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
Regulates activation of NF-kappa-B and JNK and plays acentral role in the regulation of cell survival and apoptosisRequired for normal antibody isotype switching from IgM to IgGHas E3 ubiquitin-protein ligase activity and promotes 'Lys-63'-linked ubiquitination of target proteins, such as BIRC3, RIPK1 andTICAM1 Is an essential constituent of several E3 ubiquitin-protein ligase complexes, where it promotes the ubiquitination oftarget proteins by bringing them into contact with other E3ubiquitin ligases Regulates BIRC2 and BIRC3 protein levels byinhibiting their autoubiquitination and subsequent degradation;this does not depend on the TRAF2 RING-type zinc finger domainPlays a role in mediating activation of NF-kappa-B by EIF2AK2/PKRIn complex with BIRC2 or BIRC3, promotes ubiquitination of IKBKE
The mitogen-activated protein kinase (MAPK) cascade is a highly conserved module that is involved in various cellular functions, including cell proliferation, differentiation and migration. Mammals express at least four distinctly regulated groups of MAPKs, extracellular signal-related kinases (ERK)-1/2, Jun amino-terminal kinases (JNK1/2/3), p38 proteins (p38alpha/beta/gamma/delta) and ERK5, that are activated by specific MAPKKs: MEK1/2 for ERK1/2, MKK3/6 for the p38, MKK4/7 (JNKK1/2) for the JNKs, and MEK5 for ERK5. Each MAPKK, however, can be activated by more than one MAPKKK, increasing the complexity and diversity of MAPK signalling. Presumably each MAPKKK confers responsiveness to distinct stimuli. For example, activation of ERK1/2 by growth factors depends on the MAPKKK c-Raf, but other MAPKKKs may activate ERK1/2 in response to pro-inflammatory stimuli.
Nuclear factor-kappa B (NF-kappa B) is the generic name of a family of transcription factors that function as dimers and regulate genes involved in immunity, inflammation and cell survival. There are several pathways leading to NF-kappa B-activation. The canonical pathway is induced by tumour necrosis factor-alpha (TNF-alpha), interleukin-1 (IL-1) or byproducts of bacterial and viral infections. This pathway relies on IKK- mediated IkappaB-alpha phosphorylation on Ser32 and 36, leading to its degradation, which allows the p50/p65 NF-kappa B dimer to enter the nucleus and activate gene transcription. Atypical pathways are IKK-independent and rely on phosphorylation of IkappaB-alpha on Tyr42 or on Ser residues in IkappaB-alpha PEST domain. The non-canonical pathway is triggered by particular members of the TNFR superfamily, such as lymphotoxin-beta (LT-beta) or BAFF. It involves NIK and IKK-alpha-mediated p100 phosphorylation and processing to p52, resulting in nuclear translocation of p52/RelB heterodimers.
Sphingomyelin (SM) and its metabolic products are now known to have second messenger functions in a variety of cellular signaling pathways. Particularly, the sphingolipid metabolites, ceramide (Cer) and sphingosine-1-phosphate (S1P), have emerged as a new class of potent bioactive molecules. Ceramide can be generated de novo or by hydrolysis of membrane sphingomyelin by sphingomyelinase (SMase). Ceramide is subsequently metabolized by ceramidase to generate sphingosine (Sph) which in turn produces S1P through phosphorylation by sphingosine kinases 1 and 2 (SphK1, 2). Both ceramide and S1P regulate cellular responses to stress, with generally opposing effects. S1P functions as a growth and survival factor, acting as a ligand for a family of G protein-coupled receptors, whereas ceramide activates intrinsic and extrinsic apoptotic pathways through receptor-independent mechanisms.
The endoplasmic reticulum (ER) is a subcellular organelle where proteins are folded with the help of lumenal chaperones. Newly synthesized peptides enter the ER via the sec61 pore and are glycosylated. Correctly folded proteins are packaged into transport vesicles that shuttle them to the Golgi complex. Misfolded proteins are retained within the ER lumen in complex with molecular chaperones. Proteins that are terminally misfolded bind to BiP and are directed toward degradation through the proteasome in a process called ER-associated degradation (ERAD). Accumulation of misfolded proteins in the ER causes ER stress and activates a signaling pathway called the unfolded protein response (UPR). In certain severe situations, however, the protective mechanisms activated by the UPR are not sufficient to restore normal ER function and cells die by apoptosis.
Apoptosis is a genetically programmed process for the elimination of damaged or redundant cells by activation of caspases (aspartate-specific cysteine proteases). The onset of apoptosis is controlled by numerous interrelating processes. The 'extrinsic' pathway involves stimulation of members of the tumor necrosis factor (TNF) receptor subfamily, such as TNFRI, CD95/Fas or TRAILR (death receptors), located at the cell surface, by their specific ligands, such as TNF-alpha, FasL or TRAIL, respectively. The 'intrinsic' pathway is activated mainly by non-receptor stimuli, such as DNA damage, ER stress, metabolic stress, UV radiation or growth-factor deprivation. The central event in the 'intrinsic' pathway is the mitochondrial outer membrane permeabilization (MOMP), which leads to the release of cytochrome c. These two pathways converge at the level of effector caspases, such as caspase-3 and caspase-7. The third major pathway is initiated by the constituents of cytotoxic granules (e.g. Perforin and Granzyme B) that are released by CTLs (cytotoxic T-cells) and NK (natural killer) cells. Granzyme B, similarly to the caspases, cleaves its substrates after aspartic acid residues, suggesting that this protease has the ability to activate members of the caspase family directly. It is the balance between the pro-apoptotic and anti-apoptotic signals that eventually determines whether cells will undergo apoptosis, survive or proliferate. TNF family of ligands activates anti-apoptotic or cell-survival signals as well as apoptotic signals. NGF and Interleukin-3 promotes the survival, proliferation and differentiation of neurons or hematopoietic cells, respectively. Withdrawal of these growth factors leads to cell death, as described above.
