1
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Watanabe Y, Hashishin T, Sato H, Matsuyama T, Nakajima M, Haruta JI, Uchiyama M. DFT Study on Retigerane-Type Sesterterpenoid Biosynthesis: Initial Conformation of GFPP Regulates Biosynthetic Pathway, Ring-Construction Order and Stereochemistry. JACS AU 2024; 4:3484-3491. [PMID: 39328767 PMCID: PMC11423320 DOI: 10.1021/jacsau.4c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/29/2024] [Accepted: 07/01/2024] [Indexed: 09/28/2024]
Abstract
Retigerane-type sesterterpenoids, which feature a unique 5/6/5/5/5 fused pentacyclic structure with an angular-type triquinane moiety, are biosynthesized via successive carbocation-mediated reactions triggered by terpene cyclases. However, the precise biosynthetic pathways/mechanisms, wherein steric inversion of the carbon skeleton occurs at least once, remain elusive. Two plausible reaction pathways have been proposed, which differ in the order of ring cyclization: A → B/C → D/E-ring(s) (Route 1) and A → E → B → C/D-ring(s) (Route 2). Since the reaction intermediates of these complicated domino-type reaction sequences are experimentally inaccessible, we employed comprehensive density functional theory (DFT) calculations to evaluate these routes. The results indicate that retigeranin biosynthesis proceeds via Route 2 involving a multistep carbocation cascade, in which the order of ring cyclization (A → E → B → C/D) is the key to constructing the angular 5/5/5 triquinane structure with the correct stereochemistry at C3. The result also suggests that slight differences in the initial conformation have a significant effect on the order of cyclization and steric inversion. The computed pathway/mechanism also provides a rational basis for the formation of various related terpenes/terpenoids.
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Affiliation(s)
- Yuichiro Watanabe
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Graduate
School of Pharmaceutical Sciences, Osaka
University, Suita-shi, Osaka 565-0871, Japan
| | - Takahiro Hashishin
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hajime Sato
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Interdisciplinary
Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Yamanashi 400-8510, Japan
| | - Taro Matsuyama
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masaya Nakajima
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Jun-ichi Haruta
- Graduate
School of Pharmaceutical Sciences, Osaka
University, Suita-shi, Osaka 565-0871, Japan
| | - Masanobu Uchiyama
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Research
Initiative for Supra-Materials (RISM), Shinshu
University, 3-15-1 Tokida, Ueda, Nagano 386-8567, Japan
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2
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Li J, Chen B, Fu Z, Mao J, Liu L, Chen X, Zheng M, Wang CY, Wang C, Guo YW, Xu B. Discovery of a terpene synthase synthesizing a nearly non-flexible eunicellane reveals the basis of flexibility. Nat Commun 2024; 15:5940. [PMID: 39009563 PMCID: PMC11250809 DOI: 10.1038/s41467-024-50209-z] [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: 02/05/2024] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
Eunicellane diterpenoids, containing a typical 6,10-bicycle, are bioactive compounds widely present in marine corals, but rarely found in bacteria and plants. The intrinsic macrocycle exhibits innate structural flexibility resulting in dynamic conformational changes. However, the mechanisms controlling flexibility remain unknown. The discovery of a terpene synthase, MicA, that is responsible for the biosynthesis of a nearly non-flexible eunicellane skeleton, enable us to propose a feasible theory about the flexibility in eunicellane structures. Parallel studies of all eunicellane synthases in nature discovered to date, including 2Z-geranylgeranyl diphosphate incubations and density functional theory-based Boltzmann population computations, reveale that a trans-fused bicycle with a 2Z-configuration alkene restricts conformational flexibility resulting in a nearly non-flexible eunicellane skeleton. The catalytic route and the enzymatic mechanism of MicA are also elucidated by labeling experiments, density functional theory calculations, structural analysis of the artificial intelligence-based MicA model, and mutational studies.
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Affiliation(s)
- Jinfeng Li
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong, 264117, China
- Key Laboratory of Marine Drugs, The Ministry of Education of China, Institute of Evolution & Marine Biodiversity, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Bao Chen
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong, 264117, China
| | - Zunyun Fu
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhangjiang Hi-Tech Park, Shanghai, 201203, China
| | - Jingjing Mao
- CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Shanghai, 200031, China
- Department of Pathogen Biology, School of Medicine and Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Lijun Liu
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong, 264117, China
| | - Xiaochen Chen
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong, 264117, China
| | - Mingyue Zheng
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhangjiang Hi-Tech Park, Shanghai, 201203, China
| | - Chang-Yun Wang
- Key Laboratory of Marine Drugs, The Ministry of Education of China, Institute of Evolution & Marine Biodiversity, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China.
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Chengyuan Wang
- CAS Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Shanghai, 200031, China.
| | - Yue-Wei Guo
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong, 264117, China.
- School of Medicine, Shanghai University, Shanghai, 200444, China.
| | - Baofu Xu
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong, 264117, China.
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhangjiang Hi-Tech Park, Shanghai, 201203, China.
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3
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Li W, Chen Y, Yang R, Hu Z, Wei S, Hu S, Xiong X, Wang M, Lubeiny A, Li X, Feng M, Dong S, Xie X, Nie C, Zhang J, Luo Y, Zhou Y, Liu R, Pan J, Kong DX, Hu X. A terpenoids database with the chemical content as a novel agronomic trait. Database (Oxford) 2024; 2024:baae027. [PMID: 38776380 PMCID: PMC11110934 DOI: 10.1093/database/baae027] [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: 07/28/2023] [Revised: 12/02/2023] [Accepted: 05/18/2024] [Indexed: 05/25/2024]
Abstract
Natural products play a pivotal role in drug discovery, and the richness of natural products, albeit significantly influenced by various environmental factors, is predominantly determined by intrinsic genetics of a series of enzymatic reactions and produced as secondary metabolites of organisms. Heretofore, few natural product-related databases take the chemical content into consideration as a prominent property. To gain unique insights into the quantitative diversity of natural products, we have developed the first TerPenoids database embedded with Content information (TPCN) with features such as compound browsing, structural search, scaffold analysis, similarity analysis and data download. This database can be accessed through a web-based computational toolkit available at http://www.tpcn.pro/. By conducting meticulous manual searches and analyzing over 10 000 reference papers, the TPCN database has successfully integrated 6383 terpenoids obtained from 1254 distinct plant species. The database encompasses exhaustive details including isolation parts, comprehensive molecule structures, chemical abstracts service registry number (CAS number) and 7508 content descriptions. The TPCN database accentuates both the qualitative and quantitative dimensions as invaluable phenotypic characteristics of natural products that have undergone genetic evolution. By acting as an indispensable criterion, the TPCN database facilitates the discovery of drug alternatives with high content and the selection of high-yield medicinal plant species or phylogenetic alternatives, thereby fostering sustainable, cost-effective and environmentally friendly drug discovery in pharmaceutical farming. Database URL: http://www.tpcn.pro/.
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Affiliation(s)
- Wenqian Li
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Yinliang Chen
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruofei Yang
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Zilong Hu
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Shaozhong Wei
- Colorectal cancer clinical research center of HuBei Province,Colorectal cancer clinical research center of Wuhan, Hubei Cancer Hospital,Tongji Medical College, Huazhong University of Science and Technology,, Wuhan, Hubei 430069, China
| | - Sheng Hu
- Colorectal cancer clinical research center of HuBei Province,Colorectal cancer clinical research center of Wuhan, Hubei Cancer Hospital,Tongji Medical College, Huazhong University of Science and Technology,, Wuhan, Hubei 430069, China
| | - Xinjun Xiong
- Research Center for Rural Revitalization, Power China Kunming Engineering Corporation Limited, Kunming 650051, China
| | - Meijuan Wang
- Shennongjia Academy of Forestry, Shennongjia, Hubei 442400 China
| | | | - Xiaohua Li
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Minglei Feng
- Research Center for Rural Revitalization, Power China Kunming Engineering Corporation Limited, Kunming 650051, China
| | - Shuang Dong
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Xinlu Xie
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Chao Nie
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Jingyi Zhang
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Yunhao Luo
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Yichen Zhou
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Ruodi Liu
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinhai Pan
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
| | - De-Xin Kong
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuebo Hu
- Institute for Medicinal Plants, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Innovation Academy of International Traditional Chinese Medicinal Materials, Huazhong Agricultural University, Wuhan 430070, China
- National-Regional Joint Engineering Research Center in Hubei for Medicinal Plant Breeding and Cultivation, Huazhong Agricultural University, Wuhan 430070, China
- Medicinal Plant Engineering Research Center of Hubei Province, Huazhong Agricultural University, Wuhan 430070, China
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4
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Yang L, Wang H, Lang M, Wang J, Peng S. B(C 6F 5) 3-Catalyzed Formal ( n + 3) ( n = 5 and 6) Cycloaddition of Bicyclo[1.1.0]butanes to Medium Bicyclo[ n.1.1]alkanes. Org Lett 2024; 26:4104-4110. [PMID: 38700913 DOI: 10.1021/acs.orglett.4c01219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Herein, a B(C6F5)3-catalyzed formal (n + 3) (n = 5 and 6) cycloaddition of bicyclo[1.1.0]butanes (BCBs) with imidazolidines/hexahydropyrimidines is described. The reaction provides a modular, atom-economical, and efficient strategy to two libraries of synthetically challenging medium-bridged rings, 2,5-diazabicyclo[5.1.1]nonanes and 2,6-diazabicyclo[6.1.1]decanes, in moderate to excellent yields. This reaction also features simple operation, mild reaction conditions, and broad substrate scope. A scale-up experiment and various synthetic transformations of products further highlight the synthetic utility.
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Affiliation(s)
- Liangliang Yang
- School of Pharmacy and Food Engineering, Wuyi University, Jiangmen, Guangdong 529020, People's Republic of China
| | - Haiyang Wang
- School of Pharmacy and Food Engineering, Wuyi University, Jiangmen, Guangdong 529020, People's Republic of China
| | - Ming Lang
- School of Pharmacy and Food Engineering, Wuyi University, Jiangmen, Guangdong 529020, People's Republic of China
| | - Jian Wang
- School of Pharmacy and Food Engineering, Wuyi University, Jiangmen, Guangdong 529020, People's Republic of China
- School of Pharmaceutical Sciences, Key Laboratory of Bioorganic Phosphorous Chemistry & Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, People's Republic of China
| | - Shiyong Peng
- School of Pharmacy and Food Engineering, Wuyi University, Jiangmen, Guangdong 529020, People's Republic of China
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5
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Wang X, Zhang J, Lu X, Bai Y, Wang G. Two diversities meet in the rhizosphere: root specialized metabolites and microbiome. J Genet Genomics 2024; 51:467-478. [PMID: 37879496 DOI: 10.1016/j.jgg.2023.10.004] [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: 06/15/2023] [Revised: 10/15/2023] [Accepted: 10/15/2023] [Indexed: 10/27/2023]
Abstract
Plants serve as rich repositories of diverse chemical compounds collectively referred to as specialized metabolites. These compounds are of importance for adaptive processes, including interactions with various microbes both beneficial and harmful. Considering microbes as bioreactors, the chemical diversity undergoes dynamic changes when root-derived specialized metabolites (RSMs) and microbes encounter each other in the rhizosphere. Recent advancements in sequencing techniques and molecular biology tools have not only accelerated the elucidation of biosynthetic pathways of RSMs but also unveiled the significance of RSMs in plant-microbe interactions. In this review, we provide a comprehensive description of the effects of RSMs on microbe assembly in the rhizosphere and the influence of corresponding microbial changes on plant health, incorporating the most up-to-date information available. Additionally, we highlight open questions that remain for a deeper understanding of and harnessing the potential of RSM-microbe interactions to enhance plant adaptation to the environment. Finally, we propose a pipeline for investigating the intricate associations between root exometabolites and the rhizomicrobiome.
