phagophore

Phagophore, also known as the isolation membrane, is the initial membrane structure in macroautophagy that engulfs cytoplasmic material during autophagosome formation. It is the precursor membrane that expands and closes to sequester cargo, ultimately forming the autophagosome.

Biogenesis: In nutrient-rich conditions, the ULK1 kinase complex is suppressed by mTOR, but under autophagy-inducing conditions it becomes active and recruits a class III PI3K complex (VPS34, Beclin-1/ATG6, VPS15, ATG14). This complex generates PI3P at the assembly site, attracting downstream effectors such as WIPI proteins and ATG proteins that contribute membranes. The phagophore can originate from multiple donor membranes, with the endoplasmic reticulum (via omegasomes) playing a major role in mammalian cells; other sources include mitochondria-associated membranes, Golgi, and the plasma membrane. The growth involves the ATG conjugation systems, including the LC3/ATG8 conjugation (involving ATG7, ATG3, and the ATG5-ATG12-ATG16L1 complex) that attach LC3 to lipids on the expanding membrane, aiding expansion and cargo recruitment.

Cargo recruitment and closure: Selective autophagy uses cargo receptors (such as p62/SQSTM1, NDP52) that bind ubiquitinated cargo and LC3, guiding sequestration. As the phagophore expands, it eventually closes around the cargo to form a complete autophagosome, a double-membrane vesicle.

Maturation and function: The autophagosome then fuses with lysosomes to form autolysosomes, where cargo is degraded and recycled. Phagophore formation is central to macroautophagy and is essential for cellular homeostasis, stress response, and quality control. Defects in autophagy are linked to neurodegeneration, infections, and cancer. Experimental studies commonly monitor markers such as LC3-II, p62, and PI3P-binding proteins to assess phagophore dynamics.