Journal
NUCLEIC ACIDS RESEARCH
Volume 35, Issue 1, Pages 165-174Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkl1033
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Funding
- NIAID NIH HHS [T32 AI051967] Funding Source: Medline
- NIGMS NIH HHS [R01 GM058859, R05 GM58859, R21 GM068123] Funding Source: Medline
- NLM NIH HHS [F37 LM008333, F37 LM8333] Funding Source: Medline
- NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES [R01GM058859, R21GM068123] Funding Source: NIH RePORTER
- NATIONAL LIBRARY OF MEDICINE [F37LM008333] Funding Source: NIH RePORTER
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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.
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