Necroptosis is a programmed form of necrosis. It can be initiated by different stimuli, such as tumor necrosis factor (TNF), TNF-related apoptosis-inducing ligand (TRAIL), Fas ligand (FasL), interferon (IFN), LPS, viral DNA or RNA, DNA-damage agent and requires the kinase activity of receptor-interacting protein 1 (RIPK1) and RIPK3. Its execution involves ROS generation, calcium overload, the opening of the mitochondrial permeability transition pore, mitochondrial fission, inflammatory response and chromatinolysis. Necroptosis participates in many pathogenesis of diseases, including neurological diseases, retinal disorders, acute kidney injury, inflammatory diseases and microbial infections.
The osteoclasts, multinucleared cells originating from the hematopoietic monocyte-macrophage lineage, are responsible for bone resorption. Osteoclastogenesis is mainly regulated by signaling pathways activated by RANK and immune receptors, whose ligands are expressed on the surface of osteoblasts. Signaling from RANK changes gene expression patterns through transcription factors like NFATc1 and characterizes the active osteoclast.
Specific families of pattern recognition receptors are responsible for detecting various pathogens and generating innate immune responses. The intracellular NOD-like receptor (NLR) family contains more than 20 members in mammals and plays a pivotal role in the recognition of intracellular ligands. NOD1 and NOD2, two prototypic NLRs, sense the cytosolic presence of the bacterial peptidoglycan fragments that escaped from endosomal compartments, driving the activation of NF-{kappa}B and MAPK, cytokine production and apoptosis. On the other hand, a different set of NLRs induces caspase-1 activation through the assembly of multiprotein complexes called inflammasomes. The activated of caspase-1 regulates maturation of the pro-inflammatory cytokines IL-1B, IL-18 and drives pyroptosis.
Specific families of pattern recognition receptors are responsible for detecting viral pathogens and generating innate immune responses. Non-self RNA appearing in a cell as a result of intracellular viral replication is recognized by a family of cytosolic RNA helicases termed RIG-I-like receptors (RLRs). The RLR proteins include RIG-I, MDA5, and LGP2 and are expressed in both immune and nonimmune cells. Upon recognition of viral nucleic acids, RLRs recruit specific intracellular adaptor proteins to initiate signaling pathways that lead to the synthesis of type I interferon and other inflammatory cytokines, which are important for eliminating viruses.
The interleukin 17 (IL-17) family, a subset of cytokines consisting of IL-17A-F, plays crucial roles in both acute and chronic inflammatory responses. IL-17A, the hallmark cytokine of the newly defined T helper 17 (TH17) cell subset, has important roles in protecting the host against extracellular pathogens, but also promotes inflammatory pathology in autoimmune disease, whereas IL-17F is mainly involved in mucosal host defense mechanisms. IL-17E (IL-25) is an amplifier of Th2 immune responses. IL-17C has biological functions similar to those of IL-17A. The functions of IL-17B and IL-17D remain largely elusive. The IL-17 family signals via their correspondent receptors and activates downstream pathways that include NF-kappaB, MAPKs and C/EBPs to induce the expression of antimicrobial peptides, cytokines and chemokines. The receptor proximal adaptor Act1 (an NF-kappaB activator 1) is considered as the master mediator in IL-17A signaling. It is likely that Act1 is a common signal adaptor also shared by other members mediated signalings in this family.
Tumor necrosis factor (TNF), as a critical cytokine, can induce a wide range of intracellular signal pathways including apoptosis and cell survival as well as inflammation and immunity. Activated TNF is assembled to a homotrimer and binds to its receptors (TNFR1, TNFR2) resulting in the trimerization of TNFR1 or TNFR2. TNFR1 is expressed by nearly all cells and is the major receptor for TNF (also called TNF-alpha). In contrast, TNFR2 is expressed in limited cells such as CD4 and CD8 T lymphocytes, endothelial cells, microglia, oligodendrocytes, neuron subtypes, cardiac myocytes, thymocytes and human mesenchymal stem cells. It is the receptor for both TNF and LTA (also called TNF-beta). Upon binding of the ligand, TNFR mediates the association of some adaptor proteins such as TRADD or TRAF2, which in turn initiate recruitment of signal transducers. TNFR1 signaling induces activation of many genes, primarily controlled by two distinct pathways, NF-kappa B pathway and the MAPK cascade, or apoptosis and necroptosis. TNFR2 signaling activates NF-kappa B pathway including PI3K-dependent NF-kappa B pathway and JNK pathway leading to survival.
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.
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.
Hepatitis C virus (HCV) is a major cause of chronic liver disease. The HCV employ several strategies to perturb host cell immunity. After invasion, HCV RNA genome functions directly as an mRNA in the cytoplasm of the host cell and forms membrane-associated replication complexes along with non-structural proteins. Viral RNA can trigger the RIG-I pathway and interferon production during this process. Translated HCV protein products regulate immune response to inhibit the action of interferon. HCV core and NS5A proteins appear to be the most important molecules with regulatory functions that modulate transcription, cellular proliferation, and apoptosis.
