Root of the universal tree of life based on ancient aminoacyl-tRNA synthetase gene duplications.

Universal trees based on sequences of single gene homologs cannot be rooted. Iwabe et al. [Iwabe, N., Kuma, K.-I., Hasegawa, M., Osawa, S. & Miyata, T. (1989) Proc. Natl. Acad. Sci. USA 86, 9355-9359] circumvented this problem by using ancient gene duplications that predated the last common ancestor of all living things. Their separate, reciprocally rooted gene trees for elongation factors and ATPase subunits showed Bacteria (eubacteria) as branching first from the universal tree with Archaea (archaebacteria) and Eucarya (eukaryotes) as sister groups. Given its topical importance to evolutionary biology and concerns about the appropriateness of the ATPase data set, an evaluation of the universal tree root using other ancient gene duplications is essential. In this study, we derive a rooting for the universal tree using aminoacyl-tRNA synthetase genes, an extensive multigene family whose divergence likely preceded that of prokaryotes and eukaryotes. An approximately 1600-bp conserved region was sequenced from the isoleucyl-tRNA synthetases of several species representing deep evolutionary branches of eukaryotes (Nosema locustae), Bacteria (Aquifex pyrophilus and Thermotoga maritima) and Archaea (Pyrococcus furiosus and Sulfolobus acidocaldarius). In addition, a new valyl-tRNA synthetase was characterized from the protist Trichomonas vaginalis. Different phylogenetic methods were used to generate trees of isoleucyl-tRNA synthetases rooted by valyl- and leucyl-tRNA synthetases. All isoleucyl-tRNA synthetase trees showed Archaea and Eucarya as sister groups, providing strong confirmation for the universal tree rooting reported by Iwabe et 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 mitochondrial genome to the nuclear genome, suggesting that this amitochondrial trichomonad once harbored an endosymbiotic bacterium. IMAGES:

基于单基因同源序列构建的通用系统发育树无法进行定根（rooting）。Iwabe等人[Iwabe, N., Kuma, K.-I., Hasegawa, M., Osawa, S. & Miyata, T. (1989) 美国国家科学院院刊, 86卷, 9355-9359页]通过利用早于所有生物最后共同祖先的古老基因重复事件规避了这一难题。他们针对延伸因子与ATP酶（ATPase）亚基构建的独立且互为定根的基因树显示，细菌（Bacteria，即真细菌eubacteria）率先从通用系统发育树中分支而出，古菌（Archaea，即古细菌archaebacteria）与真核生物（Eucarya，即真核生物eukaryotes）则构成姊妹群。鉴于该研究方向对进化生物学的重要价值，以及学界对ATP酶数据集适用性的担忧，利用其他古老基因重复事件对通用系统发育树开展定根评估实属必要。本研究利用氨酰-tRNA合成酶（aminoacyl-tRNA synthetase）基因推导得到通用系统发育树的定根方案；该基因家族属于庞大的多基因家族，其分化事件很可能早于原核生物与真核生物的分化。本研究对代表真核生物、细菌与古菌三大类群深层进化分支的多个物种的异亮氨酰-tRNA合成酶（isoleucyl-tRNA synthetase）基因进行测序，获得了一段长约1600 bp的保守区域。其中真核生物代表为Nosema locustae，细菌代表为Aquifex pyrophilus与Thermotoga maritima，古菌代表为Pyrococcus furiosus与Sulfolobus acidocaldarius。此外，本研究还对原生生物Trichomonas vaginalis（阴道毛滴虫）的新型缬氨酰-tRNA合成酶（valyl-tRNA synthetase）进行了功能鉴定。本研究采用多种系统发育分析方法，以缬氨酰-tRNA合成酶与亮氨酰-tRNA合成酶作为外类群，对异亮氨酰-tRNA合成酶构建系统发育树。所有异亮氨酰-tRNA合成酶系统发育树均显示古菌与真核生物为姊妹群，这为Iwabe等人提出的通用系统发育树定根方案提供了强有力的支持证据。同时，本研究也为古菌的单系群（monophyly，遵循亨尼希（Hennig）的分类学定义）属性提供了强有力的支持。来自阴道毛滴虫的缬氨酰-tRNA合成酶基因与其他真核生物的ValRS基因聚为一支，该基因可能从线粒体基因组转移至核基因组，这表明这种无线粒体的毛滴虫曾携带内共生细菌。附图：