合成生物学 ›› 2023, Vol. 4 ›› Issue (4): 756-778.DOI: 10.12211/2096-8280.2023-032
程真真1,2, 张健1,2, 高聪1,2, 刘立明1,2, 陈修来1,2
收稿日期:
2023-04-17
修回日期:
2023-05-22
出版日期:
2023-08-31
发布日期:
2023-09-14
通讯作者:
陈修来
作者简介:
基金资助:
Zhenzhen CHENG1,2, Jian ZHANG1,2, Cong GAO1,2, Liming LIU1,2, Xiulai CHEN1,2
Received:
2023-04-17
Revised:
2023-05-22
Online:
2023-08-31
Published:
2023-09-14
Contact:
Xiulai CHEN
摘要:
微生物利用甲酸生产高附加值产品,是实现碳资源回收利用与绿色产业发展的重要策略之一。然而,在微生物利用甲酸过程中存在甲酸利用效率偏低、细胞生长速率缓慢、目标代谢物产量不高等问题。为了解决上述问题,本文从甲酸利用的微生物、代谢路径与代谢工程策略三个方面,系统总结分析了代谢工程改造微生物利用甲酸的研究进展。在甲酸利用微生物方面,概述了天然甲酸利用微生物的代谢特点以及模式微生物的代谢工程改造潜能;在甲酸利用代谢路径方面,梳理了天然的甲酸利用路径、重构与优化的甲酸利用路径与人工的甲酸利用路径的关键步骤、能量/还原力消耗与特点;在甲酸利用代谢工程策略方面,阐述了提高甲酸同化效率与改善甲酸利用微生物细胞生长的关键方法。最后,从甲酸利用的微生物、代谢路径与代谢工程策略三个方面,展望了微生物利用甲酸的发展方向,为甲酸生物经济的发展奠定了基础。
中图分类号:
程真真, 张健, 高聪, 刘立明, 陈修来. 代谢工程改造微生物利用甲酸研究进展[J]. 合成生物学, 2023, 4(4): 756-778.
Zhenzhen CHENG, Jian ZHANG, Cong GAO, Liming LIU, Xiulai CHEN. Progress in metabolic engineering of microorganisms for the utilization of formate[J]. Synthetic Biology Journal, 2023, 4(4): 756-778.
图1 天然甲酸利用微生物CBB cycle—Calvin-Benson-Bassham循环;THF—四氢叶酸;THMPT—四氢甲基蝶呤
Fig. 1 Natural formate-utilizing microorganismsCBB cycle—Calvin-Benson-Bassham cycle; THF—tetrahydrofolate; THMPT—tetrahydromethanopterin
微生物种类 | 需氧类型 | 模式菌株 | 天然甲酸 代谢路径 | 应用优劣势 | 参考 文献 |
---|---|---|---|---|---|
产乙酸菌 | 专性厌氧 | 伍氏醋酸杆菌 | 还原性乙酰辅酶A途径 | 优势:能够天然利用甲酸和CO2合成乙酸、乙醇等化合物 劣势:在厌氧条件下生长,不利于工业应用;代谢研究尚不完善,代谢改造工具少 | [ |
产甲烷菌 | 专性厌氧 | 氢营养型海沼甲烷球菌 | 还原性乙酰辅酶A途径 | 优势:能够天然利用甲酸和CO2合成甲烷,在清洁能源产业方面具有应用潜能 劣势:在厌氧条件下生长,不利于工业应用;代谢研究尚不完善,代谢改造工具少 | [ |
硫酸盐还原菌 | 专型厌氧 | 普通脱硫弧菌 | 还原性乙酰辅酶A途径 | 优势:具有非常高的氢化酶活性,能够天然利用甲酸产氢,在清洁能源产业方面具有应用潜能 劣势:厌氧条件下生长,不利于工业应用;代谢研究尚不完善,代谢改造工具少 | [ |
甲基杆菌 | 好氧或 兼性厌氧 | 扭脱甲基杆菌AM1 | 丝氨酸循环 | 优势:能够天然利用甲酸、CO2与甲醇等一碳底物进行细胞生长;模式菌株的研究与改造相对充分,具有一定的改造潜能 劣势:所具有的甲酸代谢路径的能量利用效率偏低,不利于工业应用 | [ |
CBB循环 依赖型微生物 | 好氧 | 钩虫贪铜菌H16 | 还原性磷酸戊糖循环 | 优势:具有甲酸脱氢酶,能够利用甲酸作为唯一碳源和能源;模式菌株的研究与改造相对充分,具有一定的应用潜能 劣势:甲酸的氧化供能存在能量浪费,因此微生物的细胞生长速率与工业生产潜能均偏低 | [ |
表1 天然甲酸利用微生物
Table 1 Natural formate-utilizing microorganisms
微生物种类 | 需氧类型 | 模式菌株 | 天然甲酸 代谢路径 | 应用优劣势 | 参考 文献 |
---|---|---|---|---|---|
产乙酸菌 | 专性厌氧 | 伍氏醋酸杆菌 | 还原性乙酰辅酶A途径 | 优势:能够天然利用甲酸和CO2合成乙酸、乙醇等化合物 劣势:在厌氧条件下生长,不利于工业应用;代谢研究尚不完善,代谢改造工具少 | [ |
