ArticleNature2016
Codon influence on protein expression in E. coli correlates with mRNA levels.
Article in Nature, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 236 papers, 2 of them syntheses that pooled it.
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Who cites it
236 citing papers in PubMed, 2 syntheses or guidelines pooled it, 457 citations in OpenAlex.
- Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding.Annual review of biochemistry · 2021Pooled it
- Predicting Functional Effects of Synonymous Variants: A Systematic Review and Perspectives.Frontiers in genetics · 2019Pooled it
- N-terminal fusion length: The key to reliable and context-preserving regulatory sequence characterization.Synthetic and systems biotechnology · 2027Article
- Collided ribosomes are rescued by the endonuclease Rae1 andbioRxiv : the preprint server for biology · 2026Article
- Enhancing protein expression in humans through codon optimization with transformer and contrastive learning.Molecular therapy. Nucleic acids · 2026Article
- Bacterial engineering for cancer therapy.Nature cancer · 2026Review
- The leading region of many plasmids is adapted for translational efficiency.Nucleic acids research · 2026Article
- Spatial and genetic constraints govern transcription-translation coupling and mRNA degradation in bacteria.Nature microbiology · 2026Article
- Transcripts enriched in codons that trigger P-site tRNA-mediated mRNA decay possess stable mRNA.FEBS open bio · 2026Article
- Deep Learning-Guided Reverse Translation Enhances Soluble Expression of Recombinant Proteins inInternational journal of molecular sciences · 2026Article
- Transfer learning with pre-trained language models for protein expression level prediction inSynthetic and systems biotechnology · 2026Article
- Multi-gene Co-expression systems inSynthetic and systems biotechnology · 2026Review
- Scalable and cost-efficient custom gene library assembly from oligopools.Science advances · 2026Article
- Elucidating the regulatory role of the Shine-Dalgarno sequence in structural gene expression of the malolactic enzyme operon using a GFP/mCherry model.World journal of microbiology & biotechnology · 2026Article
- Essentiality and dynamic expression of the human tRNA pool during viral infection.Molecular systems biology · 2026Article
- Identification of the Mutations Spectrum in the Fumarylacetoacetate Hydrolase Gene in Tyrosinemia Type 1 Patients in Northeastern Iran.Biochemical genetics · 2026Article
- Dissecting host stress responses for predictable heterologous gene expression in E. coli.Nucleic acids research · 2026Article
- Cross-species gene redesign leveraging ortholog information and generative modeling.Nature communications · 2026Article
- Synonymous editing alters ion channel function, favoring prime editing for retinal disease correction.International journal of biological sciences · 2026Article
- QDPR rs3733570 polymorphism is associated with type 2 diabetes and diabetic kidney disease accompanied by hyperlipidemia in the Chinese Han population.Frontiers in medicine · 2026Article
176 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
14 authors at 4 institutions in 1 country.
Funding
Abstract
Degeneracy in the genetic code, which enables a single protein to be encoded by a multitude of synonymous gene sequences, has an important role in regulating protein expression, but substantial uncertainty exists concerning the details of this phenomenon. Here we analyse the sequence features influencing protein expression levels in 6,348 experiments using bacteriophage T7 polymerase to synthesize messenger RNA in Escherichia coli. Logistic regression yields a new codon-influence metric that correlates only weakly with genomic codon-usage frequency, but strongly with global physiological protein concentrations and also mRNA concentrations and lifetimes in vivo. Overall, the codon content influences protein expression more strongly than mRNA-folding parameters, although the latter dominate in the initial ~16 codons. Genes redesigned based on our analyses are transcribed with unaltered efficiency but translated with higher efficiency in vitro. The less efficiently translated native sequences show greatly reduced mRNA levels in vivo. Our results suggest that codon content modulates a kinetic competition between protein elongation and mRNA degradation that is a central feature of the physiology and also possibly the regulation of translation in E. coli.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.