CLUSTERING OF PSEUDOURIDINE RESIDUES AROUND THE PEPTIDYLTRANSFERASE CENTER OF YEAST CYTOPLASMIC AND MITOCHONDRIAL RIBOSOMES

Analysis of the high molecular weight RNAs of the large ribosomal subu nit of Saccharomyces cerevisiae cytoplasm and mitochondria by a new me thod [Bakin, A., and Ofengand, J. (1993) Biochemistry 32, 9754-9762] h as for the first time located all of the pseudouridine residues presen t in these two RNAs. Thirty pseudouridines were found in the cytoplasm ic RNA, and one was found in the mitochondrial RNA. The 30 cytoplasmic RNA pseudouridines were clustered in three regions of the RNA known t o be at or near the peptidyltransferase center. The single pseudouridi ne in yeast mitochondrial rRNA at position 2819 was also located at th e peptidyltransferase center. The localization of pseudouridines at or near the peptidyltransferase center in both cytoplasmic and mitochond rial 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 th e methylated nucleotides (both 2'-OCH3 and base-methylated) determined previously by others. In addition, this work has tentatively identifi ed the locations of two previously unknown ribothymidine residues, at positions 955 and 2920 in the cytoplasmic rRNA.