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Sharma V, Panjgotra S, Sharma N, Abrol V, Goutam U, Jaglan S. Epigenetic modifiers as inducer of bioactive secondary metabolites in fungi. Biotechnol Lett 2024; 46:297-314. [PMID: 38607602 DOI: 10.1007/s10529-024-03478-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 01/16/2024] [Accepted: 03/10/2024] [Indexed: 04/13/2024]
Abstract
Scientists are making efforts to search for new metabolites as they are essential lead molecules for the drug discovery, much required due to the evolution of multi drug resistance and new diseases. Moreover, higher production of known drugs is required because of the ever growing population. Microorganisms offer a vast collection of chemically distinct compounds that exhibit various biological functions. They play a crucial role in safeguarding crops, agriculture, and combating several infectious ailments and cancer. Research on fungi have grabbed a lot of attention after the discovery of penicillin, most of the compounds produced by fungi under normal cultivation conditions are discovered and now rarely new compounds are discovered. Treatment of fungi with the epigenetic modifiers has been becoming very popular since the last few years to boost the discovery of new molecules and enhance the production of already known molecules. Epigenetic literally means above genetics that actually does not alter the genome but alter its expression by altering the state of chromatin from heterochromatin to euchromatin. Chromatin in heterochromatin state usually doesn't express because it is closely packed by histones in this state. Epigenetic modifiers loosen the packing of chromatin by inhibiting DNA methylation and histone deacetylation and thus permit the expression of genes that usually remain dormant. This study delves into the possibility of utilizing epigenetic modifying agents to generate pharmacologically significant secondary metabolites from fungi.
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Affiliation(s)
- Vishal Sharma
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shivali Panjgotra
- Department of Environment Studies, Panjab University, Chandigarh, 160014, India
| | - Nisha Sharma
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, 180001, India
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Vidushi Abrol
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, 180001, India
| | - Umesh Goutam
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Sundeep Jaglan
- Fermentation & Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, 180001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Barreiro C, Albillos SM, García-Estrada C. Penicillium chrysogenum: Beyond the penicillin. ADVANCES IN APPLIED MICROBIOLOGY 2024; 127:143-221. [PMID: 38763527 DOI: 10.1016/bs.aambs.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
Almost one century after the Sir Alexander Fleming's fortuitous discovery of penicillin and the identification of the fungal producer as Penicillium notatum, later Penicillium chrysogenum (currently reidentified as Penicillium rubens), the molecular mechanisms behind the massive production of penicillin titers by industrial strains could be considered almost fully characterized. However, this filamentous fungus is not only circumscribed to penicillin, and instead, it seems to be full of surprises, thereby producing important metabolites and providing expanded biotechnological applications. This review, in addition to summarizing the classical role of P. chrysogenum as penicillin producer, highlights its ability to generate an array of additional bioactive secondary metabolites and enzymes, together with the use of this microorganism in relevant biotechnological processes, such as bioremediation, biocontrol, production of bioactive nanoparticles and compounds with pharmaceutical interest, revalorization of agricultural and food-derived wastes or the enhancement of food industrial processes and the agricultural production.
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Affiliation(s)
- Carlos Barreiro
- Área de Bioquímica y Biología Molecular, Departamento de Biología Molecular, Facultad de Veterinaria, Universidad de León, León, Spain; Instituto de Biología Molecular, Genómica y Proteómica (INBIOMIC), Universidad de León, León, Spain.
| | - Silvia M Albillos
- Área de Bioquímica y Biología Molecular, Departamento de Biotecnología y Ciencia de los Alimentos, Facultad de Ciencias, Universidad de Burgos, Burgos, Spain
| | - Carlos García-Estrada
- Departamento de Ciencias Biomédicas, Facultad de Veterinaria, Universidad de León, León, Spain; Instituto de Biomedicina (IBIOMED), Universidad de León, León, Spain
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Dos Reis JBA, Lorenzi AS, Pinho DB, Cortelo PC, do Vale HMM. The hidden treasures in endophytic fungi: a comprehensive review on the diversity of fungal bioactive metabolites, usual analytical methodologies, and applications. Arch Microbiol 2024; 206:185. [PMID: 38506928 DOI: 10.1007/s00203-024-03911-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 02/20/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024]
Abstract
This review provides a comprehensive overview of the key aspects of the natural metabolite production by endophytic fungi, which has attracted significant attention due to its diverse biological activities and wide range of applications. Synthesized by various fungal species, these metabolites encompass compounds with therapeutic, agricultural, and commercial significance. We delved into strategies and advancements aimed at optimizing fungal metabolite production. Fungal cultivation, especially by Aspergillus, Penicillium, and Fusarium, plays a pivotal role in metabolite biosynthesis, and researchers have explored both submerged and solid-state cultivation processes to harness the full potential of fungal species. Nutrient optimization, pH, and temperature control are critical factors in ensuring high yields of the targeted bioactive metabolites especially for scaling up processes. Analytical methods that includes High-Performance Liquid Chromatography (HPLC), Liquid Chromatography-Mass Spectrometry (LC-MS), Gas Chromatography-Mass Spectrometry (GC-MS), Nuclear Magnetic Resonance (NMR), and Mass Spectrometry (MS), are indispensable for the identification and quantification of the compounds. Moreover, genetic engineering and metabolic pathway manipulation have emerged as powerful tools to enhance metabolite production and develop novel fungal strains with increased yields. Regulation and control mechanisms at the genetic, epigenetic, and metabolic levels are explored to fine-tune the biosynthesis of fungal metabolites. Ongoing research aims to overcome the complexity of the steps involved to ensure the efficient production and utilization of fungal metabolites.
