Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, 80309-0347, USA.
J Mol Evol. 2021 Feb;89(1-2):19-44. doi: 10.1007/s00239-020-09983-9. Epub 2021 Jan 24.
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.
一个近乎普遍的标准遗传密码（SGC）意味着现在地球上生命只有一个起源。为了研究这一独特的事件，我计算了通向 SGC 的路径，比较了不同的可能历史。值得注意的是，SGC 样编码是从传统的进化机制中产生的，并且可以确定一个优越的途径。为了客观地衡量进化，从 0（随机编码）到 1（SGC 样）定义了进展值：这些值衡量随机编码到 SGC 距离的分数。进展类型是间隔/距离/差异极性要求，分别检测相同分配之间的空间/到 SGC 的突变距离/化学顺序。编码系统基于选择的 RNA 执行氨酰-RNA 合成酶反应。受体 RNA 表现出 SGC 样克里克摆动；或者，非摆动三联体独特地编码 20 种氨基酸/起始/停止。三联体通过立体化学、选择、共进化或随机获得 22 种功能。分配也通过单突变传播到被分配的三联体的邻域，但也可以衰减。一个巨大的代码宇宙使徒劳的进化路径丰富。因此，SGC 进化对随机分配的无序非常敏感。进化也不可避免地在接近编码完成时减缓。SGC 可能避免了这些困难，并且比较了两种合适的路径。在晚期摆动中，在采用摆动之前，大多数非摆动分配都已经完成。在连续摆动中，一个独特的有利早期中间产物产生有序的 SGC。经过修正的编码进化（有限的随机性、晚期摆动、集中于氨基酸编码、与化学有序的精英进行化学保守共进化）产生了具有极好联合进展值的各种完整代码。只有 600 个独立编码表的种群包括 SGC 样成员；一种更准确的 SGC 进化的贝叶斯路径是可用的。
