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Isolation and Identification of Secondary Metabolites from the Fungus Phomopsis Spp., a Pathogen Responsible for Vine Excoriosis

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Isolation and Identification of Secondary Metabolites from the Fungus Phomopsis Spp., a Pathogen Responsible for Vine Excoriosis Isolation and identification of secondary metabolites from the fungus Phomopsis spp., a pathogen responsible for vine excoriosis Thèse présentée à la Faculté des Sciences Institut de Chimie Université de Neuchâtel Pour l'obtention du grade de docteur ès sciences Par Nicolas MOTTIER Chimiste diplomé de l'Université de Genève Acceptée sur proposition du jury: Prof. Raffaele Tabacchi, directeur de thèse Université de Neuchâtel Dr. Eliane Abou-Mansour Université de Neuchâtel Dr. Brigitte Mauch-Mani Université de Neuchâtel Dr. Andrew Marston Université de Genève Dr. Olivier Viret Agroscope Changins Soutenue le 19 Août 2005 Université de Neuchâtel 2005 Isolement et identification de métabolites secondaires du champignon Phomopsis spp., un pathogène responsable de l'excoriose de la vigne Thèse présentée à la Faculté des Sciences Institut de Chimie Université de Neuchâtel Pour l'obtention du grade de docteur ès sciences Par Nicolas MOTTIER Chimiste diplomé de l'Université de Genève Acceptée sur proposition du jury: Prof. Raffaele Tabacchi, directeur de thèse Université de Neuchâtel Dr. Eliane Abou-Mansour Université de Neuchâtel Dr. Brigitte Mauch-Mani Université de Neuchâtel Dr. Andrew Marston Université de Genève Dr. Olivier Viret Agroscope Changins Soutenue le 19 Août 2005 Université de Neuchâtel 2005 i ii Remerciements Je voudrais remercier le Prof. R. Tabacchi pour m'avoir donner l'opportunité d'accomplir ce travail de recherche dans son groupe et pour la liberté et la confiance qu'il m'a accordé. Je voudrais aussi remercier les membres du jury le Dr B. Mauch-Mani, Dr E. Abou-Mansour, Dr A. Marston et Dr O. Viret pour avoir accepté de lire et réviser le présent travail et pour l'intérêt qu'ils y ont porté. Je tiens à remercier aussi D. Christen pour nous avoir fourni les souches du champignon ainsi que le Dr. D. Job et son groupe pour m'avoir permis d'utiliser son laboratoire de l'institut de Biologie. Merci aussi à Mr. F. Fehr de l'Université de Fribourg pour avoir si bien fait les analyses de RMN 500 MHz et H. Bursian pour l'analyse des composés par RMN 400 Hz. Un grand merci a Camille Perret qui m'a accueilli dans le groupe et qui a eu le temps et la patience pour m'apprendre à utiliser l'HPLC et la masse ainsi que pour sa gentillesse. Merci aussi à Manuel Tharin pour ses bougonnements légendaires et grâce à qui j'ai pu découvrir les parties les plus secrètes des HPLC et qui m'a accueilli dans mon nouveau travail. Un merci tout particulier à Eliane pour son aide, sa patience, sa disponibilité et ses conseils durant toute cette thèse. Un grand merci aussi à Jules pour la bonne ambiance qu'il aura amené dans le labo, son aide et sa patience avec la RMN et les conseils pour les purifications ainsi que pour les explications sur les différents types de Zouk. Merci aussi à Marie-Lorène Goddard pour son travail précurseur sur le champignon. Un grand merci aussi à Nathalie et David, Florence, Julie Brettar, Julie Lenoble, Sabine, pour leur encouragements et leur soutient et à Blaise pour les sorties à skis annuelles qui se sont toujours déroulées les moustaches frétillantes. Un grand merci aux membres présent et passé du groupe, Emmanuel, Sandrine, Laura, Bernard, Mustapha, Josée, Mélanie, Sabine et à tous les membres de l'Institut, doctorants ou étudiants, trop nombreux pour tous les citer ici. iii Un grand merci à ma famille, mes parents, mon frère et la famille outre-manche, pour leur soutient tout au long de ces longues années d'études. Finalement merci à Cristina pour sa patience, sa bonne humeur, ses encouragements incessants et son amour. iv Glossary 1, 2, 3… : Symbols used for the compounds isolated in this work ACN: Acetonitrile API: Atmospheric Pressure Ionisation (MS) Apical: Apex or tip of something (pl. apices) APCI: Atmospheric Pressure Chemical Ionisation (MS) APPI: Atmospheric Pressure Photo-Ionisation (MS) Apressed: Pressed closed to or lying flat against something. ATP: Adenosine triphosphate Buff: pale yellow-brown colour COSY: Correlated spectroscopy (1H NMR) Cyrrhi: Jelly made of conidia released by the ostiole of pycnidia. Conidia: Generic term referring to a spore produced in vegetative reproduction of a fungus and located on sporulating blotches. Conidia are produced and borne by specialized mycelial hyphae called conidiophores Da: Dalton DAD: Diode-array detector DEPT: Distortion enhancement by polarisation transfer (13C NMR) EtOAc: Ethyl acetate ESI: Electrospray Ionisation (MS) EI: Electron Impact Ionisation (MS) Guttule: small drop; spot like small drop HMBC: Heteronuclear multiple bond correlation spectroscopy (1H-13C NMR) HPLC: