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SNARE-fusion membrane complex proteins | |
---|---|
Identifiers | |
Symbol | SNARE |
InterPro | IPR010989 |
SCOP2 | 1kil /SCOPe /SUPFAM |
TCDB | 1.F.1 |
OPM superfamily | 197 |
OPM protein | 3hd7 |
Membranome | 198 |
SNARE proteins – "SNAPREceptors" – are a largeprotein family consisting of at least 24 members inyeasts and more than 60 members inmammalian andplant cells.[2][3][4] The primary role of SNARE proteins is to mediate thefusion of vesicles with the targetmembrane; this notably mediatesexocytosis, but can also mediate the fusion of vesicles with membrane-bound compartments (such as alysosome). The best studied SNAREs are those that mediate the release ofsynaptic vesicles containingneurotransmitters inneurons. These neuronal SNAREs are the targets of theneurotoxins responsible forbotulism andtetanus produced by certainbacteria.
SNAREs can be divided into two categories:vesicle orv-SNAREs, which are incorporated into the membranes of transport vesicles during budding, andtarget ort-SNAREs, which are associated with nerve terminal membranes. Evidence suggests that t-SNAREs form stable subcomplexes which serve as guides for v-SNARE, incorporated into the membrane of a protein-coated vesicle, binding to complete the formation of the SNARE complex.[5] Several SNARE proteins are located on both vesicles and target membranes, therefore, a more recent classification scheme takes into account structural features of SNAREs, dividing them into R-SNAREs and Q-SNAREs. Often, R-SNAREs act as v-SNAREs and Q-SNAREs act as t-SNAREs. R-SNAREs are proteins that contribute an arginine (R) residue in the formation of thezero ionic layer in the assembled core SNARE complex. One particular R-SNARE is synaptobrevin, which is located in the synaptic vesicles. Q-SNAREs are proteins that contribute a glutamine (Q) residue in the formation of the zero ionic layer in the assembled core SNARE complex. Q-SNAREs include syntaxin and SNAP-25. Q-SNAREs are further classified as Qa-, Qb-, or Qc-SNAREs depending on their location in the four-helix bundle.
Variants are known from yeasts,[6] mammals,[2][3] plants,[4]Drosophila, andCaenorhabditis elegans.[6]
SNAREs are small, abundant, sometimes tail-anchored proteins which are often post-translationally inserted into membranes via a C-terminaltransmembrane domain. Seven of the 38 known SNAREs, includingSNAP-25, do not have a transmembrane domain and are instead attached to the membrane via lipid modifications such aspalmitoylation.[7] Tail-anchored proteins can be inserted into theplasma membrane,endoplasmic reticulum,mitochondria, andperoxisomes among other membranes, though any particular SNARE is targeted to a unique membrane. The targeting of SNAREs is accomplished by altering either the composition of the C-terminal flanking amino acid residues or the length of the transmembrane domain. Replacement of the transmembrane domain with lipid anchors leads to an intermediate stage of membrane fusion where only the two contacting leaflets fuse and not the two distal leaflets of the two membrane bilayer.[8]
Although SNAREs vary considerably in structure and size, they all share a segment in their cytosolic domain called a SNAREmotif that consists of 60-70 amino acids and containsheptad repeats that have the ability to form coiled-coil structures. V- and t-SNAREs are capable of reversible assembly into tight, four-helix bundles called "trans"-SNARE complexes. In synaptic vesicles, the readily-formedmetastable "trans" complexes are composed of three SNAREs:syntaxin 1 and SNAP-25 resident in cell membrane andsynaptobrevin (also referred to asvesicle-associated membrane protein or VAMP) anchored in the vesicle membrane.
Inneuronal exocytosis, syntaxin and synaptobrevin are anchored in respective membranes by their C-terminal domains, whereas SNAP-25 is tethered to the plasma membrane via several cysteine-linked palmitoyl chains. The coretrans-SNARE complex is a four--helix bundle, where one-helix is contributed by syntaxin 1, one-helix by synaptobrevin and two-helices are contributed by SNAP-25.[9]
Theplasma membrane-resident SNAREs have been shown to be present in distinct microdomains or clusters, the integrity of which is essential for the exocytotic competence of the cell.
