Ribosomal RNA 2′- O-methylations regulate translation by impacting ribosome dynamics

Significance

The presence of RNA chemical modifications has long been known, but their precise molecular consequences remain unknown. 2′- O-methylation is an abundant modification that exists in RNA in all domains of life. Ribosomal RNA (rRNA) represents a functionally important RNA that is heavily modified by 2′- O-methylations. Although abundant at functionally important regions of the rRNA, the contribution of 2′- O-methylations to ribosome activities is unknown. By establishing a method to disturb rRNA 2′- O-methylation patterns, we show that rRNA 2′- O-methylations affect the function and fidelity of the ribosome and change the balance between different ribosome conformational states. Our work links 2′- O-methylation to ribosome dynamics and defines a set of critical rRNA 2′- O-methylations required for ribosome biogenesis and others that are dispensable.

Abstract

Protein synthesis by ribosomes is critically important for gene expression in all cells. 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, which are part of small ribonucleoprotein complexes (snoRNPs). Although 2′- O-methylations are required for the 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 RiboMethSeq 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 eukaryotic translation initiation factor 1, 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.