Protein synthesis by ribosomes is critically important for gene expression in all cells. The ribosomal RNAs (rRNAs) are marked by numerous chemical modifications. An abundant group of rRNA modifications, present in all domains of life, is 2’-O-methylation guided by box C/D small nucleolar RNAs (snoRNAs) which are part of small ribonucleoprotein complexes (snoRNPs). Although 2’-O-methylations are required for proper production of ribosomes, the mechanisms by which these modifications contribute to translation have remained elusive. Here, we show that a change in box C/D snoRNP biogenesis in actively growing yeast cells results in the production of hypo 2’-O-methylated ribosomes with distinct translational properties. Using RiboMeth-Seq for the quantitative analysis of 2’-O methylations, we identify site-specific perturbations of the rRNA 2’-O-methylation pattern and uncover sites that are not required for ribosome production under normal conditions. Characterization of the hypo 2’-O-methylated ribosomes reveals significant translational fidelity defects including frameshifting and near-cognate start codon selection. Using rRNA structural probing, we show that hypo 2’-O-methylation affects the inherent dynamics of the ribosomal subunits and impacts the binding of translation factor eIF1 thereby causing translational defects. Our data reveal an unforeseen spectrum of 2’-O-methylation heterogeneity in yeast rRNA and suggest a significant role for rRNA 2’-O-methylation in regulating cellular translation by controlling ribosome dynamics and ligand binding.

中文翻译：

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核糖体 RNA 2'-O-甲基化通过影响核糖体动力学来调节翻译

核糖体的蛋白质合成对于所有细胞中的基因表达至关重要。核糖体 RNA (rRNA) 以许多化学修饰为标志。一组丰富的 rRNA 修饰存在于生命的所有领域，是由框 C/D 小核仁 RNA (snoRNA) 引导的 2'-O-甲基化，它们是小核糖核蛋白复合物 (snoRNP) 的一部分。尽管正确生产核糖体需要 2'-O-甲基化，但这些修饰有助于翻译的机制仍然难以捉摸。在这里，我们展示了在活跃生长的酵母细胞中框 C/D snoRNP 生物发生的变化导致产生具有不同翻译特性的低 2'-O-甲基化核糖体。使用 RiboMeth-Seq 定量分析 2'-O 甲基化，我们确定了 rRNA 2'-O-甲基化模式的位点特异性扰动，并发现了在正常条件下核糖体生产不需要的位点。低 2'-O-甲基化核糖体的表征揭示了显着的翻译保真度缺陷，包括移码和近同源起始密码子选择。使用 rRNA 结构探测，我们表明低 2'-O-甲基化影响核糖体亚基的固有动力学并影响翻译因子 eIF1 的结合，从而导致翻译缺陷。我们的数据揭示了酵母 rRNA 中不可预见的 2'-O-甲基化异质性谱，并表明 rRNA 2'-O-甲基化在通过控制核糖体动力学和配体结合来调节细胞翻译中的重要作用。