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Affiliation(s)
- Xiaochen Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Xinjun Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China.
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China.
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6
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Wei G, Chen Y, Wang J, Feng L. Molecular cloning and characterization of farnesyl diphosphate synthase from Rosa rugosa Thunb associated with salinity stress. PeerJ 2024; 12:e16929. [PMID: 38435988 PMCID: PMC10909355 DOI: 10.7717/peerj.16929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 01/22/2024] [Indexed: 03/05/2024] Open
Abstract
Rosa rugosa, a renowned ornamental plant, is cultivated for its essential oil containing valuable monoterpenes, sesquiterpenes, and other compounds widely used in the floriculture industry. Farnesyl diphosphate synthase (FPPS) is a key enzyme involved in the biosynthesis of sesquiterpenes and triterpenes for abiotic or biotic stress. In this study, we successfully cloned and characterized a full-length FPPS- encoding cDNA identified as RrFPPS1 using RT-PCR from R. rugosa. Phylogenetic analysis showed that RrFPPS1 belonged to the angiosperm-FPPS clade. Transcriptomic and RT-qPCR analyses revealed that the RrFPPS1 gene had tissue-specific expression patterns. Subcellular localization analysis using Nicotiana benthamiana leaves showed that RrFPPS1 was a cytoplasmic protein. In vitro enzymatic assays combined with GC-MS analysis showed that RrFPPS1 produced farnesyl diphosphate (FPP) using isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) as substrates to provide a precursor for sesquiterpene and triterpene biosynthesis in the plant. Additionally, our research found that RrFPPS1 was upregulated under salt treatment. These substantial findings contribute to an improved understanding of terpene biosynthesis in R. rugosa and open new opportunities for advancements in horticultural practices and fragrance industries by overexpression of the RrFPPS1 gene in vivo increased FPP production and subsequently led to elevated sesquiterpene yields in the future. The knowledge gained from this study can potentially lead to the development of enhanced varieties of R. rugosa with improved aroma, medicinal properties, and resilience to environmental stressors.
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Affiliation(s)
- Guo Wei
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Yudie Chen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Jianwen Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
| | - Liguo Feng
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, China
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7
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Wei G, Xu Y, Xu M, Shi X, Wang J, Feng L. Identification of Volatile Compounds and Terpene Synthase ( TPS) Genes Reveals ZcTPS02 Involved in β-Ocimene Biosynthesis in Zephyranthes candida. Genes (Basel) 2024; 15:185. [PMID: 38397175 PMCID: PMC10887521 DOI: 10.3390/genes15020185] [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: 12/12/2023] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
Zephyranthes candida is a frequently cultivated ornamental plant containing several secondary metabolites, including alkaloids, flavonoids, and volatile organic compounds (VOCs). However, extensive research has been conducted only on non-VOCs found in the plant, whereas the production of VOCs and the molecular mechanisms underlying the biosynthesis of terpenes remain poorly understood. In this study, 17 volatile compounds were identified from Z. candida flowers using gas chromatography-mass spectrometry (GC-MS), with 16 of them being terpenoids. Transcriptome sequencing resulted in the identification of 17 terpene synthase (TPS) genes; two TPS genes, ZcTPS01 and ZcTPS02, had high expression levels. Biochemical characterization of two enzymes encoded by both genes revealed that ZcTPS02 can catalyze geranyl diphosphate (GPP) into diverse products, among which is β-ocimene, which is the second most abundant compound found in Z. candida flowers. These results suggest that ZcTPS02 plays a vital role in β-ocimene biosynthesis, providing valuable insights into terpene biosynthesis pathways in Z. candida. Furthermore, the expression of ZcTPS02 was upregulated after 2 h of methyl jasmonate (MeJA) treatment and downregulated after 4 h of the same treatment.
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Affiliation(s)
| | | | | | | | | | - Liguo Feng
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (G.W.); (Y.X.); (M.X.); (X.S.); (J.W.)
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8
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Zhou Q, Sun P, Xiong HM, Xie J, Zhu GY, Tantillo DJ, Huang AC. Insight into neofunctionalization of 2,3-oxidosqualene cyclases in B,C-ring-opened triterpene biosynthesis in quinoa. THE NEW PHYTOLOGIST 2024; 241:764-778. [PMID: 37904576 DOI: 10.1111/nph.19345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 10/04/2023] [Indexed: 11/01/2023]
Abstract
Bioactive triterpenes feature complex fused-ring structures, primarily shaped by the first-committed enzyme, 2,3-oxidosqualene cyclases (OSCs) in plant triterpene biosynthesis. Triterpenes with B,C-ring-opened skeletons are extremely rare with unknown formation mechanisms, harbouring unchartered chemistry and biology. Here, through mining the genome of Chenopodium quinoa followed by functional characterization, we identified a stress-responsive and neofunctionalized OSC capable of generating B,C-ring-opened triterpenes, including camelliol A and B and the novel (-)-quinoxide A as wax components of the specialized epidermal bladder cells, namely the quinoxide synthase (CqQS). Protein structure analysis followed by site-directed mutagenesis identified key variable amino acid sites underlying functional interconversion between pentacyclic β-amyrin synthase (CqbAS1) and B,C-ring-opened triterpene synthase CqQS. Mutation of one key residue (N612K) in even evolutionarily distant Arabidopsis β-amyrin synthase could generate quinoxides, indicating a conserved mechanism for B,C-ring-opened triterpene formation in plants. Quantum computation combined with docking experiments further suggests that conformations of conserved W613 and F413 of CqQS might be key to selectively stabilizing intermediate carbocations towards B,C-ring-opened triterpene formation. Our findings shed light on quinoa triterpene skeletal diversity and mechanisms underlying B,C-ring-opened triterpene biosynthesis, opening avenues towards accessing their chemistry and biology and paving the way for quinoa trait engineering and quality improvement.
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Affiliation(s)
- Qian Zhou
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Peng Sun
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Hao-Ming Xiong
- State Key Laboratory of Quality Research in Chinese Medicine, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, 999078, China
| | - Jiali Xie
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Guo-Yuan Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, 999078, China
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Ancheng C Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
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9
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Nickles GR, Oestereicher B, Keller NP, Drott M. Mining for a new class of fungal natural products: the evolution, diversity, and distribution of isocyanide synthase biosynthetic gene clusters. Nucleic Acids Res 2023; 51:7220-7235. [PMID: 37427794 PMCID: PMC10415135 DOI: 10.1093/nar/gkad573] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 06/16/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023] Open
Abstract
The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We amalgamated a pipeline of tools to predict BGCs based on shared promoter motifs and located 3800 ICS BGCs in 3300 genomes, making ICS BGCs the fifth largest class of specialized metabolites compared to canonical classes found by antiSMASH. ICS BGCs are not evenly distributed across fungi, with evidence of gene-family expansions in several Ascomycete families. We show that the ICS dit1/2 gene cluster family (GCF), which was prior only studied in yeast, is present in ∼30% of all Ascomycetes. The dit variety ICS exhibits greater similarity to bacterial ICS than other fungal ICS, suggesting a potential convergence of the ICS backbone domain. The evolutionary origins of the dit GCF in Ascomycota are ancient and these genes are diversifying in some lineages. Our results create a roadmap for future research into ICS BGCs. We developed a website (https://isocyanides.fungi.wisc.edu/) that facilitates the exploration and downloading of all identified fungal ICS BGCs and GCFs.
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Affiliation(s)
- Grant R Nickles
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
| | | | - Nancy P Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Plant Pathology, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - Milton T Drott
- USDA-ARS Cereal Disease Lab (CDL), St. Paul, MN 55108, USA
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10
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Jha P, Kaur T, Chhabra I, Panja A, Paul S, Kumar V, Malik T. Endophytic fungi: hidden treasure chest of antimicrobial metabolites interrelationship of endophytes and metabolites. Front Microbiol 2023; 14:1227830. [PMID: 37497538 PMCID: PMC10366620 DOI: 10.3389/fmicb.2023.1227830] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 06/26/2023] [Indexed: 07/28/2023] Open
Abstract
Endophytic fungi comprise host-associated fungal communities which thrive within the tissues of host plants and produce a diverse range of secondary metabolites with various bioactive attributes. The metabolites such as phenols, polyketides, saponins, alkaloids help to mitigate biotic and abiotic stresses, fight against pathogen attacks and enhance the plant immune system. We present an overview of the association of endophytic fungal communities with a plant host and discuss molecular mechanisms induced during their symbiotic interaction. The overview focuses on the secondary metabolites (especially those of terpenoid nature) secreted by endophytic fungi and their respective function. The recent advancement in multi-omics approaches paved the way for identification of these metabolites and their characterization via comparative analysis of extensive omics datasets. This study also elaborates on the role of diverse endophytic fungi associated with key agricultural crops and hence important for sustainability of agriculture.
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Affiliation(s)
- Priyanka Jha
- Department of Biotechnology, Lovely Faculty of Technology and Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Tamanna Kaur
- Department of Biotechnology, Lovely Faculty of Technology and Sciences, Lovely Professional University, Phagwara, Punjab, India
| | | | - Avirup Panja
- Amity Institute of Biotechnology, Amity University, Kolkata, West Bengal, India
| | - Sushreeta Paul
- Amity Institute of Biotechnology, Amity University, Kolkata, West Bengal, India
| | - Vijay Kumar
- Department of Biotechnology, Lovely Faculty of Technology and Sciences, Lovely Professional University, Phagwara, Punjab, India
| | - Tabarak Malik
- Biomedical Sciences, Institute of Health, Jimma University, Jimma, Ethiopia
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11
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Ma Y, Chen Q, Wang Y, Zhang F, Wang C, Wang G. Heteromerization of short-chain trans-prenyltransferase controls precursor allocation within a plastidial terpenoid network. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1170-1182. [PMID: 36647626 DOI: 10.1111/jipb.13454] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 01/16/2023] [Indexed: 05/13/2023]
Abstract
Terpenes are the largest and most diverse class of plant specialized metabolites. Sesterterpenes (C25), which are derived from the plastid methylerythritol phosphate pathway, were recently characterized in plants. In Arabidopsis thaliana, four genes encoding geranylfarnesyl diphosphate synthase (GFPPS) (AtGFPPS1 to 4) are responsible for the production of GFPP, which is the common precursor for sesterterpene biosynthesis. However, the interplay between sesterterpenes and other known terpenes remain elusive. Here, we first provide genetic evidence to demonstrate that GFPPSs are responsible for sesterterpene production in Arabidopsis. Blockage of the sesterterpene pathway at the GFPPS step increased the production of geranylgeranyl diphosphate (GGPP)-derived terpenes. Interestingly, co-expression of sesterTPSs in GFPPS-OE (overexpression) plants rescued the phenotypic changes of GFPPS-OE plants by restoring the endogenous GGPP. We further demonstrated that, in addition to precursor (DMAPP/IPP) competition by GFPPS and GGPP synthase (GGPPS) in plastids, GFPPS directly decreased the activity of GGPPS through protein-protein interaction, ultimately leading to GGPP deficiency in planta. Our study provides a new regulatory mechanism of the plastidial terpenoid network in plant cells.
