Identification of functional, endogenous programmed −1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae
Identification of functional, endogenous programmed −1 ribosomal frameshift signals in the genome of Saccharomyces cerevisiae
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.
- UNIVERSITY OF MARYLAND COLLEGE PK CAMPUS
- UNIV OF MARYLAND, COLLEGE PARK
- University of Maryland, College Park United States
- Rutgers, The State University of New Jersey United States
- University of Maryland United States
Internet, Base Sequence, Molecular Sequence Data, Computational Biology, Frameshifting, Ribosomal, RNA, Fungal, Genomics, Saccharomyces cerevisiae, Regulatory Sequences, Ribonucleic Acid, Data Interpretation, Statistical, Gene Expression Regulation, Fungal, Nucleic Acid Conformation, RNA, Messenger, Genome, Fungal, Databases, Nucleic Acid
Internet, Base Sequence, Molecular Sequence Data, Computational Biology, Frameshifting, Ribosomal, RNA, Fungal, Genomics, Saccharomyces cerevisiae, Regulatory Sequences, Ribonucleic Acid, Data Interpretation, Statistical, Gene Expression Regulation, Fungal, Nucleic Acid Conformation, RNA, Messenger, Genome, Fungal, Databases, Nucleic Acid
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