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Luo P, Huang JH, Lv JM, Wang GQ, Hu D, Gao H. Biosynthesis of fungal terpenoids. Nat Prod Rep 2024; 41:748-783. [PMID: 38265076 DOI: 10.1039/d3np00052d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
Covering: up to August 2023Terpenoids, which are widely distributed in animals, plants, and microorganisms, are a large group of natural products with diverse structures and various biological activities. They have made great contributions to human health as therapeutic agents, such as the anti-cancer drug paclitaxel and anti-malarial agent artemisinin. Accordingly, the biosynthesis of this important class of natural products has been extensively studied, which generally involves two major steps: hydrocarbon skeleton construction by terpenoid cyclases and skeleton modification by tailoring enzymes. Additionally, fungi (Ascomycota and Basidiomycota) serve as an important source for the discovery of terpenoids. With the rapid development of sequencing technology and bioinformatics approaches, genome mining has emerged as one of the most effective strategies to discover novel terpenoids from fungi. To date, numerous terpenoid cyclases, including typical class I and class II terpenoid cyclases as well as emerging UbiA-type terpenoid cyclases, have been identified, together with a variety of tailoring enzymes, including cytochrome P450 enzymes, flavin-dependent monooxygenases, and acyltransferases. In this review, our aim is to comprehensively present all fungal terpenoid cyclases identified up to August 2023, with a focus on newly discovered terpenoid cyclases, especially the emerging UbiA-type terpenoid cyclases, and their related tailoring enzymes from 2015 to August 2023.
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Affiliation(s)
- Pan Luo
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Jia-Hua Huang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Jian-Ming Lv
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Gao-Qian Wang
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Dan Hu
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
| | - Hao Gao
- Institute of Traditional Chinese Medicine & Natural Products, College of Pharmacy, Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education of China, Jinan University, Guangzhou 510632, China.
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2
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Zeb U, Aziz T, Azizullah A, Zan XY, Khan AA, Bacha SAS, Cui FJ. Complete mitochondrial genomes of edible mushrooms: features, evolution, and phylogeny. PHYSIOLOGIA PLANTARUM 2024; 176:e14363. [PMID: 38837786 DOI: 10.1111/ppl.14363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/15/2024] [Accepted: 02/27/2024] [Indexed: 06/07/2024]
Abstract
Edible mushrooms are an important food source with high nutritional and medicinal value. They are a useful source for studying phylogenetic evolution and species divergence. The exploration of the evolutionary relationships among these species conventionally involves analyzing sequence variations within their complete mitochondrial genomes, which range from 31,854 bp (Cordyceps militaris) to 197,486 bp (Grifolia frondosa). The study of the complete mitochondrial genomes of edible mushrooms has emerged as a critical field of research, providing important insights into fungal genetic makeup, evolution, and phylogenetic relationships. This review explores the mitochondrial genome structures of various edible mushroom species, highlighting their unique features and evolutionary adaptations. By analyzing these genomes, robust phylogenetic frameworks are constructed to elucidate mushrooms lineage relationships. Furthermore, the exploration of different variations of mitochondrial DNA presents novel opportunities for enhancing mushroom cultivation biotechnology and medicinal applications. The mitochondrial genomic features are essential for improving agricultural practices and ensuring food security through improved crop productivity, disease resistance, and nutritional qualities. The current knowledge about the mitochondrial genomes of edible mushrooms is summarized in this review, emphasising their significance in both scientific research and practical applications in bioinformatics and medicine.
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Affiliation(s)
- Umar Zeb
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
- Faculty of Biological and Biomedical Science, Department of Biology, The University of Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Tariq Aziz
- Faculty of Civil Engineering and Mechanics, Jiangsu University, Zhenjiang, PR China
| | - Azizullah Azizullah
- Faculty of Biological and Biomedical Science, Department of Biology, The University of Haripur, Khyber Pakhtunkhwa, Pakistan
| | - Xin-Yi Zan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
| | - Asif Ali Khan
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
| | - Syed Asim Shah Bacha
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
| | - Feng-Jie Cui
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, PR China
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3
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Pfütze S, Charria-Girón E, Schulzke E, Toshe R, Khonsanit A, Franke R, Surup F, Brönstrup M, Stadler M. Depicting the Chemical Diversity of Bioactive Meroterpenoids Produced by the Largest Organism on Earth. Angew Chem Int Ed Engl 2024; 63:e202318505. [PMID: 38390787 DOI: 10.1002/anie.202318505] [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: 12/03/2023] [Revised: 02/14/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
Abstract
In this investigation, we explored the diversity of melleolide-type meroterpenoids produced by Armillaria ostoyae, one of the largest and oldest organisms on Earth, using extracts from liquid and solid fermentation media. The study unveiled three unprecedented dimeric bismelleolides and three novel fatty-acid-substituted congeners, along with 11 new and 21 known derivatives. The structures were elucidated by 1D and 2D NMR spectroscopy and HRESI-MS, and ROESY spectral analysis for relative configurations. Absolute configurations were determined from crystal structures and through ECD spectra comparison. A compound library of melleolide-type meroterpenoids facilitated metabolomics-wide associations, revealing production patterns under different culture conditions. The library enabled assessments of antimicrobial and cytotoxic activities, revealing that the Δ2,4 double bond is not crucial for antifungal activity. Cytotoxicity was linked to the presence of an aldehyde at C1, but lost with hydroxylation at C13. Chemoinformatic analyses demonstrated the intricate interplay of chemical modifications on biological properties. This study marks the first systematic exploration of Armillaria spp. meroterpenoid diversity by MS-based untargeted metabolomics, offering insight into structure-activity relationships through innovative chemoinformatics.
