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Activation of Acetone by Sulfate-Reducing Bacteria – Pathway Elucidation and Enzyme Identification in Desulfococcus Biacutus

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Activation of Acetone by Sulfate-Reducing Bacteria – Pathway Elucidation and Enzyme Identification in Desulfococcus Biacutus Activation of acetone by sulfate-reducing bacteria – Pathway elucidation and enzyme identification in Desulfococcus biacutus Dissertation submitted for the degree of Doctor of Natural Sciences (Dr. rer. nat.) presented by Jasmin Renate Elisabeth Frey at the Faculty of Science Department of Biology Date of the oral examination: 27.04.2017 1. Reviewer: Prof. Dr. Bernhard Schink 2. Reviewer: Prof. Dr. Jörg Hartig Konstanzer Online-Publikations-System (KOPS) URL: http://nbn-resolving.de/urn:nbn:de:bsz:352-0-415229 „Die Definition von Wahnsinn ist, immer wieder das Gleiche zu tun und andere Ergebnisse zu erwarten.“ Albert Einstein Danksagung Die vorliegende Arbeit wurde im Zeitraum von August 2012 bis Februar 2017 am Lehrstuhl für Mikrobielle Ökologie, Limnologie und Allgemeine Mikrobiologie von Prof. Dr. Bernhard Schink angefertigt. Mein besonderer Dank gilt Prof. Dr. Bernhard Schink für die Möglichkeit, meine Doktorarbeit unter seiner Anleitung anfertigen zu können, für die Überlassung eines sehr interessanten und anspruchsvollen Themas sowie für seine stetige Unterstützung. Vielen Dank auch an Prof. Dr. Jörg Hartig für die Übernahme des Koreferats und für hilfreiche Diskussionen und Anregungen während der Fortschrittsberichtstreffen. Großer Dank gilt meinem Ko-Betreuer PD Dr. David Schleheck, der mir immer mit Rat und Tat zur Seite stand, und für seine aufbauenden Worte, wenn Experimente nicht funktionierten. Großer Dank gilt auch Dr. Thomas Huhn und Fabian Schneider für ihre unermüdlichen Synthesearbeiten zur Herstellung aller benötigten Substrate. Sehr dankbar bin ich Prof. Dr. Dieter Spiteller, der mir mit den MS-Messungen und mit interessanten Diskussionen sehr geholfen hat. Außerdem bin ich auch Prof. Dr. Bernard Golding, Prof. Dr. Wolfgang Buckel, Dr. Nicolai Müller, Dr. Alexander Schmidt und Dr. Diliana Simeonova für nützliche und anregende Diskussionen dankbar. Vielen Dank an Dr. Dominik Montag, der mir beibrachte, die HPLC zu bedienen und vor allem auch zu reparieren. Antje Wiese danke ich für ihre Hilfsbereitschaft und für das Herstellen von Medien. Vielen Dank auch an meine VTK- und Bachelor-Studenten und alle anderen Mitglieder der AG Schink. Ihr habt immer für eine tolle und herzliche Atmosphäre gesorgt. Ich möchte außerdem Sophie Ehle, Ivana Fejkova, Simone Pechmann, Kristina Ruhland, Hendrik Rusche und Marion Zetzmann danken, die immer ein offenes Ohr hatten. Ein spezieller Dank geht an Astor und Junior (“Spark of Memory”), Manfred und Renate Weh, Sonja Pfeffer und Roswitha Fochler. Ihr habt mich unterstützt und für Zerstreuung gesorgt. Sehr dankbar bin ich außerdem meiner Mutter, meinem Großvater, Esther, Felicitas, dem Rest meiner Familie und Uwe Helms dafür, dass Ihr einfach da wart, für eure Unterstützung und dass ihr immer an mich geglaubt habt. 5 Table of Contents Abbreviations ................................................................................................................... 7 Summary ....................................................................................................................... 10 Zusammenfassung ........................................................................................................ 12 CHAPTER 1 General Introduction ................................................................................. 14 1.1 Acetone ................................................................................................................ 14 1.2 Biodegradation of acetone ................................................................................... 15 1.2.1 Acetone degradation under oxic conditions ................................................... 15 1.2.2 Acetone degradation under anoxic conditions ............................................... 17 1.3 Desulfococcus biacutus ........................................................................................ 19 1.4 Sulfate-reducing bacteria ..................................................................................... 20 1.5 Complete oxidation of substrates ......................................................................... 22 1.6 Aims of this thesis ................................................................................................ 24 CHAPTER 2 .................................................................................................................. 25 Abstract ...................................................................................................................... 26 Background ................................................................................................................ 