1
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Roux I, Woodcraft C, Sbaraini N, Pepper A, Wong E, Bracegirdle J, Chooi Y. Next-generation AMA1-based plasmids for enhanced heterologous expression in filamentous fungi. Microb Biotechnol 2024; 17:e70010. [PMID: 39276061 PMCID: PMC11401059 DOI: 10.1111/1751-7915.70010] [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: 06/04/2024] [Accepted: 08/25/2024] [Indexed: 09/16/2024] Open
Abstract
Episomal AMA1-based plasmids are increasingly used for expressing biosynthetic pathways and CRISPR/Cas systems in filamentous fungi cell factories due to their high transformation efficiency and multicopy nature. However, the gene expression from AMA1 plasmids has been observed to be highly heterogeneous in growing mycelia. To overcome this limitation, here we developed next-generation AMA1-based plasmids that ensure homogeneous and strong expression. We achieved this by evaluating various degradation tags fused to the auxotrophic marker gene on the AMA1 plasmid, which introduces a more stringent selection pressure throughout multicellular fungal growth. With these improved plasmids, we observed in Aspergillus nidulans a 5-fold increase in the expression of a fluorescent reporter, a doubling in the efficiency of a CRISPRa system for genome mining, and a up to a 10-fold increase in the production of heterologous natural product metabolites. This strategy has the potential to be applied to diverse filamentous fungi.
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Affiliation(s)
- Indra Roux
- School of Molecular SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
- Present address:
Medical Research Council Toxicology UnitUniversity of CambridgeCambridgeUK
| | - Clara Woodcraft
- School of Molecular SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Nicolau Sbaraini
- School of Molecular SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Amy Pepper
- School of Molecular SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Emily Wong
- School of Molecular SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Joe Bracegirdle
- School of Molecular SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
| | - Yit‐Heng Chooi
- School of Molecular SciencesUniversity of Western AustraliaPerthWestern AustraliaAustralia
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2
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Liang X, Huang ZH, Shen WB, Lu XH, Zhang XX, Ma X, Qi SH. Prenylated indole diketopiperazine alkaloids as phosphatase inhibitors from the marine-derived fungus Talaromyces purpureogenus. PHYTOCHEMISTRY 2024; 223:114119. [PMID: 38705266 DOI: 10.1016/j.phytochem.2024.114119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 03/16/2024] [Accepted: 04/28/2024] [Indexed: 05/07/2024]
Abstract
Six previously undescribed prenylated indole diketopiperazine alkaloids, talaromyines A-F (1-6), were isolated from the marine-derived fungus Talaromyces purpureogenus SCSIO 41517. Their structures including absolute configurations were elucidated on the basis of comprehensive spectroscopic data including NMR, HR-ESI-MS, and electronic circular dichroism calculations, together with chemical analysis of hydrolysates. Compounds 1-5 represent the first example of spirocyclic indole diketopiperazines biosynthesized from the condensation of L-tryptophan and L-alanine. Compounds 2 and 4-5 showed selective inhibitory activities against phosphatases TCPTP and MEG2 with IC50 value of 17.9-29.7 μM, respectively. Compounds 4-5 exhibited mild cytotoxic activities against two human cancer cell lines H1975 and HepG-2.
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Affiliation(s)
- Xiao Liang
- 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
| | - Zhong-Hui Huang
- 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
| | - Wen-Bin Shen
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Engineering Research Center of Microbial Medicine, Hebei Industry Microbial Metabolic Technology Innovation Centre, Shijiazhuang Microbial Drugs Technology Innovation Center, Hebei Synthetic Biology High-Energy-Level Technology Innovation Center, Shijiazhuang, Hebei, 050015, China
| | - Xin-Hua Lu
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Engineering Research Center of Microbial Medicine, Hebei Industry Microbial Metabolic Technology Innovation Centre, Shijiazhuang Microbial Drugs Technology Innovation Center, Hebei Synthetic Biology High-Energy-Level Technology Innovation Center, Shijiazhuang, Hebei, 050015, China
| | - Xue-Xia Zhang
- New Drug Research & Development Center of North China Pharmaceutical Group Corporation, National Engineering Research Center of Microbial Medicine, Hebei Industry Microbial Metabolic Technology Innovation Centre, Shijiazhuang Microbial Drugs Technology Innovation Center, Hebei Synthetic Biology High-Energy-Level Technology Innovation Center, Shijiazhuang, Hebei, 050015, China
| | - Xuan Ma
- 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
| | - Shu-Hua Qi
- 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.
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3
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Meng LH, Awakawa T, Li XM, Quan Z, Yang SQ, Wang BG, Abe I. Discovery of (±)-Penindolenes Reveals an Unusual Indole Ring Cleavage Pathway Catalyzed by P450 Monooxygenase. Angew Chem Int Ed Engl 2024; 63:e202403963. [PMID: 38635317 DOI: 10.1002/anie.202403963] [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: 02/27/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 04/19/2024]
Abstract
(±)-Penindolenes A-D (1-4), the first representatives of indole terpenoids featuring a γ-lactam skeleton, were isolated from the mangrove-derived endophytic fungus Penicillium brocae MA-231. Our bioactivity tests revealed their potent antimicrobial and acetylcholinesterase inhibitory activities. The biosynthetic reactions by the five enzymes PbaABCDE leading to γ-lactam ring formation were identified with heterologous expression and in vitro enzymatic assays. Remarkably, the cytochrome P450 monooxygenase PbaB and its homolog in Aspergillus oryzae catalyzed the 2,3-cleavage of the indole ring to generate two keto groups in 1. This is the first example of the oxidative cleavage of indole by a P450 monooxygenase. In addition, rare secondary amide bond formation by the glutamine synthetase-like enzyme PbaD was reported. These findings will contribute to the engineered biosynthesis of unnatural, bioactive indole terpenoids.
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Affiliation(s)
- Ling-Hong Meng
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Nanhai Road 7, Qingdao, 266071, China
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Takayoshi Awakawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- RIKEN Center for Sustainable Resource Science 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Xiao-Ming Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Nanhai Road 7, Qingdao, 266071, China
| | - Zhiyang Quan
- RIKEN Center for Sustainable Resource Science 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Sui-Qun Yang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Nanhai Road 7, Qingdao, 266071, China
| | - Bin-Gui Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, and Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Nanhai Road 7, Qingdao, 266071, China
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, 1-1-1, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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4
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Harper CP, Day A, Tsingos M, Ding E, Zeng E, Stumpf SD, Qi Y, Robinson A, Greif J, Blodgett JAV. Critical analysis of polycyclic tetramate macrolactam biosynthetic gene cluster phylogeny and functional diversity. Appl Environ Microbiol 2024; 90:e0060024. [PMID: 38771054 PMCID: PMC11218653 DOI: 10.1128/aem.00600-24] [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: 04/06/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
Polycyclic tetramate macrolactams (PTMs) are bioactive natural products commonly associated with certain actinobacterial and proteobacterial lineages. These molecules have been the subject of numerous structure-activity investigations since the 1970s. New members continue to be pursued in wild and engineered bacterial strains, and advances in PTM biosynthesis suggest their outwardly simplistic biosynthetic gene clusters (BGCs) belie unexpected product complexity. To address the origins of this complexity and understand its influence on PTM discovery, we engaged in a combination of bioinformatics to systematically classify PTM BGCs and PTM-targeted metabolomics to compare the products of select BGC types. By comparing groups of producers and BGC mutants, we exposed knowledge gaps that complicate bioinformatics-driven product predictions. In sum, we provide new insights into the evolution of PTM BGCs while systematically accounting for the PTMs discovered thus far. The combined computational and metabologenomic findings presented here should prove useful for guiding future discovery.IMPORTANCEPolycyclic tetramate macrolactam (PTM) pathways are frequently found within the genomes of biotechnologically important bacteria, including Streptomyces and Lysobacter spp. Their molecular products are typically bioactive, having substantial agricultural and therapeutic interest. Leveraging bacterial genomics for the discovery of new related molecules is thus desirable, but drawing accurate structural predictions from bioinformatics alone remains challenging. This difficulty stems from a combination of previously underappreciated biosynthetic complexity and remaining knowledge gaps, compounded by a stream of yet-uncharacterized PTM biosynthetic loci gleaned from recently sequenced bacterial genomes. We engaged in the following study to create a useful framework for cataloging historic PTM clusters, identifying new cluster variations, and tracing evolutionary paths for these molecules. Our data suggest new PTM chemistry remains discoverable in nature. However, our metabolomic and mutational analyses emphasize the practical limitations of genomics-based discovery by exposing hidden complexity.
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Affiliation(s)
| | - Anna Day
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Maya Tsingos
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Edward Ding
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Elizabeth Zeng
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Spencer D. Stumpf
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Yunci Qi
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Adam Robinson
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Jennifer Greif
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
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5
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Wang X, Chen N, Cruz-Morales P, Zhong B, Zhang Y, Wang J, Xiao Y, Fu X, Lin Y, Acharya S, Li Z, Deng H, Sun Y, Bai L, Tang X, Keasling JD, Luo X. Elucidation of genes enhancing natural product biosynthesis through co-evolution analysis. Nat Metab 2024; 6:933-946. [PMID: 38609677 DOI: 10.1038/s42255-024-01024-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 03/06/2024] [Indexed: 04/14/2024]
Abstract
Streptomyces has the largest repertoire of natural product biosynthetic gene clusters (BGCs), yet developing a universal engineering strategy for each Streptomyces species is challenging. Given that some Streptomyces species have larger BGC repertoires than others, we proposed that a set of genes co-evolved with BGCs to support biosynthetic proficiency must exist in those strains, and that their identification may provide universal strategies to improve the productivity of other strains. We show here that genes co-evolved with natural product BGCs in Streptomyces can be identified by phylogenomics analysis. Among the 597 genes that co-evolved with polyketide BGCs, 11 genes in the 'coenzyme' category have been examined, including a gene cluster encoding for the cofactor pyrroloquinoline quinone. When the pqq gene cluster was engineered into 11 Streptomyces strains, it enhanced production of 16,385 metabolites, including 36 known natural products with up to 40-fold improvement and several activated silent gene clusters. This study provides an innovative engineering strategy for improving polyketide production and finding previously unidentified BGCs.
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Affiliation(s)
- Xinran Wang
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ningxin Chen
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Pablo Cruz-Morales
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Biming Zhong
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yangming Zhang
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jian Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, China
| | - Yifan Xiao
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xinnan Fu
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yang Lin
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China
| | - Suneil Acharya
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Zhibo Li
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Huaxiang Deng
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yuhui Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Ministry of Education), Wuhan University, Wuhan, China
- School of Pharmacy, Huazhong University of Science and Technology, Wuhan, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyu Tang
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
| | - Jay D Keasling
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, CA, USA.
