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Chin WC, Zhou YZ, Wang HY, Feng YT, Yang RY, Huang ZF, Yang YL. Bacterial polyynes uncovered: a journey through their bioactive properties, biosynthetic mechanisms, and sustainable production strategies. Nat Prod Rep 2024; 41:977-989. [PMID: 38284321 DOI: 10.1039/d3np00059a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Covering: up to 2023Conjugated polyynes are natural compounds characterized by alternating single and triple carbon-carbon bonds, endowing them with distinct physicochemical traits and a range of biological activities. While traditionally sourced mainly from plants, recent investigations have revealed many compounds originating from bacterial strains. This review synthesizes current research on bacterial-derived conjugated polyynes, delving into their biosynthetic routes, underscoring the variety in their molecular structures, and examining their potential applications in biotechnology. Additionally, we outline future directions for metabolic and protein engineering to establish more robust and stable platforms for their production.
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Affiliation(s)
- Wei-Chih Chin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Yang-Zhi Zhou
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Hao-Yung Wang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
- Department of Wood Based Materials and Design, National Chiayi University, Chiayi, Taiwan
| | - Yu-Ting Feng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Ru-Yin Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Zih-Fang Huang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
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Li L, Zhou X, Gao Z, Xiong P, Liu X. Production of succinate with two CO 2 fixation reactions from fatty acids in Cupriavidus necator H16. Microb Cell Fact 2024; 23:194. [PMID: 38970033 PMCID: PMC11225152 DOI: 10.1186/s12934-024-02470-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 07/02/2024] [Indexed: 07/07/2024] Open
Abstract
BACKGROUND Biotransformation of CO2 into high-value-added carbon-based products is a promising process for reducing greenhouse gas emissions. To realize the green transformation of CO2, we use fatty acids as carbon source to drive CO2 fixation to produce succinate through a portion of the 3-hydroxypropionate (3HP) cycle in Cupriavidus necator H16. RESULTS This work can achieve the production of a single succinate molecule from one acetyl-CoA molecule and two CO2 molecules. It was verified using an isotope labeling experiment utilizing NaH13CO3. This implies that 50% of the carbon atoms present in succinate are derived from CO2, resulting in a twofold increase in efficiency compared to prior methods of succinate biosynthesis that relied on the carboxylation of phosphoenolpyruvate or pyruvate. Meanwhile, using fatty acid as a carbon source has a higher theoretical yield than other feedstocks and also avoids carbon loss during acetyl-CoA and succinate production. To further optimize succinate production, different approaches including the optimization of ATP and NADPH supply, optimization of metabolic burden, and optimization of carbon sources were used. The resulting strain was capable of producing succinate to a level of 3.6 g/L, an increase of 159% from the starting strain. CONCLUSIONS This investigation established a new method for the production of succinate by the implementation of two CO2 fixation reactions and demonstrated the feasibility of ATP, NADPH, and metabolic burden regulation strategies in biological carbon fixation.
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Affiliation(s)
- Linqing Li
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
- International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, Zibo, 255000, China
| | - Xiuyuan Zhou
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China
- International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, Zibo, 255000, China
| | - Zhuoao Gao
- International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, Zibo, 255000, China
| | - Peng Xiong
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China.
- International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, Zibo, 255000, China.
| | - Xiutao Liu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, 255000, China.
- International Joint Laboratory on Extremophilic Bacteria and Biological Synthesis, Shandong University of Technology, Zibo, 255000, China.
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Zhu X, Wu J, Li S, Xiang L, Jin JM, Liang C, Tang SY. Artificial Biosynthetic Pathway for Efficient Synthesis of Vanillin, a Feruloyl-CoA-Derived Natural Product from Eugenol. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6463-6470. [PMID: 38501643 DOI: 10.1021/acs.jafc.3c08723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Eugenol, the main component of essential oil from the Syzygium aromaticum clove tree, has great potential as an alternative bioresource feedstock for biosynthesis purposes. Although eugenol degradation to ferulic acid was investigated, an efficient method for directly converting eugenol to targeted natural products has not been established. Herein we identified the inherent inhibitions by simply combining the previously reported ferulic acid biosynthetic pathway and vanillin biosynthetic pathway. To overcome this, we developed a novel biosynthetic pathway for converting eugenol into vanillin, by introducing cinnamoyl-CoA reductase (CCR), which catalyzes conversion of coniferyl aldehyde to feruloyl-CoA. This approach bypasses the need for two catalysts, namely coniferyl aldehyde dehydrogenase and feruloyl-CoA synthetase, thereby eliminating inhibition while simplifying the pathway. To further improve efficiency, we enhanced CCR catalytic efficiency via directed evolution and leveraged an artificialvanillin biosensor for high-throughput screening. Switching the cofactor preference of CCR from NADP+ to NAD+ significantly improved pathway efficiency. This newly designed pathway provides an alternative strategy for efficiently biosynthesizing feruloyl-CoA-derived natural products using eugenol.
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Affiliation(s)
- Xiaochong Zhu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jieyuan Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shizhong Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - La Xiang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian-Ming Jin
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing 100048, China
| | - Chaoning Liang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuang-Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Zhou H, Zhang Y, Long CP, Xia X, Xue Y, Ma Y, Antoniewicz MR, Tao Y, Lin B. A citric acid cycle-deficient Escherichia coli as an efficient chassis for aerobic fermentations. Nat Commun 2024; 15:2372. [PMID: 38491007 PMCID: PMC10943122 DOI: 10.1038/s41467-024-46655-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 03/05/2024] [Indexed: 03/18/2024] Open
Abstract
Tricarboxylic acid cycle (TCA cycle) plays an important role for aerobic growth of heterotrophic bacteria. Theoretically, eliminating TCA cycle would decrease carbon dissipation and facilitate chemicals biosynthesis. Here, we construct an E. coli strain without a functional TCA cycle that can serve as a versatile chassis for chemicals biosynthesis. We first use adaptive laboratory evolution to recover aerobic growth in minimal medium of TCA cycle-deficient E. coli. Inactivation of succinate dehydrogenase is a key event in the evolutionary trajectory. Supply of succinyl-CoA is identified as the growth limiting factor. By replacing endogenous succinyl-CoA dependent enzymes, we obtain an optimized TCA cycle-deficient E. coli strain. As a proof of concept, the strain is engineered for high-yield production of four separate products. This work enhances our understanding of the role of the TCA cycle in E. coli metabolism and demonstrates the advantages of using TCA cycle-deficient E. coli strain for biotechnological applications.
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Affiliation(s)
- Hang Zhou
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yiwen Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Christopher P Long
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE, 19716, USA
| | - Xuesen Xia
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510006, China
| | - Yanfen Xue
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China
| | - Yanhe Ma
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE, 19716, USA.
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI, USA.
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
| | - Baixue Lin
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, 100101, Beijing, China.
- University of Chinese Academy of Sciences, 100049, Beijing, China.
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Àvila-Cabré S, Pérez-Trujillo M, Albiol J, Ferrer P. Engineering the synthetic β-alanine pathway in Komagataella phaffii for conversion of methanol into 3-hydroxypropionic acid. Microb Cell Fact 2023; 22:237. [PMID: 37978380 PMCID: PMC10655335 DOI: 10.1186/s12934-023-02241-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 11/01/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND Methanol is increasingly gaining attraction as renewable carbon source to produce specialty and commodity chemicals, as it can be generated from renewable sources such as carbon dioxide (CO2). In this context, native methylotrophs such as the yeast Komagataella phaffii (syn Pichia pastoris) are potentially attractive cell factories to produce a wide range of products from this highly reduced substrate. However, studies addressing the potential of this yeast to produce bulk chemicals from methanol are still scarce. 3-Hydroxypropionic acid (3-HP) is a platform chemical which can be converted into acrylic acid and other commodity chemicals and biopolymers. 3-HP can be naturally produced by several bacteria through different metabolic pathways. RESULTS In this study, production of 3-HP via the synthetic β-alanine pathway has been established in K. phaffii for the first time by expressing three heterologous genes, namely panD from Tribolium castaneum, yhxA from Bacillus cereus, and ydfG from Escherichia coli K-12. The expression of these key enzymes allowed a production of 1.0 g l-1 of 3-HP in small-scale cultivations using methanol as substrate. The addition of a second copy of the panD gene and selection of a weak promoter to drive expression of the ydfG gene in the PpCβ21 strain resulted in an additional increase in the final 3-HP titer (1.2 g l-1). The 3-HP-producing strains were further tested in fed-batch cultures. The best strain (PpCβ21) achieved a final 3-HP concentration of 21.4 g l-1 after 39 h of methanol feeding, a product yield of 0.15 g g-1, and a volumetric productivity of 0.48 g l-1 h-1. Further engineering of this strain aiming at increasing NADPH availability led to a 16% increase in the methanol consumption rate and 10% higher specific productivity compared to the reference strain PpCβ21. CONCLUSIONS Our results show the potential of K. phaffii as platform cell factory to produce organic acids such as 3-HP from renewable one-carbon feedstocks, achieving the highest volumetric productivities reported so far for a 3-HP production process through the β-alanine pathway.
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Affiliation(s)
- Sílvia Àvila-Cabré
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Míriam Pérez-Trujillo
- Servei de Ressonància Magnètica Nuclear, Facultat de Ciències i Biociències, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Joan Albiol
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain
| | - Pau Ferrer
- Department of Chemical, Biological and Environmental Engineering, Universitat Autònoma de Barcelona, Bellaterra, Catalonia, Spain.
