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What Happens in Yeast During the Crabtree Effect? an Investigation of Work Are Discussed 8 APPLIED MICROBIOLOGY Volume 8 In this thesis a metabolic model of S. cerevisiae was enhanced with the biochemistry of volatile metabolites that have been found by a literature investigation. Not only the volatile metabolites in question have been added, but also substances and reactions that Christoph Halbfeld connect them to metabolites already present in the model. In total, 225 metabolites and 219 reactions were added to the model. Furthermore, 12 metabolic reactions could be verified by physiological and enzyme assays of knockout mutants. What happens in yeast during Additionally, volatile metabolite dynamics during the induction of the Crabtree effect in a fully respiratory growing continuous culture of S. cerevisiae were explored with real- the Crabtree effect? time analyses of the fermentation off-gas. Secondary electrospray ionization-Orbitrap- mass spectrometry was used for this endeavor. In these measurements, I detected about An investigation of S. cerevisiae’s 2,500 signals of which 16 showed a response to the perturbation of the metabolic state prior to the detection of ethanol. volatile space Furthermore, the possibility of online volatile metabolite monitoring due to multi capil- lary column–ion mobility spectrometry (MCC-IMS) analysis of yeast fermentation off-gas was established. The MCC-IMS used was developed for the detection of volatiles in human breath, and several technical adaptations were applied to allow robust detection of volatiles in the headspace of yeast fermentations. volatile space The MCC-IMS in its optimized configuration was applied to monitor volatile metabolite changes of a laboratory and an industrial yeast strain during the Crabtree effect. In ad- dition, metabolic differences in this setting were examined on transcriptional level using a cDNA microarray. The metabolic shift could be observed in the volatile space of both S. cerevisiae’s strains and in all tested conditions. The transcriptome showed differences in the leucine and isoleucine pathways, as well as in genes related to the TCA cycle and the respiratory pathways. Interestingly, the expression data indicated that the industrial strain upregula- ted its respiration during the shift, while it was downregulated in the laboratory strain. Lastly, possible applications for the knowledge gained and methods developed in this What happens in yeast during the Crabtree effect? An investigation of work are discussed. This thesis provides a blueprint for studies of the volatile space in other organisms. For example, the knowledge gained about the changes in the vola- tilome during metabolic transitions could be used to online determine and potentially control the metabolic state of a yeast. Christoph Halbfeld “What happens in yeast during the Crabtree effect? An investigation of S. cerevisiae's volatile space” Von der Fakultät für Mathematik, Informatik und Naturwissenschaften der RWTH Aachen University zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften genehmigte Dissertation vorgelegt von M. Sc. Biologie Christoph Halbfeld aus Moers, Nordrhein-Westfalen, Deutschland Berichter: Universitätsprofessor Dr.-Ing. Lars M. Blank Universitätsprofessor Dr. rer. nat. Jörg Ingo Baumbach Tag der mündlichen Prüfung: 12.04.2018 Diese Dissertation ist auf den Internetseiten der Universitätsbibliothek online verfügbar. Bibliografische Information der Deutschen Nationalbibliothek Die Deutsche Nationalbibliothek verzeichnet diese Publikation in der Deutschen Nationalbibliografie; detaillierte bibliografische Daten sind im Internet über https://portal.dnb.de abrufbar. Christoph Halbfeld: What happens in yeast during the Crabtree effect? An investigation of S. cerevisiae’s volatile space 1. Auflage, 2018 Gedruckt auf holz- und säurefreiem Papier, 100% chlorfrei gebleicht. Apprimus Verlag, Aachen, 2018 Wissenschaftsverlag des Instituts für Industriekommunikation und Fachmedien an der RWTH Aachen Steinbachstr. 25, 52074 Aachen Internet: www.apprimus-verlag.de, E-Mail: [email protected] Printed in Germany ISBN 978-3-86359-635-4 D 82 (Diss. RWTH Aachen University, 2018) Danksagung Zuerst möchte ich mich bei Prof. Lars M. Blank für die Erstkorrektur meiner Arbeit und all die Unterstützung, die ich von ihm erhalten habe bedanken. Außerdem möchte ich mich für die Möglichkeit meine Arbeit am iAMB durchführen zu dürfen bedanken. Mein Dank gilt ebenfalls Prof. Jörg-Ingo Baumbach für die Zweitkorrektur meiner Arbeit. Außerdem möchte ich mich dafür bedanken, dass ich in der B&S Analytik die Möglichkeit hatte erste Erfahrungen mit dem IMS zu sammeln und jederzeit für weitere Messungen willkommen war. Außerdem möchte ich mich für die vielen aufschlussreichen Gespräche über das IMS bedanken. Ich möchte