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Zhou L, Li C, Dong L, Liu Y, He Y, Liu G, Bai J, Ma L, Jiang Y. Construction of Multi-Enzyme Integrated Catalysts for Deracemization of Cyclic Chiral Amines. Chembiochem 2024; 25:e202400346. [PMID: 38775416 DOI: 10.1002/cbic.202400346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/19/2024] [Indexed: 07/13/2024]
Abstract
Multi-enzyme cascade catalysis has become an important technique for chemical reactions used in manufacturing and scientific study. In this research, we designed a four-enzyme integrated catalyst and used it to catalyse the deracemization reaction of cyclic chiral amines, where monoamine oxidase (MAO) catalyses the enantioselective oxidation of 1-methyl-1,2,3,4-tetrahydroisoquinoline (MTQ), imine reductase (IRED) catalyses the stereo selective reduction of 1-methyl-3,4-dihydroisoquinoline (MDQ), formate dehydrogenase (FDH) is used for the cyclic regeneration of cofactors, and catalase (CAT) is used for decomposition of oxidative reactions. The four enzymes were immobilized via polydopamine (PDA)-encapsulated dendritic organosilica nanoparticles (DONs) as carriers, resulting in the amphiphilic core-shell catalysts. The hydrophilic PDA shell ensures the dispersion of the catalyst in water, and the hydrophobic DON core creates a microenvironment with the spatial confinement effect of the organic substrate and the preconcentration effect to enhance the stability of the enzymes and the catalytic efficiency. The core-shell structure improves the stability and reusability of the catalyst and rationally arranges the position of different enzymes according to the reaction sequence to improve the cascade catalytic performance and cofactor recovery efficiency.
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Affiliation(s)
- Liya Zhou
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Chunliu Li
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Lele Dong
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Yunting Liu
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Ying He
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Guanhua Liu
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Jing Bai
- College of Food Science and Biology, Hebei University of Science & Technology, 26 Yuxiang Street, Yuhua District, Shijiazhuang, 050018, China
| | - Li Ma
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
| | - Yanjun Jiang
- School of Chemical Engineering and Technology, Hebei University of Technology, Tianjin, 300130, China
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2
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Krause J. Indolizidines from Actinomycetes: An Overview of Producers, Biosynthesis and Bioactivities. Microorganisms 2024; 12:1445. [PMID: 39065213 PMCID: PMC11278551 DOI: 10.3390/microorganisms12071445] [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: 06/18/2024] [Revised: 07/05/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
Indolizidines have long been recognized for their valuable bioactivities, their common feature being a bicyclic structure connected via a nitrogen atom. Traditionally, plants have been identified as the primary producers. However, recent discoveries have revealed that certain bacterial strains belonging to the genus of actinomycetes also possess the ability to synthesize various indolizidine-based compounds. Among these strains, Streptomyces sp. HNA39, Saccharopolyspora sp. RL78, and Streptomyces NCIB 11649 have been identified as producers of cyclizidines, characterized by their distinctive cyclopropyl moiety. Additionally, Streptomyces griseus OS-3601 synthesizes a unique class of indolizidine derivatives known as iminimycins, distinguished by their rare imine-cation structure. Protoplast fusion of a Streptomyces griseus strain with Streptomyces tenjimariensis resulted in a new indolizidine named indolizomycin. This review aims to provide an overview of known bacterial indolizidine producers, summarize current knowledge regarding the biosynthesis of cyclizidines and iminimycins, and assess their respective bioactivities.
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Affiliation(s)
- Janina Krause
- Department of Biomedical Research, Institute of Health Research and Education, School of Human Sciences, University of Osnabrueck, 49076 Osnabrueck, Germany
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3
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Shahriyary F, Amirzargar MR, Vafajoo M, Kooshari A, Basi A, Razavi SM, Gharegozlou B, Shahidi M. Resveratrol and tetrahydroisoquinoline effects on neutrophil sensitivity to NETosis formation in low-risk essential thrombocythemia patients. Eur J Haematol 2024; 113:44-53. [PMID: 38544388 DOI: 10.1111/ejh.14196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 06/04/2024]
Abstract
INTRODUCTION Recent studies scrutinize how NETosis (a unique cell death mechanism of neutrophil), impacts thrombosis patients with essential thrombocythemia (ET). This research evaluates the susceptibility of ET neutrophils to form NETs and tests two potential inhibitors, resveratrol (RSV) and tetrahydroisoquinoline (THIQ), in vitro. METHODS Platelet-rich plasma from low-risk ET patients was used, along with neutrophils from both patients and controls. NET formation assays, with or without RSV and THIQ treatment after LPS stimulation, were conducted in a CO2 incubator. Evaluation included flow cytometry and fluorescence microscopy for NET formation and ELISA for TNFα, IL8, and vWF:Ag levels in patient and control plasma. RESULTS Neutrophils from ET patients released more NETs than controls, confirmed by flow cytometry and fluorescence microscopy. Additionally, patients had significantly higher plasma levels of IL8 and TNFα compared to controls, while RSV was more effective than THIQ in reducing NETosis rates in these patients. CONCLUSIONS In ET patients, a platelet counts over 1 million indicates the need for preventive treatment against thrombotic events. Similarly, in this study, RSV and THIQ significantly reduced the rate of NETosis in ET patients with higher platelet counts, and this role was more prominent in the case of the second inhibitor (RSV).
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Affiliation(s)
- Fahimeh Shahriyary
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Amirzargar
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Mahshid Vafajoo
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Ahmad Kooshari
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
| | - Ali Basi
- Department of Oncology, Firoozgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Seyed Mohsen Razavi
- Department of Oncology, Firoozgar Hospital, Iran University of Medical Sciences, Tehran, Iran
| | - Behnaz Gharegozlou
- Department of Immunology, School of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Minoo Shahidi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Iran University of Medical Sciences, Tehran, Iran
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4
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Zhu J, Zhang K, He Y, Zhang Q, Ran Y, Tan Z, Cui L, Feng Y. Metabolic engineering of Saccharomyces cerevisiae for chelerythrine biosynthesis. Microb Cell Fact 2024; 23:183. [PMID: 38902758 PMCID: PMC11191272 DOI: 10.1186/s12934-024-02448-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 06/03/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Chelerythrine is an important alkaloid used in agriculture and medicine. However, its structural complexity and low abundance in nature hampers either bulk chemical synthesis or extraction from plants. Here, we reconstructed and optimized the complete biosynthesis pathway for chelerythrine from (S)-reticuline in Saccharomyces cerevisiae using genetic reprogramming. RESULTS The first-generation strain Z4 capable of producing chelerythrine was obtained via heterologous expression of seven plant-derived enzymes (McoBBE, TfSMT, AmTDC, EcTNMT, PsMSH, EcP6H, and PsCPR) in S. cerevisiae W303-1 A. When this strain was cultured in the synthetic complete (SC) medium supplemented with 100 µM of (S)-reticuline for 10 days, it produced up to 0.34 µg/L chelerythrine. Furthermore, efficient metabolic engineering was performed by integrating multiple-copy rate-limiting genes (TfSMT, AmTDC, EcTNMT, PsMSH, EcP6H, PsCPR, INO2, and AtATR1), tailoring the heme and NADPH engineering, and engineering product trafficking by heterologous expression of MtABCG10 to enhance the metabolic flux of chelerythrine biosynthesis, leading to a nearly 900-fold increase in chelerythrine production. Combined with the cultivation process, chelerythrine was obtained at a titer of 12.61 mg per liter in a 0.5 L bioreactor, which is over 37,000-fold higher than that of the first-generation recombinant strain. CONCLUSIONS This is the first heterologous reconstruction of the plant-derived pathway to produce chelerythrine in a yeast cell factory. Applying a combinatorial engineering strategy has significantly improved the chelerythrine yield in yeast and is a promising approach for synthesizing functional products using a microbial cell factory. This achievement underscores the potential of metabolic engineering and synthetic biology in revolutionizing natural product biosynthesis.
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Affiliation(s)
- Jiawei Zhu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Kai Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Yuanzhi He
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Qi Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Yanpeng Ran
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Zaigao Tan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Li Cui
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, China.
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Rd, Shanghai, 200240, China.
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Gou Y, Li D, Zhao M, Li M, Zhang J, Zhou Y, Xiao F, Liu G, Ding H, Sun C, Ye C, Dong C, Gao J, Gao D, Bao Z, Huang L, Xu Z, Lian J. Intein-mediated temperature control for complete biosynthesis of sanguinarine and its halogenated derivatives in yeast. Nat Commun 2024; 15:5238. [PMID: 38898098 PMCID: PMC11186835 DOI: 10.1038/s41467-024-49554-w] [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: 01/01/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
While sanguinarine has gained recognition for antimicrobial and antineoplastic activities, its complex conjugated structure and low abundance in plants impede broad applications. Here, we demonstrate the complete biosynthesis of sanguinarine and halogenated derivatives using highly engineered yeast strains. To overcome sanguinarine cytotoxicity, we establish a splicing intein-mediated temperature-responsive gene expression system (SIMTeGES), a simple strategy that decouples cell growth from product synthesis without sacrificing protein activity. To debottleneck sanguinarine biosynthesis, we identify two reticuline oxidases and facilitated functional expression of flavoproteins and cytochrome P450 enzymes via protein molecular engineering. After comprehensive metabolic engineering, we report the production of sanguinarine at a titer of 448.64 mg L-1. Additionally, our engineered strain enables the biosynthesis of fluorinated sanguinarine, showcasing the biotransformation of halogenated derivatives through more than 15 biocatalytic steps. This work serves as a blueprint for utilizing yeast as a scalable platform for biomanufacturing diverse benzylisoquinoline alkaloids and derivatives.
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Affiliation(s)
- Yuanwei Gou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Dongfang Li
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Minghui Zhao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Mengxin Li
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiaojiao Zhang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Yilian Zhou
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Feng Xiao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Gaofei Liu
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Haote Ding
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Chenfan Sun
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Cuifang Ye
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Chang Dong
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Jucan Gao
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Di Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Zehua Bao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, China.
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Holtz M, Acevedo-Rocha CG, Jensen MK. Combining enzyme and metabolic engineering for microbial supply of therapeutic phytochemicals. Curr Opin Biotechnol 2024; 87:103110. [PMID: 38503222 DOI: 10.1016/j.copbio.2024.103110] [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: 01/09/2024] [Revised: 02/27/2024] [Accepted: 02/29/2024] [Indexed: 03/21/2024]
Abstract
The history of pharmacology is deeply intertwined with plant-derived compounds, which continue to be crucial in drug development. However, their complex structures and limited availability in plants challenge drug discovery, optimization, development, and industrial production via chemical synthesis or natural extraction. This review delves into the integration of metabolic and enzyme engineering to leverage micro-organisms as platforms for the sustainable and reliable production of therapeutic phytochemicals. We argue that engineered microbes can serve a triple role in this paradigm: facilitating pathway discovery, acting as cell factories for scalable manufacturing, and functioning as platforms for chemical derivatization. Analyzing recent progress and outlining future directions, the review highlights microbial biotechnology's transformative potential in expanding plant-derived human therapeutics' discovery and supply chains.
