ArticleNucleic acids research2013
Selection on codon bias in yeast: a transcriptional hypothesis.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- Article
- Mitochondrial genomes of Mentha reveal structural complexity and evolutionary diversity.Molecular genetics and genomics : MGG · 2026Article
- Genetic Characteristics and Phylogenetic Relationships of 18 Anchovy Species Based on Mitochondrial Genomes in the Seas Around China.Ecology and evolution · 2025Article
- A New Comparative Framework for Estimating Selection on Synonymous Substitutions.Molecular biology and evolution · 2025Article
- The Complete Mitochondrial Genome ofBiomolecules · 2025Article
- A new comparative framework for estimating selection on synonymous substitutions.bioRxiv : the preprint server for biology · 2025Article
- Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains.BMC genomics · 2024Article
- Codon usage bias in yeasts and its correlation with gene expression, growth temperature, and protein structure.Frontiers in microbiology · 2024Article
- Single nucleotide polymorphisms associated with wine fermentation and adaptation to nitrogen limitation in wild and domesticated yeast strains.Biological research · 2023Article
- Synonymous Codon Variant Analysis for Autophagic Genes Dysregulated in Neurodegeneration.Molecular neurobiology · 2023Article
- Analysis of synonymous codon usage patterns in mitochondrial genomes of nineFrontiers in microbiology · 2023Article
- Assembly and analysis of the mitochondrial genome ofFrontiers in plant science · 2023Article
- Comprehensive analysis of codon bias in 13Frontiers in microbiology · 2023Article
- Stop Codon Usage as a Window into Genome Evolution: Mutation, Selection, Biased Gene Conversion and the TAG Paradox.Genome biology and evolution · 2022Article
- Response to Cold: A Comparative Transcriptomic Analysis in Eight Cold-Adapted Yeasts.Frontiers in microbiology · 2022Article
- Article
- Inferring Adaptive Codon Preference to Understand Sources of Selection Shaping Codon Usage Bias.Molecular biology and evolution · 2021Article
- Identification of permissive amber suppression sites for efficient non-canonical amino acid incorporation in mammalian cells.Nucleic acids research · 2021Article
- Article
- Further engineering of R. toruloides for the production of terpenes from lignocellulosic biomass.Biotechnology for biofuels · 2021Article
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1 author.
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No grant is acknowledged in the PubMed record.
Abstract
Codons that code for the same amino acid are often used with unequal frequencies. This phenomenon is termed codon bias. Here, we report a computational analysis of codon bias in yeast using experimental and theoretical genome-wide data. We show that the most used codons in highly expressed genes can be predicted by mRNA structural data and that the codon choice at each synonymous site within an mRNA is not random with respect to the local secondary structure. Because we also found that the folding stability of intron sequences is strongly correlated with codon bias and mRNA level, our results suggest that codon bias is linked to mRNA folding structure through a mechanism that, at least partially, operates before pre-mRNA splicing. Consistent with this, we report evidence supporting the adaptation of the tRNA pool to the codon profile of the most expressed genes rather than vice versa. We show that the correlation of codon usage with the gene expression level also includes the stop codons that are normally not decoded by aminoacyl-tRNAs. The results reported here are consistent with a role for transcriptional forces in driving codon usage bias via a mechanism that improves gene expression by optimizing mRNA folding structures.
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