Abstract
Syntaxins are a family of membrane-anchored SNARE proteins that are essential components required for membrane fusion in all eukaryotic intracellular membrane trafficking pathways. Syntaxins contain an N-terminal regulatory domain, termed the Habc domain, that is not highly conserved at the primary sequence level but folds into a three-helix bundle that is structurally conserved among family members. The syntaxin Habc domain has previously been found to be structurally very similar to the GAT domain present in GGA family members and related proteins that are otherwise completely unrelated to syntaxins. Because the GAT domain has been found to be a ubiquitin binding domain we hypothesized that the Habc domain of syntaxins may also bind to ubiquitin. Here, we report that the Habc domain of syntaxin 3 (Stx3) indeed binds to monomeric ubiquitin with low affinity. This domain binds efficiently to K63-linked poly-ubiquitin chains within a narrow range of chain lengths but not to K48-linked poly-ubiquitin chains. Other syntaxin family members also bind to K63-linked polyubiquitin chains but with different chain length specificities. Molecular modeling suggests that residues of the GGA3-GAT domain known to be important for ionic and hydrophobic interactions with ubiquitin have equivalent, conserved residues within the Habc domain of Stx3. We conclude that the syntaxin Habc domain and the GAT domain are both structurally and functionally related, and likely share a common ancestry despite sequence divergence. Binding of K63-linked poly-ubiquitin chains to the Habc domain may regulate the function of syntaxins in membrane fusion or may suggest additional functions of this protein family.
Introduction
SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) proteins are the indispensable mediators of membrane fusion reactions within the endomembrane system of eukaryotic cells [1-5]. The SNARE superfamily consists of several sub-families whose members contain one or two SNARE domains of ∽60 residue length [3, 4, 6]. Members of the syntaxin family of SNAREs are central to the formation of SNARE complexes. They contain a C-terminal transmembrane anchor, preceded by the SNARE domain. The latter engages in interactions with cognate SNAREs to form a SNARE complex in a 4-helix bundle arrangement that ultimately leads to membrane fusion [7-9].
Syntaxins also contain an N-terminal regulatory domain that consists of three a helices (a,b,c) and has been termed the Habc domain. At least 16 syntaxins are encoded in the human genome and many more in divergent species. Amongst these syntaxins, the Habc domains are poorly – or not at all - conserved at the primary sequence level. However, in the cases of syntaxin family members whose Habc domains have been structurally studied it was found that they all share a highly conserved fold. This includes Stx1A [10, 11], Stx6 [12], Sso1 [13], Stx10 [14], Vam3p [15] and several others (see Protein Data Bank) whose Habc domains fold into essentially superimposable three-helix bundles despite limited or absent sequence similarity. The Habc domains of various syntaxins have been found to be binding sites to proteins that regulate SNARE function including those of the munc18, munc13 and synaptotagmin families [16]. In addition, in some – but not all – syntaxins the Habc domains have the ability to engage in an intramolecular interaction with the SNARE domain resulting in a tetrameric helical bundle. This “closed” conformation generally inhibits the formation of complexes with cognate SNARE proteins and thereby inhibits membrane fusion [16, 17]. These findings clearly indicate that the Habc domains of syntaxins play a critical role in the regulation of membrane fusion and that this function depends on the conserved three-dimensional structure of these domains.
It was surprising when it was found that a conserved domain in a very different family of proteins shares the same fold with the syntaxin Habc domain. The GAT (GGAs and TOM) domain of GGA1 was found to be nearly superimposable with the Habc domains of Stx1A and Stx6 despite their lack of sequence similarity [18]. GGA proteins are Golgi- and endosome-associated clathrin adaptor proteins involved in cargo recruitment in membrane trafficking pathways. At the time of the discovery of the structural similarity with the syntaxin Habc domain, relatively little was known about the function of the GAT domain. Subsequently, however, the GAT domains of GGA proteins were found to be ubiquitin binding domains [19-24] which helped to explain their function in recruiting ubiquitinated membrane proteins for targeting to multivesicular bodies (MVBs) [25].
Ubiquitin, an 8 kDa protein, is covalently attached to lysine residues of target proteins via E3 ligases [26]. In the case of membrane proteins, reversible ubiquitination serves as a signal for targeting to endosomes, and then to intraluminal vesicles of MVBs. MVBs can subsequently either fuse with lysosomes leading to degradation [27] or they can fuse with the plasma membrane leading to extracellular secretion of membrane proteins in the form of exosomes [28]. Ubiquitin itself may be ubiquitinated at any of its seven lysine residues leading to target proteins being tagged with a chain of polyubiquitin molecules [29]. K48-linked polyubiquitin chains are a signal for proteasomal degradation whereas K63-linked polyubiquitin chains are another signal for trafficking of membrane proteins to the endosomal pathway, and especially into the MVB pathway [30-32]. The GAT domain of GGA proteins has been shown to be required for the sorting of membrane proteins tagged with K63-polyubiquitin chains into the MVB pathway [31, 32].
