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Lv HW, Tang JG, Wei B, Zhu MD, Zhang HW, Zhou ZB, Fan BY, Wang H, Li XN. Bioinformatics assisted construction of the link between biosynthetic gene clusters and secondary metabolites in fungi. Biotechnol Adv 2025; 81:108547. [PMID: 40024584 DOI: 10.1016/j.biotechadv.2025.108547] [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: 10/20/2024] [Revised: 02/24/2025] [Accepted: 02/24/2025] [Indexed: 03/04/2025]
Abstract
Fungal secondary metabolites are considered as important resources for drug discovery. Despite various methods being employed to facilitate the discovery of new fungal secondary metabolites, the trend of identifying novel secondary metabolites from fungi is inevitably slowing down. Under laboratory conditions, the majority of biosynthetic gene clusters, which store information for secondary metabolites, remain inactive. Therefore, establishing the link between biosynthetic gene clusters and secondary metabolites would contribute to understanding the genetic logic underlying secondary metabolite biosynthesis and alleviating the current challenges in discovering novel natural products. Bioinformatics methods have garnered significant attention due to their powerful capabilities in data mining and analysis, playing a crucial role in various aspects. Thus, we have summarized successful cases since 2016 in which bioinformatics methods were utilized to establish the link between fungal biosynthetic gene clusters and secondary metabolites, focusing on their biosynthetic gene clusters and associated secondary metabolites, with the goal of aiding the field of natural product discovery.
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Affiliation(s)
- Hua-Wei Lv
- College of Pharmaceutical Science & Zhejiang Provincial Key Laboratory of TCM for Innovative R&D and Digital Intelligent Manufacturing of TCM Great Health Products & Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hang Zhou, PR China; School of Pharmacy, Youjiang Medical University for Nationalities, Baise, PR China
| | - Jia-Gui Tang
- College of Pharmaceutical Science & Zhejiang Provincial Key Laboratory of TCM for Innovative R&D and Digital Intelligent Manufacturing of TCM Great Health Products & Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hang Zhou, PR China
| | - Bin Wei
- College of Pharmaceutical Science & Zhejiang Provincial Key Laboratory of TCM for Innovative R&D and Digital Intelligent Manufacturing of TCM Great Health Products & Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hang Zhou, PR China
| | - Meng-Di Zhu
- Research Center of Analysis and Measurement, Zhejiang University of Technology, Hang Zhou, PR China
| | - Hua-Wei Zhang
- College of Pharmaceutical Science & Zhejiang Provincial Key Laboratory of TCM for Innovative R&D and Digital Intelligent Manufacturing of TCM Great Health Products & Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hang Zhou, PR China
| | - Zhong-Bo Zhou
- School of Pharmacy, Youjiang Medical University for Nationalities, Baise, PR China
| | - Bo-Yi Fan
- School of Pharmacy, Nantong University, Nantong, PR China
| | - Hong Wang
- College of Pharmaceutical Science & Zhejiang Provincial Key Laboratory of TCM for Innovative R&D and Digital Intelligent Manufacturing of TCM Great Health Products & Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hang Zhou, PR China
| | - Xing-Nuo Li
- College of Pharmaceutical Science & Zhejiang Provincial Key Laboratory of TCM for Innovative R&D and Digital Intelligent Manufacturing of TCM Great Health Products & Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hang Zhou, PR China.