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Cheng J, Zhang C, Zhang K, Li J, Hou Y, Xin J, Sun Y, Xu C, Xu W. Cyanobacteria-Mediated Light-Driven Biotransformation: The Current Status and Perspectives. ACS OMEGA 2023; 8:42062-42071. [PMID: 38024730 PMCID: PMC10653055 DOI: 10.1021/acsomega.3c05407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/29/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023]
Abstract
Most chemicals are manufactured by traditional chemical processes but at the expense of toxic catalyst use, high energy consumption, and waste generation. Biotransformation is a green, sustainable, and cost-effective process. As cyanobacteria can use light as the energy source to power the synthesis of NADPH and ATP, using cyanobacteria as the chassis organisms to design and develop light-driven biotransformation platforms for chemical synthesis has been gaining attention, since it can provide a theoretical and practical basis for the sustainable and green production of chemicals. Meanwhile, metabolic engineering and genome editing techniques have tremendous prospects for further engineering and optimizing chassis cells to achieve efficient light-driven systems for synthesizing various chemicals. Here, we display the potential of cyanobacteria as a promising light-driven biotransformation platform for the efficient synthesis of green chemicals and current achievements of light-driven biotransformation processes in wild-type or genetically modified cyanobacteria. Meanwhile, future perspectives of one-pot enzymatic cascade biotransformation from biobased materials in cyanobacteria have been proposed, which could provide additional research insights for green biotransformation and accelerate the advancement of biomanufacturing industries.
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Affiliation(s)
- Jie Cheng
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Chaobo Zhang
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Kaidian Zhang
- State
Key Laboratory of Marine Resource Utilization in the South China Sea,
School of Marine Biology and Aquaculture, Hainan University, Haikou, Hainan 570100, China
- Xiamen
Key Laboratory of Urban Sea Ecological Conservation and Restoration,
State Key Laboratory of Marine Environmental Science, College of Ocean
and Earth Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Jiashun Li
- Xiamen
Key Laboratory of Urban Sea Ecological Conservation and Restoration,
State Key Laboratory of Marine Environmental Science, College of Ocean
and Earth Sciences, Xiamen University, Xiamen, Fujian 361005, China
| | - Yuyong Hou
- Key
Laboratory of Engineering Biology for Low-Carbon Manufacturing, Tianjin Institute of Industrial Biotech-nology, Chinese
Academy of Sciences, Tianjin 300308, China
| | - Jiachao Xin
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Yang Sun
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Chengshuai Xu
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
| | - Wei Xu
- School
of Life Sciences, Liaocheng University, Liaocheng, Shandong 252000, China
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7
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Xinrui D, Bo L, Yihong B, Weifeng L, Yong T. Metabolic engineering of Escherichia coli for high-level production of violaxanthin. Microb Cell Fact 2023; 22:115. [PMID: 37344799 DOI: 10.1186/s12934-023-02098-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/15/2023] [Indexed: 06/23/2023] Open
Abstract
BACKGROUND Xanthophylls are a large class of carotenoids that are found in a variety of organisms and play particularly important roles in the light-harvesting and photoprotection processes of plants and algae. Violaxanthin is an important plant-derived xanthophyll with wide potential applications in medicines, foods, and cosmetics because of its antioxidant activity and bright yellow color. To date, however, violaxanthins have not been produced using metabolically engineered microbes on a commercial scale. Metabolic engineering for microbial production of violaxanthin is hindered by inefficient synthesis pathway in the heterologous host. We systematically optimized the carotenoid chassis and improved the functional expression of key enzymes of violaxanthin biosynthesis in Escherichia coli. RESULTS Co-overexpression of crtY (encoding lycopene β-cyclase), crtZ (encoding β-carotene 3-hydroxylase), and ZEP (encoding zeaxanthin epoxidase) had a notable impact on their functions, resulting in the accumulation of intermediate products, specifically lycopene and β-carotene. A chassis strain that did not accumulate the intermediate was optimized by several approaches. A promoter library was used to optimize the expression of crtY and crtZ. The resulting strain DZ12 produced zeaxanthin without intermediates. The expression of ZEP was further systematically optimized by using DZ12 as the chassis host. By using a low copy number plasmid and a modified dithiol/disulfide system, and by co-expressing a full electron transport chain, we generated a strain producing violaxanthin at about 25.28 ± 3.94 mg/g dry cell weight with decreased byproduct accumulation. CONCLUSION We developed an efficient metabolically engineered Escherichia coli strain capable of producing a large amount of violaxanthin. This is the first report of a metabolically engineered microbial platform that could be used for the commercial production of violaxanthin.
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Affiliation(s)
- Dong Xinrui
- College of Forestry, Northeast Forestry University, No. 26 Hexing Road, Harbin, 150040, Heilongjiang Province, People's Republic of China
- Microcyto Co. Ltd, Beijing, People's Republic of China
| | - Liu Bo
- Microcyto Co. Ltd, Beijing, People's Republic of China.
| | - Bao Yihong
- College of Forestry, Northeast Forestry University, No. 26 Hexing Road, Harbin, 150040, Heilongjiang Province, People's Republic of China.
- Heilongjiang Key Laboratory of Forest Food Resources Utilization, No. 26 Hexing Road, Harbin, 150040, Heilongjiang Province, People's Republic of China.
| | - Liu Weifeng
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China.
| | - Tao Yong
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing, 100101, People's Republic of China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
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Production of 3-Hydroxypropionic Acid from Renewable Substrates by Metabolically Engineered Microorganisms: A Review. Molecules 2023; 28:molecules28041888. [PMID: 36838875 PMCID: PMC9960984 DOI: 10.3390/molecules28041888] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/08/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023] Open
Abstract
3-Hydroxypropionic acid (3-HP) is a platform chemical with a wide range of existing and potential applications, including the production of poly(3-hydroxypropionate) (P-3HP), a biodegradable plastic. The microbial synthesis of 3-HP has attracted significant attention in recent years due to its green and sustainable properties. In this paper, we provide an overview of the microbial synthesis of 3-HP from four major aspects, including the main 3-HP biosynthesis pathways and chassis strains used for the construction of microbial cell factories, the major carbon sources used for 3-HP production, and fermentation processes. Recent advances in the biosynthesis of 3-HP and related metabolic engineering strategies are also summarized. Finally, this article provides insights into the future direction of 3-HP biosynthesis.
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Liang B, Zhang X, Meng C, Wang L, Yang J. Directed evolution of tripartite ATP-independent periplasmic transporter for 3-Hydroxypropionate biosynthesis. Appl Microbiol Biotechnol 2023; 107:663-676. [PMID: 36525041 DOI: 10.1007/s00253-022-12330-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/28/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022]
Abstract
Our previous study's introduction of the malonic acid assimilation pathway into Escherichia coli enabled biosynthesis of 3-Hydroxypropionate (3-HP) from malonate. However, the relatively low uptake activity of tripartite ATP-independent periplasmic (TRAP) malonic acid transporter (MatPQM) is considered rate-limiting in malonate utilization. Here, to improve the transport performance of this importer, MatP variants were obtained via directed evolution and a novel developed enzyme-inhibition-based high throughput screening approach. This plate chromogenic screening method is based on the fact that malonic acid inhibits both of succinate dehydrogenase activity and further the capability of the reduction of methylene-blue to methylene-white. The best mutant E103G/S194G/Y218H/L235P/N272S showed twofold increased transport efficiency compared to the wild-type. ITC assay and structural analysis revealed that increased binding affinity of the mutant to the ligand was the reason for improved uptake activity of MatPQM. Finally, the engineered strain harboring the evolved mutant produced 20.08 g/L 3-HP with the yield of 0.87 mol/mol malonate in a bioreactor. Therefore, the well-established directed evolution strategy can be regarded as the reference work for other TRAP-type transporters engineering. And, this transporter mutant with enhanced malonic acid uptake activity has broad applications in the microbial biosynthesis of malonyl-CoA-derived valuable compounds in bacteria. KEY POINTS: • We reported directed evolution of a TRAP-type malonic acid transporter. • We found the enhanced malonate uptake activity of mutant lies in improved affinity. • We enhanced 3-HP bioproduction with high yield by employing the best mutant.
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Affiliation(s)
- Bo Liang
- College of Food Science & Engineering, Qingdao Special Food Research Institute, Qingdao Agricultural University, Qingdao, China
- Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xinping Zhang
- College of Food Science & Engineering, Qingdao Special Food Research Institute, Qingdao Agricultural University, Qingdao, China
- Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Chenfei Meng
- College of Food Science & Engineering, Qingdao Special Food Research Institute, Qingdao Agricultural University, Qingdao, China
- Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Lu Wang
- College of Food Science & Engineering, Qingdao Special Food Research Institute, Qingdao Agricultural University, Qingdao, China
- Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jianming Yang
- College of Food Science & Engineering, Qingdao Special Food Research Institute, Qingdao Agricultural University, Qingdao, China.
- Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
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10
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Lu J, Wang Y, Xu M, Fei Q, Gu Y, Luo Y, Wu H. Efficient biosynthesis of 3-hydroxypropionic acid from ethanol in metabolically engineered Escherichia coli. BIORESOURCE TECHNOLOGY 2022; 363:127907. [PMID: 36087655 DOI: 10.1016/j.biortech.2022.127907] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
Engineering microbial cell factories to convert CO2-based feedstock into chemicals and fuels provide a feasible carbon-neutral route for the third-generation biorefineries. Ethanol became one of the major products of syngas fermentation by engineered acetogens. The key building block chemical 3-hydroxypropionic acid (3-HP) can be synthesized from ethanol by the malonyl-CoA pathway with CO2 fixation. In this study, the effect of two ethanol consumption pathways on 3-HP synthesis were studied as well as the effect of TCA cycle, gluconeogenesis pathway, and transhydrogenase. And the 3-HP synthesis pathway was also optimized. The engineered strain synthesized 1.66 g/L of 3-HP with a yield of 0.24 g/g. Furthermore, the titer and the yield of 3-HP increased to 13.17 g/L and 0.57 g/g in the whole-cell biocatalysis system. This study indicated that ethanol as feedstock had the potential to synthesize 3-HP, which provided an alternative route for future biorefinery.
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Affiliation(s)
- Juefeng Lu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yuying Wang
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Mingcheng Xu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiang Fei
- School of Chemical Engineering and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Yang Gu
- Key Laboratory of Synthetic Biology, The State Key Laboratory of Plant Carbon-Nitrogen Assimilation, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yuanchan Luo
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering, School of Biotechnology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai 200237, China; Key Laboratory of Bio-based Material Engineering of China National Light Industry Council, 130 Meilong Road, Shanghai 200237, China.
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11
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Cai M, Zhao Z, Li X, Xu Y, Xu M, Rao Z. Development of a nonauxotrophic L-homoserine hyperproducer in Escherichia coli by systems metabolic engineering. Metab Eng 2022; 73:270-279. [PMID: 35961600 DOI: 10.1016/j.ymben.2022.08.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/14/2022] [Accepted: 08/03/2022] [Indexed: 11/19/2022]
Abstract
L-Homoserine is a valuable amino acid as a platform chemical in the synthesis of various important compounds. Development of microbial strains for high-level L-homoserine production is an attractive research direction in recent years. Herein, we converted a wild-type Escherichia coli to a non-auxotrophic and plasmid-free hyperproducer of L-homoserine using systematically metabolic engineer strategies. First, an initial strain was obtained through regulating L-homoserine degradation pathway and enhancing synthetic flow. To facilitate L-homoserine production, flux-control genes were tuned by optimizing the copy numbers in chromosome, and transport system was modified to promote L-homoserine efflux. Subsequently, a strategy of cofactors synergistic utilization was proposed and successfully applied to achieve L-homoserine hyperproduction. The final engineered strain could efficiently produce 85.29 g/L L-homoserine, which was the highest production level ever reported from a plasmid-free, antibiotic-free, inducer-free and nonauxotrophic strain. These strategies used here can be considered for developing microbial cell factory of other L-aspartate derivatives.
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Affiliation(s)
- Mengmeng Cai
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Zhenqiang Zhao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Xiangfei Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Yuanyi Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Meijuan Xu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China
| | - Zhiming Rao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, China.
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12
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Liang B, Sun G, Zhang X, Nie Q, Zhao Y, Yang J. Recent Advances, Challenges and Metabolic Engineering Strategies in the Biosynthesis of 3-Hydroxypropionic Acid. Biotechnol Bioeng 2022; 119:2639-2668. [PMID: 35781640 DOI: 10.1002/bit.28170] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/26/2022] [Accepted: 06/29/2022] [Indexed: 11/07/2022]
Abstract
As an attractive and valuable platform chemical, 3-hydroxypropionic acid (3-HP) can be used to produce a variety of industrially important commodity chemicals and biodegradable polymers. Moreover, the biosynthesis of 3-HP has drawn much attention in recent years due to its sustainability and environmental friendliness. Here, we focus on recent advances, challenges and metabolic engineering strategies in the biosynthesis of 3-HP. While glucose and glycerol are major carbon sources for its production of 3-HP via microbial fermentation, other carbon sources have also been explored. To increase yield and titer, synthetic biology and metabolic engineering strategies have been explored, including modifying pathway enzymes, eliminating flux blockages due to byproduct synthesis, eliminating toxic byproducts, and optimizing via genome-scale models. This review also provides insights on future directions for 3-HP biosynthesis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Bo Liang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Qingdao Agricultural University, Qingdao, China.,Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Guannan Sun
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Qingdao Agricultural University, Qingdao, China.,Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xinping Zhang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Qingdao Agricultural University, Qingdao, China.,Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Qingjuan Nie
- Foreign Languages School, Qingdao Agricultural University, Qingdao, China
| | - Yukun Zhao
- Pony Testing International Group, Qingdao, China
| | - Jianming Yang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Qingdao Agricultural University, Qingdao, China.,Shandong Key Lab of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao, China
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13
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Miao Y, Liu J, Wang X, Liu B, Liu W, Tao Y. Fatty acid feedstocks enable a highly efficient glyoxylate-TCA cycle for high-yield production of β-alanine. MLIFE 2022; 1:171-182. [PMID: 38817673 PMCID: PMC10989975 DOI: 10.1002/mlf2.12006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 06/01/2024]
Abstract
Metabolic engineering to produce tricarboxylic acid (TCA) cycle-derived chemicals is usually associated with problems of low production yield and impaired cellular metabolism. In this work, we found that fatty acid (FA) feedstocks could enable high-yield production of TCA cycle-derived chemicals, while maintaining an efficient and balanced metabolic flux of the glyoxylate-TCA cycle, which is favorable for both product synthesis and cell growth. Here, we designed a novel synthetic pathway for production of β-alanine, an important TCA cycle-derived product, from FAs with a high theortecial yield of 1.391 g/g. By introducing panD, improving aspA, and knocking out iclR, glyoxylate shunt was highly activated in FAs and the yield of β-alanine reached 0.71 g/g from FAs, much higher than from glucose. Blocking the TCA cycle at icd/sucA/fumAC nodes could increase β-alanine yield in a flask cultivation, but severely reduced cell growth and FA utilization during fed-batch processes. Replenishing oxaloacetate by knocking out aspC and recovering fumAC could restore the growth and lead to a titer of 35.57 g/l. After relieving the oxidative stress caused by FA metabolism, β-alanine production could reach 72.05 g/l with a maximum yield of 1.24 g/g, about 86% of the theoretical yield. Our study thus provides a promising strategy for the production of TCA cycle-derived chemicals.
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Affiliation(s)
- Yingchun Miao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Jiao Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Xuanlin Wang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Bo Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- Microcyto Co. Ltd.BeijingChina
| | - Weifeng Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
- College of Life ScienceUniversity of Chinese Academy of SciencesBeijingChina
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14
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Wang S, Jin X, Jiang W, Wang Q, Qi Q, Liang Q. The Expression Modulation of the Key Enzyme Acc for Highly Efficient 3-Hydroxypropionic Acid Production. Front Microbiol 2022; 13:902848. [PMID: 35633674 PMCID: PMC9130761 DOI: 10.3389/fmicb.2022.902848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
3-Hydroxypropionic acid (3-HP) is a promising high value-added chemical. Acetyl-CoA carboxylase (Acc) is a vital rate-limiting step in 3-HP biosynthesis through the malonyl-CoA pathway. However, Acc toxicity in cells during growth blocks its ability to catalyze acetyl-CoA to malonyl-CoA. The balancing of Acc and malonyl-CoA reductase (MCR) expression is another an unexplored but key process in 3-HP production. To solve these problems, in the present study, we developed a method to mitigate Acc toxicity cell growth through Acc subunits (AccBC and DtsR1) expression adjustment. The results revealed that cell growth and 3-HP production can be accelerated through the adjustment of DtsR1 and AccBC expression. Subsequently, the balancing Acc and MCR expression was also employed for 3-HP production, the engineered strain achieved the highest titer of 6.8 g/L, with a high yield of 0.566 g/g glucose and productivity of 0.13 g/L/h, in shake-flask fermentation through the malonyl-CoA pathway. Likewise, the engineered strain also had the highest productivity (1.03 g/L/h) as well as a high yield (0.246 g/g glucose) and titer (up to 38.13 g/L) in fed-batch fermentation, constituting the most efficient strain for 3-HP production through the malonyl-CoA pathway using a cheap carbon source. This strategy might facilitate the production of other malonyl-CoA-derived chemical compounds in the future.
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Affiliation(s)
- Sumeng Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Xin Jin
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Wei Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Qian Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, China
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15
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Liu X, Zhao G, Sun S, Fan C, Feng X, Xiong P. Biosynthetic Pathway and Metabolic Engineering of Succinic Acid. Front Bioeng Biotechnol 2022; 10:843887. [PMID: 35350186 PMCID: PMC8957974 DOI: 10.3389/fbioe.2022.843887] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Accepted: 02/16/2022] [Indexed: 11/25/2022] Open
Abstract
Succinic acid, a dicarboxylic acid produced as an intermediate of the tricarboxylic acid (TCA) cycle, is one of the most important platform chemicals for the production of various high value-added derivatives. As traditional chemical synthesis processes suffer from nonrenewable resources and environment pollution, succinic acid biosynthesis has drawn increasing attention as a viable, more environmentally friendly alternative. To date, several metabolic engineering approaches have been utilized for constructing and optimizing succinic acid cell factories. In this review, different succinic acid biosynthesis pathways are summarized, with a focus on the key enzymes and metabolic engineering approaches, which mainly include redirecting carbon flux, balancing NADH/NAD+ ratios, and optimizing CO2 supplementation. Finally, future perspectives on the microbial production of succinic acid are discussed.