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Affiliation(s)
- Maxence Holtz
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Carlos G Acevedo-Rocha
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Michael K Jensen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark.
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7
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Gao J, Gou Y, Huang L, Lian J. Reconstitution and optimization of complex plant natural product biosynthetic pathways in microbial expression systems. Curr Opin Biotechnol 2024; 87:103136. [PMID: 38705090 DOI: 10.1016/j.copbio.2024.103136] [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: 01/30/2024] [Revised: 03/24/2024] [Accepted: 04/12/2024] [Indexed: 05/07/2024]
Abstract
Plant natural products (PNPs) are a diverse group of chemical compounds synthesized by plants for various biological purposes and play a significant role in the fields of medicine, agriculture, and industry. In recent years, the development of synthetic biology promises the production of PNPs in microbial expression systems in a sustainable, low-cost, and large-scale manner. This review first introduces multiplex genome editing and PNP pathway assembly in microbial expression systems. Then recent technologies and examples geared toward improving PNP biosynthetic efficiency are discussed from three aspects: pathway optimization, chassis optimization, and modular coculture engineering. Finally, the review is concluded with future perspectives on the combination of machine learning and BioFoundry for the reconstitution and optimization of PNP microbial cell factories.
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Affiliation(s)
- Jucan Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310000, China
| | - Yuanwei Gou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310000, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310000, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education & National Key Laboratory of Biobased Transportation Fuel Technology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 310000, China.
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8
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Han T, Miao G. Strategies, Achievements, and Potential Challenges of Plant and Microbial Chassis in the Biosynthesis of Plant Secondary Metabolites. Molecules 2024; 29:2106. [PMID: 38731602 PMCID: PMC11085123 DOI: 10.3390/molecules29092106] [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: 03/08/2024] [Revised: 04/27/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Diverse secondary metabolites in plants, with their rich biological activities, have long been important sources for human medicine, food additives, pesticides, etc. However, the large-scale cultivation of host plants consumes land resources and is susceptible to pest and disease problems. Additionally, the multi-step and demanding nature of chemical synthesis adds to production costs, limiting their widespread application. In vitro cultivation and the metabolic engineering of plants have significantly enhanced the synthesis of secondary metabolites with successful industrial production cases. As synthetic biology advances, more research is focusing on heterologous synthesis using microorganisms. This review provides a comprehensive comparison between these two chassis, evaluating their performance in the synthesis of various types of secondary metabolites from the perspectives of yield and strategies. It also discusses the challenges they face and offers insights into future efforts and directions.
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Affiliation(s)
- Taotao Han
- Department of Bioengineering, Huainan Normal University, Huainan 232038, China;
| | - Guopeng Miao
- Department of Bioengineering, Huainan Normal University, Huainan 232038, China;
- Key Laboratory of Bioresource and Environmental Biotechnology of Anhui Higher Education Institutes, Huainan Normal University, Huainan 232038, China
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9
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Wang S, Zhao F, Yang M, Lin Y, Han S. Metabolic engineering of Saccharomyces cerevisiae for the synthesis of valuable chemicals. Crit Rev Biotechnol 2024; 44:163-190. [PMID: 36596577 DOI: 10.1080/07388551.2022.2153008] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/11/2022] [Accepted: 10/29/2022] [Indexed: 01/05/2023]
Abstract
In the twenty first century, biotechnology offers great opportunities and solutions to climate change mitigation, energy and food security and resource efficiency. The use of metabolic engineering to modify microorganisms for producing industrially significant chemicals is developing and becoming a trend. As a famous, generally recognized as a safe (GRAS) model microorganism, Saccharomyces cerevisiae is widely used due to its excellent operational convenience and high fermentation efficiency. This review summarizes recent advancements in the field of using metabolic engineering strategies to construct engineered S. cerevisiae over the past ten years. Five different types of compounds are classified by their metabolites, and the modified metabolic pathways and strategies are summarized and discussed independently. This review may provide guidance for future metabolic engineering efforts toward such compounds and analogues. Additionally, the limitations of S. cerevisiae as a cell factory and its future trends are comprehensively discussed.
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Affiliation(s)
- Shuai Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Fengguang Zhao
- School of Light Industry and Engineering, South China University of Technology, Guangzhou, China
| | - Manli Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Ying Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shuangyan Han
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
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Liu M, Wu J, Yue M, Ning Y, Guan X, Gao S, Zhou J. YaliCMulti and YaliHMulti: Stable, efficient multi-copy integration tools for engineering Yarrowia lipolytica. Metab Eng 2024; 82:29-40. [PMID: 38224832 DOI: 10.1016/j.ymben.2024.01.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/17/2024]
Abstract
Yarrowia lipolytica is widely used in biotechnology to produce recombinant proteins, food ingredients and diverse natural products. However, unstable expression of plasmids, difficult and time-consuming integration of single and low-copy-number plasmids hampers the construction of efficient production pathways and application to industrial production. Here, by exploiting sequence diversity in the long terminal repeats (LTRs) of retrotransposons and ribosomal DNA (rDNA) sequences, a set of vectors and methods that can recycle multiple and high-copy-number plasmids was developed that can achieve stable integration of long-pathway genes in Y. lipolytica. By combining these sequences, amino acids and antibiotic tags with the Cre-LoxP system, a series of multi-copy site integration recyclable vectors were constructed and assessed using the green fluorescent protein (HrGFP) reporter system. Furthermore, by combining the consensus sequence with the vector backbone of a rapidly degrading selective marker and a weak promoter, multiple integrated high-copy-number vectors were obtained and high levels of stable HrGFP expression were achieved. To validate the universality of the tools, simple integration of essential biosynthesis modules was explored, and 7.3 g/L of L-ergothioneine and 8.3 g/L of (2S)-naringenin were achieved in a 5 L fermenter, the highest titres reported to date for Y. lipolytica. These novel multi-copy genome integration strategies provide convenient and effective tools for further metabolic engineering of Y. lipolytica.
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Affiliation(s)
- Mengsu Liu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Junjun Wu
- School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Mingyu Yue
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Yang Ning
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Xin Guan
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Song Gao
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu, 214122, China.
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11
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Long Y, Han X, Meng X, Xu P, Tao F. A robust yeast chassis: comprehensive characterization of a fast-growing Saccharomyces cerevisiae. mBio 2024; 15:e0319623. [PMID: 38214535 PMCID: PMC10865977 DOI: 10.1128/mbio.03196-23] [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: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 01/13/2024] Open
Abstract
Robust chassis are critical to facilitate advances in synthetic biology. This study describes a comprehensive characterization of a new yeast isolate Saccharomyces cerevisiae XP that grows faster than commonly used research and industrial S. cerevisiae strains. The genomic, transcriptomic, and metabolomic analyses suggest that the fast growth rate is, in part, due to the efficient electron transport chain and key growth factor synthesis. A toolbox for genetic manipulation of the yeast was developed; we used it to construct l-lactic acid producers for high lactate production. The development of genetically malleable yeast strains that grow faster than currently used strains may significantly enhance the uses of S. cerevisiae in biotechnology.IMPORTANCEYeast is known as an outstanding starting strain for constructing microbial cell factories. However, its growth rate restricts its application. A yeast strain XP, which grows fast in high concentrations of sugar and acidic environments, is revealed to demonstrate the potential in industrial applications. A toolbox was also built for its genetic manipulation including gene insertion, deletion, and ploidy transformation. The knowledge of its metabolism, which could guide the designing of genetic experiments, was generated with multi-omics analyses. This novel strain along with its toolbox was then tested by constructing an l-lactic acid efficient producer, which is conducive to the development of degradable plastics. This study highlights the remarkable competence of nonconventional yeast for applications in biotechnology.
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Affiliation(s)
- Yangdanyu Long
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiao Han
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuanlin Meng
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Xu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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12
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Marchán-García J, Buxaderas E, Stratico DN, Richmond V, Cavallaro V, Murray AP, Radivoy G, Moglie Y. Green approach to the synthesis of α-aminophosphonate-tetrahydroisoquinoline hybrids and their anti-cholinesterase activity. Bioorg Chem 2024; 143:107008. [PMID: 38091720 DOI: 10.1016/j.bioorg.2023.107008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 11/12/2023] [Accepted: 11/26/2023] [Indexed: 01/24/2024]
Abstract
A series of 19 novel α-aminophosphonate-tetrahydroisoquinoline hybrids were synthesized through a cross dehydrogenative coupling reaction between N-aryl-tetrahydroisoquinolines and dialkylphosphites, using tert-butyl hydroperoxide as oxidazing agent. This simple procedure provided products with high atom economy and moderate to high yields. In vitro cholinesterase inhibitory activity of these compounds was evaluated. All the synthesized compounds showed good to excellent selective inhibition against butyrylcholinesterase. Compound 3bc was found to be the most active derivative with an IC50 of 9 nM. Molecular modelling studies suggested that the inhibitor is located in the peripheral anionic site (PAS) of the enzyme and interacts with some residue of the catalytic anionic site. Kinetic studies revealed that 3bc acts as a non-competitive inhibitor. Predicted ADME showed good pharmacokinetics and drug-likeness properties for most hybrids. Each newly synthesized compound was characterized by IR, 1H NMR, 13C NMR, 31P NMR spectral studies and also HRMS. The results of this study suggest that α-aminophosphonate-tetrahydroisoquinoline hybrids can be promising lead compounds in the discovery of new and improved drugs for the treatment of Alzheimer's disease and related neurodegenerative disorders.
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Affiliation(s)
- Joaquín Marchán-García
- Instituto de Química del Sur, INQUISUR (CONICET-UNS), Departamento de Química, Universidad Nacional del Sur, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
| | - Eduardo Buxaderas
- Instituto de Química del Sur, INQUISUR (CONICET-UNS), Departamento de Química, Universidad Nacional del Sur, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
| | - Dante Nicolás Stratico
- Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica, UMYMFOR (CONICET-UBA), Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428, Buenos Aires, Argentina; Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, 1428, Argentina
| | - Victoria Richmond
- Unidad de Microanálisis y Métodos Físicos Aplicados a Química Orgánica, UMYMFOR (CONICET-UBA), Departamento de Química Orgánica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, 1428, Buenos Aires, Argentina
| | - Valeria Cavallaro
- Instituto de Química del Sur, INQUISUR (CONICET-UNS), Departamento de Química, Universidad Nacional del Sur, Avenida Alem 1253, 8000, Bahía Blanca, Argentina.
| | - Ana Paula Murray
- Instituto de Química del Sur, INQUISUR (CONICET-UNS), Departamento de Química, Universidad Nacional del Sur, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
| | - Gabriel Radivoy
- Instituto de Química del Sur, INQUISUR (CONICET-UNS), Departamento de Química, Universidad Nacional del Sur, Avenida Alem 1253, 8000, Bahía Blanca, Argentina
| | - Yanina Moglie
- Instituto de Química del Sur, INQUISUR (CONICET-UNS), Departamento de Química, Universidad Nacional del Sur, Avenida Alem 1253, 8000, Bahía Blanca, Argentina.
