Figure 2

Codon and amino-acid responses are determined by their individual GC content. (a) Plot of response to GC content (here, the slope of the regression of absolute frequency in coding sequences on genome GC content) versus composition of the 21 codon sets (20 amino acids and termination) for archaea/bacteria (black symbols, thick lines) and eukaryotes (white symbols, thin lines). (b) A similar plot for the 64 codons. Note that, of the three measures of response, the slope is the least highly correlated with codon or amino-acid composition (see Table 2). For amino acids the composition is the mean GC content of their codons (a). For codons (b,c) the composition is the difference (ΔGC) between the codon's GC content and the mean GC content for all codons encoding the corresponding amino acid. (c) A response-composition plot of the 64 codons showing response within genomes rather than between them, for a bacterium (Synechocystis, black symbols, thick line), an archaean (Archaeoglobus, gray symbols, gray line), and a eukaryote (Drosophila, white symbols, dashed line). The gray line is almost coincident with the thick line; the points are clustered along the abscissa because the structure of the code restricts the possible GC content of the codon sets.