysterious due to the lack of exclusively neuronal factors targeting PtdIns(3,5)P₂.The Sec14 domain is an evolutionarily ancient protein module that in humans is found in more than 45 proteins encoded by at least 25 genes (17). Mutations in several Sec14 proteins lead to human diseases, including neurodegeneration (18), yet most of the Sec14 proteins in mammals remain uncharacterized. The yeast protein Sec14p is the prototype for this module (19). Sec14p is essential for the transport of proteins from the Golgi (19), but more recently it was also found to be involved in the trafficking of protein cargo, specifically the mating factor receptor Ste3, from the plasma membrane via endosomes to the yeast vacuole (17). The yeast vacuole is the equivalent of the lysosome in mammalian cells. Yeast Sec14p is a phospholipid transfer protein that extracts phosphatidylinositol and phosphatidylcholine from membranes in vitro and regulates the metabolism of these lipids in cells (19, 20). Sec14p is composed of the Sec14 domain only, whereas the majority of Sec14 proteins in mammals contain a Sec14 domain in conjunction with other modules or protein/lipid binding domains (21, 22). In the few well characterized examples, these proteins function to integrate lipid binding/metabolism with other biological functions (21, 22).In a subcellular proteomic analysis of CCVs from the brain, we identified eight novel open reading frames, including one encoding an Sec14 domain (23, 24). A subsequent bioinformatics analysis revealed a second, paralogous Sec14 protein. We now demonstrate that the proteins, which we have named clavesin (clathrin vesicle-associated Sec14 protein) 1 and 2, are neuron-specific proteins that function in the regulation of lysosome morphology.     

Analysis of Free Energy Signals Arising from Nucleotide Hybridization Between rRNA and mRNA Sequences during Translation in Eubacteria

A decoding algorithm is tested that mechanistically models the progressive alignments that arise as the mRNA moves past the rRNA tail during translation elongation. Each of these alignments provides an opportunity for hybridization between the single-stranded, -terminal nucleotides of the 16S rRNA and the spatially accessible window of mRNA sequence, from which a free energy value can be calculated. Using this algorithm we show that a periodic, energetic pattern of frequency 1/3 is revealed. This periodic signal exists in the majority of coding regions of eubacterial genes, but not in the non-coding regions encoding the 16S and 23S rRNAs. Signal analysis reveals that the population of coding regions of each bacterial species has a mean phase that is correlated in a statistically significant way with species () content. These results suggest that the periodic signal could function as a synchronization signal for the maintenance of reading frame and that codon usage provides a mechanism for manipulation of signal phase.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]     

ERS-24, a Mammalian v-SNARE Implicated in Vesicle Traffic between the ER and the Golgi

We report the identification and characterization of ERS-24 (Endoplasmic Reticulum SNARE of 24 kD), a new mammalian v-SNARE implicated in vesicular transport between the ER and the Golgi. ERS24 is incorporated into 20S docking and fusion particles and disassembles from this complex in an ATP-dependent manner. ERS-24 has significant sequence homology to Sec22p, a v-SNARE in Saccharomyces cerevisiae required for transport between the ER and the Golgi. ERS-24 is localized to the ER and to the Golgi, and it is enriched in transport vesicles associated with these organelles.Newly formed transport vesicles have to be selectively targeted to their correct destinations, implying the existence of a set of compartment-specific proteins acting as unique receptor–ligand pairs. Such proteins have now been identified (Söllner et al., 1993a ; Rothman, 1994): one partner efficiently packaged into vesicles, termed a v-SNARE,¹ and the other mainly localized to the target compartment, a t-SNARE. Cognate pairs of v- and t-SNAREs, capable of binding each other specifically, have been identified for the ER–Golgi transport step (Lian and Ferro-Novick, 1993; Søgaard et al., 1994), the Golgi–plasma membrane transport step (Aalto et al., 1993; Protopopov et al., 1993; Brennwald et al., 1994) in Saccharomyces cerevisiae, and regulated exocytosis in neuronal synapses (Söllner et al., 1993a ; for reviews see Scheller, 1995; Südhof, 1995). Additional components, like p115, rab proteins, and sec1 proteins, appear to regulate vesicle docking by controlling the assembly of SNARE complexes (Søgaard et al., 1994; Lian et al., 1994; Sapperstein et al., 1996; Hata et al., 1993; Pevsner et al., 1994).In contrast with vesicle docking, which requires compartment-specific components, the fusion of the two lipid bilayers uses a more general machinery derived, at least in part, from the cytosol (Rothman, 1994), which includes an ATPase, the N-ethylmaleimide–sensitive fusion protein (NSF) (Block et al., 1988; Malhotra et al., 1988), and soluble NSF attachment proteins (SNAPs) (Clary et al., 1990; Clary and Rothman, 1990; Whiteheart et al., 1993). Only the assembled v–t-SNARE complex provides high affinity sites for the consecutive binding of three SNAPs (Söllner et al., 1993b ; Hayashi et al., 1995) and NSF. When NSF is inactivated in vivo, v–t-SNARE complexes accumulate, confirming that NSF is needed for fusion after stable docking (Søgaard et al., 1994).The complex of SNAREs, SNAPs, and NSF can be isolated from detergent extracts of cellular membranes in the presence of ATPγS, or in the presence of ATP but in the absence of Mg²⁺, and sediments at ∼20 Svedberg (20S particle) (Wilson et al., 1992). In the presence of MgATP, the ATPase of NSF disassembles the v–t-SNARE complex and also releases SNAPs. It seems likely that this step somehow initiates fusion.To better understand vesicle flow patterns within cells, it is clearly of interest to identify new SNARE proteins. Presently, the most complete inventory is in yeast, but immunolocalization is difficult in yeast compared with animal cells, and many steps in protein transport have been reconstituted in animal extracts (Rothman, 1992) that have not yet been developed in yeast. Therefore, it is important to create an inventory of SNARE proteins in animal cells. The most unambiguous and direct method for isolating new SNAREs is to exploit their ability to assemble together with SNAPs and NSF into 20S particles and to disassemble into subunits when NSF hydrolyzes ATP. Similar approaches have already been successfully used to isolate new SNAREs implicated in ER to Golgi (Søgaard et al., 1994) and intra-Golgi transport (Nagahama et al., 1996), in addition to the original discovery of SNAREs in the context of neurotransmission (Söllner et al., 1993a ).Using this method, we now report the isolation and detailed characterization of ERS-24 (Endoplasmic Reticulum SNARE of 24 kD), a new mammalian v-SNARE that is localized to the ER and Golgi. ERS-24 is found in transport vesicles associated with the transitional areas of the ER and with the rims of Golgi cisternae, suggesting a role for ERS-24 in vesicular transport between these two compartments.     

