ArticleJournal of molecular evolution2007
The mechanisms of codon reassignments in mitochondrial genetic codes.
Article in Journal of molecular evolution, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 58 papers.
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58 citing papers in PubMed, 123 citations in OpenAlex.
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- The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes.International journal of molecular sciences · 2023Article
- Mitogenomics and mitochondrial gene phylogeny decipher the evolution of Saccharomycotina yeasts.Genome biology and evolution · 2022Article
- Probing the Role of Cysteine Thiyl Radicals in Biology: Eminently Dangerous, Difficult to Scavenge.Antioxidants (Basel, Switzerland) · 2022Review
- Formation of the Codon Degeneracy during Interdependent Development between Metabolism and Replication.Genes · 2021Article
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- Recent advances in understanding mitochondrial genome diversity.F1000Research · 2020Review
- Fungal Mitogenomes: Relevant Features to Planning Plant Disease Management.Frontiers in microbiology · 2020Review
- Evolution and Unprecedented Variants of the Mitochondrial Genetic Code in a Lineage of Green Algae.Genome biology and evolution · 2019Article
- Rapid Genetic Code Evolution in Green Algal Mitochondrial Genomes.Molecular biology and evolution · 2019Article
- The influence of different types of translational inaccuracies on the genetic code structure.BMC bioinformatics · 2019Article
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- Synthetic genome recoding: new genetic codes for new features.Current genetics · 2018Review
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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