The autophagic machinery receives inputs from several signaling pathways that modulate autophagy according to specific physiological cues such as nutritional status


The autophagic machinery receives inputs from several signaling pathways that modulate autophagy according to specific physiological cues such as nutritional status, energy level and growth factor signaling (Figure 1). Autophagy is controlled mainly as a master regulator, but not exclusively, by the kinase mammalian target of rapamycin (mTOR; also known as FRAP1), which is a downstream component of the PI3K pathway2,39. It consists of two separate complexes termed TORC1 (containing mTOR, GbL and raptor) and TORC2 (containing mTOR, GbL, rictor and SIN1), of which only the former is sensitive to rapamycin. mTOR negatively regulates autophagy by integrating the signals from growth factors, insulin, high or low nutrition level(Amherdt et al., 1974; Grinde and Seglen, 1981; Plomp et al., 1987; Samari and Seglen, 1998) (starvation), ER stress, SOS etc.

The downstream targets of TORC1 in regulation of cell growth are the elongation factor 4EBP1, which promotes mRNA translation, and p70S6K, which also promotes translation when phosphorylated, acting through eEF-2 kinase. The known TORC1 targets in autophagy are the autophagic regulator kinase ULK1 and its accessory protein ATG13, whose TORC1-mediated phosphorylation, inhibits formation of a trimeric complex required for autophagosome formation (12) and causes suppression of autophagy (Chang and Neufeld, 2009; Ganley et al., 2009; Hosokawa et al., 2009; Jung et al., 2009).
In the upstream pathway of mTORC1 – growth factors, insulin etc activates growth factor receptors and other receptor tyrosine kinases and stimulate class I PI 3-kinase by binding of the regulatory p85/PIK3R1 subunit of PI 3-kinase to tyrosine phosphorylated receptors, either directly or via adaptors such as GAB2 and IRS1 or indirectly through GRB2-SOS-mediated activation of the small GTPase RAS, whose GTP-bound form activates p110/PIK3C1, the catalytic subunit of class I PI 3-kinase, through a direct interaction (Cully et al., 2006; Pawson, 2004).
Class I PI 3-kinase, which converts PtdIns(4,5)P2 into PtdIns(3,4,5)P3 at the plasma membrane recruits the protein kinases PDK1 and AKT1 to the plasma membrane, followed by phosphorylation and activation of AKT1 by PDK1 (Sarbassov et al., 2005) it inhibits heterodimerization of TSC2 and TSC1 by phosphorylation of TSC2, which inhibits the ability of this complex to stimulate the GTPase activity of Rheb. GTP-bound Rheb activates TORC1, which inhibits autophagy, This signaling cascade is counterbalanced by the action of the tumour suppressor PTEN (phosphatase with tensin homology), which dephosphorylates PtdIns(3,4,5)P3 into PtdIns(4,5)P2.
Activation of mTOR can also occur due to loss of tumor suppressors (LKB1, PML, PTEN, and TSC1/2) or through gain-of function mutations in receptor tyrosine kinases (21). Cellular stress leads to downregulation of mTOR1 activity that triggers autophagy (11), and in this regard, mTOR inhibitors, including rapamycin Torin1, Tamox, have been shown to induce autophagy in tumor cells (20).
TORC2 phosphorylates and activates AKT1, thereby participating in a positive feedback loop for activation of this crucial regulator of metabolism and autophagy.

A decrease in intracellular energy or increase in the AMP/ATP ratio under low energy level results in activation of adenosine monophosphate kinase (AMPK), by the upstream LKB1 kinase. It’s a central metabolic sensor that has important functions in regulating lipid and glucose metabolism. AMPK in turn phosphorylates TSC2 to stimulate its GAP activity, thereby turning off Rheb and TORC1 (Inoki et al., 2003) and initiate autophagy (12). A recent study found that AMPK can directly phosphorylate ULK1, which is required for mitochondrial homeostasis and cell survival during starvation (22).
Recent studies have implicated the GTPase Rag, which interacts with TORC1 in its active, GTPbound form and mediates sensing of amino acid levels (Kim et al., 2008a; Sancak et al., 2008). Andreas Brech2009