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13
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Dror MJ, Misa J, Yee DA, Chu AM, Yu RK, Chan BB, Aoyama LS, Chaparala AP, O'Connor SE, Tang Y. Engineered biosynthesis of plant heteroyohimbine and corynantheine alkaloids in Saccharomyces cerevisiae. J Ind Microbiol Biotechnol 2024; 51:kuad047. [PMID: 38140980 PMCID: PMC10995622 DOI: 10.1093/jimb/kuad047] [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: 11/09/2023] [Accepted: 12/21/2023] [Indexed: 12/24/2023]
Abstract
Monoterpene indole alkaloids (MIAs) are a class of natural products comprised of thousands of structurally unique bioactive compounds with significant therapeutic values. Due to difficulties associated with isolation from native plant species and organic synthesis of these structurally complex molecules, microbial production of MIAs using engineered hosts are highly desired. In this work, we report the engineering of fully integrated Saccharomyces cerevisiae strains that allow de novo access to strictosidine, the universal precursor to thousands of MIAs at 30-40 mg/L. The optimization efforts were based on a previously reported yeast strain that is engineered to produce high titers of the monoterpene precursor geraniol through compartmentalization of mevalonate pathway in the mitochondria. Our approaches here included the use of CRISPR-dCas9 interference to identify mitochondria diphosphate transporters that negatively impact the titer of the monoterpene, followed by genetic inactivation; the overexpression of transcriptional regulators that increase cellular respiration and mitochondria biogenesis. Strain construction included the strategic integration of genes encoding both MIA biosynthetic and accessory enzymes into the genome under a variety of constitutive and inducible promoters. Following successful de novo production of strictosidine, complex alkaloids belonging to heteroyohimbine and corynantheine families were reconstituted in the host with introduction of additional downstream enzymes. We demonstrate that the serpentine/alstonine pair can be produced at ∼5 mg/L titer, while corynantheidine, the precursor to mitragynine can be produced at ∼1 mg/L titer. Feeding of halogenated tryptamine led to the biosynthesis of analogs of alkaloids in both families. Collectively, our yeast strain represents an excellent starting point to further engineer biosynthetic bottlenecks in this pathway and to access additional MIAs and analogs through microbial fermentation. ONE SENTENCE SUMMARY An Saccharomyces cerevisiae-based microbial platform was developed for the biosynthesis of monoterpene indole alkaloids, including the universal precursor strictosidine and further modified heteroyohimbine and corynantheidine alkaloids.
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Affiliation(s)
- Moriel J Dror
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Joshua Misa
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Danielle A Yee
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Angela M Chu
- Stanford Genome Technology Center, Stanford University, Stanford, CA 94305, USA
| | - Rachel K Yu
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Bradley B Chan
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Lauren S Aoyama
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Anjali P Chaparala
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena 07745, Germany
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA 90095, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095, USA
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14
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Mo Q, Yuan J. Minimal aromatic aldehyde reduction (MARE) yeast platform for engineering vanillin production. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:4. [PMID: 38184607 PMCID: PMC10771647 DOI: 10.1186/s13068-023-02454-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 12/19/2023] [Indexed: 01/08/2024]
Abstract
BACKGROUND Vanillin represents one of the most widely used flavoring agents in the world. However, microbial synthesis of vanillin is hindered by the host native metabolism that could rapidly degrade vanillin to the byproducts. RESULTS Here, we report that the industrial workhorse Saccharomyces cerevisiae was engineered by systematic deletion of oxidoreductases to improve the vanillin accumulation. Subsequently, we harnessed the minimal aromatic aldehyde reduction (MARE) yeast platform for de novo synthesis of vanillin from glucose. We investigated multiple coenzyme-A free pathways to improve vanillin production in yeast. The vanillin productivity in yeast was enhanced by multidimensional engineering to optimize the supply of cofactors (NADPH and S-adenosylmethionine) together with metabolic reconfiguration of yeast central metabolism. The final yeast strain with overall 24 genetic modifications produced 365.55 ± 7.42 mg l-1 vanillin in shake-flasks, which represents the best reported vanillin titer from glucose in yeast. CONCLUSIONS The success of vanillin overproduction in budding yeast showcases the great potential of synthetic biology for the creation of suitable biocatalysts to meet the requirement in industry. Our work lays a foundation for the future implementation of microbial production of aromatic aldehydes in budding yeast.
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Affiliation(s)
- Qiwen Mo
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, 361102, China
| | - Jifeng Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Fujian, 361102, China.
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15
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Gao Y, Li F, Luo Z, Deng Z, Zhang Y, Yuan Z, Liu C, Rao Y. Modular assembly of an artificially concise biocatalytic cascade for the manufacture of phenethylisoquinoline alkaloids. Nat Commun 2024; 15:30. [PMID: 38167860 PMCID: PMC10761944 DOI: 10.1038/s41467-023-44420-7] [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: 09/18/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024] Open
Abstract
Plant-derived alkaloids are an important class of pharmaceuticals. However, they still rely on phytoextraction to meet their diverse market demands. Since multistep biocatalytic cascades have begun to revolutionize the manufacture of natural or unnatural products, to address the synthetic challenges of alkaloids, herein we establish an artificially concise four-enzyme biocatalytic cascade with avoiding plant-derived P450 modification for synthesizing phenethylisoquinoline alkaloids (PEIAs) after enzyme discovery and enzyme engineering. Efficient biosynthesis of diverse natural and unnatural PEIAs is realized from readily available substrates. Most importantly, the scale-up preparation of the colchicine precursor (S)-autumnaline with a high titer is achieved after replacing the rate-limiting O-methylation by the plug-and-play strategy. This study not only streamlines future engineering endeavors for colchicine biosynthesis, but also provides a paradigm for constructing more artificial biocatalytic cascades for the manufacture of diverse alkaloids through synthetic biology.
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Affiliation(s)
- Yue Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
| | - Fei Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
| | - Zhengshan Luo
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
| | - Zhiwei Deng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
| | - Yan Zhang
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Zhenbo Yuan
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
| | - Changmei Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China
| | - Yijian Rao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China.
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16
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Ndip RA, Hanna JN, Mbah JA, Ghogomu SM, Ngemenya MN. In Vitro Synergistic Activity of Combinations of Tetrahydroisoquinolines and Treatment Antibiotics against Multidrug-Resistant Salmonella. Adv Pharmacol Pharm Sci 2023; 2023:6142810. [PMID: 38130400 PMCID: PMC10733592 DOI: 10.1155/2023/6142810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 10/31/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
The global burden of Salmonella infections remains high due to the emergence of multidrug resistance to all recommended treatment antibiotics. Tetrahydroisoquinolines (THIQs) have demonstrated promising activity against multidrug-resistant (MDR) Salmonella Typhi. Hence, their interaction with treatment antibiotics was investigated for possible synergy. Twenty combinations of five THIQs (1, 2, 3, 4, and 5) and four antibiotics were tested against each of 7 Salmonella isolates by the checkerboard method giving a total of 140 assays performed. Fractional inhibitory concentration indices (FICIs) were calculated, and isobolograms were plotted. In terms of FICI, synergism ranged from 0.078 to 0.5 and the highest magnitude (0.078) was recorded for chloramphenicol-THIQ 1 combination. In a total of 140 antibiotics-THIQs combination assays, 27 were synergistic (17%), 42 were additive (30%), 11 were antagonistic (7.8%), and 60 were indifferent (42%). The synergistic activity recorded for each antibiotic class in combination based on the total of 7 bacterial isolates tested ranged from 14.29% to 71.43%; the highest percentage was recorded for two combinations (chloramphenicol or sulphamethoxazole with THIQ 1). Ciprofloxacin-THIQ 1 combination showed additivity on all bacteria isolates tested (100%). Overall, THIQ 1 was the most synergistic and most additive in combination with three antibiotics (ampicillin, chloramphenicol, or sulphamethoxazole-trimethoprim). Some combinations of the THIQs and treatment antibiotics have shown high synergism which could potentially be efficacious against multidrug-resistant S. Typhi, hence this interaction should be further studied in vivo.
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Affiliation(s)
- Rita Ayuk Ndip
- Department of Biochemistry and Molecular Biology, University of Buea, P.O. Box 63, Buea, Cameroon
| | - Joelle Ngo Hanna
- Department of Chemistry, Faculty of Science, University of Douala, P.O. Box 24157, Douala, Cameroon
| | - James Ajeck Mbah
- Department of Chemistry, Faculty of Science, University of Buea, P.O. Box 63, Buea, Cameroon
| | - Stephen Mbigha Ghogomu
- Department of Biochemistry and Molecular Biology, University of Buea, P.O. Box 63, Buea, Cameroon
| | - Moses Njutain Ngemenya
- Department of Biochemistry and Molecular Biology, University of Buea, P.O. Box 63, Buea, Cameroon
- Department of Medical Laboratory Sciences, University of Buea, P.O. Box 63, Buea, Cameroon
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17
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Yu J, Zheng Y, Song C, Chen S. New insights into the roles of fungi and bacteria in the development of medicinal plant. J Adv Res 2023:S2090-1232(23)00394-6. [PMID: 38092299 DOI: 10.1016/j.jare.2023.12.007] [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: 08/08/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 01/02/2024] Open
Abstract
BACKGROUND The interaction between microorganisms and medicinal plants is a popular topic. Previous studies consistently reported that microorganisms were mainly considered pathogens or contaminants. However, with the development of microbial detection technology, it has been demonstrated that fungi and bacteria affect beneficially the medicinal plant production chain. AIM OF REVIEW Microorganisms greatly affect medicinal plants, with microbial biosynthesis a high regarded topic in medicinal plant-microbial interactions. However, it lacks a systematic review discussing this relationship. Current microbial detection technologies also have certain advantages and disadvantages, it is essential to compare the characteristics of various technologies. KEY SCIENTIFIC CONCEPTS OF REVIEW This review first illustrates the role of fungi and bacteria in various medicinal plant production procedures, discusses the development of microbial detection and identification technologies in recent years, and concludes with microbial biosynthesis of natural products. The relationship between fungi, bacteria, and medicinal plants is discussed comprehensively. We also propose a future research model and direction for further studies.
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Affiliation(s)
- Jingsheng Yu
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137 China; Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700 China
| | - Yixuan Zheng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137 China
| | - Chi Song
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137 China
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu 611137 China; Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700 China.
