Pseudouridines and pseudouridine synthases of the ribosome

J. Ofengand, A. Malhotra, J. Remme, N. S. Gutgsell, M. Del Campo, S. Jean-Charles, L. Peil, Y. Kaya

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Abstract

Ψ are ubiquitous in ribosomal RNA. Eubacteria, Archaea, and eukaryotes all contain Ψ, although their number varies widely, with eukaryotes having the most. The small ribosomal subunit can apparently do without Ψ in a 2′-O-methyltransferase specific for G2251 (E. coli numbering) in yeast mitochondria virtually blocks 50S subunit assembly and mitochondrial function (Sirum-Connolly et al. 1995), but the methylation activity of the enzyme is not required (T. Mason, pers. comm.). The absence of FtsJ, a heat shock protein that makes Um2552 in E. coli, makes the 50S subunit less stable at 1 mm Mg++ (Bügl et al. 2000) and inhibits subunit joining (Caldas et al. 2000), but, in this case, it is not yet known whether the effects are due to the lack of 2′-O-methylation or to the absence of the enzyme itself. Is there any role for the Ψ residues themselves? First, as noted above, the 3 Ψ made by RluD which cluster in the end-loop of helix 69 are highly conserved, with one being universal (Fig. 2B). In the 70S-tRNA structure (Yusupov et al. 2001), the loop of this helix containing the Ψ supports the anticodon arm of A-site tRNA near its juncture with the amino acid arm. The middle of helix 69 does the same thing for P-site tRNA. Unfortunately, the resolution is not yet sufficient to provide a more precise alignment of the Ψ residues with the other structural elements of the tRNA-ribosome complex so that one cannot yet determine what role, if any, is played by the N-1 H that distinguishes Ψ from U. Second, and more generally, some Ψ residues in the LSU appear to be near the site of peptide-bond formation or tRNA binding but not actually at it (Fig. 2B) (Nissen et al. 2000; Yusupov et al. 2001). For example, position 2492 is commonly Ψ and is only six residues away from A2486, the A postulated to catalyze peptide-bond formation. Position 2589 is Ψ in all the eukaryotes and is next to 2588, which base-pairs with the C75 of A-site tRNA. Residue 2620, which interacts with the A76 of A-site-bound tRNA, is a Ψ or is next to a Ψ in eukaryotes and Archaea, and is five residues away from Ψ2580 in E. coli. A2637, which is between the two CCA ends of P- and A-site tRNA, is near Ψ2639, Ψ2640, and Ψ2641, found in a number of organisms. Residue 2529, which contacts the backbone of A-site tRNA residues 74-76, is near Ψ2527Ψ2528 in H. marismortui. Residues 2505-2507, which contact A-site tRNA residues 50-53, are near Ψ2509 in higher eukaryotes, and residues 2517-2519 in contact with A-site tRNA residues 64-65 are within 1-3 nucleotides of Ψ2520 in higher eukaryotes and Ψ2514 in H. marismortui. A way to rationalize this might be to invoke the concept suggested in the Introduction that Ψ acts as a molecular glue to hold loose elements in a more rigid configuration. It may well be that this is more important near the site of peptide-bond formation and tRNA binding, accounting for the preponderance of Ψ in this vicinity. What might be the role of all the other Ψ in eukaryotes? One can only surmise that cells, having once acquired the ability to make Ψ with guide RNAs, took advantage of the system to inexpensively place Ψ wherever an undesirable loose region was found. It might be that in some of these cases, Ψ performs the role played by proteins in other regions, namely that of holding the rRNA in its proper configuration. Confirmation of this hypothesis will have to await structural determination of eukaryotic ribosomes.

Original languageEnglish (US)
Pages (from-to)147-159
Number of pages13
JournalCold Spring Harbor symposia on quantitative biology
Volume66
DOIs
StatePublished - 2001

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Genetics

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    Ofengand, J., Malhotra, A., Remme, J., Gutgsell, N. S., Del Campo, M., Jean-Charles, S., Peil, L., & Kaya, Y. (2001). Pseudouridines and pseudouridine synthases of the ribosome. Cold Spring Harbor symposia on quantitative biology, 66, 147-159. https://doi.org/10.1101/sqb.2001.66.147