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Metabolomics and Dereplication-Based Isolation of Novel Bioactive Natural Products from Marine Sponge-Associated Actinomycetes

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Metabolomics and Dereplication-Based Isolation of Novel Bioactive Natural Products from Marine Sponge-Associated Actinomycetes Metabolomics and dereplication-based isolation of novel bioactive natural products from marine sponge-associated actinomycetes Metabolomik und Dereplikations-basierte Isolierung von neuen bioaktiven Naturstoffen aus marinen, Schwamm-assoziierten Actinomyceten Doctoral thesis for a doctoral degree at the Graduate School of Life Sciences, Julius-Maximilians-Universität Würzburg, Section: Infection and Immunity submitted by Cheng Cheng from Tianjin, China Würzburg, June, 2016 Submitted on: Members of the Promotionskomitee: Chairperson: Prof. Dr. Thomas Müller Primary Supervisor: Prof. Dr. Ute Hentschel Humeida Supervisor (Second): Prof. Dr. Martin J. Mueller Supervisor (Third): Dr. RuAngelie Edrada-Ebel Supervisor (Fourth): Dr. Usama Ramadan Abdelmohsen Date of Public Defence: Date of Receipt of Certificates: Affidavit I hereby confirm that my thesis entitled "Metabolomics and dereplication-based isolation of novel bioactive natural products from marine sponge-associated actinomycetes" is the result of my own work. I did not receive any help or support from commercial consultants. All sources and / or materials applied are listed and specified in the thesis. Furthermore, I confirm that this thesis has not yet been submitted as part of another examination process neither in identical nor in similar form. th Würzburg, 6 Jun 2016 Place, Date Signature Eidesstattliche Erklärung Hiermit erkläre ich an Eides statt, die Dissertation "Metabolomik und Dereplikations- basierte Isolierung von neuen bioaktiven Naturstoffen aus marinen, Schwamm-assoziierten Actinomyceten" eigenständig, d.h. insbesondere selbständig und ohne Hilfe eines kommerziellen Promotionsberaters, angefertigt und keine anderen als die von mir angegebenen Quellen und Hilfsmittel verwendet zu haben. Ich erkläre außerdem, dass die Dissertation weder in gleicher noch in ähnlicher Form bereits in einem anderen Prüfungsverfahren vorgelegen hat. th Würzburg, 6 Jun 2016 Ort, Datum Unterschrift Acknowledgments I would like to express my deepest gratitude to all those who helped me to make this thesis possible. First, I would like to thank my supervisor Prof. Dr. Ute Hentschel Humeida for providing me with the opportunity to work on this exciting project, for being patient in teaching me my work and for supporting me even beyond the confines of my studies. I am extremely thankful that I have been able to complete my Ph.D. thesis under her excellent supervision. My great appreciation also goes out to my committee member, Dr. Usama Ramadan Abdelmohsen, who has always been very kind and patient in supporting my work, encouraging me, and providing me valuable suggestions, as well as accurate and tight guidance on my experiments and academic work. I would offer my special thanks to Dr. RuAngelie Edrada-Ebel for giving me the opportunity to join in the SeaBioTech project and to implement the metabolomics analysis in the University of Strathclyde. My gratitude also goes to Dr. Lynsey MacIntyre, Dr. Christina Viegelmann, and Dr. Tong Zhang for their kind help on metabolomics data processing and sample measurements in the University of Strathclyde. I would like to acknowledge Prof. Dr. Martin J. Mueller for providing me the chance to measure my samples in the Department of Pharmaceutical Biology, Würzburg University, and Dr. Markus Krischke, Dr. Agnes Fekete, Dr. Stefan Schäbler, and Ms. Maria Lesch for their support on mass spectrometry measurement and analysis. I am grateful to Dr. Matthias Grüne for the NMR measurements in the Department of Organic Chemistry, Würzburg University, and his vital comments on compound structure elucidation. For the sponge collections and bioassay screening, I would like to thank all the members in WP2 and WP3 within the SeaBioTech project, and Ms. Antje Fuß in the Missionsärztliches Institut Würzburg, especially for the antitrypanosomal screening. My gratitude also goes to Dr. Eman Maher Othman, Prof. Dr. Helga Stopper, Anastasija Reimer, Dr. Vera Kozjak- Pavlovic, Prof. Dr. Thomas Rudel, Srikkanth Balasubramanian, Dr. Tobias Oelschläger for their help and support in the bioactivity testings of the isolated compounds. I would like to thank Ms. Christine Gernert for her patience and kindness in teaching me the procedure of the DNA extraction and amplification. 4 My appreciation also goes to my labmates Hannes Horn for the support on phylogenetic analysis and German translation, Dr. Lucas Moitinho-Silva, Dr. Lucía Pita Galán, Beate Slaby, Dr. Kristina Bayer, and Martin Jahn for the friendship and happy time we spent together. I am thankful to the SeaBioTech and the SFB630 project for the financial support and GSLS Würzburg University for providing me the chance to participate in a variety of excellent workshops and transferable skills courses during my Ph.D. study. Lastly, I would like to thank my parents for their endless love and support throughout my life and wish to offer my best regards and blessings to all of those who supported me in any respect during the completion of the project. 5 DEDICATION THIS DISSERTATION IS DEDICATED TO MY FAMILY 6 Table of Contents Summary .............................................................................................................................10 Zusammenfassung .............................................................................................................12 中文摘要 ...............................................................................................................................14 Chapter 1 Introduction .......................................................................................................15 1.1 Natural products ........................................................................................................15 1.2 Marine sponge microbiology ....................................................................................16 1.3 Actinomycetes ...........................................................................................................19 1.3.1 Actinomycete diversity .......................................................................................19 1.3.2 Sponge-associated actinomycetes ....................................................................20 1.4 Utility of metabolomics tools for natural product discovery ..................................28 1.5 Scope of the study ....................................................................................................33 1.6 References .................................................................................................................34 Chapter 2 Isolation, biodiversity, and biological activity screening of actinomycetes isolated from Mediterranean sponges ..............................................................................45 2.1 Materials and methods ..............................................................................................45 2.1.1 Specimen collection ...........................................................................................45 2.1.2 Isolation of sponge-associated actinomycetes ................................................45 2.1.3 Molecular identification and phylogenetic analysis .........................................46 2.1.4 Bioassay screening ............................................................................................47 2.1.4.1 Antioxidant assay .........................................................................................48 2.1.4.2 Antimicrobial assay ......................................................................................48 2.1.4.3 Antitrypanosomal bioassay .........................................................................48 2.2 Results .......................................................................................................................49 2.2.1 Diversity of sponge-associated actinomycetes ................................................49 2.2.2 Phylogenetic analysis .........................................................................................54 2.2.3 Bioassay screening ............................................................................................57 2.3 References .................................................................................................................59 Chapter 3 Metabolomics and dereplication-based strain prioritization ..........................61 3.1 Materials and methods ..............................................................................................61 3.1.1 Metabolomics analysis using NMR data ............................................................61 3.1.2 Metabolomics analysis using LC-MS data ........................................................61 3.1.3 Dereplication study using LC-MS/MS data ........................................................63 7 3.1.4 HPLC profiling .....................................................................................................63 3.2 Results .......................................................................................................................64 3.2.1 Milos collection ...................................................................................................64 3.2.1.1 Metabolomics analysis .................................................................................64 3.2.1.2 HPLC profiling of solid extracts of 13 selected Milos isolates ..................74 3.2.2 Crete collection ...................................................................................................75 3.2.2.1 Metabolomics
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