Lysosomes are the major cellular site for clearance of defective organelles and digestion of internalized material. Demand on lysosomal capacity varies greatly, but the mechanisms that adjust lysosomal function to maintain cellular homeostasis are unknown. In this study, we identify an interaction between mTOR and the TFEB transcription factor on the surface of lysosomes that allows mTOR to transduce signals arising from changes in lysosomal status to TFEB and thus control the ability of TFEB to enter the nucleus. This occurs via regulation of the serine 211 phosphorylation-dependent binding of 14-3-3 proteins to TFEB. These results identify TFEB as a novel target of mTOR that couples the transcriptional regulation of genes encoding proteins of autophagosomes and lysosomes to cellular need. We further present evidence that the closely related MITF and TFE3 transcription factors are regulated in a similar manner, thus broadening the range of physiological contexts under which such regulation may prove important.

The canonical function of the Golgi-associated retrograde protein (GARP) complex is the tethering of transport carriers. GARP belongs to the complexes associated with tethering containing helical rods (CATCHR) family and is a hetero-tetrameric complex consisting of the subunits Vps51, Vps52, Vps53 and Vps54. How the activity of GARP is regulated and if it possesses other functions besides tethering remains largely unknown. Here we identify the GARP subunit Vps53 as a novel regulatory target of the S. cerevisiae AMP kinase (AMPK) homolog Snf1. We find that Vps53 is both an in vivo and in vitro target of Snf1 and show that phosphorylation depends on the nature and quantity of the available carbon source. Phosphorylation of Vps53 does not affect the canonical trafficking pathway, but results in altered mitochondrial dynamics and the formation of a previously unknown contact site between the Golgi apparatus and mitochondria, termed GoMiCS. Our results provide an example of a subunit of a CATCHR complex with a constitutive function in membrane trafficking and an inducible role in organelle contact site formation. We anticipate our results to be the starting point for the characterization of this novel contact site.

The degradative and signaling functions of lysosomes are dependent on numerous peripherally associated proteins. Targeting of lysosomes to sites of need is controlled by adaptors that link lysosomes to both dynein and kinesin motors. SKIP is one such adaptor that promotes microtubule plus-end-directed movement through its interaction with Arl8 on the lysosome surface and kinesin-1. Sequence homology between SKIP and STK11IP (also known as LIP1) led us to investigate a potential role for STK11IP at lysosomes. After first establishing that STK11IP localizes to lysosomes, we identified TMEM192, an abundant lysosomal integral membrane protein, as the major binding partner of STK11IP and demonstrated that STK11IP depends on TMEM192 for both its lysosome localization as well as its stability. Depletion studies furthermore support a role for these proteins in the control of lysosome homeostasis. Collectively, these new results define a lysosome localized complex of TMEM192 and STK11IP that we have named LyTS (lights).