241 human active and 13 inactive phosphatases in total;
194 phosphatases have substrate data;
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336 protein substrates;
83 non-protein substrates;
1215 dephosphorylation interactions;
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299 KEGG pathways;
876 Reactome pathways;
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last scientific update: 11 Mar, 2019
last maintenance update: 01 Sep, 2023
Cytoplasm Nucleus Note=In response to stress,recruited by p53/TP53 to specific promoters
Function (UniProt annotation)
Catalytic subunit of AMP-activated protein kinase(AMPK), an energy sensor protein kinase that plays a key role inregulating cellular energy metabolism In response to reduction ofintracellular ATP levels, AMPK activates energy-producing pathwaysand inhibits energy-consuming processes: inhibits protein,carbohydrate and lipid biosynthesis, as well as cell growth andproliferation AMPK acts via direct phosphorylation of metabolicenzymes, and by longer-term effects via phosphorylation oftranscription regulators Also acts as a regulator of cellularpolarity by remodeling the actin cytoskeleton; probably byindirectly activating myosin Regulates lipid synthesis byphosphorylating and inactivating lipid metabolic enzymes such asACACA, ACACB, GYS1, HMGCR and LIPE; regulates fatty acid andcholesterol synthesis by phosphorylating acetyl-CoA carboxylase(ACACA and ACACB) and hormone-sensitive lipase (LIPE) enzymes,respectively Regulates insulin-signaling and glycolysis byphosphorylating IRS1, PFKFB2 and PFKFB3 AMPK stimulates glucoseuptake in muscle by increasing the translocation of the glucosetransporter SLC2A4/GLUT4 to the plasma membrane, possibly bymediating phosphorylation of TBC1D4/AS160 Regulates transcriptionand chromatin structure by phosphorylating transcriptionregulators involved in energy metabolism such as CRTC2/TORC2,FOXO3, histone H2B, HDAC5, MEF2C, MLXIPL/ChREBP, EP300, HNF4A,p53/TP53, SREBF1, SREBF2 and PPARGC1A Acts as a key regulator ofglucose homeostasis in liver by phosphorylating CRTC2/TORC2,leading to CRTC2/TORC2 sequestration in the cytoplasm In responseto stress, phosphorylates 'Ser-36' of histone H2B (H2BS36ph),leading to promote transcription Acts as a key regulator of cellgrowth and proliferation by phosphorylating TSC2, RPTOR andATG1/ULK1: in response to nutrient limitation, negativelyregulates the mTORC1 complex by phosphorylating RPTOR component ofthe mTORC1 complex and by phosphorylating and activating TSC2 Inresponse to nutrient limitation, promotes autophagy byphosphorylating and activating ATG1/ULK1 In response to nutrientlimitation, phosphorylates transcription factor FOXO3 promotingFOXO3 mitochondrial import (By similarity) AMPK also acts as aregulator of circadian rhythm by mediating phosphorylation ofCRY1, leading to destabilize it May regulate the Wnt signalingpathway by phosphorylating CTNNB1, leading to stabilize it Alsohas tau-protein kinase activity: in response to amyloid beta A4protein (APP) exposure, activated by CAMKK2, leading tophosphorylation of MAPT/TAU; however the relevance of such dataremains unclear in vivo Also phosphorylates CFTR, EEF2K, KLC1,NOS3 and SLC12A1
Catalytic Activity (UniProt annotation)
ATP + a protein = ADP + a phosphoprotein ATP + [acetyl-CoA carboxylase] = ADP +[acetyl-CoA carboxylase] phosphate ATP + [hydroxymethylglutaryl-CoA reductase(NADPH)] = ADP + [hydroxymethylglutaryl-CoA reductase (NADPH)]phosphate ATP + [tau protein] = ADP + [tau protein]phosphate
The forkhead box O (FOXO) family of transcription factors regulates the expression of genes in cellular physiological events including apoptosis, cell-cycle control, glucose metabolism, oxidative stress resistance, and longevity. A central regulatory mechanism of FOXO proteins is phosphorylation by the serine-threonine kinase Akt/protein kinase B (Akt/PKB), downstream of phosphatidylinositol 3-kinase (PI3K), in response to insulin or several growth factors. Phosphorylation at three conserved residues results in the export of FOXO proteins from the nucleus to the cytoplasm, thereby decreasing expression of FOXO target genes. In contrast, the stress-activated c-Jun N-terminal kinase (JNK) and the energy sensing AMP-activated protein kinase (AMPK), upon oxidative and nutrient stress stimuli phosphorylate and activate FoxOs. Aside from PKB, JNK and AMPK, FOXOs are regulated by multiple players through several post-translational modifications, including phosphorylation, but also acetylation, methylation and ubiquitylation.
Autophagy (or macroautophagy) is a cellular catabolic pathway involving in protein degradation, organelle turnover, and non-selective breakdown of cytoplasmic components, which is evolutionarily conserved among eukaryotes and exquisitely regulated. This progress initiates with production of the autophagosome, a double-membrane intracellular structure of reticular origin that engulfs cytoplasmic contents and ultimately fuses with lysosomes for cargo degradation. Autophagy is regulated in response to extra- or intracellular stress and signals such as starvation, growth factor deprivation and ER stress. Constitutive level of autophagy plays an important role in cellular homeostasis and maintains quality control of essential cellular components.
