Team:TU Darmstadt/Project/Degradation

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(Degradation)
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== Degradation ==
== Degradation ==
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The [https://2012.igem.org/Team:TU_Darmstadt/Team#Degradation degradation group] consists of six undergraduates and one PhD advisor. Our objective is the expression of a fusion proteins on the surface of ''E. coli'' or as alternative ''S. cerevisiae'' to enable a microbial polyethylenterephtalate (PET) degradation.
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Die Gruppe Degradierung des TU Darmstadt iGEM Teams 2012 besteht aus 6 Studenten und 2 Doktoranden. Unserer Ziel ist es Fusionsproteine auf der Zelloberfläche von E.Coli und S.cerevisiae zu bringen um dort das Polymer Polyethylenterephthalat (PET) zu degradieren und in seine Monomere Terephthalsäure (TPA) und Ehtylenglyco zul zerlegen.
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We identified three potential PET degradation enzymes from literature. Two of them are cutinases HiC (''Humicola insolens'' cutinase) and FsC (''Fusarium solani'' cutinase) the other namely pNB-Est13 beeing an esterase. After thoroughly examination we dropped the HiC due to a temperature optimum of 80+°C.[[File:Project_overview_degradation.png|450px|thumb|right|Enzymatical degradation of polyethylen terephtalate (PET) to terephtalic acid (TPA)]]
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In order to maximise the activity we decided to anchor and display the cutinase/esterase directly on the surface of the producing bacterial cell. Surface-exposed enzymes are directly accessible to the respective substrates which no longer have to traverse the cellular membrane barriers. Furthermore, the enzyme reaction occurs in a chemically more defined environment as compared to the interior of a microbial cell. We use the outer membrane proteins of ''Pseudomonas aeruginosa'' (EstA) as a membrane anchor and the signaling sequence of PhoA translocators to display the enzyme on the outer surface of ''E. coli'' cells. In addition the fusion protein contains a his-tag for FACS detection and purification.
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Die Fusionsproteine bestehen aus einer Signalsequenz (PhoA) zur Sekretion ins Periplasma, einem His-Tag zur Detektion via FACS, verschiedenen katalytischen Domänen zur Hydrolyse des PET's und einem C-terminalen Membrananker.
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The signal sequence (PhoA), the catalytic domain (FsC/Est13) and EstA are assembled inline from their respective vectors. This is due to the fact, that by combining multiple parts in the standardized BioBrick vectors, scars with stop codons are generated that would effectively prevent the fusionproteins expression.
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In consideration of the DNA constructs length we pursued two PCR based synthesis strategies. One being the SKV (standard cloning procedure) the other being the SOE (standard overlap procedure). The first using primers and restriction sites for assembly the latter using overlapping primers. During both assembly procedures restriction sites of PstI, EcorI, SpeI or XbaI were eliminated from the coding sequence by mutagene PCR.
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After completion the fusionproteins and their subunits were transfered to the BioBrick standard and sent to the registry.  
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Die Signal Sequenz (PhoA Signal Peptid), die katalytische Domänen und der Membrananker werden aus verschiedenen Spender Vektoren entnommen, da das Standard BioBrick System des iGEM-Wettbewerbs nach jeder Insertion Stoppcodons vermittelt und somit die Synthese von Fusionsproteinen nicht erlaubt. Danach werden störende Schnittstellen (PstI, EcorI, SpeI oder XbaI) in der codierenden Sequenz entfernt. Wir bedienen uns daher beim Zusammenfügen der einzelnen Funktionselementen der herkömmlichen Klonierungsverfahren.
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For further characterisation the enzymes were overexpressed in ''E. coli'', screened on tributyrin agar and FACS. The [https://2012.igem.org/Team:TU_Darmstadt/Project/Material_Science material science group] went even further and tried to examine them using AFM.
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Nachdem die Fusionsproteine erstellt und in das BioBrick System überführt wurden und anschließend in E.coli Produktionsstämmen inseriert um hohe Mengen an Protein für die Charakterisierung zu erzeugen.
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The corresponding data is available in our [https://2012.igem.org/Team:TU_Darmstadt/Labjournal/Degradation labjournal]. If you want to know what happens with the PET after it is degradated to its TPA monomers continue with [https://2012.igem.org/Team:TU_Darmstadt/Project/Transport 2.Transport].
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Die Aktivität der auf der Zelloberfläche präsentierten Fusionsproteine wird auf Tributyrin-Agarplatten untersucht. Danach in einen Chassis Stamm eingeführt, der alle Funktionen aus den Arbeitsgurppen Degradierung, Transport und Metabolismus beinhaltet.
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Die Aktivität unserer Fusionsproteine wird erst qualitativ über die Ausplattierug auf Tributyrin-Agarplatten untersucht. Parallel dazu wird durch einen fluoreszenzmarkierten Antikörper eine quantitative Aussage über die Zelloberflächenexpression via FACS gemacht.
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Die Charackterisiertung der Enzymaktivität (Quantitative Parameter: Vmax, Km etc.) werden photometrisch über ein pNP-Assay mit dem Standardsubstrat (4-nitrophenyl Butyrat) und 2 weiteren von der Metarailwissenschafs Gruppe synthetisierten Substraten gemacht. Die Hydrolyse auf PET-Monomeren wird mittels Säure-Base Titration und HPLC gemessen. Im Anschluss dieser Untersuchungen wird die PET-spezifische Hydrolyseaktivität auf nativen PET-Mikropartikel mit verschiedenen Körnungen analysiert.
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continue with [https://2012.igem.org/Team:TU_Darmstadt/Project/Transport 2.Transport]
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Revision as of 03:00, 23 September 2012

