ArticleBMC genomics2008
Preferred and avoided codon pairs in three domains of life.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed, 118 citations in OpenAlex.
- Beyond codon optimality: codon pairs regulate mRNA stability dependent on translation.bioRxiv : the preprint server for biology · 2026Article
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- The CpG Landscape of Protein Coding DNA in Vertebrates.Evolutionary applications · 2025Article
- Mouse embryo CoCoPUTs: novel murine transcriptomic-weighted usage website featuring multiple strains, tissues, and stages.BMC bioinformatics · 2024Article
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- In silico methods for predicting functional synonymous variants.Genome biology · 2023Review
- Gene recoding by synonymous mutations creates promiscuous intragenic transcription initiation in mycobacteria.bioRxiv : the preprint server for biology · 2023Article
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- mRNA-Based Therapeutics in Cancer Treatment.Pharmaceutics · 2023Review
- Application of codon usage and context analysis in genes up- or down-regulated in neurodegeneration and cancer to combat comorbidities.Frontiers in molecular neuroscience · 2023Article
- Ten Plastomes ofBiology · 2022Article
- Codon Usage and Context Analysis of Genes Modulated during SARS-CoV-2 Infection and Dental Inflammation.Vaccines · 2022Article
- 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
- Design of typical genes for heterologous gene expression.Scientific reports · 2022Article
- Frameshift and wild-type proteins are often highly similar because the genetic code and genomes were optimized for frameshift tolerance.BMC genomics · 2022Article
- Compositional biases in RNA viruses: Causes, consequences and applications.Wiley interdisciplinary reviews. RNA · 2022Review
- Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases.Computational and structural biotechnology journal · 2022Review
- Codon usage bias.Molecular biology reports · 2022Review
- Codon Usage Bias: An Endless Tale.Journal of molecular evolution · 2021Review
6 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundAlternative synonymous codons are not used with equal frequencies. In addition, the contexts of codons - neighboring nucleotides and neighboring codons - can have certain patterns. The codon context can influence both translational accuracy and elongation rates. However, it is not known how strong or conserved the codon context preferences in different organisms are. We analyzed 138 organisms (bacteria, archaea and eukaryotes) to find conserved patterns of codon pairs.
resultsAfter removing the effects of single codon usage and dipeptide biases we discovered a set of neighboring codons for which avoidances or preferences were conserved in all three domains of life. Such biased codon pairs could be divided into subtypes on the basis of the nucleotide patterns that influence the bias. The most frequently avoided type of codon pair was nnUAnn. We discovered that 95.7% of avoided nnUAnn type patterns contain out-frame UAA or UAG triplets on the sense and/or antisense strand. On average, nnUAnn codon pairs are more frequently avoided in ORFeomes than in genomes. Thus we assume that translational selection plays a major role in the avoidance of these codon pairs. Among the preferred codon pairs, nnGCnn was the major type.
conclusionTranslational selection shapes codon pair usage in protein coding sequences by rules that are common to all three domains of life. The most frequently avoided codon pairs contain the patterns nnUAnn, nnGGnn, nnGnnC, nnCGCn, GUCCnn, CUCCnn, nnCnnA or UUCGnn. The most frequently preferred codon pairs contain the patterns nnGCnn, nnCAnn or nnUnCn.
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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.