After disrupting the E3 ligase PTR1 in Xanthophyllomyces dendrorhous CBS 6938 (Xd-ptr1), we observed a quadrupling of astaxanthin production, accompanied by increased levels of ergosterol and stellasterol. This disruption also resulted in a reduction of total lipids, a shift in fatty acid composition toward polyunsaturated species, and a decrease in triglyceride levels. To elucidate the mechanism by which PTR1 regulates carotenoid, sterol, and lipid metabolism, we conducted a ubiquitinomic analyse.