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Affiliation(s)
- Xiutao Liu
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Guang Zhao
- State Key Lab of Microbial Technology, Shandong University, Qingdao, China
| | - Shengjie Sun
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Chuanle Fan
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Xinjun Feng
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Peng Xiong
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
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16
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Avermectin B1a production in Streptomyces avermitilis is enhanced by engineering aveC and precursor supply genes. Appl Microbiol Biotechnol 2022; 106:2191-2205. [PMID: 35258669 DOI: 10.1007/s00253-022-11854-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 02/21/2022] [Accepted: 02/26/2022] [Indexed: 11/02/2022]
Abstract
Avermectins (AVEs) are economically potent anthelmintic agents produced by Streptomyces avermitilis. Among eight AVE components, B1a exhibits the highest insecticidal activity. The purpose of this study was to enhance B1a production, particularly in the high-yielding industrial strain A229, by a combination strategy involving the following steps. (i) aveC gene was engineered to increase B1a:B2a ratio. Three aveC variants (aveC2m, aveC5m, and aveC8m, respectively encoding two, five, and eight amino acid mutations) were synthesized by fusion PCR. B1a:B2a ratio in A229 derivative having kasOp*-controlled aveC8m reached 1.33 (B1a and B2a titers were 8120 and 6124 μg/mL). Corresponding values in A229 were 0.99 and 6447 and 6480 μg/mL. (ii) β-oxidation pathway genes fadD and fadAB were overexpressed in wild-type (WT) strain and A229 to increase supply of acyl-CoA precursors for AVE production. The resulting strains all showed increased B1a titer. Co-overexpression of pkn5p-driven fadD and fadAB in A229 led to B1a titer of 8537 μg/mL. (iii) Genes bicA and ecaA involved in cyanobacterial CO2-concentrating mechanism (CCM) were introduced into WT and A229 to enhance carboxylation velocity of acetyl-CoA and propionyl-CoA carboxylases, leading to increased supply of malonyl- and methylmalonyl-CoA precursors and increased B1a titer. Co-expression of bicA and ecaA in A229 led to B1a titer of 8083 μg/mL. (iv) aveC8m, fadD-fadAB, and bicA-ecaA were co-overexpressed in A229, resulting in maximal B1a titer (9613 μg/mL; 49.1% increase relative to A229). Our findings demonstrate that the combination strategy we provided here is an efficient approach for improving B1a production in industrial strains.Key points• aveC mutation increased avermectin B1a:B2a ratio and B1a titer.• Higher levels of acyl-CoA precursors contributed to enhanced B1a production.• B1a titer in an industrial strain was increased by 49.1% via a combination strategy.
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17
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Sun C, Zhang R, Xie C. Biosynthesis of (
R
)‐(+)‐perillyl alcohol by
Escherichia coli
expressing neryl pyrophosphate synthase. Eng Life Sci 2022; 22:407-416. [PMID: 35573132 PMCID: PMC9077825 DOI: 10.1002/elsc.202100135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 12/29/2021] [Accepted: 01/28/2022] [Indexed: 11/09/2022] Open
Abstract
(R)‐(+)‐perillyl alcohol is widely used in agricultural and anticarcinogenic fields. Microbial production of (R)‐(+)‐perillyl alcohol was investigated in this study. We optimized biosynthesis of (R)‐(+)‐perillyl alcohol in Escherichia coli by using neryl pyrophosphate synthase and NADPH regeneration. Engineering neryl pyrophosphate (NPP)‐supplied pathway resulted in a 4‐fold improvement of (R)‐(+)‐perillyl alcohol titer. Subsequently, combined engineering of p‐cymene monooxygenase (CymA) expression and module for NADPH regeneration exhibited a 15.4‐fold increase of titer over the initial strain S02. Finally, 453 mg/L (R)‐(+)‐perillyl alcohol was achieved in fed‐batch fermentation, which is the highest (R)‐(+)‐perillyl alcohol titer in E. coli.
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Affiliation(s)
- Chao Sun
- State Key Laboratory Base of Eco‐Chemical Engineering, College of Chemistry and Molecular Engineering Qingdao University of Science and Technology Qingdao P. R. China
- CAS Key Laboratory of Bio‐based Materials Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao P. R. China
| | - Rubing Zhang
- CAS Key Laboratory of Bio‐based Materials Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences Qingdao P. R. China
| | - Congxia Xie
- State Key Laboratory Base of Eco‐Chemical Engineering, College of Chemistry and Molecular Engineering Qingdao University of Science and Technology Qingdao P. R. China
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18
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Chang Z, Dai W, Mao Y, Cui Z, Zhang Z, Wang Z, Ma H, Chen T. Enhanced 3-Hydroxypropionic Acid Production From Acetate via the Malonyl-CoA Pathway in Corynebacterium glutamicum. Front Bioeng Biotechnol 2022; 9:808258. [PMID: 35096794 PMCID: PMC8790568 DOI: 10.3389/fbioe.2021.808258] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 12/16/2021] [Indexed: 11/20/2022] Open
Abstract
Acetate is an economical and environmental-friendly alternative carbon source. Herein, the potential of harnessing Corynebacterium glutamicum as a host to produce 3-hydroxypropionic acid (3-HP) from acetate was explored. First, the expression level of malonyl-CoA reductase from Chloroflexus aurantiacus was optimized through several strategies, strain Cgz2/sod-N-C* showed an MCR enzyme activity of 63 nmol/mg/min and a 3-HP titer of 0.66 g/L in flasks. Next, the expression of citrate synthase in Cgz2/sod-N-C* was weakened to reduce the acetyl-CoA consumption in the TCA cycle, and the resulting strain Cgz12/sod-N-C* produced 2.39 g/L 3-HP from 9.32 g/L acetate. However, the subsequent deregulation of the expression of acetyl-CoA carboxylase genes in Cgz12/sod-N-C* resulted in an increased accumulation of intracellular fatty acids, instead of 3-HP. Accordingly, cerulenin was used to inhibit fatty acid synthesis in Cgz14/sod-N-C*, and its 3-HP titer was further increased to 4.26 g/L, with a yield of 0.50 g 3-HP/g-acetate. Finally, the engineered strain accumulated 17.1 g/L 3-HP in a bioreactor without cerulenin addition, representing the highest titer achieved using acetate as substrate. The results demonstrated that Corynebacterium glutamicum is a promising host for 3-HP production from acetate.
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Affiliation(s)
- Zhishuai Chang
- Frontier Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Department of Biochemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Wei Dai
- Frontier Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Department of Biochemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yufeng Mao
- Frontier Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Department of Biochemical Engineering and Technology, Tianjin University, Tianjin, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhenzhen Cui
- Frontier Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Department of Biochemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Zhidan Zhang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zhiwen Wang
- Frontier Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Department of Biochemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Hongwu Ma
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
- *Correspondence: Hongwu Ma, ; Tao Chen,
| | - Tao Chen
- Frontier Center for Synthetic Biology and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Department of Biochemical Engineering and Technology, Tianjin University, Tianjin, China
- *Correspondence: Hongwu Ma, ; Tao Chen,
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19
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Reprogramming microbial populations using a programmed lysis system to improve chemical production. Nat Commun 2021; 12:6886. [PMID: 34824227 PMCID: PMC8617184 DOI: 10.1038/s41467-021-27226-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 11/10/2021] [Indexed: 11/08/2022] Open
Abstract
Microbial populations are a promising model for achieving microbial cooperation to produce valuable chemicals. However, regulating the phenotypic structure of microbial populations remains challenging. In this study, a programmed lysis system (PLS) is developed to reprogram microbial cooperation to enhance chemical production. First, a colicin M -based lysis unit is constructed to lyse Escherichia coli. Then, a programmed switch, based on proteases, is designed to regulate the effective lysis unit time. Next, a PLS is constructed for chemical production by combining the lysis unit with a programmed switch. As a result, poly (lactate-co-3-hydroxybutyrate) production is switched from PLH synthesis to PLH release, and the content of free PLH is increased by 283%. Furthermore, butyrate production with E. coli consortia is switched from E. coli BUT003 to E. coli BUT004, thereby increasing butyrate production to 41.61 g/L. These results indicate the applicability of engineered microbial populations for improving the metabolic division of labor to increase the efficiency of microbial cell factories.
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20
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Soma Y, Takahashi M, Fujiwara Y, Tomiyasu N, Goto M, Hanai T, Izumi Y, Bamba T. Quantitative metabolomics for dynamic metabolic engineering using stable isotope labeled internal standards mixture (SILIS). J Biosci Bioeng 2021; 133:46-55. [PMID: 34620543 DOI: 10.1016/j.jbiosc.2021.09.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 11/28/2022]
Abstract
The production of chemicals and fuels from renewable resources using engineered microbes is an attractive alternative for current fossil-dependent industries. Metabolic engineering has contributed to pathway engineering for the production of chemicals and fuels by various microorganisms. Recently, dynamic metabolic engineering harnessing synthetic biological tools has become a next-generation strategy in this field. The dynamic regulation of metabolic flux during fermentation optimizes metabolic states according to each fermentation stage such as cell growth phase and compound production phase. However, it is necessary to repeat the evaluation and redesign of the dynamic regulation system to achieve the practical use of engineered microbes. In this study, we performed quantitative metabolome analysis to investigate the effects of dynamic metabolic flux regulation on engineered Escherichia coli for γ-amino butyrate (GABA) fermentation. We prepared a stable isotope-labeled internal standard mixture (SILIS) for the stable isotope dilution method (SIDM), a mass spectrometry-based quantitative metabolome analysis method. We found multiple candidate bottlenecks for GABA production. Some metabolic reactions in the GABA production pathway should be engineered for further improvement in the direct GABA fermentation with dynamic metabolic engineering strategy.
