Potential role of omegasomes in autophagosome biogenesis. Our hypothesis is that during amino acid starvation, Vps34-containing vesicles interact with the ER and form PI(3)P on a membrane connected to the ER (step 1, green). This membrane domain associates with autophagosomal proteins (red) to create a mixed membrane domain that continues to expand but maintains its spatial separation with PI(3)P on the outside, and autophagosomal membranes inside (steps 1 and 2). Note that the connection of this membrane to the ER is not fully shown, thus the question marks at the junction. Once omegasomes reach their maximum size, the autophagosomal membranes bud inwards (steps 2 and 3), giving rise to a fully formed double-membrane autophagosome (step 4). The PI(3)P outer membrane in the intermediate of step 3 may aid the fusion reaction. Inward budding would allow the autophagosome to ingest cytoplasmic material and/or organelles indicated as autophagosome cargo. At the bottom of steps 2, 3, and 4, we have drawn cut-outs of the relevant structures to indicate the geometry of the bilayer.