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Fernando K, Reddy P, Spangenberg GC, Rochfort SJ, Guthridge KM. Metabolic Potential of Epichloë Endophytes for Host Grass Fungal Disease Resistance. Microorganisms 2021; 10:64. [PMID: 35056512 PMCID: PMC8781568 DOI: 10.3390/microorganisms10010064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/24/2021] [Indexed: 12/27/2022] Open
Abstract
Asexual species of the genus Epichloë (Clavicipitaceae, Ascomycota) form endosymbiotic associations with Pooidae grasses. This association is important both ecologically and to the pasture and turf industries, as the endophytic fungi confer a multitude of benefits to their host plant that improve competitive ability and performance such as growth promotion, abiotic stress tolerance, pest deterrence and increased host disease resistance. Biotic stress tolerance conferred by the production of bioprotective metabolites has a critical role in an industry context. While the known antimammalian and insecticidal toxins are well characterized due to their impact on livestock welfare, antimicrobial metabolites are less studied. Both pasture and turf grasses are challenged by many phytopathogenic diseases that result in significant economic losses and impact livestock health. Further investigations of Epichloë endophytes as natural biocontrol agents can be conducted on strains that are safe for animals. With the additional benefits of possessing host disease resistance, these strains would increase their commercial importance. Field reports have indicated that pasture grasses associated with Epichloë endophytes are superior in resisting fungal pathogens. However, only a few antifungal compounds have been identified and chemically characterized, and these from sexual (pathogenic) Epichloë species, rather than those utilized to enhance performance in turf and pasture industries. This review provides insight into the various strategies reported in identifying antifungal activity from Epichloë endophytes and, where described, the associated antifungal metabolites responsible for the activity.
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Affiliation(s)
- Krishni Fernando
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (K.F.); (P.R.); (G.C.S.); (S.J.R.)
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Priyanka Reddy
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (K.F.); (P.R.); (G.C.S.); (S.J.R.)
| | - German C. Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (K.F.); (P.R.); (G.C.S.); (S.J.R.)
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Simone J. Rochfort
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (K.F.); (P.R.); (G.C.S.); (S.J.R.)
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Kathryn M. Guthridge
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083, Australia; (K.F.); (P.R.); (G.C.S.); (S.J.R.)
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A classification of liquid chromatography mass spectrometry techniques for evaluation of chemical composition and quality control of traditional medicines. J Chromatogr A 2019; 1609:460501. [PMID: 31515074 DOI: 10.1016/j.chroma.2019.460501] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Revised: 08/06/2019] [Accepted: 08/29/2019] [Indexed: 12/25/2022]
Abstract
Natural products (NPs) and traditional medicines (TMs) are used for treatment of various diseases and also to develop new drugs. However, identification of drug leads within the immense biodiversity of living organisms is a challenging task that requires considerable time, labor, and computational resources as well as the application of modern analytical instruments. LC-MS platforms are widely used for both drug discovery and quality control of TMs and food supplements. Moreover, a large dataset generated during LC-MS analysis contains valuable information that could be extracted and handled by means of various data mining and statistical tools. Novel sophisticated LC-MS based approaches are being introduced every year. Therefore, this review is prepared for the scientists specialized in pharmacognosy and analytical chemistry of NPs as well as working in related areas, in order to navigate them in the world of diverse LC-MS based techniques and strategies currently employed for NP discovery and dereplication, quality control, pattern recognition and sample comparison, and also in targeted and untargeted metabolomic studies. The suggested classification system includes the following LC-MS based procedures: elemental composition determination, isotopic fine structure analysis, mass defect filtering, de novo identification, clustering of the compounds in Molecular Networking (MN), diagnostic fragment ion (or neutral loss) filtering, manual dereplication using MS/MS data, database-assisted peak annotation, annotation of spectral trees, MS fingerprinting, feature extraction, bucketing of LC-MS data, peak profiling, predicted metabolite screening, targeted quantification of biomarkers, quantitative analysis of multi-component system, construction of chemical fingerprints, multi-targeted and untargeted metabolite profiling.
