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Lv HW, Tang JG, Wei B, Zhu MD, Zhang HW, Zhou ZB, Fan BY, Wang H, Li XN. Bioinformatics assisted construction of the link between biosynthetic gene clusters and secondary metabolites in fungi. Biotechnol Adv 2025; 81:108547. [PMID: 40024584 DOI: 10.1016/j.biotechadv.2025.108547] [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: 10/20/2024] [Revised: 02/24/2025] [Accepted: 02/24/2025] [Indexed: 03/04/2025]
Abstract
Fungal secondary metabolites are considered as important resources for drug discovery. Despite various methods being employed to facilitate the discovery of new fungal secondary metabolites, the trend of identifying novel secondary metabolites from fungi is inevitably slowing down. Under laboratory conditions, the majority of biosynthetic gene clusters, which store information for secondary metabolites, remain inactive. Therefore, establishing the link between biosynthetic gene clusters and secondary metabolites would contribute to understanding the genetic logic underlying secondary metabolite biosynthesis and alleviating the current challenges in discovering novel natural products. Bioinformatics methods have garnered significant attention due to their powerful capabilities in data mining and analysis, playing a crucial role in various aspects. Thus, we have summarized successful cases since 2016 in which bioinformatics methods were utilized to establish the link between fungal biosynthetic gene clusters and secondary metabolites, focusing on their biosynthetic gene clusters and associated secondary metabolites, with the goal of aiding the field of natural product discovery.
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Affiliation(s)
- Hua-Wei Lv
- College of Pharmaceutical Science & Zhejiang Provincial Key Laboratory of TCM for Innovative R&D and Digital Intelligent Manufacturing of TCM Great Health Products & Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hang Zhou, PR China; School of Pharmacy, Youjiang Medical University for Nationalities, Baise, PR China
| | - Jia-Gui Tang
- College of Pharmaceutical Science & Zhejiang Provincial Key Laboratory of TCM for Innovative R&D and Digital Intelligent Manufacturing of TCM Great Health Products & Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hang Zhou, PR China
| | - Bin Wei
- College of Pharmaceutical Science & Zhejiang Provincial Key Laboratory of TCM for Innovative R&D and Digital Intelligent Manufacturing of TCM Great Health Products & Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hang Zhou, PR China
| | - Meng-Di Zhu
- Research Center of Analysis and Measurement, Zhejiang University of Technology, Hang Zhou, PR China
| | - Hua-Wei Zhang
- College of Pharmaceutical Science & Zhejiang Provincial Key Laboratory of TCM for Innovative R&D and Digital Intelligent Manufacturing of TCM Great Health Products & Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hang Zhou, PR China
| | - Zhong-Bo Zhou
- School of Pharmacy, Youjiang Medical University for Nationalities, Baise, PR China
| | - Bo-Yi Fan
- School of Pharmacy, Nantong University, Nantong, PR China
| | - Hong Wang
- College of Pharmaceutical Science & Zhejiang Provincial Key Laboratory of TCM for Innovative R&D and Digital Intelligent Manufacturing of TCM Great Health Products & Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hang Zhou, PR China
| | - Xing-Nuo Li
- College of Pharmaceutical Science & Zhejiang Provincial Key Laboratory of TCM for Innovative R&D and Digital Intelligent Manufacturing of TCM Great Health Products & Key Laboratory of Marine Fishery Resources Exploitment & Utilization of Zhejiang Province, Zhejiang University of Technology, Hang Zhou, PR China.
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Chiou SL, Chang CY, Chu J. "Cofactors" for Natural Products. ChemMedChem 2025; 20:e202400498. [PMID: 39822069 DOI: 10.1002/cmdc.202400498] [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: 07/01/2024] [Revised: 12/10/2024] [Accepted: 01/14/2025] [Indexed: 01/19/2025]
Abstract
Cofactors are non-protein entities necessary for proteins to operate. They provide "functional groups" beyond those of the 20 canonical amino acids and enable proteins to carry out more diverse functions. Such a viewpoint is rarely mentioned, if at all, when it comes to natural products and is the theme of this Concept. Even though the mechanisms of action (MOA) of only a few natural products are known to require cofactors, we believe that cofactor mediated MOA in natural products are far more prevalent than what we currently know. Bleomycin is a case in point. It binds iron cation to form a pseudoenzyme that generates reactive oxygen species. As another example, calcium cations induce laspartomycin to "fold" into the active conformation. Iron and calcium are bona fide cofactors for bleomycin and laspartomycin, respectively, as these natural products do not display their characteristic anticancer and antibacterial activities without Fe(II) and Ca(II). These types of cofactor mediated MOA in natural products were discovered mostly serendipitously, and being conscious of such a possibility is the first step toward identifying more novel chemistry that nature performs.
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Affiliation(s)
- Shao-Lun Chiou
- Department of Chemistry, National Taiwan University, 106319, Taipei City, Taiwan
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, 300193, Hsinchu City, Taiwan
| | - John Chu
- Department of Chemistry, National Taiwan University, 106319, Taipei City, Taiwan
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Pasinato A, Singh G. Lichens are a treasure chest of bioactive compounds: fact or fake? THE NEW PHYTOLOGIST 2025; 246:389-395. [PMID: 40013383 PMCID: PMC11923404 DOI: 10.1111/nph.70034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2024] [Accepted: 02/05/2025] [Indexed: 02/28/2025]
Affiliation(s)
- Anna Pasinato
- Department of Biology, University of Padova, Via U. Bassi, 58/B, 35121, Padova, Italy
- National Biodiversity Future Center (NBFC), Piazza Marina, 61, 90133, Palermo, Italy
| | - Garima Singh
- Department of Biology, University of Padova, Via U. Bassi, 58/B, 35121, Padova, Italy
- National Biodiversity Future Center (NBFC), Piazza Marina, 61, 90133, Palermo, Italy
- Botanical Garden, University of Padova, Via Orto Botanico, 15, 35123, Padova, Italy
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Iobbi V, Parisi V, Giacomini M, De Riccardis F, Brun P, Núñez-Pons L, Drava G, Giordani P, Monti MC, Poggi R, Murgia Y, De Tommasi N, Bisio A. Sesterterpenoids: sources, structural diversity, biological activity, and data management. Nat Prod Rep 2025; 42:443-481. [PMID: 39832137 DOI: 10.1039/d4np00041b] [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: 01/22/2025]
Abstract
Reviewing the literature published up to October 2024.Sesterterpenoids are one of the most chemically diverse and biologically promising subgroup of terpenoids, the largest family of secondary metabolites. The present review article summarizes more than seven decades of studies on isolation and characterization of more than 1600 structurally novel sesterterpenoids, supplemented by biological, pharmacological, ecological, and geographic distribution data. All the information have been implemented in eight tables available on the web and a relational database https://sesterterpenoids.unige.net/. The interface has two sections, one open to the public for reading only and the other, protected by an authentication mechanism, for timely updating of published results.
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Affiliation(s)
- Valeria Iobbi
- Department of Pharmacy, University of Genova, Viale Cembrano 4, 16148 Genova, Italy.
| | - Valentina Parisi
- Department of Pharmacy, Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy.
- NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
| | - Mauro Giacomini
- Department of Informatics, Bioengineering, Robotics and System Science, University of Genova, Via all'Opera Pia 13, 16146 Genova, Italy
| | - Francesco De Riccardis
- Department of Chemistry and Biology "A. Zambelli", Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy
| | - Paola Brun
- Department of Molecular Medicine, Section of Microbiology, University of Padova, Via A. Gabelli, 63, 35121 Padova, Italy
| | - Laura Núñez-Pons
- Department of Integrative Marine Ecology (EMI), Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Napoli, Italy
- NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
| | - Giuliana Drava
- Department of Pharmacy, University of Genova, Viale Cembrano 4, 16148 Genova, Italy.
| | - Paolo Giordani
- Department of Pharmacy, University of Genova, Viale Cembrano 4, 16148 Genova, Italy.
| | - Maria Chiara Monti
- Department of Pharmacy, University of Napoli "Federico II", Via T. De Amicis 95, 80131 Napoli, Italy
| | - Roberto Poggi
- Museo Civico di Storia Naturale Giacomo Doria, Via Brigata Liguria 9, 16121 Genova, Italy
| | - Ylenia Murgia
- Department of Informatics, Bioengineering, Robotics and System Science, University of Genova, Via all'Opera Pia 13, 16146 Genova, Italy
| | - Nunziatina De Tommasi
- Department of Pharmacy, Via Giovanni Paolo II, 132, 84084 Fisciano, Salerno, Italy.
- NBFC, National Biodiversity Future Center, 90133 Palermo, Italy
| | - Angela Bisio
- Department of Pharmacy, University of Genova, Viale Cembrano 4, 16148 Genova, Italy.
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Ragozzino C, Casella V, Coppola A, Scarpato S, Buonocore C, Consiglio A, Palma Esposito F, Galasso C, Tedesco P, Della Sala G, de Pascale D, Vitale L, Coppola D. Last Decade Insights in Exploiting Marine Microorganisms as Sources of New Bioactive Natural Products. Mar Drugs 2025; 23:116. [PMID: 40137302 PMCID: PMC11943599 DOI: 10.3390/md23030116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2025] [Revised: 02/28/2025] [Accepted: 03/03/2025] [Indexed: 03/27/2025] Open
Abstract
Marine microorganisms have emerged as prolific sources of bioactive natural products, offering a large chemical diversity and a broad spectrum of biological activities. Over the past decade, significant progress has been made in discovering and characterizing these compounds, pushed by technological innovations in genomics, metabolomics, and bioinformatics. Furthermore, innovative isolation and cultivation approaches have improved the isolation of rare and difficult-to-culture marine microbes, leading to the identification of novel secondary metabolites. Advances in synthetic biology and metabolic engineering have further optimized natural product yields and the generation of novel compounds with improved bioactive properties. This review highlights key developments in the exploitation of marine bacteria, fungi, and microalgae for the discovery of novel natural products with potential applications in diverse fields, underscoring the immense potential of marine microorganisms in the growing Blue Economy sector.
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Affiliation(s)
- Costanza Ragozzino
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio, Ferdinando Acton 55, 80133 Naples, Italy; (C.R.); (V.C.); (A.C.); (S.S.); (C.B.); (A.C.); (F.P.E.); (P.T.); (G.D.S.); (D.d.P.)
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres, 31, 98166 Messina, Italy
| | - Vincenza Casella
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio, Ferdinando Acton 55, 80133 Naples, Italy; (C.R.); (V.C.); (A.C.); (S.S.); (C.B.); (A.C.); (F.P.E.); (P.T.); (G.D.S.); (D.d.P.)
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres, 31, 98166 Messina, Italy
| | - Alessandro Coppola
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio, Ferdinando Acton 55, 80133 Naples, Italy; (C.R.); (V.C.); (A.C.); (S.S.); (C.B.); (A.C.); (F.P.E.); (P.T.); (G.D.S.); (D.d.P.)
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d’Alcontres, 31, 98166 Messina, Italy
| | - Silvia Scarpato
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio, Ferdinando Acton 55, 80133 Naples, Italy; (C.R.); (V.C.); (A.C.); (S.S.); (C.B.); (A.C.); (F.P.E.); (P.T.); (G.D.S.); (D.d.P.)
| | - Carmine Buonocore
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio, Ferdinando Acton 55, 80133 Naples, Italy; (C.R.); (V.C.); (A.C.); (S.S.); (C.B.); (A.C.); (F.P.E.); (P.T.); (G.D.S.); (D.d.P.)
| | - Antonella Consiglio
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio, Ferdinando Acton 55, 80133 Naples, Italy; (C.R.); (V.C.); (A.C.); (S.S.); (C.B.); (A.C.); (F.P.E.); (P.T.); (G.D.S.); (D.d.P.)
| | - Fortunato Palma Esposito
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio, Ferdinando Acton 55, 80133 Naples, Italy; (C.R.); (V.C.); (A.C.); (S.S.); (C.B.); (A.C.); (F.P.E.); (P.T.); (G.D.S.); (D.d.P.)
| | - Christian Galasso
- Department of Ecosustainable Marine Biotechnology, Calabria Marine Centre, CRIMAC, Stazione Zoologica Anton Dohrn, C. da Torre Spaccata, 87071 Amendolara, Italy;
| | - Pietro Tedesco
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio, Ferdinando Acton 55, 80133 Naples, Italy; (C.R.); (V.C.); (A.C.); (S.S.); (C.B.); (A.C.); (F.P.E.); (P.T.); (G.D.S.); (D.d.P.)
| | - Gerardo Della Sala
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio, Ferdinando Acton 55, 80133 Naples, Italy; (C.R.); (V.C.); (A.C.); (S.S.); (C.B.); (A.C.); (F.P.E.); (P.T.); (G.D.S.); (D.d.P.)
| | - Donatella de Pascale
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio, Ferdinando Acton 55, 80133 Naples, Italy; (C.R.); (V.C.); (A.C.); (S.S.); (C.B.); (A.C.); (F.P.E.); (P.T.); (G.D.S.); (D.d.P.)
| | - Laura Vitale
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio, Ferdinando Acton 55, 80133 Naples, Italy; (C.R.); (V.C.); (A.C.); (S.S.); (C.B.); (A.C.); (F.P.E.); (P.T.); (G.D.S.); (D.d.P.)
| | - Daniela Coppola
- Department of Ecosustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Via Ammiraglio, Ferdinando Acton 55, 80133 Naples, Italy; (C.R.); (V.C.); (A.C.); (S.S.); (C.B.); (A.C.); (F.P.E.); (P.T.); (G.D.S.); (D.d.P.)
