Anticodon-dependent conservation of bacterial tRNA gene sequences

The residues in tRNA that account for its tertiary fold and for its specific aminoacylation are well understood. In contrast, relatively little is known about the residues in tRNA that dictate its ability to transit the different sites of the ribosome. Yet protein synthesis cannot occur unless tRNA properly engages with the ribosome. This study analyzes tRNA gene sequences from 145 fully sequenced bacterial genomes. Grouping the sequences according to the anticodon triplet reveals that many residues in tRNA, including some that are distal to the anticodon loop, are conserved in an anticodon-dependent manner. These residues evade detection when tRNA genes are grouped according to amino acid family. The conserved residues include those at positions 32, 38, and 37 of the anticodon loop, which are already known to influence tRNA translational performance. Therefore, it seems likely that the newly detected anticodon-associated residues also influence tRNA performance on the ribosome. Remarkably, tRNA genes that belong to the same amino acid family and therefore share identical residues at the second and third anticodon positions have diverged, during bacterial evolution, into highly conserved groups that are defined by the residue at the first (wobble) anticodon position. Current ideas about the properties of tRNA and the translation mechanism do not fully account for this phenomenon. The results of the present study provide a foundation for studying the adaptation of individual tRNAs to the translation machinery and for future studies of the translation mechanism.