Do anticodons of misacylated tRNAs preferentially mismatch codons coding for the misloaded amino acid?

Abstract

BackgroundAccurate amino acid insertion during peptide elongation requires tRNAs loaded by cognate amino acids and that anticodons match codons. However, tRNA misloading does not necessarily cause misinsertions: misinsertion is avoided when anticodons mismatch codons coding for misloaded amino acids.Presentation of the hypothesisOccasional compensation of misacylation by codon-anticodon mismatch necessarily occurs. Putatively, occasional error compensation may be enhanced beyond the random combination of independent errors in tRNA loading and codon-anticodon interactions: tRNA misacylation might alter potentials for codon-anticodon mismatches, perhaps specifically increasing potentials for mismatching those codons coding for the misacylated non-cognate amino acid. This hypothetical phenomenon is called 'error coordination', in distinction from 'error compensation' that assumes independence between misacylation and mismatch.Testing the hypothesisEventually, the hypothesis should be tested for each combination of amino acid misacylation and codon-anticodon mismatch, by comparing stabilities or frequencies of mismatched codon-anticodon duplexes formed by tRNAs loaded by their cognate amino acid with stabilities formed by that tRNA when misloaded with the amino acid coded by the mismatched codon. Competitive mismatching experiments between misloaded and correctly loaded tRNAs could also be useful, yet more sophisticated experiments.Implications of the hypothesisDetecting error coordination implies estimating error compensation, which also promotes protein synthesis accuracy. Hence even in the absence of evidence for error coordination, experiments would yield very useful insights into misacylation and mismatch processes. In case experiments consider post-transcriptional RNA modifications (especially at wobble positions), results on codon-anticodon mismatches would enable significant improvements and sophistications of secondary structure prediction softwares. Positive results would show that protein translation enhances accuracies of products, not of single steps in the production. Ancient translational machineries putatively optimized error coordination, especially before tRNA editing by tRNA synthetases evolved: few primitive, but functionally versatile tRNA species perhaps executed low accuracy translation. Systems artificially designed/selected for low complexity and high efficiency could make use of this property for anticodons with high levels of error compensation and coordination.