An extended signal involved in eukaryotic -1 frameshifting operates through modification of the E site tRNA.
By using a sensitive search program based on hidden Markov models (HMM), we identified 74 viruses carrying frameshift sites among 1500 fully sequenced virus genomes. These viruses are clustered in specific families or genera. Sequence analysis of the frameshift sites identified here, along with previously characterized sites, identified a strong bias toward the two nucleotides 5' of the shifty heptamer signal. Functional analysis in the yeast Saccharomyces cerevisiae demonstrated that high frameshifting efficiency is correlated with the presence of a Psi39 modification in the tRNA present in the E site of the ribosome at the time of frameshifting. These results demonstrate that an extended signal is involved in eukaryotic frameshifting and suggest additional interactions between tRNAs and the ribosome during decoding.
Bekaert
Michaël
M
Institut de Génétique et Microbiologie, Centre National de la Recherche Scientifique-Unité Mixte de Recherche 8621, Bâtiment 400, Université Paris-Sud, 91405 Orsay Cedex, France.
Rousset
Jean-Pierre
JP
D001483:Base Sequence; D018965:Frameshifting, Ribosomal; D016679:Genome, Viral; D019751:Intramolecular Transferases; D010942:Plant Viruses / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics*; D012367:RNA, Viral / Q000235:genetics*; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000378:metabolism; D014780:Viruses / Q000235:genetics*
D012367:RNA, Viral; D029701:Saccharomyces cerevisiae Proteins; D012343:RNA, Transfer; D019751:Intramolecular Transferases; C068903:DEG1 protein, S cerevisiae