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Yin M, Xie L, Chen K, Zhang L, Yue Q, Wang C, Zeng J, Hao X, Gu X, Molnár I, Xu Y. Re-Engineering Fungal Nonribosomal Peptide Synthetases by Module Dissection and Duplicated Thiolation Domains. Angew Chem Int Ed Engl 2024; 63:e202406360. [PMID: 38822735 DOI: 10.1002/anie.202406360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/31/2024] [Accepted: 05/31/2024] [Indexed: 06/03/2024]
Abstract
Unnatural product (uNP) nonribosomal peptides promise to be a valuable source of pharmacophores for drug discovery. However, the extremely large size and complexity of the nonribosomal peptide synthetase (NRPS) enzymes pose formidable challenges to the production of such uNPs by combinatorial biosynthesis and synthetic biology. Here we report a new NRPS dissection strategy that facilitates the engineering and heterologous production of these NRPSs. This strategy divides NRPSs into "splitting units", each forming an enzyme subunit that contains catalytically independent modules. Functional collaboration between the subunits is then facilitated by artificially duplicating, at the N-terminus of the downstream subunit, the linker - thiolation domain - linker fragment that is resident at the C-terminus of the upstream subunit. Using the suggested split site that follows a conserved motif in the linker connecting the adenylation and the thiolation domains allows cognate or chimeric splitting unit pairs to achieve productivities that match, and in many cases surpass those of hybrid chimeric enzymes, and even those of intact NRPSs, upon production in a heterologous chassis. Our strategy provides facile options for the rational engineering of fungal NRPSs and for the combinatorial reprogramming of nonribosomal peptide production.
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Affiliation(s)
- Miaomiao Yin
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, P.R. China
| | - Linan Xie
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, P.R. China
- Zhongyuan Research Center, The Chinese Academy of Agricultural Sciences, Xinxiang, 453000, P.R. China
| | - Kang Chen
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, P.R. China
| | - Liwen Zhang
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, P.R. China
- Zhongyuan Research Center, The Chinese Academy of Agricultural Sciences, Xinxiang, 453000, P.R. China
| | - Qun Yue
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, P.R. China
- Zhongyuan Research Center, The Chinese Academy of Agricultural Sciences, Xinxiang, 453000, P.R. China
| | - Chen Wang
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, P.R. China
- Zhongyuan Research Center, The Chinese Academy of Agricultural Sciences, Xinxiang, 453000, P.R. China
| | - Juntian Zeng
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, P.R. China
| | - Xiaoyang Hao
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, P.R. China
| | - Xiaofeng Gu
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, P.R. China
| | - István Molnár
- VTT Technical Research Centre of Finland, Espoo, 02150, Finland
| | - Yuquan Xu
- National Key Laboratory of Agricultural Microbiology, Biotechnology Research Institute, The Chinese Academy of Agricultural Sciences, 12 Zhongguancun South Street, Beijing, 100081, P.R. China
- Zhongyuan Research Center, The Chinese Academy of Agricultural Sciences, Xinxiang, 453000, P.R. China
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2
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Liu Q, Gao S, Fang J, Gong Y, Zheng Y, Xu Y, Zhang D, Wei J, Liao L, Yao M, Wang W, Han X, Chen F, Molnár I, Yang X. Novel fungal diphenyl ether biosynthetic gene clusters encode a promiscuous oxidase for elevated antibacterial activities. Chem Sci 2024:d4sc01435a. [PMID: 39144458 PMCID: PMC11320064 DOI: 10.1039/d4sc01435a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 07/22/2024] [Indexed: 08/16/2024] Open
Abstract
Diphenyl ethers (DPEs) are produced by filamentous fungi using polyketide synthases (PKSs) directly, or via Cu oxidase-catalyzed oxidative rearrangements of benzophenone intermediates. Here, we use heterologous expression to reveal a third route towards DPEs in Preussia isomera that relies on an oxidative multienzyme cascade to convert a PKS-generated, ester-linked didepside to depsidones and further to DPEs, and apply comparative genomics to identify conserved biosynthetic gene clusters for this pathway in multiple fungi. The distribution of DPE products is modulated by the expression chassis upon pathway reconstitution. Among the post-PKS enzymes, the DpeH tyrosinase shows considerable substrate promiscuity towards synthetic DPE analogues. By creating hybrid enzymes with a DpeH orthologue from Aspergillus nidulans, we identify the C-terminal region of DpeH to alter substrate recognition. Our work highlights an evolutionarily conserved way to produce DPEs, and provides enzymatic tools to generate DPE analogues with broad spectrum antibiotic activity against multidrug-resistant human pathogens.