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2
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Liu Y, Tang Y, Fu Z, Zhu W, Wang H, Zhang H. BGC heteroexpression strategy for production of novel microbial secondary metabolites. Metab Eng 2025; 91:1-29. [PMID: 40158686 DOI: 10.1016/j.ymben.2025.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Revised: 03/13/2025] [Accepted: 03/27/2025] [Indexed: 04/02/2025]
Abstract
Biosynthetic gene clusters (BGCs) in microbial genomes play a crucial role in the biosynthesis of diverse secondary metabolites (SMs) with pharmaceutical potential. However, most BGCs remain silent under conventional conditions, resulting in the frequently repeated discovery of known SMs. Fortunately, in the past two decades, the heterologous expression of BGCs in genetically tractable hosts has emerged as a powerful strategy to awaken microbial metabolic pathways for making novel microbial SMs. In this review, we comprehensively delineated the development and application of this strategy, highlighting various BGC cloning and assembly techniques and their technical characteristics. We also summarized 519 novel SMs from BGC hetero-expression-derived strains and described their occurrence, bioactivity, mode of action, and biosynthetic logic. Lastly, current challenges and future perspectives for developing more efficient BGC hetero-expression strategies were discussed in this review.
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Affiliation(s)
- Yuanyuan Liu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Yuqi Tang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Zhiyang Fu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Wangjie Zhu
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Hong Wang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, China.
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3
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Kong D, Wang X, Liu L. Biosynthesis of a Novel Diketopiperazine Aspkyncin Incorporating a Kynurenine Unit from Aspergillus aculeatus. J Fungi (Basel) 2025; 11:171. [PMID: 40137209 PMCID: PMC11942691 DOI: 10.3390/jof11030171] [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: 01/24/2025] [Revised: 02/15/2025] [Accepted: 02/19/2025] [Indexed: 03/27/2025] Open
Abstract
The simplest cyclo-peptides, also known as diketopiperazines (DKPs), are widespread in nature. The growing interest in these simplest cyclo-peptides is driven by their significant potential for therapeutic applications. In this study, we identified a biosynthetic gene cluster from Aspergillus aculeatus CRI323-04 through genome mining and heterologous expression in Aspergillus nidulans. The two core genes, aacA and aacB, within the gene cluster were characterized for their role in the biossoynthesis of aspkyncin, a novel DKP compound that incorporates a l-kynurenine (l-Kyn) unit. Furthermore, we successfully reconstituted the activities of the minimal bimodular non-ribosomal peptide synthetase (NRPS) AacA and the methyltransferase AacB both in vivo and in vitro. Our findings demonstrate that AacA catalyzes the condensation and cyclization of two non-proteinogenic amino acids, l-Kyn and N-methyl-l-alanine, to produce aspkyncin without the involvement of any release domain. Notably, the N-methyl-l-alanine is generated by a specialized l-alanine N-methyltransferase AacB prior to NRP assembly. This study reveals an unconventional pathway for the biosynthesis of fungal DKPs.
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Affiliation(s)
- Dekun Kong
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China;
| | - Xin Wang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400715, China;
| | - Li Liu
- Laboratory of Biochemistry and Molecular Biology, Lab Teaching and Management Center, Chongqing Medical University, Chongqing 400016, China
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4
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Ji Q, Wei X, Liu S, Matsuda Y. Involvement of a Noncanonical Polyketide Synthase-Nonribosomal Peptide Synthetase Hybrid in the Biosynthesis of Sterol-C4-methyl Oxidase Inhibitor PF1163A. Org Lett 2025; 27:36-40. [PMID: 39719272 PMCID: PMC11731387 DOI: 10.1021/acs.orglett.4c03675] [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: 10/01/2024] [Revised: 11/12/2024] [Accepted: 11/15/2024] [Indexed: 12/26/2024]
Abstract
PF1163A (1) is a fungal metabolite that inhibits sterol-C4-methyl oxidase. In this study, we identified the biosynthetic gene cluster of 1 and elucidated its biosynthetic pathway through heterologous expression experiments. Polyketide synthase-nonribosomal synthetase hybrid PfaA, which is responsible for the biosynthesis of PF1163A, harbors an unusual domain organization with tandem condensation (C) domains and a terminal condensation domain. Mutagenesis studies suggest that both C domains are required for the function of PfaA.
