ArticleJournal of molecular evolution2005
Mitochondrial genetic codes evolve to match amino acid requirements of proteins.
Article in Journal of molecular evolution, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Analysis of the Entire Mitogenome of the Threatened Freshwater StingrayInternational journal of molecular sciences · 2025Article
- Cysteine Is the Only Universally Affected and Disfavored Proteomic Amino Acid under Oxidative Conditions in Animals.Antioxidants (Basel, Switzerland) · 2024Article
- Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies.Scientific reports · 2022Article
- Global Characterization of Fungal Mitogenomes: New Insights on Genomic Diversity and Dynamism of Coding Genes and Accessory Elements.Frontiers in microbiology · 2021Article
- Disrupted architecture and fast evolution of the mitochondrial genome of Argeia pugettensis (Isopoda): implications for speciation and fitness.BMC genomics · 2020Article
- The influence of different types of translational inaccuracies on the genetic code structure.BMC bioinformatics · 2019Article
- Blastocystis Mitochondrial Genomes Appear to Show Multiple Independent Gains and Losses of Start and Stop Codons.Genome biology and evolution · 2016Article
- Ancient DNA sequence revealed by error-correcting codes.Scientific reports · 2015Article
- Pathways of Genetic Code Evolution in Ancient and Modern Organisms.Journal of molecular evolution · 2015Review
- Mutation and selection cause codon usage and bias in mitochondrial genomes of ribbon worms (Nemertea).PloS one · 2014Article
- Revisiting the physico-chemical hypothesis of code origin: an analysis based on code-sequence coevolution in a finite population.Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life · 2013Article
- An alternative look at code evolution: using non-canonical codes to evaluate adaptive and historic models for the origin of the genetic code.Journal of molecular evolution · 2013Article
- Stops making sense: translational trade-offs and stop codon reassignment.BMC evolutionary biology · 2011Article
- Dual functions of codons in the genetic code.Critical reviews in biochemistry and molecular biology · 2010Review
- Genome wide exploration of the origin and evolution of amino acids.BMC evolutionary biology · 2010Article
- Article
- Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Broad genomic and transcriptional analysis reveals a highly derived genome in dinoflagellate mitochondria.BMC biology · 2007Article
- The mechanisms of codon reassignments in mitochondrial genetic codes.Journal of molecular evolution · 2007Article
- Selection on synthesis cost affects interprotein amino acid usage in all three domains of life.Journal of molecular evolution · 2007Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mitochondria often use genetic codes different from the standard genetic code. Now that many mitochondrial genomes have been sequenced, these variant codes provide the first opportunity to examine empirically the processes that produce new genetic codes. The key question is: Are codon reassignments the sole result of mutation and genetic drift? Or are they the result of natural selection? Here we present an analysis of 24 phylogenetically independent codon reassignments in mitochondria. Although the mutation-drift hypothesis can explain reassignments from stop to an amino acid, we found that it cannot explain reassignments from one amino acid to another. In particular--and contrary to the predictions of the mutation-drift hypothesis--the codon involved in such a reassignment was not rare in the ancestral genome. Instead, such reassignments appear to take place while the codon is in use at an appreciable frequency. Moreover, the comparison of inferred amino acid usage in the ancestral genome with the neutral expectation shows that the amino acid gaining the codon was selectively favored over the amino acid losing the codon. These results are consistent with a simple model of weak selection on the amino acid composition of proteins in which codon reassignments are selected because they compensate for multiple slightly deleterious mutations throughout the mitochondrial genome. We propose that the selection pressure is for reduced protein synthesis cost: most reassignments give amino acids that are less expensive to synthesize. Taken together, our results strongly suggest that mitochondrial genetic codes evolve to match the amino acid requirements of proteins.
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