FLIP(S) is a short-lived protein which is sensitive to ubiquitination and proteasomal degradation (Poukkula M et al. 2005). Protein kinase C (PKC)- mediated phosphorylation of FLIP(S) at Ser193 was shown to prolongs the half-life of FLIP(S) by inhibiting its polyubiquitination (Kaunisto A et al. 2009).", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q12933-1", "Q14790-1", "Q13546-1" ], "evidence": [ { "id": "R-HSA-3465429", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-3465429" } ] }, { "id": "R-HSA-3465448", "name": "Caspase-8 and FLIP(L) processing at DISC", "equation": "", "summary": "In the presence of FLIP(L), both caspase-8 and FLIP(L) are recruited and partially processed at the death-inducing signaling complex (DISC). The partially processed proteins stay bound to the DISC.
The long cellular FLIP (FLIP(L) or c-FLIPL) has two death effector domains (DED) and a caspase-like domain that lacks catalytic activity due to absence of a cysteine residue. Processing of FLIP(L) occurs at the DISC and depends on caspase-8 activity (zymogen and mature form). Upon activation FLIP(L) is cleaved to generate N-terminal FLIP(p43) and C-terminal FLIP(p12)(Irmler M et al. 1997; Jong WY et al. 2009). Processed FLIP(L) can enhance the proteolytic activity of procaspase-8 (Chang DW et al. 2002; Jong WY et al. 2009; Pop C et al. 2011). However, the increased FLIP(L) protein levels in cells have been found to limit caspase-8 activity and inhibit apoptotic signaling pathway,", "cellular_location": "cytosol", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q12933-1", "Q14790-1", "Q13546-1" ], "evidence": [ { "id": "R-HSA-3465448", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-3465448" } ] }, { "id": "R-HSA-5213462", "name": "RIPK3 binds RIPK1", "equation": "", "summary": "Necroptosis is a regulated form of necrotic cell death that is mediated by receptor-interacting serine/threonine-protein kinase 1 (RIPK1), RIPK3 and mixed-lineage kinase domain-like protein (MLKL). 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 ligands for toll like receptors 3 (TLR3) and TLR4 (Holler N et al. 2000; He S et al. 2009; Feoktistova M et al. 2011; Voigt S et al. 2014). In contrast to apoptosis, however, necroptosis is optimally induced when caspases are inhibited (Holler N et al. 2000; Sawai H 2014). Otherwise active caspase 8 (CASP8) blocks necroptosis by the proteolytic cleavage of RIPK1 and RIPK3 (Kalai M et al. 2002; Degterev A et al. 2008; Feng S et al. 2007). When CASP8 activity is inhibited under certain pathophysiological conditions or by pharmacological agents, RIPK1 is engaged in physical and functional interactions with its homolog RIPK3 leading to formation of the necrosome, a cytosolic necroptosis-inducing complex consisting of RIPK1 and RIPK3 (Sawai H 2013; Moquin DM et al. 2013; Kalai M et al. 2002; He S et al. 2009, Zhang DW et al. 2009). RIPK3 was found to be essential for necroptosis (He S et al. 2009; Cho YC et al. 2009; Zhang DW et al. 2009). Embryonic fibroblasts from RIPK3 knockout mice were resistant to necrosis induced by TNF or during virus infection (He S et al. 2009; Cho YC et al. 2009). RIPK3-/- mice exhibited severely impaired vaccinia virus (VV)-induced tissue necrosis, inflammation, and control of viral replication (Cho YC et al. 2009). RIPK3 knockout animals were devoid of inflammation inflicted tissue damage in an acute pancreatitis model (He S et al. 2009). Further, RIPK3 knockdown in the human colorectal adenocarcinoma (HT-29) cell line, that stably expressed a shRNA targeting RIPK3, led to blockage of TNF-alpha, TRAIL or FAS-induced pronecrotic signaling pathway (He S et al. 2009). Knockdown of RIPK3 in human keratinocyte HaCaT cells blocked TLR3-mediated necroptosis without affecting the apoptotic response. Moreover, overexpression of RIPK3 in human epithelial carcinoma (HeLa) cells led to increased caspase-independent TLR3-induced cell death in the absence of inhibitors of apoptosis (IAPs) (Feoktistova M et al. 2011). Within the necrosome RIPK1 and RIPK3 bind to each other through their RIP homotypic interaction motif (RHIM) domains (Sun X et al. 2002; Li J et al. 2012; Mompean M et al. 2018). The RHIMs can facilitate RIPK1:RIPK3 oligomerization, allowing them to form amyloid-like fibrillar structures (Li J et al. 2012; Mompean M et al. 2018). RIPK1 serves as a scaffold to enable RIPK3 to assemble into homooligomers. Owing to the size and the toxicity arising from overexpressing RIPK1 and RIPK3 in cells, this has been problematic to study in detail. The underlying mechanism is still debated, but RIPK3 transphosphorylation is believed to be crucial for MLKL activation (Orozco S et al. 2014; Cook WD et al. 2014). Necroptosis is a tightly regulated process. The balance between caspase-dependent apoptosis and RIPK-dependent necroptosis was found to depend on the levels of CASP8 and cellular FADD-like interleukin-1 beta converting enzyme (FLICE)-inhibitory protein (cFLIP, encoded by the CFLAR gene) (Feoktistova M et al. 2011). cFLIP exists in two main isoforms: long cFLIP(L) and short cFLIP(S) forms. cFLIP(L) (CFLAR) prevented apoptosis and necroptosis, whereas FLIP(S) inhibited apoptosis but promoted necroptosis (Feoktistova M et al. 2011; Dillon CP et al. 2012). A blockage of CASP8 activity in the presence of viral FLIP-like protein was found to switch signaling to necrotic cell death (Sawai H 2013). Cell level of free active RIPK1 can be controlled by targeting RIPK1 for proteasomal degradation via K48-linked polyubiquitination mediated by baculoviral IAP repeat containing proteins BIRC2 and BIRC3 (also known as cellular inhibitor of apoptosis proteins cIAP1 and cIAP2) (Varfolomeev E et al, 2008; Bertrand MJM et al. 2008; Tenev T et al. 2011). The carboxyl terminus of Hsp70-interacting protein (CHIP or STUB1) was shown to negatively regulate necroptosis by ubiquitylation-mediated degradation of RIPK3 (Seo J et al. 2016). Further, O-linked \u03b2-N-acetylglucosamine (O-GlcNAc) transferase (OGT) was found to prevent necroptosis by suppressing RIPK3 activity (Li X et al. 2019; Zhang B et al. 2019). During infection in human cells, herpes simplex virus (HSV)-1 and HSV-2 can modulate cell death pathways using the large subunit (R1) of viral ribonucleotide reductase (RIR1 or UL39). Viral RIR1 blocked necroptosis in infected human cells by interactions with RIPK1, RIPK3 and CASP8 (Guo H et al. 2015; Mocarski ES et al. 2015).
This Reactome event shows RHIM-dependent interaction of RIPK1 and RIPK3.