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Affiliation(s)
- Yihua Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Qingwen Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yaoyao Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Fengxia Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chengyuan Wang
- Center for Microbes, Development and Health, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
- Center for Microbes, Development and Health, Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, 200031, China
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12
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Nickles GR, Oestereicher B, Keller NP, Drott MT. Mining for a New Class of Fungal Natural Products: The Evolution, Diversity, and Distribution of Isocyanide Synthase Biosynthetic Gene Clusters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537281. [PMID: 37131656 PMCID: PMC10153163 DOI: 10.1101/2023.04.17.537281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The products of non-canonical isocyanide synthase (ICS) biosynthetic gene clusters (BGCs) have notable bioactivities that mediate pathogenesis, microbial competition, and metal-homeostasis through metal-associated chemistry. We sought to enable research into this class of compounds by characterizing the biosynthetic potential and evolutionary history of these BGCs across the Fungal Kingdom. We developed the first genome-mining pipeline to identify ICS BGCs, locating 3,800 ICS BGCs in 3,300 genomes. Genes in these clusters share promoter motifs and are maintained in contiguous groupings by natural selection. ICS BGCs are not evenly distributed across fungi, with evidence of gene-family expansions in several Ascomycete families. We show that the ICS dit1 / 2 gene cluster family (GCF), which was thought to only exist in yeast, is present in ∼30% of all Ascomycetes, including many filamentous fungi. The evolutionary history of the dit GCF is marked by deep divergences and phylogenetic incompatibilities that raise questions about convergent evolution and suggest selection or horizontal gene transfers have shaped the evolution of this cluster in some yeast and dimorphic fungi. Our results create a roadmap for future research into ICS BGCs. We developed a website ( www.isocyanides.fungi.wisc.edu ) that facilitates the exploration, filtering, and downloading of all identified fungal ICS BGCs and GCFs.
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Affiliation(s)
- Grant R. Nickles
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
| | | | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Plant Pathology, University of Wisconsin—Madison, Madison, WI 53706, USA
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13
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Gu B, Goldfuss B, Dickschat JS. Mechanistic Characterisation and Engineering of Sesterviolene Synthase from Streptomyces violens. Angew Chem Int Ed Engl 2023; 62:e202215688. [PMID: 36350768 PMCID: PMC10107272 DOI: 10.1002/anie.202215688] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Indexed: 11/10/2022]
Abstract
The sesterviolene synthase from Streptomyces violens was identified and represents the second known sesterterpene synthase from bacteria. Isotopic labelling experiments in conjunction with DFT calculations were performed that provided detailed insight into its complex cyclisation mechanism. Enzyme engineering through site-directed mutagenesis gave access to a high-yielding enzyme variant that provided six additional minor products and the main product in sufficient quantities to study its chemistry.
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Affiliation(s)
- Binbin Gu
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
| | - Bernd Goldfuss
- Department for Chemistry, University of Cologne, Greinstraße 4, 50939, Cologne, Germany
| | - Jeroen S Dickschat
- Kekulé-Institute for Organic Chemistry and Biochemistry, University of Bonn, Gerhard-Domagk-Straße 1, 53121, Bonn, Germany
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14
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Zhang J, Ma Y, Chen Q, Yang M, Feng D, Zhou F, Wang G, Wang C. Functional Prediction of trans-Prenyltransferases Reveals the Distribution of GFPPSs in Species beyond the Brassicaceae Clade. Int J Mol Sci 2022; 23:ijms23169471. [PMID: 36012736 PMCID: PMC9409350 DOI: 10.3390/ijms23169471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/11/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Terpenoids are the most diverse class of plant primary and specialized metabolites, and trans-prenyltransferases (trans-PTs) are the first branch point to synthesize precursors of various chain lengths for further metabolism. Whereas the catalytic mechanism of the enzyme is known, there is no reliable method for precisely predicting the functions of trans-PTs. With the exponentially increasing number of available trans-PTs genes in public databases, an in silico functional prediction method for this gene family is urgently needed. Here, we present PTS-Pre, a web tool developed on the basis of the “three floors” model, which shows an overall 86% prediction accuracy for 141 experimentally determined trans-PTs. The method was further validated by in vitro enzyme assays for randomly selected trans-PTs. In addition, using this method, we identified nine new GFPPSs from different plants which are beyond the previously reported Brassicaceae clade, suggesting these genes may have occurred via convergent evolution and are more likely lineage-specific. The high accuracy of our blind prediction validated by enzymatic assays suggests that PTS-Pre provides a convenient and reliable method for genome-wide functional prediction of trans-PTs enzymes and will surely benefit the elucidation and metabolic engineering of terpenoid biosynthetic pathways.
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Affiliation(s)
- Jing Zhang
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yihua Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Qingwen Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Mingxia Yang
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Deyu Feng
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Fei Zhou
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (G.W.); (C.W.)
| | - Chengyuan Wang
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology and Immunology, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- Correspondence: (G.W.); (C.W.)
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15
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Shen SM, Yang Q, Zang Y, Li J, Liu X, Guo YW. Anti-inflammatory aromadendrane- and cadinane-type sesquiterpenoids from the South China Sea sponge Acanthella cavernosa. Beilstein J Org Chem 2022; 18:916-925. [PMID: 35957756 PMCID: PMC9344550 DOI: 10.3762/bjoc.18.91] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/14/2022] [Indexed: 11/23/2022] Open
Abstract
One new aromadendrane-type sesquiterpenoid, namely ximaocavernosin P [(+)-1], and three new cadinane-type sesquiterpenoids, namely (+)-maninsigin D [(+)-4], (+)- and (−)-ximaocavernosin Q [(+)- and (−)-5], together with five related known ones [2, 3, (−)-4, 6, and 7], were isolated from the Hainan sponge Acanthella cavernosa. Compounds 4 and 5 were isolated as racemic forms, which were further separated to the corresponding enantiomers [(+)-4/(−)-4 and (+)-5/(−)-5], respectively, by using chiral-phase HPLC. The structures of new compounds were elucidated by extensive spectroscopic analysis and comparison with the reported data. In addition, the absolute configuration of optically pure (+)-1 and 2 were determined by time-dependent density functional theory/electronic circular dichroism (TDDFT-ECD) calculations or X-ray diffraction analysis. A plausible biosynthetic pathway of these sesquiterpenoids and their internal correlation were proposed and discussed. In an in vitro bioassay, (+)-aristolone (3) exhibited promising anti-inflammatory activity by the inhibition of LPS-induced TNF-α and CCL2 release in RAW 264.7 macrophages.
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Affiliation(s)
- Shou-Mao Shen
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Qing Yang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Pharmaceutical Science, Nanchang University, Nanchang 330006, China
| | - Yi Zang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jia Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yue-Wei Guo
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing 210023, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China
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16
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Cao S, Duan H, Sun Y, Hu R, Wu B, Lin J, Deng W, Li Y, Zheng H. Genome-Wide Association Study With Growth-Related Traits and Secondary Metabolite Contents in Red- and White-Heart Chinese Fir. FRONTIERS IN PLANT SCIENCE 2022; 13:922007. [PMID: 35845628 PMCID: PMC9280351 DOI: 10.3389/fpls.2022.922007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 05/27/2022] [Indexed: 06/15/2023]
Abstract
Chinese fir [Cunninghamia lanceolata (Lamb.) Hook] is an important evergreen coniferous tree species that is widely distributed in many southern provinces of China and has important economic value. The Chinese fir accounts for 1/4 and 1/3 of the total artificial forest area and stock volume, respectively. Red-heart Chinese fir is popular in the market because of its high density and red heartwood. The long-growth cycle hindered the breeding process of Chinese fir, while molecular marker-assisted breeding could accelerate it. However, Chinese fir, a perennial conifer species, has a large genome, which has not yet been published. In this study, the growth-related traits and secondary metabolite contents of red- and white-heart Chinese fir were measured and found to be different between them. There are extremely significant differences among growth-related traits (p < 0.001), but secondary metabolite contents have different correlations due to differences in chemical structure. Moreover, genotype effect analysis of the substantially correlated single nucleotide polymorphisms (SNPs) revealed that most of the loci related to each growth-related traits were different from each other, indicating a type specificity of the genes regulated different growth-related traits. Furthermore, among the loci related to secondary metabolite contents, nine loci associated with multiple metabolite phenotypes such as Marker21022_4, Marker21022_172, Marker24559_31, Marker27425_37, Marker20748_85, Marker18841_115, Marker18841_198, Marker65846_146, and Marker21486_163, suggesting the presence of pleiotropic genes. This study identified the potential SNP markers associated with secondary metabolites in Chinese fir, thus setting the basis for molecular marker-assisted selection.
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Affiliation(s)
- Sen Cao
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hongjing Duan
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Experimental School Affiliated to Chinese Academy of Sciences, Beijing, China
| | - Yuhan Sun
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Ruiyang Hu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Experimental Center of Forestry in North China, Chinese Academy of Forestry, Beijing, China
| | - Bo Wu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jun Lin
- Longshan State Forest Farm of Lechang, Lechang, China
| | - Wenjian Deng
- Longshan State Forest Farm of Lechang, Lechang, China
| | - Yun Li
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Huiquan Zheng
- Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, China
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17
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Han X, Tsuda K. Evolutionary footprint of plant immunity. CURRENT OPINION IN PLANT BIOLOGY 2022; 67:102209. [PMID: 35430538 DOI: 10.1016/j.pbi.2022.102209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/24/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
There are pieces of evidence from genomic footprints and fossil records indicating that plants have co-evolved with microbes after terrestrialization for more than 407 million years. Therefore, to truly comprehend plant evolution, we need to understand the co-evolutionary process and history between plants and microbes. Recent developments in genomes and transcriptomes of a vast number of plant species as well as microbes have greatly expanded our knowledge of the evolution of the plant immune system. In this review, we summarize recent advances in the co-evolution between plants and microbes with emphasis on the plant side and point out future research needed for understanding plant-microbial co-evolution. Knowledge of the evolution and variation of the plant immune system will better equip us on designing crops with boosted performance in agricultural fields.
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Affiliation(s)
- Xiaowei Han
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Kenichi Tsuda
- State Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China; Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China; Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China.
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18
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Feng K, Kan XY, Li R, Yan YJ, Zhao SP, Wu P, Li LJ. Integrative Analysis of Long- and Short-Read Transcriptomes Identify the Regulation of Terpenoids Biosynthesis Under Shading Cultivation in Oenanthe javanica. Front Genet 2022; 13:813216. [PMID: 35464839 PMCID: PMC9022222 DOI: 10.3389/fgene.2022.813216] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Water dropwort (Oenanthe javanica) is a popular vegetable with high nutritional value and distinctive flavor. The flavor is mainly correlate with the biosynthesis of terpenoids. Shading cultivation was used to improve the flavor in the production of water dropwort. However, the changes of terpenoids and the genes involved in terpenoids biosynthesis under shading treatment remains unclear. In this study, the long- and short-reads transcriptomes of water dropwort were constructed. In total, 57,743 non-redundant high-quality transcripts were obtained from the transcriptome. 28,514 SSRs were identified from non-redundant transcripts and the mono-nucleotide repeats were the most abundant SSRs. The lncRNAs of water dropwort were recognized and their target genes were predicted. The volatile compound contents in petioles and leaf blades of water dropwort were decreased after the shading treatment. The DEGs analysis was performed to identify the terpenoids biosynthesis genes. The results indicated that 5,288 DEGs were differentially expressed in petiole, of which 22 DEGs were enriched in the terpenoids backbone biosynthesis pathway. A total of 12 DEGs in terpenoids biosynthesis pathway were selected and further verified by qRT-PCR assay, demonstrating that the terpenoids biosynthesis genes were down-regulated under shading treatment. Here, the full-length transcriptome was constructed and the regulatory genes related to terpenoids biosynthesis in water dropwort were also investigated. These results will provide useful information for future researches on functional genomics and terpenoids biosynthesis mechanism in water dropwort.