GGA proteins themselves are also mono-ubiquitinated in a manner dependent on the binding of ubiquitin to their GAT domain [19]. A large number of ubiquitin-binding proteins have been found to also be ubiquitinated themselves. The reasons for this are not always completely clear but it is thought that concurrent ubiquitin-binding and ubiquitination of sorting proteins aids in the establishment of protein networks to create sorting domains [25, 33].
We have recently reported that syntaxin 3, a SNARE involved in membrane fusion at the apical plasma membrane of polarized epithelial cells, undergoes mono-ubiquitination at lysine residues adjacent to its transmembrane domain [34]. Ubiquitination of Stx3 leads to endocytosis from the basolateral plasma membrane, direction into the endosomal/MVB pathway and eventually excretion with exosomes [34]. Functional studies using a nonubiquitinatable Stx3 mutant suggested that Stx3 may function to sort specific cargo proteins into the MVB/exosomal pathway [34]. Such a function is unexpected for a protein thought to be involved in membrane fusion.
The structural similarity between the Habc domain of syntaxins and the GAT domain suggests a common ancestry and related function. Given this structural similarity, and given the finding that Stx3 – like GGA proteins - is mono-ubiquitinated and appears to play a role in cargo sorting in the MVB/exosomal pathway, we hypothesized that the Habc domain of Stx3 may be a ubiquitin-binding domain. We report here that Stx3 indeed binds to ubiquitin with low affinity, and with much higher affinity to K63-linked polyubiquitin chains, but not K48-linked polyubiquitin chains. Structural modeling and mutagenesis experiments suggest that the mode of ubiquitin binding is similar to that of the GAT domain and may involve conserved hydrophobic interactions and a salt bridge. These results suggest that syntaxin function may be regulated by polyubiquitin binding, and that syntaxins may function in protein sorting in addition to their established role in membrane fusion.
Results
Stx3 binds non-covalently to ubiquitin
To investigate the possibility that Stx3 may bind to ubiquitin we incubated a purified GST-fusion protein of the entire cytoplasmic domain (1-265) of Stx3 with ubiquitin-coated beads to observe any interaction in a pull-down assay. A GST-fusion protein of the GGA3-GAT domain served as a positive control. As shown in Fig. 1A, GGA3-GAT interacts strongly with ubiquitin-coated beads as expected. GST-Stx3 also interacts with ubiquitin-coated beads although with reduced efficiency as compared to GGA3-GAT. A GST-fusion protein containing only the Habc domain (1-146) of Stx3 pulls down with ubiquitin-coated beads much more efficiently than the entire Stx3 cytoplasmic domain (Fig. 1B). This suggests that the Habc domain directly binds to ubiquitin, and that this interaction is inhibited by intramolecular binding between the Habc and SNARE domains in the “closed conformation” of Stx3. To test this possibility, we introduced the LE165/166AA mutation that has previously been shown to prevent the closed conformation in the highly conserved Stx1A leading to a constitutively open conformation [17]. The observed increase in binding of the open-mutant vs. wild-type Stx3 (Fig. 1B) suggests that the Habc domain preferentially binds to ubiquitin when it is not engaged in binding to the SNARE domain.
To assess the affinity of the Habc domain of Stx3 for ubiquitin, we utilized a surface plasmon resonance assay using immobilized GST-Stx3-Habc in comparison with GST-GGA3-GAT as a positive control. The measured Kd for the binding of GST-GGA3-GAT to ubiquitin is 0.211 mM which is consistent with previously published values of 0.231 mM [24] and 0.181 mM [23]. This interaction has been described as a “high-affinity” interaction for a ubiquitin binding protein [29]. In comparison, the measured Kd for the Habc domain of Stx3 is approximately four times weaker (1.36 mM) (Fig. 1D) indicating that the binding of Stx3 to mono-ubiquitin in solution is a low-affinity interaction.
Altogether, these results suggest that the similarity between the GAT domain of GGA proteins and the Habc region of Stx3 is not only structural, but also functional with respect to ubiquitin binding.
