| No. | Title | Authors | Journal |
|---|---|---|---|
| 192 | Comparative Analysis of Codon Optimization Tools: Advancing toward a Multi-Criteria Framework for Synthetic Gene Design | Eden A. Demissie, Seo-Young Park, Je Hun Moon, Dong-Yup Lee | JMB 2025(35): e2411066 |
Abstract
Abstract
Codon optimization is an essential technique in synthetic biology and biopharmaceutical production, enhancing recombinant protein expression by fine-tuning genetic sequences to match the translational machinery and codon usage preferences of specific host organisms. This study presents a comprehensive comparative analysis of widely used codon optimization tools, focusing on their capacity to reflect host-specific codon biases, design principles, and parameters. Industrially relevant target proteins were evaluated in Escherichia coli, Saccharomyces cerevisiae, and CHO cells, uncovering significant variability in sequence design and clustering patterns across tools. Tools such as JCat, OPTIMIZER, ATGme, and GeneOptimizer demonstrated strong alignment with genome-wide and highly expressed gene-level codon usage, achieving high codon adaptation index (CAI) values and efficient codon-pair utilization. Conversely, tools like TISIGNER and IDT employed different optimization strategies that frequently produced divergent results. Other key parameters, including GC content, mRNA secondary structure stability (ΔG), and codon-pair bias (CPB), were analyzed to elucidate their influence on translational efficiency. While increased GC content enhanced mRNA stability in E. coli, A/T-rich codons in S. cerevisiae minimized secondary structure formation, and moderate GC content in CHO cells balanced mRNA stability and translation efficiency. Our findings highlight the limitations of single-metric approaches and advocate for a multi-criteria framework that integrates CAI, GC content, mRNA folding energy, and codon-pair considerations. This integrative strategy enables the design of tailored genetic sequences that meet host-specific requirements, advancing synthetic gene design for biotechnological innovation and precision biopharmaceutical applications.
Date: 2026.5.26 (화) 12:00 ~ 15:00
Presenter: Yeoncheon Yu & Youbi Noh
유연천 학생과 노유비 학생의 주도로, 다양한 Host system에서의 단백질 발현 효율 향상을 위한 코돈 최적화(codon optimization) 전략 및 관련 알고리즘들에 대해 저널클럽을 진행했습니다.
Abstract
Codon optimization is an essential technique in synthetic biology and biopharmaceutical production, enhancing recombinant protein expression by fine-tuning genetic sequences to match the translational machinery and codon usage preferences of specific host organisms. This study presents a comprehensive comparative analysis of widely used codon optimization tools, focusing on their capacity to reflect host-specific codon biases, design principles, and parameters. Industrially relevant target proteins were evaluated in Escherichia coli, Saccharomyces cerevisiae, and CHO cells, uncovering significant variability in sequence design and clustering patterns across tools. Tools such as JCat, OPTIMIZER, ATGme, and GeneOptimizer demonstrated strong alignment with genome-wide and highly expressed gene-level codon usage, achieving high codon adaptation index (CAI) values and efficient codon-pair utilization. Conversely, tools like TISIGNER and IDT employed different optimization strategies that frequently produced divergent results. Other key parameters, including GC content, mRNA secondary structure stability (ΔG), and codon-pair bias (CPB), were analyzed to elucidate their influence on translational efficiency. While increased GC content enhanced mRNA stability in E. coli, A/T-rich codons in S. cerevisiae minimized secondary structure formation, and moderate GC content in CHO cells balanced mRNA stability and translation efficiency. Our findings highlight the limitations of single-metric approaches and advocate for a multi-criteria framework that integrates CAI, GC content, mRNA folding energy, and codon-pair considerations. This integrative strategy enables the design of tailored genetic sequences that meet host-specific requirements, advancing synthetic gene design for biotechnological innovation and precision biopharmaceutical applications.
Date: 2026.5.26 (화) 12:00 ~ 15:00
Presenter: Yeoncheon Yu & Youbi Noh
유연천 학생과 노유비 학생의 주도로, 다양한 Host system에서의 단백질 발현 효율 향상을 위한 코돈 최적화(codon optimization) 전략 및 관련 알고리즘들에 대해 저널클럽을 진행했습니다.