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Tan ZQ, Leow HY, Lee DCW, Karisnan K, Song AAL, Mai CW, Yap WS, Lim SHE, Lai KS. Co-Culture Systems for the Production of Secondary Metabolites: Current and Future Prospects. ACTA ACUST UNITED AC 2019. [DOI: 10.2174/1874070701913010018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Microorganisms are the great sources of Natural Products (NPs); these are imperative to their survival apart from conferring competitiveness amongst each other within their environmental niches. Primary and secondary metabolites are the two major classes of NPs that help in cell development, where antimicrobial activity is closely linked with secondary metabolites. To capitalize on the effects of secondary metabolites, co-culture methods have been often used to develop an artificial microbial community that promotes the action of these metabolites. Different analytical techniques will subsequently be employed based on the metabolite specificity and sensitivity to further enhance the metabolite induction. Liquid Chromatography-Mass Spectrometry (LC-MS) and Gas Chromatography (GC)-MS are commonly used for metabolite separation while Nuclear Magnetic Resonance (NMR) and Mass Spectrometry (MS) have been used as tools to elucidate the structure of compounds. This review intends to discuss current systems in use for co-culture in addition to its advantages, with discourse into the investigation of specific techniques in use for the detailed study of secondary metabolites. Further advancements and focus on co-culture technologies are required to fully realize the massive potential in synthetic biological systems.
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Tabudravu JN, Pellissier L, Smith AJ, Subko K, Autréau C, Feussner K, Hardy D, Butler D, Kidd R, Milton EJ, Deng H, Ebel R, Salonna M, Gissi C, Montesanto F, Kelly SM, Milne BF, Cimpan G, Jaspars M. LC-HRMS-Database Screening Metrics for Rapid Prioritization of Samples to Accelerate the Discovery of Structurally New Natural Products. JOURNAL OF NATURAL PRODUCTS 2019; 82:211-220. [PMID: 30735391 DOI: 10.1021/acs.jnatprod.8b00575] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In order to accelerate the isolation and characterization of structurally new or novel secondary metabolites, it is crucial to develop efficient strategies that prioritize samples with greatest promise early in the workflow so that resources can be utilized in a more efficient and cost-effective manner. We have developed a metrics-based prioritization approach using exact LC-HRMS, which uses data for 24 618 marine natural products held in the PharmaSea database. Each sample was evaluated and allocated a metric score by a software algorithm based on the ratio of new masses over the total (sample novelty), ratio of known masses over the total (chemical novelty), number of peaks above a defined peak area threshold (sample complexity), and peak area (sample diversity). Samples were then ranked and prioritized based on these metric scores. To validate the approach, eight marine sponges and six tunicate samples collected from the Fiji Islands were analyzed, metric scores calculated, and samples targeted for isolation and characterization of new compounds. Structures of new compounds were elucidated by spectroscopic techniques, including 1D and 2D NMR, MS, and MS/MS. Structures were confirmed by computer-assisted structure elucidation methods (CASE) using the ACD/Structure Elucidator Suite.
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Affiliation(s)
- Jioji N Tabudravu
- School of Forensic and Applied Sciences, Faculty of Science & Technology , University of Central Lancashire , Preston , Lancashire PR1 2HE , U.K
- Marine Biodiscovery Centre, Department of Chemistry , University of Aberdeen , Aberdeen AB24 3UE , Scotland, U.K
| | - Léonie Pellissier
- Marine Biodiscovery Centre, Department of Chemistry , University of Aberdeen , Aberdeen AB24 3UE , Scotland, U.K
| | - Alan James Smith
- Marine Biodiscovery Centre, Department of Chemistry , University of Aberdeen , Aberdeen AB24 3UE , Scotland, U.K
| | - Karolina Subko
- Marine Biodiscovery Centre, Department of Chemistry , University of Aberdeen , Aberdeen AB24 3UE , Scotland, U.K
| | - Caroline Autréau
- Marine Biodiscovery Centre, Department of Chemistry , University of Aberdeen , Aberdeen AB24 3UE , Scotland, U.K
