Progress in microbial utilization of one-carbon feedstocks for biomanufacturing

doi:10.16085/j.issn.1000-6613.2022-1639

Abstract

Abstract:

One-carbon compounds (C₁, including CO₂, CO, methane, formate and methanol) have been considered as ideal alternative feedstocks for biomanufacturing, due to their abundance and low production cost. Microbes that could use C₁ substrates has been widely studied and engineered for production of biofuels and chemicals from C₁ feedstocks. This review briefly summarized the sources of C₁ feedstocks including traditional coal, oil and natural gas, and renewable resources. Microbes that utilize C₁ compounds as energy and carbon sources, and various C₁ compounds utilization pathways in these microbes were detailed. Achievements in production of value-added products from C₁ feedstocks in various hosts, as well as challenges in this area and further efforts needed were also discussed.

Key words: one-carbon compounds, biomanufacturing, carbon dioxide, carbon fixation, carbon neutrality, renewable energy

摘要：

一碳化合物（包括CO₂、CO、甲烷、甲醇、甲酸等）来源广泛，价格低廉，并且有望通过光催化、电催化等实现绿色、可持续生产，被认为是下一代生物制造的理想原料。自然界中广泛存在多种能够天然利用一碳化合物的微生物，对这些微生物开展研究，并进行改造和利用，使其以一碳资源为原料合成能源和化学品，对于降低对传统化石资源的依赖，实现绿色、可持续发展具有重要意义。本文主要概述各种一碳化合物的原料来源，包括传统化石资源和可再生原料、一碳化合物微生物利用途径以及各种一碳利用微生物及其改造合成燃料和化学品的相关研究进展，并对近年来构建合成型一碳转化体系的相关研究进行总结，最后分析了一碳化合物生物转化面临的挑战并对未来研究方向进行展望。

关键词: 一碳化合物, 生物制造, 二氧化碳, 碳固定, 碳中和, 再生能源

CLC Number:

Q819

YAO Lun, ZHOU Yongjin. Progress in microbial utilization of one-carbon feedstocks for biomanufacturing[J]. Chemical Industry and Engineering Progress, 2023, 42(1): 16-29.

姚伦, 周雍进. 一碳化合物生物利用和转化研究进展[J]. 化工进展, 2023, 42(1): 16-29.

Figures/Tables 4

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一碳利用微生物	代表物种	一碳底物	一碳利用途径	遗传操作	主要产物	参考文献
微藻	Chlamydomonas reinhardtii、Phaeodactylum tricornutum、Nannochloropsis oceanica	CO₂	CBB循环	大部分菌株难以进行遗传改造	三酰甘油等	[39-41]
蓝细菌	Synechocystis sp. PCC6803、Synechococcuselongatus PCC 7942、Synechococcus sp. PCC7002	CO₂	CBB循环	具备成熟的遗传操作体系	短链醇、长链脂肪酸及其衍生物等	[42-44]
一氧化碳自养菌（需氧型）	Oligotropha carboxidovorans、Hydrogenophaga pseudoflava	CO、CO₂（+H₂）	CBB循环	仅少数菌株能够进行遗传操作	PHA/PHB等	[45-47]
产乙酸菌	Clostridium autoethanogenum、 Clostridium ljungdahlii、 Clostridium carboxidivorans、Acetobacterium woodii	CO、CO₂（+H₂）、甲醇、甲酸	Wood-Ljungdahl途径	仅少数菌株能够进行遗传操作	有机酸、短链醇等	[48-53]
甲烷氧化菌	Methylomicrobium alcaliphilum、 Methylotuvimicrobium buryatense、 Methylococcus capsulatus	甲烷、甲醇、CO₂	RuMP途径、丝氨酸循环、 CBB循环	遗传操作工具相对有限	PHB、有机酸、短链醇等	[54-56]
甲醇细菌	Methylobacterium extorquens、Bacillus methanolicus	甲醇	RuMP途径、丝氨酸循环	遗传操作相对成熟	有机酸、PHA、氨基酸及其衍生物等	[57-61]
甲醇酵母	Komagataella phaffii、 Ogataea polymorpha	甲醇	XuMP途径	具备成熟的遗传操作系统	有机酸、脂肪酸及其衍生物等	[62-68]
钩虫贪铜菌	Cupriavidus necator	CO₂（+H₂）、甲酸	CBB循环	遗传操作相对成熟	PHB、短链醇等	[69-73]

