ArticleBMC systems biology2014
A condition-specific codon optimization approach for improved heterologous gene expression in Saccharomyces cerevisiae.
Article in BMC systems biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 112 citations in OpenAlex.
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- Comparative Analysis of Codon Optimization Tools: Advancing toward a Multi-Criteria Framework for Synthetic Gene Design.Journal of microbiology and biotechnology · 2025Article
- Mirages in continuous directed enzyme evolution: a cautionary case study with plantized bacterial THI4 enzymes.Plant biotechnology journal · 2025Article
- Amino acid sequence encodes protein abundance shaped by protein stability at reduced synthesis cost.Protein science : a publication of the Protein Society · 2025Article
- Strangers in a foreign land: 'Yeastizing' plant enzymes.Microbial biotechnology · 2024Review
- EngineeringEngineering microbiology · 2024Review
- Relative synonymous codon usage and codon pair analysis of depression associated genes.Scientific reports · 2024Article
- Engineering strategies for enhanced heterologous protein production by Saccharomyces cerevisiae.Microbial cell factories · 2024Review
- Harnessing synthetic biology for advancing RNA therapeutics and vaccine design.NPJ systems biology and applications · 2023Review
- The ribosome quality control factor Asc1 determines the fate of HSP70 mRNA on and off the ribosome.Nucleic acids research · 2023Article
- Optimization of ribosome utilization inPNAS nexus · 2023Article
- Yeast as a tool for membrane protein production and structure determination.FEMS yeast research · 2022Article
- Design of typical genes for heterologous gene expression.Scientific reports · 2022Article
- Saccharomyces cerevisiae as a Heterologous Host for Natural Products.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Boosting lignan-precursor synthesis in yeast cell factories through co-factor supply optimization.Frontiers in bioengineering and biotechnology · 2022Article
- CHARMING: Harmonizing synonymous codon usage to replicate a desired codon usage pattern.Protein science : a publication of the Protein Society · 2022Article
- Codon pair optimization (CPO): a software tool for synthetic gene design based on codon pair bias to improve the expression of recombinant proteins in Pichia pastoris.Microbial cell factories · 2021Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 2 countries.
Funding
Abstract
backgroundHeterologous gene expression is an important tool for synthetic biology that enables metabolic engineering and the production of non-natural biologics in a variety of host organisms. The translational efficiency of heterologous genes can often be improved by optimizing synonymous codon usage to better match the host organism. However, traditional approaches for optimization neglect to take into account many factors known to influence synonymous codon distributions.
resultsHere we define an alternative approach for codon optimization that utilizes systems level information and codon context for the condition under which heterologous genes are being expressed. Furthermore, we utilize a probabilistic algorithm to generate multiple variants of a given gene. We demonstrate improved translational efficiency using this condition-specific codon optimization approach with two heterologous genes, the fluorescent protein-encoding eGFP and the catechol 1,2-dioxygenase gene CatA, expressed in S. cerevisiae. For the latter case, optimization for stationary phase production resulted in nearly 2.9-fold improvements over commercial gene optimization algorithms.
conclusionsCodon optimization is now often a standard tool for protein expression, and while a variety of tools and approaches have been developed, they do not guarantee improved performance for all hosts of applications. Here, we suggest an alternative method for condition-specific codon optimization and demonstrate its utility in Saccharomyces cerevisiae as a proof of concept. However, this technique should be applicable to any organism for which gene expression data can be generated and is thus of potential interest for a variety of applications in metabolic and cellular engineering.
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