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18
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Black WB, Perea S, Li H. Design, construction, and application of noncanonical redox cofactor infrastructures. Curr Opin Biotechnol 2023; 84:103019. [PMID: 37939631 DOI: 10.1016/j.copbio.2023.103019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023]
Abstract
Controlling the flow of carbon and reducing power in biological systems is a central theme in metabolic engineering. Often, trade-offs in pushing carbon flux through targeted pathways while operating in conditions agreeable to the host are required due to the central pools of the shared native redox cofactors NAD(P)/H. Noncanonical redox cofactors (NRCs) have emerged as promising tools to transform how engineers develop biotransformation systems. These new-to-Nature redox cofactors have been demonstrated to function orthogonally to the endogenous cofactors, support pathway thermodynamics optimization, and achieve product scopes previously difficult to reach due to endogenous pathway crosstalk. This review will discuss the development of NRC infrastructures, comprising NRC pools, cofactor reduction sources, and cofactor oxidation sinks, the (pool-source-sink) infrastructure.
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Affiliation(s)
- William B Black
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA 92697-3900, United States of America
| | - Sean Perea
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA 92697-3900, United States of America
| | - Han Li
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, CA 92697-3900, United States of America; Department of Biomedical Engineering, University of California, Irvine, Irvine, CA 92697-3900, United States of America; Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92697-3900, United States of America.
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19
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Gao M, Zhao Y, Yao Z, Su Q, Van Beek P, Shao Z. Xylose and shikimate transporters facilitates microbial consortium as a chassis for benzylisoquinoline alkaloid production. Nat Commun 2023; 14:7797. [PMID: 38016984 PMCID: PMC10684500 DOI: 10.1038/s41467-023-43049-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 10/30/2023] [Indexed: 11/30/2023] Open
Abstract
Plant-sourced aromatic amino acid (AAA) derivatives are a vast group of compounds with broad applications. Here, we present the development of a yeast consortium for efficient production of (S)-norcoclaurine, the key precursor for benzylisoquinoline alkaloid biosynthesis. A xylose transporter enables the concurrent mixed-sugar utilization in Scheffersomyces stipitis, which plays a crucial role in enhancing the flux entering the highly regulated shikimate pathway located upstream of AAA biosynthesis. Two quinate permeases isolated from Aspergillus niger facilitates shikimate translocation to the co-cultured Saccharomyces cerevisiae that converts shikimate to (S)-norcoclaurine, resulting in the maximal titer (11.5 mg/L), nearly 110-fold higher than the titer reported for an S. cerevisiae monoculture. Our findings magnify the potential of microbial consortium platforms for the economical de novo synthesis of complex compounds, where pathway modularization and compartmentalization in distinct specialty strains enable effective fine-tuning of long biosynthetic pathways and diminish intermediate buildup, thereby leading to increases in production.
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Affiliation(s)
- Meirong Gao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Yuxin Zhao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Zhanyi Yao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA
| | - Qianhe Su
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Payton Van Beek
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, USA.
- NSF Engineering Research Center for Biorenewable Chemicals, Iowa State University, Ames, IA, USA.
- Interdepartmental Microbiology Program, Iowa State University, Ames, IA, USA.
- Bioeconomy Institute, Iowa State University, Ames, IA, USA.
- The Ames Laboratory, Ames, IA, USA.
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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20
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Watkins JL, Li Q, Yeaman S, Facchini PJ. Elucidation of the mescaline biosynthetic pathway in peyote (Lophophora williamsii). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:635-649. [PMID: 37675639 DOI: 10.1111/tpj.16447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/08/2023]
Abstract
Peyote (Lophophora williamsii) is an entheogenic and medicinal cactus native to the Chihuahuan desert. The psychoactive and hallucinogenic properties of peyote are principally attributed to the phenethylamine derivative mescaline. Despite the isolation of mescaline from peyote over 120 years ago, the biosynthetic pathway in the plant has remained undiscovered. Here, we use a transcriptomics and homology-guided gene discovery strategy to elucidate a near-complete biosynthetic pathway from l-tyrosine to mescaline. We identified a cytochrome P450 that catalyzes the 3-hydroxylation of l-tyrosine to l-DOPA, a tyrosine/DOPA decarboxylase yielding dopamine, and four substrate-specific and regiospecific substituted phenethylamine O-methyltransferases. Biochemical assays with recombinant enzymes or functional analyses performed by feeding putative precursors to engineered yeast (Saccharomyces cerevisiae) strains expressing candidate peyote biosynthetic genes were used to determine substrate specificity, which served as the basis for pathway elucidation. Additionally, an N-methyltransferase displaying broad substrate specificity and leading to the production of N-methylated phenethylamine derivatives was identified, which could also function as an early step in the biosynthesis of tetrahydroisoquinoline alkaloids in peyote.
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Affiliation(s)
- Jacinta L Watkins
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Qiushi Li
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Sam Yeaman
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
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21
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Cigan E, Pletz J, Berger SA, Hierzberger B, Grilec-Zlamal M, Steiner A, Oroz-Guinea I, Kroutil W. Concise synthesis of ( R)-reticuline and (+)-salutaridine by combining early-stage organic synthesis and late-stage biocatalysis. Chem Sci 2023; 14:9863-9871. [PMID: 37736642 PMCID: PMC10510765 DOI: 10.1039/d3sc02304d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/10/2023] [Indexed: 09/23/2023] Open
Abstract
Efficient access to the morphinan scaffold remains a major challenge in both synthetic chemistry and biotechnology. Here, a biomimetic chemo-enzymatic strategy to synthesize the natural promorphinan intermediate (+)-salutaridine is demonstrated. By combining early-stage organic synthesis with enzymatic asymmetric key step transformations, the prochiral natural intermediate 1,2-dehydroreticuline was prepared and subsequently stereoselectively reduced by the enzyme 1,2-dehydroreticuline reductase obtaining (R)-reticuline in high ee and yield (>99% ee, up to quant. conversion, 92% isol. yield). In the final step, membrane-bound salutaridine synthase was used to perform the selective ortho-para phenol coupling to give (+)-salutaridine. The synthetic route shows the potential of combining early-stage advanced organic chemistry to minimize protecting group techniques with late-stage multi-step biocatalysis to provide an unprecedented access to the medicinally important compound class of promorphinans.
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Affiliation(s)
- Emmanuel Cigan
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz Heinrichstrasse 28/II 8010 Graz Austria
| | - Jakob Pletz
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz Heinrichstrasse 28/II 8010 Graz Austria
| | - Sarah A Berger
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz Heinrichstrasse 28/II 8010 Graz Austria
| | - Bettina Hierzberger
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz Heinrichstrasse 28/II 8010 Graz Austria
| | - Michael Grilec-Zlamal
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz Heinrichstrasse 28/II 8010 Graz Austria
| | - Alexander Steiner
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz Heinrichstrasse 28/II 8010 Graz Austria
| | - Isabel Oroz-Guinea
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz Heinrichstrasse 28/II 8010 Graz Austria
| | - Wolfgang Kroutil
- Institute of Chemistry, University of Graz, NAWI Graz, BioTechMed Graz Heinrichstrasse 28/II 8010 Graz Austria
- Field of Excellence BioHealth, University of Graz 8010 Graz Austria
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22
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Dykstra CB, Pyne ME, Martin VJJ. CRAPS: Chromosomal-Repair-Assisted Pathway Shuffling in Yeast. ACS Synth Biol 2023; 12:2578-2587. [PMID: 37584634 DOI: 10.1021/acssynbio.3c00170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
A fundamental challenge of metabolic engineering involves assembling and screening vast combinations of orthologous enzymes across a multistep biochemical pathway. Current pathway assembly workflows involve combining genetic parts ex vivo and assembling one pathway configuration per tube or well. Here, we present CRAPS, Chromosomal-Repair-Assisted Pathway Shuffling, an in vivo pathway engineering technique that enables the self-assembly of one pathway configuration per cell. CRAPS leverages the yeast chromosomal repair pathway and utilizes a pool of inactive, chromosomally integrated orthologous gene variants corresponding to a target multistep pathway. Supplying gRNAs to the CRAPS host activates the expression of one gene variant per pathway step, resulting in a unique pathway configuration in each cell. We deployed CRAPS to build more than 1000 theoretical combinations of a four-step carotenoid biosynthesis network. Sampling the CRAPS pathway space yielded strains with distinct color phenotypes and carotenoid product profiles. We anticipate that CRAPS will expedite strain engineering campaigns by enabling the generation and sampling of vast biochemical spaces.
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Affiliation(s)
- Christien B Dykstra
- Department of Biology, Concordia University, Montréal, Quebec, Canada H4B 1R6
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Quebec, Canada H4B 1R6
| | - Michael E Pyne
- Department of Biology, Concordia University, Montréal, Quebec, Canada H4B 1R6
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Quebec, Canada H4B 1R6
| | - Vincent J J Martin
- Department of Biology, Concordia University, Montréal, Quebec, Canada H4B 1R6
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Quebec, Canada H4B 1R6
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23
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Pyne ME, Bagley JA, Narcross L, Kevvai K, Exley K, Davies M, Wang Q, Whiteway M, Martin VJJ. Screening non-conventional yeasts for acid tolerance and engineering Pichia occidentalis for production of muconic acid. Nat Commun 2023; 14:5294. [PMID: 37652930 PMCID: PMC10471774 DOI: 10.1038/s41467-023-41064-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/22/2023] [Indexed: 09/02/2023] Open
Abstract
Saccharomyces cerevisiae is a workhorse of industrial biotechnology owing to the organism's prominence in alcohol fermentation and the suite of sophisticated genetic tools available to manipulate its metabolism. However, S. cerevisiae is not suited to overproduce many bulk bioproducts, as toxicity constrains production at high titers. Here, we employ a high-throughput assay to screen 108 publicly accessible yeast strains for tolerance to 20 g L-1 adipic acid (AA), a nylon precursor. We identify 15 tolerant yeasts and select Pichia occidentalis for production of cis,cis-muconic acid (CCM), the precursor to AA. By developing a genome editing toolkit for P. occidentalis, we demonstrate fed-batch production of CCM with a maximum titer (38.8 g L-1), yield (0.134 g g-1 glucose) and productivity (0.511 g L-1 h-1) that surpasses all metrics achieved using S. cerevisiae. This work brings us closer to the industrial bioproduction of AA and underscores the importance of host selection in bioprocessing.
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Affiliation(s)
- Michael E Pyne
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Department of Biology, University of Western Ontario, Ontario, Canada
| | - James A Bagley
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
| | - Lauren Narcross
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Amyris, Inc., Emeryville, CA, USA
| | - Kaspar Kevvai
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Pivot Bio, Berkeley, CA, USA
| | - Kealan Exley
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Novo Nordisk Foundation Center for Biosustainability, Lyngby, Denmark
| | - Meghan Davies
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- BenchSci, Toronto, ON, Canada
| | | | - Malcolm Whiteway
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada
| | - Vincent J J Martin
- Department of Biology, Concordia University, Montréal, QC, H4B 1R6, Canada.
- Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B 1R6, Canada.
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24
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Nasr MA, Martin VJJ, Kwan DH. Divergent directed evolution of a TetR-type repressor towards aromatic molecules. Nucleic Acids Res 2023; 51:7675-7690. [PMID: 37377432 PMCID: PMC10415137 DOI: 10.1093/nar/gkad503] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 05/18/2023] [Accepted: 06/25/2023] [Indexed: 06/29/2023] Open
Abstract
Reprogramming cellular behaviour is one of the hallmarks of synthetic biology. To this end, prokaryotic allosteric transcription factors (aTF) have been repurposed as versatile tools for processing small molecule signals into cellular responses. Expanding the toolbox of aTFs that recognize new inducer molecules is of considerable interest in many applications. Here, we first establish a resorcinol responsive aTF-based biosensor in Escherichia coli using the TetR-family repressor RolR from Corynebacterium glutamicum. We then perform an iterative walk along the fitness landscape of RolR to identify new inducer specificities, namely catechol, methyl catechol, caffeic acid, protocatechuate, L-DOPA, and the tumour biomarker homovanillic acid. Finally, we demonstrate the versatility of these engineered aTFs by transplanting them into the model eukaryote Saccharomyces cerevisiae. This work provides a framework for efficient aTF engineering to expand ligand specificity towards novel molecules on laboratory timescales, which, more broadly, is invaluable across a wide range of applications such as protein and metabolic engineering, as well as point-of-care diagnostics.
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Affiliation(s)
- Mohamed A Nasr
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
- PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec City, Québec, Canada
| | - Vincent J J Martin
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | - David H Kwan
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
- PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec City, Québec, Canada
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25
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Bui VH, Rodríguez-López CE, Dang TTT. Integration of discovery and engineering in plant alkaloid research: Recent developments in elucidation, reconstruction, and repurposing biosynthetic pathways. CURRENT OPINION IN PLANT BIOLOGY 2023; 74:102379. [PMID: 37182414 DOI: 10.1016/j.pbi.2023.102379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/17/2023] [Accepted: 03/22/2023] [Indexed: 05/16/2023]
Abstract
Plants synthesize tens of thousands of bioactive nitrogen-containing compounds called alkaloids, including some clinically important drugs in modern medicine. The discovery of new alkaloid structures and their metabolism in plants have provided ways to access these rich sources of bioactivities including new-to-nature compounds relevant to therapeutic and industrial applications. This review discusses recent advances in alkaloid biosynthesis discovery, including complete pathway elucidations. Additionally, the latest developments in the production of new and established plant alkaloids based on either biosynthesis or semisynthesis are discussed.
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Affiliation(s)
- Van-Hung Bui
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, 3247 University Way, Kelowna, BC V1V 1V7, Canada
| | - Carlos Eduardo Rodríguez-López
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey, N.L. 64849, Mexico.
| | - Thu-Thuy T Dang
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, 3247 University Way, Kelowna, BC V1V 1V7, Canada.
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26
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De Sousa JPM, Oliveira NCSA, Fernandes PA. Rational Engineering of ( S)-Norcoclaurine Synthase for Efficient Benzylisoquinoline Alkaloids Biosynthesis. Molecules 2023; 28:molecules28114265. [PMID: 37298742 DOI: 10.3390/molecules28114265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/11/2023] [Accepted: 05/20/2023] [Indexed: 06/12/2023] Open
Abstract
(S)-Norcoclaurine is synthesized in vivo through a metabolic pathway that ends with (S)-norcoclaurine synthase (NCS). The former constitutes the scaffold for the biosynthesis of all benzylisoquinoline alkaloids (BIAs), including many drugs such as the opiates morphine and codeine and the semi-synthetic opioids oxycodone, hydrocodone, and hydromorphone. Unfortunately, the only source of complex BIAs is the opium poppy, leaving the drug supply dependent on poppy crops. Therefore, the bioproduction of (S)-norcoclaurine in heterologous hosts, such as bacteria or yeast, is an intense area of research nowadays. The efficiency of (S)-norcoclaurine biosynthesis is strongly dependent on the catalytic efficiency of NCS. Therefore, we identified vital NCS rate-enhancing mutations through the rational transition-state macrodipole stabilization method at the Quantum Mechanics/Molecular Mechanics (QM/MM) level. The results are a step forward for obtaining NCS variants able to biosynthesize (S)-norcoclaurine on a large scale.
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Affiliation(s)
- João P M De Sousa
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Nuno C S A Oliveira
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
| | - Pedro A Fernandes
- LAQV/REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências Universidade do Porto, Rua do Campo Alegre, s/n, 4169-007 Porto, Portugal
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27
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Butler ND, Anderson SR, Dickey RM, Nain P, Kunjapur AM. Combinatorial gene inactivation of aldehyde dehydrogenases mitigates aldehyde oxidation catalyzed by E. coli resting cells. Metab Eng 2023; 77:294-305. [PMID: 37100193 DOI: 10.1016/j.ymben.2023.04.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/11/2023] [Accepted: 04/23/2023] [Indexed: 04/28/2023]
Abstract
Aldehydes are attractive chemical targets both as end products in the flavors and fragrances industry and as intermediates due to their propensity for C-C bond formation. Here, we identify and address unexpected oxidation of a model collection of aromatic aldehydes, including many that originate from biomass degradation. When diverse aldehydes are supplemented to E. coli cells grown under aerobic conditions, as expected they are either reduced by the wild-type MG1655 strain or stabilized by a strain engineered for reduced aromatic aldehyde reduction (the E. coli RARE strain). Surprisingly, when these same aldehydes are supplemented to resting cell preparations of either E. coli strain, under many conditions we observe substantial oxidation. By performing combinatorial inactivation of six candidate aldehyde dehydrogenase genes in the E. coli genome using multiplexed automatable genome engineering (MAGE), we demonstrate that this oxidation can be substantially slowed, with greater than 50% retention of 6 out of 8 aldehydes when assayed 4 h after their addition. Given that our newly engineered strain exhibits reduced oxidation and reduction of aromatic aldehydes, we dubbed it the E. coli ROAR strain. We applied the new strain to resting cell biocatalysis for two kinds of reactions - the reduction of 2-furoic acid to furfural and the condensation of 3-hydroxy-benzaldehyde and glycine to form a beta hydroxylated non-standard amino acid. In each case, we observed substantial improvements in product titer 20 h after reaction initiation (9-fold and 10-fold, respectively). Moving forward, the use of this strain to generate resting cells should allow aldehyde product isolation, further enzymatic conversion, or chemical reactivity under cellular contexts that better accommodate aldehyde toxicity.
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Affiliation(s)
- Neil D Butler
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newar, DE, 19716, USA
| | - Shelby R Anderson
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newar, DE, 19716, USA
| | - Roman M Dickey
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newar, DE, 19716, USA
| | - Priyanka Nain
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newar, DE, 19716, USA
| | - Aditya M Kunjapur
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newar, DE, 19716, USA.
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28
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Pyne ME, Gold ND, Martin VJJ. Pathway elucidation and microbial synthesis of proaporphine and bis-benzylisoquinoline alkaloids from sacred lotus (Nelumbo nucifera). Metab Eng 2023; 77:162-173. [PMID: 37004909 DOI: 10.1016/j.ymben.2023.03.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/07/2023] [Accepted: 03/25/2023] [Indexed: 04/03/2023]
Abstract
Sacred lotus (Nelumbo nucifera) has been utilized as a food, medicine, and spiritual symbol for nearly 3000 years. The medicinal properties of lotus are largely attributed to its unique profile of benzylisoquinoline alkaloids (BIAs), which includes potential anti-cancer, anti-malarial and anti-arrhythmic compounds. BIA biosynthesis in sacred lotus differs markedly from that of opium poppy and other members of the Ranunculales, most notably in an abundance of BIAs possessing the (R)-stereochemical configuration and the absence of reticuline, a major branchpoint intermediate in most BIA producers. Owing to these unique metabolic features and the pharmacological potential of lotus, we set out to elucidate the BIA biosynthesis network in N. nucifera. Here we show that lotus CYP80G (NnCYP80G) and a superior ortholog from Peruvian nutmeg (Laurelia sempervirens; LsCYP80G) stereospecifically convert (R)-N-methylcoclaurine to the proaporphine alkaloid glaziovine, which is subsequently methylated to pronuciferine, the presumed precursor to nuciferine. While sacred lotus employs a dedicated (R)-route to aporphine alkaloids from (R)-norcoclaurine, we implemented an artificial stereochemical inversion approach to flip the stereochemistry of the core BIA pathway. Exploiting the unique substrate specificity of dehydroreticuline synthase from common poppy (Papaver rhoeas) and pairing it with dehydroreticuline reductase enabled de novo synthesis of (R)-N-methylcoclaurine from (S)-norcoclaurine and its subsequent conversion to pronuciferine. We leveraged our stereochemical inversion approach to also elucidate the role of NnCYP80A in sacred lotus metabolism, which we show catalyzes the stereospecific formation of the bis-BIA nelumboferine. Screening our collection of 66 plant O-methyltransferases enabled conversion of nelumboferine to liensinine, a potential anti-cancer bis-BIA from sacred lotus. Our work highlights the unique benzylisoquinoline metabolism of N. nucifera and enables the targeted overproduction of potential lotus pharmaceuticals using engineered microbial systems.
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Affiliation(s)
- Michael E Pyne
- Department of Biology, Concordia University, Montréal, Québec, Canada; Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada.
| | - Nicholas D Gold
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada; Concordia Genome Foundry, Concordia University, Montréal, Québec, Canada
| | - Vincent J J Martin
- Department of Biology, Concordia University, Montréal, Québec, Canada; Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada.
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29
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Elucidation of the (R)-enantiospecific benzylisoquinoline alkaloid biosynthetic pathways in sacred lotus (Nelumbo nucifera). Sci Rep 2023; 13:2955. [PMID: 36805479 PMCID: PMC9940101 DOI: 10.1038/s41598-023-29415-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 02/03/2023] [Indexed: 02/22/2023] Open
Abstract
Benzylisoquinoline alkaloids (BIAs) are a structurally diverse group of plant specialized metabolites found mainly in members of the order Ranunculales, including opium poppy (Papaver somniferum), for which BIA biosynthetic pathways leading to the critical drugs morphine, noscapine, and sanguinarine have been elucidated. Sacred lotus (Nelumbo nucifera), in the order Proteales, accumulates medicinal BIAs in the proaporphine, aporphine, and bisbenzylisoquinoline structural subgroups with a prevalence of R enantiomers, opposed to the dominant S configuration occurring in the Ranunculales. Nevertheless, distinctive BIA biosynthetic routes in sacred lotus have not been explored. In planta labeling experiments and in vitro assays with recombinant enzymes and plant protein extracts showed that dopamine and 4-hydroxyphenylacetaldehyde derived from L-tyrosine serve as precursors for the formation of (R,S)-norcoclaurine in sacred lotus, whereas only (R)-norcoclaurine byproducts are favored in the plant by action of R-enantiospecific methyltransferases and cytochrome P450 oxidoreductases (CYPs). Enzymes responsible for the R-enantiospecific formation of proaporphine (NnCYP80Q1) and bisbenzylisoquinoline (NnCYP80Q2) scaffolds, and a methylenedioxy bridge introduction on aporphine substrates (NnCYP719A22) were identified, whereas additional aspects of the biosynthetic pathways leading to the distinctive alkaloid profile are discussed. This work expands the availability of molecular tools that can be deployed in synthetic biology platforms for the production of high-value alkaloids.