",
"cellular_location": "cytosol",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q9UNE7-1",
"Q14790-1",
"P98170-1",
"Q13546-1",
"O15294-1",
"Q13490-1",
"Q13489-1",
"Q9Y572-1"
],
"evidence": [
{
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}
]
},
{
"id": "R-HSA-5357757",
"name": "BIRC(cIAP1/2) ubiquitinates RIPK1",
"equation": "",
"summary": "Receptor-interacting protein 1 (RIPK1) polyubiquitination is required for the recruitment of the downstream signaling complexes such as the IkB kinase (IKK) complex in the response to TNFR1 stimulation (Ea CK et al. 2006; Blackwell K et al. 2013). RIPK1 is polyubiquitinated at Lys377 (K377, equivalent to K376 of mouse RIPK1) (Ea CK et al. 2006). A point mutation of RIPK1 at Lys377 (K377R) was found to abolish its polyubiquitination and prevent the recruitment and activation of IKK and the TGF-\u03b2 activated kinase 1 (TAK1) complex (Ea CK et al. 2006). TNF\u03b1-induced recruitment of the IKK complex to TNFR1 is completely impaired, recruitment of TAK1 is severely reduced, and recruitment of the LUBAC E3 ligase complex, is also reduced in human RIPK1-deficient Jukart T-cells (Blackwell K et al. 2013). In vivo studies showed that RIPK1 K376R mutation activated cell death resulting in embryonic lethality in mice (Tang Y et al. 2019; Zhang X et al. 2019; Kist M et al. 2021). These data suggest that K63-linked ubiquitylation of RIPK1 at K377 prevents TNF-induced cell death.
Several E3 ligases are involved in TNF-\u03b1 signaling to initiate an immediate and effective host response to infection or injury. Among them are anti-apoptotic regulators BIRC2 and BIRC3, also known as inhibitor of apoptosis proteins (cIAP1/2). BIRC2/3 were found to constitutively associate with TRAF2 and via TRAF2 they were recruited to the TNFR1 signaling complex (Samuel T et al. 2006; Bertrand et al, 2008; Varfolomeev E et al, 2008). BIRC2/3 can directly ubiquitinate RIPK1 within the TNFR1 receptor complex allowing it to bind to the TAB2:TAK1 complex, a process reversed by the deubiquitinase CYLD and A20 (Bertrand et al, 2008; Varfolomeev et al, 2008; Moquin DM et al. 2013; Shembade N et al. 2010; Wertz IE et al. 2004). In conjunction with the ubiquitin conjugating enzyme (E2) enzyme UbcH5a, BIRC2/3 was shown to mediate polymerization of both K63-linked and linear Met1-linked chains on RIPK1 (Varfolomeev E et al, 2008; Bertrand et al, 2008; Blackwell K et al. 2013). TRAF2 promotes BIRC-mediated linear and K63-linked ubiquitination of RIP1 (Blackwell K et al. 2013). K11-linked polyubiquitination of RIPK1 may also depend on BIRC2 and BIRC3 (Dynek JN et al. 2010).", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q12933-1", "P98170-1", "Q13546-1", "Q13490-1", "Q13489-1" ], "evidence": [ { "id": "R-HSA-5357757", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5357757" } ] }, { "id": "R-HSA-5357776", "name": "TNF:TNFR1:TRADD:TRAF2:K63polyUb-RIPK1:BIRC2,3:LUBAC recruits IKKA:IKBKB:IKBKG", "equation": "", "summary": "K63-polyubiquitinated RIPK1 binds to IKBKG (NEMO), resulting in the recruitment of the IKK complex to the TNF-alpha receptor 1 (TNFR1) signaling complex (Ea CK et al. 2006).
In addition, the linear polyubiquitination has been implicated in the NF-kappa-B activation. The linear ubiquitin chain assembly complex (LUBAC) ligase consisting of HOIL-1L, HOIP, and SHARPIN, specifically generates linear polyubiquitin chains (Kirisako T et al. 2006; Walczak H et al. 2012). IKBKG (NEMO), a regulatory component of the I\u03baB kinase (IKK) complex, is a substrate of LUBAC. LUBAC-mediated IKBKG ubiquitination enhances IKBKG interaction with the TNFR1 complex and stabilizes this protein complex to promote activation of NF-kappa-B (Haas TL et al. 2009).
Structural analysis revealed that NPL4 zinc finger 1 (NZF1) of HOIP can simultaneously bind both leucine zipper domains of NEMO (IKBKG) and ubiquitin and that both interactions are involved in the TNF alpha-mediated NF-kappa-B activation (Fujita H et al. 2014). In addition, NEMO (IKBKG) ubiquitination required RING-between-RING (RBR) domain of HOIL-1L (Smit JJ et al. 2013)", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q96EP0-1", "Q9BYM8-1", "Q5VV17-1", "Q12933-1", "Q13107-1", "O75604-1", "O15111-1", "P98170-1", "Q13546-1", "P21580-1", "O14920-1", "Q13490-1", "Q13489-1", "Q6GQQ9-1", "Q9NQC7-1", "Q9UK80-1" ], "evidence": [ { "id": "R-HSA-5357776", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5357776" } ] }, { "id": "R-HSA-5357780", "name": "TNF:TNFR1:TRADD:TRAF2:RIPK1 recruits BIRC2/3 (cIAP1/2)", "equation": "", "summary": "Activation of tumor necrosis factor receptor 1 (TNFR1) stimulates the formation of complex that consists of TNFR1, TNFR-associated via death domain (TRADD), RIPK1, TNFR-associated factor 2 (TRAF2) and cellular inhibitor of apoptosis (BIRC2/3 also known as cIAP1/2). TRAF2 and BIRC (cIAP1) were found to form a complex in solution (Zheng et al. 2010), suggesting that TNFR1:TRADD:RIPK1 receptor complex recruits the TRAF2:BIRC complex. Following TNF-\u03b1 stimulation, RIPK1 is promptly K63-ubiquitinated at Lys377 residue by E3 ubiquitin ligases, such as BIRC2/3, to allow recruitment of the TAB2:TAK1 complex, the LUBAC and the IKK complex and eventually to stimulate the canonical NFkB activation.", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q12933-1", "P98170-1", "Q13546-1", "Q13490-1", "Q13489-1" ], "evidence": [ { "id": "R-HSA-5357780", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5357780" } ] }, { "id": "R-HSA-5357828", "name": "RIPK1 is cleaved by CASP8", "equation": "", "summary": "Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) can be a part of cell death and survival signaling complexes. Whether RIPK1 functions in apoptosis, necroptosis or NF\u03baB signaling is dependent on autocrine/paracrine signals, on the cellular context and tightly regulated by posttranslational modifications of RIP1 itself. The pro-survival function of RIPK1 is achieved by polyubiquitination which is required for recruitment of signaling molecules/complexes such as the IKK complex and the TAB2:TAK1 complex to mediate activation of NF\u03baB signaling (Ea CK et al. 2006). CYLD-mediated deubiquitination of RIPK1 switches its pro-survival function to caspase-mediated pro-apoptotic signaling (Fujikura D et al. 2012; Moquin DM et al. 2013). Caspase-8 (CASP8) in human and rodent cells facilitates the cleavage of kinases RIPK1 and RIPK3 and prevents RIPK1/RIPK3-dependent necroptosis (Lin Y et al. 1999; Hopkins-Donaldson S et al. 2000; Newton K et al. 2019; Zhang X et al. 2019; Lalaoui N et al. 2020). CASP8-mediated cleavage of human RIPK1 after D324 (D325 in mice) separates the amino-terminal kinase domain from the carboxy-terminal part of the molecule preventing RIPK1 kinase activation through dimerization via the carboxy-terminal death domain and leads to the dissociation of the complex TRADD:TRAF2:RIP1:FADD:CASP8 (Lin Y et al. 1999; Meng H et al. 2018). The lack of CASP8 proteolytic activity in the presence of viral (e.g. CrmA and vICA) or pharmacological caspase inhibitors results in necroptosis induction via RIPK1 and RIPK3 (Tewari M & Dixit VM 1995; Fliss PM & Brune W 2012; Hopkins-Donaldson S et al. 2000). Cellular FLICE-like inhibitory protein (cFLIP), which is an NF-\u03baB target gene, form heterodimer with procaspase-8 and inhibits activation of CASP8 within the the TRADD:TRAF2:RIP1:FADD:CASP8:FLIP complex (Yu JW et al. 2009; Pop C et al. 2011). The presence of cFLIP (long