Abstract
BackgroundCodon bias is a phenomenon that refers to the differences in the frequencies of synonymous codons among different genes. In many organisms, natural selection is considered to be a cause of codon bias because codon usage in highly expressed genes is biased toward optimal codons. Methods have previously been developed to predict the expression level of genes from their nucleotide sequences, which is based on the observation that synonymous codon usage shows an overall bias toward a few codons called major codons. However, the relationship between codon bias and gene expression level, as proposed by the translation-selection model, is less evident in mammals.FindingsWe investigated the correlations between the expression levels of 1,182 mouse genes and amino acid composition, as well as between gene expression and codon preference. We found that a weak but significant correlation exists between gene expression levels and amino acid composition in mouse. In total, less than 10% of variation of expression levels is explained by amino acid components. We found the effect of codon preference on gene expression was weaker than the effect of amino acid composition, because no significant correlations were observed with respect to codon preference.ConclusionThese results suggest that it is difficult to predict expression level from amino acid components or from codon bias in mouse.
Highlights
Codon bias is a phenomenon that refers to the differences in the frequencies of synonymous codons among different genes
Natural selection is considered to be a cause of codon bias, because codon usage in highly expressed genes is biased toward “optimal” codons, i.e., codons corresponding to more abundant tRNAs in many organisms [2,3,4,5,6]
Methods have previously been developed to predict the expression level of genes from their nucleotide sequences, which is based on the observation that synonymous codon usage shows an overall bias toward a few codons called major codons [2,3,4,5,6,7,8,9,10,11,12]
Summary
Codon bias is a phenomenon that refers to the differences in the frequencies of synonymous codons among different genes. Natural selection is considered to be a cause of codon bias because codon usage in highly expressed genes is biased toward optimal codons. The relationship between codon bias and gene expression level, as proposed by the translation-selection model, is less evident in mammals. Natural selection is considered to be a cause of codon bias, because codon usage in highly expressed genes is biased toward “optimal” codons, i.e., codons corresponding to more abundant tRNAs in many organisms [2,3,4,5,6]. The relationship between codon bias and expression level as proposed by the translation-selection model is less evident in mammals [22,23,24,25,26,27,28,29,30]. Urrutia and Hurst [23] found a weak correlation between gene expression levels and codon bias in human, but failed to find a relationship between this correlation and tRNA-gene copy numbers
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