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Cochereau B, Le Strat Y, Ji Q, Pawtowski A, Delage L, Weill A, Mazéas L, Hervé C, Burgaud G, Gunde-Cimerman N, Pouchus YF, Demont-Caulet N, Roullier C, Meslet-Cladiere L. Heterologous Expression and Biochemical Characterization of a New Chloroperoxidase Isolated from the Deep-Sea Hydrothermal Vent Black Yeast Hortaea werneckii UBOCC-A-208029. Mar Biotechnol (NY) 2023; 25:519-536. [PMID: 37354383 PMCID: PMC10427571 DOI: 10.1007/s10126-023-10222-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/04/2023] [Indexed: 06/26/2023]
Abstract
The initiation of this study relies on a targeted genome-mining approach to highlight the presence of a putative vanadium-dependent haloperoxidase-encoding gene in the deep-sea hydrothermal vent fungus Hortaea werneckii UBOCC-A-208029. To date, only three fungal vanadium-dependent haloperoxidases have been described, one from the terrestrial species Curvularia inaequalis, one from the fungal plant pathogen Botrytis cinerea, and one from a marine derived isolate identified as Alternaria didymospora. In this study, we describe a new vanadium chloroperoxidase from the black yeast H. werneckii, successfully cloned and overexpressed in a bacterial host, which possesses higher affinity for bromide (Km = 26 µM) than chloride (Km = 237 mM). The enzyme was biochemically characterized, and we have evaluated its potential for biocatalysis by determining its stability and tolerance in organic solvents. We also describe its potential three-dimensional structure by building a model using the AlphaFold 2 artificial intelligence tool. This model shows some conservation of the 3D structure of the active site compared to the vanadium chloroperoxidase from C. inaequalis but it also highlights some differences in the active site entrance and the volume of the active site pocket, underlining its originality.
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Affiliation(s)
- Bastien Cochereau
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France
| | - Yoran Le Strat
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France
| | - Qiaolin Ji
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France
| | - Audrey Pawtowski
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
| | - Ludovic Delage
- Integrative Biology of Marine Models (LBI2M), UMR8227, Station Biologique de Roscoff (SBR), CNRS, Université, 29680, Roscoff, Sorbonne, France
| | - Amélie Weill
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
- Univ Brest, UBO Culture Collection (UBOCC), F-29280, Plouzané, France
| | - Lisa Mazéas
- Integrative Biology of Marine Models (LBI2M), UMR8227, Station Biologique de Roscoff (SBR), CNRS, Université, 29680, Roscoff, Sorbonne, France
| | - Cécile Hervé
- Integrative Biology of Marine Models (LBI2M), UMR8227, Station Biologique de Roscoff (SBR), CNRS, Université, 29680, Roscoff, Sorbonne, France
| | - Gaëtan Burgaud
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France
| | - Nina Gunde-Cimerman
- Molecular Genetics and Biology of Microorganisms, Dept. Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Yves François Pouchus
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France
| | - Nathalie Demont-Caulet
- INRAE, University of Paris, UMR ECOSYS, INRAE, Université Paris-Saclay, 78026, Versailles, AgroParisTech, France
| | - Catherine Roullier
- Institut des Substances et Organismes de la Mer, Nantes Université, ISOMER, UR, 2160, F-44000, Nantes, France.
| | - Laurence Meslet-Cladiere
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, F-29280, Plouzané, France.
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Hoang TPT, Roullier C, Evanno L, Kerzaon I, Gentil E, Robiou du Pont T, Nazih EH, Pouchus YF, Bertrand S, Poupon E, Grovel O. Nature-Inspired Chemistry of Complex Alkaloids: Combining Targeted Molecular Networking Approach and Semisynthetic Strategy to Access Rare Communesins in a Marine-Derived Penicillium expansum. Chemistry 2023:e202300103. [PMID: 36893323 DOI: 10.1002/chem.202300103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/11/2023]
Abstract
Communesins are rare alkaloids isolated from fungi of the genus Penicillium. In this work, the extract of a marine-derived Penicillium expansum strain was studied using targeted molecular networking approach allowing to detect 65 communesins including 55 novels. A fragmentation pattern for dimethylvinyl communesins was established and a script was implemented allowing to predict the structure and map all communesins in a global molecular network. A semisynthetic strategy was carried out to obtain some minor congeners from the two isolated communesins A and B. Nine communesins were then synthetised: two of them were already described as produced by the studied strain; four are new natural products which occurrence in the extracts was confirmed; three are new semi-synthetic analogues never described so far. These communesins were evaluated for their cytotoxicity on two human cancer cell lines KB and MCF-7 leading to a preliminary study of their structure-activity relationships.
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Affiliation(s)
| | - Catherine Roullier
- Nantes University: Universite de Nantes, UR2160 - ISOMer, UFR Sciences pharmaceutiques et Biologiques, 9 rue Bias, 44000, Nantes, FRANCE
| | - Laurent Evanno
- Université Paris-Saclay Faculté de Pharmacie: Universite Paris-Saclay Faculte de Pharmacie, Chimie des Substances Naturelles, BioCIS, FRANCE
| | - Isabelle Kerzaon
- Lyon 1 University: Universite Claude Bernard Lyon 1, Laboratoire d'écologie microbienne, LEM, UMR5557, FRANCE
| | - Emmanuel Gentil
- Nantes University: Universite de Nantes, UR2160 - ISOMer, FRANCE
| | | | - El-Hassane Nazih
- Nantes University: Universite de Nantes, UR2160 - ISOMer, FRANCE
| | | | - Samuel Bertrand
- Nantes University: Universite de Nantes, UR2160 - ISOMer, FRANCE
| | - Erwan Poupon
- Université Paris-Saclay: Universite Paris-Saclay, Chimie des Substances Naturelles, BioCIS, FRANCE
| | - Olivier Grovel
- Nantes University: Universite de Nantes, UR2160 - ISOMer, FRANCE
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Toure S, Millot M, Ory L, Roullier C, Khaldi Z, Pichon V, Girardot M, Imbert C, Mambu L. Access to Anti-Biofilm Compounds from Endolichenic Fungi Using a Bioguided Networking Screening. J Fungi (Basel) 2022; 8:jof8101012. [PMID: 36294577 PMCID: PMC9604612 DOI: 10.3390/jof8101012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Endolichenic microorganisms represent a new source of bioactive natural compounds. Lichens, resulting from a symbiotic association between algae or cyanobacteria and fungi, constitute an original ecological niche for these microorganisms. Endolichenic fungi inhabiting inside the lichen thallus have been isolated and characterized. By cultivation on three different culture media, endolichenic fungi gave rise to a wide diversity of bioactive metabolites. A total of 38 extracts were screened for their anti-maturation effect on Candida albicans biofilms. The 10 most active ones, inducing at least 50% inhibition, were tested against 24 h preformed biofilms of C. albicans, using a reference strain and clinical isolates. The global molecular network was associated to bioactivity data in order to identify and priorize active natural product families. The MS-targeted isolation led to the identification of new oxygenated fatty acid in Preussia persica endowed with an interesting anti-biofilm activity against C. albicans yeasts.
