氨酰tRNA合成酶(aaRS),也称为tRNA连接酶,是翻译中必不可少的酶。由于它们的功能重要性,这些酶在生命的所有领域都是保守的,并用作追踪细胞生物进化历史的信息标记。与细胞生物不同,病毒通常缺乏aaRS,因为它们具有专性的寄生性质,但是核子细胞病毒门中的几种巨大的DNA病毒在其基因组中编码aaRS。病毒aaaRS的发现导致了这样的想法,即aaRS的系统发育分析可以揭示古代病毒的进化。然而,以前的系统发育研究报告了相互矛盾的结果:有人认为核细胞病毒最近从宿主真核生物中获得了aaRS,而另一个人假设病毒aaRS有古老的起源。这里,我们调查了4,168个核细胞病毒基因组,包括来自大规模宏基因组研究的宏基因组组装基因组。总的来说,我们在273个病毒基因组中鉴定出780个病毒aaRS序列.我们用大量细胞序列生成并检查了这些aaRS的系统发育树,以追踪病毒和细胞aaRS之间的进化关系。分析表明,某些病毒aaRS的起源早于最后一个共同的真核祖先。在病毒aaRS进化枝内部,我们确定了具有水平转移的病毒aaRS的复杂进化轨迹,损失,和流离失所。总的来说,这些结果表明,在原真核生物时代,祖先的核细胞病毒已经发展出复杂的基因组,并扩展了aaRSs.
Aminoacyl-tRNA synthetases (aaRSs), also known as tRNA ligases, are essential enzymes in translation. Owing to their functional essentiality, these enzymes are conserved in all domains of life and used as informative markers to trace the evolutionary history of cellular organisms. Unlike cellular organisms, viruses generally lack aaRSs because of their obligate parasitic nature, but several large and giant DNA viruses in the phylum Nucleocytoviricota encode aaRSs in their genomes. The discovery of viral aaRSs led to the idea that the phylogenetic analysis of aaRSs can shed light on ancient viral evolution. However, conflicting results have been reported from previous phylogenetic studies: one posited that nucleocytoviruses recently acquired their aaRSs from their host eukaryotes, while another hypothesized that the viral aaRSs have ancient origins. Here, we investigated 4,168 nucleocytovirus genomes, including metagenome-assembled genomes (MAGs) derived from large-scale metagenomic studies. In total, we identified 780 viral aaRS sequences in 273 viral genomes. We generated and examined phylogenetic trees of these aaRSs with a large set of cellular sequences to trace evolutionary relationships between viral and cellular aaRSs. The analyses suggest that the origins of some viral aaRSs predate the last common eukaryotic ancestor. Inside viral aaRS clades, we identify intricate evolutionary trajectories of viral aaRSs with horizontal transfers, losses, and displacements. Overall, these results suggest that ancestral nucleocytoviruses already developed complex genomes with an expanded set of aaRSs in the proto-eukaryotic era.