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Affiliation(s)
- Qingpei Liu
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Shuaibiao Gao
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Jin Fang
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Yifu Gong
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Yiling Zheng
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Yao Xu
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Dan Zhang
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Jiayuan Wei
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Liangxiu Liao
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Ming Yao
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Wenjing Wang
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
| | - Xiaole Han
- School of Chemistry and Materials Science, South-Central Minzu University Wuhan 430074 P.R. China
| | - Fusheng Chen
- School of Life Sciences, Guizhou Normal University Guiyang 550025 P.R. China
- College of Food Science and Technology, Huazhong Agricultural University Wuhan 430070 P.R. China
| | - István Molnár
- VTT Technical Research Centre of Finland FI-02044 VTT Espoo Finland
| | - Xiaolong Yang
- School of Pharmaceutical Sciences, South-Central Minzu University Wuhan 430074 P.R. China
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3
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Ji Q, Xiang H, Wang WG, Matsuda Y. Mechanism Behind the Programmed Biosynthesis of Heterotrimeric Fungal Depside Thielavin A. Angew Chem Int Ed Engl 2024; 63:e202402663. [PMID: 38467568 DOI: 10.1002/anie.202402663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/13/2024]
Abstract
Thielavin A (1) is a fungal depside composed of one 3-methylorsellinic acid and two 3,5-dimethylorsellinic acid units. It displays diverse biological activities. However, the mechanism underlying the assembly of the heterotrimeric structure of 1 remains to be clarified. In this study, we identified the polyketide synthase (PKS) involved in the biosynthesis of 1. This PKS, designated as ThiA, possesses an unusual domain organization with the C-methyltransferase (MT) domain situated at the C-terminus following the thioesterase (TE) domain. Our findings indicated that the TE domain is solely responsible for two rounds of ester bond formation, along with subsequent chain hydrolysis. We identified a plausible mechanism for TE-catalyzed reactions and obtained insights into how a single PKS can selectively yield a specific heterotrimeric product. In particular, the tandem acyl carrier protein domains of ThiA are critical for programmed methylation by the MT domain. Overall, this study highlighted the occurrence of highly optimized domain-domain communication within ThiA for the selective synthesis of 1, which can advance our understanding of the programming rules of fungal PKSs.
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Affiliation(s)
- Qiaolin Ji
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, 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
| | - 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
| | - Yudai Matsuda
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong SAR, China
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4
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Skellam E, Rajendran S, Li L. Combinatorial biosynthesis for the engineering of novel fungal natural products. Commun Chem 2024; 7:89. [PMID: 38637654 PMCID: PMC11026467 DOI: 10.1038/s42004-024-01172-9] [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: 01/21/2024] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
Natural products are small molecules synthesized by fungi, bacteria and plants, which historically have had a profound effect on human health and quality of life. These natural products have evolved over millions of years resulting in specific biological functions that may be of interest for pharmaceutical, agricultural, or nutraceutical use. Often natural products need to be structurally modified to make them suitable for specific applications. Combinatorial biosynthesis is a method to alter the composition of enzymes needed to synthesize a specific natural product resulting in structurally diversified molecules. In this review we discuss different approaches for combinatorial biosynthesis of natural products via engineering fungal enzymes and biosynthetic pathways. We highlight the biosynthetic knowledge gained from these studies and provide examples of new-to-nature bioactive molecules, including molecules synthesized using combinations of fungal and non-fungal enzymes.
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Affiliation(s)
- Elizabeth Skellam
- Department of Chemistry, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA.
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA.
