MAPPING TO NUCLEOTIDE RESOLUTION OF PSEUDOURIDINE RESIDUES IN LARGE SUBUNIT RIBOSOMAL-RNAS FROM REPRESENTATIVE EUKARYOTES, PROKARYOTES, ARCHAEBACTERIA, MITOCHONDRIA AND CHLOROPLASTS

The pseudouridine (Psi) residues present in the high molecular mass RN A from the large ribosomal subunit (LSU) have been sequenced from repr esentative species of the eukaryotes, prokaryotes and archaebacteria, and from mitochondrial and chloroplast organelles. Ribosomes from Baci llus subtilis, Halobacter halobium, Drosophila melanogaster, Mus muscu lus, Homo sapiens, mitochondria of M. musculus, H. sapiens and Trypano soma brucei, and Zea mays chloroplasts were examined, resulting in the exact localization of 190 Psi residues. The number of Psi residues pe r RNA varied from one in the mitochondrial RNAs to 57 in the cytoplasm ic LSU RNA of D. melanogaster and M. musculus. Despite this, all of th e Psi residues were found in three domains, II, IV and V. All three ar e at or have been linked to the peptidyl transferase center according to the literature. Comparison of the sites for Psi among the species e xamined revealed four conserved or semi-conserved segments. One is the region 1911 to 1917, which contains three Psi or modified Psi in almo st all species examined. This site is also juxtaposed to the decoding site of the 30 S subunit in the 70 S ribosome and has been implicated in the fidelity of codon recognition. Three additional sites were at t he peptidyl transferase center itself. The juxtaposition of the conser ved sites for Psi with the two important functions of the ribosome, co don recognition and peptide bond formation, implies an important role for Psi in ribosome function. We report some new putative modified nuc leosides in LSU RNAs as detected by reverse transcription, correct a s egment of the sequence of Z. mays chloroplasts and D. melanogaster LSU RNA, correlate the secondary structural context for all known Psi res idues in ribosomal RNA, and compare the sites for Psi with those known for methylated nucleosides in H. sapiens. (C) 1997 Academic Press Lim ited.