Global impacts of peroxisome and pexophagy dysfunction revealed through multi‐omics analyses of <i>lon2</i> and <i>atg2</i> mutants

Peroxisomes house diverse metabolic pathways that are essential for plant and animal survival, including enzymes that produce or inactivate toxic byproducts. Despite the importance of peroxisomes and their collaborations with other organelles, the mechanisms that trigger or prevent peroxisome turnover and the cellular impacts of impaired peroxisomes are incompletely understood. When Arabidopsis thaliana LON2, a peroxisomal protein with chaperone and protease capacity, is disrupted, metabolic dysfunction and protein instability in peroxisomes ensue. Paradoxically, preventing autophagy in lon2 mutants appears to normalize peroxisomal metabolism and stabilize peroxisomal proteins-hinting at a role for autophagy in causing the peroxisomal defects observed in lon2 seedlings. Using a combination of transcriptomics, proteomics, and in silico investigations, we compared wild type to lon2 and autophagy null mutants and double mutants. Through this analysis, we found that impeding autophagy via an atg2 null mutation alleviated several of the global defects observed when LON2 is absent. Moreover, we revealed processes influenced by LON2 that are independent of autophagy, including impacts on lipid droplet and chloroplast protein levels. Finally, we identified and classified potential LON2 substrates, which include proteins that might provide signal(s) for pexophagy.