Biokatalytische Diversität Der Terpenbildung in Pflanzen Und Bakterien”

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Biokatalytische Diversität Der Terpenbildung in Pflanzen Und Bakterien” Biokatalytische Diversität der Terpenbildung in Pflanzen und Bakterien Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften der Fakultät für Chemie und Biochemie an der Graduate School for Chemistry and Biochemistry der Ruhr-Universität Bochum angefertigt in der Nachwuchsgruppe für Mikrobielle Biotechnologie vorgelegt von Octavia Natascha Kracht aus Unna Bochum Juli 2017 Erstgutachter: Prof. Dr. Robert Kourist Zweitgutachter: Jun.-Prof. Dr. Simon Ebbinghaus Diese Arbeit wurde in der Zeit von Mai 2014 bis Juli 2017 unter der Leitung von Jun.- Prof. Dr. Robert Kourist in der Nachwuchsgruppe für Mikrobielle Biotechnologie an der Ruhr-Universität Bochum durchgeführt. 2 Danksagung An dieser Stelle möchte ich mich bei den Personen bedanken, die mich während der Anfertigung dieser Arbeit immer unterstützt und damit einen Großteil zum Gelingen dieses Projektes beigetragen haben. Mein größter Dank gilt meinem Doktorvater Prof. Dr. Robert Kourist für die interessante Themenstellung und die Möglichkeit der Anfertigung dieser Dissertation in seiner Arbeitsgruppe. Vielen Dank für das Vertrauen, dass du mir entgegengebracht hast und deine sowohl fachliche als auch persönliche Unterstützung während meiner gesamten Promotion. Auch auf langen Durststrecken hast du immer an unser Projekt geglaubt und mich stets motiviert. Vielen Dank für deine ständige Gesprächsbereitschaft, die konstruktiven Beiträge und vor allem die Ermöglichung meines Auslandsaufenthaltes in Kanada. Ich werde meine Zeit in deiner Gruppe immer in guter Erinnerung behalten. Ich möchte mich außerdem ganz herzlich bei Jun.-Prof. Dr. Simon Ebbinghaus für die freundliche Übernahme des Koreferates bedanken. Einen ganz großen Dank möchte ich unseren Gärtnern Andreas Aufermann und Martin Pullack (LS Pflanzenphysiologie, RUB) ausprechen. Ohne euch wäre die Anfertigung dieser Arbeit gar nicht erst möglich gewesen! Egal ob Weiße Fliege, Läuse oder Behandlung mit Methanol, ihr habt nie aufgegeben und euch immer etwas Neues einfallen lassen, um unsere Pflanzen zu erhalten. Euer Einsatz bei der Kultivierung der Eremophila Spezies war beeindruckend. Ein weiterer Dank gilt unseren Kooperationspartnern des OMCBP-Projektes. Hierbei möchte ich vor allem PD Dr. Markus Piotrowski (RUB), Prof. Dr. Thomas Brück (TUM) und Dr. Michael Hofer (Fraunhofer IGB) für die fachliche Unterstützung während der gesamten Projektlaufzeit danken. Die fachlichen Diskussionen während der OMCBP-Meetings haben zu einem Mehrwert dieser Arbeit beigetragen. Ein ganz besonderer Dank gilt ebenfalls unseren kanadischen Kooperationspartnern: Many thanks to Prof. Russell Kerr, Brad Haltli and Dr. Fabrice Berrué for your support on my project and the nice research stay in your lab. Desweiteren möchte ich mich ganz herzlich bei Prof. Dr. Julia Bandow und Christoph Senges für die angenehme Kooperationsarbeit bezüglich des Streptomyceten-Projektes bedanken. Einen ganz besonderen Dank möchte ich ebenfalls meinen Studenten Julia Stockmann, Dennis Sander und Pia Fiegenbaum ausprechen: Eure Leistungsbereitschaft und Motivation