塑造低碳经济的第三代固碳生物炼制

doi:10.12211/2096-8280.2020-015

合成生物学 ›› 2020, Vol. 1 ›› Issue (1): 44-59.DOI: 10.12211/2096-8280.2020-015

塑造低碳经济的第三代固碳生物炼制

史硕博¹^,², 孟琼宇¹, 乔玮博¹, 赵惠民³

^1.北京化工大学北京软物质科学与工程高精尖创新中心，北京 100029
^2.北京化工大学秦皇岛环渤海生物产业研究院，河北秦皇岛 066000
^3.美国伊利诺伊大学香槟分校化学与生物分子工程系，伊利诺伊州厄巴纳-香槟市 IL618 01

收稿日期:2020-03-02 修回日期:2020-04-14 出版日期:2020-02-29 发布日期:2020-07-07
通讯作者: 赵惠民
作者简介:史硕博（1981-），男，博士，教授，主要从事微生物代谢工程及合成生物学研究。E-mail：shishuobo@mail.buct.edu.cn
赵惠民（1969-），男，博士，现为伊利诺伊大学香槟分校化学与生物分子工程系Steven L. Miller讲座教授，主要从事合成生物学研究。E-mail：zhao5@illinois.edu
基金资助:
国家自然科学基金(21878013);国家重点研发计划(2018YFA0901800)

Establishing carbon dioxide-based third-generation biorefinery for a sustainable low-carbon economy

SHI Shuobo¹^,², MENG Qiongyu¹, QIAO Weibo¹, ZHAO Huimin³

^1.Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
^2.Qinhuangdao Bohai Biological Research Institute, Beijing University of Chemical Technology, Qinhuangdao, 066000, Hebei, China
^3.Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL618 01, USA

Received:2020-03-02 Revised:2020-04-14 Online:2020-02-29 Published:2020-07-07
Contact: ZHAO Huimin

摘要/Abstract

摘要：

目前人类社会面临的两大挑战是如何实现非化石来源化学品和燃料的可持续生产以及如何应对大量二氧化碳排放造成的温室效应。第三代固碳生物炼制利用细胞工厂可将二氧化碳固定为一系列化学品和燃料，有望解决这一问题，从而建立以低能耗、低污染、低排放为基础的低碳经济模式。构建可利用二氧化碳的细胞工厂是迈向建立第三代固碳生物炼制平台的重要一步。随着生命科学的飞速发展，越来越多的二氧化碳固定机制被揭示。为了提高固碳效率，研究人员利用合成生物学改造天然固碳途径，并在此基础上设计人工固碳途径，或引入新颖的能源供应模式，甚至使异养模式生物变为合成自养生物。本文将对上述领域进行总结，并讨论微生物固定二氧化碳的主要挑战及其未来前景。

关键词: 合成生物学, 生物炼制, 二氧化碳, 低碳经济, 细胞工厂

Abstract:

Due to the sharply increased greenhouse gas (GHG) emissions, there is an urgent need to transit from the traditional ‘take-make-dispose’ economy to a sustainable economy with ecological balances through circular green technologies such as biorefineries. Based on the source of the feedstocks, existing biorefineries can be classified into three types: starch-based first-generation biorefinery, cellulosic biomass-based second-generation biorefinery, and carbon dioxide (CO₂)-based third-generation biorefinery. Compared to the first- and second-generation biorefineries, the third-generation biorefinery will not only significantly reduce the GHG emissions but also have no issues on food and water security. However, one of the major challenges in establishing the third-generation biorefinery is the design and engineering of microbial cell factories capable of efficiently utilizing CO₂ for the production of chemicals, fuels, and materials. In the past decades, a variety of CO₂ fixation pathways have been discovered in naturally occurring CO₂ fixation microorganisms (autotrophs) such as microalgae, cyanobacteria, and acetogens, and significant progress has been made in engineering these autotrophs to extend the product portfolio or improve the carbon fixation efficiencies. Recently, some of these CO₂ fixation pathways were successfully incorporated into heterotrophic microorganisms commonly used as microbial cell factories such as Escherichia coli and Pichia pastoris. In this review, we will first introduce both the naturally occurring and artificially designed CO₂ fixation pathways, and then discuss the application of synthetic biology strategies and tools for engineering autotrophs and heterotrophs to convert CO₂ into a variety of industrially important compounds. Finally, we will briefly comment on the prospects of CO₂-based biorefinery and the relevant scientific opportunities and challenges.