| | - Klaus Feussner
- Institute of Applied Sciences, Faculty of Science, Technology and Environment , University of the South Pacific , Laucala Campus, Private Mail Bag, Suva , Fiji Islands
| | - David Hardy
- Thermo Fisher Scientific , Altrincham Business Park, 1 St George's Court , Altrincham WA14 5TP , U.K
| | - Daniel Butler
- Advanced Chemistry Development , UK Ltd. Venture House, Arlington Square, Downshire Way, Bracknell, Berks RG12 1WA , U.K
| | - Richard Kidd
- Publisher, Data & Databases , Royal Society of Chemistry , Thomas Graham House, Science Park, Milton Road , Cambridge CB4 0WF , U.K
| | - Edward J Milton
- Advanced Chemistry Development , UK Ltd. Venture House, Arlington Square, Downshire Way, Bracknell, Berks RG12 1WA , U.K
| | - Hai Deng
- Marine Biodiscovery Centre, Department of Chemistry , University of Aberdeen , Aberdeen AB24 3UE , Scotland, U.K
| | - Rainer Ebel
- Marine Biodiscovery Centre, Department of Chemistry , University of Aberdeen , Aberdeen AB24 3UE , Scotland, U.K
| | - Marika Salonna
- Department of Biosciences, Biotechnologies and Biopharmaceutics , University of Bari "A. Moro" , Via Orabona 4 , 70125 Bari , Italy
| | - Carmela Gissi
- Department of Biosciences, Biotechnologies and Biopharmaceutics , University of Bari "A. Moro" , Via Orabona 4 , 70125 Bari , Italy
- IBIOM, Istituto di Biomembrane, Bioenergetica e Biotecnologie Molecolari, CNR , Via Amendola 165/A , 70126 Bari , Italy
| | - Federica Montesanto
- Department of Biology - LRU CoNISMa , University of Bari , Via Orabona 4 , 70125 Bari , Italy
| | - Sharon M Kelly
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences , University of Glasgow , Glasgow G128QQ , U.K
| | - Bruce F Milne
- CFisUC, Department of Physics , University of Coimbra , Rua Larga, 3004-516 , Coimbra , Portugal
| | - Gabriela Cimpan
- Advanced Chemistry Development , UK Ltd. Venture House, Arlington Square, Downshire Way, Bracknell, Berks RG12 1WA , U.K
| | - Marcel Jaspars
- Marine Biodiscovery Centre, Department of Chemistry , University of Aberdeen , Aberdeen AB24 3UE , Scotland, U.K
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Sonnenschein EC, Stierhof M, Goralczyk S, Vabre FM, Pellissier L, Hanssen KØ, de la Cruz M, Díaz C, de Witte P, Copmans D, Andersen JH, Hansen E, Kristoffersen V, Tormo JR, Ebel R, Milne BF, Deng H, Gram L, Jaspars M, Tabudravu JN. Pseudochelin A, a siderophore of Pseudoalteromonas piscicida S2040. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.03.051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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6
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Rakshith D, Santosh P, Pradeep TP, Gurudatt DM, Baker S, Yashavantha Rao HC, Pasha A, Satish S. Application of Bioassay-Guided Fractionation Coupled with a Molecular Approach for the Dereplication of Antimicrobial Metabolites. Chromatographia 2016. [DOI: 10.1007/s10337-016-3188-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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7
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de Medeiros LS, Abreu LM, Nielsen A, Ingmer H, Larsen TO, Nielsen KF, Rodrigues-Filho E. Dereplication-guided isolation of depsides thielavins S-T and lecanorins D-F from the endophytic fungus Setophoma sp. PHYTOCHEMISTRY 2015; 111:154-162. [PMID: 25586883 DOI: 10.1016/j.phytochem.2014.12.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 11/13/2014] [Accepted: 12/16/2014] [Indexed: 06/04/2023]
Abstract
Dereplication methodology using UHPLC-DAD-QTOFMS was applied during the metabolic profiling investigation of the endophyte Setophoma sp., a fungus isolated from symptomless guava fruits. The approach performed allowed a fast analysis of the microbial secondary metabolites. From this fungus, seven highly C-alkylated depsides were isolated and identified as polyketides thielavins S, T, U and V and lecanorins D, E and F. Their structures were elucidated through spectroscopic methods including NMR, HRMS and especially with assistance of HRMS/MS experiments. The compounds were tested for quorum sensing regulation activity in the virulence gene expression of Staphylococcus aureus, but no inhibitory effect was detected. Nevertheless, moderate antibacterial activity was encountered in three of tested depsides, particularly with thielavin T, whose MIC was 6.25 μg/mL against S. aureus.
