Different tRNA modifications are likely to correlate with the codon pairing patterns observed in bacteria.

<p>The location of a black dot represents the codon recognized by a cognate tRNA through Watson-Crick pairing, and the first anticodon base (with or without modifications) of the tRNA is provided next to the black dot. According to wobble rule, the tRNA is able to recognize other synonymous codons (white circles). However, our analysis of the synonymous codon pairing pattern in bacteria supports the hypothesis that the other synonymous codons are recognized in a discriminated way. In the Ala, Leu4, Pro, Ser4, Thr, and Val codon families, the tRNA with a modified cmo⁵U at the wobble position would prefer A- and U-ending codons (linked with solid lines), but avoid C- and G-ending codons (linked with dashed lines). However, in Arg2, Arg4, Gly, and Leu2 codon families the tRNA with a modified mnm⁵U (not confirmed for Arg4 as yet) at the wobble position would prefer A- and G-ending codons instead (linked with solid lines). In the Gln, Glu and Lys codon families, the tRNA with a modified mnm⁵S²U at the wobble base would only prefer A-ending codons and avoid G-ending codons (linked with dashed lines).