war beeindruckend und ich hoffe, dass ihr nie eure Freude an der Wissenschaft verlieren werdet. Ich bin glücklich, euch in meinem „Team Eremophila“ gehabt zu haben und danke 3 euch für eure Unterstützung! Vor allem Julia Stockmann sei gedankt für die Unterstützung bei der Anfertigung der unzähligen Stämmbäume während und sogar nach ihrer Masterarbeit. Vielen Dank an Ann-Christin Ammann und Nicole Schmelzer für die Hilfe bei der RNA- Extraktion und die Unterstüzung bei den zahlreichen RACE-PCRs. Für die schöne Zeit auf der zweiten Etage möchte ich mich ganz herzlich bei der Arbeitsgruppe von Prof. Dr. Ute Krämer bedanken. Ein ganz großer Dank gilt hierbei Klaus Hagemann, der mich regelmäßig über drei Jahre lang mit Trinkwasser versorgte. Vielen Dank auch an Petra Düchting für die Unterstützung mit dem GC/MS. Desweiteren danke ich PD Dr. Minou Nowrousian und ihrem gesamten Team für das freundliche Miteinander auf der sechsten Etage sowie die Unterstützung bei der Gerätebenutzung. Der gesamten Nachwuchsgruppe für Mikrobielle Biotechnologie möchte ich für das freundliche, stets positive Arbeitsklima danken, sowie für viele lustige Momente, beim Wasserski, Lasertag und nicht zuletzt natürlich auch im Labor. Ich freue mich über die tollen Freundschaften, die sich auch über die Arbeit hinaus entwickelt haben. Zuletzt danke ich meiner Familie für die Unterstützung während meiner gesamten Promotion. 4 Inhaltsverzeichnis 1. Zusammenfassung 11 1. Abstract 14 2. Einleitung 17 2.1 Die Bedeutung der Biotechnologie 17 2.1.1. Bereitstellung von Enzymen in der Biotechnologie 18 2.2 Bedeutung und Biosynthese von Terpenen 19 2.2.1. Die Naturstoffgruppe der Terpene 19 2.2.2. Die Bedeutung von Terpenen in der Industrie 23 2.2.3. Entstehung und Generierung von Terpendiversität 25 2.2.4. Entstehung von Terpendiversität in Bakterien 50 2.3. Zielsetzung 53 3. Material und Methoden 54 3.1. Material 54 3.2. Methoden 63 3.2.1. Molekularbiologische Methoden 63 3.2.2. Proteinbiochemische Methoden 72 3.2.3. Analytische Methoden 73 4. Ergebnisse 78 4.1. Identifizierung und Charakterisierung neuer TPS aus der australischen 78 Wüstenpflanze E. serrulata 4.1.1. Naturstoffextraktion 78 4.1.2. Etablierung einer Methode zur Isolierung von Nukleinsäuren 82 aus den Blättern der Pflanze E. serrulata 4.1.3. Transkriptomdaten 88 4.1.4. Bestimmung potentieller TPS aus E. serrulata 90 5 4.1.5. Resquenzierung der NGS Daten und Entdeckung 96 potentieller Isoenzyme 4.1.6. RACE-PCR zur Generierung von Volllängen-Genen 103 4.1.7. Phylogenetische Einordnung der E. serrulata 104 4.1.8. Heterologe Genexpression potentieller TPS in E. coli 106 4.1.9. Aktivitätsmessungen mit isotopenmarkierten Substraten 108 4.1.10. Produktbestimmung der potentiellen TPS 109 4.1.11. Enzym-Charakterisierung von OK 4a und OK 1a 118 4.2. Entdeckung und Identifzierung neuer TPS aus S. chartreusis 122 4.2.1. Generierung der genomischen DNA und NGS 122 4.2.2. Bestimmung potentieller TPS 123 4.2.3. Phylogenetische Einordnung der TPS 125 4.2.4. Heterologe Expression der potentiellen TPS in E. coli 126 4.2.5. Produktbestimmung der TPS 129 4.3. Mutagenesestudien einer pflanzlichen TPS 135 4.3.1. Modellierung von TPS4 135 4.3.2. Generierung der TPS4 Mutanten 136 4.3.3. Heterologe Expression von TPS4 und