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Luo P, Huang JH, Lv JM, Wang GQ, Hu D, Gao H. Biosynthesis of fungal terpenoids. Nat Prod Rep 2024; 41:748-783. [PMID: 38265076 DOI: 10.1039/d3np00052d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Covering: up to August 2023Terpenoids, which are widely distributed in animals, plants, and microorganisms, are a large group of natural products with diverse structures and various biological activities. They have made great contributions to human health as therapeutic agents, such as the anti-cancer drug paclitaxel and anti-malarial agent artemisinin. Accordingly, the biosynthesis of this important class of natural products has been extensively studied, which generally involves two major steps: hydrocarbon skeleton construction by terpenoid cyclases and skeleton modification by tailoring enzymes. Additionally, fungi (Ascomycota and Basidiomycota) serve as an important source for the discovery of terpenoids. With the rapid development of sequencing technology and bioinformatics approaches, genome mining has emerged as one of the most effective strategies to discover novel terpenoids from fungi. To date, numerous terpenoid cyclases, including typical class I and class II terpenoid cyclases as well as emerging UbiA-type terpenoid cyclases, have been identified, together with a variety of tailoring enzymes, including cytochrome P450 enzymes, flavin-dependent monooxygenases, and acyltransferases. In this review, our aim is to comprehensively present all fungal terpenoid cyclases identified up to August 2023, with a focus on newly discovered terpenoid cyclases, especially the emerging UbiA-type terpenoid cyclases, and their related tailoring enzymes from 2015 to August 2023.
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Affiliation(s)
- Pan Luo
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Jia-Hua Huang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Jian-Ming Lv
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Gao-Qian Wang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Dan Hu
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Hao Gao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
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Frey M, Bathe U, Meink L, Balcke GU, Schmidt J, Frolov A, Soboleva A, Hassanin A, Davari MD, Frank O, Schlagbauer V, Dawid C, Tissier A. Combinatorial biosynthesis in yeast leads to over 200 diterpenoids. Metab Eng 2024; 82:193-200. [PMID: 38387676 DOI: 10.1016/j.ymben.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/24/2024] [Accepted: 02/12/2024] [Indexed: 02/24/2024]
Abstract
Diterpenoids form a diverse group of natural products, many of which are or could become pharmaceuticals or industrial chemicals. The modular character of diterpene biosynthesis and the promiscuity of the enzymes involved make combinatorial biosynthesis a promising approach to generate libraries of diverse diterpenoids. Here, we report on the combinatorial assembly in yeast of ten diterpene synthases producing (+)-copalyl diphosphate-derived backbones and four cytochrome P450 oxygenases (CYPs) in diverse combinations. This resulted in the production of over 200 diterpenoids. Based on literature and chemical database searches, 162 of these compounds can be considered new-to-Nature. The CYPs accepted most substrates they were given but remained regioselective with few exceptions. Our results provide the basis for the systematic exploration of the diterpenoid chemical space in yeast using sequence databases.
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Affiliation(s)
- Maximilian Frey
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Ulschan Bathe
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany; Department of Horticultural Sciences, University of Florida, 2550 Hull Road, Gainesville, FL 32611, USA
| | - Luca Meink
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Gerd U Balcke
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Jürgen Schmidt
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Andrej Frolov
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Alena Soboleva
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Ahmed Hassanin
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany; Department of Pharmacognosy, Faculty of Pharmacy, Assiut University, Assiut 71526, Egypt
| | - Mehdi D Davari
- Department of Bioorganic Chemistry Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany
| | - Oliver Frank
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Verena Schlagbauer
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Corinna Dawid
- Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
| | - Alain Tissier
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Weinberg 3, 06120, Halle (Saale), Germany; Martin-Luther University Halle-Wittenberg, Institute of Pharmacy, Kurt-Mothes-Strasse 3, 06120 Halle, Germany.