form) limits CASP8 to cleave CASP3/7 but allow cleavage of RIPK1 to cause the dissociation of the TRADD:TRAF2:RIP1:FADD:CASP8, thereby inhibiting both apoptosis and necroptosis (Boatright KM et al. 2004; Yu JW et al. 2009; Pop C et al. 2011; Feoktistova M et al. 2011). Mice that lack CASP8 or knock-in mice that express catalytically inactive CASP8 (C362A) die in a RIPK3- and MLKL-dependent manner during embryogenesis (Kaiser WJ et al. 2011; Newton K et al. 2019). Studies using mice that express RIPK1(D325A), in which the CASP8 cleavage site Asp325 had been mutated, further confirmed that cleavage of RIPK1 by CASP8 is a mechanism for dismantling death-inducing complexes for limiting aberrant cell death in response to stimuli (Newton K et al. 2019; Lalaoui N et al. 2020). Disrupted cleavage of RIPK1 variants with mutations at D324 by CASP8 in humans leads to an autoinflammatory response by promoting the activation of RIPK1 (Tao P et al. 2020; Lalaoui N et al. 2020).", "cellular_location": "cytosol", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q12933-1", "Q14790-1", "Q13546-1" ], "evidence": [ { "id": "R-HSA-5357828", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5357828" } ] }, { "id": "R-HSA-5357845", "name": "K63polyUb-RIPK1 is deubiquitinated", "equation": "", "summary": "K63-deubiquitination of RIP1 abolishes its ability to activate NF-kappa-B upon TNF-alpha stimulation and leads to the formation of the cytosolic caspase-8 containing complex II and subsequent apoptosis.", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q5VV17-1", "Q12933-1", "Q13107-1", "O75604-1", "P98170-1", "Q13546-1", "P21580-1", "Q13490-1", "Q13489-1", "Q6GQQ9-1", "Q9NQC7-1", "Q9UK80-1" ], "evidence": [ { "id": "R-HSA-5357845", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5357845" } ] }, { "id": "R-HSA-5357860", "name": "TNF:TNFR1:TRADD:TRAF2:K63polyUb-RIPK1:BIRC2/3:LUBAC recruits TAK1 complex", "equation": "", "summary": "Polyubiquitinated RIPK1 binds to TAB2 resulting in the recruitment of the TAB2:TAK1 complex. The K63-linked ubiqitination on Lys377 of RIPK1 was shown to mediate the association of RIPK1 with the TAB2:TAK1 complex (Li H et al. 2006)", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q96EP0-1", "Q9BYM8-1", "Q5VV17-1", "O43318-1", "Q12933-1", "Q13107-1", "O75604-1", "P98170-1", "Q13546-1", "P21580-1", "Q13490-1", "Q13489-1", "Q6GQQ9-1", "Q9NQC7-1", "Q9UK80-1" ], "evidence": [ { "id": "R-HSA-5357860", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5357860" } ] }, { "id": "R-HSA-5357904", "name": "TNF:TNFR1:TRADD:TRAF2:RIPK1 binds LUBAC", "equation": "", "summary": "Ubiquitinated TRAF2 and BIRC2/3 were reported to recruit an additional E3 ligase complex, the linear ubiquitin (Ub) chain assembly complex (LUBAC). LUBAC is thought to bind K63 chains on BIRC2/3 but produce Met1 (M1)-linked (also known as linear) Ub chains to facilitate recruitment and Met1-linked ubiquitination of NEMO (IKBKG), the regulatory subunit of the IKK complex (Haas TL et al. 2009). LUBAC enhances NEMO interaction with the TNFR1 receptor signaling complex and thus IKK complex, stabilizes this protein complex, and promotes efficient TNF-induced activation of NFkappaB resulting in apoptosis inhibition (Haas TL et al. 2009)
LUBAC consists of the chain-assembling E3 ligase HOIP as well as HOIL-1 and SHARPIN (Kirisako T et al. 2006; Walczak H et al. 2012). Importantly, deletion of the LUBAC component SHARPIN in mice or mutation of HOIL-1 in humans, lead to hyperinflammatory phenotypes, indicating key roles of LUBAC and linear Ub chains in the response to infection and inflammation (Gerlach B et al. 2011; Ikeda F et al. 2011; Tokunaga F et al. 2011; Boisson B et al. 2012).
HOIP belongs to the RING-between-RING (RBR) family of E3 ligases and is the catalytic component of LUBAC (Spratt DE et al. 2014). RBR E3 ligase domain and a conserved C-terminal extension of HOIP are responsible for assembling Met1-linked chains (Smit JJ et al., 2012; Stieglitz B et al. 2012 and 2013). HOIP was reported to act as RING/HECT hybrids, employing RING1 to recognize ubiquitin-loaded E2 while a conserved cysteine in RING2 domain subsequently forms a thioester intermediate with the transferred or \u201cdonor\u201d ubiquitin (Stieglitz B et al. 2013). A Ub-associated (UBA) domain mediates interactions with HOIL-1L (Yagi H et al. 2012), while N-terminal PUB domain may be involved in interaction with regulatory proteins such as OTULIN to control NFkappaB signaling (Elliott PR et al. 2014). HOIP also comprises several NPL4 zinc finger (NZF) Ub binding domains (UBDs) that target it to ubiquitinated proteins (Haas et al. 2009; Fujita H et al. 2014).
Structural analysis revealed that NZF1 of HOIP can simultaneously bind both leucine zipper (CoZi) domains of NEMO (IKBKG) and ubiquitin and that both interactions are involved in TNF \u03b1-mediated NFkappaB activation (Fujita H et al. 2014). In addition, NEMO (IKBKG) ubiquitination required RBR domain of HOIL-1L (Smit JJ et al. 2013).", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q96EP0-1", "Q9BYM8-1", "Q12933-1", "P98170-1", "Q13546-1", "Q13490-1", "Q13489-1" ], "evidence": [ { "id": "R-HSA-5357904", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5357904" } ] }, { "id": "R-HSA-5357928", "name": "CLIP3 and CYLD bind TNF signaling complex", "equation": "", "summary": "CAP-GLY domain containing linker protein 3 (CLIP3 or CLIPR-59) is thought to function as an adaptor protein recruiting CYLD into the TNFR1 signaling to facilitate CYLD-mediated deubiquitination of RIPK1 in TNFalpha signaling (Fujikura D et al. 2012). CLIP3-assisted CYLD-mediated K63-deubiquitination of RIPK1 may promote caspase-8 activation to induce apoptosis by TNFalpha. The effects of CLIP3 (CLIPR-59) knockdown on apoptosis induction by TNFalpha were more effective in human cervical cancer HeLa cells than in human alveolar basal epithelial A549 cells or human fibrosarcoma HT1080 cells. These findings suggest that the role of CLIP3 on TNF-alpha-induced and RIP1-mediated pro-apoptotic signaling is dependent on cell type and context (Fujikura D et al. 2012). Further, low expression levels of CLIP3 (CLIPR-59) were detected in human glioblastoma multiforme (GBM) cells, such as U87MG, and high grade glioma biopsy samples (Ding Z et al. 2015). In malignant gliomas, a negative relationship between overexpression of speedy protein A (SPDYA or SPY1) and CLIP3 downregulation was associated with a highly aggressive phenotype of glioma (Ding Z et al. 2015; Kang H et al. 2021). In GBM cells, CLIP3 interacted with SPDYA, resulting in decreased association of CLIP3 with CYLD (Ding Z et al. 2015). This in turn led to reduced CYLD-mediated deubiquitination of RIPK1 suppressing TNF-\u03b1-induced cell death of glioma cells (Ding Z et al. 2015).", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q12933-1", "P98170-1", "Q13546-1", "Q13490-1", "Q13489-1", "Q9NQC7-1" ], "evidence": [ { "id": "R-HSA-5357928", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5357928" } ] }, { "id": "R-HSA-5634221", "name": "TRAF1 binds TRAF2 within TNFR1 signaling complex", "equation": "", "summary": "TNF-induced NFkappaB activates a group of gene products including TNF receptor associated factor (TRAF) family members and inhibitor of apoptosis proteins (BIRC or cIAP1/2). TRAFs and cIAP1/2 proteins may function cooperatively at the earliest checkpoint to suppress TNF-\u03b1-induced apoptosis (Rothe M et al. 1994,1995; Wang CU et al. 1998).
