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Gong X, Teng Y, Zhang J, Gan Q, Song M, Alaraj A, Kner P, Yan Y. Architecting a Transcriptional Repressor-based Genetic Inverter for Tryptophan Derived Pathway Regulation in Escherichia coli. Metab Eng 2024:S1096-7176(24)00123-X. [PMID: 39293710 DOI: 10.1016/j.ymben.2024.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 09/15/2024] [Indexed: 09/20/2024]
Abstract
Efficient microbial cell factories require intricate and precise metabolic regulations for optimized production, which can be significantly aided by implementing regulatory genetic circuits with versatile functions. However, constructing functionally diverse genetic circuits in host strains is challenging. Especially, functional diversification based on transcriptional repressors has been rarely explored due to the difficulty in inverting their repression properties. To address this, we proposed a design logic to create transcriptional repressor-based genetic inverters for functional enrichment. As proof of concept, a tryptophan-inducible genetic inverter was constructed by integrating two sets of transcriptional repressors, PtrpO1-TrpR1 and PtetO1-TetR. In this genetic inverter, the repression of TetR towards PtetO1 could be alleviated by the tryptophan-TrpR1 complex in the presence of tryptophan, leading to the activated output. Subsequently, we optimized the dynamic performance of the inverter and constructed tryptophan-triggered dynamic activation systems. Further coupling of the original repression function of PtrpO1-TrpR1 with inverter variants realized the tryptophan-triggered bifunctional regulation system. Finally, the dynamic regulation systems enabled tryptophan production monitoring. These systems also remarkably increased the titers of the tryptophan derivatives tryptamine and violacein by 2.0-fold and 7.4-fold, respectively. The successful design and application of the genetic inverter enhanced the applicability of transcriptional repressors.
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Affiliation(s)
- Xinyu Gong
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Yuxi Teng
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Jianli Zhang
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Qi Gan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Ming Song
- School of Electrical and Computer Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Ameen Alaraj
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Peter Kner
- School of Electrical and Computer Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA
| | - Yajun Yan
- School of Chemical, Materials and Biomedical Engineering, College of Engineering, The University of Georgia, Athens, GA 30602, USA.
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2
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Eun H, Lee SY. Metabolic engineering and fermentation of microorganisms for carotenoids production. Curr Opin Biotechnol 2024; 87:103104. [PMID: 38447325 DOI: 10.1016/j.copbio.2024.103104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/11/2024] [Accepted: 02/18/2024] [Indexed: 03/08/2024]
Abstract
Carotenoids are natural pigments that exhibit a wide range of red, orange, and yellow colors and are extensively used in the food, nutraceuticals, cosmetics, and aquaculture industries. While advances in systems metabolic engineering have established a foundation for constructing carotenoid-producing microbial cell factories at a laboratory scale, translating these technologies to industrial scales remains a big challenge. Moreover, there is a need to devise cost-effective methods for downstream processing and purification of carotenoids. In this review, we discuss recent strategies in metabolic engineering, such as metabolic flux optimization, enzyme assembly, and storage capacity engineering, aimed at constructing high-performance carotenoid-producing microbial strains. We also review recent approaches for cost-effective downstream processing and purification of carotenoids.
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Affiliation(s)
- Hyunmin Eun
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), KAIST Institute for BioCentury, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon 34141, Republic of Korea; Graduate School of Engineering Biology, KAIST, Daejeon 34141, Republic of Korea.
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3
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Wu T, Jiang J, Zhang H, Liu J, Ruan H. Transcending membrane barriers: advances in membrane engineering to enhance the production capacity of microbial cell factories. Microb Cell Fact 2024; 23:154. [PMID: 38796463 PMCID: PMC11128114 DOI: 10.1186/s12934-024-02436-8] [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: 03/15/2024] [Accepted: 05/21/2024] [Indexed: 05/28/2024] Open
Abstract
Microbial cell factories serve as pivotal platforms for the production of high-value natural products, which tend to accumulate on the cell membrane due to their hydrophobic properties. However, the limited space of the cell membrane presents a bottleneck for the accumulation of these products. To enhance the production of intracellular natural products and alleviate the burden on the cell membrane caused by product accumulation, researchers have implemented various membrane engineering strategies. These strategies involve modifying the membrane components and structures of microbial cell factories to achieve efficient accumulation of target products. This review summarizes recent advances in the application of membrane engineering technologies in microbial cell factories, providing case studies involving Escherichia coli and yeast. Through these strategies, researchers have not only improved the tolerance of cells but also optimized intracellular storage space, significantly enhancing the production efficiency of natural products. This article aims to provide scientific evidence and references for further enhancing the efficiency of similar cell factories.
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Affiliation(s)
- Tao Wu
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.
| | - Jingjing Jiang
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Hongyang Zhang
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Jiazhi Liu
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China
| | - Haihua Ruan
- Tianjin Key Laboratory of Food Science and Biotechnology, College of Biotechnology and Food Science, Tianjin University of Commerce, Tianjin, China.
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4
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Guo Q, Peng QQ, Li YW, Yan F, Wang YT, Ye C, Shi TQ. Advances in the metabolic engineering of Saccharomyces cerevisiae and Yarrowia lipolytica for the production of β-carotene. Crit Rev Biotechnol 2024; 44:337-351. [PMID: 36779332 DOI: 10.1080/07388551.2023.2166809] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/20/2022] [Accepted: 12/08/2022] [Indexed: 02/14/2023]
Abstract
β-Carotene is one kind of the most important carotenoids. The major functions of β-carotene include the antioxidant and anti-cardiovascular properties, which make it a growing market. Recently, the use of metabolic engineering to construct microbial cell factories to synthesize β-carotene has become the latest model for its industrial production. Among these cell factories, yeasts including Saccharomyces cerevisiae and Yarrowia lipolytica have attracted the most attention because of the: security, mature genetic manipulation tools, high flux toward carotenoids using the native mevalonate pathway and robustness for large-scale fermentation. In this review, the latest strategies for β-carotene biosynthesis, including protein engineering, promoters engineering and morphological engineering are summarized in detail. Finally, perspectives for future engineering approaches are proposed to improve β-carotene production.
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Affiliation(s)
- Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Qian-Qian Peng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Ya-Wen Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Fang Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Yue-Tong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
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Wang J, Ma W, Ma W, Fang Z, Jiang Y, Jiang W, Kong X, Xin F, Zhang W, Jiang M. Strategies for the efficient biosynthesis of β-carotene through microbial fermentation. World J Microbiol Biotechnol 2024; 40:160. [PMID: 38607448 DOI: 10.1007/s11274-024-03955-7] [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: 01/26/2024] [Accepted: 03/12/2024] [Indexed: 04/13/2024]
Abstract
β-Carotene is an orange fat-soluble compound, which has been widely used in fields such as food, medicine and cosmetics owing to its anticancer, antioxidant and cardiovascular disease prevention properties. Currently, natural β-carotene is mainly extracted from plants and algae, which cannot meet the growing market demand, while chemical synthesis of β-carotene cannot satisfy the pursuit for natural products of consumers. The β-carotene production through microbial fermentation has become a promising alternative owing to its high efficiency and environmental friendliness. With the rapid development of synthetic biology and in-depth study on the synthesis pathway of β-carotene, microbial fermentation has shown promising applications in the β-carotene synthesis. Accordingly, this review aims to summarize the research progress and strategies of natural carotenoid producing strain and metabolic engineering strategies in the heterologous synthesis of β-carotene by engineered microorganisms. Moreover, it also summarizes the adoption of inexpensive carbon sources to synthesize β-carotene as well as proposes new strategies that can further improve the β-carotene production.
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Affiliation(s)
- Jingnan Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Wenqi Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Weixu Ma
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Zhanyang Fang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Xiangping Kong
- Key Laboratory for Crop and Animal Integrated Farming, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, People's Republic of China.
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
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Su B, Deng MR, Zhu H. Advances in the Discovery and Engineering of Gene Targets for Carotenoid Biosynthesis in Recombinant Strains. Biomolecules 2023; 13:1747. [PMID: 38136618 PMCID: PMC10742120 DOI: 10.3390/biom13121747] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/29/2023] [Accepted: 12/02/2023] [Indexed: 12/24/2023] Open
Abstract
Carotenoids are naturally occurring pigments that are abundant in the natural world. Due to their excellent antioxidant attributes, carotenoids are widely utilized in various industries, including the food, pharmaceutical, cosmetic industries, and others. Plants, algae, and microorganisms are presently the main sources for acquiring natural carotenoids. However, due to the swift progress in metabolic engineering and synthetic biology, along with the continuous and thorough investigation of carotenoid biosynthetic pathways, recombinant strains have emerged as promising candidates to produce carotenoids. The identification and manipulation of gene targets that influence the accumulation of the desired products is a crucial challenge in the construction and metabolic regulation of recombinant strains. In this review, we provide an overview of the carotenoid biosynthetic pathway, followed by a summary of the methodologies employed in the discovery of gene targets associated with carotenoid production. Furthermore, we focus on discussing the gene targets that have shown potential to enhance carotenoid production. To facilitate future research, we categorize these gene targets based on their capacity to attain elevated levels of carotenoid production.