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Affiliation(s)
- Qiaolin Ji
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Xingxing Wei
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Shengkun Liu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
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5
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Janevska S, Weiser S, Huang Y, Lin J, Hoefgen S, Jojić K, Barber AE, Schäfer T, Fricke J, Hoffmeister D, Regestein L, Valiante V, Kufs JE. Optimized psilocybin production in tryptophan catabolism-repressed fungi. Microb Biotechnol 2024; 17:e70039. [PMID: 39487767 PMCID: PMC11530996 DOI: 10.1111/1751-7915.70039] [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: 06/01/2024] [Accepted: 10/10/2024] [Indexed: 11/04/2024] Open
Abstract
The high therapeutic potential of psilocybin, a prodrug of the psychotropic psilocin, holds great promise for the treatment of mental disorders such as therapy-refractory depression, alcohol use disorder and anorexia nervosa. Psilocybin has been designated a 'Breakthrough Therapy' by the US Food and Drug Administration, and therefore a sustainable production process must be established to meet future market demands. Here, we present the development of an in vivo psilocybin production chassis based on repression of l-tryptophan catabolism. We demonstrate the proof of principle in Saccharomyces cerevisiae expressing the psilocybin biosynthetic genes. Deletion of the two aminotransferase genes ARO8/9 and the indoleamine 2,3-dioxygenase gene BNA2 yielded a fivefold increase of psilocybin titre. We transferred this knowledge to the filamentous fungus Aspergillus nidulans and identified functional ARO8/9 orthologs involved in fungal l-tryptophan catabolism by genome mining and cross-complementation. The double deletion mutant of A. nidulans resulted in a 10-fold increased psilocybin production. Process optimization based on respiratory activity measurements led to a final psilocybin titre of 267 mg/L in batch cultures with a space-time-yield of 3.7 mg/L/h. These results demonstrate the suitability of our engineered A. nidulans to serve as a production strain for psilocybin and other tryptamine-derived pharmaceuticals.
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Affiliation(s)
- Slavica Janevska
- (Epi‐)Genetic Regulation of Fungal VirulenceLeibniz Institute for Natural Product Research and Infection Biology–Hans Knöll InstituteJenaGermany
| | - Sophie Weiser
- Bio Pilot PlantLeibniz Institute for Natural Product Research and Infection Biology–Hans Knöll InstituteJenaGermany
- Faculty of Biological SciencesFriedrich Schiller UniversityJenaGermany
| | - Ying Huang
- Biobricks of Microbial Natural Product SynthesesLeibniz Institute for Natural Product Research and Infection Biology–Hans Knöll InstituteJenaGermany
- PaleobiotechnologyLeibniz Institute for Natural Product Research and Infection Biology–Hans Knöll InstituteJenaGermany
| | - Jun Lin
- Biobricks of Microbial Natural Product SynthesesLeibniz Institute for Natural Product Research and Infection Biology–Hans Knöll InstituteJenaGermany
| | - Sandra Hoefgen
- Biobricks of Microbial Natural Product SynthesesLeibniz Institute for Natural Product Research and Infection Biology–Hans Knöll InstituteJenaGermany
| | - Katarina Jojić
- Biobricks of Microbial Natural Product SynthesesLeibniz Institute for Natural Product Research and Infection Biology–Hans Knöll InstituteJenaGermany
| | | | - Tim Schäfer
- Pharmaceutical MicrobiologyFriedrich Schiller UniversityJenaGermany
- Pharmaceutical MicrobiologyLeibniz Institute for Natural Product Research and Infection Biology–Hans Knöll InstituteJenaGermany
| | - Janis Fricke
- Pharmaceutical MicrobiologyFriedrich Schiller UniversityJenaGermany
- Pharmaceutical MicrobiologyLeibniz Institute for Natural Product Research and Infection Biology–Hans Knöll InstituteJenaGermany
| | - Dirk Hoffmeister
- Pharmaceutical MicrobiologyFriedrich Schiller UniversityJenaGermany
- Pharmaceutical MicrobiologyLeibniz Institute for Natural Product Research and Infection Biology–Hans Knöll InstituteJenaGermany
| | - Lars Regestein
- Bio Pilot PlantLeibniz Institute for Natural Product Research and Infection Biology–Hans Knöll InstituteJenaGermany
| | - Vito Valiante
- Biobricks of Microbial Natural Product SynthesesLeibniz Institute for Natural Product Research and Infection Biology–Hans Knöll InstituteJenaGermany
| | - Johann E. Kufs
- Bio Pilot PlantLeibniz Institute for Natural Product Research and Infection Biology–Hans Knöll InstituteJenaGermany
- Present address:
AG Genome Engineering and EditingBielefeld UniversityBielefeldGermany
