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Metabolische Modellierung Thermophiler Prokaryoten

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Metabolische Modellierung Thermophiler Prokaryoten Metabolische Modellierung thermophiler Prokaryoten Von der Fakultät für Lebenswissenschaften der Technischen Universität Carolo-Wilhelmina zu Braunschweig zur Erlangung des Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigte D i s s e r t a t i o n von Helge Sebastian Stark aus Braunschweig 1. Referent: Prof. Dr. Dietmar Schomburg 2. Referent Prof. Dr. Dieter Jahn eingereicht am: 26.04.2017 mündliche Prüfung (Disputation) am: 27.06.2017 Druckjahr 2017 Vorveröffentlichung der Dissertation Teilergebnisse aus dieser Arbeit wurden mit Genehmigung der Fakultät für Lebenswissenschaften, vertreten durch den Mentor der Arbeit, in folgenden Beiträgen vorab veröffentlicht. Publikationen Stark, H., Wolf, J., Albersmeier, A., Pham, T. K., Hofmann, J. D., Siebers, B., Kalinowski, J., Wright, P. C., Neumann-Schaal, M. and Schomburg, D. (2017), Oxidative Stickland reactions in an obligate aerobic organism – amino acid catabolism in the Crenarchaeon Sulfolobus solfataricus. FEBS J, 284: 2078–2095. Wolf, J., Stark, H., Fafenrot, K., Albersmeier, A., Pham, T. K., Müller, K. B., Meyer, B. H., Hoffmann, L., Shen, L., Albaum, S. P., Kouril, T., Schmidt-Hohagen, K., Neumann-Schaal, M., Bräsen, C., Kalinowski, J., Wright, P. C., Albers, S.-V., Schomburg, D. and Siebers, B. (2016), A systems biology approach reveals major metabolic changes in the thermoacidophilic archaeon Sulfolobus solfataricus in response to the carbon source L-fucose versus D-glucose. Molecular Microbiology, 102: 882–908. Posterbeiträge Stark, H., Wolf, J., Müller, K., Albaum, S., Albersmeier, A., Pham, T.K., Schomburg, D. (2015), Systems biology reveals a novel L-fucose degradation pathway in the archaeon Sulfolobus solfataricus. Poster präsentiert auf dem e:Bio Innovation Competition Systems Biology Status Seminar, Berlin, Deutschland. I Gewidmet meiner Lebenspartnerin Jacqueline Hermann II Inhaltsverzeichnis Zusammenfassung................................................................................................VI Abstract................................................................................................................VIII 1 Einleitung.............................................................................................................1 1.1 Metabolische Modellierung.....................................................................1 1.2 Genomannotationen................................................................................4 1.3 Anpassungsstrategien thermophiler Prokaryoten...............................4 1.4 Thermus thermophilus............................................................................6 1.5 Sulfolobus solfataricus...........................................................................7 1.6 Ziel der Arbeit...........................................................................................8 2 Material und Methoden.......................................................................................9 2.1 Metabolische Modellierung.....................................................................9 2.1.1 Repräsentation metabolischer Netzwerke.....................................9 2.1.2 Einschränkungsbasierte Modellierung.........................................10 2.1.3 Das metano-Softwarepaket..........................................................12 2.1.4 Informationsquellen und Datenbanken........................................13 2.1.5 Erweiterung der Ausgangsmodelle..............................................14 2.1.6 Modell-Nomenklatur.....................................................................15 2.1.7 Semi-automatische Genom-Annotation.......................................16 2.2 Analyse der metabolischen Modelle....................................................17 2.2.1 Flux Balance Analysis..................................................................17 2.2.2 Flux Variability Analysis................................................................19 2.2.3 Minimisation Of Metabolic Adjustment.........................................20 2.2.4 Thermodynamisch verbotene Zyklen...........................................22 2.2.5 „Dead end“-Analyse.....................................................................23 2.2.6 Metabolitzentrische Flussanalyse................................................23 2.2.7 Metabolitfluss-Minimierung...........................................................24 2.3 Programmierung....................................................................................24 2.3.1 Bestehende Software...................................................................25 2.3.2 Standardisierte Speicherung von Modellparametern...................25 2.3.3 Erstellung einer