Covalent conjugation of ubiquitin is a widespread post-translational modification. It has long been thought that targets of ubiquitination are limited to proteins. We recently discovered that ubiquitin is conjugated to phospholipids in endosomal and lysosomal membranes (Sakamaki et al., Mol Cell 2022). Similar to lysine ubiquitination, ubiquitin forms an amide bond with the head group of phosphatidylethanolamine (PE) via the canonical ubiquitin-conjugation enzymes. A recent series of studies has shown that non-proteinaceous substrates such as bacterial glycolipids, carbohydrates, and nucleotides are also ubiquitinated via an ester linkage, highlighting that the chemical diversity of ubiquitination substrates is broader than previously appreciated (Sakamaki and Mizushima, Trends Cell Biol 2023). However, it remains unknown whether membrane lipids other than PE are ubiquitinated.
Here, we show that lipid ubiquitination is not limited to PE, and that membrane lipids are ubiquitinated upon lysosomal damage. This process is mediated by a lysosomal transmembrane ubiquitin ligase. Depletion of this E3 ligase inhibits lipid and protein ubiquitination at lysosomes and impairs recruitment of the autophagy machinery, thereby suppressing autophagic clearance of damaged lysosomes. Our findings suggest that ubiquitination may be a widespread modification of membrane lipids and provide new insights into the chemistry and function of this well-established post-translational modification.