endocytosis, autophagy, and phagocytosis through the concerted action of more than 50 acid hydrolases ( 1 ). To maintain their function, lysosomes require a continuous replenishment of newly synthesized components transported from the endoplasmic reticulum (ER) via the Golgi apparatus to the endosomal/lysosomal compartment. The effi cient transport of soluble lysosomal enzymes to lysosomes requires mannose 6-phosphate (M6P) residues on their N -linked glycans, which serve as recognition markers for M6P-specifi c receptors (MPRs) ( 2 ). The formation of M6P residues is catalyzed by two enzymes, the N -acetylglucosamine-1-phosphotransferase (termed "GlcNAc-1-phosphotransferase") and the GlcNAc-1-phosphodiester ␣ -N -acetylglucosaminidase (termed "uncovering enzyme") localized in the cis -Golgi apparatus and trans -Golgi network, respectively ( 3 ).The GlcNAc-1-phosphotransferase is a heterohexameric complex of three subunits ( ␣ 2  2 ␥ 2 ), which are encoded by two genes ( 4-6 ). The ␣ -and  -subunits of the GlcNAc-1-phosphotransferase are synthesized in the ER as a single, highly N -glycosylated, 190 kDa, type III membrane protein ( 6 ). For the transport to the Golgi apparatus, combinatorial dileucine and dibasic sorting motifs in the N-and C-terminal cytosolic domains, respectively, are required ( 7 ). Upon arrival in the cis -Golgi compartment, the ␣ /  -subunit precursor is proteolytically cleaved by the site-1 protease (S1P) into mature ␣ -and  -subunits ( 8 ), which are prerequisite for the enzymatic activity of the GlcNAc-1-phosphotransferase complex ( 9 ).Abstract Site-1 protease (S1P) cleaves membrane-bound lipogenic sterol regulatory element-binding proteins (SREBPs) and the ␣ /  -subunit precursor protein of the N -acetylglucosamine-1-phosphotransferase forming mannose 6-phosphate (M6P) targeting markers on lysosomal enzymes. The translocation of SREBPs from the endoplasmic reticulum (ER) to the Golgi-resident S1P depends on the intracellular sterol content, but it is unknown whether the ER exit of the ␣ /  -subunit precursor is regulated. Here, we investigated the effect of cholesterol depletion (atorvastatin treatment) and elevation (LDL overload) on ER-Golgi transport, S1P-mediated cleavage of the ␣ /  -subunit precursor, and the subsequent targeting of lysosomal enzymes along the biosynthetic and endocytic pathway to lysosomes. The data showed that the proteolytic cleavage of the ␣ /  -subunit precursor into mature and enzymatically active subunits does not depend on the cholesterol content. In either treatment, lysosomal enzymes are normally decorated with M6P residues, allowing the proper sorting to lysosomes. In addition, we found that, in fi broblasts of mucolipidosis type II mice and Niemann-Pick type C patients characterized by aberrant cholesterol accumulation, the proteolytic cleavage of the ␣ /  -subunit precursor was not impaired. We conclude that S1P substrate-dependent regulatory mechanisms for lipid synthesis and biogenesis of lysosomes are different. T.B., and S.P.) and GR...