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Affiliation(s)
| | - Ming-Rong Deng
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China;
| | - Honghui Zhu
- Key Laboratory of Agricultural Microbiomics and Precision Application (MARA), Key Laboratory of Agricultural Microbiome (MARA), State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou 510070, China;
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Luo Z, Shi JT, Chen XL, Chen J, Liu F, Wei LJ, Hua Q. Iterative gene integration mediated by 26S rDNA and non-homologous end joining for the efficient production of lycopene in Yarrowia lipolytica. BIORESOUR BIOPROCESS 2023; 10:83. [PMID: 38647953 PMCID: PMC10992032 DOI: 10.1186/s40643-023-00697-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/23/2023] [Indexed: 04/25/2024] Open
Abstract
Because of its potent antioxidant effects, lycopene has been used in various industries including, but not limited to, food, medical, and cosmetic industries. Yarrowia lipolytica, a non-conventional yeast species, is a promising chassis due to its natural mevalonate (MVA) pathway, abundant precursor acetyl coenzyme A content, and oleaginous properties. Several gene editing tools have been developed for Y. lipolytica along with engineering strategies for tetraterpenoid production. In this study, we engineered Y. lipolytica following multi-level strategies for efficient lycopene accumulation. We first evaluated the performance of the key lycopene biosynthetic genes crtE, crtB, and crtI, expressed via ribosomal DNA (rDNA) mediated multicopy random integration in the HMG1- and GGS1-overexpressing background strain. Further improvement in lycopene production was achieved by overexpressing the key genes for MVA synthesis via non-homologous end joining (NHEJ) mediated multi-round iterative transformation. Efficient strategies in the MVA and lipid synthesis pathways were combined to improve lycopene production with a yield of 430.5 mg/L. This strain produced 121 mg/g dry cell weight of lycopene in a 5-L fed-batch fermentation system. Our findings demonstrated iterative gene integration mediated by 26S rDNA and NHEJ for the efficient production of lycopene in Y. lipolytica. These strategies can be applied to induce Y. lipolytica to produce other tetraterpenoids.
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Affiliation(s)
- Zhen Luo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Jiang-Ting Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Xin-Liang Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Jun Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Feng Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Liu-Jing Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai, 200237, China.
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Fordjour E, Bai Z, Li S, Li S, Sackey I, Yang Y, Liu CL. Improved Membrane Permeability via Hypervesiculation for In Situ Recovery of Lycopene in Escherichia coli. ACS Synth Biol 2023; 12:2725-2739. [PMID: 37607052 DOI: 10.1021/acssynbio.3c00306] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Lycopene biosynthesis is frequently hampered by downstream processing hugely due to its inability to be secreted out from the producing chassis. Engineering cell factories can resolve this issue by secreting this hydrophobic compound. A highly permeable E. coli strain was developed for a better release rate of lycopene. Specifically, the heterologous mevalonate pathway and crtEBI genes from Corynebacterium glutamicum were overexpressed in Escherichia coli BL21 (DE3) for lycopene synthesis. To ensure in situ lycopene production, murein lipoprotein, lipoprotein NlpI, inner membrane permease protein, and membrane-anchored protein in TolA-TolQ-TolR were deleted for improved membrane permeability. The final strain, LYC-8, produced 438.44 ± 8.11 and 136.94 ± 1.94 mg/L of extracellular and intracellular lycopene in fed-batch fermentation. Both proteomics and lipidomics analyses of secreted outer membrane vesicles were perfect indicators of hypervesiculation. Changes in the ratio of saturated fatty acids, unsaturated fatty acids, and cyclopropane fatty acids coupled with the branching and acyl chain lengths altered the membrane fatty acid composition. This ensured membrane fluidity and permeability for in situ lycopene release. The combinatorial deletion of these genes altered the cellular morphology. The structural and morphological changes in cell shape, size, and length were associated with changes in the mechanical strength of the cell envelope. The enhanced lycopene production and secretion mediated by improved membrane permeability established a cell lysis-free system for an efficient releasing rate and downstream processing, demonstrating the importance of vesicle-associated membrane permeability in efficient lycopene production.
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Affiliation(s)
- Eric Fordjour
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Zhonghu Bai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Sihan Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Shijie Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Isaac Sackey
- Department of Biological Sciences, Faculty of Biosciences, University for Development Studies, P.O. Box TL1350, NT-0272-1946 Tamale, Ghana
| | - Yankun Yang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
| | - Chun-Li Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center of Cereal Fermentation, and Food Biomanufacturing, Jiangnan University, Wuxi 214122, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi 214122, China
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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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10
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Xu S, Gao S, An Y. Research progress of engineering microbial cell factories for pigment production. Biotechnol Adv 2023; 65:108150. [PMID: 37044266 DOI: 10.1016/j.biotechadv.2023.108150] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 03/14/2023] [Accepted: 04/06/2023] [Indexed: 04/14/2023]
Abstract
Pigments are widely used in people's daily life, such as food additives, cosmetics, pharmaceuticals, textiles, etc. In recent years, the natural pigments produced by microorganisms have attracted increased attention because these processes cannot be affected by seasons like the plant extraction methods, and can also avoid the environmental pollution problems caused by chemical synthesis. Synthetic biology and metabolic engineering have been used to construct and optimize metabolic pathways for production of natural pigments in cellular factories. Building microbial cell factories for synthesis of natural pigments has many advantages, including well-defined genetic background of the strains, high-density and rapid culture of cells, etc. Until now, the technical means about engineering microbial cell factories for pigment production and metabolic regulation processes have not been systematically analyzed and summarized. Therefore, the studies about construction, modification and regulation of synthetic pathways for microbial synthesis of pigments in recent years have been reviewed, aiming to provide an up-to-date summary of engineering strategies for microbial synthesis of natural pigments including carotenoids, melanins, riboflavins, azomycetes and quinones. This review should provide new ideas for further improving microbial production of natural pigments in the future.
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Affiliation(s)
- Shumin Xu
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China; College of Food Science, Shenyang Agricultural University, Shenyang, China
| | - Song Gao
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yingfeng An
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang, China; College of Food Science, Shenyang Agricultural University, Shenyang, China; Shenyang Key Laboratory of Microbial Resources Mining and Molecular Breeding, Shenyang, China; Liaoning Provincial Key Laboratory of Agricultural Biotechnology, Shenyang, China.
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11
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Eroglu A, Al'Abri IS, Kopec RE, Crook N, Bohn T. Carotenoids and Their Health Benefits as Derived via Their Interactions with Gut Microbiota. Adv Nutr 2023; 14:238-255. [PMID: 36775788 DOI: 10.1016/j.advnut.2022.10.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/21/2022] [Accepted: 10/28/2022] [Indexed: 12/23/2022] Open
Abstract
Carotenoids have been related to a number of health benefits. Their dietary intake and circulating levels have been associated with a reduced incidence of obesity, diabetes, certain types of cancer, and even lower total mortality. Their potential interaction with the gut microbiota (GM) has been generally overlooked but may be of relevance, as carotenoids largely bypass absorption in the small intestine and are passed on to the colon, where they appear to be in part degraded into unknown metabolites. These may include apo-carotenoids that may have biological effects because of higher aqueous solubility and higher electrophilicity that could better target transcription factors, i.e., NF-κB, PPARγ, and RAR/RXRs. If absorbed in the colon, they could have both local and systemic effects. Certain microbes that may be supplemented were also reported to produce carotenoids in the colon. Although some bactericidal aspects of carotenoids have been shown in vitro, a few studies have also demonstrated a prebiotic-like effect, resulting in bacterial shifts with health-associated properties. Also, stimulation of IgA could play a role in this respect. Carotenoids may further contribute to mucosal and gut barrier health, such as stabilizing tight junctions. This review highlights potential gut-related health-beneficial effects of carotenoids and emphasizes the current research gaps regarding carotenoid-GM interactions.
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Affiliation(s)
- Abdulkerim Eroglu
- Department of Molecular and Structural Biochemistry, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC, USA; Plants for Human Health Institute, North Carolina Research Campus, North Carolina State University, Kannapolis, NC, USA.
| | - Ibrahim S Al'Abri
- Department of Chemical and Biomolecular Engineering, College of Engineering, North Carolina State University, Raleigh, NC, USA
| | - Rachel E Kopec
- Human Nutrition Program, Department of Human Sciences, The Ohio State University, Columbus, OH, USA; Foods for Health Discovery Theme, The Ohio State University, Columbus, OH, USA
| | - Nathan Crook
- Department of Chemical and Biomolecular Engineering, College of Engineering, North Carolina State University, Raleigh, NC, USA
| | - Torsten Bohn
- Nutrition and Health Research Group, Department of Precision Health, Luxembourg Institute of Health, rue 1 A-B, Thomas Edison, L-1445 Strassen, Luxembourg.
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12
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Chen L, Xiao W, Yao M, Wang Y, Yuan Y. Compartmentalization engineering of yeasts to overcome precursor limitations and cytotoxicity in terpenoid production. Front Bioeng Biotechnol 2023; 11:1132244. [PMID: 36911190 PMCID: PMC9997727 DOI: 10.3389/fbioe.2023.1132244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
Metabolic engineering strategies for terpenoid production have mainly focused on bottlenecks in the supply of precursor molecules and cytotoxicity to terpenoids. In recent years, the strategies involving compartmentalization in eukaryotic cells has rapidly developed and have provided several advantages in the supply of precursors, cofactors and a suitable physiochemical environment for product storage. In this review, we provide a comprehensive analysis of organelle compartmentalization for terpenoid production, which can guide the rewiring of subcellular metabolism to make full use of precursors, reduce metabolite toxicity, as well as provide suitable storage capacity and environment. Additionally, the strategies that can enhance the efficiency of a relocated pathway by increasing the number and size of organelles, expanding the cell membrane and targeting metabolic pathways in several organelles are also discussed. Finally, the challenges and future perspectives of this approach for the terpenoid biosynthesis are also discussed.
