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.

De Novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae

“…BSC4 has no significant homolog when we used tBLASTN to search against genome sequences of S. bayanus, S. kudriavzevii, S. mikatae, and S. paradoxus under the standard parameters. Even if we use the putative translation product of the stop codon bypass event predicted by Namy et al (2003), which is a peptide of 237 amino acids, there is still no significant homolog in these sibling species. The absence of homolog might be the false negative result due to incompleteness of the genomic databases of those species.…”

“…This gene first caught our attention as a species-specific protein-coding gene in our genome comparison analysis among Saccharomyces species (H.-F. Jiang and W. Wang, unpublished data). Previously the BSC4 gene was found as one of the stop codon readthrough genes in baker's yeast by Namy et al (2003). They found that BSC4 has a typical readthrough nucleotide context around its stop codon and its readthrough frequency is 9% when cloned into a plasmid with reporter genes (Namy et al 2003).…”

“…Previously the BSC4 gene was found as one of the stop codon readthrough genes in baker's yeast by Namy et al (2003). They found that BSC4 has a typical readthrough nucleotide context around its stop codon and its readthrough frequency is 9% when cloned into a plasmid with reporter genes (Namy et al 2003). Although the BSC4 gene has been included in many large-scale studies, no specific study has been done with an aim to characterize it.…”

Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae

“…The eRF1, composed of three domains, functionally mimics a tRNA with the N-terminal domain recognizing the stop codon (Bertram et al 2000), the central domain with its methylated GGQ motif promotes hydrolysis of the peptidyl-tRNA bond (Heurgue-Hamard et al 2005), and the C-terminal domain interacts with eRF3. Recognition of all three stop codons by eRF1 is mediated by the YxCxxxF and TASNIKS motifs, as well as by other binding pockets/cavities in the N domain Namy et al 2001;Namy et al 2002;Namy et al 2003;Beznoskova et al 2015 Genes are grouped by publication/similar mechanism. Many examples given rely on a single publication and detailed mechanisms remain unknown.…”

An engineered nonsense URA3 allele provides a versatile system to detect the presence, absence and appearance of the [PSI+] prion in Saccharomyces cerevisiae

“…Previous studies indicated that the context in which a nonsense codon exists affects the efficiency with which it can be read through (Namy et al, 2003). …”