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Affiliation(s)
- Lívia S de Medeiros
- Department of Chemistry, Universidade Federal de São Carlos, LaBioMMi, Rod. Washington Luís, Km 265, 13565-905 São Carlos, SP, Brazil.
| | - Lucas M Abreu
- Department of Phytopathology, Universidade Federal de Lavras, 37200-000 Lavras, MG, Brazil
| | - Anita Nielsen
- Department of Veterinary Disease Biology, Food Safety and Zoonoses Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg, Copenhagen, Denmark
| | - Hanne Ingmer
- Department of Veterinary Disease Biology, Food Safety and Zoonoses Faculty of Health and Medical Sciences, University of Copenhagen, Stigbøjlen 4, DK-1870 Frederiksberg, Copenhagen, Denmark
| | - Thomas O Larsen
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads Building 221, 2800 Kgs. Lyngby, Denmark
| | - Kristian F Nielsen
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Søltofts Plads Building 221, 2800 Kgs. Lyngby, Denmark
| | - Edson Rodrigues-Filho
- Department of Chemistry, Universidade Federal de São Carlos, LaBioMMi, Rod. Washington Luís, Km 265, 13565-905 São Carlos, SP, Brazil
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Wolfender JL, Marti G, Thomas A, Bertrand S. Current approaches and challenges for the metabolite profiling of complex natural extracts. J Chromatogr A 2015; 1382:136-64. [DOI: 10.1016/j.chroma.2014.10.091] [Citation(s) in RCA: 352] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 10/23/2014] [Accepted: 10/26/2014] [Indexed: 12/11/2022]
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9
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Bertrand S, Bohni N, Schnee S, Schumpp O, Gindro K, Wolfender JL. Metabolite induction via microorganism co-culture: a potential way to enhance chemical diversity for drug discovery. Biotechnol Adv 2014; 32:1180-204. [PMID: 24651031 DOI: 10.1016/j.biotechadv.2014.03.001] [Citation(s) in RCA: 297] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 02/28/2014] [Accepted: 03/03/2014] [Indexed: 02/08/2023]
Abstract
Microorganisms have a long track record as important sources of novel bioactive natural products, particularly in the field of drug discovery. While microbes have been shown to biosynthesize a wide array of molecules, recent advances in genome sequencing have revealed that such organisms have the potential to yield even more structurally diverse secondary metabolites. Thus, many microbial gene clusters may be silent under standard laboratory growth conditions. In the last ten years, several methods have been developed to aid in the activation of these cryptic biosynthetic pathways. In addition to the techniques that demand prior knowledge of the genome sequences of the studied microorganisms, several genome sequence-independent tools have been developed. One of these approaches is microorganism co-culture, involving the cultivation of two or more microorganisms in the same confined environment. Microorganism co-culture is inspired by the natural microbe communities that are omnipresent in nature. Within these communities, microbes interact through signaling or defense molecules. Such compounds, produced dynamically, are of potential interest as new leads for drug discovery. Microorganism co-culture can be achieved in either solid or liquid media and has recently been used increasingly extensively to study natural interactions and discover new bioactive metabolites. Because of the complexity of microbial extracts, advanced analytical methods (e.g., mass spectrometry methods and metabolomics) are key for the successful detection and identification of co-culture-induced metabolites. This review focuses on co-culture studies that aim to increase the diversity of metabolites obtained from microbes. The various strategies are summarized with a special emphasis on the multiple methods of performing co-culture experiments. The analytical approaches for studying these interaction phenomena are discussed, and the chemical diversity and biological activity observed among the induced metabolites are described.
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Affiliation(s)
- Samuel Bertrand
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland; Groupe Mer, Molécules, Santé-EA 2160, Faculté des Sciences pharmaceutiques et biologiques, Université de Nantes, 9 rue Bias, BP 53508, F-44035 Nantes Cedex 01, France
| | - Nadine Bohni
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland
| | - Sylvain Schnee
- Mycology and Biotechnology group, Institute for Plant Production Sciences IPS, Agroscope, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Olivier Schumpp
- Mycology and Biotechnology group, Institute for Plant Production Sciences IPS, Agroscope, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Katia Gindro
- Mycology and Biotechnology group, Institute for Plant Production Sciences IPS, Agroscope, Route de Duillier 50, P.O. Box 1012, 1260 Nyon, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland.
