During autophagy, double-membrane autophagosomes sequester intracellular components and then fuse with lysosomes to form autolysosomes in which cargo is degraded. Under starvation conditions, the nutrient-responsive kinase, target of rapamycin (TOR), is inhibited, which results in an induction of autophagy. In this study, Yu et al. report a negative feedback mechanism by which lysosomes are reformed after the termination of autophagy. They demonstrate that upon prolonged starvation conditions, mTOR is reactivated, which attenuates autophagy and results in the formation of tubules and vesicles that extrude from autolysosomes. These mature into functional lysosomes, thereby restoring lysosome numbers in the cell. This feedback mechanism tightly couples nutritional status with the induction and termination of autophagy. When cells are starved, the enzyme TOR is inhibited, inducing autophagy. In this process, autophagosomes sequester intracellular components and then fuse with lysosomes, producing autolysosomes in which cargo is degraded to regenerate nutrients. Now, a mechanism is revealed by which lysosomes are re-formed. When starvation conditions are prolonged, mTOR is re-activated; this attenuates autophagy and results in tubules and vesicles extruding from the autolysosome and maturing into functional lysosomes. Autophagy is an evolutionarily conserved process by which cytoplasmic proteins and organelles are catabolized1,2. During starvation, the protein TOR (target of rapamycin), a nutrient-responsive kinase, is inhibited, and this induces autophagy. In autophagy, double-membrane autophagosomes envelop and sequester intracellular components and then fuse with lysosomes to form autolysosomes, which degrade their contents to regenerate nutrients. Current models of autophagy terminate with the degradation of the autophagosome cargo in autolysosomes3,4,5, but the regulation of autophagy in response to nutrients and the subsequent fate of the autolysosome are poorly understood. Here we show that mTOR signalling in rat kidney cells is inhibited during initiation of autophagy, but reactivated by prolonged starvation. Reactivation of mTOR is autophagy-dependent and requires the degradation of autolysosomal products. Increased mTOR activity attenuates autophagy and generates proto-lysosomal tubules and vesicles that extrude from autolysosomes and ultimately mature into functional lysosomes, thereby restoring the full complement of lysosomes in the cell—a process we identify in multiple animal species. Thus, an evolutionarily conserved cycle in autophagy governs nutrient sensing and lysosome homeostasis during starvation.

Leucine‐rich repeat kinase 2 (LRRK2) has been associated with Parkinson9s disease (PD) and other disorders. However, its normal physiological functions and pathogenic properties remain elusive. Here we show that LRRK2 regulates the anterograde ER–Golgi transport through anchoring Sec16A at the endoplasmic reticulum exit sites (ERES). LRRK2 interacted and co‐localized with Sec16A, a key protein in the formation of ERES. Lrrk2 depletion caused a dispersion of Sec16A from ERES and impaired ER export. In neurons, LRRK2 and Sec16A showed extensive co‐localization at the dendritic ERES (dERES) that locally regulate the transport of proteins to the dendritic spines. A loss of Lrrk2 affected the association of Sec16A with dERES and impaired the activity‐dependent targeting of glutamate receptors onto the cell/synapse surface. Furthermore, the PD‐related LRRK2 R1441C missense mutation in the GTPase domain interfered with the interaction of LRRK2 with Sec16A and also affected ER–Golgi transport, while LRRK2 kinase activity was not required for these functions. Therefore, our findings reveal a new physiological function of LRRK2 in ER–Golgi transport, suggesting ERES dysfunction may contribute to the pathogenesis of PD. Synopsis Parkinson9s disease (PD)‐associated LRRK2 functions by associating with Sec16A at ER exit sites, facilitating COPII‐mediated anterograde vesicle transport; a PD‐associated LRRK2 mutant lacks this function. LRRK2 interacts and co‐localizes with Sec16A at ER exit sites (ERES). LRRK2 regulates the attachment of Sec16A to ERES. LRRK2 regulates dendritic ERES and activity‐dependent cell surface targeting of glutamate receptors in neurons. Parkinson9s disease‐related R1441C mutation compromises LRRK29s regulatory function on Sec16A and ER export.

Long-range communication between intestinal symbiotic bacteria and extra-intestinal organs can occur through circulating bacterial signal molecules, through neural circuits, or through cytokines or hormones from host cells. Here we report that Nod1 ligands derived from intestinal bacteria act as signal molecules and directly modulate insulin trafficking in pancreatic beta cells. The cytosolic peptidoglycan receptor Nod1 and its downstream adapter Rip2 are required for insulin trafficking in beta cells in a cell-autonomous manner. Mechanistically, upon recognizing cognate ligands, Nod1 and Rip2 localize to insulin vesicles, recruiting Rab1a to direct insulin trafficking through the cytoplasm. Importantly, intestinal lysozyme liberates Nod1 ligands into the circulation, thus enabling long-range communication between intestinal microbes and islets. The intestine-islet crosstalk bridged by Nod1 ligands modulates host glucose tolerance. Our study defines a new type of inter-organ communication based on circulating bacterial signal molecules, which has broad implications for understanding the mutualistic relationship between microbes and host.