- Joint BioEnergy Institute, Emeryville, CA, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Xiaozhou Luo
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- Shenzhen Infrastructure for Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
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6
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Zhang YH, Du HF, Liu YF, Cao F, Luo DQ, Wang CY. Novel anti-inflammatory diketopiperazine alkaloids from the marine-derived fungus Penicillium brasilianum. Appl Microbiol Biotechnol 2024; 108:194. [PMID: 38315417 PMCID: PMC10844341 DOI: 10.1007/s00253-024-13026-4] [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: 08/25/2023] [Revised: 12/30/2023] [Accepted: 01/22/2024] [Indexed: 02/07/2024]
Abstract
Diketopiperazine alkaloids have proven the most abundant heterocyclic alkaloids up to now, which usually process diverse scaffolds and rich biological activities. In our search for bioactive diketopiperazine alkaloids from marine-derived fungi, two novel diketopiperazine alkaloids, penipiperazine A (1) and its biogenetically related new metabolite (2), together with a known analogue neofipiperzine C (3), were obtained from the strain Penicillium brasilianum. Their planar structures and absolute configurations were elucidated by extensive spectroscopic analyses, 13C NMR calculation, Marfey's, ECD, and ORD methods. Compound 1 featured a unique 6/5/6/6/5 indole-pyrazino-pyrazino-pyrrolo system, and its plausible biogenetic pathway was also proposed. Additionally, compounds 1-3 have been tested for their inflammatory activities. 1 and 2 significantly inhibited the release of NO and the expression of related pro-inflammatory cytokines on LPS-stimulated RAW264.7 cells, suggesting they could be attracting candidate for further development as anti-inflammatory agent. KEY POINTS: • A novel diketopiperazine alkaloid featuring a unique 6/5/6/6/5 indole-pyrazino-pyrazino-pyrrolo system was isolated from the marine fungus Penicillium brasilianum. • The structure of 1 was elucidated by detailed analysis of 2D NMR data, 13C NMR calculation, Marfey's, ECD, and ORD methods. • Compounds 1 and 2 significantly inhibited the release of NO and the expression of related pro-inflammatory cytokines on LPS-stimulated RAW264.7 cells.
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Affiliation(s)
- Ya-Hui Zhang
- College of Life Sciences, Key Laboratory of Medicinal Chemistry and Molecular Diagnostics of Education Ministry of China, Hebei University, Baoding, 071002, China
| | - Hui-Fang Du
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, 071002, China
| | - Yun-Feng Liu
- College of Life Sciences, Key Laboratory of Medicinal Chemistry and Molecular Diagnostics of Education Ministry of China, Hebei University, Baoding, 071002, China
| | - Fei Cao
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, 071002, China.
| | - Du-Qiang Luo
- College of Life Sciences, Key Laboratory of Medicinal Chemistry and Molecular Diagnostics of Education Ministry of China, Hebei University, Baoding, 071002, China.
| | - Chang-Yun Wang
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drugs, the Ministry of Education of China, School of Medicine and Pharmacy, Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
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7
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Shi X, Zhao G, Li H, Zhao Z, Li W, Wu M, Du YL. Hydroxytryptophan biosynthesis by a family of heme-dependent enzymes in bacteria. Nat Chem Biol 2023; 19:1415-1422. [PMID: 37653171 DOI: 10.1038/s41589-023-01416-0] [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: 11/27/2022] [Accepted: 08/03/2023] [Indexed: 09/02/2023]
Abstract
Hydroxytryptophan serves as a chemical precursor to a variety of bioactive specialized metabolites, including the human neurotransmitter serotonin and the hormone melatonin. Although the human and animal routes to hydroxytryptophan have been known for decades, how bacteria catalyze tryptophan indole hydroxylation remains a mystery. Here we report a class of tryptophan hydroxylases that are involved in various bacterial metabolic pathways. These enzymes utilize a histidine-ligated heme cofactor and molecular oxygen or hydrogen peroxide to catalyze regioselective hydroxylation on the tryptophan indole moiety, which is mechanistically distinct from their animal counterparts from the nonheme iron enzyme family. Through genome mining, we also identify members that can hydroxylate the tryptophan indole ring at alternative positions. Our results not only reveal a conserved way to synthesize hydroxytryptophans in bacteria but also provide a valuable enzyme toolbox for biocatalysis. As proof of concept, we assemble a highly efficient pathway for melatonin in a bacterial host.
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Affiliation(s)
- Xinjie Shi
- The Fourth Affiliated Hospital and Department of Microbiology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Guiyun Zhao
- The Fourth Affiliated Hospital and Department of Microbiology, School of Medicine, Zhejiang University, Hangzhou, China
- Department of Pharmacy, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, China
| | - Hu Li
- Polytechnic Institute, Zhejiang University, Hangzhou, China
| | - Zhijie Zhao
- The Fourth Affiliated Hospital and Department of Microbiology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Wei Li
- The Fourth Affiliated Hospital and Department of Microbiology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Miaolian Wu
- Department of Pharmacy, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, China
| | - Yi-Ling Du
- The Fourth Affiliated Hospital and Department of Microbiology, School of Medicine, Zhejiang University, Hangzhou, China.
- Department of Pharmacy, The Fourth Affiliated Hospital, School of Medicine, Zhejiang University, Yiwu, China.
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China.
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Hangzhou, China.
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8
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Shende VV, Harris NR, Sanders JN, Newmister SA, Khatri Y, Movassaghi M, Houk KN, Sherman DH. Molecular Dynamics Simulations Guide Chimeragenesis and Engineered Control of Chemoselectivity in Diketopiperazine Dimerases. Angew Chem Int Ed Engl 2023; 62:e202210254. [PMID: 36610039 PMCID: PMC10159983 DOI: 10.1002/anie.202210254] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 12/14/2022] [Accepted: 01/05/2023] [Indexed: 01/09/2023]
Abstract
In the biosynthesis of the tryptophan-linked dimeric diketopiperazines (DKPs), cytochromes P450 selectively couple DKP monomers to generate a variety of intricate and isomeric frameworks. To determine the molecular basis for selectivity of these biocatalysts we obtained a high-resolution crystal structure of selective Csp2 -N bond forming dimerase, AspB. Overlay of the AspB structure onto C-C and C-N bond forming homolog NzeB revealed no significant structural variance to explain their divergent chemoselectivities. Molecular dynamics (MD) simulations identified a region of NzeB with increased conformational flexibility relative to AspB, and interchange of this region along with a single active site mutation led to a variant that catalyzes exclusive C-N bond formation. MD simulations also suggest that intermolecular C-C or C-N bond formation results from a change in mechanism, supported experimentally through use of a substrate mimic.
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Affiliation(s)
- Vikram V Shende
- Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109, USA
| | - Natalia R Harris
- Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109, USA
| | - Jacob N Sanders
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Sean A Newmister
- Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109, USA
| | - Yogan Khatri
- Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109, USA
| | - Mohammad Movassaghi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kendall N Houk
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MÌ 48109, USA
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9
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Permana D, Kitaoka T, Ichinose H. Conversion and synthesis of chemicals catalyzed by fungal cytochrome P450 monooxygenases: A review. Biotechnol Bioeng 2023. [PMID: 37139574 DOI: 10.1002/bit.28411] [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: 02/06/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 05/05/2023]
Abstract
Cytochrome P450s (also called CYPs or P450s) are a superfamily of heme-containing monooxygenases. They are distributed in all biological kingdoms. Most fungi have at least two P450-encoding genes, CYP51 and CYP61, which are housekeeping genes that play important roles in the synthesis of sterols. However, the kingdom fungi is an interesting source of numerous P450s. Here, we review reports on fungal P450s and their applications in the bioconversion and biosynthesis of chemicals. We highlight their history, availability, and versatility. We describe their involvement in hydroxylation, dealkylation, oxygenation, C═C epoxidation, C-C cleavage, C-C ring formation and expansion, C-C ring contraction, and uncommon reactions in bioconversion and/or biosynthesis pathways. The ability of P450s to catalyze these reactions makes them promising enzymes for many applications. Thus, we also discuss future prospects in this field. We hope that this review will stimulate further study and exploitation of fungal P450s for specific reactions and applications.
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Affiliation(s)
- Dani Permana
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Research Center for Environmental and Clean Technology, The National Research and Innovation Agency of the Republic of Indonesia (Badan Riset dan Inovasi Nasional (BRIN)), Bandung Advanced Science and Creative Engineering Space (BASICS), Kawasan Sains dan Teknologi (KST) Prof. Dr. Samaun Samadikun, Bandung, Indonesia
| | - Takuya Kitaoka
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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10
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Nguyen TAM, Grzech D, Chung K, Xia Z, Nguyen TD, Dang TTT. Discovery of a cytochrome P450 enzyme catalyzing the formation of spirooxindole alkaloid scaffold. FRONTIERS IN PLANT SCIENCE 2023; 14:1125158. [PMID: 36818833 PMCID: PMC9936145 DOI: 10.3389/fpls.2023.1125158] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Spirooxindole alkaloids feature a unique scaffold of an oxindole ring sharing an atom with a heterocyclic moiety. These compounds display an extensive range of biological activities such as anticancer, antibiotics, and anti-hypertension. Despite their structural and functional significance, the establishment and rationale of the spirooxindole scaffold biosynthesis are yet to be elucidated. Herein, we report the discovery and characterization of a cytochrome P450 enzyme from kratom (Mitragyna speciosa) responsible for the formation of the spirooxindole alkaloids 3-epi-corynoxeine (3R, 7R) and isocorynoxeine (3S, 7S) from the corynanthe-type (3R)-secoyohimbane precursors. Expression of the newly discovered enzyme in Saccharomyces cerevisiae yeast allows for the efficient in vivo and in vitro production of spirooxindoles. This discovery highlights the versatility of plant cytochrome P450 enzymes in building unusual alkaloid scaffolds and opens a gateway to access the prestigious spirooxindole pharmacophore and its derivatives.
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Affiliation(s)
- Tuan-Anh M. Nguyen
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
| | - Dagny Grzech
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Khoa Chung
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Zhicheng Xia
- Department of Chemistry, Faculty of Science, University of British Columbia, Vancouver, BC, Canada
| | - Trinh-Don Nguyen
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
| | - Thu-Thuy T. Dang
- Department of Chemistry, Irving K. Barber Faculty of Science, University of British Columbia, Kelowna, BC, Canada
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11
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Deng H, Liang X, Liu J, Zheng X, Fan TP, Cai Y. Advances and perspectives on perylenequinone biosynthesis. Front Microbiol 2022; 13:1070110. [PMID: 36605511 PMCID: PMC9808054 DOI: 10.3389/fmicb.2022.1070110] [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: 10/14/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Under illumination, the fungal secondary metabolites, perylenequinones (PQs) react with molecular oxygen to generate reactive oxygen species (ROS), which, in excess can damage cellular macromolecules and trigger apoptosis. Based on this property, PQs have been widely used as photosensitizers and applied in pharmaceuticals, which has stimulated research into the discovery of new PQs and the elucidation of their biosynthetic pathways. The PQs-associated literature covering from April 1967 to September 2022 is reviewed in three sections: (1) the sources, structural diversity, and biological activities of microbial PQs; (2) elucidation of PQ biosynthetic pathways, associated genes, and mechanisms of regulation; and (3) advances in pathway engineering and future potential strategies to modify cellular metabolism and improve PQ production.
