The presence of multiple homologues of the same yeast Atg protein endows an additional layer of complexity on the autophagy pathway in higher eukaryotes. The physiological function of the individual genes, however, remains largely unknown. Here we investigated the role of the two Caenorhabditis elegans homologues of the cysteine protease Atg4 in the pathway responsible for degradation of protein aggregates. Loss of
atg-4.1 activity causes defective degradation of a variety of protein aggregates, whereas
atg-4.2 mutants remove these substrates normally. LGG-1 precursors accumulate in
atg-4.1 mutants, but not
atg-4.2 mutants. LGG-1 puncta, formation of which depends on lipidation of LGG-1, are present in
atg-4.1 and
atg-4.2 single mutants, but are completely absent in
atg-4.1;
atg-4.2 double mutants. In vitro enzymatic analysis revealed that ATG-4.1 processes LGG-1 precursors about 100-fold more efficiently than ATG-4.2. Expression of a mutant form LGG-1, which mimics the processed precursor, rescues the defective autophagic degradation of protein aggregates in
atg-4.1 mutants and, to a lesser extent, in
atg-4.1;
atg-4.2 double mutants. Our study reveals that ATG-4.1 and ATG-4.2 are functionally redundant yet display differential LGG-1 processing and deconjugating activity in the aggrephagy pathway in C. elegans.