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Affiliation(s)
- Kai Feng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Xia-Yue Kan
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Rui Li
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Ya-Jie Yan
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Shu-Ping Zhao
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Peng Wu
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Liang-Jun Li
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
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19
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Rodríguez-López CE, Jiang Y, Kamileen MO, Lichman BR, Hong B, Vaillancourt B, Buell CR, O'Connor SE. Phylogeny-aware chemoinformatic analysis of chemical diversity in the Lamiaceae enables iridoid pathway assembly and discovery of aucubin synthase. Mol Biol Evol 2022; 39:6550147. [PMID: 35298643 PMCID: PMC9048965 DOI: 10.1093/molbev/msac057] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Countless reports describe the isolation and structural characterization of natural products, yet this information remains disconnected and under-utilized. Using a cheminformatics approach, we leverage the reported observations of iridoid glucosides with the known phylogeny of a large iridoid producing plant family (Lamiaceae), to generate a set of biosynthetic pathways that best explain the extant iridoid chemical diversity. We developed a pathway reconstruction algorithm that connects iridoid reports via reactions, and prunes this solution space by considering phylogenetic relationships between genera. We formulate a model that emulates the evolution of iridoid glucosides to create a synthetic dataset, used to select the parameters that would best reconstruct the pathways, and apply them to the iridoid dataset to generate Pathway Hypotheses. These computationally generated pathways were then used as the basis by which to select and screen biosynthetic enzyme candidates. Our model was successfully applied to discover a cytochrome P450 enzyme from Callicarpa americana that catalyzes the oxidation of bartsioside to aucubin, predicted by our model despite neither molecule having been observed in the genus. We also demonstrate aucubin synthase activity in orthologues of Vitex agnus-castus, and the outgroup Paulownia tomentosa, further strengthening the hypothesis, enabled by our model, that the reaction was present in the ancestral biosynthetic pathway. This is the first systematic hypothesis on the epi-iridoid glucosides biosynthesis in 25 years, and sets the stage for streamlined work on the iridoid pathway. This work highlights how curation and computational analysis of widely available structural data can facilitate hypothesis-based gene discovery.
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Affiliation(s)
- Carlos E Rodríguez-López
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany.,Escuela de Ingenieria y Ciencias, Tecnologico de Monterrey, 64849 Monterrey, Mexico
| | - Yindi Jiang
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Mohamed O Kamileen
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Benjamin R Lichman
- Department of Biology, University of York, YO10 5DD York, United Kingdom
| | - Benke Hong
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
| | - Brieanne Vaillancourt
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA
| | - C Robin Buell
- Department of Crop & Soil Sciences, University of Georgia, Athens, GA 30602, USA
| | - Sarah E O'Connor
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, 07745 Jena, Germany
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20
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Luo F, Yu Z, Zhou Q, Huang A. Multi-Omics-Based Discovery of Plant Signaling Molecules. Metabolites 2022; 12:metabo12010076. [PMID: 35050197 PMCID: PMC8777911 DOI: 10.3390/metabo12010076] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 02/01/2023] Open
Abstract
Plants produce numerous structurally and functionally diverse signaling metabolites, yet only relatively small fractions of which have been discovered. Multi-omics has greatly expedited the discovery as evidenced by increasing recent works reporting new plant signaling molecules and relevant functions via integrated multi-omics techniques. The effective application of multi-omics tools is the key to uncovering unknown plant signaling molecules. This review covers the features of multi-omics in the context of plant signaling metabolite discovery, highlighting how multi-omics addresses relevant aspects of the challenges as follows: (a) unknown functions of known metabolites; (b) unknown metabolites with known functions; (c) unknown metabolites and unknown functions. Based on the problem-oriented overview of the theoretical and application aspects of multi-omics, current limitations and future development of multi-omics in discovering plant signaling metabolites are also discussed.
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Affiliation(s)
| | | | - Qian Zhou
- Correspondence: (Q.Z.); (A.H.); Tel.: +86-755-8801-8496 (Q.Z. & A.H.)
| | - Ancheng Huang
- Correspondence: (Q.Z.); (A.H.); Tel.: +86-755-8801-8496 (Q.Z. & A.H.)
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21
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Hanson SJ, Dawson JC, Goldman IL. Beta vulgaris ssp. vulgaris chromosome 8 shows significant association with geosmin concentration in table beet. G3 (BETHESDA, MD.) 2021; 11:jkab344. [PMID: 34586384 PMCID: PMC8664477 DOI: 10.1093/g3journal/jkab344] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022]
Abstract
Geosmin, a degraded sesquiterpene molecule with earthy and musty odor, imbues table beet with its characteristic aroma. Geosmin is heritable and endogenously produced in table beet; its earthy aroma is sought by some consumers but deters others. Geosmin biosynthesis is catalyzed by a bifunctional geosmin synthase enzyme in diverse bacteria and fungi, but a mechanism for geosmin biosynthesis in plants has not been reported. This work employed association analysis and selective genotyping of a segregating F2:3 mapping population to seek QTL associated with geosmin concentration in table beet. GBS reads were aligned to sugar beet reference genome EL10.2, and association analysis revealed two QTL for geosmin concentration on Beta vulgaris ssp. vulgaris chromosome 8. QTL at EL10.2 positions 28,017,624 and 38,488,687 each show effect size 8.7 μg·kg-1 geosmin and explain 8.5% and 6.4% of total variation in geosmin concentration, respectively. Resolution was low due to large recombination bin size and imperfect alignment between the reference genome and mapping population, but population size and selection proportion were sufficient to detect moderate to large effect QTL. This study, the first molecular genetic mapping experiment in table beet, succeeded in finding QTL for geosmin concentration in table beet, and it provides the basis for fine mapping or candidate gene investigation of functional loci for this distinctive sensory trait.
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Affiliation(s)
- Solveig J Hanson
- Centre for Sustainable Food Systems, The University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Julie C Dawson
- Department of Horticulture, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - Irwin L Goldman
- Department of Horticulture, University of Wisconsin—Madison, Madison, WI 53706, USA
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22
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Chen Y, Li D, Ling Y, Liu Y, Zuo Z, Gan L, Luo S, Hua J, Chen D, Xu F, Li M, Guo K, Liu Y, Gershenzon J, Li S. A Cryptic Plant Terpene Cyclase Producing Unconventional 18‐ and 14‐Membered Macrocyclic C
25
and C
20
Terpenoids with Immunosuppressive Activity. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yue‐Gui Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy Chengdu University of Traditional Chinese Medicine Chengdu 611137 P. R. China
- State Key Laboratory of Phytochemistry and Plant Resources in West China & Yunnan Key Laboratory of Natural Medicinal Chemistry Kunming Institute of Botany, Chinese Academy of, Sciences Kunming 650201 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - De‐Sen Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy Chengdu University of Traditional Chinese Medicine Chengdu 611137 P. R. China
- State Key Laboratory of Phytochemistry and Plant Resources in West China & Yunnan Key Laboratory of Natural Medicinal Chemistry Kunming Institute of Botany, Chinese Academy of, Sciences Kunming 650201 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Yi Ling
- State Key Laboratory of Phytochemistry and Plant Resources in West China & Yunnan Key Laboratory of Natural Medicinal Chemistry Kunming Institute of Botany, Chinese Academy of, Sciences Kunming 650201 P. R. China
| | - Yan‐Chun Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China & Yunnan Key Laboratory of Natural Medicinal Chemistry Kunming Institute of Botany, Chinese Academy of, Sciences Kunming 650201 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Zhi‐Li Zuo
- State Key Laboratory of Phytochemistry and Plant Resources in West China & Yunnan Key Laboratory of Natural Medicinal Chemistry Kunming Institute of Botany, Chinese Academy of, Sciences Kunming 650201 P. R. China
| | - Li‐She Gan
- School of Biotechnology and Health Sciences Wuyi University Jiangmen 529020 P. R. China
| | - Shi‐Hong Luo
- State Key Laboratory of Phytochemistry and Plant Resources in West China & Yunnan Key Laboratory of Natural Medicinal Chemistry Kunming Institute of Botany, Chinese Academy of, Sciences Kunming 650201 P. R. China
| | - Juan Hua
- State Key Laboratory of Phytochemistry and Plant Resources in West China & Yunnan Key Laboratory of Natural Medicinal Chemistry Kunming Institute of Botany, Chinese Academy of, Sciences Kunming 650201 P. R. China
| | - Ding‐Yuan Chen
- State Key Laboratory of Phytochemistry and Plant Resources in West China & Yunnan Key Laboratory of Natural Medicinal Chemistry Kunming Institute of Botany, Chinese Academy of, Sciences Kunming 650201 P. R. China
| | - Fan Xu
- School of Biotechnology and Health Sciences Wuyi University Jiangmen 529020 P. R. China
| | - Man Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China & Yunnan Key Laboratory of Natural Medicinal Chemistry Kunming Institute of Botany, Chinese Academy of, Sciences Kunming 650201 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Kai Guo
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy Chengdu University of Traditional Chinese Medicine Chengdu 611137 P. R. China
| | - Yan Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy Chengdu University of Traditional Chinese Medicine Chengdu 611137 P. R. China
- State Key Laboratory of Phytochemistry and Plant Resources in West China & Yunnan Key Laboratory of Natural Medicinal Chemistry Kunming Institute of Botany, Chinese Academy of, Sciences Kunming 650201 P. R. China
| | | | - Sheng‐Hong Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, and Innovative Institute of Chinese Medicine and Pharmacy Chengdu University of Traditional Chinese Medicine Chengdu 611137 P. R. China
- State Key Laboratory of Phytochemistry and Plant Resources in West China & Yunnan Key Laboratory of Natural Medicinal Chemistry Kunming Institute of Botany, Chinese Academy of, Sciences Kunming 650201 P. R. China
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23
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Chen YG, Li DS, Ling Y, Liu YC, Zuo ZL, Gan LS, Luo SH, Hua J, Chen DY, Xu F, Li M, Guo K, Liu Y, Gershenzon J, Li SH. A Cryptic Plant Terpene Cyclase Producing Unconventional 18- and 14-Membered Macrocyclic C 25 and C 20 Terpenoids with Immunosuppressive Activity. Angew Chem Int Ed Engl 2021; 60:25468-25476. [PMID: 34580976 DOI: 10.1002/anie.202110842] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/20/2021] [Indexed: 11/09/2022]
Abstract
A versatile terpene synthase (LcTPS2) producing unconventional macrocyclic terpenoids was characterized from Leucosceptrum canum. Engineered Escherichia coli and Nicotiana benthamiana expressing LcTPS2 produced six 18-/14-membered sesterterpenoids including five new ones and two 14-membered diterpenoids. These products represent the first macrocyclic sesterterpenoids from plants and the largest sesterterpenoid ring system identified to date. Two variants F516A and F516G producing approximately 3.3- and 2.5-fold, respectively, more sesterterpenoids than the wild-type enzyme were engineered. Both 18- and 14-membered ring sesterterpenoids displayed significant inhibitory activity on the IL-2 and IFN-γ production of T cells probably via inhibition of the MAPK pathway. The findings will contribute to the development of efficient biocatalysts to create bioactive macrocyclic sesterterpenoids, and also herald a new potential in the well-trodden territory of plant terpenoid biosynthesis.
