MAPPING OF THE 13-PSEUDOURIDINE RESIDUES IN SACCHAROMYCES-CEREVISIAE SMALL-SUBUNIT RIBOSOMAL-RNA TO NUCLEOTIDE RESOLUTION

The number and location of all of the pseudouridine (Psi) residues in Saccharomyces cerevisiae small subunit (SSU) ribosomal RNA have been d etermined by a reverse transcriptase sequencing method [Bakin, A, and Ofengand, J., 1993, Biochemistry, 32, 9754-9762], Thirteen residues we re found in addition to the previously described m(1)acp(3) Psi 1189. The residues were scattered throughout the molecule with three being i n expansion segments, No Psi was found in the three highly conserved s ingle-stranded sequence elements common to all SSU RNAs. Specifically, Psi 563, the analog of Psi 516 (Escherichia coli) and Psi 517 (Bacill us subtilis) were not found, Eight of the Psi were located identically to those in mammalian SSU RNA and three were near to mammalian Psi re sidues in the secondary structure, There was no discernible correlatio n between the sites for Psi and the known locations of the methylated nucleosides as exists in large subunit (LSU) RNAs. Comparison of the s tructural context in which Psi was found in SSU RNA with that in LSU R NA showed a differential bias suggestive of possible different roles f or Psi in the two rRNAs. This work also identified the locations of th ree putative new modified bases in SSU rRNA, and revealed 15 sequence differences between the yeast strain used here and the reported sequen ce (GenBank, Release 88.0, April 1995, accession.no.J01353).