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Bacterial Degradation Pathways for Xenobiotic and Natural Organosulfonates

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Bacterial Degradation Pathways for Xenobiotic and Natural Organosulfonates Bacterial degradation pathways for xenobiotic and natural organosulfonates Dissertation zur Erlangung des akademischen Grades des Doktors der Naturwissenschaften (Dr. rer. nat.) an der Universität Konstanz Mathematisch-Naturwissenschaftliche Sektion Fachbereich Biologie vorgelegt von Michael Weiß Tag der mündlichen Prüfung: 17. Dezember 2014 1. Referent: Prof. Dr. Bernhard Schink 2. Referent: Prof. Dr. Dieter Spiteller 3. Referent: Prof. Dr. Jörg Hartig Konstanzer Online-Publikations-System (KOPS) URL: http://nbn-resolving.de/urn:nbn:de:bsz:352-0-267999 DANKSAGUNG Mein herzlichster Dank geht an Dr. David Schleheck für die Möglichkeit meine Doktorarbeit zu diesem Thema anzufertigen, für seine herausragende Betreuung, für sein Vertrauen und die akademische Freiheit, die ich genießen durfte. Vielen Dank auch für die Gastfreundschaft bei zahlreichen Grillabenden. Vielen Dank an Herrn Prof. Dr. Bernhard Schink für die Übernahme des Referats, seine Betreuung im Rahmen des Graduiertenprogamms und der als kompetenter Ansprechpartner immer ein offenes Ohr für meine Fragen hatte. Vielen Dank an Herrn Prof. Dr. Jörg Hartig, dass er sich für mein Betreuungs- und Prüfungskomitee zur Verfügung gestellt hat. Vielen Dank an Herrn Prof. Dr. Dieter Spiteller für die spontane Übernahme des Referats, für die Möglichkeit, seine äußerst hilfreichen Geräte (GC-MS, LC-MS, NanoPhotometer) mitbenutzen zu können sowie für seine stete Diskussionsbereitschaft. Vielen herzlichen Dank an Ann-Katrin Felux. Es ist schön, mit einer zuverlässigen und hilfsbereiten Kollegin zusammenzuarbeiten, mit der man auch viel Spaß haben kann. Vielen Dank an die AG Spiteller (Daniela, Dieter, Karin, Kathrin und Ralf) für das freundschaftliche Verhältnis in unserem Flügel; insbesondere an Karin Denger für ihre tatkräftige Unterstützung vor allem während meiner Startphase an der Universität Konstanz sowie für Racletteabende und dafür, dass sie nicht vergisst, dass ihre Kollegen rechtzeitig in die Mensa kommen, an Ralf Schlesiger für seine kritische Durchsicht dieser Arbeit, für seine großartige Hilfe bei dem Bedienen sämtlicher Geräte und für glutenfreie Crêpes und Kuchen, an Kathrin Schmidt, besonders für ihre Gastfreundschaft bei manch torreichen WM-Spielen. Vielen Dank an Herrn Prof. Dr. Alasdair M. Cook, dessen Geist als Graue Eminenz die Grundlage manch erfolgreicher Arbeiten darstellte. Vielen Dank an die eifrigen Teilnehmer des Fehlerfindespiels (Ralf, Ann-Katrin, Anna und Karin). Vielen Dank an Sabine Lehmann für das ausgesprochen gute und freundschaftliche Verhältnis, selbst als wir um die letzten Sauerstoffanteile in der Denkzelle konkurrierten. Vielen Dank an meine Vertiefungskurs- und Hiwi-Studentinnen Lena Wurmthaler, Anna Rist und Silvie Berthelot für ihre tatkräftige Mitarbeit. Vielen Dank an Dr. Thomas Huhn, der mit seinen chemischen Synthesen (3-C4-SPC, 4-C6-SPC, SQ) erst die Möglichkeit eröffnete, bestimmte Fragestellungen zu bearbeiten. Meinen herzlichen Dank der Graduiertenschule KoRS-CB für die Möglichkeit, im Rahmen eines Doktorandenstipendiums, diese Arbeit anzufertigen, für finanzielle Unterstützungen für Sach- und Reisemittel sowie für die Möglichkeit auf den Retreats und insbesondere beim Besuch der Harvard University interessante Bekanntschaften und Erfahrungen zu machen. Vielen Dank Frau Dr. Heike Brandstädter, Frau Renée Rummel und Frau Katharina Magerkurth für ihre Hilfe und Unterstützung. Vielen Dank an Herrn Dr. Roland Kissmehl, für seine vielen kompetenten Antworten. Vielen Dank dem Zukunftskolleg der Universität Konstanz, insbesondere für die finanzielle Unterstützung in der Endphase meiner Arbeit. Vielen Dank an die Arbeitsgruppe van Kleunen für die freundschaftliche Nachbarschaft, der Mitbenutzung ihrer Räumlichkeiten und dass ich ihre botanische Exkursion begleiten durfte. Vielen herzlichen Dank den Arbeitsgruppen von M9 (AG Adamska, AG Kroth, AG Schink) für ihre freundliche Inklusion in ihre Aktivitäten, insbesondere in ihre Weihnachtsfeier sowie für das freundliche Teilen von Geräten (Ultrazentrifuge, Elektroporator, French Press), von Chemikalien und für Plasmid pGWB408 (Dr. Dietmar Funck). Der AG Schink sei auch besonders herzlich für die Aufnahme in ihr Seminarprogramm (inkl. lehrreicher Nachsitzungen) und zu ihren Betriebsausflügen gedankt. Vielen Dank an Tobias Erb (Zürich) und an Ivan Berg (Freiburg), bei denen ich immer Antworten auf meine Fragen finden konnte und dass sie sich die Zeit genommen haben, Vorträge zu verschiedenen Anlässen zu halten. Tobi, vielen Dank auch für die ASKA-Klone und die zahlreichen Publikationen, zu denen ich keinen Zugang hatte. Vielen Dank an Maike Voges für