Dokument: Establishing regulatable expression systems in the acetic acid bacterium Gluconobacter oxydans 621H
| Titel: | Establishing regulatable expression systems in the acetic acid bacterium Gluconobacter oxydans 621H | |||||||
| Weiterer Titel: | Etablierung regulierbarer Expressionssysteme in dem Essigsäurebakterium Gluconobacter oxydans 621H | |||||||
| URL für Lesezeichen: | https://docserv.uni-duesseldorf.de/servlets/DocumentServlet?id=58806 | |||||||
| URN (NBN): | urn:nbn:de:hbz:061-20220307-105908-0 | |||||||
| Kollektion: | Dissertationen | |||||||
| Sprache: | Englisch | |||||||
| Dokumententyp: | Wissenschaftliche Abschlussarbeiten » Dissertation | |||||||
| Medientyp: | Text | |||||||
| Autor: | Dr. Fricke, Philipp Moritz [Autor] | |||||||
| Dateien: |
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| Beitragende: | Prof. Dr. Bott, Michael [Gutachter] Prof. Dr. Urlacher, Vlada [Gutachter] | |||||||
| Stichwörter: | Bacteria, Acetic acid bacteria, Gluconobacter oxydans, Biotechnology, Genetics, Expression system, Fluorescence protein | |||||||
| Dewey Dezimal-Klassifikation: | 500 Naturwissenschaften und Mathematik » 570 Biowissenschaften; Biologie | |||||||
| Beschreibungen: | Das Essigsäurebakterium Gluconobacter oxydans wird unter den industriell relevanten Mikroorganismen für seine Fähigkeit geschätzt, eine Vielzahl von Kohlenhydraten stereo- und regiospezifisch unvollständig zu oxidieren. Bisherige biotechnologische Verfahren mit G. oxydans verwendeten für die zielgerichtete Genexpression ausschließlich konstitutive Promotoren. Die regulierbaren Promotoren, die in G. oxydans oder anderen Essigsäurebakterien untersucht wurden, zeigten eine sehr hohe Basalaktivität unter nicht induzierten Bedingungen, was zu einem geringen Induktionsverhältnis führte. Das Ziel dieser Doktorarbeit war es, ein regulierbares Promotorsystem in G. oxydans zu etablieren, dass die Expression ausgewählter Gene durch die Konzentration eines Induktors steuern kann. Zu diesem Zweck wurden vier bekannte und gut charakterisierte Regulator-Promotor-Paare in G.oxydans mit Hilfe von Expressionsplasmiden getestet. Außerdem wurde versucht, regulierbare endogene G. oxydans-Promotoren zu identifizieren, die auf die Zugabe eines Metaboliten als externen Stimulus reagieren und so für eine kontrollierte Genexpression geeignet sind.
In G. oxydans getestet, ermöglichte das AraC-ParaBAD-System aus Escherichia coli MC4100 eine starke Repression der Transkription in Abwesenheit von L-Arabinose sowie eine bis zu 480-fach erhöhte Genexpression bei vollständiger Induktion mit L-Arabinose. Die Genexpression von ParaBAD war durch den Einsatz von Induktorkonzentrationen von 0,1-1% (w/v) L-Arabinose gut modulierbar. Außerdem wurde gezeigt, dass die Oxidation von L-Arabinose zu L-Arabinsäure durch die membrangebundene Glucose-Dehydrogenase GdhM zu einer Ansäuerung des Mediums und damit zu einem pH-abhängigen Verlust der Reporterproteinaktivität führte. In pH-kontrollierten Fermentationen oder durch die Verwendung des GdhM-Deletionsstamms BP.6 konnte dieser Verlust umgangen werden. Das Oxidationsprodukt L-Arabinsäure ist ein wertvoller Rohstoff, der in vielen Prozessen unter anderem bei der Herstellung bestimmter Pharmazeutika, Halbleiter- materialien und Verbundzementen Anwendung findet. Durch die Verwendung von G. oxydans 621H wurde in pH-kontrollierten Fed-Batch-Kultivierungen innerhalb von 144 Stunden mehr als 120 g/L L-Arabinsäure aus 160 g/L L-Arabinose hergestellt. Dieser hohe Titer übertraf die Titer, die zuvor für gentechnisch veränderte E. coli oder Saccharomyces cerevisiae berichtet wurden, um mehr als das Dreifache. Die Plasmid-basierte Überexpression von gdhM zur Erhöhung der Enzymaktivität führte, möglicherweise aufgrund nachteiliger Auswirkungen auf die Membranintegrität, zu keiner Verbesserung der Produktivität. Neben dem AraC-ParaBAD-System wurden mit dem Transposon Tn10-basiertem TetR- Ptet-System und dem LacI-PlacUV5-System zwei weitere induzierbare Expressionssysteme aus E. coli in G. oxydans getestet. Im Gegensatz zu AraC-ParaBAD beruhen diese induzierbaren Expressionssysteme auf der Transkriptionsrepression von Zielgenen. Die Leistung des TetR- Ptet-Systems übertraf die des AraC-ParaBAD-Systems. Unter nicht induzierten Bedingungen zeigte das TetR-Ptet-System eine sehr geringe basale Expression, die durch die Konzentration des Induktors graduell gesteigert werden konnte. Unter Verwendung von 200ng/ml Anhydrotetracyclin wurde ein maximales Induktionsverhältnis von 3.500 