The DOI matches its Crossref record; 94 of the 94 references it cites were found in a registry or an index.
The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes
Open accessAbstract
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.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“There is no evidence that any modern code modifications are adaptive. Most likely, these change evolved neutrally, through genetic drift and mutational pressure that drives small genomes toward high AT-content.”
From Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code (2017) · cites this paper as [24]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Thompson, J. (1997) · Nucleic Acids Research · doi:10.1093/nar/25.24.4876 · Cited by 38,685 · cited 2×
“The rRNA sequences were aligned initially using ClustalX ( Thompson et al. 1997 ).”
MethodPHYLIP-Phylogeny inference package (Version 3.2)
Felsenstein, J. (1989) · Cladistics · Cited by 17,682
The origin of the genetic code
Crick, F. H. C. (1968) · Journal of Molecular Biology · doi:10.1016/0022-2836(68)90392-6 · Cited by 2,320
A kingdom-level phylogeny of eukaryotes based on combined protein data.
Baldauf, S., Roger, A., Wenk-Siefert, I., & Doolittle, W. (2000) · Science · doi:10.1126/science.290.5493.972 · Cited by 1,243 · cited 6×
“Dictyostelium discoideum and Acanthamoeba castellanii are thought to be more distant relatives of this group that diverge before the split of fungi and metazoa ( Baldauf et al. 2000; Van der Peer et al. 2000; Lang et al. 2002).”
BackgroundInfluentialUniversal rules and idiosyncratic features in tRNA identity
Giege, R., Sissler, M., & Florentz, C. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.22.5017 · Cited by 769 · cited 2×
“The identity elements and antideterminants of tRNAs are key aspects of the molecules that play a crucial role in the proper aminoacylation and prevention of misacylation of a tRNA (Giegé et al. 1998).”
BackgroundKurtzman, C. P., & Robnett, C. J. (2003) · FEMS Yeast Research · doi:10.1016/s1567-1356(03)00012-6 · Cited by 652 · cited 2×
“The branching order of the species within Ascomycota agrees with Bullerwell et al. (2003a) and Kurtzman and Robnett (2003), and that within Chytridiomycota agrees with Bullerwell et al. (2003b).”
BackgroundAnimals and fungi are each other's closest relatives: congruent evidence from multiple proteins.
Baldauf, S. L., & Palmer, J. D. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.24.11558 · Cited by 543 · cited 2×
“The grouping of fungi and metazoa, proposed by Baldauf & Palmer (1993), is supported by all the studies cited in the previous paragraph.”
BackgroundThe New View of Animal Phylogeny
Halanych, K. M. (2004) · Annual Review of Ecology, Evolution, and Systematics · doi:10.1146/annurev.ecolsys.35.112202.130124 · Cited by 489 · cited 2×
“Winchell (2002) and Halanych (2004) for the relationship between the animal phyla.”
BackgroundRewiring the keyboard: evolvability of the genetic code
Knight, R. D., Freeland, S. J., & Landweber, L. F. (2001) · Nature Reviews Genetics · doi:10.1038/35047500 · Cited by 435 · cited 14×
“(v) Ascomycota (group containing Yarrowia and relatives) Knight et al. (2001a) list a single change in the ancestor of Metazoa, Acanthamoeba and Fungi.”
BackgroundMethodResultInfluentialAsymmetrical directional mutation pressure in the mitochondrial genome of mammals
Reyes, A., Gissi, C., Pesole, G., & Saccone, C. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026011 · Cited by 415
Cited by
Sorted by citations
Origin and evolution of the genetic code: The universal enigma
Koonin, E. V., & Novozhilov, A. S. (2009) · IUBMB Life · doi:10.1002/iub.146 · Cited by 392
“The three theories explaining codon reassignment are not exclusive considering that the ‘‘ambiguous intermediate’’ stage can be preceded by a significant decrease in the content of GCrich codons, so that codon reassignment might be driven by a combination of evolutionary mechanisms (56), often under the pressure for g…”
BackgroundGrosjean, H., de Crécy‐Lagard, V., & Marck, C. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.11.052 · Cited by 308
“changes, for reviews see [24–26]).”
BackgroundMcCutcheon, J. P., McDonald, B. R., & Moran, N. A. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000565 · Cited by 275
“This tRNA-Trp mutation has also been observed in mitochondrial genomes that have the UGA StopRTrp recoding [24].”
BackgroundOrigin and Evolution of the Universal Genetic Code
Koonin, E. V., & Novozhilov, A. S. (2017) · Annual Review of Genetics · doi:10.1146/annurev-genet-120116-024713 · Cited by 200
A Thermodynamic Basis for Prebiotic Amino Acid Synthesis and the Nature of the First Genetic Code
Higgs, P. G., & Pudritz, R. E. (2009) · Astrobiology · doi:10.1089/ast.2008.0280 · Cited by 218
“Splitting a two-codon family into separate single codons is possible in the case of Met and Trp codons, but this does not increase the number of amino acids encoded in either case; and, in many mitochondrial codes, Met and Trp both have two codons (Sengupta et al., 2007).”
Self-citation
Metadata
- Authors
- Sengupta, S., Yang, X., & Higgs, P. G.
- Affiliations
- McMaster University (CA)
- Corresponding author
- Higgs, Paul G.
- Venue
- Journal of Molecular Evolution
- Published
- 2007-05-29
- Volume
- 64
- Issue
- 6
- Pages
- 662-688
- ISSN
- 0022-2844 (ISSN-L)
- 1432-1432
- PMC
- PMC1894752
- OpenAlex
- W2171069213
- Cited by
- 121
- References
- 94
- Citations by year
- 2026: 4 · 2025: 4 · 2024: 4 · 2023: 4 · 2022: 2 · 2021: 3 · 2020: 7 · 2019: 4 · 2018: 4 · 2017: 12 · 2016: 9 · 2015: 9 · 2014: 5 · 2013: 7 · 2012: 5
- FWCI
- 3.57
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Journal of Molecular Evolution (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- arXiv (Cornell University) (submittedVersion)
- arXiv (Cornell University)
- Funders
- Canada Research Chairs
- Natural Sciences and Engineering Research Council of Canada
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Protist diversity and phylogeny
- Keywords
- codon reassignment, mitochondrial genetic code, codon usage, tRNA, stop codon reassignment, mitochondrial genome, phylogeny
- MeSH terms
- Animals, Codon, Cytoplasm, DNA, Mitochondrial, Fungi, Genetic Code, Introns, Phylogeny, Plants, RNA, Transfer, Ile, Open Reading Frames, Codon, Terminator, Mitochondrial Proteins, Eukaryota
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