一碳利用微生物	代表物种	一碳底物	一碳利用途径	遗传操作	主要产物	参考文献
微藻	Chlamydomonas reinhardtii、Phaeodactylum tricornutum、Nannochloropsis oceanica	CO₂	CBB循环	大部分菌株难以进行遗传改造	三酰甘油等	[39-41]
蓝细菌	Synechocystis sp. PCC6803、Synechococcuselongatus PCC 7942、Synechococcus sp. PCC7002	CO₂	CBB循环	具备成熟的遗传操作体系	短链醇、长链脂肪酸及其衍生物等	[42-44]
一氧化碳自养菌（需氧型）	Oligotropha carboxidovorans、Hydrogenophaga pseudoflava	CO、CO₂（+H₂）	CBB循环	仅少数菌株能够进行遗传操作	PHA/PHB等	[45-47]
产乙酸菌	Clostridium autoethanogenum、 Clostridium ljungdahlii、 Clostridium carboxidivorans、Acetobacterium woodii	CO、CO₂（+H₂）、甲醇、甲酸	Wood-Ljungdahl途径	仅少数菌株能够进行遗传操作	有机酸、短链醇等	[48-53]
甲烷氧化菌	Methylomicrobium alcaliphilum、 Methylotuvimicrobium buryatense、 Methylococcus capsulatus	甲烷、甲醇、CO₂	RuMP途径、丝氨酸循环、 CBB循环	遗传操作工具相对有限	PHB、有机酸、短链醇等	[54-56]
甲醇细菌	Methylobacterium extorquens、Bacillus methanolicus	甲醇	RuMP途径、丝氨酸循环	遗传操作相对成熟	有机酸、PHA、氨基酸及其衍生物等	[57-61]
甲醇酵母	Komagataella phaffii、 Ogataea polymorpha	甲醇	XuMP途径	具备成熟的遗传操作系统	有机酸、脂肪酸及其衍生物等	[62-68]
钩虫贪铜菌	Cupriavidus necator	CO₂（+H₂）、甲酸	CBB循环	遗传操作相对成熟	PHB、短链醇等	[69-73]

宿主	一碳原料	代谢途径	参考文献
E. coli	CO₂/甲酸	CBB循环	[102-103]
	CO₂/甲酸	还原甘氨酸途径	[104-109]
	CO₂	POAP循环	[110]
	甲酸/甲醛/甲醇	FORCE途径	[111]
	甲醇	RuMP途径	[112-117]
	甲酸/甲醇	丝氨酸循环	[118]
	甲醇	SACA途径	[119]
Saccharomyces cerevisiae	CO₂/甲酸	还原甘氨酸途径	[120]
Saccharomyces cerevisiae	甲醇	XuMP途径	[121]
Methylorubrumextorquens	CO₂	CBB循环	[122]
Clostridium pasteurianum	CO₂/甲酸	还原甘氨酸途径	[123]
Cupriavidus necator	甲酸/CO₂	还原甘氨酸途径	[100]
Corynebacteriumglutamicum	甲醇	RuMP途径	[124-126]
Yarrowia lipolytica	甲醇	RuMP/XuMP途径	[127]
酶催化体系	CO₂	甲醛裂合酶途径	[128]
	CO₂	CETCH循环	[129-131]
	CO₂	rGPS-MCG循环	[132]
	甲醇	MCC途径	[133]
	甲醇	ASAP途径	[134]

宿主	一碳原料	代谢途径	参考文献
E. coli	CO₂/甲酸	CBB循环	[102-103]
	CO₂/甲酸	还原甘氨酸途径	[104-109]
	CO₂	POAP循环	[110]
	甲酸/甲醛/甲醇	FORCE途径	[111]
	甲醇	RuMP途径	[112-117]
	甲酸/甲醇	丝氨酸循环	[118]
	甲醇	SACA途径	[119]
Saccharomyces cerevisiae	CO₂/甲酸	还原甘氨酸途径	[120]
Saccharomyces cerevisiae	甲醇	XuMP途径	[121]
Methylorubrumextorquens	CO₂	CBB循环	[122]
Clostridium pasteurianum	CO₂/甲酸	还原甘氨酸途径	[123]
Cupriavidus necator	甲酸/CO₂	还原甘氨酸途径	[100]
Corynebacteriumglutamicum	甲醇	RuMP途径	[124-126]
Yarrowia lipolytica	甲醇	RuMP/XuMP途径	[127]
酶催化体系	CO₂	甲醛裂合酶途径	[128]
	CO₂	CETCH循环	[129-131]
	CO₂	rGPS-MCG循环	[132]
	甲醇	MCC途径	[133]
	甲醇	ASAP途径	[134]

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