第二类 tRNA 可变环的起源、来自远端决定因素的氨基酰-tRNA 合成酶异构体以及生命的多样化

DNA Pub Date : 2024-08-09 DOI:10.3390/dna4030017
Lei Lei, Zachary Frome Burton
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引用次数: 0

摘要

三个 31 核苷酸小螺旋 tRNA 演化定理描述了 I 型和 II 型 tRNA 演化到最后一个核苷酸的过程。在数据库中,I型和II型tRNA的V环(V代表变量)排列不当,但基于该定理的排列是准确的。II 型 tRNA V 臂是一个 3′受体茎(最初为 CCGCCGC)连接到一个 5′受体茎(最初为 GCGGCGG)。II 型 V 臂进化成茎-环-茎。在古生菌中,tRNALeu 和 tRNASer 属于 II 型。在细菌中,tRNALeu、tRNASer 和 tRNATyr 都是 II 型。II 型 V 臂的轨迹由莱维特碱基 5′ 处的未配对碱基数量(Vmax)决定。对于古菌,tRNALeu 有两个未配对碱基,tRNASer 有一个未配对碱基。细菌的 tRNATyr 有两个未配对碱基,tRNALeu 有一个未配对碱基,而 tRNASer 的未配对碱基为零。因此,同义的第二类 tRNA 组的数量受到臂的可能轨迹集点的限制。从对氨基酰-tRNA 合成酶结构的分析来看,与 II 型 V 臂的接触似乎主要是通过 tRNA 与氨基酰化和编辑活性位点的沟通来调整异构张力。为了增强异构张力,II 型 V 臂末端环接触似乎倾向于演变为 V 臂茎接触。
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Origin of Type II tRNA Variable Loops, Aminoacyl-tRNA Synthetase Allostery from Distal Determinants, and Diversification of Life
The three 31 nucleotide minihelix tRNA evolution theorem describes the evolution of type I and type II tRNAs to the last nucleotide. In databases, type I and type II tRNA V loops (V for variable) were improperly aligned, but alignment based on the theorem is accurate. Type II tRNA V arms were a 3′-acceptor stem (initially CCGCCGC) ligated to a 5′-acceptor stem (initially GCGGCGG). The type II V arm evolved to form a stem–loop–stem. In Archaea, tRNALeu and tRNASer are type II. In Bacteria, tRNALeu, tRNASer, and tRNATyr are type II. The trajectory of the type II V arm is determined by the number of unpaired bases just 5′ of the Levitt base (Vmax). For Archaea, tRNALeu has two unpaired bases, and tRNASer has one unpaired base. For Bacteria, tRNATyr has two unpaired bases, tRNALeu has one unpaired base, and tRNASer has zero unpaired bases. Thus, the number of synonymous type II tRNA sets is limited by the possible trajectory set points of the arm. From the analysis of aminoacyl-tRNA synthetase structures, contacts to type II V arms appear to adjust allosteric tension communicated primarily via tRNA to aminoacylating and editing active sites. To enhance allostery, it appears that type II V arm end loop contacts may tend to evolve to V arm stem contacts.
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DNA
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