Phylogenetic Analysis of the vesicular fusion SNARE machinery revealing its functional divergence across Eukaryotes

Proteins of the SNARE (Soluble N-ethylmaleimide-sensitive factor attachment protein receptors) family play a significant role in all vesicular fusion events involved in endocytic and exocytic pathways. These proteins act as molecular machines that assemble into tight four-helix bundle complex, bridging the opposing membranes into close proximity forming membrane fusion. Almost all SNARE proteins share a 53 amino acid coiled-coil domain, which is mostly linked to the transmembrane domain at the C-terminal end. Despite significant variations between SNARE sequences across species, the SNARE mediated membrane fusion is evolutionary conserved in all eukaryotes. It is of interest to compare the functional divergence of SNARE proteins across various eukaryotic groups during evolution. Here, we report an exhaustive phylogeny of the SNARE proteins retrieved from SNARE database including plants, animals, fungi and protists. The Initial phylogeny segregated SNARE protein sequences into five well-supported clades Qa, Qb, Qc, Qbc and R reflective of their positions in the four-helix SNARE complex. Further to improve resolution the Qa, Qb, Qc and R family specific trees were reconstructed, each of these were further segregated into organelle specific clades at first and later diverged into lineage specific subgroups. This revealed that most of the SNARE orthologs are conserved at subcellular locations or at trafficking pathways across various species during eukaryotic evolution. The paralogous expansion in SNARE repertoire was observed at metazoans (animals) and plants independently during eukaryotic evolution. However, results also show that the multi-cellular and saprophytic fungi have limited SNAREs.