Structure, lipid scrambling activity and role in autophagosome formation of ATG9A
Open accessAbstract
De novo formation of the double-membrane compartment autophagosome is seeded by small vesicles carrying membrane protein autophagy-related 9 (ATG9), the function of which remains unknown. Here we find that ATG9A scrambles phospholipids of membranes in vitro. Cryo-EM structures of human ATG9A reveal a trimer with a solvated central pore, which is connected laterally to the cytosol through the cavity within each protomer. Similarities to ABC exporters suggest that ATG9A could be a transporter that uses the central pore to function. Moreover, molecular dynamics simulation suggests that the central pore opens laterally to accommodate lipid headgroups, thereby enabling lipids to flip. Mutations in the pore reduce scrambling activity and yield markedly smaller autophagosomes, indicating that lipid scrambling by ATG9A is essential for membrane expansion. We propose ATG9A acts as a membrane-embedded funnel to facilitate lipid flipping and to redistribute lipids added to the outer leaflet of ATG9 vesicles, thereby enabling growth into autophagosomes.
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ATG9A knockout in HeLa cells and mouse embryonic fibroblasts resulted in fewer but larger LC3 puncta that colocalize with ubiquitin and p62.
“ATG9A knockout in HeLa cells and mouse embryonic fibroblasts resulted in fewer but larger LC3 puncta that colocalize with ubiquitin and p62 [50, 55].”
From miRNA family miR-29 inhibits PINK1-PRKN signaling via ATG9A (2026) · cites this paper as [50]
The Results section (‘Mutations in the central pore reduce autophagosome size,’ Fig. 4c) reports large GFP-LC3 puncta in ATG9A-knockout HeLa cells and mouse embryonic fibroblasts, describing them as likely p62–ubiquitin–LC3 condensates. It does not report that the puncta were fewer or demonstrate colocalization with p62 and ubiquitin; the latter is presented as a likely interpretation. (LLM, conf=0.86)
Experimental — accuracy not yet measuredATG9A forms a homotrimer with a wide, solvated central pore and a lateral cavity.
“ATG9A forms a homotrimer with a wide, solvated central pore and a lateral cavity [50].”
From miRNA family miR-29 inhibits PINK1-PRKN signaling via ATG9A (2026) · cites this paper as [50]
ATG9A acts as a lipid scramblase facilitating membrane expansion.
“ATG9A was more recently shown to act as a lipid scramblase facilitating membrane expansion [50, 51].”
From miRNA family miR-29 inhibits PINK1-PRKN signaling via ATG9A (2026) · cites this paper as [50]
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Autophagy in health and disease: From molecular mechanisms to therapeutic target
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ATG9 vesicles comprise the seed membrane of mammalian autophagosomes
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The Groovy TMEM16 Family: Molecular Mechanisms of Lipid Scrambling and Ion Conduction
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Toward Understanding the Molecular Role of SNX27/Retromer in Human Health and Disease
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Lipid Dynamics at Membrane Contact Sites
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- Authors
- Maeda, S., Yamamoto, H., Kinch, L. N., Garza, C. M., Takahashi, S., Otomo, C., Grishin, N. V., Forli, S., Mizushima, N., & Otomo, T.
- Affiliations
- Scripps Research Institute (US)
- The University of Tokyo (JP)
- Howard Hughes Medical Institute (US)
- Tokyo Medical and Dental University (JP)
- Corresponding author
- Otomo, Takanori
- ORCID
- Venue
- Nature Structural & Molecular Biology
- Published
- 2020-10-26
- Volume
- 27
- Issue
- 12
- Pages
- 1194-1201
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- PMC
- PMC7718406
- OpenAlex
- W3093507769
- Cited by
- 305
- References
- 88
- Citations by year
- 2026: 35 · 2025: 48 · 2024: 50 · 2023: 59 · 2022: 60 · 2021: 52 · 2020: 1
- FWCI
- 31.02
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health (1s10od021634-01)
- National Institute of General Medical Sciences (R35GM127390, R01GM069832, R01GM092740)
- Topics
- Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Lipid Membrane Structure and Behavior
- Keywords
- ATG9A, autophagosome formation, lipid scrambling, membrane protein structure, ABC transporters, central pore, membrane expansion, cryo-EM structure, molecular dynamics simulation
- MeSH terms
- Autophagosomes, Autophagy-Related Proteins, Protein Conformation, alpha-Helical, Protein Conformation, beta-Strand, Red Fluorescent Protein, Animals, Binding Sites, Biological Transport, Cell Line, Fibroblasts, HeLa Cells, Humans, Lipid Bilayers, Luminescent Proteins, Membrane Proteins, Phospholipids, Protein Binding, Proteolipids, Recombinant Fusion Proteins, Gene Expression, Cryoelectron Microscopy, Vesicular Transport Proteins, Green Fluorescent Proteins, Mice, Protein Interaction Domains and Motifs, Protein Multimerization, Molecular Dynamics Simulation, HEK293 Cells
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