Codon Bias As indicated by Figure , the major effect of nucleotide content is at the third position. Arginine and lysine are used as an example in Fig. For arginine, a six-fold degenerate amino acid, the situation is more complex. However, organisms fall into distinct clusters in their use of arginine and lysine codons. A number of measures of codon bias have been proposed to answer these questions.
None are entirely satisfactory.
Furthermore, it is not always clear what null hypothesis should be used to assess synonymous codon bias. Dong et al. It is evident that either the synonymous codon choices of highly expressed genes have evolved to match tRNA expression or tRNA expression has evolved to match a biased set of of highly expressed genes. Lacking any explanation for why highly expressed genes should have different synonymous choices, most people prefer the former explanation. They used a set of highly expressed genes in E. coli as their reference set, the idea being to determine if codon use was correlated with gene expression.