Hierarchical evolution of endosomal trafficking proteins reveals conserved catalytic cores and lineage-specific divergent regulatory layers across eukaryotes

Abstract

Membrane trafficking proteins are essential for organelle communication. However, whether different functional classes evolve under distinct evolutionary pressures remains unclear. In order to investigate this, eight protein families (ESCRT-0, ESCRT-I, ESCRT-II, ESCRT-III, Rab GTPases, VPS4, SNAREs and tetraspanins) were taken across Saccharomyces cerevisiae, Arabidopsis thaliana and Homo sapiens. Sequence identity, domain architecture, motif conservation, phylogenetic relationship, structural overlays and intrinsic disorder patterns were inspected to find out which features remain conserved and which are not. The investigation showed a clear hierarchy where the catalytic proteins (Rab GTPases, VPS4) showed high sequence identity, near perfect motif conservation along with strong structural similarity. However, structural proteins (ESCRT-I, II, III and SNAREs) showed moderate conservation with preserved folds despite sequence divergence. And finally the regulatory adaptor proteins (ESCRT-0, tetraspanins) showed the greatest divergence, including missing domains, very low sequence identity, and increased disorder. These results from our investigation led us to believe that conservation in the membrane trafficking systems is not uniform. Rather, it follows a hierarchy in which it offers compensation in the structural and adaptor regions while remaining highly conserved for the catalytic roles.