Anticodon-dependent conservation of bacterial tRNA gene sequences

Abstract

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.

FIGURE 1.

A comparison of the extent to which tRNA gene sequences are conserved when they are grouped according to the amino acid identity versus the anticodon triplet of the encoded tRNA. (A) The sequences are grouped by the amino acid identity of the encoded tRNA. (B) The sequences for the tRNAs in each amino acid family are separated according to their encoded anticodon triplet. (C) The extent of sequence conservation as a function of the number of different anticodon triplets (isoacceptors) in each amino acid family; Pearson's product moment correlation coefficient, r = −0.851, p < 0.01. Different colors are assigned to each amino acid family, and the colors are consistent across the three panels.

FIGURE 2.

Sequence conservation among tRNA genes from 145 species, which represent the major lineages of the bacteria. The conserved residues are displayed on cloverleaf diagrams of alanine, arginine, glycine, leucine, proline, serine, threonine, and valine tRNA gene sequences that have been grouped according to the encoded anticodon triplet. The standard single-letter abbreviations are used to indicate the residues that are conserved at each position: (G) guanine, (A) adenine, (C) cytosine, (T) thymine; periods indicate that no residue is conserved. Nucleotide frequencies at positions that are conserved on the basis of amino acid family are indicated as: (black) 90%–100%; (blue) 80%–89%; and (gray) 70%–79%. Nucleotide frequencies at positions that are detected as conserved once the tRNAs for each amino acid family are separated according to the anticodon triplet are indicated as (red, large font) 90%–100%; (dark pink) 80%–89%; and (orange) 70%–89%. Symbols at the variable positions (17, 17a, 20a, 20b, and 47, the variable arm of leucine and serine tRNAs) indicate whether the position is conserved as (o) occupied; (*) unoccupied; or (period, .) neither. The 3′-terminal CCA was not included in the analyses.