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Hu Y, Zhao X, Song Y, Jiang J, Long T, Cong M, Miao Y, Liu Y, Yang Z, Zhu Y, Wang J. Anti-inflammatory and Neuroprotective α-Pyrones from a Marine-Derived Strain of the Fungus Arthrinium arundinis and Their Heterologous Expression. JOURNAL OF NATURAL PRODUCTS 2024. [PMID: 38687877 DOI: 10.1021/acs.jnatprod.4c00393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
Fungal linear polyketides, such as α-pyrones with a 6-alkenyl chain, have been a rich source of biologically active compounds. Two new (1 and 2) and four known (3-6) 6-alkenylpyrone polyketides were isolated from a marine-derived strain of the fungus Arthrinium arundinis. Their structures were determined based on extensive spectroscopic analysis. The biosynthetic gene cluster (alt) for alternapyrones was identified from A. arundinis ZSDS-F3 and validated by heterologous expression in Aspergillus nidulans A1145 ΔSTΔEM, which revealed that the cytochrome P450 monooxygenase Alt2' could convert the methyl group 26-CH3 to a carboxyl group to produce 4 from 3. Another cytochrome P450 monooxygenase, Alt3', catalyzed successive hydroxylation, epoxidation, and oxidation steps to produce 1, 2, 5, and 6 from 4. Alternapyrone G (1) not only suppressed M1 polarization in lipopolysaccharide (LPS)-stimulated BV2 microglia but also stimulated dendrite regeneration and neuronal survival after Aβ treatment, suggesting alternapyrone G may be utilized as a privileged scaffold for Alzheimer's disease drug discovery.
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Affiliation(s)
- Yiwei Hu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Xiaoyang Zhao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yue Song
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Jiahui Jiang
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Ocean University, Zhanjiang 524088, China
| | - Ting Long
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Mengjing Cong
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Yuhua Miao
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
| | - Yonghong Liu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Marine Ecology and Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Zhiyou Yang
- College of Food Science and Technology, Guangdong Provincial Key Laboratory of Aquatic Product Processing and Safety, Guangdong Province Engineering Laboratory for Marine Biological Products, Guangdong Provincial Engineering Technology Research Center of Seafood, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yiguang Zhu
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Marine Ecology and Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Junfeng Wang
- CAS Key Laboratory of Tropical Marine Bio-resources and Ecology/Guangdong Key Laboratory of Marine Materia Medica, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
- Sanya Institute of Marine Ecology and Engineering, Yazhou Scientific Bay, Sanya 572000, China
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Sousa TF, Vieira Reça BNP, Castro GS, da Silva IJS, Caniato FF, de Araújo Júnior MB, Yamagishi MEB, Koolen HHF, Bataglion GA, Hanada RE, da Silva GF. Trichoderma agriamazonicum sp. nov. (Hypocreaceae), a new ally in the control of phytopathogens. Microbiol Res 2023; 275:127469. [PMID: 37543005 DOI: 10.1016/j.micres.2023.127469] [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: 03/28/2023] [Revised: 07/23/2023] [Accepted: 08/01/2023] [Indexed: 08/07/2023]
Abstract
The genus Trichoderma comprises more than 500 valid species and is commonly used in agriculture for the control of plant diseases. In the present study, a Trichoderma species isolated from Scleronema micranthum (Malvaceae) has been extensively characterized and the morphological and phylogenetic data support the proposition of a new fungal species herein named Trichoderma agriamazonicum. This species inhibited the mycelial growth of all the nine phytopathogens tested both by mycoparasitism and by the production of VOCs, with a highlight for the inhibition of Corynespora cassiicola and Colletotrichum spp. The VOCs produced by T. agriamazonicum were able to control Capsicum chinense fruit rot caused by Colletotrichum scovillei and no symptoms were observed after seven days of phytopathogen inoculation. GC-MS revealed the production of mainly 6-amyl-α-pyrone, 1-octen-3-ol and 3-octanone during interaction with C. scovillei in C. chinense fruit. The HLPC-MS/MS analysis allowed us to annotate trikoningin KBII, hypocrenone C, 5-hydroxy-de-O-methyllasiodiplodin and unprecedented 7-mer peptaibols and lipopeptaibols. Comparative genomic analysis of five related Trichoderma species reveals a high number of proteins shared only with T. koningiopsis, mainly the enzymes related to oxidative stress. Regarding the CAZyme composition, T. agriamazonicum is most closely related to T. atroviride. A high protein copy number related to lignin and chitin degradation is observed for all Trichoderma spp. analyzed, while the presence of licheninase GH12 was observed only in T. agriamazonicum. Genome mining analysis identified 33 biosynthetic gene clusters (BGCs) of which 27 are new or uncharacterized, and the main BGCs are related to the production of polyketides. These results demonstrate the potential of this newly described species for agriculture and biotechnology.
