The Nutrient-Responsive Transcription Factor TFE3 Promotes Autophagy, Lysosomal Biogenesis, and Clearance of Cellular Debris

Abstract

The discovery of a gene network regulating lysosomal biogenesis and its transcriptional regulator TFEB revealed that cells monitor lysosomal function and respond to degradation requirements and environmental cues. Here, we report the identification of transcription factor E3 (TFE3) as another regulator of lysosomal homeostasis that induced expression of genes encoding proteins involved in autophagy and lysosomal biogenesis in ARPE-19 cells in response to starvation and lysosomal stress. We found that in nutrient-replete cells, TFE3 was recruited to lysosomes through interaction with active Rag GTPases and exhibited mTORC1-dependent phosphorylation. Phosphorylated TFE3 was retained in the cytosol through its interaction with the cytosolic chaperone 14-3-3. Following starvation, TFE3 rapidly translocated to the nucleus and bound to the CLEAR elements present in the promoter region of many lysosomal genes, thereby inducing lysosomal biogenesis. Depletion of endogenous TFE3 entirely abolished the response of ARPE-19 cells to starvation, suggesting that TFE3 plays a critical role in nutrient sensing and regulation of energy metabolism. Furthermore, overexpression of TFE3 triggered lysosomal exocytosis and resulted in efficient cellular clearance in a cellular model of a lysosomal storage disorder, Pompe disease, thus identifying TFE3 as a potential therapeutic target for the treatment of lysosomal disorders.

The MITF family of transcription factors: Role in endolysosomal biogenesis, Wnt signaling, and oncogenesis

“…When active, mTOR phosphorylates TFE3 causing its cytoplasmic retention. In conditions of nutritional deprivation, mTORC is inhibited and unphosphorylated TFE3 can enter the nucleus and activate the transcription of genes containing CLEAR elements in their promoters [37]. TFE3 has also been recently described to play a role in the maintenance of pluripotency [19].…”

“…In addition, the CLEAR element also contains a 5 flanking T known to be crucial for MITF binding [49]. A further layer of mystery is added by the fact that in RPE cells MITF-A, which can be regulated by nutrient starvation, activates autophagy but not lysosomal genes [37].…”

“…Thus, MITF-M is a constitutively nuclear transcription factor. MITF-A overexpressed in the human retinal pigment epithelium cell line ARPE-19 effectively activates the expression of many autophagy genes in this cell type [37].…”

MiT/TFE transcription factors are activated during mitophagy downstream of Parkin and Atg5

“…Rag GTPases play a central regulatory role for MiT/TFE transcription factors during starvation (Settembre et al, 2012;Martina and Puertollano, 2013;Martina et al, 2014b). To examine their contribution to mitophagy-induced TFEB activation, we expressed a dominant-negative (RagB GDP /RagD GTP ) or constitutively active (RagB GTP /RagD GDP ; Sancak et al, 2008) heterodimer in WT and mCherry-Parkin HeLa cells, respectively.…”

Lysosome enlargement during inhibition of the lipid kinase PIKfyve proceeds through lysosome coalescence

“…In addition, nutrient depletion, protein aggregation, and phagocytosis activate a family of transcription factors that can enhance expression of lysosome genes and adjust lysosome activity (Gray et al, 2016;Pastore et al, 2016;Sardiello et al, 2009;Tsunemi et al, 2012;Medina et al, 2011;Settembre et al, 2012;Roczniak-Ferguson et al, 2012). This is best understood for the related transcription factors, TFEB and TFE3, which are recruited to the surface of lysosomes and subject to phosphorylation by various kinases including mTORC1 to modulate their nucleo-cytoplasmic transport (Li et al, 2016b;Martina et al, 2012;Peña-Llopis et al, 2011;Martina et al, 2014Martina et al, , 2016Roczniak-Ferguson et al, 2012).…”