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Ito T, Masubuchi M. Dereplication of microbial extracts and related analytical technologies. J Antibiot (Tokyo) 2014; 67:353-60. [PMID: 24569671 DOI: 10.1038/ja.2014.12] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 01/06/2014] [Accepted: 01/27/2014] [Indexed: 02/07/2023]
Abstract
Natural products still continue to have an important role as a resource of various biologically active substances. Dereplication is a key process in natural product screening that analyzes the extracts of microbial fermentation broths or plant samples. In this review article, we describe and discuss the analytical techniques of dereplication and related technologies in the following sections: 1. Direct detection from microbial colonies. 2. Ultra high performance liquid chromatography (UHPLC)-MS profiling for library construction. 3. Micro-fractionation to identify active peaks. 4. Quantification of small-amount compounds. 5. Structure identification from small amounts. Using these techniques, the desired compound in the mixture library can be rapidly identified.
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Affiliation(s)
- Tatsuya Ito
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
| | - Miyako Masubuchi
- Research Division, Chugai Pharmaceutical Co., Ltd., Kamakura, Kanagawa, Japan
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Bertrand S, Azzollini A, Schumpp O, Bohni N, Schrenzel J, Monod M, Gindro K, Wolfender JL. Multi-well fungal co-culture for de novo metabolite-induction in time-series studies based on untargeted metabolomics. ACTA ACUST UNITED AC 2014; 10:2289-98. [DOI: 10.1039/c4mb00223g] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A multi-well approach was developed for time series studies of de novo metabolite-induction by fungal co-culture using untargeted metabolomics.
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Affiliation(s)
- Samuel Bertrand
- School of Pharmaceutical Sciences
- EPGL
- University of Geneva
- University of Lausanne
- CH-1211 Geneva 4, Switzerland
| | - Antonio Azzollini
- School of Pharmaceutical Sciences
- EPGL
- University of Geneva
- University of Lausanne
- CH-1211 Geneva 4, Switzerland
| | - Olivier Schumpp
- Mycology and Biotechnology Group
- Institute for Plant Production Sciences IPS
- 1260 Nyon, Switzerland
| | - Nadine Bohni
- School of Pharmaceutical Sciences
- EPGL
- University of Geneva
- University of Lausanne
- CH-1211 Geneva 4, Switzerland
| | - Jacques Schrenzel
- Clinical Microbiology Laboratory
- Service of Infectious Diseases
- Geneva University Hospital
- CH-1211 Geneva 4, Switzerland
| | - Michel Monod
- Department of Dermatology and Venereology
- Laboratory of Mycology
- CHUV
- CH-1011 Lausanne, Switzerland
| | - Katia Gindro
- Mycology and Biotechnology Group
- Institute for Plant Production Sciences IPS
- 1260 Nyon, Switzerland
| | - Jean-Luc Wolfender
- School of Pharmaceutical Sciences
- EPGL
- University of Geneva
- University of Lausanne
- CH-1211 Geneva 4, Switzerland
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12
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Chemical dereplication of marine actinomycetes by liquid chromatography-high resolution mass spectrometry profiling and statistical analysis. Anal Chim Acta 2013; 805:70-9. [PMID: 24296145 DOI: 10.1016/j.aca.2013.10.029] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 10/02/2013] [Accepted: 10/11/2013] [Indexed: 12/15/2022]
Abstract
Discovery of novel bioactive metabolites from marine bacteria is becoming increasingly challenging, and the development of novel approaches to improve the efficiency of early steps in the microbial drug discovery process is therefore of interest. For example, current protocols for the taxonomic dereplication of microbial strains generally use molecular tools which do not take into consideration the ability of these selected bacteria to produce secondary metabolites. As the identification of novel chemical entities is one of the key elements driving drug discovery programs, this study reports a novel methodology to dereplicate microbial strains by a metabolomics approach using liquid chromatography-high resolution mass spectrometry (LC-HRMS). In order to process large and complex three dimensional LC-HRMS datasets, the reported method uses a bucketing and presence-absence standardization strategy in addition to statistical analysis tools including principal component analysis (PCA) and cluster analysis. From a closely related group of Streptomyces isolated from geographically varied environments, we demonstrated that grouping bacteria according to the chemical diversity of produced metabolites is reproducible and provides greatly improved resolution for the discrimination of microbial strains compared to current molecular dereplication techniques. Importantly, this method provides the ability to identify putative novel chemical entities as natural product discovery leads.
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Henrich CJ, Beutler JA. Matching the power of high throughput screening to the chemical diversity of natural products. Nat Prod Rep 2013; 30:1284-98. [PMID: 23925671 PMCID: PMC3801163 DOI: 10.1039/c3np70052f] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Covering up to 2013. Application of high throughput screening technologies to natural product samples demands alterations in assay design as well as sample preparation in order to yield meaningful hit structures at the end of the campaign.