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Affiliation(s)
- Thiago Fernandes Sousa
- Programa de Pós-graduação em Biotecnologia, Universidade Federal do Amazonas (UFAM), 69080-900 Manaus, Brazil; Embrapa Amazônia Ocidental, 69010-970 Manaus, Brazil
| | - Bruna Nayara Pantoja Vieira Reça
- Programa de Pós-graduação em Agricultura no Trópico Úmido (ATU), Instituto Nacional de Pesquisas da Amazônia (INPA), 69067-375 Manaus, Brazil
| | - Gleucinei Santos Castro
- Grupo de Pesquisas em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas (UEA), 690065-130 Manaus, Brazil
| | - Ingride Jarline Santos da Silva
- Programa de Pós-graduação em Biotecnologia, Universidade Federal do Amazonas (UFAM), 69080-900 Manaus, Brazil; Embrapa Amazônia Ocidental, 69010-970 Manaus, Brazil
| | - Fernanda Fátima Caniato
- Departamento de Ciências Fundamentais e Desenvolvimento Agrícola, Faculdade de Ciências Agrárias, Universidade Federal do Amazonas (UFAM), 69080-900 Manaus, Brazil
| | | | | | - Hector Henrique Ferreira Koolen
- Grupo de Pesquisas em Metabolômica e Espectrometria de Massas, Universidade do Estado do Amazonas (UEA), 690065-130 Manaus, Brazil
| | - Giovana Anceski Bataglion
- Departamento de Química do Instituto de Ciências Exatas, Universidade Federal do Amazonas (UFAM), 69080-900 Manaus, Brazil
| | - Rogério Eiji Hanada
- Instituto Nacional de Pesquisas da Amazônia (INPA), 69067-375 Manaus, Brazil.
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Fang Z, Zhang Q, Xiong W, Sun L, Tan B, Zhu M, Ma L, Zhang L, Zhu Y, Zhang C. Discovery of Tetronate-Containing Kongjuemycins from a Coral-Associated Actinomycete and Elucidation of Their Biosynthetic Origin. Org Lett 2023; 25:6346-6351. [PMID: 37606755 DOI: 10.1021/acs.orglett.3c02231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Tetronate antibiotics make up a growing family of natural products with a wide variety of biological activities. Herein, we report four new tetronates kongjuemycins (KJMs, 5-8) from a coral-associated actinomycete Pseudonocardia kongjuensis SCSIO 11457, and the identification and characterization of the KJM biosynthetic gene cluster (kjm) by heterologous expression, comparative genomic analysis, isotope labeling, and gene knockout studies. The biosynthesis of KJMs is demonstrated to harness diverse precursors from primary metabolism for building secondary metabolites.
