Soutenance de thèse Jérémy Le Reun

I am pleased to invite you to my thesis defense, which will take place on Wednesday, 25 February 2026, at 2 p.m. in room 401 of TBI.

The thesis is entitled “Enzyme and microbial engineering for tailored chain-length fatty acid production in the yeast Yarrowia lipolytica” (abstract below).

The presentation will be in French, with slides written in English.

Please note that the defense and its content will be confidential. You will be required to sign a non-disclosure agreement before entering the room. Please plan to arrive a few minutes early !


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Jury composition:

Mr Sébastien BAUD, Directeur de recherche CNRS, Reviewer
Mr Frédéric CARRIERE, Directeur de recherche CNRS, Reviewer
Mme Fayza DABOUSSI, Directrice de recherche INRAe, Examiner
Mr Frédéric DOMERGUE, Chargé de recherche CNRS, Examiner
Mme Young-Kyoung PARK, Chargée de recherche INRAe, Examiner
Mme Isabelle ANDRÉ, Directrice de recherche CNRS, PhD supervisor
Mme Florence BORDES, Maitre de Conférence INSA Toulouse, PhD co-supervisor

Abstract:

Fatty acids containing 20 or more carbon atoms are generally referred to as very-long chain fatty acids (VLCFAs). Although their abundance in living organisms is low, these compounds are essential biological components and valuable chemicals for various industrial applications. Microbial production of VLCFAs have thus gained in interest over the past years, in particular using metabolic engineering approaches to fine-tune fatty acid composition towards desired VLCFA. Such approaches involve modulating with precision the fatty acid elongation pathway and using enzymes endowed with the appropriate substrate and product specificities.

This study focuses on a family of enzymes named fatty acid elongases (ELOs), whose specificity and activity governs the maximal chain length of fatty acids that can be produced. This thesis aimed at better understanding the molecular determinants controlling the product specificity of ELOs, with the goal in fine to use these enzymes to produce VLCFAs of tailored chain length. To achieve this objective, a combination of computational and experimental approaches was employed, using the oleaginous yeast Yarrowia lipolytica as a chassis for both ELO characterization and VLCFA production.

In this work, a sequence-based analysis was first performed to mine the natural diversity of ELO enzymes and to understand their sequence-function relationships, revealing clusters of sequences associated with distinct specificities. To complete this bioinformatics analysis with experimental data, an improved workflow for the characterization of ELO specificity in vivo in Y. lipolytica was developed and used to provide data on the specificity of 37 ELO enzymes covering major subfamilies, including 9 new enzymes characterized for the first time.

The determinants controlling ELOs specificity were then investigated at molecular level on some of these subfamilies, combining molecular modeling and sequence analyses. Fungal elongases active on saturated fatty acids were used as enzyme models to explain chain length specificity. Three amino acid positions located at the bottom of the substrate pocket that could limit the maximum size of the accommodated substrate were identified. ELOs active on polyunsaturated fatty acids but specific to the position of the unsaturation were then studied, revealing a cluster of four amino acid residues situated at the center of the enzyme that could control the topology of the tunnel for substrate positioning. The amino acid positions identified were further validated experimentally by site-directed mutagenesis, enabling to evaluate their role on the modulation of the specificity of the enzymes studied.

Through the expression of elongases in Yarrowia lipolytica, it was possible to modify the fatty acid profile and diversify the VLCFAs obtained. To understand the impact of these modifications on the physiology and lipid metabolism of the strains, lipidomic analyses were initiated. The results obtained provide novel insights into the redistribution of new fatty acids across lipid pools, opening up prospects for strain improvement by metabolic engineering.