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Affiliation(s)
- Seinde Toure
- Laboratoire PEIRENE, University Limoges, UR 22722, F-87000 Limoges, France
| | - Marion Millot
- Laboratoire PEIRENE, University Limoges, UR 22722, F-87000 Limoges, France
| | - Lucie Ory
- Institut des Substances et Organismes de la Mer (ISOMer), Nantes Université, UR 2160, F-44000 Nantes, France
| | - Catherine Roullier
- Institut des Substances et Organismes de la Mer (ISOMer), Nantes Université, UR 2160, F-44000 Nantes, France
| | - Zineb Khaldi
- Laboratoire PEIRENE, University Limoges, UR 22722, F-87000 Limoges, France
| | - Valentin Pichon
- Laboratoire PEIRENE, University Limoges, UR 22722, F-87000 Limoges, France
| | - Marion Girardot
- Laboratoire Ecologie et Biologie des Interactions (EBI), University Poitiers, UMR CNRS 7267, F-86000 Poitiers, France
| | - Christine Imbert
- Laboratoire Ecologie et Biologie des Interactions (EBI), University Poitiers, UMR CNRS 7267, F-86000 Poitiers, France
| | - Lengo Mambu
- Laboratoire PEIRENE, University Limoges, UR 22722, F-87000 Limoges, France
- Correspondence: ; Tel.: +33-5-55-43-58-34
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Cochereau B, Meslet-Cladière L, Pouchus YF, Grovel O, Roullier C. Halogenation in Fungi: What Do We Know and What Remains to Be Discovered? Molecules 2022; 27:molecules27103157. [PMID: 35630634 PMCID: PMC9144378 DOI: 10.3390/molecules27103157] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/09/2022] [Accepted: 05/10/2022] [Indexed: 02/04/2023] Open
Abstract
In nature, living organisms produce a wide variety of specialized metabolites to perform many biological functions. Among these specialized metabolites, some carry halogen atoms on their structure, which can modify their chemical characteristics. Research into this type of molecule has focused on how organisms incorporate these atoms into specialized metabolites. Several families of enzymes have been described gathering metalloenzymes, flavoproteins, or S-adenosyl-L-methionine (SAM) enzymes that can incorporate these atoms into different types of chemical structures. However, even though the first halogenation enzyme was discovered in a fungus, this clade is still lagging behind other clades such as bacteria, where many enzymes have been discovered. This review will therefore focus on all halogenation enzymes that have been described in fungi and their associated metabolites by searching for proteins available in databases, but also by using all the available fungal genomes. In the second part of the review, the chemical diversity of halogenated molecules found in fungi will be discussed. This will allow the highlighting of halogenation mechanisms that are still unknown today, therefore, highlighting potentially new unknown halogenation enzymes.
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Affiliation(s)
- Bastien Cochereau
- Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, Nantes Université, F-44000 Nantes, France; (B.C.); (Y.F.P.); (O.G.)
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France;
| | - Laurence Meslet-Cladière
- Laboratoire Universitaire de Biodiversité et Écologie Microbienne, INRAE, University Brest, F-29280 Plouzané, France;
| | - Yves François Pouchus
- Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, Nantes Université, F-44000 Nantes, France; (B.C.); (Y.F.P.); (O.G.)
| | - Olivier Grovel
- Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, Nantes Université, F-44000 Nantes, France; (B.C.); (Y.F.P.); (O.G.)
| | - Catherine Roullier
- Institut des Substances et Organismes de la Mer, ISOMer, UR 2160, Nantes Université, F-44000 Nantes, France; (B.C.); (Y.F.P.); (O.G.)
- Correspondence: ; Tel.: +33-251-125-686
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Pisapia F, Sibat M, Watanabe R, Roullier C, Suzuki T, Hess P, Herrenknecht C. Characterization of maitotoxin-4 (MTX4) using electrospray positive mode ionization high-resolution mass spectrometry and UV spectroscopy. Rapid Commun Mass Spectrom 2020; 34:e8859. [PMID: 32530533 DOI: 10.1002/rcm.8859] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/09/2020] [Accepted: 06/10/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE The dinoflagellate genera Gambierdiscus and Fukuyoa are producers of toxins responsible for Ciguatera Poisoning (CP). Although having very low oral potency, maitotoxins (MTXs) are very toxic following intraperitoneal injection and feeding studies have shown they may accumulate in fish muscle. To date, six MTX congeners have been described but two congeners (MTX2 and MTX4) have not yet been structurally elucidated. The aim of the present study was to further characterize MTX4. METHODS Chemical analysis was performed using liquid chromatography coupled to a diode-array detector (DAD) and positive ion mode high-resolution mass spectrometry (LC/HRMS) on partially purified extracts of G. excentricus (strain VGO792). HRMS/MS studies were also carried out to tentatively explain the fragmentation pathways of MTX and MTX4. RESULTS The comparison of UV and HRMS (ESI+ ) spectra between MTX and MTX4 led us to propose the elemental formula of MTX4 (C157 H241 NO68 S2 , as the unsalted molecule). The comparison of the theoretical and measured m/z values of the doubly charged ions of the isotopic profile in ESI+ were coherent with the proposed elemental formula of MTX4. The study of HRMS/MS spectra on the tri-ammoniated adduct ([M - H + 3NH4 ]2+ ) of both molecules gave additional information about structural features. The cleavage observed, probably located at C99 -C100 in both MTX and MTX4, highlighted the same A-side product ion shared by the two molecules. CONCLUSIONS All these investigations on the characterization of MTX4 contribute to highlighting that MTX4 belongs to the same structural family of MTXs. However, to accomplish a complete structural elucidation of MTX4, an NMR-based study and LC/HRMSn investigation will have to be carried out.
