Seligmann Hervé
Unité de Recherche sur les Maladies Infectieuses et Tropicales Émergentes, Faculté de Médecine, URMITE CNRS-IRD 198 UMER 6236, Université de la Méditerranée, Marseille, France.
Biosystems. 2015 Mar;129:36-43. doi: 10.1016/j.biosystems.2015.01.003. Epub 2015 Jan 16.
Punctuation codons (starts, stops) delimit genes, reflect translation apparatus properties. Most codon reassignments involve punctuation. Here two complementary approaches classify natural genetic codes: (A) properties of amino acids assigned to codons (classical phylogeny), coding stops as X (A1, antitermination/suppressor tRNAs insert unknown residues), or as gaps (A2, no translation, classical stop); and (B) considering only punctuation status (start, stop and other codons coded as -1, 0 and 1 (B1); 0, -1 and 1 (B2, reflects ribosomal translational dynamics); and 1, -1, and 0 (B3, starts/stops as opposites)). All methods separate most mitochondrial codes from most nuclear codes; Gracilibacteria consistently cluster with metazoan mitochondria; mitochondria co-hosted with chloroplasts cluster with nuclear codes. Method A1 clusters the euplotid nuclear code with metazoan mitochondria; A2 separates euplotids from mitochondria. Firmicute bacteria Mycoplasma/Spiroplasma and Protozoan (and lower metazoan) mitochondria share codon-amino acid assignments. A1 clusters them with mitochondria, they cluster with the standard genetic code under A2: constraints on amino acid ambiguity versus punctuation-signaling produced the mitochondrial versus bacterial versions of this genetic code. Punctuation analysis B2 converges best with classical phylogenetic analyses, stressing the need for a unified theory of genetic code punctuation accounting for ribosomal constraints.
标点密码子（起始密码子、终止密码子）界定基因，反映翻译装置的特性。大多数密码子重新分配都涉及标点。本文采用两种互补方法对天然遗传密码进行分类：（A）分配给密码子的氨基酸特性（经典系统发育），将终止密码子编码为X（A1，抗终止/抑制性tRNA插入未知残基），或编码为空位（A2，无翻译，经典终止）；以及（B）仅考虑标点状态（起始、终止和其他密码子分别编码为-1、0和1（B1）；0、-1和1（B2，反映核糖体翻译动力学）；以及1、-1和0（B3，起始/终止为相反状态））。所有方法都能将大多数线粒体密码与大多数核密码区分开来；纤细杆菌始终与后生动物线粒体聚类；与叶绿体共宿主的线粒体与核密码聚类。方法A1将真核生物核密码与后生动物线粒体聚类；A2将真核生物与线粒体分开。厚壁菌门细菌支原体/螺旋体和原生动物（及低等后生动物）线粒体共享密码子-氨基酸分配。A1将它们与线粒体聚类，在A2下它们与标准遗传密码聚类：氨基酸歧义性与标点信号的限制产生了这种遗传密码的线粒体版本和细菌版本。标点分析B2与经典系统发育分析的收敛性最佳，强调需要一种统一的遗传密码标点理论来解释核糖体的限制。
