Lysosomes are cellular organelles that house a host of lytic enzymes, serving numerous functions such as degradation of unneeded proteins and catabolism of endocytosed extracellular proteins to provide the cell with a supply of amino acid nutrients — a pathway that is particularly active during nutrient scarcity. During viral infections, lysosomes can be hijacked by viruses that utilize the resident proteases of the lysosome to cleave viral proteins into their mature forms, which are needed for a productive viral infection.

Writing in Science, two independent studies use genetic screens to identify a membrane protein that plays an essential role in trafficking of lysosomal proteases into the lysosome, and thereby influences the ability of the lysosome to perform its various functions. The two groups renamed this protein (originally called TMEM251) as lysosomal enzyme trafficking factor, or LYSET.

Pechincha et al. (Science; 2022) used pancreatic adenocarcinoma cells to identify genes that are required for the acquisition of amino-acid nutrients through catabolism of extracellular proteins in the lysosome, which commonly occurs in nutrient-deficient milieus — for example, in the microenvironments of tumors. To enforce this pathway, Pechincha et al. deprived the cells of essential amino acids and instead provided serum protein albumin as an amino-acid source. The authors then used a CRISPR–Cas9 screen to search for genes that are needed for the intact function of this lysosomal catabolic pathway. Their screen identified LYSET as an essential player in this pathway. Using fluorescently labelled albumin to trace its fate after its uptake into the cell, they found that LYSET is needed for lysosomal degradation of endocytosed albumin. They then investigated changes in cellular proteomic signatures following knockout of the LYSET gene. Although this did not significantly alter the general constituents of the proteome, they observed a marked mistrafficking of lysosomal enzymes to the cell surface. This correlated with a loss of the mannose-6-phosphate (M6P) post-translational modification on lysosomal enzymes — a mark that is needed for the efficient targeting of these enzymes for uptake into the lysosome where they perform their catabolic functions.

To understand how LYSET is needed for the deposition of the M6P mark on a molecular level, Pechincha et al. looked at its interaction with GlcNAc-1-phosphotransferase, the enzyme that deposits M6P on lysosomal enzymes. They found that LYSET co-localizes with GlcNAc-1-phosphotransferase at Golgi membranes, and helps stabilize to stabilize the compound by interacting with its otherwise exposed hydrophilic transmembrane domain.

In a parallel study, Richards, Jabs and Qiao et al. (Science; 2022) set out to investigate factors that support the infectivity of viruses that require the lysosomal enzyme cathepsin for their maturation, such as SARS-CoV-2. They performed a genome-scale CRISPR–Cas9 screen in human glioblastoma cells, which are known to die following productive viral infection, providing a simple readout for viral infection. Similar to the findings of Pechincha et al., the screen implicated LYSET in this lysosome-dependent process. LYSET knockout compromised the ability of viruses to achieve productive infection. More in-depth molecular investigation similarly delineated the functional interaction of LYSET with GlcNAc-1-phosphotransferase to support M6P deposition on cathepsin and other lysosomal enzymes, which in turn is needed for targeting of the enzymes to the lysosome. As such, the authors conclude that LYSET is essential for productive viral infection, through its ability to equip lysosomes with the enzymes needed for viral maturation.

A generalizable role for LYSET in lysosomal transport emerges from these two studies, with both studies corroborating its vital role in marking and trafficking lysosomal enzymes into the lysosomes, thereby supporting lysosome-dependent processes in the contexts of both health and disease.