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Shen X, Lei C, Zhang A, Wang L, Chen D, Qi L, Hu Y, Chen G, Ran H, Yin WB. Stimulating Novel and Bioactive Metabolite Production by Cocultivation of Two Fungi ─Aspergillus oryzae and Epicoccum dendrobii. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024. [PMID: 39020512 DOI: 10.1021/acs.jafc.4c04764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/19/2024]
Abstract
Fungi produce various bioactive secondary metabolites (SMs) as protective and weaponized tools to enhance survival in shared ecological niches. By mimicking a competitive ecosystem, cocultivation has been proven to be particularly successful in stimulating SM discovery. Here, we reported the identification of four novel metabolites, epiclactones A and B, epioxochromane and aoergostane, from the coculture of two biotechnologically important strains, Aspergillus oryzae and Epicoccum dendrobii. Transcriptome and metabolome analyses revealed widespread silent gene activation during fungal-fungal interaction. The majority of differentially expressed gene clusters were summarized for both strains. Based on these highly activated biosynthetic pathways, we suggested that a bidirectional chemical defense occurred under cocultivation. E. dendrobii enhanced the production of the spore inhibitor, fumigermin. Moreover, A. oryzae highly accumulated the antifungal agent kojic acid with a yield of up to 1.10 g/L. This study provides an excellent example for the discovery of hidden natural products by cocultivation.
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Affiliation(s)
- Xiangrui Shen
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, PR China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Chengzhi Lei
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- Medical School, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Anxin Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Long Wang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Denghui Chen
- Henan Academy of Science Institute of Biology, Zhengzhou 450008, PR China
| | - Landa Qi
- Henan Academy of Science Institute of Biology, Zhengzhou 450008, PR China
| | - Yiliang Hu
- Henan Academy of Science Institute of Biology, Zhengzhou 450008, PR China
| | - Guocan Chen
- Henan Academy of Science Institute of Biology, Zhengzhou 450008, PR China
| | - Huomiao Ran
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- Henan Academy of Science Institute of Biology, Zhengzhou 450008, PR China
| | - Wen-Bing Yin
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, PR China
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
- Medical School, University of Chinese Academy of Sciences, Beijing 100049, PR China
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Wu J, Danko D, Afshinnekoo E, Bezdan D, Bhattacharyya M, Castro-Nallar E, Chmielarczyk A, Hazrin-Chong NH, Deng Y, Dias-Neto E, Frolova A, Mason-Buck G, Iraola G, Jang S, Łabaj P, Lee PKH, Nieto-Caballero M, Osuolale OO, Ouzounis CA, Perlin MH, Prithiviraj B, Rascovan N, Różańska A, Schriml LM, Semmler T, Suzuki H, Ugalde JA, Young B, Werner J, Zambrano MM, Zhao Y, Mason C, Shi T. Annotating unknown species of urban microorganisms on a global scale unveils novel functional diversity and local environment association. ENVIRONMENTAL RESEARCH 2022; 207:112183. [PMID: 34637759 DOI: 10.1016/j.envres.2021.112183] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
In urban ecosystems, microbes play a key role in maintaining major ecological functions that directly support human health and city life. However, the knowledge about the species composition and functions involved in urban environments is still limited, which is largely due to the lack of reference genomes in metagenomic studies comprises more than half of unclassified reads. Here we uncovered 732 novel bacterial species from 4728 samples collected from various common surface with the matching materials in the mass transit system across 60 cities by the MetaSUB Consortium. The number of novel species is significantly and positively correlated with the city population, and more novel species can be identified in the skin-associated samples. The in-depth analysis of the new gene catalog showed that the functional terms have a significant geographical distinguishability. Moreover, we revealed that more biosynthetic gene clusters (BGCs) can be found in novel species. The co-occurrence relationship between BGCs and genera and the geographical specificity of BGCs can also provide us more information for the synthesis pathways of natural products. Expanded the known urban microbiome diversity and suggested additional mechanisms for taxonomic and functional characterization of the urban microbiome. Considering the great impact of urban microbiomes on human life, our study can also facilitate the microbial interaction analysis between human and urban environment.