Metabolitdatenbank............................................26 III 2.3.4 Automatisierte Erstellung von Szenarien.....................................27 2.3.5 Automatisierte Graphenerstellung................................................28 2.3.6 Elementzentrische Flussanalyse..................................................29 3 Ergebnisse und Diskussion.............................................................................30 3.1 Entwicklung einer Modellierungsplattform.........................................30 3.1.1 Klassenstruktur.............................................................................33 3.1.2 Datenbankstruktur........................................................................35 3.1.3 Verbesserung der automatisierten Genomannotation.................38 3.1.4 Bündelung von Metabolit-Informationen......................................38 3.1.5 Standardisierte Speicherung von Modellierungsparametern.......39 3.1.6 Automatisierte Batch-Simulationen..............................................40 3.1.7 Erweiterte Analysefunktionen.......................................................43 3.2 Modellierung von Thermus thermophilus...........................................50 3.2.1 Erweiterung und Validierung des Modells....................................50 3.2.2 Charakterisierung des Stoffwechsels für verschiedene Kohlenstoffquellen........................................................................57 3.2.2.1 Glucose........................................................................58 3.2.2.2 Glycerol........................................................................67 3.2.2.3 Succinat.......................................................................74 3.2.2.4 Phenylacetat................................................................81 3.2.2.5 3-Hydroxybutanoat......................................................89 3.2.3 Auswirkungen temperaturabhängiger Parameter........................96 3.3 Modellierung von Sulfolobus solfataricus........................................103 3.3.1 Erweiterung und Validierung des Modells..................................103 3.3.2 Charakterisierung des Stoffwechsels für verschiedene Kohlenstoffquellen......................................................................108 3.3.2.1 Glucose, Lactose und Mannose................................111 3.3.2.2 Acetoin.......................................................................122 3.3.2.3 Phenol........................................................................128 3.3.2.4 L- und D-Arabinose...................................................133 3.3.2.5 L-Fucose....................................................................141 3.3.2.6 Caseinhydrolysat.......................................................153 IV 4 Zusammenfassung.........................................................................................164 Danksagung.........................................................................................................167 Abkürzungen.......................................................................................................168 Abbildungsverzeichnis.......................................................................................169 Tabellenverzeichnis............................................................................................173 Anhang.................................................................................................................176 Literaturverzeichnis............................................................................................192 V Zusammenfassung In der Systembiologie werden durch die mathematische Modellierung unterschiedlichster molekularer Prozesse neue Erkenntnisse über biologische Netzwerke gewonnen. So kann durch die Rekonstruktion genomweiter metabolischer Modelle der Stoffwechsel von Organismen bioinformatisch analysiert werden. Metabolische Modelle werden heutzutage unter Anderem zur Identifizierung von Angriffspunkten für Pharmazeutika in pathogenen Zellen und zur Optimierung biotechnologischer Prozesse eingesetzt. Darüber hinaus können metabolische Modelle als Wissenssammlung über die biochemischen Prozesse innerhalb eines Organismus angesehen werden und die experimentelle Versuchsplanung gezielt unterstützen. Hochinteressant für biotechnologische Fragestellungen ist dabei besonders der Stoffwechsel thermophiler Prokaryoten, für die allerdings nur eine sehr geringe Anzahl genomweiter metabolischer Modelle existiert. In dieser Arbeit wurden zwei Ziele verfolgt. Zum Einen sollten etablierte Softwarepakete für die metabolische Modellierung zu einer Modellierungsplattform zusammengefügt werden. Zum Anderen sollten verfügbare metabolische Modelle thermophiler Prokaryoten erweitert und der Kohlenhydratstoffwechsel dieser Organismen erstmals für viele verschiedene
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