The mammalian (mechanistic) target of rapamycin (mTOR) is a highly conserved serine/threonine protein kinase, which exists in two complexes termed mTOR complex 1 (mTORC1) and 2 (mTORC2). mTORC1 contains mTOR, Raptor, PRAS40, Deptor, mLST8, Tel2 and Tti1. mTORC1 is activated by the presence of growth factors, amino acids, energy status, stress and oxygen levels to regulate several biological processes, including lipid metabolism, autophagy, protein synthesis and ribosome biogenesis. On the other hand, mTORC2, which consists of mTOR, mSin1, Rictor, Protor, Deptor, mLST8, Tel2 and Tti1, responds to growth factors and controls cytoskeletal organization, metabolism and survival.
The phosphatidylinositol 3' -kinase(PI3K)-Akt signaling pathway is activated by many types of cellular stimuli or toxic insults and regulates fundamental cellular functions such as transcription, translation, proliferation, growth, and survival. The binding of growth factors to their receptor tyrosine kinase (RTK) or G protein-coupled receptors (GPCR) stimulates class Ia and Ib PI3K isoforms, respectively. PI3K catalyzes the production of phosphatidylinositol-3,4,5-triphosphate (PIP3) at the cell membrane. PIP3 in turn serves as a second messenger that helps to activate Akt. Once active, Akt can control key cellular processes by phosphorylating substrates involved in apoptosis, protein synthesis, metabolism, and cell cycle.
AMP-activated protein kinase (AMPK) is a serine threonine kinase that is highly conserved through evolution. AMPK system acts as a sensor of cellular energy status. It is activated by increases in the cellular AMP:ATP ratio caused by metabolic stresses that either interfere with ATP production (eg, deprivation for glucose or oxygen) or that accelerate ATP consumption (eg, muscle contraction). Several upstream kinases, including liver kinase B1 (LKB1), calcium/calmodulin kinase kinase-beta (CaMKK beta), and TGF-beta-activated kinase-1 (TAK-1), can activate AMPK by phosphorylating a threonine residue on its catalytic alpha-subunit. Once activated, AMPK leads to a concomitant inhibition of energy-consuming biosynthetic pathways, such as protein, fatty acid and glycogen synthesis, and activation of ATP-producing catabolic pathways, such as fatty acid oxidation and glycolysis.
Regulation of longevity depends on genetic and environmental factors. Caloric restriction (CR), that is limiting food intake, is recognized in mammals as the best characterized and most reproducible strategy for extending lifespan. Four pathways have been implicated in mediating the CR effect. These are the insulin like growth factor (IGF-1)/insulin signaling pathway, the sirtuin pathway, the adenosine monophosphate (AMP) activated protein kinase (AMPK) pathway and the target of rapamycin (TOR) pathway. The collective response of these pathways to CR is believed to promote cellular fitness and ultimately longevity via activation of autophagy, stress defense mechanisms, and survival pathways while attenuating proinflammatory mediators and cellular growth. Furthermore, there is evidence supporting that life span extension can be achieved with pharmacologic agents that mimic the effects of caloric restriction, such as rapamycin, via mTOR signaling blockade, resveratrol, by activating SIRT1 activity, and metformin, which seems to be a robust stimulator of AMPK activity. As an aging suppressor, Klotho is an important molecule in aging processes and its overexpression results in longevity.
Aging is a complex process of accumulation of molecular, cellular, and organ damage, leading to loss of function and increased vulnerability to disease and death. Despite the complexity of aging, recent work has shown that dietary restriction (DR) and genetic down-regulation of nutrient-sensing pathways, namely IIS (insulin/insulin-like growth factor signalling) and TOR (target-of- rapamycin) can substantially increase healthy life span of laboratory model organisms. These nutrient signaling pathways are conserved in various organisms. In worms, flies, and mammals, DR reduces signalling through IIS/TOR pathways, deactivating the PI3K/Akt/TOR intracellular signalling cascade and consequently activating the antiaging FOXO family transcription factor(s). In yeast, the effects of DR on life- span extension are associated with reduced activities of the TOR/Sch9 and Ras/PKA pathways and require the serine-threonine kinase Rim15 and transcription factors Gis1 and Msn2/4. These transcription factors (FOXO, DAF-16, Gis1, and Msn2/4) transactivate genes involved in resistance to oxidative stress, energy metabolism, DNA damage repair, glucose metabolism, autophagy and protection of proteins by chaperones.
Apelin is an endogenous peptide capable of binding the apelin receptor (APJ), which was originally described as an orphan G-protein-coupled receptor. Apelin and APJ are widely expressed in various tissues and organ systems. They are implicated in different key physiological processes such as angiogenesis, cardiovascular functions, cell proliferation and energy metabolism regulation. On the other hand, this ligand receptor couple is also involved in several pathologies including diabetes, obesity, cardiovascular disease and cancer.
