Mapping of the 13 pseudouridine residues inSaccharomyces cerevisiaesmall subunit ribosomal RNA to nucleotide resolution

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Abstract
The number and location of all of the pseudouridine (ψ) residues in Saccharomyces cerevisiae small subunit (SSU) ribosomal RNA have been determined by a reverse transcriptase sequencing method [Bakin, A. and Ofengand, J., 1993, Biochemistry, 32, 9754-9762]. Thirteen residues were found in addition to the previously described m1acp3ψ1189. The esidues were scattered throughout the molecule with three being in expansion segments. No ψ was found in the three highly conserved single-stranded sequence elements common to all SSU RNAs. Specifically, ψ563, the analog of ψ516 (Escherichia colt) and ψ517 (Bacillus subtllls) were not found. Eight of the T were located identically to those in ammalian SSU RNA and three were near to mammalian ψ residues In the secondary structure. There was no iscernible correlation between the sites for ψ and the known locations of the methylated nucleosides as exists in large subunit (LSU) RNAs. Comparison of the structural context in which ψ was found in SSU RNA with that in LSU RNA showed a ifferential bias suggestive of possible different roles for T in the two rRNAs. This work also Identified the locations of three putative new modified bases in SSU rRNA, and revealed 15 sequence differences between the yeast strain used here and the reported sequence (GenBank, Release 88.0, April 1995, accession, no. J01353).