The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.
Translationally Optimal Codons Associate with Structurally Sensitive Sites in Proteins
Open accessAbstract
The mistranslation-induced protein misfolding hypothesis predicts that selection should prefer high-fidelity codons at sites at which translation errors are structurally disruptive and lead to protein misfolding and aggregation. To test this hypothesis, we analyzed the relationship between codon usage bias and protein structure in the genomes of four model organisms, Escherichia coli, yeast, fly, and mouse. Using both the Mantel-Haenszel procedure, which applies to categorical data, and a newly developed association test for continuous variables, we find that translationally optimal codons associate with buried residues and also with residues at sites where mutations lead to large changes in free energy (DeltaDeltaG). In each species, only a subset of all amino acids show this signal, but most amino acids show the signal in at least one species. By repeating the analysis on a reduced data set that excludes interdomain linkers, we show that our results are not caused by an association of rare codons with solvent-accessible linker regions. Finally, we find that our results depend weakly on expression level; the association between optimal codons and buried sites exists at all expression levels, but increases in strength as expression level increases.
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Cites
Kabsch, W., & Sander, C. (1983) · Biopolymers · doi:10.1002/bip.360221211 · Cited by 15,320
Statistical Aspects of the Analysis of Data From Retrospective Studies of Disease
(1959) · JNCI: Journal of the National Cancer Institute · doi:10.1093/jnci/22.4.719 · Cited by 14,689
A gene atlas of the mouse and human protein-encoding transcriptomes
Su, A. I., Wiltshire, T., Batalov, S., Lapp, H., Ching, K. A., Block, D., Zhang, J., Soden, R., Hayakawa, M., Kreiman, G., et al. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400782101 · Cited by 3,475
Integrating high-throughput and computational data elucidates bacterial networks
Covert, M. W., Knight, E. M., Reed, J. L., Herrgard, M. J., & Palsson, B. O. (2004) · Nature · doi:10.1038/nature02456 · Cited by 792
Highly Expressed Genes in Yeast Evolve Slowly
Pál, C., Papp, B., & Hurst, L. D. (2001) · Genetics · doi:10.1093/genetics/158.2.927 · Cited by 635
Tissue-Specific Differences in Human Transfer RNA Expression
Dittmar, K. A., Goodenbour, J. M., & Pan, T. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020221 · Cited by 601
Protein Folding Theory: From Lattice to All-Atom Models
Mirny, L., & Shakhnovich, E. (2001) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.30.1.361 · Cited by 341
Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution
Goldman, N., Thorne, J. L., & Jones, D. T. (1998) · Genetics · doi:10.1093/genetics/149.1.445 · Cited by 281
Cited by
Codon Optimality Is a Major Determinant of mRNA Stability
Presnyak, V., Alhusaini, N., Chen, Y.-H., Martin, S., Morris, N., Kline, N., Olson, S., Weinberg, D., Baker, K. E., Graveley, B. R., et al. (2015) · Cell · doi:10.1016/j.cell.2015.02.029 · Cited by 1,078
“The term codon optimality has been introduced in an attempt to define the differential recognition of codons by the translational apparatus (Zhou et al., 2009; Pechmann and Frydman, 2013).”
BackgroundCodon optimality, bias and usage in translation and mRNA decay
Hanson, G., & Coller, J. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.91 · Cited by 825
The evolutionary consequences of erroneous protein synthesis
Allan Drummond, D., & Wilke, C. O. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2662 · Cited by 515
Self-citationDeterminants of translation efficiency and accuracy
Gingold, H., & Pilpel, Y. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.14 · Cited by 489
Gu, W., Zhou, T., & Wilke, C. O. (2010) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000664 · Cited by 313
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Metadata
- Authors
- Zhou, T., Weems, M., & Wilke, C. O.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2009-04-06
- Volume
- 26
- Issue
- 7
- Pages
- 1571-1580
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2042548693
- Cited by
- 210
- References
- 8
- FWCI
- 5.76
- Type
- journal article
- Language
- en
- Open access
- bronze
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