The TRAFs (TRAF1 to TRAF6) are a group of structurally similar adaptor proteins, in most cases with E3 ligase activity, that are involved in downstream signaling of various cell surface receptors such as TNFR1, TNFR2, CD40, TLRs and TCR (Jang HD et al. 2001; Fotin-Mleczek M et al. 2004; Su X et al. 2006). The hallmark feature of all TRAFs is a C-terminal TRAF-domain of approximately 230 amino acids, which is responsible for homo- and heterooligomerization of TRAF molecules (Rothe M et al. 1994). The differences in amino acid sequences in TRAF-domains define the range of TRAF interaction partners. Another important structural element of TRAFs, with an exception of TRAF1, is the N-terminal RING finger domain that modulates induction of NFkappaB and MAPK activities. As TRAF1 has no RING finger domain, the effects of TRAF1 on NFkB activation are rather unclear. It is believed that TRAF1 regulates TNF receptor activity through its ability to interact with TRAF2 (Rothe M et al.1995; Zheng C et al. 2010; Fotin-Mleczek M et al. 2004). Structural and biochemical studies showed that TRAF1:TRAF2 heterotrimer (1:2) binds BIRC (cIAP2) more strongly than TRAF2 homotrimers, suggesting that TRAF1 may modulate the interaction between TRAF2 and BIRC (cIAP1/2) and thus suppress TNF-alpha induced apoptosis (Zheng C et al. 2010). Noteworthy, TRAF1:TRAF2 heterotrimers and TRAF2 homotrimers also differ in their capability with certain receptors but there seems to be no difference with respect to TNFR1 recruitment (Fotin-Mleczek M et al. 2004). On the contrary, TNF-induced caspase-mediated cleavage of TRAF1 generates a C-terminal fragment with NFkB-inhibitory, pro-apoptotic activity (Leo e et al. 2001; Jang HD et al. 2001; Henkler F et al. 2003). Thus, the current data suggest that depending on its cleavage status TRAF1 may exert either cytoprotective or cytotoxic effect in death domain-containing receptor signaling pathways.
The heteromeric complex TRAF1:TRAF2 has been also implicated in the cross-talk of TNFR1 and TNFR2 (Wicovsky A et al. 2009).",
"cellular_location": "cytosol, plasma membrane",
"input_participant_list": [],
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"evidence": [
{
"id": "R-HSA-5634221",
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}
]
},
{
"id": "R-HSA-5668414",
"name": "TRAF2 ubiquitinates cIAP1,2 in cIAP1,2:TRAF1:TRAF2:TRAF3:NIK",
"equation": "",
"summary": "Following recruitment to receptor, TRAF2 mediates K63-linked polyubiquitination of cIAP1 and cIAP2. In addition to being an adaptor that recruits cIAP1/2 and TRAF3 to the receptor TRAF2 is also an E3 that activates cIAP1/2, through their K63-linked ubiquitination. This K63-linked ubiquitination stimulates the K48-ubiquitin ligase function of cIAP1/2 and may impose a change in the substrate specificity of cIAP1/2. Thus, rather than ubiquitinating NIK, cIAP1/2 ubiquitinates TRAF3 leading to its degradation (Vallabhapurapu et al. 2008, Wallach & Kovalenko 2008).",
"cellular_location": "cytosol, plasma membrane",
"input_participant_list": [],
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"Q12933-1",
"Q13490-1",
"Q13489-1",
"Q13114-1",
"Q99558-1"
],
"evidence": [
{
"id": "R-HSA-5668414",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5668414"
}
]
},
{
"id": "R-HSA-5668417",
"name": "cIAP1,2:TRAF2:TRAF3:NIK complex binds TNFR2 trimer",
"equation": "",
"summary": "Tumor necrosis factor receptor 2 (TNFR2) signalling starts with recruitment of the adaptor protein TNF receptor-associated factor 2 (TRAF2) to the intracellular TRAF-binding motif and consequently to indirect recruitment of the TRAF2 associated proteins cellular inhibitors of apoptosis 1 and 2 (cIAP1 and cIAP2), along with a complex of TRAF3 and NF-kB-inducing kinase (NIK) which already interact with TRAF2 in unstimulated cells (Song & Donner. 1994, Rothe et al. 1995, Rothe et al. 1994). In resting cells usually NIK is targeted for ubiquitination and proteasomal degradation however in stimulated cells NIK escapes the ubiquitination by the cIAP1,2:TRAF2::TRAF3 complex due to rapid degradation of TRAF3.",
"cellular_location": "cytosol, plasma membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q13490-1",
"Q13489-1",
"Q13114-1",
"Q99558-1"
],
"evidence": [
{
"id": "R-HSA-5668417",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5668417"
}
]
},
{
"id": "R-HSA-5668454",
"name": "K63polyUb-cIAP1,2 ubiquitinates TRAF3",
"equation": "",
"summary": "cIAP1,2 targets NIK for ubiquitination and degradation under unstimulated conditions but redirects its destructive action towards TRAF3 in response to receptor signals. K63polyUb-cIAP1,2 catalyses K48-linked polyubiquitination of TRAF3 leading to signal-induced TARF3 degradation.",
"cellular_location": "cytosol, plasma membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q13490-1",
"Q13489-1",
"Q13114-1",
"Q99558-1"
],
"evidence": [
{
"id": "R-HSA-5668454",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5668454"
}
]
},
{
"id": "R-HSA-5668481",
"name": "Protesomal degradation of K48polyUb-TRAF3",
"equation": "",
"summary": "K48-linked ubiquitination of TRAF3 further leads to its proteasome-dependent degradation. The resultant degradation of TRAF3 releases NIK from the cIAPs ubiquitin-ligase complex. NIK can escape from ubiquitination and subsequent degradation resulting in accumulation in the cytosol (Sas et al. 2012).",
"cellular_location": "cytosol, plasma membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"A5LHX3-1",
"O00487-1",
"P28074-1",
"Q99436-1",
"Q12933-1",
"P28072-1",
"Q13490-1",
"Q13489-1",
"P40306-1",
"Q13114-1",
"Q99558-1",
"P28065-1",
"P28062-1"
],
"evidence": [
{
"id": "R-HSA-5668481",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5668481"
}
]
},
{
"id": "R-HSA-5668534",
"name": "cIAP1,2 ubiquitinates NIK in cIAP1,2:TRAF2::TRAF3:NIK",
"equation": "",
"summary": "TNF receptor-associated factor 2 (TRAF2) and cellular inhibitors of apoptosis 1 and 2 (cIAP1,2) are both RING-containing ubiquitin protein ligase (E3), and the interplay between these two protein families and other molecules in the receptor complex is critical in the propagation of downstream signals (Rothe et al. 1995, Yang et al., 2000). cIAP1,2 initiates proteasomal degradation of NIK by mediating its K48-linked ubiquitination (K48-(Ub)n).",
"cellular_location": "cytosol",
"input_participant_list": [],
"output_participant_list": [
"R-HSA-5668525",
"R-HSA-914241"
],
"enzyme_list": [
"Q12933-1",
"Q13490-1",
"Q13489-1",
"Q13114-1",
"Q99558-1"
],
"evidence": [
{
"id": "R-HSA-5668534",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5668534"
}
]
},
{
"id": "R-HSA-5668543",
"name": "TRAF3:NIK binds TRAF2:cIAP1/2",
"equation": "",
