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Investigation of the Biosynthesis of Bacterial Natural Products

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Investigation of the Biosynthesis of Bacterial Natural Products Investigation of the biosynthesis of bacterial natural products Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften vorgelegt beim Fachbereich für Biowissenschaften (15) der Johann Wolfgang Goethe-Universität in Frankfurt am Main von Sebastian Winfried Fuchs aus Hanau (2013) (D 30) vom Fachbereich für Biowissenschaften (15) der Johann Wolfgang Goethe-Universität als Dissertation angenommen. Dekanin: Professorin Anna Starzinski-Powitz Gutachter: Professor Dr. Helge B. Bode, Professor Dr. Eckhard Boles, Professor Dr. Christian Hertweck Datum der Disputation: 16.12.2013 ii Danksagung Danksagung Meinen Eltern und Großeltern möchte ich meinen herzlichen Dank für ihre Unterstützung ausdrücken. Herrn Professor Dr. Helge B. Bode und der gesamten Arbeitsgruppe danke ich für die überaus freundliche und motivierende Arbeitsatmosphäre, und die Unterstützung, die mir im Laufe der Zeit von Euch zugekommen ist. Herrn Professor Dr. Helge B. Bode möchte ich besonders für die Möglichkeit zur Bearbeitung der hierin beschriebenen Projekte danken. Herrn Professor Dr. Eckhard Boles danke ich für die Übernahme des Zweitgutachtens zu dieser Arbeit. Herrn Professor Dr. Michael Karas möchte ich für die Möglichkeit zur Nutzung der MALDI- Massenspektrometer danken. Herrn Dr. Thorsten Jaskolla möchte ich für seine freundliche Unterstützung danken, die mir das Feld der Massenspektrometrie näher gebracht hat. Weiterhin möchte ich meinen Freunden für unsere gemeinsamen Erlebnisse danken. iii Table of contents Table of contents Danksagung ............................................................................................................................... iii Table of contents ....................................................................................................................... iv Table of abbreviations .............................................................................................................. vii 1. Summary ................................................................................................................................ 1 1.1. Zusammenfassung ............................................................................................................. 3 2. Introduction ............................................................................................................................ 8 2.1. Natural products and research ........................................................................................... 9 The natural activity of antibiotics ............................................................................... 10 Traditional natural product sources ........................................................................... 11 Historical aspects of pharmaceutical natural product research ................................ 12 2.2. Alternative organisms as source of novel bioactive natural products ............................. 13 2.3. Additional strategies to novel bioactive natural products ............................................... 18 2.3.1. Contemporary strategies ................................................................................... 19 2.3.2. Mass spectrometric strategies and applications ................................................ 22 2.3.3. Mass spectrometric principles of peptide fragmentation .................................. 26 2.3.4. Additional strategies for the production of bioactive natural products ............ 27 2.4. Biosynthesis of natural products ..................................................................................... 28 2.4.1. Peptide biosynthesis .......................................................................................... 28 Adenylation domains ................................................................................................... 30 Peptidyl carrier protein domains ................................................................................ 31 Condensation domains ................................................................................................ 32 Epimerization domains ............................................................................................... 33 Thioesterase domains and other chain release mechanisms ...................................... 33 Additional domains ..................................................................................................... 35 Collinearity and exceptions ........................................................................................ 35 Three dimensional studies of NRPS ............................................................................ 36 2.4.2. Polyketide and fatty acid biosynthesis .............................................................. 36 Architectural organization of PKS and FAS ............................................................... 38 Acyltransferases .......................................................................................................... 39 β-ketoacyl-ACP-synthases .......................................................................................... 40 Acyl carrier proteins ................................................................................................... 43 iv Table of contents Thioesterases .............................................................................................................. 44 Tailoring enzymes ....................................................................................................... 44 Type I PKS/FAS .......................................................................................................... 45 Type II PKS ................................................................................................................. 46 Type III PKS ................................................................................................................ 47 Collinearity and exceptions/Beyond the type I, II, III stereotypes .............................. 51 Mixed NRPS-PKS ....................................................................................................... 52 2.5. Aims of this work ............................................................................................................ 52 3. Publications .......................................................................................................................... 55 3.1. Structure elucidation and biosynthesis of lysine-rich cyclic peptides in Xenorhabdus nematophila .................................................................................................................... 55 3.2. Neutral loss fragmentation pattern based screening for arginine-rich natural products in Xenorhabdus and Photorhabdus .................................................................................... 56 3.3. Formation of 1,3-cyclohexanediones and resorcinols catalyzed by a widely occurring ketosynthase ................................................................................................................... 57 4. Additional results ................................................................................................................. 58 4.1. Natural products of Paenibacillus larvae as potential American foulbrood virulence factors ............................................................................................................................. 58 Entomotoxicity of Paenibacillus larvae natural products ........................................... 61 4.2. The xenoGUFamines from Xenorhabdus budapestensis DSM 16342 ........................... 68 5. Discussion ............................................................................................................................ 74 5.1. Structure elucidation and biosynthesis of lysine-rich cyclic peptides in Xenorhabdus nematophila .................................................................................................................... 74 5.2. Entomotoxicity of Paenibacillus larvae extracts against Apis mellifera ........................ 77 5.3. Neutral loss fragmentation pattern based screening for arginine-rich natural products in Xenorhabdus and Photorhabdus .................................................................................... 78 5.4. The xenoGUFamine biosynthesis gene cluster ............................................................... 80 Bioactivity of the xenoGUFamines ............................................................................. 86 5.5. Formation of cyclohexane-1,3-diones and resorcinols catalyzed by a widely occurring ketosynthase ................................................................................................................... 89 Flexirubin biosynthesis machinery: comparison with other PKSs/FASs ................... 95 The wide distribution and possible functions of darAB gene clusters ........................ 95 6. References .......................................................................................................................... 100 7. Attachments ........................................................................................................................ 122 7.1. Structure elucidation and biosynthesis of lysine-rich cyclic peptides in Xenorhabdus nematophila .................................................................................................................. 122 v Table of contents 7.1.2. Supplementary information ............................................................................ 132 7.2. Neutral loss fragmentation
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