ermittelt. Terminatorsequenzen, Wahl des Expressionsplasmids, Antibiotikaresistenzgen und die Insertion einer zusätzlichen, bekannten Ribosomenbindestelle beeinflussten die Leistungsfähigkeit dieses Systems. Die deutlich geringere Induzierbarkeit von PlacUV5 in G. oxydans hingegen machte dieses System zum schwächsten der hier getesteten Regulator- Promotor-Paare. Aufgrund der hohen Basalaktivität wurde mit PlacUV5 nur eine 40-fache Induktion mit 1 mM IPTG erzielt. Mit dem RhaSR-PrhaBAD-System von E. coli wurde ein Regulator-Promotor-Paar gefunden, das – im Gegensatz zu E. coli – einen L-Rhamnose-abhängigen Knockdown anstelle einer Induktion der Genexpression in G. oxydans ermöglichte. PrhaBAD führte in G. oxydans zu einer sehr starken Expression und wurde durch die Anwesenheit von RhaS in Abwesenheit von L-Rhamnose aktiviert. Mit steigender L-Rhamnose-Konzentration wurde die PrhaBAD-Aktivität RhaS-abhängig um bis zu 92% reduziert. Im Gegensatz dazu war die Expression des RhaS-abhängigen Permease-Promotors PrhaT in G. oxydans genauso wie in E. coli induzierbar. PrhaT zeigte in G. oxydans eine schwache Expressionsstärke, welche durch die L-Rhamnosekonzentration maximal 10-fach induziert werden konnte. Ein derartiger Promotor wäre möglicherweise für die Expression von „schwierigen“ Enzymen von Vorteil. In DNA-Microarray-basierten genomweiten Stimulon-Screenings auf regulierte endogene Promotoren wurde gezeigt, dass sich die Transkription der G. oxydans-Gene GOX0532 und GOX0536 um das 45-fache erhöhte, wenn dem Medium 1% (w/v) Citrat zugesetzt wurde. Die Gene GOX0532 und GOX0536 kodieren für ExbB und einen Eisen- Siderophore Rezeptor, die beide wahrscheinlich an der Eisenaufnahme beteiligt sind. Die Supplementierung des Mediums mit 8 μM FeSO4 reduzierte die basale Expression beider Promotoren und erhöhte dadurch die Induktionsraten. Wahrscheinlich induziert durch Eisenlimitierung verursacht durch Citrate-Fe3+-Chelatierung, konnte die Expression von PGOX0532 und PGOX0536 >270-fach hochreguliert werden, wenn das Medium mit 5 x 50 mM Citrat in Intervallen von 1,5 Stunden versetzt wurden. ChAP-Seq Analysen bestätigten, dass der Transkriptionsfaktor Fur (ferric uptake regulator) (GOX0771) Promotorbereiche von PGOX0536 bindet. Neben diesen Originalstudien wurde in einem Minireview ein Überblick über Expressionssysteme und ihre Anwendungen in Essigsäurebakterien veröffentlicht, der die Jahre von 1985, als die ersten Plasmide in Essigsäurebakterien verwendet wurden, bis Ende 2020 umfasste. In 6.097 Veröffentlichungen zu Essigsäurebakterien wurde lediglich für neun von 49 beschriebenen Gattungen über die Verwendung von Expressionsplasmiden berichtet. Innerhalb der beschriebenen Expressionsplasmide wurden sechs Hauptplasmidlinien identifiziert. Gemäß der Literaturrecherche sind die für G. oxydans entwickelten Systeme AraC-ParaBAD und TetR-Ptet die ersten regulierbaren Expressionssystem in dieser Bakteriengruppe, die eine >40-fach Induktion erlauben. Sie bieten neue Optionen für die zukünftige Stammentwicklung von G. oxydans und können möglicherweise auf andere Essigsäurebakterien-Arten übertragen werden.Among industrially relevant microorganisms, the acetic acid bacterium Gluconobacter oxydans is valued for its ability to incompletely oxidize a vast number of carbohydrates stereo- and regio-specifically. Biotechnological production processes involving G. oxydans strains so far utilized exclusively constitutive target gene expression. Regulatable promoters used in G. oxydans suffered from low induction fold-changes and relatively high basal promoter activity already when not induced. This study aimed to establish regulatable promoter systems in G. oxydans that allow tuned target gene expression in an effector-dependent manner. For this purpose, expression plasmids were constructed to test four well-characterized heterologous regulator-promoter pairs in G. oxydans. Additionally, screenings were performed to identify regulatable endogenous G. oxydans promoters responding to a metabolite given as an external stimulus and suitable for controlled gene expression. When transferred into G. oxydans, the AraC-ParaBAD system from Escherichia coli MC4100 permitted tight repression of target gene expression in the absence of L-arabinose and up to 480-fold induction when maximally induced with L-arabinose. At inducer concentrations from 0.1 to 1% (w/v) L-arabinose, reporter gene expression from ParaBAD was highly tunable. Furthermore, L-arabinose was found to be oxidized to L-arabinonic acid by the