Selective Charging of tRNA Isoacceptors Explains Patterns of Codon Usage
Abstract
We modeled how the charged levels of different transfer RNAs (tRNAs) that carry the same amino acid (isoacceptors) respond when this amino acid becomes growth-limiting. The charged levels will approach zero for some isoacceptors (such as tRNA2Leu) and remain high for others (such as tRNA4Leu), as determined by the concentrations of isoacceptors and how often their codons occur in protein synthesis. The theory accounts for (synonymous) codons for the same amino acid that are used in ribosome-mediated transcriptional attenuation, the choices of synonymous codons in trans-translating transfermessenger RNA, and the overrepresentation of rare codons in messenger RNAs for amino acid biosynthetic enzymes.
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tRNA concentration is a major selective force on codon usage patterns.
“suggesting that this is a major selective force on codon usage patterns [31-33].”
From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [33]
Codon frequencies correlate with tRNA concentrations.
“Codon frequencies correlate with tRNA concentrations, suggesting that this is a major selective force on codon usage patterns [31-33].”
From Preferred and avoided codon pairs in three domains of life (2008) · cites this paper as [33]
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References 23 · Cited by 260
- Authors
- Elf, J., Nilsson, D., Tenson, T., & Ehrenberg, M.
- Affiliations
- Uppsala University (SE)
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, 751 24 Uppsala, Sweden.
- Venue
- Science
- Published
- 2003-06-13
- Volume
- 300
- Issue
- 5626
- Pages
- 1718-1722
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2079136072
- Cited by
- 260
- References
- 23
- Citations by year
- 2026: 8 · 2025: 10 · 2024: 4 · 2023: 11 · 2022: 3 · 2021: 14 · 2020: 13 · 2019: 14 · 2018: 20 · 2017: 13 · 2016: 15 · 2015: 14 · 2014: 16 · 2013: 13 · 2012: 21
- FWCI
- 3.56
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- 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 › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- tRNA isoacceptors, codon usage, synonymous codons, rare codons, protein synthesis
- MeSH terms
- Amino Acids, Amino Acyl-tRNA Synthetases, Codon, Escherichia coli, Kinetics, Mathematics, Models, Genetic, Operon, Pyrophosphatases, Ribosomes, RNA, Bacterial, RNA, Messenger, RNA, Transfer, RNA, Transfer, Amino Acyl, Protein Biosynthesis, Gene Expression Regulation, Bacterial, Frameshifting, Ribosomal, Escherichia coli Proteins
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