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Codon optimality, bias and usage in translation and mRNA decay
Open accessAbstract
The advent of ribosome profiling and other tools to probe mRNA translation has revealed that codon bias - the uneven use of synonymous codons in the transcriptome - serves as a secondary genetic code: a code that guides the efficiency of protein production, the fidelity of translation and the metabolism of mRNAs. Recent advancements in our understanding of mRNA decay have revealed a tight coupling between ribosome dynamics and the stability of mRNA transcripts; this coupling integrates codon bias into the concept of codon optimality, or the effects that specific codons and tRNA concentrations have on the efficiency and fidelity of the translation machinery. In this Review, we first discuss the evidence for codon-dependent effects on translation, beginning with the basic mechanisms through which translation perturbation can affect translation efficiency, protein folding and transcript stability. We then discuss how codon effects are leveraged by the cell to tailor the proteome to maintain homeostasis, execute specific gene expression programmes of growth or differentiation and optimize the efficiency of protein production.
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“elements including the relative frequencies of codon use for each amino acid, local and global GC composition, mRNA secondary structure stability, and the presence of cryptic termination signals or splice sites are significant factors impacting the degree of protein expression”
From Codon optimization is an essential parameter for the efficient allotopic expression of mtDNA genes (2020) · cites this paper as [61]
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“The translation elongation rate is controlled by the accessibility of cognate tRNA species and the codon usage modification to prevent the match rare tRNA sequence of species and integrate sequences that match more common tRNA species (Hanson and Coller 2018).”
From Modifications of mRNA vaccine structural elements for improving mRNA stability and translation efficiency (2022) · cites this paper as Hanson and Coller 2018
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“To improve the safety, efficacy, and stability of mRNA vaccines, researchers usually performed codon optimization172,239–243 on the antigen-coding sequence to enhance translation efficiency.”
From Advances in COVID-19 mRNA vaccine development (2022) · cites this paper as [239]
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Metadata
- Authors
- Hanson, G., & Coller, J.
- Affiliations
- Case Western Reserve University (US)
- Corresponding author
- Hanson, Gavin
- Coller, Jeff
- Venue
- Nature Reviews Molecular Cell Biology
- Published
- 2017-10-11
- Volume
- 19
- Issue
- 1
- Pages
- 20-30
- ISSN
- 1471-0072 (ISSN-L)
- 1471-0080
- PMC
- PMC6594389
- OpenAlex
- W2762868004
- Cited by
- 825
- References
- 143
- Citations by year
- 2026: 92 · 2025: 114 · 2024: 108 · 2023: 113 · 2022: 93 · 2021: 122 · 2020: 78 · 2019: 58 · 2018: 46
- FWCI
- 4.66
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Reviews Molecular Cell Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of General Medical Sciences (R01GM118018, R01GM125086, T32GM007250)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA modifications and cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- codon usage bias, codon optimality, synonymous codons, tRNA abundance, translation efficiency, translation fidelity, ribosome profiling, mRNA degradation, transcript stability, protein folding, ribosome dynamics, gene expression regulation
- MeSH terms
- Animals, Codon, Homeostasis, Humans, Proteins, Ribosomes, RNA, Messenger, Protein Biosynthesis, Protein Folding, RNA Stability
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