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Affiliation(s)
- Huaxiang Deng
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China,The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China,*Correspondence: Huaxiang Deng,
| | - Xinxin Liang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jinbin Liu
- School of Marine and Bioengineering, Yancheng Institute of Technology, Yancheng, Jiangsu, China
| | - Xiaohui Zheng
- College of Life Sciences, Northwest University, Xi’an, Shanxi, China
| | - Tai-Ping Fan
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Yujie Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China,Yujie Cai,
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12
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Chen XW, Rao L, Chen JL, Zou Y. Unexpected assembly machinery for 4(3H)-quinazolinone scaffold synthesis. Nat Commun 2022; 13:6522. [PMID: 36316336 PMCID: PMC9622831 DOI: 10.1038/s41467-022-34340-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 10/21/2022] [Indexed: 11/06/2022] Open
Abstract
4(3H)-quinazolinone is the core scaffold in more than 200 natural alkaloids and numerous drugs. Many chemosynthetic methodologies have been developed to generate it; however, investigation of its native enzymatic formation mechanism in fungi has been largely limited to fumiquinazolines, where the two nitrogen atoms come from anthranilate (N-1) and the α-NH2 of amino acids (N-3). Here, via biochemical investigation of the chrysogine pathway, unexpected assembly machinery for 4(3H)-quinazolinone is unveiled, which involves a fungal two-module nonribosomal peptide synthase ftChyA with an unusual terminal condensation domain catalysing tripeptide formation; reveals that N-3 originates from the inorganic ammonium ions or the amide of L-Gln; demonstrates an unusual α-ketoglutarate-dependent dioxygenase ftChyM catalysis of the C-N bond oxidative cleavage of a tripeptide to form a dipeptide. Our study uncovers a unique release and tailoring mechanism for nonribosomal peptides and an alternative route for the synthesis of 4(3H)-quinazolinone scaffolds.
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Affiliation(s)
- Xi-Wei Chen
- grid.263906.80000 0001 0362 4044College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715 P. R. China
| | - Li Rao
- grid.263906.80000 0001 0362 4044College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715 P. R. China
| | - Jia-Li Chen
- grid.263906.80000 0001 0362 4044College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715 P. R. China
| | - Yi Zou
- grid.263906.80000 0001 0362 4044College of Pharmaceutical Sciences, Southwest University, Chongqing, 400715 P. R. China
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13
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Chiang YM, Lin TS, Wang CCC. Total Heterologous Biosynthesis of Fungal Natural Products in Aspergillus nidulans. JOURNAL OF NATURAL PRODUCTS 2022; 85:2484-2518. [PMID: 36173392 PMCID: PMC9621686 DOI: 10.1021/acs.jnatprod.2c00487] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Fungal natural products comprise a wide range of bioactive compounds including important drugs and agrochemicals. Intriguingly, bioinformatic analyses of fungal genomes have revealed that fungi have the potential to produce significantly more natural products than what have been discovered so far. It has thus become widely accepted that most biosynthesis pathways of fungal natural products are silent or expressed at very low levels under laboratory cultivation conditions. To tap into this vast chemical reservoir, the reconstitution of entire biosynthetic pathways in genetically tractable fungal hosts (total heterologous biosynthesis) has become increasingly employed in recent years. This review summarizes total heterologous biosynthesis of fungal natural products accomplished before 2020 using Aspergillus nidulans as heterologous hosts. We review here Aspergillus transformation, A. nidulans hosts, shuttle vectors for episomal expression, and chromosomal integration expression. These tools, collectively, not only facilitate the discovery of cryptic natural products but can also be used to generate high-yield strains with clean metabolite backgrounds. In comparison with total synthesis, total heterologous biosynthesis offers a simplified strategy to construct complex molecules and holds potential for commercial application.
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Affiliation(s)
- Yi-Ming Chiang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department of Pharmacy, Chia Nan University of Pharmacy and Science, Tainan 71710, Taiwan
| | - Tzu-Shyang Lin
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
| | - Clay C C Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, California 90089, United States
- Department of Chemistry, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, California 90089, United States
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14
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Kelly SP, Shende VV, Flynn AR, Dan Q, Ye Y, Smith JL, Tsukamoto S, Sigman MS, Sherman DH. Data Science-Driven Analysis of Substrate-Permissive Diketopiperazine Reverse Prenyltransferase NotF: Applications in Protein Engineering and Cascade Biocatalytic Synthesis of (-)-Eurotiumin A. J Am Chem Soc 2022; 144:19326-19336. [PMID: 36223664 PMCID: PMC9831672 DOI: 10.1021/jacs.2c06631] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Prenyltransfer is an early-stage carbon-hydrogen bond (C-H) functionalization prevalent in the biosynthesis of a diverse array of biologically active bacterial, fungal, plant, and metazoan diketopiperazine (DKP) alkaloids. Toward the development of a unified strategy for biocatalytic construction of prenylated DKP indole alkaloids, we sought to identify and characterize a substrate-permissive C2 reverse prenyltransferase (PT). As the first tailoring event within the biosynthesis of cytotoxic notoamide metabolites, PT NotF catalyzes C2 reverse prenyltransfer of brevianamide F. Solving a crystal structure of NotF (in complex with native substrate and prenyl donor mimic dimethylallyl S-thiolodiphosphate (DMSPP)) revealed a large, solvent-exposed active site, intimating NotF may possess a significantly broad substrate scope. To assess the substrate selectivity of NotF, we synthesized a panel of 30 sterically and electronically differentiated tryptophanyl DKPs, the majority of which were selectively prenylated by NotF in synthetically useful conversions (2 to >99%). Quantitative representation of this substrate library and development of a descriptive statistical model provided insight into the molecular origins of NotF's substrate promiscuity. This approach enabled the identification of key substrate descriptors (electrophilicity, size, and flexibility) that govern the rate of NotF-catalyzed prenyltransfer, and the development of an "induced fit docking (IFD)-guided" engineering strategy for improved turnover of our largest substrates. We further demonstrated the utility of NotF in tandem with oxidative cyclization using flavin monooxygenase, BvnB. This one-pot, in vitro biocatalytic cascade enabled the first chemoenzymatic synthesis of the marine fungal natural product, (-)-eurotiumin A, in three steps and 60% overall yield.
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Affiliation(s)
- Samantha P. Kelly
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.,Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA.,These authors contributed equally: Samantha P. Kelly, Vikram V. Shende
| | - Vikram V. Shende
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.,Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109, USA.,These authors contributed equally: Samantha P. Kelly, Vikram V. Shende
| | - Autumn R. Flynn
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Qingyun Dan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ying Ye
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Janet L. Smith
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Sachiko Tsukamoto
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kumamoto 862-0973, Japan
| | - Matthew S. Sigman
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
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15
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Zhang N, Wu J, Zhang S, Yuan M, Xu H, Li J, Zhang P, Wang M, Kempher ML, Tao X, Zhang LQ, Ge H, He YX. Molecular basis for coordinating secondary metabolite production by bacterial and plant signaling molecules. J Biol Chem 2022; 298:102027. [PMID: 35568198 PMCID: PMC9163588 DOI: 10.1016/j.jbc.2022.102027] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/03/2022] [Accepted: 05/05/2022] [Indexed: 11/28/2022] Open
Abstract
The production of secondary metabolites is a major mechanism used by beneficial rhizobacteria to antagonize plant pathogens. These bacteria have evolved to coordinate the production of different secondary metabolites due to the heavy metabolic burden imposed by secondary metabolism. However, for most secondary metabolites produced by bacteria, it is not known how their biosynthesis is coordinated. Here, we showed that PhlH from the rhizobacterium Pseudomonas fluorescens is a TetR-family regulator coordinating the expression of enzymes related to the biosynthesis of several secondary metabolites, including 2,4-diacetylphloroglucinol (2,4-DAPG), mupirocin, and pyoverdine. We present structures of PhlH in both its apo form and 2,4-DAPG-bound form and elucidate its ligand-recognizing and allosteric switching mechanisms. Moreover, we found that dissociation of 2,4-DAPG from the ligand-binding domain of PhlH was sufficient to allosterically trigger a pendulum-like movement of the DNA-binding domains within the PhlH dimer, leading to a closed-to-open conformational transition. Finally, molecular dynamics simulations confirmed that two distinct conformational states were stabilized by specific hydrogen bonding interactions and that disruption of these hydrogen bonds had profound effects on the conformational transition. Our findings not only reveal a well-conserved route of allosteric signal transduction in TetR-family regulators but also provide novel mechanistic insights into bacterial metabolic coregulation.
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Affiliation(s)
- Nannan Zhang
- School of Life Sciences, Anhui University, Hefei 230601, P.R. China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China.
| | - Jin Wu
- School of Life Sciences, Anhui University, Hefei 230601, P.R. China; Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, P.R. China
| | - Siping Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, P.R. China
| | - Maoran Yuan
- School of Life Sciences, Anhui University, Hefei 230601, P.R. China; Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, P.R. China
| | - Hang Xu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, P.R. China
| | - Jie Li
- School of Life Sciences, Anhui University, Hefei 230601, P.R. China; Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, P.R. China
| | - Pingping Zhang
- School of Life Sciences, Anhui University, Hefei 230601, P.R. China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China
| | - Mingzhu Wang
- School of Life Sciences, Anhui University, Hefei 230601, P.R. China; Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, P.R. China
| | - Megan L Kempher
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Ok, USA
| | - Xuanyu Tao
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, Ok, USA
| | - Li-Qun Zhang
- College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Honghua Ge
- School of Life Sciences, Anhui University, Hefei 230601, P.R. China; Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Material Science and Information Technology, Anhui University, Hefei 230601, P.R. China.
| | - Yong-Xing He
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, P.R. China.