mich ebenfalls bei Prof. Alan Slusarenko für die Übernahme der Drittprüferschafft bedanken. Ich danke ebenfalls meiner Betreuerin Dr. Birgitta E. Ebert an die ich mich jederzeit wenden konnte. Durch ihre Unterstützung war ich in der Lage die Art, wie ich Experimente plane und Texte schreibe wesentlich zu verbessern. Vielen Dank ebenfalls an alle Projektpartner für die gute Zusammenarbeit. Jessica Kuhlmann danke ich für die gute Zusammenarbeit bei der Verbesserung des IMS und der IMS-Analytik. Ann-Kathrin Sippel möchte ich für die Zusammenarbeit bei der IMS-Analytik und der Vermessung von GC- Proben danken. Prof. Sven Rahmann und Elias Kuthe möchte ich für die Hilfe bei der Auswertung der cDNA-Microarrays danken. Sven Wegerhoff und Prof. Sebastian Engell möchte ich für die interessanten Diskussionen während den Projekttreffen danken. Dr. Michael Quantz und Dr. Erik Pollmann möchte ich für die immerwährende Hilfe in der Erkundung der unendlich großen Hefeliteratur, für die Hilfe bei Fermentationsproblemen sowie für die gute Zusammenarbeit und die Unterbringung bei der VH-Berlin danken. Mein Dank gilt ebenfalls Prof. Pablo Martinez-Lozano Sinues für die Möglichkeit Experimente an der SESI-Orbitrap-MS in Zürich durchzuführen. Ebenfalls danke ich der Zenobi-Gruppe für die freundliche Arbeitsatmosphäre. Außerdem danke ich allen Studenten, die im Verlauf meiner Arbeit mit mir zusammengearbeitet haben: Christina Redmers, Daniela Dey, Christiane Sonntag, Sandrine Nankia Tatepo, Kai Büchner, Mathis Wolter, Niklas Kitschen und Birthe Halmschlag. Durch sie wurde meine Arbeit bereichert, da mehr Arbeitspakete bearbeitet werden konnten, als ich alleine hätte schaffen können. Ebenfalls danke ich allen, die während meiner Zeit am iAMB gearbeitet haben, durch alle wurde eine einzigartige Arbeitsatmosphäre geschaffen, die die oftmals langen Tage teils sehr unterhaltsam gemacht haben. Besonders möchte ich hierbei Dr. Thiemo Zambanini, Benedikt Wienands, Hamed Tehrani, Mathias Lehnen, Vanessa Bayer und Birthe Halmschlag danken, durch sie wurde die Zeit unvergesslich. Ebenfalls möchte ich mich bei Eik Czarnotta für die Starthilfe bei Hefefermentationen bedanken. Ein besonderer Dank gilt Dr. Martin Zimmermann, der mich schon während meines Studiums, aber auch in der Phase der Promotion immer wieder mit motivierenden Gesprächen auf dem Weg begleitet hat. Ich möchte mich auch bei den Mitarbeitern der Mechanischen und Elektrotechnik Werkstatt bedanken. Mit Hilfe des Teams war ich dazu in der Lage Ideen zu realisieren, die ich alleine nicht hätte umsetzen können. Ich möchte ebenfalls meiner Freundin Dr. Sandra Jumpertz danken, sie hat mich auch in schwierigen Phasen der Promotion immer aufgebaut und mir die Stärke gegeben die Promotion erfolgreich abzuschließen. Zuletzt möchte ich meiner Familie danken, die es mir ermöglicht hat diesen Weg zu beschreiten und mir immer Rückhalt gegeben haben. Funding The project was funded by the German Federal Ministry of Education and Research (BMBF). Eidesstattliche Erklärung „Hiermit erkläre ich, Christoph Halbfeld, an Eides statt, dass ich die vorliegende Dissertation selbstständig verfasst und keine anderen als die angegebenen Quellen und Hilfsmittel benutzt habe.“ Table of Contents SUMMARY ....................................................................................................................................... V ZUSAMMENFASSUNG ............................................................................................................... VII LIST OF ABBREVIATIONS ........................................................................................................ IX LIST OF FIGURES ..................................................................................................................... XIII LIST OF TABLES ......................................................................................................................... XV GENERAL INTRODUCTION ............................................................................................... 5 SUMMARY .......................................................................................................................... 5 INTRODUCTION ................................................................................................................... 5 VOLATILE ORGANIC COMPOUNDS ....................................................................................... 5 BREAD ............................................................................................................................... 6 WINE ................................................................................................................................. 6 Wine flavors............................................................................................................
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