Abstract:

The construction of microbial cell factories plays a critical role in green biomanufacturing. The production of chemicals can be achieved using microbial cell factories, instead of traditional production methods that rely on plants and land resources. In recent years, synthetic biology has made significant advancements in biological manufacturing, including the successful biosynthesis and commercialization of natural products derived from plants, such as artemisinin and cannabidiol. However, the construction of engineered microbial cell factories still faces challenges due to the high complexity of living systems, the iterative nature of experimental processes, and low experimental throughput. To overcome these obstacles, the application of high-throughput, automated, and intelligent hardware, and software platforms, as well as standard, modular libraries of synthetic biology parts and processes, has led to the emergence of automated synthetic biotechnology. This breakthrough allows for low-cost, high-throughput, rapid, and iterative experimentation to efficiently construct large-scale engineering prototypes of microbial cell factories, thereby facilitating related research and applications in this field. To this end, dozens of automated biofoundries have been built around the world. This article primarily focuses on the application of automated synthetic biotechnology in the most critical and time-consuming step of "build" in the "design-build-test-learn" cycle of synthetic biology. The automated building of microbial cell factory demands both the automated construction of engineered DNA and the automated manipulation of microbial chassis, including gene synthesis, PCR amplification, enzymatic digestion, DNA assembly, transformation and plating, colony picking, cell lysis, nucleotide purification, and sequencing. In this review, we summarized the state-of-the-art automated processes and platforms for DNA assembly and microbial chassis manipulation, provided recent advances of automated synthetic biotechnology in the mining and characterization of biosynthetic gene clusters, the combinatorial optimization of metabolic pathways, and the engineering of microbial chassis. We also discussed the challenges and opportunities in automating the construction of microbial cell factories, putting forward to one of most important future directions in full process automation, including the construction of non-model microbial cell factories. The localization and independent research and development of automated biofoundry would make significant contributions to this process.

Key words: rapid construction of cell factories, automated synthetic biotechnology, DNA assembly, chassis manipulation

摘要：

基于绿色生物制造进行物质能量生产，有望减少对天然植被、耕地、石化等资源的依赖，而微生物细胞工厂是绿色生物制造过程的“芯片”。合成生物学为微生物细胞工厂的研究提供了重要的使能技术，但目前仍面临生命系统高度复杂、实验过程需要反复试错、实验通量较低等限制因素。自动化合成生物技术借助高通量、自动化和智能化的软硬件设施平台，基于标准化、模块化的生物元件库和合成生物工艺，可低成本、高通量、快速、多循环地完成海量工程试错性实验，加速特定性能人工细胞工厂的设计和优化，支撑相关研究和应用。本文主要针对细胞工厂“设计-构建-测试-学习”循环中最关键、最耗时的“构建”环节，对DNA组装和底盘细胞操作自动化工艺和设施平台进行了总结，对自动化合成生物技术应用于生物合成基因簇挖掘、代谢通路优化和底盘细胞优化的最新进展进行了介绍。最后展望了微生物细胞工厂自动化构建面临的挑战和未来发展，讨论了包括非模式微生物在内的全流程自动化的发展趋势，而自动化装备的国产化自主研发将为此做出重要贡献。

关键词: 细胞工厂快速构建, 自动化合成生物技术, DNA组装, 底盘细胞操作