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Affiliation(s)
- Yue-Gui Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, and, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, P. R. China.,State Key Laboratory of Phytochemistry and Plant Resources in West China &, Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of, Sciences, Kunming, 650201, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - De-Sen Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, and, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, P. R. China.,State Key Laboratory of Phytochemistry and Plant Resources in West China &, Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of, Sciences, Kunming, 650201, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Yi Ling
- State Key Laboratory of Phytochemistry and Plant Resources in West China &, Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of, Sciences, Kunming, 650201, P. R. China
| | - Yan-Chun Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China &, Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of, Sciences, Kunming, 650201, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Zhi-Li Zuo
- State Key Laboratory of Phytochemistry and Plant Resources in West China &, Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of, Sciences, Kunming, 650201, P. R. China
| | - Li-She Gan
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China
| | - Shi-Hong Luo
- State Key Laboratory of Phytochemistry and Plant Resources in West China &, Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of, Sciences, Kunming, 650201, P. R. China
| | - Juan Hua
- State Key Laboratory of Phytochemistry and Plant Resources in West China &, Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of, Sciences, Kunming, 650201, P. R. China
| | - Ding-Yuan Chen
- State Key Laboratory of Phytochemistry and Plant Resources in West China &, Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of, Sciences, Kunming, 650201, P. R. China
| | - Fan Xu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China
| | - Man Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China &, Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of, Sciences, Kunming, 650201, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Kai Guo
- State Key Laboratory of Southwestern Chinese Medicine Resources, and, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, P. R. China
| | - Yan Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, and, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, P. R. China.,State Key Laboratory of Phytochemistry and Plant Resources in West China &, Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of, Sciences, Kunming, 650201, P. R. China
| | | | - Sheng-Hong Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, and, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, P. R. China.,State Key Laboratory of Phytochemistry and Plant Resources in West China &, Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of, Sciences, Kunming, 650201, P. R. China
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24
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Tsugawa H, Rai A, Saito K, Nakabayashi R. Metabolomics and complementary techniques to investigate the plant phytochemical cosmos. Nat Prod Rep 2021; 38:1729-1759. [PMID: 34668509 DOI: 10.1039/d1np00014d] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Plants and their associated microbial communities are known to produce millions of metabolites, a majority of which are still not characterized and are speculated to possess novel bioactive properties. In addition to their role in plant physiology, these metabolites are also relevant as existing and next-generation medicine candidates. Elucidation of the plant metabolite diversity is thus valuable for the successful exploitation of natural resources for humankind. Herein, we present a comprehensive review on recent metabolomics approaches to illuminate molecular networks in plants, including chemical isolation and enzymatic production as well as the modern metabolomics approaches such as stable isotope labeling, ultrahigh-resolution mass spectrometry, metabolome imaging (spatial metabolomics), single-cell analysis, cheminformatics, and computational mass spectrometry. Mass spectrometry-based strategies to characterize plant metabolomes through metabolite identification and annotation are described in detail. We also highlight the use of phytochemical genomics to mine genes associated with specialized metabolites' biosynthesis. Understanding the metabolic diversity through biotechnological advances is fundamental to elucidate the functions of the plant-derived specialized metabolome.
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Affiliation(s)
- Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. .,RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei, Tokyo 184-8588, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Amit Rai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. .,Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. .,Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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25
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Li DS, Hua J, Luo SH, Liu YC, Chen YG, Ling Y, Guo K, Liu Y, Li SH. An extremely promiscuous terpenoid synthase from the Lamiaceae plant Colquhounia coccinea var. mollis catalyzes the formation of sester-/di-/sesqui-/mono-terpenoids. PLANT COMMUNICATIONS 2021; 2:100233. [PMID: 34746763 PMCID: PMC8554039 DOI: 10.1016/j.xplc.2021.100233] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/03/2021] [Accepted: 08/10/2021] [Indexed: 05/05/2023]
Abstract
Terpenoids are the largest class of natural products with complex structures and extensive bioactivities; their scaffolds are generated by diverse terpenoid synthases (TPSs) from a limited number of isoprenoid diphosphate precursors. Promiscuous TPSs play important roles in the evolution of terpenoid chemodiversity, but they remain largely unappreciated. Here, an extremely promiscuous terpenoid synthase (CcTPS1) of the TPS-b subfamily was cloned and functionally characterized from a leaf-specific transcriptome of the Lamiaceae plant Colquhounia coccinea var. mollis. CcTPS1 is the first sester-/di-/sesqui-/mono-TPS identified from the plant kingdom, accepting C25/C20/C15/C10 diphosphate substrates to generate a panel of sester-/di-/sesqui-/mono-terpenoids. Engineered Escherichia coli expressing CcTPS1 produced three previously unreported terpenoids (two sesterterpenoids and a diterpenoid) with rare cyclohexane-containing skeletons, along with four sesquiterpenoids and one monoterpenoid. Their structures were elucidated by extensive nuclear magnetic resonance spectroscopy. Nicotiana benthamiana transiently expressing CcTPS1 also produced the diterpenoid and sesquiterpenoids, demonstrating the enzyme's promiscuity in planta. Its highly leaf-specific expression pattern combined with detectable terpenoid products in leaves of C. coccinea var. mollis and N. benthamiana expressing CcTPS1 suggested that CcTPS1 was mainly responsible for diterpenoid and sesquiterpenoid biosynthesis in plants. CcTPS1 expression and the terpenoid products could be induced by methyl jasmonate, suggesting their possible role in plant-environment interaction. CcTPS1 was localized to the cytosol and may differ from mono-TPSs in subcellular compartmentalization and substrate tolerance. These findings will greatly aid our understanding of plant TPS evolution and terpenoid chemodiversity; they also highlight the enormous potential of transcriptome mining and heterologous expression for the exploration of unique enzymes and natural products hidden in plants.
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Affiliation(s)
- De-Sen Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Juan Hua
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P. R. China
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shengyang 110866, P. R. China
| | - Shi-Hong Luo
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P. R. China
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shengyang 110866, P. R. China
| | - Yan-Chun Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P. R. China
| | - Yue-Gui Chen
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Yi Ling
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P. R. China
| | - Kai Guo
- State Key Laboratory of Southwestern Chinese Medicine Resources and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P. R. China
| | - Yan Liu
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P. R. China
- State Key Laboratory of Southwestern Chinese Medicine Resources and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P. R. China
| | - Sheng-Hong Li
- State Key Laboratory of Phytochemistry and Plant Resources in West China and Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P. R. China
- State Key Laboratory of Southwestern Chinese Medicine Resources and Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P. R. China
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26
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Chen Q, Li J, Ma Y, Yuan W, Zhang P, Wang G. Occurrence and biosynthesis of plant sesterterpenes (C25), a new addition to terpene diversity. PLANT COMMUNICATIONS 2021; 2:100184. [PMID: 34746758 PMCID: PMC8553974 DOI: 10.1016/j.xplc.2021.100184] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/03/2021] [Accepted: 03/28/2021] [Indexed: 05/21/2023]
Abstract
Terpenes, the largest group of plant-specialized metabolites, have received considerable attention for their highly diverse biological activities. Monoterpenes (C10), sesquiterpenes (C15), diterpenes (C20), and triterpenes (C30) have been extensively investigated at both the biochemical and molecular levels over the past two decades. Sesterterpenes (C25), an understudied terpenoid group, were recently described by plant scientists at the molecular level. This review summarizes the plant species that produce sesterterpenes and describes recent developments in the field of sesterterpene biosynthesis, placing a special focus on the catalytic mechanism and evolution of geranylfarnesyl diphosphate synthase and sesterterpene synthase. Finally, we propose several questions to be addressed in future studies, which may help to elucidate sesterterpene metabolism in plants.
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Affiliation(s)
- Qingwen Chen
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxu Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yihua Ma
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Weiliang Yuan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China
- Corresponding author
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27
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Medema MH, de Rond T, Moore BS. Mining genomes to illuminate the specialized chemistry of life. Nat Rev Genet 2021; 22:553-571. [PMID: 34083778 PMCID: PMC8364890 DOI: 10.1038/s41576-021-00363-7] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/09/2021] [Indexed: 02/07/2023]
Abstract
All organisms produce specialized organic molecules, ranging from small volatile chemicals to large gene-encoded peptides, that have evolved to provide them with diverse cellular and ecological functions. As natural products, they are broadly applied in medicine, agriculture and nutrition. The rapid accumulation of genomic information has revealed that the metabolic capacity of virtually all organisms is vastly underappreciated. Pioneered mainly in bacteria and fungi, genome mining technologies are accelerating metabolite discovery. Recent efforts are now being expanded to all life forms, including protists, plants and animals, and new integrative omics technologies are enabling the increasingly effective mining of this molecular diversity.
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Affiliation(s)
- Marnix H Medema
- Bioinformatics Group, Wageningen University, Wageningen, The Netherlands
| | - Tristan de Rond
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Bradley S Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
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28
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Plant geranylgeranyl diphosphate synthases: every (gene) family has a story. ABIOTECH 2021; 2:289-298. [PMID: 36303884 PMCID: PMC9590577 DOI: 10.1007/s42994-021-00050-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 05/18/2021] [Indexed: 12/20/2022]
Abstract
Plant isoprenoids (also known as terpenes or terpenoids) are a wide family of primary and secondary metabolites with multiple functions. In particular, most photosynthesis-related isoprenoids (including carotenoids and chlorophylls) as well as diterpenes and polyterpenes derive from geranylgeranyl diphosphate (GGPP) produced by GGPP synthase (GGPPS) enzymes in several cell compartments. Plant genomes typically harbor multiple copies of differentially expressed genes encoding GGPPS-like proteins. While sequence comparisons allow to identify potential GGPPS candidates, experimental evidence is required to ascertain their enzymatic activity and biological function. Actually, functional analyses of the full set of potential GGPPS paralogs are only available for a handful of plant species. Here we review our current knowledge on the GGPPS families of the model plant Arabidopsis thaliana and the crop species rice (Oryza sativa), pepper (Capsicum annuum) and tomato (Solanum lycopersicum). The results indicate that a major determinant of the biological role of particular GGPPS paralogs is the expression profile of the corresponding genes even though specific interactions with other proteins (including GGPP-consuming enzymes) might also contribute to subfunctionalization. In some species, however, a single GGPPS isoforms appears to be responsible for the production of most if not all GGPP required for cell functions. Deciphering the mechanisms regulating GGPPS activity in particular cell compartments, tissues, organs and plant species will be very useful for future metabolic engineering approaches aimed to manipulate the accumulation of particular GGPP-derived products of interest without negatively impacting the levels of other isoprenoids required to sustain essential cell functions.
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Sato H, Li BX, Takagi T, Wang C, Miyamoto K, Uchiyama M. DFT Study on the Biosynthesis of Verrucosane Diterpenoids and Mangicol Sesterterpenoids: Involvement of Secondary-Carbocation-Free Reaction Cascades. JACS AU 2021; 1:1231-1239. [PMID: 34467361 PMCID: PMC8397367 DOI: 10.1021/jacsau.1c00178] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Indexed: 05/03/2023]
Abstract
Some experimental observations indicate that a sequential formation of secondary (2°) carbocations might be involved in some biosynthetic pathways, including those of verrucosane-type diterpenoids and mangicol-type sesterterpenoids, but it remains controversial whether or not such 2° cations are viable intermediates. Here, we performed comprehensive density functional theory calculations of these biosynthetic pathways. The results do not support previously proposed pathways/mechanisms: in particular, we find that none of the putative 2° carbocation intermediates is involved in either of the biosynthetic pathways. In verrucosane biosynthesis, the proposed 2° carbocations (II and IV) in the early stage are bypassed by the formation of the adjacent 3° carbocations and by unusual skeletal rearrangement reactions, and in the later stage, the putative 2° carbocation intermediates (VI, VII, and VIII) are not present as the proposed forms but as nonclassical structures between homoallyl and cyclopropylcarbinyl cations. In the mangicol biosynthesis, one of the two proposed 2° carbocations (X) is bypassed by a C-C bond-breaking reaction to generate a 3° carbocation with a C=C bond, while the other (XI) is bypassed by a strong hyperconjugative interaction leading to a nonclassical carbocation. We propose new biosynthetic pathways/mechanisms for the verrucosane-type diterpenoids and mangicol-type sesterterpenoids. These pathways are in good agreement with the findings of previous biosynthetic studies, including isotope-labeling experiments and byproducts analysis, and moreover can account for the biosynthesis of related terpenes.