"summary": "Mitogen-activated protein kinase kinase kinase 14 (MAP3K14 also named as NIK) is a central signalling component of the non-canonical pathway which integrates signals from TNFR2 and activates IkB kinase-alpha (IkBA) for triggering p100 phosphorylation and processing (Sun 2011). A tight control of NIK stability is essential to achieve controlled activation of the noncanonical NF-kB signalling upon TNFR2 activation. In unstimulated cells the level of NIK protein is extremely low, which is due to constant degradation by a ubiquitination-dependent mechanism (Liao et al. 2004). Proteasomal degradation of NIK occurs on assembly of a regulatory complex through TRAF3 complexed with NIK and TRAF2 which exists in a preassembled complex with cellular Inhibitor of apoptosis 1 (cIAP1) and cIAP2 (cIAP1,2:TRAF2::TRAF3:NIK). The c-IAPs do not directly contact TNFR2, but rather associate with TRAF2 through their N-terminal BIR motif-comprising domain (Rothe et al. 1995, Shu et al. 1996). TRAF3 functions as a bridging factor between cIAP1/2-TRAF2 E3 complex and NIK enabling cIAP to mediate K48 linked ubiquitination of NIK (Zarnegar et al. 2008, Vallabhapurapu et al. 2008, Li et al. 2004).",
"cellular_location": "cytosol",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q13490-1",
"Q13489-1",
"Q13114-1",
"Q99558-1"
],
"evidence": [
{
"id": "R-HSA-5668543",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5668543"
}
]
},
{
"id": "R-HSA-5675456",
"name": "FLIP(L) and procaspase-8 form heterodimer",
"equation": "",
"summary": "The balance between caspase-dependent apoptosis and RIPK-dependent necroptosis was found to depend on the levels of caspase-8 (CASP8) and cellular FADD-like interleukin-1 beta converting enzyme (FLICE)-inhibitory protein (cFLIP, encoded by the CFLAR gene) (Feoktistova M et al. 2011; Hughes MA et al. 2016; reviewed in Tummers B & Green DR 2017). cFLIP exists in two main isoforms: long FLIP(L) and short FLIP(S) forms. Both FLIP(L) and FLIP(S) form heterodimers with procaspase-8, however they differentially regulate CASP8 activation (Feoktistova M et al. 2011; Dillon CP et al. 2012). The pseudoprotease FLIP(L) interacts with procaspase-8 through both death effector domains (DED) and caspase-like domain (CLD) that lacks catalytic activity due to absence of a cysteine residue in FLIP(L). The procaspase-8 catalytic domain prefers heterodimerization with the CLD of FLIP(L) over homodimerization with catalytic domains of other procaspase-8 molecules (Boatright KM et al. 2004; Yu JW et al. 2009). Heterodimerization to FLIP(L) rearranges the catalytic site of procaspase-8, producing a conformation that renders the heterodimer highly active even in the absence of proteolytic processing of either caspase-8 or cFLIPL (Micheau O et al. 2002; Yu JW et al. 2009; reviewed in Tummers B & Green DR 2017). The regulatory function of FLIP(L) has been found to differ depending on its expression levels. FLIP(L) was shown to inhibit death receptor (DR)-mediated apoptosis only when expressed at high levels, while low cell levels of FLIP(L) enhanced DR signaling to apoptosis (Boatright KM et al. 2004; Okano H et al. 2003; Yerbes R et al. 2011; Hughes MA et al. 2016). When FLIP(L) is expressed at high levels, the enzymatic activity of the FLIP(L):CASP8 heterodimer with procaspase-8 being an active unit is insufficient to generate active CASP8 heterotetramers for the apoptosis induction in mammalian cells. In contrary, the residual catalytic activity of FLIP(L):CASP8 is sufficient for RIPK1/RIPK3 cleavage, which inhibited the necroptotic cell death mode (Feoktistova M et al. 2011; Dillon CP et al. 2012; Oberst A et al. 2011).",
"cellular_location": "cytosol, plasma membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q14790-1",
"Q13546-1"
],
"evidence": [
{
"id": "R-HSA-5675456",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5675456"
}
]
},
{
"id": "R-HSA-5676593",
"name": "TRAF2:TRAF1:cIAP1,2:TRAF3:NIK regulatory complex binds LTBR",
"equation": "",
"summary": "After clustering or dimerisation lymphotoxin-beta receptor (LTBR) initiates signal transduction by recruiting different TNF receptor-associated factor (TRAF) adaptors to the cytoplasmic domain. LTBR directly binds to several TRAFs, including TRAF2 and TRAF3 through its TRAF-interacting peptide motif (VanArsdale et al. 1997, Nakano et al. 1996, Sanjo et al. 2010).
Mitogen-activated protein kinase kinase kinase 14 (MAP3K14 also named as NIK) is a central signalling component of the non-canonical pathway and a tight control of NIK activation by TRAFs is essential to achieve controlled activation of the noncanonical NF-kB signalling. In unstimulated cells ubiquitin:NIK E3 ligase complex catalyses K48-linked ubiquitination of NIK, leading to constitutive NIK degradation. The ubiquitin:NIK E3 ligase is a multisubunit complex comprised of TRAF3 and TRAF2 in association with cellular inhibitors of apoptosis (cIAP1,2). In the activated state the TRAF2:cIAP1,2:TRAF3:NIK complex is recruited to the receptor upon ligand binding whereupon TRAF2-mediated, K63-linked ubiquitination of cIAP1,2 switches its K48 ubiquitin ligase activity from NIK to TRAF3. The resultant TRAF3 degradation destabilizes the TRAF-cIAP complex, so allowing the accumulation of newly synthesised NIK (Razani et al. 2011, Sun 2011).",
"cellular_location": "cytosol, plasma membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q13490-1",
"Q13489-1",
"Q13114-1",
"Q99558-1"
],
"evidence": [
{
"id": "R-HSA-5676593",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5676593"
}
]
},
{
"id": "R-HSA-5676595",
"name": "TRAFs bind RANK:RANKL",
"equation": "",
"summary": "Upon activation, RANK on osteoclasts sends signals into the cells by recruiting adapter proteins like tumor necrosis factor receptor-associated factors (TRAFs) and mediates activation of noncanonical NF-kB signalling pathways (Novack et al. 2003, Chaisson ML et al. 2004, Vaira et al. 2007). RANK interacts with TRAFs 1, 2, 3, 5, and 6 however, only TRAF2, TRAF5, and TRAF6 are functionally competent to activate signaling pathways (Kanazawa & Kudi 2004, Galibert et al. 1998, Darnay et al.1999, Darnay et al. 2000).",
"cellular_location": "cytosol, plasma membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q13490-1",
"Q13489-1",
"Q13114-1",
"Q99558-1"
],
"evidence": [
{
"id": "R-HSA-5676595",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5676595"
}
]
},
{
"id": "R-HSA-5676596",
"name": "TRAF3 binds BAFFR:BAFF",
"equation": "",
"summary": "In the absence of BAFFR (TNFSF13C) ligation to BAFF (TNFSF13B) ligand, NFkB-inducing kinase (NIK) forms a complex with TNF receptor associated factor 3 (TRAF3) and TRAF2 which exists in a preassembled complex with cellular Inhibitor of apoptosis 1 (cIAP1) and cIAP2 in the cytosol. cIAP1/2 targets NIK for degradation by ubiquitylation, there by inhibiting non-canonical NFkB pathway (Vallabhapurapu et al. 2008, Zarnegar et al. 2008). Upon BAFF trimer binding to BAFFR, TRAF3 but not TRAF2 is recruited to the receptor via a 'PVPAT' binding site. This unique feature of BAFFR to recruit TRAF3 instead of TRAF2 is primarily due to its possession of an atypical TRAF-binding sequence (Morrison et al 2005). Following recruitment to BAFFR, TRAF3 undergoes proteasomal degradation, a process which requires TRAF2 and cIAP1/2.",
