FLCN may act as a molecular switch

Chromosome translocations involving the transcription factor TFE3, leading to its overexpression, cause roughly 15% of renal cell carcinomas in patients under 45 years of age (Kuroda et al., 2012). TFE3 is constitutively activated in FLCN-null cells (Hong et al., 2010), indicating that FLCN may regulate TFE3. While investigating the role of TFE3 in lysosome homeostasis and autophagy, Martina et al. (2014) demonstrated that although FLCN does not directly interact with TFE3, it controls TFE3 via mTORC1 signalling.

Martina et al. (2014) show that under amino acid sufficiency, active GTP-bound Rag proteins recruit TFE3 to the lysosome, where it is phosphorylated at S311 by mTORC1 and remains in the cytoplasm in ARPE-19, HeLa and HepG2 cells. Under amino acid starvation, the Rag proteins and mTORC1 are no longer active, and unphosphorylated TFE3 translocates to the nucleus where it activates the transcription of target genes, including lysosome and autophagy genes. Thus, under starvation conditions, autophagy is initiated by TFE3.

The authors found that FLCN was required for correct phosphorylation of TFE3 by mTORC1, with FLCN knock down leading to aberrant autophagy in cells during nutrient sufficiency. It has previously been shown by two independent groups that the Rag proteins recruit FLCN to lysosomes during amino acid starvation, where it activates mTORC1 and dissociates from the lysosome once amino acid levels are restored. Martina et al. also observed this pattern of activity. Additionally, TFE3 overexpression led to increased mRNA levels of FLCN, FNIP1 and FNIP2, suggesting that TFE3 autoregulates its activity via FLCN. Taken together, FLCN seems to act as a molecular switch, making starved cells poised to quickly reactivate mTOR signalling and inhibit TFE3 induced autophagy as soon as nutrients become available.

This corresponds well with previous studies that have suggested that FLCN inhibits autophagy, which are summarised here. Additionally, a number of studies either directly or indirectly suggest that FLCN may act as a molecular switch to regulate cell homeostasis or differentiation in response to external stimuli.

In exactly the same way that FLCN regulates TFE3 localisation via mTORC1 in upon amino acid restimulation, FLCN also regulates TFEB – another transcription factor from the same family as TFE3 (Petit et al., 2013).  Furthermore, Betschinger et al. (2013) reported that the FLCN-FNIP1-FNIP2 complex controls exit from pluripotency by precluding TFE3 from the nucleus in response to differentiation signals.

Martina et al. show that elevated TFE3 activity led to increased exocytosis of lysosomes, and an increase in the acidity of growth medium. Under hypoxia, VHL conserves ATP by causing cells to acidify their environment and inhibiting rRNA synthesis. FLCN also inhibits rRNA synthesis and is known to be an effector protein of VHL under certain circumstances. It is therefore possible that under hypoxia, FLCN also acts to conserve cellular energy by inhibiting rRNA synthesis and activating acidosis by allowing TFE3 to increase lysosome exocytosis.

Finally, loss of FNIP1 leads to a block in B-cell differentiation in mice, while TFE3-null B-cells show impaired activation (Merrell et al., 1997), suggesting that this pathway might be responsible for correct B-cell maturation during development or following exposure to an antigen.

Precisely how FLCN is able to act as a molecular switch is currently unknown. However, the alternative splicing of FNIP1 is evolutionarily conserved and happens in response to differentiation signals during mesoderm differentiation, making this a viable and intriguing possibility.


  • Betschinger J, Nichols J, Dietmann S, Corrin PD, Paddison PJ, & Smith A (2013). Exit from pluripotency is gated by intracellular redistribution of the bHLH transcription factor Tfe3. Cell, 153 (2), 335-47 PMID: 23582324
  • Kuroda N, Mikami S, Pan CC, Cohen RJ, Hes O, Michal M, Nagashima Y, Tanaka Y, Inoue K, Shuin T, & Lee GH (2012). Review of renal carcinoma associated with Xp11.2 translocations/TFE3 gene fusions with focus on pathobiological aspect. Histology and histopathology, 27 (2), 133-40 PMID: 22207547
  • Martina JA, Diab HI, Lishu L, Jeong-A L, Patange S, Raben N, & Puertollano R (2014). The nutrient-responsive transcription factor TFE3 promotes autophagy, lysosomal biogenesis, and clearance of cellular debris. Science signaling, 7 (309) PMID: 24448649
  • Merrell K, Wells S, Henderson A, Gorman J, Alt F, Stall A, & Calame K (1997). The absence of the transcription activator TFE3 impairs activation of B cells in vivo. Molecular and cellular biology, 17 (6), 3335-44 PMID: 9154832
  • Petit CS, Roczniak-Ferguson A, & Ferguson SM (2013). Recruitment of folliculin to lysosomes supports the amino acid-dependent activation of Rag GTPases. The Journal of cell biology, 202 (7), 1107-22 PMID: 24081491

www.bhdsyndrome.org – the primary online resource for anyone interested in BHD Syndrome.

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