During membrane fusion, v-SNARE and t-SNARE proteins on separate membranes combine to form a trans-SNARE complex, also known as a "SNAREpin". Depending on the stage of fusion of the membranes, these complexes may be referred to differently.
During fusion oftrans-SNARE complexes, the membranes merge and SNARE proteins involved in complex formation after fusion are then referred to as a "cis"-SNARE complex, because they now reside in a single (orcis) resultant membrane. After fusion, thecis-SNARE complex is bound and disassembled by an adaptor protein,alpha-SNAP. Then, the hexamericATPase (of theAAA type) calledNSF catalyzes theATP-dependent unfolding of the SNARE proteins and releases them into the cytosol for recycling.
SNAREs are thought to be the core required components of the fusion machinery and can function independently of additional cytosolic accessory proteins. This was demonstrated by engineering "flipped" SNAREs, where the SNARE domains face the extracellular space rather than the cytosol. When cells containing v-SNAREs contact cells containing t-SNAREs,trans-SNARE complexes form and cell-cell fusion ensues.[10]
The core SNARE complex is a 4--helix bundle.[11] Synaptobrevin and syntaxin contribute one-helix each, while SNAP-25 participates with two-helices (abbreviated as Sn1 and Sn2). The interacting amino acid residues that zip the SNARE complex can be grouped into layers. Each layer has 4 amino acid residues – one residue per each of the 4-helices. In the center of the complex is thezero ionic layer composed of one arginine (R) and three glutamine (Q) residues, and it is flanked byleucine zippering. Layers '-1', '+1' and '+2' at the centre of the complex most closely follow ideal leucine-zipper geometry and aminoacid composition.[12]
Thezero ionic layer is composed of R56 from VAMP-2, Q226 from syntaxin-1A, Q53 from Sn1 and Q174 from Sn2, and is completely buried within the leucine-zipper layers. The positively chargedguanidino group of thearginine (R) residue interact with thecarboxyl groups of each of the threeglutamine (Q) residues.
The flanking leucine-zipper layers act as a water-tight seal to shield theionic interactions from the surroundingsolvent. Exposure of thezero ionic layer to the water solvent by breaking the flanking leucine zipper leads to instability of the SNARE complex and is the putative mechanism by which-SNAP andNSF recycle the SNARE complexes after the completion ofsynaptic vesicleexocytosis.
SNARE proteins must assemble intotrans-SNARE complexes to provide the force that is necessary forvesicle fusion. The fourα-helix domains (1 each fromsynaptobrevin andsyntaxin, and 2 fromSNAP-25) come together to form acoiled-coil motif. Therate-limiting step in the assembly process is the association of the syntaxin SNARE domain, since it is usually found in a "closed" state where it is incapable of interacting with other SNARE proteins.[13] When syntaxin is in an open state,trans-SNARE complex formation begins with the association of the four SNARE domains at theirN-termini. The SNARE domains proceed in forming a coiled-coil motif in the direction of theC-termini of their respective domains.SNAP andNSF also associate with the complex formed by SNAREs during this step and participate in the later events of priming and disassembly.
The SM proteinMunc18 is thought to play a role in assembly of the SNARE complex, although the exact mechanism by which it acts is still under debate. It is known that the clasp of Munc18 locks syntaxin in a closed conformation by binding to itsα-helical SNARE domains, which inhibits syntaxin from entering SNARE complexes (thereby inhibitingfusion).[13] The clasp is also capable, however, of binding the entire four-helix bundle of thetrans-SNARE complex. One hypothesis suggests that, during SNARE-complex assembly, the Munc18 clasp releases closed syntaxin, remains associated with theN-terminal peptide of syntaxin (allowing association of the syntaxin SNARE domain with other SNARE proteins), and then reattaches to the newly formed four-helix SNARE complex.[14] This possible mechanism of dissociation and subsequent re-association with the SNARE domains could be calcium-dependent.[15] This supports the idea that Munc18 plays a key regulatory role invesicle fusion; under normal conditions the SNARE complex will be prevented from forming by Munc18, but when triggered the Munc18 will actually assist in SNARE-complex assembly and thereby act as a fusioncatalyst.[14]
Membrane fusion is an energetically demanding series of events, which requires translocation of proteins in the membrane and disruption of the lipid bilayer, followed by reformation of a highly curved membrane structure. The process of bringing together two membranes requires input energy to overcome the repulsive electrostatic forces between the membranes. The mechanism that regulates the movement of membrane associated proteins away from the membrane contact zone prior to fusion is unknown, but the local increase in membrane curvature is thought to contribute in the process. SNAREs generate energy through protein-lipid and protein-protein interactions which act as a driving force for membrane fusion.