Tight junctions (TJs) are essential for establishing a selectively permeable barrier to diffusion through the paracellular space between neighboring cells. TJs are composed of at least three types of transmembrane protein -occludin, claudin and junctional adhesion molecules (JAMs)- and a cytoplasmic 'plaque' consisting of many different proteins that form large complexes. These are proposed to be involved in junction assembly, barrier regulation, cell polarity, gene transcription, and other pathways.
Circadian rhythm is an internal biological clock, which enables to sustain an approximately 24-hour rhythm in the absence of environmental cues. In mammals, the circadian clock mechanism consists of cell-autonomous transcription-translation feedback loops that drive rhythmic, 24-hour expression patterns of core clock components. The first negative feedback loop is a rhythmic transcription of period genes (PER1, PER2, and PER3) and chryptochrome genes (CRY1 and CRY2). PER and CRY proteins form a heterodimer, which acts on the CLOCK/BMAL1 heterodimer to repress its own transcription. PER and CRY proteins are phosphorylated by casein kinase epsilon (CKIepsilon), which leads to degradation and restarting of the cycle. The second loop is a positive feedback loop driven by the CLOCK/BMAL1 heterodimer, which initiates transcription of target genes containing E-box cis-regulatory enhancer sequences.
Thermogenesis is essential for warm-blooded animals, ensuring normal cellular and physiological function under conditions of environmental challenge. Thermogenesis in brown and beige adipose tissue is mainly controlled by norepinephrine, which is released from sympathetic nervous system in response to cold or dietary stimuli. The mitochondrial uncoupling protein 1 (UCP1) is responsible for the process whereby chemical energy is converted into heat in these adipocytes. Activation of these adipocytes leads to an increase in calorie consumption and is expected to improve overweight conditions, providing a potential strategy for treating obesity and its related metabolic disorders.
Insulin binding to its receptor results in the tyrosine phosphorylation of insulin receptor substrates (IRS) by the insulin receptor tyrosine kinase (INSR). This allows association of IRSs with the regulatory subunit of phosphoinositide 3-kinase (PI3K). PI3K activates 3-phosphoinositide-dependent protein kinase 1 (PDK1), which activates Akt, a serine kinase. Akt in turn deactivates glycogen synthase kinase 3 (GSK-3), leading to activation of glycogen synthase (GYS) and thus glycogen synthesis. Activation of Akt also results in the translocation of GLUT4 vesicles from their intracellular pool to the plasma membrane, where they allow uptake of glucose into the cell. Akt also leads to mTOR-mediated activation of protein synthesis by eIF4 and p70S6K. The translocation of GLUT4 protein is also elicited through the CAP/Cbl/TC10 pathway, once Cbl is phosphorylated by INSR.Other signal transduction proteins interact with IRS including GRB2. GRB2 is part of the cascade including SOS, RAS, RAF and MEK that leads to activation of mitogen-activated protein kinase (MAPK) and mitogenic responses in the form of gene transcription. SHC is another substrate of INSR. When tyrosine phosphorylated, SHC associates with GRB2 and can thus activate the RAS/MAPK pathway independently of IRS-1.
Increased adipocyte volume and number are positively correlated with leptin production, and negatively correlated with production of adiponectin.Leptin is an important regulator of energy intake and metabolic rate primarily by acting at hypothalamic nuclei. Leptin exerts its anorectic effects by modulating the levels of neuropeptides such as NPY, AGRP, and alpha-MSH. This leptin action is through the JAK kinase, STAT3 phosphorylation, and nuclear transcriptional effect.Adiponectin lowers plasma glucose and FFAs. These effects are partly accounted for by adiponectin-induced AMPK activation, which in turn stimulates skeletal muscle fatty acid oxidation and glucose uptake. Furthermore, activation of AMPK by adiponectin suppresses endogenous glucose production, concomitantly with inhibition of PEPCK and G6Pase expression.The proinflammatory cytokine TNFalpha has been implicated as a link between obesity and insulin resistance. TNFalpha interferes with early steps of insulin signaling. Several data have shown that TNFalpha inhibits IRS1 tyrosine phosphorylation by promoting its serine phosphorylation. Among the serine/threonine kinases activated by TNFalpha, JNK, mTOR and IKK have been shown to be involved in this phosphorylation.
Oxytocin (OT) is a nonapeptide synthesized by the magno-cellular neurons located in the supraoptic (SON) and paraventricular (PVN) nuclei of the hypothalamus. It exerts a wide variety of central and peripheral effects. However, its best-known and most well-established roles are stimulation of uterine contractions during parturition and milk release during lactation. Oxytocin also influences cardiovascular regulation and various social behaviors. The actions of OT are all mediated by one type of OT receptor (OTR). This is a transmembrane receptor belonging to the G-protein-coupled receptor superfamily. The main signaling pathway is the Gq/PLC/Ins3 pathway, but the MAPK and the RhoA/Rho kinase pathways are also activated, contributing to increased prostaglandin production and direct contractile effect on myometrial cells. In the cardiovascular system, OTR is associated with the ANP-cGMP and NO-cGMP pathways, which reduce the force and rate of contraction and increase vasodilatation.
