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Son SH, Kang J, Shin Y, Lee C, Sung BH, Lee JY, Lee W. Sustainable production of natural products using synthetic biology: Ginsenosides. J Ginseng Res 2024; 48:140-148. [PMID: 38465212 PMCID: PMC10920010 DOI: 10.1016/j.jgr.2023.12.006] [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: 11/17/2023] [Revised: 12/23/2023] [Accepted: 12/30/2023] [Indexed: 03/12/2024] Open
Abstract
Synthetic biology approaches offer potential for large-scale and sustainable production of natural products with bioactive potency, including ginsenosides, providing a means to produce novel compounds with enhanced therapeutic properties. Ginseng, known for its non-toxic and potent qualities in traditional medicine, has been used for various medical needs. Ginseng has shown promise for its antioxidant and neuroprotective properties, and it has been used as a potential agent to boost immunity against various infections when used together with other drugs and vaccines. Given the increasing demand for ginsenosides and the challenges associated with traditional extraction methods, synthetic biology holds promise in the development of therapeutics. In this review, we discuss recent developments in microorganism producer engineering and ginsenoside production in microorganisms using synthetic biology approaches.
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Affiliation(s)
- So-Hee Son
- Research Center for Bio-Based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, Republic of Korea
| | - Jin Kang
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, Korea National University of Science and Technology (UST), Daejeon, Republic of Korea
| | - YuJin Shin
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - ChaeYoung Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - Bong Hyun Sung
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
- Biosystems and Bioengineering Program, Korea National University of Science and Technology (UST), Daejeon, Republic of Korea
- Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Ju Young Lee
- Research Center for Bio-Based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan, Republic of Korea
| | - Wonsik Lee
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
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2
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Chen Z, Wu T, Yu S, Li M, Fan X, Huo YX. Self-assembly systems to troubleshoot metabolic engineering challenges. Trends Biotechnol 2024; 42:43-60. [PMID: 37451946 DOI: 10.1016/j.tibtech.2023.06.009] [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] [Received: 04/19/2023] [Revised: 06/18/2023] [Accepted: 06/23/2023] [Indexed: 07/18/2023]
Abstract
Enzyme self-assembly is a technology in which enzyme units can aggregate into ordered macromolecules, assisted by scaffolds. In metabolic engineering, self-assembly strategies have been explored for aggregating multiple enzymes in the same pathway to improve sequential catalytic efficiency, which in turn enables high-level production. The performance of the scaffolds is critical to the formation of an efficient and stable assembly system. This review comprehensively analyzes these scaffolds by exploring how they assemble, and it illustrates how to apply self-assembly strategies for different modules in metabolic engineering. Functional modifications to scaffolds will further promote efficient strategies for production.
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Affiliation(s)
- Zhenya Chen
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Tong Wu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Shengzhu Yu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Min Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Xuanhe Fan
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081, Beijing, China.
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3
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Liu N, Dong W, Yang H, Li JH, Chiu TY. Application of artificial scaffold systems in microbial metabolic engineering. Front Bioeng Biotechnol 2023; 11:1328141. [PMID: 38188488 PMCID: PMC10771841 DOI: 10.3389/fbioe.2023.1328141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/12/2023] [Indexed: 01/09/2024] Open
Abstract
In nature, metabolic pathways are often organized into complex structures such as multienzyme complexes, enzyme molecular scaffolds, or reaction microcompartments. These structures help facilitate multi-step metabolic reactions. However, engineered metabolic pathways in microbial cell factories do not possess inherent metabolic regulatory mechanisms, which can result in metabolic imbalance. Taking inspiration from nature, scientists have successfully developed synthetic scaffolds to enhance the performance of engineered metabolic pathways in microbial cell factories. By recruiting enzymes, synthetic scaffolds facilitate the formation of multi-enzyme complexes, leading to the modulation of enzyme spatial distribution, increased enzyme activity, and a reduction in the loss of intermediate products and the toxicity associated with harmful intermediates within cells. In recent years, scaffolds based on proteins, nucleic acids, and various organelles have been developed and employed to facilitate multiple metabolic pathways. Despite varying degrees of success, synthetic scaffolds still encounter numerous challenges. The objective of this review is to provide a comprehensive introduction to these synthetic scaffolds and discuss their latest research advancements and challenges.
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Affiliation(s)
- Nana Liu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
| | - Wei Dong
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
| | - Huanming Yang
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
| | - Jing-Hua Li
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
| | - Tsan-Yu Chiu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou, China
- HIM-BGI Omics Center, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences (CAS), Hangzhou, China
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Qiu S, Blank LM. Recent Advances in Yeast Recombinant Biosynthesis of the Triterpenoid Protopanaxadiol and Glycosylated Derivatives Thereof. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2197-2210. [PMID: 36696911 DOI: 10.1021/acs.jafc.2c06888] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Plant natural products are a seemingly endless resource for novel chemical structures. However, their extraction often results in high prices, fluctuation in both quantity and quality, and negative environmental impact. The latter might result from the extraction procedure but more often from the high amount of plant biomass required. With the advent of synthetic biology, producing natural plant products in large quantities using yeasts as hosts has become possible. Here, we focus on the recent advances in metabolic engineering of the yeasts species Saccharomyces cerevisiae and Yarrowia lipolytica for the synthesis of ginsenoside triterpenoids, namely, dammarenediol-II, protopanaxadiol, protopanaxatriol, compound K, ginsenoside Rh1, ginsenoside Rh2, ginsenoside Rg3, and ginsenoside F1. A discussion is provided on advanced synthetic biology, bioprocess strategies, and current challenges for the biosynthesis of ginsenoside triterpenoids. Finally, future directions in metabolic and process engineering are summarized and may help reify sustainable ginsenoside production.