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Affiliation(s)
| | - Adriana Sturion Lorenzi
- Department of Cellular Biology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
| | - Danilo Batista Pinho
- Department of Phytopathology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
| | | | - Helson Mario Martins do Vale
- Department of Phytopathology, Institute of Biological Sciences, University of Brasília (UnB), Brasília, DF, Brazil
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Shi X, Li X, He X, Zhang D, Quan C, Xiu Z, Dong Y. Chemical Epigenetic Regulation Secondary Metabolites Derived from Aspergillus sydowii DL1045 with Inhibitory Activities for Protein Tyrosine Phosphatases. Molecules 2024; 29:670. [PMID: 38338416 PMCID: PMC10856041 DOI: 10.3390/molecules29030670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 01/29/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Protein tyrosine phosphatases (PTPs) are ubiquitous in living organisms and are promising drug targets for cancer, diabetes/obesity, and autoimmune disorders. In this study, a histone deacetylase inhibitor called suberoylanilide hydroxamic acid (SAHA) was added to a culture of marine fungi (Aspergillus sydowii DL1045) to identify potential drug candidates related to PTP inhibition. Then, the profile of the induced metabolites was characterized using an integrated metabolomics strategy. In total, 46% of the total SMs were regulated secondary metabolites (SMs), among which 20 newly biosynthesized metabolites (10% of the total SMs) were identified only in chemical epigenetic regulation (CER) broth. One was identified as a novel compound, and fourteen compounds were identified from Aspergillus sydowii first. SAHA derivatives were also biotransformed by A. sydowii DL1045, and five of these derivatives were identified. Based on the bioassay, some of the newly synthesized metabolites exhibited inhibitory effects on PTPs. The novel compound sydowimide A (A11) inhibited Src homology region 2 domain-containing phosphatase-1 (SHP1), T-cell protein tyrosine phosphatase (TCPTP) and leukocyte common antigen (CD45), with IC50 values of 1.5, 2.4 and 18.83 μM, respectively. Diorcinol (A3) displayed the strongest inhibitory effect on SHP1, with an IC50 value of 0.96 μM. The structure-activity relationship analysis and docking studies of A3 analogs indicated that the substitution of the carboxyl group reduced the activity of A3. Research has demonstrated that CER positively impacts changes in the secondary metabolic patterns of A. sydowii DL1045. The compounds produced through this approach will provide valuable insights for the creation and advancement of novel drug candidates related to PTP inhibition.
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Affiliation(s)
- Xuan Shi
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China; (X.S.); (X.L.); (X.H.); (D.Z.); (Z.X.)
| | - Xia Li
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China; (X.S.); (X.L.); (X.H.); (D.Z.); (Z.X.)
| | - Xiaoshi He
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China; (X.S.); (X.L.); (X.H.); (D.Z.); (Z.X.)
| | - Danyang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China; (X.S.); (X.L.); (X.H.); (D.Z.); (Z.X.)
| | - Chunshan Quan
- College of Life Science, Dalian Minzu University, Dalian 116600, China;
| | - Zhilong Xiu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China; (X.S.); (X.L.); (X.H.); (D.Z.); (Z.X.)
| | - Yuesheng Dong
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China; (X.S.); (X.L.); (X.H.); (D.Z.); (Z.X.)
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Gurgel RS, de Melo Pereira DÍ, Garcia AVF, Fernandes de Souza AT, Mendes da Silva T, de Andrade CP, Lima da Silva W, Nunez CV, Fantin C, de Lima Procópio RE, Albuquerque PM. Antimicrobial and Antioxidant Activities of Endophytic Fungi Associated with Arrabidaea chica (Bignoniaceae). J Fungi (Basel) 2023; 9:864. [PMID: 37623634 PMCID: PMC10455555 DOI: 10.3390/jof9080864] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/04/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023] Open
Abstract
The endophytic fungal community of the Amazonian medicinal plant Arrabidaea chica (Bignoniaceae) was evaluated based on the hypothesis that microbial communities associated with plant species in the Amazon region may produce metabolites with interesting bioactive properties. Therefore, the antimicrobial and antioxidant activities of the fungal extracts were investigated. A total of 107 endophytic fungi were grown in liquid medium and the metabolites were extracted with ethyl acetate. In the screening of fungal extracts for antimicrobial activity, the fungus identified as Botryosphaeria mamane CF2-13 was the most promising, with activity against E. coli, S. epidermidis, P. mirabilis, B. subtilis, S. marcescens, K. pneumoniae, S. enterica, A. brasiliensis, C. albicans, C. tropicalis and, especially, against S. aureus and C. parapsilosis (MIC = 0.312 mg/mL). Screening for antioxidant potential using the DPPH elimination assay showed that the Colletotrichum sp. CG1-7 endophyte extract exhibited potential activity with an EC50 of 11 µg/mL, which is equivalent to quercetin (8 µg/mL). The FRAP method confirmed the antioxidant potential of the fungal extracts. The presence of phenolic compounds and flavonoids in the active extracts was confirmed using TLC. These results indicate that two of the fungi isolated from A. chica exhibit significant antimicrobial and antioxidant potential.
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Affiliation(s)
- Raiana Silveira Gurgel
- Programa Graduate Program in Biodiversity and Biotechnology of the Bionorte Network, School of Health Sciences, Amazonas State University, Manaus 69050-010, Brazil; (R.S.G.); (D.Í.d.M.P.); (C.P.d.A.)
- Research Group on Chemistry Applied to Technology, School of Technology, Amazonas State University, Manaus 69050-020, Brazil; (A.V.F.G.); (A.T.F.d.S.); (T.M.d.S.); (R.E.d.L.P.)
| | - Dorothy Ívila de Melo Pereira
- Programa Graduate Program in Biodiversity and Biotechnology of the Bionorte Network, School of Health Sciences, Amazonas State University, Manaus 69050-010, Brazil; (R.S.G.); (D.Í.d.M.P.); (C.P.d.A.)
- Research Group on Chemistry Applied to Technology, School of Technology, Amazonas State University, Manaus 69050-020, Brazil; (A.V.F.G.); (A.T.F.d.S.); (T.M.d.S.); (R.E.d.L.P.)
| | - Ana Vyktória França Garcia
- Research Group on Chemistry Applied to Technology, School of Technology, Amazonas State University, Manaus 69050-020, Brazil; (A.V.F.G.); (A.T.F.d.S.); (T.M.d.S.); (R.E.d.L.P.)
| | - Anne Terezinha Fernandes de Souza
- Research Group on Chemistry Applied to Technology, School of Technology, Amazonas State University, Manaus 69050-020, Brazil; (A.V.F.G.); (A.T.F.d.S.); (T.M.d.S.); (R.E.d.L.P.)
