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Microbial Olefin Production – Towardsa Biorefinery Approach

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Microbial Olefin Production – Towardsa Biorefinery Approach TECHNISCHE UNIVERSITÄT MÜNCHEN Lehrstuhl für Chemie Biogener Rohstoffe MICROBIAL OLEFIN PRODUCTION – TOWARDS A BIOREFINERY APPROACH Michael Emil Loscar Vollständiger Abdruck von der promotionsführenden Einrichtung Campus Straubing für Biotechnologie und Nachhaltigkeit der Technischen Universitat München zur Erlangung des akademischen Grades eines Doktors der Naturwissenschaften (Dr. rer. nat.) genehmigten Dissertation. Vorsitzender: Prof. Dr. Magnus Fröhling Prüfer der Dissertation: 1. Prof. Dr. Volker Sieber 2. Prof. Dr. Bastian Blombach Die Dissertation wurde am 16.10.2019 bei der Technischen Universität München eingereicht und durch die promotionsführende Einrichtung Campus Straubing für Biotechnologie und Nachhaltigkeit am 10.02.2020 angenommen. dummy TO ALL LOVED ONES, ESPECIALLY TO MY TWINS JANNIS AND KILIAN „YESTERDAY´S the past, The Family Circus TOMORROW`S the future, TODAY is a . GIFT ! That`s why it´s called: The PRESENT“ by Bil Keane Zusammenfassung In Zeiten des Klimawandels wird fieberhaft nach Alternativen zu fossilen Rohstoffen gesucht. Hierbei liegt ein Fokus auf nachwachsenden Rohstoffen. Die Hof- Bioraffinerie soll die gasförmigen Chemikalien Ethylen, Propylen und Isopren aus Silage bereitstellen. Hierzu sollen diese Chemikalien mittels Fermentation hergestellt werden. Die mikrobielle Bildung von Ethylen wurde bisher von drei Substraten beschrieben: (1) α-Ketoglutarat aus dem Zitratzyklus, (2) 1-Aminocyclopropan-1-Carbonsäure (ACC) aus dem Yang-Zyklus und (3) aus 2-keto-4-Methylthio Buttersäure (KMBA). Allen Stoffwechselwegen gemein ist eine suboptimale Stöchiometrie von Glukose ausgehend. Um wirtschaftliche Mengen bereitzustellen bedarf es der Erforschung neuer Stoffwechselwege zum Ethylen. Ziel der vorliegenden Arbeit ist die Suche nach stöchiometrisch optimaleren Wegen und enzymatischen Reaktionen. Hierzu wurde die lehrstuhlinterne Stammsammlung mittels headspace Gaschromatographie nach ethylenogenen und propylenogenen Mikroorganismen durchmustert. Im Anschluss wurde ein Teil der entdeckten Stämme weiter charakterisiert. Die Biosynthese des Isoprens ist verhältnismäßig gut verstanden, sodass diese Arbeit die Optimierung der Isoprenproduktion in Cupriavidus necator und die Etablierung der Isoprenproduktion in Pichia pastoris zum Ziel hatte. Als Substrate für die Ethylenproduktion kamen 3-Phosphonooxy-Propansäure und β-Alanin zum Einsatz. Für Propylen 3-Phosphonooxy-Butansäure und 3-Sulfonooxy- Butansäure. Diese lassen sich aus nachwachsenden Rohstoffen herstellen und könnten von Decarboxylasen in Alkene umgewandlet werden. Die Stämme wurden drei Tage inkubiert, anschließend geerntet, gewaschen und zehnfach in Phosphatpuffer konzentriert. Nach dem Aufschluss der Zellen durch Hitze/Einfrier-Zyklen wurde das Zelllysat zusammen mit den Substraten in einem verschlossenen Gaschromatographie- Vial vier Stunden bei 30 ◦C inkubiert. Anschließend wurde die Ethylen- bzw. Propylenbildung analysiert. Die Ethylenogenen wurden weiter charakterisiert. Hierzu wurden Substrate (ACC, L-Methionin, α-Ketoglutarat, KMBA, S-Adenosylmethionin) der bekannten Stoffwechselwege in verschiedenen Kombinationen eingesetzt. Weiterhin wurde von drei Mikroorganismen das Genom sequenziert und eine Proteinaufreinigung durchgeführt. Für die Optimierung der Isoprenproduktion in Cupriavidus necator wurde zuerst ein Expressionsvektor mit (e)GFP als Reportergen identifiziert. Anschließend wurde die Isoprensynthase von Pueraria montana sowie das Mev-Operon, welche alle Gene für den MEP-Stoffelwechelweg enthält, in den Vektor pJeM1TcR und pMS137 kloniert. Für die Etablierung der Isoprenproduktion in Pichia pastoris X-33 wurde die Isoprensynthase aus Pueraria montana in das Integrationsplasmid pPICZa kloniert. Die Isoprenproduktion wurde mittels Gaschromatographie nach verschiedenen Inkubationszeiten und Medien nachgewiesen. Proylenogene Mikroorganismen konnten nicht gefunden werden. Von 524 Stämmen zeigten 31 eine sehr geringe Ethylenproduktion. Die vier Bacillus thurengiensis Stämme SR-769, SR-778, SR-780, SR-792, Lysinibacillus xylanilyticus SR-86, Bacillus cereus SR-772, Providencia sp. SR-782 and Bacillus luti SR-783 produzieren Ethylen ii über den KMBA-Weg, was ebenfalls auf Lactobacillus brevis SR-416 zutrifft. Pichia fermentans SR-265 zeigte hingegen ein Substratspektrum, welches zu erwarten ist, wenn Ethylen über den Yang-Zyklus gebildet wird. Die Genome von Lysinibacillus xylanilyticus SR-86, Bacillus cereus SR-772 sowie Pichia fermentans SR-265 wurden sequenziert. Dabei konnten nur in Pichia fermentans SR-265 homologe Proteine zur ethylenbildenden ACC Oxidase im Apfel (Malus domestica) gefunden werden. Diese zeigen die typische Triade aus