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Yazid SNE, Selamat J, Ismail SI, Sanny M, Samsudin NIP. Efficacy of fungal antagonists against aflatoxins, ochratoxin A, and fumonisins at different pathogen:antagonist inoculum ratios on grain corn agar and grain corn kernel. J Appl Microbiol 2025; 136:lxaf049. [PMID: 40042983 DOI: 10.1093/jambio/lxaf049] [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: 06/10/2024] [Revised: 01/03/2025] [Accepted: 03/04/2025] [Indexed: 03/14/2025]
Abstract
AIM The present work investigated the efficacy of native biocontrol candidates (antagonists) against aflatoxins, ochratoxin A (OTA), and fumonisins produced by native mycotoxigenic fungi isolated from Malaysia at different pathogen: antagonist inoculum ratios on grain corn agar and grain corn kernels. METHODS AND RESULTS Five pathogen: antagonist inoculum ratios (100:0, 75:25, 50:50, 25:75, and 0:100) were employed. Non-aflatoxigenic Aspergillus flavus Af1KD and Af5TD, and Penicillium janthinellum were used against aflatoxin B1 (AFB1) and aflatoxin B2 (AFB2) by A. flavus. Against OTA by A. niger, and fumonisin B1 (FB1) and fumonisin B2 (FB2) by Fusarium verticillioides and F. proliferatum, respectively, the antagonists Trichoderma asperelloides, T. asperellum, and T. harzianum were used. Non-aflatoxigenic A. flavus Af1KD was the most effective against AFB1 and AFB2 at all tested ratios and substrates. All Trichoderma spp. were effective against OTA by A. niger on grain corn agar at all tested ratios. Trichoderma asperelloides and T. asperellum were effective against FB1 and FB2 produced by F. verticillioides at all tested ratios and substrates. Trichoderma asperelloides was effective against FB1 and FB2 by F. proliferatum at all tested ratios and substrates. CONCLUSION The native biocontrol candidates were effective against mycotoxigenic fungi and mycotoxin production on grain corn agar and grain corn kernels, and could be developed into biocontrol agents.
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Affiliation(s)
- Siti Nur Ezzati Yazid
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Jinap Selamat
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Izera Ismail
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Maimunah Sanny
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Nik Iskandar Putra Samsudin
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Ceballos Rodriguez-Conde F, Zhu S, Dikicioglu D. Harnessing microbial division of labor for biomanufacturing: a review of laboratory and formal modeling approaches. Crit Rev Biotechnol 2025:1-19. [PMID: 39972973 DOI: 10.1080/07388551.2025.2455607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 12/13/2024] [Accepted: 12/28/2024] [Indexed: 02/21/2025]
Abstract
Bioprocess industries aim to meet the increasing demand for product complexity by designing enhanced cellular and metabolic capabilities for the host. Monocultures, standard biomanufacturing workhorses, are often restricted in their capability to meet these demands, and the solution often involves the genetic modification of the host. Synthetic microbial communities are a promising alternative to monocultures because they exhibit division of labor, enabling efficient resource utilization and pathway modularity. This specialization minimizes metabolic burden and enhances robustness to perturbations, providing a competitive advantage. Despite this potential, their utilization in biotechnological or bioprocessing applications remains limited. The recent emergence of new and innovative community design tools and strategies, particularly those harnessing the division of labor, holds promise to change this outlook. Understanding the microbial interactions governing natural microbial communities can be used to identify complementary partners, informing synthetic community design. Therefore, we particularly consider engineering division of labor in synthetic microbial communities as a viable solution to accelerate progress in the field. This review presents the current understanding of how microbial interactions enable division of labor and how this information can be used to design synthetic microbial communities to perform tasks otherwise unfeasible to individual organisms. We then evaluate laboratory and formal modeling approaches specifically developed to: elucidate microbial community physiology, guide experimental design, and improve our understanding of complex community interactions assisting synthetic community design. By synthesizing these insights, we aim to present a comprehensive framework that advances the use of microbial communities in biomanufacturing applications.
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Affiliation(s)
| | - Sophie Zhu
- Department of Biochemical Engineering, University College London, London, UK
| | - Duygu Dikicioglu
- Department of Biochemical Engineering, University College London, London, UK
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Saez JM, Raimondo EE, Costa-Gutierrez SB, Aparicio JD, Mosca Angelucci D, Donati E, Polti MA, Tomei MC, Benimeli CS. Enhancing environmental decontamination and sustainable production through synergistic and complementary interactions of actinobacteria and fungi. Heliyon 2025; 11:e42135. [PMID: 39991206 PMCID: PMC11847236 DOI: 10.1016/j.heliyon.2025.e42135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 01/19/2025] [Accepted: 01/20/2025] [Indexed: 02/25/2025] Open
Abstract
Actinobacteria and fungi are renowned for their metabolic diversity and adaptability to various environments, thus exhibiting significant potential for environmental decontamination and sustainable production. Both actinobacteria and fungi excel in producing diverse secondary metabolites and enzymes, offering valuable tools for industrial and environmental applications. Their ability to detoxify metals and degrade a wide range of organic pollutants, such as pesticides, hydrocarbons, and dyes, positions them as promising candidates for bioremediation. Recent shifts in microbiological sciences emphasize research on mixed microbial populations. Microbial interactions in mixed communities emulate natural processes and yield emergent properties such as stability, robustness, and enhanced metabolism. Co-cultures of actinobacteria and fungi harness a broader range of genes and metabolic capabilities through their distinctive interactions, opening new avenues for developing novel products and/or technologies. This review provides a critical analysis of the present status of knowledge regarding the potential of actinobacteria-fungi co-cultures with a particular focus on novel functionalities and heightened production efficiency. These consortia are promising in several fields, from environmental applications to the biosynthesis of industrially relevant metabolites and enzymes, and enhancements in agricultural production. Although challenges still exist, their potential to address complex problems has been demonstrated and deserves further investigation.
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Affiliation(s)
- Juliana M. Saez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, 4000, Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, 4000, Tucumán, Argentina
| | - Enzo E. Raimondo
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, 4000, Tucumán, Argentina
- Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 491, 4000, Tucumán, Argentina
| | - Stefanie B. Costa-Gutierrez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, 4000, Tucumán, Argentina
| | - Juan D. Aparicio
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, 4000, Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, 4000, Tucumán, Argentina
| | - Domenica Mosca Angelucci
- Water Research Institute, National Research Council (CNR-IRSA), Via Salaria km 29.300, CP 10, Monterotondo Stazione, 00015, Rome, Italy
| | - Enrica Donati
- Institute for Biological Systems, National Research Council (CNR-ISB), Via Salaria km 29.300, CP 10, Monterotondo Stazione, 00015, Rome, Italy
| | - Marta A. Polti
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, 4000, Tucumán, Argentina
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Miguel Lillo 205, 4000, Tucumán, Argentina
| | - Maria C. Tomei
- Water Research Institute, National Research Council (CNR-IRSA), Via Salaria km 29.300, CP 10, Monterotondo Stazione, 00015, Rome, Italy
| | - Claudia S. Benimeli
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI-CONICET), Avenida Belgrano y Pasaje Caseros, 4000, Tucumán, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Catamarca, Belgrano 300, 4700, Catamarca, Argentina
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Thissera B, Soldatou S, Belbahri L, Ebel R, Jaspars M, Rateb ME. Unconventional approaches for the induction of microbial natural products. J Appl Microbiol 2025; 136:lxaf014. [PMID: 39794282 DOI: 10.1093/jambio/lxaf014] [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: 09/03/2024] [Revised: 12/11/2024] [Accepted: 01/09/2025] [Indexed: 01/13/2025]
Abstract
Expansion of the microbial drug discovery pipeline has been impeded by a limited and skewed appreciation of the microbial world and its full chemical capabilities and by an inability to induce silent biosynthetic gene clusters (BGCs). Typically, these silent genes are not expressed under standard laboratory conditions, instead requiring particular interventions to activate them. Genetic, physical, and chemical strategies have been employed to trigger these BGCs, and some have resulted in the induction of novel secondary metabolites. This review encompasses a wide range of literature and emphasizes selected successful induction of microbial secondary metabolites examples through unconventional approaches such as quorum sensing, epigenetic modulation, and ribosome engineering. Whenever applicable, we will also discuss their mechanisms and optimizations to improve the microbial drug discovery process.
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Affiliation(s)
- Bathini Thissera
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, High Street, Paisley PA1 2BE, Scotland, UK
| | - Sylvia Soldatou
- Department of Chemistry, Marine Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, UK
| | - Lassaad Belbahri
- University Institute of Teacher Education (IUFE), University of Geneva, 24 Rue du Général-Dufour, 1211 Geneva, Switzerland
| | - Rainer Ebel
- Department of Chemistry, Marine Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, UK
| | - Marcel Jaspars
- Department of Chemistry, Marine Biodiscovery Centre, University of Aberdeen, Meston Walk, Aberdeen AB24 3UE, UK
| | - Mostafa E Rateb
- School of Computing, Engineering & Physical Sciences, University of the West of Scotland, High Street, Paisley PA1 2BE, Scotland, UK
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Fan J, Wei PL, Li Y, Zhang S, Ren Z, Li W, Yin WB. Developing filamentous fungal chassis for natural product production. BIORESOURCE TECHNOLOGY 2025; 415:131703. [PMID: 39477163 DOI: 10.1016/j.biortech.2024.131703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 10/09/2024] [Accepted: 10/23/2024] [Indexed: 11/07/2024]
Abstract
The growing demand for green and sustainable production of high-value chemicals has driven the interest in microbial chassis. Recent advances in synthetic biology and metabolic engineering have reinforced filamentous fungi as promising chassis cells to produce bioactive natural products. Compared to the most used model organisms, Escherichia coli and Saccharomyces cerevisiae, most filamentous fungi are natural producers of secondary metabolites and possess an inherent pre-mRNA splicing system and abundant biosynthetic precursors. In this review, we summarize recent advances in the application of filamentous fungi as chassis cells. Emphasis is placed on strategies for developing a filamentous fungal chassis, including the establishment of mature genetic manipulation and efficient genetic tools, the catalogue of regulatory elements, and the optimization of endogenous metabolism. Furthermore, we provide an outlook on the advanced techniques for further engineering and application of filamentous fungal chassis.
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Affiliation(s)
- Jie Fan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China.
| | - Peng-Lin Wei
- 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
| | - Yuanyuan Li
- 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
| | - Shengquan Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Zedong Ren
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wei Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China
| | - Wen-Bing Yin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, PR China; Medical School, University of Chinese Academy of Sciences, Beijing 100049, PR China.
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11
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Gonzalez-Silva A, San Juan-Mendo M, Delgado-Prudencio G, Hernández-García JA, Larios-Serrato V, Aguilar C, Villa-Tanaca L, Hernández-Rodríguez C. Comparative Genomics and Biosynthetic Cluster Analysis of Antifungal Secondary Metabolites of Three Strains of Streptomyces albidoflavus Isolated from Rhizospheric Soils. Microorganisms 2024; 12:2637. [PMID: 39770839 PMCID: PMC11678301 DOI: 10.3390/microorganisms12122637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2024] [Revised: 12/01/2024] [Accepted: 12/17/2024] [Indexed: 01/11/2025] Open
Abstract
Streptomyces is a genus of Gram-positive bacteria with high GC content. It remains attractive for studying and discovering new antibiotics, antifungals, and chemotherapeutics. Streptomyces genomes can contain more than 30 cryptic and expressed biosynthetic gene clusters (BGC) encoding secondary metabolites. In this study, three Streptomyces strains isolated from jungle rhizospheric soil exhibited supernatants that can inhibit sensitive and fluconazole-resistant Candida spp. The genomes of the strains Streptomyces sp. A1, J25, J29 ori2 were sequenced, assembled de novo, and analyzed. The genome assemblies revealed that the size of the genomes was 6.9 Mb, with linear topology and 73.5% GC. A phylogenomic approach identified the strains with high similitudes between 98.5 and 98.7% with Streptomyces albidoflavus SM254 and R-53649 strains, respectively. Pangenomic analysis of eight genomes of S. albidoflavus strains deposited in the Genomes database recognized 4707 core protein orthogroups and 745 abundant accessory and exclusive protein orthogroups, suggesting an open pangenome in this species. The antiSMASH software detected candicidin and surugamide BGC-encoding polyene and octapeptide antifungal secondary metabolites in other S. albidoflavus. CORASON software was used to compare the synteny, and the abundance of genes harbored in the clusters was used. In conclusion, although the three strains belong to the same species, each possesses a distinct genome, as evidenced by the different phenotypes, including antifungal and extracellular enzymatic activities.
