ArticleScientific reports2017
Predicting synonymous codon usage and optimizing the heterologous gene for expression in E. coli.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 44 citations in OpenAlex.
- Leaky recombinant expression reveals design constraints of bicistronic synthetic operons in Escherichia coli.Scientific reports · 2026Article
- Hurdles to horizontal gene transfer: species-specific effects of synonymous variation and plasmid copy number determine antibiotic resistance phenotype.Microbiology (Reading, England) · 2026Article
- OPT: Codon optimize gene sequences for E. coli protein overexpression.Journal of molecular biology · 2025Article
- Escherichia coli Nissle 1917 efficiently expresses the RBD domain of SARS-CoV-2 spike protein without codon optimization.Scientific reports · 2025Article
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- Repositioning microbial biotechnology against COVID-19: the case of microbial production of flavonoids.Microbial biotechnology · 2021Review
- Strategies for enhancing gene expression in Escherichia coli.Applied microbiology and biotechnology · 2020Review
- Computational Tools for Discovering and Engineering Natural Product Biosynthetic Pathways.iScience · 2020Review
- Codon optimization, expression inPeerJ · 2020Article
- Optimization of culture conditions for the expression of three different insoluble proteins in Escherichia coli.Scientific reports · 2019Article
- Applications of Protein Engineering and Directed Evolution in Plant Research.Plant physiology · 2019Review
- Tuning recombinant protein expression to match secretion capacity.Microbial cell factories · 2018Article
- Presyncodon, a Web Server for Gene Design with the Evolutionary Information of the Expression Hosts.International journal of molecular sciences · 2018Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Of the 20 common amino acids, 18 are encoded by multiple synonymous codons. These synonymous codons are not redundant; in fact, all of codons contribute substantially to protein expression, structure and function. In this study, the codon usage pattern of genes in the E. coli was learned from the sequenced genomes of E. coli. A machine learning based method, Presyncodon was proposed to predict synonymous codon selection in E. coli based on the learned codon usage patterns of the residue in the context of the specific fragment. The predicting results indicate that Presycoden could be used to predict synonymous codon selection of the gene in the E. coli with the high accuracy. Two reporter genes (egfp and mApple) were designed with a combination of low- and high-frequency-usage codons by the method. The fluorescence intensity of eGFP and mApple expressed by the (egfp and mApple) designed by this method was about 2.3- or 1.7- folds greater than that from the genes with only high-frequency-usage codons in E. coli. Therefore, both low- and high-frequency-usage codons make positive contributions to the functional expression of the heterologous proteins. This method could be used to design synthetic genes for heterologous gene expression in biotechnology.
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