Stx3 binds to K63-linked but not K48-linked polyubiquitin chains
Ubiquitin-binding domains commonly have weak affinities for mono-ubiquitin but the presence of multiple ubiquitin binding sites in the same molecule often results in much higher affinities for polyubiquitin chains [29]. Since the affinity of the Habc domain of Stx3 for mono-ubiquitin was low, we next investigated whether Stx3 may exhibit higher affinity for polyubiquitin chains. The two predominant chain-linkages are via the K48 or K63 residues of ubiquitin, respectively. GST-Stx3 was incubated with either K48- or K63-linked polyubiquitin chains covering a range of lengths from monomeric to 7-mers. As shown in Fig. 2A, Stx3 interacts with K63-linked polyubiquitin chains of lengths between 3-5. In this assay, no binding is detected to monomeric ubiquitin consistent with the weak affinity of Stx3 to monomeric ubiquitin measured above (Fig. 1D). Stx3 also does not exhibit interaction with K63-linked ubiquitin chains longer than 5 units suggesting selectivity to a narrow range of chain lengths. Importantly, no interaction between Stx3 and K48-linked chains of any length is detected suggesting that Stx3 shows strong preference to the K63 linkage.
Next, we tested whether the ability to interact with K63-linked ubiquitin chains is unique to Stx3 or may also be a feature of other syntaxins. We compared GST-fusion proteins of Stx1A, Stx2, and Stx4 side-by-side with Stx3. Stx1A and Stx2 interact with K63-linked ubiquitin chains similarly to Stx3 albeit with somewhat differing preferences for different chain lengths (Fig. 2B). Stx4 only exhibits very weak interaction with Ubi5. None of these syntaxins show binding to monomeric ubiquitin in this assay. Altogether, these data suggest that the Habc domains of several syntaxins are capable of binding to ubiquitin chains and that Stx3 shows strong preference for K63-linked ubiquitin chains of a narrow range of lengths.
Structural modeling
The GAT domain of GGA3 has been to shown have two distinct binding sites for ubiquitin. Site 1 has been studied in most detail and encompasses residues from the C-terminal half of helix A and the N-terminal half of helix B (Fig. 3A). X-ray structure analysis of ubiquitin in complex with the GGA3-GAT domain revealed prominent hydrophobic interactions with ubiquitin involving L227, M231 and L247 of GGA3, and a salt bridge involving E246 and E250 of GGA3 [23, 24]. These residues interact closely with I44 and R42, respectively, of ubiquitin. The other ubiquitin binding site of GGA3 (site 2) is located on the opposite face of the 3-helix bundle of the GAT domain and encompasses residues in helices B and C [24], but no 3D structure is available for this interaction.
To better understand how the Habc domain of Stx3 may interact with ubiquitin we constructed a model based on the X-ray structure of ubiquitin in association with site 1 of the GGA3 GAT domain [23, 24]. We modeled the Stx3 sequence into the known structure of the Habc domain of the closely related Stx1A [10, 11], and then fitted this Stx3 Habc domain onto the GGA3 GAT domain. The resulting model is shown in Fig. 4. This allowed us to identify Stx3 residues that correspond most closely to the known hydrophobic and ionic interactions between GGA3-GAT and ubiquitin. As shown in Fig. 4, the Stx3 Habc domain has two glutamic acid residues (E78 and E83) in very similar positions as E246 and E250 of GGA3-GAT, and these residues maybe be predicted to engage in a salt bridge with R42 of ubiquitin. Similarly, L59, L77 and L80 of Stx3 would form a hydrophobic pocket that may interact with I44 of ubiquitin, analogous to the hydrophobic pocket formed by L227, M231 and L247 of GGA3 (Fig. 4).
Due to the lack of similarity between Stx3 and GGA3 at the primary sequence level (Fig. 3A) these predictions would have been difficult or impossible to make. However, we note that E78 and E83 of Stx3 and E246 and E250 of GGA3 can be aligned closely with each other (Fig. 3A). Sequence alignment of Stx3 orthologs from numerous species indicates that all of the residues that may potentially interact with ubiquitin are highly conserved (Fig. 3B).
Mutational analysis
Based on this model, we decided to mutate residues L77, E78, L80, and E83 of Stx3 to alanine residues and test any effects on the ability to interact with ubiquitin chains. GST fusion proteins with the cytoplasmic domain of Stx3 containing either double leucine (L77A/L80A) or double glutamate (E79A/E83A) mutations were generated. Introducing all four mutations simultaneously resulted in an insoluble GST fusion protein that could not be analyzed.