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16
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Study on Secondary Metabolites of Endophytic Fungus, Aspergillus fumigatus, from Crocus sativus L. Guided byUHPLC-HRMS/MS-Based Molecular Network. Int J Anal Chem 2022; 2022:7067665. [PMID: 35586120 PMCID: PMC9110225 DOI: 10.1155/2022/7067665] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/22/2022] [Indexed: 11/24/2022] Open
Abstract
As a traditional Chinese medicine, Crocus sativus Linn has been used for a long time in China. However, the studies on secondary metabolites of its endophytic fungi were not fully sufficient. Thus, the endophytic fungus, Aspergillus fumigatus, collected from the lateral buds of C. sativus, was here investigated. An approach combining UHPLC-HRMS/MS (ultra-high performance liquid chromatography-high resolution mass spectrometry) with molecular network was carried out to construct a molecular network of crude EtOAc extract (CEE) of A. fumigatus, in which 32 chemical compounds were annotated. On the basis of analysis results, a total of 15 known natural compounds were isolated from CEE. Among them, compounds 11 and 12 were isolated for the first time from the genus Aspergillus. Moreover, CEE and compound 7 exhibited moderate inhibitory activity against Erwinia sp. with a MIC value of 100 μg/mL. This study provided a more convenient and rapid approach to investigating the crude extract with complex components of A. fumigatus, which is of great benefit to the further study and utilization of secondary metabolites of the genus Aspergillus.
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17
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Mori T, Nakashima Y, Chen H, Hoshino S, Mitsuhashi T, Abe I. Structure-based redesign of Fe(II)/2-oxoglutarate-dependent oxygenase AndA to catalyze spiro-ring formation. Chem Commun (Camb) 2022; 58:5510-5513. [PMID: 35420093 DOI: 10.1039/d2cc00736c] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Structure- and mechanism-based redesign of the Fe(II)/2-oxoglutarate-dependent oxygenase AndA was performed. The function of AndA was expanded to catalyze a spiro-ring formation reaction from an isomerization reaction. The redesigned AndA variants produced two unnatural novel spiro-ring containing compounds through two and three consecutive oxidation reactions.
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Affiliation(s)
- Takahiro Mori
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.,PRESTO, Japan Science and Technology Agency (JST), Kawaguchi, Saitama 332-0012, Japan
| | - Yu Nakashima
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Heping Chen
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Shotaro Hoshino
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Takaaki Mitsuhashi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Ikuro Abe
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan. .,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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18
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Wang G, Ran H, Fan J, Keller NP, Liu Z, Wu F, Yin WB. Fungal-fungal cocultivation leads to widespread secondary metabolite alteration requiring the partial loss-of-function VeA1 protein. SCIENCE ADVANCES 2022; 8:eabo6094. [PMID: 35476435 PMCID: PMC9045611 DOI: 10.1126/sciadv.abo6094] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/11/2022] [Indexed: 05/02/2023]
Abstract
Microbial communication has attracted notable attention as an indicator of microbial interactions that lead to marked alterations of secondary metabolites (SMs) in varied environments. However, the mechanisms responsible for SM regulation are not fully understood, especially in fungal-fungal interactions. Here, cocultivation of an endophytic fungus Epicoccum dendrobii with the model fungus Aspergillus nidulans and several other filamentous fungi triggered widespread alteration of SMs. Multiple silent biosynthetic gene clusters in A. nidulans were activated by transcriptome and metabolome analysis. Unprecedentedly, gene deletion and replacement proved that a partial loss-of-function VeA1 protein, but not VeA, was associated with the widespread SM changes in both A. nidulans and A. fumigatus during cocultivation. VeA1 regulation required the transcription factor SclB and the velvet complex members LaeA and VelB for producing aspernidines as representative formation of SMs in A. nidulans. This study provides new insights into the mechanism that trigger metabolic changes during fungal-fungal interactions.
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Affiliation(s)
- Gang Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Huomiao Ran
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Jie Fan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zhiguo Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Fan Wu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, PR China
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19
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Okamoto T, Kishimoto S, Watanabe K. Isolation of Natural Prodrug-Like Metabolite by Simulating Human Prodrug Activation in Filamentous Fungus. Chem Pharm Bull (Tokyo) 2022; 70:304-308. [DOI: 10.1248/cpb.c21-01099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Takumi Okamoto
- Department of Pharmaceutical Sciences, University of Shizuoka
| | | | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka
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20
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Biosynthesis of Fungal Natural Products Involving Two Separate Pathway Crosstalk. J Fungi (Basel) 2022; 8:jof8030320. [PMID: 35330322 PMCID: PMC8948627 DOI: 10.3390/jof8030320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 03/17/2022] [Accepted: 03/17/2022] [Indexed: 01/21/2023] Open
Abstract
Fungal natural products (NPs) usually possess complicated structures, exhibit satisfactory bioactivities, and are an outstanding source of drug leads, such as the cholesterol-lowering drug lovastatin and the immunosuppressive drug mycophenolic acid. The fungal NPs biosynthetic genes are always arranged within one single biosynthetic gene cluster (BGC). However, a rare but fascinating phenomenon that a crosstalk between two separate BGCs is indispensable to some fungal dimeric NPs biosynthesis has attracted increasing attention. The hybridization of two separate BGCs not only increases the structural complexity and chemical diversity of fungal NPs, but also expands the scope of bioactivities. More importantly, the underlying mechanism for this hybridization process is poorly understood and needs further exploration, especially the determination of BGCs for each building block construction and the identification of enzyme(s) catalyzing the two biosynthetic precursors coupling processes such as Diels–Alder cycloaddition and Michael addition. In this review, we summarized the fungal NPs produced by functional crosstalk of two discrete BGCs, and highlighted their biosynthetic processes, which might shed new light on genome mining for fungal NPs with unprecedented frameworks, and provide valuable insights into the investigation of mysterious biosynthetic mechanisms of fungal dimeric NPs which are constructed by collaboration of two separate BGCs.
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21
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Yan D, Wang K, Bai S, Liu B, Bai J, Qi X, Hu Y. Flavin-Dependent Monooxygenase-Mediated 1,2-Oxazine Construction via Meisenheimer Rearrangement in the Biosynthesis of Paeciloxazine. J Am Chem Soc 2022; 144:4269-4276. [PMID: 35192348 DOI: 10.1021/jacs.2c00881] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The [1,2]-Meisenheimer rearrangement is well known as the [1,2]-migration of an O-substituted hydroxylamine from a tertiary amine N-oxide, and it is frequently employed in organic synthesis to enforce adjacent carbon oxidation or install a 1,2-oxazine core, which is a prevalent structural feature and pharmacophore of many bioactive natural products. Although the [1,2]-Meisenheimer rearrangement was proposed to occur in the biosynthesis of a number of 1,2-oxazine-containing natural products, it has never been proved biosynthetically. Here, we identified the biosynthetic gene cluster of an insecticidal natural product, paeciloxazine (1), from Penicillium janthinellum and characterized a flavin-dependent monooxygenase, PaxA, as the first example that mediates the formation of a 1,2-oxazine moiety via Meisenheimer rearrangement. In vitro biochemical assays, site-directed mutations, docking and molecular dynamics simulations, and density functional theory calculations support the mechanism that PaxA first catalyzes N-oxidation to form an N-oxide intermediate, which undergoes [1,2]-Meisenheimer rearrangement with the assistance of an amino acid with proton transfer property. This study expands the repertoire of rearrangement reactions during the biosynthesis of natural products and provides a new strategy for discovering natural products with N-O tethers by genome mining.
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Affiliation(s)
- Daojiang Yan
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Kunya Wang
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Songlin Bai
- National Institute of Biological Sciences, Beijing 102206, China
| | - Bingyu Liu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Jian Bai
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xiangbing Qi
- National Institute of Biological Sciences, Beijing 102206, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 100084, China
| | - Youcai Hu
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.,NHC Key Laboratory of Biosynthesis of Natural Products, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.,CAMS Key Laboratory of Enzyme and Catalysis of Natural Drugs, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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22
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Madhavan A, Arun KB, Sindhu R, Alphonsa Jose A, Pugazhendhi A, Binod P, Sirohi R, Reshmy R, Kumar Awasthi M. Engineering interventions in industrial filamentous fungal cell factories for biomass valorization. BIORESOURCE TECHNOLOGY 2022; 344:126209. [PMID: 34715339 DOI: 10.1016/j.biortech.2021.126209] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/18/2021] [Accepted: 10/20/2021] [Indexed: 05/15/2023]
Abstract
Filamentous fungi possess versatile capabilities for synthesizing a variety of valuable bio compounds, including enzymes, organic acids and small molecule secondary metabolites. The advancements of genetic and metabolic engineering techniques and the availability of sequenced genomes discovered their potential as expression hosts for recombinant protein production. Remarkably, plant-biomass degrading filamentous fungi show the unique capability to decompose lignocellulose, an extremely recalcitrant biopolymer. The basic biochemical approaches have motivated several industrial processes for lignocellulose biomass valorisation into fermentable sugars and other biochemical for biofuels, biomolecules, and biomaterials. The review gives insight into current trends in engineering filamentous fungi for enzymes, fuels, and chemicals from lignocellulose biomass. This review describes the variety of enzymes and compounds that filamentous fungi produce, engineering of filamentous fungi for biomass valorisation with a special focus on lignocellulolytic enzymes and other bulk chemicals.
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Affiliation(s)
- Aravind Madhavan
- Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum 695 014, India.
| | - K B Arun
- Rajiv Gandhi Centre for Biotechnology, Jagathy, Trivandrum 695 014, India
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| | - Anju Alphonsa Jose
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| | | | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| | - Ranjna Sirohi
- Department of Chemical & Biological Engineering, Korea University, Seoul 136713, Republic of Korea; Centre for Energy & Environmental Sustainability, Lucknow 226001. Uttar Pradesh, India
| | - R Reshmy
- Post Graduate and Research Department of Chemistry, Bishop Moore College, Mavelikara 690 110, Kerala, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712 100, PR China
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23
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Roux I, Chooi YH. Heterologous Expression of Fungal Biosynthetic Pathways in Aspergillus nidulans Using Episomal Vectors. Methods Mol Biol 2022; 2489:75-92. [PMID: 35524046 DOI: 10.1007/978-1-0716-2273-5_5] [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: 06/14/2023]
Abstract
Filamentous fungi produce a wide diversity of secondary metabolites, whose biosynthesis is encoded in biosynthetic gene clusters (BGCs). As novel BGCs are often found in fungal species that are genetically intractable or difficult to cultivate, heterologous expression is increasingly being used for compound discovery. In addition, heterologous expression is a useful strategy to elucidate the function of the genes within a BGC and shed light on their enzymatic mechanisms. Here, we describe a method for BGC elucidation using multi-marker AMA1-based pYFAC vectors for episomal expression in the fungal host Aspergillus nidulans. The pYFAC vectors have the advantage of high transformation efficiency and support high compound production. In addition, different pathway intermediates can be easily evaluated by testing different vector combinations. This protocol encompasses different AMA1-based strategies for BGC expression such as cloning of a BGC native sequence, promoter exchange or transcription factor overexpression. We also describe procedures for A. nidulans protoplasting, transformation, and small-scale culture analysis of strains containing AMA1 vectors.