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Affiliation(s)
- Adilene Gonzalez-Silva
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Carpio y Plan de Ayala S/N, Mexico City CP 11430, Mexico; (A.G.-S.); (M.S.J.-M.); (J.A.H.-G.); (L.V.-T.)
| | - Magali San Juan-Mendo
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Carpio y Plan de Ayala S/N, Mexico City CP 11430, Mexico; (A.G.-S.); (M.S.J.-M.); (J.A.H.-G.); (L.V.-T.)
| | - Gustavo Delgado-Prudencio
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca CP 62210, Mexico;
| | - Juan Alfredo Hernández-García
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Carpio y Plan de Ayala S/N, Mexico City CP 11430, Mexico; (A.G.-S.); (M.S.J.-M.); (J.A.H.-G.); (L.V.-T.)
| | - Violeta Larios-Serrato
- Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Carpio y Plan de Ayala S/N, Mexico City CP 11430, Mexico;
| | - César Aguilar
- Department of Chemistry, Purdue University, 575 Stadium Mall Dr. West Lafayette, Indiana, IN 47907, USA;
| | - Lourdes Villa-Tanaca
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Carpio y Plan de Ayala S/N, Mexico City CP 11430, Mexico; (A.G.-S.); (M.S.J.-M.); (J.A.H.-G.); (L.V.-T.)
| | - César Hernández-Rodríguez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prol. Carpio y Plan de Ayala S/N, Mexico City CP 11430, Mexico; (A.G.-S.); (M.S.J.-M.); (J.A.H.-G.); (L.V.-T.)
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12
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Netherway T, Bahram M. Melanized root-associated fungi: key players in plant-soil systems. Trends Microbiol 2024; 32:1190-1199. [PMID: 38987052 DOI: 10.1016/j.tim.2024.06.006] [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: 04/30/2024] [Revised: 06/03/2024] [Accepted: 06/21/2024] [Indexed: 07/12/2024]
Abstract
Melanized root-associated fungi are a group of fungi that produce melanized structures and form root associations, including different mycorrhizal and endophytic symbioses with plants. They are pervasive across terrestrial ecosystems and play an important role in the prevailing soil carbon (C) and nutrient cycling syndromes through direct and indirect mechanisms, where they may strongly modulate plant-microbe interactions and structure root and soil microbiomes. Furthermore, melanized root-associated fungi can confer on plants an enhanced ability to tolerate abiotic and biotic stressors such as drought, extreme temperatures, heavy metals, and pathogen attacks. We propose that melanized root-associated fungi are a cohesive and ecologically relevant grouping that can be an indicator of plant-soil system functioning, and considering them will advance research on plant-soil interactions.
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Affiliation(s)
- Tarquin Netherway
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden.
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls väg 16, 756 51 Uppsala, Sweden; Department of Agroecology, Aarhus University, Slagelse, Denmark; Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, Tartu, Estonia
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13
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Ujie Y, Saito S, Fukaya K, Urabe D, Yaguchi T, Arai MA. Aspergillus terreus IFM 65899-THP-1 cells interaction triggers production of the natural product butyrolactone Ia, an immune suppressive compound. Sci Rep 2024; 14:28278. [PMID: 39550448 PMCID: PMC11569209 DOI: 10.1038/s41598-024-79837-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2024] [Accepted: 11/12/2024] [Indexed: 11/18/2024] Open
Abstract
We focused on the possibility that pathogenic microorganisms might produce immune suppressors to evade the action of immune cells. Based on this possibility, we have recently developed new co-culture method of pathogenic actinomyces and immune cells, however, the interaction mechanism between pathogens and cells was still unclear. In this report, co-culturing pathogenic fungi and immune cells were investigated. Pathogenic fungus Aspergillus terreus IFM 65899 and THP-1 cells were co-cultured and isolated a co-culture specific compound, butyrolactone Ia (1). 1 inhibits the production of nitric oxide by RAW264 cells and exhibits regulatory effects on autophagy, suggesting 1 plays a defensive role in the response of A. terreus IFM 65899 to immune cells. Furthermore, dialysis experiments and micrographs indicated that "physical interaction" between A. terreus IFM 65899 and THP-1 cells may be required for the production of 1. This is the first report of co-culture method of fungi with immune cells and its interaction mechanism.
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Affiliation(s)
- Yukiko Ujie
- Faculty of Science and Technology, Keio University, Yokohama, 223-8522, Japan
| | - Shun Saito
- Faculty of Science and Technology, Keio University, Yokohama, 223-8522, Japan
| | - Keisuke Fukaya
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University, Toyama, 939-0398, Japan
| | - Daisuke Urabe
- Biotechnology Research Center, Department of Biotechnology, Toyama Prefectural University, Toyama, 939-0398, Japan
| | - Takashi Yaguchi
- Medical Mycology Research Center, Chiba University, Chiba, 260-8673, Japan
| | - Midori A Arai
- Faculty of Science and Technology, Keio University, Yokohama, 223-8522, Japan.
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14
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Yu G, Ge X, Li W, Ji L, Yang S. Interspecific cross-talk: The catalyst driving microbial biosynthesis of secondary metabolites. Biotechnol Adv 2024; 76:108420. [PMID: 39128577 DOI: 10.1016/j.biotechadv.2024.108420] [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: 03/02/2024] [Revised: 06/07/2024] [Accepted: 08/04/2024] [Indexed: 08/13/2024]
Abstract
Microorganisms co-exist and co-evolve in nature, forming intricate ecological communities. The interspecies cross-talk within these communities creates and sustains their great biosynthetic potential, making them an important source of natural medicines and high-value-added chemicals. However, conventional investigations into microbial metabolites are typically carried out in pure cultures, resulting in the absence of specific activating factors and consequently causing a substantial number of biosynthetic gene clusters to remain silent. This, in turn, hampers the in-depth exploration of microbial biosynthetic potential and frequently presents researchers with the challenge of rediscovering compounds. In response to this challenge, the coculture strategy has emerged to explore microbial biosynthetic capabilities and has shed light on the study of cross-talk mechanisms. These elucidated mechanisms will contribute to a better understanding of complex biosynthetic regulations and offer valuable insights to guide the mining of secondary metabolites. This review summarizes the research advances in microbial cross-talk mechanisms, with a particular focus on the mechanisms that activate the biosynthesis of secondary metabolites. Additionally, the instructive value of these mechanisms for developing strategies to activate biosynthetic pathways is discussed. Moreover, challenges and recommendations for conducting in-depth studies on the cross-talk mechanisms are presented.
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Affiliation(s)
- Guihong Yu
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China.
| | - Xiaoxuan Ge
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China
| | - Wanting Li
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China
| | - Linwei Ji
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China
| | - Song Yang
- School of Life Sciences, Shandong Province Key Laboratory of Applied Mycology, and Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao 266109, Shandong Province, People's Republic of China.
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15
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Zulfiqar M, Singh V, Steinbeck C, Sorokina M. Review on computer-assisted biosynthetic capacities elucidation to assess metabolic interactions and communication within microbial communities. Crit Rev Microbiol 2024; 50:1053-1092. [PMID: 38270170 DOI: 10.1080/1040841x.2024.2306465] [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: 03/13/2023] [Revised: 11/17/2023] [Accepted: 01/12/2024] [Indexed: 01/26/2024]
Abstract
Microbial communities thrive through interactions and communication, which are challenging to study as most microorganisms are not cultivable. To address this challenge, researchers focus on the extracellular space where communication events occur. Exometabolomics and interactome analysis provide insights into the molecules involved in communication and the dynamics of their interactions. Advances in sequencing technologies and computational methods enable the reconstruction of taxonomic and functional profiles of microbial communities using high-throughput multi-omics data. Network-based approaches, including community flux balance analysis, aim to model molecular interactions within and between communities. Despite these advances, challenges remain in computer-assisted biosynthetic capacities elucidation, requiring continued innovation and collaboration among diverse scientists. This review provides insights into the current state and future directions of computer-assisted biosynthetic capacities elucidation in studying microbial communities.
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Affiliation(s)
- Mahnoor Zulfiqar
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Vinay Singh
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
| | - Christoph Steinbeck
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Maria Sorokina
- Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- Data Science and Artificial Intelligence, Research and Development, Pharmaceuticals, Bayer, Berlin, Germany
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16
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Sbaraini N, Crombie A, Kalaitzis JA, Vuong D, Bracegirdle J, Windsor F, Lau A, Chen R, Tan YP, Lacey A, Lacey E, Piggott AM, Chooi YH. The aquastatin biosynthetic gene cluster encodes a versatile polyketide synthase capable of synthesising heteromeric depsides with diverse alkyl side chains. Chem Sci 2024:d4sc05557h. [PMID: 39479171 PMCID: PMC11514314 DOI: 10.1039/d4sc05557h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Accepted: 10/18/2024] [Indexed: 11/02/2024] Open
Abstract
Depsides have garnered substantial interest due to the diverse biological activities exhibited by members of this class. Among these are the antibacterial aquastatins, glycosylated heteromeric depsides formed through the condensation of orsellinic acid with corticiolic acid. In this work, we isolated aquastatins and the recently described geministatins, along with several novel aquastatin-related depsides with different alkyl side chains from the fungus Austroacremonium gemini MST-FP2131. The structures were determined through comprehensive spectroscopic analysis and chemical degradation. Genome mining and heterologous expression in Aspergillus nidulans and Saccharomyces cerevisiae revealed that aquastatin biosynthesis requires only two genes: a non-reducing polyketide synthase (SAT-KS-AT-PT-ACP-TE) and a glycosyltransferase. We demonstrated that the single polyketide synthase can synthesise an acetyl-primed orsellinic acid and alkylresorcylate with various chain lengths (C14, C16, or C18) by incorporating different long-chain acyl-CoAs as starter units, and then join these as heteromeric depsides. Using chemical degradation, we generated a series of analogues and showed that several aglycone depsides exhibit antibacterial activity against Staphylococcus aureus and methicillin-resistant S. aureus (MRSA), as well as antifungal and cytotoxic activities. Interestingly, heterologous expression of the aquastatin gene cluster in A. nidulans produced higher levels of geministatins with Δ15,16 and Δ18,19 double bonds, which have superior bioactivities compared to the aquastatins but are only present as minor compounds in the native fungus A. gemini.
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Affiliation(s)
- Nicolau Sbaraini
- School of Molecular Sciences, The University of Western Australia Perth WA 6009 Australia
| | - Andrew Crombie
- Microbial Screening Technologies Pty. Ltd Smithfield NSW 2164 Australia
| | - John A Kalaitzis
- School of Natural Sciences, Macquarie University Sydney NSW 2109 Australia
| | - Daniel Vuong
- Microbial Screening Technologies Pty. Ltd Smithfield NSW 2164 Australia
| | - Joe Bracegirdle
- School of Molecular Sciences, The University of Western Australia Perth WA 6009 Australia
- Microbial Screening Technologies Pty. Ltd Smithfield NSW 2164 Australia
| | - Fraser Windsor
- School of Molecular Sciences, The University of Western Australia Perth WA 6009 Australia
| | - Ashli Lau
- School of Molecular Sciences, The University of Western Australia Perth WA 6009 Australia
| | - Rachel Chen
- Microbial Screening Technologies Pty. Ltd Smithfield NSW 2164 Australia
| | - Yu Pei Tan
- Department of Agriculture and Fisheries, Plant Pathology Herbarium Dutton Park QLD 4102 Australia
- Centre for Crop Health, University of Southern Queensland Toowoomba QLD 4350 Australia
| | - Alastair Lacey
- Microbial Screening Technologies Pty. Ltd Smithfield NSW 2164 Australia
| | - Ernest Lacey
- Microbial Screening Technologies Pty. Ltd Smithfield NSW 2164 Australia
- School of Natural Sciences, Macquarie University Sydney NSW 2109 Australia
| | - Andrew M Piggott
- School of Natural Sciences, Macquarie University Sydney NSW 2109 Australia
| | - Yit-Heng Chooi
- School of Molecular Sciences, The University of Western Australia Perth WA 6009 Australia
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17
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Li W, Wang X, Jiang Y, Cui S, Hu J, Wei Y, Li J, Wu Y. Volatile Organic Compounds Produced by Co-Culture of Burkholderia vietnamiensis B418 with Trichoderma harzianum T11-W Exhibits Improved Antagonistic Activities against Fungal Phytopathogens. Int J Mol Sci 2024; 25:11097. [PMID: 39456879 PMCID: PMC11507488 DOI: 10.3390/ijms252011097] [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: 09/25/2024] [Revised: 10/13/2024] [Accepted: 10/14/2024] [Indexed: 10/28/2024] Open
Abstract
Recently, there has been a growing interest in the biocontrol activity of volatile organic compounds (VOCs) produced by microorganisms. This study specifically focuses on the effects of VOCs produced by the co-culture of Burkholderia vietnamiensis B418 and Trichoderma harzianum T11-W for the control of two phytopathogenic fungi, Botrytis cinerea and Fusarium oxysporum f. sp. cucumerium Owen. The antagonistic activity of VOCs released in mono- and co-culture modes was evaluated by inhibition assays on a Petri dish and in detached fruit experiments, with the co-culture demonstrating significantly higher inhibitory effects on the phytopathogens on both the plates and fruits compared with the mono-cultures. Metabolomic profiles of VOCs were conducted using the solid-liquid microextraction technique, revealing 341 compounds with significant changes in their production during the co-culture. Among these compounds, linalool, dimethyl trisulfide, dimethyl disulfide, geranylacetone, 2-phenylethanol, and acetophenone were identified as having strong antagonistic activity through a standard inhibition assay. These key compounds were found to be related to the improved inhibitory effect of the B418 and T11-W co-culture. Overall, the results suggest that VOCs produced by the co-culture of B. vietnamiensis B418 and T. harzianum T11-W possess great potential in biological control.