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Affiliation(s)
- Zhuangjie Fang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Weiliang Xiong
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Lili Sun
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bin Tan
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Mengyi Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
| | - Liang Ma
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
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4
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Lin C, Feng XL, Liu Y, Li ZC, Li XZ, Qi J. Bioinformatic Analysis of Secondary Metabolite Biosynthetic Potential in Pathogenic Fusarium. J Fungi (Basel) 2023; 9:850. [PMID: 37623621 PMCID: PMC10455296 DOI: 10.3390/jof9080850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/11/2023] [Accepted: 08/13/2023] [Indexed: 08/26/2023] Open
Abstract
Fusarium species are among the filamentous fungi with the most pronounced impact on agricultural production and human health. The mycotoxins produced by pathogenic Fusarium not only attack various plants including crops, causing various plant diseases that lead to reduced yields and even death, but also penetrate into the food chain of humans and animals to cause food poisoning and consequent health hazards. Although sporadic studies have revealed some of the biosynthetic pathways of Fusarium toxins, they are insufficient to satisfy the need for a comprehensive understanding of Fusarium toxin production. In this study, we focused on 35 serious pathogenic Fusarium species with available genomes and systematically analyzed the ubiquity of the distribution of identified Fusarium- and non-Fusarium-derived fungal toxin biosynthesis gene clusters (BGCs) in these species through the mining of core genes and the comparative analysis of corresponding BGCs. Additionally, novel sesterterpene synthases and PKS_NRPS clusters were discovered and analyzed. This work is the first to systematically analyze the distribution of related mycotoxin biosynthesis in pathogenic Fusarium species. These findings enhance the knowledge of mycotoxin production and provide a theoretical grounding for the prevention of fungal toxin production using biotechnological approaches.
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Affiliation(s)
- Chao Lin
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xi-long Feng
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Yu Liu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Zhao-chen Li
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
| | - Xiu-Zhang Li
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Academy of Animal and Veterinary Sciences, Qinghai University, Xining 810016, China
| | - Jianzhao Qi
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, Xianyang 712100, China
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Zhang H, Guo L, Su Y, Wang R, Yang W, Mu W, Xuan L, Huang L, Wang J, Gao W. Hosts engineering and in vitro enzymatic synthesis for the discovery of novel natural products and their derivatives. Crit Rev Biotechnol 2023:1-19. [PMID: 37574211 DOI: 10.1080/07388551.2023.2236787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/23/2023] [Accepted: 06/17/2023] [Indexed: 08/15/2023]
Abstract
Novel natural products (NPs) and their derivatives are important sources for drug discovery, which have been broadly applied in the fields of agriculture, livestock, and medicine, making the synthesis of NPs and their derivatives necessarily important. In recent years, biosynthesis technology has received increasing attention due to its high efficiency in the synthesis of high value-added novel products and its advantages of green, environmental protection, and controllability. In this review, the technological advances of biosynthesis strategies in the discovery of novel NPs and their derivatives are outlined, with an emphasis on two areas of host engineering and in vitro enzymatic synthesis. In terms of hosts engineering, multiple microorganisms, including Streptomyces, Aspergillus, and Penicillium, have been used as the biosynthetic gene clusters (BGCs) provider and host strain for the expression of BGCs to discover new compounds over the past years. In addition, the use of in vitro enzymatic synthesis strategy to generate novel compounds such as triterpenoid saponins and flavonoids is also hereby described.
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Affiliation(s)
- Huanyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
| | - Lanping Guo
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, P.R. China
| | - Yaowu Su
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
| | - Rubing Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
| | - Wenqi Yang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
| | - Wenrong Mu
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, P.R. China
| | - Liangshuang Xuan
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, P.R. China
| | - Luqi Huang
- National Resource Center for Chinese Meteria Medica, China Academy of Chinese Medical Sciences, Beijing, P.R. China
| | - Juan Wang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
| | - Wenyuan Gao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, P.R. China
- Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, P.R. China
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Han W, Wu Z, Zhong Z, Williams J, Jacobsen SE, Sun Z, Tang Y. Assessing the Biosynthetic Inventory of the Biocontrol Fungus Trichoderma afroharzianum T22. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37471583 DOI: 10.1021/acs.jafc.3c03240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Natural products biosynthesized from biocontrol fungi in the rhizosphere can have both beneficial and deleterious effects on plants. Herein, we performed a comprehensive analysis of natural product biosynthetic gene clusters (BGCs) from the widely used biocontrol fungus Trichoderma afroharzianum T22 (ThT22). This fungus encodes at least 64 BGCs, yet only seven compounds and four BGCs were previously characterized or mined. We correlated 21 BGCs of ThT22 with known primary and secondary metabolites through homologous BGC comparison and characterized one unknown BGC involved in the biosynthesis of eujavanicol A using heterologous expression. In addition, we performed untargeted transcriptomics and metabolic analysis to demonstrate the activation of silent ThT22 BGCs via the "one strain many compound" (OSMAC) approach. Collectively, our analysis showcases the biosynthetic capacity of ThT22 and paves the way for fully exploring the roles of natural products of ThT22.
