Autophagy and Development
Topics
LC3/Gabarap functions during selective autophagy
The family of Atg8/LC3 “ubiquitin-like” proteins appears to have key roles for mediating the selectivity of autophagy. Among multiple roles, Atg8/LC3 are involved in the formation of the autophagosomes and the recognition of the cargoes to be degraded.
With only one LC3 and one Gabarap homolog, C. elegans is a good paradigm to understand their specific functions. We have shown that they are essential for multiple physiological processes during development, stress and aging and have a synergistic role in several aspects of development. We demonstrated that LGG-1 is essential for the formation of autophagosomes and acts upstream of LGG-2 which interacts directly with the HOPS complex and favors fusion with lysosome, a cellular acidic compartment.
Quinet G, Génin P, Belgareh-Touzé N, et al. Analysis of ATG8 Family Members Using LC3-Interacting Regions (LIR)-Based Molecular Traps. Methods Mol Biol. 2023;2602:191-204. doi:10.1007/978-1-0716-2859-1_14
Quinet G, Génin P, Ozturk O, et al. Exploring selective autophagy events in multiple biologic models using LC3-interacting regions (LIR)-based molecular traps. Sci Rep. 2022;12(1):7652. Published 2022 May 10. doi:10.1038/s41598-022-11417-z
Leboutet, Largeau C, Prigent M, Quinet G, Rodriguez MS, Cuif MH, Culetto E, Lefebvre C, Legouis R. LGG-1/GABARAP lipidation is dispensable for autophagy and development in C. elegans. bioRxiv 2021.10.05.462725; doi: https://doi.org/10.1101/2021.10.05.462725
Leboutet R, Chen Y, Legouis R*, Culetto E*. Mitophagy during development and stress in C. elegans. Mech Ageing Dev. 2020 May 23;189:111266.111266. Review
Jenzer C, Simionato E, LARGEAU C, Scarcelli V, Lefebvre C, Legouis R. Autophagy mediates phosphatidylserine exposure and phagosome degradation during apoptosis through specific functions of GABARAP/LGG-1 and LC3/LGG-2. Autophagy. 2019 Feb;15(2):228-241.
Chen Y, Scarcelli V, Legouis R. Approaches for Studying Autophagy in Caenorhabditis elegans. Cells. 2017 Aug 30;6(3). Review
Jenzer C, Legouis R. Multiple functions of autophagy during development. Med Sci (Paris). 2017 Mar;33(3):238-245. Review
Yi Z, Manil-Ségalen M, Sago L, Glatigny A, Redeker V, Legouis R*, Mucchielli-Giorgi MH*. SAFER, an Analysis Method of Quantitative Proteomic Data, Reveals New Interactors of the C. elegans Autophagic Protein LGG-1. J Proteome Res. 2016 May 6;15(5):1515-23.
Zhang H, Chang JT, Guo B, Hansen M, Jia K, Kovács AL, Kumsta C, Lapierre LR, Legouis R, Lin L, Lu Q, Meléndez A, O’Rourke EJ, Sato K, Sato M, Wang X, Wu F. Guidelines for monitoring autophagy in Caenorhabditis elegans. Autophagy. 2015;11(1):9-27.
Jenzer C, Simionato E, Legouis R. Tools and methods to analyze autophagy in C. elegans. Methods. 2015 Mar;75:162-71.
Manil-Ségalen M, LEFEBVRE C, Jenzer C, Trichet M, Boulogne C, Satiat-Jeunemaitre B, Legouis R. The C. elegans LC3 acts downstream of GABARAP to degrade autophagosomes by interacting with the HOPS subunit VPS39. Dev Cell. 2014 Jan 13;28(1):43-55.
Al Rawi S, Louvet-Vallée S, Djeddi A, Sachse M, Culetto E, Hajjar C, Boyd L, Legouis R.*, Galy V*. Postfertilization autophagy of sperm organelles prevents paternal mitochondrial DNA transmission. Science. 2011 Nov 25;334(6059):1144-7
Role of Drp-1 during heat-stress induced Autophagy
We have developed a new paradigm for studying the adaptation of C. elegans larvae to an acute heat-stress (aHS) that induces a strong developmental defect but no lethality or sterility. We describe how C. elegans copes with aHS, which induces the fragmentation of mitochondria. A DRP-1-dependent autophagy process takes place as part of the worm adaptive mechanism to heat-stress. DRP-1 participates to the coordination between mitochondria fission and autophagosome biogenesis.
Leboutet R, Legouis R. Autophagy facilitates mitochondrial network rebuilding after heat stress in the nematode C. elegans. Med Sci (Paris). 2022;38(6-7):517-519. doi:10.1051/medsci/2022074
Chen Y, Culetto E, Legouis R. The strange case of Drp1 in autophagy: Jekyll and Hyde?. Bioessays. 2022;44(4):e2100271. doi:10.1002/bies.202100271
Chen Y, Leboutet R, Largeau C, Zentout S, Lefebvre C, Delahodde A, Culetto E, Legouis R. Autophagy facilitates mitochondrial rebuilding after acute heat stress via a DRP-1-dependent process. J Cell Biol. 2021 Apr 5;220(4).
Roles of RabGAP (RabGTPase Activating Protein) and N-BAR (Bin-Amphyphysin-Rvs167) proteins in adaptation to nutrients starvation in the yeast S. cerevisiae
Once detected the depletion of one or more nutrients, yeasts stop their cell cycle in G1 (START checkpoint) and rapidly adapt their metabolism and intracellular traffic. At a molecular level, how yeast cells detect nutrients depletion and then how deficiency signals cause cell cycle arrest is known; but the mechanisms which relay these signals to the membrane traffic actors are less understood.
