The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

Abstract

Abstract. Many cases of nonstandard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The ''gain'' represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The ''loss'' represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is codon disappearance (CD), where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the unassigned codon mechanism, the loss occurs first, whereas in the ambiguous intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. CD is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense-to-sense reassignments cannot be explained by CD. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the unassigned codon and the ambiguous intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.

Mitochondrial Genomes Provide Insights into the Phylogeny of Lauxanioidea (Diptera: Cyclorrhapha)

“…Most cyclorrhaphan tRNAs used the standard anticodon for each gene, but tRNA Asn in Procecidochares utilis (Tephritidae) (Wu et al unpublished) was predicted to have the anticodon UUU, and tRNA Phe in Liriomyza huidobrensis (Agromyzidae) 15 used GAG as anticodon. Although the genetic code is nearly universal, more than 10 variants have been described in metazoan mt genomes [62][63][64][65][66][67]. The above two patterns detected in cyclorrhapha mt genomes were unique amongst arthropods, while these variations on 'wobble' position within the anticodon did not necessarily make changes to the genetic code.…”

Expanded use of sense codons is regulated by modified cytidines in tRNA

“…In this case, a modification of cytidine, 5-formylcytidine (f modified nucleosides | ribosome crystallography | tautomerism T he genetic code was initially deemed to be universal and frozen in time (1). However, deviations in sense and nonsense codon use are found in bacteria, archaea, and both nuclear and organellar eukaryotic genomes (2,3). Use of genetic codes that deviate from the universal code provides insight into its evolution (4) and possibilities for investigator-initiated manipulation (synthetic biology) (5).…”

Codon-reading specificities of mitochondrial release factors and translation termination at non-standard stop codons

“…Although evolution has led to a universal genetic code, many examples of deviations exist 7,8 . In vertebrate mitochondria, the standard stop codon UGA has been reassigned to encode tryptophan, whereas the two arginine codons AGA and AGG have no cognate tRNAs and have instead been reassigned to stop codons in many organisms 2 .…”