Key words: synthetic biology, biorefinery, carbon dioxide, low-carbon economy, microbial cell factory

中图分类号:

Q819

史硕博, 孟琼宇, 乔玮博, 赵惠民. 塑造低碳经济的第三代固碳生物炼制[J]. 合成生物学, 2020, 1(1): 44-59.

SHI Shuobo, MENG Qiongyu, QIAO Weibo, ZHAO Huimin. Establishing carbon dioxide-based third-generation biorefinery for a sustainable low-carbon economy[J]. Synthetic Biology Journal, 2020, 1(1): 44-59.

图/表 4

图1 大气中二氧化碳浓度和温度变化（1880—2020年）（柱状图表示当年的全球平均温度，曲线表示当年大气中的二氧化碳浓度。数据来源于美国国家海洋和大气管理局[3]）

Fig. 1 The global average concentration of carbon dioxide and temperature in the atmosphere (1880—2020) (The histogram shows the global average temperature of the year, and the curve shows the concentration of carbon dioxide in the atmosphere. The data came from the National Oceanic and Atmospheric Administration of USA [3])

图2 天然二氧化碳固定途径[黑色表示CBB循环（CBB cycle），是自然界中普遍的固碳途径；红色表示还原性甘氨酸通路（reductive glycine pathway），可以利用CO2和甲酸盐合成甘氨酸，是一个最新发现的潜在天然固碳途径；棕色表示还原性乙酰辅酶A通路（Wood-Ljungdahl pathway），可被产甲烷菌和产乙酸菌使用；其他几条途径虽然是分别在不同物种中独立进化得到的，但均使用乙酰CoA/琥珀酰CoA之间的循环进行固碳，且共享一些反应和中间代谢物，包括：浅蓝色表示的还原性三羧酸循环（reductive TCA cycle）、绿色表示的二羧酸/4-羟基丁酸循环（DC/HB cycle）、橙色表示的3-羟基丙酸/4-羟基丁酸循环（HP/HB cycle）和紫色表示的3-羟基丙酸循环（3-HPA bicycle）]

Fig. 2 Natural carbon dioxide fixation pathways identified[The black color indicates the CBB cycle, which is a universal carbon fixation pathway in nature. The red indicates the reductive Glycine pathway that can utilize CO2 and formate to synthesize glycine, which is a newly discovered potential natural carbon fixation pathway. The brown color indicates the reduced acetyl-CoA pathway (Wood-Ljungdahl pathway), which can be used by methanogens and acetogens. Moreover, the reductive TCA cycle (in light blue), the DC/HB cycle (in green), the HP/HB cycle (in orange) and the 3-HPA bicycle (in purple) all use the cycle between acetyl CoA / succinyl CoA to fix carbon and share some reactions and intermediate metabolites, although evolved independently in different ecological niches]

图3 人工设计二氧化碳固定途径

Fig. 3 Artificially designed carbon dioxide fixation pathways

表1 合成生物学在改造和设计固碳途径方面的应用

Tab. 1 Synthetic biology strategies in designing and engineering CO2-fixation pathways

