Putative anticodons in mitochondrial tRNA sidearm loops: Pocketknife tRNAs?

Abstract

The hypothesis that tRNA sidearm loops bear anticodons assumes crossovers between anticodon and sidearms, or translation by expressed aminoacylated tRNA halves forming single stem-loops. Only the latter might require ribosomal adaptations. Drosophila mitochondrial codon usages coevolve with sidearm numbers bearing matching putative anticodons (comparing different codon families in one genome, macroevolution) and when comparing different genomes for single codon families (microevolution). Coevolution between Drosophila and yeast mitochondrial antisense tRNAs and codon usages partly confounds microevolutionary patterns for putative sidearm anticodons. Some tRNA sidearm loops have more than seven nucleotides, putative expanded anticodons potentially matching quadruplet codons (tetracodons, codons expanded by a fourth silent position, forming tetragenes (predicted by alignment analyses of Drosophila mitochondrial genomes)). Tetracodon numbers coevolve with expanded tRNA sidearm loops. Sidearm coevolution with amino acid usages and tetragenes occurs for putative anticodons in 5′ and 3′ sidearms loops (D and TΨC loops, respectively), are stronger for the D-loop. Results slightly favour isolated stem-loops upon crossover hypotheses. An alternative hypothesis, that patterns observed for sidearm ‘anticodons’ do not imply translational activity, but recognition signals for tRNA synthetases that aminoacylate tRNAs, is incompatible with tetracodon/tetra-anticodon coevolution. Hence analyses strengthen translational hypotheses for tRNA sidearm anticodons, tetragenes, and antisense tRNAs.