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Deng L, Zhong M, Li Y, Hu G, Zhang C, Peng Q, Zhang Z, Fang J, Yu X. High hydrostatic pressure harnesses the biosynthesis of secondary metabolites via the regulation of polyketide synthesis genes of hadal sediment-derived fungi. Front Microbiol 2023; 14:1207252. [PMID: 37383634 PMCID: PMC10293889 DOI: 10.3389/fmicb.2023.1207252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/24/2023] [Indexed: 06/30/2023] Open
Abstract
Deep-sea fungi have evolved extreme environmental adaptation and possess huge biosynthetic potential of bioactive compounds. However, not much is known about the biosynthesis and regulation of secondary metabolites of deep-sea fungi under extreme environments. Here, we presented the isolation of 15 individual fungal strains from the sediments of the Mariana Trench, which were identified by internal transcribed spacer (ITS) sequence analysis as belonging to 8 different fungal species. High hydrostatic pressure (HHP) assays were performed to identify the piezo-tolerance of the hadal fungi. Among these fungi, Aspergillus sydowii SYX6 was selected as the representative due to the excellent tolerance of HHP and biosynthetic potential of antimicrobial compounds. Vegetative growth and sporulation of A. sydowii SYX6 were affected by HHP. Natural product analysis with different pressure conditions was also performed. Based on bioactivity-guided fractionation, diorcinol was purified and characterized as the bioactive compound, showing significant antimicrobial and antitumor activity. The core functional gene associated with the biosynthetic gene cluster (BGC) of diorcinol was identified in A. sydowii SYX6, named as AspksD. The expression of AspksD was apparently regulated by the HHP treatment, correlated with the regulation of diorcinol production. Based on the effect of the HHP tested here, high pressure affected the fungal development and metabolite production, as well as the expression level of biosynthetic genes which revealed the adaptive relationship between the metabolic pathway and the high-pressure environment at the molecular level.
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Affiliation(s)
- Ludan Deng
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Maosheng Zhong
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Yongqi Li
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Guangzhao Hu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Changhao Zhang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Qingqing Peng
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Zhizhen Zhang
- Ocean College, Zhoushan Campus, Zhejiang University, Zhoushan, China
| | - Jiasong Fang
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
| | - Xi Yu
- Shanghai Engineering Research Center of Hadal Science and Technology, College of Marine Sciences, Shanghai Ocean University, Shanghai, China
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Scesa PD, Lin Z, Schmidt EW. Ancient defensive terpene biosynthetic gene clusters in the soft corals. Nat Chem Biol 2022; 18:659-663. [PMID: 35606556 DOI: 10.1038/s41589-022-01027-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/30/2022] [Indexed: 11/09/2022]
Abstract
Diterpenes are major defensive small molecules that enable soft corals to survive without a tough exterior skeleton, and, until now, their biosynthetic origin has remained intractable. Furthermore, biomedical application of these molecules has been hampered by lack of supply. Here, we identify and characterize coral-encoded terpene cyclase genes that produce the eunicellane precursor of eleutherobin and cembrene, representative precursors for the >2,500 terpenes found in octocorals. Related genes are found in all sequenced octocorals and form their own clade, indicating a potential ancient origin concomitant with the split between the hard and soft corals. Eleutherobin biosynthetic genes are colocalized in a single chromosomal region. This demonstrates that, like plants and microbes, animals also harbor defensive biosynthetic gene clusters, supporting a recombinational model to explain why specialized or defensive metabolites are adjacently encoded in the genome.
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Affiliation(s)
- Paul D Scesa
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Zhenjian Lin
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, USA
| | - Eric W Schmidt
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT, USA.
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5
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Chen HY, Lei JY, Li SL, Guo LQ, Lin JF, Wu GH, Lu J, Ye ZW. Progress in biological activities and biosynthesis of edible fungi terpenoids. Crit Rev Food Sci Nutr 2022; 63:7288-7310. [PMID: 35238261 DOI: 10.1080/10408398.2022.2045559] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The edible fungi have both edible and medicinal functions, in which terpenoids are one of the most important active ingredients. Terpenoids possess a wide range of biological activities and show great potential in the pharmaceutical and healthcare industries. In this review, the diverse biological activities of edible fungi terpenoids were summarized with emphasis on the mechanism of anti-cancer and anti-inflammation. Subsequently, this review focuses on advances in knowledge and understanding of the biosynthesis of terpenoids in edible fungi, especially in the generation of sesquiterpenes, diterpenes, and triterpenes. This paper is aim to provide an overview of biological functions and biosynthesis developed for utilizing the terpenoids in edible fungi.