seinen Varianten 139 4.3.4. Produktbestimmung von TPS4 140 4.3.5. Mutanten mit einem veränderten Produktspektrum 147 5. Diskussion 152 5.1. Entdeckung neuer TPS aus der australischen Wüstenpflanze 152 E. serrulata 5.1.1. Naturstoffextraktion und Induktion der E. serrulata 152 5.1.2. Betrachtung der NGS Daten und der 160 Transkriptomzusammensetzung 6 5.1.3. Generierung von Volllängen-Genen mittels RACE-PCR 164 5.1.4. Heterologe Genexpression pflanzlicher TPS in E. coli 164 5.1.5. Produktbestimmung der TPS 166 5.2. Entdeckung und Identifzierung neuer TPS aus S. chartreusis 169 5.2.1. Bakterien als alternative Terpenproduzenten 169 5.2.2. Heterologe Genexpression und Aktivität der bakteriellen 171 TPS 5.2.3. Identifzierung der potentiellen TPS 171 5.3. Mutagenesestudien zur pflanzlichen Sesquiterpensynthase TPS4 174 5.3.1. Strukturbestimmung und Analyse potentieller 175 plastizierbarer Reste 5.3.2. Auswirkung der Mutagenese auf das Produktspektrum 176 6. Fazit 178 7. Literatur 181 8. Anhang 199 Lebenslauf 203 Eidesstattliche Erklärung 206 7 Abkürzungsverzeichnis Abkürzungsverzeichnis Amp Ampicillin antiSMASH antibiotics and Secondary Metabolite Analysis SHell Software AS Aminosäure cDNA copy-Desoxyribonukleinsäure Cm Chloramphenicol FD Fast digest DMAPP Dimethylallylpyrophosphat DMSO Dimethylsulfoxid DNA Desoxyribonukleinsäure dNTP Desoxyribonukleosidtriphosphat ds-DNA double-stranded-DNA E. coli Escherichia coli E. serrulata Eremphila serrulata (A. DC.) Druce et al. et alii FPP Farnesylpyrophosphat GC/FID Gaschromatographie mit Flammenionisations-Detektor GC/MS Gaschromatographie mit Massenspektrometrie-Detektor gDNA Genomische DNA GPP Geranylpyrophosphat GGPP Geranylgeranylpyrophosphat Hep n-Heptan IPP Isopentylpyrophosphat 8 Abkürzungsverzeichnis IPTG Isopropyl-β-D-thiogalactopyranosid ITS Internal transcribed spacer Kan Kanamycin LB Lysogeny broth LC Flüssigchromatographie MeJa Methyljasmonat MEP Methylerythritolphosphat MEV Mevalonat mRNA messenger RNA MRSA Methicillin-resistenter Staphylococcus aureus n.b. nicht bestimmt NGS Next generation sequencing Ni-NTA Nickel-Nitrilotriessigsäure OPP Diphosphat ORF open reading frame PacBio Pacific Biosciences PDB Protein Datenbank PCR Polymerase-Kettenreaktion RACE Rapid amplification of cDNA ends RI Retentionsindex RNA Ribonukleinsäure rRNA Ribosomale RNA S. chartreusis Streptomyces chartreusis SDS-PAGE Natriumdodecylsulfat-Polyacrylamidgelelektrophorese ss-DNA single-stranded-DNA Std Stunde tBME tert-Butylmethylether TCEP Tris(2-Carboxyethyl)-Phosphin 9 Abkürzungsverzeichnis TIRF-Mikroskopie Interne Totalreflexionsfluoreszenz-Mikroskopie TPS Terpensynthase tRNA transfer-RNA TXS Taxadien-Synthase UHPLC/MS Ultra high performance liquid chromatography mit Massenspektrometrie VRE Vancomycin-resistente Enterokokken 10 Zusammenfassung 1. Zusammenfassung Mit über 50.000 Vertretern gehören die Terpenoide zu der bedeutendsten Klasse der Naturstoffe. Aufgrund ihrer diversen Bioaktivitäten und ihrer einzigartigen Gerüche finden sie bereits breite Anwendung in der Pharma- und Kosmetikindustrie. Zahlreiche Terpenoide können derzeit nur durch die klassische Naturstoffextraktion unter Verwendung großer Lösemittelmengen gewonnen werden,
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