Human cytomegalovirus (HCMV) is an enveloped, double-stranded DNA virus that is a member of beta-herpesvirus family. HCMV is best known for causing significant morbidity and mortality in immunocompromised populations. As with other herpesviruses, HCMV gB and gH/gL envelope glycoproteins are essential for virus entry. HCMV gB could activate the PDGFRA, and induce activation of the oncogenic PI3-K/AKT pathway. Though it is unlikely that HCMV by itself can act as an oncogenic factor, HCMV may have an oncomodulatory role, to catalyze an oncogenic process that has already been initiated. US28, one of the four HCMV-encoded vGPCRs (US27, US28, UL33 and UL78), also has a specific role in the oncomodulatory properties. In addition, HCMV has developed numerous mechanisms for manipulating the host immune system. The virally encoded US2, US3, US6 and US11 gene products all interfere with major histocompatibility complex (MHC) class I antigen presentation. HCMV encodes several immediate early (IE) antiapoptotic proteins (IE1, IE2, vMIA and vICA). These proteins might avoid immune clearance of infected tumor cells by cytotoxic lymphocytes and NK cells.
Kaposi sarcoma-associated herpesvirus (KSHV), also known as human herpesvirus 8 (HHV-8), is the most recently identified human tumor virus, and is associated with the pathogenesis of Kaposi's sarcoma (KS), primary effusion lymphoma (PEL), and Multicentric Castleman's disease (MCD). Like all other herpesviruses, KSHV displays two modes of life cycle, latency and lytic replication, which are characterized by the patterns of viral gene expression. Genes expressed in latency (LANA, v-cyclin, v-FLIP, Kaposins A, B and C and viral miRNAs) are mainly thought to facilitate the establishment of life long latency in its host and survival against the host innate, and adaptive immune surveillance mechanisms. Among the viral proteins shown to be expressed during lytic replication are potent signaling molecules such as vGPCR, vIL6, vIRFs, vCCLs, K1 and K15, which have been implicated experimentally in the angiogenic and inflammatory phenotype observed in KS lesions. Several of these latent viral and lytic proteins are known to transform host cells, linking KSHV with the development of severe human malignancies.
Herpes simplex virus (HSV) infections are very common worldwide, with the prevalence of HSV-1 reaching up to 80%-90%. Primary infection with HSV takes place in the mucosa, followed by the establishment of latent infection in neuronal ganglia. HSV is the main cause of herpes infections that lead to the formation of characteristic blistering lesion. HSV express multiple viral accessory proteins that interfere with host immune responses and are indispensable for viral replication. Among these proteins, the immediate early (IE) gene ICP0, ICP4, and ICP27 are essential for regulation of HSV gene expression in productive infection. On the other hand, ORF P and ORF O gene are transcribed during latency and blocks the expression of the IE genes, thus maintaining latent infection.
Epstein-Barr virus (EBV) is a gamma-herpes virus that widely infects human populations predominantly at an early age but remains mostly asymptomatic. EBV has been linked to a wide spectrum of human malignancies, including nasopharyngeal carcinoma and other hematologic cancers, like Hodgkin's lymphoma, Burkitt's lymphoma (BL), B-cell immunoblastic lymphoma in HIV patients, and posttransplant-associated lymphoproliferative diseases. EBV has the unique ability to establish life-long latent infection in primary human B lymphocytes. During latent infection, EBV expresses a small subset of genes, including 6 nuclear antigens (EBNA-1, -2, -3A, -3B, -3C, and -LP), 3 latent membrane proteins (LMP-1, -2A, and -2B), 2 small noncoding RNAs (EBER-1 and 2). On the basis of these latent gene expression, three different latency patterns associated with the types of cancers are recognized.
Human immunodeficiency virus type 1 (HIV-1) , the causative agent of AIDS (acquired immunodeficiency syndrome), is a lentivirus belonging to the Retroviridae family. The primary cell surface receptor for HIV-1, the CD4 protein, and the co-receptor for HIV-1, either CCR5 or CXCR4, are found on macrophages and T lymphocytes. At the earliest step, sequential binding of virus envelope (Env) glycoprotein gp120 to CD4 and the co-receptor CCR5 or CXCR4 facilitates HIV-1 entry and has the potential to trigger critical signaling that may favor viral replication. At advanced stages of the disease, HIV-1 infection results in dramatic induction of T-cell (CD4+ T and CD8+ T cell) apoptosis both in infected and uninfected bystander T cells, a hallmark of HIV-1 pathogenesis. On the contrary, macrophages are resistant to the cytopathic effect of HIV-1 and produce virus for longer periods of time.
There is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C virus (HCV), human papilloma virus (HPV), human T-cell lymphotropic virus (HTLV-1) and Kaposi's associated sarcoma virus (KSHV) contribute to 10-15% of the cancers worldwide. Via expression of many potent oncoproteins, these tumor viruses promote an aberrant cell-proliferation via modulating cellular cell-signaling pathways and escape from cellular defense system such as blocking apoptosis. Human tumor virus oncoproteins can also disrupt pathways that are necessary for the maintenance of the integrity of host cellular genome. Viruses that encode such activities can contribute to initiation as well as progression of human cancers.