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Affiliation(s)
- Shangkun Qiu
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, 52074 Aachen, Germany
| | - Lars M Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, 52074 Aachen, Germany
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Microorganisms for Ginsenosides Biosynthesis: Recent Progress, Challenges, and Perspectives. Molecules 2023; 28:molecules28031437. [PMID: 36771109 PMCID: PMC9921939 DOI: 10.3390/molecules28031437] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/24/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Ginsenosides are major bioactive compounds present in the Panax species. Ginsenosides exhibit various pharmaceutical properties, including anticancer, anti-inflammatory, antimetastatic, hypertension, and neurodegenerative disorder activities. Although several commercial products have been presented on the market, most of the current chemical processes have an unfriendly environment and a high cost of downstream processing. Compared to plant extraction, microbial production exhibits high efficiency, high selectivity, and saves time for the manufacturing of industrial products. To reach the full potential of the pharmaceutical resource of ginsenoside, a suitable microorganism has been developed as a novel approach. In this review, cell biological mechanisms in anticancer activities and the present state of research on the production of ginsenosides are summarized. Microbial hosts, including native endophytes and engineered microbes, have been used as novel and promising approaches. Furthermore, the present challenges and perspectives of using microbial hosts to produce ginsenosides have been discussed.
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Luo G, Lin Y, Chen S, Xiao R, Zhang J, Li C, Sinskey AJ, Ye L, Liang S. Overproduction of Patchoulol in Metabolically Engineered Komagataella phaffii. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:2049-2058. [PMID: 36681940 DOI: 10.1021/acs.jafc.2c08228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Patchoulol, a plant-derived sesquiterpene compound, is widely used in perfumes, cosmetics, and pharmaceuticals. Microbial production provides a promising alternative approach for the efficient and sustainable production of patchoulol. However, there are no systematic engineering studies on Komagataella phaffii aimed at achieving high-yield patchoulol production. Herein, by fusion overexpression of FPP synthase and patchoulol synthase (ERG20LPTS), increasing the precursor supply, adjusting the copy number of ERG20LPTS and PTS, and combined with adding auxiliary carbon source and methanol concentration optimization, we constructed a high-yield patchoulol-producing strain P6H53, which produced 149.64 mg/L patchoulol in shake-flask fermentation with methanol as the substrate. In fed-batch fermentation, strain P6H53 achieved the highest production (2.47 g/L, 21.48 mg/g DCW, and 283.25 mg/L/d) to date in a 5 L fermenter. This study will lay a good foundation for the development of K. phaffii as a promising chassis microbial cell for the synthesis of patchoulol and other sesquiterpenes with methanol as the carbon source.
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Affiliation(s)
- Guangjuan Luo
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong research center of Industrial enzyme and Green manufacturing technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong research center of Industrial enzyme and Green manufacturing technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Shuting Chen
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong research center of Industrial enzyme and Green manufacturing technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Ruiming Xiao
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong research center of Industrial enzyme and Green manufacturing technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Jiaxin Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong research center of Industrial enzyme and Green manufacturing technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
| | - Cheng Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong research center of Industrial enzyme and Green manufacturing technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anthony J Sinskey
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Lei Ye
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, P. R. China
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
- Guangdong research center of Industrial enzyme and Green manufacturing technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, P. R. China
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7
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Li F, Chen MM, Zhang HM, Wu QP, Han YB. Production of ginsenoside compound K by microbial cell factory using synthetic biology-based strategy: a review. Biotechnol Lett 2023; 45:163-174. [PMID: 36550334 DOI: 10.1007/s10529-022-03326-y] [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] [Received: 07/25/2022] [Revised: 10/24/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022]
Abstract
Ginsenoside compound K (CK) is a major intestinal bacterial metabolite of the protopanaxadiol-type ginsenoside family that can be absorbed in the systemic circulation. CK possesses diverse and important pharmacological properties. The low production and high cost of traditional manufacturing methods based on the extraction and biotransformation of total ginsenosides from ginseng have limited their medical application. However, considerable progress has been made in the area of de novo CK production via microbial cell factories using synthetic biology-based strategies. By introducing key enzymes responsible for CK biosynthesis into microbial cells, CK was produced via a series of in vivo enzymatic reactions that utilize the inherent precursors in microbial cells. After systematic optimization using various metabolic engineering strategies, the yield of CK increased significantly and exceeded the traditional plant extraction-biotransformation method, implying the commercial feasibility of this approach. This review summarizes recent novel advancements in the production of CK using microbial cell factories.
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Affiliation(s)
- Feng Li
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Meng Meng Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Hui Min Zhang
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qing Ping Wu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yun Bin Han
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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Zhao J, Guo Y, Li Q, Chen J, Niu D, Liu J. Reconstruction of a Cofactor Self-Sufficient Whole-Cell Biocatalyst System for Efficient Biosynthesis of Allitol from d-Glucose. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:3775-3784. [PMID: 35298165 DOI: 10.1021/acs.jafc.2c00440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The combined catalysis of glucose isomerase (GI), d-psicose 3-epimerase (DPEase), ribitol dehydrogenase (RDH), and formate dehydrogenase (FDH) provides a convenient route for the biosynthesis of allitol from d-glucose; however, the low catalytic efficiency restricts its industrial applications. Here, the supplementation of 0.32 g/L NAD+ significantly promoted the cell catalytic activity by 1.18-fold, suggesting that the insufficient intracellular NAD(H) content was a limiting factor in allitol production. Glucose dehydrogenase (GDH) with 18.13-fold higher activity than FDH was used for reconstructing a cofactor self-sufficient system, which was combined with the overexpression of the rate-limiting genes involved in NAD+ salvage metabolic flow to expand the available intracellular NAD(H) pool. Then, the multienzyme self-assembly system with SpyTag and SpyCatcher effectively channeled intermediates, leading to an 81.1% increase in allitol titer to 15.03 g/L from 25 g/L d-glucose. This study provided a facilitated strategy for large-scale and efficient biosynthesis of allitol from a low-cost substrate.
