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Bridging the Gap Between Genomics- and Metabolomics-Based Perspectives of Myxobacterial Secondary Metabolite Production Capabili

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Bridging the Gap Between Genomics- and Metabolomics-Based Perspectives of Myxobacterial Secondary Metabolite Production Capabili Bridging the gap between genomics - and metabolomics - based perspectives of myxobacterial secondary metabolite production capability Dissertation zur Erlangung des Grades des Doktors der Naturwissenschaften der Naturwissenschaftlich - T echnischen Fakultät der Universität des Saarlandes. von Fabian Panter Saarbrücken 2018 2 Tag des Kolloquiums: 01.04.2019 Dekan : Prof. Dr. Guido Kickelbick Berichterstatter: Prof. Dr. Rolf Müller Prof. Dr. Christian Ducho Prof. Dr. Tobias Gulder Vorsitz: Prof. Dr. Uli Kazmaier Akad. Mitarbeiter : Dr. Judith Becker 3 Diese Arbeit entstand unter der Anleitung von Prof. Dr. Rolf Müller am Institut für Pharmazeutische Biotechnologie der Naturwissenschaftlich - Technischen Fakultät der Universität des Saarlandes von Dezember 2014 bis November 2018 . 4 Ο ἶ δα ο ὐ κ ε ἰ δώς Ich weiß, dass ich unwissend bin . entlehnt aus der Apologie des Sokrates, V olksgericht von Athen 399 v. Chr . 5 Danksagung Als erstes möchte ich mich bei meinem Doktorvater Prof. Dr. Rolf Müller für die Möglichkeit be danken , meine Dissertation in dieser Arbeitsgruppe durchzuführen. Das entgegengebrachte Vertrauen für die Bearbeitung anspruchsvoller Themen im Bereich des bakteriellen Sekundärstoffwechsels und die immerwährende Unterstützung im Rahmen wissenschaftlicher Diskus sionen waren sehr hilfreich und motivierend. Zudem möchte ich mich bei Prof. Dr. Christian Ducho für die Annahme des Co - Referats und Unterstützung als wissenschaftlicher Begleiter bedanken. Zudem möchte ich mich bei meinem Betreuer Dr. Daniel Krug für die tatkräftige Unterstützung meiner Dissertation, durch wissenschaftliche Diskussionen und innovative Lösungsansätze für Probleme meiner Doktorarbeit, sowie für kritische Überarbeitung meiner Manuskripte bedanken. Darüber hinaus möchte ich mich bei allen beda nken die mir in den vergangenen fast 4 Jahren mit Rat und Tat zur Seite standen und es mir ermöglichten in sehr vielen Bereichen der Naturstoffforschung dazu zu lernen. Zunächst zu nennen sind hier das ehemalige ‚Analytik Team‘ bestehend aus Dr. Thomas Hof fmann, Dr. Michael Hoffmann und Dr. David Auerbach die mir einen tiefen Einblick sowohl in die Bedienung der vielen verschiedenen Massenspektrometer und Chromatographieanlagen des Instituts gaben als auch wichtige Expertentipps verteilten um diese Anlagen optimal einzusetzen. Weiterhin möchte ich Dr. Thomas Hoffmann für Tipps und Tricks in statistischer Analyse von Massenspektrometriedaten danken. Zudem möchte ich Dr. Louise Kjaerulf für Hilfe sowie Tipps und Tricks bei der Interpretation der NMR Spektren d anken. Nicht zuletzt möchte ich mich bei Dr. Sascha Baumann, Dr. Konrad Viehrig und Dr. Alexander von Tesmar für die Einführung in Klonierungstechniken sowie unkonventionelle und zeitsparende Methoden zur Gencluster Assemblierung bedanken. Schließlich möc hte ich mich für die tolle Zeit mit der gesamten Arbeitsgruppe bedanken, vor allem bei den Mitgliedern des Freitagsbierbüros. Dies gilt