TORC1 Determines Fab1 Lipid Kinase Function at Signaling Endosomes and Vacuoles

Zilei Chen,Pedro Carpio Malia,Riko Hatakeyama,Raffaele Nicastro,Zehan Hu,Marie-Pierre Péli-Gulli,Jieqiong Gao,Taki Nishimura,Elja Eskes,Christopher J Stefan,Joris Winderickx,Jörn Dengjel,Claudio De Virgilio,Christian Ungermann

doi:10.1016/j.cub.2020.10.026

Abstract

Organelles of the endomembrane system maintain their identity and integrity during growth or stress conditions by homeostatic mechanisms that regulate membrane flux and biogenesis. At lysosomes and endosomes, the Fab1 lipid kinase complex and the nutrient-regulated target of rapamycin complex 1 (TORC1) control the integrity of the endolysosomal homeostasis and cellular metabolism. Both complexes are functionally connected as Fab1-dependent generation of PI(3,5)P2 supports TORC1 activity. Here, we identify Fab1 as a target of TORC1 on signaling endosomes, which are distinct from multivesicular bodies, and provide mechanistic insight into their crosstalk. Accordingly, TORC1 can phosphorylate Fab1 proximal to its PI3P-interacting FYVE domain, which causes Fab1 to shift to signaling endosomes, where it generates PI(3,5)P2. This, in turn, regulates (1) vacuole morphology, (2) recruitment of TORC1 and the TORC1-regulatory Rag GTPase-containing EGO complex to signaling endosomes, and (3) TORC1 activity. Thus, our study unravels a regulatory feedback loop between TORC1 and the Fab1 complex that controls signaling at endolysosomes.

Highlights

Eukaryotic organelles differ in the lipid and protein composition of their surfaces and maintain a unique identity
The Fab[1] lipid kinase complex and the nutrient-regulated target of rapamycin complex 1 (TORC1) control the integrity of the endolysosomal homeostasis and cellular metabolism. Both complexes are functionally connected as Fab1-dependent generation of PI(3,5)P2 supports TORC1 activity
We identify Fab[1] as a target of TORC1 on signaling endosomes, which are distinct from multivesicular bodies, and provide mechanistic insight into their crosstalk

Summary

Introduction

Eukaryotic organelles differ in the lipid and protein composition of their surfaces and maintain a unique identity. Proteins are transported by vesicles that are generated at the donor compartment and fuse with an acceptor organelle. Despite this active transport between organelles, each organelle maintains its identity. Apart from the fusion and fission machineries involved in each transport step, organelle-specific phosphatidylinositol phosphates (PIPs) are important markers that contribute to the identity of distinct organelles.[1] PIPs are phosphorylated derivatives of phosphatidylinositol (PI), which can be modified at three positions by specific lipid kinases and phosphatases to generate seven distinct isoforms.[2] Organelle-specific PIPs are proposed to recruit specific proteins to their surface, which have decisive roles in cell signaling, membrane trafficking, and lipid metabolism. PIP production and turnover is tightly controlled to maintain organelle identity.[2]

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