Glucagon is conventionally regarded as a counterregulatory hormone for insulin and plays a critical anti-hypoglycemic role by maintaining glucose homeostasis in both animals and humans. To increase blood glucose, glucagon promotes hepatic glucose output by increasing glycogenolysis and gluconeogenesis and by decreasing glycogenesis and glycolysis in a concerted fashion via multiple mechanisms. Glucagon also stimulates hepatic mitochondrial beta-oxidation to supply energy for glucose production. Glucagon performs its main effect via activation of adenylate cyclase. The adenylate-cyclase-derived cAMP activates protein kinase A (PKA), which then phosphorylates downstream targets, such as cAMP response element binding protein (CREB) and the bifunctional enzyme 6-phosphofructo-2-kinase/ fructose-2,6-bisphosphatase (one of the isoforms being PFK/FBPase 1, encoded by PFKFB1).
Insulin resistance is a condition where cells become resistant to the effects of insulin. It is often found in people with health disorders, including obesity, type 2 diabetes mellitus, non-alcoholic fatty liver disease, and cardiovascular diseases. In this diagram multiple mechanisms underlying insulin resistance are shown: (a) increased phosphorylation of IRS (insulin receptor substrate) protein through serine/threonine kinases, such as JNK1 and IKKB, and protein kinase C, (b) increased IRS-1 proteasome degradation via mTOR signaling pathway, (c) decreased activation of signaling molecules including PI3K and AKT, (d) increase in activity of phosphatases including PTPs, PTEN, and PP2A. Regulatory actions such as oxidative stress, mitochondrial dysfunction, accumulation of intracellular lipid derivatives (diacylglycrol and ceramides), and inflammation (via IL-6 and TNFA) contribute to these mechanisms. Consequently, insulin resistance causes reduced GLUT4 translocation, resulting in glucose takeup and glycogen synthesis in skeletal muscle as well as increased hepatic gluconeogenesis and decreased glycogen synthesis in liver. At the bottom of the diagram, interplay between O-GlcNAcylation and serine/threonine phosphorylation is shown. Studies suggested that elevated O-GlcNAc level was correlated to high glucose-induced insulin resistance. Donor UDP-GlcNAc is induced through hexosamine biosynthesis pathway and added to proteins by O-GlcNAc transferase. Elevation of O-GlcNAc modification alters phosphorylation and function of key insulin signaling proteins including IRS-1, PI3K, PDK1, Akt and other transcription factor and cofactors, resulting in the attenuation of insulin signaling cascade.
Non-alcoholic fatty liver disease (NAFLD) represents a spectrum ranging from simple steatosis to more severe steatohepatitis with hepatic inflammation and fibrosis, known as nonalcoholic steatohepatitis (NASH). NASH may further lead to cirrhosis and hepatocellular carcinoma (HCC). This map shows a stage-dependent progression of NAFLD. In the first stage of NAFLD, excess lipid accumulation has been demonstrated. The main cause is the induction of insulin resistance, which leads to a defect in insulin suppression of free fatty acids (FAAs) disposal. In addition, two transcription factors, SREBP-1c and PPAR-alpha, activate key enzymes of lipogenesis and increase the synthesis of FAAs in liver. In the second stage, as a consequence of the progression to NASH, the production of reactive oxygen species (ROS) is enhanced due to oxidation stress through mitochondrial beta-oxidation of fatty acids and endoplamic reticulum (ER) stress, leading to lipid peroxidation. The lipid peroxidation can further cause the production of cytokines (Fas ligand, TNF-alpha, IL-8 and TGF), promoting cell death, inflammation and fibrosis. The activation of JNK, which is induced by ER stress, TNF-alpha and FAAs, is also associated with NAFLD progression. Increased JNK promotes cytokine production and initiation of HCC.
Hypertrophic cardiomyopathy (HCM) is a primary myocardial disorder with an autosomal dominant pattern of inheritance that is characterized by hypertrophy of the left ventricles with histological features of myocyte hypertrophy, myfibrillar disarray, and interstitial fibrosis. HCM is one of the most common inherited cardiac disorders, with a prevalence in young adults of 1 in 500. Hundreds of mutations in the genes that encode protein constituents of the sarcomere have been identified in HCM. These mutations increase the Ca2+ sensitivity of cardiac myofilaments. Increased myofilament Ca2+ sensitivity is expected to increase the ATP utilization by actomyosin at submaximal Ca2+ concentrations, which might cause an imbalance in energy supply and demand in the heart under severe stress. The inefficient use of ATP suggests that an inability to maintain normal ATP levels could be the central abnormality. This theory might be supported by the discovery of the role of a mutant PRKAG2 gene in HCM, which in active form acts as a central sensing mechanism protecting cells from depletion of ATP supplies. The increase in the myfilament Ca2+ sensitivity well account for the diastolic dysfunction of model animals as well as human patients of HCM. It has been widely proposed that left ventricular hypertrophy is not a primary manifestation but develops as compensatory response to sarcomere dysfunction.