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Affiliation(s)
- Wenyu Han
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Zhongshou Wu
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, California 90095, United States
- Howard Hughes Medical Institute, University of California, Los Angeles, California 90095, United States
| | - Zhenhui Zhong
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, California 90095, United States
- Howard Hughes Medical Institute, University of California, Los Angeles, California 90095, United States
| | - Jason Williams
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Steven E Jacobsen
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, California 90095, United States
- Howard Hughes Medical Institute, University of California, Los Angeles, California 90095, United States
- Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, California 90095, United States
- Department of Biological Chemistry, University of California, Los Angeles, California 90095, United States
| | - Zuodong Sun
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
| | - Yi Tang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
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Tian W, Chen X, Zhang J, Zheng M, Wei G, Deng Z, Qu X. Biosynthesis of Tetronates by a Nonribosomal Peptide Synthetase-Polyketide Synthase System. Org Lett 2023; 25:1628-1632. [PMID: 36876998 DOI: 10.1021/acs.orglett.3c00103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
A cryptic tetronate biosynthetic pathway was identified in Kitasatospora niigatensis DSM 44781 via heterologous expression. Distinct from the currently known biosynthetic pathways, this system utilizes a partially functional nonribosomal peptide synthetase and a broadly selective polyketide synthase to direct the assembly and lactonization of the tetronate scaffold. By employing a permissive crotonyl-CoA reductase/carboxylase to provide different extender units, seven new tetronates (kitaniitetronins A-G) were obtained via precursor-directed biosynthesis.
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Affiliation(s)
- Wenya Tian
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinru Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Jun Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Mengmeng Zheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Guangzheng Wei
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Xudong Qu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 200240, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
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8
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Characterization of Peptaibols Produced by a Marine Strain of the Fungus Trichoderma endophyticum via Mass Spectrometry, Genome Mining and Phylogeny-Based Prediction. Metabolites 2023; 13:metabo13020221. [PMID: 36837841 PMCID: PMC9961477 DOI: 10.3390/metabo13020221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
Trichoderma is recognized as a prolific producer of nonribosomal peptides (NRPs) known as peptaibols, which have remarkable biological properties, such as antimicrobial and anticancer activities, as well as the ability to promote systemic resistance in plants against pathogens. In this study, the sequencing of 11-, 14- and 15-res peptaibols produced by a marine strain of Trichoderma isolated from the ascidian Botrylloides giganteus was performed via liquid chromatography coupled to high-resolution tandem mass spectrometry (LC-MS/MS). Identification, based on multilocus phylogeny, revealed that our isolate belongs to the species T. endophyticum, which has never been reported in marine environments. Through genome sequencing and genome mining, 53 biosynthetic gene clusters (BGCs) were identified as being related to bioactive natural products, including two NRP-synthetases: one responsible for the biosynthesis of 11- and 14-res peptaibols, and another for the biosynthesis of 15-res. Substrate prediction, based on phylogeny of the adenylation domains in combination with molecular networking, permitted extensive annotation of the mass spectra related to two new series of 15-res peptaibols, which are referred to herein as "endophytins". The analyses of synteny revealed that the origin of the 15-module peptaibol synthetase is related to 18, 19 and 20-module peptaibol synthetases, and suggests that the loss of modules may be a mechanism used by Trichoderma species for peptaibol diversification. This study demonstrates the importance of combining genome mining techniques, mass spectrometry analysis and molecular networks for the discovery of new natural products.
