Disease-causing missense mutations within the N-terminal transmembrane domain of GlcNAc-1-phosphotransferase impair endoplasmic reticulum translocation or Golgi retention

LYSET facilitates integration of both the N- and C-terminal transmembrane helices/cytoplasmic domains of GlcNAc-1-phosphotransferase

LYSET is a recently identified Golgi transmembrane (TM) protein, and inactivating mutations in the LYSET gene phenocopy mucolipidosis II (MLII), the lysosomal storage disease caused by loss of function of GlcNAc-1-phosphotransferase αβ (GNPTαβ), which tags lysosomal hydrolases with the mannose 6-phosphate (M6P) tag for delivery to lysosomes. It is conceivable that LYSET facilitates integration of both hydrophilic TM helices (TMHs) of GNPTαβ and retain the latter in the Golgi, although this has only been directly demonstrated for the N-terminal TMH wherein a membrane-stabilized GNPTαβ variant restores lysosomal function in cells lacking LYSET. Here we show that the C-terminal TMH of GNPTαβ also contributes to LYSET-mediated Golgi retention. In addition, disease-causing patient mutations in the N-terminal TMH of GNPTαβ, which increase the hydrophilicity of the helix, are partly rescued by overexpression of LYSET. Finally, we show that a membrane-stabilized GNPTαβ variant, despite overcoming the requirement for LYSET, still requires COPI-mediated recycling via the N-terminal cytosolic domain (CD) for GNPTαβ retention and function in the Golgi.

Structure of a truncated human GlcNAc-1-phosphotransferase variant reveals the basis for its hyperactivity

Mutations that cause loss of function of GlcNAc-1-phosphotransferase (PTase) lead to the lysosomal storage disorder mucolipidosis II. PTase is the key enzyme of the mannose 6-phosphate (M6P) targeting system that is responsible for tagging lysosomal hydrolases with the M6P moiety for their delivery to the lysosome. We had previously generated a truncated hyperactive form of PTase termed S1S3 which was shown to notably increase the phosphorylation level of secreted lysosomal enzymes and enhance their uptake by cells. Here, we report the 3.4 Å cryo-EM structure of soluble S1S3 lacking both transmembrane domains and cytosolic tails. The structure reveals a high degree of conservation of the catalytic core to full-length PTase. In this dimeric structure, the EF-hand of one protomer is observed interacting with the conserved region four of the other. In addition, we present a high-quality EM 3D map of the UDP-GlcNAc bound form of the full-length soluble protein showing the key molecular interactions between the nucleotide sugar donor and side chain amino acids of the protein. Finally, although the domain organization of S1S3 is very similar to that of the Drosophila melanogaster (fruit fly) PTase homolog, we establish that the latter does not act on lysosomal hydrolases.

The human disease gene LYSET is essential for lysosomal enzyme transport and viral infection

Lysosomes are key degradative compartments of the cell. Transport to lysosomes relies on GlcNAc-1-phosphotransferase-mediated tagging of soluble enzymes with mannose 6-phosphate (M6P). GlcNAc-1-phosphotransferase deficiency leads to the severe lysosomal storage disorder mucolipidosis II (MLII). Several viruses require lysosomal cathepsins to cleave structural proteins and thus depend on functional GlcNAc-1-phosphotransferase. Here, we used genome-scale CRISPR screens to identify Lysosomal Enzyme Trafficking factor (LYSET) as essential for infection by cathepsin-dependent viruses including SARS-CoV-2. LYSET deficiency resulted in global loss of M6P tagging and mislocalization of GlcNAc-1-phosphotransferase from the Golgi complex to lysosomes. Lyset knockout mice exhibited MLII-like phenotypes and human pathogenic LYSET alleles failed to restore lysosomal sorting defects. Thus, LYSET is required for correct functioning of the M6P trafficking machinery, and mutations in LYSET can explain the phenotype of the associated disorder.