The pseudouridine residues of ribosomal RNA

Abstract

Pseudouridine (psi), 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 psi residues have been compared. Many sites for psi are the same among species, but others are distinct. In general, the percentage psi in multicellular eukaryotes is greater than in prokaryotes. In LSU RNA, the psi 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 psi in SSU RNA. The psi sites in LSU RNA overlap those for the methylated nucleosides, but this is not the case in SSU RNA. There are 265 psi sites known to nucleotide resolution, of which 246 are in defined secondary structures, and 112 of these are in nonidentical structural contexts. All 246 psi sites can be classified into five structural types. Two Escherichia coli psi synthases have been cloned and characterized, one for psi 516 in SSU RNA and one for psi 746 in LSU RNA. The psi 746 synthase recognizes free RNA, but the psi 516 enzyme requires an intermediate RNP particle. Possible functional roles for psi in the ribosome are discussed.

Identities and Phylogenetic Comparisons of Posttranscriptional Modifications in 16 S Ribosomal RNA from Haloferax volcanii

“…The only previously established placement of m 6 A in SSU rRNA in other phylogenetic domains was in eukaryotes: X. laevis and human (11) and Rattus norvegicus (16,45), at positions analogous to that in which it occurs in H. volcanii, in the highly conserved mRNA decoding region of the SSU rRNA. Interestingly, this nearly universally conserved A (position 1500 in the E. coli numbering system) appears from the limited data available to be commonly modified in other archaea (various methanogens (17,27) and sulfur-dependent thermophiles (25)) but not in bacteria (18,24,40,41,46), yeast (11,47), or Dictyostelium discoideum (48). The extent to which the modified A at this location in archaea is specifically m 6 A (an uncommon modification in both rRNA and tRNA) remains to be determined.…”

Pseudouridine in RNA: What, Where, How, and Why

“…1). A recent in ux of information about W is providing structural insights and new experimental tools as well as data on the intriguing pattern of occurrence of W in various RNA species (tRNA, 1 rRNA, snRNA, and snoRNA), the unusual mode of selection of U residues for conversion to W , and, most importantly, possible biological roles of W in RNA (for detailed perspectives on the history, chemistry, and biology of W , see [1][2][3][4][5][6][7][8].…”

The box H+ACA snoRNAs carry Cbf5p, the putative rRNA pseudouridine synthase

“…The most numerous modifications are methylation of the 2Ј-hydroxyl residue in the ribose moieties (2Ј-O-methylation) and isomerization of uracil residues to pseudouridine (⌿). Formation of ⌿ residues is thought to occur through base rotation about the C 3 -C 6 axis after cleavage of the glycosyl bond (Goldwasser and Heinrikson 1966; for review, see Ofengand et al 1995). Additionally, a few positions are modified at the base level; the best described example being the universally conserved m 6 2 Am 6 2 A doublet at the 3Ј-end of the 18S rRNA (Lafontaine et al 1995).…”