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Affiliation(s)
| | - Manoëlla Sibat
- Ifremer, DYNECO, Rue de l'Île d'Yeu, Nantes, 44311, France
| | - Ryuichi Watanabe
- NRIFS, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Catherine Roullier
- MMS EA2160, Faculté de Pharmacie, Université de Nantes, 9 rue Bias, Nantes, 44035, France
| | - Toshiyuki Suzuki
- NRIFS, Japan Fisheries Research and Education Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Philipp Hess
- Ifremer, DYNECO, Rue de l'Île d'Yeu, Nantes, 44311, France
| | - Christine Herrenknecht
- MMS EA2160, Faculté de Pharmacie, Université de Nantes, 9 rue Bias, Nantes, 44035, France
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6
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Ory L, Gentil E, Kumla D, Kijjoa A, Nazih EH, Roullier C. Detection of ergosterol using liquid chromatography/electrospray ionization mass spectrometry: Investigation of unusual in-source reactions. Rapid Commun Mass Spectrom 2020; 34:e8780. [PMID: 32154942 DOI: 10.1002/rcm.8780] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/18/2020] [Accepted: 03/08/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE In the field of natural products, de-replication of complex mixtures has become a usual practice to annotate known compounds and avoid their re-isolation. For this purpose, many groups rely on liquid chromatography coupled to high-resolution mass spectrometry (HPLC/MS) to deduce molecular formulae of compounds allowing comparison with public or in-house databases. Electrospray ionization (ESI) is usually considered as the method of choice for investigating a large panel of compounds but, in some cases, it may lead to unusual results as described in this article for ergosterol. METHODS Ergosterol and other fungal sterols in methanolic solution were analysed using various chromatographic gradients with HPLC/MS using both ion trap time-of-flight MS and Orbitrap MS instruments fitted with an ESI source. Further flow injection analyses were performed to investigate the influence of the solvent composition. MS/MS fragmentation data were acquired to annotate the various ions observed. RESULTS Contrary to other fungal sterols, ergosterol was found to be highly sensitive to oxidation during ESI. Putative structures were proposed based on MS/MS studies and known oxidation mechanisms of ergosterol by reactive oxygen species that could be formed in the ESI process. The proportion of acetonitrile in the eluent was found to influence this in-source oxidation, with an increased proportion of oxidized sodium adducts with higher proportions of acetonitrile. CONCLUSIONS While ergosterol is a major sterol found in fungi, this study investigates its ionization by electrospray for the first time. The results reported here will help further detection and annotation of this compound in fungal extracts after HPLC/ESI-MS analyses.
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Affiliation(s)
- Lucie Ory
- EA2160 - MMS, Nantes University, 9 rue Bias, Nantes, 44035, France
| | - Emmanuel Gentil
- EA2160 - MMS, Nantes University, 9 rue Bias, Nantes, 44035, France
- Corsaire - ThalassOMICS, Biogenouest, Université de Nantes, Nantes, 44000, France
| | - Decha Kumla
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar and CIIMAR, Universidade do Porto, Porto, 4050-313, Portugal
| | - Anake Kijjoa
- ICBAS - Instituto de Ciências Biomédicas Abel Salazar and CIIMAR, Universidade do Porto, Porto, 4050-313, Portugal
| | - El-Hassane Nazih
- EA2160 - MMS, Nantes University, 9 rue Bias, Nantes, 44035, France
| | - Catherine Roullier
- EA2160 - MMS, Nantes University, 9 rue Bias, Nantes, 44035, France
- Corsaire - ThalassOMICS, Biogenouest, Université de Nantes, Nantes, 44000, France
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Aron AT, Gentry EC, McPhail KL, Nothias LF, Nothias-Esposito M, Bouslimani A, Petras D, Gauglitz JM, Sikora N, Vargas F, van der Hooft JJJ, Ernst M, Kang KB, Aceves CM, Caraballo-Rodríguez AM, Koester I, Weldon KC, Bertrand S, Roullier C, Sun K, Tehan RM, Boya P CA, Christian MH, Gutiérrez M, Ulloa AM, Tejeda Mora JA, Mojica-Flores R, Lakey-Beitia J, Vásquez-Chaves V, Zhang Y, Calderón AI, Tayler N, Keyzers RA, Tugizimana F, Ndlovu N, Aksenov AA, Jarmusch AK, Schmid R, Truman AW, Bandeira N, Wang M, Dorrestein PC. Reproducible molecular networking of untargeted mass spectrometry data using GNPS. Nat Protoc 2020; 15:1954-1991. [PMID: 32405051 DOI: 10.1038/s41596-020-0317-5] [Citation(s) in RCA: 263] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/03/2020] [Indexed: 02/06/2023]
Abstract
Global Natural Product Social Molecular Networking (GNPS) is an interactive online small molecule-focused tandem mass spectrometry (MS2) data curation and analysis infrastructure. It is intended to provide as much chemical insight as possible into an untargeted MS2 dataset and to connect this chemical insight to the user's underlying biological questions. This can be performed within one liquid chromatography (LC)-MS2 experiment or at the repository scale. GNPS-MassIVE is a public data repository for untargeted MS2 data with sample information (metadata) and annotated MS2 spectra. These publicly accessible data can be annotated and updated with the GNPS infrastructure keeping a continuous record of all changes. This knowledge is disseminated across all public data; it is a living dataset. Molecular networking-one of the main analysis tools used within the GNPS platform-creates a structured data table that reflects the molecular diversity captured in tandem mass spectrometry experiments by computing the relationships of the MS2 spectra as spectral similarity. This protocol provides step-by-step instructions for creating reproducible, high-quality molecular networks. For training purposes, the reader is led through a 90- to 120-min procedure that starts by recalling an example public dataset and its sample information and proceeds to creating and interpreting a molecular network. Each data analysis job can be shared or cloned to disseminate the knowledge gained, thus propagating information that can lead to the discovery of molecules, metabolic pathways, and ecosystem/community interactions.