产甲烷菌 | 专性厌氧 | 氢营养型海沼甲烷球菌 | 还原性乙酰辅酶A途径 | 优势:能够天然利用甲酸和CO2合成甲烷,在清洁能源产业方面具有应用潜能 劣势:在厌氧条件下生长,不利于工业应用;代谢研究尚不完善,代谢改造工具少 | [ |
硫酸盐还原菌 | 专型厌氧 | 普通脱硫弧菌 | 还原性乙酰辅酶A途径 | 优势:具有非常高的氢化酶活性,能够天然利用甲酸产氢,在清洁能源产业方面具有应用潜能 劣势:厌氧条件下生长,不利于工业应用;代谢研究尚不完善,代谢改造工具少 | [ |
甲基杆菌 | 好氧或 兼性厌氧 | 扭脱甲基杆菌AM1 | 丝氨酸循环 | 优势:能够天然利用甲酸、CO2与甲醇等一碳底物进行细胞生长;模式菌株的研究与改造相对充分,具有一定的改造潜能 劣势:所具有的甲酸代谢路径的能量利用效率偏低,不利于工业应用 | [ |
CBB循环 依赖型微生物 | 好氧 | 钩虫贪铜菌H16 | 还原性磷酸戊糖循环 | 优势:具有甲酸脱氢酶,能够利用甲酸作为唯一碳源和能源;模式菌株的研究与改造相对充分,具有一定的应用潜能 劣势:甲酸的氧化供能存在能量浪费,因此微生物的细胞生长速率与工业生产潜能均偏低 | [ |
微生物 | 非天然甲酸代谢路径 | 主要的应用优势 | 改造潜能 | 参考文献 |
---|---|---|---|---|
大肠杆菌 | 重构的卡尔文循环; 改良的丝氨酸循环; 高丝氨酸循环; rTHF-rgcv途径及关键模块 合成乙酰辅酶A途径等 | 生长周期短; 遗传背景清晰; 代谢工程改造工具种类丰富且高效 | 设计并构建更加高效的甲酸利用路径; 通过实验室适应性进化与培养条件优化等策略提高菌株对甲酸的耐受性 | [ |
酿酒酵母 | rTHF-rgcv途径 的关键模块 | 遗传背景清晰; 分子遗传操作工具与技术成熟且高效; 具有内源性甲酸脱氢酶,对甲酸的耐受性较高 | 通过代谢改造进一步提高rTHF-rgcv途径对甲酸的利用效率,开发以甲酸为唯一碳源和能源的工程菌株 | [ |
毕赤酵母 | 以甲酸作为P AOX1 的诱导物 | 能够利用甲醇作为唯一碳源和能源进行细胞生长; 在生物医药产业和工业酶生产方面具有巨大潜力 | 通过代谢改造进一步提高菌株对甲酸的利用效率; 基于菌株的代谢网络,设计并构建更加高效的甲酸利用路径 | [ |
恶臭假单胞菌 | rTHF-rgcv途径 | 能够编码多种天然甲酸脱氢酶; 具有灵活的代谢机制,能够抵抗氧化应激和多种有毒化合物 | 开发更高效的分子遗传操作工具,进一步完善菌株的甲酸代谢网络 | [ |
表2 代谢工程改造的微生物
Table 2 Metabolically engineered microorganisms
微生物 | 非天然甲酸代谢路径 | 主要的应用优势 | 改造潜能 | 参考文献 |
---|---|---|---|---|
大肠杆菌 | 重构的卡尔文循环; 改良的丝氨酸循环; 高丝氨酸循环; rTHF-rgcv途径及关键模块 合成乙酰辅酶A途径等 | 生长周期短; 遗传背景清晰; 代谢工程改造工具种类丰富且高效 | 设计并构建更加高效的甲酸利用路径; 通过实验室适应性进化与培养条件优化等策略提高菌株对甲酸的耐受性 | [ |
酿酒酵母 | rTHF-rgcv途径 的关键模块 | 遗传背景清晰; 分子遗传操作工具与技术成熟且高效; 具有内源性甲酸脱氢酶,对甲酸的耐受性较高 | 通过代谢改造进一步提高rTHF-rgcv途径对甲酸的利用效率,开发以甲酸为唯一碳源和能源的工程菌株 | [ |
毕赤酵母 | 以甲酸作为P AOX1 的诱导物 | 能够利用甲醇作为唯一碳源和能源进行细胞生长; 在生物医药产业和工业酶生产方面具有巨大潜力 | 通过代谢改造进一步提高菌株对甲酸的利用效率; 基于菌株的代谢网络,设计并构建更加高效的甲酸利用路径 | [ |
恶臭假单胞菌 | rTHF-rgcv途径 | 能够编码多种天然甲酸脱氢酶; 具有灵活的代谢机制,能够抵抗氧化应激和多种有毒化合物 | 开发更高效的分子遗传操作工具,进一步完善菌株的甲酸代谢网络 | [ |
图3 天然甲酸利用路径(绿色底色的化合物为路径底物,粉色底色的化合物为路径产物)Ack—乙酸激酶;Acs—乙酰辅酶A合成酶;COdh—CO脱氢酶;CoFeSP—钴铁硫蛋白;Eno—烯醇化酶;Fch—次甲基四氢叶酸环水解酶;Fdh—甲酸脱氢酶;Ftl—甲酸四氢叶酸连接酶;Fts—甲酰四氢叶酸合成酶;Gapdh—3-磷酸甘油醛脱氢酶;GCS—甘氨酸裂解系统;Gk—甘油酸激酶;GlyA—丝氨酸羟甲基转移酶;GR—甘氨酸还原酶复合体;Hpr—羟基丙酮还原酶;Madh—苹果酸脱氢酶;Mcl—苹果酰辅酶A裂解酶;Metr—甲基转移酶;Mtd—亚甲基四氢叶酸脱氢酶;Mtk—苹果酸裂解酶;Mtr—亚甲基四氢叶酸还原酶;PFOR—丙酮酸铁氧还蛋白氧化还原酶;Pgk—磷酸甘油酸激酶;Ppc—PEP羧化酶;Prk—磷酸核酮糖激酶;Rubisco—核酮糖-1,5-二磷酸羧化酶/加氧酶;Sda—丝氨酸脱氨酶;Sgt—丝氨酸-乙醛酸转氨酶;THF—四氢叶酸