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Affiliation(s)
- Sebastian Pfütze
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Esteban Charria-Girón
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Esther Schulzke
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Rita Toshe
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124, Braunschweig, Germany
- Institute of Pharmaceutical Biology Pharm. Biotechnology, Universität des Saarlandes Campus C2 3, 66123, Saarbrücken, Germany
| | - Artit Khonsanit
- BIOTEC, National Science and Technology Development, Agency (NSTDA), 111 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Raimo Franke
- Department Chemical Biology, Helmholtz Centre for Infection Research (HZI), and German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Frank Surup
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
| | - Mark Brönstrup
- Department Chemical Biology, Helmholtz Centre for Infection Research (HZI), and German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Marc Stadler
- Department Microbial Drugs, Helmholtz Centre for Infection Research (HZI), and German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstrasse 7, 38124, Braunschweig, Germany
- Institute of Microbiology, Technische Universität Braunschweig, Spielmannstraße 7, 38106, Braunschweig, Germany
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Hasan NS, Ling JG, Bakar MFA, Seman WMKW, Murad AMA, Bakar FDA, Khalid RM. The Lichen Flavin-Dependent Halogenase, DnHal: Identification, Heterologous Expression and Functional Characterization. Appl Biochem Biotechnol 2023; 195:6708-6736. [PMID: 36913095 DOI: 10.1007/s12010-022-04304-w] [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] [Accepted: 12/16/2022] [Indexed: 03/14/2023]
Abstract
Enzymatic halogenation captures scientific interest considering its feasibility in modifying compounds for chemical diversity. Currently, majority of flavin-dependent halogenases (F-Hals) were reported from bacterial origin, and as far as we know, none from lichenized fungi. Fungi are well-known producers of halogenated compounds, so using available transcriptomic dataset of Dirinaria sp., we mined for putative gene encoding for F-Hal. Phylogenetic-based classification of the F-Hal family suggested a non-tryptophan F-Hals, similar to other fungal F-Hals, which mainly act on aromatic compounds. However, after the putative halogenase gene from Dirinaria sp., dnhal was codon-optimized, cloned, and expressed in Pichia pastoris, the ~63 kDa purified enzyme showed biocatalytic activity towards tryptophan and an aromatic compound methyl haematommate, which gave the tell-tale isotopic pattern of a chlorinated product at m/z 239.0565 and 241.0552; and m/z 243.0074 and 245.0025, respectively. This study is the start of understanding the complexities of lichenized fungal F-hals and its ability to halogenate tryptophan and other aromatic. compounds which can be used as green alternatives for biocatalysis of halogenated compounds.
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Affiliation(s)
- Nurain Shahera Hasan
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Jonathan Guyang Ling
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Mohd Faizal Abu Bakar
- Malaysia Genome & Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, 43000, Kajang, Selangor, Malaysia
| | - Wan Mohd Khairulikhsan Wan Seman
- Malaysia Genome & Vaccine Institute, National Institutes of Biotechnology Malaysia, Jalan Bangi, 43000, Kajang, Selangor, Malaysia
| | - Abdul Munir Abdul Murad
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Farah Diba Abu Bakar
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Rozida Mohd Khalid
- Department of Chemical Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia.
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Fukaya M, Nagamine S, Ozaki T, Liu Y, Ozeki M, Matsuyama T, Miyamoto K, Kawagishi H, Uchiyama M, Oikawa H, Minami A. Total Biosynthesis of Melleolides from Basidiomycota Fungi: Mechanistic Analysis of the Multifunctional GMC Oxidase Mld7. Angew Chem Int Ed Engl 2023; 62:e202308881. [PMID: 37534412 DOI: 10.1002/anie.202308881] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/04/2023]
Abstract
Mushroom terpenoids are biologically and chemically diverse fungal metabolites. Among them, melleolides are representative sesquiterpenoids with a characteristic protoilludane skeleton. In this study, we applied a recently established hot spot knock-in method to elucidate the biosynthetic pathway leading to 1α-hydroxymelleolide. The biosynthesis of the sesquiterpene core involves the cytochrome P450 catalyzing stepwise hydroxylation of the Δ6 -protoilludene framework and a stereochemical inversion process at the C5 position catalyzed by short-chain dehydrogenase/reductase family proteins. The highlight of the biosynthesis is that the flavoprotein Mld7 catalyzes an oxidation-triggered double-bond shift accompanying dehydration and acyl-group-assisted substitution with two different nucleophiles at the C6 position to afford the Δ7 -protoilludene derivatives, such as melleolide and armillarivin. The complex reaction mechanism was proposed by DFT calculations. Of particular importance is that product distribution is regulated by interaction with the cell membrane.
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Affiliation(s)
- Mitsunori Fukaya
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Shota Nagamine
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Taro Ozaki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Yaping Liu
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Miina Ozeki
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Taro Matsuyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Kazunori Miyamoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hirokazu Kawagishi
- Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8526, Japan
- Research Institute for Mushroom Science, Shizuoka, 422-8529, Japan
| | - Masanobu Uchiyama
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
- Innovation Center of Marine Biotechnology and Pharmaceuticals, School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, China
| | - Atsushi Minami
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, 060-0810, Japan
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6
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Löhr NA, Urban MC, Eisen F, Platz L, Hüttel W, Gressler M, Müller M, Hoffmeister D. The Ketosynthase Domain Controls Chain Length in Mushroom Oligocyclic Polyketide Synthases. Chembiochem 2023; 24:e202200649. [PMID: 36507600 PMCID: PMC10108026 DOI: 10.1002/cbic.202200649] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022]
Abstract
The nonreducing iterative type I polyketide synthases (NR-PKSs) CoPKS1 and CoPKS4 of the webcap mushroom Cortinarius odorifer share 88 % identical amino acids. CoPKS1 almost exclusively produces a tricyclic octaketide product, atrochrysone carboxylic acid, whereas CoPKS4 shows simultaneous hepta- and octaketide synthase activity and also produces the bicyclic heptaketide 6-hydroxymusizin. To identify the region(s) controlling chain length, four chimeric enzyme variants were constructed and assayed for activity in Aspergillus niger as heterologous expression platform. We provide evidence that the β-ketoacyl synthase (KS) domain determines chain length in these mushroom NR-PKSs, even though their KS domains differ in only ten amino acids. A unique proline-rich linker connecting the acyl carrier protein with the thioesterase domain varies most between these two enzymes but is not involved in chain length control.
