对RNA家族的比较分析揭示了每个生活领域的不同储备
Comparative Analysis of RNA Families Reveals Distinct Repertoires for Each Domain of Life
摘要：
RNA世界假说，即RNA基因组和催化剂先于DNA基因组和遗传编码的蛋白质催化剂，一直是地球生命早期进化模型的核心。这种模型的一个关键部分是生命进化的最早阶段与现存谱系的RNA库之间的连续性。一些评估似乎与多样化的RNA世界一致，但现代RNA和RNA世界之间的直接连续性尚未被证明为大多数RNA家族，而且，有趣的是，许多RNA功能似乎在其分布中受到限制。尽管对RNA家族可能的古老性进行了大量讨论，但尚未对RNA家族分布进行系统分析。为了绘制已知RNA家族的广泛进化历史，我们对Rfam 10数据库中跨越1446个家族的超过300万个RNA注释进行了比较基因组分析。我们报告说，99%的已知RNA家族仅限于一个单一的生活领域，揭示了每个领域的离散剧目。对于存在于一个以上结构域中的1%的RNA家族/氏族，超过一半显示出水平基因转移的证据，其余的显示出垂直痕迹，表明在最后的普遍共同祖先（LUCA）中存在复杂的蛋白质合成机制，并与最古老的蛋白质编码基因的进化历史相一致。然而，有限的域间转移和几个RNA家族表现出明显的古老性预测下RNA世界的连续性，我们的研究结果表明，大多数现代细胞RNA库主要是在一个特定的域的方式演变。
英文摘要：
The RNA world hypothesis, that RNA genomes and catalysts preceded DNA genomes and genetically-encoded protein catalysts, has been central to models for the early evolution of life on Earth. A key part of such models is continuity between the earliest stages in the evolution of life and the RNA repertoires of extant lineages. Some assessments seem consistent with a diverse RNA world, yet direct continuity between modern RNAs and an RNA world has not been demonstrated for the majority of RNA families, and, anecdotally, many RNA functions appear restricted in their distribution. Despite much discussion of the possible antiquity of RNA families, no systematic analyses of RNA family distribution have been performed. To chart the broad evolutionary history of known RNA families, we performed comparative genomic analysis of over 3 million RNA annotations spanning 1446 families from the Rfam 10 database. We report that 99% of known RNA families are restricted to a single domain of life, revealing discrete repertoires for each domain. For the 1% of RNA families/clans present in more than one domain, over half show evidence of horizontal gene transfer, and the rest show a vertical trace, indicating the presence of a complex protein synthesis machinery in the Last Universal Common Ancestor (LUCA) and consistent with the evolutionary history of the most ancient protein-coding genes. However, with limited interdomain transfer and few RNA families exhibiting demonstrable antiquity as predicted under RNA world continuity, our results indicate that the majority of modern cellular RNA repertoires have primarily evolved in a domain-specific manner.
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