Poster Presentation 11th International Symposium on Autophagy 2025

Proteomic Landscape of LC3 and GABARAP Reveals Lipidation-Dependent Differential Roles in Neurons (#226)

Haneul Choi 1 , Sang-Won Park2 2 , Pureum Jeon 1 , Akinori Yamasaki 3 , Ji Young Mun 4 , Yong-Woo Jun 2 , Seung-Hwan Lee 2 , Michael Lazarou 5 , Dohyun Han 6 , Nobuo N Noda 3 7 , Deok-Jin Jang 2 , Jin-A Lee 1
  1. Hannam university, Yuseong-gu, DAEJEON, South Korea
  2. Department of Ecological Science, College of Ecology and Environment, Kyungpook National University, Sangju, Korea
  3. Institute of Microbial Chemistry (BIKAKEN), Tokyo, Japan
  4. Korea Brain Research Institute, Daegu, Korea
  5. Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia
  6. Department of Transdiciplinary Medicine, Seoul National University Hospital, Seoul, Korea
  7. Hokkaido University, Sapporo, Japan

Neuronal autophagy is essential for maintaining protein and organelle turnover, thereby safeguarding neuronal health. Mammalian ATG8 proteins consisting of LC3 and GABARAP subfamilies, orchestrate selective autophagy by recognizing LIR-containing cargo and adaptor proteins. Despite their shared lipidation mechanism, the neuron-specific roles of LC3 and GABARAP and how lipidation alters their functional networks are still not well understood. Neuronal autophagy plays a critical role in maintaining the turnover of proteins and organelles, thereby protecting neuronal health. Mammalian ATG8 (mATG8) proteins consisting of LC3 and GABARAP subfamilies, orchestrate selective autophagy by recognizing LC3-interacting region (LIR)-containing cargo and adaptor proteins. Despite their shared lipidation mechanism, the neuron-specific roles of LC3 and GABARAP and how lipidation alters their functional networks are still not well understood. To address this gap, we utilized TurboID tagged LC3B and GABARAPL1 to profile their overall interactomes in post-mitotic neurons. In addition, we employed previously validated LIR-based probes that selectively bind to membrane-anchored(lipidated) LC3 and GABARAP. By fusing these probes with TurboID, we specifically captured the interactomes of the lipidated forms. This dual approach enabled us to distinguish protein interactions determined by subfamily identity from those uniquely dependent on lipidation. Our proteomic analysis revealed that the LC3B interactome is enriched in cytoskeletal and trafficking regulators, highlighting its predominant role in autophagosome dynamics. In contrast, GABARAPL1 interactome was more strongly associated with neuronal signaling pathways, including post synapse organization, modulation of chemical synaptic transmission. Interestingly, lipidation profoundly reshaped the interactomes of both LC3 and GABARAP, uncovering functional modules. Our tool provieds a unique proteomic landscape of LC3 and GABARAP, revealing isoform- and lipidation-specific interactomes that suggest previously unrecognized functions in neuronal physiology. In addition, this approach can be further applied to disease models to uncover novel autophagy regulators and signaling pathways, facilitating the discovery of therapeutic targets in neurodegenerative disease.