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Woodcraft C, Chooi YH, Roux I. The expanding CRISPR toolbox for natural product discovery and engineering in filamentous fungi. Nat Prod Rep 2023; 40:158-173. [PMID: 36205232 DOI: 10.1039/d2np00055e] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Covering: up to May 2022Fungal genetics has transformed natural product research by enabling the elucidation of cryptic metabolites and biosynthetic steps. The enhanced capability to add, subtract, modulate, and rewrite genes via CRISPR/Cas technologies has opened up avenues for the manipulation of biosynthetic gene clusters across diverse filamentous fungi. This review discusses the innovative and diverse strategies for fungal natural product discovery and engineering made possible by CRISPR/Cas-based tools. We also provide a guide into multiple angles of CRISPR/Cas experiment design, and discuss current gaps in genetic tool development for filamentous fungi and the promising opportunities for natural product research.
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Affiliation(s)
- Clara Woodcraft
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Indra Roux
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
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10
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Xiao Z, Zhao Q, Li W, Gao L, Liu G. Strain improvement of Trichoderma harzianum for enhanced biocontrol capacity: Strategies and prospects. Front Microbiol 2023; 14:1146210. [PMID: 37125207 PMCID: PMC10134904 DOI: 10.3389/fmicb.2023.1146210] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/20/2023] [Indexed: 05/02/2023] Open
Abstract
In the control of plant diseases, biocontrol has the advantages of being efficient and safe for human health and the environment. The filamentous fungus Trichoderma harzianum and its closely related species can inhibit the growth of many phytopathogenic fungi, and have been developed as commercial biocontrol agents for decades. In this review, we summarize studies on T. harzianum species complex from the perspective of strain improvement. To elevate the biocontrol ability, the production of extracellular proteins and compounds with antimicrobial or plant immunity-eliciting activities need to be enhanced. In addition, resistance to various environmental stressors should be strengthened. Engineering the gene regulatory system has the potential to modulate a variety of biological processes related to biocontrol. With the rapidly developing technologies for fungal genetic engineering, T. harzianum strains with increased biocontrol activities are expected to be constructed to promote the sustainable development of agriculture.
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Affiliation(s)
- Ziyang Xiao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Qinqin Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wei Li
- Shanghai Tobacco Group Beijing Cigarette Factory Co., Ltd., Beijing, China
| | - Liwei Gao
- Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
- Liwei Gao,
| | - Guodong Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- *Correspondence: Guodong Liu,
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11
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Mózsik L, Iacovelli R, Bovenberg RAL, Driessen AJM. Transcriptional Activation of Biosynthetic Gene Clusters in Filamentous Fungi. Front Bioeng Biotechnol 2022; 10:901037. [PMID: 35910033 PMCID: PMC9335490 DOI: 10.3389/fbioe.2022.901037] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
Filamentous fungi are highly productive cell factories, many of which are industrial producers of enzymes, organic acids, and secondary metabolites. The increasing number of sequenced fungal genomes revealed a vast and unexplored biosynthetic potential in the form of transcriptionally silent secondary metabolite biosynthetic gene clusters (BGCs). Various strategies have been carried out to explore and mine this untapped source of bioactive molecules, and with the advent of synthetic biology, novel applications, and tools have been developed for filamentous fungi. Here we summarize approaches aiming for the expression of endogenous or exogenous natural product BGCs, including synthetic transcription factors, assembly of artificial transcription units, gene cluster refactoring, fungal shuttle vectors, and platform strains.
