Biological carbon fixation: from natural to synthetic

doi:10.12211/2096-8280.2022-042

Abstract

Abstract:

In recent years, the increase in the atmospheric concentration of CO₂ has caused serious environmental problems such as climate change, and carbon neutrality is presently a topic of global interest. Achieving carbon neutrality means to convert the atmospheric CO₂ into carbon-based compounds. Converting CO₂ into organics that can be used by humans is one of the effective ways to utilize CO₂. Among them, biological carbon fixation has received great interest. In nature, plants and microbes can fix CO₂ through carbon fixation pathways. Researchers have also designed several novel artificial carbon fixation pathways for CO₂ fixation. Research on biological carbon fixation has mainly focused on the modification of natural carbon fixation pathways and the design and synthesis of artificial carbon fixation pathways. Since the carbon atom in the CO₂ is in the highest oxidation state and the reduction of CO₂ into organics requires energy input, the input of reducing power and energy is one of the key factors determining the efficiency of carbon biofixation. This review summarizes the advances achieved in recent years in the engineering of natural carbon fixation pathways and the design and construction of artificial carbon fixation pathways. The efficiencies of the artificial carbon fixation pathways, including the utilization of CO₂-derived one carbon compounds, and the natural carbon fixation pathways are compared. Subsequently, we highlight the importance of reducing power and energy supply in the process of artificial biological carbon fixation, including chemical energy such as ATP and reducing power, light energy and electric energy. Finally, we analyze the challenges and trends of biological carbon fixation in terms of pathways and energy, and propose strategies for future research on biological carbon fixation.

Key words: biological carbon fixation, natural carbon fixation pathway, artificial carbon fixation pathway, energy, reducing equivalent

摘要：

近年来，大气中二氧化碳浓度上升引起了气候变化等一系列环境问题，“碳中和”成为各国发展目标之一。实现碳中和，意味着要将空气中的二氧化碳固定下来，作为生产碳基化合物的原料。将二氧化碳转化为人类可以利用的有机物是利用二氧化碳的有效途径之一，这使得二氧化碳的生物固定和转化成为当前研究热点，重点聚焦在天然固碳途径的改造和人工固碳途径的设计合成。由于二氧化碳中的碳原子处于最高氧化态，二氧化碳还原成有机物需要能量输入，如何输入还原力和能量是决定生物固碳效率的关键因素。本文总结了近年来天然固碳途径改造、人工固碳途径设计合成方面取得的进展，对天然固碳途径和人工固碳途径进行了比较分析，并重点讨论了人工生物固碳过程中的还原力和能量输入问题，包括还原力、ATP等化学能、光能和电能等。最后，从途径和能量两方面分析了生物固碳面临的问题和发展趋势，并据此提出了一些可能的研究方向。

关键词: 生物固碳, 天然固碳途径, 人工固碳途径, 能量, 还原力

CLC Number:

Lu XIAO, Yin LI. Biological carbon fixation: from natural to synthetic[J]. Synthetic Biology Journal, 2022, 3(5): 833-846.

肖璐, 李寅. 生物固碳：从自然生物到人工合成[J]. 合成生物学, 2022, 3(5): 833-846.

Figures/Tables 4

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途径	厌氧/ 好氧	反应数	产物	固碳酶	ATP/CO₂/(mol/mol)	NAD(P)H/CO₂/(mol/mol)
卡尔文循环^[8]	好氧	11	3-PGA	Rubisco	3	2
还原性TCA 循环^[9]	厌氧	9	乙酰辅酶A	2-oxoglutarate synthase and isocitrate dehydrogenase	1	2
WL途径^[10]	厌氧	8	乙酰辅酶A	Formate dehydrogenase and CO dehydrogenate/ Acetyl-CoA synthase	0.5	2
3-羟基丙酸双循环^[11]	好氧	16	丙酮酸	Acetyl-CoA carboxylase and propionyl-CoA carboxylase	1.67	1.67
3-羟基丙酸/4-羟基丁酸循环^[12]	好氧	16	乙酰辅酶A	Acetyl-CoA carboxylase and propionyl-CoA carboxylase	2	2
二羧酸/4-羟基丁酸循环^[13]	厌氧	14	乙酰辅酶A	Pyruvate synthase and Phosphoenolpyruvate carboxylase	1.5	2