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Affiliation(s)
- Lifei Chen
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Wenhai Xiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China.,Georgia Tech Shenzhen Institute, Tianjin University, Shenzhen, China
| | - Mingdong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Ying Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
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13
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Metibemu DS, Ogungbe IV. Carotenoids in Drug Discovery and Medicine: Pathways and Molecular Targets Implicated in Human Diseases. Molecules 2022; 27:6005. [PMID: 36144741 PMCID: PMC9503763 DOI: 10.3390/molecules27186005] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 09/01/2022] [Accepted: 09/12/2022] [Indexed: 11/23/2022] Open
Abstract
Carotenoids are isoprenoid-derived natural products produced in plants, algae, fungi, and photosynthetic bacteria. Most animals cannot synthesize carotenoids because the biosynthetic machinery to create carotenoids de novo is absent in animals, except arthropods. Carotenoids are biosynthesized from two C20 geranylgeranyl pyrophosphate (GGPP) molecules made from isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) via the methylerythritol 4-phosphate (MEP) route. Carotenoids can be extracted by a variety of methods, including maceration, Soxhlet extraction, supercritical fluid extraction (SFE), microwave-assisted extraction (MAE), accelerated solvent extraction (ASE), ultrasound-assisted extraction (UAE), pulsed electric field (PEF)-assisted extraction, and enzyme-assisted extraction (EAE). Carotenoids have been reported to exert various biochemical actions, including the inhibition of the Akt/mTOR, Bcl-2, SAPK/JNK, JAK/STAT, MAPK, Nrf2/Keap1, and NF-κB signaling pathways and the ability to increase cholesterol efflux to HDL. Carotenoids are absorbed in the intestine. A handful of carotenoids and carotenoid-based compounds are in clinical trials, while some are currently used as medicines. The application of metabolic engineering techniques for carotenoid production, whole-genome sequencing, and the use of plants as cell factories to produce specialty carotenoids presents a promising future for carotenoid research. In this review, we discussed the biosynthesis and extraction of carotenoids, the roles of carotenoids in human health, the metabolism of carotenoids, and carotenoids as a source of drugs and supplements.
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Affiliation(s)
| | - Ifedayo Victor Ogungbe
- Department of Chemistry, Physics, and Atmospheric Sciences, Jackson State University, Jackson, MS 39217-0095, USA
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14
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Li M, Zhou P, Chen M, Yu H, Ye L. Spatiotemporal Regulation of Astaxanthin Synthesis in S. cerevisiae. ACS Synth Biol 2022; 11:2636-2649. [PMID: 35914247 DOI: 10.1021/acssynbio.2c00044] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
As a high-valued antioxidant, astaxanthin biosynthesis using microbial cell factories has attracted increasing attention. However, its lipophilic nature conflicts with the limited storage capacity for lipophilic substances of model microorganisms such as Saccharomyces cerevisiae. Expansion of lipid droplets by enhancing lipid synthesis provides more storage room while diverting the metabolic flux from the target pathway. Therefore, proper spatial regulation is required. In this study, a library of genes related to lipid metabolism were screened using the trifunctional CRISPR system, identifying opi3 and hrd1 as new engineering targets to promote astaxanthin synthesis by moderately rather than excessively upregulating lipid synthesis. The astaxanthin yield reached 9.79 mg/g DCW after lipid engineering and was further improved to 10.21 mg/g DCW by balancing the expression of β-carotene hydroxylase and ketolase. Finally, by combining spatial regulation through lipid droplet engineering and temporal regulation via temperature-responsive pathway expression, 446.4 mg/L astaxanthin was produced in fed-batch fermentation.
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Affiliation(s)
- Min Li
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Pingping Zhou
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.,College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
| | - Mingkai Chen
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China.,ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou 311200, China
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15
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Yang D, Eun H, Prabowo CPS, Cho S, Lee SY. Metabolic and cellular engineering for the production of natural products. Curr Opin Biotechnol 2022; 77:102760. [PMID: 35908315 DOI: 10.1016/j.copbio.2022.102760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/14/2022] [Accepted: 06/30/2022] [Indexed: 11/25/2022]
Abstract
Increased awareness of the environmental and health concerns of consuming chemically synthesized products has led to a rising demand for natural products that are greener and more sustainable. Despite their importance, however, industrial-scale production of natural products has been challenging due to the low yield and high cost of the bioprocesses. To cope with this problem, systems metabolic engineering has been employed to efficiently produce natural products from renewable biomass. Here, we review the recent systems metabolic engineering strategies employed for enhanced production of value-added natural products, together with accompanying examples. Particular focus is set on systems-level engineering and cell physiology engineering strategies. Future perspectives are also discussed.
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Affiliation(s)
- Dongsoo Yang
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KAIST Institute for the BioCentury and KAIST Institute for Artificial Intelligence, KAIST, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon 34141, Republic of Korea.
| | - Hyunmin Eun
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KAIST Institute for the BioCentury and KAIST Institute for Artificial Intelligence, KAIST, Daejeon 34141, Republic of Korea
| | - Cindy Pricilia Surya Prabowo
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KAIST Institute for the BioCentury and KAIST Institute for Artificial Intelligence, KAIST, Daejeon 34141, Republic of Korea
| | - Sumin Cho
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KAIST Institute for the BioCentury and KAIST Institute for Artificial Intelligence, KAIST, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory and Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KAIST Institute for the BioCentury and KAIST Institute for Artificial Intelligence, KAIST, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon 34141, Republic of Korea.
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16
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Basiony M, Ouyang L, Wang D, Yu J, Zhou L, Zhu M, Wang X, Feng J, Dai J, Shen Y, Zhang C, Hua Q, Yang X, Zhang L. Optimization of microbial cell factories for astaxanthin production: Biosynthesis and regulations, engineering strategies and fermentation optimization strategies. Synth Syst Biotechnol 2022; 7:689-704. [PMID: 35261927 PMCID: PMC8866108 DOI: 10.1016/j.synbio.2022.01.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/08/2021] [Accepted: 01/03/2022] [Indexed: 12/29/2022] Open
Abstract
The global market demand for natural astaxanthin is rapidly increasing owing to its safety, the potential health benefits, and the diverse applications in food and pharmaceutical industries. The major native producers of natural astaxanthin on industrial scale are the alga Haematococcus pluvialis and the yeast Xanthopyllomyces dendrorhous. However, the natural production via these native producers is facing challenges of limited yield and high cost of cultivation and extraction. Alternatively, astaxanthin production via metabolically engineered non-native microbial cell factories such as Escherichia coli, Saccharomyces cerevisiae and Yarrowia lipolytica is another promising strategy to overcome these limitations. In this review we summarize the recent scientific and biotechnological progresses on astaxanthin biosynthetic pathways, transcriptional regulations, the interrelation with lipid metabolism, engineering strategies as well as fermentation process control in major native and non-native astaxanthin producers. These progresses illuminate the prospects of producing astaxanthin by microbial cell factories on industrial scale.
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Affiliation(s)
- Mostafa Basiony
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Liming Ouyang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Danni Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiaming Yu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Liming Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Mohan Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xuyuan Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jie Feng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Jing Dai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Yijie Shen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Chengguo Zhang
- Shandong Jincheng Bio-Pharmaceutical Co., Ltd., No. 117 Qixing River Road, Zibo, 255130, Shandong, China
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Xiuliang Yang
- Shandong Jincheng Bio-Pharmaceutical Co., Ltd., No. 117 Qixing River Road, Zibo, 255130, Shandong, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
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17
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Jin K, Xia H, Liu Y, Li J, Du G, Lv X, Liu L. Compartmentalization and transporter engineering strategies for terpenoid synthesis. Microb Cell Fact 2022; 21:92. [PMID: 35599322 PMCID: PMC9125818 DOI: 10.1186/s12934-022-01819-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/12/2022] [Indexed: 12/18/2022] Open
Abstract
Microbial cell factories for terpenoid synthesis form a less expensive and more environment-friendly approach than chemical synthesis and extraction, and are thus being regarded as mainstream research recently. Organelle compartmentalization for terpenoid synthesis has received much attention from researchers owing to the diverse physiochemical characteristics of organelles. In this review, we first systematically summarized various compartmentalization strategies utilized in terpenoid production, mainly plant terpenoids, which can provide catalytic reactions with sufficient intermediates and a suitable environment, while bypassing competing metabolic pathways. In addition, because of the limited storage capacity of cells, strategies used for the expansion of specific organelle membranes were discussed. Next, transporter engineering strategies to overcome the cytotoxic effects of terpenoid accumulation were analyzed. Finally, we discussed the future perspectives of compartmentalization and transporter engineering strategies, with the hope of providing theoretical guidance for designing and constructing cell factories for the purpose of terpenoid production.
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Affiliation(s)
- Ke Jin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Hongzhi Xia
- Richen Bioengineering Co., Ltd, Nantong, 226000, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China.
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China.
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18
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Rational Engineering of Non-Ubiquinone Containing Corynebacterium glutamicum for Enhanced Coenzyme Q10 Production. Metabolites 2022; 12:metabo12050428. [PMID: 35629932 PMCID: PMC9145305 DOI: 10.3390/metabo12050428] [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: 04/27/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 11/17/2022] Open
Abstract
Coenzyme Q10 (CoQ10) is a lipid-soluble compound with important physiological functions and is sought after in the food and cosmetic industries owing to its antioxidant properties. In our previous proof of concept, we engineered for CoQ10 biosynthesis the industrially relevant Corynebacterium glutamicum, which does not naturally synthesize any CoQ. Here, liquid chromatography–mass spectrometry (LC–MS) analysis identified two metabolic bottlenecks in the CoQ10 production, i.e., low conversion of the intermediate 10-prenylphenol (10P-Ph) to CoQ10 and the accumulation of isoprenologs with prenyl chain lengths of not only 10, but also 8 to 11 isopentenyl units. To overcome these limitations, the strain was engineered for expression of the Ubi complex accessory factors UbiJ and UbiK from Escherichia coli to increase flux towards CoQ10, and by replacement of the native polyprenyl diphosphate synthase IspB with a decaprenyl diphosphate synthase (DdsA) to select for prenyl chains with 10 isopentenyl units. The best strain UBI6-Rs showed a seven-fold increased CoQ10 content and eight-fold increased CoQ10 titer compared to the initial strain UBI4-Pd, while the abundance of CoQ8, CoQ9, and CoQ11 was significantly reduced. This study demonstrates the application of the recent insight into CoQ biosynthesis to improve metabolic engineering of a heterologous CoQ10 production strain.