Degradation

The degradation group consists of six undergraduates and one PhD advisor. Our objective is the expression of a fusion proteins on the surface of E. coli or as alternative S. cerevisiae to enable a microbial polyethylenterephtalate (PET) degradation.

We identified three potential PET degradation enzymes from literature. Two of them are cutinases HiC (Humicola insolens cutinase) and FsC (Fusarium solani cutinase) the other namely pNB-Est13 beeing an esterase. After thoroughly examination we dropped the HiC due to a temperature optimum of 80+°C.
Enzymatical degradation of polyethylen terephtalate (PET) to terephtalic acid (TPA)

In order to maximise the activity we decided to anchor and display the cutinase/esterase directly on the surface of the producing bacterial cell. Surface-exposed enzymes are directly accessible to the respective substrates which no longer have to traverse the cellular membrane barriers. Furthermore, the enzyme reaction occurs in a chemically more defined environment as compared to the interior of a microbial cell. We use the outer membrane proteins of Pseudomonas aeruginosa (EstA) as a membrane anchor and the signaling sequence of PhoA translocators to display the enzyme on the outer surface of E. coli cells. In addition the fusion protein contains a his-tag for FACS detection and purification.

The signal sequence (PhoA), the catalytic domain (FsC/Est13) and EstA are assembled inline from their respective vectors. This is due to the fact, that by combining multiple parts in the standardized BioBrick vectors, scars with stop codons are generated that would effectively prevent the fusionproteins expression. In consideration of the DNA constructs length we pursued two PCR based synthesis strategies. One being the SKV (standard cloning procedure) the other being the SOE (standard overlap procedure). The first using primers and restriction sites for assembly the latter using overlapping primers. During both assembly procedures restriction sites of PstI, EcorI, SpeI or XbaI were eliminated from the coding sequence by mutagene PCR. After completion the fusionproteins and their subunits were transfered to the BioBrick standard and sent to the registry.

For further characterisation the enzymes were overexpressed in E. coli, screened on tributyrin agar and FACS. The material science group went even further and tried to examine them using AFM.

The corresponding data is available in our labjournal. If you want to know what happens with the PET after it is degradated to its TPA monomers continue with 2.Transport.