"cellular_location": "cytosol, plasma membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q13490-1",
"Q13489-1",
"Q13114-1",
"Q99558-1"
],
"evidence": [
{
"id": "R-HSA-5676596",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5676596"
}
]
},
{
"id": "R-HSA-5676597",
"name": "TRAF2:TRAF1:cIAP1,2:TRAF3:NIK regulatory complex binds CD40",
"equation": "",
"summary": "After its ligation with CD40 ligand (CD40L), CD40 is activated and triggers direct recruitment of multiple TRAF proteins and initiate non-canonical NF-kB pathway. TRAF1, TRAF2, TRAF3, and TRAF6, but not TRAF4 or TRAF5, shown to bind directly to the CD40 cytoplasmic domain (Pullen et al. 1998). TRAF2 is part of the regulatory complex which includes cellular inhibitor of apoptosis (cIAP) 1 and 2 and which in turn interacts with TRAF3 and NFkB-inducing kinase (NIK). In unstimulated cells this regulatory complex acts as a negative regulator of non-canonical NFkB pathway by constantly degrading NIK, whereas up on recruitment to CD40 this complex leads to accumulation of NIK (Elgueta et al. 2009, Schonbeck & Libby 2001).",
"cellular_location": "cytosol, plasma membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q13490-1",
"Q13489-1",
"Q13114-1",
"Q99558-1"
],
"evidence": [
{
"id": "R-HSA-5676597",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5676597"
}
]
},
{
"id": "R-HSA-5676598",
"name": "TRAF2:cIAP1/2 complex binds FN14:TWEAK",
"equation": "",
"summary": "The FN14 (TNFRSF12A) intracellular domain lacks the characteristic death domain of TNF receptor superfamily (TNFRSF) but contains TNFR-associated factor (TRAF) binding sites. Upon TWEAK binding, FN14 recruits TRAF2 and TRAF3 to activate both canonical and non-canonical nuclear factor-kappa B (NF-kB) pathway (Brown et al. 2003, Saitoh et al. 2003, Sanz et al. 2010). NF-kB activation plays a key role in TWEAK-elicited inflammatory responses. TWEAK/FN14 binding induces NIK activation through targeting the degradation of TRAF2/cellular inhibitor of apoptosis (cIAP) 1 and 2 complex (Vince et al. 2008). TWEAK activation of the non-canonical NF-kB pathways promotes inflammatory responses in tubular cells. In cultured renal tubular cells TWEAK increases nuclear RelB/p52 accumulation, RelB and p52 DNA-binding activity, and NIK- and RelB-dependent CCL21 and CCL19 expression (Poveda et al. 2010).",
"cellular_location": "cytosol, plasma membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q13490-1",
"Q13489-1",
"Q13114-1",
"Q99558-1"
],
"evidence": [
{
"id": "R-HSA-5676598",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5676598"
}
]
},
{
"id": "R-HSA-5693055",
"name": "TAX1BP1:TNFAIP3(A20) binds RIPK1-containing complexes",
"equation": "",
"summary": "Expression of TNFAIP3 (also known as A20) is upregulated by NFkappaB activation. TNFAIP3 (A20) is believed to inhibit NFkappaB with the help of its ubiquitin-editing functions (Wertz IE et al, 2004). The N-terminal half of TNFAIP3 harbors a deubiquitinating (DUB) domain that mediates the deubiquitination of K63-polyubiquitinated substrates such as receptor interacting protein 1 (RIPK1), an essential mediator of the proximal TNFR1 signalling complex (Shembade N et al. 2010; Wertz IE et al. 2004). The carboxy-terminal domain of TNFAIP3 (A20), composed of seven C2/C2 zinc fingers, functions as a ubiquitin ligase by polyubiquitinating target proteins with K48-linked ubiquitin chains, thereby targeting them for proteasomal degradation (Wertz IE et al. 2004). TNFAIP3 zinc fingers have been also shown to support TNFAIP3's binding to different ubiquitinated molecules (Wertz IE et al. 2004; Shembade N et al. 2010; Lu TT et al. 2013).
The Reactome pathway shows that upon TNF receptor 1 (TNFR1) stimulation, the E3 ubiquitin ligases such as baculoviral IAP repeat-containing protein (BIRC2/3 or cIAP1/2) mediate polyubiquitination of RIPK1 generating K63-linked chains. TNFAIP3 removes these K63-linked polyubiquitin chains, preventing the interaction of RIPK1 with NFkappaB essential modulator (NEMO) (Wertz IE et al. 2004). Subsequently, TNFAIP3 facilitates addition of K48-linked polyubiquitin chains to RIPK1, targeting it for proteasomal degradation (Wertz IE et al. 2004). In this way, TNFAIP3 restricts TNF-induced NFkappaB signaling by sequential deubiquitination and ubiquitin-mediated degradation of RIPK1.
TNFAIP3 (A20) is thought to limit NFkappaB activation, however the inhibitory mechanisms for TNFAIP3 are not fully understood and are partially contradicting. A study with knockin mice expressing DUB-inactive Tnfaip3 C103A mutant reported that the deubiquitinase (DUB) activity was dispensable for LPS- or TNF-stimulated NFkappaB signaling (De A et al 2014). In contrast to Tnfaip3 knockout mice that develop perinatal lethality, the knockin Tnfaip3 C103A mice were normal and did not have an inflammatory phenotype (De A et al 2014). These finding are in agreement with an earlier study reporting that the Tnfaip3 C103A knockin mice were grossly normal for at least 4 months and contained a normal number of lymphocytes (Lu TT et al. 2013). In addition, bone marrow-derived macrophage cells (BMDM) from the knockin mice showed normal LPS- and TNF-induced NFkappaB activation and downstream gene expression, comparable to cells from wild-type mice (De A et al 2014). The study suggests that the deubiquitinase activity of TNFAIP3 in general is not obligate for most of the regulatory functions of TNFAIP3 and alternative mechanisms might be involved in TNFAIP3-mediated NFkappaB regulation (De A et al 2014). Indeed, there is biochemical evidence for different mechanisms that may contribute to TNFAIP3 inhibitory effects on TNFR1 pro-inflammatory signaling in a cell type-dependent manner:
TAX1BP1 functions as an adaptor molecule for TNFAIP3 (A20) to block TNF-alpha-stimulated signaling to NFkappaB (Shembade N et al. 2007).", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q12933-1", "P98170-1", "Q13546-1", "P21580-1", "Q13490-1", "Q13489-1" ], "evidence": [ { "id": "R-HSA-5693055", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5693055" } ] }, { "id": "R-HSA-5693108", "name": "TNFAIP3 (A20) ubiquitinates RIPK1 with K48-linked Ub chains", "equation": "", "summary": "TNFAIP3 (A20) is ubiquitin-editing enzyme with distinct peptidase and ligase domains. The amino-terminal domain of TNFAIP3 (A20), which is a de-ubiquitinating (DUB) enzyme of the OTU (ovarian tumour) family, removes K63-linked ubiquitin chains from adaptor proteins such as receptor interacting protein 1 (RIPK1) (Shembade N et al. 2010; Wertz IE et al. 2004; He KL&Ting AT 2002). The carboxy-terminal domain of TNFAIP3 (A20), composed of seven C2/C2 zinc fingers, functions as a ubiquitin ligase by polyubiquitinating target proteins with K48-linked ubiquitin chains, thereby targeting them for proteasomal degradation (Wertz IE et al. 2004). TNFAIP3 zinc fingers have been also shown to support TNFAIP3's binding to different ubiquitinated molecules (Wertz IE et al. 2004; Shembade N et al. 2010; Lu TT et al. 2013).