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Affiliation(s)
- Nikolai A. Löhr
- Department Pharmaceutical MicrobiologyHans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Maximilian C. Urban
- Department Pharmaceutical MicrobiologyHans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Frederic Eisen
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Lukas Platz
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Wolfgang Hüttel
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Markus Gressler
- Department Pharmaceutical MicrobiologyHans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Michael Müller
- Institute of Pharmaceutical SciencesAlbert-Ludwigs-Universität FreiburgAlbertstrasse 2579104FreiburgGermany
| | - Dirk Hoffmeister
- Department Pharmaceutical MicrobiologyHans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
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Zhang T, Cai G, Rong X, Wang Y, Gong K, Liu W, Wang L, Pang X, Yu L. A Combination of Genome Mining with an OSMAC Approach Facilitates the Discovery of and Contributions to the Biosynthesis of Melleolides from the Basidiomycete Armillaria tabescens. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:12430-12441. [PMID: 36134616 DOI: 10.1021/acs.jafc.2c04079] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Genome mining revealed that the genomes of basidiomycetes may include a considerable number of biosynthetic gene clusters (BGCs), yet numerous clusters remain unidentified. Herein, we report a combination of genome mining with an OSMAC (one strain, many compounds) approach to characterize the spectrum of melleolides produced by Armillaria tabescens CPCC 401429. Using F1 fermentation medium, the metabolic pathway of the gene cluster mel was successfully upregulated. From the extracts of the wild-type strain, two new melleolides (1 and 2), along with five new orsellinic acid-derived lactams (10-14), were isolated, and their structures were elucidated by LC-HR-ESIMS/MS and 2D-NMR. Several melleolides exhibited moderate anti-carcinoma (A549, NCI-H520, and H1299) effects with IC50 values of 4.0-48.8 μM. RNA-sequencing based transcriptomic profiling broadened our knowledge of the genetic background, regulation, and mechanisms of melleolide biosynthesis. These results may promote downstream metabolic engineering studies of melleolides. Our study demonstrates the approach is effective for discovering new secondary metabolites from Armillaria sp. and will facilitate the mining of the unexploited biosynthetic potential in other basidiomycetes.
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Affiliation(s)
- Tao Zhang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Guowei Cai
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- Medical Research Center, Binzhou Medical University Hospital, Binzhou, Shandong 256603, China
| | - Xiaoting Rong
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu 212003, China
| | - Yuquan Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - KaiKai Gong
- Medical Research Center, Binzhou Medical University Hospital, Binzhou, Shandong 256603, China
| | - Wancang Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Lu Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Xu Pang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Liyan Yu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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Dörner S, Rogge K, Fricke J, Schäfer T, Wurlitzer JM, Gressler M, Pham DNK, Manke DR, Chadeayne AR, Hoffmeister D. Genetic Survey of Psilocybe Natural Products. Chembiochem 2022; 23:e202200249. [PMID: 35583969 PMCID: PMC9400892 DOI: 10.1002/cbic.202200249] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/17/2022] [Indexed: 11/07/2022]
Abstract
Psilocybe magic mushrooms are best known for their main natural product, psilocybin, and its dephosphorylated congener, the psychedelic metabolite psilocin. Beyond tryptamines, the secondary metabolome of these fungi is poorly understood. The genomes of five species (P. azurescens, P. cubensis, P. cyanescens, P. mexicana, and P. serbica) were browsed to understand more profoundly common and species-specific metabolic capacities. The genomic analyses revealed a much greater and yet unexplored metabolic diversity than evident from parallel chemical analyses. P. cyanescens and P. mexicana were identified as aeruginascin producers. Lumichrome and verpacamide A were also detected as Psilocybe metabolites. The observations concerning the potential secondary metabolome of this fungal genus support pharmacological and toxicological efforts to find a rational basis for yet elusive phenomena, such as paralytic effects, attributed to consumption of some magic mushrooms.
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Affiliation(s)
- Sebastian Dörner
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Kai Rogge
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Janis Fricke
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Tim Schäfer
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Jacob M. Wurlitzer
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Markus Gressler
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
| | - Duyen N. K. Pham
- Department of Chemistry & BiochemistryUniversity of Massachusetts285 Old Westport RoadDartmouthMA02747USA
| | - David R. Manke
- Department of Chemistry & BiochemistryUniversity of Massachusetts285 Old Westport RoadDartmouthMA02747USA
| | | | - Dirk Hoffmeister
- Department Pharmaceutical Microbiology at the Hans-Knöll-InstituteFriedrich-Schiller-UniversitätBeutenbergstrasse 11a07745JenaGermany
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9
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Cochereau B, Meslet-Cladière L, Pouchus YF, Grovel O, Roullier C. Halogenation in Fungi: What Do We Know and What Remains to Be Discovered? Molecules 2022; 27:3157. [PMID: 35630634 PMCID: PMC9144378 DOI: 10.3390/molecules27103157] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 02/04/2023] Open
Abstract
In nature, living organisms produce a wide variety of specialized metabolites to perform many biological functions. Among these specialized metabolites, some carry halogen atoms on their structure, which can modify their chemical characteristics. Research into this type of molecule has focused on how organisms incorporate these atoms into specialized metabolites. Several families of enzymes have been described gathering metalloenzymes, flavoproteins, or S-adenosyl-L-methionine (SAM) enzymes that can incorporate these atoms into different types of chemical structures. However, even though the first halogenation enzyme was discovered in a fungus, this clade is still lagging behind other clades such as bacteria, where many enzymes have been discovered. This review will therefore focus on all halogenation enzymes that have been described in fungi and their associated metabolites by searching for proteins available in databases, but also by using all the available fungal genomes. In the second part of the review, the chemical diversity of halogenated molecules found in fungi will be discussed. This will allow the highlighting of halogenation mechanisms that are still unknown today, therefore, highlighting potentially new unknown halogenation enzymes.