Lung cancer is a leading cause of cancer death among men and women in industrialized countries. Small cell lung carcinoma (SCLC) is a highly aggressive neoplasm, which accounts for approximately 25% of all lung cancer cases. Molecular mechanisms altered in SCLC include induced expression of oncogene, MYC, and loss of tumorsuppressor genes, such as p53, PTEN, RB, and FHIT. The overexpression of MYC proteins in SCLC is largely a result of gene amplification. Such overexpression leads to more rapid proliferation and loss of terminal differentiation. Mutation or deletion of p53 or PTEN can lead to more rapid proliferation and reduced apoptosis. The retinoblastoma gene RB1 encodes a nuclear phosphoprotein that helps to regulate cell-cycle progression. The fragile histidine triad gene FHIT encodes the enzyme diadenosine triphosphate hydrolase, which is thought to have an indirect role in proapoptosis and cell-cycle control.
Caspase-8 is synthesized as zymogen (procaspase-8) and is formed from procaspase-8 as a cleavage product. However, the cleavage itself appears not to be sufficient for the formation of an active caspase-8. Only the coordinated dimerization and cleavage of the zymogen produce efficient activation in vitro and apoptosis in cellular systems [Boatright KM and Salvesen GS 2003; Keller N et al 2010; Oberst A et al 2010].
The caspase-8 zymogens are present in the cells as inactive monomers, which are recruited to the death-inducing signaling complex (DISC) by homophilic interactions with the DED domain of FADD. The monomeric zymogens undergo dimerization and the subsequent conformational changes at the receptor complex, which results in the formation of catalytically active form of procaspase-8.[Boatright KM et al 2003; Donepudi M et al 2003; Keller N et al 2010; Oberst A et al 2010]
c-FLIP proteins (CASP8 and FADD-like apoptosis regulators or c-FLICE inhibitory proteins) are death effector domain (DED)-containing proteins that are recruited to the death-inducing signaling complex (DISC) to regulate activation of caspases-8. Three out of 13 distinct spliced variants of c-FLIP had been found to be expressed at the protein level, the 26 kDa short form FLIP(S), the 24 kDa form FLIP(R), and the 55 kDa long form FLIP(L) (Irmler M et al. 1997; Shu HB et al. 1997; Srinivasula SM et al. 1997; Scaffidi C et al. 1999; Golks A et al. 2005; Haag C et al. 2011)
All c-FLIP proteins carry two DEDs at their N termini, which can bind FADD and procaspase-8. In addition to two DEDs, FLIP(L) contains a large (p20) and a small (p12) caspase-like domain without catalytic activity. FLIP(S) and FLIP(R) consist of two DEDs and a small C terminus. Depending on its level of expression FLIP(L) may function as an anti-apoptotic or pro-apoptotic factor, while FLIP(S) and FLIP(R) protect cells from apoptosis by blocking the processing of caspase-8 at the receptor level (Scaffidi C et al. 1999; Golks A et al. 2005; Toivonen HT et al. 2011; Fricker N et al. 2010)
Receptor-interacting kinase protein 1 (RIPK1) and RIPK3-dependent necrosis is called necroptosis or programmed necrosis. The kinase activities of RIPK1 and RIPK3 are essential for the necroptotic cell death in human, mouse cell lines and genetic mice models (Cho YS et al. 2009; He S et al. 2009, 2011; Zhang DW et al. 2009; McQuade T et al. 2013; Newton et al. 2014). The initiation of necroptosis can be stimulated by the same death ligands that activate apoptosis, such as tumor necrosis factor (TNF) alpha, Fas ligand (FasL), and TRAIL (TNF-related apoptosis-inducing ligand) or toll like receptors 3 and 4 ligands (Holler N et al. 2000; He S et al. 2009; Feoktistova M et al. 2011; Voigt S et al. 2014). In contrast to apoptosis, necroptosis represents a form of cell death that is optimally induced when caspases are inhibited (Holler N et al. 2000; Hopkins?Donaldson S et al. 2000; Sawai H 2014). Specific inhibitors of caspase-independent necrosis, necrostatins, have recently been identified (Degterev A et al. 2005, 2008). Necrostatins have been shown to inhibit the kinase activity of RIPK1 (Degterev A et al. 2008). Importantly, cell death of apoptotic morphology can be shifted to a necrotic phenotype when caspase 8 activity is compromised, otherwise active caspase 8 blocks necroptosis by the proteolytic cleavage of RIPK1 and RIPK3 (Kalai M et al. 2002; Degterev A et al. 2008; Lin Y et al. 1999; Feng S et al. 2007). When caspase activity is inhibited under certain pathophysiological conditions or by pharmacological agents, deubiquitinated RIPK1 is engaged in physical and functional interactions with its homolog RIPK3 leading to formation of necrosome, a necroptosis-inducing complex consisting of RIPK1 and RIPK3 (Sawai H 2013; Moquin DM et al. 2013; Kalai M et al. 2002; Cho YS et al. 2009, He S et al. 2009, Zhang DW et al. 2009). Within the necrosome RIPK1 and RIPK3 bind to each other through their RIP homotypic interaction motif (RHIM) domains. The RHIMs can facilitate RIPK1:RIPK3 oligomerization, allowing them to form amyloid?like fibrillar structures (Li J et al. 2012). RIPK3 in turn interacts with mixed lineage kinase domain?like protein (MLKL) (Sun L et al. 2012; Zhao J et al. 2012). The complex of RIPK1:RIPK3:MLKL is crucial for an execution phase of necroptosis which is strictly dependent on RIPK3-mediated phosphorylation of MLKL followed by MLKL oligomerization and translocation to membrane surfaces (Sun L et al. 2012; Wang H et al. 2014). Immunoblot analysis of cell fractions obtained by differential centrifugation of human colorectal adenocarcinoma (HT29) whole cell extracts suggests that upon necroptosis RIPK1:RIPK3:MLKL complexes shift to the plasma membrane and membranous organelles such as mitochondria, lysosome, endosome and ER (Wang H et al. 2014). These findings are supported by immunofluorescent imaging of subcellular distribution of necrosome components expressed in human cells (Wang H et al. 2014; Cai Z et al. 2014). The mechanisms of necroptosis regulation and execution downstream of MLKL remain elusive. MLKL has been proposed to induce necrosis execution in human cells (shown for HeLA and HT29 cell lines) by binding and activating phosphoglycerate mutase 5 (PGAM5) resulting in the induction of mitochondrial fission (Wang Z et al 2012). However, other studies showed that PGAM5-mediated mitochondrial fragmentation was dispensable for RIP?mediated necrosis in mouse cells (Murphy et al. 2013, Remijsen Q et al. 2014; Moujalled DM et al. 2014). Moreover, mitochondria-depleted 3T3 mouse embryo fibroblast cells were found to undergo necroptosis, suggesting that mitochondria axis may not be required for this process (Tait SW et al. 2013). Finally, RIPK3-activated MLKL has been also reported to translocate to lipid rafts of the plasma membrane where it facilitate cell death through membrane permeabilization (Cai Z et al. 2014; Dondelinger Y et al. 2014).