The Reactome pathway shows that upon TNF receptor 1 (TNFR1) stimulation, the E3 ubiquitin ligases such as baculoviral IAP repeat-containing protein (BIRC2/3 or cIAP1/2) mediate polyubiquitination of RIPK1 generating K63-linked chains. TNFAIP3 removes these K63-linked polyubiquitin chains, preventing the interaction of RIPK1 with NFkappaB essential modulator (NEMO) (Wertz IE et al. 2004). Subsequently, TNFAIP3 facilitates addition of K48-linked polyubiquitin chains to RIP1, targeting it for proteasomal degradation (Wertz IE et al. 2004). In this way, TNFAIP3 restricts TNF-induced NFkappaB signaling by sequential deubiquitination and ubiquitin-mediated degradation of RIPK1.
TNFAIP3 (A20) is thought to limit NFkappaB activation, however the inhibitory mechanisms for TNFAIP3 are not fully understood and are partially contradicting. A study with knockin mice expressing DUB-inactive Tnfaip3 C103A mutant reported that the deubiquitinase (DUB) activity was dispensable for LPS- or TNF-stimulated NFkappaB signaling (De A et al 2014). In contrast to Tnfaip3 knockout mice that develop perinatal lethality, the knockin Tnfaip3 C103A mice were normal and did not have an inflammatory phenotype (De A et al 2014). These finding are in agreement with an earlier study reporting that the Tnfaip3 C103A knockin mice were grossly normal for at least 4 months and contained a normal number of lymphocytes (Lu TT et al. 2013). In addition, bone marrow-derived macrophage cells (BMDM) from the knockin mice showed normal LPS- and TNF-induced NFkappaB activation and downstream gene expression, comparable to cells from wild-type mice (De A et al 2014). The study suggests that the deubiquitinase activity of TNFAIP3 in general is not obligate for most of the regulatory functions of TNFAIP3 and alternative mechanisms might be involved in TNFAIP3-mediated NFkappaB regulation (De A et al 2014). Indeed, there is biochemical evidence for different mechanisms that may contribute to TNFAIP3 inhibitory effects on TNFR1 pro-inflammatory signaling in a cell type-dependent manner:
This Reactome event shows pro-CASP8 binding to the cytosolic TRADD:TRAF2:RIPK1:FADD complex. This binding event is negatively regulated by optineurin (OPTN) (Nakazawa S et al. 2016).
",
"cellular_location": "cytosol",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q14790-1",
"Q13546-1"
],
"evidence": [
{
"id": "R-HSA-75240",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-75240"
}
]
},
{
"id": "R-HSA-83582",
"name": "TRADD:TRAF2:RIP1 complex dissociates from the TNF-:TNF-R1 complex.",
"equation": "",
"summary": "Once formed in context of the TNFR1 signaling complex the TRADD:TRAF2:RIPK1 complex may dissociate from the TNF:TNFR1 platform. With the recruitment of FADD and caspase-8 to the TRADD:TRAF2:RIPK1 complex the cell is pushed along the apoptotic pathway provided that the protective FLIP protein and TRAF2-associated BIRC (cIAPs) do not inhibit caspase-8 activation by RIPK1 and RIPK3-mediated activation of the necroptotic pathway.",
"cellular_location": "cytosol, plasma membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q96EP0-1",
"Q9BYM8-1",
"Q96AX9-1",
"Q12933-1",
"Q14164-1",
"Q9UHD2-1",
"P98170-1",
"Q13546-1",
"Q13490-1",
"Q13489-1",
"Q9NQC7-1"
],
"evidence": [
{
"id": "R-HSA-83582",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-83582"
}
]
},
{
"id": "R-HSA-83656",
"name": "TNF:TNFR1 binds TRADD, TRAF2 and RIPK1",
"equation": "",
"summary": "Once the TNF-\u03b1:TNFR1:TRADD:RIPK1 complex has been formed there is concomitant recruitment of TRAF2, BIRC2/3 (cIAP1/2) and then of the TAB2:TAK1 and the IKK complex. TRAF2 and BIRC (cIAP1) were found to form a complex in solution (Zheng C et al. 2010), suggesting that TNFR1:TRADD:RIPK1 receptor complex recruits the TRAF2:BIRC complex as a whole. However, the expression levels of BIRCs are typically lower compared to TRAF2 suggesting that TNF-stimulated TNFR1 complex may also recruit TRAF2 alone. RIPK1 and the TRAF2:cIAP1/2 can be released from TNFR1 receptor complex in a poorly understood process associated with internalization and after that there is the formation of a so called complex II containing the adapter protein FADD, caspase-8 and RIPK1. Complex II has the potential to activate caspase-8 (Micheau O & Tschopp J 2003). The steps leading to the JUN, NF kappaB or apoptotic pathways are rife with opportunities for modulation.",
"cellular_location": "cytosol, plasma membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q13546-1"
],
"evidence": [
{
"id": "R-HSA-83656",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-83656"
}
]
},
{
"id": "R-HSA-8862184",
"name": "USP48 cleaves polyubiquitin",
"equation": "",
"summary": "USP48 (confusingly referred to as USP31 in some literature) is a deubiquitinating enzyme that cleaves preferentially lysine-63-linked polyubiquitin chains. USP48 can also cleave lysine-48-linked polyubiquitin chains albeit to a lesser extent. USP48 can interact with TRAF2, and overexpression of USP48 inhibits NF-?B activation suggesting that it may remove ubiquitin from TRAF2, TRAF6 or another essential intermediate that lies downstream of TRAFs.",
"cellular_location": "nucleoplasm",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q86UV5-1"
],
"evidence": [
{
"id": "R-HSA-8862184",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-8862184"
}
]
},
{
"id": "R-HSA-8869456",
"name": "USP4 deubiquitinate TRAF2,TRAF6",
"equation": "",
"summary": "USP4 specifically interacts with tumor necrosis factor (TNF) receptor-associated factor 2 (TRAF2) and TRAF6 but not TRAF3. It deubiquitinates both TRAF2 and TRAF6 in vivo and in vitro, negatively regulating TNFalpha and IL-1beta-induced NF-kappaB activation and cancer cell migration (Xiao et al. 2012). USP25, a negative regulator of the virus-triggered type I IFN signaling pathway, cleaves lysine 48- and lysine 63-linked polyubiquitin chains in vitro and in vivo from DDX58 (Retinoic acid-inducible gene I (RIG-I)), TRAF2, and TRAF6 to inhibit RIG-I-like receptor-mediated IFN signaling (Zhong et al. 2013).",
"cellular_location": "cytosol",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q13107-1",
"Q9Y4K3-1"
],
"evidence": [
{
"id": "R-HSA-8869456",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-8869456"
}
]
},
{
"id": "R-HSA-918230",
"name": "Recruitment of TRAF6/TRAF2 to IPS-1",
"equation": "",
"summary": "IPS-1 interacts with TRAF2 and TRAF6 through its consensus TRAF-interaction motif (TIM) (TRAF2 143-PVGET-147 and TRAF6 153-PGENSE-158 & 455-PEENEY-460). Although IPS-1 can bind to both TRAF6 and TRAF2, TRAF2 binding is not required for IPS-1 activation of NF-kB.",
"cellular_location": "cytosol, mitochondrial outer membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q9Y4K3-1",
"Q8IUD6-1",
"Q9BYX4-1",
"Q14258-1",
"O95786-1",
"Q9C037-1"
],
"evidence": [
{
"id": "R-HSA-918230",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-918230"
}
]
},
{