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Affiliation(s)
- Jingyi Zhao
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Yan Guo
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Qiufeng Li
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Jing Chen
- South Subtropical Agricultural Scientific Research Institute of Guangxi, Longzhou, Guangxi 532415, China
| | - Debao Niu
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
| | - Jidong Liu
- College of Light Industry and Food Engineering, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, China
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Du MM, Zhu ZT, Zhang GG, Zhao YQ, Gao B, Tao XY, Liu M, Ren YH, Wang FQ, Wei DZ. Engineering Saccharomyces cerevisiae for Hyperproduction of β-Amyrin by Mitigating the Inhibition Effect of Squalene on β-Amyrin Synthase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:229-237. [PMID: 34955018 DOI: 10.1021/acs.jafc.1c06712] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The study aims to enhance β-amyrin production in Saccharomyces cerevisiae by peroxisome compartmentalization. First, overaccumulated squalene was determined as a key limiting factor for the production of β-amyrin since it could inhibit the activity of β-amyrin synthase GgbAs1. Second, to mitigate the inhibition effect, the enhanced squalene synthesis pathway was compartmentalized into peroxisomes to insulate overaccumulated squalene from GgbAs1, and thus the specific titer of β-amyrin reached 57.8 mg/g dry cell weight (DCW), which was 2.6-fold higher than that of the cytosol engineering strain. Third, by combining peroxisome compartmentalization with the "push-pull-restrain" strategy (ERG1 and GgbAs1 overexpression and ERG7 weakening), the production of β-amyrin was further increased to 81.0 mg/g DCW (347.0 mg/L). Finally, through fed-batch fermentation in a 5 L fermenter, the titer of β-amyrin reached 2.6 g/L, which is the highest reported to date. The study provides a new perspective to engineering yeasts as a platform for triterpene production.
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Affiliation(s)
- Meng-Meng Du
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, P.O. Box 311, 130 Meilong Road, Shanghai 200237, China
| | - Zhan-Tao Zhu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, P.O. Box 311, 130 Meilong Road, Shanghai 200237, China
| | - Ge-Ge Zhang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, P.O. Box 311, 130 Meilong Road, Shanghai 200237, China
| | - Yun-Qiu Zhao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, P.O. Box 311, 130 Meilong Road, Shanghai 200237, China
| | - Bei Gao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, P.O. Box 311, 130 Meilong Road, Shanghai 200237, China
| | - Xin-Yi Tao
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, P.O. Box 311, 130 Meilong Road, Shanghai 200237, China
| | - Min Liu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, P.O. Box 311, 130 Meilong Road, Shanghai 200237, China
| | - Yu-Hong Ren
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, P.O. Box 311, 130 Meilong Road, Shanghai 200237, China
| | - Feng-Qing Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, P.O. Box 311, 130 Meilong Road, Shanghai 200237, China
| | - Dong-Zhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, P.O. Box 311, 130 Meilong Road, Shanghai 200237, China
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Zhang X, Gu S, Zheng X, Peng S, Li Y, Lin Y, Liang S. A Novel and Efficient Genome Editing Tool Assisted by CRISPR-Cas12a/Cpf1 for Pichia pastoris. ACS Synth Biol 2021; 10:2927-2937. [PMID: 34644057 DOI: 10.1021/acssynbio.1c00172] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pichia pastoris has been widely exploited for the heterologous expression of proteins in both industry and academia. Recently, it has been shown to be a potentially good chassis host for the production of high-value chemicals and pharmaceuticals. Effective synthetic biology tools for genetic engineering are essential for industrial and biotechnological research in this yeast. Here, we describe a novel and efficient genome editing method mediated by the CRISPR-Cpf1 system, which could facilitate the deletion of large DNA fragments and integration of multiplexed gene fragments. The CRISPR-Cpf1 system exhibited a precise and high editing efficiency for single-gene disruption (99 ± 0.8%), duplex genome editing (65 ± 2.5% to 80 ± 3%), and triplex genome editing (30 ± 2.5%). In addition, the deletion of large DNA fragments of 20kb and one-step integration of multiple genes were first achieved using the developed CRISPR-Cpf1 system. Taken together, this study provides an efficient and simple gene editing tool for P. pastoris. The novel multiloci gene integration method mediated by CRISPR-Cpf1 may accelerate the ability to engineer this methylotrophic yeast for metabolic engineering and genome evolution in both biotechnological and biomedical applications.
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Affiliation(s)
- Xinying Zhang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Songjie Gu
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Xueyun Zheng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Siqi Peng
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yanru Li
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Ying Lin
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Shuli Liang
- Guangdong Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
- Guangdong Research Center of Industrial Enzyme and Green Manufacturing Technology, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
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11
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Calzini MA, Malico AA, Mitchler MM, Williams GJ. Protein engineering for natural product biosynthesis and synthetic biology applications. Protein Eng Des Sel 2021; 34:gzab015. [PMID: 34137436 PMCID: PMC8209613 DOI: 10.1093/protein/gzab015] [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: 03/15/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 11/14/2022] Open
Abstract
As protein engineering grows more salient, many strategies have emerged to alter protein structure and function, with the goal of redesigning and optimizing natural product biosynthesis. Computational tools, including machine learning and molecular dynamics simulations, have enabled the rational mutagenesis of key catalytic residues for enhanced or altered biocatalysis. Semi-rational, directed evolution and microenvironment engineering strategies have optimized catalysis for native substrates and increased enzyme promiscuity beyond the scope of traditional rational approaches. These advances are made possible using novel high-throughput screens, including designer protein-based biosensors with engineered ligand specificity. Herein, we detail the most recent of these advances, focusing on polyketides, non-ribosomal peptides and isoprenoids, including their native biosynthetic logic to provide clarity for future applications of these technologies for natural product synthetic biology.