27 Methods ..................................................................................................................... 28 Results ....................................................................................................................... 32 Discussion .................................................................................................................. 39 References ................................................................................................................. 46 CHAPTER 3 .................................................................................................................. 50 ABSTRACT ................................................................................................................ 51 INTRODUCTION ........................................................................................................ 52 RESULTS ................................................................................................................... 55 DISCUSSION ............................................................................................................. 62 MATERIAL AND METHODS ...................................................................................... 65 References ................................................................................................................. 91 CHAPTER 4 .................................................................................................................. 94 Abstract ...................................................................................................................... 95 1. Introduction............................................................................................................. 95 2. Methods/Experimental section ............................................................................... 96 3. Results and discussion ......................................................................................... 103 4. Conclusions .......................................................................................................... 109 6 References ............................................................................................................... 117 CHAPTER 5 General Discussion ................................................................................ 119 Outlook ........................................................................................................................ 125 Scientific contributions list ............................................................................................ 126 Record of Achievement ............................................................................................... 128 References .................................................................................................................. 129 Abbreviations 7 Abbreviations 2D-PAGE two dimensional polyacrylamide gel electrophoresis α alpha A ampere aa amino acids AdoCbl adenosylcobalamine, vitamine B12 ADP adenosine diphosphate Amp ampicillin AMP adenosine monophosphate ATP adenosine triphosphate ß beta B12 vitamine B12, adenosylcobalamine bp base pairs BSA bovine serum albumin °C degree centigrade C carbon cm centimeter Cm chloramphenicol CO carbon monoxide CO2 carbon dioxide CoA coenzyme A DNA desoxyribonucleic acid DNPH dinitrophenylhydrazine E. coli Escherichia coli ESI electrospray ionization et al. and others (et alii) γ gamma h hour Abbreviations 8 H hydrogen H2O chemical formula of water IPTG isopropyl β-D-1-thiogalactopyranoside l litre LB lysogenic broth µ micro (10-6) m meter, milli (10-3) M molar, mol per litre; mega (106) max. maximal, maximum MDR medium-chain dehydrogenase/reductase superfamily alcohol dehydrogenase min minute mol 6.022 x 1023 particles MS mass spectrometry n nano (10-9) N nitrogen NAD+(H) nicotinamide adenine dinucleotide (reduced form) NADP+(H) nicotinamide adenine dinucleotide phosphate (reduced form) NCBI National Center for Biotechnology Information Ni nickel NTA nitrilotriacetic acid NMR Nuclear magnetic resonance (spectroscopy) O oxygen OD optical density P phosphorus; phosphate PAGE polyacrylamide gel electrophoresis PCR polymerase chain reaction pH potential of hydrogen PMF peptide mass fingerprinting Abbreviations 9 rt room temperature S sulfur TDP thiamine diphosphate (formerly TPP; thiamine pyrophosphate) THF tetrahydrofolate U unit UK United Kingdom USA United States of America UV ultra violet V volt vol volume v/v volume per volume w/v weight per volume x g gravity of Earth Summary 10 Summary Acetone degradation is a well understood process in aerobic and nitrate-reducing bacteria, whereas only little is known about the degradation of acetone by sulfate-reducing bacteria. Aerobes and nitrate reducers activate acetone via carboxylation to acetoacetate, spending at least two ATP. Such an energy-expensive activation reaction is hardly
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