Research progress of constructing efficient biomanufacturing system based on synthetic biotechnology

doi:10.12211/2096-8280.2021-015

Abstract

Abstract:

Efficient and environmentally friendly biomanufacturing system based on synthetic biotechnology is an important approach to achieve sustainable development. Synthetic biology is expected to bring revolutionary technological breakthroughs in various industries, such as food, pharmacy and chemistry, as well as farming and animal husbandry. In this paper, the latest advances of technologies and strategies in synthetic biology used in the progress of constructing efficient biomanufacturing systems were introduced. Four aspects, namely metabolic regulation of key genes, enzyme engineering, cofactor engineering and fermentation optimization, were discussed. Through these technologies, engineered microorganisms with high robustness and excellent performance were constructed. Secondly, an emphasis was put on the summary of diverse metabolic characteristics of typical model organisms at present. In this part, as many as seven strains were mentioned, such as Escherichia coli, Bacillus subtilis, Bacillus amyloliquefaciens, Bacillus licheniformis, Corynebacterium glutamicum, Pichia pastoris and Saccharomyces cerevisiae. And for each strain, the advantages and disadvantages of different typical model organisms were discussed to clarify the scope of their most suitable products. Escherichia coli is the most intensively studied typical model organism system, making it the preferred expression system for proteins of interest. However, insufficient post-translational processing limits its applications for expressing eukaryotic-derived proteins. Saccharomyces cerevisiae and Pichia pastoris make up for this deficiency. Yeast expression system has significant advantages for the synthesis of natural products from plant, due to the extensive and in-depth research of P450 enzymes, such as the biosynthesis of artemisinin. Lastly, application prospects of synthetic biology in constructing efficient biomanufacturing systems were discussed. With the developments in standard synthetic biology components and data, standard automated work platforms, precise and generally applicable engineering strategies, emerging of machine learning and synthetic biology, it is expected to facilitate efficient biological manufacturing system construction. Precise and various metabolic engineering technology, flexible and convenient enzyme engineering strategies and whole cell microorganism modeling would be the new driving force for efficient biomanufacturing system construction.

Key words: synthetic biotechnology, biomanufacturing systems, typical model microorganisms, metabolic engineering

摘要：

基于合成生物技术构建绿色高效的生物制造系统是实现可持续化发展的重要途径，该技术的发展应用有望为食品、能源、医药、化工以及畜牧养殖等行业带来革命性的技术变革。本文针对基于合成生物技术构建高效生物制造系统进行系统性的总结与讨论。首先概述了代谢工程、酶工程、辅助系统优化以及发酵过程控制等技术的研究进展；其次，着重对比总结了大肠杆菌、芽孢杆菌属、谷氨棒酸杆菌以及酵母属等典型模式宿主的代谢特性，探究了各微生物制造系统的适用范围。最后，对合成生物技术在构建高效生物制造系统领域中的应用前景进行了展望。精细多元的代谢工程技术、高效简便的酶工程策略以及数字化的微生物系统将是促进高效生物制造系统构建的新引擎与新动力。

关键词: 合成生物技术, 生物制造系统, 典型模式宿主, 代谢工程

CLC Number:

Q815

Xiaolong ZHANG, Chenyun WANG, Yanfeng LIU, Jianghua LI, Long LIU, Guocheng DU. Research progress of constructing efficient biomanufacturing system based on synthetic biotechnology[J]. Synthetic Biology Journal, 2021, 2(6): 863-875.

张晓龙, 王晨芸, 刘延峰, 李江华, 刘龙, 堵国成. 基于合成生物技术构建高效生物制造系统的研究进展[J]. 合成生物学, 2021, 2(6): 863-875.

