Abstract
Eukaryotic cells have two categories of transport factors. One is the membranous transport factor, which is involved in the cross-membrane transport pathways. The other is the non-membranous transport factor, which is not involved in such cross-membrane transport pathways. The evolutionary functional differentiation and the natural selection of the transport factor genes might have been played an important role for the advancement of cellular structures and the diversification of cellular functions of eukaryotic cells. In this study, with the aim of elucidating the evolution of the intracellular protein transport machinery, we estimate the nucleotide substitution rates and construct the molecular phylogenetic tree of the transport factor genes. As a result, it is possible that the membranous transport factor genes are under much stronger purifying selection than the non-membranous ones. Based on this result, we will discuss about the evolution of the intracellular protein transport machinery.