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30
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Ozber N, Yu L, Hagel JM, Facchini PJ. Strong Feedback Inhibition of Key Enzymes in the Morphine Biosynthetic Pathway from Opium Poppy Detectable in Engineered Yeast. ACS Chem Biol 2023; 18:419-430. [PMID: 36735832 DOI: 10.1021/acschembio.2c00873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Systematic screening of morphine pathway intermediates in engineered yeast revealed key biosynthetic enzymes displaying potent feedback inhibition: 3'-hydroxy-N-methylcoclaurine 4'-methyltransferase (4'OMT), which yields (S)-reticuline, and the coupled salutaridinol-7-O-acetyltransferase (SalAT) and thebaine synthase (THS2) enzyme system that produces thebaine. The addition of deuterated reticuline-d1 to a yeast strain able to convert (S)-norcoclaurine to (S)-reticuline showed reduced product accumulation in response to the feeding of all four successive pathway intermediates. Similarly, the addition of deuterated thebaine-d3 to a yeast strain able to convert salutaridine to thebaine showed reduced product accumulation from exogenous salutaridine or salutaridinol. In vitro analysis showed that reticuline is a noncompetitive inhibitor of 4'OMT, whereas thebaine exerts mixed inhibition on SalAT/THS2. In a yeast strain capable of de novo morphine biosynthesis, the addition of reticuline and thebaine resulted in the accumulation of several pathway intermediates. In contrast, morphine had no effect, suggesting that circumventing the interaction of reticuline and thebaine with 4'OMT and SalAT/THS2, respectively, could substantially increase opiate alkaloid titers in engineered yeast.
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Affiliation(s)
- Natali Ozber
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Lisa Yu
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Jillian M Hagel
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
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31
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Abbate E, Andrion J, Apel A, Biggs M, Chaves J, Cheung K, Ciesla A, Clark-ElSayed A, Clay M, Contridas R, Fox R, Hein G, Held D, Horwitz A, Jenkins S, Kalbarczyk K, Krishnamurthy N, Mirsiaghi M, Noon K, Rowe M, Shepherd T, Tarasava K, Tarasow TM, Thacker D, Villa G, Yerramsetty K. Optimizing the strain engineering process for industrial-scale production of bio-based molecules. J Ind Microbiol Biotechnol 2023; 50:kuad025. [PMID: 37656881 PMCID: PMC10548853 DOI: 10.1093/jimb/kuad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 08/29/2023] [Indexed: 09/03/2023]
Abstract
Biomanufacturing could contribute as much as ${\$}$30 trillion to the global economy by 2030. However, the success of the growing bioeconomy depends on our ability to manufacture high-performing strains in a time- and cost-effective manner. The Design-Build-Test-Learn (DBTL) framework has proven to be an effective strain engineering approach. Significant improvements have been made in genome engineering, genotyping, and phenotyping throughput over the last couple of decades that have greatly accelerated the DBTL cycles. However, to achieve a radical reduction in strain development time and cost, we need to look at the strain engineering process through a lens of optimizing the whole cycle, as opposed to simply increasing throughput at each stage. We propose an approach that integrates all 4 stages of the DBTL cycle and takes advantage of the advances in computational design, high-throughput genome engineering, and phenotyping methods, as well as machine learning tools for making predictions about strain scale-up performance. In this perspective, we discuss the challenges of industrial strain engineering, outline the best approaches to overcoming these challenges, and showcase examples of successful strain engineering projects for production of heterologous proteins, amino acids, and small molecules, as well as improving tolerance, fitness, and de-risking the scale-up of industrial strains.
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Affiliation(s)
- Eric Abbate
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Jennifer Andrion
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Amanda Apel
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Matthew Biggs
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Julie Chaves
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Kristi Cheung
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Anthony Ciesla
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Alia Clark-ElSayed
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Michael Clay
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Riarose Contridas
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Richard Fox
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Glenn Hein
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Dan Held
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Andrew Horwitz
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Stefan Jenkins
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | | | | | - Mona Mirsiaghi
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Katherine Noon
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Mike Rowe
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Tyson Shepherd
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Katia Tarasava
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Theodore M Tarasow
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Drew Thacker
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
| | - Gladys Villa
- Inscripta, Inc., 5720 Stoneridge Dr, Suite 300, Pleasanton, CA 94588, USA
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32
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Li B, Wang J, Yuan M, Miao Y, Zhang H, Zhang J. Design, synthesis, and biological evaluation of tetrahydroisoquinoline stilbene derivatives as potential antitumor candidates. Chem Biol Drug Des 2023; 101:364-379. [PMID: 36054251 DOI: 10.1111/cbdd.14134] [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: 03/29/2022] [Revised: 07/31/2022] [Accepted: 08/14/2022] [Indexed: 01/14/2023]
Abstract
Herein, a novel class of tetrahydroisoquinoline stilbene derivatives were synthesized, and their potential in vitro anticancer activities were evaluated. Most of the compounds displayed inhibitory activity against one or more representative human cancer cell lines (lung cancer A549 cells, breast cancer MCF-7 cells, and human colorectal carcinoma HT-29 cells), especially compound 16e, which exhibited outstanding cytotoxicity to A549 cells. The tubulin polymerization assay demonstrated that compound 16e displayed better inhibition than colchicine when tested at the same concentration. It was found that 16e arrested A549 cells in G2/M phase by downregulating the expression of cell division cycle 2 (Cdc2) and upregulating the expression of proliferating cell nuclear antigen (PCNA) and cyclin B1. Flow cytometry and Western blot analysis indicated that 16e caused apoptosis via the mitochondrial-dependent apoptotic pathway by reducing mitochondrial membrane potential, inducing ROS accumulation, promoting the release of cytochrome C from the mitochondria into the cytoplasm, and further increasing the protein level of cleaved caspase-3. This work may inspire new ideas for the further improvement of tubulin-related anticancer drugs and treatments.
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Affiliation(s)
- Bo Li
- Department of Chemistry, Bengbu Medical College, Bengbu, China
| | - Jie Wang
- Department of Chemistry, Bengbu Medical College, Bengbu, China
| | - Ming Yuan
- Department of Chemistry, Bengbu Medical College, Bengbu, China
| | - Yuchen Miao
- Department of Chemistry, Bengbu Medical College, Bengbu, China
| | - Hui Zhang
- Department of Chemistry, Bengbu Medical College, Bengbu, China
| | - Junjie Zhang
- Department of Chemistry, Bengbu Medical College, Bengbu, China
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33
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Ahmadi F, Simchi M, Perry JM, Frenette S, Benali H, Soucy JP, Massarweh G, Shih SCC. Integrating machine learning and digital microfluidics for screening experimental conditions. LAB ON A CHIP 2022; 23:81-91. [PMID: 36416045 DOI: 10.1039/d2lc00764a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Digital microfluidics (DMF) has the signatures of an ideal liquid handling platform - as shown through almost two decades of automated biological and chemical assays. However, in the current state of DMF, we are still limited by the number of parallel biological or chemical assays that can be performed on DMF. Here, we report a new approach that leverages design-of-experiment and numerical methodologies to accelerate experimental optimization on DMF. The integration of the one-factor-at-a-time (OFAT) experimental technique with machine learning algorithms provides a set of recommended optimal conditions without the need to perform a large set of experiments. We applied our approach towards optimizing the radiochemistry synthesis yield given the large number of variables that affect the yield. We believe that this work is the first to combine such techniques which can be readily applied to any other assays that contain many parameters and levels on DMF.
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Affiliation(s)
- Fatemeh Ahmadi
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada.
- PERFORM Centre, Concordia University, 7200 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
| | - Mohammad Simchi
- Department of Mechanical & Industrial Engineering, University of Toronto, 5 King's College Rd, Toronto, Ontario, M5S 3G8, Canada
| | - James M Perry
- PERFORM Centre, Concordia University, 7200 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
| | - Stephane Frenette
- PERFORM Centre, Concordia University, 7200 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
| | - Habib Benali
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada.
- PERFORM Centre, Concordia University, 7200 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
| | - Jean-Paul Soucy
- PERFORM Centre, Concordia University, 7200 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, 3801 University Street, Montréal, Québec, H3A 2B4, Canada
| | - Gassan Massarweh
- McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University, 3801 University Street, Montréal, Québec, H3A 2B4, Canada
| | - Steve C C Shih
- Department of Electrical and Computer Engineering, Concordia University, 1455 de Maisonneuve Blvd. West, Montréal, Québec, H3G 1M8, Canada.
- PERFORM Centre, Concordia University, 7200 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke Street West, Montréal, Québec, H4B 1R6, Canada
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34
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Perrin J, Besseau S, Papon N, Courdavault V. Boosting lignan-precursor synthesis in yeast cell factories through co-factor supply optimization. Front Bioeng Biotechnol 2022; 10:1079801. [DOI: 10.3389/fbioe.2022.1079801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022] Open
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Mukherjee M, Blair RH, Wang ZQ. Machine-learning guided elucidation of contribution of individual steps in the mevalonate pathway and construction of a yeast platform strain for terpenoid production. Metab Eng 2022; 74:139-149. [DOI: 10.1016/j.ymben.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/16/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
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36
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LIU S, YU B, DAI J, CHEN R. Targeting the biological activity and biosynthesis of hyperforin: a mini-review. Chin J Nat Med 2022; 20:721-728. [DOI: 10.1016/s1875-5364(22)60189-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Indexed: 11/03/2022]
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37
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Hanna JN, Ndip RA, Ngemenya MN, Simons CR, Toze FA, Ghogomu SM, Mbah JA. Promising activity of tetrahydroisoquinolines against multidrug-resistant clinical Salmonella isolates and cytotoxicity against monkey kidney cells. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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38
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Scharf MJ, List B. A Catalytic Asymmetric Pictet-Spengler Platform as a Biomimetic Diversification Strategy toward Naturally Occurring Alkaloids. J Am Chem Soc 2022; 144:15451-15456. [PMID: 35976162 PMCID: PMC9446894 DOI: 10.1021/jacs.2c06664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Tetrahydroisoquinoline (THIQ) alkaloids constitute a
large and
diverse class of bioactive natural products, with the parent compounds
and related downstream biosynthetic secondary metabolites spanning
thousands of isolated structures. Chemoenzymatic synthetic approaches
toward the relevant THIQs rely on Pictet–Spenglerases such
as norcoclaurine synthase (NCS), the scope of which is strictly limited
to dopamine-related phenolic substrates. To overcome these limitations
in the context of chemical synthesis, we herein report asymmetric
Pictet–Spengler reactions of N-carbamoyl-β-arylethylamines
with diverse aldehydes toward enantioenriched THIQs. The obtained
products proved to be competent intermediates in the synthesis of
THIQ, aporphine, tetrahydroberberine, morphinan, and androcymbine
natural products. Novel catalyst design with regard to the stabilization
of cationic intermediates was crucial to accomplish high reactivity
while simultaneously achieving unprecedented stereoselectivity for
the reaction of biologically relevant substrates.