- Graduate Program in Biotechnology and Natural Resources of the Amazon, School of Health Sciences, Amazonas State University, Manaus 69050-010, Brazil; (C.V.N.); (C.F.)
| | - Thaysa Mendes da Silva
- Research Group on Chemistry Applied to Technology, School of Technology, Amazonas State University, Manaus 69050-020, Brazil; (A.V.F.G.); (A.T.F.d.S.); (T.M.d.S.); (R.E.d.L.P.)
| | - Cleudiane Pereira de Andrade
- Programa Graduate Program in Biodiversity and Biotechnology of the Bionorte Network, School of Health Sciences, Amazonas State University, Manaus 69050-010, Brazil; (R.S.G.); (D.Í.d.M.P.); (C.P.d.A.)
- Research Group on Chemistry Applied to Technology, School of Technology, Amazonas State University, Manaus 69050-020, Brazil; (A.V.F.G.); (A.T.F.d.S.); (T.M.d.S.); (R.E.d.L.P.)
| | - Weison Lima da Silva
- Bioprospection and Biotechnology Laboratory, National Institute of Amazonian Research, Manaus 69067-375, Brazil;
| | - Cecilia Veronica Nunez
- Graduate Program in Biotechnology and Natural Resources of the Amazon, School of Health Sciences, Amazonas State University, Manaus 69050-010, Brazil; (C.V.N.); (C.F.)
- Bioprospection and Biotechnology Laboratory, National Institute of Amazonian Research, Manaus 69067-375, Brazil;
| | - Cleiton Fantin
- Graduate Program in Biotechnology and Natural Resources of the Amazon, School of Health Sciences, Amazonas State University, Manaus 69050-010, Brazil; (C.V.N.); (C.F.)
- Multicentric Graduate Program in Biochemistry and Molecular Biology, School of Health Sciences, Amazonas State University, Manaus 69050-010, Brazil
| | - Rudi Emerson de Lima Procópio
- Research Group on Chemistry Applied to Technology, School of Technology, Amazonas State University, Manaus 69050-020, Brazil; (A.V.F.G.); (A.T.F.d.S.); (T.M.d.S.); (R.E.d.L.P.)
- Graduate Program in Biotechnology and Natural Resources of the Amazon, School of Health Sciences, Amazonas State University, Manaus 69050-010, Brazil; (C.V.N.); (C.F.)
| | - Patrícia Melchionna Albuquerque
- Programa Graduate Program in Biodiversity and Biotechnology of the Bionorte Network, School of Health Sciences, Amazonas State University, Manaus 69050-010, Brazil; (R.S.G.); (D.Í.d.M.P.); (C.P.d.A.)
- Research Group on Chemistry Applied to Technology, School of Technology, Amazonas State University, Manaus 69050-020, Brazil; (A.V.F.G.); (A.T.F.d.S.); (T.M.d.S.); (R.E.d.L.P.)
- Graduate Program in Biotechnology and Natural Resources of the Amazon, School of Health Sciences, Amazonas State University, Manaus 69050-010, Brazil; (C.V.N.); (C.F.)
- Multicentric Graduate Program in Biochemistry and Molecular Biology, School of Health Sciences, Amazonas State University, Manaus 69050-010, Brazil
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Makhwitine JP, Kumalo HM, Ndlovu SI, Mkhwanazi NP. Epigenetic Induction of Secondary Metabolites Production in Endophytic Fungi Penicillium chrysogenum and GC-MS Analysis of Crude Metabolites with Anti-HIV-1 Activity. Microorganisms 2023; 11:1404. [PMID: 37374906 DOI: 10.3390/microorganisms11061404] [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: 04/25/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
The continuous burden of human immunodeficiency virus-1 in Sub-Saharan Africa, coupled with the inability of antiretroviral agents to eradicate HIV-1 from viral reservoirs, the potential risks of drug resistance development, and the development of adverse effects, emphasizes the need to develop a new class of HIV-1 inhibitors. Here, we cultivated four endophytic fungal isolates from a medicinal plant, Albizia adianthifolia with the addition of small epigenetic modifiers, sodium butyrate, and valproic acid, to induce the expression of biosynthetic gene clusters encoding active secondary metabolites with probable anti-HIV activities. We identified a non-toxic crude extract of the endophytic fungus Penicillium chrysogenum treated with sodium butyrate to possess significantly greater anti-HIV activity than the untreated extracts. Penicillium chrysogenum P03MB2 showed anti-HIV activity with an IC50 of 0.6024 µg/mL compared to untreated fungal crude extract (IC50 5.053 µg/mL) when treated with sodium butyrate. The profile of secondary metabolite compounds from the bioactive, partially purified extracts were identified by gas chromatography-mass spectrometry (GC-MS), and more bioactive compounds were detected in treated P. chrysogenum P03MB2 fractions than in untreated fractions. Pyrrolo[1,2-a]pyrazine-1,4-dione, hexahydro (13.64%), cyclotrisiloxane, hexamethyl (8.18%), cyclotetrasiloxane, octamethyl (7.23%), cyclopentasiloxane, decamethyl (6.36%), quinoline, 1,2-dihydro-2,24-trimethyl (5.45%), propanenitrile (4.55%), deca-6,9-diene (4.55%), dibutyl phthalate (4.55%), and silane[1,1-dimethyl-2-propenyl)oxy]dimethyl (2.73%) were the most abundant compounds. These results indicate that treatment of endophytic fungi with small epigenetic modifiers enhances the secretion of secondary metabolites with stronger anti-HIV-1 properties, acknowledging the feasibility of epigenetic modification as an innovative approach for the discovery of cryptic fungal metabolites which can be developed into therapeutic compounds.
