title: Identification of stop codon readthrough genes in Saccharomyces cerevisiae.
abstract: We specifically sought genes within the yeast genome controlled by a non-conventional translation mechanism involving the stop codon. For this reason, we designed a computer program using the yeast database genomic regions, and seeking two adjacent open reading frames separated only by a unique stop codon (called SORFs). Among the 58 SORFs identified, eight displayed a stop codon bypass level ranging from 3 to 25%. For each of the eight sequences, we demonstrated the presence of a poly(A) mRNA. Using isogenic [PSI(+)] and [psi(-)] yeast strains, we showed that for two of the sequences the mechanism used is a bona fide readthrough. However, the six remaining sequences were not sensitive to the PSI state, indicating either a translation termination process independent of eRF3 or a new stop codon bypass mechanism. Our results demonstrate that the presence of a stop codon in a large ORF may not always correspond to a sequencing error, or a pseudogene, but can be a recoding signal in a functional gene. This emphasizes that genome annotation should take into account the fact that recoding signals could be more frequently used than previously expected.
authors.affiliation: Laboratoire de Génétique Moléculaire de la Traduction, Institut de Génétique et Microbiologie, Université Paris-Sud, 91405 Orsay Cedex, France. on205@mole.bio.cam.ac.uk
authors.forename: Olivier
authors.initials: O
authors.lastname: Namy
authors.forename: Guillemette
authors.initials: G
authors.lastname: Duchateau-Nguyen
authors.forename: Isabelle
authors.initials: I
authors.lastname: Hatin
authors.forename: Sylvie
authors.initials: S
authors.lastname: Hermann-Le Denmat
authors.forename: Michel
authors.initials: M
authors.lastname: Termier
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Rousset
mesh_terms: D001483:Base Sequence; D018388:Codon, Terminator / Q000235:genetics*; D005800:Genes, Fungal / Q000235:genetics*; D007763:Lac Operon / Q000235:genetics; D008156:Luciferases / Q000235:genetics / Q000378:metabolism; D016366:Open Reading Frames / Q000235:genetics; D010957:Plasmids / Q000235:genetics; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D011993:Recombinant Fusion Proteins / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D012984:Software; D001616:beta-Galactosidase / Q000235:genetics / Q000378:metabolism
chemical_list: D018388:Codon, Terminator; D012333:RNA, Messenger; D011993:Recombinant Fusion Proteins; D008156:Luciferases; D001616:beta-Galactosidase