负碳人工光合群落的设计、优化与应用

doi:10.12211/2096-8280.2024-001

合成生物学 ›› 2024, Vol. 5 ›› Issue (5): 1189-1210.DOI: 10.12211/2096-8280.2024-001

负碳人工光合群落的设计、优化与应用

郑皓天¹^,², 李朝风¹^,², 刘良叙¹^,², 王嘉伟¹^,², 李恒润¹^,², 倪俊¹^,²

^1.上海交通大学生命科学技术学院，微生物代谢国家重点实验室，上海 200240
^2.上海交通大学张江高等研究院，上海 201203

收稿日期:2024-01-02 修回日期:2024-04-16 出版日期:2024-10-31 发布日期:2024-11-20
通讯作者: 倪俊
作者简介:郑皓天（2000—），男，硕士研究生。研究方向为人工光合群落和光合细胞工厂的设计与优化。 E-mail：zhenghtjames@sjtu.edu.cn
倪俊（1987—），男，副教授，博士生导师。研究方向为合成生物学；人工光合群落；多酶级联组装；负碳生物合成等。 E-mail：tearroad@sjtu.edu.cn
基金资助:
国家自然科学基金(32071418);国家重点研发计划(2019YFA0904603)

Design, optimization and application of synthetic carbon-negative phototrophic community

Haotian ZHENG¹^,², Chaofeng LI¹^,², Liangxu LIU¹^,², Jiawei WANG¹^,², Hengrun LI¹^,², Jun NI¹^,²

^1.State Key Laboratory of Microbial Metabolism，School of Life Science and Technology，Shanghai Jiaotong University，Shanghai 200240，China
^2.Zhangjiang Institute for Advanced Study，Shanghai Jiaotong University，Shanghai 201203，China

Received:2024-01-02 Revised:2024-04-16 Online:2024-10-31 Published:2024-11-20
Contact: Jun NI

摘要/Abstract

摘要：

CO₂生物转化技术的开发为解决能源转型和气候变化问题提供了可能。人工光合群落是由密切协作的光合自养微生物与异养微生物组成的新一代生物炼制平台，能够通过群落成员间的互利代谢分工，高效地利用光能将CO₂直接转化为生物质和多种化学品，是实现负碳生物制造的潜在途径之一，因其在适用性和鲁棒性方面的优势受到了广泛的关注。近年来，随着系统生物学研究和合成生物技术的快速发展，多种研究策略被用于人工光合群落的设计与优化，取得了长远的进展，促进了对光合群落生产的理解。本文综述了光合群落的互作机制、独到优势和系统生物学研究方法，着重介绍人工光合群落的底盘升级、固定化/区室化技术、加强内部多层次调控等设计与优化策略以及在不同领域的应用进展。在此基础上，探讨了进一步将人工光合群落规模化应用所面临的光合效率和中间碳水化合物限制以及外源生物污染等潜在挑战，对纳米半导体材料杂合、物种间精细互作关系调控、基于多组学数据的群落模型构建等未来的改造方向和研究策略进行了展望。

关键词: 合成生物学, 光合群落, 负碳生物合成, CO₂利用, 系统生物学, 群体感应

Abstract:

The extensive consumption of fossil oil and the rapid accumulation of greenhouse gas emissions have caused long-term changes in the global climate and environment, sparking widespread interest in society for CO₂ bioconversion technologies as a means to address energy transition and climate change. As a new-generation biorefinery platform based on synthetic biology, the synthetic phototrophic community comprises closely cooperating phototrophic and heterotrophic microorganisms. This community is capable of efficiently converting light energy directly into biomass and a variety of chemicals through mutualistic metabolic division of labor among community members. Synthetic phototrophic community is one of the potential ways to achieve sustainable carbon-negative biomanufacturing, and has attracted widespread attention attributed to its advantages in applicability and robustness. In recent years, with the rapid development of systems biology and synthetic biotechnology, a variety of research efforts have been applied to the design and optimization of synthetic phototrophic communities, achieving stable progress and promoting the understanding of phototrophic community production. In this review, we briefly introduced an overview of the advances and current status of synthetic phototrophic community, including mutualistic mechanisms related to element, energy, and information flow. Subsequently, the unique advantages of phototrophic community were outlined. Meanwhile, recent systems biology approaches of phototrophic community were summarized, such as integrative analysis of multi-omics data, genome-scale metabolic modelling, flux balance analysis and community performance predictive algorithms. We also focused on the design and optimization strategies, such as chassis upgrading, immobilization/compartmentalization techniques, and enhanced internal multilayer regulation of synthetic phototrophic community, as well as the progress of their applications in various fields. Furthermore, we analyzed and discussed the constraints and challenges for the further deployment of synthetic phototrophic community on a larger scale, ranging from photosynthetic carbon production rate, intermediate organic matter selection, external predator invasion, to light distribution under high density cultivation. Finally, the future research strategies and engineering directions of synthetic phototrophic community encompassing semiconductor biohybrids, fine regulation of interspecies interaction and multi-omics community model construction were proposed. We conclude by providing a perspective on the future application scenarios of synthetic phototrophic communities in biochemistry, biomedicine, bioremediation and bioagriculture.