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Affiliation(s)
- Bastien Cochereau
- Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, Nantes Université, F-44000 Nantes, France; (B.C.); (Y.F.P.); (O.G.)
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France;
| | - Laurence Meslet-Cladière
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France;
| | - Yves François Pouchus
- Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, Nantes Université, F-44000 Nantes, France; (B.C.); (Y.F.P.); (O.G.)
| | - Olivier Grovel
- Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, Nantes Université, F-44000 Nantes, France; (B.C.); (Y.F.P.); (O.G.)
| | - Catherine Roullier
- Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, Nantes Université, F-44000 Nantes, France; (B.C.); (Y.F.P.); (O.G.)
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10
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Liu Z, Lu H, Zhang X, Chen Q. The Genomic and Transcriptomic Analyses of Floccularia luteovirens, a Rare Edible Fungus in the Qinghai-Tibet Plateau, Provide Insights into the Taxonomy Placement and Fruiting Body Formation. J Fungi (Basel) 2021; 7:jof7110887. [PMID: 34829176 PMCID: PMC8618933 DOI: 10.3390/jof7110887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/16/2021] [Accepted: 10/16/2021] [Indexed: 12/13/2022] Open
Abstract
Floccularia luteovirens is a famous and precious edible mushroom (Huang Mogu) on the Qinghai–Tibet plateau that has a unique flavor and remarkable medical functions. Herein, we report a reference-grade 27 Mb genome of F. luteovirens containing 7068 protein-coding genes. The genome component and gene functions were predicted. Genome ontology enrichment and pathway analyses indicated the potential production capacity for terpenoids, polyketides and polysaccharides. Moreover, 16 putative gene clusters and 145 genes coding for secondary metabolites were obtained, including guadinomine and melleolides. In addition, phylogenetic and comparative genomic analyses shed light on the precise classification of F. luteovirens suggesting that it belongs to the genus Floccularia instead of Armillaria. RNA-sequencing and comparative transcriptomic analysis revealed differentially expressed genes during four developmental stages of F. luteovirens, that of which helps to identify important genes regulating fruiting body formation for strain modification. This study will provide insight into artificial cultivation and increase the production of useful metabolites.
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Affiliation(s)
- Zhengjie Liu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (Z.L.); (H.L.); (X.Z.)
- College of Food and Pharmacy, Zhejiang Ocean University, Zhoushan 316022, China
| | - Hongyun Lu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (Z.L.); (H.L.); (X.Z.)
| | - Xinglin Zhang
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (Z.L.); (H.L.); (X.Z.)
| | - Qihe Chen
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (Z.L.); (H.L.); (X.Z.)
- Correspondence: ; Tel.: +86-0571-8698-4316
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11
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Gressler M, Löhr NA, Schäfer T, Lawrinowitz S, Seibold PS, Hoffmeister D. Mind the mushroom: natural product biosynthetic genes and enzymes of Basidiomycota. Nat Prod Rep 2021; 38:702-722. [PMID: 33404035 DOI: 10.1039/d0np00077a] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Covering: up to September 2020 Mushroom-forming fungi of the division Basidiomycota have traditionally been recognised as prolific producers of structurally diverse and often bioactive secondary metabolites, using the methods of chemistry for research. Over the past decade, -omics technologies were applied on these fungi, and sophisticated heterologous gene expression platforms emerged, which have boosted research into the genetic and biochemical basis of the biosyntheses. This review provides an overview on experimentally confirmed natural product biosyntheses of basidiomycete polyketides, amino acid-derived products, terpenoids, and volatiles. We also present challenges and solutions particular to natural product research with these fungi. 222 references are cited.
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Affiliation(s)
- Markus Gressler
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Nikolai A Löhr
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Tim Schäfer
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Stefanie Lawrinowitz
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Paula Sophie Seibold
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
| | - Dirk Hoffmeister
- Department of Pharmaceutical Microbiology at the Hans Knöll Institute, Friedrich-Schiller-University Jena, Winzerlaer Strasse 2, 07745 Jena, Germany.
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12
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Engels B, Heinig U, McElroy C, Meusinger R, Grothe T, Stadler M, Jennewein S. Isolation of a gene cluster from Armillaria gallica for the synthesis of armillyl orsellinate-type sesquiterpenoids. Appl Microbiol Biotechnol 2021; 105:211-224. [PMID: 33191459 PMCID: PMC7778616 DOI: 10.1007/s00253-020-11006-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 09/29/2020] [Accepted: 11/04/2020] [Indexed: 11/27/2022]
Abstract
Melleolides and armillyl orsellinates are protoilludene-type aryl esters that are synthesized exclusively by parasitic fungi of the globally distributed genus Armillaria (Agaricomycetes, Physalacriaceae). Several of these compounds show potent antimicrobial and cytotoxic activities, making them promising leads for the development of new antibiotics or drugs for the treatment of cancer. We recently cloned and characterized the Armillaria gallica gene Pro1 encoding protoilludene synthase, a sesquiterpene cyclase catalyzing the pathway-committing step to all protoilludene-type aryl esters. Fungal enzymes representing secondary metabolic pathways are sometimes encoded by gene clusters, so we hypothesized that the missing steps in the pathway to melleolides and armillyl orsellinates might be identified by cloning the genes surrounding Pro1. Here we report the isolation of an A. gallica gene cluster encoding protoilludene synthase and four cytochrome P450 monooxygenases. Heterologous expression and functional analysis resulted in the identification of protoilludene-8α-hydroxylase, which catalyzes the first committed step in the armillyl orsellinate pathway. This confirms that ∆-6-protoilludene is a precursor for the synthesis of both melleolides and armillyl orsellinates, but the two pathways already branch at the level of the first oxygenation step. Our results provide insight into the synthesis of these valuable natural products and pave the way for their production by metabolic engineering. KEY POINTS: • Protoilludene-type aryl esters are bioactive metabolites produced by Armillaria spp. • The pathway-committing step to these compounds is catalyzed by protoilludene synthase. • We characterized CYP-type enzymes in the cluster and identified novel intermediates.
