ArticleGenetics2009
Measuring and detecting molecular adaptation in codon usage against nonsense errors during protein translation.
Article in Genetics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding.Annual review of biochemistry · 2021Pooled it
- The importance of nonsense errors: Estimating the rates and implications of ribosome drop-off during protein synthesis.PLoS genetics · 2026Article
- Intragenomic variation in non-adaptive nucleotide biases causes underestimation of selection on synonymous codon usage.PLoS genetics · 2022Article
- Quantifying shifts in natural selection on codon usage between protein regions: a population genetics approach.BMC genomics · 2022Article
- Population Genetics Based Phylogenetics Under Stabilizing Selection for an Optimal Amino Acid Sequence: A Nested Modeling Approach.Molecular biology and evolution · 2019Article
- Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts.Molecular biology and evolution · 2017Article
- ChloroMitoCU: Codon patterns across organelle genomes for functional genomics and evolutionary applications.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Discrepancy among the synonymous codons with respect to their selection as optimal codon in bacteria.DNA research : an international journal for rapid publication of reports on genes and genomes · 2016Article
- Estimating Gene Expression and Codon-Specific Translational Efficiencies, Mutation Biases, and Selection Coefficients from Genomic Data Alone.Genome biology and evolution · 2015Article
- Multiple roles of the coding sequence 5' end in gene expression regulation.Nucleic acids research · 2015Review
- scnRCA: a novel method to detect consistent patterns of translational selection in mutationally-biased genomes.PloS one · 2013Article
- The distribution of synonymous codon choice in the translation initiation region of dengue virus.PloS one · 2013Article
- Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids.Nucleic acids research · 2012Article
- CBDB: the codon bias database.BMC bioinformatics · 2012Article
- Interspecific and intragenic differences in codon usage bias among vertebrate myosin heavy-chain genes.Journal of molecular evolution · 2011Article
- Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Codon usage in vertebrates is associated with a low risk of acquiring nonsense mutations.Journal of translational medicine · 2011Article
- Determinants of translation efficiency and accuracy.Molecular systems biology · 2011Review
- Effect of correlated tRNA abundances on translation errors and evolution of codon usage bias.PLoS genetics · 2010Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Codon usage bias (CUB) has been documented across a wide range of taxa and is the subject of numerous studies. While most explanations of CUB invoke some type of natural selection, most measures of CUB adaptation are heuristically defined. In contrast, we present a novel and mechanistic method for defining and contextualizing CUB adaptation to reduce the cost of nonsense errors during protein translation. Using a model of protein translation, we develop a general approach for measuring the protein production cost in the face of nonsense errors of a given allele as well as the mean and variance of these costs across its coding synonyms. We then use these results to define the nonsense error adaptation index (NAI) of the allele or a contiguous subset thereof. Conceptually, the NAI value of an allele is a relative measure of its elevation on a specific and well-defined adaptive landscape. To illustrate its utility, we calculate NAI values for the entire coding sequence and across a set of nonoverlapping windows for each gene in the Saccharomyces cerevisiae S288c genome. Our results provide clear evidence of adaptation to reduce the cost of nonsense errors and increasing adaptation with codon position and expression. The magnitude and nature of this adaptation are also largely consistent with simulation results in which nonsense errors are the only selective force driving CUB evolution. Because NAI is derived from mechanistic models, it is both easier to interpret and more amenable to future refinement than other commonly used measures of codon bias. Further, our approach can also be used as a starting point for developing other mechanistically derived measures of adaptation such as for translational accuracy.
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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.