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Affiliation(s)
- Yuki Soma
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Masatomo Takahashi
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuri Fujiwara
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Noriyuki Tomiyasu
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Maiko Goto
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Taizo Hanai
- Laboratory for Synthetic Biology, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, W5-729, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yoshihiro Izumi
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takeshi Bamba
- Division of Metabolomics, Research Center for Transomics Medicine, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan.
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21
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De novo biosynthesis and gram-level production of m-cresol in Aspergillus nidulans. Appl Microbiol Biotechnol 2021; 105:6333-6343. [PMID: 34423409 DOI: 10.1007/s00253-021-11490-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 07/26/2021] [Accepted: 08/03/2021] [Indexed: 10/20/2022]
Abstract
The industrially important meta-cresol (m-cresol, 3-methylphenol) is mainly produced from fossil resources by chemical methods. The microbial production of m-cresol was rarely investigated. Herein, we constructed a platform for the overproduction of m-cresol in a modified fungus Aspergillus nidulans FGSC no. A1145∆ST∆EM, which gave a gram-level titer using starch as carbon resource. For the biosynthesis of m-cresol, the 6-methyl salicylic acid synthase (MSAS)-encoding gene patK and 6-methyl salicylic acid decarboxylase-encoding gene patG from A. clavatus were co-expressed in the host A. nidulans. Multiple strategies, including promotor engineering, gene multiplication, and fed-batch fermentation, were applied to raise the production of m-cresol, which resulted in the titers of 1.29 g/L in shaking flasks and 2.03 g/L in fed-batch culture. The chassis cell A. nidulans A1145∆ST∆EM was proved to possess better tolerance to m-cresol than yeast, as it could grow in the liquid medium containing up to 2.5 g/L of m-cresol. These results showed that A. nidulans has great potential to be further engineered for industrial production of m-cresol.Key points• m-Cresol was de novo biosynthesized by a fungal chassis cell Aspergillus nidulans.• Promoter engineering and gene multiplication implemented the fine-tuned genes expression.• The titer of m-cresol reached 2.03 g/L via fed-batch culture.
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22
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Li Y, Cheng Z, Zhao C, Gao C, Song W, Liu L, Chen X. Reprogramming Escherichia coli Metabolism for Bioplastics Synthesis from Waste Cooking Oil. ACS Synth Biol 2021; 10:1966-1979. [PMID: 34337931 DOI: 10.1021/acssynbio.1c00155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The recycle and reutilization of food wastes is a promising alternative for supporting and facilitating circular economy. However, engineering industrially relevant model organisms to use food wastes as their sole carbon source has remained an outstanding challenge so far. Here, we reprogrammed Escherichia coli metabolism using modular pathway engineering followed by laboratory adaptive evolution to establish a strain that can efficiently utilize waste cooking oil (WCO) as the sole carbon source to produce monomers of bioplastics, namely, medium-chain α,ω-dicarboxylic acids (MCDCAs). First, the biosynthetic pathway of MCDCAs was designed and rewired by modifying the β-oxidation pathway and introducing an ω-oxidation pathway. Then, metabolic engineering and laboratory adaptive evolution were applied for improving the pathway efficiency of fatty acids utilization. Finally, the engineered strain E. coli AA0306 was able to produce 15.26 g/L MCDCAs with WCO as the sole carbon source. This study provides an economically attractive strategy for biomanufacturing bioplastics from food wastes, which has a great potentiality to be developed as a wide range of enabling biotechnologies for achieving green revolution.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122 Wuxi, China
| | - Zhenzhen Cheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122 Wuxi, China
| | - Chunlei Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122 Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122 Wuxi, China
- International Joint Laboratory on Food Safety, Jiangnan University, 214122 Wuxi, China
| | - Wei Song
- School of Pharmaceutical Science, State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122 Wuxi, China
- International Joint Laboratory on Food Safety, Jiangnan University, 214122 Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 214122 Wuxi, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, 214122 Wuxi, China
- International Joint Laboratory on Food Safety, Jiangnan University, 214122 Wuxi, China
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L-valine production in Corynebacterium glutamicum based on systematic metabolic engineering: progress and prospects. Amino Acids 2021; 53:1301-1312. [PMID: 34401958 DOI: 10.1007/s00726-021-03066-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/11/2021] [Indexed: 10/20/2022]
Abstract
L-valine is an essential branched-chain amino acid that cannot be synthesized by the human body and has a wide range of applications in food, medicine and feed. Market demand has stimulated people's interest in the industrial production of L-valine. At present, the mutagenized or engineered Corynebacterium glutamicum is an effective microbial cell factory for producing L-valine. Because the biosynthetic pathway and metabolic network of L-valine are intricate and strictly regulated by a variety of key enzymes and genes, highly targeted metabolic engineering can no longer meet the demand for efficient biosynthesis of L-valine. In recent years, the development of omics technology has promoted the upgrading of traditional metabolic engineering to systematic metabolic engineering. This whole-cell-scale transformation strategy has become a productive method for developing L-valine producing strains. This review provides an overview of the biosynthesis and regulation mechanism of L-valine, and summarizes the current metabolic engineering techniques and strategies for constructing L-valine high-producing strains. Finally, the opinion of constructing a cell factory for efficiently biosynthesizing L-valine was proposed.
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Lee JY, Cha S, Lee JH, Lim HG, Noh MH, Kang CW, Jung GY. Plug-in repressor library for precise regulation of metabolic flux in Escherichia coli. Metab Eng 2021; 67:365-372. [PMID: 34333137 DOI: 10.1016/j.ymben.2021.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 07/10/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022]
Abstract
In metabolic engineering, enhanced production of value-added chemicals requires precise flux control between growth-essential competing and production pathways. Although advances in synthetic biology have facilitated the exploitation of a number of genetic elements for precise flux control, their use requires expensive inducers, or more importantly, needs complex and time-consuming processes to design and optimize appropriate regulator components, case-by-case. To overcome this issue, we devised the plug-in repressor libraries for target-specific flux control, in which expression levels of the repressors were diversified using degenerate 5' untranslated region (5' UTR) sequences employing the UTR Library Designer. After we validated a wide expression range of the repressor libraries, they were applied to improve the production of lycopene from glucose and 3-hydroxypropionic acid (3-HP) from acetate in Escherichia coli via precise flux rebalancing to enlarge precursor pools. Consequently, we successfully achieved optimal carbon fluxes around the precursor nodes for efficient production. The most optimized strains were observed to produce 2.59 g/L of 3-HP and 11.66 mg/L of lycopene, which were improved 16.5-fold and 2.82-fold, respectively, compared to those produced by the parental strains. These results indicate that carbon flux rebalancing using the plug-in library is a powerful strategy for efficient production of value-added chemicals in E. coli.
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Affiliation(s)
- Ji Yeon Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Sanghak Cha
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Ji Hoon Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Hyun Gyu Lim
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Myung Hyun Noh
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Chae Won Kang
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk, 37673, South Korea.
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25
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Mu Q, Zhang S, Mao X, Tao Y, Yu B. Highly efficient production of L-homoserine in Escherichia coli by engineering a redox balance route. Metab Eng 2021; 67:321-329. [PMID: 34329706 DOI: 10.1016/j.ymben.2021.07.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/30/2021] [Accepted: 07/26/2021] [Indexed: 12/29/2022]
Abstract
L-Homoserine is a nonessential chiral amino acid and the precursor of L-threonine and L-methionine. It has great potential to be used in the pharmaceutical, agricultural, cosmetic, and fragrance industries. However, the current low efficiency in the fermentation process of L-homoserine drives up the cost and therefore limits applications. Here, we systematically analyzed the L-homoserine production network in Escherichia coli to design a redox balance route for L-homoserine fermentation from glucose. Production of L-homoserine from L-aspartate via reduction of the tricarboxylic acid cycle intermediate oxaloacetate lacks reducing power. This deficiency could be corrected by activating the glyoxylate shunt and driving the flux from fumarate to L-aspartate with excess reducing power. This redox balance route decreases cell growth pressure and the theoretical yield of L-homoserine is 1.5 mol/mol of glucose without carbon loss. We fine-tuned the flux from fumarate to L-aspartate, deleted competitive and degradative pathways, enhanced L-homoserine efflux, and generated 84.1 g/L L-homoserine with 1.96 g/L/h productivity and 0.50 g/g glucose yield in a fed-batch fermentation. This study proposes a novel balanced redox metabolic network strategy for highly efficient production of L-homoserine and its derivative amino acids.