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Affiliation(s)
- Indra Roux
- School of Molecular Sciences, University of Western Australia, Perth, WA, Australia
| | - Yit Heng Chooi
- School of Molecular Sciences, University of Western Australia, Perth, WA, Australia.
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24
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Cao F, Tao WT, Yu Q, Xu CX, Cheng JT, Liu RX, Zhao QW, Jiang XH, Liu Y, Li YQ, Zhan ZJ, Shi T, Mao XM. Discovery of Semi-Pinacolases from the Epoxide Hydrolase Family during Efficient Assembly of a Fungal Polyketide. ACS Catal 2021. [DOI: 10.1021/acscatal.1c03899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Fei Cao
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Zhejiang University, Hangzhou 310058, China
| | - Wen-Tao Tao
- 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
- Clinical Research Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Qian Yu
- 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
| | - Chu-Xuan Xu
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Zhejiang University, Hangzhou 310058, China
| | - Jin-Tao Cheng
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Zhejiang University, Hangzhou 310058, China
| | - Ruo-Xi Liu
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
| | - Qing-Wei Zhao
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Zhejiang University, Hangzhou 310058, China
| | - Xin-Hang Jiang
- Equipment and Technology Service Platform, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Yu Liu
- Equipment and Technology Service Platform, College of Life Science, Zhejiang University, Hangzhou 310058, China
| | - Yong-Quan Li
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Zhejiang University, Hangzhou 310058, China
| | - Zha-Jun Zhan
- College of Pharmaceutical Science, Zhejiang University of Technology, Hangzhou 310014, China
| | - Ting Shi
- 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
| | - Xu-Ming Mao
- Research Center for Clinical Pharmacy, The First Affiliated Hospital & Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou 310058, China
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, Zhejiang University, Hangzhou 310058, China
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25
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Meng X, Fang Y, Ding M, Zhang Y, Jia K, Li Z, Collemare J, Liu W. Developing fungal heterologous expression platforms to explore and improve the production of natural products from fungal biodiversity. Biotechnol Adv 2021; 54:107866. [PMID: 34780934 DOI: 10.1016/j.biotechadv.2021.107866] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/04/2021] [Accepted: 11/05/2021] [Indexed: 12/14/2022]
Abstract
Natural products from fungi represent an important source of biologically active metabolites notably for therapeutic agent development. Genome sequencing revealed that the number of biosynthetic gene clusters (BGCs) in fungi is much larger than expected. Unfortunately, most of them are silent or barely expressed under laboratory culture conditions. Moreover, many fungi in nature are uncultivable or cannot be genetically manipulated, restricting the extraction and identification of bioactive metabolites from these species. Rapid exploration of the tremendous number of cryptic fungal BGCs necessitates the development of heterologous expression platforms, which will facilitate the efficient production of natural products in fungal cell factories. Host selection, BGC assembly methods, promoters used for heterologous gene expression, metabolic engineering strategies and compartmentalization of biosynthetic pathways are key aspects for consideration to develop such a microbial platform. In the present review, we summarize current progress on the above challenges to promote research effort in the relevant fields.
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Affiliation(s)
- Xiangfeng Meng
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Yu Fang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Mingyang Ding
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Yanyu Zhang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Kaili Jia
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Zhongye Li
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China
| | - Jérôme Collemare
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, No. 72 Binhai Road, Qingdao 266237, PR China.
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26
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Song H, Song J, Yan L, He W, Wang P, Xu Y, Wei H, Xie W. A concise synthesis of (-)-dihydrospirotryprostatin B via tandem Michael addition. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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27
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Tippelt A, Nett M. Saccharomyces cerevisiae as host for the recombinant production of polyketides and nonribosomal peptides. Microb Cell Fact 2021; 20:161. [PMID: 34412657 PMCID: PMC8374128 DOI: 10.1186/s12934-021-01650-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/05/2021] [Indexed: 01/30/2023] Open
Abstract
As a robust, fast growing and genetically tractable organism, the budding yeast Saccharomyces cerevisiae is one of the most widely used hosts in biotechnology. Its applications range from the manufacturing of vaccines and hormones to bulk chemicals and biofuels. In recent years, major efforts have been undertaken to expand this portfolio to include structurally complex natural products, such as polyketides and nonribosomally synthesized peptides. These compounds often have useful pharmacological properties, which make them valuable drugs for the treatment of infectious diseases, cancer, or autoimmune disorders. In nature, polyketides and nonribosomal peptides are generated by consecutive condensation reactions of short chain acyl-CoAs or amino acids, respectively, with the substrates and reaction intermediates being bound to large, multidomain enzymes. For the reconstitution of these multistep catalytic processes, the enzymatic assembly lines need to be functionally expressed and the required substrates must be supplied in reasonable quantities. Furthermore, the production hosts need to be protected from the toxicity of the biosynthetic products. In this review, we will summarize and evaluate the status quo regarding the heterologous production of polyketides and nonribosomal peptides in S. cerevisiae. Based on a comprehensive literature analysis, prerequisites for a successful pathway reconstitution could be deduced, as well as recurring bottlenecks in this microbial host.
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Affiliation(s)
- Anna Tippelt
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227, Dortmund, Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227, Dortmund, Germany.
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28
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Chen H, Zhou A, Sun D, Zhao Y, Wang Y. Theoretical Investigation on the Elusive Reaction Mechanism of Spirooxindole Formation Mediated by Cytochrome P450s: A Nascent Feasible Charge-Shift C-O Bond Makes a Difference. J Phys Chem B 2021; 125:8419-8430. [PMID: 34313131 DOI: 10.1021/acs.jpcb.1c04088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Spirooxindoles are pivotal biofunctional groups widely distributed in natural products and clinic drugs. However, construction of such subtle chiral skeletons is a long-standing challenge to both organic and bioengineering scientists. The knowledge of enzymatic spirooxindole formation in nature may inspire rational design of new catalysts. To this end, we presented a theoretical investigation on the elusive mechanism of the spiro-ring formation at the 3-position of oxindole mediated by cytochrome P450 enzymes (P450). Our calculated results demonstrated that the electrophilic attack of CpdI, the active species of P450, to the substrate, shows regioselectivity, i.e., the attack at the C9 position forms a tetrahedral intermediate involving an unusual feasible charge-shift C9δ+-Oδ- bond, while the attack at the C1 position forms an epoxide intermediate. The predominant route is the first route with the charge-shift bonding intermediate due to holding a relatively lower barrier by >5 kcal mol-1 than the epoxide route, which fits the experimental observations. Such a delocalized charge-shift bond facilitates the formation of a spiro-ring mainly through elongation of the C1-C9 bond to eliminate the aromatization of the tricyclic beta-carboline. Our theoretical results shed profound mechanistic insights for the first time into the elusive spirooxindole formation mediated by P450s.
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Affiliation(s)
- Huanhuan Chen
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Anran Zhou
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Dongru Sun
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Yong Wang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China.,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
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29
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Liu Z, Zhao F, Zhao B, Yang J, Ferrara J, Sankaran B, Venkataram Prasad BV, Kundu BB, Phillips GN, Gao Y, Hu L, Zhu T, Gao X. Structural basis of the stereoselective formation of the spirooxindole ring in the biosynthesis of citrinadins. Nat Commun 2021; 12:4158. [PMID: 34230497 PMCID: PMC8260726 DOI: 10.1038/s41467-021-24421-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/17/2021] [Indexed: 11/09/2022] Open
Abstract
Prenylated indole alkaloids featuring spirooxindole rings possess a 3R or 3S carbon stereocenter, which determines the bioactivities of these compounds. Despite the stereoselective advantages of spirooxindole biosynthesis compared with those of organic synthesis, the biocatalytic mechanism for controlling the 3R or 3S-spirooxindole formation has been elusive. Here, we report an oxygenase/semipinacolase CtdE that specifies the 3S-spirooxindole construction in the biosynthesis of 21R-citrinadin A. High-resolution X-ray crystal structures of CtdE with the substrate and cofactor, together with site-directed mutagenesis and computational studies, illustrate the catalytic mechanisms for the possible β-face epoxidation followed by a regioselective collapse of the epoxide intermediate, which triggers semipinacol rearrangement to form the 3S-spirooxindole. Comparing CtdE with PhqK, which catalyzes the formation of the 3R-spirooxindole, we reveal an evolutionary branch of CtdE in specific 3S spirocyclization. Our study provides deeper insights into the stereoselective catalytic machinery, which is important for the biocatalysis design to synthesize spirooxindole pharmaceuticals.
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Affiliation(s)
- Zhiwen Liu
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Fanglong Zhao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Boyang Zhao
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Jie Yang
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | | | - Banumathi Sankaran
- Department of Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - B V Venkataram Prasad
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Biki Bapi Kundu
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, TX, USA
- Department of Chemistry, Rice University, Houston, TX, USA
| | - Yang Gao
- Department of Biosciences, Rice University, Houston, TX, USA
| | - Liya Hu
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Tong Zhu
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
| | - Xue Gao
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.
- Department of Chemistry, Rice University, Houston, TX, USA.
- Department of Bioengineering, Rice University, Houston, TX, USA.
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30
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Jamieson CS, Misa J, Tang Y, Billingsley JM. Biosynthesis and synthetic biology of psychoactive natural products. Chem Soc Rev 2021; 50:6950-7008. [PMID: 33908526 PMCID: PMC8217322 DOI: 10.1039/d1cs00065a] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Psychoactive natural products play an integral role in the modern world. The tremendous structural complexity displayed by such molecules confers diverse biological activities of significant medicinal value and sociocultural impact. Accordingly, in the last two centuries, immense effort has been devoted towards establishing how plants, animals, and fungi synthesize complex natural products from simple metabolic precursors. The recent explosion of genomics data and molecular biology tools has enabled the identification of genes encoding proteins that catalyze individual biosynthetic steps. Once fully elucidated, the "biosynthetic pathways" are often comparable to organic syntheses in elegance and yield. Additionally, the discovery of biosynthetic enzymes provides powerful catalysts which may be repurposed for synthetic biology applications, or implemented with chemoenzymatic synthetic approaches. In this review, we discuss the progress that has been made toward biosynthetic pathway elucidation amongst four classes of psychoactive natural products: hallucinogens, stimulants, cannabinoids, and opioids. Compounds of diverse biosynthetic origin - terpene, amino acid, polyketide - are identified, and notable mechanisms of key scaffold transforming steps are highlighted. We also provide a description of subsequent applications of the biosynthetic machinery, with an emphasis placed on the synthetic biology and metabolic engineering strategies enabling heterologous production.