membrane-bound glucose dehydrogenase GdhM, resulting in an acidification of the medium and pH-dependent loss of intracellular reporter protein activity. This loss could be circumvented by pH-controlled cultivation or use of the gdhM deletion strain BP.6. The oxidation product L-arabinonic acid is a valuable compound with potential use in various applications ranging from the production of pharmaceuticals to semi-conductor materials and composite cements. By using G. oxydans 621H, more than 120 g/L L-arabinonic acid could be produced from 160 g/L L-arabinose within 144 h in pH-controlled fed-batch cultivations. This high titer exceeded the ones previously reported for engineered E. coli or Saccharomyces cerevisiae strains more than threefold. Plasmid-based overexpression of gdhM to increase the enzyme activity did not improve the productivity possibly due to detrimental effects on the membrane integrity. Besides the AraC-ParaBAD system, the suitability of the transposon Tn10-based TetR- Ptet system and of the LacI-PlacUV5 system, both originating from E. coli, was tested in G. oxydans. In contrast to AraC-ParaBAD, these inducible expression systems rely on target gene repression. The TetR-Ptet system outperformed the AraC-ParaBAD system, since in G. oxydans it showed extremely low basal expression and a concentration-dependent gradual increase of target gene expression upon induction with anhydrotetracycline. A maximal induction of up to 3,500-fold was obtained with 200 ng/mL anhydrotetracycline. Terminator sequences, plasmid backbone, antibiotic resistance gene, and the insertion of an additional known ribosome-binding site affected the performance of this system. In G. oxydans, only moderate inducible gene expression from PlacUV5 made this system the weakest of the regulator-promoter pairs tested in this work. Due to relatively high leakiness of non-induced PlacUV5, induction with 1 mM IPTG was only 40-fold. With the RhaSR-PrhaBAD system from E. coli, a regulator-promoter pair was found that – contrary to E. coli – allows L-rhamnose-dependent knockdown of gene expression in G. oxydans instead of induction. PrhaBAD was very strong in G. oxydans and activated by the presence of RhaS in the absence of L-rhamnose, while with increasing L-rhamnose concentrations the PrhaBAD activity was reduced by 92% in a RhaS-dependent manner. In contrast, expression from the RhaS-dependent promoter PrhaT was L-rhamnose-inducible in G. oxydans as in E. coli. Since PrhaT was rather weak in G. oxydans, the induction was tunable up to 10-fold. This could be of advantage for expression of ‘difficult’ enzymes. In the DNA microarray-based genome-wide stimulon screenings for regulated endogenous promotors, transcription of GOX0532 and GOX0536 encoding ExbB and a ferrisiderophore receptor both likely involved in iron uptake were found to be increased 45-fold when exposed to 1% (w/v) citrate as stimulus. Supplementation of the growth medium with 8 μM FeSO4 reduced the basal expression from both promoters und thereby increased induction ratios. Probably induced by iron-limitation through Fe3+-citrate chelation, expression from PGOX0532 and PGOX0536 could be upregulated >270-fold when 5 x 50 mM citrate was added to the medium in intervals of 1.5 h. ChAP-Seq experiments confirmed that the ferric uptake regulator Fur (GOX0771) binds to the promoter region PGOX0536. Beside these original studies, a review on expression systems and their applications in acetic acid bacteria (AAB) was published covering the years from 1985, when the first plasmids were used in AAB, up to the end of 2020. Screening of 6097 AAB-related publications revealed that expression plasmids have been reported for merely nine out of 49 AAB genera currently described, and six major expression plasmid lineages were identified. According to this AAB-related literature search, the AraC-ParaBAD and TetR-Ptet systems developed by us for G. oxydans are the first regulatable expression system with induction ratios >40-fold in this group of bacteria. They provide new options in future strain development and may be transferable to other AAB species. | |||||||
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| Lizenz: |  Urheberrechtsschutz | |||||||
| Fachbereich / Einrichtung: | Mathematisch- Naturwissenschaftliche Fakultät » WE Biologie » Mikrobiologie | |||||||
| Dokument erstellt am: | 07.03.2022 | |||||||
| Dateien geändert am: | 07.03.2022 | |||||||
| Promotionsantrag am: | 10.11.2021 | |||||||
| Datum der Promotion: | 07.02.2022 |