The Reactome module describes MLKL-mediated necroptotic events on the plasma membrane
Cell death triggered by extrinsic stimuli via death receptors or toll-like receptors (e.g., TLR3, TLR4) may result in either apoptosis or regulated necrosis (necroptosis) (Holler N et al. 2000; Kalai M et al. 2002; Kaiser WJ and Offermann MK 2005; Yang P et al. 2007). Caspase-8 (CASP8) is a cysteine peptidase, which functions as a key mediator for determining which form of cell death will occur (Kalai M et al. 2002; ). The proteolytic activity of a fully processed, heterotetrameric form of CASP8 in human and rodent cells is required for proapoptotic signaling and also for a cleavage of kinases RIPK1 and RIPK3, while at the same time preventing RIPK1/RIPK3-dependent regulated necrosis (Juo P et al. 1998; Lin Y et al. 1999; Holler N et al. 2000; Hopkins-Donaldson S et al. 2000). A blockage of CASP8 activity in the presence of caspase inhibitors such as Z-VAD-FMK (pan-caspase inhibitor), endogenous FLIP(S) or viral FLIP-like protein was found to switch signaling to necrotic cell death (Thome M et al. 1997; Kalai M et al. 2002; Feoktistova M et al. 2011; Sawai H 2013)
Activation of tumor necrosis factor receptor 1 (TNFR1) can trigger multiple signal transduction pathways to induce cell survival or cell death (Ward C et al. 1999; Micheau O and Tschopp J 2003; Widera D et al. 2006). While pro-survival signaling is initiated and regulated via the activated TNFR1 receptor complex at the cell membrane, cell death signals are induced upon the release of TRADD:TRAF2:RIP1 complex from the membrane to the cytosol where it forms death-inducing signaling complex (DISC) (Micheau O and Tschopp J 2003; Schneider-Brachert W et al. 2004). Upon apoptotic stimulation procaspase-8 or 10 is recruited into the DISC, and close proximity promotes the dimerization, autocatalytic processing, and activation of the initiator caspase-8 (and/or caspase-10) (Wang J et al. 2001; Boatright KM and Salvesen GS 2003). The initiator caspases then process and activate the downstream effector caspases such as caspase-3 in a proteolytic cascade (Stennicke HR et al. 1998). The effector caspases in turn cleave many diverse substrates, ultimately inducing cell death
Tumor necrosis factor-alpha (TNFalpha) is an inflammatory cytokine, that activates either cell survival (e.g.,inflammation, proliferation) or cell death upon association with TNF receptor 1 (TNFR1). Stimuli and the cellular context dictate cell fate decisions between survival and death which rely on tightly regulated mechanisms with checkpoints on many levels. TNFR1-mediated NFkappaB activation leads to the pro-survival transcriptional program that is both anti-apoptotic and highly proinflammatory. The constitutive NFkappaB or AP1 activation may lead to excessive inflammation which has been associated with a variety of aggressive tumor types (Jackson-Bernitsas DG et al. 2007; Zhang JY et al. 2007). Thus, the tight regulation of TNFalpha:TNFR1 signaling is required to ensure the appropriate cell response to stimuli
Activation of tumor necrosis factor receptor 1 (TNFR1) can trigger multiple signal transduction pathways to induce inflammation, cell proliferation, survival or cell death (Ward C et al. 1999; Micheau O and Tschopp J 2003; Widera D et al. 2006). Whether a TNF-alpha-stimulated cell will survive or die is dependent on the cellular context. TNF-alpha-induced signals lead to the activation of transcriptional factors such as nuclear factor-kappa B (NFkappaB) and activator protein-1 (AP1) (Ward C et al. 1999; Widera D et al. 2006; Tsou HK et al. 2012).
