The DOI matches its Crossref record; 10 of the 10 references it cites were found in a registry or an index.
Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding
Open accessAbstract
Summary Codon usage bias is a universal feature of eukaryotic and prokaryotic genomes and has been proposed to regulate translation efficiency, accuracy and protein folding based on the assumption that codon usage affects translation dynamics. The roles of codon usage in translation, however, are not clear and have been challenged by recent ribosome profiling studies. Here we used a Neurospora cell-free translation system to directly monitor the velocity of mRNA translation. We demonstrated that the preferred codons enhance rate of translation elongation, whereas non-optimal codons slow elognatioon. Codon usage also controls ribosome traffic on mRNA. These conclusions were further supported by ribosome profiling results in vitro and in vivo with template mRNAs designed to increase signal to noise. Finally, we demonstrate that codon usage regulates protein function by affecting co-translational protein folding. These results resolve a long-standing fundamental question and suggest the existence of a codon usage code for protein folding.
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Cites
The Sequence Alignment/Map format and SAMtools
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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 · cited 1×
“It was recently shown that codon usage plays a role in determining yeast mRNA half-lives, likely due to its role in affecting elongation speed (Presnyak et al., 2015).”
Translation efficiency is determined by both codon bias and folding energy
Tuller, T., Waldman, Y. Y., Kupiec, M., & Ruppin, E. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0909910107 · Cited by 584 · cited 4×
“However, recent studies are not consistent with such a hypothesis and suggested that overall translation efficiency is mainly determined by translation initiation efficiency, a process that is mostly determined by the RNA structure near the translational start site (Kudla et al., 2009; Pop et al., 2014; Tuller et al.,…”
InfluentialGerashchenko, M. V., Lobanov, A. V., & Gladyshev, V. N. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120799109 · Cited by 302
Silent Substitutions Predictably Alter Translation Elongation Rates and Protein Folding Efficiencies
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mRNA vaccines — a new era in vaccinology
Pardi, N., Hogan, M. J., Porter, F. W., & Weissman, D. (2018) · Nature Reviews Drug Discovery · doi:10.1038/nrd.2017.243 · Cited by 4,667
Codon 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
Synonymous Codons Direct Cotranslational Folding toward Different Protein Conformations
Buhr, F., Jha, S., Thommen, M., Mittelstaet, J., Kutz, F., Schwalbe, H., Rodnina, M. V., & Komar, A. A. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.01.008 · Cited by 395
Codon Usage and 3′ UTR Length Determine Maternal mRNA Stability in Zebrafish
Mishima, Y., & Tomari, Y. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.02.027 · Cited by 293
Translation affects mRNA stability in a codon-dependent manner in human cells
Wu, Q., Medina, S. G., Kushawah, G., DeVore, M. L., Castellano, L. A., Hand, J. M., Wright, M., & Bazzini, A. A. (2019) · eLife · doi:10.7554/elife.45396 · Cited by 283
Metadata
- Authors
- Yu, C.-H., Dang, Y., Zhou, Z., Wu, C., Zhao, F., Sachs, M. S., & Liu, Y.
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2015-09
- Volume
- 59
- Issue
- 5
- Pages
- 744-754
- ISSN
- 1097-2765 (ISSN-L)
- OpenAlex
- W1956613997
- Cited by
- 619
- References
- 10
- FWCI
- 18.14
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Yu, C.-H., Dang, Y., Zhou, Z., Wu, C., Zhao, F., Sachs, M. S., & Liu, Y. (2015). Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding. Molecular Cell. https://doi.org/10.1016/j.molcel.2015.07.018
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