Shear stress represents the frictional force that the flow of blood exerts at the endothelial surface of the vessel wall and plays a central role in vascular biology and contributes to the progress of atherosclerosis. Sustained laminar flow with high shear stress upregulates expressions of endothelial cell (EC) genes and proteins that are protective against atherosclerosis. The key shear stress-induced transcription factors that govern the expression of these genes are Kruppel-like factor 2 (KLF2) and nuclear factor erythroid 2-like 2 (Nrf2). On the other hand, disturbed flow with associated reciprocating, low shear stress generally upregulates the EC genes and proteins that promote oxidative and inflammatory states in the artery wall, resulting in atherogenesis. Important transcriptional events that reflect this condition of ECs in disturbed flow include the activation of activator protein 1 (AP-1) and nuclear factor kappaB (NF-kappaB).
Macroautophagy (hereafter referred to as autophagy) acts as a buffer against starvation by liberating building materials and energy sources from cellular components. It has additional roles in embryonic development, removal of apoptotic cells or organelles, antigen presentation, protection against toxins and as a degradation route for aggregate-prone proteins and infectious agents. The dysregulation of autophagy is involved in several human diseases, for example, Crohn's disease, cancer and neurodegeneration (Ravikumar et al. 2010).Autophagy is highly conserved from yeast to humans; much of the machinery was first identified in yeast (see Klionsky et al. 2011). Initially, double-membraned cup-shaped structures called the isolation membrane or phagophore engulf portions of cytoplasm. The membranes fuse to form the autophagosome. In yeast cells, autophagosomes are formed at the phagophore assembly site (PAS) next to the vacuole. In mammals, autophagosomes appear throughout the cytoplasm then move along microtubules towards the microtubule-organising centre. This transport requires microtubules and the function of dynein motor proteins; depolymerization of microtubules or inhibition of dynein-dependent transport results in inhibition of autophagy (Kochl et al. 2006, Kimura et al. 2008). Autophagosomes fuse with lysosomes forming autolysosomes whose contents are degraded by lysosomal hydrolases (Mizushima et al. 2011).The origins of the autophagosomal membrane and the incorporation of existing membrane material have been extensively debated. The endoplasmic reticulum (ER), mitochondria, mitochondria-associated ER membranes (MAMs), the Golgi, the plasma membrane and recycling endosomes have all been implicated in the nucleation of the isolation membrane and subsequent growth of the membrane (Lamb et al. 2013). Recently 3D tomographic imaging of isolation membranes has shown the cup-shaped isolation membrane tightly sandwiched between two sheets of ER and physically connected to the ER through a narrow membrane tube (Hayashi-Nishino et al. 2009, Yla-Anttila et al. 2009). This suggests that isolation membrane formation and elongation are guided by adjacent ER sheets, supporting the now prevalent 'ER cradle' model, which suggests that the isolation membrane arises from the ER (Hayashi-Nishino et al. 2009, Shibutani & Yoshimori 2014).Autophagy is tightly regulated. The induction of autophagy in response to starvation is partly mediated by inactivation of the mammalian target of rapamycin (mTOR) (Noda & Ohsumi 1998) and activation of Jun N-terminal kinase (JNK), while energy loss induces autophagy by activation of AMP kinase (AMPK). Other pathways regulating autophagy are regulated by calcium, cyclic AMP, calpains and the inositol trisphosphate (IP3) receptor (Rubinsztein et al. 2012). In mammals, two complexes cooperatively produce the isolation membrane. The ULK complex consists of ULK1/2, ATG13, (FIP200) and ATG101 (Alers et al. 2012). The PIK3C3-containing Beclin-1 complex consists of PIK3C3 (Vps34), BECN1 (Beclin-1, Atg6), PIK3R4 (p150, Vps15) and ATG14 (Barkor) (Matsunaga et al. 2009, Zhong et al. 2009). A similar complex where ATG14 is replaced by UVRAG functions later in autophagosome maturation and endocytic traffic (Itakura et al. 2008, Liang et al. 2008). Binding of KIAA0226 to this complex negatively regulates the maturation process (Matsunaga et al. 2009). The ULK and Beclin-1 complexes are recruited to specific autophagosome nucleation regions where they stimulate phosphatidylinositol-3-phosphate (PI3P) production and facilitate the elongation and initial membrane curvature of the phagophore membrane (Carlsson & Simonsen 2015).The ULK complex is considered the most upstream component of the mammalian autophagy pathway (Itakura & Mizushima 2010), acting as an integrator of the autophagy signals downstream of mTORC1. It is not fully understood how ULK1 is modulated in response to environmental cues. Phosphorylation plays an essential role (Dunlop & Tee 2013) but it is not clear how phosphorylation regulates ULK1 activities (Ravikumar et al. 2010). ULK1 kinase activity is required for autophagy, but the substrate(s) of