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Affiliation(s)
- Wenzhe Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (W.L.); (X.W.); (Y.J.); (S.C.); (J.H.); (Y.W.); (J.L.)
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Xinyue Wang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (W.L.); (X.W.); (Y.J.); (S.C.); (J.H.); (Y.W.); (J.L.)
| | - Yanqing Jiang
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (W.L.); (X.W.); (Y.J.); (S.C.); (J.H.); (Y.W.); (J.L.)
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Shuning Cui
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (W.L.); (X.W.); (Y.J.); (S.C.); (J.H.); (Y.W.); (J.L.)
- School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Jindong Hu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (W.L.); (X.W.); (Y.J.); (S.C.); (J.H.); (Y.W.); (J.L.)
| | - Yanli Wei
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (W.L.); (X.W.); (Y.J.); (S.C.); (J.H.); (Y.W.); (J.L.)
| | - Jishun Li
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (W.L.); (X.W.); (Y.J.); (S.C.); (J.H.); (Y.W.); (J.L.)
| | - Yuanzheng Wu
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, China; (W.L.); (X.W.); (Y.J.); (S.C.); (J.H.); (Y.W.); (J.L.)
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18
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Brakhage AA. Microbial hub signaling compounds: natural products disproportionally shape microbiome composition and structure. MICROLIFE 2024; 5:uqae017. [PMID: 39318451 PMCID: PMC11421377 DOI: 10.1093/femsml/uqae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Revised: 07/05/2024] [Accepted: 09/12/2024] [Indexed: 09/26/2024]
Abstract
Microbiomes are shaped by abiotic factors like nutrients, oxygen availability, pH, temperature, and so on, but also by biotic factors including low molecular weight organic compounds referred to as natural products (NPs). Based on genome analyses, millions of these compounds are predicted to exist in nature, some of them have found important applications e.g. as antibiotics. Based on recent data I propose a model that some of these compounds function as microbial hub signaling compounds, i.e. they have a higher hierarchical influence on microbiomes. These compounds have direct effects e.g. by inhibiting microorganisms and thereby exclude them from a microbiome (excluded). Some microorganisms do not respond at all (nonresponder), others respond by producing themselves NPs like a second wave of information molecules (message responder) influencing other microorganisms, but conceivably a more limited spectrum. Some microorganisms may respond to the hub compounds with their chemical modification (message modifiers). This way, the modified NPs may have themselves signaling function for a subset of microorganisms. Finally, it is also likely that NPs act as food source (C- and/or N-source) for microorganisms specialized on their degradation. As a consequence, such specialized microorganisms are selectively recruited to the microbiota.
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Affiliation(s)
- Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), 07745 Jena, Germany
- Department of Microbiology and Molecular Biology, Institute of Microbiology, Friedrich Schiller University, 07745 Jena, Germany
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19
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Hu Z, Cui H, Wang Q, Li C, Chen S, Gao Z, Liu L, Peng B, Li J. Induced production of defensive secondary metabolites from Aspergillus fumigatiaffinis by co-culture with Aspergillus alabamensis. PHYTOCHEMISTRY 2024; 225:114187. [PMID: 38889845 DOI: 10.1016/j.phytochem.2024.114187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 06/05/2024] [Accepted: 06/11/2024] [Indexed: 06/20/2024]
Abstract
Seven previously undescribed compounds, including four diketomorpholine alkaloids (1‒4), one indole diketopiperazine alkaloid (9), one chromone (10), and one benzoic acid derivative (13), and nine known compounds (5-8, 11, 12, and 14-16) were isolated from two different fungal sources. Nine of these metabolites (1-9) were obtained from a seagrass-derived Aspergillus alabamensis SYSU-6778, while the others were obtained from a mixed culture of A. alabamensis SYSU-6778 and a co-isolated fungus A. fumigatiaffinis SYSU-6786. The chemical structures of the compounds were deduced via spectroscopic techniques (including HRESIMS, 1D and 2D NMR), chemical reactions, and ECD calculations. It is worth noting that compound 10 was identified as a defensive secondary metabolite of strain SYSU-6786, produced through the induction of compound 8 under co-culture conditions. Compounds 3 and 4 possessed a naturally rare isotryptophan core. Moreover, compounds 1 and 2 exhibited potent inhibitory activities against fish pathogenic bacterium Edwardsiella ictalurid, with minimum inhibitory concentration values of 10.0 μg/mL for both compounds.
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Affiliation(s)
- Zhibo Hu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, PR China
| | - Haishan Cui
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, PR China
| | - Qiang Wang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, PR China
| | - Cheng Li
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, PR China
| | - Senhua Chen
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, PR China
| | - Zhizeng Gao
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, PR China
| | - Lan Liu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, PR China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519000, PR China; Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, 519082, PR China
| | - Bo Peng
- Institute for Environmental and Climate Research, Jinan University, Guangzhou, 511443, PR China
| | - Jing Li
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, 519082, PR China; Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Zhuhai, 519082, PR China.
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20
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Anjum K, Huang X, Zhou L, Zhu T, Che Q, Zhang G, Li D. New cyclic dipeptide discovered from deep-sea derived Aspergillus sp. HDN20-1401. Nat Prod Res 2024; 38:3231-3236. [PMID: 37384587 DOI: 10.1080/14786419.2023.2227754] [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: 02/03/2023] [Revised: 06/07/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023]
Abstract
A new alkaloid named aspergilalkaloid A (1) with pyridoindole hydroxymethyl piperazine dione structure along with six known compounds 2-7 were isolated from deep-sea derived fungus Aspergillus sp. HDN20-1401. The structure including absolute configuration was elucidated by extensive NMR analyses, HRESIMS, ECD calculation, and theoretical NMR calculation with DP4+ analysis. All isolated compounds were tested for antimicrobial and anticancer activity. Aspergilalkaloid A (1) showed inhibitive activity against Bacillus cereus with MIC value of 12.5 μM and weak activity against MRCNS.
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Affiliation(s)
- Komal Anjum
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Xiaofei Huang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Luning Zhou
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Tianjiao Zhu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Qian Che
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
| | - Guojian Zhang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- Marine Biomedical Research Institute of Qingdao, Qingdao, China
| | - Dehai Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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21
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Ishikawa F, Uchida C, Tanabe G. Proteolytic Regulation in the Biosynthesis of Natural Product Via a ClpP Protease System. ACS Chem Biol 2024; 19:1794-1802. [PMID: 39096241 DOI: 10.1021/acschembio.4c00304] [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: 08/05/2024]
Abstract
Protein degradation is a tightly regulated biological process that maintains bacterial proteostasis. ClpPs are a highly conserved family of serine proteases that associate with the AAA + ATPase (an ATPase associated with diverse cellular activities) to degrade protein substrates. Identification and biochemical characterization of protein substrates for the AAA + ATPase-dependent ClpP degradation systems are considered essential for gaining an understanding of the molecular operation of the complex ClpP degradation machinery. Consequently, expanding the repertoire of protein substrates that can be degraded in vitro and within bacterial cells is necessary. Here, we report that AAA + ATPase-ClpP proteolytic complexes promote degradation of the secondary metabolite surfactin synthetases SrfAA, SrfAB, and SrfAC in Bacillus subtilis. On the basis of in vitro and in-cell studies coupled with activity-based protein profiling of nonribosomal peptide synthetases, we showed that SrfAC is targeted to the ClpC-ClpP proteolytic complex, whereas SrfAA is hydrolyzed not only by the ClpC-ClpP proteolytic complex but also by different ClpP proteolytic complexes. Furthermore, SrfAB does not appear to be a substrate for the ClpC-ClpP proteolytic complex, thereby implying that other ClpP proteolytic complexes are involved in the degradation of this surfactin synthetase. Natural product biosynthesis is regulated by the AAA + ATPase-ClpP degradation system, indicating that protein degradation plays a role in the regulatory stages of biosynthesis. However, few studies have examined the regulation of protein degradation levels. Furthermore, SrfAA, SrfAB, and SrfAC were identified as protein substrates for AAA + ATPase-ClpP degradation systems, thereby contributing to a better understanding of the complex ClpP degradation machinery.
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Affiliation(s)
- Fumihiro Ishikawa
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka 577-8502, Japan
| | - Chiharu Uchida
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka 577-8502, Japan
| | - Genzoh Tanabe
- Faculty of Pharmacy, Kindai University, 3-4-1 Kowakae, Higashi-osaka, Osaka 577-8502, Japan
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22
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Pawlowska TE. Symbioses between fungi and bacteria: from mechanisms to impacts on biodiversity. Curr Opin Microbiol 2024; 80:102496. [PMID: 38875733 PMCID: PMC11323152 DOI: 10.1016/j.mib.2024.102496] [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: 07/10/2023] [Revised: 05/20/2024] [Accepted: 05/31/2024] [Indexed: 06/16/2024]
Abstract
Symbiotic interactions between fungi and bacteria range from positive to negative. They are ubiquitous in free-living as well as host-associated microbial communities worldwide. Yet, the impact of fungal-bacterial symbioses on the organization and dynamics of microbial communities is uncertain. There are two reasons for this uncertainty: (1) knowledge gaps in the understanding of the genetic mechanisms underpinning fungal-bacterial symbioses and (2) prevailing interpretations of ecological theory that favor antagonistic interactions as drivers stabilizing biological communities despite the existence of models emphasizing contributions of positive interactions. This review synthesizes information on fungal-bacterial symbioses common in the free-living microbial communities of the soil as well as in host-associated polymicrobial biofilms. The interdomain partnerships are considered in the context of the relevant community ecology models, which are discussed critically.
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Affiliation(s)
- Teresa E Pawlowska
- School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
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23
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Guo L, Xi B, Lu L. Strategies to enhance production of metabolites in microbial co-culture systems. BIORESOURCE TECHNOLOGY 2024; 406:131049. [PMID: 38942211 DOI: 10.1016/j.biortech.2024.131049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 06/06/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
Increasing evidence shows that microbial synthesis plays an important role in producing high value-added products. However, microbial monoculture generally hampers metabolites production and limits scalability due to the increased metabolic burden on the host strain. In contrast, co-culture is a more flexible approach to improve the environmental adaptability and reduce the overall metabolic burden. The well-defined co-culturing microbial consortia can tap their metabolic potential to obtain yet-to-be discovered and pre-existing metabolites. This review focuses on the use of a co-culture strategy and its underlying mechanisms to enhance the production of products. Notably, the significance of comprehending the microbial interactions, diverse communication modes, genetic information, and modular co-culture involved in co-culture systems were highlighted. Furthermore, it addresses the current challenges and outlines potential future directions for microbial co-culture. This review provides better understanding the diversity and complexity of the interesting interaction and communication to advance the development of co-culture techniques.
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Affiliation(s)
- Lichun Guo
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214122, PR China; State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China
| | - Bingwen Xi
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214122, PR China
| | - Liushen Lu
- Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, Jiangsu 214122, PR China.
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24
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Krysenko S, Wohlleben W. Role of Carbon, Nitrogen, Phosphate and Sulfur Metabolism in Secondary Metabolism Precursor Supply in Streptomyces spp. Microorganisms 2024; 12:1571. [PMID: 39203413 PMCID: PMC11356490 DOI: 10.3390/microorganisms12081571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 09/03/2024] Open
Abstract
The natural soil environment of Streptomyces is characterized by variations in the availability of nitrogen, carbon, phosphate and sulfur, leading to complex primary and secondary metabolisms. Their remarkable ability to adapt to fluctuating nutrient conditions is possible through the utilization of a large amount of substrates by diverse intracellular and extracellular enzymes. Thus, Streptomyces fulfill an important ecological role in soil environments, metabolizing the remains of other organisms. In order to survive under changing conditions in their natural habitats, they have the possibility to fall back on specialized enzymes to utilize diverse nutrients and supply compounds from primary metabolism as precursors for secondary metabolite production. We aimed to summarize the knowledge on the C-, N-, P- and S-metabolisms in the genus Streptomyces as a source of building blocks for the production of antibiotics and other relevant compounds.
