Clustering of pseudouridine residues around the peptidyltransferase center of yeast cytoplasmic and mitochondrial ribosomes.

Analysis of the high molecular weight RNAs of the larger ribosomal subunit of Saccharomyces cerevisiae cytoplasm and mitochondria by a new method [Bakin, A., & Ofengand, J. (1993) Biochemistry 32, 9754-9762] has for the first time located all of the pseudouridine residues present in these two RNAs. Thirty pseudouridines were found in the cytoplasmic RNA, and one was found in the mitochondrial RNA. The 30 cytoplasmic RNA pseudouridines were clustered in three regions of the RNA known to be at or near the peptidyltransferase center. The single pseudouridine in yeast mitochondrial rRNA at position 2819 was also located at the peptidyltransferase center. The localization of pseudouridines at or near the peptidyltransferase center in both cytoplasmic and mitochondrial ribosomes implies a functional role for pseudouridine in peptide bond formation. A correlation was shown to exist between the locations of the pseudouridines determined in this work and the positions of the methylated nucleotides (both 2'-OCH3 and base-methylated) determined previously by others. In addition, this work has tentatively identified the locations of two previously unknown ribothymidine residues, at positions 955 and 2920 in the cytoplasmic rRNA.