ULK1 that mediate its autophagic function are not certain. ULK1 may also have kinase-independent functions in autophagy (Wong et al. 2013). PIK3C3 (Vps34) is a class III phosphatidylinositol 3-kinase that produces PI3P. It is essential for the early stages of autophagy and colocalizes strongly with early autophagosome markers (Axe et al. 2008). BECN1 binds several further proteins that affect autophagosome formation. Partners that induce autophagy include AMBRA1 (Fimia et al. 2007), UVRAG (Liang et al. 2006) and SH3GLB1 (Takahashi et al. 2007). Binding of BCL2 or BCL2L1 (Bcl-xL) inhibit autophagy (Pattingre et al. 2005, Ciechomska et al. 2009). The inositol 1,4,5-trisphosphate receptor complex that binds BCL2 also interacts with BECN1, inhibiting autophagy (Vincencio et al. 2009). CISD2 (Nutrient-deprivation autophagy factor-1, NAF1), a component in the IP3R complex, interacts with BCL2 at the ER and stabilizes the BCL2-BECN1 interaction (Chang et al. 2010). Starvation leads to activation of c-Jun NH2-terminal kinase-1 (JNK1), which results in the phosphorylation of BCL2 and BCL2L1, which release their binding to BECN1 and thus induces autophagosome formation (Wei et al. 2008). AMBRA1 can simultaneously bind dynein and the Beclin-1 complex. During nutrient starvation, AMBRA1 is phosphorylated in a ULK1-dependent manner (Di Bartolomeo et al. 2010). This phosphorylation releases AMBRA1-associated Beclin-1 complexes from dynein and the microtubule network, freeing the complex to translocate to autophagy initiation sites (Di Bartolomeo et al. 2010). A characteristic of this early phase of autophagosome formation is the formation of PI3P-enriched ER-associated structures called omegasomes (Axe et al. 2008) or cradles (Hayashi-Nishino et al. 2009). Omegasomes appear to concentrate at or near the connected mitochondria-associated ER membrane (Hamasaki et al. 2013). However, the phagophore also can incorporate existing material from other membrane sources such as ER exit sites (ERES), the ER-Golgi intermediate compartment (ERGIC), the Golgi, the plasma membrane and recycling endosomes (Carlsson & Simonsen 2015). Omegasomes lead to the formation of the isolation membrane or phagophore, which is thought to form de novo by an unknown mechanism (Simonsen & Stenmark 2008, Roberts & Ktistakis 2013). Phagophore expansion is probably mediated by membrane uptake from endomembranes and semi-autonomous organelles (Lamb et al. 2013, Shibutani & Yoshimori 2014).ATG9 is a direct target of ULK1. In nutrient-rich conditions mammalian ATG9 is localized to the trans-Golgi network and endosomes (including early, late and recycling endosomes), whereas under starvation conditions it is localized to autophagosomes, in a process that is dependent on ULK1 (Young et al. 2006). ATG9 is believed to play a role in the delivery of vesicles derived from existing membranes to the expanding phagophore (Lamb et al. 2013). Yeast Atg9 forms a complex with Atg2 and Atg18 (Reggiori et al. 2004). PI3P produced at the initiation site is sensed by WIPI2b, the mammalian homologue of Atg18 (Polson et al. 2010). WIPI2b then recruits Atg16L1 (Dooley et al. 2014). There are four WIPI proteins in mammalian cells (Proikas-Cezanne et al. 2015). They are all likely bind PI3P and be recruited to membranes but the function of WIPI1, 3 and 4 in autophagy is not yet clear. WIPI4 (WDR45) has been shown to bind Atg2 and to be involved in lipid droplet formation (Velikkakath et al. 2012); mutations in WIPI4 have been shown to cause a neurodegenerative disease (Saitsu et al. 2013).The elongation of the membrane that will become the autophagosome is regulated by two ubiquitination-like reactions. First, the ubiquitin-like molecule ATG12 is conjugated to ATG5 by ATG7, which acts as an E1-like activating enzyme, and ATG10, which has a role similar to an E2 ubiquitin-conjugating enzyme. The ATG5:ATG12 complex then interacts non-covalently with ATG16L1. This complex associates with the forming autophagosome but dissociates from completed autophagosomes (Geng & Klionski 2008). The second ubiquitin-like reaction involves the conjugation of ubiquitin-like molecules of the LC3 family (Weidberg et al. 2010). LC3 proteins are conjugated through their C-terminal glycine residues with PE by the E1-like ATG7 and E2-like ATG3. This allows LC3 proteins to associate with the autophagosome membrane. The ATG12:ATG5:ATG16L1 complex (Mizushima et al., 2011) acts as an E3 like enzyme for the conjugation of LC3 family proteins (mammalian homologues of yeast Atg8) to phosphatidylethanolamine (PE) (Hanada et al. 2007, Fujita et al. 2008). LC3 PE can be deconjugated by the protease ATG4 (Li et al. 2011, 2012). ATG4 is also responsible for priming LC3 proteins by cleaving the C terminus to expose a glycine residue (Kirisako et al, 2000, Scherz Shouval et al. 2007). LC3 proteins remain associated with autophagosomes until they fuse with lysosomes. The LC3-like proteins inside the resulting autolysosomes are degraded, while those on the cytoplasmic surface are delipidated and recycled. ATG5:ATG12:ATG16L1-positive LC3-negative vesicles