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Affiliation(s)
- Miles A Calzini
- Department of Chemistry, NC State University, Raleigh, NC 27695-8204, USA
| | - Alexandra A Malico
- Department of Chemistry, NC State University, Raleigh, NC 27695-8204, USA
| | - Melissa M Mitchler
- Department of Chemistry, NC State University, Raleigh, NC 27695-8204, USA
| | - Gavin J Williams
- Department of Chemistry, NC State University, Raleigh, NC 27695-8204, USA
- Comparative Medicine Institute, NC State University Raleigh, Raleigh, NC 27695-8204, USA
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12
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Rahmat E, Kang Y. Yeast metabolic engineering for the production of pharmaceutically important secondary metabolites. Appl Microbiol Biotechnol 2020; 104:4659-4674. [DOI: 10.1007/s00253-020-10587-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 01/30/2020] [Accepted: 03/24/2020] [Indexed: 11/29/2022]
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13
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Xu L, Han F, Dong Z, Wei Z. Engineering Improves Enzymatic Synthesis of L-Tryptophan by Tryptophan Synthase from Escherichia coli. Microorganisms 2020; 8:microorganisms8040519. [PMID: 32260519 PMCID: PMC7232222 DOI: 10.3390/microorganisms8040519] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 11/20/2022] Open
Abstract
To improve the thermostability of tryptophan synthase, the molecular modification of tryptophan synthase was carried out by rational molecular engineering. First, B-FITTER software was used to analyze the temperature factor (B-factor) of each amino acid residue in the crystal structure of tryptophan synthase. A key amino acid residue, G395, which adversely affected the thermal stability of the enzyme, was identified, and then, a mutant library was constructed by site-specific saturation mutation. A mutant (G395S) enzyme with significantly improved thermal stability was screened from the saturated mutant library. Error-prone PCR was used to conduct a directed evolution of the mutant enzyme (G395S). Compared with the parent, the mutant enzyme (G395S /A191T) had a Km of 0.21 mM and a catalytic efficiency kcat/Km of 5.38 mM−1∙s−1, which was 4.8 times higher than that of the wild-type strain. The conditions for L-tryptophan synthesis by the mutated enzyme were a L-serine concentration of 50 mmol/L, a reaction temperature of 40 °C, pH of 8, a reaction time of 12 h, and an L-tryptophan yield of 81%. The thermal stability of the enzyme can be improved by using an appropriate rational design strategy to modify the correct site. The catalytic activity of tryptophan synthase was increased by directed evolution.
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Affiliation(s)
- Lisheng Xu
- Department of Life and Food Science, Suzhou University, Suzhou 234000, China; (F.H.); (Z.D.)
- Correspondence: ; Tel.: +86-557-287-1681
| | - Fangkai Han
- Department of Life and Food Science, Suzhou University, Suzhou 234000, China; (F.H.); (Z.D.)
| | - Zeng Dong
- Department of Life and Food Science, Suzhou University, Suzhou 234000, China; (F.H.); (Z.D.)
| | - Zhaojun Wei
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China;
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Ma W, Zhao L, Ma Y, Li Y, Qin S, He B. Oriented efficient biosynthesis of rare ginsenoside Rh2 from PPD by compiling UGT-Yjic mutant with sucrose synthase. Int J Biol Macromol 2020; 146:853-859. [DOI: 10.1016/j.ijbiomac.2019.09.208] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/01/2019] [Accepted: 09/20/2019] [Indexed: 11/29/2022]
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15
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Chu LL, Montecillo JAV, Bae H. Recent Advances in the Metabolic Engineering of Yeasts for Ginsenoside Biosynthesis. Front Bioeng Biotechnol 2020; 8:139. [PMID: 32158753 PMCID: PMC7052115 DOI: 10.3389/fbioe.2020.00139] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 02/11/2020] [Indexed: 01/03/2023] Open
Abstract
Ginsenosides are a group of glycosylated triterpenes isolated from Panax species. Ginsenosides are promising candidates for the prevention and treatment of cancer as well as food additives. However, owing to a lack of efficient approaches for ginsenoside production from plants and chemical synthesis, ginsenosides may not yet have reached their full potential as medicinal resources. In recent years, an alternative approach for ginsenoside production has been developed using the model yeast Saccharomyces cerevisiae and non-conventional yeasts such as Yarrowia lipolytica and Pichia pastoris. In this review, various metabolic engineering strategies, including heterologous gene expression, balancing, and increasing metabolic flux, and enzyme engineering, have been described as recent advanced engineering techniques for improving ginsenoside production. Furthermore, the usefulness of a systems approach and fermentation strategy has been presented. Finally, the present challenges and future research direction for industrial cell factories have been discussed.
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Affiliation(s)
- Luan Luong Chu
- Department of Biotechnology, Yeungnam University, Gyeongsan-si, South Korea
| | | | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan-si, South Korea
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16
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Vilela A, Bacelar E, Pinto T, Anjos R, Correia E, Gonçalves B, Cosme F. Beverage and Food Fragrance Biotechnology, Novel Applications, Sensory and Sensor Techniques: An Overview. Foods 2019; 8:E643. [PMID: 31817355 PMCID: PMC6963671 DOI: 10.3390/foods8120643] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/29/2019] [Accepted: 12/03/2019] [Indexed: 12/19/2022] Open
Abstract
Flavours and fragrances are especially important for the beverage and food industries. Biosynthesis or extraction are the two main ways to obtain these important compounds that have many different chemical structures. Consequently, the search for new compounds is challenging for academic and industrial investigation. This overview aims to present the current state of art of beverage fragrance biotechnology, including recent advances in sensory and sensor methodologies and statistical techniques for data analysis. An overview of all the recent findings in beverage and food fragrance biotechnology, including those obtained from natural sources by extraction processes (natural plants as an important source of flavours) or using enzymatic precursor (hydrolytic enzymes), and those obtained by de novo synthesis (microorganisms' respiration/fermentation of simple substrates such as glucose and sucrose), are reviewed. Recent advances have been made in what concerns "beverage fragrances construction" as also in their application products. Moreover, novel sensory and sensor methodologies, primarily used for fragrances quality evaluation, have been developed, as have statistical techniques for sensory and sensors data treatments, allowing a rapid and objective analysis.