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Affiliation(s)
- Allegra T Aron
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Emily C Gentry
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kerry L McPhail
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Louis-Félix Nothias
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Mélissa Nothias-Esposito
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Amina Bouslimani
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Daniel Petras
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Julia M Gauglitz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Nicole Sikora
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Fernando Vargas
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Madeleine Ernst
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Kyo Bin Kang
- College of Pharmacy, Sookmyung Women's University, Seoul, Korea
| | - Christine M Aceves
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | | | - Irina Koester
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Kelly C Weldon
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
- Center of Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
| | - Samuel Bertrand
- Groupe Mer, Molécules, Santé-EA 2160, UFR des Sciences Pharmaceutiques et Biologiques, Université de Nantes, Nantes, France
- ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, Nantes, France
| | - Catherine Roullier
- College of Pharmacy, Sookmyung Women's University, Seoul, Korea
- ThalassOMICS Metabolomics Facility, Plateforme Corsaire, Biogenouest, Nantes, France
| | - Kunyang Sun
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Richard M Tehan
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Corvallis, OR, USA
| | - Cristopher A Boya P
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Nagarjuna Nagar, India
| | - Martin H Christian
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
| | - Marcelino Gutiérrez
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
| | | | | | - Randy Mojica-Flores
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
- Departamento de Química, Universidad Autónoma de Chiriquí (UNACHI), David, Chiriquí, Panama
| | - Johant Lakey-Beitia
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
| | - Victor Vásquez-Chaves
- Centro de Investigaciones en Productos Naturales (CIPRONA), Universidad de Costa Rica, San José, Costa Rica
| | - Yilue Zhang
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Angela I Calderón
- Department of Drug Discovery and Development, Harrison School of Pharmacy, Auburn University, Auburn, AL, USA
| | - Nicole Tayler
- Centro de Biodiversidad y Descubrimiento de Drogas, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT AIP), Panama City, Panama
- Department of Biotechnology, Acharya Nagarjuna University, Guntur, Nagarjuna Nagar, India
| | - Robert A Keyzers
- School of Chemical & Physical Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Fidele Tugizimana
- Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
- International R&D Division, Omnia Group (Pty) Ltd., Johannesburg, South Africa
| | - Nombuso Ndlovu
- Centre for Plant Metabolomics Research, Department of Biochemistry, University of Johannesburg, Auckland Park, South Africa
| | - Alexander A Aksenov
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Alan K Jarmusch
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Robin Schmid
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Andrew W Truman
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
| | - Mingxun Wang
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
| | - Pieter C Dorrestein
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA.
- Center for Computational Mass Spectrometry, University of California, San Diego, La Jolla, CA, USA.
- Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA.
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
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8
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Arora D, Gupta P, Jaglan S, Roullier C, Grovel O, Bertrand S. Expanding the chemical diversity through microorganisms co-culture: Current status and outlook. Biotechnol Adv 2020; 40:107521. [PMID: 31953204 DOI: 10.1016/j.biotechadv.2020.107521] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 11/29/2019] [Accepted: 01/13/2020] [Indexed: 12/17/2022]
Abstract
Natural products (NPs) are considered as a cornerstone for the generation of bioactive leads in drug discovery programs. However, one of the major limitations of NP drug discovery program is "rediscovery" of known compounds, thereby hindering the rate of drug discovery efficiency. Therefore, in recent years, to overcome these limitations, a great deal of attention has been drawn towards understanding the role of microorganisms' co-culture in inducing novel chemical entities. Such induction could be related to activation of genes which might be silent or expressed at very low levels (below detection limit) in pure-strain cultures under normal laboratory conditions. In this review, chemical diversity of compounds isolated from microbial co-cultures, is discussed. For this purpose, chemodiversity has been represented as a chemical-structure network based on the "Tanimoto Structural Similarity Index". This highlights the huge structural diversity induced by microbial co-culture. In addition, the current trends in microbial co-culture research are highlighted. Finally, the current challenges (1 - induction monitoring, 2 - reproducibility, 3 - growth time effect and 4 - up-scaling for isolation purposes) are discussed. The information in this review will support researchers to design microbial co-culture strategies for future research efforts. In addition, guidelines for co-culture induction reporting are also provided to strengthen future reporting in this NP field.
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Affiliation(s)
- Divya Arora
- Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Jammu Campus, Jammu 180001, India; 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
| | - Prasoon Gupta
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Jammu Campus, Jammu 180001, India
| | - Sundeep Jaglan
- Microbial Biotechnology Division, CSIR-Indian Institute of Integrative Medicine, Jammu 180001, India; Academy of Scientific and Innovative Research (AcSIR), Jammu Campus, Jammu 180001, India
| | - Catherine Roullier
- 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
| | - Olivier Grovel
- 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
| | - Samuel Bertrand
- 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.
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9
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Ory L, Nazih EH, Daoud S, Mocquard J, Bourjot M, Margueritte L, Delsuc MA, Bard JM, Pouchus YF, Bertrand S, Roullier C. Targeting bioactive compounds in natural extracts - Development of a comprehensive workflow combining chemical and biological data. Anal Chim Acta 2019; 1070:29-42. [DOI: 10.1016/j.aca.2019.04.038] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/19/2019] [Accepted: 04/18/2019] [Indexed: 02/07/2023]
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10
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Hoang TPT, Roullier C, Boumard MC, Robiou du Pont T, Nazih H, Gallard JF, Pouchus YF, Beniddir MA, Grovel O. Metabolomics-Driven Discovery of Meroterpenoids from a Mussel-Derived Penicillium ubiquetum. J Nat Prod 2018; 81:2501-2511. [PMID: 30407813 DOI: 10.1021/acs.jnatprod.8b00569] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Penicillium ubiquetum MMS330 isolated from the blue mussel Mytilus edulis collected on the Loire estuary in France was here investigated. As very few secondary metabolites have been documented for this species, its metabolome was studied following the OSMAC approach to enhance as many biosynthetic pathways as possible. Interestingly, HPLC-HRMS based hierarchical clustering analysis together with MS/MS molecular networking highlighted the selective overproduction of some structurally related compounds when the culture was performed on seawater CYA (Czapek Yeast extract Agar) medium. Mass-guided purification from large scale cultivation on this medium led to the isolation of nine meroterpenoids including two new analogues, 22-deoxyminiolutelide A (1) and 4-hydroxy-22-deoxyminiolutelide B (2), together with seven known compounds (3-9). The structures of 1 and 2 were elucidated on the basis of HR-ESIMS and NMR spectroscopic data analysis. Furthermore, NMR signals of 22-deoxyminiolutelide B (3) were reassigned.
