Identification of stop codon readthrough genes in Saccharomyces cerevisiae.
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.
Namy
Olivier
O
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
Duchateau-Nguyen
Guillemette
G
Hatin
Isabelle
I
Hermann-Le Denmat
Sylvie
S
Termier
Michel
M
Rousset
Jean-Pierre
JP
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
D018388:Codon, Terminator; D012333:RNA, Messenger; D011993:Recombinant Fusion Proteins; D008156:Luciferases; D001616:beta-Galactosidase