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Affiliation(s)
- Qingxuan Mu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shasha Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xianjun Mao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bo Yu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
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26
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Zhao P, Tian P. Biosynthesis pathways and strategies for improving 3-hydroxypropionic acid production in bacteria. World J Microbiol Biotechnol 2021; 37:117. [PMID: 34128152 DOI: 10.1007/s11274-021-03091-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 06/08/2021] [Indexed: 12/01/2022]
Abstract
3-Hydroxypropionic acid (3-HP) represents an economically important platform compound from which a panel of bulk chemicals can be derived. Compared with petroleum-dependent chemical synthesis, bioproduction of 3-HP has attracted more attention due to utilization of renewable biomass. This review outlines bacterial production of 3-HP, covering aspects of host strains (e.g., Escherichia coli and Klebsiella pneumoniae), metabolic pathways, key enzymes, and hurdles hindering high-level production. Inspired by the state-of-the-art advances in metabolic engineering and synthetic biology, we come up with protocols to overcome the hurdles constraining 3-HP production. The protocols range from rewiring of metabolic networks, alleviation of metabolite toxicity, to dynamic control of cell size and density. Especially, this review highlights the substantial contribution of microbial growth to 3-HP production, as we recognize the synchronization between cell growth and 3-HP formation. Accordingly, we summarize the following growth-promoting strategies: (i) optimization of fermentation conditions; (ii) construction of gene circuits to alleviate feedback inhibition; (iii) recruitment of RNA polymerases to overexpress key enzymes which in turn boost cell growth and 3-HP production. Lastly, we propose metabolic engineering approaches to simplify downstream separation and purification. Overall, this review aims to portray a picture of bacterial production of 3-HP.
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Affiliation(s)
- Peng Zhao
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Pingfang Tian
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China.
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Li Z, Wu Z, Cen X, Liu Y, Zhang Y, Liu D, Chen Z. Efficient Production of 1,3-Propanediol from Diverse Carbohydrates via a Non-natural Pathway Using 3-Hydroxypropionic Acid as an Intermediate. ACS Synth Biol 2021; 10:478-486. [PMID: 33625207 DOI: 10.1021/acssynbio.0c00486] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
1,3-Propanediol (1,3-PDO) is a promising platform chemical used to manufacture various polyesters, polyethers, and polyurethanes. Microbial production of 1,3-PDO using non-natural producers often requires adding expensive cofactors such as vitamin B12, which increases the whole production cost. In this study, we proposed and engineered a non-natural 1,3-PDO synthetic pathway derived from acetyl-CoA, enabling efficient accumulation of 1,3-PDO in Escherichia coli without adding expensive cofactors. This functional pathway was established by introducing the malonyl-CoA-dependent 3-hydroxypropionic acid (3-HP) module and screening the key enzymes to convert 3-HP to 1,3-PDO. The best engineered strain can produce 2.93 g/L 1,3-PDO with a yield of 0.35 mol/mol glucose in shake flask cultivation (and 7.98 g/L in fed-batch fermentation), which is significantly higher than previous reports based on homoserine- or malate-derived non-natural pathways. We also demonstrated for the first time the feasibility of producing 1,3-PDO from diverse carbohydrates including xylose, glycerol, and acetate based on the same pathway. Thus, this study provides an alternative route for 1,3-PDO production.
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Affiliation(s)
- Zihua Li
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ziyi Wu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Xuecong Cen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Yu Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ye Zhang
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Dehua Liu
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Tsinghua Innovation Center in Dongguan, Dongguan 523808, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
| | - Zhen Chen
- Key Laboratory of Industrial Biocatalysis (Ministry of Education), Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
- Tsinghua Innovation Center in Dongguan, Dongguan 523808, China
- Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
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28
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Zhang X, He Y, Wu Z, Liu G, Tao Y, Jin JM, Chen W, Tang SY. Whole-Cell Biosensors Aid Exploration of Vanillin Transmembrane Transport. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3114-3123. [PMID: 33666081 DOI: 10.1021/acs.jafc.0c07886] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Transcriptional regulatory protein (TRP)-based whole-cell biosensors are widely used nowadays. Here, they were demonstrated to have great potential application in screening cell efflux and influx pumps for small molecules. First, a vanillin whole-cell biosensor was developed by altering the specificity of a TRP, VanR, and strains with improved vanillin productions that were selected from a random genome mutagenesis library by using this biosensor as a high-throughput screening tool. A high intracellular vanillin concentration was found to accumulate due to the inactivation of the AcrA protein, indicating the involvement of this protein in vanillin efflux. Then, the application of this biosensor was extended to explore efflux and influx pumps, combined with directed genome evolution. Elevated intracellular vanillin levels resulting from efflux pump inactivation or influx pump overexpression could be rapidly detected by the whole-cell biosensor, markedly facilitating the identification of genome targets related to small-molecule transmembrane transport, which is of great importance in metabolic engineering.
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Affiliation(s)
- Xuanxuan Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yang He
- School of Pharmacy, Chengdu University, Chengdu 610106, China
| | - Zhe Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guoxia Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian-Ming Jin
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing 100048, China
| | - Wei Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- State Key Laboratory of Transducer Technology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuang-Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Salvador López JM, Van Bogaert INA. Microbial fatty acid transport proteins and their biotechnological potential. Biotechnol Bioeng 2021; 118:2184-2201. [PMID: 33638355 DOI: 10.1002/bit.27735] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 01/08/2021] [Accepted: 02/24/2021] [Indexed: 12/11/2022]
Abstract
Fatty acid metabolism has been widely studied in various organisms. However, fatty acid transport has received less attention, even though it plays vital physiological roles, such as export of toxic free fatty acids or uptake of exogenous fatty acids. Hence, there are important knowledge gaps in how fatty acids cross biological membranes, and many mechanisms and proteins involved in these processes still need to be determined. The lack of information is more predominant in microorganisms, even though the identification of fatty acids transporters in these cells could lead to establishing new drug targets or improvements in microbial cell factories. This review provides a thorough analysis of the current information on fatty acid transporters in microorganisms, including bacteria, yeasts and microalgae species. Most available information relates to the model organisms Escherichia coli and Saccharomyces cerevisiae, but transport systems of other species are also discussed. Intracellular trafficking of fatty acids and their transport through organelle membranes in eukaryotic organisms is described as well. Finally, applied studies and engineering efforts using fatty acids transporters are presented to show the applied potential of these transporters and to stress the need for further identification of new transporters and their engineering.
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Affiliation(s)
- José M Salvador López
- BioPort Group, Faculty of Bioscience Engineering, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
| | - Inge N A Van Bogaert
- BioPort Group, Faculty of Bioscience Engineering, Centre for Synthetic Biology (CSB), Ghent University, Ghent, Belgium
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30
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Chang C, Liu B, Bao Y, Tao Y, Liu W. Efficient bioconversion of raspberry ketone in Escherichia coli using fatty acids feedstocks. Microb Cell Fact 2021; 20:68. [PMID: 33706766 PMCID: PMC7953670 DOI: 10.1186/s12934-021-01551-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 02/21/2021] [Indexed: 02/02/2023] Open
Abstract
Background Phenylpropanoid including raspberry ketone, is a kind of important natural plant product and widely used in pharmaceuticals, chemicals, cosmetics, and healthcare products. Bioproduction of phenylpropanoid in Escherichia coli and other microbial cell factories is an attractive approach considering the low phenylpropanoid contents in plants. However, it is usually difficult to produce high titer phenylpropanoid production when fermentation using glucose as carbon source. Developing novel bioprocess using alternative sources might provide a solution to this problem. In this study, typical phenylpropanoid raspberry ketone was used as the target product to develop a biosynthesis pathway for phenylpropanoid production from fatty acids, a promising alternative low-cost feedstock. Results A raspberry ketone biosynthesis module was developed and optimized by introducing 4-coumarate-CoA ligase (4CL), benzalacetone synthase (BAS), and raspberry ketone reductase (RZS) in Escherichia coli strains CR1–CR4. Then strain CR5 was developed by introducing raspberry ketone biosynthesis module into a fatty acids-utilization chassis FA09 to achieve production of raspberry ketone from fatty acids feedstock. However, the production of raspberry ketone was still limited by the low biomass and unable to substantiate whole-cell bioconversion process. Thus, a process by coordinately using fatty-acids and glycerol was developed. In addition, we systematically screened and optimized fatty acids-response promoters. The optimized promoter Pfrd3 was then successfully used for the efficient expression of key enzymes of raspberry ketone biosynthesis module during bioconversion from fatty acids. The final engineered strain CR8 could efficiently produce raspberry ketone repeatedly using bioconversion from fatty acids feedstock strategy, and was able to produce raspberry ketone to a concentration of 180.94 mg/L from soybean oil in a 1-L fermentation process. Conclusion Metabolically engineered Escherichia coli strains were successfully developed for raspberry ketone production from fatty acids using several strategies, including optimization of bioconversion process and fine-tuning key enzyme expression. This study provides an essential reference to establish the low-cost biological manufacture of phenylpropanoids compounds. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01551-0.
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Affiliation(s)
- Chen Chang
- College of Forestry, Northeast Forestry University, No. 26 Hexing Road, Harbin, Heilongjiang Province, 150040, PR China.,CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, NO. 1 Beichen West Road, Chaoyang District, Beijing, 100101, PR China
| | - Bo Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, NO. 1 Beichen West Road, Chaoyang District, Beijing, 100101, PR China
| | - Yihong Bao
- College of Forestry, Northeast Forestry University, No. 26 Hexing Road, Harbin, Heilongjiang Province, 150040, PR China. .,Heilongjiang Key Laboratory of Forest Food Resources Utilization, No. 26 Hexing Road, Harbin, Heilongjiang Province, 150040, PR China.
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, NO. 1 Beichen West Road, Chaoyang District, Beijing, 100101, PR China. .,University of Chinese Academy of Sciences, Shijingshan District, NO. 19A Yuquan Road, Beijing, 100049, PR China.
| | - Weifeng Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, NO. 1 Beichen West Road, Chaoyang District, Beijing, 100101, PR China. .,University of Chinese Academy of Sciences, Shijingshan District, NO. 19A Yuquan Road, Beijing, 100049, PR China.
