ROOT OF THE UNIVERSAL TREE OF LIFE BASED ON ANCIENT AMINOACYL-TRANSFER-RNA SYNTHETASE GENE DUPLICATIONS

Universal trees based on sequences of single gene homologs cannot be r ooted, Iwabe ef al, [Iwabe, N., Kuma, K.-I., Hasegawa, M., Osawa, S. a nd Miyata a, T. (1989) Proc. Natl. Acad. Sci. USA 86, 9355-9359] circu mvented this problem by using ancient gene duplications that predated the last common ancestor of all living things. Their separate, recipro cally rooted gene trees for elongation factors and ATPase subunits sho wed Bacteria (eubacteria) as branching first from the universal tree w ith Archaea (archaebacteria) and Eucarya (eukaryotes) as sister groups , Given its topical importance to evolutionary biology and concerns ab out the appropriateness of the ATPase data set, an evaluation of the u niversal tree root using other ancient gene duplications is essential. In this study, we derive a rooting for the universal tree using amino acyl-tRNA synthetase genes, an extensive multigene family whose diverg ence likely preceded that of prokaryotes and eukaryotes. An approximat ely 1600-bp conserved region was sequenced from the isoleucyl-tRNA syn thetases of several species representing deep evolutionary branches of eukaryotes (Nosema locustae), Bacteria (Aquifex pyrophilus and Thermo toga maritima) and Archaea (Pyrococcus furiosus and Sulfolobus acidoca ldarius). In addition, a new valyl-tRNA synthetase was characterized f rom the protist Trichomonas vaginalis. Different phylogenetic methods were used to generate trees of isoleucyl-tRNA synthetases rooted by va lyl- and leucyl-tRNA synthetases. All isoleucyl-tRNA synthetase trees showed Archaea and Eucarya as sister groups, providing strong confirma tion for the universal tree rooting reported by Iwabe ct al. As well, there was strong support for the monophyly (sensu Hennig) of Archaea, The valyl-tRNA synthetase gene from Tr. vaginalis clustered with other eukaryotic ValRS genes, which may have been transferred from the mito chondrial genome to the nuclear genome, suggesting that this amitochon drial trichomonad once harbored an endosymbiotic bacterium.