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Affiliation(s)
- Hai-Ying Chen
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Jin-Yu Lei
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Shu-Li Li
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Li-Qiong Guo
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Jun-Fang Lin
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Guang-Hong Wu
- College of Food Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Jun Lu
- Faculty of Health and Environmental Sciences, Auckland University of Technology, Auckland, New Zealand
| | - Zhi-Wei Ye
- College of Food Science, South China Agricultural University, Guangzhou, China
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou, China
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Comparative Genomic and Metabolomic Analysis of Termitomyces Species Provides Insights into the Terpenome of the Fungal Cultivar and the Characteristic Odor of the Fungus Garden of Macrotermes natalensis Termites. mSystems 2022; 7:e0121421. [PMID: 35014870 PMCID: PMC8751386 DOI: 10.1128/msystems.01214-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Macrotermitinae termites have domesticated fungi of the genus Termitomyces as food for their colony, analogously to human farmers growing crops. Termites propagate the fungus by continuously blending foraged and predigested plant material with fungal mycelium and spores (fungus comb) within designated subterranean chambers. To test the hypothesis that the obligate fungal symbiont emits specific volatiles (odor) to orchestrate its life cycle and symbiotic relations, we determined the typical volatile emission of fungus comb biomass and Termitomyces nodules, revealing α-pinene, camphene, and d-limonene as the most abundant terpenes. Genome mining of Termitomyces followed by gene expression studies and phylogenetic analysis of putative enzymes related to secondary metabolite production encoded by the genomes uncovered a conserved and specific biosynthetic repertoire across strains. Finally, we proved by heterologous expression and in vitro enzymatic assays that a highly expressed gene sequence encodes a rare bifunctional mono-/sesquiterpene cyclase able to produce the abundant comb volatiles camphene and d-limonene. IMPORTANCE The symbiosis between macrotermitinae termites and Termitomyces is obligate for both partners and is one of the most important contributors to biomass conversion in the Old World tropic’s ecosystems. To date, research efforts have dominantly focused on acquiring a better understanding of the degradative capabilities of Termitomyces to sustain the obligate nutritional symbiosis, but our knowledge of the small-molecule repertoire of the fungal cultivar mediating interspecies and interkingdom interactions has remained fragmented. Our omics-driven chemical, genomic, and phylogenetic study provides new insights into the volatilome and biosynthetic capabilities of the evolutionarily conserved fungal genus Termitomyces, which allows matching metabolites to genes and enzymes and, thus, opens a new source of unique and rare enzymatic transformations.
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7
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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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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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Biosynthesis and regulation of terpenoids from basidiomycetes: exploration of new research. AMB Express 2021; 11:150. [PMID: 34779947 PMCID: PMC8594250 DOI: 10.1186/s13568-021-01304-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/16/2021] [Indexed: 12/15/2022] Open
Abstract
Basidiomycetes, also known as club fungi, consist of a specific group of fungi. Basidiomycetes produce a large number of secondary metabolites, of which sesquiterpenoids, diterpenoids and triterpenoids are the primary components. However, these terpenoids tend to be present in low amounts, which makes it difficult to meet application requirements. Terpenoid biosynthesis improves the quantity of these secondary metabolites. However, current understanding of the biosynthetic mechanism of terpenoids in basidiomycetes is insufficient. Therefore, this article reviews the latest research on the biosynthesis of terpenoids in basidiomycetes and summarizes the CYP450 involved in the biosynthesis of terpenoids in basidiomycetes. We also propose opportunities and challenges for chassis microbial heterologous production of terpenoids in basidiomycetes and provide a reference basis for the better development of basidiomycete engineering.