Autophagy can be induced by hypoxia, a stimulus for AMPK, that is mediated by hypoxia-inducible factor (HIF) and its target gene BNIP3 (21).BNIP3 activate Beclin1 by inhibiting the Bcl-2.
Autophagy can be potently induced by the unfolded protein response, a component of the endoplasmic reticulum (ER) stress pathway. The binding of misfolded proteins to the ER chaperone Bip/GRP78 leads to the release of 3 ER membrane-associated proteins: PKR-like eIF2a kinase (PERK), activating transcription factor-6 (ATF6), and inositol-requiring enzyme 1 (IRE1; ref. 23). Whereas PERK and ATF6 are autophagy inducers, IRE1 negatively regulates autophagy. Other factors that link cellular stress with autophagy include the transcription factor NF-kB and its upstream regulators IKK complex and TAK1, which integrate diverse stress signals, such as starvation and ER stress,with the autophagy pathway (24).
The tumor suppressor p53 protein can modulate autophagy depending on its cellular localization. Nuclear p53 acts as a transcription factor that transactivates several autophagy inducers, including DRAM1 and Sestrin2, to activate autophagy (25), whereas cytoplasmic p53 inhibits autophagy by an unknown mechanism. Inducers of autophagy can stimulate proteasome mediated degradation of p53 (26). Recently, some novel regulators of autophagy have been found. Ataxia telangiectasia mutated (ATM) is a cellular damage sensor that coordinates the cell cycle with DNA damage response checkpoints and DNA repair, and engages the TSC2/mTORC1 signaling axis to regulate autophagy (27). Additionally, high mobility group box 1 (HMGB1) is an immune modulator and regulator of stress-induced autophagy that directly interacts with Beclin 1 (28). Yang et al 2011
Now in this para we talk about the regulation of autophagy through transcriptional regulation. Some factor acts as transcriptional upregulator or some downregulators of autophagy. For example, TFEB(transcription factor EB),E2F1,ATF4(activating transcription factor 4),FOXO3(forkhead box O),NRF2,HIF(hypoxia induced factor),p53,PPAR?(peroxisome proliferation factor-activated receptor ?) are upregulators whereas ZKSCAN3(The zinc-finger protein with KRAB and SCAN domains 3 ), HSF(Heat shock factor),TCF4,XBP1,FXR(farnesoid X receptor), NF-?B(r kappa-light-chain-enhancer of activated B cells)
TFEB is a master regulator of lysosomal biogenesis, gets activated by dephosphorylation during starvation and allows to enter into the nucleus to induce transcription of its targets which include Atg4, Atg16, LC3, p62, WIPI proteins, ULK1, some Cathepsins and upregulate autophagy.
E2F1 involved in stress related mechanism and is inhibited by NF-?B, it upregulate BNIP3,ULK1,LC3,Atg5 and prautophagosome initiation.
ATF4 itself upregulated and activated by severe hypoxia, it enters into the nucleus and upregulate autophagy machinery componentsULK1, LC3, Atg5.
FOXO3 itself inhibited by Akt (which is activated by PI3K). Activated FOXO (suppressed Akt, PI3K) enter nucleus and activate Atg4, At2 itself regulg5, Atg12, Beclin1, LC3, ULK1.
NRF2 itself regulated by amino acid content, nutrient signalling and upregulate p62
HIF activated by mild hypoxia whereas ATF4 at severe. It enters into nucleus and activate BNIP3 which activates beclin1 by inhibiting bcl-2
P53 comes into picture during DNA damage, it upregulates Atg4, Atg7, ULK1
PPAR? activated during starvation, in fed state it is suppressed by FXR. PPAR? induce Atg3, Atg5, Atg7, Beclin1, LC3, TFEB, ULK1
ZKSCAN3 is a negative and major regulator of TFEB. In fed state it enters nucleus and bind to autophagy machinery target genes such as ULK1, LC3, WIPI,
HSF is opposite to NFR2, it supresses p62
TCF4 is regulated by ?-catenin. TCF4 suppress p62 when ?-catenin bound to TCF4. But when LC3 bind to ?-catenin, it leads to proteasomal degradation. So ?-catenin suppress TCF4
XBP activated by ER stress and enter nucleus. It has dual function it upregulates Beclin1 and suppress FOXO which in turn supress Atg4, Atg5, Atg12, LC3, ULK1.
FXR is a negative transcriptional repressor of PPAR? and it inhibit genes of Atg3, Atg5, Atg7, Beclin1, L3, ULK1, TFEB
NF-?B has dual effects it enters nucleus and upregulate Beclin1, p62 whereas it inhibits E2F1 i.e. inhibit Atg5, LC3, ULK1.

During starvation calcium ions are released out into the cytoplasm from lysosome and activate phosphatase calcineurin and remove phosphate from TFEB (phosphorylated by mTOR in fed state) and activated. During starvation ZKSCAN and FXR kicked out of the nucleus, it allows to enter ZKSCAN3 and PPAR? into the nucleus, binds to its targets and induce autophagy by induction of many autophagy proteins. During starvation Jun translocate into nucleus and induce expression of ANAXA2 (annexin A2, important for increased secure autophagic trafficking. Transcriptional regulation of mammalian autophagy at a glance Jens Füllgrabe, Ghita Ghislat, Dong-Hyung Cho, David C. Rubinsztein J Cell Sci 2016 129: 3059-3066; doi: 10.1242/jcs.188920