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Affiliation(s)
- Curtis J. Henrich
- Basic Science Program, SAIC-Frederick, Inc. Frederick National Lab
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA
| | - John A. Beutler
- Molecular Targets Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702 USA
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14
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Rao M, Wei W, Ge M, Chen D, Sheng X. A new antibacterial lipopeptide found by UPLC-MS from an actinomycete Streptomyces sp. HCCB10043. Nat Prod Res 2013; 27:2190-5. [PMID: 23815473 DOI: 10.1080/14786419.2013.811661] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
It is an attractive and interesting thing for us to mine the diversity of microbial metabolites by means of ultra performance liquid chromatography tandem quadrupole and time of flight high-resolution mass spectrometry. Through this method, two trace compounds, a new lipopeptide, named arylomycin A6 (1), and a known lipopeptide (arylomycin A5, 2) were found and isolated from an actinomycete Streptomyces parvus HCCB10043. The structure of the new lipopeptide was elucidated by a combination of 1D, 2D NMR (correlation spectroscopy, heteronuclear multiple quantum correlation and heteronuclear multiple bond coherence) techniques, high-resolution electrospray ionization mass spectrometry and MS/MS spectrometry and fatty acid analyses. Arylomycin A6 exhibited antibacterial activity against Staphylococcus epidermidis HCCB20256 with the minimum inhibitory concentration of 1 μg/mL. Till now, arylomycins are the third series of active secondary metabolites we found in S. parvus HCCB10043. The results strongly support and encourage the studies for mining trace natural active products from microorganisms like Streptomyces.
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Affiliation(s)
- Min Rao
- a College of Life Sciences, Nanjing Agricultural University , Nanjing , 210095 , Jiangsu Province People's Republic of China
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15
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Bertrand S, Schumpp O, Bohni N, Monod M, Gindro K, Wolfender JL. De novo production of metabolites by fungal co-culture of Trichophyton rubrum and Bionectria ochroleuca. JOURNAL OF NATURAL PRODUCTS 2013; 76:1157-1165. [PMID: 23734767 DOI: 10.1021/np400258f] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The co-cultivation of fungi has recently been described as a promising strategy to induce the production of novel metabolites through possible gene activation. A large screening of fungal co-cultures in solid media has identified an unusual long-distance growth inhibition between Trichophyton rubrum and Bionectria ochroleuca. To study metabolite induction in this particular fungal interaction, differential LC-MS-based metabolomics was performed on pure strain cultures and on their co-cultures. The comparison of the resulting fingerprints highlighted five de novo induced compounds, which were purified using software-oriented semipreparative HPLC-MS. One metabolite was successfully identified as 4″-hydroxysulfoxy-2,2″-dimethylthielavin P (a substituted trimer of 3,5-dimethylorsellinic acid). The nonsulfated form, as well as three other related compounds, were found in the pure strain culture of B. ochroleuca.
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Affiliation(s)
- Samuel Bertrand
- School of Pharmaceutical Sciences, EPGL, University of Geneva, University of Lausanne, Quai Ernest-Ansermet 30, CH-1211 Geneva 4, Switzerland
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Figueroa M, Raja H, Falkinham JO, Adcock AF, Kroll DJ, Wani MC, Pearce CJ, Oberlies NH. Peptaibols, tetramic acid derivatives, isocoumarins, and sesquiterpenes from a Bionectria sp. (MSX 47401). JOURNAL OF NATURAL PRODUCTS 2013; 76:1007-15. [PMID: 23806109 PMCID: PMC3736820 DOI: 10.1021/np3008842] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
An extract of the filamentous fungus Bionectria sp. (MSX 47401) showed both promising cytotoxic activity (>90% inhibition of H460 cell growth at 20 μg/mL) and antibacterial activity against methicillin-resistant Staphylococcus aureus (MRSA). A bioactivity-directed fractionation study yielded one new peptaibol (1) and one new tetramic acid derivative (2), and the fungus biosynthesized diverse secondary metabolites with mannose-derived units. Five known compounds were also isolated: clonostachin (3), virgineone (4), virgineone aglycone (5), AGI-7 (6), and 5,6-dihydroxybisabolol (7). Compounds 5 and 7 have not been described previously from natural sources. Compound 1 represents the second member of the peptaibol structural class that contains an ester-linked sugar alcohol (mannitol) instead of an amide-linked amino alcohol, and peptaibols and tetramic acid derivatives have not been isolated previously from the same fungus. The structures of the new compounds were elucidated primarily by high-field NMR (950 and 700 MHz), HRESIMS/MS, and chemical degradations (Marfey's analysis). All compounds (except 6) were examined for antibacterial and antifungal activities. Compounds 2, 4, and 5 showed antimicrobial activity against S. aureus and several MRSA isolates.
