ArticleNucleic acids research2009
Selection for minimization of translational frameshifting errors as a factor in the evolution of codon usage.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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Who cites it
20 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
- From Codons to Protein Structure: Evolutionary Constraints of Mitochondrial Proteins in Corvides.Biology · 2026Article
- The importance of nonsense errors: Estimating the rates and implications of ribosome drop-off during protein synthesis.PLoS genetics · 2026Article
- Genome-wide impact of codon usage bias on translation optimization in Drosophila melanogaster.Nature communications · 2024Article
- Next-generation development and application of codon model in evolution.Frontiers in genetics · 2023Review
- A Code Within a Code: How Codons Fine-Tune Protein Folding in the Cell.Biochemistry. Biokhimiia · 2021Review
- Multiple origins of a frameshift insertion in a mitochondrial gene in birds and turtles.GigaScience · 2021Article
- Robustness by intrinsically disordered C-termini and translational readthrough.Nucleic acids research · 2018Article
- Forces acting on codon bias in malaria parasites.Scientific reports · 2018Article
- Article
- Codon optimality, bias and usage in translation and mRNA decay.Nature reviews. Molecular cell biology · 2018Review
- The Yin and Yang of codon usage.Human molecular genetics · 2016Review
- Dependency of codon usage on protein sequence patterns: a statistical study.Theoretical biology & medical modelling · 2014Article
- The Purine Bias of Coding Sequences is Determined by Physicochemical Constraints on Proteins.Bioinformatics and biology insights · 2014Article
- Genetic code-guided protein synthesis and folding in Escherichia coli.The Journal of biological chemistry · 2013Article
- Determinants of translation elongation speed and ribosomal profiling biases in mouse embryonic stem cells.PLoS computational biology · 2012Article
- Determinants of translation efficiency and accuracy.Molecular systems biology · 2011Review
- Relative codon adaptation index, a sensitive measure of codon usage bias.Evolutionary bioinformatics online · 2010Article
- The rate of the molecular clock and the cost of gratuitous protein synthesis.Genome biology · 2010Article
- Unique cost dynamics elucidate the role of frameshifting errors in promoting translational robustness.Genome biology and evolution · 2010Article
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Authors and funding
4 authors.
Funding
Abstract
In a wide range of genomes, it was observed that the usage of synonymous codons is biased toward specific codons and codon patterns. Factors that are implicated in the selection for codon usage include facilitation of fast and accurate translation. There are two types of translational errors: missense errors and processivity errors. There is considerable evidence in support of the hypothesis that codon usage is optimized to minimize missense errors. In contrast, little is known about the relationship between codon usage and frameshifting errors, an important form of processivity errors, which appear to occur at frequencies comparable to the frequencies of missense errors. Based on the recently proposed pause-and-slip model of frameshifting, we developed Frameshifting Robustness Score (FRS). We used this measure to test if the pattern of codon usage indicates optimization against frameshifting errors. We found that the FRS values of protein-coding sequences from four analyzed genomes (the bacteria Bacillus subtilis and Escherichia coli, and the yeasts Saccharomyces cerevisiae and Schizosaccharomyce pombe) were typically higher than expected by chance. Other properties of FRS patterns observed in B. subtilis, S. cerevisiae and S. pombe, such as the tendency of FRS to increase from the 5'- to 3'-end of protein-coding sequences, were also consistent with the hypothesis of optimization against frameshifting errors in translation. For E. coli, the results of different tests were less consistent, suggestive of a much weaker optimization, if any. Collectively, the results fit the concept of selection against mistranslation-induced protein misfolding being one of the factors shaping the evolution of both coding and non-coding sequences.
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