Fig. 3 Natural formate-utilizing pathways(compounds with a green background are pathway substrates; compounds with a pink background are pathway products) Ack—Acetate kinase; Acs—acetyl-CoA synthase; COdh—CO dehydrogenase; CoFeSP—corrinoid ironsulfur protein; Eno—enolase; Fch—methenyl-tetrahydrofolate cyclohydrolase; Fdh—formate dehydrogenase; Ftl—formate-tetrahydrofolate ligase; Fts—formyl-tetrahydrofolate synthetase; Gapdh—glyceraldehyde-3-phosphate dehydrogenase; GCS—glycine cleavage system; Gk—glycerate kinase; GlyA—serine hydroxymethyltransferase; GR—Glycine reductase complex; Hpr—hydroxypyruvate reductase; Madh—malate dehydrogenase; Mcl—malyl-CoA lyase; Metr—methyltransferase; Mtd—methylene-tetrahydrofolate dehydrogenase; Mtk—malate thiokinase; Mtr—methylene-tetrahydrofolate reductase; PFOR—Pyruvate ferredoxin oxidoreductase; Pgk—Phosphoglycerate kinase; Ppc—phosphoenolpyruvate carboxylase; Prk—phosphoribulo kinase; Rubisco—Ribulose-1,5-bisphosphate carboxylase/oxygenase; Sda—serine deaminase; Sgt—serine-glyoxylate transaminase; THF—tetrahydrofolate
图4 重构优化甲酸利用路径(绿色底色的化合物为路径底物,粉色底色的化合物为路径产物)Acdh—乙醛脱氢酶;Acs—乙酰辅酶A合成酶;Agt—丙氨酸-乙醛酸转氨酶;CA—碳酸酐酶;Faldh—甲醛脱氢酶;Fch—次甲基四氢叶酸环水解酶;Fdh—甲酸脱氢酶;Fthfl—甲酸四氢叶酸连接酶;Ftl—甲酸四氢叶酸连接酶;GCS—甘氨酸裂解系统;Gldh—谷氨酸脱氢酶;GlyA—丝氨酸羟甲基转移酶;Gpt—谷氨酸-丙酮酸转氨酶;Hal—HOB醛缩酶;Hat—HOB转氨酶;Hsk—高丝氨酸激酶;Lta—苏氨酸醛缩酶;Madh—苹果酸脱氢酶;Mcl—苹果酰辅酶A裂解酶;Medh—甲醇脱氢酶;Mtd—亚甲基四氢叶酸脱氢酶;Mthfs—5,10-亚甲基四氢叶酸合成酶;Mtk—苹果酸硫激酶;Oxidative PPP—氧化戊糖磷酸途径;Pfk—磷酸果糖激酶;Ppc—PEP羧化酶;Pps—PEP合成酶;Prk—磷酸核酮糖激酶;Rubisco—核酮糖-1,5-二磷酸羧化酶;Sal—丝氨酸醛缩酶;Sda—丝氨酸脱氨酶;THF—四氢叶酸;Ts—苏氨酸合成酶;Zwf—6-磷酸葡萄糖脱氢酶
Fig. 4 Reconstruction and optimization of formate-utilizing pathways(compounds with a green background are pathway substrates; compounds with a pink background are pathway products) Acdh—acetaldehyde dehydrogenase; Acs—acetyl-CoA synthase; Agt—alanine-glyoxylate transaminase; CA—carbonic anhydrase; Faldh—formaldehyde dehydrogenase; Fch—methenyl-tetrahydrofolate cyclohydrolase; Fdh—formate dehydrogenase; Fthfl—formate-tetrahydrofolate ligase; Ftl—formate-tetrahydrofolate ligase; GCS—glycine cleavage