The binding of TNF-alpha to TNFR1 leads to recruitment of the adapter protein TNFR1-associated death domain (TRADD) and of receptor‑interacting protein 1 (RIPK1). TRADD subsequently recruits also TNF receptor-associated factor 2 (TRAF2). RIPK1 is promptly K63-polyubiquitinated which results in the recruitment of the TAB2:TAK1 complex and the IkB kinase (IKK) complex to TNFR1. The activated IKK complex mediates phosphorylation of the inhibitor of NFkappaB (IkB), which targets IkB for ubiquitination and subsequent degradation. Released NFkappaB induces the expression of a variety of genes including inflammation-related genes and anti-apoptotic genes encoding proteins such as inhibitor of apoptosis proteins cIAP1/2, Bcl-2, Bcl-xL or cellular FLICE-like inhibitory protein (FLIP) (Blonska M et al. 2005; Ea CK et al. 2006; Wu CJ et al. 2006; Chen C et al. 2000; Manna SK et al. 2000; Kreuz S et al. 2001; Micheau O et al. 2001). NFkB-mediated inhibition of cell death also involves attenuating TNF-induced activation of c-Jun activating kinase (JNK). Whereas transient activation of JNK upon TNF treatment is associated with cellular survival, prolonged JNK activation contributes to cell death. However, as caspases activate JNK quite efficiently, JNKs are also regularly stimulated in course of apoptosis without being essential for cell death (Wicovsky A et al. 2007). AP1-mediated gene induction results from activation of JNK via TRAF2 (not shown here) (Tsou HK et al. 2012). While pro-survival signaling is initiated and regulated via the activated TNFR1 receptor complex at the cell membrane, cell death signals are induced by internalization-associated fashion upon the release of RIPK1 from the membrane complex (Micheau O and Tschopp J 2003; Schneider-Brachert W et al. 2004; Tchikov V et al. 2011).
TNFR1-mediated transcriptional activity of NFkB is both antiapoptotic and highly proinflammatory and thus must be tightly regulated to prevent constitutive activation that leads to persistent inflammation and cancer (Ward C et al. 1999; Fujihara S et al. 2002; Pekalski J et al. 2013; Kankaanranta H et al. 2014; Shukla S and Gupta S 2004; Jackson-Bernitsas DG et al. 2007; Zhang JY et al. 2007). Multiple mechanisms normally ensure the proper control of NFkappaB activation including two negative feedback loops mediated by NFkappaB inducible inhibitors, IkB-alpha (NFKBIA) and ubiquitin-editing protein A20 (He KL & Ting AT 2002; Wertz IE et al. 2004; Vereecke L et al. 2009; Pekalski J et al. 2013)
Tumor necrosis factor-alpha (TNFA) exerts a wide range of biological effects through TNF receptor 1 (TNFR1) and TNF receptor 2 (TNFR2). Under normal physiological conditions TNFR2 exhibits more restricted expression, being found on certain subpopulation of immune cells and few other cell types (Grell et al. 1995 ). TNFR1 mediated signalling pathways have been very well characterized but, TNFR2 has been much less well studied. TNFR1 upon activation by TNFA activates apoptosis through two pathways, involving the adaptor proteins TNFR1-associated death domain (TRADD) and fas-associated death domain (FADD). In contrast, TNFR2 signalling especially in highly activated T cells, induces cell survival pathways that can result in cell proliferation by activating transcription factor NF-kB (nuclear factor-kB) via the alternative non-canonical route. TNFR2 signalling seems to play an important role, in particular for the function of regulatory T cells. It offers protective roles in several disorders, including autoimmune diseases, heart diseases, demyelinating and neurodegenerative disorders and infectious diseases (Faustman & Davis 2010).Activation of the non-canonical pathway by TNFR2 is mediated through a signalling complex that includes TNF receptor-associated factor (TRAF2 and TRAF3), cellular inhibitor of apoptosis (cIAP1 and cIAP2), and NF-kB-inducing kinase (NIK). In this complex TRAF3 functions as a bridging factor between the cIAP1/2:TRAF2 complex and NIK. In resting cells cIAP1/2 in the signalling complex mediates K48-linked polyubiquitination of NIK and subsequent proteasomal degradation making NIK levels invisible. Upon TNFR2 stimulation, TRAF2 is recruited to the intracellular TRAF binding motif and this also indirectly recruits TRAF1 and cIAP1/2, as well as TRAF3 and NIK which are already bound to TRAF2 in unstimulated cells. TRAF2 mediates K63-linked ubiquitination of cIAP1/2 and this in turn mediates cIAP dependent K48-linked ubiquitination of TRAF3 leading to the proteasome-dependent degradation of the latter. As TRAF3 is degraded, NIK can no longer interact with TRAF1/2:cIAP complex. As a result NIK concentration in the cytosol increases and NIK gets stabilised and activated. Activated NIK phosphorylates IKKalpha, which in turn phosphorylates p100 (NFkB2) subunit. Phosphorylated p100 is also ubiquitinated by the SCF-beta-TRCP ubiquitin ligase complex and is subsequently processed by the proteaseome to p52, which is a transcriptionally competent NF-kB subunit in conjunction with RelB (Petrus et al. 2011, Sun 2011, Vallabhapurapu & Karin 2009)
A regulated balance between cell survival and cell death is essential for normal development and homeostasis of multicellular organisms. Defects in control of this balance may contribute to autoimmune disease, neurodegeneration and cancer