- Department of Biological Sciences, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA.
| | - Sanjeevan Rajendran
- Department of Chemistry, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
| | - Lei Li
- Department of Chemistry, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
- BioDiscovery Institute, University of North Texas, 1155 Union Circle, Denton, TX, 76203, USA
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5
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Chen D, Song Z, Han J, Liu J, Liu H, Dai J. Targeted Discovery of Glycosylated Natural Products by Tailoring Enzyme-Guided Genome Mining and MS-Based Metabolome Analysis. J Am Chem Soc 2024; 146:9614-9622. [PMID: 38545685 DOI: 10.1021/jacs.3c12895] [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: 04/11/2024]
Abstract
Glycosides make up a biomedically important class of secondary metabolites. Most naturally occurring glycosides were isolated from plants and bacteria; however, the chemical diversity of glycosylated natural products in fungi remains largely unexplored. Herein, we present a paradigm to specifically discover diverse and bioactive glycosylated natural products from fungi by combining tailoring enzyme-guided genome mining with mass spectrometry (MS)-based metabolome analysis. Through in vivo genes deletion and heterologous expression, the first fungal C-glycosyltransferase AuCGT involved in the biosynthesis of stromemycin was identified from Aspergillus ustus. Subsequent homology-based genome mining for fungal glycosyltransferases by using AuCGT as a probe revealed a variety of biosynthetic gene clusters (BGCs) containing its homologues in diverse fungi, of which the glycoside-producing capability was corroborated by high-performance liquid chromatography-mass spectrometry (HPLC-MS) analysis. Consequently, 28 fungal aromatic polyketide C/O-glycosides, including 20 new compounds, were efficiently discovered and isolated from the three selected fungi. Moreover, several novel fungal C/O-glycosyltransferases, especially three novel α-pyrone C-glycosyltransferases, were functionally characterized and verified in the biosynthesis of these glycosides. In addition, a proof of principle for combinatorial biosynthesis was applied to design the production of unnatural glycosides in Aspergillus nidulans. Notably, the newly discovered glycosides exhibited significant antiviral, antibacterial, and antidiabetic activities. Our work demonstrates the promise of tailoring enzyme-guided genome-mining approach for the targeted discovery of fungal glycosides and promotes the exploration of a broader chemical space for natural products with a target structural motif in microbial genomes.
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Affiliation(s)
- Dawei Chen
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs and NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Zhijun Song
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs and NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Junjie Han
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jimei Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs and NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
| | - Hongwei Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jungui Dai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, CAMS Key Laboratory of Enzyme and Biocatalysis of Natural Drugs and NHC Key Laboratory of Biosynthesis of Natural Products, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
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6
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Huang Z, Liu D, Chen S, Ren J, Gao C, Li Z, Fan A, Lin W. Brominated Depsidones with Antibacterial Effects from a Deep-Sea-Derived Fungus Spiromastix sp. Mar Drugs 2024; 22:78. [PMID: 38393049 PMCID: PMC10890614 DOI: 10.3390/md22020078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Eleven new brominated depsidones, namely spiromastixones U-Z5 (1-11) along with five known analogues (12-16), were isolated from a deep-sea-derived fungus Spiromastix sp. through the addition of sodium bromide during fermentation. Their structures were elucidated by extensive analysis of the spectroscopic data including high-resolution MS and 1D and 2D NMR data. Compounds 6-10 and 16 exhibited significant inhibition against Gram-positive bacteria including methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant Enterococcus faecium (VRE) with MIC values ranging from 0.5 to 2.0 μM. Particularly, tribrominated 7 displayed the strongest activity against MRSA and VRE with a MIC of 0.5 and 1.0 μM, respectively, suggesting its potential for further development as a new antibacterial agent.
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Affiliation(s)
- Zequan Huang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; (Z.H.); (D.L.); (S.C.)
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, China;
| | - Dong Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; (Z.H.); (D.L.); (S.C.)
| | - Shang Chen
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; (Z.H.); (D.L.); (S.C.)
| | - Jinwei Ren
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China;
| | - Chenghai Gao
- Institute of Marine Drugs, Guangxi University of Chinese Medicine, Nanning 530200, China;
| | - Zhiyong Li
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Aili Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; (Z.H.); (D.L.); (S.C.)
| | - Wenhan Lin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China; (Z.H.); (D.L.); (S.C.)