system; Gldh—glutamate dehydrogenase; GlyA—serine hydroxymethyltransferase; Gpt—glutamate-pyruvate transaminase; Hal—4-hydroxy-2-oxobutanoate aldolase; Hat—4-hydroxy-2-oxobutanoate aminotransferase; Hsk—homoserine kinase; Lta—threonine aldolase; Madh—malate dehydrogenase; Mcl—malyl-CoA lyase; Medh—methanol dehydrogenase; Mtd—methylene-tetrahydrofolate dehydrogenase; Mthfs—5,10-methylene-tetrahydrofolate synthase; Mtk—malate thiokinase; Oxidative PPP—Oxidative pentose-phosphate pathway; Pfk—phosphofructokinase; Ppc—phosphoenolpyruvate carboxylase; Pps—phosphoenolpyruvate synthase; Prk—phosphoribulo kinase; Rubisco—ribulose-1,5-bisphosphate carboxylase; Sal—serine aldolase; Sda—serine deaminase; THF—tetrahydrofolate; Ts—threonine synthase; Zwf—glucose-6-phosphate dehydrogenase
菌株 | 路径酶来源 | 参考文献 |
---|---|---|
Escherichia coli | Ftl、Fch、Mtd(源自Clostridium ljungdahalii) GCS、GlyA、Sda(内源酶) | [ |
Escherichia coli | Ftl、Fch、Mtd(源自Methylobacterium extorquens AM1) GCS、GlyA(内源酶) | [ |
Escherichia coli | Ftl、Fch、Mtd(源自Methylobacterium extorquens CM4) GCS、GlyA、Sda(内源酶) Fdh(源自Candida boidinii) | [ |
Escherichia coli | Ftl(源自Clostridium kluyveri) FolD(Fch/ Mtd)、GCS、GlyA(内源酶) | [ |
Escherichia coli | Ftl、Fch、Mtd(源自Methylobacterium extorquens AM1) GCS、GlyA、Sda(内源酶) Fdh(源自Pseudomonas sp.) | [ |
Escherichia coli (Bang等[ | Ftl、Fch、Mtd(源自Methylobacterium extorquens CM4) GCS、GlyA、Sda(内源酶) Fdh(源自Candida boidinii、Arabidopsis thaliana) | [ |
Escherichia coli (Döring等[ | Ftl(源自Clostridium kluyveri) FolD(Fch/ Mtd)、GCS、GlyA(内源酶) | [ |
Escherichia coli (Kim等[ | Ftl、Fch、Mtd(源自Methylobacterium extorquens AM1) GCS、GlyA、Sda(内源酶) Fdh(源自Pseudomonas sp. ) | [ |
Saccharomyces cerevisiae | MIS1(Ftl/ Fch/ Mtd)、GCS(内源酶) Fdh(内源酶) | [ |
Cupriavidus necator | Ftl、Fch、Mtd(源自Methylobacterium extorquens AM1) GCS、GlyA、Sda(内源酶) Fdh(内源酶) | [ |
Clostridium pasteurianum | GCS(源自Gottschalkia acidurici) Ftl、Fch、Mtd、GlyA、Sda(内源酶) | [ |
Pseudomonas putida | Ftl、Fch、Mtd(源自Methylobacterium extorquens AM1) GCS、GlyA、Sda(内源酶) Fdh(内源酶) | [ |
表3 rTHF-rgcv途径的路径酶来源
Table 3 Source of pathway enzymes of the rTHF-rgcv pathway
菌株 | 路径酶来源 | 参考文献 |
---|---|---|