One model hypothesizes that the force required to bring twomembranes together duringfusion comes from theconformational change intrans-SNARE complexes to formcis-SNARE complexes. The current hypothesis that describes this process is referred to as SNARE "zippering."[16]
When thetrans-SNARE complex is formed, the SNARE proteins are still found on opposing membranes. As the SNARE domains continue coiling in aspontaneous process, they form a much tighter, more stable four-helix bundle. During this "zippering" of the SNARE complex, a fraction of the released energy from binding is thought to be stored as molecular bending stress in the individual SNARE motifs. This mechanical stress is postulated to be stored in the semi-rigid linker regions between the transmembrane domains and the SNARE helical bundle.[17][18] The energetically unfavorable bending is minimized when the complex moves peripherally to the site of membrane fusion. As a result, relief of the stress overcomes the repulsive forces between thevesicle and thecell membrane and presses the two membranes together.[19]
Several models to explain the subsequent step – the formation of stalk and fusion pore – have been proposed. However, the exact nature of these processes remains debated. In accordance with the "zipper" hypothesis, as the SNARE complex forms, the tightening helix bundle puts torsional force on thetransmembrane (TM) domains ofsynaptobrevin andsyntaxin.[20] This causes the TM domains to tilt within the separate membranes as the proteins coil more tightly. The unstable configuration of the TM domains eventually causes the two membranes to fuse and the SNARE proteins come together within the same membrane, which is referred to as a "cis"-SNARE complex.[21] As a result of the lipid rearrangement, afusion pore opens and allows the chemical contents of thevesicle to leak into the outside environment.
The continuum explanation of stalk formation suggests that membrane fusion begins with an infinitesimal radius until it radially expands into a stalk-like structure. However, such a description fails to take into account the molecular dynamics of membrane lipids. Recent molecular simulations show that the close proximity of the membranes allows the lipids to splay, where a population of lipids insert their hydrophobic tails into the neighboring membrane – effectively keeping a "foot" in each membrane. The resolution of the splayed lipid state proceeds spontaneously to form the stalk structure. In this molecular view, the splayed-lipid intermediate state is the rate determining barrier rather than the formation of the stalk, which now becomes the free energy minimum. The energetic barrier for establishment of the splayed-lipid conformation is directly proportional to the intermembrane distance. The SNARE complexes and their pressing of the two membranes together, therefore, could provide the free energy required to overcome the barrier.[22]
The energy input that is required for SNARE-mediated fusion to take place comes from SNARE-complex disassembly. The suspected energy source isN-ethylmaleimide-sensitive factor (NSF), anATPase that is involved withmembrane fusion. NSF homohexamers, along with the NSFcofactorα-SNAP, bind and dissociate the SNARE complex by coupling the process withATP hydrolysis.[23] This process allows for reuptake ofsynaptobrevin for further use invesicles, whereas the other SNARE proteins remain associated with thecell membrane.
The dissociated SNARE proteins have a higher energy state than the more stablecis-SNARE complex. It is believed that the energy that drivesfusion is derived from the transition to a lower energycis-SNARE complex. The ATP hydrolysis-coupled dissociation of SNARE complexes is an energy investment that can be compared to "cocking the gun" so that, oncevesicle fusion is triggered, the process takes placespontaneously and at optimum velocity. A comparable process takes place in muscles, in which the myosin heads must first hydrolyzeATP in order to adapt the necessary conformation for interaction with actin and the subsequent power stroke to occur.
The Q-SNARE protein Synaptosomal-associated protein 25 (SNAP-25) is composed of twoα-helical domains connected by arandom coil linker. The random coil linker region is most notable for its fourcysteine residues.[24] The α-helical domains combine with those of bothsyntaxin andsynaptobrevin (also known asvesicle associated membrane protein or VAMP) to form the 4-α-helix coiled-coil SNARE complex critical to efficientexocytosis.