- Ningbo Institute of Marine Medicine, Peking University, Ningbo 315832, China
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7
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Zhao X, Chen Y, Long T, Liu Z, Zhang Q, Zhang H, Yan Y, Zhang C, Zhu Y. Genome Mining and Biosynthetic Reconstitution of Fungal Depsidone Mollicellins Reveal a Dual Functional Cytochrome P450 for Ether Formation. JOURNAL OF NATURAL PRODUCTS 2023; 86:2046-2053. [PMID: 37566707 DOI: 10.1021/acs.jnatprod.3c00609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
Depsidones are significant in structural diversity and broad in biological activities; however, their biosynthetic pathways have not been well understood and have attracted considerable attention. Herein, we heterologously reconstituted a depsidone encoding gene cluster from Ovatospora sp. SCSIO SY280D in Aspergillus nidulans A1145, leading to production of mollicellins, a representative family of depsidones, and discovering a bifunctional P450 monooxygenase that catalyzes both ether formation and hydroxylation in the biosynthesis of the mollicellins. The functions of a decarboxylase and an aromatic prenyltransferase are also characterized to understand the tailoring modification steps. This work provides important insights into the biosynthesis of mollicellins.
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Affiliation(s)
- Xiaoyang Zhao
- 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, Beijing 100049, China
| | - Youzhe Chen
- 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
| | - Ting Long
- 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, Beijing 100049, China
| | - Zhiying Liu
- 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
| | - Qingbo Zhang
- 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, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Haibo Zhang
- 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, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
| | - Yan Yan
- 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, 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, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 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
| | - Yiguang Zhu
- 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, Beijing 100049, China
- Sanya Institute of Ocean Eco-Environmental Engineering, Yazhou Scientific Bay, Sanya 572000, China
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8
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Löhr NA, Rakhmanov M, Wurlitzer JM, Lackner G, Gressler M, Hoffmeister D. Basidiomycete non-reducing polyketide synthases function independently of SAT domains. Fungal Biol Biotechnol 2023; 10:17. [PMID: 37542286 PMCID: PMC10401856 DOI: 10.1186/s40694-023-00164-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/16/2023] [Indexed: 08/06/2023] Open
Abstract
BACKGROUND Non-reducing polyketide synthases (NR-PKSs) account for a major share of natural product diversity produced by both Asco- and Basidiomycota. The present evolutionary diversification into eleven clades further underscores the relevance of these multi-domain enzymes. Following current knowledge, NR-PKSs initiate polyketide assembly by an N-terminal starter unit:acyl transferase (SAT) domain that catalyzes the transfer of an acetyl starter from the acetyl-CoA thioester onto the acyl carrier protein (ACP). RESULTS A comprehensive phylogenetic analysis of NR-PKSs established a twelfth clade from which three representatives, enzymes CrPKS1-3 of the webcap mushroom Cortinarius rufoolivaceus, were biochemically characterized. These basidiomycete synthases lack a SAT domain yet are fully functional hepta- and octaketide synthases in vivo. Three members of the other clade of basidiomycete NR-PKSs (clade VIII) were produced as SAT-domainless versions and analyzed in vivo and in vitro. They retained full activity, thus corroborating the notion that the SAT domain is dispensable for many basidiomycete NR-PKSs. For comparison, the ascomycete octaketide synthase atrochrysone carboxylic acid synthase (ACAS) was produced as a SAT-domainless enzyme as well, but turned out completely inactive. However, a literature survey revealed that some NR-PKSs of ascomycetes carry mutations within the catalytic motif of the SAT domain. In these cases, the role of the domain and the origin of the formal acetate unit remains open. CONCLUSIONS The role of SAT domains differs between asco- and basidiomycete NR-PKSs. For the latter, it is not part of the minimal set of NR-PKS domains and not required for function. This knowledge may help engineer compact NR-PKSs for more resource-efficient routes. From the genomic standpoint, seemingly incomplete or corrupted genes encoding SAT-domainless NR-PKSs should not automatically be dismissed as non-functional pseudogenes, but considered during genome analysis to decipher the potential arsenal of natural products of a given fungus.
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Affiliation(s)
- Nikolai A Löhr
- Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Department Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Malik Rakhmanov
- Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Department Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Jacob M Wurlitzer
- Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Department Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Gerald Lackner
- Synthetic Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Markus Gressler
- Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Department Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Dirk Hoffmeister
- Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany.
- Department Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany.
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