Escherichia coli | Ftl、Fch、Mtd(源自Clostridium ljungdahalii) GCS、GlyA、Sda(内源酶) | [ |
Escherichia coli | Ftl、Fch、Mtd(源自Methylobacterium extorquens AM1) GCS、GlyA(内源酶) | [ |
Escherichia coli | Ftl、Fch、Mtd(源自Methylobacterium extorquens CM4) GCS、GlyA、Sda(内源酶) Fdh(源自Candida boidinii) | [ |
Escherichia coli | Ftl(源自Clostridium kluyveri) FolD(Fch/ Mtd)、GCS、GlyA(内源酶) | [ |
Escherichia coli | Ftl、Fch、Mtd(源自Methylobacterium extorquens AM1) GCS、GlyA、Sda(内源酶) Fdh(源自Pseudomonas sp.) | [ |
Escherichia coli (Bang等[ | Ftl、Fch、Mtd(源自Methylobacterium extorquens CM4) GCS、GlyA、Sda(内源酶) Fdh(源自Candida boidinii、Arabidopsis thaliana) | [ |
Escherichia coli (Döring等[ | Ftl(源自Clostridium kluyveri) FolD(Fch/ Mtd)、GCS、GlyA(内源酶) | [ |
Escherichia coli (Kim等[ | Ftl、Fch、Mtd(源自Methylobacterium extorquens AM1) GCS、GlyA、Sda(内源酶) Fdh(源自Pseudomonas sp. ) | [ |
Saccharomyces cerevisiae | MIS1(Ftl/ Fch/ Mtd)、GCS(内源酶) Fdh(内源酶) | [ |
Cupriavidus necator | Ftl、Fch、Mtd(源自Methylobacterium extorquens AM1) GCS、GlyA、Sda(内源酶) Fdh(内源酶) | [ |
Clostridium pasteurianum | GCS(源自Gottschalkia acidurici) Ftl、Fch、Mtd、GlyA、Sda(内源酶) | [ |
Pseudomonas putida | Ftl、Fch、Mtd(源自Methylobacterium extorquens AM1) GCS、GlyA、Sda(内源酶) Fdh(内源酶) | [ |
图5 人工设计甲酸利用路径Acdh—乙醛脱氢酶;Acs—乙酰辅酶A合成酶;Acps—乙酰磷酸合成酶;Dhak—二羟基丙酮激酶;Fls—甲醛酶;Gals—乙醇醛合成酶;Pta—磷酸转乙酰酶(绿色底色的化合物为路径底物,粉色底色的化合物为路径产物)
Fig. 5 Artificial formate-utilizing pathwaysAcdh—acetaldehyde dehydrogenase; Acs—acetyl-CoA synthase; Acps—acetyl phosphate synthase; Dhak—dihydroxyacetone kinase; Fls—formolase; Gals—glycolaldehyde synthase; Pta—phosphate acetyltransferase (compounds with a green background are pathway substrates, compounds with a pink background are pathway products)
图6 提高甲酸同化效率的关键方法FDH—甲酸脱氢酶;Hint—H蛋白的氨甲基化形式;Hox—H蛋白的氧化形式;Hred—H蛋白的还原形式;TCA cycle—三羧酸循环;THF—四氢叶酸
Fig. 6 Key methods to improve the efficiency of formate assimilationFDH—formate dehydrogenase; Hint—aminomethylated form of H protein; Hox—oxidized form of H protein; Hred—reduced form of H protein; TCA cycle—tricarboxylic acid cycle; THF—tetrahydrofolate;
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摘要 |
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