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Affiliation(s)
- Jun Wu
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - David Danko
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Ebrahim Afshinnekoo
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Daniela Bezdan
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Malay Bhattacharyya
- Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India; Centre for Artificial Intelligence and Machine Learning, Indian Statistical Institute, Kolkata, India
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Argentina
| | | | - Nur Hazlin Hazrin-Chong
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia
| | - Youping Deng
- University of Hawaii, John A. Burns School of Mecidine, USA
| | - Emmanuel Dias-Neto
- Medical Genomics Group, A.C. Camargo Cancer Center and LIM-27 Faculdade de Medicina, USP, São Paulo, Brazil
| | - Alina Frolova
- Institute of Molecular Biology and Genetics of National Academy of Science of Ukraine, Ukraine
| | - Gabriella Mason-Buck
- Department of Analytical, Environmental and Forensic Sciences, King's College London, UK
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Uruguay; Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile; Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | - Paweł Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Poland
| | - Patrick K H Lee
- School of Energy and Environment, City University of Hong Kong, Hong Kong SAR, China
| | - Marina Nieto-Caballero
- University of Colorado at Boulder, Civil, Environmental and Architectural Department, Boulder, 80303, USA
| | - Olayinka O Osuolale
- Applied Environmental Metagenomics and Infectious Diseases Research (AEMIDR), Department of Biological Sciences, Elizade University, Nigeria
| | - Christos A Ouzounis
- BCPL-CPERI, Centre for Research & Technology Hellas, Thessalonica, GR, 57001, Greece
| | - Michael H Perlin
- Department of Biology, Program on Disease Evolution, University of Louisville, Louisville, KY, 40292, USA
| | - Bharath Prithiviraj
- Reckitt Health, Montvale, NJ, USA; Dept. of Biology, City University of New York, Brooklyn, 11210, NY, USA
| | - Nicolás Rascovan
- Aix-Marseille Université, IRD, AP-HM, IHU Méditerranée Infection, France
| | - Anna Różańska
- Jagiellonian University, Faculty of Medicine, Department of Microbiology, Poland
| | - Lynn M Schriml
- University of Maryland School of Medicine, Institute for Genome Sciences, USA
| | | | - Haruo Suzuki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Kanagawa, Japan
| | - Juan A Ugalde
- Millennium Initiative for Collaborative Research on Bacterial Resistance, Germany
| | - Ben Young
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Johannes Werner
- High Performance and Cloud Computing Group, Zentrum für Datenverarbeitung (ZDV), Eberhard Karls University of Tübingen, Wächterstraße 76, 72074, Tübingen, Germany
| | | | - Yongxiang Zhao
- Biological Targeting Diagnosis and Therapy Research Center, Guangxi Medical University, Nanning, 530021, China
| | - Christopher Mason
- Weill Cornell Medicine, USA; The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, USA
| | - Tieliu Shi
- Center for Bioinformatics and Computational Biology, and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China; Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China.
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Xu X, Feng J, Zhang P, Fan J, Yin WB. A CRISPR/Cas9 Cleavage System for Capturing Fungal Secondary Metabolite Gene Clusters. J Microbiol Biotechnol 2021; 31:8-15. [PMID: 33144546 PMCID: PMC9705949 DOI: 10.4014/jmb.2008.08040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/22/2020] [Accepted: 10/26/2020] [Indexed: 12/15/2022]
Abstract
More and more available fungal genome sequence data reveal a large amount of secondary metabolite (SM) biosynthetic 'dark matter' to be discovered. Heterogeneous expression is one of the most effective approaches to exploit these novel natural products, but it is limited by having to clone entire biosynthetic gene clusters (BGCs) without errors. So far, few effective technologies have been developed to manipulate the specific large DNA fragments in filamentous fungi. Here, we developed a fungal BGC-capturing system based on CRISPR/Cas9 cleavage in vitro. In our system, Cas9 protein was purified and CRISPR guide sequences in combination with in vivo yeast assembly were rationally designed. Using targeted cleavages of plasmid DNAs with linear (8.5 kb) or circular (8.5 kb and 28 kb) states, we were able to cleave the plasmids precisely, demonstrating the high efficiency of this system. Furthermore, we successfully captured the entire Nrc gene cluster from the genomic DNA of Neosartorya fischeri. Our results provide an easy and efficient approach to manipulate fungal genomic DNA based on the in vitro application of Cas9 endonuclease. Our methodology will lay a foundation for capturing entire groups of BGCs in filamentous fungi and accelerate fungal SMs mining.
