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基于密码子使用的突变稳健性的系统发育分析支持标准遗传密码不偏爱极端环境。

Phylogenetic analysis of mutational robustness based on codon usage supports that the standard genetic code does not prefer extreme environments.

机构信息

Department of Plant Systematics, Ecology and Theoretical Biology, Institute of Biology, Eötvös Loránd University, Budapest, Hungary.

Evolutionary Systems Research Group, Centre for Ecological Research, Institute of Evolution, Budapest, Hungary.

出版信息

Sci Rep. 2021 May 26;11(1):10963. doi: 10.1038/s41598-021-90440-y.

Abstract

The mutational robustness of the genetic code is rarely discussed in the context of biological diversity, such as codon usage and related factors, often considered as independent of the actual organism's proteome. Here we put the living beings back to picture and use distortion as a metric of mutational robustness. Distortion estimates the expected severities of non-synonymous mutations measuring it by amino acid physicochemical properties and weighting for codon usage. Using the biological variance of codon frequencies, we interpret the mutational robustness of the standard genetic code with regards to their corresponding environments and genomic compositions (GC-content). Employing phylogenetic analyses, we show that coding fidelity in physicochemical properties can deteriorate with codon usages adapted to extreme environments and these putative effects are not the artefacts of phylogenetic bias. High temperature environments select for codon usages with decreased mutational robustness of hydrophobic, volumetric, and isoelectric properties. Selection at high saline concentrations also leads to reduced fidelity in polar and isoelectric patterns. These show that the genetic code performs best with mesophilic codon usages, strengthening the view that LUCA or its ancestors preferred lower temperature environments. Taxonomic implications, such as rooting the tree of life, are also discussed.

摘要

遗传密码的突变稳健性在生物多样性的背景下很少被讨论,例如密码子使用和相关因素,它们通常被认为与实际生物体的蛋白质组无关。在这里,我们将生物放回图片中,并使用扭曲作为衡量突变稳健性的指标。扭曲通过氨基酸的物理化学性质和密码子使用的权重来衡量非同义突变的预期严重程度。利用密码子频率的生物学方差,我们根据环境和基因组组成(GC 含量)解释了标准遗传密码的突变稳健性。通过系统发育分析,我们表明在物理化学性质方面的编码保真度可能会随着适应极端环境的密码子使用而恶化,并且这些潜在的影响不是系统发育偏差的人为产物。高温环境选择具有降低疏水性、体积和等电性质的突变稳健性的密码子使用。高盐浓度的选择也会导致极性和等电模式的保真度降低。这些表明遗传密码在嗜温密码子使用下表现最佳,这加强了 LUCA 或其祖先更喜欢低温环境的观点。还讨论了分类学意义,例如确定生命之树的根。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/2d22/8154912/009cf38fb964/41598_2021_90440_Fig1_HTML.jpg

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