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Affiliation(s)
- Cooper S Jamieson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Joshua Misa
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Yi Tang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA, USA. and Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA.
| | - John M Billingsley
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, Los Angeles, CA, USA. and Invizyne Technologies, Inc., Monrovia, CA, USA
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31
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Sbaraini N, Hu J, Roux I, Phan CS, Motta H, Rezaee H, Schrank A, Chooi YH, Staats CC. Polyketides produced by the entomopathogenic fungus Metarhizium anisopliae induce Candida albicans growth. Fungal Genet Biol 2021; 152:103568. [PMID: 33991663 DOI: 10.1016/j.fgb.2021.103568] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/16/2021] [Accepted: 04/18/2021] [Indexed: 11/15/2022]
Abstract
Metarhizium anisopliae is an important entomopathogenic species and model for arthropod-fungus interaction studies. This fungus harbors a diverse arsenal of unexplored secondary metabolite biosynthetic gene clusters, which are suggested to perform diverse roles during host interaction and soil subsistence as a saprophytic species. Here we explored an unusual carnitine acyltransferase domain-containing highly reducing polyketide synthase found in the genome of M. anisopliae. Employing heterologous expression in Aspergillus nidulans, two new polyketides were obtained, named BAA and BAB, as well as one known polyketide [(2Z,4E,6E)-octa-2,4,6-trienedioic acid]. Intra-hemocoel injection of the most abundant compound (BAA) in the model-arthropod Galleria mellonella larvae did not induce mortality or noticeable alterations, suggesting that this compound may not harbor insecticidal activity. Also, the potential role of such molecules in polymicrobial interactions was evaluated. Determination of minimum inhibitory concentration assays using distinct fungal species revealed that BAA and BAB did not alter Cryptococcus neoformans growth, while BAA exhibited weak antifungal activity against Saccharomyces cerevisiae. Unexpectedly, these compounds increased Candida albicans growth compared to control conditions. Furthermore, BAA can mitigate the fungicidal effects of fluconazole over C. albicans. Although the exact role of these compounds on the M. anisopliae life cycle is elusive, the described results add up to the complexity of secondary metabolites produced by Metarhizium spp. Moreover, up to our knowledge, these are the first polyketides isolated from filamentous fungi that can boost the growth of another fungal species.
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Affiliation(s)
- Nicolau Sbaraini
- Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil; School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Jinyu Hu
- 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
| | - Chin-Soon Phan
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Heryk Motta
- Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Hamideh Rezaee
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Augusto Schrank
- Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia.
| | - Charley Christian Staats
- Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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32
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Tsunematsu Y, Maeda N, Sato M, Hara K, Hashimoto H, Watanabe K, Hertweck C. Specialized Flavoprotein Promotes Sulfur Migration and Spiroaminal Formation in Aspirochlorine Biosynthesis. J Am Chem Soc 2020; 143:206-213. [PMID: 33351612 DOI: 10.1021/jacs.0c08879] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Epidithiodiketopiperazines (ETPs) are a class of ecologically and medicinally important cyclodipeptides bearing a reactive transannular disulfide bridge. Aspirochlorine, an antifungal and toxic ETP isolated from Aspergillus oryzae used in sake brewing, deviates from the common ETP scaffold owing to its unusual ring-enlarged disulfide bridge linked to a spiroaminal ring system. Although this disulfide ring system is implicated in the biological activity of ETPs the biochemical basis for this derailment has remained a mystery. Here we report the discovery of a novel oxidoreductase (AclR) that represents the first-in-class enzyme catalyzing both a carbon-sulfur bond migration and spiro-ring formation, and that the acl pathway involves a cryptic acetylation as a prerequisite for the rearrangement. Genetic screening in A. oryzae identified aclR as the candidate for the complex biotransformation, and the aclR-deficient mutant provided the biosynthetic intermediate, unexpectedly harboring an acetyl group. In vitro assays showed that AclR alone promotes 1,2-sulfamyl migration, elimination of the acetoxy group, and spiroaminal formation. AclR features a thioredoxin oxidoreductase fold with a noncanonical CXXH motif that is distinct from the CXXC in the disulfide forming oxidase for the ETP biosynthesis. Crystallographic and mutational analyses of AclR revealed that the CXXH motif is crucial for catalysis, whereas the flavin-adenine dinucleotide is required as a support of the protein fold, and not as a redox cofactor. AclR proved to be a suitable bioinformatics handle to discover a number of related fungal gene clusters that potentially code for the biosynthesis of derailed ETP compounds. Our results highlight a specialized role of the thioredoxin oxidoreductase family enzyme in the ETP pathway and expand the chemical diversity of small molecules bearing an aberrant disulfide pharmacophore.
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Affiliation(s)
- Yuta Tsunematsu
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan.,Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany
| | - Naoya Maeda
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Michio Sato
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kodai Hara
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Hiroshi Hashimoto
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Christian Hertweck
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Chemistry and Infection Biology (HKI), Beutenbergstrasse 11a, 07745 Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743 Jena, Germany
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33
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Matsushita T, Kishimoto S, Hara K, Hashimoto H, Watanabe K. Structural and Functional Analyses of a Spiro-Carbon-Forming, Highly Promiscuous Epoxidase from Fungal Natural Product Biosynthesis. Biochemistry 2020; 59:4787-4792. [DOI: 10.1021/acs.biochem.0c00896] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Takuma Matsushita
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Shinji Kishimoto
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kodai Hara
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Hiroshi Hashimoto
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
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34
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El Hajj Assaf C, Zetina-Serrano C, Tahtah N, Khoury AE, Atoui A, Oswald IP, Puel O, Lorber S. Regulation of Secondary Metabolism in the Penicillium Genus. Int J Mol Sci 2020; 21:E9462. [PMID: 33322713 PMCID: PMC7763326 DOI: 10.3390/ijms21249462] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
Penicillium, one of the most common fungi occurring in a diverse range of habitats, has a worldwide distribution and a large economic impact on human health. Hundreds of the species belonging to this genus cause disastrous decay in food crops and are able to produce a varied range of secondary metabolites, from which we can distinguish harmful mycotoxins. Some Penicillium species are considered to be important producers of patulin and ochratoxin A, two well-known mycotoxins. The production of these mycotoxins and other secondary metabolites is controlled and regulated by different mechanisms. The aim of this review is to highlight the different levels of regulation of secondary metabolites in the Penicillium genus.
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Affiliation(s)
- Christelle El Hajj Assaf
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (C.E.H.A.); (C.Z.-S.); (N.T.); (I.P.O.); (S.L.)
- Institute for Agricultural and Fisheries Research (ILVO), member of Food2Know, Brusselsesteenweg 370, 9090 Melle, Belgium
| | - Chrystian Zetina-Serrano
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (C.E.H.A.); (C.Z.-S.); (N.T.); (I.P.O.); (S.L.)
| | - Nadia Tahtah
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (C.E.H.A.); (C.Z.-S.); (N.T.); (I.P.O.); (S.L.)
- Centre D’analyse et de Recherche, Unité de Recherche Technologies et Valorisations Agro-Alimentaires, Faculté des Sciences, Université Saint-Joseph, P.O. Box 17-5208, Mar Mikhael, Beirut 1104, Lebanon;
| | - André El Khoury
- Centre D’analyse et de Recherche, Unité de Recherche Technologies et Valorisations Agro-Alimentaires, Faculté des Sciences, Université Saint-Joseph, P.O. Box 17-5208, Mar Mikhael, Beirut 1104, Lebanon;
| | - Ali Atoui
- Laboratory of Microbiology, Department of Life and Earth Sciences, Faculty of Sciences I, Lebanese University, Hadath Campus, P.O. Box 5, Beirut 1104, Lebanon;
| | - Isabelle P. Oswald
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (C.E.H.A.); (C.Z.-S.); (N.T.); (I.P.O.); (S.L.)
| | - Olivier Puel
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (C.E.H.A.); (C.Z.-S.); (N.T.); (I.P.O.); (S.L.)
| | - Sophie Lorber
- Toxalim (Research Centre in Food Toxicology), Université de Toulouse, INRAE, ENVT, INP-Purpan, UPS, 31027 Toulouse, France; (C.E.H.A.); (C.Z.-S.); (N.T.); (I.P.O.); (S.L.)
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Genomics-directed activation of cryptic natural product pathways deciphers codes for biosynthesis and molecular function. J Nat Med 2020; 75:261-274. [PMID: 33274411 PMCID: PMC7902601 DOI: 10.1007/s11418-020-01466-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/06/2020] [Indexed: 12/22/2022]
Abstract
Natural products, which can be isolated from living organisms worldwide, have played a pivotal role in drug discovery since ancient times. However, it has become more challenging to identify a structurally novel molecule with promising biological activity for pharmaceutical development, mainly due to the limited methodologies for their acquisition. In this review, we summarize our recent studies that activate the biosynthetic potential of filamentous fungi by genetic engineering to harness the metabolic flow for the efficient production of unprecedented natural products. The recent revolution in genome sequencing technology enables the accumulation of vast amounts of information on biosynthetic genes, the blueprint of the molecular construction. Utilizing the established heterologous expression system, activation of the pathway-specific transcription factor coupled with a knockout strategy, and manipulating the global regulatory gene, the biosynthetic genes were exploited to activate biosynthetic pathways and decipher the encoded enzyme functions. We show that this methodology was beneficial for acquiring fungal treasures for drug discovery. These studies also enabled the investigation of the molecular function of natural products in fungal development.
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Gataullin RR. Advances in the Synthesis of Benzo‐Fused Spiro Nitrogen Heterocycles: New Approaches and Modification of Old Strategies. Helv Chim Acta 2020. [DOI: 10.1002/hlca.202000137] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Rail R. Gataullin
- Ufa Federal Research Centre Ufa Institute of Chemistry of the Russian Academy of Sciences Prospect Oktyabrya, 71 Ufa 450054 Russian Federation
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37
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Zhang Z, Qiao T, Watanabe K, Tang Y. Concise Biosynthesis of Phenylfuropyridones in Fungi. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202008321] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Zhuan Zhang
- Department of Chemical and Biomolecular Engineering University of California Los Angeles CA 90095 USA
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095 USA
| | - Tianzhang Qiao
- Department of Chemical and Biomolecular Engineering University of California Los Angeles CA 90095 USA
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences University of Shizuoka Shizuoka Japan
| | - Yi Tang
- Department of Chemical and Biomolecular Engineering University of California Los Angeles CA 90095 USA
- Department of Chemistry and Biochemistry University of California Los Angeles CA 90095 USA
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Concise Biosynthesis of Phenylfuropyridones in Fungi. Angew Chem Int Ed Engl 2020; 59:19889-19893. [DOI: 10.1002/anie.202008321] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/28/2020] [Indexed: 01/13/2023]
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Fraley AE, Tran HT, Kelly SP, Newmister SA, Tripathi A, Kato H, Tsukamoto S, Du L, Li S, Williams RM, Sherman DH. Flavin-Dependent Monooxygenases NotI and NotI' Mediate Spiro-Oxindole Formation in Biosynthesis of the Notoamides. Chembiochem 2020; 21:2449-2454. [PMID: 32246875 PMCID: PMC7483341 DOI: 10.1002/cbic.202000004] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 04/04/2020] [Indexed: 11/08/2022]
Abstract
The fungal indole alkaloids are a unique class of complex molecules that have a characteristic bicyclo[2.2.2]diazaoctane ring and frequently contain a spiro-oxindole moiety. While various strains produce these compounds, an intriguing case involves the formation of individual antipodes by two unique species of fungi in the generation of the potent anticancer agents (+)- and (-)-notoamide A. NotI and NotI' have been characterized as flavin-dependent monooxygenases that catalyze epoxidation and semi-pinacol rearrangement to form the spiro-oxindole center within these molecules. This work elucidates a key step in the biosynthesis of the notoamides and provides an evolutionary hypothesis regarding a common ancestor for production of enantiopure notoamides.