Whilesyntaxin andsynaptobrevin both containtransmembrane domains which allow for docking with target and vesiclemembranes respectively,SNAP-25 relies on thepalmitoylation ofcysteine residues found in its random coil region for docking to the target membrane. Some studies have suggested that association withsyntaxin via SNARE interactions precludes the need for such docking mechanisms.Syntaxinknockdown studies however, failed to show a decrease in membrane bound SNAP-25 suggesting alternate docking means exist.[25] Thecovalent bonding offatty acid chains to SNAP-25 viathioester linkages with one or morecysteine residues therefore, provides for regulation of docking and ultimately SNARE mediatedexocytosis. This process is mediated by a specialized enzyme calledDHHC palmitoyl transferase.[26] Thecysteine rich domain ofSNAP-25 has also been shown to weakly associate with theplasma membrane possibly allowing it to be localized near theenzyme for subsequentpalmitoylation. The reverse of this process is carried out by another enzyme calledpalmitoyl protein thioesterase (see figure).
The availability of SNAP-25 in the SNARE complex is also theorized to possibly be spatially regulated via localization oflipid microdomains in the target membrane. Palmitoylated cysteine residues could be localized to the desired target membrane region via a favorable lipid environment (possiblycholesterol rich) complementary to thefatty acid chains bonded to the cysteine residues of SNAP-25.[25]
As anaction potential reaches theaxon terminal,depolarization events stimulate the opening ofvoltage-gated calcium channels (VGCCs) allowing the rapid influx ofcalcium down itselectrochemical gradient. Calcium goes on to stimulateexocytosis via binding withsynaptotagmin 1.SNAP-25 however, has been shown to negatively regulateVGCC function inglutamatergic neuronal cells. SNAP-25 leads to a reduction ofcurrent density throughVGCC's and therefore a decrease in the amount ofcalcium that is binding thesynaptotagmin, causing a decrease in neuronalglutamatergicexocytosis. Conversely,underexpression of SNAP-25 allows for an increase in VGCC current density and increase in exocytosis.[27]
Further investigation has suggested possible relationships between SNAP-25 over/underexpression and a variety ofbrain diseases. Inattention-deficit/hyperactivity disorder or ADHD,polymorphisms at the SNAP-25gene locus in humans have been linked to the disease suggesting a potential role in its manifestation.[28] This is further suggested byheterogeneous SNAP-25knockout studies performed oncoloboma mutant mice, which led tophenotypic characteristics of ADHD.[29] Studies have also shown a correlation of SNAP-25 over/underexpression and the onset ofschizophrenia.[30][31]
Syntaxin consists of atransmembrane domain (TMD),alpha-helical SNARE domain, a short linker region, and the Habc domain which consists of three alpha-helical regions. The SNARE domain in syntaxin serves as a target site for docking ofSNAP-25 andsynaptobrevin in order to form the four helix bundle requisite to the SNARE complex and subsequentfusion. The Habc domain, however, serves as an autoinhibitory domain in syntaxin. It has been shown to fold over and associate with the SNARE domain of syntaxin inducing a "closed" state, creating a physical barrier to the formation of the SNAREmotif. Conversely, the Habc domain can again disassociate with the SNARE domain leaving syntaxin free to associate with bothSNAP-25 andsynaptobrevin.[32]
There is an immense diversity ofsyntaxin subtypes, with 15 varieties in the human genome.[33] It has been suggested thatsyntaxin1B has a role in regulating number of synaptic vesicles ready for exocytosis in the axon terminal. This is also called thereadily releasable pool (RRP) of vesicles. Aknock out study in 2014 showed that the lack of syntaxin1B led to a significant decrease in RRP size.[34]
Manyneurotoxins directly affect SNARE complexes. Such toxins as thebotulinum andtetanus toxins work by targeting the SNARE components. These toxins prevent proper vesicle recycling and result in poor muscle control, spasms, paralysis, and even death.