sowohl für Chantal Bader, Patrick Haak und Nicolas Frank , sowie für Ex - Alumni David Auerbach und Michael Hoffmann , als a uch Büromitglieder h.c. wie Sebastian Groß, Joachim Hug , Markus Neuber und Jan Schlemmer, die durch aggressiv gute Laune jede Form von Dissertationsdepression vertreiben konnten. Zum Schluss möchte ich noch meiner ganzen Patchworkgroßfamilie danken auf die ich in jeder Situation zählen kann. Ihr alle habt mitgeholfen mich durch alle Hochs und Tiefs der Dissertation zu manövrieren. Auch möchte ich mich bei Sophia für seelische und moralische Unterstützung bei allen gescheiterten Experimenten und während der etwas kurzfristig anberaumten Anfertigung der Druckversion dieser Doktorarbeit bedanken. Ohne dich hätte ich das alles so nicht geschafft. 6 Vorveröffentlichungen aus dieser Dissertation Teile dieser Arbeit wurden vorab mit Genehmigung der Naturwissenschaft lich - Technischen Fakultät en , vertreten durch den Mentor der Arbeit, in folgenden Beiträgen veröffentlicht oder sind derzeit in Vorbereitung zur Veröffentlichung: Publikationen Fabian Panter , Daniel Krug , Sascha Baumann and Rolf Müller* : Self - resistance guided genome mining uncovers new topoisomerase inhibitors from myxobacteria . Chem. Sci. , 2018 May 3; 9 (21): 4898 - 4908 DOI: 10.1039/C8SC01325J Fabian Panter , Daniel Krug and Rolf Müller*: Novel methoxymethacrylate natural products uncovered by statistics - b ased mining of the Myxococcus fulvus secondary metabolome. ACS chem . biol . 2019 Jan 18; 14 (1):88 - 98 DOI: 10.1021/acschembio.8b00948 Jan Gorges, 1 Fabian Panter, 1 Louise Kjaerulff, 1 Thomas Hoffmann, Uli Kazmaier * and Rolf Müller* : Structure, Total Synthesis and Biosynthesis of Chloromyxamides - Myxobacterial Tetrapeptides Featuring an Uncommon 6 - Chloromethyl - 5 - methoxypipecolic Acid Building Bloc . Angew. Chem. Int. Ed. Engl. 2018 Oct 22; 57 (43):14270 - 14275 DOI: 10.1002/anie.201808028 Louise Kjaerulff, 1 Ritesh Raju, 1 Fabian Panter , Ullrich Scheid, Ronald Garcia, Jennifer Herrmann, and Rolf Müller* : Pyxipyrrolones: Novel cytotoxic myxobacterial metabolites. Structure elucidation and biosynthesis proposal. Angew. Chem. Int. Ed. Engl. 2017 Aug 1; 56 (32):9614 - 9618 DOI: 10.1002/anie.201704790 Michael Hoffmann , 1 David Auerbach , 1 Fabian Panter , Thomas Hoffmann , Pieter C. Dorrestein and Rolf Müller * : Homospermidine Lipids: A Compound Class Specifically Formed during Fruiting Body Formation of Myxococcus xan thus DK1622. ACS Chem. Biol. 2018 Jan 19; 13 (1):273 - 280 DOI: 10.1021/acschembio.7b00816 1 These Authors contributed equally to the manuscript 7 Marvin Meusel , Franziska Hufsky , Fabian Panter , Daniel Krug , Rolf Müller and Sebastian Böcker * : Predicting the Presence of Uncommon Elements in Unknown Biomolecules from Isotope Patterns . Anal. Chem. 2016 Aug 2; 88 (15):7556 - 66 DOI: 10.1021/acs.analchem.6b01015 Publikationen die nicht Teil dieser Arbeit sind E ilien Schulz, Adriely Goes, Ronald Garcia, Fabian Panter , Marcus Koch, Rolf Müller, Kathrin Fuhrmann and Gregor Fuhrmann*: Biocompatible bacteria - derived vesicles show inherent antimicrobial activity. J . Control. Release 2018 Nov 28; 290 :46 - 55 DOI: 10.1016/j.jconrel.2018.09.030 Joachim J. Hug , Fabian Panter , Daniel Krug and Rolf Mü ller * : Genome mining reveals Uncommon Alkylpyrones as Type