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Affiliation(s)
- Alice Vilela
- CQ-VR, Chemistry Research Centre, Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, P-5000-801 Vila Real, Portugal;
| | - Eunice Bacelar
- CITAB, Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, P-5000-801 Vila Real, Portugal; (E.B.); (T.P.); (R.A.); (B.G.)
| | - Teresa Pinto
- CITAB, Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, P-5000-801 Vila Real, Portugal; (E.B.); (T.P.); (R.A.); (B.G.)
| | - Rosário Anjos
- CITAB, Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, P-5000-801 Vila Real, Portugal; (E.B.); (T.P.); (R.A.); (B.G.)
| | - Elisete Correia
- CQ-VR, Chemistry Research Centre, Department of Mathematics, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, P-5000-801 Vila Real, Portugal;
- Center for Computational and Stochastic Mathematics (CEMAT), Department of Mathematics, IST-UL, Av. Rovisco Pais 1, 1049-001 Lisboa, Portugal
| | - Berta Gonçalves
- CITAB, Centre for the Research and Technology of Agro-Environmental and Biological Sciences, Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, P-5000-801 Vila Real, Portugal; (E.B.); (T.P.); (R.A.); (B.G.)
| | - Fernanda Cosme
- CQ-VR, Chemistry Research Centre, Department of Biology and Environment, School of Life Sciences and Environment, University of Trás-os-Montes and Alto Douro, P-5000-801 Vila Real, Portugal;
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Xu W, Klumbys E, Ang EL, Zhao H. Emerging molecular biology tools and strategies for engineering natural product biosynthesis. Metab Eng Commun 2019; 10:e00108. [PMID: 32547925 PMCID: PMC7283510 DOI: 10.1016/j.mec.2019.e00108] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/05/2019] [Accepted: 11/05/2019] [Indexed: 02/08/2023] Open
Abstract
Natural products and their related derivatives play a significant role in drug discovery and have been the inspiration for the design of numerous synthetic bioactive compounds. With recent advances in molecular biology, numerous engineering tools and strategies were established to accelerate natural product synthesis in both academic and industrial settings. However, many obstacles in natural product biosynthesis still exist. For example, the native pathways are not appropriate for research or production; the key enzymes do not have enough activity; the native hosts are not suitable for high-level production. Emerging molecular biology tools and strategies have been developed to not only improve natural product titers but also generate novel bioactive compounds. In this review, we will discuss these emerging molecular biology tools and strategies at three main levels: enzyme level, pathway level, and genome level, and highlight their applications in natural product discovery and development.
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Affiliation(s)
- Wei Xu
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology, and Research, Singapore
| | - Evaldas Klumbys
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology, and Research, Singapore
| | - Ee Lui Ang
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology, and Research, Singapore
| | - Huimin Zhao
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology, and Research, Singapore.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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18
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Liu Q, Shi X, Song L, Liu H, Zhou X, Wang Q, Zhang Y, Cai M. CRISPR-Cas9-mediated genomic multiloci integration in Pichia pastoris. Microb Cell Fact 2019; 18:144. [PMID: 31434578 PMCID: PMC6704636 DOI: 10.1186/s12934-019-1194-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/14/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Pichia pastoris (syn. Komagataella phaffii) is a widely used generally recognized as safe host for heterologous expression of proteins in both industry and academia. Recently, it has been shown to be a potentially good chassis host for the production of high-value pharmaceuticals and chemicals. Nevertheless, limited availability of selective markers and low efficiency of homologous recombination make this process difficult and time-consuming, particularly in the case of multistep biosynthetic pathways. Therefore, it is crucial to develop an efficient and marker-free multiloci gene knock-in method in P. pastoris. RESULTS A non-homologous-end-joining defective strain (Δku70) was first constructed using the CRISPR-Cas9 based gene deficiency approach. It was then used as a parent strain for multiloci gene integration. Ten guide RNA (gRNA) targets were designed within 100 bp upstream of the promoters or downstream of terminator, and then tested using an eGFP reporter and confirmed as suitable single-locus integration sites. Three high-efficiency gRNA targets (PAOX1UP-g2, PTEF1UP-g1, and PFLD1UP-g1) were selected for double- and triple-locus co-integration. The integration efficiency ranged from 57.7 to 70% and 12.5 to 32.1% for double-locus and triple-locus integration, respectively. In addition, biosynthetic pathways of 6-methylsalicylic acid and 3-methylcatechol were successfully assembled using the developed method by one-step integration of functional genes. The desired products were obtained, which further established the effectiveness and applicability of the developed CRISPR-Cas9-mediated gene co-integration method in P. pastoris. CONCLUSIONS A CRISPR-Cas9-mediated multiloci gene integration method was developed with efficient gRNA targets in P. pastoris. Using this method, multiple gene cassettes can be simultaneously integrated into the genome without employing selective markers. The multiloci integration strategy is beneficial for pathway assembly of complicated pharmaceuticals and chemicals expressed in P. pastoris.