Key words: synthetic biology, phototrophic communities, carbon-negative biosynthesis, CO₂ utilization, systems biology, quorum sensing

中图分类号:

Q819

郑皓天, 李朝风, 刘良叙, 王嘉伟, 李恒润, 倪俊. 负碳人工光合群落的设计、优化与应用[J]. 合成生物学, 2024, 5(5): 1189-1210.

Haotian ZHENG, Chaofeng LI, Liangxu LIU, Jiawei WANG, Hengrun LI, Jun NI. Design, optimization and application of synthetic carbon-negative phototrophic community[J]. Synthetic Biology Journal, 2024, 5(5): 1189-1210.

图/表 5

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自养微生物	异养微生物	中间碳	产物	滴度/(mg/L)	产率/[mg/(L·d)]	参考文献
S. elongatus PCC 7942	S. cerevisiae	蔗糖	促进生长	—	—	[102]
S. elongatus PCC 7942	A. vinelandii	蔗糖	PHB	< 40	< 8	[103]
S. elongatus PCC 7942	H. boliviensis	蔗糖	PHB	未指明	28.3	[25]
S. elongatus PCC 7942	R. glutinis	蔗糖	游离脂肪酸	39	1.2	[82]
S. elongatus PCC 7942	P. putida	蔗糖	PHA	156	9.8	[104]
S. elongatus PCC 7942	S. cerevisiae	蔗糖	促进生长	—	—	[105]
S. elongatus PCC 7942	E. coli	蔗糖	PHB	< 1	< 0.15	[105]
S. elongatus PCC 7942	B. subtilis	蔗糖	α-淀粉酶	未指明	未指明	[105]
S. elongatus PCC 7942	P. putida	蔗糖	PHA；降解2,4-DNT	5.1	5.1	[83]
S. elongatus PCC 7942	P. putida	蔗糖	HMF转化为FDCA	约750	约250	[106]
S. elongatus PCC 7942	E. coli	蔗糖	促进生长	—	—	[96]
S. elongatus PCC 7942	Y. lipolytica	蔗糖	促进生长	—	—	[96]
S. elongatus PCC 7942	B. subtilis	蔗糖	促进生长	—	—	[96]
S. elongatus PCC 7942	E. coli	蔗糖	异戊二烯	400	15.4	[87]
S. elongatus PCC 7942	P. putida	蔗糖	PHA	393	42.1	[24]
S. elongatus PCC 7942	E. coli	蔗糖	乙烯	1.2	0.6	[84]
S. elongatus PCC 7942	E. coli	蔗糖	异戊二烯	0.051	0.026	[84]
S. elongatus PCC 7942	E. coli	蔗糖	促进生长	—	—	[27]
S. elongatus PCC 7942	V. natriegens	蔗糖	乳酸	313.3	52.2	[28]
S. elongatus PCC 7942	V. natriegens	蔗糖	2,3-丁二醇	137.3	22.9	[28]
S. elongatus PCC 7942	V. natriegens	蔗糖	对香豆酸	24.7	4.1	[28]
S. elongatus PCC 7942	V. natriegens	蔗糖	黑色素	9.1	1.5	[28]
S. elongatus PCC 7942	A. nidulans	蔗糖	Neosartoricin B	0.2	0.05	[107]
S. elongatus PCC 7942	E. coli	蔗糖	构建方法开发	—	—	[108]
S. elongatus PCC 7942	E. coli	蔗糖	匹配度预测	—	—	[101]
S. elongatus PCC 7942	E. coli	蔗糖	群体感应工具箱开发	—	—	[78]
S. elongatus UTEX 2973	E. coli	蔗糖	3-羟基丙酸	68.3	9.8	[26]
S. elongatus UTEX 2973	P. putida	蔗糖	天然蓝色素	7500	1250	[29]
S. elongatus UTEX 2973	Y. lipolytica	蔗糖	β-胡萝卜素	1300	260	[29]
Synechococcus sp. WH7803	R. pomeroyi	光合产物	促进生长	—	—	[109]
Synechococcus sp. PCC 7002	S. putrefaciens	光合产物	促进生长	—	—	[110]
Synechococcus sp. PCC 7002	M. alcaliphilum	光合产物	甲烷降解	—	—	[111]
T. elongates PKUAC-SCTE542	E. coli	蔗糖	乙烯	1.5	0.74	[84]
T. elongates PKUAC-SCTE542	E. coli	蔗糖	异戊二烯	0.027	0.013	[84]
T. elongatus BP-1	M. ruber	光合产物	促进生长	—	—	[112]
Nostoc sp. PCC 6720	A. nidulans	光合产物	促进生长	—	—	[113]
Nostoc sp. PCC 7413	A. niger	光合产物	促进生长	—	—	[114]
Nostocaceae sp. SAB-B866	P. cypripedii	光合产物	促进植物生长	—	—	[115]
Nostocaceae sp. SAB-B866	P. putida	光合产物	促进植物生长	—	—	[115]
S. hyalinum	废水内源微生物	光合产物	废水处理	—	—	[116]
P. keutzingium	活性污泥微生物	光合产物	氢气；废水处理	89.9	14.9	[117]
T. obliquus IS2	V. paradoxus	光合产物	废水处理	—	—	[118]
Chlorella sp. GY-H4	S. cerevisiae	光合产物	苯乙醇	2130	710	[119]