High-Performance liquid chromatography Hyaline: Transparent, glassy or vitreous J: Coupling constant (Hz) LC-MS: High-Performance liquid chromatography coupled to mass spectrometry MeOH: Methanol Mycelium: Microscopic filaments of the vegetative system of fungi which make a thick network. MW: molecular weight (in Da) (MS) i m/z: mass to charge ratio (MS) NMR: Nuclear magnetic resonance Ostiole: Small opening, pore. PDA: Potato dextrose agar q: quadruplet (NMR) Pycnidia: A rounded, or flask-shaped, asexual fungal fructification that produces conidia (pycnidiospores) characteristic of the imperfect stages of some fungi and of one main group of the Fungi Imperfecti. s: singlet (NMR) sp: unspecified species Spore: A small, usually microscopic, reproductive cell, either sexual or asexual, used for its own preservation and spread. Teleomorph: Describes a fungus that reproduces sexually (as opposed to anamorph) TLC: Thin-layer chromatography t : triplet (NMR) Umbonate: An umbo is a softly curved bump in a flat cap of a mushroom. A cap with an umbo is said to be umbonate UV: Ultra-violet ii Table of contents 1. Introduction..................................................................................................................1 1.1. Phomopsis viticola (Sacc.) Sacc. ...............................................................................2 1.1.1. Disease symptoms..........................................................................................5 1.1.2. Disease cycle..................................................................................................7 1.1.3. Disease management....................................................................................10 1.2. Aim of the work.......................................................................................................10 1.3. Secondary metabolites from Phomopsis sp. ............................................................11 1.4. Analytical techniques...............................................................................................13 1.4.1. Electrospray ionisation.................................................................................16 1.4.2. Atmospheric pressure chemical ionisation ..................................................18 1.4.3. Atmospheric pressure photoionisation.........................................................19 1.4.4. The ion trap..................................................................................................22 1.4.5. NMR techniques..........................................................................................24 2. Material and methods................................................................................................27 2.1. Fungal strains...........................................................................................................27 2.1.1. Fungal cultures and extraction.....................................................................27 2.2. Fungal cultures on grapevine wood .........................................................................28 2.3. Bioassays..................................................................................................................29 2.4. Solvents....................................................................................................................29 2.5. TLC..........................................................................................................................30 2.6. Open columns..........................................................................................................30 2.7. HPLC .......................................................................................................................31 2.7.1. Analytical HPLC..........................................................................................31 2.7.2. Semi-preparative HPLC...............................................................................32 2.8. Mass spectrometry ...................................................................................................32 2.9. LC-MS .....................................................................................................................33 2.10. NMR ....................................................................................................................34 iii 3. Results .........................................................................................................................35 3.1. Strain selection.........................................................................................................35 3.2. Strain growth time....................................................................................................39 3.3. Isolated compounds.................................................................................................42 3.3.1. Compound 1: 1-carboxymethyl-6-(hydroxymethyl)-8-hydroxy-xanthone (Sydowinin
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