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Affiliation(s)
- Qi Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Xiaona Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Lili Song
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Haifeng Liu
- Chinare Resources Angde Biotech Pharmaceutical Co., Ltd., 78 E-jiao Street, Liaocheng, China
| | - Xiangshan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
- Chinare Resources Angde Biotech Pharmaceutical Co., Ltd., 78 E-jiao Street, Liaocheng, China
| | - Qiyao Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
| | - Yuanxing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
- Shanghai Collaborative Innovation Center for Biomanufacturing, 130 Meilong Road, Shanghai, 200237 China
| | - Menghao Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237 China
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Moser S, Pichler H. Identifying and engineering the ideal microbial terpenoid production host. Appl Microbiol Biotechnol 2019; 103:5501-5516. [PMID: 31129740 PMCID: PMC6597603 DOI: 10.1007/s00253-019-09892-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022]
Abstract
More than 70,000 different terpenoid structures are known so far; many of them offer highly interesting applications as pharmaceuticals, flavors and fragrances, or biofuels. Extraction of these compounds from their natural sources or chemical synthesis is-in many cases-technically challenging with low or moderate yields while wasting valuable resources. Microbial production of terpenoids offers a sustainable and environment-friendly alternative starting from simple carbon sources and, frequently, safeguards high product specificity. Here, we provide an overview on employing recombinant bacteria and yeasts for heterologous de novo production of terpenoids. Currently, Escherichia coli and Saccharomyces cerevisiae are the two best-established production hosts for terpenoids. An increasing number of studies have been successful in engineering alternative microorganisms for terpenoid biosynthesis, which we intend to highlight in this review. Moreover, we discuss the specific engineering challenges as well as recent advances for microbial production of different classes of terpenoids. Rationalizing the current stages of development for different terpenoid production hosts as well as future prospects shall provide a valuable decision basis for the selection and engineering of the cell factory(ies) for industrial production of terpenoid target molecules.
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Affiliation(s)
- Sandra Moser
- Austrian Centre of Industrial Biotechnology (acib GmbH), Petersgasse 14, 8010, Graz, Austria
- Institute of Molecular Biotechnology, NAWI Graz, BioTechMed Graz, Graz University of Technology, Petersgasse 14/2, 8010, Graz, Austria
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology (acib GmbH), Petersgasse 14, 8010, Graz, Austria.
- Institute of Molecular Biotechnology, NAWI Graz, BioTechMed Graz, Graz University of Technology, Petersgasse 14/2, 8010, Graz, Austria.
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20
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Kim JE, Jang IS, Sung BH, Kim SC, Lee JY. Rerouting of NADPH synthetic pathways for increased protopanaxadiol production in Saccharomyces cerevisiae. Sci Rep 2018; 8:15820. [PMID: 30361526 PMCID: PMC6202386 DOI: 10.1038/s41598-018-34210-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/11/2018] [Indexed: 11/17/2022] Open
Abstract
Ginseng (Panax ginseng) and its bioactive components, ginsenosides, are popular medicinal herbal products, exhibiting various pharmacological effects. Despite their advocated use for medication, the long cultivation periods of ginseng roots and their low ginsenoside content prevent mass production of this compound. Yeast Saccharomyces cerevisiae was engineered for production of protopanaxadiol (PPD), a type of aglycone characterizing ginsenoside. PPD-producing yeast cell factory was further engineered by obtaining a balance between enzyme expressions and altering cofactor availability. Different combinations of promoters (PGPD, PCCW12, and PADH2) were utilized to construct the PPD biosynthetic pathway. Rerouting the redox metabolism to improve NADPH availability in the engineered S. cerevisiae also increased PPD production. Combining these approaches resulted in more than an 11-fold increase in PPD titer over the initially constructed strain. The series of metabolic engineering strategies of this study provides a feasible approach for the microbial production of PPD and development of microbial platforms producing other industrially-relevant terpenoids.
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Affiliation(s)
- Jae-Eung Kim
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), 406-30, Jongga-ro, Jung-gu, Ulsan, 44429, Republic of Korea
| | - In-Seung Jang
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), 406-30, Jongga-ro, Jung-gu, Ulsan, 44429, Republic of Korea
| | - Bong Hyun Sung
- Cell Factory Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.
| | - Ju Young Lee
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), 406-30, Jongga-ro, Jung-gu, Ulsan, 44429, Republic of Korea.
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21
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Moser S, Strohmeier GA, Leitner E, Plocek TJ, Vanhessche K, Pichler H. Whole-cell (+)-ambrein production in the yeast Pichia pastoris. Metab Eng Commun 2018; 7:e00077. [PMID: 30197866 PMCID: PMC6127371 DOI: 10.1016/j.mec.2018.e00077] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 11/30/2022] Open
Abstract
The triterpenoid (+)-ambrein is a natural precursor for (-)-ambrox, which constitutes one of the most sought-after fragrances and fixatives for the perfume industry. (+)-Ambrein is a major component of ambergris, an intestinal excretion of sperm whales that is found only serendipitously. Thus, the demand for (-)-ambrox is currently mainly met by chemical synthesis. A recent study described for the first time the applicability of an enzyme cascade consisting of two terpene cyclases, namely squalene-hopene cyclase from Alicyclobacillus acidocaldarius (AaSHC D377C) and tetraprenyl-β-curcumene cyclase from Bacillus megaterium (BmeTC) for in vitro (+)-ambrein production starting from squalene. Yeasts, such as Pichia pastoris, are natural producers of squalene and have already been shown in the past to be excellent hosts for the biosynthesis of hydrophobic compounds such as terpenoids. By targeting a central enzyme in the sterol biosynthesis pathway, squalene epoxidase Erg1, intracellular squalene levels in P. pastoris could be strongly enhanced. Heterologous expression of AaSHC D377C and BmeTC and, particularly, development of suitable methods to analyze all products of the engineered strain provided conclusive evidence of whole-cell (+)-ambrein production. Engineering of BmeTC led to a remarkable one-enzyme system that was by far superior to the cascade, thereby increasing (+)-ambrein levels approximately 7-fold in shake flask cultivation. Finally, upscaling to 5 L bioreactor yielded more than 100 mg L-1 of (+)-ambrein, demonstrating that metabolically engineered yeast P. pastoris represents a valuable, whole-cell system for high-level production of (+)-ambrein.
