Matheus Montrazi

Titre de la thèse: The function of acyl-chain length of lipids in cell signaling and denovo organogenesis

Encadrante : Yohann Boutte

Date de début de thèse : 1er octobre 2022
Financement : ANR
Ecole Doctorale des Sciences de la Vie et de la Santé

In cell signaling, extracellular signals are transmitted across the plasma membrane to activate downstream elements inside the cell. These signaling processes are based on protein complexes e.g. activation of receptor-like kinases, transmembrane kinases and/or membrane associated kinase regulators. However, it now appears that lipids play a major role for signal transduction across membranes. Indeed, they could act on protein activity or activation, mobility, clustering or interaction with other proteins. An additional layer of complexity relies on regulatory networks that robustly control the organogenesis and functional patterning of developing tissues in a hormone-dependent manner. Recent advances in the field indicate that the expression of lipid biosynthesis genes, and more particularly those encoding proteins that regulate the acyl-chain length of lipids, is restricted both in time and space to specific targeted area of new developing organs. During my PhD thesis I will be using the denovo organogenesis of the lateral root primordium as a model to:

1/ Study the involvement of acyl-chain length of lipids in mediating hormone signaling across the two leaflets of the plasma membrane.

2/ Identify the cellular mechanisms acting both during and downstream membrane lipid-mediated signaling.

3/ Characterize how these mechanisms are coordinated both in time and space in the developing lateral root primordium.

Julie Castets

Titre de la thèse: Characterizing the contribution of lipid remodeling to plant autophagy

Encadrante : Amélie Bernard

Date de début de thèse : 1er octobre 2021
Financement : ERC Lip-ATG
Ecole Doctorale des Sciences de la Vie et de la Santé

Autophagy is an intracellular degradation process critical for plant adaptation to environmental stresses. During autophagy, unwanted/toxic cytosolic material is engulfed by a growing membrane which ultimately closes to form a vesicle, the autophagosome. Autophagosomes are critical to autophagy by selecting and trafficking cargo the lytic vacuole where it will be degraded; reduction in size or numbers of autophagosomes lead to defects in rates of autophagy flux and plant survival. Yet the molecular mechanisms underlying autophagosome formation remain largely unresolved in plants. Specifically, our view on autophagy is limited by the lack of knowledge concerning the functional implication of lipids in the formation and dynamics of autophagosome membranes. Our recent work identified the association between a small family of lipid-remodeling proteins and autophagy in Arabidopsis. Using a transdisciplinary approach combining cell biology, biochemistry and reverse genetics, the overall objectives of this project are (1) to explore the localization of these proteins and the relevance of their interactions with the autophagy machinery, (2) to characterize the function of these proteins in the autophagy pathway and notably, in autophagosome formation and structure, (3) to address the functional relevance of the crosstalks between lipid metabolism and autophagy to support plant adaptation to stress.

Claire Le Ruyet

Titre de la thèse: Identification and validation of potential herbicide targets in the very-long-chain fatty acid biosynthetic pathway in order to support the development of new environmental friendly herbicides

Encadrant : J. Joubès
Date de début de thèse : 1er Juin 2021
Financement : CIFRE
Ecole Doctorale des Sciences de la Vie et de la Santé

Very-long-chain fatty acids are important molecules with crucial physiological and structural roles in plants. VLCFA are required for the production of membrane lipids and are essential for membrane homeostasis. They are also stored in triacylglycerols in seeds and are thus essential for seed germination. Furthermore, in epidermal cells, VLCFA are converted into several derivatives such as cuticular waxes for the formation of the plant cuticle which prevents water-loss and pathogen attacks. VLFCA are also found in other surface lipid barriers such as the pollen coat or the root suberin. VLCFA are produced by the acyl-CoA elongase activity (FAE complexes). Biochemical and genetic studies in Arabidopsis led to the idea that multiple elongase complexes with distinct chain-length specificities perform sequential and parallel reactions to produce the wide range of VLCFA found in plants. Because FAE complexes are known to be the targets of various herbicides, the project will lead to identify and validate the inhibitory activity of various herbicides in order to better understand the differences between target and non-targeted plants allowing the development of new environmentally friendly herbicides.

Louise Fougère

Titre de la thèse: Unraveling new structures, dynamics and functions of the Golgi apparatus to better understand protein sorting and cell polarity

Encadrant : Y. Boutté
Date de début de thèse : 1er Octobre 2021
Financement : Ministère de la Recherche et de l’Enseignement
Ecole Doctorale des Sciences de la Vie et de la Santé

In eukaryotic cells, sorting of integral membrane proteins within the secretory system regulates their final localization as well as degradation. A major sorting hub in eukaryotic cells is the Golgi apparatus that plays fundamental functions to organize and regulate delivery fluxes of proteins and lipids from the endoplasmic reticulum (ER) to their final destination. As such the Golgi is a key regulatory component of cell-cell signalling, development and environmental responses. The main events of protein sorting occur both at the pre-Golgi and post-Golgi. In animal cells, the pre-Golgi is composed from ER-derived tubulo-vesicular transport carriers that act as a ER-Golgi intermediate compartment (ERGIC). In plants, as the existence of the ERGIC is debated, a hurdle is now to address whether an equivalent or similar compartment to the ERGIC actually exists in plants cells and identify its nature, structure and function. My PhD thesis project employs a combination of immuno-purification of endomembrane compartments including pre- and post-Golgi subdomains for subsequent proteomic and lipidomic analysis, improved resolution Airyscan microscopy coupled with dynamic tracking of Golgi entities in living cells, lifetime 𝛕-STED super-resolution microscopy and novel imaging quantification methods to:

1/ Decipher the dynamics and structure of the potential ERGIC in plant cells.

2/ Visualize, track and quantify the dynamics of the pre-Golgi and test its interaction with other Golgi entities or other membrane compartments.

3/ Identify the lipid composition and function at pre- and post-Golgi in protein sorting during trafficking of cargos that localize in a polar fashion within the cell.

Ziqiang Li

Titre de thèse: ER defines intercellular communication in plants

Encadrante: E. Bayer

Date début de thèse: Nov 2019
Financement: ERC BRIDGING

In multicellular organisms, stable intercellular bridges arise from incomplete cytokinesis provide direct cytoplasmic connections between sibling cells. Through these membrane-lined canals, cells exchange signals, nutrients, and organelles to coordinate cell fate decisions and growth. In plants, stable intercellular bridges, named plasmodesmata (PD), are spanned by a modified endoplasmic reticulum (ER) that runs continuously through the entire plant body. Cell to cell ER continuity has been observed for more than a century, yet very little is known about how ER is maintained inside PD to bridge neighbor cells together. Historically, this ER has been considered as a non-functional element, and its presence is due to ‘accidental’ trapping by the intercellular bridges during cytokinesis. However, it is hard to imagine how ER, one highly dynamic organelle, can be physically immobilized inside of intercellular bridges during and post cytokinesis.  This objective of the thesis is to investigate how plants generate ER continuity  cell to cell continuity using Arabidopsis thaliana as a model, genetics, live-cell imaging, and electron microscope,  to understand a) what steps and molecules are needed to immobilize and remodel ER inside intercellular bridges during cytokinesis a) Would the ER involve in making decisions between abscission and intercellular bridges stabilization to create PD c) finally, why plants create this ER continuity? Would the ER provide a path for on-demand communication, and is there a barrier to prevent unwanted exchanges between sibling cells?