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Affiliation(s)
- Amy E Fraley
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 28104, USA
- Department of Medicinal Chemistry, University of Michigan, 428 Church St., Ann Arbor, MI 48109, USA
| | - Hong T Tran
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 28104, USA
- Program in Chemical Biology, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109, USA
| | - Samantha P Kelly
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 28104, USA
- Program in Chemical Biology, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 48109, USA
| | - Sean A Newmister
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 28104, USA
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 28104, USA
- Department of Medicinal Chemistry, University of Michigan, 428 Church St., Ann Arbor, MI 48109, USA
| | - Hikaru Kato
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kumamoto, 862-0973, Japan
| | - Sachiko Tsukamoto
- Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-honmachi, Kumamoto, 862-0973, Japan
| | - Lei Du
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong, 266237, China
| | - Robert M Williams
- Department of Chemistry, Colorado State University, 1301 Center Ave., Fort Collins, CO 80523, USA
| | - David H Sherman
- Life Sciences Institute, University of Michigan, 210 Washtenaw Ave., Ann Arbor, MI 28104, USA
- Department of Medicinal Chemistry, University of Michigan, 428 Church St., Ann Arbor, MI 48109, USA
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150W. Medical Center Drive, Ann Arbor, MI 48109
- Department of Chemistry, University of Michigan, 930N. University Ave., Ann Arbor, MI 48109, USA
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Zhu Y, Zhang Q, Fang C, Zhang Y, Ma L, Liu Z, Zhai S, Peng J, Zhang L, Zhu W, Zhang C. Refactoring the Concise Biosynthetic Pathway of Cyanogramide Unveils Spirooxindole Formation Catalyzed by a P450 Enzyme. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004978] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology Guangdong Key Laboratory of Marine Materia Medica Innovation Academy of South China Sea Ecology and Environmental Engineering South China Sea Institute of Oceanology Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) 1119 Haibin Rd. Nansha District Guangzhou 511458 China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology Guangdong Key Laboratory of Marine Materia Medica Innovation Academy of South China Sea Ecology and Environmental Engineering South China Sea Institute of Oceanology Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) 1119 Haibin Rd. Nansha District Guangzhou 511458 China
| | - Chunyan Fang
- Key Laboratory of Tropical Marine Bio-resources and Ecology Guangdong Key Laboratory of Marine Materia Medica Innovation Academy of South China Sea Ecology and Environmental Engineering South China Sea Institute of Oceanology Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 China
| | - Yingli Zhang
- College of Life Sciences Hebei Normal University Shijiazhuang 050024 China
| | - Liang Ma
- Key Laboratory of Tropical Marine Bio-resources and Ecology Guangdong Key Laboratory of Marine Materia Medica Innovation Academy of South China Sea Ecology and Environmental Engineering South China Sea Institute of Oceanology Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) 1119 Haibin Rd. Nansha District Guangzhou 511458 China
| | - Zhiwen Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology Guangdong Key Laboratory of Marine Materia Medica Innovation Academy of South China Sea Ecology and Environmental Engineering South China Sea Institute of Oceanology Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 China
| | - Shilan Zhai
- Key Laboratory of Tropical Marine Bio-resources and Ecology Guangdong Key Laboratory of Marine Materia Medica Innovation Academy of South China Sea Ecology and Environmental Engineering South China Sea Institute of Oceanology Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 China
| | - Jing Peng
- Key Laboratory of Tropical Marine Bio-resources and Ecology Guangdong Key Laboratory of Marine Materia Medica Innovation Academy of South China Sea Ecology and Environmental Engineering South China Sea Institute of Oceanology Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology Guangdong Key Laboratory of Marine Materia Medica Innovation Academy of South China Sea Ecology and Environmental Engineering South China Sea Institute of Oceanology Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) 1119 Haibin Rd. Nansha District Guangzhou 511458 China
| | - Weiming Zhu
- Key Laboratory of Marine Drugs Chinese Ministry of Education School of Medicine and Pharmacy Ocean University of China Qingdao 266003 China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology Guangdong Key Laboratory of Marine Materia Medica Innovation Academy of South China Sea Ecology and Environmental Engineering South China Sea Institute of Oceanology Chinese Academy of Sciences 164 West Xingang Road Guangzhou 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou) 1119 Haibin Rd. Nansha District Guangzhou 511458 China
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Asai S, Tsunematsu Y, Masuya T, Otaka J, Osada H, Watanabe K. Uncovering hidden sesquiterpene biosynthetic pathway through expression boost area-mediated productivity enhancement in basidiomycete. J Antibiot (Tokyo) 2020; 73:721-728. [DOI: 10.1038/s41429-020-0355-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/13/2020] [Accepted: 07/13/2020] [Indexed: 11/09/2022]
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42
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Roux I, Woodcraft C, Hu J, Wolters R, Gilchrist CLM, Chooi YH. CRISPR-Mediated Activation of Biosynthetic Gene Clusters for Bioactive Molecule Discovery in Filamentous Fungi. ACS Synth Biol 2020; 9:1843-1854. [PMID: 32526136 DOI: 10.1021/acssynbio.0c00197] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Accessing the full biosynthetic potential encoded in the genomes of fungi is limited by the low expression of most biosynthetic gene clusters (BGCs) under common laboratory culture conditions. CRISPR-mediated transcriptional activation (CRISPRa) of fungal BGCs could accelerate genomics-driven bioactive secondary metabolite discovery. In this work, we established the first CRISPRa system for filamentous fungi. First, we constructed a CRISPR/dLbCas12a-VPR-based system and demonstrated the activation of a fluorescent reporter in Aspergillus nidulans. Then, we targeted the native nonribosomal peptide synthetase-like (NRPS-like) gene micA in both chromosomal and episomal contexts, achieving increased production of the compound microperfuranone. Finally, multigene CRISPRa led to the discovery of the mic cluster product as dehydromicroperfuranone. Additionally, we demonstrated the utility of the variant dLbCas12aD156R-VPR for CRISPRa at room temperature culture conditions. Different aspects that influence the efficiency of CRISPRa in fungi were investigated, providing a framework for the further development of fungal artificial transcription factors based on CRISPR/Cas.
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Affiliation(s)
- Indra Roux
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Clara Woodcraft
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Jinyu Hu
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Rebecca Wolters
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Cameron L M Gilchrist
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, University of Western Australia, Perth, WA 6009, Australia
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43
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Genome-Inspired Chemical Exploration of Marine Fungus Aspergillus fumigatus MF071. Mar Drugs 2020; 18:md18070352. [PMID: 32640519 PMCID: PMC7401266 DOI: 10.3390/md18070352] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 06/30/2020] [Accepted: 07/02/2020] [Indexed: 01/01/2023] Open
Abstract
The marine-derived fungus Aspergillus fumigatus MF071, isolated from sediment collected from the Bohai Sea, China, yielded two new compounds 19S,20-epoxy-18-oxotryprostatin A (1) and 20-hydroxy-18-oxotryprostatin A (2), in addition to 28 known compounds (3-30). The chemical structures were established on the basis of 1D, 2D NMR and HRESIMS spectroscopic data. This is the first report on NMR data of monomethylsulochrin-4-sulphate (4) and pseurotin H (10) as naturally occurring compounds. Compounds 15, 16, 20, 23, and 30 displayed weak antibacterial activity (minimum inhibitory concentration: 100 μg/mL). Compounds 18 and 19 exhibited strong activity against S. aureus (minimum inhibitory concentration: 6.25 and 3.13 μg/mL, respectively) and E. coli (minimum inhibitory concentration: 6.25 and 3.13 μg/mL, respectively). A genomic data analysis revealed the putative biosynthetic gene clusters ftm for fumitremorgins, pso for pseurotins, fga for fumigaclavines, and hel for helvolinic acid. These putative biosynthetic gene clusters fundamentally underpinned the enzymatic and mechanistic function study for the biosynthesis of these compounds. The current study reported two new compounds and biosynthetic gene clusters of fumitremorgins, pseurotins, fumigaclavines and helvolinic acid from Aspergillus fumigatus MF071.
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44
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Zhu Y, Zhang Q, Fang C, Zhang Y, Ma L, Liu Z, Zhai S, Peng J, Zhang L, Zhu W, Zhang C. Refactoring the Concise Biosynthetic Pathway of Cyanogramide Unveils Spirooxindole Formation Catalyzed by a P450 Enzyme. Angew Chem Int Ed Engl 2020; 59:14065-14069. [PMID: 32329169 DOI: 10.1002/anie.202004978] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/19/2020] [Indexed: 12/12/2022]
Abstract
Cyanogramide (1) from the marine actinomycete Actinoalloteichus cyanogriseus WH1-2216-6 features a unique spirooxindole skeleton and exhibits significant bioactivity to efficiently reverse drug resistance in tumor cells. The biosynthetic gene cluster of 1 in A. cyanogriseus WH1-2216-6 was identified and refactored by promoter engineering for heterologous expression in Streptomyces coelicolor YF11, thereby enabling the production of 1 and five new derivatives. Interesting, four of them, including 1, were identified as enantiomeric mixtures in different ratios. The functions of tailoring enzymes, including two methyltransferases (CyaEF), and three cytochrome P450 monooxygenases (CyaGHI) were confirmed by gene inactivation and feeding experiments, leading to the elucidation of a concise biosynthetic pathway for 1. Notably, CyaH was biochemically verified to catalyze the formation of the spirooxindole skeleton in 1 through an unusual carbocation-mediated semipinacol-type rearrangement reaction.
