Figure 5. Codon context model.

This model explains how the first codon of a codon-pair affects the outcome of the codon-context bias. The 3^rd nucleotide (N₃) of the first codon of codon-pairs is the major modulator of the codon-context bias (adjusted residual value), as has already been shown by our group in a previous study (see text). Changing this nucleotide can revert the context signal of a particular codon pair, turning it from positive to negative or vice versa. For example, a U-ending codon such as UCU next to the Ala GCC codon produces a preferred context, conversely to the other UCN codons (panel A). In order to maintain the context signal, the first codon of the pair is sometimes altered to another codon ending with the same nucleotide of the original first codon (AGU in the example of panel A), even if the amino acid is different (ACU, GCU or UCU in the example of panel B). In cases where there is more than one synonymous codon resulting in the same context signal (e.g. AGU and UCU), first codon alteration may maintain the amino acid (panel A). The figure shows codon context biases of S. cerevisiae as an example to illustrate the concept outlined in the model.