Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan 61-704, Poland.
Center for the Origins of Life, Georgia Institute of Technology, Atlanta, GA 30332, USA.
Nucleic Acids Res. 2022 Oct 14;50(18):10717-10732. doi: 10.1093/nar/gkac844.
The ribosomal core is universally conserved across the tree of life. However, eukaryotic ribosomes contain diverse rRNA expansion segments (ESs) on their surfaces. Sites of ES insertions are predicted from sites of insertion of micro-ESs in archaea. Expansion segment 7 (ES7) is one of the most diverse regions of the ribosome, emanating from a short stem loop and ranging to over 750 nucleotides in mammals. We present secondary and full-atom 3D structures of ES7 from species spanning eukaryotic diversity. Our results are based on experimental 3D structures, the accretion model of ribosomal evolution, phylogenetic relationships, multiple sequence alignments, RNA folding algorithms and 3D modeling by RNAComposer. ES7 contains a distinct motif, the 'ES7 Signature Fold', which is generally invariant in 2D topology and 3D structure in all eukaryotic ribosomes. We establish a model in which ES7 developed over evolution through a series of elementary and recursive growth events. The data are sufficient to support an atomic-level accretion path for rRNA growth. The non-monophyletic distribution of some ES7 features across the phylogeny suggests acquisition via convergent processes. And finally, illustrating the power of our approach, we constructed the 2D and 3D structure of the entire LSU rRNA of Mus musculus.
核糖体核心在生命之树上普遍存在。然而，真核核糖体在其表面含有多样化的 rRNA 扩展片段（ES）。ES 插入位点是根据古菌中微 ES 的插入位点预测的。扩展片段 7（ES7）是核糖体中最多样化的区域之一，从一个短茎环发出，在哺乳动物中延伸超过 750 个核苷酸。我们展示了跨越真核生物多样性的物种的 ES7 的二级和全原子 3D 结构。我们的结果基于实验 3D 结构、核糖体进化的积累模型、系统发育关系、多重序列比对、RNA 折叠算法和 RNAComposer 的 3D 建模。ES7 包含一个独特的基序，即“ES7 特征折叠”，在所有真核核糖体的 2D 拓扑和 3D 结构中通常是不变的。我们建立了一个模型，其中 ES7 通过一系列基本和递归的生长事件在进化过程中发展。这些数据足以支持 rRNA 生长的原子级积累途径。一些 ES7 特征在系统发育中的非单系分布表明是通过趋同过程获得的。最后，通过说明我们方法的强大功能，我们构建了 Mus musculus 的整个 LSU rRNA 的 2D 和 3D 结构。
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