Department of Crop Sciences, University of Illinois at Urbana-Champaign, 332 National Soybean Research Center, 1101 West Peabody Drive, Urbana, IL 61801, USA.
J Mol Evol. 2009 Nov;69(5):430-43. doi: 10.1007/s00239-009-9264-z. Epub 2009 Jul 29.
5S rRNA is the smallest nucleic acid component of the large ribosomal subunit, contributing to ribosomal assembly, stability, and function. Despite being a model for the study of RNA structure and RNA-protein interactions, the evolution of this universally conserved molecule remains unclear. Here, we explore the history of the three-domain structure of 5S rRNA using phylogenetic trees that are reconstructed directly from molecular structure. A total of 46 structural characters describing the geometry of 666 5S rRNAs were used to derive intrinsically rooted trees of molecules and molecular substructures. Trees of molecules revealed the tripartite nature of life. In these trees, superkingdom Archaea formed a paraphyletic basal group, while Bacteria and Eukarya were monophyletic and derived. Trees of molecular substructures supported an origin of the molecule in a segment that is homologous to helix I (alpha domain), its initial enhancement with helix III (beta domain), and the early formation of the three-domain structure typical of modern 5S rRNA in Archaea. The delayed formation of the branched structure in Bacteria and Eukarya lends further support to the archaeal rooting of the tree of life. Remarkably, the evolution of molecular interactions between 5S rRNA and associated ribosomal proteins inferred from a census of domain structure in hundreds of genomes established a tight relationship between the age of 5S rRNA helices and the age of ribosomal proteins. Results suggest 5S rRNA originated relatively quickly but quite late in evolution, at a time when primordial metabolic enzymes and translation machinery were already in place. The molecule therefore represents a late evolutionary addition to the ribosomal ensemble that occurred prior to the early diversification of Archaea.
5S rRNA 是大亚基核糖体的最小核酸成分，有助于核糖体的组装、稳定性和功能。尽管它是研究 RNA 结构和 RNA-蛋白质相互作用的模型，但这个普遍保守的分子的进化仍然不清楚。在这里，我们使用直接从分子结构重建的系统发育树来探索 5S rRNA 三域结构的历史。总共使用了 46 个描述 666 个 5S rRNA 几何形状的结构特征，以获得分子和分子亚结构的内在根系树。分子树揭示了生命的三分体性质。在这些树中，超界古菌形成了一个并系的基础群，而细菌和真核生物则是单系的，并从中衍生而来。分子亚结构树支持该分子起源于与螺旋 I（alpha 结构域）同源的片段，其最初与螺旋 III（beta 结构域）增强，并在古菌中形成了典型的现代 5S rRNA 的三结构域结构。在细菌和真核生物中分支结构的形成延迟进一步支持了生命之树的古菌生根。值得注意的是，从数百个基因组的结构域结构普查中推断出的 5S rRNA 与相关核糖体蛋白之间的分子相互作用的进化，建立了 5S rRNA 螺旋的年龄与核糖体蛋白的年龄之间的紧密关系。结果表明，5S rRNA 的起源相对较快，但在进化过程中相当晚，当时原始的代谢酶和翻译机制已经存在。因此，该分子代表了核糖体集合的一个晚期进化添加物，发生在古菌早期多样化之前。
