Optimizing multicopy chromosomal integration for stable high-performing strains

IF 12.9 1区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Nature chemical biology Pub Date : 2024-06-10 DOI:10.1038/s41589-024-01650-0

Fei Du, Zijia Li, Xin Li, Duoduo Zhang, Feng Zhang, Zixu Zhang, Yingshuang Xu, Jin Tang, Yongqian Li, Xingxu Huang, Yang Gu, Xiaoman Sun, He Huang

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Abstract

The copy number of genes in chromosomes can be modified by chromosomal integration to construct efficient microbial cell factories but the resulting genetic systems are prone to failure or instability from triggering homologous recombination in repetitive DNA sequences. Finding the optimal copy number of each gene in a pathway is also time and labor intensive. To overcome these challenges, we applied a multiple nonrepetitive coding sequence calculator that generates sets of coding DNA sequence (CDS) variants. A machine learning method was developed to calculate the optimal copy number combination of genes in a pathway. We obtained an engineered Yarrowia lipolytica strain for eicosapentaenoic acid biosynthesis in 6 months, producing the highest titer of 27.5 g l⁻¹ in a 50-liter bioreactor. Moreover, the lycopene production in Escherichia coli was also greatly improved. Importantly, all engineered strains of Y. lipolytica, E. coli and Saccharomyces cerevisiae constructed with nonrepetitive CDSs maintained genetic stability.

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优化多拷贝染色体整合，培育稳定的高效菌株

染色体中基因的拷贝数可以通过染色体整合来改变，从而构建高效的微生物细胞工厂，但由此产生的基因系统很容易因引发重复 DNA 序列的同源重组而失效或不稳定。寻找通路中每个基因的最佳拷贝数也需要耗费大量时间和人力。为了克服这些挑战，我们采用了一种多重非重复编码序列计算器，它能生成一组编码 DNA 序列（CDS）变体。我们开发了一种机器学习方法来计算通路中基因的最佳拷贝数组合。我们在 6 个月内获得了一株可进行二十碳五烯酸生物合成的工程化脂肪溶解亚罗茨菌株，在 50 升生物反应器中产生的最高滴度为 27.5 g l-1。此外，在大肠杆菌中番茄红素的产量也大大提高。重要的是，所有利用非重复性 CDS 构建的脂溶性酵母菌、大肠杆菌和酿酒酵母工程菌株都保持了遗传稳定性。

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来源期刊

Nature chemical biology 生物-生化与分子生物学

CiteScore

23.90

自引率

1.40%

发文量

238

审稿时长

12 months

期刊介绍： Nature Chemical Biology stands as an esteemed international monthly journal, offering a prominent platform for the chemical biology community to showcase top-tier original research and commentary. Operating at the crossroads of chemistry, biology, and related disciplines, chemical biology utilizes scientific ideas and approaches to comprehend and manipulate biological systems with molecular precision. The journal embraces contributions from the growing community of chemical biologists, encompassing insights from chemists applying principles and tools to biological inquiries and biologists striving to comprehend and control molecular-level biological processes. We prioritize studies unveiling significant conceptual or practical advancements in areas where chemistry and biology intersect, emphasizing basic research, especially those reporting novel chemical or biological tools and offering profound molecular-level insights into underlying biological mechanisms. Nature Chemical Biology also welcomes manuscripts describing applied molecular studies at the chemistry-biology interface due to the broad utility of chemical biology approaches in manipulating or engineering biological systems. Irrespective of scientific focus, we actively seek submissions that creatively blend chemistry and biology, particularly those providing substantial conceptual or methodological breakthroughs with the potential to open innovative research avenues. The journal maintains a robust and impartial review process, emphasizing thorough chemical and biological characterization.

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