Lysosomal microautophagic pathway links proteostasis to protein aggregation disease

Constitutive lysosomal degradation of cytosolic proteins is fundamental to proteostasis, but how these substrates are delivered into the lysosomal lumen remains incompletely understood. In mammals, the contribution of microautophagy to basal lysosomal protein degradation and the molecular machinery that mediates this process remain poorly defined. Here we identify a mammalian microautophagic pathway that is mediated by the lysosomal membrane protein SIDT2 and directly delivers cytosolic proteins, including disease-associated aggregation-prone proteins, into the lysosomal lumen for degradation. This pathway functions independently of macroautophagy and chaperone-mediated autophagy. Reconstitution and imaging analyses showed that SIDT2 mediates direct lysosomal uptake and subsequent degradation of cytosolic proteins and increases the prevalence and size of intraluminal vesicles, with the resulting vesicles exhibiting a topology consistent with inward sequestration of cytosol. A conserved catalytic serine residue was required for SIDT2 ATPase activity in vitro and was also essential for these increases in prevalence and size of intraluminal vesicles and for protein degradation. Loss of SIDT2 impaired lysosomal substrate uptake without altering luminal acidification or proteolytic activity. We further identified a dominant-negative SIDT2 mutation in familial neuromyopathy with rimmed vacuoles. Both Sidt2-deficient mice and knock-in mice carrying the patient mutation recapitulated key pathological features, including accumulation of aggregation-prone proteins and rimmed vacuole-like lesions. These findings establish SIDT2-dependent microautophagy as a pathway for basal lysosomal protein degradation and show that its failure can underlie human protein aggregation disease.