Proinsulin and the Genetics of Diabetes Mellitus

Insulin plays a central role in the regulation of vertebrate metabolism. The hormone, the post-translational product of a single-chain precursor, is a globular protein containing two chains, A (21 residues) and B (30 residues). Recent advances in human genetics have identified dominant mutations in the insulin gene causing permanent neonatal-onset DM² (1–4). The mutations are predicted to block folding of the precursor in the ER of pancreatic β-cells. Although expression of the wild-type allele would in other circumstances be sufficient to maintain homeostasis, studies of a corresponding mouse model (5–7) suggest that the misfolded variant perturbs wild-type biosynthesis (8, 9). Impaired β-cell secretion is associated with ER stress, distorted organelle architecture, and cell death (10). These findings have renewed interest in insulin biosynthesis (11–13) and the structural basis of disulfide pairing (14–19). Protein evolution is constrained not only by structure and function but also by susceptibility to toxic misfolding.Insulin plays a central role in the regulation of vertebrate metabolism. The hormone, the post-translational product of a single-chain precursor, is a globular protein containing two chains, A (21 residues) and B (30 residues). Recent advances in human genetics have identified dominant mutations in the insulin gene causing permanent neonatal-onset DM² (1–4). The mutations are predicted to block folding of the precursor in the ER of pancreatic β-cells. Although expression of the wild-type allele would in other circumstances be sufficient to maintain homeostasis, studies of a corresponding mouse model (5–7) suggest that the misfolded variant perturbs wild-type biosynthesis (8, 9). Impaired β-cell secretion is associated with ER stress, distorted organelle architecture, and cell death (10). These findings have renewed interest in insulin biosynthesis (11–13) and the structural basis of disulfide pairing (14–19). Protein evolution is constrained not only by structure and function but also by susceptibility to toxic misfolding.     

Algorithms for Finding Small Attractors in Boolean Networks

A Boolean network is a model used to study the interactions between different genes in genetic regulatory networks. In this paper, we present several algorithms using gene ordering and feedback vertex sets to identify singleton attractors and small attractors in Boolean networks. We analyze the average case time complexities of some of the proposed algorithms. For instance, it is shown that the outdegree-based ordering algorithm for finding singleton attractors works in time for , which is much faster than the naive time algorithm, where is the number of genes and is the maximum indegree. We performed extensive computational experiments on these algorithms, which resulted in good agreement with theoretical results. In contrast, we give a simple and complete proof for showing that finding an attractor with the shortest period is NP-hard.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32]     

Molecular Architecture and Function of the SEA Complex,a Modulator of the TORC1 Pathway