策略	出发菌株	描述	年份	参考文献
改造自养微生物
调控RuBisCO酶	微拟球藻（Nannochloropsis oceanica）	提高了微拟球藻46%的生物量和32%的生长速率	2017	[58]
减小捕光天线蛋白	莱茵衣藻（Chlamydomonas reinhardtii）	减小天线蛋白，提高了10%的光能利用率	2014	[59]
减小捕光天线蛋白	小球藻（Chlorella vulgaris）	减小天线蛋白，提高了65%的光能利用率	2016	[60]
过表达RuBisCO酶， SBPase， FBA，TK	胞藻（Synechocystis sp. PCC 6803）	提升52%的生物量积累	2016	[61]
RuBisCO酶工程改造	胞藻（Synechocystis sp. PCC 6803）	提升55%的光合效率	2015	[31]
HP/HB途径	强烈炽热球菌 (Pyrococcusfuriosus)	引入异源固碳途径，利用CO₂ 生产3-羟基丙酸	2013	[62]
引入电化学系统	罗尔斯通菌（Ralstonia eutropha）	实现利用CO₂作为唯一碳源和电能作为唯一能量来源生产异丁醇和3-甲基-1-丁醇	2012	[57]
改造异养模式微生物
引入3-羟基丙酸循环	大肠杆菌(E. coli)	分4步将3-羟基丙酸循环在大肠杆菌中表达，并验证了每一步的活性	2013	[63]
引入还原性三羧酸循环	大肠杆菌(E. coli)	在大肠杆菌表达了还原性三羧酸循环以增强马来酸的产量	2018	[64]
引入还原性乙酰辅酶A通路	大肠杆菌(E. coli)	实现了从甲酸和CO₂合成甘氨酸和丝氨酸	2018	[47]
重建CBB循环部分途径	酿酒酵母（Saccharomyces cerevisiae）	CO₂作为碳源之一生产乙醇	2013/2017	[65,66]
引入CBB循环及相应代谢网络改造和适应性进化	大肠杆菌(E. coli)	利用CO₂合成了大约35%的生物质	2016	[67]
引入CBB循环及适应性进化	大肠杆菌(E. coli)	利用CO₂作为唯一碳源和甲酸作为唯一能量来源的“自养”生长	2019	[68]
引入过氧化物酶体甲醇同化途径及CBB循环改造	毕赤酵母（Pichia pastoris）	利用CO₂作为唯一碳源和甲醇作为唯一能量来源的“自养”生长	2019	[69]

表1 合成生物学在改造和设计固碳途径方面的应用

Tab. 1 Synthetic biology strategies in designing and engineering CO2-fixation pathways

策略	出发菌株	描述	年份	参考文献
改造自养微生物
调控RuBisCO酶	微拟球藻（Nannochloropsis oceanica）	提高了微拟球藻46%的生物量和32%的生长速率	2017	[58]
减小捕光天线蛋白	莱茵衣藻（Chlamydomonas reinhardtii）	减小天线蛋白，提高了10%的光能利用率	2014	[59]
减小捕光天线蛋白	小球藻（Chlorella vulgaris）	减小天线蛋白，提高了65%的光能利用率	2016	[60]
过表达RuBisCO酶， SBPase， FBA，TK	胞藻（Synechocystis sp. PCC 6803）	提升52%的生物量积累	2016	[61]
RuBisCO酶工程改造	胞藻（Synechocystis sp. PCC 6803）	提升55%的光合效率	2015	[31]
HP/HB途径	强烈炽热球菌 (Pyrococcusfuriosus)	引入异源固碳途径，利用CO₂ 生产3-羟基丙酸	2013	[62]
引入电化学系统	罗尔斯通菌（Ralstonia eutropha）	实现利用CO₂作为唯一碳源和电能作为唯一能量来源生产异丁醇和3-甲基-1-丁醇	2012	[57]
改造异养模式微生物
引入3-羟基丙酸循环	大肠杆菌(E. coli)	分4步将3-羟基丙酸循环在大肠杆菌中表达，并验证了每一步的活性	2013	[63]
引入还原性三羧酸循环	大肠杆菌(E. coli)	在大肠杆菌表达了还原性三羧酸循环以增强马来酸的产量	2018	[64]
引入还原性乙酰辅酶A通路	大肠杆菌(E. coli)	实现了从甲酸和CO₂合成甘氨酸和丝氨酸	2018	[47]
重建CBB循环部分途径	酿酒酵母（Saccharomyces cerevisiae）	CO₂作为碳源之一生产乙醇	2013/2017	[65,66]
引入CBB循环及相应代谢网络改造和适应性进化	大肠杆菌(E. coli)	利用CO₂合成了大约35%的生物质	2016	[67]
引入CBB循环及适应性进化	大肠杆菌(E. coli)	利用CO₂作为唯一碳源和甲酸作为唯一能量来源的“自养”生长	2019	[68]
引入过氧化物酶体甲醇同化途径及CBB循环改造	毕赤酵母（Pichia pastoris）	利用CO₂作为唯一碳源和甲醇作为唯一能量来源的“自养”生长	2019	[69]

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塑造低碳经济的第三代固碳生物炼制

Establishing carbon dioxide-based third-generation biorefinery for a sustainable low-carbon economy

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