Botulinum Toxin (BoNT) is one of the most potent toxins to have ever been discovered.[35] It is a proteolytic enzyme that cleavesSNARE proteins inneurons. Itsprotein structure is composed of two peptide subunits, a heavy chain (100kDas) and a light chain (50kDas), which are held together by adisulfide bond. The action of BoNT follows a 4-step mechanism including binding to the neuronal membrane,endocytosis, membrane translocation, andproteolysis of SNARE proteins.[36]
In its mechanism of action, the heavy chain of BoNT is first used to find its neuronal targets and bind to the gangliosides and membrane proteins of presynaptic neurons. Next, the toxin is then endocytosed into the cell membrane. The heavy chain undergoes a conformational change important for translocating the light chain into thecytosol of the neuron. Finally, after the light chain of BoNT is brought into the cytosol of the targeted neuron, it is released from the heavy chain so that it can reach its active cleavage sites on the SNARE proteins.[36] The light chain is released from the heavy chain by the reduction of the disulfide bond holding the two together. The reduction of this disulfide bond is mediated by the NADPH-thioredoxin reductase-thioredoxin system.[38] The light chain of BoNT acts as ametalloprotease on SNARE proteins that is dependent on Zn(II) ions,[39] cleaving them and eliminating their function inexocytosis.
There are 8 known isotypes of BoNT, BoNT/A – BoNT/H, each with different specific cleavage sites on SNARE proteins.SNAP25, a member of the SNARE protein family located in the membrane of cells, is cleaved by BoNT isotypes A, C, and E. The cleavage of SNAP-25 by these isotypes of BoNT greatly inhibits their function in forming the SNARE complex for fusion of vesicles to the synaptic membrane. BoNT/C also targetsSyntaxin-1, another SNARE protein located in the synaptic membrane. It degenerates these Syntaxin proteins with a similar outcome as with SNAP-25. A third SNARE protein,Synaptobrevin (VAMP), is located on cellvesicles.VAMP2 is targeted and cleaved by BoNT isotypes B, D, and F in synaptic neurons.[35] The targets of these various isotypes of BoNT as well as Tetanus Neurotoxin (TeNT) are shown in the figure to the right.
In each of these cases, Botulinum Neurotoxin causes functional damage to SNARE proteins, which has significant physiological and medical implications. By damaging SNARE proteins, the toxin preventssynaptic vesicles from fusing to the synaptic membrane and releasing theirneurotransmitters into thesynaptic cleft. With the inhibition of neurotransmitter release into the synaptic cleft,action potentials cannot be propagated to stimulate muscle cells. This result inparalysis of those infected and in serious cases, it can cause death. Although the effects of Botulinum Neurotoxin can be fatal, it has also been used as a therapeutic agent in medical and cosmetic treatments.[40][41]
Tetanus toxin, or TeNT, is composed of a heavy chain (100KDa) and a light chain (50kDa) connected by adisulfide bond. The heavy chain is responsible for neurospecific binding of TeNT to the nerve terminal membrane,endocytosis of the toxin, andtranslocation of the light chain into the cytosol. The light chain has zinc-dependentendopeptidase or more specificallymatrix metalloproteinase (MMP) activity through which cleaveage ofsynaptobrevin or VAMP is carried out.[42]
For the light chain of TeNT to be activated one atom ofzinc must be bound to every molecule of toxin.[43] When zinc is boundreduction of the disulfide bond will be carried out primarily via theNADPH-thioredoxin reductase-thioredoxin redox system.[44] Then the light chain is free to cleave the Gln76-Phe77 bond of synaptobrevin.[42] Cleavage of synaptobrevin affects the stability of the SNARE core by restricting it from entering the low energy conformation which is the target forNSF binding.[45] This cleavage of synaptobrevin is the final target of TeNT and even in low doses the neurotoxin will inhibit neurotransmitterexocytosis.
Neurotransmitters are stored inreadily releasable pools ofvesicles confined within thepresynaptic terminal. Duringneurosecretion/exocytosis, SNAREs play a crucial role in vesicle docking, priming, fusion, and synchronization of neurotransmitter release into thesynaptic cleft.
The first step in synaptic vesicle fusion is tethering, where the vesicles are translocated from thereserve pool into physical contact with the membrane. At the membrane,Munc-18 is initially bound tosyntaxin 1A in a closed structure. It is postulated that the dissociation of Munc-18 from the complex frees syntaxin 1A to bind with the v-SNARE proteins.[46] The next step in release is the docking of vesicles, where the v- and t-SNARE proteins transiently associate in a calcium-independent manner. The vesicles are then primed, wherein the SNAREmotifs form a stable interaction between the vesicle and membrane.Complexins stabilize the primed SNARE-complex rendering the vesicles ready for rapid exocytosis.
