Chaperone and protease functions of LON protease 2 modulate the peroxisomal transition and degradation with autophagy

Balancing repair and degradation is essential for maintaining organellar and cellular homeostasis. Peroxisomes are ubiquitous organelles in eukaryotic cells that play pivotal roles in cell survival. However, the quality control mechanism used to maintain peroxisomes is unclear. Here, we demonstrate that LON protease 2 (LON2), which is encoded by ABERRANT PEROXISOME MORPHOLOGY 10 (APEM10), is responsible for the functional transition of peroxisomes with autophagy. The Arabidopsis apem10 mutant displayed accelerated peroxisome degradation and a dramatically reduced number of peroxisomes. LON2 deficiency caused enhanced peroxisome degradation by autophagy, and peroxisomal proteins accumulated in the cytosol due to a decrease in the number of peroxisomes. We also show the proteolytic consequence of LON2 for the degradation of peroxisomal proteins, and we demonstrated that unnecessary proteins are eliminated by LON2- and autophagy-dependent degradation pathways during the functional transition of peroxisomes. LON2 plays dual roles as an ATP-dependent protease and a chaperone. We show that the chaperone domain of LON2 is essential for the suppression of autophagy, whereas its peptidase domain interferes with this chaperone function, indicating that intramolecular modulation between the proteolysis and chaperone functions of LON2 regulates degradation of peroxisomes by autophagy.