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Key Words
- (+)-ambrein
- AOX1, alcohol oxidase
- AaSHC, Alicyclobacillus acidocaldarius squalene-hopene cyclase
- BSM, basal salt medium
- BmeTC, Bacillus megaterium terpene cyclase
- CDW, cell dry weight
- FLD1, formaldehyde dehydrogenase 1
- HRP, horse radish peroxidase
- Metabolic engineering
- PTM1, Pichia trace metals
- Pichia pastoris
- Squalene
- Terpene cyclase
- Triterpenoid
- YNB, yeast nitrogen base
- YPD, yeast extract peptone dextrose medium
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Affiliation(s)
- Sandra Moser
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| | - Gernot A Strohmeier
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria.,Institute of Organic Chemistry, NAWI Graz, Stremayrgasse 9, 8010 Graz, Austria
| | - Erich Leitner
- Institute of Analytical Chemistry and Food Chemistry, Graz University of Technology, NAWI Graz, Stremayrgasse 9, 8010 Graz, Austria
| | - Thomas J Plocek
- ACS International S.A., 184 Route de St-Julien, CH-1228 Plan-les-Ouates, Switzerland
| | - Koenraad Vanhessche
- ACS International S.A., 184 Route de St-Julien, CH-1228 Plan-les-Ouates, Switzerland
| | - Harald Pichler
- Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria.,Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, BioTechMed Graz, Petersgasse 14/2, 8010 Graz, Austria
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22
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Metabolic engineering of Pichia pastoris. Metab Eng 2018; 50:2-15. [PMID: 29704654 DOI: 10.1016/j.ymben.2018.04.017] [Citation(s) in RCA: 135] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 04/16/2018] [Accepted: 04/23/2018] [Indexed: 12/11/2022]
Abstract
Besides its use for efficient production of recombinant proteins the methylotrophic yeast Pichia pastoris (syn. Komagataella spp.) has been increasingly employed as a platform to produce metabolites of varying origin. We summarize here the impressive methodological developments of the last years to model and analyze the metabolism of P. pastoris, and to engineer its genome and metabolic pathways. Efficient methods to insert, modify or delete genes via homologous recombination and CRISPR/Cas9, supported by modular cloning techniques, have been reported. An outstanding early example of metabolic engineering in P. pastoris was the humanization of protein glycosylation. More recently the cell metabolism was engineered also to enhance the productivity of heterologous proteins. The last few years have seen an increased number of metabolic pathway design and engineering in P. pastoris, mainly towards the production of complex (secondary) metabolites. In this review, we discuss the potential role of P. pastoris as a platform for metabolic engineering, its strengths, and major requirements for future developments of chassis strains based on synthetic biology principles.
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Dai L, Li J, Yang J, Zhu Y, Men Y, Zeng Y, Cai Y, Dong C, Dai Z, Zhang X, Sun Y. Use of a Promiscuous Glycosyltransferase from Bacillus subtilis 168 for the Enzymatic Synthesis of Novel Protopanaxatriol-Type Ginsenosides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:943-949. [PMID: 29338263 DOI: 10.1021/acs.jafc.7b03907] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ginsenosides are the principal bioactive ingredients of Panax ginseng and possess diverse notable pharmacological activities. UDP-glycosyltransferase (UGT)-mediated glycosylation of the C6-OH and C20-OH of protopanaxatriol (PPT) is the prominent biological modification that contributes to the immense structural and functional diversity of PPT-type ginsenosides. In this study, the glycosylation of PPT and PPT-type ginsenosides was achieved using a promiscuous glycosyltransferase (Bs-YjiC) from Bacillus subtilis 168. PPT was selected as the probe for the in vitro glycodiversification of PPT-type ginsenosides using diverse UDP-sugars as sugar donors. Structural analysis of the newly biosynthesized products demonstrated that Bs-YjiC can transfer a glucosyl moiety to the free C3-OH, C6-OH, and C12-OH of PPT. Five PPT-type ginsenosides were biosynthesized, including ginsenoside Rh1 and four unnatural ginsenosides. The present study suggests flexible microbial UGTs play an important role in the enzymatic synthesis of novel ginsenosides.