途径	厌氧/ 好氧	反应数	产物	固碳酶	ATP/CO₂/(mol/mol)	NAD(P)H/CO₂/(mol/mol)
卡尔文循环^[8]	好氧	11	3-PGA	Rubisco	3	2
还原性TCA 循环^[9]	厌氧	9	乙酰辅酶A	2-oxoglutarate synthase and isocitrate dehydrogenase	1	2
WL途径^[10]	厌氧	8	乙酰辅酶A	Formate dehydrogenase and CO dehydrogenate/ Acetyl-CoA synthase	0.5	2
3-羟基丙酸双循环^[11]	好氧	16	丙酮酸	Acetyl-CoA carboxylase and propionyl-CoA carboxylase	1.67	1.67
3-羟基丙酸/4-羟基丁酸循环^[12]	好氧	16	乙酰辅酶A	Acetyl-CoA carboxylase and propionyl-CoA carboxylase	2	2
二羧酸/4-羟基丁酸循环^[13]	厌氧	14	乙酰辅酶A	Pyruvate synthase and Phosphoenolpyruvate carboxylase	1.5	2

Strain	Fermentation time	Fermentation mode	Product	Titer or productivity	Ref
Clostridium ljungdahlii	560 h	Cell recycle in the CSTR	Ethanol	48 g/L	[33]
Acetobacterium woodii	11 d	A batch-operated stirred-tank bioreactor	Acetate	44 g/L	[34]
Acetobacterium woodii	-	Continuous fermentation	Acetone	26.4 mg/(L·h)	[35]
Clostridium sp. MTButOH365	6 d	Single-stage continuous fermentation	Butanol	21.98 g/L	[36]
Clostridium sp. MAceT113	5 d	Single-stage continuous fermentation	Acetone	104 g/L	[32]
Clostridium sp. MT1802	25 d	Single-stage continuous fermentation	2,3-butanediol	9.18 g/L	[37]
Clostridium sp. MT1424	25 d	Single-stage continuous fermentation	Methanol	70.4 g/L	[38]
Clostridium sp. MT1424	25 d	Single-stage continuous fermentation	Formate	4.3 g/L	[38]
Clostridium sp. MT1243	25 d	Single-stage continuous fermentation	Mevalonate	97 mmol/L	[39]

Strain	Fermentation time	Fermentation mode	Product	Titer or productivity	Ref
Clostridium ljungdahlii	560 h	Cell recycle in the CSTR	Ethanol	48 g/L	[33]
Acetobacterium woodii	11 d	A batch-operated stirred-tank bioreactor	Acetate	44 g/L	[34]
Acetobacterium woodii	-	Continuous fermentation	Acetone	26.4 mg/(L·h)	[35]
Clostridium sp. MTButOH365	6 d	Single-stage continuous fermentation	Butanol	21.98 g/L	[36]
Clostridium sp. MAceT113	5 d	Single-stage continuous fermentation	Acetone	104 g/L	[32]
Clostridium sp. MT1802	25 d	Single-stage continuous fermentation	2,3-butanediol	9.18 g/L	[37]
Clostridium sp. MT1424	25 d	Single-stage continuous fermentation	Methanol	70.4 g/L	[38]
Clostridium sp. MT1424	25 d	Single-stage continuous fermentation	Formate	4.3 g/L	[38]
Clostridium sp. MT1243	25 d	Single-stage continuous fermentation	Mevalonate	97 mmol/L	[39]

途径	体内/体外	反应数	底物	产物	固碳酶	固碳速率 /[nmol C/(min·mg总酶量)]	ATP/CO₂/(mol/mol)	NAD(P)H /CO₂/(mol/mol)
MCG途径	体内	8	CO₂、PEP	乙酰辅酶A	Phosphoenolpyruvate carboxylase	—	3	3
CETCH循环	体外	12	CO₂	乙醛酸	Enoyl-CoA carboxylases/ reductases	3.87 [5 nmol C/(min·mg核心酶)]	1	1
SACA途径	体外	3	甲醛	乙酰辅酶A	—	—	—	—
POAP循环	体外	4	CO₂	草酸	Pyruvate synthase and pyruvate carboxylase	6.8	1	0.5
ASAP途径	体外	11	CO₂	淀粉	Formolase	17.2	0.5	2