His177, Arg179 und His234 für die Fe(II) Bindestelle. Die typische Bikarbonat-Bindestelle ist mit den Aminosäuren Thr157, Arg244 und Ser246 teilweise vorhanden. Weitere Versuche mit Aminosäuren und Metallen zeigten für die Proteinextrakte von Lysini, Lacto und Bacillus cereus, dass die Ethylenproduktion aus ACC durch die Anwesenheit von α-Ketoglutarat und Mn(II) gesteigert wird. Um Proteine zu identifizieren wurde eine Proteinaufreinigung mittels AEKTA vorgenommen. Das putative Ethylenbildene Enzym konnte aus Lysini über eine QXL- und QFF- Sepharose Anionentauscher gebunden und eluiert werden. Die Untersuchung der Fraktion brachte die 4-Oxalocrotonat Tautomerase hervor. Diese wurde in Escherichia coli BL21 kloniert und auf ihre Aktivität hin getestet. Es zeigte sich, dass sie nicht für die Ethylenbildung verantwortlich ist. Weitere Versuche zur Natur der Ethylenbildung über den Verdau der Proteine mittels Proteinase K zeigte, dass die Ethylenproduktion abnimmt. Kontrollversuche mit Bovines Serum Albumin (BSA) in Puffer nahm die Ethylenproduktion ebenfalls ab. Die Bildung von Ethylen aus KMBA wurde durch die Zugabe von EDTA, NAD(P)H und Fe(III) stimuliert. Die besten Vektoren für eine Genexpression in Cupriavidus necator waren pJeM1TcR und pMS137. Die Expression des Mev-Operons sowie der Isoprensynthase brachte jedoch keine Steigerung der Isoprenproduktion. Die Isoprenproduktion konnte in Pichia pastoris X-33 etabliert werden, war nach sechstägiger Inkubation jedoch sehr gering. Die Ethylenproduktion in Lysinibacillus xylanilyticus SR-86, Lactobacillus brevis SR-416 und Bacillus cereus SR-772 aus ACC erwies sich als chemische Reaktion von ACC und α-Ketoglutarat, katalysiert durch Mn(II). Die Ethylenbildung aus KMBA ist in der Literatur für andere Mikroorganismen beschrieben und entspricht diesen. Eine Sequenz ist allerdings nicht publiziert. Die Aktivität der homologen Proteine in Pichia fermentans SR-265 kann mittels Expression überprüft werden. Um in der Hof-Bioraffinerie Ethylen produzieren zu können, muss weiterhin nach stöchiometrisch optimalen Stoffwechselwegen gesucht werden. Basierend auf den Ergebnissen lässt sich ableiten, dass weiterhin nach effizienteren Stoffwechselwegen für die Produktion von Ethylen und Proyplen für die Hof-Bioraffinerie gesucht werden muss. Ebenfalls muss die Isoprenproduktion geeigneter Stämme für die Hof-Bioraffinerie verbessert werden. Summary In times of climate change the world is looking for alternative resources to move away from fossil resources. The farm-stead biorefinery aims to produce the gaseous chemicals ethylene, propylene and isoprene by fermentation from the renewable resource silage, in contrast to the recent production from fossil resources. A simple fermentation process would be desirable to provide the above-mentioned chemicals. This work has two major objectives: (1) find stoichiometrically favorable reactions to ethylene and propylene and their further characterization; (2) enhance the isoprene production in Cupriavidus necator and Pichia pastoris X-33. There are three pathways for the biosynthesis of ethylene known: the formation from α-keto-γ-methylthio- butyrate (KMBA), the ethylene-forming enzyme (EFE) reaction from α-ketoglutarate and the Yang-cycle in plants, in which ethylene is derived from 1-aminocyclopropane- 1-carboxylic acid (ACC). From a biotechnological point of view, all pathways have a suboptimal stoichiometry. There is no pathway for the biological propylene production elucidated so far, but 3-hydroxyalkanoic acids converted by the mevalonate diphosphate decarboxylase are involved. Isoprene is biosynthesized via the mevalonate-independent and mevalonate-dependent pathway and optimization is in progress. The screening for ethylenogenic and propylenogenic microorganisms in the department culture collection was examined by using gas chromatography. After three days of growth the culture was harvested, washed, concentrated ten-times and disrupted using heat/freeze cycles in phosphate buffer. Afterwards, the cell lysate was incubated with 3-phosphonooxy-propanoic and beta-alanine for ethylene production, and 3-phosphonooxy-butanoic acid and 3-sulfooxy-butanoic acid for propylene production in a sealed gas chromatography vial for four hours at 30 ◦C. Ethylene and propylene production were examined using headspace gas chromatography. The above-mentioned substrates can be produced from renewable resources and could be converted into alkenes by decarboxylation. Further characterization was done using molecular phylogenetic analysis, genomic sequencing and protein purification using AEKTA. Enhancing isoprene production in Cupriavidus necator started with the identification of versatile expression vectors by using (e)GFP as reporter gene. The next step was to clone the isoprene synthase from Pueraria montana and a codon optimized Mev- operon into
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