ArticleNature structural & molecular biology2013
Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding.
Article in Nature structural & molecular biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 295 papers, 3 of them syntheses that pooled it.
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Who cites it
295 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding.Annual review of biochemistry · 2021Pooled it
- Differential proteostatic regulation of insoluble and abundant proteins.Bioinformatics (Oxford, England) · 2019Pooled it
- Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives.Frontiers in genetics · 2019Pooled it
- Codon Optimality Modulates Cellular Stress and Innate Immune Responses Triggered by Exogenous RNAs.Journal of molecular biology · 2026Article
- Puf3 contributes to changes in mRNA solubility, translation elongation dynamics at rare arginine codons and loss of protein homeostasis in cells lacking Not4.RNA (New York, N.Y.) · 2026Article
- The Tor pathway, ribosome concentration, and wobble decoding mediate inhibitory effects of the Leu-Pro CUC-CCG codon pair inRNA (New York, N.Y.) · 2026Article
- A detailed molecular picture of protein folding during active translation.bioRxiv : the preprint server for biology · 2026Article
- Heat stress promotes pre-tRNA capping to modulate cap-dependent translation in Saccharomyces cerevisiae.Nature communications · 2026Article
- Synonymous mutations in essential genes infrequently produce fitness effects in human cell lines.Nucleic acids research · 2026Article
- Approaches for Studying Context Specificity of Translation Inhibitor Action.International journal of molecular sciences · 2026Review
- Co-translational protein targeting to mitochondria in the context of co-translational protein maturation.Protein science : a publication of the Protein Society · 2026Review
- Reading Between the ABCs: Intrinsic Disorder and Evolutionary Dynamics of Non-Canonical Regions in ABC Transporters.International journal of molecular sciences · 2026Article
- Evidence for Non-optimal Codon Choice in Highly Transcribed Sex-Biased Genes of Drosophila melanogaster.Genome biology and evolution · 2026Article
- Translational regulation by oxidative desulfuration of tRNA modifications.Nature communications · 2026Article
- Mapping the inter- and intra-genic codon-usage landscape inNAR genomics and bioinformatics · 2026Article
- Unveiling ribosomal dysfunction and impaired signaling pathways in the cortical region of 5xFAD mice.Acta neuropathologica communications · 2026Article
- A giant virus forms a specialized subcellular environment within its amoeba host for efficient translation.Nature microbiology · 2026Article
- Synonymous editing alters ion channel function, favoring prime editing for retinal disease correction.International journal of biological sciences · 2026Article
- Acute glucose stimulation drives coordinated translational reprogramming in primary pancreatic islets: from global remodeling to fine-tuned insulin synthesis.Frontiers in endocrinology · 2026Article
- Transfer RNA regulation during herpesvirus infection: Wielding a sword or raising a shield?PLoS pathogens · 2025Article
235 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
The choice of codons can influence local translation kinetics during protein synthesis. Whether codon preference is linked to cotranslational regulation of polypeptide folding remains unclear. Here, we derive a revised translational efficiency scale that incorporates the competition between tRNA supply and demand. Applying this scale to ten closely related yeast species, we uncover the evolutionary conservation of codon optimality in eukaryotes. This analysis reveals universal patterns of conserved optimal and nonoptimal codons, often in clusters, which associate with the secondary structure of the translated polypeptides independent of the levels of expression. Our analysis suggests an evolved function for codon optimality in regulating the rhythm of elongation to facilitate cotranslational polypeptide folding, beyond its previously proposed role of adapting to the cost of expression. These findings establish how mRNA sequences are generally under selection to optimize the cotranslational folding of corresponding polypeptides.
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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.