Activation of NF-kB is fundamental to signal transduction by members of the TNFRSF. Expression of NF-kB target genes is essential for mounting innate immune responses to infectious microorganisms but is also important for the proper development and cellular compartmentalization of secondary lymphoid organs necessary to orchestrate an adaptive immune response. NF-kB transcription factor family is activated by two distinct pathways: the canonical pathway involving NF-kB1 and the non-canonical pathway involving NF-kB2. Unlike NF-kB1 signalling, which can be activated by a wide variety of receptors, the NF-kB2 pathway is typically activated by a subset of receptor and ligand pairs belonging to the tumor necrosis factor receptor (TNF) super family (TNFRSF) members. These members include TNFR2 (Rauert et al. 2010), B cell activating factor of the TNF family receptor (BAFFR also known as TNFRSF13C) (Kayagaki et al. 2002, CD40 (also known as TNFRSF5) (Coope et al. 2002, lymphotoxin beta-receptor (LTBR also known as TNFRSF3) (Dejardin et al. 2002), receptor activator for nuclear factor kB (RANK also known as TNFRSF11A) (Novack et al. 2003), CD27 and Fibroblast growth factor-inducible immediate-early response protein 14 (FN14 also known as TNFRSF12A) etc. These receptors each mediate specific biological roles of the non-canonical NF-kB. These non-canonical NF-kB-stimulating receptors have one thing in common and is the presence of a TRAF-binding motif, which recruits different TNF receptor-associated factor (TRAF) members, particularly TRAF2 and TRAF3, to the receptor complex during ligand ligation (Grech et al. 2004, Bishop & Xie 2007). Receptor recruitment of these TRAF members leads to their degradation which is a critical step leading to the activation of NIK and induction of p100 processing (Sun 2011, 2012)
Ub-specific processing proteases (USPs) are the largest of the DUB families with more than 50 members in humans. The USP catalytic domain varies considerably in size and consists of six conserved motifs with N- or C-terminal extensions and insertions occurring between the conserved motifs (Ye et al. 2009). Two highly conserved regions comprise the catalytic triad, the Cys-box (Cys) and His-box (His and Asp/Asn) (Nijman et al. 2005, Ye et al. 2009, Reyes-Turcu & Wilkinson 2009). They recognize their substrates by interactions of the variable regions with the substrate protein directly, or via scaffolds or adapters in multiprotein complexes
Procaspase-8 monomers undergo dimerization. The dimerization event occurs at death-inducing signaling complex (DISC) and results in a reposition of the procaspase-8 inter-subunit linker to become accessible for intermolecular processing by the associated procaspase-8 molecule [Keller N et al 2010; Oberst A et al 2010]
The inflammatory cytokine tumor necrosis factor alpha (TNF-alpha) is expressed in immune and nonimmune cell types including macrophages, T cells, mast cells, granulocytes, natural killer (NK) cells, fibroblasts, neurons, keratinocytes and smooth muscle cells as a response to tissue injury or upon immune responses to pathogenic stimuli (Köck A. et al. 1990; Dubravec DB et al. 1990; Walsh LJ et al. 1991; te Velde AA et al. 1990; Imaizumi T et al. 2000). TNF-alpha interacts with two receptors, namely TNF receptor 1 (TNFR1) and TNF receptor 2 (TNFR2). Activation of TNFR1 can trigger multiple signal transduction pathways inducing inflammation, proliferation, survival or cell death (Ward C et al. 1999; Micheau O and Tschopp J 2003; Widera D et al. 2006). Whether a TNF-alpha-stimulated cell will survive or die is dependent on autocrine/paracrine signals, and on the cellular context.
TRAF6 is crucial for both RIG-I- and MDA5-mediated antiviral responses. The absence of TRAF6 resulted in enhanced viral replication and a significant reduction in the production of type I IFNs and IL6 after infection with RNA virus. Activation of NF-kB and IRF7, but not that of IRF3, was significantly impaired during RIG-like helicases (RLHs) signaling in the absence of TRAF6. TRAF6-induced activation of IRF is likely to be specific for IRF7, while TRAF3 is thought to activate both IRF3 and IRF7. These results strongly suggest that the TRAF6- and TRAF3-dependent pathways are likely to bifurcate at IPS-1, but to converge later at IRF7 in order to co-operatively induce sufficient production of type I IFNs during RLH signaling
The TRAF6/TAK1 signal activates a canonical IKK complex, resulting in the activation of NF-kB as well as MAPK cascades leading to the activation of AP-1. Although TRAF6/TAK1 has been implicated in Tool like receptor (TLR) mediated cytokine production, the involvement of these molecules in the regulation of type I IFN induction mediated by RIG-I/MDA5 pathway is largely unknown. According to the study done by Yoshida et al RIG-I/IPS-1 pathway requires TRAF6 and MAP3K, MEKK1 to activate NF-kB and MAP Kinases for optimal induction of type I IFNs
Affinity Capture-Western, Two-hybrid, two hybrid array, two hybrid bait and prey pooling approach, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Biochemical Activity, Co-localization, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, proximity ligation assay, pull down, two hybrid, two hybrid array, two hybrid pooling approach, two hybrid prey pooling approach
Co-localization, Two-hybrid, proximity ligation assay, two hybrid array, two hybrid bait and prey pooling approach, two hybrid pooling approach, validated two hybrid
Affinity Capture-Western, Co-localization, Reconstituted Complex, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, proximity ligation assay, pull down
Affinity Capture-MS, Affinity Capture-Western, Biochemical Activity, Reconstituted Complex, anti tag coimmunoprecipitation, tandem affinity purification
Affinity Capture-Western, Biochemical Activity, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, coimmunoprecipitation, two hybrid, two hybrid array, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Reconstituted Complex, Two-hybrid, anti tag coimmunoprecipitation, tandem affinity purification, two hybrid
Two-hybrid, anti tag coimmunoprecipitation, two hybrid, two hybrid array, two hybrid pooling approach, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Co-crystal Structure, Reconstituted Complex, Two-hybrid, anti tag coimmunoprecipitation, coimmunoprecipitation, tandem affinity purification, two hybrid, two hybrid array, two hybrid prey pooling approach, x-ray crystallography
association, direct interaction, physical, physical association
Affinity Capture-Western, Biochemical Activity, Co-crystal Structure, FRET, Reconstituted Complex, Two-hybrid, anti tag coimmunoprecipitation, tandem affinity purification, two hybrid, two hybrid array, two hybrid pooling approach, two hybrid prey pooling approach
