Identification of functional, endogenous programmed −1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae

Abstract

In viruses, programmed −1 ribosomal frameshifting (−1 PRF) signals direct the translation of alternative proteins from a single mRNA. Given that many basic regulatory mechanisms were first discovered in viral systems, the current study endeavored to: (i) identify −1 PRF signals in genomic databases, (ii) apply the protocol to the yeast genome and (iii) test selected candidates at the bench. Computational analyses revealed the presence of 10 340 consensus −1 PRF signals in the yeast genome. Of the 6353 yeast ORFs, 1275 contain at least one strong and statistically significant −1 PRF signal. Eight out of nine selected sequences promoted efficient levels of PRF in vivo. These findings provide a robust platform for high throughput computational and laboratory studies and demonstrate that functional −1 PRF signals are widespread in the genome of Saccharomyces cerevisiae. The data generated by this study have been deposited into a publicly available database called the PRFdb. The presence of stable mRNA pseudoknot structures in these −1 PRF signals, and the observation that the predicted outcomes of nearly all of these genomic frameshift signals would direct ribosomes to premature termination codons, suggest two possible mRNA destabilization pathways through which −1 PRF signals could post-transcriptionally regulate mRNA abundance.

Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning

“…Indeed, a strong evolutionary selection is observed that eliminates sequences that are strongly prone to frameshifting in protein-coding genes 111 . Such selection is also observed for some 112 , but not all, weakly frameshiftprone sequences [113][114][115] , and in both cases they are frequently found among coding regions [112][113][114][115] . These patterns of occurrence suggest that abortive frameshifting at low frequency might also be beneficial for regulatory purposes under certain conditions.…”

Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae

“…Whereas +1 frameshifting can be triggered when the A site contains a stop codon or a sense codon decoded by a rare tRNA, 21 frameshifting relies on a slippery sequence that allows repairing of the A-and P-site tRNAs with the mRNA and on a downstream secondary structure that impedes forward movement of the ribosome. Computational approaches to identify slippery sites and potential downstream pseudoknot structures predict that as many as 10% of yeast genes, including several genes controlling telomere maintenance (Table 3, Advani et al 2013), contain a frameshift signal (Jacobs et al 2007;Belew et al 2008) and that frameshifting on these sites impacts mRNA levels by activating the nonsense-mediated decay pathway (Belew et al 2011).…”

Bypass of the pre-60S ribosomal quality control as a pathway to oncogenesis

“…Computational analyses suggest that ∼10% of eukaryotic cellular mRNAs harbor operational −1 PRF signals (30). Over 95% of these frameshift events are predicted to function as mRNA destabilizing elements through the nonsensemediated mRNA decay pathway by directing translating ribosomes to premature termination codons (31). More recently, −1 PRF was implicated in telomere maintenance in yeast (23).…”