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.