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Affiliation(s)
- Benedikt Engels
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany
- Jennewein Biotechnologie GmbH, Maarweg 32, Rheinbreitbach, Germany
| | - Uwe Heinig
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany
- Department of Plant & Environmental Sciences, Weizmann Institute of Science, P.O. Box 26, 7610001, Rehovot, Israel
| | - Christopher McElroy
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany
| | - Reinhard Meusinger
- Clemens Schöpf Institute of Organic Chemistry and Biochemistry, Technical University of Darmstadt, 64287, Darmstadt, Germany
| | - Torsten Grothe
- Mibelle Group Biochemistry, Bolimattstrasse 1, 5033, Buchs, Switzerland
| | - Marc Stadler
- Department of Microbial Drugs, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Stefan Jennewein
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Forckenbeckstrasse 6, 52074, Aachen, Germany.
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13
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Redox Coenzyme F 420 Biosynthesis in Thermomicrobia Involves Reduction by Stand-Alone Nitroreductase Superfamily Enzymes. Appl Environ Microbiol 2020; 86:AEM.00457-20. [PMID: 32276981 DOI: 10.1128/aem.00457-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 04/07/2020] [Indexed: 12/17/2022] Open
Abstract
Coenzyme F420 is a redox cofactor involved in hydride transfer reactions in archaea and bacteria. Since F420-dependent enzymes are attracting increasing interest as tools in biocatalysis, F420 biosynthesis is being revisited. While it was commonly accepted for a long time that the 2-phospho-l-lactate (2-PL) moiety of F420 is formed from free 2-PL, it was recently shown that phosphoenolpyruvate is incorporated in Actinobacteria and that the C-terminal domain of the FbiB protein, a member of the nitroreductase (NTR) superfamily, converts dehydro-F420 into saturated F420 Outside the Actinobacteria, however, the situation is still unclear because FbiB is missing in these organisms and enzymes of the NTR family are highly diversified. Here, we show by heterologous expression and in vitro assays that stand-alone NTR enzymes from Thermomicrobia exhibit dehydro-F420 reductase activity. Metabolome analysis and proteomics studies confirmed the proposed biosynthetic pathway in Thermomicrobium roseum These results clarify the biosynthetic route of coenzyme F420 in a class of Gram-negative bacteria, redefine functional subgroups of the NTR superfamily, and offer an alternative for large-scale production of F420 in Escherichia coli in the future.IMPORTANCE Coenzyme F420 is a redox cofactor of Archaea and Actinobacteria, as well as some Gram-negative bacteria. Its involvement in processes such as the biosynthesis of antibiotics, the degradation of xenobiotics, and asymmetric enzymatic reductions renders F420 of great relevance for biotechnology. Recently, a new biosynthetic step during the formation of F420 in Actinobacteria was discovered, involving an enzyme domain belonging to the versatile nitroreductase (NTR) superfamily, while this process remained blurred in Gram-negative bacteria. Here, we show that a similar biosynthetic route exists in Thermomicrobia, although key biosynthetic enzymes show different domain architectures and are only distantly related. Our results shed light on the biosynthesis of F420 in Gram-negative bacteria and refine the knowledge about sequence-function relationships within the NTR superfamily of enzymes. Appreciably, these results offer an alternative route to produce F420 in Gram-negative model organisms and unveil yet another biochemical facet of this pathway to be explored by synthetic microbiologists.
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14
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Oikawa H. Reconstitution of biosynthetic machinery of fungal natural products in heterologous hosts. Biosci Biotechnol Biochem 2020; 84:433-444. [DOI: 10.1080/09168451.2019.1690976] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
ABSTRACT
Ascomycota and basidiomycota fungi are prolific sources of biologically active natural products. Recent genomic data and bioinformatic analysis indicate that fungi possess a large number of biosynthetic gene clusters for bioactive natural products but more than 90% are silent. Heterologous expression in the filamentous fungi as hosts is one of the powerful tools to expression of the silent gene clusters. This review introduces recent studies on the total biosynthesis of representative family members via common platform intermediates, genome mining of novel di- and sesterterpenoids including detailed cyclization pathway, and development of expression host for basidiomycota genes with efficient genome editing method. In addition, this review will discuss the several strategies, for the generation of structural diversity, which are found through these studies.
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Affiliation(s)
- Hideaki Oikawa
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
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15
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Fisher B, Snodgrass HM, Jones KA, Andorfer MC, Lewis JC. Site-Selective C-H Halogenation Using Flavin-Dependent Halogenases Identified via Family-Wide Activity Profiling. ACS CENTRAL SCIENCE 2019; 5:1844-1856. [PMID: 31807686 PMCID: PMC6891866 DOI: 10.1021/acscentsci.9b00835] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Indexed: 05/19/2023]
Abstract
Enzymes are powerful catalysts for site-selective C-H bond functionalization. Identifying suitable enzymes for this task and for biocatalysis in general remains challenging, however, due to the fundamental difficulty of predicting catalytic activity from sequence information. In this study, family-wide activity profiling was used to obtain sequence-function information on flavin-dependent halogenases (FDHs). This broad survey provided a number of insights into FDH activity, including halide specificity and substrate preference, that were not apparent from the more focused studies reported to date. Regions of FDH sequence space that are most likely to contain enzymes suitable for halogenating small-molecule substrates were also identified. FDHs with novel substrate scope and complementary regioselectivity on large, three-dimensionally complex compounds were characterized and used for preparative-scale late-stage C-H functionalization. In many cases, these enzymes provide activities that required several rounds of directed evolution to accomplish in previous efforts, highlighting that this approach can achieve significant time savings for biocatalyst identification and provide advanced starting points for further evolution.
