Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT.
Department of Chemistry, Yale University, New Haven, CT.
Mol Biol Evol. 2018 Jul 1;35(7):1588-1598. doi: 10.1093/molbev/msy021.
Ribosomal proteins are indispensable components of a living cell, and yet their structures are remarkably diverse in different species. Here we use manually curated structural alignments to provide a comprehensive catalog of structural variations in homologous ribosomal proteins from bacteria, archaea, eukaryotes, and eukaryotic organelles. By resolving numerous ambiguities and errors of automated structural and sequence alignments, we uncover a whole new class of structural variations that reside within seemingly conserved segments of ribosomal proteins. We then illustrate that these variations reflect an apparent adaptation of ribosomal proteins to the specific environments and lifestyles of living species. Finally, we show that most of these structural variations reside within nonglobular extensions of ribosomal proteins-protein segments that are thought to promote ribosome biogenesis by stabilizing the proper folding of ribosomal RNA. We show that although the extensions are thought to be the most ancient peptides on our planet, they are in fact the most rapidly evolving and most structurally and functionally diverse segments of ribosomal proteins. Overall, our work illustrates that, despite being long considered as slowly evolving and highly conserved, ribosomal proteins are more complex and more specialized than is generally recognized.
核糖体蛋白是活细胞中不可或缺的组成部分，但它们在不同物种中的结构却有显著的差异。在这里，我们使用经过精心整理的结构比对，提供了来自细菌、古菌、真核生物和真核细胞器的同源核糖体蛋白结构变异的全面目录。通过解决自动结构和序列比对的许多歧义性和错误，我们发现了一类全新的结构变异，这些变异存在于核糖体蛋白中看似保守的区域内。然后，我们说明这些变异反映了核糖体蛋白对生活物种特定环境和生活方式的明显适应。最后，我们表明，这些结构变异中的大多数都存在于核糖体蛋白的非球形延伸部分——这些肽段被认为通过稳定核糖体 RNA 的正确折叠来促进核糖体的生物发生。我们表明，尽管这些延伸被认为是我们星球上最古老的肽段，但实际上它们是核糖体蛋白中进化最快、结构和功能最多样化的部分。总的来说，我们的工作表明，尽管核糖体蛋白长期以来被认为是缓慢进化和高度保守的，但它们比人们普遍认为的要复杂和专业化得多。