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Affiliation(s)
- John P Makhwitine
- Discipline of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Hezekiel M Kumalo
- Drug Research and Innovation Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban 4000, South Africa
| | - Sizwe I Ndlovu
- Department of Biotechnology and Food Technology, Faculty of Science, University of Johannesburg, Johannesburg 2028, South Africa
| | - Nompumelelo P Mkhwanazi
- HIV Pathogenesis Programme, Doris Duke Medical Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban 4000, South Africa
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Pacheco-Tapia R, Ortíz S, Jargeat P, Amasifuen C, Vansteelandt M, Haddad M. Exploration of the Production of Three Thiodiketopiperazines by an Endophytic Fungal Strain of Cophinforma mamane. Chem Biodivers 2023; 20:e202201087. [PMID: 36919620 DOI: 10.1002/cbdv.202201087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 03/10/2023] [Accepted: 03/12/2023] [Indexed: 03/16/2023]
Abstract
Endophytic fungi possess a versatile metabolism which is related to their ability to live in diverse ecological niches. While culturing under laboratory conditions, their metabolism is mainly influenced by the culture media, time of incubation and other physicochemical factors. In this study, we focused on the production of 3 thiodiketopiperazines (TDKPs) botryosulfuranols A-C produced by an endophytic strain of Cophinforma mamane isolated from the leaves of Bixa orellana L collected in the Peruvian Amazon. We studied the time-course production of botryosulfuranols A-C during 28 days and evaluated the variations in the production of secondary metabolites, including the TDKPs, produced by C. mamane in response to different culture media, light versus dark conditions and different incubation times. We observed a short time-frame production of botryosulfuranol C while its production was significantly affected by the light conditions and nutrients of the culture media. Botryosulfuranols A and B showed a similar production pattern and a similar response to culturing conditions. Molecular networking allowed us to detect three compounds related to TDKPs that will be the focus of future experiments.
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Affiliation(s)
- Romina Pacheco-Tapia
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, France
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Sergio Ortíz
- Therapeutic Innovation Laboratory UMR CNRS 7200, Faculty of Pharmacy, Université de Strasbourg, Strasbourg, France
| | - Patricia Jargeat
- Laboratoire Evolution et Diversité Biologique UMR 5174, Université de Toulouse, CNRS, IRD, France
| | - Carlos Amasifuen
- Instituto Nacional de Innovación Agraria, Dirección de Recursos Genéticos y Biotecnología, Avenida La Molina 1981, Lima, 15024, Perú
- Present address: Epigénomique Fonctionnelle et Physiologie Moléculaire Du Diabète et Maladies Associées UMR 1283/8199, Université de Lille, Lille, France
| | | | - Mohamed Haddad
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, France
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Xue M, Hou X, Fu J, Zhang J, Wang J, Zhao Z, Xu D, Lai D, Zhou L. Recent Advances in Search of Bioactive Secondary Metabolites from Fungi Triggered by Chemical Epigenetic Modifiers. J Fungi (Basel) 2023; 9:jof9020172. [PMID: 36836287 PMCID: PMC9961798 DOI: 10.3390/jof9020172] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/31/2023] Open
Abstract
Genomic analysis has demonstrated that many fungi possess essential gene clusters for the production of previously unobserved secondary metabolites; however, these genes are normally reduced or silenced under most conditions. These cryptic biosynthetic gene clusters have become treasures of new bioactive secondary metabolites. The induction of these biosynthetic gene clusters under stress or special conditions can improve the titers of known compounds or the production of novel compounds. Among the inducing strategies, chemical-epigenetic regulation is considered a powerful approach, and it uses small-molecule epigenetic modifiers, which mainly act as the inhibitors of DNA methyltransferase, histone deacetylase, and histone acetyltransferase, to promote changes in the structure of DNA, histones, and proteasomes and to further activate cryptic biosynthetic gene clusters for the production of a wide variety of bioactive secondary metabolites. These epigenetic modifiers mainly include 5-azacytidine, suberoylanilide hydroxamic acid, suberoyl bishydroxamic acid, sodium butyrate, and nicotinamide. This review gives an overview on the method of chemical epigenetic modifiers to trigger silent or low-expressed biosynthetic pathways to yield bioactive natural products through external cues of fungi, mainly based on the research progress in the period from 2007 to 2022. The production of about 540 fungal secondary metabolites was found to be induced or enhanced by chemical epigenetic modifiers. Some of them exhibited significant biological activities such as cytotoxic, antimicrobial, anti-inflammatory, and antioxidant activity.
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Triastuti A, Vansteelandt M, Barakat F, Amasifuen C, Jargeat P, Haddad M. Untargeted metabolomics to evaluate antifungal mechanism: a study of Cophinforma mamane and Candida albicans interaction. NATURAL PRODUCTS AND BIOPROSPECTING 2023; 13:1. [PMID: 36595109 PMCID: PMC9810774 DOI: 10.1007/s13659-022-00365-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Microbial interactions between filamentous fungi and yeast are still not fully understood. To evaluate a potential antifungal activity of a filamentous fungus while highlighting metabolomic changes, co-cultures between an endophytic strain of Cophinforma mamane (CM) and Candida albicans (CA) were performed. The liquid cultures were incubated under static conditions and metabolite alterations during the course were investigated by ultra-performance liquid chromatography-tandem mass spectrophotometry (UPLC-MS/MS). Results were analyzed using MS-DIAL, MS-FINDER, METLIN, Xcalibur, SciFinder, and MetaboAnalyst metabolomics platforms. The metabolites associated with catabolic processes, including the metabolism of branched-chain amino acids, carnitine, and phospholipids were upregulated both in the mono and co-cultures, indicating fungal adaptability to environmental stress. Several metabolites, including C20 sphinganine 1-phosphate, myo-inositol, farnesol, gamma-undecalactone, folinic acid, palmitoleic acid, and MG (12:/0:0/0:0) were not produced by CA during co-culture with CM, demonstrating the antifungal mechanism of CM. Our results highlight the crucial roles of metabolomics studies to provide essential information regarding the antifungal mechanism of C. mamane against C. albicans, especially when the lost/undetected metabolites are involved in fungal survival and pathogenicity.
