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

• Authors: Sohail Khoshnevis, Emory University; Elizabeth Dreggors-Walker, Emory University; Virginie Marchand, Université de Lorraine; Yuri Motorin, Université de Lorraine; Homa Ghalei, Emory University
• Journal Title: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• Volume: Volume 119, Number 12
• Publisher: NATL ACAD SCIENCES | 2022-03-22, Pages e2117334119-e2117334119
• Type of Work: Article | Final Publisher PDF
• Publisher DOI: http://doi.org/10.1073/pnas.2117334119
• Subjects: Chemistry, Biochemistry; Biology, Cell
• Keywords: Science & Technology; Multidisciplinary Sciences; Science & Technology - Other Topics; 2 '-O-methylation; rRNA modification; ribosome biogenesis; ribosome dynamics; translation regulation; BOX C/D; SACCHAROMYCES-CEREVISIAE; PREINITIATION COMPLEXES; SOLUTION CONFORMATION; INITIATION-FACTORS; STRUCTURAL BASIS; YEAST; METHYLATION; PROTEIN; FIBRILLARIN

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 20-O-methylation guided by box C/D small nucleolar RNAs, which are part of small ribonucleoprotein complexes (snoRNPs). Although 20-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-20-O-methylated ribosomes with distinct translational properties. Using RiboMethSeq for the quantitative analysis of 20-O-methylations, we identify site-specific perturbations of the rRNA 20-O-methylation pattern and uncover sites that are not required for ribosome production under normal conditions. Characterization of the hypo-20-O-methylated ribosomes reveals significant translational fidelity defects, including frameshifting and near-cognate start codon selection. Using rRNA structural probing, we show that hypo-20-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 20-O-methylation heterogeneity in yeast rRNA and suggest a significant role for rRNA 20-O-methylation in regulating cellular translation by controlling ribosome dynamics and ligand binding.