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Affiliation(s)
- László Mózsik
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Riccardo Iacovelli
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Roel A. L. Bovenberg
- DSM Biotechnology Center, Delft, Netherlands
- Department of Synthetic Biology and Cell Engineering, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Arnold J. M. Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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12
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Genome Mining of α-Pyrone Natural Products from Ascidian-Derived Fungus Amphichordafelina SYSU-MS7908. Mar Drugs 2022; 20:md20050294. [PMID: 35621945 PMCID: PMC9146101 DOI: 10.3390/md20050294] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 01/24/2023] Open
Abstract
Culturing ascidian-derived fungus Amphichorda felina SYSU-MS7908 under standard laboratory conditions mainly yielded meroterpenoid, and nonribosomal peptide-type natural products. We sequenced the genome of Amphichorda felina SYSU-MS7908 and found 56 biosynthetic gene clusters (BGCs) after bioinformatics analysis, suggesting that the majority of those BGCSs are silent. Here we report our genome mining effort on one cryptic BGC by heterologous expression in Aspergillus oryzae NSAR1, and the identification of two new α-pyrone derivatives, amphichopyrone A (1) and B (2), along with a known compound, udagawanone A (3). Anti-inflammatory activities were performed, and amphichopyrone A (1) and B (2) displayed potent anti-inflammatory activity by inhibiting nitric oxide (NO) production in RAW264.7 cells with IC50 values 18.09 ± 4.83 and 7.18 ± 0.93 μM, respectively.
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13
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Skellam E. Biosynthesis of fungal polyketides by collaborating and trans-acting enzymes. Nat Prod Rep 2022; 39:754-783. [PMID: 34842268 DOI: 10.1039/d1np00056j] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Covering: 1999 up to 2021Fungal polyketides encompass a range of structurally diverse molecules with a wide variety of biological activities. The giant multifunctional enzymes that synthesize polyketide backbones remain enigmatic, as do many of the tailoring enzymes involved in functional modifications. Recent advances in elucidating biosynthetic gene clusters (BGCs) have revealed numerous examples of fungal polyketide synthases that require the action of collaborating enzymes to synthesize the carbon backbone. This review will discuss collaborating and trans-acting enzymes involved in loading, extending, and releasing polyketide intermediates from fungal polyketide synthases, and additional modifications introduced by trans-acting enzymes demonstrating the complexity encountered when investigating natural product biosynthesis in fungi.
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Affiliation(s)
- Elizabeth Skellam
- Department of Chemistry, BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX 76203, USA.
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14
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Vicente I, Baroncelli R, Hermosa R, Monte E, Vannacci G, Sarrocco S. Role and genetic basis of specialised secondary metabolites in Trichoderma ecophysiology. FUNGAL BIOL REV 2022. [DOI: 10.1016/j.fbr.2021.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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15
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Sarrocco S, Vicente I, Staropoli A, Vinale F. Genes Involved in the Secondary Metabolism of Trichoderma and the Biochemistry of These Compounds. Fungal Biol 2022. [DOI: 10.1007/978-3-030-91650-3_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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16
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Cheng X, Ma L. Enzymatic synthesis of fluorinated compounds. Appl Microbiol Biotechnol 2021; 105:8033-8058. [PMID: 34625820 PMCID: PMC8500828 DOI: 10.1007/s00253-021-11608-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/16/2021] [Accepted: 09/18/2021] [Indexed: 12/31/2022]
Abstract
Fluorinated compounds are widely used in the fields of molecular imaging, pharmaceuticals, and materials. Fluorinated natural products in nature are rare, and the introduction of fluorine atoms into organic compound molecules can give these compounds new functions and make them have better performance. Therefore, the synthesis of fluorides has attracted more and more attention from biologists and chemists. Even so, achieving selective fluorination is still a huge challenge under mild conditions. In this review, the research progress of enzymatic synthesis of fluorinated compounds is summarized since 2015, including cytochrome P450 enzymes, aldolases, fluoroacetyl coenzyme A thioesterases, lipases, transaminases, reductive aminases, purine nucleoside phosphorylases, polyketide synthases, fluoroacetate dehalogenases, tyrosine phenol-lyases, glycosidases, fluorinases, and multienzyme system. Of all enzyme-catalyzed synthesis methods, the direct formation of the C-F bond by fluorinase is the most effective and promising method. The structure and catalytic mechanism of fluorinase are introduced to understand fluorobiochemistry. Furthermore, the distribution, applications, and future development trends of fluorinated compounds are also outlined. Hopefully, this review will help researchers to understand the significance of enzymatic methods for the synthesis of fluorinated compounds and find or create excellent fluoride synthase in future research.Key points• Fluorinated compounds are distributed in plants and microorganisms, and are used in imaging, medicine, materials science.• Enzyme catalysis is essential for the synthesis of fluorinated compounds.• The loop structure of fluorinase is the key to forming the C-F bond.