III PKS Products from Myxobacteria. J. Ind. Microbiol. Biotechnol. Accepted manuscript, online preview DOI: 10.1007/s10295 - 018 - 2105 - 6 Domen Pogorevc, Fabian Panter , Carolina Schillinger , Silke C. Wenzel and Rolf Müller * : Production optimization and biosynthesis revision of Corallopyronin A, a potent anti - fil arial antibiotic . M anuscript in preparation Tagungsbeiträge Fabian Panter , Daniel Krug und Rolf Müller (2016) The Fulvuthiacenes – Secondary metabolites from Myxococcus fulvus with an unprecedented structural feature . (Poster) Vereinigung für Allgemeine und Angewandte Mikrobiologie (VAAM) Workshop , Freiburg , Germany Fabian Panter , Daniel Krug und Rolf Müller (2017) The Fulvuthiacenes – Secondary metabolites from Myxococcus fulvus with an unprecedented terminal ketene acetal moiety . (Oral Communication) V ereinigung für Allgemeine und Angewandte Mikrobiologie (VAAM) Workshop , Tübingen , Germany 8 Fabian Panter , Daniel Krug und Rolf Müller (2017) The Fulvuthiacenes – Secondary metabolites from Myxococcus fulvus with an unprecedented structural feature. (Poster) VI . Symposium of the Interdisciplinary Graduate School of Natural Product Research , Saarbrücken, Germany Fabian Panter , Daniel Krug, Sascha Baumann und Rolf Müller (2018) Self - resistance guided genome mining uncovers the pyxidicycline class of my xobacterial natural products . (Poster) 30. Irseer Naturstofftage, Gesellschaft für C hemische Technik und Biotechnologie e.V. (DECHEMA) , Irsee , Germany Fabian Panter , Daniel Krug und Rolf Müller (2018) Mass spectrometrical observation of the fulvuthiacene biosynthesis (Poster) European Mass Spectrometry Conference (EMSC) , Saarbrücken , Germany Fabian Panter , Daniel Krug, Sascha Baumann und Rolf Müller (2018) Self - resistance guided genome mining uncovers new topoisomerase inhibitors from myxobacteria ( Oral Communication ) 8 th Helmholtz Institut für Pharmazeutische Forschung Saarland ( HIPS ) Symposium , Saarbrücken, Germany Fabian Panter , Daniel Krug, Sascha Baumann und Rolf Müller (2018) Self - resistance guided genome mining uncovers the pyxidicycline class of myxobacterial natural products (Poster) VII. Symposium of the Interdisciplinary Graduate School of Natural Product Research , Saarbrücken, Germany Fabian Panter , Daniel Krug, Sascha Baumann und Rolf Müller (2018) Self - resistance guided Genome Mining uncovers the Pyxidicycline Class of Myxobacterial N atural P roducts ( Oral Communication ) Vereinigung für Allgemeine und Angewandte Mikrobiologie (VAAM) Workshop, Frankfurt am Main , Germany Fabian Panter , D aniel Krug, Sascha Baumann und Rolf Müller (2018) Self - resistance guided Genome Mining uncovers the Pyxidicycline Class of Myxobacterial N atural P roducts (Poster) 3rd European Conference on Natural Products, Gesellschaft für Chemische Technik und Biotechnologie e.V. (DECHEMA) , Frankfurt am Main , Germany 9 Zusammenfassung Bakterielle Sekundärmetabolite haben oft starke biologische Aktivität und hohe „ Target “ - s pezifität , weshalb sie wertvolle Wirkstoffleitstrukturen darstellen . Es besteht jedoch eine große Diskrepanz zwischen der Anzahl der aus Bakterien unter Laborbedingungen nachweisbaren Sekundärmetabolite n und der in ihrem Genom codierten Produktionskapazität für
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