The p97 ATPase and its adaptor UBXD8 maintain peroxisome pools by preventing pexophagy.

Peroxisomes perform key metabolic functions in eukaryotic cells. Loss of peroxisome function causes peroxisome biogenesis disorders and severe childhood diseases with disrupted lipid metabolism. One mechanism regulating peroxisome abundance is degradation via selective autophagy (pexophagy). However, the mechanisms regulating pexophagy remain poorly understood in mammalian cells. Here, we find that the evolutionarily conserved AAA-ATPase p97/VCP and its adaptor UBXD8/FAF2 are essential for maintaining peroxisome abundance. From quantitative proteomics studies, we show that loss of UBXD8 affects the abundance of many peroxisomal proteins and that the depletion of UBXD8 results in a loss of peroxisomes. Loss of p97-UBXD8 and inhibition of p97 catalytic activity increase peroxisomal turnover through autophagy and can be rescued by depleting key autophagy proteins and E3 ligases or overexpressing the deubiquitylase USP30. We find increased ubiquitylation of PMP70 and PEX5 in cells lacking UBXD8 or p97. Our findings identify a new role of the p97-UBXD8 in regulating peroxisome abundance by removing ubiquitylated peroxisome membrane proteins to prevent pexophagy.