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Affiliation(s)
- Hajime Sato
- Interdisciplinary
Graduate School of Medicine and Engineering, University of Yamanashi, 4-4-37 Takeda, Kofu, Yamanashi 400-8510, Japan
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Bi-Xiao Li
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Taisei Takagi
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Chao Wang
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kazunori Miyamoto
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masanobu Uchiyama
- Graduate
School of Pharmaceutical Sciences, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Research
Initiative for Supra-Materials, Shinshu
University, 3-15-1 Tokida,
Ueda, Nagano 386-8567, Japan
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Bharadwaj R, Kumar SR, Sharma A, Sathishkumar R. Plant Metabolic Gene Clusters: Evolution, Organization, and Their Applications in Synthetic Biology. FRONTIERS IN PLANT SCIENCE 2021; 12:697318. [PMID: 34490002 PMCID: PMC8418127 DOI: 10.3389/fpls.2021.697318] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/05/2021] [Indexed: 05/21/2023]
Abstract
Plants are a remarkable source of high-value specialized metabolites having significant physiological and ecological functions. Genes responsible for synthesizing specialized metabolites are often clustered together for a coordinated expression, which is commonly observed in bacteria and filamentous fungi. Similar to prokaryotic gene clustering, plants do have gene clusters encoding enzymes involved in the biosynthesis of specialized metabolites. More than 20 gene clusters involved in the biosynthesis of diverse metabolites have been identified across the plant kingdom. Recent studies demonstrate that gene clusters are evolved through gene duplications and neofunctionalization of primary metabolic pathway genes. Often, these clusters are tightly regulated at nucleosome level. The prevalence of gene clusters related to specialized metabolites offers an attractive possibility of an untapped source of highly useful biomolecules. Accordingly, the identification and functional characterization of novel biosynthetic pathways in plants need to be worked out. In this review, we summarize insights into the evolution of gene clusters and discuss the organization and importance of specific gene clusters in the biosynthesis of specialized metabolites. Regulatory mechanisms which operate in some of the important gene clusters have also been briefly described. Finally, we highlight the importance of gene clusters to develop future metabolic engineering or synthetic biology strategies for the heterologous production of novel metabolites.
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Affiliation(s)
- Revuru Bharadwaj
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Sarma R. Kumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
| | - Ashutosh Sharma
- Tecnologico de Monterrey, Centre of Bioengineering, Querétaro, Mexico
| | - Ramalingam Sathishkumar
- Plant Genetic Engineering Laboratory, Department of Biotechnology, Bharathiar University, Coimbatore, India
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Das A, Begum K, Akhtar S, Ahmed R, Kulkarni R, Banu S. Genome-wide detection and classification of terpene synthase genes in Aquilaria agallochum. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1711-1729. [PMID: 34539112 PMCID: PMC8405786 DOI: 10.1007/s12298-021-01040-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/28/2021] [Accepted: 07/23/2021] [Indexed: 06/05/2023]
Abstract
Agarwood, one of the precious woods in the globe, is produced by Aquilaria plant species during an upshot of wounding and infection. Produced as a defence response, the dark, fragrant resin gets secreted in the plant's duramen, which is impregnated with fragrant molecules with the due course. Agarwood has gained worldwide popularity due to its high aromatic oil, fragrance, and pharmaceutical value, which makes it highly solicited by numerous industries. Predominant chemical constituents of agarwood, sesquiterpenoids, and 2-(2-phenylethyl) chromones have been scrutinized to comprehend the scientific nature of the fragrant wood and develop novel products. However, the genes involved in the biosynthesis of these aromatic compounds are still not comprehensively studied in Aquilaria. In this study, publicly available genomic and transcriptomics data of Aquilaria agallochum were integrated to identify putative functional terpene synthase genes (TPSs). The in silico study enabled us to identify ninety-six TPSs, of which thirty-nine full-length genes were systematically classified into TPS-a, TPS-b, TPS-c, TPS-e, TPS-f, and TPS-g subfamilies based on their gene structure, conserve motif, and phylogenetic comparison with TPSs from other plant species. Analysis of the cis-regulatory elements present upstream of AaTPSs revealed their association with hormone, stress and light responses. In silico expression studies detected their up-regulation in stress induced tissue. This study provides a basic understanding of terpene synthase gene repertoire in Aquilaria agallochum and unlatches opportunities for the biochemical characterization and biotechnological exploration of these genes. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01040-z.
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Affiliation(s)
- Ankur Das
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014 India
| | - Khaleda Begum
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014 India
| | - Suraiya Akhtar
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014 India
| | - Raja Ahmed
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014 India
| | - Ram Kulkarni
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune, India
| | - Sofia Banu
- Department of Bioengineering and Technology, Gauhati University, Guwahati, Assam 781014 India
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Huang ZY, Ye RY, Yu HL, Li AT, Xu JH. Mining methods and typical structural mechanisms of terpene cyclases. BIORESOUR BIOPROCESS 2021; 8:66. [PMID: 38650244 PMCID: PMC10992375 DOI: 10.1186/s40643-021-00421-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/24/2021] [Indexed: 12/13/2022] Open
Abstract
Terpenoids, formed by cyclization and/or permutation of isoprenes, are the most diverse and abundant class of natural products with a broad range of significant functions. One family of the critical enzymes involved in terpenoid biosynthesis is terpene cyclases (TCs), also known as terpene synthases (TSs), which are responsible for forming the ring structure as a backbone of functionally diverse terpenoids. With the recent advances in biotechnology, the researches on terpene cyclases have gradually shifted from the genomic mining of novel enzyme resources to the analysis of their structures and mechanisms. In this review, we summarize both the new methods for genomic mining and the structural mechanisms of some typical terpene cyclases, which are helpful for the discovery, engineering and application of more and new TCs.
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Affiliation(s)
- Zheng-Yu Huang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, China
| | - Ru-Yi Ye
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, China
| | - Hui-Lei Yu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, China
| | - Ai-Tao Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing, Frontiers Science Center for Materiobiology and Dynamic Chemistry, East China University of Science and Technology, Shanghai, 200237, China.
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Systematic mining of fungal chimeric terpene synthases using an efficient precursor-providing yeast chassis. Proc Natl Acad Sci U S A 2021; 118:2023247118. [PMID: 34257153 PMCID: PMC8307374 DOI: 10.1073/pnas.2023247118] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Chimeric terpene synthases, termed PTTSs, are a unique family of enzymes occurring only in fungi. Characterizing PTTSs is challenging due to the complex reactions they catalyze and the structural complexity of their products. Here, by devising an efficient precursor-providing yeast chassis and incorporating a high-throughput automated platform, we identified 34 active PTTSs, which was considerably more than the number of known functional PTTSs. This effective and rapid pipeline can be employed for the characterization of other PTTSs or related terpenoid biosynthetic enzymes. By systematically analyzing the presence/absence of PTTS genes together with phylogenetic analysis, the ancestral PTTS gene was inferred to have undergone duplication and functional divergence, which led to the development of two distinct cyclization mechanisms. Chimeric terpene synthases, which consist of C-terminal prenyltransferase (PT) and N-terminal class I terpene synthase (TS) domains (termed PTTSs here), is unique to fungi and produces structurally diverse di- and sesterterpenes. Prior to this study, 20 PTTSs had been functionally characterized. Our understanding of the origin and functional evolution of PTTS genes is limited. Our systematic search of sequenced fungal genomes among diverse taxa revealed that PTTS genes were restricted to Dikarya. Phylogenetic findings indicated different potential models of the origin and evolution of PTTS genes. One was that PTTS genes originated in the common Dikarya ancestor and then underwent frequent gene loss among various subsequent lineages. To understand their functional evolution, we selected 74 PTTS genes for biochemical characterization in an efficient precursor-providing yeast system employing chassis-based, robot-assisted, high-throughput automatic assembly. We found 34 PTTS genes that encoded active enzymes and collectively produced 24 di- and sesterterpenes. About half of these di- and sesterterpenes were also the products of the 20 known PTTSs, indicating functional conservation, whereas the PTTS products included the previously unknown sesterterpenes, sesterevisene (1), and sesterorbiculene (2), suggesting that a diversity of PTTS products awaits discovery. Separating functional PTTSs into two monophyletic groups implied that an early gene duplication event occurred during the evolution of the PTTS family followed by functional divergence with the characteristics of distinct cyclization mechanisms.
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Scherlach K, Hertweck C. Mining and unearthing hidden biosynthetic potential. Nat Commun 2021; 12:3864. [PMID: 34162873 PMCID: PMC8222398 DOI: 10.1038/s41467-021-24133-5] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 06/04/2021] [Indexed: 12/11/2022] Open
Abstract
Genetically encoded small molecules (secondary metabolites) play eminent roles in ecological interactions, as pathogenicity factors and as drug leads. Yet, these chemical mediators often evade detection, and the discovery of novel entities is hampered by low production and high rediscovery rates. These limitations may be addressed by genome mining for biosynthetic gene clusters, thereby unveiling cryptic metabolic potential. The development of sophisticated data mining methods and genetic and analytical tools has enabled the discovery of an impressive array of previously overlooked natural products. This review shows the newest developments in the field, highlighting compound discovery from unconventional sources and microbiomes. Natural products are an important source of bioactive compounds and have versatile applications in different fields, but their discovery is challenging. Here, the authors review the recent developments in genome mining for discovery of natural products, focusing on compounds from unconventional microorganisms and microbiomes.
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Affiliation(s)
- Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology, HKI, Jena, Germany. .,Faculty of Biological Sciences, Friedrich Schiller University Jena, Jena, Germany.