Among adaptations to the deficiency, we focus specifically on autophagy as well as lipid droplets metabolism, and we study specifically the roles of two types of proteins : – RabGAP proteins, negative regulators of the Rab GTPases (Fig.A), and – N-BAR proteins, able to bend and tubulate membranes (Fig. B).
We have previously shown that two RabGAP proteins, Gyp5 and Gyl1, are involved in the control of exocytosis, specifically at the bud tip during the very beginning of bud growth (Chesneau, 2004; 2008). One of their roles is to recruit the N-BAR protein Rvs167 for exocytosis (Prigent, 2011). Depletion of Gyp5, Gyl1 or Rvs167 leads to a transient acumulation of exocytosis vesicles (Fig. C).
We have shown also that yeast N-BAR domain proteins can form different forms of multimers according to the cellular organelle (FigD; Prigent, 2020).
Our recent data show that during nutrients depletion, Gyp5, Gyl1 and Rvs167 redistribute in the cell, interact with new partners and play roles in autophagy, lipid droplets dynamics and cell cycle control.
Prigent M., Chaillot J., Tisserand A., Boy-Marcotte E., Cuif M.H.. Three members of the yeast N-BAR proteins family form heterogeneous lattices in vivo and interact differentially with two RabGAP proteins. Sci. Rep., 2020, vol. 10 1698.
Prigent M., Boy-Marcotte E., Chesneau L., Dupré-Crochet S., Gibson K., Tisserand H., Verbavatz J.M., Cuif M.H. The RabGAP proteins Gyp5p and Gyl1p recruit the BAR domain protein Rvs167p for polarized exocytosis. Traffic, 2011, vol.12, 1084-1097.
Chesneau L., Prigent M., Boy-Marcotte E., Daraspe J., Fortier G., Jacquet M., Verbavatz J.M., Cuif M.H. Interdependence of the Ypt/RabGAP Gyp5p and Gyl1p for recruitment to the sites of polarized growth. Traffic, 2008, vol.8, 608-622.
Chesneau L., Dupré S., Burdina A., Roger J., Lepanse S., Jacquet M., Cuif M.H. Gyp5p and Gyl1p are involved in the control of polarized exocytosis in budding yeast. J. Cell Science, 2004, vol. 117, 4757-4767.
Interaction between endocytosis and autophagy
We have analyzed the role of the ESCRT machinery and the functional links between endosomal maturation and autophagy. We reported the first evidence of amphisomes in C. elegans but showed that autophagosomes preferentially directly fuse with lysosomes. We also discovered a novel function of ESCRT-II components in the maintenance of the sarcoplasmic reticulum (SR) integrity in muscles. The characterization of ESCRT-II mutants revealed a fragmentation of the SR network, associated with a calcium dynamics alteration, providing evidence that ESCRT-II proteins are involved in SR shaping.
Lefebvre C, Legouis R*, Culetto E*. ESCRT and autophagies: Endosomal functions and beyond. Semin Cell Dev Biol. 2018 Feb;74:21-28. *Last Co-authors. Review
Largeau C, Culetto E, Legouis R. Subcellular Localization of ESCRT-II in the Nematode C. elegans by Correlative Light Electron Microscopy. Methods Mol Biol. 2019;1998:49-61.
Lefebvre C, Largeau C, Michelet X, Fourrage C, Maniere X, Matic I, Legouis R*, Culetto E. The ESCRT-II proteins are involved in shaping the sarcoplasmic reticulum in C. elegans. J Cell Sci. 2016 Apr 1;129(7):1490-9.
Manil-Ségalen M, Culetto E, Legouis R*, Lefebvre C*. Interactions between endosomal maturation and autophagy: analysis of ESCRT machinery during Caenorhabditis elegans development. Methods Enzymol. 2014;534:93-118. *Last Co-authors
Djeddi A, Michelet X, Culetto E, Alberti A, Barois N, Legouis R. Induction of autophagy in ESCRT mutants is an adaptive response for cell survival in C. elegans. J Cell Sci. 2012 Feb 1;125(Pt 3):685-94.
A dual role for autophagy during the phagocytosis of apoptotic cells
Phagocytosis and autophagy are involved in lysosome-mediated clearance of extracellular and intracellular components, respectively. Recent studies have identified the recruitment of the autophagic protein LC3 during phagocytosis of apoptotic corpses in the so-called LC3-associated phagocytosis (LAP). We discovered that both LGG-1 and LGG-2 are involved in the correct elimination of apoptotic corpses and are enriched in apoptotic corpses and phagocytic cells, respectively. LGG-1 is involved in the exposure of the “eat-me signal” phosphatidylserine at the surface of the apoptotic cell, whereas LGG-2 is involved in mediating the maturation/degradation of the phagosome.
Jenzer C, Manil-Ségalen M, Lefebvre C, Largeau C, Glatigny A, Legouis R. Human GABARAP can restore autophagosome biogenesis in a C. elegans lgg-1 mutant. Autophagy. 2014 Oct 1;10:1868-72.
Largeau C, Legouis R. Correlative Light and Electron Microscopy to Analyze LC3 Proteins in Caenorhabditis elegans Embryo. Methods Mol Biol. 2019;1880:281-293.