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Affiliation(s)
- Xinran Xu
- State Key Laboratory of Mycology and CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 000, P.R. China,Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Jin Feng
- State Key Laboratory of Mycology and CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 000, P.R. China
| | - Peng Zhang
- State Key Laboratory of Mycology and CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 000, P.R. China
| | - Jie Fan
- State Key Laboratory of Mycology and CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 000, P.R. China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology and CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 000, P.R. China,Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, P.R. China,Corresponding author Phone: +86-10-64806170 E-mail:
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Simoben CV, Qaseem A, Moumbock AFA, Telukunta KK, Günther S, Sippl W, Ntie‐Kang F. Pharmacoinformatic Investigation of Medicinal Plants from East Africa. Mol Inform 2020; 39:e2000163. [PMID: 32964659 PMCID: PMC7685152 DOI: 10.1002/minf.202000163] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/22/2020] [Indexed: 12/18/2022]
Abstract
Medicinal plants have widely been used in the traditional treatment of ailments and have been proven effective. Their contribution still holds an important place in modern drug discovery due to their chemical, and biological diversities. However, the poor documentation of traditional medicine, in developing African countries for instance, can lead to the loss of knowledge related to such practices. In this study, we present the Eastern Africa Natural Products Database (EANPDB) containing the structural and bioactivity information of 1870 unique molecules isolated from about 300 source species from the Eastern African region. This represents the largest collection of natural products (NPs) from this geographical region, covering literature data of the period from 1962 to 2019. The computed physicochemical properties and toxicity profiles of each compound have been included. A comparative analysis of some physico-chemical properties like molecular weight, H-bond donor/acceptor, logPo/w , etc. as well scaffold diversity analysis has been carried out with other published NP databases. EANPDB was combined with the previously published Northern African Natural Products Database (NANPDB), to form a merger African Natural Products Database (ANPDB), containing ∼6500 unique molecules isolated from about 1000 source species (freely available at http://african-compounds.org). As a case study, latrunculins A and B isolated from the sponge Negombata magnifica (Podospongiidae) with previously reported antitumour activities, were identified via substructure searching as molecules to be explored as putative binders of histone deacetylases (HDACs).
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Affiliation(s)
- Conrad V. Simoben
- Institute of PharmacyMartin-Luther University of Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
| | - Ammar Qaseem
- Institute of Pharmaceutical Sciences, Research Group Pharmaceutical BioinformaticsAlbert-Ludwigs-University FreiburgHermann-Herder-Straße 979104FreiburgGermany
| | - Aurélien F. A. Moumbock
- Institute of Pharmaceutical Sciences, Research Group Pharmaceutical BioinformaticsAlbert-Ludwigs-University FreiburgHermann-Herder-Straße 979104FreiburgGermany
| | - Kiran K. Telukunta
- ELIXIR@PSB, VIB-UGent Center for Plant Systems BiologyTechnologiepark 719052GhentBelgium
| | - Stefan Günther
- Institute of Pharmaceutical Sciences, Research Group Pharmaceutical BioinformaticsAlbert-Ludwigs-University FreiburgHermann-Herder-Straße 979104FreiburgGermany
| | - Wolfgang Sippl
- Institute of PharmacyMartin-Luther University of Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
| | - Fidele Ntie‐Kang
- Institute of PharmacyMartin-Luther University of Halle-WittenbergKurt-Mothes-Str. 306120Halle/SaaleGermany
- Department of Chemistry, Faculty of ScienceUniversity of BueaP.O. Box 63Buea CM00237Cameroon
- Institut für BotanikTechnische Universität DresdenZellescherWeg 20b01217DresdenGermany
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