ArticlePloS one2011
Species-specific codon context rules unveil non-neutrality effects of synonymous mutations.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 24 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
24 citing papers in PubMed, 39 citations in OpenAlex.
- Evolution of Resistance to Avian Malaria Infection in an Endemic Hawaiian Honeycreeper.Ecology and evolution · 2026Article
- Holostean genomes reveal evolutionary novelty in the vertebrate immunoproteasome that have implications for MHCI function.Molecular biology and evolution · 2026Article
- In silico methods for predicting functional synonymous variants.Genome biology · 2023Review
- Mechanisms governing codon usage bias and the implications for protein expression in the chloroplast of Chlamydomonas reinhardtii.The Plant journal : for cell and molecular biology · 2022Review
- Codon Pattern and Compositional Constraints Determination of Genes Associated with Chronic Periodontitis.Genes · 2022Article
- The Codon Usage Bias Analysis of Free-Living Ciliates' Macronuclear Genomes and Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 Vector Construction ofFrontiers in microbiology · 2022Article
- Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris.Microbial cell factories · 2021Article
- Harnessing the Genetic Plasticity of Porcine Circovirus Type 2 to Target Suicidal Replication.Viruses · 2021Article
- A comparative genomics-based study of positive strand RNA viruses emphasizing on SARS-CoV-2 utilizing dinucleotide signature, codon usage and codon context analyses.Gene reports · 2021Article
- A Modelling Framework Linking Resource-Based Stochastic Translation to the Optimal Design of Synthetic Constructs.Biology · 2021Article
- Synonymous genome recoding: a tool to explore microbial biology and new therapeutic strategies.Nucleic acids research · 2019Review
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- Plasmodium apicoplast tyrosyl-tRNA synthetase recognizes an unusual, simplified identity set in cognate tRNATyr.PloS one · 2018Article
- Attenuation of Viruses by Large-Scale Recoding of their Genomes: the Selection Is Always Biased.Current clinical microbiology reports · 2018Review
- Dynamics of translation can determine the spatial organization of membrane-bound proteins and their mRNA.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Codon usage and codon pair patterns in non-grass monocot genomes.Annals of botany · 2017Review
- The Yin and Yang of codon usage.Human molecular genetics · 2016Review
- Effects of tRNA modification on translational accuracy depend on intrinsic codon-anticodon strength.Nucleic acids research · 2016Article
- Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate.Nucleic acids research · 2015Article
Corrections and comments
- Erratum issued
Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCodon pair usage (codon context) is a species specific gene primary structure feature whose evolutionary and functional roles are poorly understood. The data available show that codon-context has direct impact on both translation accuracy and efficiency, but one does not yet understand how it affects these two translation variables or whether context biases shape gene evolution. METHODOLOGIES/PRINCIPAL
findingsHere we study codon-context biases using a set of 72 orthologous highly conserved genes from bacteria, archaea, fungi and high eukaryotes to identify 7 distinct groups of codon context rules. We show that synonymous mutations, i.e., neutral mutations that occur in synonymous codons of codon-pairs, are selected to maintain context biases and that non-synonymous mutations, i.e., non-neutral mutations that alter protein amino acid sequences, are also under selective pressure to preserve codon-context biases.
conclusionsSince in vivo studies provide evidence for a role of codon context on decoding fidelity in E. coli and for decoding efficiency in mammalian cells, our data support the hypothesis that, like codon usage, codon context modulates the evolution of gene primary structure and fine tunes the structure of open reading frames for high genome translational fidelity and efficiency in the 3 domains of life.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.