The TORC1 signaling pathway plays a major role in the control of cell growth and response to stress. Here we demonstrate that the SEA complex physically interacts with TORC1 and is an important regulator of its activity. During nitrogen starvation, deletions of SEA complex components lead to Tor1 kinase delocalization, defects in autophagy, and vacuolar fragmentation. TORC1 inactivation, via nitrogen deprivation or rapamycin treatment, changes cellular levels of SEA complex members. We used affinity purification and chemical cross-linking to generate the data for an integrative structure modeling approach, which produced a well-defined molecular architecture of the SEA complex and showed that the SEA complex comprises two regions that are structurally and functionally distinct. The SEA complex emerges as a platform that can coordinate both structural and enzymatic activities necessary for the effective functioning of the TORC1 pathway.The highly conserved Target of Rapamycin Complex 1 (TORC1)¹ controls eukaryotic cell growth and cellular responses to a variety of signals, including nutrients, hormones, and stresses (1, 2). In a nutrient-rich environment, TORC1 promotes anabolic processes including ribosome biogenesis and translation. Nutrient limitation or treatment with rapamycin inhibits the Tor1 kinase and initiates autophagy, a catabolic process that mediates the degradation and recycling of cytoplasmic components. However, the nutrient-sensing function of TORC1 is not fully understood, and the mechanisms of TORC1 modulation by amino acid and nitrogen availability are not yet clear.In the yeast Saccharomyces cerevisiae, the TOR1 complex is composed of four subunits (Tor1, Kog1, Tco89, and Lst8) and is localized to the vacuole membrane. Amino acid levels are signaled to TORC1 (at least partially) via the EGO complex (Ragulator-Rag in mammals), which consists of Ego1, Ego3, Gtr1 (RagA/RagB), and Gtr2 (RagC/RagD) (3–6). The small GTPases Gtr1 and Gtr2 function as heterodimers and in their active form exist as the Gtr1-GTP/Gtr2-GDP complex. Amino acid sensing via the EGO complex involves the conserved vacuolar membrane protein Vam6, a member of the HOPS tethering complex. Vam6 is a GDP exchange factor that regulates the nucleotide-binding status of Gtr1 (6). At the same time, the GTP-bound state of Gtr1 is controlled by a leucyl t-RNA synthetase (7). In mammals, amino acids promote interaction of Ragulator-Rag with mTORC1 and its translocation to the lysosomal membrane (3, 4). Ragulator interacts with the v-ATPase complex at the lysosomal membrane (8), and leucyl t-RNA synthetase binds to RagD to activate mTORC1 (9).A genome-wide screen for TORC1 regulators in yeast identified two proteins, Npr2 and Npr3, as proteins that mediate amino acid starvation signal to TORC1 (10). Npr2 and Npr3 are both members of the SEA complex that we discovered recently (11–13). Besides Npr2 and Npr3, the SEA complex also contains four previously uncharacterized proteins (Sea1–Sea4) and two proteins also found in the nuclear pore complex, Seh1 and Sec13, the latter of which is additionally a component of the endoplasmic-reticulum-associated COPII coated vesicle. However, the SEA complex localizes to the vacuole membrane, and not to the nuclear pore complex or endoplasmic reticulum.The Sea proteins contain numerous structural elements present in intracellular structural trafficking complexes (11). For example, proteins Sea2–Sea4 are predicted to possess β-propeller/α-solenoid folds and contain RING domains, architectural combinations characteristic to protein complexes that form coats around membranes (e.g. coated vesicles, nuclear pore complexes) or participate in membrane tethering (e.g. HOPS, CORVET complexes). Npr2 and Npr3 possess a longin domain, found in many guanine nucleotide exchange factors (GEFs) (14–16), and Sea1/Iml1 is a GTPase activating protein (GAP) for Gtr1 (17). These structural characteristics, taken together with functional data, indicate a role for the SEA complex in intracellular trafficking, amino acid biogenesis, regulation of the TORC1 pathway, and autophagy (11–13, 17–20). A mammalian analog of the SEA complex, termed GATOR1/GATOR2, has recently been identified (21). GATORS are localized at the lysosome membrane and serve as upstream regulators of mammalian TORC1 via GATOR1 GAP activity toward RagA and RagB (21).In this study, we characterized the structural and functional organization of the yeast SEA complex. We present here a well-defined molecular architecture of the SEA complex obtained via an integrative modeling approach based on a variety of biochemical data. The structure reveals the relative positions and orientations of two SEA subcomplexes, Sea1/Npr2/Npr3 (or SEACIT (19)) and Sea2/Sea3/Sea4/Sec13/Seh1 (or SEACAT (19)), and identifies the Sea3/Sec13 dimer as a major interacting hub within the complex. We describe how the SEA complex interacts physically with TORC1 and the vacuole and is required for the relocalization of Tor1, and how every member of the Sea1/Npr2/Npr3 subcomplex is required for general autophagy.