CDC48A and the ubiquitin-associated domain protein PUX10 regulate the ubiquitin-dependent degradation of peroxisomal proteins in Arabidopsis

Homeostasis of peroxisomes and their constituents maintains peroxisome function during plant growth, development, and environmental responses. Protein degradation maintains peroxisome homeostasis by eliminating misfolded or damaged proteins and precisely regulating the abundance of specific proteins. However, the mechanism by which a subset of peroxisomal proteins is transported from the peroxisome to the Proteasome for degradation remains unclear. Here, we show that CELL DIVISION CONTROL PROTEIN 48 HOMOLOG A (CDC48A) and its cofactor, the plant UBX domain-containing (PUX) protein PUX10, play a critical role in the degradation of certain peroxisomal proteins in Arabidopsis thaliana. The inducible expression of a CDC48A dominant-negative (CDC48A-DN) mutant or a deficiency of PUX10 (pux10 mutant) caused the accumulation of ubiquitinated proteins and defective degradation of peroxisomal proteins, including the peroxin (PEX) PEX5, a receptor responsible for cytosolic cargo delivery to the peroxisomal matrix, and the peroxisomal matrix protein CATALASE 3 (CAT3). We further reveal that PUX10 is an integral peroxisomal membrane protein that interacts with PEX5 and CAT3 via its ubiquitin-associated domain. Functional analysis demonstrates that CDC48A is required for peroxisomal metabolism and abundance, whereas loss of PUX10 only affects peroxisome abundance. Overall, these findings establish that the CDC48A-PUX10 complex is a key component in the ubiquitin-dependent peroxisome-associated degradation machinery, which governs the turnover of a subset of peroxisomal proteins.