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Analysis of flanking nucleotide contributions to translation start codon selection in yeast
Author(s) -
Pittman Yvette Renee,
Dever Thomas E.
Publication year - 2010
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.24.1_supplement.467.6
Subject(s) - start codon , codon usage bias , genetics , context (archaeology) , nucleotide , eukaryotic translation , biology , translation (biology) , genetic code , yeast , selection (genetic algorithm) , stop codon , genome , messenger rna , amino acid , gene , computer science , paleontology , artificial intelligence
Nearly all protein synthesis occurring in organisms from bacteria to humans initiates at an AUG start codon. Interestingly, the nucleotides flanking the AUG start codon are not random. In mammals, there is a strong preference for A or G at position ‐3 and G at position +4 relative to the A(+1) of the AUG codon. Our analysis of the yeast S. cerevisiae genome revealed a clear bias for A at positions −4 to −1 preceding the AUG codon, and a bias against C at position +4. Studies of mammalian translation established a start codon consensus sequence, (A/G)‐C‐C‐AUG‐G, and mutating this optimal sequence drastically impairs translation. However, previous studies concluded that flanking nucleotides are not important for AUG codon selection in yeast. Using a reporter assay based on leaky scanning of an upstream AUG codon in the GCN4 mRNA, we systematically re‐examined the impact of flanking nucleotides on start codon selection in yeast. Similar to mammals, substituting U at position ‐3 had the most severe impact on translation. In addition, we found that replacing the optimal context A‐A‐A‐AUG‐G with the least preferred U‐U‐U‐AUG‐C context reduced translation over 100‐fold. We are exploiting this strong dependence on flanking nucleotides by using yeast genetic analyses to identify factors that influence start site selection and to reveal the mechanism of how flanking nucleotides govern AUG selection.