Lipids Regulate Export of Lysosomal Enzymes from the Endoplasmic Reticulum

Abstract Lysosomal enzymes are synthesized in the Endoplasmic Reticulum (ER) and transported to lysosomes to execute their functions. Deficiencies in lysosomal enzymes or components of the lysosomal transport machinery result in lysosomal storage disorders. While mannose-6-phosphate mediated lysosomal enzymes sorting in the Golgi has been extensively characterized, the mechanisms governing their export from the ER remain elusive. Here, we show that de novo lipogenesis, a metabolic pathway responsible for fatty acid synthesis, regulates lysosomal enzyme transport. Inhibition of de novo lipogenesis leads to the retention of lysosomal enzymes within the ER. Mechanistically, fatty acid derived from de novo lipogenesis is used for Arf1 myristoylation. Myristoylated Arf1 promotes retrograde vesicle trafficking from the Golgi to the ER, thereby maintaining the homeostatic bidirectional flux required for efficient ER export of lysosomal enzymes. Our findings uncover a critical functional link between lipid metabolism and lysosomal enzyme trafficking. Significance Proper intracellular protein trafficking is essential for cellular homeostasis, yet how cellular metabolism regulates this process remains poorly understood. In this study, we show that inhibition of fatty acid synthesis disrupts lysosomal enzyme trafficking by causing these enzymes to accumulate in the endoplasmic reticulum instead of reaching lysosomes. Fatty acids are required for protein lipidation that supports vesicle trafficking and export of lysosomal enzymes from the endoplasmic reticulum. In addition, interactome screening identified other regulators of lysosomal enzyme transport. These findings reveal a direct link between fatty acid metabolism and lysosomal protein trafficking, expanding our understanding of how metabolic pathways coordinate intracellular transport processes.