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Evolution of the standard genetic code
bioRxiv - Molecular Biology Pub Date : 2020-10-09 , DOI: 10.1101/2020.02.20.958546
Michael Yarus

A near-universal Standard Genetic Code (SGC) implies a single origin for Earthly 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 path 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. A coding system was based on known RNAs performing aminoacyl-RNA synthetase reactions. Acceptor RNAs exhibit SGC-like wobble; alternatively, non-wobbling triplets uniquely encode 20 amino acids/start/stop. Triplets acquire 22 functions by stereochemistry, selection, coevolution, or randomly. Assignments also propagate to an assigned triplets neighborhood via single mutations, but can also decay. Futile evolutionary paths are plentiful due to the vast code universe. Thus SGC evolution is critically sensitive to disorder from random assignments. Evolution also inevitably slows near coding completion. Coding 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 supplies the gateway to 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)暗示着地球生命的单一起源。为了研究这个独特的事件,我计算了到SGC的路径,比较了不同的合理历史。值得注意的是,类似SGC的编码是从传统的进化机制中出现的,并且可以找到一条更好的途径。为了客观地衡量演进,定义了从0(随机编码)到1(类似于SGC)的进度值:这些度量了随机码到SGC距离的分数。进度类型是间距/距离/增量极地要求,分别检测相同分配之间的间距/到SGC /化学顺序的突变距离。编码系统基于进行氨酰基-RNA合成酶反应的已知RNA。受体RNA表现出类似SGC的摆动;或者,不摇动的三胞胎唯一编码20个氨基酸/起始/终止。三联体通过立体化学,选择,协同进化或随机获得22种功能。分配还会通过单个突变传播到分配的三元组邻域,但也会衰减。由于广阔的代码领域,无用的进化途径很多。因此,SGC进化对随机分配的疾病极为敏感。演进也不可避免地会减慢编码完成的速度。编码可能避免了这些困难,并比较了两个合适的路径。在后期摆动中,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,一个独特的优势是,早期的中间设备将网关提供给有序的SGC。修订的编码演变(有限的随机性,后期摆动,对氨基酸编码的集中,与化学有序的精英进行化学保守的协同进化)会产生各种完整的代码,并具有出色的联合进度值。只有600个独立的编码表,包括类似SGC的成员。有一条通往更精确的SGC演化的贝叶斯方法。
更新日期:2020-10-11
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