Structure and Function of TM6SF1 Reveal Role in mTORC1 Signaling

The Transmembrane 6 Superfamily (TM6SF) comprises two members: TM6SF1, a ubiquitously expressed lysosomal membrane protein of unknown function, and TM6SF2, an endoplasmic reticulum protein required for bulk lipidation of Apolipoprotein B-containing lipoproteins. Here we used cryo-electron microscopy (cryo-EM) to determine the structure of human TM6SF1 at 2.9- [A] resolution. TM6SF1 forms a polytopic homodimer, with each protomer comprising ten transmembrane helices (TMs). TMs 1-6 form a pocket that accommodates a cholesterol molecule. Cell-based assays revealed that loss of TM6SF1 perturbs mTORC1 signaling, resulting in reduced phosphorylation of S6 kinase 1 and 4E-BP1 and constitutive activation of Transcription Factor EB (TFEB) and that cholesterol is required for these effects. Biochemical analyses support the model that TM6SF1 directly engages LAMTOR1, a component of Ragulator complex, in a cholesterol-dependent manner. Together, these findings identify TM6SF1 as a lysosomal cholesterol binding protein involved in regulating mTORC1 signaling. Significance StatementWe determine the cryo-EM structure of TM6SF1 and show that it is a lysosomal membrane protein that associates with LAMTOR1, a component of Ragulator complex, in a cholesterol-dependent manner. Loss of TM6SF1 impairs mTORC1 signaling and promotes nuclear accumulation of TFEB, suggesting a role for TM6SF1 in lysosome-dependent nutrient sensing and signaling. Together, our findings suggest that TM6SF1 is involved in the regulation of mTORC1 activity and provide insight into the functional diversification of the TM6SF protein family.