Neofunctionalization of VAMP7 opened up a plant-unique vacuolar transport pathway

Each eukaryotic cell possesses a specialized membrane trafficking system that emerged through paralogous expansion followed by the neofunctionalization of trafficking machinery components, including soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) proteins, during evolution. We discovered that the acquisition of an acidic insertion in the polypeptide converted the secretory R-SNARE vesicle-associated membrane protein (VAMP)72 into a major component of plant vacuolar transport. The moderately acidic insertion, originating from alternative splicing in the common ancestor of zygnematophytes and embryophytes, conferred binding ability to the clathrin adapter protein complex-4 (AP-4) at the trans-Golgi network (TGN), partially redirecting the VAMP72 protein from the secretory to the vacuolar transport pathway. Increased acidity of the insertion in angiosperms further reinforced the interaction with AP-4, leading VAMP727 to discrete zoning during sorting at the TGN and a definitive conversion to endosomal localization. This stepwise neofunctionalization of VAMP72 provided an option for the development of the intricate and complex vacuolar transport system in extant angiosperms.