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31
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Li S, Liang C, Liu G, Jin JM, Tao Y, Tang SY. De Novo Biosynthesis of Chlorogenic Acid Using an Artificial Microbial Community. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:2816-2825. [PMID: 33629856 DOI: 10.1021/acs.jafc.0c07588] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Engineering an artificial microbial community for natural product production is a promising strategy. As mono- and dual-culture systems only gave non-detectable or minimal chlorogenic acid (CGA) biosynthesis, here, a polyculture of three recombinant Escherichia coli strains, acting as biosynthetic modules of caffeic acid (CA), quinic acid (QA), and CGA, was designed and used for de novo CGA biosynthesis. An influx transporter of 3-dehydroshikimic acid (DHS)/shikimic acid (SA), ShiA, was introduced into the QA module-a DHS auxotroph. The QA module proportion in the polyculture and CGA production were found to be dependent on ShiA expression, providing an alternative approach for controlling microbial community composition. The polyculture strategy avoids metabolic flux competition in the biosynthesis of two CGA precursors, CA and QA, and allows production improvement by balancing module proportions. The performance of this polyculture approach was superior to that of previously reported approaches of de novo CGA production.
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Affiliation(s)
- Shizhong Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chaoning Liang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guoxia Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jian-Ming Jin
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing 100048, China
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuang-Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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32
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Liu H, Qi Y, Zhou P, Ye C, Gao C, Chen X, Liu L. Microbial physiological engineering increases the efficiency of microbial cell factories. Crit Rev Biotechnol 2021; 41:339-354. [PMID: 33541146 DOI: 10.1080/07388551.2020.1856770] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Microbial cell factories provide vital platforms for the production of chemicals. Advanced biotechnological toolboxes have been developed to enhance their efficiency. However, these tools have limitations in improving physiological functions, and therefore boosting the efficiency (e.g. titer, rate, and yield) of microbial cell factories remains a challenge. In this review, we propose a strategy of microbial physiological engineering (MPE) to improve the efficiency of microbial cell factories. This strategy integrates tools from synthetic and systems biology to characterize and regulate physiological functions during chemical synthesis. MPE strategies mainly focus on the efficiency of substrate utilization, growth performance, stress tolerance, and the product export capacity of cell factories. In short, this review provides a new framework for resolving the bottlenecks that currently exist in low-efficiency cell factories.
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Affiliation(s)
- Hui Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Yanli Qi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Pei Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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Li Y, Yang S, Ma D, Song W, Gao C, Liu L, Chen X. Microbial engineering for the production of C 2-C 6 organic acids. Nat Prod Rep 2021; 38:1518-1546. [PMID: 33410446 DOI: 10.1039/d0np00062k] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Covering: up to the end of 2020Organic acids, as building block compounds, have been widely used in food, pharmaceutical, plastic, and chemical industries. Until now, chemical synthesis is still the primary method for industrial-scale organic acid production. However, this process encounters some inevitable challenges, such as depletable petroleum resources, harsh reaction conditions and complex downstream processes. To solve these problems, microbial cell factories provide a promising approach for achieving the sustainable production of organic acids. However, some key metabolites in central carbon metabolism are strictly regulated by the network of cellular metabolism, resulting in the low productivity of organic acids. Thus, multiple metabolic engineering strategies have been developed to reprogram microbial cell factories to produce organic acids, including monocarboxylic acids, hydroxy carboxylic acids, amino carboxylic acids, dicarboxylic acids and monomeric units for polymers. These strategies mainly center on improving the catalytic efficiency of the enzymes to increase the conversion rate, balancing the multi-gene biosynthetic pathways to reduce the byproduct formation, strengthening the metabolic flux to promote the product biosynthesis, optimizing the metabolic network to adapt the environmental conditions and enhancing substrate utilization to broaden the substrate spectrum. Here, we describe the recent advances in producing C2-C6 organic acids by metabolic engineering strategies. In addition, we provide new insights as to when, what and how these strategies should be taken. Future challenges are also discussed in further advancing microbial engineering and establishing efficient biorefineries.
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Affiliation(s)
- Yang Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Road, Wuxi 214122, China.
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34
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Cao Z, Meng R, Wang P, Zhu G. Heterologous expression and enzymatic identification of two novel soluble pyridine nucleotide transhydrogenases from Acidobacteria bacterium KBS 146 and Nocardia jiangxiensis. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1988708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Zhengyu Cao
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
| | - Rui Meng
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
| | - Peng Wang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
| | - Guoping Zhu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases and Key Laboratory of Biomedicine in Gene Diseases and Health of Anhui Higher Education Institutes, College of Life Sciences, Anhui Normal University, Wuhu, Anhui, PR China
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Hao Y, Ma Q, Liu X, Fan X, Men J, Wu H, Jiang S, Tian D, Xiong B, Xie X. High-yield production of L-valine in engineered Escherichia coli by a novel two-stage fermentation. Metab Eng 2020; 62:198-206. [DOI: 10.1016/j.ymben.2020.09.007] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 08/24/2020] [Accepted: 09/16/2020] [Indexed: 01/27/2023]
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36
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Characterization and directed evolution of propionyl-CoA carboxylase and its application in succinate biosynthetic pathway with two CO2 fixation reactions. Metab Eng 2020; 62:42-50. [DOI: 10.1016/j.ymben.2020.08.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 07/18/2020] [Accepted: 08/24/2020] [Indexed: 11/20/2022]
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Wu J, Chen W, Zhang Y, Zhang X, Jin JM, Tang SY. Metabolic Engineering for Improved Curcumin Biosynthesis in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10772-10779. [PMID: 32864959 DOI: 10.1021/acs.jafc.0c04276] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The biosynthetic efficiency of curcumin, a highly bioactive compound from the plant Curcuma longa, needs to be improved. In this study, we performed host cell and biosynthetic pathway engineering to improve curcumin biosynthesis. Using in vivo-directed evolution, the expression level of curcuminoid synthase (CUS), the rate-limiting enzyme in the curcumin biosynthetic pathway, was significantly improved. Furthermore, as curcumin is a highly hydrophobic compound, two cell membrane engineering strategies were applied to optimize the biosynthetic efficiency. Curcumin storage was increased by overexpression of monoglucosyldiacylglycerol synthase from Acholeplasma laidlawii, which optimized the cell membrane morphology. Furthermore, unsaturated fatty acid supplementation was used to enhance membrane fluidity, which greatly ameliorated the damaging effect of curcumin on the cell membrane. These two strategies enhanced curcumin biosynthesis and demonstrated an additive effect.
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Affiliation(s)
- Jieyuan Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yutong Zhang
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing 100048, China
| | - Xuanxuan Zhang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Ming Jin
- Beijing Key Laboratory of Plant Resources Research and Development, Beijing Technology and Business University, Beijing 100048, China
| | - Shuang-Yan Tang
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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38
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Sun S, Ding Y, Liu M, Xian M, Zhao G. Comparison of Glucose, Acetate and Ethanol as Carbon Resource for Production of Poly(3-Hydroxybutyrate) and Other Acetyl-CoA Derivatives. Front Bioeng Biotechnol 2020; 8:833. [PMID: 32850713 PMCID: PMC7396591 DOI: 10.3389/fbioe.2020.00833] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/29/2020] [Indexed: 01/11/2023] Open
Abstract
Poly(3-hydroxybutyrate) (PHB) is a biodegradable and biocompatible thermoplastic, and synthesized from the central metabolite acetyl-CoA. The acetyl-CoA synthesis from glucose presents low atomic economy due to the release of CO2 in pyruvate decarboxylation. As ethanol and acetate can be converted into acetyl-CoA directly, they were used as carbon source for PHB production in this study. The reductase mutant AdhE A267T/E568K was introduced into Escherichia coli to enable growth on ethanol, and acetate utilization was improved by overexpression of acetyl-CoA synthetase ACS. Comparison of the PHB production using glucose, ethanol or acetate as sole carbon source showed that the production and yield from ethanol was much higher than those from glucose and acetate, and metabolome analysis revealed the differences in metabolism of glucose, ethanol and acetate. Furthermore, other acetyl-CoA derived chemicals including 3-hydroxypropionate and phloroglucinol were produced from those three feedstocks, and similar results were achieved, suggesting that ethanol could be a suitable carbon source for the production of acetyl-CoA derivatives.
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Affiliation(s)
- Shenmei Sun
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yamei Ding
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Min Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Guang Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China.,State Key Lab of Microbial Technology, Shandong University, Qingdao, China
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39
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Xian WD, Salam N, Li MM, Zhou EM, Yin YR, Liu ZT, Ming YZ, Zhang XT, Wu G, Liu L, Xiao M, Jiang HC, Li WJ. Network-directed efficient isolation of previously uncultivated Chloroflexi and related bacteria in hot spring microbial mats. NPJ Biofilms Microbiomes 2020; 6:20. [PMID: 32350263 PMCID: PMC7190741 DOI: 10.1038/s41522-020-0131-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 04/07/2020] [Indexed: 12/16/2022] Open
Abstract
The perplexity of the complex multispecies community interactions is one of the many reasons why majority of the microorganisms are still uncultivated. We analyzed the entire co-occurrence networks between the OTUs of Tibet and Yunnan hot spring samples, and found that less abundant OTUs such as genus Tepidimonas (relative abundant <1%) had high-degree centricity (key nodes), while dominant OTUs particularly genus Chloroflexus (relative abundant, 13.9%) formed the peripheral vertexes. A preliminary growth-promotion assay determined that Tepidimonas sp. strain SYSU G00190W enhanced the growth of Chloroflexus sp. SYSU G00190R. Exploiting this result, an ameliorated isolation medium containing 10% spent-culture supernatant of Tepidimonas sp. strain SYSU G00190W was prepared for targeted isolation of Chloroflexi in the Tibet and Yunnan hot spring samples. 16S rRNA gene fingerprinting characterized majority of the colonies isolated from these media as previously uncultivated Chloroflexi, of which 36 are potential novel species (16S rRNA sequence identity <98.5%). Metabolomes studies indicated that the spent-culture supernatant comprises several low-molecular-weight organic substrates that can be utilized as potential nutrients for the growth of these bacteria. These findings suggested that limited knowledge on the interaction of microbes provide threshold to traditional isolation method.