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6
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Tang J, Matsuda Y. Discovery of fungal onoceroid triterpenoids through domainless enzyme-targeted global genome mining. Nat Commun 2024; 15:4312. [PMID: 38773118 PMCID: PMC11109268 DOI: 10.1038/s41467-024-48771-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 05/09/2024] [Indexed: 05/23/2024] Open
Abstract
Genomics-guided methodologies have revolutionized the discovery of natural products. However, a major challenge in the field of genome mining is determining how to selectively extract biosynthetic gene clusters (BGCs) for untapped natural products from numerous available genome sequences. In this study, we developed a fungal genome mining tool that extracts BGCs encoding enzymes that lack a detectable protein domain (i.e., domainless enzymes) and are not recognized as biosynthetic proteins by existing bioinformatic tools. We searched for BGCs encoding a homologue of Pyr4-family terpene cyclases, which are representative examples of apparently domainless enzymes, in approximately 2000 fungal genomes and discovered several BGCs with unique features. The subsequent characterization of selected BGCs led to the discovery of fungal onoceroid triterpenoids and unprecedented onoceroid synthases. Furthermore, in addition to the onoceroids, a previously unreported sesquiterpene hydroquinone, of which the biosynthesis involves a Pyr4-family terpene cyclase, was obtained. Our genome mining tool has broad applicability in fungal genome mining and can serve as a beneficial platform for accessing diverse, unexploited natural products.
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Affiliation(s)
- Jia Tang
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China.
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7
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Tang J, Matsuda Y. Functional analysis of transmembrane terpene cyclases involved in fungal meroterpenoid biosynthesis. Methods Enzymol 2024; 699:419-445. [PMID: 38942513 DOI: 10.1016/bs.mie.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Pyr4-family terpene cyclases are noncanonical transmembrane class II terpene cyclases that catalyze a variety of cyclization reactions in the biosynthesis of microbial terpenoids, such as meroterpenoids. However, although these cyclases are widely distributed in microorganisms, their three-dimensional structures have not been determined, possibly due to the transmembrane locations of these enzymes. In this chapter, we describe procedures for the functional analysis of transmembrane terpene cyclases based on their model structures generated using AlphaFold2. We used AdrI, the Pyr4-family terpene cyclase required for the biosynthesis of andrastin A and its homologs, as an example.
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Affiliation(s)
- Jia Tang
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, P.R. China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, P.R. China.
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8
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Yang R, Feng J, Xiang H, Cheng B, Shao LD, Li YP, Wang H, Hu QF, Xiao WL, Matsuda Y, Wang WG. Ketoreductase Domain-Catalyzed Polyketide Chain Release in Fungal Alkyl Salicylaldehyde Biosynthesis. J Am Chem Soc 2023; 145:11293-11300. [PMID: 37172192 DOI: 10.1021/jacs.3c02011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Alkyl salicylaldehyde derivatives are polyketide natural products, which are widely distributed in fungi and exhibit great structural diversity. Their biosynthetic mechanisms have recently been intensively studied; however, how the polyketide synthases (PKSs) involved in the fungal alkyl salicylaldehyde biosyntheses release their products remained elusive. In this study, we discovered an orphan biosynthetic gene cluster of salicylaldehyde derivatives in the fungus Stachybotrys sp. g12. Intriguingly, the highly reducing PKS StrA, encoded by the gene cluster, performs a reductive polyketide chain release, although it lacks a C-terminal reductase domain, which is typically required for such a reductive release. Our study revealed that the chain release is achieved by the ketoreductase (KR) domain of StrA, which also conducts cannonical β-keto reductions during polyketide chain elongation. Furthermore, we found that the cupin domain-containing protein StrC plays a critical role in the aromatization reaction. Collectively, we have provided an unprecedented example of a KR domain-catalyzed polyketide chain release and a clearer image of how the salicylaldehyde scaffold is generated in fungi.
