The pseudouridine residues of ribosomal RNA

Pseudouridine (Ψ), the most common single modified nucleoside in ribosomal RNA, has been positioned in the small subunit (SSU) and large subunit (LSU) RNAs of a number of representative species. Most of the information has been obtained by application of a rapid primed reverse transcriptase sequencing technique. The locations of these Ψ residues have been compared. Many sites for Ψ are the same among species, but others are distinct. In general, the percentage Ψ in multicellular eukaryotes is greater than in prokaryotes. In LSU RNA, the Ψ residues are strongly clustered in three domains, all of which are near or connected to the peptidyl transferase center. There is no apparent clustering of Ψ in SSU RNA. The Ψ sites in LSU RNA overlap those for the methylated nucleosides, but this is not the case in SSU RNA. There are 265 Ψ sites known to nucleotide resolution, of which 246 are in defined secondary structures, and 112 of these are in nonidentical structural contexts. All 246 Ψ sites can be classified int...