A code within the genetic code: codon usage regulates co-translational protein folding
Open accessAbstract
The genetic code is degenerate, and most amino acids are encoded by two to six synonymous codons. Codon usage bias, the preference for certain synonymous codons, is a universal feature of all genomes examined. Synonymous codon mutations were previously thought to be silent; however, a growing body evidence now shows that codon usage regulates protein structure and gene expression through effects on co-translational protein folding, translation efficiency and accuracy, mRNA stability, and transcription. Codon usage regulates the speed of translation elongation, resulting in non-uniform ribosome decoding rates on mRNAs during translation that is adapted to co-translational protein folding process. Biochemical and genetic evidence demonstrate that codon usage plays an important role in regulating protein folding and function in both prokaryotic and eukaryotic organisms. Certain protein structural types are more sensitive than others to the effects of codon usage on protein folding, and predicted intrinsically disordered domains are more prone to misfolding caused by codon usage changes than other domain types. Bioinformatic analyses revealed that gene codon usage correlates with different protein structures in diverse organisms, indicating the existence of a codon usage code for co-translational protein folding. This review focuses on recent literature on the role and mechanism of codon usage in regulating translation kinetics and co-translational protein folding. Video abstract.
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Codon optimization can result in an improvement in protein expression yield, antibody assembly, affinity, and biological activity.
“Codon optimization can not only result in an improvement in protein expression yield, but also antibody assembly, affinity, and biological activity [85,86].”
From Computational and artificial intelligence-based methods for antibody development (2023) · cites this paper as [86]
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- Authors
- Liu, Y.
- Affiliations
- The University of Texas Southwestern Medical Center (US)
- Corresponding author
- Liu, Yi
- ORCID
- Liu, Yi
- Venue
- Cell Communication and Signaling
- Published
- 2020-09-09
- Volume
- 18
- Issue
- 1
- Pages
- 145-145
- ISSN
- 1478-811X (ISSN-L)
- PMC
- PMC7488015
- OpenAlex
- W3083874241
- Cited by
- 252
- References
- 105
- Citations by year
- 2026: 29 · 2025: 54 · 2024: 63 · 2023: 48 · 2022: 36 · 2021: 21 · 2020: 1
- FWCI
- 2.54
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Cell Communication and Signaling (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institute of General Medical Sciences (R35GM118118)
- Welch Foundation (I-1560)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- codon usage bias, co-translational folding, synonymous codons, genetic code degeneracy, translation elongation rate, intrinsically disordered regions, protein misfolding, translation efficiency, mRNA stability
- MeSH terms
- Codon Usage, Animals, Genetic Code, Humans, Protein Conformation, Proteins, RNA, Messenger, Protein Biosynthesis, Protein Folding, Intrinsically Disordered Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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