The complex relationship between TFEB transcription factor phosphorylation and subcellular localization

Abstract

The MiT-TFE family of basic helix-loop-helix leucine-zipper transcription factors includes four members: TFEB, TFE3, TFEC, and MITF Originally described as oncogenes, these factors play a major role as regulators of lysosome biogenesis, cellular energy homeostasis, and autophagy. An important mechanism by which these transcription factors are regulated involves their shuttling between the surface of lysosomes, the cytoplasm, and the nucleus. Such dynamic changes in subcellular localization occur in response to nutrient fluctuations and various forms of cell stress and are mediated by changes in the phosphorylation of multiple conserved amino acids. Major kinases responsible for MiT-TFE protein phosphorylation include mTOR, ERK, GSK3, and AKT In addition, calcineurin de-phosphorylates MiT-TFE proteins in response to lysosomal calcium release. Thus, through changes in the phosphorylation state of MiT-TFE proteins, lysosome function is coordinated with the cellular metabolic state and cellular demands. This review summarizes the evidence supporting MiT-TFE regulation by phosphorylation at multiple key sites. Elucidation of such regulatory mechanisms is of fundamental importance to understand how these transcription factors contribute to both health and disease.

Keywords: TFEB; autophagy; lysosome; mTOR; nucleo‐cytoplasmic shuttling.

Figure 1. TFEB subcellular localization is both nutrient‐ and phosphorylation‐dependent

(A) HeLa cells cultured in either normal or starved medium were stained for Flag‐TFEB (green; Settembre et al, 2011). (B) 3D reconstruction of Airyscan super‐resolution imaging of HeLa cells stained for TFEB (green) and LAMP1 (red; Image courtesy of Jlenia Monfregola and A.B.). (C) TFEB phosphorylation of specific serine residues controls its subcellular localization. Flag immunostaining (red) of HeLa cells transfected with WT TFEB and treated with Torin 1 and of HeLa cells transfected with serine‐to‐alanine mutated versions of 3xFlag‐TFEB and grown in normal medium (Settembre et al, 2012).

Figure 2. Relevant TFEB phosphorylation sites and their regulatory role

Figure 3. Sequence conservation of TFEB, TFE3, MITF and TFEC phosphorylation sites

Multiple sequence alignment highlights the conservation of critical domains and phosphorylation sites between human TFEB (Uniprot P19484), TFE3 (Uniprot 19532), MITF (O75030, “D” splice variant shown here), and TFEC (Uniprot O14948) proteins. Red asterisks highlight phosphorylation sites that inhibit nuclear translocation of TFEB, while those shown in green have been found to promote TFEB nuclear localization.