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Affiliation(s)
- Longhai Dai
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 Xiqi Road, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Jiao Li
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 Xiqi Road, Tianjin Airport Economic Area, Tianjin 300308, China
- University of Chinese Academy of Sciences , Beijing 100049, China
| | - Jiangang Yang
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 Xiqi Road, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yueming Zhu
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 Xiqi Road, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Men
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 Xiqi Road, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yan Zeng
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 Xiqi Road, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yi Cai
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 Xiqi Road, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Caixia Dong
- Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnosis, School of Pharmacy, Tianjin Medical University , Tianjin 300070, China
| | - Zhubo Dai
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 Xiqi Road, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Xueli Zhang
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 Xiqi Road, Tianjin Airport Economic Area, Tianjin 300308, China
| | - Yuanxia Sun
- National Engineering Laboratory for Industrial Enzymes, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , 32 Xiqi Road, Tianjin Airport Economic Area, Tianjin 300308, China
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Ping LF, Chen XY, Yuan XL, Zhang M, Chai YJ, Shan SD. Application and comparison in biosynthesis and biodegradation by Fusarium solani and Aspergillus fumigatus cutinases. Int J Biol Macromol 2017; 104:1238-1245. [DOI: 10.1016/j.ijbiomac.2017.06.118] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/29/2017] [Accepted: 06/29/2017] [Indexed: 12/29/2022]
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25
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Schwarzhans JP, Luttermann T, Geier M, Kalinowski J, Friehs K. Towards systems metabolic engineering in Pichia pastoris. Biotechnol Adv 2017; 35:681-710. [DOI: 10.1016/j.biotechadv.2017.07.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 12/30/2022]
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26
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Vickers CE, Williams TC, Peng B, Cherry J. Recent advances in synthetic biology for engineering isoprenoid production in yeast. Curr Opin Chem Biol 2017. [DOI: 10.1016/j.cbpa.2017.05.017] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Wang Z, Zhuang W, Cheng J, Sun W, Wu J, Chen Y, Ying H. In Vivo Multienzyme Complex Coconstruction of N-Acetylneuraminic Acid Lyase and N-Acetylglucosamine-2-epimerase for Biosynthesis of N-Acetylneuraminic Acid. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:7467-7475. [PMID: 28791861 DOI: 10.1021/acs.jafc.7b02708] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Metabolic channeling enables efficient transfer of the intermediates by forming a multienzyme complex. To leverage the metabolic channeling for improved biosynthesis, we coexpressed N-acetylneuraminic acid lyase from C. glutamicum ATCC 13032 (CgNal) and N-acetylglucosamine-2-epimerase from Anabaena sp. CH1 (anAGE) in Escherichia coli and used the whole cell to synthesize N-acetylneuraminic acid (Neu5Ac) from N-acetylglucosamine (GlcNAc) and pyruvate. To get the multienzyme complex, polycistronic plasmid with high levels of CgNal and anAGE expression was constructed by tuning the orders of the genes. The Shine-Dalgarno (SD) sequence and aligned spacing (AS) distance were optimized. The E. coli Rosetta harboring the polycistronic plasmid pET-28a-SD2-AS1-CgNal-SD-AS-anAGE increased the production of Neu5Ac by 58.7% to 92.5 g/L in 36 h by whole-cell catalysis and by 21.9% up to 112.8 g/L in 24 h with the addition of Triton X-100.
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Affiliation(s)
- Zhenfu Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , No. 5 Xinmofan Road, Nanjing 210009, China
- College of Biotechnology and Pharmaceutical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
- Synergetic Innovation Center for Advanced Materials, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
| | - Wei Zhuang
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , No. 5 Xinmofan Road, Nanjing 210009, China
- College of Biotechnology and Pharmaceutical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
- Synergetic Innovation Center for Advanced Materials, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
| | - Jian Cheng
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , No. 5 Xinmofan Road, Nanjing 210009, China
- College of Biotechnology and Pharmaceutical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
| | - Wujin Sun
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill and North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Jinglan Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , No. 5 Xinmofan Road, Nanjing 210009, China
- College of Biotechnology and Pharmaceutical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
| | - Yong Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , No. 5 Xinmofan Road, Nanjing 210009, China
- College of Biotechnology and Pharmaceutical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
- Synergetic Innovation Center for Advanced Materials, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
| | - Hanjie Ying
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University , No. 5 Xinmofan Road, Nanjing 210009, China
- College of Biotechnology and Pharmaceutical Engineering, National Engineering Technique Research Center for Biotechnology, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
- Synergetic Innovation Center for Advanced Materials, Nanjing Tech University , No. 30 Puzhu South Road, Nanjing 211816, China
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Zhang DH, Jiang LX, Li N, Yu X, Zhao P, Li T, Xu JW. Overexpression of the Squalene Epoxidase Gene Alone and in Combination with the 3-Hydroxy-3-methylglutaryl Coenzyme A Gene Increases Ganoderic Acid Production in Ganoderma lingzhi. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:4683-4690. [PMID: 28530827 DOI: 10.1021/acs.jafc.7b00629] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The squalene epoxidase (SE) gene from the biosynthetic pathway of ganoderic acid (GA) was cloned and overexpressed in Ganoderma lingzhi. The strain that overexpressed the SE produced approximately 2 times more GA molecules than the wild-type (WT) strain. Moreover, SE overexpression upregulated lanosterol synthase gene expression in the biosynthetic pathway. These results indicated that SE stimulates GA accumulation. Then, the SE and 3-hydroxy-3-methylglutaryl coenzyme A (HMGR) genes were simultaneously overexpressed in G. lingzhi. Compared with the individual overexpression of SE or HMGR, the combined overexpression of the two genes further enhanced individual GA production. The overexpressing strain produced maximum GA-T, GA-S, GA-Mk, and GA-Me contents of 90.4 ± 7.5, 35.9 ± 5.4, 6.2 ± 0.5, and 61.8 ± 5.8 μg/100 mg dry weight, respectively. These values were 5.9, 4.5, 2.4, and 5.8 times higher than those produced by the WT strain. This is the first example of the successful manipulation of multiple biosynthetic genes to improve GA content in G. lingzhi.
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Affiliation(s)
- De-Huai Zhang
- Faculty of Life Science and Technology, Kunming University of Science and Technology , Kunming, 650500, China
| | - Lu-Xi Jiang
- Faculty of Life Science and Technology, Kunming University of Science and Technology , Kunming, 650500, China
| | - Na Li
- Faculty of Science, Kunming University of Science and Technology , Kunming, 650500, China
| | - Xuya Yu
- Faculty of Life Science and Technology, Kunming University of Science and Technology , Kunming, 650500, China
| | - Peng Zhao
- Faculty of Life Science and Technology, Kunming University of Science and Technology , Kunming, 650500, China
| | - Tao Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology , Kunming, 650500, China
| | - Jun-Wei Xu
- Faculty of Life Science and Technology, Kunming University of Science and Technology , Kunming, 650500, China
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