Cargo levels control endosomal PI(3)P homeostasis through direct feedback between SNX17 and MTM1

The sorting of internalised cell surface proteins through the endosomal network is crucial for cellular function. Phosphatidylinositol-3-phosphate (PI(3)P) is a critical lipid identity cue for organising endosomal sorting but there is limited understanding of how PI(3)P homeostasis is regulated. Here, we show that free PI(3)P is segregated into distinct endosomal subdomains and that depletion of the disease-relevant lipid phosphatase Myotubularin1 (MTM1) leads to its accumulation and mis-segregation, impairing cargo recycling. Complementary imaging and reconstitution approaches show that MTM1 recruitment and activity are controlled by binding to the endosomal cargo adaptor SNX17. This interaction is mediated by sorting motifs in the C-Terminal tail of MTM1 and is in competition with the same sorting motifs in cargo that bind to SNX17. This competitive binding mechanistically links cargo sorting to PI(3)P depletion and because SNX17 is itself a PI(3)P effector, establishes negative feedback regulating local PI(3)P levels. Importantly, we demonstrate that this feedback couples endosomal cargo levels to PI(3)P depletion. We propose that cargo levels thereby modulate endosomal phosphoinositide identity through cargo sensitive feedback between SNX17 and MTM1.