Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae

A total of 274 transfer RNA genes, representing the entire tRNA gene set of the yeast Saccharomyces cerevisiae, has been extracted from the whole genome sequence of this organism using a dedicated search algorithm (Pol3scan). All tRNA genes were assigned to 42 classes of distinct codon specificity. Accordingly, four deviations from previously proposed rules for third position wobble pairing in yeast, three G:U and one A:I codon-anticodon pairings, were found to be required to account for the reading of 61 coding triplets. The gene copy number for individual tRNA species, which ranges from one to 16, correlates well with both the frequency of codon occurrence in a sample of 1756 distinct protein coding sequences (r = 0.82) and the previously measured intracellular content of 21 tRNA species. A close link between tRNA gene redundancy and the overall amino acid composition of yeast proteins was also observed. Regression analysis values for individual protein coding sequences proved to be effective descriptions of the translational selective pressure operating on a particular gene. A significantly stronger co-adaptation between codon choice and tRNA gene copy number was observed in highly expressed genes. These observations strongly support the notion that intracellular tRNA levels in normally growing yeast cells are mainly determined by gene copy number, which, along with codon choice, is the key parameter acted upon by translational selection.