ihre Begleitung nach Boston. Trotz unserer Interessen, die nicht unterschiedlicher sein könnten, waren es drei äußerst harmonische und erfahrungsreiche Wochen. Vielen Dank an Caro Bogs, die mir durch ihren Eindruck, dass ich doch schon immer hier sei, zum schnellen Einleben und Wohlfühlen verhalf. Vielen Dank an alle meine Konstanzer Mitbewohner, an Lisa, Bernd, Anke, Björn, Verena, Gerald, Judith und Hakan. Es war mir immer eine große Freude mit euch zusammenzuwohnen. Vielen Dank an meine ganze Familie, insbesondere an meine Eltern Gertrud und Karl, an meine Geschwister Monika, Christian und Fabian und an meine Tante Rosemarie, die mich immer unterstützt haben. Vielen Dank Anna, schön, dass es dich gibt! CHAPTERS OF THIS THESIS ARE PUBLISHED IN: Denger, K., M. Weiss, A. K. Felux, A. Schneider, C. Mayer, D. Spiteller, T. Huhn, A. M. Cook and D. Schleheck (2014). Sulfoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulfur cycle. Nature 507(7490): 114-117. Weiss, M., A. I. Kesberg, K. M. LaButti, S. Pitluck, D. Bruce, L. Hauser, A. Copeland, T. Woyke, S. Lowry, S. Lucas, M. Land, L. Goodwin, S. Kjelleberg, A. M. Cook, M. Buhmann, T. Thomas and D. Schleheck (2013). Permanent draft genome sequence of Comamonas testosteroni KF-1. Stand. Genomic Sci. 8(2): 239-254. Weiss, M., K. Denger, T. Huhn and D. Schleheck (2012). Two enzymes of a complete degradation pathway for linear alkylbenzenesulfonate (LAS) surfactants: 4-sulfoacetophenone Baeyer-Villiger monooxygenase and 4-sulfophenylacetate esterase in Comamonas testosteroni KF-1. Appl. Environ. Microbiol. 78: 8254-8263. Schleheck, D., M. Weiss, S. Pitluck, D. Bruce, M. L. Land, S. Han, E. Saunders, R. Tapia, C. Detter, T. Brettin, J. Han, T. Woyke, L. Goodwin, L. Pennacchio, M. Nolan, A. M. Cook, S. Kjelleberg and T. Thomas (2011). Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1T). Stand. Genomic Sci. 5(3): 298-310. FURTHER PUBLICATIONS NOT INCLUDED IN THIS THESIS: Felux, A.-K., K. Denger, M. Weiss, A. M. Cook and D. Schleheck (2013). Paracoccus denitrificans PD1222 utilizes hypotaurine via transamination followed by spontaneous desulfination to yield acetaldehyde, and finally acetate for growth. J. Bacteriol. 195: 2921- 2930. TABLE OF CONTENTS I TABLE OF CONTENTS SUMMARY ............................................................................................................................... 1 ZUSAMMENFASSUNG ........................................................................................................... 3 CHAPTER 1 ............................................................................................................................... 5 General introduction CHAPTER 2 ............................................................................................................................. 11 Complete genome sequence of Parvibaculum lavamentivorans type strain DS-1T CHAPTER 3 ............................................................................................................................. 25 Permanent draft genome sequence of Comamonas testosteroni KF-1 CHAPTER 4 ............................................................................................................................. 41 Complete genome sequence of Delftia acidovorans SPH-1 CHAPTER 5 ............................................................................................................................. 55 Two enzymes of a complete degradation pathway for linear alkylbenzenesulfonate (LAS) surfactants: 4-sulfoacetophenone Baeyer-Villiger monooxygenase and 4-sulfophenylacetate esterase in Comamonas testosteroni KF-1 CHAPTER 6 ............................................................................................................................. 83 Characterization of a steroid Baeyer-Villiger monooxygenase and esterase in Comamonas testosteroni KF-1 CHAPTER 7 ........................................................................................................................... 119 A proteomic approach to unravel enzymes of the sulfophenylcarboxylate degradation pathway in Comamonas testosteroni KF-1 and identification of a hydroxyquinol ring cleavage dioxygenase CHAPTER 8 ........................................................................................................................... 149 Sulfoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulfur cycle CHAPTER 9 ........................................................................................................................... 171 General discussion II TABLE OF CONTENTS CHAPTER 10 ......................................................................................................................... 177 Appendix Abbreviations ........................................................................................................................
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