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Affiliation(s)
- Asih Triastuti
- UMR 152 Pharma Dev, IRD, UPS, Université de Toulouse, 31400, Toulouse, France.
- Department of Pharmacy, Universitas Islam Indonesia, Yogyakarta, 55584, Indonesia.
| | | | - Fatima Barakat
- UMR 152 Pharma Dev, IRD, UPS, Université de Toulouse, 31400, Toulouse, France
| | - Carlos Amasifuen
- Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria, Avenida La Molina 1981, La Molina, Lima, 15024, Peru
| | - Patricia Jargeat
- Laboratoire Evolution et Diversité Biologique UMR 5174, CNRS, IRD, UPS, Université de Toulouse, 31062, Toulouse, France
| | - Mohamed Haddad
- UMR 152 Pharma Dev, IRD, UPS, Université de Toulouse, 31400, Toulouse, France.
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Complementary Strategies to Unlock Biosynthesis Gene Clusters Encoding Secondary Metabolites in the Filamentous Fungus Podospora anserina. J Fungi (Basel) 2022; 9:jof9010009. [PMID: 36675830 PMCID: PMC9864250 DOI: 10.3390/jof9010009] [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: 11/08/2022] [Revised: 12/09/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The coprophilous ascomycete Podospora anserina is known to have a high potential to synthesize a wide array of secondary metabolites (SMs). However, to date, the characterization of SMs in this species, as in other filamentous fungal species, is far less than expected by the functional prediction through genome mining, likely due to the inactivity of most SMs biosynthesis gene clusters (BGCs) under standard conditions. In this work, our main objective was to compare the global strategies usually used to deregulate SM gene clusters in P. anserina, including the variation of culture conditions and the modification of the chromatin state either by genetic manipulation or by chemical treatment, and to show the complementarity of the approaches between them. In this way, we showed that the metabolomics-driven comparative analysis unveils the unexpected diversity of metabolic changes in P. anserina and that the integrated strategies have a mutual complementary effect on the expression of the fungal metabolome. Then, our results demonstrate that metabolite production is significantly influenced by varied cultivation states and epigenetic modifications. We believe that the strategy described in this study will facilitate the discovery of fungal metabolites of interest and will improve the ability to prioritize the production of specific fungal SMs with an optimized treatment.
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Munusamy M, Ching KC, Yang LK, Crasta S, Gakuubi MM, Chee ZY, Wibowo M, Leong CY, Kanagasundaram Y, Ng SB. Chemical elicitation as an avenue for discovery of bioactive compounds from fungal endophytes. Front Chem 2022; 10:1024854. [PMID: 36505735 PMCID: PMC9727085 DOI: 10.3389/fchem.2022.1024854] [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: 08/22/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022] Open
Abstract
The present study investigated the molecular phylogeny, antimicrobial and cytotoxic activities of fungal endophytes obtained from the A*STAR Natural Organism Library (NOL) and previously isolated from Sungei Buloh Wetland Reserve, Singapore. Phylogenetic analysis based on ITS2 gene suggests that these isolates belong to 46 morphotypes and are affiliated to 23 different taxa in 17 genera of the Ascomycota phylum. Colletotrichum was the most dominant fungal genus accounting for 37% of all the isolates, followed by Diaporthe (13%), Phyllosticta (10.9%) and Diplodia (8.7%). Chemical elicitation using 5-azacytidine, a DNA methyltransferase inhibitor and suberoylanilide hydroxamic acid, a histone deacetylase inhibitor resulted in an increase in the number of active strains. Bioassay-guided isolation and structural elucidation yielded pestahivin and two new analogues from Bartalinia sp. F9447. Pestahivin and its related analogues did not exhibit antibacterial activity against Staphylococcus aureus but displayed strong antifungal activities against Candida albicans and Aspergillus brasiliensis, with IC50 values ranging from 0.46 ± 0.06 to 144 ± 18 µM. Pestahivin and its two analogues furthermore exhibited cytotoxic activity against A549 and MIA PACA-2 cancer cell lines with IC50 values in the range of 0.65 ± 0.12 to 42 ± 5.2 µM. The finding from this study reinforces that chemical epigenetic induction is a promising approach for the discovery of bioactive fungal secondary metabolites encoded by cryptic gene clusters.
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Affiliation(s)
- Madhaiyan Munusamy
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Kuan Chieh Ching
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lay Kien Yang
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Sharon Crasta
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Martin Muthee Gakuubi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Zhao Yan Chee
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mario Wibowo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Chung Yan Leong
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore,*Correspondence: Siew Bee Ng,
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Schüller A, Studt-Reinhold L, Strauss J. How to Completely Squeeze a Fungus-Advanced Genome Mining Tools for Novel Bioactive Substances. Pharmaceutics 2022; 14:1837. [PMID: 36145585 PMCID: PMC9505985 DOI: 10.3390/pharmaceutics14091837] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
Fungal species have the capability of producing an overwhelming diversity of bioactive substances that can have beneficial but also detrimental effects on human health. These so-called secondary metabolites naturally serve as antimicrobial "weapon systems", signaling molecules or developmental effectors for fungi and hence are produced only under very specific environmental conditions or stages in their life cycle. However, as these complex conditions are difficult or even impossible to mimic in laboratory settings, only a small fraction of the true chemical diversity of fungi is known so far. This also implies that a large space for potentially new pharmaceuticals remains unexplored. We here present an overview on current developments in advanced methods that can be used to explore this chemical space. We focus on genetic and genomic methods, how to detect genes that harbor the blueprints for the production of these compounds (i.e., biosynthetic gene clusters, BGCs), and ways to activate these silent chromosomal regions. We provide an in-depth view of the chromatin-level regulation of BGCs and of the potential to use the CRISPR/Cas technology as an activation tool.