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Affiliation(s)
- Mario Figueroa
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, Unites States
| | - Huzefa Raja
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, Unites States
| | - Joseph O. Falkinham
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, Unites States
| | - Audrey F. Adcock
- Department of Pharmaceutical Sciences, BRITE, North Carolina Central University, Durham, NC 27707, Unites States
| | - David J. Kroll
- Department of Pharmaceutical Sciences, BRITE, North Carolina Central University, Durham, NC 27707, Unites States
| | - Mansukh C. Wani
- Natural Products Laboratory, Research Triangle Institute, Research Triangle Park, NC 27709
| | | | - Nicholas H. Oberlies
- Department of Chemistry and Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402, Unites States
- To whom correspondence should be addressed. . Tel: 336-334-5474
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Detection of metabolite induction in fungal co-cultures on solid media by high-throughput differential ultra-high pressure liquid chromatography-time-of-flight mass spectrometry fingerprinting. J Chromatogr A 2013; 1292:219-28. [PMID: 23466199 DOI: 10.1016/j.chroma.2013.01.098] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 01/23/2013] [Accepted: 01/24/2013] [Indexed: 01/18/2023]
Abstract
Access to new biological sources is a key element of natural product research. A particularly large number of biologically active molecules have been found to originate from microorganisms. Very recently, the use of fungal co-culture to activate the silent genes involved in metabolite biosynthesis was found to be a successful method for the induction of new compounds. However, the detection and identification of the induced metabolites in the confrontation zone where fungi interact remain very challenging. To tackle this issue, a high-throughput UHPLC-TOF-MS-based metabolomic approach has been developed for the screening of fungal co-cultures in solid media at the petri dish level. The metabolites that were overexpressed because of fungal interactions were highlighted by comparing the LC-MS data obtained from the co-cultures and their corresponding mono-cultures. This comparison was achieved by subjecting automatically generated peak lists to statistical treatments. This strategy has been applied to more than 600 co-culture experiments that mainly involved fungal strains from the Fusarium genera, although experiments were also completed with a selection of several other filamentous fungi. This strategy was found to provide satisfactory repeatability and was used to detect the biomarkers of fungal induction in a large panel of filamentous fungi. This study demonstrates that co-culture results in consistent induction of potentially new metabolites.
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Duarte K, Rocha-Santos TA, Freitas AC, Duarte AC. Analytical techniques for discovery of bioactive compounds from marine fungi. Trends Analyt Chem 2012. [DOI: 10.1016/j.trac.2011.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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19
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Frisvad JC. Media and growth conditions for induction of secondary metabolite production. Methods Mol Biol 2012; 944:47-58. [PMID: 23065607 DOI: 10.1007/978-1-62703-122-6_3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Growth media and incubation conditions have a very strong influence of secondary metabolite production. There is no consensus on which media are the optimal for metabolite production, but a series of useful and effective media and incubation conditions have been listed here. Chemically well-defined media are suited for biochemical studies, but in order to get chemical diversity expressed in filamentous fungi, sources rich in amino acids, vitamins, and trace metals have to be added, such as yeast extract and oatmeal. A battery of solid agar media is recommended for exploration of chemical diversity as agar plug samples are easily analyzed to get an optimal representation of the qualitative secondary metabolome. Standard incubation for a week at 25°C in darkness is recommended, but optimal conditions have to be modified depending on the ecology and physiology of different filamentous fungi.
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Affiliation(s)
- Jens C Frisvad
- Department of Systems Biology, Center for Microbial Biotechnology, Technical University of Denmark, Kongens Lyngby, Denmark.
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Affiliation(s)
- Cedric Pearce
- Associate Editor, Journal of Natural Products, Adjunct Professor, University of North Carolina-Greensboro, CEO, Mycosynthetix Inc., North Carolina, USA E-mail:
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