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Evolution of the Standard Genetic Code
Journal of Molecular Evolution ( IF 2.1 ) Pub Date : 2021-01-24 , DOI: 10.1007/s00239-020-09983-9
Michael Yarus 1
Affiliation  

A near-universal Standard Genetic Code (SGC) implies a single origin for present Earth life. To study this unique event, I compute paths to the SGC, comparing different plausible histories. Notably, SGC-like coding emerges from traditional evolutionary mechanisms, and a superior route can be identified. To objectively measure evolution, progress values from 0 (random coding) to 1 (SGC-like) are defined: these measure fractions of random-code-to-SGC distance. Progress types are spacing/distance/delta Polar Requirement, detecting space between identical assignments/mutational distance to the SGC/chemical order, respectively. The coding system is based on selected RNAs performing aminoacyl-RNA synthetase reactions. Acceptor RNAs exhibit SGC-like Crick wobble; alternatively, non-wobbling triplets uniquely encode 20 amino acids/start/stop. Triplets acquire 22 functions by stereochemistry, selection, coevolution, or at random. Assignments also propagate to an assigned triplet’s neighborhood via single mutations, but can also decay. A vast code universe makes futile evolutionary paths plentiful. Thus, SGC evolution is critically sensitive to disorder from random assignments. Evolution also inevitably slows near coding completion. The SGC likely avoided these difficulties, and two suitable paths are compared. In late wobble, a majority of non-wobble assignments are made before wobble is adopted. In continuous wobble, a uniquely advantageous early intermediate yields an ordered SGC. Revised coding evolution (limited randomness, late wobble, concentration on amino acid encoding, chemically conservative coevolution with a chemically ordered elite) produces varied full codes with excellent joint progress values. A population of only 600 independent coding tables includes SGC-like members; a Bayesian path toward more accurate SGC evolution is available.



中文翻译:

标准遗传密码的演变

近乎通用的标准遗传密码 (SGC) 暗示了当前地球生命的单一起源。为了研究这个独特的事件,我计算了 SGC 的路径,比较了不同的似是而非的历史。值得注意的是,类 SGC 编码是从传统的进化机制中出现的,并且可以确定一条优越的路线。为了客观地测量进化,定义了从 0(随机编码)到 1(类 SGC)的进度值:这些测量随机代码到 SGC 距离的分数。进展类型间隔/距离/ d ELTA P OLAR ř要求,分别检测到 SGC/化学顺序的相同分配/突变距离之间的空间。编码系统基于进行氨酰-RNA 合成酶反应的选定RNA。受体 RNA 表现出类似 SGC 的克里克摆动;或者,非摆动三元组独特地编码 20 个氨基酸/起始/终止。三胞胎通过立体化学、选择、共同进化或随机获得 22 种功能。分配也通过单个突变传播到分配的三元组的邻域,但也可以衰减。一个庞大的代码世界使徒劳的进化路径变得丰富。因此,SGC 进化对随机分配的无序非常敏感。进化在接近编码完成时也不可避免地变慢。SGC 可能避免了这些困难,并比较了两条合适的路径。在晚摇,大多数非摆动分配是在采用摆动之前进行的。在连续摆动中,独特有利的早期中间体产生有序的 SGC。修改后的编码进化(有限的随机性、晚期摆动、氨基酸编码的集中、与化学有序精英的化学保守共同进化)产生具有优异联合进展值的各种完整代码。仅有 600 个独立编码表的总体包括类 SGC 成员;可以获得更准确的 SGC 进化的贝叶斯路径。

更新日期:2021-01-24
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