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Affiliation(s)
- Sergii Krysenko
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
| | - Wolfgang Wohlleben
- Department of Microbiology/Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany;
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, 72076 Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
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25
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Bogdanov A, Salib MN, Chase AB, Hammerlindl H, Muskat MN, Luedtke S, da Silva EB, O'Donoghue AJ, Wu LF, Altschuler SJ, Molinski TF, Jensen PR. Small molecule in situ resin capture provides a compound first approach to natural product discovery. Nat Commun 2024; 15:5230. [PMID: 38898025 PMCID: PMC11187115 DOI: 10.1038/s41467-024-49367-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: 08/24/2023] [Accepted: 06/04/2024] [Indexed: 06/21/2024] Open
Abstract
Culture-based microbial natural product discovery strategies fail to realize the extraordinary biosynthetic potential detected across earth's microbiomes. Here we introduce Small Molecule In situ Resin Capture (SMIRC), a culture-independent method to obtain natural products directly from the environments in which they are produced. We use SMIRC to capture numerous compounds including two new carbon skeletons that were characterized using NMR and contain structural features that are, to the best of our knowledge, unprecedented among natural products. Applications across diverse marine habitats reveal biome-specific metabolomic signatures and levels of chemical diversity in concordance with sequence-based predictions. Expanded deployments, in situ cultivation, and metagenomics facilitate compound discovery, enhance yields, and link compounds to candidate producing organisms, although microbial community complexity creates challenges for the later. This compound-first approach to natural product discovery provides access to poorly explored chemical space and has implications for drug discovery and the detection of chemically mediated biotic interactions.
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Affiliation(s)
- Alexander Bogdanov
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Mariam N Salib
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Alexander B Chase
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Earth Sciences, Southern Methodist University, Dallas, TX, 75275, USA
| | - Heinz Hammerlindl
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Mitchell N Muskat
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Stephanie Luedtke
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anthony J O'Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Steven J Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Tadeusz F Molinski
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA.
| | - Paul R Jensen
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, 92093, USA.
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26
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Hsieh YYP, Sun W, Young JM, Cheung R, Hogan DA, Dandekar AA, Malik HS. Widespread fungal-bacterial competition for magnesium lowers bacterial susceptibility to polymyxin antibiotics. PLoS Biol 2024; 22:e3002694. [PMID: 38900845 PMCID: PMC11218974 DOI: 10.1371/journal.pbio.3002694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/02/2024] [Accepted: 05/29/2024] [Indexed: 06/22/2024] Open
Abstract
Fungi and bacteria coexist in many polymicrobial communities, yet the molecular basis of their interactions remains poorly understood. Here, we show that the fungus Candida albicans sequesters essential magnesium ions from the bacterium Pseudomonas aeruginosa. To counteract fungal Mg2+ sequestration, P. aeruginosa expresses the Mg2+ transporter MgtA when Mg2+ levels are low. Thus, loss of MgtA specifically impairs P. aeruginosa in co-culture with C. albicans, but fitness can be restored by supplementing Mg2+. Using a panel of fungi and bacteria, we show that Mg2+ sequestration is a general mechanism of fungal antagonism against gram-negative bacteria. Mg2+ limitation enhances bacterial resistance to polymyxin antibiotics like colistin, which target gram-negative bacterial membranes. Indeed, experimental evolution reveals that P. aeruginosa evolves C. albicans-dependent colistin resistance via non-canonical means; antifungal treatment renders resistant bacteria colistin-sensitive. Our work suggests that fungal-bacterial competition could profoundly impact polymicrobial infection treatment with antibiotics of last resort.
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Affiliation(s)
- Yu-Ying Phoebe Hsieh
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Wanting Sun
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Janet M. Young
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Robin Cheung
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Deborah A. Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States of America
| | - Ajai A. Dandekar
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Harmit S. Malik
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
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27
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Liang D, Jiang Y, Zhang Y, Mao C, Ma T, Zhang C. The Comparative Genomics of Botryosphaeriaceae Suggests Gene Families of Botryosphaeria dothidea Related to Pathogenicity on Chinese Hickory Tree. J Fungi (Basel) 2024; 10:299. [PMID: 38667970 PMCID: PMC11051394 DOI: 10.3390/jof10040299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/07/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
Trunk canker poses a major threat to the production of Chinese hickory tree (Carya cathayensis Sarg.), which is primarily determined by Botryosphaeriaceae. In our previous work, we identified Botryosphaeria dothidea as the predominant pathogen of this disease. However, it is still unclear about corresponding gene families and mechanisms associated with B. dothidea's pathogenicity on Chinese hickory tree. Here, we present a comparative analysis of high-quality genome assemblies of Botryosphaeria dothidea and other isolated pathogens, showing highly syntenic relationships between B. dothidea and its closely related species and the conservative evolution of the Botryosphaeriaceae family. Higher GC contents were found in the genomes of B. dothidea and three other isolated pathogens (Botryshaeria cortices, Botryshaeria fabicerciana, and Botryshaeria qingyuanensis) compared to Macrophomina phaseolina, Neofusicoccum parvum, Diplodia corticola, and Lasiodiplodia theobromae. An investigation of genes specific to or expanded in B. dothidea revealed that one secreted glucanase, one orsellinic acid biosynthesis enzyme, and two MFS transporters positively regulated B. dothidea's pathogenicity. We also observed an overrepresentation of viral integrase like gene and heterokaryon incompatibility proteins in the B. dothidea's genome. In addition, we observed one LRR-domain-containing protein and two Sec-domain-containing proteins (Sec_1 and Sec_7) that underwent positive selection. This study will help to understand B. dothidea's pathogenicity and potential influence on the infection of Chinese hickory, which will help in the development of disease control and ensure the security of Chinese hickory production.
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Affiliation(s)
| | | | | | | | - Tianlin Ma
- College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forest University, Hangzhou 311300, China; (D.L.); (Y.J.); (Y.Z.); (C.M.)
| | - Chuanqing Zhang
- College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forest University, Hangzhou 311300, China; (D.L.); (Y.J.); (Y.Z.); (C.M.)
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28
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Seo HW, Wassano NS, Amir Rawa MS, Nickles GR, Damasio A, Keller NP. A Timeline of Biosynthetic Gene Cluster Discovery in Aspergillus fumigatus: From Characterization to Future Perspectives. J Fungi (Basel) 2024; 10:266. [PMID: 38667937 PMCID: PMC11051388 DOI: 10.3390/jof10040266] [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: 03/08/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
In 1999, the first biosynthetic gene cluster (BGC), synthesizing the virulence factor DHN melanin, was characterized in Aspergillus fumigatus. Since then, 19 additional BGCs have been linked to specific secondary metabolites (SMs) in this species. Here, we provide a comprehensive timeline of A. fumigatus BGC discovery and find that initial advances centered around the commonly expressed SMs where chemical structure informed rationale identification of the producing BGC (e.g., gliotoxin, fumigaclavine, fumitremorgin, pseurotin A, helvolic acid, fumiquinazoline). Further advances followed the transcriptional profiling of a ΔlaeA mutant, which aided in the identification of endocrocin, fumagillin, hexadehydroastechrome, trypacidin, and fumisoquin BGCs. These SMs and their precursors are the commonly produced metabolites in most A. fumigatus studies. Characterization of other BGC/SM pairs required additional efforts, such as induction treatments, including co-culture with bacteria (fumicycline/neosartoricin, fumigermin) or growth under copper starvation (fumivaline, fumicicolin). Finally, four BGC/SM pairs were discovered via overexpression technologies, including the use of heterologous hosts (fumicycline/neosartoricin, fumihopaside, sphingofungin, and sartorypyrone). Initial analysis of the two most studied A. fumigatus isolates, Af293 and A1160, suggested that both harbored ca. 34-36 BGCs. However, an examination of 264 available genomes of A. fumigatus shows up to 20 additional BGCs, with some strains showing considerable variations in BGC number and composition. These new BGCs present a new frontier in the future of secondary metabolism characterization in this important species.
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Affiliation(s)
- Hye-Won Seo
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; (H.-W.S.); (N.S.W.); (M.S.A.R.); (G.R.N.)
| | - Natalia S. Wassano
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; (H.-W.S.); (N.S.W.); (M.S.A.R.); (G.R.N.)
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), São Paulo 13083-970, Brazil;
| | - Mira Syahfriena Amir Rawa
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; (H.-W.S.); (N.S.W.); (M.S.A.R.); (G.R.N.)
| | - Grant R. Nickles
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; (H.-W.S.); (N.S.W.); (M.S.A.R.); (G.R.N.)
| | - André Damasio
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), São Paulo 13083-970, Brazil;
| | - Nancy P. Keller
- Department of Medical Microbiology and Immunology, University of Wisconsin, Madison, WI 53706, USA; (H.-W.S.); (N.S.W.); (M.S.A.R.); (G.R.N.)
- Department of Plant Pathology, University of Wisconsin, Madison, WI 53706, USA
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29
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Hoskisson PA, Barona-Gómez F, Rozen DE. Phenotypic heterogeneity in Streptomyces colonies. Curr Opin Microbiol 2024; 78:102448. [PMID: 38447313 DOI: 10.1016/j.mib.2024.102448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
Streptomyces are a large genus of multicellular bacteria best known for their prolific production of bioactive natural products. In addition, they play key roles in the mineralisation of insoluble resources, such as chitin and cellulose. Because of their multicellular mode of growth, colonies of interconnected hyphae extend over a large area that may experience different conditions in different parts of the colony. Here, we argue that within-colony phenotypic heterogeneity can allow colonies to simultaneously respond to divergent inputs from resources or competitors that are spatially and temporally dynamic. We discuss causal drivers of heterogeneity, including competitors, precursor availability, metabolic diversity and division of labour, that facilitate divergent phenotypes within Streptomyces colonies. We discuss the adaptive causes and consequences of within-colony heterogeneity, highlight current knowledge (gaps) and outline key questions for future studies.
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Affiliation(s)
- Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | | | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, The Netherlands.
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30
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Yurchenko AN, Nesterenko LE, Popov RS, Kirichuk NN, Chausova VE, Chingizova EA, Isaeva MP, Yurchenko EA. The Metabolite Profiling of Aspergillus fumigatus KMM4631 and Its Co-Cultures with Other Marine Fungi. Metabolites 2023; 13:1138. [PMID: 37999234 PMCID: PMC10673247 DOI: 10.3390/metabo13111138] [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: 09/30/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/25/2023] Open
Abstract
An Aspergillus fumigatus KMM 4631 strain was previously isolated from a Pacific soft coral Sinularia sp. sample and was found to be a source of a number of bioactive secondary metabolites. The aims of this work are the confirmation of this strain' identification based on ITS, BenA, CaM, and RPB2 regions/gene sequences and the investigation of secondary metabolite profiles of Aspergillus fumigatus KMM 4631 culture and its co-cultures with Penicillium hispanicum KMM 4689, Amphichorda sp. KMM 4639, Penicillium sp. KMM 4672, and Asteromyces cruciatus KMM 4696 from the Collection of Marine Microorganisms (PIBOC FEB RAS, Vladivostok, Russia). Moreover, the DPPH-radical scavenging activity, urease inhibition, and cytotoxicity of joint fungal cultures' extracts on HepG2 cells were tested. The detailed UPLC MS qTOF investigation resulted in the identification and annotation of indolediketopiperazine, quinazoline, and tryptoquivaline-related alkaloids as well as a number of polyketides (totally 20 compounds) in the extract of Aspergillus fumigatus KMM 4631. The metabolite profiles of the co-cultures of A. fumigatus with Penicillium hispanicum, Penicillium sp., and Amphichorda sp. were similar to those of Penicillium hispanicum, Penicillium sp., and Amphichorda sp. monocultures. The metabolite profile of the co-culture of A. fumigatus with Asteromyces cruciatus differed from that of each monoculture and may be more promising for the isolation of new compounds.
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Affiliation(s)
- Anton N. Yurchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Prospect 100-Letiya Vladivostoka, 159, Vladivostok 690022, Russia; (L.E.N.); (R.S.P.); (N.N.K.); (V.E.C.); (E.A.C.); (M.P.I.)
| | | | | | | | | | | | | | - Ekaterina A. Yurchenko
- G.B. Elyakov Pacific Institute of Bioorganic Chemistry, Far Eastern Branch of the Russian Academy of Sciences, Prospect 100-Letiya Vladivostoka, 159, Vladivostok 690022, Russia; (L.E.N.); (R.S.P.); (N.N.K.); (V.E.C.); (E.A.C.); (M.P.I.)
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31
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Dominique S, Alex PG, Christiane EY, Dodehe Y, Adèle KN. Diversity of Endophytic Fungi Isolated from the Bark of Ceiba pentandra (L.) Gaertn., (Bombacaceae) and Antibacterial Potential of Secalonic Acid A Produced by Diaporthe searlei EC 321. Chem Biodivers 2023; 20:e202301010. [PMID: 37814192 DOI: 10.1002/cbdv.202301010] [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: 07/12/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/11/2023]
Abstract
The objective of this study was to study the diversity of endophytic fungi isolated from Ceiba pentandra and to isolate their bioactive chemical compounds. The methodology used during this study consisted in isolating endophytic fungi from the bark of C. pentandra on Potato Agar. The isolates obtained were identified on the basis of the ITS regions of their ribosomal DNA. Antibacterial screening of the mycelium of endophytic fungi isolated was evaluated against multidrug-resistant E. coli and S. aureus strains. This screening led to the selection of isolates EC 321 and EC 28 for their ability to effectively inhibit the growth of the bacterial strains tested. EC 321 was grown and fermented on rice medium. Secondary metabolites were extracted with ethyl acetate. From the crude extract, secalonic acid A was isolated and identified by chromatographic and NMR. The in vitro activity of secalonic acid A against the growth of multiresistant bacterial strains was evaluated. Secalonic acid A was active against all multidrug-resistant bacterial strains E. coli 942, E. coli 4814, S. aureus 931, S. aureus 934, S. aureus MRSA 1872 and K. pneumonia 815 with respective MICs of 18.75; 18.75; 18.75; 4.7; 37.5 and 37.5 μg/mL.
