Aravind L, Iyer Lakshminarayan M, Koonin Eugene V
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
Curr Opin Struct Biol. 2006 Jun;16(3):409-19. doi: 10.1016/j.sbi.2006.04.006. Epub 2006 May 5.
Eukaryotes encode numerous proteins that either have no detectable homologs in prokaryotes or have only distant homologs. These molecular innovations of eukaryotes may be classified into three categories: proteins and domains inherited from prokaryotic precursors without drastic changes in biochemical function, but often recruited for novel roles in eukaryotes; new superfamilies or distinct biochemical functions emerging within pre-existing protein folds; and domains with genuinely new folds, apparently 'invented' at the outset of eukaryotic evolution. Most new folds emerging in eukaryotes are either alpha-helical or stabilized by metal chelation. Comparative genomics analyses point to an early phase of rapid evolution, and dramatic changes between the origin of the eukaryotic cell and the advent of the last common ancestor of extant eukaryotes. Extensive duplication of numerous genes, with subsequent functional diversification, is a distinctive feature of this turbulent era. Evolutionary analysis of ancient eukaryotic proteins is generally compatible with a two-symbiont scenario for eukaryotic origin, involving an alpha-proteobacterium (the ancestor of the mitochondria) and an archaeon, as well as key contributions from their selfish elements.
真核生物编码了许多蛋白质，这些蛋白质在原核生物中要么没有可检测到的同源物，要么只有远缘同源物。真核生物的这些分子创新可分为三类：从原核生物前体继承而来的蛋白质和结构域，其生化功能没有剧烈变化，但通常在真核生物中被赋予了新的功能；在已有的蛋白质折叠中出现的新超家族或独特的生化功能；以及具有全新折叠的结构域，显然是在真核生物进化之初“发明”的。真核生物中出现的大多数新折叠要么是α螺旋结构，要么是通过金属螯合稳定的。比较基因组学分析表明，在真核细胞起源和现存真核生物的最后一个共同祖先出现之间，存在一个快速进化的早期阶段以及巨大变化。众多基因的广泛复制以及随后的功能多样化，是这个动荡时期的一个显著特征。对古代真核生物蛋白质的进化分析总体上与真核生物起源的双共生体假说相符，该假说涉及一种α变形菌（线粒体的祖先）和一个古菌，以及它们自私元件的关键贡献。
