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Autophagy

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Goup leader : Amélie Bernard, researcher CNRS

contact :
Phone : 00 33 5 57 12 25 74
E-mail : amelie.bernard@u-bordeaux.fr

Amélie Bernard obtained her PhD in plant biology in 2011. She worked as a post-doctoral research fellow in the Klionsky Lab at the Life Sciences Institute, University of Michigan, Ann Arbor, USA (2012-2016). In 2016, she obtained a full position at the CNRS (CR1) and joined the LBM. 











Group members : Amélie Bernard (CR), Jérôme Joubes (PU), Frédéric Domergue (CR), Stéphanie Pascal (AI), Rodrigo Enrique-Gomez (PhD).































Functional characterization of lipids associated with autophagy in plants
Life of every organism is dependent on its adaptation to environmental stresses. Over the last years, global warming has started to cause aridity as well as reduction and impoverishment of agricultural land. In that context, understanding the molecular mechanisms of plant adaptation to environmental constraints is one of the major challenges that have to be addressed to keep feeding humanity. Macroautophagy, hereafter referred to as autophagy, is one of these mechanisms. Highly conserved among eukaryotes, from yeast to plants and mammals, autophagy organizes the delivery of portions of the cell to the lytic vacuole for degradation and subsequent recycling of resulting molecules. Kept at a basal level when environmental conditions are optimal, autophagy is highly induced upon multiple stresses during which it plays critical roles. In particular, upon nutrient starvation, molecules resulting form autophagic degradation, are reuse by the cell to maintain a basal metabolism and promote adaptation and survival. Defects in autophagy are also associated with a hypersensitivity to saline stress, drought, oxidative stresses or necrotrophic pathogens.

Autophagy is based on the biogenesis of a double membrane defining the space and material to be engulfed. In this context, it seems obvious that lipids play key roles in this process : the quantity and molecular structure of lipids would presumably regulate the number, the morphology and the size of APs as well as the recruitment and functions of ATG proteins. A specific lipid composition is also likely necessary to maintain special features. Similar to a unique protein composition, we propose that a unique lipid composition regulates the ultra-specialization of the autophagic membranes. Nevertheless, while tremendous research focused on the characterization of ATG proteins, the identity, the composition and the function of lipids composing autophagic membranes remain almost completely unknown in all organisms to date.

Thus, in our model, in response to environmental constraints, plant adaptation is dependent on the remodeling and mobilization of lipids towards the PAS for autophagy. What are these lipids ? How are they mobilized towards the autophagy pathway ? How are these mobilization processes regulated ? Which steps of the autophagy pathway are affected by the different lipid species and to which extent does the lipid composition of autophagic membranes influence plant response to stresses ? Our work is addressing these questions using Arabidopsis as a model organism.


(A) Schematic of the autophagy pathway in plant cells. (B) Hypothetical representation of lipid- and protein-driven curvature within the phagophore. A specific lipid composition and distribution could shape the phagophore and especially drive the high curvature of the membranes at the rim. BAR-domain-containing proteins (represented in red) and amphipatic proteins (represented in brown) could create, force or stabilize membrane deformation. Adapted from Gomez et al., 2018.


Key publications :


- Gomez ER, Joubès J, Valentin N, Batoko H, Satiat-Jeunemaître B, Bernard A. Lipids in membrane dynamics during autophagy in plants. J Exp Bot 2018 ; 69:1287-1299.
- Eapen VV , Waterman DP , Bernard A , Schiffman N , Sayas E , Kamber R, Lemos B, Memisoglu G, Ang J, Mazella A, Chuartzman SG, Loewith R, Schuldiner M, Denic V , Klionsky DJ, Haber, JE. A novel pathway of targeted autophagy is induced by DNA damage in budding yeast. PNAS 2017 ; 114, E1158-E1167.
- Bernard A*, Jin M*, Xu Z, Klionsky DJ. A large-scale analysis of autophagy related gene expression identifies new regulators of autophagy. Autophagy 2015 ; 2114-2122.
- Hu G*, McQuiston T*, Bernard A*, Park YD, Qiu J, Vural A, Zhang N, Waterman SR, Blewett NH, Myers TG, Maraia RJ, Kehrl JH, Uzel G, Klionsky DJ, Williamson PR. A conserved mechanism of TOR-dependent RCK-mediated mRNA degradation regulates autophagy. Nature Cell Biology 2015 ; 17:930-942
- Bernard A, Jin M, González-Rodriguez P, Füllgrabe J, Delorme-Axford E, Backues SK, Joseph B, Klionsky DJ. Rph1/KDM4 mediates nutrient-limitation signaling that leads to the transcriptional induction of autophagy. Current Biology 2015 ; 25:546-555.