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Affiliation(s)
- Xinkuan Cheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Laboratory of Metabolic Control Fermentation Technology, College of Biotechnology, Tianjin University of Science & Technology, No. 29, Thirteenth Street, Binhai New District, Tianjin, 300457, China
| | - Long Ma
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Industrial Microbiology, Ministry of Education, Tianjin Key Laboratory of Industry Microbiology, National and Local United Engineering Laboratory of Metabolic Control Fermentation Technology, College of Biotechnology, Tianjin University of Science & Technology, No. 29, Thirteenth Street, Binhai New District, Tianjin, 300457, China.
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Abstract
4-Hydroxy-2-pyridone alkaloids have attracted attention for synthetic and biosynthetic studies due to their broad biological activities and structural diversity. Here, we elucidated the pathway and chemical logic of (-)-sambutoxin (1) biosynthesis. In particular, we uncovered the enzymatic origin of the tetrahydropyran moiety and showed that the p-hydroxyphenyl group is installed via a late-stage, P450-catalyzed oxidation of the phenylalanine-derived side chain rather than via a direct incorporation of tyrosine.
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Affiliation(s)
- Eun Bin Go
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Lee Joon Kim
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
| | - Hosea M Nelson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Chemistry, California Institute of Technology, Pasadena, California 91125, United States
| | - Masao Ohashi
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
| | - Yi Tang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, United States
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, California 90095, United States
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18
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Xie L, Zang X, Cheng W, Zhang Z, Zhou J, Chen M, Tang Y. Harzianic Acid from Trichoderma afroharzianum Is a Natural Product Inhibitor of Acetohydroxyacid Synthase. J Am Chem Soc 2021; 143:10.1021/jacs.1c03988. [PMID: 34132537 PMCID: PMC8674378 DOI: 10.1021/jacs.1c03988] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Acetohydroxyacid synthase (AHAS) is the first enzyme in the branched-chain amino acid biosynthetic pathway and is a validated target for herbicide and fungicide development. Here we report harzianic acid (HA, 1) produced by the biocontrol fungus Trichoderma afroharzianum t-22 (Tht22) as a natural product inhibitor of AHAS. The biosynthetic pathway of HA was elucidated with heterologous reconstitution. Guided by a putative self-resistance enzyme in the genome, HA was biochemically demonstrated to be a selective inhibitor of fungal AHAS, including those from phytopathogenic fungi. In addition, HA can inhibit a common resistant variant of AHAS in which the active site proline is mutated. Structural analysis of AHAS complexed with HA revealed the molecular basis of competitive inhibition, which differs from all known commercial AHAS inhibitors. The alternative binding mode also rationalizes the selectivity of HA, as well as effectiveness toward resistant mutants. A proposed role of HA biosynthesis by Tht22 in the rhizosphere is discussed based on the data.
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Affiliation(s)
- Linan Xie
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States
- Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing 100081, P.R. China
| | - Xin Zang
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Wei Cheng
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States
- State Key Laboratory of Natural and Biomimetic Drugs, Peking University, Beijing 100191, China
| | - Zhuan Zhang
- Texas Therapeutics Institute, the Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, Texas 77054, United States
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Mengbin Chen
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States
- Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, California 90095, United States
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19
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Hill RA, Sutherland A. Hot off the press. Nat Prod Rep 2021. [DOI: 10.1039/d1np90013g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as eurysoloid A from Eurysolen gracilis.
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Affiliation(s)
- Robert A. Hill
- School of Chemistry, Glasgow University, Glasgow, G12 8QQ, UK
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