Mechanisms regulating TFEB activity
TFEB, together with MITF (melanogenesis associated transcription factor), TFE3 and TFEC constitute the MiT/TFE subfamily of transcription factors; it participates in cell metabolism and intracellular clearance by modulating the processes of lysosomal biogenesis, autophagy and lysosomal exocytosis. TFEB regulates biological processes by regulating the expression of downstream genes. The activity of TFEB is strictly controlled by post-translational modifications and protein-protein interactions.(13) Normally, TFEB is primarily located in cytoplasmic. Under the conditions of starvation, it is transported to the nucleus, binds to its target genes, promotes the transcription and expression of autophagy and lysosomal related proteins, which can improve the functions of autophagy and lysosome.(10) Recent studies have shown that TFEB and TFE3 not only respond to changes in nutritional levels, but also a variety of internal and external stress factors, including mitochondrial damage,(14) the accumulation of unfolded proteins in endoplasmic reticulum, (15) pathogens(16, 17) and physical exercise.(18) TFEB is mainly regulated post-translation via phosphorylation. Many factors involve in regulate TFEB through phosphorylation of specific amino acid residues. To date, at least six kinases, including mTOR, MAPK1,GSK3b, AKT, MAP4K3, and PKCβ have been identified to regulate TFEB function by phosphorylation. The activity of TFEB and TFE3 factors is negatively regulated by nutrient and growth factor-sensitive kinases (such as mTORC1, AKT, ERK2, and GSK3B) and positively regulated by the phosphatase calcineurin through the modulation of the phosphorylation status of multiple serine residues .(19, 20) Activated TFEB binds to promoter sequence named CLEAR sequenced elements to form CLEAR gene networks. This gene network enriches the genes encoding lysosomes endosomes and autophagy proteins. Therefore, stress-induced TFEB activation can adapt and expand the activity of the endosomal system by driving lysosomal biogenesis and autophagy flux.
The highly conserved sequence mTOR(mammalian target of rapamycin ) is an atypical serine/threonine kinase, belong to PI3K related protein kinases family.it is a key upstream kinase regulating autophagy(21) and also is a key upstream kinase that directly phosphorylates TFEB and inhibits its activity and expression.(22) It can phosphorylate two particular serine residues Ser142 and Ser211 in the TFEB protein, inducing the TFEB retained in cytoplasm, block the generation of new lysosomes, and decreases autophagic flux. Under conditions of amino acid satiety, Rag GTPases-Ragulator complex recruited TFEB to lysosomal membranes, and mammalian target of rapamycin complex 1 (mTORC1) phosphorylates TFEB at serine 211. the Phosphorylated TFEB is sequestered by chaperones of the 14-3-3 family, which actively prevent its translocation to the nucleus.(23) while Under starvation conditions, inactivation of mTORC1 allows nuclear translocation of TFEB to mediate cellular adaptation to stress. S142 is also dephosphorylated in the presence of MTORC1 inhibition,But its exact function is unclear. A recent study reported that S122 is the direct phosphorylation site of mTOR, which coordinates with S211 to regulate TFEB nuclear localization.(24) Therefore, mTOR can regulate TFEB by acting on different sites. Another serine/threonine phosphatase, calcineurin, is also involved in regulating TFEB activity, (25) In a state of nutritional deficiency or stress, Ca2+ is released from lysosomal MCOLN1 (a member of the transient receptor potential channel family), thereby exciting calcineurin, leading to TFEB dephosphorylation and nuclear translocation.(26) Serine/threonine kinase AMP-activated protein kinase (AMPK) complex is a sensor of energy in cells to regulate a variety of metabolic processes, including autophagy. It can regulate TFEB in different ways. AMPK can directly phosphorylate the upstream regulator TSC2 of mTOR and the mTORC1 subunit raptor. These two phosphorylation events lead to a decrease in mTOR activity,(27) which promoted TFEB nuclear translocation. This is a mTOR dependent way to activate TFEB. Recent studies have also shown that AMPK activates SIRT1(silent information regulator 1). SIRT1 is a highly conserved member of the histone deacetylase family, which can directly deacetylate TFEB (28) or indirectly activate TFEB via deacetylating the downstream protein PGC-1α(peroxisome proliferator-activated receptor gamma, coactivator 1 alpha) .(29, 30) It is a coactivator that interacts with a broad range of transcription factors involved in various biological responses, including adaptive thermogenesis, mitochondrial biogenesis, oxidative metabolism and steroidogenesis. PGC-1a has a parallel effect on TFEB, overexpression of PGC-1a increased the abundance of TFEB protein, and knockout decreased the transcription and protein abundance of TFEB,(31, 32) such as In Huntington’s disease, PGC-1α promotes the elimination of protein aggregates by activating the transcription factor EB (TFEB).(33) These are mTOR independent pathways that activate TFEB. In addition, P53 has been shown to be positively correlated with TFEB, But the exact mechanism is unclear.