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Affiliation(s)
| | | | - Joseph Strauss
- Institute of Microbial Genetics, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences Vienna, A-3430 Tulln/Donau, Austria
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Sequeira P, Rothkegel M, Domingos P, Martins I, Leclercq CC, Renaut J, Goldman GH, Silva Pereira C. Untargeted Metabolomics Sheds Light on the Secondary Metabolism of Fungi Triggered by Choline-Based Ionic Liquids. Front Microbiol 2022; 13:946286. [PMID: 35958129 PMCID: PMC9361774 DOI: 10.3389/fmicb.2022.946286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Fungal secondary metabolites constitute a rich source of yet undiscovered bioactive compounds. Their production is often silent under standard laboratory conditions, but the production of some compounds can be triggered simply by altering the cultivation conditions. The usage of an organic salt – ionic liquid – as growth medium supplement can greatly impact the biosynthesis of secondary metabolites, leading to higher diversity of compounds accumulating extracellularly. This study examines if such supplements, specifically cholinium-based ionic liquids, can support the discovery of bioactive secondary metabolites across three model species: Neurospora crassa, Aspergillus nidulans, and Aspergillus fumigatus. Enriched organic extracts obtained from medium supernatant revealed high diversity in metabolites. The supplementation led apparently to increased levels of either 1-aminocyclopropane-1-carboxylate or α-aminoisobutyric acid. The extracts where bioactive against two major foodborne bacterial strains: Staphylococcus aureus and Escherichia coli. In particular, those retrieved from N. crassa cultures showed greater bactericidal potential compared to control extracts derived from non-supplemented cultures. An untargeted mass spectrometry analysis using the Global Natural Product Social Molecular Networking tool enabled to capture the chemical diversity driven by the ionic liquid stimuli. Diverse macrolides, among other compounds, were putatively associated with A. fumigatus; whereas an unexpected richness of cyclic (depsi)peptides with N. crassa. Further studies are required to understand if the identified peptides are the major players of the bioactivity of N. crassa extracts, and to decode their biosynthesis pathways as well.
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Affiliation(s)
- Patrícia Sequeira
- Applied and Environmental Mycology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
| | - Maika Rothkegel
- Applied and Environmental Mycology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
| | - Patrícia Domingos
- Applied and Environmental Mycology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
| | - Isabel Martins
- Applied and Environmental Mycology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
| | - Céline C. Leclercq
- Integrative Biology Platform, Environmental Research and Technology Platform, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Jenny Renaut
- Integrative Biology Platform, Environmental Research and Technology Platform, Luxembourg Institute of Science and Technology, Belvaux, Luxembourg
| | - Gustavo H. Goldman
- Applied and Environmental Mycology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Cristina Silva Pereira
- Applied and Environmental Mycology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, Portugal
- *Correspondence: Cristina Silva Pereira,
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Gakuubi MM, Ching KC, Munusamy M, Wibowo M, Liang ZX, Kanagasundaram Y, Ng SB. Enhancing the Discovery of Bioactive Secondary Metabolites From Fungal Endophytes Using Chemical Elicitation and Variation of Fermentation Media. Front Microbiol 2022; 13:898976. [PMID: 35733953 PMCID: PMC9207341 DOI: 10.3389/fmicb.2022.898976] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/05/2022] [Indexed: 11/26/2022] Open
Abstract
Endophytic microorganisms are an important source of bioactive secondary metabolites. In this study, fungal endophytes obtained from A*STAR’s Natural Product Library (NPL) and previously isolated from different habitats of Singapore were investigated for their diversity, antimicrobial, and cytotoxic activities. A total of 222 fungal strains were identified on the basis of sequence analysis of ITS region of the rDNA gene. The identified fungal strains belong to 59 genera distributed in 20 orders. Majority of the identified strains (99%; 219 strains) belong to the phylum Ascomycota, while two strains belonged to the phylum Basidiomycota, and only one strain was from Mucoromycota phylum. The most dominant genus was Colletotrichum accounting for 27% of all the identified strains. Chemical elicitation using 5-azacytidine and suberoylanilide hydroxamic acid (SAHA) and variation of fermentation media resulted in the discovery of more bioactive strains. Bioassay-guided isolation and structure elucidation of active constituents from three prioritized fungal strains: Lophiotrema sp. F6932, Muyocopron laterale F5912, and Colletotrichum tropicicola F10154, led to the isolation of a known compound; palmarumycin C8 and five novel compounds; palmarumycin CP30, muyocopronol A-C and tropicicolide. Tropicicolide displayed the strongest antifungal activity against Aspergillus fumigatus with an IC50 value of 1.8 μg/ml but with a weaker activity against the Candida albicans presenting an IC50 of 7.1 μg/ml. Palmarumycin C8 revealed the best antiproliferative activity with IC50 values of 1.1 and 2.1 μg/ml against MIA PaCa-2 and PANC-1 cells, respectively.
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Affiliation(s)
- Martin Muthee Gakuubi
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Kuan Chieh Ching
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Madhaiyan Munusamy
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Mario Wibowo
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Yoganathan Kanagasundaram
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Siew Bee Ng
- Singapore Institute of Food and Biotechnology Innovation (SIFBI), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- *Correspondence: Siew Bee Ng,
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Pacheco-Tapia R, Vásquez-Ocmín P, Duthen S, Ortiz S, Jargeat P, Amasifuen C, Haddad M, Vansteelandt M. Chemical modulation of the metabolism of an endophytic fungal strain of Cophinforma mamane using epigenetic modifiers and amino-acids. Fungal Biol 2022; 126:385-394. [DOI: 10.1016/j.funbio.2022.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 02/03/2022] [Accepted: 02/25/2022] [Indexed: 11/26/2022]
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16
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Sun Y, Liu WC, Shi X, Zheng HZ, Zheng ZH, Lu XH, Xing Y, Ji K, Liu M, Dong YS. Inducing secondary metabolite production of Aspergillus sydowii through microbial co-culture with Bacillus subtilis. Microb Cell Fact 2021; 20:42. [PMID: 33579268 PMCID: PMC7881642 DOI: 10.1186/s12934-021-01527-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 01/22/2021] [Indexed: 01/25/2023] Open
Abstract
Background The co-culture strategy which mimics natural ecology by constructing an artificial microbial community is a useful tool to activate the biosynthetic gene clusters to generate new metabolites. However, the conventional method to study the co-culture is to isolate and purify compounds separated by HPLC, which is inefficient and time-consuming. Furthermore, the overall changes in the metabolite profile cannot be well characterized. Results A new approach which integrates computational programs, MS-DIAL, MS-FINDER and web-based tools including GNPS and MetaboAnalyst, was developed to analyze and identify the metabolites of the co-culture of Aspergillus sydowii and Bacillus subtilis. A total of 25 newly biosynthesized metabolites were detected only in co-culture. The structures of the newly synthesized metabolites were elucidated, four of which were identified as novel compounds by the new approach. The accuracy of the new approach was confirmed by purification and NMR data analysis of 7 newly biosynthesized metabolites. The bioassay of newly synthesized metabolites showed that four of the compounds exhibited different degrees of PTP1b inhibitory activity, and compound N2 had the strongest inhibition activity with an IC50 value of 7.967 μM. Conclusions Co-culture led to global changes of the metabolite profile and is an effective way to induce the biosynthesis of novel natural products. The new approach in this study is one of the effective and relatively accurate methods to characterize the changes of metabolite profiles and to identify novel compounds in co-culture systems.