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19
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Production of natural colorants by metabolically engineered microorganisms. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.04.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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20
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Liu J, Wang X, Dai G, Zhang Y, Bian X. Microbial chassis engineering drives heterologous production of complex secondary metabolites. Biotechnol Adv 2022; 59:107966. [PMID: 35487394 DOI: 10.1016/j.biotechadv.2022.107966] [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: 01/15/2022] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/27/2022]
Abstract
The cryptic secondary metabolite biosynthetic gene clusters (BGCs) far outnumber currently known secondary metabolites. Heterologous production of secondary metabolite BGCs in suitable chassis facilitates yield improvement and discovery of new-to-nature compounds. The two juxtaposed conventional model microorganisms, Escherichia coli, Saccharomyces cerevisiae, have been harnessed as microbial chassis to produce a bounty of secondary metabolites with the help of certain host engineering. In last decade, engineering non-model microbes to efficiently biosynthesize secondary metabolites has received increasing attention due to their peculiar advantages in metabolic networks and/or biosynthesis. The state-of-the-art synthetic biology tools lead the way in operating genetic manipulation in non-model microorganisms for phenotypic optimization or yields improvement of desired secondary metabolites. In this review, we firstly discuss the pros and cons of several model and non-model microbial chassis, as well as the importance of developing broader non-model microorganisms as alternative programmable heterologous hosts to satisfy the desperate needs of biosynthesis study and industrial production. Then we highlight the lately advances in the synthetic biology tools and engineering strategies for optimization of non-model microbial chassis, in particular, the successful applications for efficient heterologous production of multifarious complex secondary metabolites, e.g., polyketides, nonribosomal peptides, as well as ribosomally synthesized and post-translationally modified peptides. Lastly, emphasis is on the perspectives of chassis cells development to access the ideal cell factory in the artificial intelligence-driven genome era.
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Affiliation(s)
- Jiaqi Liu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China; Present address: Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Saarland University, Campus E8 1, 66123 Saarbrücken, Germany
| | - Xue Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Guangzhi Dai
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, PR China.
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21
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Wu J, Tian X, Xu X, Gu X, Kong J, Guo T. Engineered Probiotic Lactococcus lactis for Lycopene Production against ROS Stress in Intestinal Epithelial Cells. ACS Synth Biol 2022; 11:1568-1576. [PMID: 35289165 DOI: 10.1021/acssynbio.1c00639] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lactococcus lactis is a food-grade chassis for delivery of bioactive molecules to the intestinal mucosa in situ, while its ability to produce lycopene for detoxification of reactive oxidative species (ROS) is not realized yet. Here, L. lactis NZ9000 was engineered to synthesize lycopene by heterologous expression of a gene cluster crtEBI in plasmids or chromosomes, yielding the recombinant strains NZ4 and NZ5 with 0.59 and 0.54 mg/L lycopene production, respectively. To reroute the pyruvate flux to lycopene, the main lactate dehydrogenase and α-acetolactate synthase pathways were sequentially disrupted. The resultant strains NZΔldh-1 and NZΔldhΔals-1 increased lycopene accumulation to 0.70 and 0.73 mg/L, respectively, while their biomasses were reduced by 12.42% and the intracellular NADH/NAD+ ratios increased by 3.05- and 2.10-fold. To increase the biomasses of these engineered strains, aerobic respiration was activated and tuned by the addition of exogenous heme and oxygen. As a result, the engineered L. lactis strains partly recovered the growth and redox balance, yielding the lycopene levels of 0.91-1.09 mg/L. The engineered L. lactis strain protected the intestinal epithelial cells NCM460 against H2O2 challenge, with a 30.09% increase of cell survival and a 29.2% decrease of the intracellular ROS level compared with strain NZ9000 treatment. In summary, this work established the use of the engineered probiotic L. lactis for lycopene production and prospected its potential in the prevention of intestinal oxidative damage.
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Affiliation(s)
- Jiapeng Wu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Xingfang Tian
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Xiaoning Xu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Xinyi Gu
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
| | - Tingting Guo
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao 266237, P. R. China
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22
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Singh RV, Sambyal K. An overview of β-carotene production: Current status and future prospects. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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23
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Li S, Ma L, Fu W, Su R, Zhao Y, Deng Y. Programmable Synthetic Upstream Activating Sequence Library for Fine-Tuning Gene Expression Levels in Saccharomyces cerevisiae. ACS Synth Biol 2022; 11:1228-1239. [PMID: 35195994 DOI: 10.1021/acssynbio.1c00511] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A wide dynamic range of promoters is necessary for fine-tuning transcription levels. However, weak intensity and narrow dynamic range limit transcriptional regulation via constitutive promoters. The upstream activation sequence (UAS) located upstream of the core promoter is a crucial region that could obviously enhance promoter strength. Herein, we created a random mutagenesis library consisting of 330 different variants based on the UAS of the TDH3 promoter with an ∼37-fold dynamic range by error-prone polymerase chain reaction (PCR) and obtained strong intensity mutant UAS, which was ∼12-fold greater than the wild-type UASTDH3. Analysis of the mutant library revealed 15 strength-enhancing sites and their corresponding bases of the UASTDH3 regions, which provided the impetus for a synthetic library. The resulting 32 768 mutant UAS library was constructed by permutation and combination of the bases of the 15 enhancing sites. To characterize the library, a strength prediction model was built by correlating DNA structural features and UAS strength, which provided a model between UAS sequence and intensity. Following characterization, the UAS library was applied to precisely regulate gene expression in the production of β-carotene, proving that the UAS library would be a useful tool for gene tuning in metabolic engineering. In summary, we designed, constructed, and characterized a UAS library that facilitated precise tuning of transcription levels of target proteins.
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Affiliation(s)
- Shiyun Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Lizhou Ma
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Wenxuan Fu
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Ruifang Su
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yunying Zhao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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24
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Abstract
Terpenoids represent the largest group of secondary metabolites with variable structures and functions. Terpenoids are well known for their beneficial application in human life, such as pharmaceutical products, vitamins, hormones, anticancer drugs, cosmetics, flavors and fragrances, foods, agriculture, and biofuels. Recently, engineering microbial cells have been provided with a sustainable approach to produce terpenoids with high yields. Noticeably, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) system has emerged as one of the most efficient genome-editing technologies to engineer microorganisms for improving terpenoid production. In this review, we summarize the application of the CRISPR-Cas system for the production of terpenoids in microbial hosts such as Escherichia coli, Saccharomyces cerevisiae, Corynebacterium glutamicum, and Pseudomonas putida. CRISPR-Cas9 deactivated Cas9 (dCas9)-based CRISPR (CRISPRi), and the dCas9-based activator (CRISPRa) have been used in either individual or combinatorial systems to control the metabolic flux for enhancing the production of terpenoids. Finally, the prospects of using the CRISPR-Cas system in terpenoid production are also discussed.
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Affiliation(s)
- Luan Luong Chu
- Faculty of Biotechnology, Chemistry and Environmental Engineering, Phenikaa University, Hanoi, Viet Nam.,Bioresource Research Center, Phenikaa University, Hanoi, Viet Nam
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25
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Lyu X, Lyu Y, Yu H, Chen W, Ye L, Yang R. Biotechnological advances for improving natural pigment production: a state-of-the-art review. BIORESOUR BIOPROCESS 2022; 9:8. [PMID: 38647847 PMCID: PMC10992905 DOI: 10.1186/s40643-022-00497-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/17/2022] [Indexed: 12/14/2022] Open
Abstract
In current years, natural pigments are facing a fast-growing global market due to the increase of people's awareness of health and the discovery of novel pharmacological effects of various natural pigments, e.g., carotenoids, flavonoids, and curcuminoids. However, the traditional production approaches are source-dependent and generally subject to the low contents of target pigment compounds. In order to scale-up industrial production, many efforts have been devoted to increasing pigment production from natural producers, via development of both in vitro plant cell/tissue culture systems, as well as optimization of microbial cultivation approaches. Moreover, synthetic biology has opened the door for heterologous biosynthesis of pigments via design and re-construction of novel biological modules as well as biological systems in bio-platforms. In this review, the innovative methods and strategies for optimization and engineering of both native and heterologous producers of natural pigments are comprehensively summarized. Current progress in the production of several representative high-value natural pigments is also presented; and the remaining challenges and future perspectives are discussed.
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Affiliation(s)
- Xiaomei Lyu
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Yan Lyu
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China
| | - Hongwei Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
| | - WeiNing Chen
- School of Chemical and Biomedical Engineering, College of Engineering, Nanyang Technological University, Singapore, 637459, Singapore
| | - Lidan Ye
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China.
| | - Ruijin Yang
- School of Food Science and Technology, Jiangnan University, Wuxi, 214122, People's Republic of China.
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26
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Rinaldi MA, Ferraz CA, Scrutton NS. Alternative metabolic pathways and strategies to high-titre terpenoid production in Escherichia coli. Nat Prod Rep 2022; 39:90-118. [PMID: 34231643 PMCID: PMC8791446 DOI: 10.1039/d1np00025j] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Terpenoids are a diverse group of chemicals used in a wide range of industries. Microbial terpenoid production has the potential to displace traditional manufacturing of these compounds with renewable processes, but further titre improvements are needed to reach cost competitiveness. This review discusses strategies to increase terpenoid titres in Escherichia coli with a focus on alternative metabolic pathways. Alternative pathways can lead to improved titres by providing higher orthogonality to native metabolism that redirects carbon flux, by avoiding toxic intermediates, by bypassing highly-regulated or bottleneck steps, or by being shorter and thus more efficient and easier to manipulate. The canonical 2-C-methyl-D-erythritol 4-phosphate (MEP) and mevalonate (MVA) pathways are engineered to increase titres, sometimes using homologs from different species to address bottlenecks. Further, alternative terpenoid pathways, including additional entry points into the MEP and MVA pathways, archaeal MVA pathways, and new artificial pathways provide new tools to increase titres. Prenyl diphosphate synthases elongate terpenoid chains, and alternative homologs create orthogonal pathways and increase product diversity. Alternative sources of terpenoid synthases and modifying enzymes can also be better suited for E. coli expression. Mining the growing number of bacterial genomes for new bacterial terpenoid synthases and modifying enzymes identifies enzymes that outperform eukaryotic ones and expand microbial terpenoid production diversity. Terpenoid removal from cells is also crucial in production, and so terpenoid recovery and approaches to handle end-product toxicity increase titres. Combined, these strategies are contributing to current efforts to increase microbial terpenoid production towards commercial feasibility.