自养微生物	异养微生物	中间碳	产物	滴度/(mg/L)	产率/[mg/(L·d)]	参考文献
S. elongatus PCC 7942	S. cerevisiae	蔗糖	促进生长	—	—	[102]
S. elongatus PCC 7942	A. vinelandii	蔗糖	PHB	< 40	< 8	[103]
S. elongatus PCC 7942	H. boliviensis	蔗糖	PHB	未指明	28.3	[25]
S. elongatus PCC 7942	R. glutinis	蔗糖	游离脂肪酸	39	1.2	[82]
S. elongatus PCC 7942	P. putida	蔗糖	PHA	156	9.8	[104]
S. elongatus PCC 7942	S. cerevisiae	蔗糖	促进生长	—	—	[105]
S. elongatus PCC 7942	E. coli	蔗糖	PHB	< 1	< 0.15	[105]
S. elongatus PCC 7942	B. subtilis	蔗糖	α-淀粉酶	未指明	未指明	[105]
S. elongatus PCC 7942	P. putida	蔗糖	PHA；降解2,4-DNT	5.1	5.1	[83]
S. elongatus PCC 7942	P. putida	蔗糖	HMF转化为FDCA	约750	约250	[106]
S. elongatus PCC 7942	E. coli	蔗糖	促进生长	—	—	[96]
S. elongatus PCC 7942	Y. lipolytica	蔗糖	促进生长	—	—	[96]
S. elongatus PCC 7942	B. subtilis	蔗糖	促进生长	—	—	[96]
S. elongatus PCC 7942	E. coli	蔗糖	异戊二烯	400	15.4	[87]
S. elongatus PCC 7942	P. putida	蔗糖	PHA	393	42.1	[24]
S. elongatus PCC 7942	E. coli	蔗糖	乙烯	1.2	0.6	[84]
S. elongatus PCC 7942	E. coli	蔗糖	异戊二烯	0.051	0.026	[84]
S. elongatus PCC 7942	E. coli	蔗糖	促进生长	—	—	[27]
S. elongatus PCC 7942	V. natriegens	蔗糖	乳酸	313.3	52.2	[28]
S. elongatus PCC 7942	V. natriegens	蔗糖	2,3-丁二醇	137.3	22.9	[28]
S. elongatus PCC 7942	V. natriegens	蔗糖	对香豆酸	24.7	4.1	[28]
S. elongatus PCC 7942	V. natriegens	蔗糖	黑色素	9.1	1.5	[28]
S. elongatus PCC 7942	A. nidulans	蔗糖	Neosartoricin B	0.2	0.05	[107]
S. elongatus PCC 7942	E. coli	蔗糖	构建方法开发	—	—	[108]
S. elongatus PCC 7942	E. coli	蔗糖	匹配度预测	—	—	[101]
S. elongatus PCC 7942	E. coli	蔗糖	群体感应工具箱开发	—	—	[78]
S. elongatus UTEX 2973	E. coli	蔗糖	3-羟基丙酸	68.3	9.8	[26]
S. elongatus UTEX 2973	P. putida	蔗糖	天然蓝色素	7500	1250	[29]
S. elongatus UTEX 2973	Y. lipolytica	蔗糖	β-胡萝卜素	1300	260	[29]
Synechococcus sp. WH7803	R. pomeroyi	光合产物	促进生长	—	—	[109]
Synechococcus sp. PCC 7002	S. putrefaciens	光合产物	促进生长	—	—	[110]
Synechococcus sp. PCC 7002	M. alcaliphilum	光合产物	甲烷降解	—	—	[111]
T. elongates PKUAC-SCTE542	E. coli	蔗糖	乙烯	1.5	0.74	[84]
T. elongates PKUAC-SCTE542	E. coli	蔗糖	异戊二烯	0.027	0.013	[84]
T. elongatus BP-1	M. ruber	光合产物	促进生长	—	—	[112]
Nostoc sp. PCC 6720	A. nidulans	光合产物	促进生长	—	—	[113]
Nostoc sp. PCC 7413	A. niger	光合产物	促进生长	—	—	[114]
Nostocaceae sp. SAB-B866	P. cypripedii	光合产物	促进植物生长	—	—	[115]
Nostocaceae sp. SAB-B866	P. putida	光合产物	促进植物生长	—	—	[115]
S. hyalinum	废水内源微生物	光合产物	废水处理	—	—	[116]
P. keutzingium	活性污泥微生物	光合产物	氢气；废水处理	89.9	14.9	[117]
T. obliquus IS2	V. paradoxus	光合产物	废水处理	—	—	[118]
Chlorella sp. GY-H4	S. cerevisiae	光合产物	苯乙醇	2130	710	[119]

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负碳人工光合群落的设计、优化与应用

Design, optimization and application of synthetic carbon-negative phototrophic community

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