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Affiliation(s)
- Yiguang Zhu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd. Nansha District, Guangzhou, 511458, China
| | - Qingbo Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd. Nansha District, Guangzhou, 511458, China
| | - Chunyan Fang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Yingli Zhang
- College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Liang Ma
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd. Nansha District, Guangzhou, 511458, China
| | - Zhiwen Liu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Shilan Zhai
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Jing Peng
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Liping Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd. Nansha District, Guangzhou, 511458, China
| | - Weiming Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Changsheng Zhang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, Innovation Academy of South China Sea Ecology and Environmental Engineering, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), 1119 Haibin Rd. Nansha District, Guangzhou, 511458, China
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45
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Fraley AE, Sherman DH. Enzyme evolution in fungal indole alkaloid biosynthesis. FEBS J 2020; 287:1381-1402. [PMID: 32118354 PMCID: PMC7317620 DOI: 10.1111/febs.15270] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/24/2019] [Accepted: 02/27/2020] [Indexed: 12/28/2022]
Abstract
The class of fungal indole alkaloids containing the bicyclo[2.2.2]diazaoctane ring is comprised of diverse molecules that display a range of biological activities. While much interest has been garnered due to their therapeutic potential, this class of molecules also displays unique chemical functionality, making them intriguing synthetic targets. Many elegant and intricate total syntheses have been developed to generate these alkaloids, but the selectivity required to produce them in high yield presents great barriers. Alternatively, if we can understand the molecular mechanisms behind how fungi make these complex molecules, we can leverage the power of nature to perform these chemical transformations. Here, we describe the various studies regarding the evolutionary development of enzymes involved in fungal indole alkaloid biosynthesis.
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Affiliation(s)
- Amy E. Fraley
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
| | - David H. Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, United States
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46
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Fraley AE, Caddell Haatveit K, Ye Y, Kelly SP, Newmister SA, Yu F, Williams RM, Smith JL, Houk KN, Sherman DH. Molecular Basis for Spirocycle Formation in the Paraherquamide Biosynthetic Pathway. J Am Chem Soc 2020; 142:2244-2252. [PMID: 31904957 DOI: 10.1021/jacs.9b09070] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The paraherquamides are potent anthelmintic natural products with complex heptacyclic scaffolds. One key feature of these molecules is the spiro-oxindole moiety that lends a strained three-dimensional architecture to these structures. The flavin monooxygenase PhqK was found to catalyze spirocycle formation through two parallel pathways in the biosynthesis of paraherquamides A and G. Two new paraherquamides (K and L) were isolated from a ΔphqK strain of Penicillium simplicissimum, and subsequent enzymatic reactions with these compounds generated two additional metabolites, paraherquamides M and N. Crystal structures of PhqK in complex with various substrates provided a foundation for mechanistic analyses and computational studies. While it is evident that PhqK can react with various substrates, reaction kinetics and molecular dynamics simulations indicated that the dioxepin-containing paraherquamide L is the favored substrate. Through this effort, we have elucidated a key step in the biosynthesis of the paraherquamides and provided a rationale for the selective spirocyclization of these powerful anthelmintic agents.
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Affiliation(s)
| | - Kersti Caddell Haatveit
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , United States
| | | | | | | | | | - Robert M Williams
- Department of Chemistry , Colorado State University , Fort Collins , Colorado 80523 , United States.,University of Colorado Cancer Center , Aurora , Colorado 80045 , United States
| | | | - K N Houk
- Department of Chemistry and Biochemistry , University of California , Los Angeles , California 90095 , United States
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Chevrette MG, Gutiérrez-García K, Selem-Mojica N, Aguilar-Martínez C, Yañez-Olvera A, Ramos-Aboites HE, Hoskisson PA, Barona-Gómez F. Evolutionary dynamics of natural product biosynthesis in bacteria. Nat Prod Rep 2019; 37:566-599. [PMID: 31822877 DOI: 10.1039/c9np00048h] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Covering: 2008 up to 2019The forces of biochemical adaptive evolution operate at the level of genes, manifesting in complex phenotypes and the global biodiversity of proteins and metabolites. While evolutionary histories have been deciphered for some other complex traits, the origins of natural product biosynthesis largely remain a mystery. This fundamental knowledge gap is surprising given the many decades of research probing the genetic, chemical, and biophysical mechanisms of bacterial natural product biosynthesis. Recently, evolutionary thinking has begun to permeate this otherwise mechanistically dominated field. Natural products are now sometimes referred to as 'specialized' rather than 'secondary' metabolites, reinforcing the importance of their biological and ecological functions. Here, we review known evolutionary mechanisms underlying the overwhelming chemical diversity of bacterial secondary metabolism, focusing on enzyme promiscuity and the evolution of enzymatic domains that enable metabolic traits. We discuss the mechanisms that drive the assembly of natural product biosynthetic gene clusters and propose formal definitions for 'specialized' and 'secondary' metabolism. We further explore how biosynthetic gene clusters evolve to synthesize related molecular species, and in turn how the biological and ecological roles that emerge from metabolic diversity are acted on by selection. Finally, we reconcile chemical, functional, and genetic data into an evolutionary model, the dynamic chemical matrix evolutionary hypothesis, in which the relationships between chemical distance, biomolecular activity, and relative fitness shape adaptive landscapes.
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Affiliation(s)
- Marc G Chevrette
- Wisconsin Institute for Discovery, Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI, USA.
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Li H, Hu J, Wei H, Solomon PS, Stubbs KA, Chooi YH. Biosynthesis of a Tricyclo[6.2.2.0 2,7 ]dodecane System by a Berberine Bridge Enzyme-Like Aldolase. Chemistry 2019; 25:15062-15066. [PMID: 31553484 DOI: 10.1002/chem.201904360] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Indexed: 11/06/2022]
Abstract
The aldol reaction is one of the most fundamental stereocontrolled carbon-carbon bond-forming reactions and is mainly catalyzed by aldolases in nature. Despite the fact that the aldol reaction has been widely proposed to be involved in fungal secondary metabolite biosynthesis, a dedicated aldolase that catalyzes stereoselective aldol reactions has only rarely been reported in fungi. Herein, we activated a cryptic polyketide biosynthetic gene cluster that was upregulated in the fungal wheat pathogen Parastagonospora nodorum during plant infection; this resulted in the production of the phytotoxic stemphyloxin II (1). Through heterologous reconstruction of the biosynthetic pathway and in vitro assay by using cell-free lysate from Aspergillus nidulans, we demonstrated that a berberine bridge enzyme (BBE)-like protein SthB catalyzes an intramolecular aldol reaction to establish the bridged tricyclo[6.2.2.02,7 ]dodecane skeleton in the post-assembly tailoring step. The characterization of SthB as an aldolase enriches the catalytic toolbox of classic reactions and the functional diversities of the BBE superfamily of enzymes.
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Affiliation(s)
- Hang Li
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Jinyu Hu
- School of Molecular Sciences, The University of Western Australia, Perth, WA, 6009, Australia
| | - Haochen Wei
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Peter S Solomon
- Division of Plant Science, Research School of Biology, The Australian National University, Canberra, ACT, 2601, Australia
| | - Keith A Stubbs
- 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
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Vassaux A, Meunier L, Vandenbol M, Baurain D, Fickers P, Jacques P, Leclère V. Nonribosomal peptides in fungal cell factories: from genome mining to optimized heterologous production. Biotechnol Adv 2019; 37:107449. [PMID: 31518630 DOI: 10.1016/j.biotechadv.2019.107449] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/06/2019] [Accepted: 09/09/2019] [Indexed: 12/15/2022]
Abstract
Fungi are notoriously prolific producers of secondary metabolites including nonribosomal peptides (NRPs). The structural complexity of NRPs grants them interesting activities such as antibiotic, anti-cancer, and anti-inflammatory properties. The discovery of these compounds with attractive activities can be achieved by using two approaches: either by screening samples originating from various environments for their biological activities, or by identifying the related clusters in genomic sequences thanks to bioinformatics tools. This genome mining approach has grown tremendously due to recent advances in genome sequencing, which have provided an incredible amount of genomic data from hundreds of microbial species. Regarding fungal organisms, the genomic data have revealed the presence of an unexpected number of putative NRP-related gene clusters. This highlights fungi as a goldmine for the discovery of putative novel bioactive compounds. Recent development of NRP dedicated bioinformatics tools have increased the capacity to identify these gene clusters and to deduce NRPs structures, speeding-up the screening process for novel metabolites discovery. Unfortunately, the newly identified compound is frequently not or poorly produced by native producers due to a lack of expression of the related genes cluster. A frequently employed strategy to increase production rates consists in transferring the related biosynthetic pathway in heterologous hosts. This review aims to provide a comprehensive overview about the topic of NRPs discovery, from gene cluster identification by genome mining to the heterologous production in fungal hosts. The main computational tools and methods for genome mining are herein presented with an emphasis on the particularities of the fungal systems. The different steps of the reconstitution of NRP biosynthetic pathway in heterologous fungal cell factories will be discussed, as well as the key factors to consider for maximizing productivity. Several examples will be developed to illustrate the potential of heterologous production to both discover uncharacterized novel compounds predicted in silico by genome mining, and to enhance the productivity of interesting bio-active natural products.
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Affiliation(s)
- Antoine Vassaux
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France
| | - Loïc Meunier
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium; InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Micheline Vandenbol
- TERRA Teaching and Research Centre, Microbiologie et Génomique, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Denis Baurain
- InBioS-PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liege, Boulevard du Rectorat 27, B-4000 Liège, Belgium
| | - Patrick Fickers
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Philippe Jacques
- TERRA Teaching and Research Centre, Microbial Processes and Interactions, Gembloux Agro-Bio Tech, University of Liege, Avenue de la Faculté d'Agronomie, B5030 Gembloux, Belgium
| | - Valérie Leclère
- Univ. Lille, INRA, ISA, Univ. Artois, Univ. Littoral Côte d'Opale, EA 7394-ICV-Institut Charles Viollette, F-59000 Lille, France.
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Discovery of Bioactive Indole-Diketopiperazines from the Marine-Derived Fungus Penicillium brasilianum Aided by Genomic Information. Mar Drugs 2019; 17:md17090514. [PMID: 31480589 PMCID: PMC6781160 DOI: 10.3390/md17090514] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/27/2019] [Accepted: 08/29/2019] [Indexed: 12/22/2022] Open
Abstract
Identification and analysis of the whole genome of the marine-derived fungus Penicillium brasilianum HBU-136 revealed the presence of an interesting biosynthetic gene cluster (BGC) for non-ribosomal peptide synthetases (NRPS), highly homologous to the BGCs of indole-diketopiperazine derivatives. With the aid of genomic analysis, eight indole-diketopiperazines (1−8), including three new compounds, spirotryprostatin G (1), and cyclotryprostatins F and G (2 and 3), were obtained by large-scale cultivation of the fungal strain HBU-136 using rice medium with 1.0% MgCl2. The absolute configurations of 1−3 were determined by comparison of their experimental electronic circular dichroism (ECD) with calculated ECD spectra. Selective cytotoxicities were observed for compounds 1 and 4 against HL-60 cell line with the IC50 values of 6.0 and 7.9 μM, respectively, whereas 2, 3, and 5 against MCF-7 cell line with the IC50 values of 7.6, 10.8, and 5.1 μM, respectively.
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