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Affiliation(s)
- Mauro A Rinaldi
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Clara A Ferraz
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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27
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Fordjour E, Mensah EO, Hao Y, Yang Y, Liu X, Li Y, Liu CL, Bai Z. Toward improved terpenoids biosynthesis: strategies to enhance the capabilities of cell factories. BIORESOUR BIOPROCESS 2022; 9:6. [PMID: 38647812 PMCID: PMC10992668 DOI: 10.1186/s40643-022-00493-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 01/04/2022] [Indexed: 02/22/2023] Open
Abstract
Terpenoids form the most diversified class of natural products, which have gained application in the pharmaceutical, food, transportation, and fine and bulk chemical industries. Extraction from naturally occurring sources does not meet industrial demands, whereas chemical synthesis is often associated with poor enantio-selectivity, harsh working conditions, and environmental pollutions. Microbial cell factories come as a suitable replacement. However, designing efficient microbial platforms for isoprenoid synthesis is often a challenging task. This has to do with the cytotoxic effects of pathway intermediates and some end products, instability of expressed pathways, as well as high enzyme promiscuity. Also, the low enzymatic activity of some terpene synthases and prenyltransferases, and the lack of an efficient throughput system to screen improved high-performing strains are bottlenecks in strain development. Metabolic engineering and synthetic biology seek to overcome these issues through the provision of effective synthetic tools. This review sought to provide an in-depth description of novel strategies for improving cell factory performance. We focused on improving transcriptional and translational efficiencies through static and dynamic regulatory elements, enzyme engineering and high-throughput screening strategies, cellular function enhancement through chromosomal integration, metabolite tolerance, and modularization of pathways.
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Affiliation(s)
- Eric Fordjour
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Emmanuel Osei Mensah
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Yunpeng Hao
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Yankun Yang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Xiuxia Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Ye Li
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China
| | - Chun-Li Liu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China.
| | - Zhonghu Bai
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
- Jiangsu Provincial Research Centre for Bioactive Product Processing Technology, Jiangnan University, Wuxi, China.
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28
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Microbial cell surface engineering for high-level synthesis of bio-products. Biotechnol Adv 2022; 55:107912. [PMID: 35041862 DOI: 10.1016/j.biotechadv.2022.107912] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/28/2021] [Accepted: 01/09/2022] [Indexed: 02/08/2023]
Abstract
Microbial cell surface layers, which mainly include the cell membrane, cell wall, periplasmic space, outer membrane, capsules, S-layers, pili, and flagella, control material exchange between the cell and the extracellular environment, and have great impact on production titers and yields of various bio-products synthesized by microbes. Recent research work has made exciting achievements in metabolic engineering using microbial cell surface components as novel regulation targets without direct modifications of the metabolic pathways of the desired products. This review article will summarize the accomplishments obtained in this emerging field, and will describe various engineering strategies that have been adopted in bacteria and yeasts for the enhancement of mass transfer across the cell surface, improvement of protein expression and folding, modulation of cell size and shape, and re-direction of cellular resources, all of which contribute to the construction of more efficient microbial cell factories toward the synthesis of a variety of bio-products. The existing problems and possible future directions will also be discussed.
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29
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Bu X, Lin JY, Duan CQ, Koffas MAG, Yan GL. Dual regulation of lipid droplet-triacylglycerol metabolism and ERG9 expression for improved β-carotene production in Saccharomyces cerevisiae. Microb Cell Fact 2022; 21:3. [PMID: 34983533 PMCID: PMC8725481 DOI: 10.1186/s12934-021-01723-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/14/2021] [Indexed: 12/05/2022] Open
Abstract
Background The limitation of storage space, product cytotoxicity and the competition for precursor are the major challenges for efficiently overproducing carotenoid in engineered non-carotenogenic microorganisms. In this work, to improve β-carotene accumulation in Saccharomyces cerevisiae, a strategy that simultaneous increases cell storage capability and strengthens metabolic flux to carotenoid pathway was developed using exogenous oleic acid (OA) combined with metabolic engineering approaches. Results The direct separation of lipid droplets (LDs), quantitative analysis and genes disruption trial indicated that LDs are major storage locations of β-carotene in S. cerevisiae. However, due to the competition for precursor between β-carotene and LDs-triacylglycerol biosynthesis, enlarging storage space by engineering LDs related genes has minor promotion on β-carotene accumulation. Adding 2 mM OA significantly improved LDs-triacylglycerol metabolism and resulted in 36.4% increase in β-carotene content. The transcriptome analysis was adopted to mine OA-repressible promoters and IZH1 promoter was used to replace native ERG9 promoter to dynamically down-regulate ERG9 expression, which diverted the metabolic flux to β-carotene pathway and achieved additional 31.7% increase in β-carotene content without adversely affecting cell growth. By inducing an extra constitutive β-carotene synthesis pathway for further conversion precursor farnesol to β-carotene, the final strain produced 11.4 mg/g DCW and 142 mg/L of β-carotene, which is 107.3% and 49.5% increase respectively over the parent strain. Conclusions This strategy can be applied in the overproduction of other heterogeneous FPP-derived hydrophobic compounds with similar synthesis and storage mechanisms in S. cerevisiae. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01723-y.
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Affiliation(s)
- Xiao Bu
- Centre for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.,Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083, China.,Jiangsu Key Laboratory for High-Tech Research and Development of Veterinary Biopharmaceuticals, Jiangsu Agri-Animal Husbandry Vocational College, Taizhou, 225300, People's Republic of China
| | - Jing-Yuan Lin
- Centre for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.,Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083, China
| | - Chang-Qing Duan
- Centre for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.,Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083, China
| | - Mattheos A G Koffas
- Center for Biotechnology and Interdisciplinary Studies and Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Guo-Liang Yan
- Centre for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China. .,Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083, China. .,Innovation Research Center of Future Foods, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China. .,Key Laboratory of Food Bioengineering (China National Light Industry), China Agricultural University, Beijing, 100083, China.
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30
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Li C, Swofford CA, Rückert C, Chatzivasileiou AO, Ou RW, Opdensteinen P, Luttermann T, Zhou K, Stephanopoulos G, Jones Prather KL, Zhong-Johnson EZL, Liang S, Zheng S, Lin Y, Sinskey AJ. Heterologous production of α-Carotene in Corynebacterium glutamicum using a multi-copy chromosomal integration method. BIORESOURCE TECHNOLOGY 2021; 341:125782. [PMID: 34419880 DOI: 10.1016/j.biortech.2021.125782] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
The carotenoid, α-carotene, is very beneficial for human health and wellness, but microbial production of this compound is notoriously difficult, due to the asymmetric rings on either end of its terpenoid backbone. Here, we report for the first time the efficient production of α-carotene in the industrial bacterium Corynebaterium glutamicum by using a combined pathway engineering approach including evaluation of the performance of different cyclases and analysis of key metabolic intermediates to determine flux bottlenecks in the carotenoid biosynthesis pathway. A multi-copy chromosomal integration method was pivotal in achieving stable expression of the cyclases. In fed-batch fermentation, 1,054 mg/L of α-carotene was produced by the best strain, which is the highest reported titer achieved in microbial fermentation. The success of increased α-carotene production suggests that the multi-copy chromosomal integration method can be a useful metabolic engineering tool for overexpression of key enzymes in C. glutamicum and other bacterium as well.
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Affiliation(s)
- Cheng Li
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA; Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore; Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, PR China
| | - Charles A Swofford
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA; Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
| | - Christian Rückert
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA; Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
| | - Alkiviadis Orfefs Chatzivasileiou
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Rui Wen Ou
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA; Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
| | - Patrick Opdensteinen
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Tobias Luttermann
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Kang Zhou
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585 Singapore
| | - Gregory Stephanopoulos
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Kristala L Jones Prather
- Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | | | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, PR China
| | - Suiping Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, PR China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Bioscience and Bioengineering, South China University of Technology, Guangzhou 510006, PR China
| | - Anthony J Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139 USA; Disruptive & Sustainable Technologies for Agricultural Precision, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore.
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31
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Seong J, Shin J, Kim K, Cho BK. Microbial production of nematicidal agents for controlling plant-parasitic nematodes. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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32
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Wang J, Zhao D, Li J, Hu M, Xin X, Price MA, Li Q, Liu L, Li S, Rosser SJ, Zhang C, Bi C, Zhang X. Helicase-AID: A novel molecular device for base editing at random genomic loci. Metab Eng 2021; 67:396-402. [PMID: 34411701 DOI: 10.1016/j.ymben.2021.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/06/2021] [Accepted: 08/14/2021] [Indexed: 01/09/2023]
Abstract
CRISPR-enabled deaminase base editing has become a powerful tool for precisely editing nucleotides on the chromosome. In this study DNA helicases, such as Escherichia coli DnaB, were fused to activation-induced cytidine deaminase (AID) to form enzyme complexes which randomly introduces edited bases throughout the chromosome. DnaB-AID was found to increase 2.5 × 103 fold relative to the mutagenesis frequency of wildtype. 97.9% of these edits were observed on the leading strand during DNA replication suggesting deamination to be highly coordinated with DNA replication. Using DnaB-AID, a 371.4% increase in β-carotene production was obtained following four rounds of editing. In Saccharomyces cerevisiae Helicase-AID was constructed by fusing AID to one of the subunits of eukaryotic helicase Mcm2-7 complex, MCM5. Using MCM5-AID, the average editing efficiency of five strains was 2.1 ± 0.4 × 103 fold higher than the native genomic mutation rate. MCM5-AID was able to improve β-carotene production of S. cerevisiae 4742crt by 75.4% following eight rounds of editing. The S. cerevisiae MCM5-AID technique is the first biological tool for generating and accumulating single base mutations in eukaryotic chromosomes. Since the helicase complex is highly conservative in all eukaryotes, Helicase-AID could be adapted for various applications and research in all eukaryotic cells.