Figures/Tables 2

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典型模式微生物	优缺点	适用范围	产品应用
大肠杆菌	发酵周期短，遗传背景清晰，具有成熟的基因编辑工具以及多元化的代谢调控策略；但不适于表达需要翻译后修饰的蛋白及膜蛋白	非糖基化重组蛋白表达系统	类胡萝卜素、紫杉醇、青蒿酸、丹参素、1,3-丙二醇、1,4-丁二醇以及1,3-丁二醇
枯草芽孢杆菌	出色的蛋白质分泌系统；同时具有典型的芽孢形成能力、细胞分裂以及生物膜系统；但极易形成不溶性包涵体，潜在的脂多糖和内毒素风险	碱性丝氨酸蛋白酶与中温淀粉酶制备生产；为微生物机理研究的首选微生物之一	核苷酸、维生素、表面活性剂、维生素B₂复合物、D-（-）-2,3-丁二醇、透明质酸^[53]以及抗生素（例如杆菌肽和枯草杆菌素）
地衣芽孢杆菌	清晰的遗传背景，出色的蛋白质分泌系统，在高温培养环境中拥有极佳的液化和糊化特性；但极易形成不溶性包涵体，潜在的脂多糖和内毒素风险	高温淀粉酶的工业化生产	耐热碱性蛋白酶、银纳米颗粒、生物絮凝剂、聚γ-谷氨酸、2,3-丁二醇
解淀粉芽孢杆菌	出色的蛋白质分泌系统；但极易形成不溶性包涵体，潜在的脂多糖和内毒素风险	中性或碱性蛋白酶的工业化生产	表面活性、果聚糖、S-腺苷甲硫氨酸、银纳米颗粒
谷氨酸棒杆菌	耗糖迅速，易于高密度发酵，无碳源分解代谢阻遏效应，且对有毒醇和芳香族化合物有较高耐受性；但遗传背景清晰，有成熟的调控工具	芳香族化合物的工业化生产	L-谷氨酸、L-赖氨酸以及透明质酸
酿酒酵母	遗传背景清晰，胞内代谢机制高度解析，拥有内质网、线粒体等细胞器，且有较好的pH与渗透压耐受性；但其糖基化过高，较低的蛋白表达能力限制其工业化生产	适合生产生物能源、蛋白质、萜类、脂肪酸和脂肪醇、芳香族化合物等生物制品	乙酰辅酶A、香叶醇、柠檬烯、白藜芦醇、柚皮素、胰岛素等
巴斯德毕赤酵母	极佳的蛋白分泌能力，优异的翻译后修饰（糖基化与二硫键），并且胞外内源性蛋白极少	适合异源蛋白表达	人促红细胞生成素、磷脂酶C、人超氧化物歧化酶、胰蛋白酶、人血清白蛋白、胶原蛋白和人单克隆抗体3H6 Fab片段

典型模式微生物	优缺点	适用范围	产品应用
大肠杆菌	发酵周期短，遗传背景清晰，具有成熟的基因编辑工具以及多元化的代谢调控策略；但不适于表达需要翻译后修饰的蛋白及膜蛋白	非糖基化重组蛋白表达系统	类胡萝卜素、紫杉醇、青蒿酸、丹参素、1,3-丙二醇、1,4-丁二醇以及1,3-丁二醇
枯草芽孢杆菌	出色的蛋白质分泌系统；同时具有典型的芽孢形成能力、细胞分裂以及生物膜系统；但极易形成不溶性包涵体，潜在的脂多糖和内毒素风险	碱性丝氨酸蛋白酶与中温淀粉酶制备生产；为微生物机理研究的首选微生物之一	核苷酸、维生素、表面活性剂、维生素B₂复合物、D-（-）-2,3-丁二醇、透明质酸^[53]以及抗生素（例如杆菌肽和枯草杆菌素）
地衣芽孢杆菌	清晰的遗传背景，出色的蛋白质分泌系统，在高温培养环境中拥有极佳的液化和糊化特性；但极易形成不溶性包涵体，潜在的脂多糖和内毒素风险	高温淀粉酶的工业化生产	耐热碱性蛋白酶、银纳米颗粒、生物絮凝剂、聚γ-谷氨酸、2,3-丁二醇
解淀粉芽孢杆菌	出色的蛋白质分泌系统；但极易形成不溶性包涵体，潜在的脂多糖和内毒素风险	中性或碱性蛋白酶的工业化生产	表面活性、果聚糖、S-腺苷甲硫氨酸、银纳米颗粒
谷氨酸棒杆菌	耗糖迅速，易于高密度发酵，无碳源分解代谢阻遏效应，且对有毒醇和芳香族化合物有较高耐受性；但遗传背景清晰，有成熟的调控工具	芳香族化合物的工业化生产	L-谷氨酸、L-赖氨酸以及透明质酸
酿酒酵母	遗传背景清晰，胞内代谢机制高度解析，拥有内质网、线粒体等细胞器，且有较好的pH与渗透压耐受性；但其糖基化过高，较低的蛋白表达能力限制其工业化生产	适合生产生物能源、蛋白质、萜类、脂肪酸和脂肪醇、芳香族化合物等生物制品	乙酰辅酶A、香叶醇、柠檬烯、白藜芦醇、柚皮素、胰岛素等
巴斯德毕赤酵母	极佳的蛋白分泌能力，优异的翻译后修饰（糖基化与二硫键），并且胞外内源性蛋白极少	适合异源蛋白表达	人促红细胞生成素、磷脂酶C、人超氧化物歧化酶、胰蛋白酶、人血清白蛋白、胶原蛋白和人单克隆抗体3H6 Fab片段

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