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Affiliation(s)
- Yu Sun
- School of Bioengineering, Dalian University of Technology, DalianLiaoning, 116024, China
| | - Wen-Cai Liu
- Shandong New Time Pharmaceutical Co., Ltd, Shandong, 255000, China
| | - Xuan Shi
- School of Bioengineering, Dalian University of Technology, DalianLiaoning, 116024, China
| | - Hai-Zhou Zheng
- New Drug Research and Development Center, North China Pharmaceutical Group Corporation and National Microbial Medicine Engineering and Research Center, Shijiazhuang, 050015, Hebei, China
| | - Zhi-Hui Zheng
- New Drug Research and Development Center, North China Pharmaceutical Group Corporation and National Microbial Medicine Engineering and Research Center, Shijiazhuang, 050015, Hebei, China
| | - Xin-Hua Lu
- New Drug Research and Development Center, North China Pharmaceutical Group Corporation and National Microbial Medicine Engineering and Research Center, Shijiazhuang, 050015, Hebei, China
| | - Yan Xing
- School of Bioengineering, Dalian University of Technology, DalianLiaoning, 116024, China
| | - Kai Ji
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Mei Liu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Yue-Sheng Dong
- School of Bioengineering, Dalian University of Technology, DalianLiaoning, 116024, China.
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17
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Triastuti A, Haddad M, Barakat F, Mejia K, Rabouille G, Fabre N, Amasifuen C, Jargeat P, Vansteelandt M. Dynamics of Chemical Diversity during Co-Cultures: An Integrative Time-Scale Metabolomics Study of Fungal Endophytes Cophinforma mamane and Fusarium solani. Chem Biodivers 2021; 18:e2000672. [PMID: 33289281 DOI: 10.1002/cbdv.202000672] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/07/2020] [Indexed: 11/07/2022]
Abstract
A rapid and efficient metabolomic study of Cophinforma mamane and Fusarium solani co-cultivation in time-series based analysis was developed to study metabolome variations during their fungal interactions. The fungal metabolomes were studied through the integration of four metabolomic tools: MS-DIAL, a chromatographic deconvolution of liquid-chromatography-mass spectrometry (LC/MS); MS-FINDER, a structure-elucidation program with a wide range metabolome database; GNPS, an effective method to organize MS/MS fragmentation spectra, and MetaboAnalyst, a comprehensive web application for metabolomic data analysis and interpretation. Co-cultures of C. mamane and F. solani induced different patterns of metabolite production over 10 days of incubation and induced production of five de novo compounds not occurring in monocultures. These results emphasize that co-culture in time-frame analysis is an interesting method to unravel hidden metabolome in the investigation of fungal chemodiversity.
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Affiliation(s)
- Asih Triastuti
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, 31400, Toulouse, France.,Department of Pharmacy, Universitas Islam Indonesia, Yogyakarta, 55584, Indonesia
| | - Mohamed Haddad
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, 31400, Toulouse, France
| | - Fatima Barakat
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, 31400, Toulouse, France
| | - Kember Mejia
- Instituto de Investigaciones de la Amazonía Peruana, Avenida Abelardo Quiñonez Km. 4.5, Iquitos, 1600, Peru
| | - Gabriel Rabouille
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, 31400, Toulouse, France
| | - Nicolas Fabre
- UMR 152 Pharma Dev, Université de Toulouse, IRD, UPS, 31400, Toulouse, France
| | - Carlos Amasifuen
- Facultad de Ingeniería Civil y Ambiental [FICIAM], Escuela de Ingeniería Ambiental, Universidad Nacional Toribio Rodríguez de Mendoza [UNTRM, Chachapoyas, 01001, Peru
| | - Patricia Jargeat
- Laboratoire Evolution et Diversité Biologique UMR 5174, Université de Toulouse, CNRS, IRD, UPS, 31062, Toulouse, France
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Chen XL, Sun MC, Chong SL, Si JP, Wu LS. Transcriptomic and Metabolomic Approaches Deepen Our Knowledge of Plant-Endophyte Interactions. FRONTIERS IN PLANT SCIENCE 2021; 12:700200. [PMID: 35154169 PMCID: PMC8828500 DOI: 10.3389/fpls.2021.700200] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 12/22/2021] [Indexed: 05/10/2023]
Abstract
In natural systems, plant-symbiont-pathogen interactions play important roles in mitigating abiotic and biotic stresses in plants. Symbionts have their own special recognition ways, but they may share some similar characteristics with pathogens based on studies of model microbes and plants. Multi-omics technologies could be applied to study plant-microbe interactions, especially plant-endophyte interactions. Endophytes are naturally occurring microbes that inhabit plants, but do not cause apparent symptoms in them, and arise as an advantageous source of novel metabolites, agriculturally important promoters, and stress resisters in their host plants. Although biochemical, physiological, and molecular investigations have demonstrated that endophytes confer benefits to their hosts, especially in terms of promoting plant growth, increasing metabolic capabilities, and enhancing stress resistance, plant-endophyte interactions consist of complex mechanisms between the two symbionts. Further knowledge of these mechanisms may be gained by adopting a multi-omics approach. The involved interaction, which can range from colonization to protection against adverse conditions, has been investigated by transcriptomics and metabolomics. This review aims to provide effective means and ways of applying multi-omics studies to solve the current problems in the characterization of plant-microbe interactions, involving recognition and colonization. The obtained results should be useful for identifying the key determinants in such interactions and would also provide a timely theoretical and material basis for the study of interaction mechanisms and their applications.