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Affiliation(s)
- Thi Phuong Thuy Hoang
- EA 2160 - Mer Molécules Santé , Université de Nantes , 44035 Nantes Cedex 1 , France
- Phu Tho College of Pharmacy , 290000 Phu Tho , Vietnam
| | - Catherine Roullier
- EA 2160 - Mer Molécules Santé , Université de Nantes , 44035 Nantes Cedex 1 , France
- Corsaire-ThalassOMICS Metabolomics Facility, Biogenouest , Université de Nantes , Nantes , France
| | - Marie-Claude Boumard
- EA 2160 - Mer Molécules Santé , Université de Nantes , 44035 Nantes Cedex 1 , France
| | | | - Hassan Nazih
- EA 2160 - Mer Molécules Santé , Université de Nantes , 44035 Nantes Cedex 1 , France
| | - Jean-François Gallard
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris Saclay , 91198 Gif-sur-Yvette , France
| | - Yves François Pouchus
- EA 2160 - Mer Molécules Santé , Université de Nantes , 44035 Nantes Cedex 1 , France
| | - Mehdi A Beniddir
- Équipe "Pharmacognosie-Chimie des Substances Naturelles" BioCIS , Univ. Paris-Sud, CNRS, Université Paris Saclay , 92290 Châtenay-Malabry , France
| | - Olivier Grovel
- EA 2160 - Mer Molécules Santé , Université de Nantes , 44035 Nantes Cedex 1 , France
- Corsaire-ThalassOMICS Metabolomics Facility, Biogenouest , Université de Nantes , Nantes , France
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11
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Castro-Falcón G, Millán-Aguiñaga N, Roullier C, Jensen PR, Hughes CC. Nitrosopyridine Probe To Detect Polyketide Natural Products with Conjugated Alkenes: Discovery of Novodaryamide and Nocarditriene. ACS Chem Biol 2018; 13:3097-3106. [PMID: 30272441 DOI: 10.1021/acschembio.8b00598] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An optimized nitroso-based probe that facilitates the discovery of conjugated alkene-containing natural products in unprocessed extracts was developed. It chemoselectively reacts with conjugated olefins via a nitroso-Diels-Alder cyclization to yield derivatives with a distinct chromophore and an isotopically unique bromine atom that can be rapidly identified using liquid chromatography/mass spectrometry and a bioinformatics tool called MeHaloCoA (Marine Halogenated Compound Analysis). The probe is ideally employed when genome-mining techniques identify strains containing polyketide gene clusters with two or more repeating KS-AT-DH-KR-ACP domain sequences, which are required for the biosynthesis of conjugated alkenes. Comparing the reactivity and spectral properties of five brominated arylnitroso reagents with model compounds spiramycin, bufalin, rapamycin, and rifampicin led to the identification of 5-bromo-2-nitrosopyridine as the most suitable probe structure. The utility of the dienophile probe was then demonstrated in bacterial extracts. Tylactone, novodaryamide and daryamide A, piperazimycin A, and the saccharamonopyrones A and B were cleanly labeled in extracts from their respective bacterial producers, in high regioselectivity but with varying degrees of diastereoselectivity. Further application of the method led to the discovery of a new natural product called nocarditriene, containing an unprecedented epoxy-2,3,4,5-tetrahydropyridine structure, from marine-derived Nocardiopsis strain CNY-503.
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Affiliation(s)
- Gabriel Castro-Falcón
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Natalie Millán-Aguiñaga
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Catherine Roullier
- Mer Molécules Santé - EA2160, Université de Nantes, 44035 Nantes-cedex 1, France
| | - Paul R. Jensen
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
| | - Chambers C. Hughes
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, California 92093, United States
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12
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Staerck C, Landreau A, Herbette G, Roullier C, Bertrand S, Siegler B, Larcher G, Bouchara JP, Fleury MJJ. The secreted polyketide boydone A is responsible for the anti-Staphylococcus aureus activity of Scedosporium boydii. FEMS Microbiol Lett 2017; 364:4563577. [DOI: 10.1093/femsle/fnx223] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/21/2017] [Indexed: 11/13/2022] Open
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13
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Pisapia F, Sibat M, Herrenknecht C, Lhaute K, Gaiani G, Ferron PJ, Fessard V, Fraga S, Nascimento SM, Litaker RW, Holland WC, Roullier C, Hess P. Maitotoxin-4, a Novel MTX Analog Produced by Gambierdiscus excentricus. Mar Drugs 2017; 15:E220. [PMID: 28696398 PMCID: PMC5532662 DOI: 10.3390/md15070220] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 06/30/2017] [Accepted: 07/05/2017] [Indexed: 11/17/2022] Open
Abstract
Maitotoxins (MTXs) are among the most potent toxins known. These toxins are produced by epi-benthic dinoflagellates of the genera Gambierdiscus and Fukuyoa and may play a role in causing the symptoms associated with Ciguatera Fish Poisoning. A recent survey revealed that, of the species tested, the newly described species from the Canary Islands, G. excentricus, is one of the most maitotoxic. The goal of the present study was to characterize MTX-related compounds produced by this species. Initially, lysates of cells from two Canary Island G. excentricus strains VGO791 and VGO792 were partially purified by (i) liquid-liquid partitioning between dichloromethane and aqueous methanol followed by (ii) size-exclusion chromatography. Fractions from chromatographic separation were screened for MTX toxicity using both the neuroblastoma neuro-2a (N2a) cytotoxicity and Ca2+ flux functional assays. Fractions containing MTX activity were analyzed using liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS) to pinpoint potential MTX analogs. Subsequent non-targeted HRMS analysis permitted the identification of a novel MTX analog, maitotoxin-4 (MTX4, accurate mono-isotopic mass of 3292.4860 Da, as free acid form) in the most toxic fractions. HRMS/MS spectra of MTX4 as well as of MTX are presented. In addition, crude methanolic extracts of five other strains of G. excentricus and 37 other strains representing one Fukuyoa species and ten species, one ribotype and one undetermined strain/species of Gambierdiscus were screened for the presence of MTXs using low resolution tandem mass spectrometry (LRMS/MS). This targeted analysis indicated the original maitotoxin (MTX) was only present in one strain (G. australes S080911_1). Putative maitotoxin-2 (p-MTX2) and maitotoxin-3 (p-MTX3) were identified in several other species, but confirmation was not possible because of the lack of reference material. Maitotoxin-4 was detected in all seven strains of G. excentricus examined, independently of their origin (Brazil, Canary Islands and Caribbean), and not detected in any other species. MTX4 may therefore serve as a biomarker for the highly toxic G. excentricus in the Atlantic area.