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Affiliation(s)
- Manuel J Scharf
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470Mülheim an der Ruhr, Germany
| | - Benjamin List
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470Mülheim an der Ruhr, Germany
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Abstract
Tetrahydropapaverine (THP) and papaverine are plant natural products with clinically significant roles. THP is a precursor in the production of the drugs atracurium and cisatracurium, and papaverine is used as an antispasmodic during vascular surgery. In recent years, metabolic engineering advances have enabled the production of natural products through heterologous expression of pathway enzymes in yeast. Heterologous biosynthesis of THP and papaverine could play a role in ensuring a stable supply of these clinically significant products. Biosynthesis of THP and papaverine has not been achieved to date, in part because multiple pathway enzymes have not been elucidated. Here, we describe the development of an engineered yeast strain for de novo biosynthesis of THP. The production of THP is achieved through heterologous expression of two enzyme variants with activity on nonnative substrates. Through protein engineering, we developed a variant of N-methylcoclaurine hydroxylase with activity on coclaurine, enabling de novo norreticuline biosynthesis. Similarly, we developed a variant of scoulerine 9-O-methyltransferase capable of O-methylating 1-benzylisoquinoline alkaloids at the 3' position, enabling de novo THP biosynthesis. Flux through the heterologous pathway was improved by knocking out yeast multidrug resistance transporters and optimization of media conditions. Overall, strain engineering increased the concentration of biosynthesized THP 600-fold to 121 µg/L. Finally, we demonstrate a strategy for papaverine semisynthesis using hydrogen peroxide as an oxidizing agent. Through optimizing pH, temperature, reaction time, and oxidizing agent concentration, we demonstrated the ability to produce semisynthesized papaverine through oxidation of biosynthesized THP.
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40
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White LV, Hu N, He Y, Banwell MG, Lan P. Expeditious Access to Morphinans by Chemical Synthesis. Angew Chem Int Ed Engl 2022; 61:e202203186. [DOI: 10.1002/anie.202203186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Lorenzo V. White
- Institute for Advanced and Applied Chemical Synthesis Jinan University Guangzhou Guangdong 510632 China
- College of Pharmacy Jinan University Guangzhou Guangdong 510632 China
| | - Nan Hu
- Institute for Advanced and Applied Chemical Synthesis Jinan University Guangzhou Guangdong 510632 China
- College of Pharmacy Jinan University Guangzhou Guangdong 510632 China
| | - Yu‐Tao He
- Institute for Advanced and Applied Chemical Synthesis Jinan University Guangzhou Guangdong 510632 China
- College of Pharmacy Jinan University Guangzhou Guangdong 510632 China
| | - Martin G. Banwell
- Institute for Advanced and Applied Chemical Synthesis Jinan University Guangzhou Guangdong 510632 China
- College of Pharmacy Jinan University Guangzhou Guangdong 510632 China
| | - Ping Lan
- Institute for Advanced and Applied Chemical Synthesis Jinan University Guangzhou Guangdong 510632 China
- College of Pharmacy Jinan University Guangzhou Guangdong 510632 China
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41
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Agnès SA, Okpekon T, Kouadio YA, Jagora A, Bréard D, Costa EV, da Silva FMA, Koolen HHF, Le Ray-Richomme AM, Richomme P, Champy P, Beniddir MA, Le Pogam P. Implementation of a MS/MS database for isoquinoline alkaloids and other annonaceous metabolites. Sci Data 2022; 9:270. [PMID: 35668110 PMCID: PMC9170680 DOI: 10.1038/s41597-022-01345-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 05/04/2022] [Indexed: 12/22/2022] Open
Abstract
This data descriptor reports on the upload to a public repository (GNPS) of the IQAMDB, IsoQuinoline and Annonaceous Metabolites Data Base, comprising 320 tandem mass spectra. This project originated from our in-house collection of isoquinolines. The diversity of compounds included in this database was further extended through the contribution of two additional laboratories involved in isoquinoline alkaloids research: University of Angers and University of Manaus. The generated MS/MS data were processed and annotated on an individual basis to promote their straightforward reuse by natural product chemists interested in either the description of new isoquinoline alkaloids or the dereplication of isoquinoline-containing samples. The interest of the current repertoire for dereplication purposes has been validated based on the molecular networking of the well-investigated plant model Annona montana against the IQAMDB‐implemented GNPS. Measurement(s) | electrospray ionization | Technology Type(s) | Ultra High-performance Liquid Chromatography • Tandem Mass Spectrometry |
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Affiliation(s)
- Salemon Akpa Agnès
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.,Laboratoire de Constitution et Réaction de la Matière (LCRM), UFR Sciences des Structures de la Matière et Technologie, Université Félix Houphouët-Boigny, BP 582, Abidjan 22, Côte d'Ivoire
| | - Timothée Okpekon
- Laboratoire de Constitution et Réaction de la Matière (LCRM), UFR Sciences des Structures de la Matière et Technologie, Université Félix Houphouët-Boigny, BP 582, Abidjan 22, Côte d'Ivoire
| | - Yvette Affoué Kouadio
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.,Laboratoire de Constitution et Réaction de la Matière (LCRM), UFR Sciences des Structures de la Matière et Technologie, Université Félix Houphouët-Boigny, BP 582, Abidjan 22, Côte d'Ivoire
| | - Adrien Jagora
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France
| | | | - Emmanoel V Costa
- Departamento de Química, Universidade Federal do Amazonas, Av. Rodrigo Otávio 1200, 69067-005, Manaus, AM, Brazil
| | - Felipe M A da Silva
- Centro de Apoio Multidisciplinar (CAM), Universidade Federal do Amazonas, Av. Rodrigo Otávio 1200, 69067-005, Manaus, Brazil
| | - Hector H F Koolen
- Grupo de Pesquisa em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas, Av. Carvalho Leal 1777, 69065-001, Manaus, Brazil
| | | | | | - Pierre Champy
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France
| | - Mehdi A Beniddir
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France
| | - Pierre Le Pogam
- Équipe "Chimie des Substances Naturelles" Université Paris-Saclay, CNRS, BioCIS, 5 rue J.-B. Clément, 92290, Châtenay-Malabry, France.
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42
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Bean BDM, Mulvihill CJ, Garge RK, Boutz DR, Rousseau O, Floyd BM, Cheney W, Gardner EC, Ellington AD, Marcotte EM, Gollihar JD, Whiteway M, Martin VJJ. Functional expression of opioid receptors and other human GPCRs in yeast engineered to produce human sterols. Nat Commun 2022; 13:2882. [PMID: 35610225 PMCID: PMC9130329 DOI: 10.1038/s41467-022-30570-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 05/09/2022] [Indexed: 12/12/2022] Open
Abstract
The yeast Saccharomyces cerevisiae is powerful for studying human G protein-coupled receptors as they can be coupled to its mating pathway. However, some receptors, including the mu opioid receptor, are non-functional, which may be due to the presence of the fungal sterol ergosterol instead of cholesterol. Here we engineer yeast to produce cholesterol and introduce diverse mu, delta, and kappa opioid receptors to create sensitive opioid biosensors that recapitulate agonist binding profiles and antagonist inhibition. Additionally, human mu opioid receptor variants, including those with clinical relevance, largely display expected phenotypes. By testing mu opioid receptor-based biosensors with systematically adjusted cholesterol biosynthetic intermediates, we relate sterol profiles to biosensor sensitivity. Finally, we apply sterol-modified backgrounds to other human receptors revealing sterol influence in SSTR5, 5-HTR4, FPR1, and NPY1R signaling. This work provides a platform for generating human G protein-coupled receptor-based biosensors, facilitating receptor deorphanization and high-throughput screening of receptors and effectors.
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Affiliation(s)
- Björn D M Bean
- Department of Biology, Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B1R6, Canada
| | - Colleen J Mulvihill
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Riddhiman K Garge
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Daniel R Boutz
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, 78712, USA
- DEVCOM Army Research Laboratory-South, Austin, 78712, TX, USA
| | - Olivier Rousseau
- Department of Biology, Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B1R6, Canada
| | - Brendan M Floyd
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - William Cheney
- Department of Biology, Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B1R6, Canada
| | - Elizabeth C Gardner
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Andrew D Ellington
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Edward M Marcotte
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Jimmy D Gollihar
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX, 78712, USA.
- DEVCOM Army Research Laboratory-South, Austin, 78712, TX, USA.
- Center for Molecular and Translational Human Infectious Diseases Research, Department of Pathology and Genomic Medicine, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, TX, USA.
| | - Malcolm Whiteway
- Department of Biology, Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B1R6, Canada
| | - Vincent J J Martin
- Department of Biology, Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, H4B1R6, Canada.
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43
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Kumar B, Babu JN, Chowhan LR. Sustainable Synthesis of Highly Diastereoselective & Fluorescent Active Spirooxindoles Catalyzed by Copper Oxide Nanoparticle Immobilized on Microcrystalline Cellulose. Appl Organomet Chem 2022. [DOI: 10.1002/aoc.6742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Bhupender Kumar
- School for Applied Material Sciences Central University of Gujarat, Sector 30 Gandhinagar Gujarat India
| | - J. Nagendra Babu
- Department of Chemistry School for Basic and Applied Sciences, Central University of Punjab, VPO Ghudda Bathinda Punjab India
| | - L. Raju Chowhan
- School for Applied Material Sciences Central University of Gujarat, Sector 30 Gandhinagar Gujarat India
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44
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Kumokita R, Bamba T, Inokuma K, Yoshida T, Ito Y, Kondo A, Hasunuma T. Construction of an l-Tyrosine Chassis in Pichia pastoris Enhances Aromatic Secondary Metabolite Production from Glycerol. ACS Synth Biol 2022; 11:2098-2107. [PMID: 35575690 DOI: 10.1021/acssynbio.2c00047] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Bioactive plant-based secondary metabolites such as stilbenoids, flavonoids, and benzylisoquinoline alkaloids (BIAs) are produced from l-tyrosine (l-Tyr) and have a wide variety of commercial applications. Therefore, building a microorganism with high l-Tyr productivity (l-Tyr chassis) is of immense value for large-scale production of various aromatic compounds. The aim of this study was to develop an l-Tyr chassis in the nonconventional yeast Pichia pastoris (Komagataella phaffii) to produce various aromatic secondary metabolites (resveratrol, naringenin, norcoclaurine, and reticuline). Overexpression of feedback-inhibition insensitive variants of 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase (ARO4K229L) and chorismate mutase (ARO7G141S) enhanced l-Tyr titer from glycerol in P. pastoris. These engineered P. pastoris strains increased the titer of resveratrol, naringenin, and norcoclaurine by 258, 244, and 3400%, respectively, after expressing the corresponding heterologous pathways. The titer of resveratrol and naringenin further increased by 305 and 249%, resulting in yields of 1825 and 1067 mg/L, respectively, in fed-batch fermentation, which is the highest titer from glycerol reported to date. Furthermore, the resveratrol-producing strain accumulated intermediates in the shikimate pathway. l-Tyr-derived aromatic compounds were produced using crude glycerol byproducts from biodiesel fuel (BDF) production. Constructing an l-Tyr chassis is a promising strategy to increase the titer of various aromatic secondary metabolites and P. pastoris is an attractive host for high-yield production of l-Tyr-derived aromatic compounds from glycerol.