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Affiliation(s)
- Run Yang
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Key Laboratory of Chemistry in Ethnic Medicinal Resources, Ministry of Education, Yunnan Minzu University, Kunming 650031, Yunnan, China
| | - Jian Feng
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Key Laboratory of Chemistry in Ethnic Medicinal Resources, Ministry of Education, Yunnan Minzu University, Kunming 650031, Yunnan, China
| | - Hao Xiang
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Key Laboratory of Chemistry in Ethnic Medicinal Resources, Ministry of Education, Yunnan Minzu University, Kunming 650031, Yunnan, China
| | - Bin Cheng
- Key Laboratory of Medicinal Chemistry for Natural Resource of Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory and Yunnan Provincial Center of Natural Products, School of Pharmacy, Yunnan University, Kunming 650091, Yunnan, China
| | - Li-Dong Shao
- Yunnan Key Laboratory of Southern Medicinal Utilization, School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500 Yunnan, China
| | - Yan-Ping Li
- Yunnan Key Laboratory of Southern Medicinal Utilization, School of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500 Yunnan, China
| | - Hang Wang
- School of Life Science and Technology, China Pharmaceutical University, Nanjing 210009, China
| | - Qiu-Fen Hu
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Key Laboratory of Chemistry in Ethnic Medicinal Resources, Ministry of Education, Yunnan Minzu University, Kunming 650031, Yunnan, China
| | - Wei-Lie Xiao
- Key Laboratory of Medicinal Chemistry for Natural Resource of Ministry of Education, Yunnan Characteristic Plant Extraction Laboratory and Yunnan Provincial Center of Natural Products, School of Pharmacy, Yunnan University, Kunming 650091, Yunnan, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
- City University of Hong Kong Shenzhen Research Institute, Shenzhen, Guangdong 518057, China
| | - Wei-Guang Wang
- Key Laboratory of Natural Products Synthetic Biology of Ethnic Medicinal Endophytes, State Ethnic Affairs Commission, Key Laboratory of Chemistry in Ethnic Medicinal Resources, Ministry of Education, Yunnan Minzu University, Kunming 650031, Yunnan, China
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9
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Zhang W, Zhang X, Feng D, Liang Y, Wu Z, Du S, Zhou Y, Geng C, Men P, Fu C, Huang X, Lu X. Discovery of a Unique Flavonoid Biosynthesis Mechanism in Fungi by Genome Mining. Angew Chem Int Ed Engl 2023; 62:e202215529. [PMID: 36704842 DOI: 10.1002/anie.202215529] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 01/28/2023]
Abstract
Flavonoids are important plant natural products with variable structures and bioactivities. All known plant flavonoids are generated under the catalysis of a type III polyketide synthase (PKS) followed by a chalcone isomerase (CHI) and a flavone synthase (FNS). In this study, the biosynthetic gene cluster of chlorflavonin, a fungal flavonoid with acetolactate synthase inhibitory activity, was discovered using a self-resistance-gene-directed strategy. A novel flavonoid biosynthetic pathway in fungi was revealed. A core nonribosomal peptide synthetase-polyketide synthase (NRPS-PKS) is responsible for the generation of the key precursor chalcone. Then, a new type of CHI catalyzes the conversion of a chalcone into a flavanone by a histidine-mediated oxa-Michael addition mechanism. Finally, the desaturation of flavanone to flavone is catalyzed by a new type of FNS, a flavin mononucleotide (FMN)-dependent oxidoreductase.