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Affiliation(s)
- Sagou Dominique
- Biology and Health Laboratory, UFR des Biosciences, Félix Houphouët-Boigny University, 22 BP 582, Abidjan 22, Côte d'Ivoire
| | - Pakora Gilles Alex
- Biology and Health Laboratory, UFR des Biosciences, Félix Houphouët-Boigny University, 22 BP 582, Abidjan 22, Côte d'Ivoire
| | - Essoh You Christiane
- Department of Biochemistry-Genetics, UFR o f Biological Sciences, Péléforo Gon Coulibaly University, BP 1328, Korhogo, Côte d'Ivoire
| | - Yeo Dodehe
- Biology and Health Laboratory, UFR des Biosciences, Félix Houphouët-Boigny University, 22 BP 582, Abidjan 22, Côte d'Ivoire
| | - Kacou N'douba Adèle
- Department of Fundamental Sciences, UFR of Medical Sciences, BPV 166, Abidjan, Côte d'Ivoire
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Cowled MS, Kalaitzis JA, Crombie A, Chen R, Sbaraini N, Lacey E, Piggott AM. Fungal Duel between Penicillium brasilianum and Aspergillus nomius Results in Dual Induction of Miktospiromide A and Kitrinomycin A. JOURNAL OF NATURAL PRODUCTS 2023; 86:2398-2406. [PMID: 37737825 DOI: 10.1021/acs.jnatprod.3c00593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Cocultivation of the fungi Penicillium brasilianum MST-FP1927 and Aspergillus nomius MST-FP2004 resulted in the reciprocal induction of two new compounds, miktospiromide A (1) from A. nomius and kitrinomycin A (2) from P. brasilianum. A third new compound, kitrinomycin B (3), was also identified from an axenic culture of P. brasilianum, along with the previously reported compounds austalide K (4), 17S-dihydroaustalide K (5), verruculogen (6), and fumitremorgin B (7). The structures of 1-3 were elucidated by detailed spectroscopic analysis and DFT calculations, while 4-7 were identified by comparison to authentic standards. The genome of A. nomius MST-FP2004 was sequenced, and a putative biosynthetic gene cluster for 1 was identified. Compound 2 showed activity against murine melanoma NS-1 cells (LD99 7.8 μM) and the bovine parasite Tritrichomonas foetus (LD99 4.8 μM).
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Affiliation(s)
- Michael S Cowled
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - John A Kalaitzis
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Andrew Crombie
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - Rachel Chen
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - Nicolau Sbaraini
- School of Molecular Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - Ernest Lacey
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Microbial Screening Technologies Pty. Ltd., Smithfield, NSW 2164, Australia
| | - Andrew M Piggott
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
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Santamaría RI, Martínez-Carrasco A, Tormo JR, Martín J, Genilloud O, Reyes F, Díaz M. Interactions of Different Streptomyces Species and Myxococcus xanthus Affect Myxococcus Development and Induce the Production of DK-Xanthenes. Int J Mol Sci 2023; 24:15659. [PMID: 37958645 PMCID: PMC10649082 DOI: 10.3390/ijms242115659] [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: 09/19/2023] [Revised: 10/19/2023] [Accepted: 10/24/2023] [Indexed: 11/15/2023] Open
Abstract
The co-culturing of microorganisms is a well-known strategy to study microbial interactions in the laboratory. This approach facilitates the identification of new signals and molecules produced by one species that affects other species' behavior. In this work, we have studied the effects of the interaction of nine Streptomyces species (S. albidoflavus, S. ambofaciens, S. argillaceus, S. griseus, S. lividans, S. olivaceus, S. parvulus, S. peucetius, and S. rochei) with the predator bacteria Myxococcus xanthus, five of which (S. albidoflavus, S. griseus, S. lividans, S. olivaceus, and S. argillaceus) induce mound formation of M. xanthus on complex media (Casitone Yeast extract (CYE) and Casitone tris (CTT); media on which M. xanthus does not form these aggregates under normal culture conditions. An in-depth study on S. griseus-M. xanthus interactions (the Streptomyces strain producing the strongest effect) has allowed the identification of two siderophores produced by S. griseus, demethylenenocardamine and nocardamine, responsible for this grouping effect over M. xanthus. Experiments using pure commercial nocardamine and different concentrations of FeSO4 show that iron depletion is responsible for the behavior of M. xanthus. Additionally, it was found that molecules, smaller than 3 kDa, produced by S. peucetius can induce the production of DK-xanthenes by M. xanthus.
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Affiliation(s)
- Ramón I. Santamaría
- Instituto de Biología Funcional y Genómica (IBFG), Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, C/Zacarías González, nº 2, 37007 Salamanca, Spain;
| | - Ana Martínez-Carrasco
- Instituto de Biología Funcional y Genómica (IBFG), Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, C/Zacarías González, nº 2, 37007 Salamanca, Spain;
| | - José R. Tormo
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (J.R.T.); (J.M.); (O.G.); (F.R.)
| | - Jesús Martín
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (J.R.T.); (J.M.); (O.G.); (F.R.)
| | - Olga Genilloud
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (J.R.T.); (J.M.); (O.G.); (F.R.)
| | - Fernando Reyes
- Fundación MEDINA, Centro de Excelencia en Investigación de Medicamentos Innovadores en Andalucía, Avda. del Conocimiento 34, 18016 Granada, Spain; (J.R.T.); (J.M.); (O.G.); (F.R.)
| | - Margarita Díaz
- Instituto de Biología Funcional y Genómica (IBFG), Departamento de Microbiología y Genética, Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Salamanca, C/Zacarías González, nº 2, 37007 Salamanca, Spain;
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Embacher J, Zeilinger S, Kirchmair M, Rodriguez-R LM, Neuhauser S. Wood decay fungi and their bacterial interaction partners in the built environment – A systematic review on fungal bacteria interactions in dead wood and timber. FUNGAL BIOL REV 2023. [DOI: 10.1016/j.fbr.2022.100305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Kato-Noguchi H. The Impact and Invasive Mechanisms of Pueraria montana var. lobata, One of the World's Worst Alien Species. PLANTS (BASEL, SWITZERLAND) 2023; 12:3066. [PMID: 37687313 PMCID: PMC10490251 DOI: 10.3390/plants12173066] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/10/2023]
Abstract
Pueraria montana var. lobata is native to East Asia, and was introduced to many countries due to its potential for multiple uses. This species escaped under the management conditions soon after its introduction, and became a harmful weed species. This species has been listed in the top 100 of the world's worst invasive alien species. P. montana stands expand quickly and threaten the native flora and fauna including microbiota. This species affects the concentration of carbon and nitrogen in soil and aquatic environments, and increases the amount of pollutants in the local atmosphere. Its infestation also causes serious economic losses on forestry and agriculture. Its characteristics of fast growth, thick canopy structure, enormous vegetative reproduction, and adaptative ability to the various environmental conditions may contribute to the invasiveness and naturalization of this species. The characteristics of P. montana regarding their defense functions against their natural enemies and pathogens, and allelopathy may also contribute to the invasiveness of this species. Potential allelochemicals such as xanthoxins, p-coumaric acid, caffeic acid, methyl caffeate and daidzein, and two isoflavones with anti-virus activity were identified in this species. In addition, fewer herbivore insects were found in the introduced ranges. These characteristics of P. montana may be involved in the invasive mechanisms of the species. This is the first review article focusing on the invasive mechanisms of this species.
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Affiliation(s)
- Hisashi Kato-Noguchi
- Department of Applied Biological Science, Faculty of Agriculture, Kagawa University, Miki 761-0795, Kagawa, Japan
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Seibold PS, Lawrinowitz S, Raztsou I, Gressler M, Arndt HD, Stallforth P, Hoffmeister D. Bifurcate evolution of quinone synthetases in basidiomycetes. Fungal Biol Biotechnol 2023; 10:14. [PMID: 37400920 PMCID: PMC10316625 DOI: 10.1186/s40694-023-00162-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/14/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND The terphenylquinones represent an ecologically remarkable class of basidiomycete natural products as they serve as central precursors of pigments and compounds that impact on microbial consortia by modulating bacterial biofilms and motility. This study addressed the phylogenetic origin of the quinone synthetases that assemble the key terphenylquinones polyporic acid and atromentin. RESULTS The activity of the Hapalopilus rutilans synthetases HapA1, HapA2 and of Psilocybe cubensis PpaA1 were reconstituted in Aspergilli. Liquid chromatography and mass spectrometry of the culture extracts identified all three enzymes as polyporic acid synthetases. PpaA1 is unique in that it features a C-terminal, yet catalytically inactive dioxygenase domain. Combined with bioinformatics to reconstruct the phylogeny, our results demonstrate that basidiomycete polyporic acid and atromentin synthetases evolved independently, although they share an identical catalytic mechanism and release structurally very closely related products. A targeted amino acid replacement in the substrate binding pocket of the adenylation domains resulted in bifunctional synthetases producing both polyporic acid and atromentin. CONCLUSIONS Our results imply that quinone synthetases evolved twice independently in basidiomycetes, depending on the aromatic α-keto acid substrate. Furthermore, key amino acid residues for substrate specificity were identified and changed which led to a relaxed substrate profile. Therefore, our work lays the foundation for future targeted enzyme engineering.
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Affiliation(s)
- Paula Sophie Seibold
- Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Department Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Stefanie Lawrinowitz
- Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Department Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Ihar Raztsou
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-Universität Jena, Humboldtstrasse 10, 07743, Jena, Germany
| | - Markus Gressler
- Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany
- Department Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Hans-Dieter Arndt
- Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich-Schiller-Universität Jena, Humboldtstrasse 10, 07743, Jena, Germany
| | - Pierre Stallforth
- Department Paleobiotechnology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany
| | - Dirk Hoffmeister
- Institute of Pharmacy, Department Pharmaceutical Microbiology, Friedrich Schiller University Jena, Winzerlaer Strasse 2, 07745, Jena, Germany.
- Department Pharmaceutical Microbiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Knöll Institute, Winzerlaer Strasse 2, 07745, Jena, Germany.
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Luu GT, Little JC, Pierce EC, Morin M, Ertekin CA, Wolfe BE, Baars O, Dutton RJ, Sanchez LM. Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms. Analyst 2023; 148:3002-3018. [PMID: 37259951 PMCID: PMC10330857 DOI: 10.1039/d3an00408b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that metabolomic profiles are mainly comprised of fungi derived features, indicating that fungi are the key contributors to small molecules in BFIs. LC-inductively coupled plasma MS (LC-ICP-MS) and MS/MS based dereplication using database searching revealed the presence of several known fungal specialized metabolites and structurally related analogues in these extracts, including siderophores such as desferrichrome, desferricoprogen, and palmitoylcoprogen. Among these analogues, a novel putative coprogen analogue possessing a terminal carboxylic acid motif was identified from Scopulariopsis sp. JB370, a common cheese rind fungus, and its structure was elucidated via MS/MS fragmentation. Based on these findings, filamentous fungal species appear to be capable of producing multiple siderophores with potentially different biological roles (i.e. various affinities for different forms of iron). These findings highlight that fungal species are important contributors to microbiomes via their production of abundant specialized metabolites and that elucidating their role in complex communities should continue to be a priority.
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Affiliation(s)
- Gordon T Luu
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064, USA.
| | - Jessica C Little
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, 60612, USA
| | - Emily C Pierce
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093, USA
| | - Manon Morin
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093, USA
| | - Celine A Ertekin
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064, USA.
| | - Benjamin E Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, 02155, USA
- Tufts University Sensory and Science Center, Medford, Massachusetts, 02155, USA
| | - Oliver Baars
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, 27607, USA
| | - Rachel J Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093, USA
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, 92093, USA
| | - Laura M Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064, USA.
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Krespach MKC, Stroe MC, Netzker T, Rosin M, Zehner LM, Komor AJ, Beilmann JM, Krüger T, Scherlach K, Kniemeyer O, Schroeckh V, Hertweck C, Brakhage AA. Streptomyces polyketides mediate bacteria-fungi interactions across soil environments. Nat Microbiol 2023:10.1038/s41564-023-01382-2. [PMID: 37322111 DOI: 10.1038/s41564-023-01382-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 04/13/2023] [Indexed: 06/17/2023]
Abstract
Although the interaction between prokaryotic and eukaryotic microorganisms is crucial for the functioning of ecosystems, information about the processes driving microbial interactions within communities remains scarce. Here we show that arginine-derived polyketides (arginoketides) produced by Streptomyces species mediate cross-kingdom microbial interactions with fungi of the genera Aspergillus and Penicillium, and trigger the production of natural products. Arginoketides can be cyclic or linear, and a prominent example is azalomycin F produced by Streptomyces iranensis, which induces the cryptic orsellinic acid gene cluster in Aspergillus nidulans. Bacteria that synthesize arginoketides and fungi that decode and respond to this signal were co-isolated from the same soil sample. Genome analyses and a literature search indicate that arginoketide producers are found worldwide. Because, in addition to their direct impact, arginoketides induce a secondary wave of fungal natural products, they probably contribute to the wider structure and functioning of entire soil microbial communities.
