PEX11 mediates intralumenal vesicle formation in peroxisomes

Peroxisomes are eukaryotic organelles that compartmentalize crucial metabolic reactions. Peroxisome size, shape, and number are governed by the peroxisomal membrane protein PEX11. PEX11 is encoded in multiple isoforms across diverse eukaryotes, including five in Arabidopsis, but the functional distinctions among these isoforms are largely uncharacterized. Here we report null pex11 mutants in plants expressing reporters that mark peroxisome membranes and lumen to illuminate distinct functions for PEX11 isoforms. We find that PEX11C/D/E promotes the formation of peroxisomal intralumenal vesicles, limits peroxisome size throughout development, and is required for efficient fatty acid β-oxidation in germinating seedlings. Unlike the pervasive roles of PEX11C/D/E, we find that PEX11A/B promotes the formation of peroxisomal intralumenal vesicles and limits peroxisome enlargement specifically during seedling lipid mobilization. Complete loss of the PEX11 family confers seedling lethality, even though peroxisomes remain abundant. Our findings reveal that Arabidopsis PEX11 isoforms shape internal peroxisome membranes and have distinct functions in cellular physiology that are essential for plant development. These results extend the roles of PEX11 beyond its canonical function in peroxisome division.