The Lipid Kinase PIKfyve Controls Lysosome Gene Transcription

Lysosomes are degradative organelles responsible for molecular degradation, eliminating pathogens, digesting cellular debris and salvaging energy during autophagy. Upscaling of lysosome activity has been observed in autophagy where the transcription factor EB (TFEB), a master regulator of lysosome biogenesis, is stimulated to enhance lysosomal gene expression. The most well characterized regulator of TFEB is the mammalian target of rapamycin complex one (mTORC1). Under nutrient sufficiency, mTORC1 is active and phosphorylates TFEB, resulting in its cytosolic retention. During starvation, mTORC1 is inactivated, TFEB becomes dephosphorylated and it enters the nucleus, upregulating lysosomal gene transcription. Recently, mTORC1 was shown to be recruited by the lysosomal lipid phosphatidylinositol 3,5‐bisphosphate [PtdIns(3,5) P 2 ]. Therefore, we postulated that PtdIns(3,5) P 2 may help repress TFEB function by maintaining an active mTORC1. To do this, we used apilimod to inhibit PIKfyve, the enzyme that synthesizes PtdIns(3,5) P 2 . Depletion of PtdIns(3,5) P 2 caused TFEB‐GFP to translocate from the cytosol to the nucleus within 40 minutes and enhanced expression of various lysosomal genes, including cathepsin D. Additionally, apilimod treatment appeared to cause TFEB dephosphorylation similar to mTORC1 inhibition, judged by the faster TFEB gel mobility. However, and strikingly, mTORC1 remained active in apilimod‐treated cells as reported by phosphorylation of two downstream effectors, S6K and ULK. Thus, PtdIns(3,5) P 2 appears to control TFEB‐mediated lysosome gene expression, independently of mTORC1 activity. Currently, we are testing whether PtdIns(3,5) P 2 binds to and presents TFEB to mTORC1 on lysosomes. This work was funded by Canadian Research Chairs.