During the last few years there have been advances in our understanding of the functions of SNARE proteins, especially in the membrane fusion and vesicle transport pathways. However, the functional redundancy between SNAREs makes it hard to define precisely their fusion specificity in relation to specific cellular or developmental events. For example, functional redundancy exists between VTI11 and VTI12 [54, 55], SYP121 and SYP122 [56, 57], and VAMP721 and VAMP722 R-SNAREs [28]. Homozygous double mutants of each show embryo lethal or severe growth defects, but single gene knockout mutations do not show any obvious phenotypes. SYP22 and SYP23 [58], VAMP711, VAMP712 and VAMP713 [59] may either form distinct SNARE complexes or they could have overlapping functions for specific developmental roles. The redundancy between SNAREs makes it difficult to identify specific SNARE functions if we use traditional experimental approaches [60].
Our phylogenetic analysis provides insights into patterns and drivers of SNARE family gene diversification across green plants. Each SNARE class could be broken down into subclades, many of which had genes representating all studied species, attesting to their ancient evolutionary origins. Some sets of homologous genes including: Qa-SYP32, SYP42, SYP81; Qb-SEC20, GOS12, MEMB12, VTI14, NPSN13; Qc-SYP61, SYP73, BS14a, USE11, SFT11; Qb+c-SNAP29 and R-SEC22, YKT62, VAMP714, VAMP727 are found in all angiosperms examined, and also in the chlorophyte algae, indicating that this complex was inherited vertically through the green plant lineage [12]. Many of these subclades were diverse, with relatively high numbers of gene duplications is some species. Species specific gene duplications frequently occurred in higher plants. It has also been pointed out that a large number of SNAREs, and particularly the SYP1 and VAMP7 SNARE clades, has appeared during the evolution of multicellular green plants, with a similar story for syntaxins in higher animals [12]. Therefore one reason for the diversification of SNAREs be related to the increased complexity of inter- and intracellular communication systems that are associated with multicellularity. For other SNARE classes, for example Qa-SNAREs, it is less clear why basal green plants such as moss have species-specific subclades with as many as 7 genes. Understanding these phylogenetic relationships will help address our understanding of the evolution of SNARE function. Gene duplications in Arabidopsis seem to be more associated with sub-functionalization to different tissue types as neo-functionalization in terms of the accumulation of amino acid changes.
However, some valuable functional information is available. Depending on the specific intracellular trafficking process, different v-/t-SNARE complexes are correspondingly formed [18]. This specificity of t-SNARE and v-SNARE complex formation ensures that vesicles are targeted to the correct compartment and induce membrane fusion [61]. For example, SYP111 takes part in membrane fusion events forming the cell plate and the transport of secretory vesicles at the plasma membrane [34, 62–64]. SYP122 plays a role in cell wall deposition and in tethering of donor and target membrane [65]. SYP81, SYP31, SYP32, GOS11, GOS12, MEMB11, SFT11, SFT12, BS14a, BS14b, SEC22, YKT61 and YKT62 mediate anterograde traffic between ER and Golgi and retrograde traffic within the Golgi apparatus [5, 48, 66–71]. SEC20, MEMB12, USE11, USE12, SYP71, SYP72 and SYP73 mediate retrograde traffic from Golgi to ER for protein recycling and balance maintenance [12, 29, 72–75]. SYP51 and SYP52 take part in direct membrane transport from ER to tonoplast and Golgi to mediate vesicle trafficking [76, 77]. VAMP714 interacts with SYP121 and SYP22 to mediate vesicle transport from the Golgi apparatus to the vacuole [78, 79].
Furthermore, Q-SNAREs have roles as key proteins in gravitropic responses (VTI11, VTI14) [27, 54], in cytokinesis (SYP31, SYP32, NPSN11, NPSN12, NPSN13) [4, 10, 80–82], in auxin homeostasis (VTI11, SYP41, SYP42, SYP43) [83–88], and in cell plate formation and pathogen resistance (SYP121, SYP131, SYP132, SNAP33) [35, 37, 56, 89–95].
SYP121 mediates vesicle fusion at the Arabidopsis plasma membrane, and binds the K+ channels voltage sensors to coordinate membrane trafficking with K+ uptake for growth [96]. Karnik et al. [30, 97, 98] and Zhang et al. [99] found that SM protein SEC11 binds and selectively regulates secretory traffic mediated by N terminus of SYP121 and is important for assembling and recycling of the SNARE during membrane fusion. And Sec1/Munc18 proteins interact with some SNARE proteins form the exocyst complex, which initiates membrane fusion [100, 101]. Moreover, Waghmare et al. [42] found that the membrane traffic mediated by SYP121 and SYP122 is associated differentially with lots of cargo proteins. Xue et al. [26] found that VAMP711 regulates ABA-mediated inhibition of PM H+-ATPase activity and drought stress response by regulating stoma closure. Zhang et al. [19, 64] found that VAMP721 and VAMP722 interact with the same K+ channels and that this interaction suppresses channel activity, and VAMP721 assembles with SYP121 to coordinate K+ channel gating during SNARE assembly and vesicle fusion. Kim et al. [102] found that CALRETICULIN 1 (CRT1) and CRT2 are critical components in the accumulation of VAMP721 and VAMP722 during ER stress responses. Zhang et al. [103] found that SYP22 and VAMP727 mediate the BRI trafficking to PM.
These studies show that SNARE proteins likely function in trafficking at most membranes, but especially at the vacuole and plasma membrane. And VAMP727 forms a complex with SYP22, VTI11, SYP121 and SYP51 to drive membrane fusion and vesicle transport pathways between PVCs and vacuoles [32, 33, 104]. Löfke et al. [88] found that auxin can increase the amount of SNARE proteins in the vacuolar membrane. Shirakawa et al. [105] found that SYP22 functions in the polarized localization of the auxin efflux carrier PIN1 in the Arabidopsis leaf. Xia et al. [106] found that SYP132 and associated endocytosis play significant roles in auxin-regulated H+-ATPase traffic and associated functions at the plasma membrane. Moreover, we have recently found that AtVAMP714 is also required for the exocytic localization of PIN1 and PIN2 proteins to the plasmamembrane via the Golgi, and for polar auxin transport; and the related genes VAMP711, VAMP712 and VAMP713 are also inducible by auxin [107].