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Affiliation(s)
- Mario K C Krespach
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Maria C Stroe
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
- Department of Microbiology, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Tina Netzker
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Maira Rosin
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Lukas M Zehner
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Anna J Komor
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Johanna M Beilmann
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
| | - Thomas Krüger
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Kirstin Scherlach
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Olaf Kniemeyer
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Volker Schroeckh
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Christian Hertweck
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany
- Department of Biomolecular Chemistry, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany
| | - Axel A Brakhage
- Department of Molecular and Applied Microbiology, Leibniz Institute for Natural Product Research and Infection Biology (Leibniz-HKI), Jena, Germany.
- Institute of Microbiology, Friedrich Schiller University Jena, Jena, Germany.
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Bogdanov A, Salib MN, Chase AB, Hammerlindl H, Muskat MN, Luedtke S, Barbosa da Silva E, O’Donoghue AJ, Wu LF, Altschuler SJ, Molinski TF, Jensen PR. Small Molecule in situ Resin Capture - A Compound First Approach to Natural Product Discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.02.530684. [PMID: 37398257 PMCID: PMC10312467 DOI: 10.1101/2023.03.02.530684] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Microbial natural products remain an important resource for drug discovery. Yet, commonly employed discovery techniques are plagued by the rediscovery of known compounds, the relatively few microbes that can be cultured, and laboratory growth conditions that do not elicit biosynthetic gene expression among myriad other challenges. Here we introduce a culture independent approach to natural product discovery that we call the Small Molecule In situ Resin Capture (SMIRC) technique. SMIRC exploits in situ environmental conditions to elicit compound production and represents a new approach to access poorly explored chemical space by capturing natural products directly from the environments in which they are produced. In contrast to traditional methods, this compound-first approach can capture structurally complex small molecules across all domains of life in a single deployment while relying on Nature to provide the complex and poorly understood environmental cues needed to elicit biosynthetic gene expression. We illustrate the effectiveness of SMIRC in marine habitats with the discovery of numerous new compounds and demonstrate that sufficient compound yields can be obtained for NMR-based structure assignment. Two new compound classes are reported including one novel carbon skeleton that possesses a functional group not previously observed among natural products and a second that possesses potent biological activity. We introduce expanded deployments, in situ cultivation, and metagenomics as methods to facilitate compound discovery, enhance yields, and link compounds to producing organisms. This compound first approach can provide unprecedented access to new natural product chemotypes with broad implications for drug discovery.
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Affiliation(s)
- Alexander Bogdanov
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mariam N. Salib
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexander B. Chase
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
- Department of Earth Sciences, Southern Methodist University, Dallas, TX 75275, USA
| | - Heinz Hammerlindl
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Mitchell N. Muskat
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephanie Luedtke
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Elany Barbosa da Silva
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Anthony J. O’Donoghue
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093
| | - Lani F. Wu
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Steven J. Altschuler
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Tadeusz F. Molinski
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Paul R. Jensen
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA 92093, USA
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Yazid SNE, Tajudin NI, Razman NAA, Selamat J, Ismail SI, Sanny M, Samsudin NIP. Mycotoxigenic fungal growth inhibition and multi-mycotoxin reduction of potential biological control agents indigenous to grain maize. Mycotoxin Res 2023:10.1007/s12550-023-00484-4. [PMID: 37219742 PMCID: PMC10204017 DOI: 10.1007/s12550-023-00484-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 05/03/2023] [Accepted: 05/09/2023] [Indexed: 05/24/2023]
Abstract
The present work investigated the potential of fungal species from grain maize farms in Malaysia as antagonists against the indigenous mycotoxigenic fungal species and their subsequent mycotoxin production. Dual-culture assay was conducted on grain maize agar (GMA) with 12 strains of potential fungal antagonists namely Bjerkandra adusta, Penicillium janthinellum, Schizophyllum commune, Trametes cubensis, Trichoderma asperelloides, Trichoderma asperellum, Trichoderma harzianum, and Trichoderma yunnanense against seven mycotoxigenic strains namely Aspergillus flavus, Aspergillus niger, Fusarium verticillioides, and Fusarium proliferatum producing aflatoxins, ochratoxin A, and fumonisins, respectively. Based on fungal growth inhibition, Trichoderma spp. showed the highest inhibitory activity (73-100% PIRG, Percentage Inhibition of Radial Growth; 28/0 ID, Index of Dominance) against the tested mycotoxigenic strains. Besides, B. adusta and Tra. cubensis showed inhibitory activity against some of the tested mycotoxigenic strains. All fungal antagonists showed varying degrees of mycotoxin reduction. Aflatoxin B1 produced by A. flavus was mainly reduced by P. janthinellum, Tra. cubensis, and B. adusta to 0 ng/g. Ochratoxin A produced by A. niger was mainly reduced by Tri. harzianum and Tri. asperellum to 0 ng/g. Fumonisin B1 and FB2 produced by F. verticillioides was mainly reduced by Tri. harzianum, Tri. asperelloides, and Tri. asperellum to 59.4 and 0 µg/g, respectively. Fumonisin B1 and FB2 produced by F. proliferatum were mainly reduced by Tri. asperelloides and Tri. harzianum to 244.2 and 0 µg/g, respectively. This is the first study that reports on the efficacy of Tri. asperelloides against FB1, FB2, and OTA, P. janthinellum against AFB1, and Tra. cubensis against AFB1.
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Affiliation(s)
- Siti Nur Ezzati Yazid
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Nur Izzah Tajudin
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Nur Aina Aribah Razman
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Jinap Selamat
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Siti Izera Ismail
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Plant Protection, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Maimunah Sanny
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia
| | - Nik Iskandar Putra Samsudin
- Laboratory of Food Safety and Food Integrity, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 UPM, Serdang, Selangor, Malaysia.
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Gasparek M, Steel H, Papachristodoulou A. Deciphering mechanisms of production of natural compounds using inducer-producer microbial consortia. Biotechnol Adv 2023; 64:108117. [PMID: 36813010 DOI: 10.1016/j.biotechadv.2023.108117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/22/2023]
Abstract
Living organisms produce a wide range of metabolites. Because of their potential antibacterial, antifungal, antiviral, or cytostatic properties, such natural molecules are of high interest to the pharmaceutical industry. In nature, these metabolites are often synthesized via secondary metabolic biosynthetic gene clusters that are silent under the typical culturing conditions. Among different techniques used to activate these silent gene clusters, co-culturing of "producer" species with specific "inducer" microbes is a particularly appealing approach due to its simplicity. Although several "inducer-producer" microbial consortia have been reported in the literature and hundreds of different secondary metabolites with attractive biopharmaceutical properties have been described as a result of co-cultivating inducer-producer consortia, less attention has been devoted to the understanding of the mechanisms and possible means of induction for production of secondary metabolites in co-cultures. This lack of understanding of fundamental biological functions and inter-species interactions significantly limits the diversity and yield of valuable compounds using biological engineering tools. In this review, we summarize and categorize the known physiological mechanisms of production of secondary metabolites in inducer-producer consortia, and then discuss approaches that could be exploited to optimize the discovery and production of secondary metabolites.
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Affiliation(s)
- Miroslav Gasparek
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom.
| | - Harrison Steel
- Department of Engineering Science, University of Oxford, Parks Road, Oxford OX1 3PJ, United Kingdom
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Jo C, Bernstein DB, Vaisman N, Frydman HM, Segrè D. Construction and Modeling of a Coculture Microplate for Real-Time Measurement of Microbial Interactions. mSystems 2023; 8:e0001721. [PMID: 36802169 PMCID: PMC10134821 DOI: 10.1128/msystems.00017-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 01/24/2023] [Indexed: 02/23/2023] Open
Abstract
The dynamic structures of microbial communities emerge from the complex network of interactions between their constituent microorganisms. Quantitative measurements of these interactions are important for understanding and engineering ecosystem structure. Here, we present the development and application of the BioMe plate, a redesigned microplate device in which pairs of wells are separated by porous membranes. BioMe facilitates the measurement of dynamic microbial interactions and integrates easily with standard laboratory equipment. We first applied BioMe to recapitulate recently characterized, natural symbiotic interactions between bacteria isolated from the Drosophila melanogaster gut microbiome. Specifically, the BioMe plate allowed us to observe the benefit provided by two Lactobacillus strains to an Acetobacter strain. We next explored the use of BioMe to gain quantitative insight into the engineered obligate syntrophic interaction between a pair of Escherichia coli amino acid auxotrophs. We integrated experimental observations with a mechanistic computational model to quantify key parameters associated with this syntrophic interaction, including metabolite secretion and diffusion rates. This model also allowed us to explain the slow growth observed for auxotrophs growing in adjacent wells by demonstrating that, under the relevant range of parameters, local exchange between auxotrophs is essential for efficient growth. The BioMe plate provides a scalable and flexible approach for the study of dynamic microbial interactions. IMPORTANCE Microbial communities participate in many essential processes from biogeochemical cycles to the maintenance of human health. The structure and functions of these communities are dynamic properties that depend on poorly understood interactions among different species. Unraveling these interactions is therefore a crucial step toward understanding natural microbiota and engineering artificial ones. Microbial interactions have been difficult to measure directly, largely due to limitations of existing methods to disentangle the contribution of different organisms in mixed cocultures. To overcome these limitations, we developed the BioMe plate, a custom microplate-based device that enables direct measurement of microbial interactions, by detecting the abundance of segregated populations of microbes that can exchange small molecules through a membrane. We demonstrated the possible application of the BioMe plate for studying both natural and artificial consortia. BioMe is a scalable and accessible platform that can be used to broadly characterize microbial interactions mediated by diffusible molecules.
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Affiliation(s)
- Charles Jo
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - David B. Bernstein
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Natalie Vaisman
- Department of Biology, Boston University, Boston, Massachusetts, USA
- CAPES Foundation, Ministry of Education of Brazil, Brasília, Brazil
| | | | - Daniel Segrè
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Biological Design Center, Boston University, Boston, Massachusetts, USA
- Department of Biology, Boston University, Boston, Massachusetts, USA
- Program in Bioinformatics, Boston University, Boston, Massachusetts, USA
- Department of Physics, Boston University, Boston, Massachusetts, USA
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Alanzi A, Elhawary EA, Ashour ML, Moussa AY. Aspergillus co-cultures: A recent insight into their secondary metabolites and microbial interactions. Arch Pharm Res 2023; 46:273-298. [PMID: 37032397 DOI: 10.1007/s12272-023-01442-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 02/28/2023] [Indexed: 04/11/2023]
Abstract
There is an urgent need for novel antibiotics to combat emerging resistant microbial strains. One of the most pressing resources is Aspergillus microbial cocultures. The genome of Aspergillus species comprises a far larger number of novel gene clusters than previously expected, and novel strategies and approaches are essential to exploit this potential source of new drugs and pharmacological agents. This is the first review consulting recent developments and chemical diversity of Aspergillus cocultures and highlighting its untapped richness. The analyzed data revealed that cocultivation of several Aspergillus species with other microorganisms, including bacteria, plants, and fungi, is a source of novel bioactive natural products. Various vital chemical skeleton leads were newly produced or augmented in Aspergillus cocultures, among which were taxol, cytochalasans, notamides, pentapeptides, silibinin, and allianthrones. The possibility of mycotoxin production or complete elimination in cocultivations was detected, which pave the way for better decontamination strategies. Most cocultures revealed a remarkable improvement in their antimicrobial or cytotoxic behavior due to their produced chemical patterns; for instance, weldone and asperterrin whose antitumor and antibacterial activities, respectively, were superior. Microbial cocultivation elicited the upregulation or production of specific metabolites whose importance and significance are yet to be revealed. With more than 155 compounds isolated from Aspergillus cocultures in the last 10 years, showing overproduction, reduction, or complete suppression under the optimized coculture circumstances, this study filled a gap for medicinal chemists searching for new lead sources or bioactive molecules as anticancer agents or antimicrobials.
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Affiliation(s)
- Abdullah Alanzi
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Esraa A Elhawary
- Department of Pharmacognosy, Faculty of Pharmacy, Ain shams University, Cairo, 11566, Egypt
| | - Mohamed L Ashour
- Department of Pharmacognosy, Faculty of Pharmacy, Ain shams University, Cairo, 11566, Egypt
- Pharmacy Program, Department of Pharmaceutical Science, Batterjee Medical College, 21442, Jeddah, Saudi Arabia
| | - Ashaimaa Y Moussa
- Department of Pharmacognosy, Faculty of Pharmacy, Ain shams University, Cairo, 11566, Egypt.