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Affiliation(s)
- Jie Wang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Ju Li
- College of Life Science, Tianjin Normal University, Tianjin, China
| | - Muzi Hu
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Xiuqing Xin
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Marcus A Price
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological Sciences, University of Edinburgh, UK
| | - Qingyan Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Li Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Siwei Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Technology Innovation Center of Synthetic Biology, Tianjin, China
| | - Susan J Rosser
- Centre for Synthetic and Systems Biology and UK Centre for Mammalian Synthetic Biology, School of Biological Sciences, University of Edinburgh, UK
| | - Chunzhi Zhang
- School of Biological Engineering, Dalian Polytechnic University, Dalian, China.
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Technology Innovation Center of Synthetic Biology, Tianjin, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, China; National Technology Innovation Center of Synthetic Biology, Tianjin, China.
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33
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Ferraz L, Sauer M, Sousa MJ, Branduardi P. The Plasma Membrane at the Cornerstone Between Flexibility and Adaptability: Implications for Saccharomyces cerevisiae as a Cell Factory. Front Microbiol 2021; 12:715891. [PMID: 34434179 PMCID: PMC8381377 DOI: 10.3389/fmicb.2021.715891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/19/2021] [Indexed: 11/23/2022] Open
Abstract
In the last decade, microbial-based biotechnological processes are paving the way toward sustainability as they implemented the use of renewable feedstocks. Nonetheless, the viability and competitiveness of these processes are often limited due to harsh conditions such as: the presence of feedstock-derived inhibitors including weak acids, non-uniform nature of the substrates, osmotic pressure, high temperature, extreme pH. These factors are detrimental for microbial cell factories as a whole, but more specifically the impact on the cell’s membrane is often overlooked. The plasma membrane is a complex system involved in major biological processes, including establishing and maintaining transmembrane gradients, controlling uptake and secretion, intercellular and intracellular communication, cell to cell recognition and cell’s physical protection. Therefore, when designing strategies for the development of versatile, robust and efficient cell factories ready to tackle the harshness of industrial processes while delivering high values of yield, titer and productivity, the plasma membrane has to be considered. Plasma membrane composition comprises diverse macromolecules and it is not constant, as cells adapt it according to the surrounding environment. Remarkably, membrane-specific traits are emerging properties of the system and therefore it is not trivial to predict which membrane composition is advantageous under certain conditions. This review includes an overview of membrane engineering strategies applied to Saccharomyces cerevisiae to enhance its fitness under industrially relevant conditions as well as strategies to increase microbial production of the metabolites of interest.
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Affiliation(s)
- Luís Ferraz
- Center of Molecular and Environmental Biology, University of Minho, Braga, Portugal.,Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
| | - Michael Sauer
- Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, BOKU University of Natural Resources and Life Sciences, Vienna, Austria
| | - Maria João Sousa
- Center of Molecular and Environmental Biology, University of Minho, Braga, Portugal
| | - Paola Branduardi
- Department of Biotechnology and Biosciences, University of Milano Bicocca, Milan, Italy
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34
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Ciurkot K, Gorochowski TE, Roubos JA, Verwaal R. Efficient multiplexed gene regulation in Saccharomyces cerevisiae using dCas12a. Nucleic Acids Res 2021; 49:7775-7790. [PMID: 34197613 PMCID: PMC8287914 DOI: 10.1093/nar/gkab529] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 06/02/2021] [Accepted: 06/09/2021] [Indexed: 12/27/2022] Open
Abstract
CRISPR Cas12a is an RNA-programmable endonuclease particularly suitable for gene regulation. This is due to its preference for T-rich PAMs that allows it to more easily target AT-rich promoter sequences, and built-in RNase activity which can process a single CRISPR RNA array encoding multiple spacers into individual guide RNAs (gRNAs), thereby simplifying multiplexed gene regulation. Here, we develop a flexible dCas12a-based CRISPRi system for Saccharomyces cerevisiae and systematically evaluate its design features. This includes the role of the NLS position, use of repression domains, and the position of the gRNA target. Our optimal system is comprised of dCas12a E925A with a single C-terminal NLS and a Mxi1 or a MIG1 repression domain, which enables up to 97% downregulation of a reporter gene. We also extend this system to allow for inducible regulation via an RNAP II-controlled promoter, demonstrate position-dependent effects in crRNA arrays, and use multiplexed regulation to stringently control a heterologous β-carotene pathway. Together these findings offer valuable insights into the design constraints of dCas12a-based CRISPRi and enable new avenues for flexible and efficient gene regulation in S. cerevisiae.
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Affiliation(s)
- Klaudia Ciurkot
- DSM Biotechnology Center, Delft 2613 AX, The Netherlands.,Department of Chemistry, University of Hamburg, Hamburg 20146, Germany
| | - Thomas E Gorochowski
- School of Biological Sciences, University of Bristol, Tyndall Avenue, Bristol BS8 1TQ, UK
| | | | - René Verwaal
- DSM Biotechnology Center, Delft 2613 AX, The Netherlands
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35
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Yang D, Park SY, Lee SY. Production of Rainbow Colorants by Metabolically Engineered Escherichia coli. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100743. [PMID: 34032018 PMCID: PMC8261500 DOI: 10.1002/advs.202100743] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/08/2021] [Indexed: 05/07/2023]
Abstract
There has been much interest in producing natural colorants to replace synthetic colorants of health concerns. Escherichia coli has been employed to produce natural colorants including carotenoids, indigo, anthocyanins, and violacein. However, production of natural green and navy colorants has not been reported. Many natural products are hydrophobic, which are accumulated inside or on the cell membrane. This causes cell growth limitation and consequently reduces production of target chemicals. Here, integrated membrane engineering strategies are reported for the enhanced production of rainbow colorants-three carotenoids and four violacein derivatives-as representative hydrophobic natural products in E. coli. By integration of systems metabolic engineering, cell morphology engineering, inner- and outer-membrane vesicle formation, and fermentation optimization, production of rainbow colorants are significantly enhanced to 322 mg L-1 of astaxanthin (red), 343 mg L-1 of β-carotene (orange), 218 mg L-1 of zeaxanthin (yellow), 1.42 g L-1 of proviolacein (green), 0.844 g L-1 of prodeoxyviolacein (blue), 6.19 g L-1 of violacein (navy), and 11.26 g L-1 of deoxyviolacein (purple). The membrane engineering strategies reported here are generally applicable to microbial production of a broader range of hydrophobic natural products, contributing to food, cosmetic, chemical, and pharmaceutical industries.
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Affiliation(s)
- Dongsoo Yang
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross‐Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCenturyKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- BioProcess Engineering Research CenterKAISTDaejeon34141Republic of Korea
| | - Seon Young Park
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross‐Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCenturyKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- BioProcess Engineering Research CenterKAISTDaejeon34141Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Systems Metabolic Engineering and Systems Healthcare Cross‐Generation Collaborative Laboratory, Department of Chemical and Biomolecular Engineering (BK21 plus program), Institute for the BioCenturyKorea Advanced Institute of Science and Technology (KAIST)Daejeon34141Republic of Korea
- BioProcess Engineering Research CenterKAISTDaejeon34141Republic of Korea
- BioInformatics Research CenterKAISTDaejeon34141Republic of Korea
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Wang Y, Wang Y, Wang Y, Chen X, Liu C, Zhang M, Liu K, Zhao Y, Li Z. Untargeted Global Metabolomic Analysis Reveals the Mechanism of Tripropylamine-Enhanced Lycopene Accumulation in Blakeslea trispora. Front Bioeng Biotechnol 2021; 9:673225. [PMID: 34150732 PMCID: PMC8207141 DOI: 10.3389/fbioe.2021.673225] [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: 02/27/2021] [Accepted: 04/22/2021] [Indexed: 11/13/2022] Open
Abstract
We previously determined that the cyclase inhibitor tripropylamine (TPA) significantly enhances lycopene accumulation in Blakeslea trispora. To elucidate the mechanism of TPA-enhanced lycopene accumulation, the untargeted metabolome of B. trispora treated with TPA was analyzed by UHPLC-Q-TOF/MS. Forty-two differential metabolites were identified, of which 15 significantly differential metabolites meeting the following parameters were screened: variable importance for the projection > 1, P < 0.05, and fold change > 1.5. The down-regulated metabolites were mainly cyclic dipeptides, bacteriostatic compounds, and lipids, while the up-regulated metabolites were mainly unsaturated fatty acid. Furthermore, the bacteriostatic ability was poor, the extracellular and intracellular pH levels were high, and hyphae with vesicles were swollen locally in B. trispora after treatment with TPA. Our data suggest that the TPA enhances lycopene accumulation not only by inhibiting the cyclization of β-carotene but also by down-regulating cyclic dipeptides for quorum sensing; up-regulating unsaturated fatty acids, 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine, and 4-hydroxybenzoate and down-regulating choline, resulting in locally swelling mycelium with vacuoles; and down-regulating bacteriostatic metabolites for metabolic flux redistribution.
