Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum

Abstract

Autophagy is the engulfment of cytosol and organelles by double-membrane vesicles termed autophagosomes. Autophagosome formation is known to require phosphatidylinositol 3-phosphate (PI(3)P) and occurs near the endoplasmic reticulum (ER), but the exact mechanisms are unknown. We show that double FYVE domain–containing protein 1, a PI(3)P-binding protein with unusual localization on ER and Golgi membranes, translocates in response to amino acid starvation to a punctate compartment partially colocalized with autophagosomal proteins. Translocation is dependent on Vps34 and beclin function. Other PI(3)P-binding probes targeted to the ER show the same starvation-induced translocation that is dependent on PI(3)P formation and recognition. Live imaging experiments show that this punctate compartment forms near Vps34-containing vesicles, is in dynamic equilibrium with the ER, and provides a membrane platform for accumulation of autophagosomal proteins, expansion of autophagosomal membranes, and emergence of fully formed autophagosomes. This PI(3)P-enriched compartment may be involved in autophagosome biogenesis. Its dynamic relationship with the ER is consistent with the idea that the ER may provide important components for autophagosome formation.

Autophagy at the crossroads of catabolism and anabolism

“…Although evidence supports the idea that nucleation of the isolation membrane occurs at a distinct site emanating from the endoplasmic reticulum (ER), termed the omegasome 17 , other sources of membrane contribute to autophagosome formation, including ER-Golgi intermediate compartments, ERmitochondri a junctions, mitochondria, endosomes and the plasma membrane [17][18][19][20][21][22] . Taken together, these studies highlight the complexities of autophagy initiation in mammals.…”

Autophagy and regulation of cilia function and assembly

“…Recent studies have shown that phagophore elongation takes place at the endoplasmic reticulum in a structure called the omegasome characterized by the presence of the phosphatidylinositol 3-phosphate binding protein DFCP1. 58,61,62 In addition, other membrane sources also contribute to the biogenesis of the autophagosome, including those of the endosomes and the Golgi apparatus, the contact site between the endoplasmic reticulum and mitochondria, endoplasmic reticulum transition elements, and the plasma membrane (for recent reviews, Lamb et al 58 ; Shibutani and Yoshimori 61 ; and Puri et al 63 ). Each functional module from the initiation of the autophagosome formation to the elongation/closure step involves different ATG proteins.…”

SNX 18 regulates ATG 9A trafficking from recycling endosomes by recruiting Dynamin‐2

“…The biogenesis of the phagophore is not fully understood, but it is generally believed to originate from specific omega‐shaped domains in the ER called omegasomes 13, 14, 15, found in close proximity to ER–mitochondria contact sites 16, 17. The phagophore expands by receiving membrane input through vesicle transport or membrane contact sites from different membrane sources, including ER‐exit sites (ERES) and the ER–Golgi intermediate compartment (ERGIC) 18, 19, 20, the Golgi apparatus 21, 22, mitochondria 23, 24 and the plasma membrane 21, 22, 25.…”