direct interaction, physical, physical association
Affinity Capture-MS, Affinity Capture-Western, Two-hybrid, cosedimentation through density gradient, two hybrid, two hybrid array, two hybrid pooling approach, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, two hybrid, two hybrid pooling approach
Affinity Capture-Western, Two-hybrid, two hybrid array, two hybrid bait and prey pooling approach, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Biochemical Activity, Co-localization, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, proximity ligation assay, pull down, two hybrid, two hybrid array, two hybrid pooling approach, two hybrid prey pooling approach
Co-localization, Two-hybrid, proximity ligation assay, two hybrid array, two hybrid bait and prey pooling approach, two hybrid pooling approach, validated two hybrid
Affinity Capture-Western, Co-localization, Reconstituted Complex, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, proximity ligation assay, pull down
Affinity Capture-MS, Affinity Capture-Western, Biochemical Activity, Reconstituted Complex, anti tag coimmunoprecipitation, tandem affinity purification
Affinity Capture-Western, Biochemical Activity, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, coimmunoprecipitation, two hybrid, two hybrid array, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Reconstituted Complex, Two-hybrid, anti tag coimmunoprecipitation, tandem affinity purification, two hybrid
Two-hybrid, anti tag coimmunoprecipitation, two hybrid, two hybrid array, two hybrid pooling approach, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Co-crystal Structure, Reconstituted Complex, Two-hybrid, anti tag coimmunoprecipitation, coimmunoprecipitation, tandem affinity purification, two hybrid, two hybrid array, two hybrid prey pooling approach, x-ray crystallography
association, direct interaction, physical, physical association
Affinity Capture-Western, Biochemical Activity, Co-crystal Structure, FRET, Reconstituted Complex, Two-hybrid, anti tag coimmunoprecipitation, tandem affinity purification, two hybrid, two hybrid array, two hybrid pooling approach, two hybrid prey pooling approach
direct interaction, physical, physical association
Affinity Capture-MS, Affinity Capture-Western, Two-hybrid, cosedimentation through density gradient, two hybrid, two hybrid array, two hybrid pooling approach, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, two hybrid, two hybrid pooling approach
Affinity Capture-MS, Affinity Capture-Western, Biochemical Activity, Co-localization, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, proximity ligation assay, pull down, two hybrid, two hybrid array, two hybrid pooling approach, two hybrid prey pooling approach
Affinity Capture-Western, Biochemical Activity, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, coimmunoprecipitation, two hybrid, two hybrid array, two hybrid prey pooling approach, validated two hybrid
Two-hybrid, anti tag coimmunoprecipitation, two hybrid, two hybrid array, two hybrid pooling approach, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Co-crystal Structure, Reconstituted Complex, Two-hybrid, anti tag coimmunoprecipitation, coimmunoprecipitation, tandem affinity purification, two hybrid, two hybrid array, two hybrid prey pooling approach, x-ray crystallography
association, direct interaction, physical, physical association
Affinity Capture-MS, Affinity Capture-Western, Two-hybrid, cosedimentation through density gradient, two hybrid, two hybrid array, two hybrid pooling approach, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-Western, Two-hybrid, two hybrid array, two hybrid bait and prey pooling approach, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Biochemical Activity, Co-localization, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, proximity ligation assay, pull down, two hybrid, two hybrid array, two hybrid pooling approach, two hybrid prey pooling approach
Co-localization, Two-hybrid, proximity ligation assay, two hybrid array, two hybrid bait and prey pooling approach, two hybrid pooling approach, validated two hybrid
Affinity Capture-Western, Co-localization, Reconstituted Complex, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, proximity ligation assay, pull down
Affinity Capture-MS, Affinity Capture-Western, Biochemical Activity, Reconstituted Complex, anti tag coimmunoprecipitation, tandem affinity purification
Affinity Capture-Western, Biochemical Activity, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, coimmunoprecipitation, two hybrid, two hybrid array, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Reconstituted Complex, Two-hybrid, anti tag coimmunoprecipitation, tandem affinity purification, two hybrid
Two-hybrid, anti tag coimmunoprecipitation, two hybrid, two hybrid array, two hybrid pooling approach, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Co-crystal Structure, Reconstituted Complex, Two-hybrid, anti tag coimmunoprecipitation, coimmunoprecipitation, tandem affinity purification, two hybrid, two hybrid array, two hybrid prey pooling approach, x-ray crystallography
association, direct interaction, physical, physical association
Affinity Capture-Western, Biochemical Activity, Co-crystal Structure, FRET, Reconstituted Complex, Two-hybrid, anti tag coimmunoprecipitation, tandem affinity purification, two hybrid, two hybrid array, two hybrid pooling approach, two hybrid prey pooling approach
direct interaction, physical, physical association
Affinity Capture-MS, Affinity Capture-Western, Two-hybrid, cosedimentation through density gradient, two hybrid, two hybrid array, two hybrid pooling approach, two hybrid prey pooling approach, validated two hybrid
Affinity Capture-MS, Affinity Capture-Western, Reconstituted Complex, Two-hybrid, anti bait coimmunoprecipitation, anti tag coimmunoprecipitation, two hybrid, two hybrid pooling approach