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Affiliation(s)
- Yanlong Wang
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Yulong Wang
- College of Teacher Education, Qilu Normal University, Jinan, China
| | - Yicun Wang
- Shandong Institute for Product Quality Inspection, Jinan, China
| | - Xin Chen
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Cunping Liu
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Meng Zhang
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Keying Liu
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Yuechao Zhao
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Zexu Li
- Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
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Guardini Z, Dall’Osto L, Barera S, Jaberi M, Cazzaniga S, Vitulo N, Bassi R. High Carotenoid Mutants of Chlorella vulgaris Show Enhanced Biomass Yield under High Irradiance. PLANTS 2021; 10:plants10050911. [PMID: 34062906 PMCID: PMC8147269 DOI: 10.3390/plants10050911] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/30/2022]
Abstract
Microalgae represent a carbon-neutral source of bulk biomass, for extraction of high-value compounds and production of renewable fuels. Due to their high metabolic activity and reproduction rates, species of the genus Chlorella are highly productive when cultivated in photobioreactors. However, wild-type strains show biological limitations making algal bioproducts expensive compared to those extracted from other feedstocks. Such constraints include inhomogeneous light distribution due to high optical density of the culture, and photoinhibition of the surface-exposed cells. Thus, the domestication of algal strains for industry makes it increasingly important to select traits aimed at enhancing light-use efficiency while withstanding excess light stress. Carotenoids have a crucial role in protecting against photooxidative damage and, thus, represent a promising target for algal domestication. We applied chemical mutagenesis to Chlorella vulgaris and selected for enhanced tolerance to the carotenoid biosynthesis inhibitor norflurazon. The NFR (norflurazon-resistant) strains showed an increased carotenoid pool size and enhanced tolerance towards photooxidative stress. Growth under excess light revealed an improved carbon assimilation rate of NFR strains with respect to WT. We conclude that domestication of Chlorella vulgaris, by optimizing both carotenoid/chlorophyll ratio and resistance to photooxidative stress, boosted light-to-biomass conversion efficiency under high light conditions typical of photobioreactors. Comparison with strains previously reported for enhanced tolerance to singlet oxygen, reveals that ROS resistance in Chlorella is promoted by at least two independent mechanisms, only one of which is carotenoid-dependent.
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Liu L, Qu YL, Dong GR, Wang J, Hu CY, Meng YH. Elevated β-Carotene Production Using Codon-Adapted CarRA&B and Metabolic Balance in Engineered Yarrowia lipolytica. Front Microbiol 2021; 12:627150. [PMID: 33746920 PMCID: PMC7970187 DOI: 10.3389/fmicb.2021.627150] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 01/22/2021] [Indexed: 11/13/2022] Open
Abstract
β-carotene is a precursor of vitamin A and has multiple physiological functions. Producing β-carotene by microbial fermentation has attracted much attention to consumers' preference for natural products. This study focused on improving β-carotene production by constructing codon-adapted genes and minimizing intermediate accumulation. The codon-adapted CarRA and CarB genes from the industrial strain of Blakeslea trispora were integrated into the genome of the Yarrowia lipolytica to construct YL-C0, the baseline strain for producing β-carotene. Thereafter, the β-carotene biosynthetic pathway's metabolic balance was accurately regulated to reduce the intermediates' accumulation. Notably, the β-carotene content increased by 21 times to reach 12.5 dry cell weight (DCW) mg/g when minimizing HMG-CoA and FPP accumulation. Further, we improved the expression levels of the CarRA and CarB genes to minimize the accumulation of phytoene and lycopene. Total production of β-carotene of 1.7 g/L and 21.6 mg/g DCW was achieved. These results reveal that the rate-limiting enzymes CarRA and CarB of B. trispora exhibited higher catalytic activity than the same enzymes from other microorganisms. Promoting metabolic balance by minimizing the accumulation of intermediates is a very effective strategy for increasing β-carotene. The β-carotene-producing strain constructed in this study has established the foundation for its potential use in industrial production. These successful engineering strategies also provide a foundation for large-scale production of other terpenoids.
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Affiliation(s)
- Liang Liu
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, National Research and Development Center of Apple Processing Technology, Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Yu Ling Qu
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, National Research and Development Center of Apple Processing Technology, Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Gui Ru Dong
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, National Research and Development Center of Apple Processing Technology, Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Jing Wang
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, National Research and Development Center of Apple Processing Technology, Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
| | - Ching Yuan Hu
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, National Research and Development Center of Apple Processing Technology, Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China.,Department of Human Nutrition, Food and Animal Sciences, College of Tropical Agriculture and Human Resources, University of Hawai'i at Mānoa, Honolulu, HI, United States
| | - Yong Hong Meng
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, National Research and Development Center of Apple Processing Technology, Shaanxi Engineering Laboratory for Food Green Processing and Safety Control, College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, China
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Wang J, Ma W, Wang X. Insights into the structure of Escherichia coli outer membrane as the target for engineering microbial cell factories. Microb Cell Fact 2021; 20:73. [PMID: 33743682 PMCID: PMC7980664 DOI: 10.1186/s12934-021-01565-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/12/2021] [Indexed: 12/16/2022] Open
Abstract
Escherichia coli is generally used as model bacteria to define microbial cell factories for many products and to investigate regulation mechanisms. E. coli exhibits phospholipids, lipopolysaccharides, colanic acid, flagella and type I fimbriae on the outer membrane which is a self-protective barrier and closely related to cellular morphology, growth, phenotypes and stress adaptation. However, these outer membrane associated molecules could also lead to potential contamination and insecurity for fermentation products and consume lots of nutrients and energy sources. Therefore, understanding critical insights of these membrane associated molecules is necessary for building better microbial producers. Here the biosynthesis, function, influences, and current membrane engineering applications of these outer membrane associated molecules were reviewed from the perspective of synthetic biology, and the potential and effective engineering strategies on the outer membrane to improve fermentation features for microbial cell factories were suggested.
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Affiliation(s)
- Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,International Joint Laboratory On Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wenjian Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
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Xie Q, Li S, Zhao D, Ye L, Li Q, Zhang X, Zhu L, Bi C. Manipulating the position of DNA expression cassettes using location tags fused to dCas9 (Cas9-Lag) to improve metabolic pathway efficiency. Microb Cell Fact 2020; 19:229. [PMID: 33317552 PMCID: PMC7737257 DOI: 10.1186/s12934-020-01496-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/05/2020] [Indexed: 02/02/2023] Open
Abstract
Background Deactivated Cas9 (dCas9) led to significant improvement of CRISPR/Cas9-based techniques because it can be fused with a variety of functional groups to form diverse molecular devices, which can manipulate or modify target DNA cassettes. One important metabolic engineering strategy is to localize the enzymes in proximity of their substrates for improved catalytic efficiency. In this work, we developed a novel molecular device to manipulate the cellular location of specific DNA cassettes either on plasmids or on the chromosome, by fusing location tags to dCas9 (Cas9-Lag), and applied the technique for synthetic biology applications. Carotenoids like β-carotene serve as common intermediates for the synthesis of derivative compounds, which are hydrophobic and usually accumulate in the membrane compartment. Results Carotenoids like β-carotene serve as common intermediates for the synthesis of derivative compounds, which are hydrophobic and usually accumulate in the membrane components. To improve the functional expression of membrane-bound enzymes and localize them in proximity to the substrates, Cas9-Lag was used to pull plasmids or chromosomal DNA expressing carotenoid enzymes onto the cell membrane. For this purpose, dCas9 was fused to the E. coli membrane docking tag GlpF, and gRNA was designed to direct this fusion protein to the DNA expression cassettes. With Cas9-Lag, the zeaxanthin and astaxanthin titer increased by 29.0% and 26.7% respectively. Due to experimental limitations, the electron microscopy images of cells expressing Cas9-Lag vaguely indicated that GlpF-Cas9 might have pulled the target DNA cassettes in close proximity to membrane. Similarly, protein mass spectrometry analysis of membrane proteins suggested an increased expression of carotenoid-converting enzymes in the membrane components. Conclusion This work therefore provides a novel molecular device, Cas9-Lag, which was proved to increase zeaxanthin and astaxanthin production and might be used to manipulate DNA cassette location.
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Affiliation(s)
- Qianwen Xie
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, P. R. China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, P. R. China
| | - Siwei Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, P. R. China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Dongdong Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, P. R. China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Lijun Ye
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, P. R. China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Qingyan Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, P. R. China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, P. R. China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Li Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Biotechnology, Beijing, 100071, China.
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, P. R. China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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Zhao J, Fang H, Zhang D. Expanding application of CRISPR-Cas9 system in microorganisms. Synth Syst Biotechnol 2020; 5:269-276. [PMID: 32913902 PMCID: PMC7451738 DOI: 10.1016/j.synbio.2020.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/24/2020] [Accepted: 08/04/2020] [Indexed: 11/08/2022] Open
Abstract
The development of CRISPR-Cas9 based genetic manipulation tools represents a huge breakthrough in life sciences and has been stimulating research on metabolic engineering, synthetic biology, and systems biology. The CRISPR-Cas9 and its derivative tools are one of the best choices for precise genome editing, multiplexed genome editing, and reversible gene expression control in microorganisms. However, challenges remain for applying CRISPR-Cas9 in novel microorganisms, especially those industrial microorganism hosts that are intractable using traditional genetic manipulation tools. How to further extend CRISPR-Cas9 to these microorganisms is being an urgent matter. In this review, we first introduce the mechanism and application of CRISPR-Cas9, then discuss how to optimize CRISPR-Cas9 as genome editing tools, including but not limited to how to reduce off-target effects and Cas9 related toxicity, and how to increase on-target efficiency by optimizing crRNA and sgRNA design.
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Affiliation(s)
- Jing Zhao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Huan Fang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
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Li M, Xia Q, Zhang H, Zhang R, Yang J. Metabolic Engineering of Different Microbial Hosts for Lycopene Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:14104-14122. [PMID: 33207118 DOI: 10.1021/acs.jafc.0c06020] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
As a result of the extensive use of lycopene in a variety of fields, especially the dietary supplement and health food industries, the production of lycopene has attracted considerable interest. Lycopene can be obtained through extraction from vegetables and chemical synthesis. Alternatively, the microbial production of lycopene has been extensively researched in recent years. Various types of microbial hosts have been evaluated for their potential to accumulate a high level of lycopene. Metabolic engineering of the hosts and optimization of culture conditions are performed to enhance lycopene production. After years of research, great progress has been made in lycopene production. In this review, strategies used to improve lycopene production in different microbial hosts and the advantages and disadvantages of each microbial host are summarized. In addition, future perspectives of lycopene production in different microbial hosts are discussed.
