Cited by 835RNA and protein synthesis mechanismsRNA modifications and cancerRNA Research and Splicing

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Codon optimality, bias and usage in translation and mRNA decay

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Hanson, Gavin, Coller, Jeff·2018·Nature Reviews Molecular Cell Biology

DOI 10.1038/nrm.2017.91PMC PMC6594389

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Abstract

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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Authors: Hanson, G., & Coller, J.
Affiliations: Case Western Reserve University (US)
Corresponding author: Hanson, Gavin
Coller, Jeff
ORCID: Hanson, Gavin
Coller, Jeff
Venue: Nature Reviews Molecular Cell Biology
Publisher: Springer Science and Business Media LLC
Published: 2017-10-11
Volume: 19
Issue: 1
Pages: 20-30
ISSN: 1471-0072 (ISSN-L)
1471-0080
DOI: 10.1038/nrm.2017.91
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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Codon optimality, bias and usage in translation and mRNA decay

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