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Affiliation(s)
- Brian
F. Fisher
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Harrison M. Snodgrass
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krysten A. Jones
- Department
of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Mary C. Andorfer
- Department
of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jared C. Lewis
- Department
of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
- E-mail:
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16
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Slot JC, Gluck-Thaler E. Metabolic gene clusters, fungal diversity, and the generation of accessory functions. Curr Opin Genet Dev 2019; 58-59:17-24. [DOI: 10.1016/j.gde.2019.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 07/01/2019] [Accepted: 07/16/2019] [Indexed: 10/26/2022]
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17
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18
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Zhelifonova VP, Antipova TV, Litvinova EA, Baskunov BP, Litovka YA, Pavlov IN, Kozlovsky AG. Biosynthesis of Protoilludene Sesquiterpene Aryl Esters by Siberian Strains of the Genus Armillaria Fungi. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819030153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Genome- and MS-based mining of antibacterial chlorinated chromones and xanthones from the phytopathogenic fungus Bipolaris sorokiniana strain 11134. Appl Microbiol Biotechnol 2019; 103:5167-5181. [PMID: 31001746 DOI: 10.1007/s00253-019-09821-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 12/18/2022]
Abstract
Halogen substituents are important for biological activity in many compounds. Genome-based mining of halogenase along with its biosynthetic gene cluster provided an efficient approach for the discovery of naturally occurring organohalogen compounds. Analysis of the genome sequence of a phytopathogenic fungus Bipolaris sorokiniana 11134 revealed a polyketide gene cluster adjacent to a flavin-dependent halogenase capable of encoding halogenated polyketides, which are rarely reported in phytopathogenic fungi. Furthermore, MS- and UV-guided isolation and purification led to the identification of five chlorine-containing natural products together with seven other chromones and xanthones. Two of the chlorinated compounds and four chromones are new compounds. Their structures were elucidated by NMR spectroscopic analysis and HRESIMS data. The biosynthetic gene clusters of isolated compounds and their putative biosynthetic pathway are also proposed. One new chlorinated compound showed activity against Staphylococcus aureus, methicillin-resistant S. aureus, and three clinical-resistant S. aureus strains with a shared minimum inhibitory concentration (MIC) of 12.5 μg/mL. Genome-based mining of halogenases combined with high-resolution MS- and UV-guided identification provides an efficient approach to discover new halogenated natural products from microorganisms.
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20
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Biological and chemical diversity go hand in hand: Basidiomycota as source of new pharmaceuticals and agrochemicals. Biotechnol Adv 2019; 37:107344. [PMID: 30738916 DOI: 10.1016/j.biotechadv.2019.01.011] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/30/2019] [Accepted: 01/31/2019] [Indexed: 12/20/2022]
Abstract
The Basidiomycota constitutes the second largest higher taxonomic group of the Fungi after the Ascomycota and comprises over 30.000 species. Mycelial cultures of Basidiomycota have already been studied since the 1950s for production of antibiotics and other beneficial secondary metabolites. Despite the fact that unique and selective compounds like pleuromutilin were obtained early on, it took several decades more until they were subjected to a systematic screening for antimicrobial and anticancer activities. These efforts led to the discovery of the strobilurins and several hundreds of further compounds that mainly constitute terpenoids. In parallel the traditional medicinal mushrooms of Asia were also studied intensively for metabolite production, aimed at finding new therapeutic agents for treatment of various diseases including metabolic disorders and the central nervous system. While the evaluation of this organism group has in general been more tedious as compared to the Ascomycota, the chances to discover new metabolites and to develop them further to candidates for drugs, agrochemicals and other products for the Life Science industry have substantially increased over the past decade. This is owing to the revolutionary developments in -OMICS techniques, bioinformatics, analytical chemistry and biotechnological process technology, which are steadily being developed further. On the other hand, the new developments in polythetic fungal taxonomy now also allow a more concise selection of previously untapped organisms. The current review is dedicated to summarize the state of the art and to give an outlook to further developments.
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21
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Fraley AE, Sherman DH. Halogenase engineering and its utility in medicinal chemistry. Bioorg Med Chem Lett 2018; 28:1992-1999. [PMID: 29731363 DOI: 10.1016/j.bmcl.2018.04.066] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 10/17/2022]
Abstract
Halogenation is commonly used in medicinal chemistry to improve the potency of pharmaceutical leads. While synthetic methods for halogenation present selectivity and reactivity challenges, halogenases have evolved over time to perform selective reactions under benign conditions. The optimization of halogenation biocatalysts has utilized enzyme evolution and structure-based engineering alongside biotransformation in a variety of systems to generate stable site-selective variants. The recent improvements in halogenase-catalyzed reactions has demonstrated the utility of these biocatalysts for industrial purposes, and their ability to achieve a broad substrate scope implies a synthetic tractability with increasing relevance in medicinal chemistry.