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Affiliation(s)
- Meijie Li
- Energy-Rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, 700 Changchen Road, Qingdao, Shandong 266109, People's Republic of China
| | - Qingqing Xia
- Energy-Rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, 700 Changchen Road, Qingdao, Shandong 266109, People's Republic of China
| | - Haibo Zhang
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 135 Songling Road, Qingdao, Shandong 266101, People's Republic of China
| | - Rubing Zhang
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 135 Songling Road, Qingdao, Shandong 266101, People's Republic of China
| | - Jianming Yang
- Energy-Rich Compound Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, 700 Changchen Road, Qingdao, Shandong 266109, People's Republic of China
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Lv PJ, Qiang S, Liu L, Hu CY, Meng YH. Dissolved-oxygen feedback control fermentation for enhancing β-carotene in engineered Yarrowia lipolytica. Sci Rep 2020; 10:17114. [PMID: 33051539 PMCID: PMC7555900 DOI: 10.1038/s41598-020-74074-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/16/2020] [Indexed: 01/06/2023] Open
Abstract
The DO-stat fed-batch fermentation was carried out to explore the volumetric productivity of β-carotene in engineered Yarrowia lipolytica C11 strain. Using DO-stat fed-batch fermentation, we achieved 94 g/L biomass and 2.01 g/L β-carotene. Both biomass and β-carotene were about 1.28-fold higher than that in fed-batch fermentation. The ATP, NADP+/NADPH, and gene expression levels of tHMG, GGS1, carRA, and carB were promoted as compared to that in fed-batch fermentation. As for as the kinetic parameters in DO-stat fed-batch fermentation, μm', Yx/s', and Yp/s' was 0.527, 0.353, and 0.158, respectively. The μm' was elevated 4.66-fold than that in fed-batch fermentation. These data illustrate that more dissolved oxygen increased the biomass. The Yx/s' and Yp/s' were increased 1.15 and 22.57-fold, which suggest that the DO-stat fed-batch fermentation reduced the Crabtree effect and improved the utilization rate of glucose. Therefore, DO-stat fed-batch fermentation is a promising strategy in the industrialized production of β-carotene.
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Affiliation(s)
- Peng Jun Lv
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, 620 West Changan Avenue, Changan, Xian, 710119, P.R. China
| | - Shan Qiang
- Xian Healthful Biotechnology Co., Ltd., Hang Tuo Road, Changan, Xi'an, 710100, People's Republic of China
| | - Liang Liu
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, 620 West Changan Avenue, Changan, Xian, 710119, P.R. China
| | - Ching Yuan Hu
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, 620 West Changan Avenue, Changan, Xian, 710119, P.R. China
| | - Yong Hong Meng
- Engineering Research Center of High Value Utilization of Western China Fruit Resources, Ministry of Education, National Research and Development Center of Apple Processing Technology, College of Food Engineering and Nutritional Science, Shaanxi Normal University, 620 West Changan Avenue, Changan, Xian, 710119, P.R. China.
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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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Liu Y, Su A, Li J, Ledesma-Amaro R, Xu P, Du G, Liu L. Towards next-generation model microorganism chassis for biomanufacturing. Appl Microbiol Biotechnol 2020; 104:9095-9108. [DOI: 10.1007/s00253-020-10902-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/03/2020] [Accepted: 09/10/2020] [Indexed: 11/29/2022]
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Chen X, Zhang C, Lindley ND. Metabolic Engineering Strategies for Sustainable Terpenoid Flavor and Fragrance Synthesis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:10252-10264. [PMID: 31865696 DOI: 10.1021/acs.jafc.9b06203] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Terpenoids derived from plant material are widely applied in the flavor and fragrance industry. Traditional extraction methods are unsustainable, but microbial synthesis offers a promising solution to attain efficient production of natural-identical terpenoids. Overproduction of terpenoids in microbes requires careful balancing of the synthesis pathway constituents within the constraints of host cell metabolism. Advances in metabolic engineering have greatly facilitated overcoming the challenges of achieving high titers, rates, and yields (TRYs). The review summarizes recent development in the molecular biology toolbox to achieve high TRYs for terpenoid biosynthesis, mainly in the two industrial platform microorganisms: Escherichia coli and Saccharomyces cerevisiae. The biosynthetic pathways, including alternative pathway designs, are briefly introduced, followed by recently developed methodologies used for pathway, genome, and strain optimization. Integrated applications of these tools are important to achieve high "TRYs" of terpenoid production and pave the way for translating laboratory research into successful commercial manufacturing.
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Affiliation(s)
- Xixian Chen
- Biotransformation Innovation Platform, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138673
| | - Congqiang Zhang
- Biotransformation Innovation Platform, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138673
| | - Nicholas D Lindley
- Biotransformation Innovation Platform, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Singapore 138673
- TBI, Université de Toulouse, CNRS, INRA, INSA,31077 Toulouse, France
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48
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Meng Y, Shao X, Wang Y, Li Y, Zheng X, Wei G, Kim S, Wang C. Extension of cell membrane boosting squalene production in the engineered
Escherichia coli. Biotechnol Bioeng 2020; 117:3499-3507. [DOI: 10.1002/bit.27511] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/10/2020] [Accepted: 07/19/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Yunhe Meng
- School of Biology and Basic Medical Sciences Soochow University Suzhou China
| | - Xixi Shao
- School of Biology and Basic Medical Sciences Soochow University Suzhou China
| | - Yan Wang
- School of Biology and Basic Medical Sciences Soochow University Suzhou China
| | - Yumei Li
- School of Biology and Basic Medical Sciences Soochow University Suzhou China
| | - Xiaojian Zheng
- School of Biology and Basic Medical Sciences Soochow University Suzhou China
| | - Gongyuan Wei
- School of Biology and Basic Medical Sciences Soochow University Suzhou China
| | - Seon‐Won Kim
- Division of Applied Life Science (BK21 Plus) PMBBRC, Gyeongsang National University Jinju Republic of Korea
| | - Chonglong Wang
- School of Biology and Basic Medical Sciences Soochow University Suzhou China
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49
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Parveen S, Akhtar N, Ghauri MA, Akhtar K. Conventional genetic manipulation of desulfurizing bacteria and prospects of using CRISPR-Cas systems for enhanced desulfurization activity. Crit Rev Microbiol 2020; 46:300-320. [PMID: 32530374 DOI: 10.1080/1040841x.2020.1772195] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Highly active and stable biocatalysts are the prerequisite for industrial scale application of the biodesulfurization process. Scientists are making efforts for increasing the desulfurizing activity of native strains by employing various genetic engineering approaches. Nevertheless, the achieved desulfurization rate is lower than the industrial requirements. Thus, there is a dire need to use efficient genetic tools for precise genome editing of desulfurizing bacteria for enhanced efficiency. In comparison to the previously used genetic engineering tools the newly developed CRISPR-Cas is a more efficient and simple genetic tool that has been successfully applied for targeted genome modification of eukaryotes as well as prokaryotes. In this paper, we have reviewed the approaches, previously used to enhance the biodesulfurization rates of the sulfur metabolizing microorganisms and have discussed the potential of CRISPR-Cas systems in engineering desulfurizing biocatalysts. We have also proposed a model to construct competent desulfurizing recombinants involving use of CRISPR-Cas technology. The model can be used to over-express the dsz genes under a constitutive promoter in a suitable heterologous host, to get a steady expression of desulfurization pathway. This may serve as an inducement to develop better performing desulfurizing recombinant strains using CRISPR-Cas systems, which can be helpful in increasing the rate of biodesulfurization in future.
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Affiliation(s)
- Sana Parveen
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Nasrin Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad A Ghauri
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Kalsoom Akhtar
- Industrial Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
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50
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Wu Y, Yan P, Li Y, Liu X, Wang Z, Chen T, Zhao X. Enhancing β-Carotene Production in Escherichia coli by Perturbing Central Carbon Metabolism and Improving the NADPH Supply. Front Bioeng Biotechnol 2020; 8:585. [PMID: 32582683 PMCID: PMC7296177 DOI: 10.3389/fbioe.2020.00585] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/13/2020] [Indexed: 01/12/2023] Open
Abstract
Beta (β)-carotene (C40H56; a provitamin) is a particularly important carotenoid for human health. Many studies have focused on engineering Escherichia coli as an efficient heterologous producer of β-carotene. Moreover, several strains with potential for use in the industrial production of this provitamin have already been constructed via different metabolic engineering strategies. In this study, we aimed to improve the β-carotene-producing capacity of our previously engineered E. coli strain ZF43ΔgdhA through further gene deletion and metabolic pathway manipulations. Deletion of the zwf gene increased the resultant strain's β-carotene production and content by 5.1 and 32.5%, respectively, relative to the values of strain ZF43ΔgdhA, but decreased the biomass by 26.2%. Deletion of the ptsHIcrr operon further increased the β-carotene production titer from 122.0 to 197.4 mg/L, but the provitamin content was decreased. Subsequently, comparative transcriptomic analysis was used to explore the dynamic transcriptional responses of the strains to the blockade of the pentose phosphate pathway and inactivation of the phosphotransferase system. Lastly, based on the analyses of comparative transcriptome and reduction cofactor, several strategies to increase the NADPH supply were evaluated for enhancement of the β-carotene content. The combination of yjgB gene deletion and nadK overexpression led to increased β-carotene production and content. The best strain, ECW4/p5C-nadK, produced 266.4 mg/L of β-carotene in flask culture and 2,579.1 mg/L in a 5-L bioreactor. The latter value is the highest reported from production via the methylerythritol phosphate pathway in E. coli. Although the strategies applied is routine in this study, the combinations reported were first implemented, are simple but efficient and will be helpful for the production of many other natural products, especially isoprenoids. Importantly, we demonstrated that the use of the methylerythritol phosphate pathway alone for efficient β-carotene biosynthesis could be achieved via appropriate modifications of the cell metabolic functions.
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Affiliation(s)
- Yuanqing Wu
- Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Panpan Yan
- Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Yang Li
- Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
- College of Life Science, Shihezi University, Shihezi, China
| | - Xuewei Liu
- Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Zhiwen Wang
- Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Tao Chen
- Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - Xueming Zhao
- Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin, China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
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