Autophagy is an intracellular degradation mechanism in eukaryotes. The autophagosome, which encloses damaged or excess cellular material for degradation, is constructed from lipids supplied by the endoplasmic reticulum (ER), via the lipid transfer protein Atg2. Researchers have identified an activation mechanism that enables Atg2 localization to the ER, facilitating efficient lipid transfer. This activation mechanism was found to be conserved across fungi and mammals and may be a crucial part of autophagosome formation.
Autophagy is the process by which eukaryotic cells—plants, animals, fungi—remove damaged or superfluous cellular components. “Upon induction of autophagy, a cup-shaped lipid membrane called the isolation membrane emerges in the cytoplasm, expands into a spherical structure while engulfing a portion of the cytoplasm, and finally closes to form an autophagosome,” says Dr. Tetsuya Kotani, Specially Appointed Lecturer at the Cell Biology Center, Institute of Integrated Research, Institute of Science Tokyo (Science Tokyo), Japan.
The autophagy-related proteins (Atg in fungi, ATG in mammals) regulate autophagosome formation. Several Atg proteins combine to form a pre-autophagosomal structure (PAS), which expands into the isolation membrane mediated by Atg1, a protein kinase. The PAS uses lipids from the endoplasmic reticulum (ER) to eventually form the autophagosome. This lipid transfer is mediated by Atg2. However, the mechanism behind Atg2 identifying and docking to the ER membrane, and the regulation of its activity, is not well understood.
Dr. Kotani and Professor Hitoshi Nakatogawa of the Cell Biology Center, Science Tokyo, together with Specially Appointed Associate Professor Akiko Kuma of the Graduate School of Medicine, The University of Osaka, have discovered how Atg2 recognizes and binds to the ER. Their findings were made available online on July 29, 2026, and published in Volume 123, Issue 31 of the journal Proceedings of the National Academy of Sciences of the United States of America (PNAS) on August 4, 2026.
The research team first studied Atg2 in the yeast Saccharomyces cerevisiae . They found that cytosolic Atg2 did not bind to the ER. It was only after Atg2 localized to the PAS that it acquired the ability to bind to the ER. This showed that localization to the PAS activated Atg2 in some way. Further analyses showed that Atg1 phosphorylates a region of Atg2 called the FFAT or two phenylalanines in an acidic tract. Once phosphorylated, the Atg2 FFAT region could bind to the major sperm protein (MSP) domain of an ER-resident protein Scs2, anchoring the PAS to the ER to facilitate lipid transfer. This phosphorylation of Atg2 by Atg1 functions as a spatiotemporal switch that ensures that lipid transfer specifically occurs at sites of autophagosome formation. Scs2 belongs to a class of proteins called Vesicle-associated membrane protein-Associated Protein (VAP), a highly conserved class of intracellular proteins found in many eukaryotes.
But how important is the Atg2-Scs2 interaction in autophagosome formation? Mutation in the phospho-FFAT motif of Atg2 weakened its binding to Scs2. However, this mutation alone did not impair autophagic activity. Previous studies showed that the N-terminal region of Atg2 is involved in ER association in a Scs2-independent manner. While a partial deletion of the Atg2 N-terminal region caused only a partial reduction in autophagic activity, combining this deletion with the phospho-FFAT mutation resulted in an almost complete loss of autophagy. Overall, these findings suggest that the N-terminal of Atg2 along with its binding to Scs2 mediated by the phospho-FFAT region synergistically modulates the association of Atg2 with ER and subsequent lipid transfer.
The team also studied ATG2 in HEK293T cells, an immortalized human embryonic kidney cell line. They found that human ATG2A/B bind with Scs2 homologs MOSPD1/3 through a phospho-FFAT-like motif similar to the Atg2-Scs2 interaction in yeast. Evidently, this mechanism of Atg2-VAP interaction is conserved across fungi and animals, which means it may be a vital part of autophagosome formation across all eukaryotes.
Describing these findings, Kotani says, “This study revealed that two distinct mechanisms operate to establish the ER association of Atg2. The mechanism involving the Atg2 N-terminal region appears to establish a robust association of Atg2 with the ER membrane. Besides, the VAP-mediated mechanism could enhance ER specificity of membrane association.”
To conclude, further research into these two mechanisms and their activation will deepen our understanding of autophagosome formation.
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About Institute of Science Tokyo (Science Tokyo)
Institute of Science Tokyo (Science Tokyo) was established on October 1, 2024, following the merger between Tokyo Medical and Dental University (TMDU) and Tokyo Institute of Technology (Tokyo Tech), with the mission of “Advancing science and human wellbeing to create value for and with society.”
Proceedings of the National Academy of Sciences
Experimental study
Cells
Spatiotemporal control of Atg2 association with the ER during autophagosome formation
4-Aug-2026