The ability of the mutants to bind to K63-linked polyubiquitin chains was assessed using the same assay as in Figure 2. Introducing the E79A/E83A mutations had no discernible effect on polyubiquitin binding as compared to wild-type Stx3 (Fig. 5). Introducing the L77A/L80A mutations had only a seemingly minor effect in that it eliminated a very weak interaction with K63-linked Ubi2 (Fig. 5). Given that similar mutagenesis experiments with GGA GAT domains frequently lead only to minor disruption of ubiquitin binding [19, 21, 23], however, these results may not be surprising. First, the interactions between the GAT domain and ubiquitin involve numerous contacts with multiple residues. Second, the fact that the GAT domain has two separate ubiquitin binding sites suggests that mutations of one site alone will have little effect on overall ubiquitin binding, especially for the binding of polyubiquitin chains. We predict that polyubiquitin chains wrap around the entire surface of the GAT domain, and by analogy also the Habc domain of syntaxins, and engage in numerous contacts that are difficult to completely disrupt by mutagenesis. Such a binding mode may also explain why similar structures (GAT and Habc domains) could bind to polyubiquitin even in the absence of highly conserved primary sequence similarity. In this regard, it is interesting that the L77A/L80A mutations in Stx3 appear to disrupt only the binding to ubiquitin dimers, which may suggest that longer ubiquitin chains can compensate by interacting with additional residues simultaneously.
Discussion
This study illuminates a novel characteristic of syntaxins, ubiquitin binding. This is a surprising finding because, to our knowledge, ubiquitin-binding has not previously been reported for any SNARE protein, nor has there been any indication that ubiquitin-binding could affect SNARE-mediated membrane fusion events. On the other hand, the fact that the 3D structures of the GAT and Habc domains are highly similar, and the fact that critical hydrophobic and ionic residues known to mediate ubiquitin-binding of the GAT domain have equivalent residues in the Habc domain of Stx3 (Fig. 4) makes it plausible that both domains share a similar function.
Besides in GGA proteins, GAT domains are also present in the more distantly related proteins TOM1 and TOM1-L1, both of which also bind to ubiquitin [35]. The degree of primary sequence similarity among these GAT domains is low but the overall structures of these 3-helix bundles are highly conserved. The finding that Habc domains of syntaxins not only share the same fold with GAT domains but also function in ubiquitin-binding strongly suggests that all of these domains share a common ancestry.
While the purpose of the ability of syntaxins to bind to K63-linked polyubiquitin chains remains to be elucidated, several possibilities can be envisioned. Binding of K63-linked polyubiquitin chains to the Habc domain of a syntaxin may interfere with the ability of that syntaxin to bind to other regulatory proteins that are known to interact with the Habc domain such as members of the munc13, synaptotagmin and munc18 families of SNARE regulators. Thereby K63-linked polyubiquitin chains, possibly attached to specific regulatory proteins, may regulate SNARE function and therefore membrane fusion in certain vesicle trafficking pathways. Another possibility is that binding of K63-linked polyubiquitin chains to the Habc domain of a syntaxin would interfere with the ability of the Habc domain to engage in an intramolecular interaction with the SNARE domain of that syntaxin. This would result in a “constitutively open” conformation of that syntaxin and, again, may regulate membrane fusion functions. Another possibility emerges from our recent finding that Stx3 can undergo ubiquitination at a cluster of lysine residues located between its SNARE domain and transmembrane domain [34]. It may be possible that the Habc domain could engage in an intramolecular interaction with this covalently attached ubiquitin thereby locking such modified Stx3 in a “constitutively closed” conformation. Finally, it is possible that binding of K63-linked polyubiquitin chains to the Habc domain of Stx3 may be unrelated to a function in membrane fusion but rather relates to a different function. Such a possibility may be supported by our recent finding that Stx3 that is covalently ubiquitinated at the lysine cluster proximal to its transmembrane domain enters the endosomal pathway, intraluminal vesicles of MVBs, and is eventually excreted with exosomes [34]. We reported that a non-ubiquitinatable mutant of Stx3 (termed Stx3-5R) is not only unable to enter the MVB/exosomal pathway but also interferes with the recruitment of a specific apical exosomal cargo protein, the orphan G-protein coupled receptor GPRC5B, into this pathway. This suggested that Stx3 normally plays a role in cargo recruitment in a fashion that is dependent on its ability to be ubiquitinated. Interestingly, the Stx3-5R mutant was also found to disrupt the secretion of human cytomegalovirus (hCMV) virions, a result that - combined with other findings - suggests that hCMV exploits the MVB/exosomal pathways for virion production and secretion [34]. In this regard, Stx3 bears striking similarities to GGA proteins. Both contain a similarly structured ubiquitin-binding domain, both undergo ubiquitination themselves, and both are involved in recruitment of membrane proteins into the MVB pathway. In the case of GGA proteins, this sorting function requires cargo proteins to be tagged with K63-linked polyubiquitin chains [31, 32].