represent pre-autophagosomal structures (pre-phagophores and possibly early phagophores), ATG5:ATG12:ATG16L1-positive LC3-positive structures can be considered to be phagophores, and ATG5:ATG12:ATG16L1-negative LC3-positive vesicles can be regarded as mature autophagosomes (Tandia et al. 2011).Phagophore expansion is probably mediated by membrane uptake from endomembranes as well as from semiautonomous organelles (Lamb et al. 2013, Shibutani & Yoshimori 2014).The mechanisms involved in the closure of the phagophore membrane are poorly understood. As the phagophore is a double-membraned structure, its closure involves the fusion of a narrow opening, a process that is distinct from other membrane fusion events (Carlsson & Simonsen 2015). The topology of the phagophore is similar to that of cytokinesis, viral budding or multivesicular body (MVB) formation. These processes rely on the Endosomal Sorting Complex Required for Transport (ESCRT) (Rusten et al. 2012). ESCRT and associated proteins facilitate membrane budding away from the cytosol and subsequent cleavage of the bud neck (Hurley & Hanson 2010). Several studies have shown that depletion of ESCRT subunits or the regulatory ATPase Vps4 causes an accumulation of autophagosomes (Filimonenko et al. 2007, Rusten et al. 2007) but it is not clear whether ESCRTs are required for autophagosome closure or for autophagosome to endosome fusion. UVRAG is also involved in the maturation step, recruiting proteins that bring about membrane fusion such as the class C Vps proteins, which activate Rab7 thereby promoting fusion with late endosomes and lysosomes (Liang et al. 2008)
Upon formation of a trimeric LKB1:STRAD:MO25 complex, LKB1 phosphorylates and activates AMPK. This phosphorylation is immediately removed in basal conditions by PP2C, but if the cellular AMP:ATP ratio rises, this activation is maintained, as AMP binding by AMPK inhibits the dephosphorylation. AMPK then activates the TSC complex by phosphorylating TSC2. Active TSC activates the intrinsic GTPase activity of Rheb, resulting in GDP-loaded Rheb and inhibition of mTOR pathway
While the p53 tumor suppressor protein (TP53) is known to inhibit cell growth by inducing apoptosis, senescence and cell cycle arrest, recent studies have found that p53 is also able to influence cell metabolism to prevent tumor development. TP53 regulates transcription of many genes involved in the metabolism of carbohydrates, nucleotides and amino acids, protein synthesis and aerobic respiration.
TP53 stimulates transcription of TIGAR, a D-fructose 2,6-bisphosphatase. TIGAR activity decreases glycolytic rate and lowers ROS (reactive oxygen species) levels in cells (Bensaad et al. 2006). TP53 may also negatively regulate the rate of glycolysis by inhibiting the expression of glucose transporters GLUT1, GLUT3 and GLUT4 (Kondoh et al. 2005, Schwartzenberg-Bar-Yoseph et al. 2004, Kawauchi et al. 2008).
TP53 negatively regulates several key points in PI3K/AKT signaling and downstream mTOR signaling, decreasing the rate of protein synthesis and, hence, cellular growth. TP53 directly stimulates transcription of the tumor suppressor PTEN, which acts to inhibit PI3K-mediated activation of AKT (Stambolic et al. 2001). TP53 stimulates transcription of sestrin genes, SESN1, SESN2, and SESN3 (Velasco-Miguel et al. 1999, Budanov et al. 2002, Brynczka et al. 2007). One of sestrin functions may be to reduce and reactivate overoxidized peroxiredoxin PRDX1, thereby reducing ROS levels (Budanov et al. 2004, Papadia et al. 2008, Essler et al. 2009). Another function of sestrins is to bind the activated AMPK complex and protect it from AKT-mediated inactivation. By enhancing AMPK activity, sestrins negatively regulate mTOR signaling (Budanov and Karin 2008, Cam et al. 2014). The expression of DDIT4 (REDD1), another negative regulator of mTOR signaling, is directly stimulated by TP63 and TP53. DDIT4 prevents AKT-mediated inactivation of TSC1:TSC2 complex, thus inhibiting mTOR cascade (Cam et al. 2014, Ellisen et al. 2002, DeYoung et al. 2008). TP53 may also be involved, directly or indirectly, in regulation of expression of other participants of PI3K/AKT/mTOR signaling, such as PIK3CA (Singh et al. 2002), TSC2 and AMPKB (Feng et al. 2007).
TP53 regulates mitochondrial metabolism through several routes. TP53 stimulates transcription of SCO2 gene, which encodes a mitochondrial cytochrome c oxidase assembly protein (Matoba et al. 2006). TP53 stimulates transcription of RRM2B gene, which encodes a subunit of the ribonucleotide reductase complex, responsible for the conversion of ribonucleotides to deoxyribonucleotides and essential for the maintenance of mitochondrial DNA content in the cell (Tanaka et al. 2000, Bourdon et al. 2007, Kulawiec et al. 2009). TP53 also transactivates mitochondrial transcription factor A (TFAM), a nuclear-encoded gene important for mitochondrial DNA (mtDNA) transcription and maintenance (Park et al. 2009). Finally, TP53 stimulates transcription of the mitochondrial glutaminase GLS2, leading to increased mitochondrial respiration rate and reduced ROS levels (Hu et al. 2010).
