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Études d’un mécanisme enzymatique et d’interactions inter-protéiques au sein de voies complexes de biosynthèse de polycétides

Abstract : Complex polyketides are secondary metabolites which are produced by a range of different organisms, and which present a broad spectrum of therapeutic activity. The modular organization of the enzymes responsible for their synthesis, the polyketide synthases (PKS), makes them attractive targets for synthetic biology aimed at obtaining new polyketide structures. One of the most promising strategies to date consists in swapping of whole sub-units between different PKS systems. However, the success of this strategy critically depends on understanding and exploiting ‘docking domains’  the protein sequences at the C- and N-terminal extremities of the subunits which are responsible for correctly ordering the polypeptides, and therefore for faithful chain transfer. To increase our knowledge of DDs, we investigated several interfaces in both trans-AT and cis-AT PKSs. This work led notably to the identification of the first family of DDs from trans-AT PKSs, and we were further able to characterize a complete interface formed between two consecutive subunits within the virginiamycin PKS. In addition, we showed that at least one DD of matched pairs is often an intrinsically disordered region (IDR), as this type of interaction motif allows for specific but medium affinity contacts. Indeed, in the enacyloxin hybrid cis-AT/trans-AT PKS which we also investigated extensively, docking at every interface is mediated by a C-terminal IDR. In addition, we demonstrated that multiple structural classes of DD are present within the system, but that variations of the electrostatic ‘code’ within an individual structural class can also be used to ensure specificity. Taken together, these results provide important guidelines for future attempts to deploy DDs in subunit engineering. Another attractive target for synthetic biology are the so-called ‘post-PKS’ enzymes, which chemically decorate the initially-formed structure, and are often essential for their bioactivity. In this context, we studied LkcE, a bi-functional enzyme that catalyzes a rare amide oxidation followed by an intramolecular Mannich reaction to yield the lankacidin macrocycle – both to understand its unusual mechanism and to evaluate its suitability as a general polyketide modifying enzyme. We solved four crystal structures of the enzyme, and characterized it kinetically. Together, our data allowed us to propose a detailed catalytic mechanism for LkcE, involving a large-scale conformational change of the enzyme to bring the substrate into a cyclisation-ready state. Moreover, we showed that LkcE displays a certain tolerance toward its substrate structures, suggesting its usefulness as a general catalyst for cyclisation/ligation reaction in synthetic biology and chemical synthesis.
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Fanny Risser. Études d’un mécanisme enzymatique et d’interactions inter-protéiques au sein de voies complexes de biosynthèse de polycétides. Biochimie, Biologie Moléculaire. Université de Lorraine, 2019. Français. ⟨NNT : 2019LORR0296⟩. ⟨tel-02928579⟩



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