ArticleProteomics2010
Translationally optimal codons associate with aggregation-prone sites in proteins.
Article in Proteomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
26 citing papers in PubMed, 44 citations in OpenAlex.
- Aggregation is a Context-Dependent Constraint on Protein Evolution.Frontiers in molecular biosciences · 2021Article
- Structural analysis of SARS-CoV-2 genome and predictions of the human interactome.Nucleic acids research · 2020Article
- RNA-binding and prion domains: the Yin and Yang of phase separation.Nucleic acids research · 2020Article
- Thermodynamic and Evolutionary Coupling between the Native and Amyloid State of Globular Proteins.Cell reports · 2020Article
- Codon bias confers stability to human mRNAs.EMBO reports · 2019Article
- A Shift in Aggregation Avoidance Strategy Marks a Long-Term Direction to Protein Evolution.Genetics · 2019Article
- The stop-and-go traffic regulating protein biogenesis: How translation kinetics controls proteostasis.The Journal of biological chemistry · 2019Review
- Codon usage clusters correlation: towards protein solubility prediction in heterologous expression systems in E. coli.Scientific reports · 2018Article
- Selective Constraints on Coding Sequences of Nervous System Genes Are a Major Determinant of Duplicate Gene Retention in Vertebrates.Molecular biology and evolution · 2017Article
- Evidence of evolutionary selection for cotranslational folding.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Functional and Structural Consequence of Rare Exonic Single Nucleotide Polymorphisms: One Story, Two Tales.Genome biology and evolution · 2015Article
- Nonoptimal codon usage influences protein structure in intrinsically disordered regions.Molecular microbiology · 2015Article
- Protein functional features are reflected in the patterns of mRNA translation speed.BMC genomics · 2015Article
- Interrelation between protein synthesis, proteostasis and life span.Current genomics · 2014Article
- Estimating selection on synonymous codon usage from noisy experimental data.Molecular biology and evolution · 2013Article
- Three independent determinants of protein evolutionary rate.Journal of molecular evolution · 2013Review
- The ribosome as a hub for protein quality control.Molecular cell · 2013Review
- Evolutionary conservation of codon optimality reveals hidden signatures of cotranslational folding.Nature structural & molecular biology · 2013Article
- The signatures of selection for translational accuracy in plant genes.Genome biology and evolution · 2013Article
- Cellular strategies for regulating functional and nonfunctional protein aggregation.Cell reports · 2012Article
Corrections and comments
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Authors and funding
5 authors at 4 institutions in 3 countries.
Funding
Abstract
We analyze the relationship between codon usage bias and residue aggregation propensity in the genomes of four model organisms, Escherichia coli, yeast, fly, and mouse, as well as the archaeon Halobacterium species NRC-1. Using the Mantel-Haenszel procedure, we find that translationally optimal codons associate with aggregation-prone residues. Our results are qualitatively and quantitatively similar to those of an earlier study where we found an association between translationally optimal codons and buried residues. We also combine the aggregation-propensity data with solvent-accessibility data. Although the resulting data set is small, and hence statistical power low, results indicate that the association between optimal codons and aggregation-prone residues exists both at buried and at exposed sites. By comparing codon usage at different combinations of sites (exposed, aggregation-prone sites versus buried, non-aggregation-prone sites; buried, aggregation-prone sites versus exposed, non-aggregation-prone sites), we find that aggregation propensity and solvent accessibility seem to have independent effects of (on average) comparable magnitude on codon usage. Finally, in fly, we assess whether optimal codons associate with sites at which amino acid substitutions lead to an increase in aggregation propensity, and find only a very weak effect. These results suggest that optimal codons may be required to reduce the frequency of translation errors at aggregation-prone sites that coincide with certain functional sites, such as protein-protein interfaces. Alternatively, optimal codons may be required for rapid translation of aggregation-prone regions.
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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.