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de Amorim MR, Wijeratne EMK, Zhou S, Arnold AE, Batista ANL, Batista JM, Dos Santos LC, Gunatilaka AAL. An epigenetic modifier induces production of 3-(4-oxopyrano)-chromen-2-ones in Aspergillus sp. AST0006, an endophytic fungus of Astragalus lentiginosus. Tetrahedron 2020; 76:131525. [PMID: 33716326 PMCID: PMC7945046 DOI: 10.1016/j.tet.2020.131525] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Incorporation of the epigenetic modifier suberoylanilide hydroxamic acid (SAHA) into a potato dextrose broth culture of the endophytic fungus Aspergillus sp. AST0006 affected its polyketide biosynthetic pathway providing two new 3-(4-oxopyrano)-chromen-2-ones, aspyranochromenones A (1) and B (2), and the isocoumarin, (-)-6,7-dihydroxymellein (3). Eight additional metabolites (4-11) and two biotransformation products of SAHA (12-13) were also encountered. The planar structures and relative configurations of the new metabolites 1-2 were elucidated with the help of high-resolution mass, 1D and 2D NMR spectroscopic data and the absolute configurations of 1-3 were determined by comparison of experimental and calculated ECD data. Possible biosynthetic pathways to 1 and 2 are presented.
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Affiliation(s)
- Marcelo R de Amorim
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
- Institute of Chemistry, São Paulo State University, Araraquara, São Paulo 14800-900, Brazil
| | - E M Kithsiri Wijeratne
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
| | - Shengliang Zhou
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
- The Key Laboratory of Biotechnology for Medicinal Plants of Jiangsu Province, Jiangsu Normal University, 101 Shanghai Rd, Xuzhou 221116, P. R. China
| | - A Elizabeth Arnold
- School of Plant Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson, Arizona 85721, United States
| | - Andrea N L Batista
- Department of Organic Chemistry, Chemistry Institute, Fluminense Federal University, Niterói, RJ 24020-141, Brazil
| | - João M Batista
- Institute of Science and Technology, Federal University of São Paulo, São José dos Campos, São Paulo 12231-280, Brazil
| | - Lourdes C Dos Santos
- Institute of Chemistry, São Paulo State University, Araraquara, São Paulo 14800-900, Brazil
| | - A A Leslie Gunatilaka
- Southwest Center for Natural Products Research, School of Natural Resources and the Environment, College of Agriculture and Life Sciences, University of Arizona, 250 E. Valencia Road, Tucson, Arizona 85706, United States
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An anticonvulsive drug, valproic acid (valproate), has effects on the biosynthesis of fatty acids and polyketides in microorganisms. Sci Rep 2020; 10:9300. [PMID: 32518288 PMCID: PMC7283484 DOI: 10.1038/s41598-020-66251-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/18/2020] [Indexed: 12/20/2022] Open
Abstract
Valproic acid or valproate (VPA) is an anticonvulsive drug used for treatments of epilepsy, bipolar disorder, and migraine headaches. VPA is also an epigenetic modulator, inhibiting histone deacetylase, and it has been subjected to clinical study for cancer treatment. During the investigation of VPA on a metabolite profile in a fungus, we found that VPA has significant effects on the production of some fatty acids. Further exploration of VPA on fatty acid profiles of microorganisms, fungi, yeast, and bacteria, as well as representative gut microbiome, revealed that VPA could enhance or reduce the production of some fatty acids. VPA was found to induce the production of trans-9-elaidic acid, a fatty acid that was previously reported to have cellular effects in human macrophages. VPA could also inhibit the production of some polyketides produced by a model fungus. The present work suggests that the induction or inhibition of fatty acid biosynthesis by VPA (100 µM) in gut microbiome could give effects to patients treated with VPA because high doses of VPA oral administration (up to 600 mg to 900 mg) are used by patients; the concentration of VPA in the human gut may reach a concentration of 100 µM, which may give effects to gut microorganisms.
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21
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Collemare J, Seidl MF. Chromatin-dependent regulation of secondary metabolite biosynthesis in fungi: is the picture complete? FEMS Microbiol Rev 2019; 43:591-607. [PMID: 31301226 PMCID: PMC8038932 DOI: 10.1093/femsre/fuz018] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 06/18/2019] [Indexed: 01/07/2023] Open
Abstract
Fungal secondary metabolites are small molecules that exhibit diverse biological activities exploited in medicine, industry and agriculture. Their biosynthesis is governed by co-expressed genes that often co-localize in gene clusters. Most of these secondary metabolite gene clusters are inactive under laboratory conditions, which is due to a tight transcriptional regulation. Modifications of chromatin, the complex of DNA and histone proteins influencing DNA accessibility, play an important role in this regulation. However, tinkering with well-characterised chemical and genetic modifications that affect chromatin alters the expression of only few biosynthetic gene clusters, and thus the regulation of the vast majority of biosynthetic pathways remains enigmatic. In the past, attempts to activate silent gene clusters in fungi mainly focused on histone acetylation and methylation, while in other eukaryotes many other post-translational modifications are involved in transcription regulation. Thus, how chromatin regulates the expression of gene clusters remains a largely unexplored research field. In this review, we argue that focusing on only few well-characterised chromatin modifications is significantly hampering our understanding of the chromatin-based regulation of biosynthetic gene clusters. Research on underexplored chromatin modifications and on the interplay between different modifications is timely to fully explore the largely untapped reservoir of fungal secondary metabolites.
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Affiliation(s)
| | - Michael F Seidl
- Corresponding author: Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands. E-mail: ; Present address: Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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