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The process of autophagic membrane expansion is regulated by a number of different Atg proteins that includes ubiquitinlike (Ubl) proteins, which participate in the two conjugation reactions. Both systems include proteins displaying three different enzymatic activities: ubiquitin-activating enzyme (E1), ubiquitin-conjugating enzyme (E2) and ubiquitin-protein ligase (E3). The first Ubl system essential for autophagy and membrane expansion is responsible for generating an Atg12- Atg5 protein conjugate. A second Ubl system involves the processing and subsequent conjugation of Atg8 (MAP1LC3 or simply LC3) to phosphatidyl-ethanolamine (PE) by sequential action of three Atg proteins: Atg4, Atg7 and Atg3. LC3 is proteolytically processed by the cysteine protease Atg4 (ATG4D or Autophagin-4), forming an intermediate, cytosolically localized LC3-I. A subpopulation of LC3-I is subsequently converted to a smaller form (form II). Form II, with a revealed C-terminal glycine, is considered to be the phosphatidylethanolamine (PE)-conjugated form associates tight to the membrane and promotes formation of the autophagosomes. (ribbon structure and cleavage is shown below)

Fluorescent image of U251 cells stained with ATG4D (C-term) antibody. U251 cells were treated with Chloroquine (50 µM,16h), then fixed with 4% PFA (20 min), permeabilized with Triton X-100 (0.2%, 30 min). Cells were then incubated with AP1811c ATG4D (C-term) primary antibody (1:100, 2 h at room temperature). For secondary antibody, Alexa Fluor® 488 conjugated donkey anti-rabbit antibody (green) was used (1:1000, 1h). Nuclei were counterstained with Hoechst 33342 (blue) (10 µg/ml, 5 min). ATG4D immunoreactivity is localized to autophagic vacuoles in the cytoplasm of U251 cells.

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ATG4 ()