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Codon assignment evolvability in theoretical minimal RNA rings
Gene ( IF 2.6 ) Pub Date : 2020-10-05 , DOI: 10.1016/j.gene.2020.145208
Jacques Demongeot , Hervé Seligmann

Genetic code codon-amino acid assignments evolve for 15 (AAA, AGA, AGG, ATA, CGG, CTA, CTG. CTC, CTT, TAA, TAG, TCA, TCG, TGA and TTA (GNN codons notably absent)) among 64 codons (23.4 %) across the 31 genetic codes (NCBI list completed with recently suggested green algal mitochondrial genetic codes). Their usage in 25 theoretical minimal RNA rings is examined. RNA rings are designed in silico to code once over the shortest length for all 22 coding signals (start and stop codons and each amino acid according to the standard genetic code). Though designed along coding constraints, RNA rings resemble ancestral tRNA loops, assigning to each RNA ring a putative anticodon, a cognate amino acid and an evolutionary genetic code integration rank for that cognate amino acid. Analyses here show 1. biases against/for evolvable codons in the two first vs last thirds of RNA ring coding sequences, 2. RNA rings with evolvable codons have recent cognates, and 3. evolvable codon and cytosine numbers in RNA ring compositions are positively correlated. Applying alternative genetic codes to RNA rings designed for nonredundant coding according to the standard genetic code reveals unsuspected properties of the standard genetic code and of RNA rings, notably on codon assignment evolvability and the special role of cytosine in relation to codon assignment evolvability and of the genetic code's coding structure.



中文翻译:

理论最小RNA环中密码子分配的可进化性

在64个密码子中,有15个(AAA,AGA,AGG,ATA,CGG,CTA,CTG.CTC,CTT,TAA,TAG,TCA,TCG,TGA和TTA(尤其是GNN密码子))的遗传密码子氨基酸分配得到了发展。 (23.4%)在31个遗传密码中(NCBI清单已完成,最近建议使用绿色藻线粒体遗传密码)。检查了它们在25个理论最小RNA环中的用法。RNA环是计算机设计在所有22种编码信号(起始密码子和终止密码子以及根据标准遗传密码的每个氨基酸)的最短长度上编码一次。尽管按照编码限制进行设计,但RNA环类似于祖先的tRNA环,为每个RNA环分配一个推定的反密码子,一个同源氨基酸,以及该同源氨基酸的进化遗传密码整合等级。此处的分析显示1. RNA环编码序列的前三分之二与后三分之二对/可进化密码子的偏倚; 2。具有可进化密码子的RNA环具有最近的认知;以及3. RNA环组成中可进化的密码子与胞嘧啶数目呈正相关。 。将替代遗传密码应用于根据标准遗传密码设计用于非冗余编码的RNA环,可以揭示标准遗传密码和RNA环的意想不到的特性,

更新日期:2020-10-05
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