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Luu GT, Little JC, Pierce EC, Morin M, Ertekin CA, Wolfe BE, Baars O, Dutton RJ, Sanchez LM. Metabolomics of bacterial-fungal pairwise interactions reveal conserved molecular mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.532449. [PMID: 36993360 PMCID: PMC10054941 DOI: 10.1101/2023.03.13.532449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Bacterial-fungal interactions (BFIs) can shape the structure of microbial communities, but the small molecules mediating these BFIs are often understudied. We explored various optimization steps for our microbial culture and chemical extraction protocols for bacterial-fungal co-cultures, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) revealed that metabolomic profiles are mainly comprised of fungi derived features, indicating that fungi are the key contributors to small molecule mediated BFIs. LC-inductively coupled plasma MS (LC-ICP-MS) and MS/MS based dereplication using database searching revealed the presence of several known fungal specialized metabolites and structurally related analogues in these extracts, including siderophores such as desferrichrome, desferricoprogen, and palmitoylcoprogen. Among these analogues, a novel putative coprogen analogue possessing a terminal carboxylic acid motif was identified from Scopulariopsis spp. JB370, a common cheese rind fungus, and its structure was elucidated via MS/MS fragmentation. Based on these findings, filamentous fungal species appear to be capable of producing multiple siderophores with potentially different biological roles (i.e. various affinities for different forms of iron). These findings highlight that fungal species are important contributors to microbiomes via their production of abundant specialized metabolites and their role in complex communities should continue to be a priority.
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Affiliation(s)
- Gordon T. Luu
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064
| | - Jessica C. Little
- Department of Pharmaceutical Sciences, University of Illinois at Chicago, Chicago, Illinois, 60612
| | - Emily C. Pierce
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093
| | - Manon Morin
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093
| | - Celine A. Ertekin
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064
| | - Benjamin E. Wolfe
- Department of Biology, Tufts University, Medford, Massachusetts, 02155
- Tufts University Sensory and Science Center, Medford Massachusetts, 02155
| | - Oliver Baars
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, North Carolina, 27607
| | - Rachel J. Dutton
- Division of Biological Sciences, University of California San Diego, La Jolla, California, 92093
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, 92093
| | - Laura M. Sanchez
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, California, 95064
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Bai X, Sheng Y, Tang Z, Pan J, Wang S, Tang B, Zhou T, Shi L, Zhang H. Polyketides as Secondary Metabolites from the Genus Aspergillus. J Fungi (Basel) 2023; 9:261. [PMID: 36836375 PMCID: PMC9962652 DOI: 10.3390/jof9020261] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Polyketides are an important class of structurally diverse natural products derived from a precursor molecule consisting of a chain of alternating ketone and methylene groups. These compounds have attracted the worldwide attention of pharmaceutical researchers since they are endowed with a wide array of biological properties. As one of the most common filamentous fungi in nature, Aspergillus spp. is well known as an excellent producer of polyketide compounds with therapeutic potential. By extensive literature search and data analysis, this review comprehensively summarizes Aspergillus-derived polyketides for the first time, regarding their occurrences, chemical structures and bioactivities as well as biosynthetic logics.
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Affiliation(s)
- Xuelian Bai
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yue Sheng
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Zhenxing Tang
- School of Culinary Arts, Tourism College of Zhejiang, Hangzhou 311231, China
| | - Jingyi Pan
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Shigui Wang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Bin Tang
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Ting Zhou
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Lu’e Shi
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Huawei Zhang
- School of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou 310014, China
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The Potential Use of Fungal Co-Culture Strategy for Discovery of New Secondary Metabolites. Microorganisms 2023; 11:microorganisms11020464. [PMID: 36838429 PMCID: PMC9965835 DOI: 10.3390/microorganisms11020464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/15/2023] Open
Abstract
Fungi are an important and prolific source of secondary metabolites (SMs) with diverse chemical structures and a wide array of biological properties. In the past two decades, however, the number of new fungal SMs by traditional monoculture method had been greatly decreasing. Fortunately, a growing number of studies have shown that co-culture strategy is an effective approach to awakening silent SM biosynthetic gene clusters (BGCs) in fungal strains to produce cryptic SMs. To enrich our knowledge of this approach and better exploit fungal biosynthetic potential for new drug discovery, this review comprehensively summarizes all fungal co-culture methods and their derived new SMs as well as bioactivities on the basis of an extensive literature search and data analysis. Future perspective on fungal co-culture study, as well as its interaction mechanism, is supplied.
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Selegato DM, Castro-Gamboa I. Enhancing chemical and biological diversity by co-cultivation. Front Microbiol 2023; 14:1117559. [PMID: 36819067 PMCID: PMC9928954 DOI: 10.3389/fmicb.2023.1117559] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/06/2023] [Indexed: 02/04/2023] Open
Abstract
In natural product research, microbial metabolites have tremendous potential to provide new therapeutic agents since extremely diverse chemical structures can be found in the nearly infinite microbial population. Conventionally, these specialized metabolites are screened by single-strain cultures. However, owing to the lack of biotic and abiotic interactions in monocultures, the growth conditions are significantly different from those encountered in a natural environment and result in less diversity and the frequent re-isolation of known compounds. In the last decade, several methods have been developed to eventually understand the physiological conditions under which cryptic microbial genes are activated in an attempt to stimulate their biosynthesis and elicit the production of hitherto unexpressed chemical diversity. Among those, co-cultivation is one of the most efficient ways to induce silenced pathways, mimicking the competitive microbial environment for the production and holistic regulation of metabolites, and has become a golden methodology for metabolome expansion. It does not require previous knowledge of the signaling mechanism and genome nor any special equipment for cultivation and data interpretation. Several reviews have shown the potential of co-cultivation to produce new biologically active leads. However, only a few studies have detailed experimental, analytical, and microbiological strategies for efficiently inducing bioactive molecules by co-culture. Therefore, we reviewed studies applying co-culture to induce secondary metabolite pathways to provide insights into experimental variables compatible with high-throughput analytical procedures. Mixed-fermentation publications from 1978 to 2022 were assessed regarding types of co-culture set-ups, metabolic induction, and interaction effects.
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Berry O, Briand E, Bagot A, Chaigné M, Meslet-Cladière L, Wang J, Grovel O, Jansen JJ, Ruiz N, du Pont TR, Pouchus YF, Hess P, Bertrand S. Deciphering interactions between the marine dinoflagellate Prorocentrum lima and the fungus Aspergillus pseudoglaucus. Environ Microbiol 2023; 25:250-267. [PMID: 36333915 PMCID: PMC10100339 DOI: 10.1111/1462-2920.16271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/28/2022] [Indexed: 11/07/2022]
Abstract
The comprehension of microbial interactions is one of the key challenges in marine microbial ecology. This study focused on exploring chemical interactions between the toxic dinoflagellate Prorocentrum lima and a filamentous fungal species, Aspergillus pseudoglaucus, which has been isolated from the microalgal culture. Such interspecies interactions are expected to occur even though they were rarely studied. Here, a co-culture system was designed in a dedicated microscale marine-like condition. This system allowed to explore microalgal-fungal physical and metabolic interactions in presence and absence of the bacterial consortium. Microscopic observation showed an unusual physical contact between the fungal mycelium and dinoflagellate cells. To delineate specialized metabolome alterations during microalgal-fungal co-culture metabolomes were monitored by high-performance liquid chromatography coupled to high-resolution mass spectrometry. In-depth multivariate statistical analysis using dedicated approaches highlighted (1) the metabolic alterations associated with microalgal-fungal co-culture, and (2) the impact of associated bacteria in microalgal metabolome response to fungal interaction. Unfortunately, only a very low number of highlighted features were fully characterized. However, an up-regulation of the dinoflagellate toxins okadaic acid and dinophysistoxin 1 was observed during co-culture in supernatants. Such results highlight the importance to consider microalgal-fungal interactions in the study of parameters regulating toxin production.
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Affiliation(s)
- Olivier Berry
- Institut des Substances et Organismes de la Mer, ISOMer, Nantes Université, UR 2160, Nantes, France
| | | | - Alizé Bagot
- Institut des Substances et Organismes de la Mer, ISOMer, Nantes Université, UR 2160, Nantes, France
- IFREMER, PHYTOX, Nantes, France
| | - Maud Chaigné
- Institut des Substances et Organismes de la Mer, ISOMer, Nantes Université, UR 2160, Nantes, France
- IFREMER, PHYTOX, Nantes, France
| | - Laurence Meslet-Cladière
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, Plouzané, France
| | - Julien Wang
- Institut des Substances et Organismes de la Mer, ISOMer, Nantes Université, UR 2160, Nantes, France
| | - Olivier Grovel
- Institut des Substances et Organismes de la Mer, ISOMer, Nantes Université, UR 2160, Nantes, France
| | - Jeroen J Jansen
- Radboud University, Institute for Molecules and Materials, Nijmegen, The Netherlands
| | - Nicolas Ruiz
- Institut des Substances et Organismes de la Mer, ISOMer, Nantes Université, UR 2160, Nantes, France
| | - Thibaut Robiou du Pont
- Institut des Substances et Organismes de la Mer, ISOMer, Nantes Université, UR 2160, Nantes, France
| | - Yves François Pouchus
- Institut des Substances et Organismes de la Mer, ISOMer, Nantes Université, UR 2160, Nantes, France
| | | | - Samuel Bertrand
- Institut des Substances et Organismes de la Mer, ISOMer, Nantes Université, UR 2160, Nantes, France
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Wang Y, Chen Y, Xin J, Chen X, Xu T, He J, Pan Z, Zhang C. Metabolomic profiles of the liquid state fermentation in co-culture of Eurotium amstelodami and Bacillus licheniformis. Front Microbiol 2023; 14:1080743. [PMID: 36778878 PMCID: PMC9909110 DOI: 10.3389/fmicb.2023.1080743] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
As an important source of new drug molecules, secondary metabolites (SMs) produced by microorganisms possess important biological activities, such as antibacterial, anti-inflammatory, and hypoglycemic effects. However, the true potential of microbial synthesis of SMs has not been fully elucidated as the SM gene clusters remain silent under laboratory culture conditions. Herein, we evaluated the inhibitory effect of Staphylococcus aureus by co-culture of Eurotium amstelodami and three Bacillus species, including Bacillus licheniformis, Bacillus subtilis, and Bacillus amyloliquefaciens. In addition, a non-target approach based on ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOF-MS) was used to detect differences in extracellular and intracellular metabolites. Notably, the co-culture of E. amstelodami and Bacillus spices significantly improved the inhibitory effect against S. aureus, with the combination of E. amstelodami and B. licheniformis showing best performance. Metabolomics data further revealed that the abundant SMs, such as Nummularine B, Lucidenic acid E2, Elatoside G, Aspergillic acid, 4-Hydroxycyclohexylcarboxylic acid, Copaene, and Pipecolic acid were significantly enhanced in co-culture. Intracellularly, the differential metabolites were involved in the metabolism of amino acids, nucleic acids, and glycerophospholipid. Overall, this work demonstrates that the co-culture strategy is beneficial for inducing biosynthesis of active metabolites in E. amstelodami and B. licheniformis.
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Affiliation(s)
| | | | | | | | | | | | | | - Chuanbo Zhang
- Laboratory of Microbial Resources and Industrial Application, College of Life Sciences, Guizhou Normal University, Guiyang, China
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Kalra R, Conlan XA, Goel M. Recent advances in research for potential utilization of unexplored lichen metabolites. Biotechnol Adv 2023; 62:108072. [PMID: 36464145 DOI: 10.1016/j.biotechadv.2022.108072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/28/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022]
Abstract
Several research studies have shown that lichens are productive organisms for the synthesis of a broad range of secondary metabolites. Lichens are a self-sustainable stable microbial ecosystem comprising an exhabitant fungal partner (mycobiont) and at least one or more photosynthetic partners (photobiont). The successful symbiosis is responsible for their persistence throughout time and allows all the partners (holobionts) to thrive in many extreme habitats, where without the synergistic relationship they would be rare or non-existent. The ability to survive in harsh conditions can be directly correlated with the production of some unique metabolites. Despite the potential applications, these unique metabolites have been underutilised by pharmaceutical and agrochemical industries due to their slow growth, low biomass availability and technical challenges involved in their artificial cultivation. However, recent development of biotechnological tools such as molecular phylogenetics, modern tissue culture techniques, metabolomics and molecular engineering are opening up a new opportunity to exploit these compounds within the lichen holobiome for industrial applications. This review also highlights the recent advances in culturing the symbionts and the computational and molecular genetics approaches of lichen gene regulation recognized for the enhanced production of target metabolites. The recent development of multi-omics novel biodiscovery strategies aided by synthetic biology in order to study the heterologous expressed lichen-derived biosynthetic gene clusters in a cultivatable host offers a promising means for a sustainable supply of specialized metabolites.
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Affiliation(s)
- Rishu Kalra
- Sustainable Agriculture Program, The Energy and Resources Institute, Gurugram, Haryana, India
| | - Xavier A Conlan
- Deakin University, School of Life and Environmental Sciences, Geelong, Victoria, Australia
| | - Mayurika Goel
- Sustainable Agriculture Program, The Energy and Resources Institute, Gurugram, Haryana, India.
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