Coding-Sequence Determinants of Gene Expression in Escherichia coli
Open accessAbstract
Synonymous mutations do not alter the encoded protein, but they can influence gene expression. To investigate how, we engineered a synthetic library of 154 genes that varied randomly at synonymous sites, but all encoded the same green fluorescent protein (GFP). When expressed in Escherichia coli , GFP protein levels varied 250-fold across the library. GFP messenger RNA (mRNA) levels, mRNA degradation patterns, and bacterial growth rates also varied, but codon bias did not correlate with gene expression. Rather, the stability of mRNA folding near the ribosomal binding site explained more than half the variation in protein levels. In our analysis, mRNA folding and associated rates of translation initiation play a predominant role in shaping expression levels of individual genes, whereas codon bias influences global translation efficiency and cellular fitness.
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Recent work has shown that mRNA structure stability in 5' region weakens as expression level increases, favoring more efficient translation initiation, and heterologous protein levels can be varied by mRNA stability near initiation site.
“Correspondingly, recent work has shown that in yeast and a wide range of other organisms, the stability of mRNA structures in the 5’ region weakens as expression level increases, favoring more efficient translation initiation [67], and wide variation in heterologous protein levels can be achieved by varying mRNA stability near the initiation site [68, 69].”
Researchers usually performed codon optimization on the antigen-coding sequence to enhance translation efficiency.
“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 [243]
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- Authors
- Kudla, G., Murray, A. W., Tollervey, D., & Plotkin, J. B.
- Affiliations
- Harvard University (US)
- Corresponding author
- Kudla, Grzegorz
- Plotkin, Joshua B.
- Venue
- Science
- Published
- 2009-04-10
- Volume
- 324
- Issue
- 5924
- Pages
- 255-258
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3902468
- OpenAlex
- W2051242197
- Cited by
- 1,458
- References
- 29
- Citations by year
- 2026: 66 · 2025: 62 · 2024: 77 · 2023: 68 · 2022: 63 · 2021: 84 · 2020: 81 · 2019: 82 · 2018: 100 · 2017: 80 · 2016: 88 · 2015: 95 · 2014: 111 · 2013: 113 · 2012: 99
- FWCI
- 38.21
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Wellcome Trust (BB/DO19621/1)
- Biotechnology and Biological Sciences Research Council (BB/D019621/1, BB/DO19621/1)
- National Institute of General Medical Sciences (P50GM068763)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Keywords
- synonymous mutations, gene expression, codon usage bias, mRNA folding, ribosome binding site, translation initiation, mRNA stability, green fluorescent protein, Escherichia coli, translation efficiency, cell fitness
- MeSH terms
- Base Composition, Cloning, Molecular, Codon, Escherichia coli, Genes, Synthetic, Mutation, Nucleic Acid Conformation, RNA, Bacterial, RNA, Messenger, Spectrometry, Fluorescence, Protein Biosynthesis, Gene Library, Gene Expression, Amino Acid Substitution, RNA Stability, Green Fluorescent Proteins
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