Altogether, these results suggest that syntaxins contain a ubiquitin binding domain similar to the GAT domain. The implications of this finding are yet to be elucidated but may relate to the regulation of membrane fusion functions and/or point towards a novel function of syntaxins in the sorting of membrane proteins.
Materials and Methods
Plasmid construction
The cytoplasmic region of rat Stx3 (1-265) and the N-terminal region of Stx3 (1-146), respectively, were cloned into pGEX-4T-3 (GE Healthcare Life Sciences). pGEX-4T-2-GGA3-GAT plasmid was a kind gift of Kazuhisa Nakayama (Graduate School of Pharmaceutical Sciences, Kyoto University). Site-directed mutagenesis (QuickChange II, Agilent Technologies) was employed to generate the open-conformation mutant (LE165/166AA) in the Stx3 (1-265) plasmid.
Protein expression and purification
GST-fusion protein plasmids were transformed into E. coli Rosetta 2 (EMD Millipore) competent cells. When the cultures reached an OD of 0.6, IPTG was added to induce expression of GST-protein. Cells were pelleted and lysed in a buffer containing 10 mM Tris-HCl, pH 8.0, 150 mM NaCl with lysozyme, RNase, DNase, Triton X-100. DTT, 5 mM EDTA, PMSF, and a protease inhibitor cocktail were subsequently added. CL2B Sepharose beads (GE Healthcare Life Sciences) were used to pre-clear the lysates, followed by incubation with glutathione-coated agarose overnight at 4°C with rotating. Beads were washed four times and eluted with glutathione. Eluate content was analyzed by SDS-PAGE. Eluates were then dialyzed into 50 mM Tris-HCl, pH 8.0, 150 mM NaCl, 1 mM EDTA and the protein concentration determined using a Nanodrop spectrophotometer (ThermoScientific).
Mono-ubiquitin binding assay
Purified GST-fusion proteins were incubated in Buffer A (25 mM HEPES-KOH, pH 7.4, 125 mM potassium acetate, 2.5 mM magnesium acetate, 5 mM EGTA) containing 1% fetal bovine serum with ubiquitin-coated agarose beads (Sigma-Aldrich) for 2 hours at room temperature. Beads were washed three times with Buffer A containing 0.005% Tween-20, re-suspended in SDS-PAGE sample buffer, boiled, separated on SDS-PAGE, and transferred to nitrocellulose membrane. Membranes were probed with a polyclonal goat anti-GST antibody (GE Healthcare Life Sciences) and a donkey anti-goat IgG HRP-conjugated secondary antibody (Jackson Immunoresearch).
Poly-ubiquitin binding assay
GST-fusion proteins were incubated in Buffer A containing FBS (25 mM HEPES-KOH, pH 7.4, 125 mM potassium acetate, 2.5 mM magnesium acetate, 5 mM EGTA, 1% FBS) while rotating at room temperature with 8 μg of a K48-linked or K63-linked mixture of polyubiquitin chains of 2-7 ubiquitins in length (Boston Biochem). After one hour, glutathione-coated agarose beads were added to the sample and incubated for one hour. Beads were washed three times with Buffer A containing 0.005% Tween-20, re-suspended in SDS-PAGE sample buffer and treated as above. Membranes were boiled for 10 minutes in H2O prior to blocking in 5% dry milk in TBST before being probed with mouse anti-ubiquitin antibody P4D1 (Santa Cruz Biotechnology).
Surface plasmon resonance measurements
All SPR measurements were performed on a Biacore 2000 instrument. All binding assays were performed at room temperature in HBS-EP buffer (10 mM HEPES, pH 7.4, 150 mM NaCl, 3 mM EDTA, 0.005% Tween-20). GST-fusion proteins were captured to a CM5 Sensor Chip (GE Healthcare Life Sciences) by using a GST capture kit (GE Healthcare Life Sciences) according to the manufacturer’s instructions. Purified bovine ubiquitin was from Sigma-Aldrich (U6253).
Acknowledgments
This work was supported by grants from the NIH (DK095248, GM66785), and the California Cancer Research Coordinating Committee to T.W., and a Postdoctoral Fellowship from the Spanish Ministry of Education and Science to E.R.