Directional Mutation Pressure and Transfer RNA in Choice of the Third Nucleotide of Synonymous Two-Codon Sets

Bacterial species have diverged into a series of families, some with high G + C content in their DNA, and others with high A + T content, resulting, respectively, from G· C- and A· T-directional mutation pressures. Such mutation pressure (G· C/A· T pressure) may be an important determinant for codon usage. It has also been suggested that tRNA acts as a selective constraint for determining codon usage. We have studied the relation between G· C/A· T pressure and tRNA constraints in determining choice of the third nucleotide of eight two-codon sets, using codon usage data obtained from protein genes in four bacterial species, Mycoplasma capricolum, Bacillus subtilis, Escherichia coli, and Micrococcus luteus, and in liverwort (Marchantia polymorpha) chloroplasts. The genomic G + C contents of these range from 25% to 74%. The results demonstrate that tRNA levels act additively to A· T and G· C pressure in affecting contents of A (pairing with *UNN anticodons, in which *U indicates a 2-thiouridine derivative) and C (pairing with GNN anticodons) or G (pairing with CNN anticodons), respectively, in third nucleotide positions of codons.