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Abstract
The fungal kingdom has provided advances in our ability to identify biosynthetic gene clusters (BGCs) and to examine how gene composition of BGCs evolves across species and genera. However, little is known about the evolution of specific BGC regulators that mediate how BGCs produce secondary metabolites (SMs). A bioinformatics search for conservation of the Aspergillus fumigatus xanthocillin BGC revealed an evolutionary trail of xan-like BGCs across Eurotiales species. Although the critical regulatory and enzymatic genes were conserved in Penicillium expansum, overexpression (OE) of the conserved xan BGC transcription factor (TF) gene, PexanC, failed to activate the putative xan BGC transcription or xanthocillin production in P. expansum, in contrast to the role of AfXanC in A. fumigatus. Surprisingly, OE::PexanC was instead found to promote citrinin synthesis in P. expansum via trans induction of the cit pathway-specific TF, ctnA, as determined by cit BGC expression and chemical profiling of ctnA deletion and OE::PexanC single and double mutants. OE::AfxanC results in significant increases of xan gene expression and metabolite synthesis in A. fumigatus but had no effect on either xanthocillin or citrinin production in P. expansum. Bioinformatics and promoter mutation analysis led to the identification of an AfXanC binding site, 5'-AGTCAGCA-3', in promoter regions of the A. fumigatus xan BGC genes. This motif was not in the ctnA promoter, suggesting a different binding site of PeXanC. A compilation of a bioinformatics examination of XanC orthologs and the presence/absence of the 5'-AGTCAGCA-3' binding motif in xan BGCs in multiple Aspergillus and Penicillium spp. supports an evolutionary divergence of XanC regulatory targets that we speculate reflects an exaptation event in the Eurotiales. IMPORTANCE Fungal secondary metabolites (SMs) are an important source of pharmaceuticals on one hand and toxins on the other. Efforts to identify the biosynthetic gene clusters (BGCs) that synthesize SMs have yielded significant insights into how variation in the genes that compose BGCs may impact subsequent metabolite production within and between species. However, the role of regulatory genes in BGC activation is less well understood. Our finding that the bZIP transcription factor XanC, located in the xanthocillin BGC of both Aspergillus fumigatus and Penicillium expansum, has functionally diverged to regulate different BGCs in these two species emphasizes that the diversification of BGC regulatory elements may sometimes occur through exaptation, which is the co-option of a gene that evolved for one function to a novel function. Furthermore, this work suggests that the loss/gain of transcription factor binding site targets may be an important mediator in the evolution of secondary-metabolism regulatory elements.
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An interpreted atlas of biosynthetic gene clusters from 1,000 fungal genomes. Proc Natl Acad Sci U S A 2021; 118:2020230118. [PMID: 33941694 DOI: 10.1073/pnas.2020230118] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Fungi are prolific producers of natural products, compounds which have had a large societal impact as pharmaceuticals, mycotoxins, and agrochemicals. Despite the availability of over 1,000 fungal genomes and several decades of compound discovery efforts from fungi, the biosynthetic gene clusters (BGCs) encoded by these genomes and the associated chemical space have yet to be analyzed systematically. Here, we provide detailed annotation and analyses of fungal biosynthetic and chemical space to enable genome mining and discovery of fungal natural products. Using 1,037 genomes from species across the fungal kingdom (e.g., Ascomycota, Basidiomycota, and non-Dikarya taxa), 36,399 predicted BGCs were organized into a network of 12,067 gene cluster families (GCFs). Anchoring these GCFs with reference BGCs enabled automated annotation of 2,026 BGCs with predicted metabolite scaffolds. We performed parallel analyses of the chemical repertoire of fungi, organizing 15,213 fungal compounds into 2,945 molecular families (MFs). The taxonomic landscape of fungal GCFs is largely species specific, though select families such as the equisetin GCF are present across vast phylogenetic distances with parallel diversifications in the GCF and MF. We compare these fungal datasets with a set of 5,453 bacterial genomes and their BGCs and 9,382 bacterial compounds, revealing dramatic differences between bacterial and fungal biosynthetic logic and chemical space. These genomics and cheminformatics analyses reveal the large extent to which fungal and bacterial sources represent distinct compound reservoirs. With a >10-fold increase in the number of interpreted strains and annotated BGCs, this work better regularizes the biosynthetic potential of fungi for rational compound discovery.
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In Depth Natural Product Discovery from the Basidiomycetes Stereum Species. Microorganisms 2020; 8:microorganisms8071049. [PMID: 32679785 PMCID: PMC7409058 DOI: 10.3390/microorganisms8071049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 01/08/2023] Open
Abstract
Natural metabolites from microorganisms play significant roles in the discovery of drugs, both for disease treatments in humans, and applications in agriculture. The Basidiomycetes Stereum genus has been a source of such bioactive compounds. Here we report on the structures and activities of secondary metabolites from Stereum. Their structural types include sesquiterpenoids, polyketides, vibralactones, triterpenoids, sterols, carboxylic acids and saccharides. Most of them showed biological activities including cytotoxic, antibacterial, antifungal, antiviral, radical scavenging activity, autophagy inducing activity, inhibiting pancreatic lipase against malarial parasite, nematocidal and so on. The syntheses of some metabolites have been studied. In this review, 238 secondary metabolites from 10 known species and various unidentified species of Stereum were summarized over the last seven decades.
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