The great majority of tumor cells generate energy through aerobic glycolysis, rather than the much more efficient aerobic mitochondrial respiration, and this metabolic change is known as the Warburg effect (Warburg 1956). Since the majority of tumor cells have impaired TP53 function, and TP53 regulates a number of genes involved in glycolysis and mitochondrial respiration, it is likely that TP53 inactivation plays an important role in the metabolic derangement of cancer cells such as the Warburg effect and the concomitant increased tumorigenicity (reviewed by Feng and Levine 2010). On the other hand, some mutations of TP53 in Li-Fraumeni syndrome may result in the retention of its wild-type metabolic activities while losing cell cycle and apoptosis functions (Wang et al. 2013). Consistent with such human data, some mutations of p53, unlike p53 null state, retain the ability to regulate energy metabolism while being inactive in regulating its classic gene targets involved in cell cycle, apoptosis and senescence. Retention of metabolic and antioxidant functions of p53 protects p53 mutant mice from early onset tumorigenesis (Li et al. 2012)
Phosphorylation of TP53 (p53) at the N-terminal serine residues S15 and S20 plays a critical role in protein stabilization as phosphorylation at these sites interferes with binding of the ubiquitin ligase MDM2 to TP53. Several different kinases can phosphorylate TP53 at S15 and S20. In response to double strand DNA breaks, S15 is phosphorylated by ATM (Banin et al. 1998, Canman et al. 1998, Khanna et al. 1998), and S20 by CHEK2 (Chehab et al. 1999, Chehab et al. 2000, Hirao et al. 2000). DNA damage or other types of genotoxic stress, such as stalled replication forks, can trigger ATR-mediated phosphorylation of TP53 at S15 (Lakin et al. 1999, Tibbetts et al. 1999) and CHEK1-mediated phosphorylation of TP53 at S20 (Shieh et al. 2000). In response to various types of cell stress, NUAK1 (Hou et al. 2011), CDK5 (Zhang et al. 2002, Lee et al. 2007, Lee et al. 2008), AMPK (Jones et al. 2005) and TP53RK (Abe et al. 2001, Facchin et al. 2003) can phosphorylate TP53 at S15, while PLK3 (Xie, Wang et al. 2001, Xie, Wu et al. 2001) can phosphorylate TP53 at S20.
Phosphorylation of TP53 at serine residue S46 promotes transcription of TP53-regulated apoptotic genes rather than cell cycle arrest genes. Several kinases can phosphorylate S46 of TP53, including ATM-activated DYRK2, which, like TP53, is targeted for degradation by MDM2 (Taira et al. 2007, Taira et al. 2010). TP53 is also phosphorylated at S46 by HIPK2 in the presence of the TP53 transcriptional target TP53INP1 (D'Orazi et al. 2002, Hofmann et al. 2002, Tomasini et al. 2003). CDK5, in addition to phosphorylating TP53 at S15, also phosphorylates it at S33 and S46, which promotes neuronal cell death (Lee et al. 2007).
MAPKAPK5 (PRAK) phosphorylates TP53 at serine residue S37, promoting cell cycle arrest and cellular senescence in response to oncogenic RAS signaling (Sun et al. 2007).
NUAK1 phosphorylates TP53 at S15 and S392, and phosphorylation at S392 may contribute to TP53-mediated transcriptional activation of cell cycle arrest genes (Hou et al. 2011). S392 of TP53 is also phosphorylated by the complex of casein kinase II (CK2) bound to the FACT complex, enhancing transcriptional activity of TP53 in response to UV irradiation (Keller et al. 2001, Keller and Lu 2002).
The activity of TP53 is inhibited by phosphorylation at serine residue S315, which enhances MDM2 binding and degradation of TP53. S315 of TP53 is phosphorylated by Aurora kinase A (AURKA) (Katayama et al. 2004) and CDK2 (Luciani et al. 2000). Interaction with MDM2 and the consequent TP53 degradation is also increased by phosphorylation of TP53 threonine residue T55 by the transcription initiation factor complex TFIID (Li et al. 2004).
Aurora kinase B (AURKB) has been shown to phosphorylate TP53 at serine residue S269 and threonine residue T284, which is possibly facilitated by the binding of the NIR co-repressor. AURKB-mediated phosphorylation was reported to inhibit TP53 transcriptional activity through an unknown mechanism (Wu et al. 2011). A putative direct interaction between TP53 and AURKB has also been described and linked to TP53 phosphorylation and S183, T211 and S215 and TP53 degradation (Gully et al. 2012)
Affinity Capture-MS, Affinity Capture-Western, Co-fractionation, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, tandem affinity purification
Affinity Capture-MS, Co-fractionation, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, tandem affinity purification, two hybrid, two hybrid array, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, tandem affinity purification, two hybrid array, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Co-fractionation, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, tandem affinity purification
Affinity Capture-MS, Co-fractionation, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, tandem affinity purification, two hybrid, two hybrid array, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, tandem affinity purification, two hybrid array, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Co-fractionation, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, tandem affinity purification
Affinity Capture-MS, Affinity Capture-Western, Co-fractionation, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, tandem affinity purification
Affinity Capture-MS, Co-fractionation, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, tandem affinity purification, two hybrid, two hybrid array, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, tandem affinity purification, two hybrid array, two hybrid prey pooling approach, validated two hybrid