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Affiliation(s)
- Wei Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,Shandong Energy Institute, Qingdao, Shandong, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuan Zhang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,Shandong Energy Institute, Qingdao, Shandong, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Dandan Feng
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,Shandong Energy Institute, Qingdao, Shandong, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Yajing Liang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,Shandong Energy Institute, Qingdao, Shandong, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Zhenying Wu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,Shandong Energy Institute, Qingdao, Shandong, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Siyu Du
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,Shandong Energy Institute, Qingdao, Shandong, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Yu Zhou
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,Shandong Energy Institute, Qingdao, Shandong, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Ce Geng
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,Shandong Energy Institute, Qingdao, Shandong, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Ping Men
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,Shandong Energy Institute, Qingdao, Shandong, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China
| | - Chunxiang Fu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,Shandong Energy Institute, Qingdao, Shandong, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuenian Huang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,Shandong Energy Institute, Qingdao, Shandong, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuefeng Lu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China.,Shandong Energy Institute, Qingdao, Shandong, 266101, China.,Qingdao New Energy Shandong Laboratory, Qingdao, Shandong, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Marine Biology and Biotechnology Laboratory, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266101, China
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10
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Furumura S, Ozaki T, Sugawara A, Morishita Y, Tsukada K, Ikuta T, Inoue A, Asai T. Identification and Functional Characterization of Fungal Chalcone Synthase and Chalcone Isomerase. JOURNAL OF NATURAL PRODUCTS 2023; 86:398-405. [PMID: 36762727 PMCID: PMC9972472 DOI: 10.1021/acs.jnatprod.2c01027] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Indexed: 05/23/2023]
Abstract
By mining fungal genomic information, a noncanonical iterative type I PKS fused with an N-terminal adenylation-thiolation didomain, which catalyzes the formation of naringenin chalcone, was found. Structural prediction and molecular docking analysis indicated that a C-terminal thioesterase domain was involved in the Claisen-type cyclization. An enzyme responsible for formation of (2S)-flavanone in the biosynthesis of fungal flavonoids was also identified. Collectively, these findings demonstrate unprecedented fungal biosynthetic machinery leading to plant-like metabolites.
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11
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Motoyama T, Nogawa T, Shimizu T, Kawatani M, Kashiwa T, Yun CS, Hashizume D, Osada H. Fungal NRPS-PKS Hybrid Enzymes Biosynthesize New γ-Lactam Compounds, Taslactams A-D, Analogous to Actinomycete Proteasome Inhibitors. ACS Chem Biol 2023; 18:396-403. [PMID: 36692171 DOI: 10.1021/acschembio.2c00830] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Proteasome inhibitors with γ-lactam structure, such as lactacystin and salinosporamide A, have been isolated from actinomycetes and have attracted attention as lead compounds for anticancer drugs. Previously, we identified a unique enzyme TAS1, which is the first reported fungal NRPS-PKS hybrid enzyme, from the filamentous fungus Pyricularia oryzae for the biosynthesis of a mycotoxin tenuazonic acid, a tetramic acid compound without γ-lactam structure. Homologues of TAS1 have been identified in several fungal genomes and classified into four groups (A-D). Here, we show that the group D TAS1 homologues from two filamentous fungi can biosynthesize γ-lactam compounds, taslactams A-D, with high similarity to actinomycete proteasome inhibitors. One of the γ-lactam compounds, taslactam C, showed potent proteasome inhibitory activity. In contrast to actinomycete γ-lactam compounds which require multiple enzymes for biosynthesis, the TAS1 homologue alone was sufficient for the biosynthesis of the fungal γ-lactam compounds.
