The catabolic process known as autophagy is essential for the maintenance of cellular health and the removal of cytotoxins, such as aberrant macromolecules, damaged organelles, and invasive bacteria. The hallmark of autophagy is de novo formation of the double-membrane vesicle called autophagosome. The process begins with assembling the precursor membrane phagophore adjacent to the endoplasmic reticulum (ER), followed by its expansion into a cup-like shape around a non-selective portion of the cytoplasm or a selected cytotoxin. During the expansion, the edges of the phagophore remain associated with the ER and at the last moment, the edges merge, resulting in the closure of the cup, thereby producing a complete autophagosome. The contribution to cellular homeostasis by autophagy hinges on the fact that the phagophore can engulf degradation substrates. For the phagophore to achieve this remarkable task, it must expand. We and others have made progress toward the goal of understanding the molecular mechanism of phagophore expansion by determining the function of ATG2, the largest protein in the group of autophagy-related proteins. We have worked on human ATG2A and demonstrated that this protein is a rod-shaped membrane tether that can transfer lipids between membranes. Our current working model is that ATG2 transports lipids from the ER to the phagophore by tethering them. The transported lipids would then serve as the building blocks the phagophore built around the substrates. This new proposal aims to build on this model and gain further mechanistic insights into this enigmatic process.
In Aim 1, we will extend our study of ATG2 to determine its structure. The goal is to explain how ATG2 transports lipids between membranes.
In Aim 2, we will focus on ATG9, the integral membrane protein of autophagy that has been known as an ATG2 interactor. Through structural and biochemical characterizations, we aim to elucidate the function of this protein and gain new insights into phagophore expansion.
In Aim 3, we will characterize the interaction between ATG2 and ATG9. The goal is to determine how these two proteins interact with each other at the structural level and explore the significance of the interaction for ATG2-mediated lipid transfer and phagophore expansion. Results from these studies will vertically advance our understanding of autophagosome biogenesis at the molecular level.

Public Health Relevance

Molecular mechanisms of autophagy are highly related to public health because autophagy plays crucial roles in the maintenance of cellular health and the control of damage. Defects in autophagy are associated with human diseases, such as cancer, neurodegeneration, infection, and inflammation. The proposed research will provide information that could allow rational intervention of autophagy for the development of new therapeutic strategies.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Membrane Biology and Protein Processing Study Section (MBPP)
Program Officer
Maas, Stefan
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Scripps Research Institute
La Jolla
United States
Zip Code
Chowdhury, Saikat; Otomo, Chinatsu; Leitner, Alexander et al. (2018) Insights into autophagosome biogenesis from structural and biochemical analyses of the ATG2A-WIPI4 complex. Proc Natl Acad Sci U S A 115:E9792-E9801
Ohashi, Kazuto; Otomo, Takanori (2015) Identification and characterization of the linear region of ATG3 that interacts with ATG7 in higher eukaryotes. Biochem Biophys Res Commun 463:447-52
Metlagel, Zoltan; Otomo, Chinatsu; Ohashi, Kazuto et al. (2014) Structural insights into E2-E3 interaction for LC3 lipidation. Autophagy 10:522-3
Otomo, Chinatsu; Metlagel, Zoltan; Takaesu, Giichi et al. (2013) Structure of the human ATG12~ATG5 conjugate required for LC3 lipidation in autophagy. Nat Struct Mol Biol 20:59-66
Metlagel, Zoltan; Otomo, Chinatsu; Takaesu, Giichi et al. (2013) Structural basis of ATG3 recognition by the autophagic ubiquitin-like protein ATG12. Proc Natl Acad Sci U S A 110:18844-9