The span of presynaptic membrane containing the primed vesicles and dense collection of SNARE proteins is referred to as theactive zone.Voltage-gated calcium channels are highly concentrated around active zones and open in response to membranedepolarization at the synapse. The influx of calcium is sensed bysynaptotagmin 1, which in turn dislodges complexin protein and allows the vesicle to fuse with the presynaptic membrane to release neurotransmitter. It has also been shown that the voltage-gated calcium channels directly interact with the t-SNAREs syntaxin 1A and SNAP-25, as well as with synaptotagmin 1. The interactions are able to inhibit calcium channel activity as well as tightly aggregate the molecules around the release site.[47]
There have been many clinical cases that link SNARE genes with neural disorders. Deficiency in SNAP-25mRNA has been observed inhippocampal tissue of someschizophrenic patients, a SNAP-25single-nucleotide polymorphism is linked to hyperactivity inautism-spectrum disorders, and overexpression ofSNAP-25B leads to the early onset ofbipolar disorder.[47]
Macroautophagy is acatabolic process involving the formation of double-membrane boundorganelles calledautophagosomes, which aid in degradation of cellular components through fusion withlysosomes. Duringautophagy, portions of thecytoplasm are engulfed by a cup-shaped double-membrane structure called a phagophore and eventually become the contents of the fully assembled autophagosome. Autophagosome biogenesis requires the initiation and growth of phagophores, a process that was once thought to occur through de novo addition of lipids. However, recent evidence suggests that the lipids that contribute to the growing phagophores originate from numerous sources of membrane, includingendoplasmic reticulum,Golgi,plasma membrane, andmitochondria.[48] SNAREs play important roles in mediating vesicle fusion during phagophore initiation and expansion as well as autophagosome-lysosome fusion in the later stages of autophagy.
Though the mechanism of phagophore initiation in mammals is unknown, SNAREs have been implicated in phagophore formation through homotypic fusion of small,clathrin-coated, single-membrane vesicles containing Atg16L, the v-SNAREVAMP7, and its partner t-SNAREs:Syntaxin-7,Syntaxin-8, andVTI1B.[49] In yeast, the t-SNAREs Sec9p and Sso2p are required for exocytosis and promote tubulovesicular budding of Atg9 positive vesicles, which are also required for autophagosome biogenesis.[50][51] Knocking out either of these SNAREs leads to accumulation of small Atg9 containing vesicles that do not fuse, therefore preventing the formation of the pre-autophagosomal structure.[51]
In addition to phagophore assembly, SNAREs are also important in mediating autophagosome-lysosome fusion. In mammals, the SNAREsVAMP7,VAMP8, andVTI1B are required in autophagosome-lysosome fusion and this process is impaired in lysosomal storage disorders where cholesterol accumulates in the lysosome and sequesters SNAREs in cholesterol rich regions of the membrane preventing their recycling.[52] Recently, syntaxin 17 (STX17) was identified as an autophagosome associated SNARE that interacts with VAMP8 andSNAP29 and is required for fusion with the lysosome.[53] STX17 is localized on the outer membrane of autophagosomes, but not phagophores or other autophagosome precursors, which prevents them from prematurely fusing with the lysosome.[53] In yeast, the fusion of autophagosomes with vacuoles (the yeast equivalent of lysosomes) requires SNAREs and related proteins such as the syntaxin homolog Vam3, SNAP-25 homolog Vam7, Ras-like GTPase Ypt7, and the NSF ortholog, Sec18.[48]
Several complexes are known to flexibly substitute one protein for another: Two Qa-SNAREs in yeasts can substitute for each other to some degree. Yeasts which lose the R-SNARE -Sec22p - automatically increase levels of ahomolog -Ykt6p - and use it the same way. AlthoughDrosophilae cannot survive the loss of theSNAP-25 component,SNAP-24 can fully replace it. And also inDrosophila, an R-SNARE not normally found insynapses can substitute forsynaptobrevin.[6]
SNAREs also occur in plants, where they are essential forvesicle transport to and from ER, Golgi, trans-Golgi network/early endosome, plasma membrane and vacuole.[54]
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