Macroautophagy, named autophagy, is a basic process that operates under physiological and pathological conditions and represents a third digestive cellular system, which is functionally connected with lysosomes. Autophagy is typically enhanced during starvation and after functional overload or cellular injury. It results in remodeling of the cytoplasm and removal of excess organelles. Although long regarded as a nonspecific process, autophagy can be selective, involving autophagic adaptor proteins. Autophagy is not only an important cellular degradation mechanism, but also plays active roles in cancer, immune defense, and apoptosis.

Autophagy results in the segregation and digestion of part of the cytoplasm, which involves the sequential formation of the isolation membrane, autophagosomes, and autolysosomes. The highly coordinated process and various machinery proteins encoded by a family of autophagy related genes (ATG) are well characterized. LC3 (Atg8 in yeast) is a useful marker for the immunocytochemical detection of autophagosomes. Initially, the double-membraned, cup-shaped isolation membrane is formed. As shown in panels A, B and C, the isolation membrane (arrowheads) may by narrow or shallow and surrounds part of the cytoplasm. The origin of the isolation membrane remains a matter of debate, but there probably is not a single source. In the maturation model, the isolation membrane is derived from plain rough endoplasmic reticulum (RER), although transitional elements of the RER and endoplasmic reticulum – mitochondria junctions may be involved as well. Isolation membranes originate from omega-shaped subdomains of the RER called omegasomes. From three-dimensional tomograms, RER subdomains have been shown to surround the isolation membrane and to be continuous with each other. Panels D and E show the intimate relation between RER and an isolation membrane (IM), of which a part is sandwiched between two RER cisterna (panel D). Panel E is representative of isolation membrane elongation, which progressively engulfs part of the cytoplasm. The expansion and finally closure of the isolation membrane by the sealing of its edges results in the formation of a unique double-membrane-limited vesicle, the autophagosome. Such a double-membrane-limited autophagosome, which contains cytoplasm, is shown in panel F (arrowheads point to cross-sectioned parts of the double membrane). The formation of the autophagosomes is a fast process and it seems that the Golgi apparatus, the plasma membrane, and endosomes contribute to the expansion process. Autophagosomes have no digestive capacity. Only following fusion with lysosomes (cf. Fig. 75) do they obtain both lysosomal membrane proteins and lysosomal enzymes, and they are then termed autolysosomes. Autolysosomes initially are double-membraned, but their inner limiting membrane is gradually digested by lysosomal enzymes (AL 1 in panel G), which results in a single-membraned autolysosome (AL 2 in panel G). Initially, autolysosomes contain well-recognizable cytoplasm, but later, as a result of lysosomal digestion, unstructured electron-dense material becomes prevalent (AL 2 in panel G), making it difficult to distinguish them from typical secondary lysosomes. Fusion between autophagosomes and endosomes may occur, resulting in the formation of amphisomes. Amphisomes contain not only cellular but also endocytosed foreign material.