Comparative Analysis of Codon Optimization Tools: Advancing toward a Multi-Criteria Framework for Synthetic Gene Design.

IF 2.5 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Eden A Demissie, Seo-Young Park, Je Hun Moon, Dong-Yup Lee
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引用次数: 0

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.

密码子优化工具的比较分析:迈向合成基因设计的多标准框架。
密码子优化是合成生物学和生物制药生产中的一项重要技术,它通过微调基因序列来匹配特定宿主生物的翻译机制和密码子使用偏好,从而增强重组蛋白的表达。本研究对广泛使用的密码子优化工具进行了全面的比较分析,重点关注它们反映宿主特异性密码子偏差、设计原则和参数的能力。工业上相关的靶蛋白在大肠杆菌、酿酒酵母和CHO细胞中进行了评估,揭示了不同工具在序列设计和聚类模式上的显著差异。JCat、OPTIMIZER、ATGme和GeneOptimizer等工具显示出与全基因组和高表达基因水平密码子使用的强一致性,实现了高密码子适应指数(CAI)值和高效的密码子对利用。相反,TISIGNER和IDT等工具采用不同的优化策略,经常产生不同的结果。分析GC含量、mRNA二级结构稳定性(ΔG)和密码子对偏倚(CPB)等其他关键参数对翻译效率的影响。大肠杆菌中GC含量的增加增强了mRNA的稳定性,酿酒酵母中富含A/ t的密码子减少了二级结构的形成,CHO细胞中GC含量的适度平衡了mRNA的稳定性和翻译效率。我们的研究结果强调了单度量方法的局限性,并提倡将CAI、GC含量、mRNA折叠能量和密码子对考虑因素集成在一起的多标准框架。这种综合策略能够设计出符合宿主特异性要求的定制基因序列,推进生物技术创新和精密生物制药应用的合成基因设计。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Journal of microbiology and biotechnology
Journal of microbiology and biotechnology BIOTECHNOLOGY & APPLIED MICROBIOLOGY-MICROBIOLOGY
CiteScore
5.50
自引率
3.60%
发文量
151
审稿时长
2 months
期刊介绍: The Journal of Microbiology and Biotechnology (JMB) is a monthly international journal devoted to the advancement and dissemination of scientific knowledge pertaining to microbiology, biotechnology, and related academic disciplines. It covers various scientific and technological aspects of Molecular and Cellular Microbiology, Environmental Microbiology and Biotechnology, Food Biotechnology, and Biotechnology and Bioengineering (subcategories are listed below). Launched in March 1991, the JMB is published by the Korean Society for Microbiology and Biotechnology (KMB) and distributed worldwide.
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