Alvarez-Carreño Claudia, Arciniega Marcelino, Ribas de Pouplana Lluís, Petrov Anton S, Hernández-González Adriana, Dimas-Torres Jorge-Uriel, Valencia-Sánchez Marco Igor, Williams Loren Dean, Torres-Larios Alfredo
NASA Center for the Origin of Life, Georgia Institute of Technology, Atlanta, Georgia, USA.
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA.
Protein Sci. 2023 Nov 27;33(3):e4844. doi: 10.1002/pro.4844.
Aminoacyl-tRNA synthetases (aaRSs) establish the genetic code. Each aaRS covalently links a given canonical amino acid to a cognate set of tRNA isoacceptors. Glycyl tRNA aminoacylation is unusual in that it is catalyzed by different aaRSs in different lineages of the Tree of Life. We have investigated the phylogenetic distribution and evolutionary history of bacterial glycyl tRNA synthetase (bacGlyRS). This enzyme is found in early diverging bacterial phyla such as Firmicutes, Acidobacteria, and Proteobacteria, but not in archaea or eukarya. We observe relationships between each of six domains of bacGlyRS and six domains of four different RNA-modifying proteins. Component domains of bacGlyRS show common ancestry with (i) the catalytic domain of class II tRNA synthetases; (ii) the HD domain of the bacterial RNase Y; (iii) the body and tail domains of the archaeal CCA-adding enzyme; (iv) the anti-codon binding domain of the arginyl tRNA synthetase; and (v) a previously unrecognized domain that we call ATL (Ancient tRNA latch). The ATL domain has been found thus far only in bacGlyRS and in the universal alanyl tRNA synthetase (uniAlaRS). Further, the catalytic domain of bacGlyRS is more closely related to the catalytic domain of uniAlaRS than to any other aminoacyl tRNA synthetase. The combined results suggest that the ATL and catalytic domains of these two enzymes are ancestral to bacGlyRS and uniAlaRS, which emerged from common protein ancestors by bricolage, stepwise accumulation of protein domains, before the last universal common ancestor of life.
氨酰 - tRNA合成酶（aaRSs）确立了遗传密码。每种aaRS将特定的标准氨基酸共价连接到一组同源的tRNA同工受体上。甘氨酰tRNA的氨酰化作用不同寻常，因为在生命之树的不同谱系中，它是由不同的aaRS催化的。我们研究了细菌甘氨酰tRNA合成酶（bacGlyRS）的系统发育分布和进化历史。这种酶存在于早期分化的细菌门类中，如厚壁菌门、酸杆菌门和变形菌门，但在古菌或真核生物中不存在。我们观察到bacGlyRS的六个结构域与四种不同RNA修饰蛋白的六个结构域之间的关系。bacGlyRS的组成结构域与以下结构域具有共同的祖先：（i）II类tRNA合成酶的催化结构域；（ii）细菌核糖核酸酶Y的HD结构域；（iii）古菌CCA添加酶的主体和尾部结构域；（iv）精氨酰tRNA合成酶的反密码子结合结构域；以及（v）一个我们称为ATL（古老tRNA锁扣）的先前未被识别的结构域。到目前为止，ATL结构域仅在bacGlyRS和通用丙氨酰tRNA合成酶（uniAlaRS）中发现。此外，bacGlyRS的催化结构域与uniAlaRS的催化结构域的关系比与任何其他氨酰tRNA合成酶的关系更密切。综合结果表明，这两种酶的ATL和催化结构域是bacGlyRS和uniAlaRS的祖先，它们在生命的最后一个普遍共同祖先之前，通过拼合，即蛋白质结构域逐步积累，从共同的蛋白质祖先中演化而来。