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Velázquez-Márquez S, De-la-Cruz IM, Tapia-López R, Núñez-Farfán J. Tropane alkaloids and terpenes synthase genes of Datura stramonium (Solanaceae). PeerJ 2021; 9:e11466. [PMID: 34178440 PMCID: PMC8212831 DOI: 10.7717/peerj.11466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 04/26/2021] [Indexed: 12/12/2022] Open
Abstract
Background Plants have evolved physical–chemical defense to prevent/diminish damage by their enemies. Chemical defense involves the synthesis’ pathways of specialized toxic, repellent, or anti-nutritive metabolites to herbivores. Molecular evolutionary studies have revealed the origin of new genes, acquisition and functional diversification along time in different plant lineages. Methods Using bioinformatic tools we analyze gene divergence of tropane alkaloids (TAs) and terpene synthases (TPSs) in Datura stramonium and other species of Solanaceae; compared gene and amino acids sequence of TAs and TPSs on genomes, cDNA and proteins sequences of Viridiplantae. We analyzed two recently assembled genomes of D. stramonium (Ticumán and Teotihuacán), transcriptomes of Datura metel and genomes of other Solanaceae. Hence, we analyzed variation of TAs and TPSs to infer genes involved in plant defense and plant responses before stress. We analyzed protein modeling and molecular docking to predict interactions between H6H and ligand; we translated the sequences (Teo19488, Tic8550 and Tic8549) obtained from the two genomes of D. stramonium by using Swiss-Model and Ramachandran plot and MolProbity structure validation of Teo19488 protein model. Results For TAs, we detected an expansion event in the tropinone reductase II (TRII) and the ratio synonymous/non-synonymous substitutions indicate positive selection. In contrast, a contraction event and negative selection was detected in tropinone reductase I (TRI). In Hy-oscyamine 6 b-hydroxylase (H6H), enzyme involved in the production of tropane alkaloids atropine and scopolamine, the synonymous/non-synonymous substitution ratio in its dominion indicates positive selection. For terpenes (TPS), we found 18 DsTPS in D. stramomiun and seven in D. metel; evolutionary analyses detected positive selection in TPS10.1 and TPS10.2 of D. stramonium and D. metel. Comparison of copies of TPSs in D. stramonium detected variation among them in the binding site. Duplication events and differentiation of TAs and TPSs of D. stramonium, as compared to other Solanaceae, suggest their possible involvement on adaptive evolution of defense to herbivores. Protein modeling and docking show that the three protein structures obtained of DsH6H from Teo19488, Tic-8550 and Tic8549 maintain the same interactions and the union site of 2OG-FeII_Oxy with the Hy-o ligand as in 6TTM of D. metel. Conclusion Our results indicate differences in the number of gene copies involved in the synthesis of tropane alkaloids, between the genomes of D. stramonium from two Mexican populations. More copies of genes related to the synthesis of tropane alkaloids (TRI, TRII, H6H, PMT) are found in D. stramonium as compared to Viridiplantae. Likewise, for terpene synthases (TPS), TPS-10 is duplicated in D. stramonium and D. metel. Further studies should be directed to experimentally assess gain (overexpression) or loss (silencing) of function of duplicated genes.
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Affiliation(s)
- Sabina Velázquez-Márquez
- Laboratorio de Genética Ecológica y Evolución, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, DF, Mexico
| | - Iván M De-la-Cruz
- Laboratorio de Genética Ecológica y Evolución, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, DF, Mexico
| | - Rosalinda Tapia-López
- Laboratorio de Genética Ecológica y Evolución, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, DF, Mexico
| | - Juan Núñez-Farfán
- Laboratorio de Genética Ecológica y Evolución, Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, DF, Mexico
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Guo K, Liu Y, Li SH. The untapped potential of plant sesterterpenoids: chemistry, biological activities and biosynthesis. Nat Prod Rep 2021; 38:2293-2314. [PMID: 34114591 DOI: 10.1039/d1np00021g] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: 1969 up to 2021Sesterterpenoids, biosynthetically derived from the precursor, namely geranylfarnesyl diphosphate (GFDP) are amongst the rarest of all isoprenoids with approximately 1300 compounds known. Most sesterterpenoids originate from marine organisms (especially sponges), while only about 15% of these compounds are isolated from several families of plants such as Lamiaceae, Gentianaceae, and Nartheciaceae. Many plant sesterterpenoids possess highly oxygenated and complex cyclic skeletons and exhibit remarkable biological activities involving cytotoxic, anti-inflammatory, antimicrobial, and antifeedant properties. Thus, due to their intrinsic chemical complexity and intriguing biological profiles, plant sesterterpenoids have attracted continuing interest from both chemists and biologists. However, the biosynthesis and distribution of sesterterpenoids in the plant kingdom still remain elusive, although substantial progress has been achieved in recent years. This review provides an overall coverage of sesterterpenoids originating from plant sources, followed by a classification of their chemical skeletons, which summarizes the distribution, chemistry, biological activities, biosynthesis and evolution of plant sesterterpenoids, aiming at strengthening the research efforts toward the untapped great potential of these unique natural product resources.
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Affiliation(s)
- Kai Guo
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P. R. China.
| | - Yan Liu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P. R. China. and State Key Laboratory of Phytochemistry and Plant Resources in West China, Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P. R. China.
| | - Sheng-Hong Li
- State Key Laboratory of Southwestern Chinese Medicine Resources, Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, P. R. China. and State Key Laboratory of Phytochemistry and Plant Resources in West China, Yunnan Key Laboratory of Natural Medicinal Chemistry, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, P. R. China.
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Jiang L, Zhang X, Sato Y, Zhu G, Minami A, Zhang W, Ozaki T, Zhu B, Wang Z, Wang X, Lv K, Zhang J, Wang Y, Gao S, Liu C, Hsiang T, Zhang L, Oikawa H, Liu X. Genome-Based Discovery of Enantiomeric Pentacyclic Sesterterpenes Catalyzed by Fungal Bifunctional Terpene Synthases. Org Lett 2021; 23:4645-4650. [DOI: 10.1021/acs.orglett.1c01361] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Lan Jiang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Xue Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Yuya Sato
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Guoliang Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Weiyan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Taro Ozaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Bin Zhu
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
- Engineering Research Centre of Pharmaceutical Process Chemistry, Ministry of Education, and Laboratory of Pharmaceutical Crystal Engineering & Technology, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhixin Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Xinye Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Kangjie Lv
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Jingyu Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Yongheng Wang
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, and Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, Jinan University, Guangzhou 510632, China
| | - Shushan Gao
- Chinese Academy of Sciences Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengwei Liu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, College of Life Sciences, Northeast Forestry University, Harbin 150040, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
| | - Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science of Technology, Shanghai 200237, China
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Mass spectrometry based untargeted metabolomics for plant systems biology. Emerg Top Life Sci 2021; 5:189-201. [DOI: 10.1042/etls20200271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/04/2021] [Accepted: 02/22/2021] [Indexed: 12/12/2022]
Abstract
Untargeted metabolomics enables the identification of key changes to standard pathways, but also aids in revealing other important and possibly novel metabolites or pathways for further analysis. Much progress has been made in this field over the past decade and yet plant metabolomics seems to still be an emerging approach because of the high complexity of plant metabolites and the number one challenge of untargeted metabolomics, metabolite identification. This final and critical stage remains the focus of current research. The intention of this review is to give a brief current state of LC–MS based untargeted metabolomics approaches for plant specific samples and to review the emerging solutions in mass spectrometer hardware and computational tools that can help predict a compound's molecular structure to improve the identification rate.
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Guo J, Cai YS, Cheng F, Yang C, Zhang W, Yu W, Yan J, Deng Z, Hong K. Genome Mining Reveals a Multiproduct Sesterterpenoid Biosynthetic Gene Cluster in Aspergillus ustus. Org Lett 2021; 23:1525-1529. [PMID: 33480256 DOI: 10.1021/acs.orglett.0c03996] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Genome mining of Aspergillus ustus 094102 enabled the discovery of a multiproduct bifunctional terpene synthase (BTS), AuAS. Heterologous expression of AuAS led to the discovery of five new sesterterpenes, and coexpression of the upstream CYP450 monooxygenase (AuAP450) generated four new sesterterpene alcohols. Additionally, aspergilol A showed cytotoxic activities against MCF-7, MDA-MB231, and HepG2 cancer cells (IC50 21.20-48.76 μM), and aspergilol B exhibited a cytotoxic effect on MCF-7 cells (IC50 27.41 μM).
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Affiliation(s)
- Jingjing Guo
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - You-Sheng Cai
- Institute of TCM and Natural Products, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Fangcai Cheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Chenjie Yang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Wenqi Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Wulin Yu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Jingjing Yan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
| | - Kui Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education and School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, People's Republic of China
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40
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Li K, Gustafson KR. Sesterterpenoids: chemistry, biology, and biosynthesis. Nat Prod Rep 2020; 38:1251-1281. [PMID: 33350420 DOI: 10.1039/d0np00070a] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Covering: July 2012 to December 2019Over the last seven years, expanding research efforts focused on sesterterpenoids has led to the isolation, identification, and characterization of numerous structurally novel and biologically active sesterterpenoids. These newly reported sesterterpenoids provide diverse structures that often incorporate unprecedented ring systems and new carbon skeletons, as well as unusual functional group arrays. Biological activities of potential biomedical importance including suppression of cancer cell growth, inhibition of enzymatic activity, and modulation of receptor signaling, as well as ecologically important functions such as antimicrobial effects and deterrence of herbivorous insects have been associated with a variety of sesterterpenoids. There has also been a rapid growth in our knowledge of the genomics, enzymology, and specific pathways associated with sesterterpene biosynthesis. This has opened up new opportunities for future sesterterpene discovery and diversification through the expression of new cryptic metabolites and the engineered manipulation of associated biosynthetic machinery and processes. In this paper we reviewed 498 new sesterterpenoids, including their structures, source organisms, country of origin, relevant bioactivities, and biosynthesis.
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Affiliation(s)
- Keke Li
- College of Life Science, Dalian Minzu University, Dalian 116600, China.
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Yang J, Li Z, Lian J, Qi G, Shi P, He J, Hu Z, Zhang M. Brassicaceae transcriptomes reveal convergent evolution of super-accumulation of sinigrin. Commun Biol 2020; 3:779. [PMID: 33328568 PMCID: PMC7745032 DOI: 10.1038/s42003-020-01523-x] [Citation(s) in RCA: 6] [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: 03/23/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022] Open
Abstract
Wasabi, horseradish and mustard are popular pungent crops in which the characteristic bioactive hydrolysis of specialized glucosinolates (GSLs) occurs. Although the metabolic pathways of GSLs are well elucidated, how plants have evolved convergent mechanisms to accumulate identical GSL components remains largely unknown. In this study, we discovered that sinigrin is predominantly synthesized in wasabi, horseradish and mustard in Brassicaceae. We de novo assembled the transcriptomes of the three species, revealing the expression patterns of gene clusters associated with chain elongation, side chain modification and transport. Our analysis further revealed that several gene clusters were convergently selected during evolution, exhibiting convergent shifts in amino acid preferences in mustard, wasabi and horseradish. Collectively, our findings provide insights into how unrelated crop species evolve the capacity for sinigrin super-accumulation and thus promise a potent strategy for engineering metabolic pathways at multiple checkpoints to fortify bioactive compounds for condiment or pharmaceutical purposes.
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Affiliation(s)
- Jinghua Yang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, 310058, Hangzhou, China
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, 310058, Hangzhou, China
| | - Zhangping Li
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, 310058, Hangzhou, China
| | - Jinmin Lian
- Biozeron Shenzhen, Inc., 518081, Shenzhen, China
| | - Guoning Qi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Pibiao Shi
- Xinyang Agricultural Experiment Station of Yancheng, 224049, Yancheng, China
| | - Jiawei He
- Alpine Economic Plant Research Institute of Yunnan Academy of Agricultural Sciences, 674199, lijiang, China
| | - Zhongyuan Hu
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, 310058, Hangzhou, China
| | - Mingfang Zhang
- Laboratory of Germplasm Innovation and Molecular Breeding, Institute of Vegetable Science, Zhejiang University, 310058, Hangzhou, China.
- Key Laboratory of Horticultural Plant Growth and Development, Ministry of Agriculture and Rural Affairs, 310058, Hangzhou, China.
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Hou A, Dickschat JS. The Biosynthetic Gene Cluster for Sestermobaraenes-Discovery of a Geranylfarnesyl Diphosphate Synthase and a Multiproduct Sesterterpene Synthase from Streptomyces mobaraensis. Angew Chem Int Ed Engl 2020; 59:19961-19965. [PMID: 32749032 PMCID: PMC7693059 DOI: 10.1002/anie.202010084] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Indexed: 01/23/2023]
Abstract
A biosynthetic gene cluster from Streptomyces mobaraensis encoding the first cases of a bacterial geranylfarnesyl diphosphate synthase and a type I sesterterpene synthase was identified. The structures of seven sesterterpenes produced by these enzymes were elucidated, including their absolute configurations. The enzyme mechanism of the sesterterpene synthase was investigated by extensive isotope labeling experiments.