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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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22
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Andorfer MC, Lewis JC. Understanding and Improving the Activity of Flavin-Dependent Halogenases via Random and Targeted Mutagenesis. Annu Rev Biochem 2018; 87:159-185. [PMID: 29589959 DOI: 10.1146/annurev-biochem-062917-012042] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Flavin-dependent halogenases (FDHs) catalyze the halogenation of organic substrates by coordinating reactions of reduced flavin, molecular oxygen, and chloride. Targeted and random mutagenesis of these enzymes have been used to both understand and alter their reactivity. These studies have led to insights into residues essential for catalysis and FDH variants with improved stability, expanded substrate scope, and altered site selectivity. Mutations throughout FDH structures have contributed to all of these advances. More recent studies have sought to rationalize the impact of these mutations on FDH function and to identify new FDHs to deepen our understanding of this enzyme class and to expand their utility for biocatalytic applications.
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Affiliation(s)
- Mary C Andorfer
- Department of Biology and Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA;
| | - Jared C Lewis
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA;
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23
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Proteomic Characterization of Armillaria mellea Reveals Oxidative Stress Response Mechanisms and Altered Secondary Metabolism Profiles. Microorganisms 2017; 5:microorganisms5030060. [PMID: 28926970 PMCID: PMC5620651 DOI: 10.3390/microorganisms5030060] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 09/08/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022] Open
Abstract
Armillaria mellea is a major plant pathogen. Yet, the strategies the organism uses to infect susceptible species, degrade lignocellulose and other plant material and protect itself against plant defences and its own glycodegradative arsenal are largely unknown. Here, we use a combination of gel and MS-based proteomics to profile A. mellea under conditions of oxidative stress and changes in growth matrix. 2-DE and LC-MS/MS were used to investigate the response of A. mellea to H2O2 and menadione/FeCl3 exposure, respectively. Several proteins were detected with altered abundance in response to H2O2, but not menadione/FeCl3 (i.e., valosin-containing protein), indicating distinct responses to these different forms of oxidative stress. One protein, cobalamin-independent methionine synthase, demonstrated a common response in both conditions, which may be a marker for a more general stress response mechanism. Further changes to the A. mellea proteome were investigated using MS-based proteomics, which identified changes to putative secondary metabolism (SM) enzymes upon growth in agar compared to liquid cultures. Metabolomic analyses revealed distinct profiles, highlighting the effect of growth matrix on SM production. This establishes robust methods by which to utilize comparative proteomics to characterize this important phytopathogen.
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Agarwal V, Miles ZD, Winter JM, Eustáquio AS, El Gamal AA, Moore BS. Enzymatic Halogenation and Dehalogenation Reactions: Pervasive and Mechanistically Diverse. Chem Rev 2017; 117:5619-5674. [PMID: 28106994 PMCID: PMC5575885 DOI: 10.1021/acs.chemrev.6b00571] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Naturally produced halogenated compounds are ubiquitous across all domains of life where they perform a multitude of biological functions and adopt a diversity of chemical structures. Accordingly, a diverse collection of enzyme catalysts to install and remove halogens from organic scaffolds has evolved in nature. Accounting for the different chemical properties of the four halogen atoms (fluorine, chlorine, bromine, and iodine) and the diversity and chemical reactivity of their organic substrates, enzymes performing biosynthetic and degradative halogenation chemistry utilize numerous mechanistic strategies involving oxidation, reduction, and substitution. Biosynthetic halogenation reactions range from simple aromatic substitutions to stereoselective C-H functionalizations on remote carbon centers and can initiate the formation of simple to complex ring structures. Dehalogenating enzymes, on the other hand, are best known for removing halogen atoms from man-made organohalogens, yet also function naturally, albeit rarely, in metabolic pathways. This review details the scope and mechanism of nature's halogenation and dehalogenation enzymatic strategies, highlights gaps in our understanding, and posits where new advances in the field might arise in the near future.
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Affiliation(s)
- Vinayak Agarwal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Zachary D. Miles
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
| | | | - Alessandra S. Eustáquio
- College of Pharmacy, Department of Medicinal Chemistry & Pharmacognosy and Center for Biomolecular Sciences, University of Illinois at Chicago
| | - Abrahim A. El Gamal
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
| | - Bradley S. Moore
- Center for Oceans and Human Health, Scripps Institution of Oceanography, University of California, San Diego
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego
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25
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Biochemical and genetic basis of orsellinic acid biosynthesis and prenylation in a stereaceous basidiomycete. Fungal Genet Biol 2017; 98:12-19. [DOI: 10.1016/j.fgb.2016.11.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/23/2016] [Accepted: 11/25/2016] [Indexed: 12/25/2022]
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26
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Making Use of Genomic Information to Explore the Biotechnological Potential of Medicinal Mushrooms. MEDICINAL AND AROMATIC PLANTS OF THE WORLD 2017. [DOI: 10.1007/978-981-10-5978-0_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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27
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Secondary Metabolites from Higher Fungi. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 106 2017; 106:1-201. [DOI: 10.1007/978-3-319-59542-9_1] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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28
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Schlegel M, Münsterkötter M, Güldener U, Bruggmann R, Duò A, Hainaut M, Henrissat B, Sieber CMK, Hoffmeister D, Grünig CR. Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles. BMC Genomics 2016; 17:1015. [PMID: 27938347 PMCID: PMC5148876 DOI: 10.1186/s12864-016-3369-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/02/2016] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Whereas an increasing number of pathogenic and mutualistic ascomycetous species were sequenced in the past decade, species showing a seemingly neutral association such as root endophytes received less attention. In the present study, the genome of Phialocephala subalpina, the most frequent species of the Phialocephala fortinii s.l. - Acephala applanata species complex, was sequenced for insight in the genome structure and gene inventory of these wide-spread root endophytes. RESULTS The genome of P. subalpina was sequenced using Roche/454 GS FLX technology and a whole genome shotgun strategy. The assembly resulted in 205 scaffolds and a genome size of 69.7 Mb. The expanded genome size in P. subalpina was not due to the proliferation of transposable elements or other repeats, as is the case with other ascomycetous genomes. Instead, P. subalpina revealed an expanded gene inventory that includes 20,173 gene models. Comparative genome analysis of P. subalpina with 13 ascomycetes shows that P. subalpina uses a versatile gene inventory including genes specific for pathogens and saprophytes. Moreover, the gene inventory for carbohydrate active enzymes (CAZymes) was expanded including genes involved in degradation of biopolymers, such as pectin, hemicellulose, cellulose and lignin. CONCLUSIONS The analysis of a globally distributed root endophyte allowed detailed insights in the gene inventory and genome organization of a yet largely neglected group of organisms. We showed that the ubiquitous root endophyte P. subalpina has a broad gene inventory that links pathogenic and saprophytic lifestyles.
