Nuclear codon reassignments in the genomics era and mechanisms behind their evolution

The canonical genetic code ubiquitously translates nucleotide into peptide sequence with several alterations known in viruses, bacteria, mitochondria, plastids, and single‐celled eukaryotes. A new hypothesis to explain genetic code changes, termed tRNA loss driven codon reassignment, has been proposed recently when the polyphyly of the yeast codon reassignment events has been uncovered. According to this hypothesis, the driving force for genetic code changes are tRNA or translation termination factor loss‐of‐function mutations or loss‐of‐gene events. The free codon can subsequently be captured by all tRNAs that have an appropriately mutated anticodon and are efficiently charged. Thus, codon capture most likely happens by near‐cognate tRNAs and tRNAs whose anticodons are not part of the recognition sites of the respective aminoacyl‐tRNA‐synthetases. This hypothesis comprehensively explains the CTG codon translation as alanine in Pachysolen yeast together with the long known translation of the same codon as serine in Candida albicans and related species, and can also be applied to most other known reassignments. With the recently discovered genetic code alterations, time has come to revisit the processes behind the genetic code diversity across the eukaryotic tree. The tRNA loss driven codon reassignment hypothesis, which attributes a special role to the charging of anticodon‐mutated tRNAs, seems to be particularly apt at explaining these events.