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Affiliation(s)
- Francesco Pisapia
- Ifremer, Phycotoxins Laboratory, rue de l'Ile d'Yeu, BP 21105, F-44311 Nantes, France.
| | - Manoëlla Sibat
- Ifremer, Phycotoxins Laboratory, rue de l'Ile d'Yeu, BP 21105, F-44311 Nantes, France.
| | - Christine Herrenknecht
- Mer Molécules Santé (MMS) Laboratory EA2160, University of Nantes, LUNAM, Pharmacy Faculty, 9 rue Bias, F-44035 Nantes, France.
| | - Korian Lhaute
- Ifremer, Phycotoxins Laboratory, rue de l'Ile d'Yeu, BP 21105, F-44311 Nantes, France.
| | - Greta Gaiani
- Department of Life Science, University of Trieste, Via Giorgieri 5, 34127 Trieste, Italy.
| | - Pierre-Jean Ferron
- Toxicology of Contaminants Unit, ANSES Laboratory-French Agency for Food, Environmental and Occupational Health and Safety, Fougères, 10 B rue Claude Bourgelat, 35133 Javené, France.
| | - Valérie Fessard
- Toxicology of Contaminants Unit, ANSES Laboratory-French Agency for Food, Environmental and Occupational Health and Safety, Fougères, 10 B rue Claude Bourgelat, 35133 Javené, France.
| | - Santiago Fraga
- Instituto Español de Oceanografía (IEO), Centro Oceanográfico de Vigo, Subida a Radio Faro 50, 36390 Vigo, Spain.
| | - Silvia M Nascimento
- Laboratório de Microalgas Marinhas, Departamento de Ecologia e Recursos Marinhos, Universidade Federal do Estado do Rio de Janeiro (UNIRIO), Rio de Janeiro 22290-240, Brazil.
| | - R Wayne Litaker
- National Oceanic and Atmospheric Administration, National Ocean Service, National Centers for Coastal Ocean Science, Center for Coastal Fisheries and Habitat Research (CCFHR), 101 Pivers Island Road, Beaufort, NC 28516, USA.
| | - William C Holland
- National Oceanic and Atmospheric Administration, National Ocean Service, National Centers for Coastal Ocean Science, Center for Coastal Fisheries and Habitat Research (CCFHR), 101 Pivers Island Road, Beaufort, NC 28516, USA.
| | - Catherine Roullier
- Mer Molécules Santé (MMS) Laboratory EA2160, University of Nantes, LUNAM, Pharmacy Faculty, 9 rue Bias, F-44035 Nantes, France.
| | - Philipp Hess
- Ifremer, Phycotoxins Laboratory, rue de l'Ile d'Yeu, BP 21105, F-44311 Nantes, France.
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14
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Bertrand S, Roullier C, Guitton Y. Successes and Pitfalls in Automated Dereplication Strategy Using Mass Spectrometry Data: a CASMI Experience. ACTA ACUST UNITED AC 2017. [DOI: 10.2174/2213235x04666160622074357] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Roullier C, Guitton Y, Valery M, Amand S, Prado S, Robiou du Pont T, Grovel O, Pouchus YF. Automated Detection of Natural Halogenated Compounds from LC-MS Profiles–Application to the Isolation of Bioactive Chlorinated Compounds from Marine-Derived Fungi. Anal Chem 2016; 88:9143-50. [DOI: 10.1021/acs.analchem.6b02128] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Catherine Roullier
- University of Nantes, Faculty of Pharmacy, MMS-EA2160, 44035 Nantes, France
- ThalassOMICS,
Plateforme Corsaire, Biogenouest, 44035 Nantes, France
| | - Yann Guitton
- University of Nantes, Faculty of Pharmacy, MMS-EA2160, 44035 Nantes, France
- ThalassOMICS,
Plateforme Corsaire, Biogenouest, 44035 Nantes, France
| | - Marine Valery
- University of Nantes, Faculty of Pharmacy, MMS-EA2160, 44035 Nantes, France
| | - Séverine Amand
- Molécules
de Communication et Adaptation des Micro-organismes, UMR 7245 MNHN/CNRS, Muséum National d’Histoire Naturelle, 75231 Paris Cedex 05, France
| | - Soizic Prado
- Molécules
de Communication et Adaptation des Micro-organismes, UMR 7245 MNHN/CNRS, Muséum National d’Histoire Naturelle, 75231 Paris Cedex 05, France
| | | | - Olivier Grovel
- University of Nantes, Faculty of Pharmacy, MMS-EA2160, 44035 Nantes, France
- ThalassOMICS,
Plateforme Corsaire, Biogenouest, 44035 Nantes, France
| | - Yves François Pouchus
- University of Nantes, Faculty of Pharmacy, MMS-EA2160, 44035 Nantes, France
- ThalassOMICS,
Plateforme Corsaire, Biogenouest, 44035 Nantes, France
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16
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Roullier C, Bertrand S, Blanchet E, Peigné M, Robiou du Pont T, Guitton Y, Pouchus YF, Grovel O. Time Dependency of Chemodiversity and Biosynthetic Pathways: An LC-MS Metabolomic Study of Marine-Sourced Penicillium. Mar Drugs 2016; 14:md14050103. [PMID: 27213411 PMCID: PMC4882577 DOI: 10.3390/md14050103] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 04/21/2016] [Accepted: 05/11/2016] [Indexed: 12/14/2022] Open
Abstract
This work aimed at studying metabolome variations of marine fungal strains along their growth to highlight the importance of the parameter “time” for new natural products discovery. An untargeted time-scale metabolomic study has been performed on two different marine-derived Penicillium strains. They were cultivated for 18 days and their crude extracts were analyzed by HPLC-DAD-HRMS (High Performance Liquid Chromatography-Diode Array Detector-High Resolution Mass Spectrometry) each day. With the example of griseofulvin biosynthesis, a pathway shared by both strains, this work provides a new approach to study biosynthetic pathway regulations, which could be applied to other metabolites and more particularly new ones. Moreover, the results of this study emphasize the interest of such an approach for the discovery of new chemical entities. In particular, at every harvesting time, previously undetected features were observed in the LC-MS (Liquid Chromatography-Mass Spectrometry) data. Therefore, harvesting times for metabolite extraction should be performed at different time points to access the hidden metabolome.