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Affiliation(s)
- Wen-Dong Xian
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Nimaichand Salam
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Meng-Meng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - En-Min Zhou
- School of Resource Environment and Earth Science, Yunnan Institute of Geography, Yunnan University, Kunming, 650091, China
| | - Yi-Rui Yin
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ze-Tao Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yu-Zhen Ming
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xiao-Tong Zhang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Geng Wu
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Lan Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Min Xiao
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Hong-Chen Jiang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, 430074, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Sciences and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China.
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40
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Lycopene production from glucose, fatty acid and waste cooking oil by metabolically engineered Escherichia coli. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107488] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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41
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Engineering Corynebacterium glutamicum for the Efficient Production of 3-Hydroxypropionic Acid from a Mixture of Glucose and Acetate via the Malonyl-CoA Pathway. Catalysts 2020. [DOI: 10.3390/catal10020203] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
3-Hydroxypropionic acid (3-HP) has been recognized as one of the top value-added building block chemicals, due to its numerous potential applications. Over the past decade, biosynthesis of 3-HP via the malonyl-CoA pathway has been increasingly favored because it is balanced in terms of ATP and reducing equivalents, does not require the addition of costly coenzymes, and can utilize renewable lignocellulosic biomass. In this study, gene mcr encoding malonyl-CoA reductase from Chloroflexus aurantiacus was introduced into Corynebacterium glutamicum ATCC13032 to construct the strain Cgz1, which accumulated 0.30 g/L 3-HP. Gene ldhA encoding lactate dehydrogenase was subsequently deleted to eliminate lactate accumulation, but this decreased 3-HP production and greatly increased acetate accumulation. Then, different acetate utilization genes were overexpressed to reuse the acetate, and the best candidate Cgz5 expressing endogenous gene pta could effectively reduce the acetate accumulation and produced 0.68 g/L 3-HP. To enhance the supply of the precursor acetyl-CoA, acetate was used as an ancillary carbon source to improve the 3-HP production, and 1.33 g/L 3-HP could be produced from a mixture of glucose and acetate, with a 2.06-fold higher yield than from glucose alone. Finally, to inhibit the major 3-HP competing pathway-fatty acid synthesis, 10 μM cerulenin was added and strain Cgz5 produced 3.77 g/L 3-HP from 15.47 g/L glucose and 4.68 g/L acetate with a yield of 187 mg/g substrate in 48 h, which was 12.57-fold higher than that of Cgz1. To our best knowledge, this is the first report on engineering C. glutamicum to produce 3-HP via the malonyl-CoA pathway. The results indicate that the innocuous biosafety level I microorganism C. glutamicum is a potential industrial 3-HP producer.
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Biocatalytic production of D-p-hydroxyphenylglycine by optimizing protein expression and cell wall engineering in Escherichia coli. Appl Microbiol Biotechnol 2019; 103:8839-8851. [DOI: 10.1007/s00253-019-10155-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/19/2019] [Accepted: 09/24/2019] [Indexed: 10/25/2022]
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43
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Zhang S, Yang W, Chen H, Liu B, Lin B, Tao Y. Metabolic engineering for efficient supply of acetyl-CoA from different carbon sources in Escherichia coli. Microb Cell Fact 2019; 18:130. [PMID: 31387584 PMCID: PMC6685171 DOI: 10.1186/s12934-019-1177-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/30/2019] [Indexed: 11/24/2022] Open
Abstract
Background Acetyl-CoA is an important metabolic intermediate and serves as an acetylation precursor for the biosynthesis of various value-added acetyl-chemicals. Acetyl-CoA can be produced from glucose, acetate, or fatty acids via metabolic pathways in Escherichia coli. Although glucose is an efficient carbon source for acetyl-CoA production, the pathway from acetate to acetyl-CoA is the shortest and fatty acids can produce acetyl-CoA through fatty acid oxidation along with abundant NADH and FADH2. In this study, metabolically engineered E. coli strains for efficiently supplying acetyl-CoA from glucose, acetate, and fatty acid were constructed and applied in one-step biosynthesis of N-acetylglutamate (NAG) from glutamate and acetyl-CoA. Results A metabolically engineered E. coli strain for NAG production was constructed by overexpressing N-acetylglutamate synthase from Kitasatospora setae in E. coli BW25113 with argB and argA knockout. The strain was further engineered to utilize glucose, acetate, and fatty acid to produce acetyl-CoA. When glucose was used as a carbon source, the combined mutants of ∆ptsG::glk, ∆galR::zglf, ∆poxB::acs, ∆ldhA, and ∆pta were more efficient for supplying acetyl-CoA. The acetyl-CoA synthetase (ACS) pathway and acetate kinase-phosphate acetyltransferase (ACK-PTA) pathway from acetate to acetyl-CoA were investigated, and the ACK-PTA pathway showed to be more efficient for supplying acetyl-CoA. When fatty acid was used as a carbon source, acetyl-CoA supply was improved by deletion of fadR and constitutive expression of fadD under the strong promoter CPA1. Comparison of acetyl-CoA supply from glucose, acetate and palmitic acid revealed that a higher conversion rate of glutamate (98.2%) and productivity (an average of 6.25 mmol/L/h) were obtained when using glucose as a carbon source. The results also demonstrated the great potential of acetate and fatty acid to supply acetyl-CoA, as the molar conversion rate of glutamate was more than 80%. Conclusions Metabolically engineered E. coli strains were developed for NAG production. The metabolic pathways of acetyl-CoA from glucose, acetate, or fatty acid were optimized for efficient acetyl-CoA supply to enhance NAG production. The metabolic strategies for efficient acetyl-CoA supply used in this study can be exploited for other chemicals that use acetyl-CoA as a precursor or when acetylation is involved. Electronic supplementary material The online version of this article (10.1186/s12934-019-1177-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shasha Zhang
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Yang
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Hao Chen
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bo Liu
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baixue Lin
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yong Tao
- Chinese Academy of Sciences Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Piao X, Wang L, Lin B, Chen H, Liu W, Tao Y. Metabolic engineering of Escherichia coli for production of L-aspartate and its derivative β-alanine with high stoichiometric yield. Metab Eng 2019; 54:244-254. [DOI: 10.1016/j.ymben.2019.04.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 04/22/2019] [Accepted: 04/27/2019] [Indexed: 12/14/2022]
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Efficient Synthesis of Methyl 3-Acetoxypropionate by a Newly Identified Baeyer-Villiger Monooxygenase. Appl Environ Microbiol 2019; 85:AEM.00239-19. [PMID: 30926727 DOI: 10.1128/aem.00239-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 03/24/2019] [Indexed: 11/20/2022] Open
Abstract
Baeyer-Villiger monooxygenases (BVMOs) are an emerging class of promising biocatalysts for the oxidation of ketones to prepare corresponding esters or lactones. Although many BVMOs have been reported, the development of highly efficient enzymes for use in industrial applications is desirable. In this work, we identified a BVMO from Rhodococcus pyridinivorans (BVMORp) with a high affinity toward aliphatic methyl ketones (Km < 3.0 μM). The enzyme was highly soluble and relatively stable, with a half-life of 23 h at 30°C and pH 7.5. The most effective substrate discovered so far is 2-hexanone (k cat = 2.1 s-1; Km = 1.5 μM). Furthermore, BVMORp exhibited excellent regioselectivity toward most aliphatic ketones, preferentially forming typical (i.e., normal) products. Using the newly identified BVMORp as the catalyst, a high concentration (26.0 g/liter; 200 mM) of methyl levulinate was completely converted to methyl 3-acetoxypropionate after 4 h, with a space-time yield of 5.4 g liter-1 h-1 Thus, BVMORp is a promising biocatalyst for the synthesis of 3-hydroxypropionate from readily available biobased levulinate to replace the conventional fermentation.IMPORTANCE BVMOs are emerging as a green alternative to traditional oxidants in the BV oxidation of ketones. Although many BVMOs are discovered and used in organic synthesis, few are really applied in industry, especially in the case of aliphatic ketones. Herein, a highly soluble and relatively stable monooxygenase from Rhodococcus pyridinivorans (BVMORp) was identified with high activity and excellent regioselectivity toward most aliphatic ketones. BVMORp possesses unusually high substrate loading during the catalysis of the oxidation of biobased methyl levulinate to 3-hydroxypropionic acid derivatives. This study indicates that the synthesis of 3-hydroxypropionate from readily available biobased levulinate by BVMORp-catalyzed oxidation holds great promise to replace traditional fermentation.
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