Phylogenetic analysis of components of the eukaryotic vesicle transport system reveals a common origin of adaptor protein complexes 1, 2, and 3 and the F subcomplex of the coatomer COPI

Eukaryotic vesicular transport requires the recognition of membranes throug h specific protein complexes. The heterotetrameric adaptor protein complexe s 1, 2, and 3 (AP1/2/3) are composed of two large, one small, and one mediu m adaptin subunit. We isolated and characterized the cDNA for Arabidopsis g amma-adaptin and performed a phylogenetic analysis of all adaptin subunits (proteins) in the context of all known homologous proteins. This analysis r evealed (i) that the large subunits of AP1/2/3 are homologous and (ii) two subunits of the heptameric coatomer I(COPI) complex belong to this gene fam ily. In addition, all small subunits and the aminoterminal domain of the me dium subunits of the heterotetramers are homologous to each other; this als o holds for two corresponding subunits of the COPI complex. AP1/2/3 and a s ubstructure (heterotetrameric, F-COPI subcomplex) of the heptameric COPI ha d a common ancestral complex (called pre-F-COPI). Since all large and all s mall/medium subunits share sequence similarity, the ancestor of this comple x is inferred to have been a heterodimer composed of one large and one smal l subunit. The situation encountered today is the result of successive roun ds of coordinated gene duplications of both the large and the small/medium subunits, with F-COPI being the first that separated from the ancestral pre -F-COPI.