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Affiliation(s)
- Ryota Kumokita
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Takahiro Bamba
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Kentaro Inokuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Takanobu Yoshida
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Yoichiro Ito
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Biomass Engineering Program, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
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45
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Nasr M, Timmins LR, Martin VJJ, Kwan DH. A Versatile Transcription Factor Biosensor System Responsive to Multiple Aromatic and Indole Inducers. ACS Synth Biol 2022; 11:1692-1698. [PMID: 35316041 PMCID: PMC9017570 DOI: 10.1021/acssynbio.2c00063] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Allosteric transcription factor (aTF) biosensors are valuable tools for engineering microbes toward a multitude of applications in metabolic engineering, biotechnology, and synthetic biology. One of the challenges toward constructing functional and diverse biosensors in engineered microbes is the limited toolbox of identified and characterized aTFs. To overcome this, extensive bioprospecting of aTFs from sequencing databases, as well as aTF ligand-specificity engineering are essential in order to realize their full potential as biosensors for novel applications. In this work, using the TetR-family repressor CmeR from Campylobacter jejuni, we construct aTF genetic circuits that function as salicylate biosensors in the model organisms Escherichia coli and Saccharomyces cerevisiae. In addition to salicylate, we demonstrate the responsiveness of CmeR-regulated promoters to multiple aromatic and indole inducers. This relaxed ligand specificity of CmeR makes it a useful tool for detecting molecules in many metabolic engineering applications, as well as a good target for directed evolution to engineer proteins that are able to detect new and diverse chemistries.
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Affiliation(s)
- Mohamed
A. Nasr
- Department
of Biology, Centre for Applied Synthetic Biology, and Centre for Structural
and Functional Genomics, Concordia University, Montréal, Quebec H4B 1R6, Canada
- PROTEO,
Quebec Network for Research on Protein Function, Structure, and Engineering, Québec City, Quebec G1 V 0A6, Canada
| | - Logan R. Timmins
- Department
of Biology, Centre for Applied Synthetic Biology, and Centre for Structural
and Functional Genomics, Concordia University, Montréal, Quebec H4B 1R6, Canada
- PROTEO,
Quebec Network for Research on Protein Function, Structure, and Engineering, Québec City, Quebec G1 V 0A6, Canada
| | - Vincent J. J. Martin
- Department
of Biology, Centre for Applied Synthetic Biology, and Centre for Structural
and Functional Genomics, Concordia University, Montréal, Quebec H4B 1R6, Canada
| | - David H. Kwan
- Department
of Biology, Centre for Applied Synthetic Biology, and Centre for Structural
and Functional Genomics, Concordia University, Montréal, Quebec H4B 1R6, Canada
- PROTEO,
Quebec Network for Research on Protein Function, Structure, and Engineering, Québec City, Quebec G1 V 0A6, Canada
- Department
of Chemistry and Biochemistry, Concordia
University, Montréal, Quebec H4B 1R6, Canada
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46
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White LV, Hu N, He YT, Banwell M, Lan P. Expeditious Access to Morphinans by Chemical Synthesis. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | - Nan Hu
- Jinan University IAACS CHINA
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47
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Tran VH, Kim HK. Facile tin(II)-catalyzed synthesis of N-heterocycles from dicarboxylic acids and arylamines. Org Biomol Chem 2022; 20:2881-2888. [PMID: 35318478 DOI: 10.1039/d2ob00330a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel efficient transformation reaction of dicarboxylic acids into N-aryl-substituted azacycles is described. In this synthetic procedure, both catalytic SnCl2 and phenylsilane were used as crucial reagents for reaction of arylamines with dicarboxylic acids to produce the desired azacycles. Using this SnCl2-catalyzed synthetic method, various N-aryl-substituted azacycles were successfully prepared from arylamines with dicarboxylic acids in high yield. This practical synthetic method using catalytic SnCl2 can provide a useful approach for preparation of the desired azacycle products from many available dicarboxylic acid starting materials.
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Affiliation(s)
- Van Hieu Tran
- Department of Nuclear Medicine, Molecular Imaging & Therapeutic Medicine Research Center, Jeonbuk National University Medical School and Hospital, Jeonju, 54907, Republic of Korea. .,Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, 54907, Republic of Korea
| | - Hee-Kwon Kim
- Department of Nuclear Medicine, Molecular Imaging & Therapeutic Medicine Research Center, Jeonbuk National University Medical School and Hospital, Jeonju, 54907, Republic of Korea. .,Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, 54907, Republic of Korea
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Biotechnological production of specialty aromatic and aromatic-derivative compounds. World J Microbiol Biotechnol 2022; 38:80. [PMID: 35338395 DOI: 10.1007/s11274-022-03263-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 03/05/2022] [Indexed: 10/18/2022]
Abstract
Aromatic compounds are an important class of chemicals with different industrial applications. They are usually produced by chemical synthesis from petroleum-derived feedstocks, such as toluene, xylene and benzene. However, we are now facing threats from the excessive use of fossil fuels causing environmental problems such as global warming. Furthermore, fossil resources are not infinite, and will ultimately be depleted. To cope with these problems, the sustainable production of aromatic chemicals from renewable non-food biomass is urgent. With this in mind, the search for alternative methodologies to produce aromatic compounds using low-cost and environmentally friendly processes is becoming more and more important. Microorganisms are able to produce aromatic and aromatic-derivative compounds from sugar-based carbon sources. Metabolic engineering strategies as well as bioprocess optimization enable the development of microbial cell factories capable of efficiently producing aromatic compounds. This review presents current breakthroughs in microbial production of specialty aromatic and aromatic-derivative products, providing an overview on the general strategies and methodologies applied to build microbial cell factories for the production of these compounds. We present and describe some of the current challenges and gaps that must be overcome in order to render the biotechnological production of specialty aromatic and aromatic-derivative attractive and economically feasible at industrial scale.
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Qiu Z, Liu X, Li J, Qiao B, Zhao GR. Metabolic Division in an Escherichia coli Coculture System for Efficient Production of Kaempferide. ACS Synth Biol 2022; 11:1213-1227. [PMID: 35167258 DOI: 10.1021/acssynbio.1c00510] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kaempferide, a plant-derived natural flavonoid, exhibits excellent pharmacological activities with nutraceutical and medicinal applications in human healthcare. Efficient microbial production of complex flavonoids suffers from metabolic crosstalk and burden, which is a big challenge for synthetic biology. Herein, we identified 4'-O-methyltransferases and divided the artificial biosynthetic pathway of kaempferide into upstream, midstream, and downstream modules. By combining heterologous genes from different sources and fine-tuning the expression, we optimized each module for the production of kaempferide. Furthermore, we designed and evaluated four division patterns of synthetic labor in coculture systems by plug-and-play modularity. The linear division of three modules in a three-strain coculture showed higher productivity of kaempferide than that in two-strain cocultures. The U-shaped division by co-distributing the upstream and downstream modules in one strain led to the best performance of the coculture system, which produced 116.0 ± 3.9 mg/L kaempferide, which was 510, 140, and 50% higher than that produced by the monoculture, two-strain coculture, and three-strain coculture with the linear division, respectively. This is the first report of efficient de novo production of kaempferide in a robust Escherichia coli coculture. The strategy of U-shaped pathway division in the coculture provides a promising way for improving the productivity of valuable and complex natural products.
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Affiliation(s)
- Zetian Qiu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
- Georgia Tech Shenzhen Institute, Tianjin University, Dashi Road 1, Nanshan
District, Shenzhen 518055, China
| | - Xue Liu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
- Georgia Tech Shenzhen Institute, Tianjin University, Dashi Road 1, Nanshan
District, Shenzhen 518055, China
| | - Jia Li
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
- Georgia Tech Shenzhen Institute, Tianjin University, Dashi Road 1, Nanshan
District, Shenzhen 518055, China
| | - Bin Qiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
| | - Guang-Rong Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
- Georgia Tech Shenzhen Institute, Tianjin University, Dashi Road 1, Nanshan
District, Shenzhen 518055, China
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Machine learning discovery of missing links that mediate alternative branches to plant alkaloids. Nat Commun 2022; 13:1405. [PMID: 35296652 PMCID: PMC8927377 DOI: 10.1038/s41467-022-28883-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 02/16/2022] [Indexed: 01/12/2023] Open
Abstract
Engineering the microbial production of secondary metabolites is limited by the known reactions of correctly annotated enzymes. Therefore, the machine learning discovery of specialized enzymes offers great potential to expand the range of biosynthesis pathways. Benzylisoquinoline alkaloid production is a model example of metabolic engineering with potential to revolutionize the paradigm of sustainable biomanufacturing. Existing bacterial studies utilize a norlaudanosoline pathway, whereas plants contain a more stable norcoclaurine pathway, which is exploited in yeast. However, committed aromatic precursors are still produced using microbial enzymes that remain elusive in plants, and additional downstream missing links remain hidden within highly duplicated plant gene families. In the current study, machine learning is applied to predict and select plant missing link enzymes from homologous candidate sequences. Metabolomics-based characterization of the selected sequences reveals potential aromatic acetaldehyde synthases and phenylpyruvate decarboxylases in reconstructed plant gene-only benzylisoquinoline alkaloid pathways from tyrosine. Synergistic application of the aryl acetaldehyde producing enzymes results in enhanced benzylisoquinoline alkaloid production through hybrid norcoclaurine and norlaudanosoline pathways. Producing plant secondary metabolites by microbes is limited by the known enzymatic reactions. Here, the authors apply machine learning to predict missing link enzymes of benzylisoquinoline alkaloid (BIA) biosynthesis in Papaver somniferum, and validate the specialized activities through heterologous production.
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