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Affiliation(s)
- Catherine Roullier
- Faculty of Pharmacy, University of Nantes, EA 2160-Mer Molécules Santé, 9 rue Bias BP 53508, Nantes-cedex 1 44035, France.
- ThalassOMICS, Plateforme Corsaire, Biogenouest, Nantes 44035, France.
| | - Samuel Bertrand
- Faculty of Pharmacy, University of Nantes, EA 2160-Mer Molécules Santé, 9 rue Bias BP 53508, Nantes-cedex 1 44035, France.
- ThalassOMICS, Plateforme Corsaire, Biogenouest, Nantes 44035, France.
| | - Elodie Blanchet
- Faculty of Pharmacy, University of Nantes, EA 2160-Mer Molécules Santé, 9 rue Bias BP 53508, Nantes-cedex 1 44035, France.
- Sorbonne Universités, UPMC Université Paris, USR 3579, LBBM, Observatoire Océanologique, Banyuls-sur-Mer 66650, France.
| | - Mathilde Peigné
- Faculty of Pharmacy, University of Nantes, EA 2160-Mer Molécules Santé, 9 rue Bias BP 53508, Nantes-cedex 1 44035, France.
| | - Thibaut Robiou du Pont
- Faculty of Pharmacy, University of Nantes, EA 2160-Mer Molécules Santé, 9 rue Bias BP 53508, Nantes-cedex 1 44035, France.
| | - Yann Guitton
- Faculty of Pharmacy, University of Nantes, EA 2160-Mer Molécules Santé, 9 rue Bias BP 53508, Nantes-cedex 1 44035, France.
- Laboratoire d'Etude des Résidus et Contaminants dans les Aliments (LABERCA), LUNAM Université, Oniris, Nantes 44307, France.
| | - Yves François Pouchus
- Faculty of Pharmacy, University of Nantes, EA 2160-Mer Molécules Santé, 9 rue Bias BP 53508, Nantes-cedex 1 44035, France.
- ThalassOMICS, Plateforme Corsaire, Biogenouest, Nantes 44035, France.
| | - Olivier Grovel
- Faculty of Pharmacy, University of Nantes, EA 2160-Mer Molécules Santé, 9 rue Bias BP 53508, Nantes-cedex 1 44035, France.
- ThalassOMICS, Plateforme Corsaire, Biogenouest, Nantes 44035, France.
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17
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Carroux A, Van Bohemen AI, Roullier C, Robiou du Pont T, Vansteelandt M, Bondon A, Zalouk-Vergnoux A, Pouchus YF, Ruiz N. Unprecedented 17-residue peptaibiotics produced by marine-derived Trichoderma atroviride. Chem Biodivers 2013; 10:772-86. [PMID: 23681725 DOI: 10.1002/cbdv.201200398] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Indexed: 11/07/2022]
Abstract
In the course of investigations on marine-derived toxigenic fungi, five strains of Trichoderma atroviride were studied for their production of peptaibiotics. While these five strains were found to produce classical 19-residue peptaibols, three of them exhibited unusual peptidic sodium-adduct [M + 2 Na](2+) ion peaks at m/z between 824 and 854. The sequencing of these peptides led to two series of unprecedented 17-residue peptaibiotics based on the model Ac-XXX-Ala-Ala-XXX-XXX-Gln-Aib-Aib-Aib-Ala/Ser-Lxx-Aib-Pro-XXX-Aib-Lxx-[C(129) ]. The C-terminus of these new peptides was common to all of them, and its elemental formula C5 H9 N2 O2 was established by HR-MS. It could correspond to the cyclized form of N(δ) -hydroxyornithine which has already been observed at the C-terminus of various peptidic siderophores. The comparison of the sequences of 17- and 19-residue peptides showed similarities for positions 1-16. This observation seems to indicate a common biosynthesis pathway. Both new 17-residue peptaibiotics and 19-residue peptaibols exhibited weak in vitro cytotoxicities against KB cells.
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Affiliation(s)
- Angélique Carroux
- University of Nantes, LUNAM, Faculty of Pharmacy, MMS, F-44000 Nantes
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18
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Vu H, Roullier C, Campitelli M, Trenholme KR, Gardiner DL, Andrews KT, Skinner-Adams T, Crowther GJ, Van Voorhis WC, Quinn RJ. Plasmodium gametocyte inhibition identified from a natural-product-based fragment library. ACS Chem Biol 2013; 8:2654-9. [PMID: 24079418 DOI: 10.1021/cb400582b] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Fragment-based screening is commonly used to identify compounds with relatively weak but efficient localized binding to protein surfaces. We used mass spectrometry to study fragment-sized three-dimensional natural products. We identified seven securinine-related compounds binding to Plasmodium falciparum 2'-deoxyuridine 5'-triphosphate nucleotidohydrolase (PfdUTPase). Securinine bound allosterically to PfdUTPase, enhancing enzyme activity and inhibiting viability of both P. falciparum gametocyte (sexual) and blood (asexual) stage parasites. Our results provide a new insight into mechanisms that may be applicable to transmission-blocking agents.
