Molecule of the Month: Aminopeptidase 1 and Autophagy

Cells are constantly changing, building new molecules when needed and breaking down others when they are finished with them. The proteasome and exosome systems recycle biomolecules one at a time, but the cell also has a system for bulk recycling, termed autophagy. The name means “self-eating,” and that’s just what the cell does. It packages up the waste and delivers it to its internal digestive system, lysosomes, where everything is broken down by a soup of digestive enzymes.

Autophagy plays many essential roles in cells. When cells are starved, they use autophagy to engulf and digest portions of their own cytoplasm, sustaining themselves by internal cannibalism. Autophagy can also be more selective, surrounding and discarding entire mitochondria or other organelles when they are damaged or no longer needed. Selective autophagy is also used in a biosynthetic mode, to deliver digestive enzymes from the cytoplasm to the lysosome. Researchers are interested in autophagy because of many connections with disease, for instance, faults in autophagy contribute to degenerative diseases whereas cancer cells upregulate autophagy to promote their own survival.

The process of selective autophagy has been widely studied in yeast cells, where a large vacuole at the center of the cell plays the role of the lysosome. The enzyme aminopeptidase 1 is delivered to the yeast vacuole in a package surrounded by two membranes, termed a phagophore. With the assistance of dozens of autophagy proteins, this double membrane is constructed closely around an aggregate of the enzyme, as shown in the illustration. The outer membrane of the phagophore then fuses with the vacuole membrane, and lipases in the vacuole break down the inner membrane, releasing the enzymes.

Aminopeptidase 1 is built as an inactive precursor, with a small “propeptide” extension at one end, as seen here from PDB entry 5jh9. This propeptide interacts with neighboring molecules to form the aggregate, and it also interacts with specific autophagy receptor proteins, ensuring that the phagophore is built around the aggregate and doesn’t also capture much of the surrounding cytoplasm. Once the enzyme is inside the vacuole, the propeptide is clipped off, activating the enzyme, as seen here from PDB entry 4r8f.