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Affiliation(s)
- Takayuki Motoyama
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Toshihiko Nogawa
- Molecular Structure Characterization Unit, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Takeshi Shimizu
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Makoto Kawatani
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan.,Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan.,Chemical Resource Development Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Takeshi Kashiwa
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Choong-Soo Yun
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Daisuke Hashizume
- Materials Characterization Support Team, RIKEN Center for Emergent Matter Science (CEMS), 2-1 Hirosawa, Saitama 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan.,Chemical Resource Development Research Unit, RIKEN Center for Sustainable Resource Science (CSRS), 2-1 Hirosawa, Saitama 351-0198, Japan.,Department of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yata, Suruga-ku, Shizuoka 422-8526, Japan
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12
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Ning Y, Xu Y, Jiao B, Lu X. Application of Gene Knockout and Heterologous Expression Strategy in Fungal Secondary Metabolites Biosynthesis. Mar Drugs 2022; 20:705. [PMID: 36355028 PMCID: PMC9699552 DOI: 10.3390/md20110705] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/12/2022] Open
Abstract
The in-depth study of fungal secondary metabolites (SMs) over the past few years has led to the discovery of a vast number of novel fungal SMs, some of which possess good biological activity. However, because of the limitations of the traditional natural product mining methods, the discovery of new SMs has become increasingly difficult. In recent years, with the rapid development of gene sequencing technology and bioinformatics, new breakthroughs have been made in the study of fungal SMs, and more fungal biosynthetic gene clusters of SMs have been discovered, which shows that the fungi still have a considerable potential to produce SMs. How to study these gene clusters to obtain a large number of unknown SMs has been a research hotspot. With the continuous breakthrough of molecular biology technology, gene manipulation has reached a mature stage. Methods such as gene knockout and heterologous expression techniques have been widely used in the study of fungal SM biosynthesis and have achieved good effects. In this review, the representative studies on the biosynthesis of fungal SMs by gene knockout and heterologous expression under the fungal genome mining in the last three years were summarized. The techniques and methods used in these studies were also briefly discussed. In addition, the prospect of synthetic biology in the future under this research background was proposed.
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Affiliation(s)
| | | | | | - Xiaoling Lu
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai 200433, China
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13
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Chen L, Wei X, Matsuda Y. Depside Bond Formation by the Starter-Unit Acyltransferase Domain of a Fungal Polyketide Synthase. J Am Chem Soc 2022; 144:19225-19230. [PMID: 36223511 DOI: 10.1021/jacs.2c08585] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Depsides are polyphenolic molecules comprising two or more phenolic acid derivatives linked by an ester bond, which is called a depside bond in these molecules. Despite more than a century of intensive research on depsides, the biosynthetic mechanism of depside bond formation remains unclear. In this study, we discovered a polyketide synthase, DrcA, from the fungus Aspergillus duricaulis CBS 481.65 and found that DrcA synthesizes CJ-20,557 (1), a heterodimeric depside composed of 3-methylorsellinic acid and 3,5-dimethylorsellinic acid. Moreover, we determined that depside bond formation is catalyzed by the starter-unit acyltransferase (SAT) domain of DrcA. Remarkably, this is a previously undescribed form of SAT domain chemistry. Further investigation revealed that 1 is transformed into duricamidepside (2), a depside-amino acid conjugate, by the single-module nonribosomal peptide synthetase DrcB.
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Affiliation(s)
- Lin Chen
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Xingxing Wei
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China.,City University of Hong Kong Shenzhen Research Institute, Shenzhen, Guangdong 518057, China
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14
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Rao L, Shi HC, Zou Y. A fungal nonribosomal peptide-polyketide hybrid synthase synthesizes 2-pyrrolidinone alkaloid. Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.133060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Hill RA, Sutherland A. Hot off the Press. Nat Prod Rep 2022. [DOI: 10.1039/d2np90034c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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 hyjapone A from Hypericum japonicum.
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Affiliation(s)
- Robert A. Hill
- School of Chemistry, Glasgow University, Glasgow, G12 8QQ, UK
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