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Affiliation(s)
- Markus Schlegel
- Institute of Integrative Biology (IBZ), Forest Pathology and Dendrology, ETH Zürich, 8092, Zürich, Switzerland
| | - Martin Münsterkötter
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany
| | - Ulrich Güldener
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany.,Department of Genome-oriented Bioinformatics, Technische Universität München, Wissenschaftszentrum Weihenstephan, 85354, Freising, Germany
| | - Rémy Bruggmann
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Berne, Baltzerstrasse 6, 3012, Bern, Switzerland
| | - Angelo Duò
- Institute of Integrative Biology (IBZ), Forest Pathology and Dendrology, ETH Zürich, 8092, Zürich, Switzerland
| | - Matthieu Hainaut
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 CNRS, Université Aix-Marseille, 163 Avenue de Luminy, 13288, Marseille, France
| | - Christian M K Sieber
- Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764, Neuherberg, Germany.,DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Dirk Hoffmeister
- Friedrich-Schiller-Universität, Pharmazeutische Mikrobiologie, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Christoph R Grünig
- Institute of Integrative Biology (IBZ), Forest Pathology and Dendrology, ETH Zürich, 8092, Zürich, Switzerland. .,Microsynth AG, Schützenstrasse 15, 9436, Balgach, Switzerland.
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29
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Schafhauser T, Kirchner N, Kulik A, Huijbers MM, Flor L, Caradec T, Fewer DP, Gross H, Jacques P, Jahn L, Jokela J, Leclère V, Ludwig-Müller J, Sivonen K, van Berkel WJ, Weber T, Wohlleben W, van Pée KH. The cyclochlorotine mycotoxin is produced by the nonribosomal peptide synthetase CctN inTalaromyces islandicus(‘Penicillium islandicum’). Environ Microbiol 2016; 18:3728-3741. [DOI: 10.1111/1462-2920.13294] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 02/15/2016] [Accepted: 03/07/2016] [Indexed: 01/08/2023]
Affiliation(s)
- Thomas Schafhauser
- Mikrobiologie und Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Norbert Kirchner
- Department of Pharmaceutical Biology; Pharmaceutical Institute, University of Tübingen; Auf der Morgenstelle 8 72076 Tübingen Germany
- German Centre for Infection Research (DZIF), Partner site Tübingen; 72076 Tübingen Germany
| | - Andreas Kulik
- Mikrobiologie und Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 28 72076 Tübingen Germany
| | - Mieke M.E. Huijbers
- Laboratory of Biochemistry; Wageningen University; Dreijenlaan 3 6703 HA Wageningen The Netherlands
| | - Liane Flor
- Allgemeine Biochemie, Technische Universität Dresden; 01069 Dresden Germany
| | - Thibault Caradec
- Research Laboratory in Agro-Food and Biotechnology; Charles Viollette Institute, Team ProBioGEM, Polytech-Lille, Université Lille1- Sciences et Technologies; 59655 Villeneuve d'Ascq France
| | - David P. Fewer
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki; Viikinkaari 9 FIN-00014 Helsinki Finland
| | - Harald Gross
- Department of Pharmaceutical Biology; Pharmaceutical Institute, University of Tübingen; Auf der Morgenstelle 8 72076 Tübingen Germany
- German Centre for Infection Research (DZIF), Partner site Tübingen; 72076 Tübingen Germany
| | - Philippe Jacques
- Research Laboratory in Agro-Food and Biotechnology; Charles Viollette Institute, Team ProBioGEM, Polytech-Lille, Université Lille1- Sciences et Technologies; 59655 Villeneuve d'Ascq France
| | - Linda Jahn
- Institut für Botanik; Technische Universität Dresden; 01062 Dresden Germany
| | - Jouni Jokela
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki; Viikinkaari 9 FIN-00014 Helsinki Finland
| | - Valérie Leclère
- Research Laboratory in Agro-Food and Biotechnology; Charles Viollette Institute, Team ProBioGEM, Polytech-Lille, Université Lille1- Sciences et Technologies; 59655 Villeneuve d'Ascq France
| | | | - Kaarina Sivonen
- Microbiology and Biotechnology Division, Department of Food and Environmental Sciences, University of Helsinki; Viikinkaari 9 FIN-00014 Helsinki Finland
| | - Willem J.H. van Berkel
- Laboratory of Biochemistry; Wageningen University; Dreijenlaan 3 6703 HA Wageningen The Netherlands
| | - Tilmann Weber
- Mikrobiologie und Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 28 72076 Tübingen Germany
- German Centre for Infection Research (DZIF), Partner site Tübingen; 72076 Tübingen Germany
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark; Kogle Alle 6 2970 Hørsholm Denmark
| | - Wolfgang Wohlleben
- Mikrobiologie und Biotechnologie, Interfakultäres Institut für Mikrobiologie und Infektionsmedizin; Eberhard Karls Universität Tübingen; Auf der Morgenstelle 28 72076 Tübingen Germany
- German Centre for Infection Research (DZIF), Partner site Tübingen; 72076 Tübingen Germany
| | - Karl-Heinz van Pée
- Allgemeine Biochemie, Technische Universität Dresden; 01069 Dresden Germany
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