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Robescu, Marina Simona (2018) Discovery and characterization of new Ene-reductases. [Ph.D. thesis]

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Abstract (italian or english)

Seven new putative ene-reductases (ERs or OYEs) have been identified and selected using bioinformatics tools from different organisms: Galdieria sulphuraria (GsOYE), Chroococcidiopsis thermalis (CtOYE), Chloroflexus aggregans (CaOYE), Botryotinia fuckeliana (BfOYE1 and BfOYE4) and Aspergillus niger (AnOYE2 and AnOYE8). Based on most updated literature, both the photosynthetic organisms (Galdieria, Chroococcidiopsis and Chloroflexus) and the fungi (Botryotinia and Aspergillus) result very interesting sources for ERs, that have not been exploited until now.
The cloning and expression strategy used was the same for all the seven putative sequences. After a first trial of expression in E. coli BL21(DE3 good over-expression and solubility were obtained for GsOYE, CtOYE, CaOYE and BfOYE1 while for the other three proteins further optimization was necessary. To overcome the low solubility of AnOYE2 and AnOYE8 and the low production of BfOYE4 many strategies have been performed such as lowering the temperature of expression and using chaperons, but also trying other expression hosts (i.e. P. pastoris).
A biocatalytic characterization was carried out for all proteins. Once verified their activity as ene-reductases in vitro, a steady-state study was performed in order to obtain the kinetics parameters. For two enzymes, GsOYE and CtOYE, bioconversions were set-up at the Biocatalysis laboratories of Graz University headed by Prof. Kurt Faber, a main expert of biocatalysis and also of ene-reductases. Finally, a biochemical characterization was carried on in order to determine the thermal stability, pH tolerance and also the three-dimensional structure of the newly discovered enzymes.
Moreover, their application for the hydride-independent isomerization of non-activated C=C-bonds and subsequent reduction is also discussed and the efforts in elucidating this new reactivity are shown in detail.
The work presented in this thesis lead to the discovery of new ERs enlarging the possibility to find out novel and promising biocatalysts for C=C-bond bioreduction but also for other unexpected biocatalytic reactivities.

Abstract (a different language)

Sette nuove ene-reduttasi putative sono state identificate attraverso mezzi bioinformatici con un approccio di “genome mining” da diversi organismi: Galdieria sulphuraria (GsOYE), Chroococcidiopsis thermalis (CtOYE), Chloroflexus aggregans (CaOYE), Botryotinia fuckeliana (BfOYE1 and BfOYE4) e Aspergillus niger (AnOYE2 and AnOYE8). In particolare gli organismi fotosintetici (Galdieria, Chroococcidiopsis e Chloroflexus) e i fungi (Botryotinia e Aspergillus) sono, ad oggi, fonti di ene-reduttasi rimaste inesplorate.
Per il clonaggio e l’espressione di tutte e sette le sequenze codificanti le proteine di interesse è stata utilizzata una strategia comune. Inizialmente tutte le proteine sono state espresse utilizzando come ospite E. coli BL21(DE3); con questa strategia, però, sovraespressione e buona solubilità sono state ottenute solo per quattro delle sette proteine, GsOYE, CtOYE, CaOYE e BfOYE1. Per le altre tre proteine è stata necessaria un’ulteriore ottimizzazione. La bassa solubilità di AnOYE2 e AnOYE8 e la scarsa espressione di BfOYE4 sono state affrontate utilizzando diverse strategie, come la diminuzione della temperatura e l’utilizzo di chaperonine ma anche l’utilizzo di altri ospiti per l’espressione proteica (P. pastoris).
Per tutte e sette le proteine ricombinanti è stata condotta una caratterizzazione biocatalitica. Una volta dimostrata la loro attività come ene-reduttasi in vitro, sono stati determinati anche i parametri cinetici per i substrati preferiti da ciascun enzima. Nel laboratorio del Professor Kurt Faber dell’Università di Graz, sono state messe a punto bioconversioni per i due enzimi GsOYE e CtOYE, al fine di capirne il profilo di selettività nei confronti di substrati standard.
Infine, è stata condotta anche una caratterizzazione biochimica che ha permesso di determinare la stabilità termica e la tolleranza a diversi pH dei nuovi enzimi identificati; per i quali è stata anche ottenuta la struttura tridimensionale.
Nella tesi è discusso l’utilizzo degli enzimi nell’isomerizzazione NADH-indipendente di substrati con legami C=C non attivati e la loro successiva riduzione, così come gli sforzi per chiarire il meccanismo d’azione di questa nuova reattività scoperta solo di recente.
Il lavoro presentato ha portato alla scoperta di nuove ene-reduttasi, ampliando così il pannello dei biocatalizzatori disponibili per la riduzione del doppio legame C=C ma anche per reattività biocatalitiche inaspettate.

EPrint type:Ph.D. thesis
Tutor:Bergantino, Elisabetta
Ph.D. course:Ciclo 31 > Corsi 31 > SCIENZE MOLECOLARI
Data di deposito della tesi:29 November 2018
Anno di Pubblicazione:01 October 2018
Key Words:Biocatalisi, Flavoproteine, Ene-reduttasi/Biocatalysis, Flavoproteins, Ene-reductases
Settori scientifico-disciplinari MIUR:Area 03 - Scienze chimiche > CHIM/06 Chimica organica
Struttura di riferimento:Dipartimenti > Dipartimento di Biologia
Codice ID:11506
Depositato il:14 Nov 2019 13:40
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