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Affiliation(s)
- Hoan Vu
- Eskitis
Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Catherine Roullier
- Eskitis
Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Marc Campitelli
- Eskitis
Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Katharine R. Trenholme
- Queensland Institute of Medical Research, Herston, Queensland, Australia
- School
of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Donald L. Gardiner
- Queensland Institute of Medical Research, Herston, Queensland, Australia
| | - Katherine T. Andrews
- Eskitis
Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Tina Skinner-Adams
- Eskitis
Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
| | - Gregory J. Crowther
- Department
of Medicine, University of Washington, Seattle, Washington, United States
| | - Wesley C. Van Voorhis
- Department
of Medicine, University of Washington, Seattle, Washington, United States
| | - Ronald J. Quinn
- Eskitis
Institute for Drug Discovery, Griffith University, Brisbane, Queensland, Australia
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19
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Roullier C, Kambouo R, Paofa J, McKey D, Lebot V. On the origin of sweet potato (Ipomoea batatas (L.) Lam.) genetic diversity in New Guinea, a secondary centre of diversity. Heredity (Edinb) 2013; 110:594-604. [PMID: 23531982 DOI: 10.1038/hdy.2013.14] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
New Guinea is considered the most important secondary centre of diversity for sweet potato (Ipomoea batatas). We analysed nuclear and chloroplast genetic diversity of 417 New Guinea sweet potato landraces, representing agro-morphological diversity collected throughout the island, and compared this diversity with that in tropical America. The molecular data reveal moderate diversity across all accessions analysed, lower than that found in tropical America. Nuclear data confirm previous results, suggesting that New Guinea landraces are principally derived from the Northern neotropical genepool (Camote and Batata lines, from the Caribbean and Central America). However, chloroplast data suggest that South American clones (early Kumara line clones or, more probably, later reintroductions) were also introduced into New Guinea and then recombined with existing genotypes. The frequency distribution of pairwise distances between New Guinea landraces suggests that sexual reproduction, rather than somaclonal variation, has played a predominant role in the diversification of sweet potato. The frequent incorporation of plants issued from true seed by farmers, and the geographical and cultural barriers constraining crop diffusion in this topographically and linguistically heterogeneous island, has led to the accumulation of an impressive number of variants. As the diversification of sweet potato in New Guinea is primarily the result of farmers' management of the reproductive biology of their crop, we argue that on-farm conservation programmes that implement distribution of core samples (clones representing the useful diversity of the species) and promote on-farm selection of locally adapted variants may allow local communities to fashion relatively autonomous strategies for coping with ongoing global change.
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Roullier C, Rossel G, Tay D, McKey D, Lebot V. Combining chloroplast and nuclear microsatellites to investigate origin and dispersal of New World sweet potato landraces. Mol Ecol 2011; 20:3963-77. [PMID: 21880085 DOI: 10.1111/j.1365-294x.2011.05229.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We analysed a representative collection of New World sweet potato landraces (329 accessions from Mexico to Peru) with both chloroplast and nuclear microsatellite markers. Both kinds of markers supported the existence of two geographically restricted genepools, corresponding to accessions from the north-western part of South America and accessions from the Caribbean and Central America region. Our conservative cpSSRs markers revealed that the divergence between the two haplotype groups is associated with numerous mutation events concerning various markers, supporting the idea that this divergence may be ancient, predating domestication. For both kinds of markers, we found no significant difference in diversity between the two genepools and detected region-specific alleles in both groups. Previous studies have favoured the hypothesis of a single domestication of this crop. Our analysis suggests at least two independent domestications, in Central/Caribbean America and in the north-western part of South America. Sweet potato was then dispersed from these centres throughout tropical America. Comparison of nuclear and chloroplast data suggests that exchanges of clones and sexual reproduction were both important processes in landrace diversification in this clonally propagated crop. Our analysis provides useful tools for rationalizing the conservation and use of sweet potato germplasm collections.
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Affiliation(s)
- C Roullier
- CIRAD Avenue Agropolis, 34398 Montpellier Cédex 5, France.
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Roullier C, Chollet-Krugler M, Pferschy-Wenzig EM, Maillard A, Rechberger GN, Legouin-Gargadennec B, Bauer R, Boustie J. Characterization and identification of mycosporines-like compounds in cyanolichens. Isolation of mycosporine hydroxyglutamicol from Nephroma laevigatum Ach. Phytochemistry 2011; 72:1348-1357. [PMID: 21550091 DOI: 10.1016/j.phytochem.2011.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 04/03/2011] [Accepted: 04/04/2011] [Indexed: 05/30/2023]
Abstract
Mycosporine-like compounds, comprising mycosporines and mycosporine-like amino acids (MAAs) are UV protecting secondary metabolites described in organisms such as fungi, algae, cyanobacteria or animals. Lichens however, were only poorly investigated for such constituents so far. Here, a method for the characterization of mycosporines and MAAs in purified aqueous extracts, involving HPTLC coupled to spectrophotodensitometry, HPLC-DAD-MS(n) and UPLC-HRMS analysis, is described. This optimized protocol was validated on three algae and one cyanolichen containing known MAAs and mycosporines, and then applied to 18 cyanolichen species. Analyses revealed the presence of five already described mycosporine-like compounds in the investigated species, including mycosporine serinol in Lichina and Peltigera species and mycosporine glutamicol in Degelia plumbea. Apart from that, eight unknown mycosporine-like compounds were detected and tentatively characterized on the basis of their DAD spectra and their MS(n) and HRMS data: two in the alga Porphyra dioica and six in cyanolichen species belonging to the genera Degelia, Nephroma and Stereocaulon. From Nephroma laevigatum, the mycosporine hydroxyglutamicol was preparatively isolated and identified through HRMS, 1D and 2D NMR spectroscopic data. The optimized analytical protocol allowed the characterization of mycosporine-like compounds in small amounts of material and confirmed the potential of cyanolichens as a source of mycosporine compounds. It should also be applicable to investigate lichen species with green algae photobionts for mycosporine-like compounds.
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Affiliation(s)
- Catherine Roullier
- Equipe PNSCM "Produits Naturels, Synthèses et Chimie Médicinale", UMR CNRS 6226, Faculté des Sciences Pharmaceutiques et Biologiques, Université de Rennes 1, 2 Av. du Pr. Léon Bernard, 35043 Rennes Cedex, France
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Roullier C, Chollet-Krugler M, Weghe PVD, Devehat FLL, Boustie J. A novel aryl-hydrazide from the marine lichen Lichina pygmaea: Isolation, synthesis of derivatives, and cytotoxicity assays. Bioorg Med Chem Lett 2010; 20:4582-6. [DOI: 10.1016/j.bmcl.2010.06.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 06/01/2010] [Accepted: 06/02/2010] [Indexed: 11/28/2022]
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Roullier C, Chollet-Krugler M, Bernard A, Boustie J. Multiple dual-mode centrifugal partition chromatography as an efficient method for the purification of a mycosporine from a crude methanolic extract of Lichina pygmaea. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:2067-73. [DOI: 10.1016/j.jchromb.2009.05.040] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 05/14/2009] [Accepted: 05/19/2009] [Indexed: 11/30/2022]
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