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Affiliation(s)
- Anwei Hou
- Kekulé-Institute of Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Strasse 153121BonnGermany
| | - Jeroen S. Dickschat
- Kekulé-Institute of Organic Chemistry and BiochemistryUniversity of BonnGerhard-Domagk-Strasse 153121BonnGermany
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43
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Yu HB, Gu BB, Iwasaki A, Jiang WL, Ecker A, Wang SP, Yang F, Lin HW. Dactylospenes A-E, Sesterterpenes from the Marine Sponge Dactylospongia elegans. Mar Drugs 2020; 18:md18100491. [PMID: 32993037 PMCID: PMC7600696 DOI: 10.3390/md18100491] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 12/03/2022] Open
Abstract
Chemical investigation on a marine sponge, Dactylospongia elegans, yielded five new γ-oxygenated butenolide sesterterpene derivatives, dactylospenes A–E (1–5), as well as two known biosynthetically related compounds, luffariellolide (6) and furospinosulin B (7). The structures of these compounds were elucidated on the basis of their spectroscopic data, experimental and calculated electronic circular dichroism (ECD) analysis, as well as comparison of the NMR data with those of known analogs. These metabolites are the first γ-oxygenated butenolide sesterterpenes to be reported from this genus. These compounds were evaluated in antimicrobial, anti-inflammatory, and cytotoxic assays. Only compounds 1, 3, and 6 exhibited moderate cytotoxicity against DU145, SW1990, Huh7, and PANC-1 cancer cell lines with IC50 values in the range of 2.11–13.35 μM. Furthermore, compound 2, without cytotoxicity, exhibited significant inhibitory effects (inhibitory rate 77.5%) on nitric oxide production induced by lipopolysaccharide at 10 μM.
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Affiliation(s)
- Hao-Bing Yu
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center of PLA, Second Military Medical University, Shanghai 200433, China;
| | - Bin-Bin Gu
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China; (B.-B.G.); (S.-P.W.)
| | - Arihiro Iwasaki
- Department of Chemistry, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan;
| | - Wen-Li Jiang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Second Military Medical University, Shanghai 200433, China;
| | - Andrew Ecker
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, CA 92093, USA;
| | - Shu-Ping Wang
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China; (B.-B.G.); (S.-P.W.)
| | - Fan Yang
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China; (B.-B.G.); (S.-P.W.)
- Correspondence: (F.Y.); (H.-W.L.); Tel.: +86-21-6838-3346 (H.-W.L.)
| | - Hou-Wen Lin
- Research Center for Marine Drugs, State Key Laboratory of Oncogenes and Related Genes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China; (B.-B.G.); (S.-P.W.)
- Correspondence: (F.Y.); (H.-W.L.); Tel.: +86-21-6838-3346 (H.-W.L.)
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Chen Q, Li J, Liu Z, Mitsuhashi T, Zhang Y, Liu H, Ma Y, He J, Shinada T, Sato T, Wang Y, Liu H, Abe I, Zhang P, Wang G. Molecular Basis for Sesterterpene Diversity Produced by Plant Terpene Synthases. PLANT COMMUNICATIONS 2020; 1:100051. [PMID: 33367256 PMCID: PMC7747971 DOI: 10.1016/j.xplc.2020.100051] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/10/2020] [Accepted: 04/26/2020] [Indexed: 05/04/2023]
Abstract
Class I terpene synthase (TPS) generates bioactive terpenoids with diverse backbones. Sesterterpene synthase (sester-TPS, C25), a branch of class I TPSs, was recently identified in Brassicaceae. However, the catalytic mechanisms of sester-TPSs are not fully understood. Here, we first identified three nonclustered functional sester-TPSs (AtTPS06, AtTPS22, and AtTPS29) in Arabidopsis thaliana. AtTPS06 utilizes a type-B cyclization mechanism, whereas most other sester-TPSs produce various sesterterpene backbones via a type-A cyclization mechanism. We then determined the crystal structure of the AtTPS18-FSPP complex to explore the cyclization mechanism of plant sester-TPSs. We used structural comparisons and site-directed mutagenesis to further elucidate the mechanism: (1) mainly due to the outward shift of helix G, plant sester-TPSs have a larger catalytic pocket than do mono-, sesqui-, and di-TPSs to accommodate GFPP; (2) type-A sester-TPSs have more aromatic residues (five or six) in their catalytic pocket than classic TPSs (two or three), which also determines whether the type-A or type-B cyclization mechanism is active; and (3) the other residues responsible for product fidelity are determined by interconversion of AtTPS18 and its close homologs. Altogether, this study improves our understanding of the catalytic mechanism of plant sester-TPS, which ultimately enables the rational engineering of sesterterpenoids for future applications.
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Affiliation(s)
- Qingwen Chen
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jianxu Li
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhixi Liu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yuting Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Haili Liu
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yihua Ma
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Juan He
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Tetsuro Shinada
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Tsutomu Sato
- Department of Applied Biological Chemistry, Faculty of Agriculture, Graduate School of Science and Technology, Niigata University, 8050 Ikarashi-2, Niigata 950-2181, Japan
| | - Yong Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hongwei Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- Corresponding author
| | - Guodong Wang
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100039, China
- Corresponding author
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Hou A, Dickschat JS. Biosynthesegencluster für Sestermobaraene – Entdeckung einer Geranylfarnesyldiphosphatsynthase und einer Multiprodukt‐Sesterterpensynthase aus
Streptomyces mobaraensis. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010084] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Anwei Hou
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Deutschland
| | - Jeroen S. Dickschat
- Kekulé-Institut für Organische Chemie und Biochemie Universität Bonn Gerhard-Domagk-Strasse 1 53121 Bonn Deutschland
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46
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Cao X, Shi Y, Wu S, Wu X, Wang K, Sun H, He S, Dickschat JS, Wu B. Polycyclic meroterpenoids, talaromyolides E − K for antiviral activity against pseudorabies virus from the endophytic fungus Talaromyces purpureogenus. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131349] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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47
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Zhou F, Pichersky E. More is better: the diversity of terpene metabolism in plants. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:1-10. [PMID: 32088555 DOI: 10.1016/j.pbi.2020.01.005] [Citation(s) in RCA: 126] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/15/2020] [Accepted: 01/21/2020] [Indexed: 05/18/2023]
Abstract
All plants synthesize a diverse array of terpenoid metabolites. Some are common to all, but many are synthesized only in specific taxa and presumably evolved as adaptations to specific ecological conditions. While the basic terpenoid biosynthetic pathways are common in all plants, recent discoveries have revealed many variations in the way plants synthesized specific terpenes. A major theme is the much greater number of substrates that can be used by enzymes belonging to the terpene synthase (TPS) family. Other recent discoveries include non-TPS enzymes that catalyze the formation of terpenes, and novel transport mechanisms.
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Affiliation(s)
- Fei Zhou
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Eran Pichersky
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA.
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48
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Lichman BR, Godden GT, Buell CR. Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:74-83. [PMID: 32344371 DOI: 10.1016/j.pbi.2020.03.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 02/19/2020] [Accepted: 03/04/2020] [Indexed: 05/28/2023]
Abstract
Plants are reservoirs of extreme chemical diversity, yet biosynthetic pathways remain underexplored in the majority of taxa. Access to improved, inexpensive genomic and computational technologies has recently enhanced our understanding of plant specialized metabolism at the biochemical and evolutionary levels including the elucidation of pathways leading to key metabolites. Furthermore, these approaches have provided insights into the mechanisms of chemical evolution, including neofunctionalization and subfunctionalization, structural variation, and modulation of gene expression. The broader utilization of genomic tools across the plant tree of life, and an expansion of genomic resources from multiple accessions within species or populations, will improve our overall understanding of chemodiversity. These data and knowledge will also lead to greater insight into the selective pressures contributing to and maintaining this diversity, which in turn will enable the development of more accurate predictive models of specialized metabolism in plants.
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Affiliation(s)
- Benjamin R Lichman
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Grant T Godden
- Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA
| | - Carol Robin Buell
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; Plant Resilience Institute, Michigan State University, 612 Wilson Road, East Lansing, MI 48824, USA; MSU AgBioResearch, Michigan State University, 446 West Circle Drive, East Lansing, MI 48824, USA.
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49
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Zhou F, Pichersky E. The complete functional characterisation of the terpene synthase family in tomato. THE NEW PHYTOLOGIST 2020; 226:1341-1360. [PMID: 31943222 PMCID: PMC7422722 DOI: 10.1111/nph.16431] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 01/05/2020] [Indexed: 05/14/2023]
Abstract
Analysis of the updated reference tomato genome found 34 full-length TPS genes and 18 TPS pseudogenes. Biochemical analysis has now identified the catalytic activities of all enzymes encoded by the 34 TPS genes: one isoprene synthase, 10 exclusively or predominantly monoterpene synthases, 17 sesquiterpene synthases and six diterpene synthases. Among the monoterpene and sesquiterpene and diterpene synthases, some use trans-prenyl diphosphates, some use cis-prenyl diphosphates and some use both. The isoprene synthase is cytosolic; six monoterpene synthases are plastidic, and four are cytosolic; the sesquiterpene synthases are almost all cytosolic, with the exception of one found in the mitochondria; and three diterpene synthases are found in the plastids, one in the cytosol and two in the mitochondria. New trans-prenyltransferases (TPTs) were characterised; together with previously characterised TPTs and cis-prenyltransferases (CPTs), tomato plants can make all cis and trans C10 , C15 and C20 prenyl diphosphates. Every type of plant tissue examined expresses some TPS genes and some TPTs and CPTs. Phylogenetic comparison of the TPS genes from tomato and Arabidopsis shows expansions in each clade of the TPS gene family in each lineage (and inferred losses), accompanied by changes in subcellular localisations and substrate specificities.
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Affiliation(s)
- Fei Zhou
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMI48109USA
| | - Eran Pichersky
- Department of Molecular, Cellular, and Developmental BiologyUniversity of MichiganAnn ArborMI48109USA
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50
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Sato H, Yamazaki M, Uchiyama M. DFT Study on the Biosynthesis of Preasperterpenoid A: Role of Secondary Carbocations in the Carbocation Cascade. Chem Pharm Bull (Tokyo) 2020; 68:487-490. [PMID: 32378547 DOI: 10.1248/cpb.c20-00037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Preasperterpenoid A, featuring a 5/7/(3)6/5 pentacyclic structure, is a C25 sesterterpenoid produced by Penicillium verruculosum. The results of density functional calculations on putative biosynthetic carbocation cyclization/rearrangements leading to preasperterpenoid A revealed a highly concerted four-step cyclization mechanism. Interestingly, two secondary carbocation structures were obtained as minima, but appeared almost as shoulders in the energy profile, and may represent essentially transient structures during the highly concerted reaction.
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Affiliation(s)
- Hajime Sato
- Graduate School of Pharmaceutical Sciences, Chiba University.,Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN
| | - Mami Yamazaki
- Graduate School of Pharmaceutical Sciences, Chiba University
| | - Masanobu Uchiyama
- Cluster of Pioneering Research (CPR), Advanced Elements Chemistry Laboratory, RIKEN.,Graduate School of Pharmaceutical Sciences, The University of Tokyo.,Research Initiative for Supra-Materials (RISM), Shinshu University
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