"id": "R-HSA-933525",
"name": "Phosphorylation and release of IRF7",
"equation": "",
"summary": "IRF7 is activated through phosphorylation of residues Ser477 and Ser479 by TBK1/IKKi kinase complex.",
"cellular_location": "cytosol, mitochondrial outer membrane",
"input_participant_list": [],
"output_participant_list": [
"R-HSA-450318"
],
"enzyme_list": [
"Q12933-1",
"Q14164-1",
"Q9UHD2-1",
"Q9Y4K3-1",
"Q8IUD6-1",
"Q9BYX4-1",
"Q14258-1",
"O95786-1",
"Q9C037-1"
],
"evidence": [
{
"id": "R-HSA-933525",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-933525"
}
]
},
{
"id": "R-HSA-933527",
"name": "Recruitment of TBK1/IKK epsilon complex to TANK:TRAF6",
"equation": "",
"summary": "TANK acts as an adapter protein and regulates the assembly of TBK1/IKK epsilon complex with upstream signaling molecules. SIKE (for Suppressor of IKKepsilon) interacts with IKKepsilon and TBK1. SIKE is associated with TBK1 under physiological condition and dissociated from TBK1 upon viral infection. Overexpression of SIKE disrupted the interactions of IKKepsilon or TBK1 with RIG-1.",
"cellular_location": "cytosol, mitochondrial outer membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q14164-1",
"Q9UHD2-1",
"Q9Y4K3-1",
"Q8IUD6-1",
"Q9BYX4-1",
"Q14258-1",
"O95786-1",
"Q9C037-1"
],
"evidence": [
{
"id": "R-HSA-933527",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-933527"
}
]
},
{
"id": "R-HSA-933528",
"name": "Interaction of MEKK1 with TRAF6",
"equation": "",
"summary": "TRAF6 requires MEKK1 (MAP3K1) to activate NF-kB and MEKK1 may interact with TRAF6, which in turn contributes to the activation of IKK and MAPKK, leading to the activation of NF-kB and AP-1. (Yoshida et al)",
"cellular_location": "cytosol, mitochondrial outer membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q13233-1",
"Q9Y4K3-1",
"Q8IUD6-1",
"Q9BYX4-1",
"Q14258-1",
"O95786-1",
"Q9C037-1"
],
"evidence": [
{
"id": "R-HSA-933528",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-933528"
}
]
},
{
"id": "R-HSA-933530",
"name": "Activation of IKK by MEKK1",
"equation": "",
"summary": "In Human, IKKs - IkB kinase (IKK) complex serves as the master regulator for the activation of NF-kB by various stimuli. It contains two catalytic subunits, IKK alpha and IKK beta, and a regulatory subunit, IKKgamma/NEMO. The activation of IKK complex and NFkB mediated antiviral responce are dependent on the phosphorylation of IKK alpha/beta at its activation loop and the ubiquitination of NEMO.[Solt et al 2009]; [Li et al 2002]. NEMO ubiquitination by TRAF6 is required for optimal activation of IKKalpha/beta; it's remained unclear if NEMO subunit undergoes K63-linked or linear ubiquitination.
This basic trimolecular complex is referred to as the IKK complex. Each catalytic IKK subunit has a N-term kinase domain a leucine zipper (LZ) motifs, a helix-loop-helix (HLH) and a C-ter NEMO binding domain (NBD). IKK catalytic subunits are dimerized through their LZ motifs.
IKK beta is the major IKK catalytic subunit for NF-kB activation. MEKK1 can activate both IKK-alpha (IKKA) and IKK-beta (IKKB) in vivo. MEKK1 phosphorylates Ser-176 and Ser-180 in IKKA and Ser-177 and Ser-181 in IKKB activation loop and thus activate the IKK kinase activity, leading to the IkB alpha phosphorylation and NF-kB activation.",
"cellular_location": "cytosol, mitochondrial outer membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"O15111-1",
"Q13233-1",
"Q9Y4K3-1",
"Q8IUD6-1",
"Q9BYX4-1",
"O14920-1",
"Q14258-1",
"O95786-1",
"Q9C037-1"
],
"evidence": [
{
"id": "R-HSA-933530",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-933530"
}
]
},
{
"id": "R-HSA-933537",
"name": "Recruitment of TANK to TRAF6",
"equation": "",
"summary": "TRAF family member-associated NF-kB activator (TANK, also known as I-TRAF) plays an important role in IFN induction through both RIG-I and Toll-like receptor-dependent pathways. TANK has been identified as a TRAF6 binding protein. Transient transfection experiments in 293T cells revealed that TRAF6 associates with IPS-1, TBK1, IKKi, and TANK (Konno et al. 2009).",
"cellular_location": "cytosol, mitochondrial outer membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q9Y4K3-1",
"Q8IUD6-1",
"Q9BYX4-1",
"Q14258-1",
"O95786-1",
"Q9C037-1"
],
"evidence": [
{
"id": "R-HSA-933537",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-933537"
}
]
},
{
"id": "R-HSA-933538",
"name": "Recruitment of IRF7 to TRAF6",
"equation": "",
"summary": "TRAF6 associates with and activates IRF7 but not IRF3.",
"cellular_location": "cytosol, mitochondrial outer membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q14164-1",
"Q9UHD2-1",
"Q9Y4K3-1",
"Q8IUD6-1",
"Q9BYX4-1",
"Q14258-1",
"O95786-1",
"Q9C037-1"
],
"evidence": [
{
"id": "R-HSA-933538",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-933538"
}
]
},
{
"id": "R-HSA-9693929",
"name": "RIPK1 variant is not cleaved by CASP8",
"equation": "",
"summary": "Activation of receptor-interacting serine/threonine-protein kinase 1 (RIPK1) controls tumor necrosis factor receptor (TNFR)- and pattern recognition receptors-mediated apoptosis, necroptosis and inflammatory pathways. RIPK1 activity is regulated post-translationally by ubiquitylation and phosphorylation events, as well as by caspase-8 (CASP8)-mediated cleavage. CASP8 facilitates the cleavage of human and mouse RIPK1 after residues D324 and D325, respectively and prevents caspase-8-dependent apoptosis and RIPK1:RIPK3-dependent necroptosis (Lin Y et al. 1999; Hopkins-Donaldson S et al. 2000; Newton K et al. 2019; Zhang X et al. 2019; Lalaoui N et al. 2020). The dominantly inherited mutations D324N, D324H, D324V and D324Y in RIPK1 prevent CASP8 from cleaving the mutated protein, thereby promoting activation of RIPK1 and leading to an autoinflammatory response in humans (Tao P et al. 2020; Lalaoui N et al. 2020).",
"cellular_location": "cytosol",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q14790-1",
"Q13546-1"
],
"evidence": [
{
"id": "R-HSA-9693929",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9693929"
}
]
},
{
"id": "R-HSA-9697747",
"name": "Caspase-8 and FLIP(L) processing at TNFR signaling complex",
"equation": "",
"summary": "The balance between caspase-dependent apoptosis and RIPK-dependent necroptosis was found to depend on the levels of FADD-like interleukin-1 beta converting enzyme (FLICE)-inhibitory protein isoforms (cFLIP, encoded by the CFLAR gene) (reviewed in Tummers B & Green DR 2017). cFLIP exists in two main isoforms: long FLIP(L) and short FLIP(S) forms. Both FLIP(L) and FLIP(S) dimerize with procaspase-8 at the death\u2011inducing signaling complex (DISC) such as TRADD:TRAF2:RIPK1: FADD:CASP8:FLIP(L), however they differentially regulate CASP8 activation (Pop C et al. 2011; Oberst A et al. 2011; Hughes MA et al. 2009, 2016). The heterodimers of FLIP(L):CASP8 inhibit CASP8 activity limiting the cleavage of CASP3/7 but allowing the cleavage of RIPK1 to cause the dissociation of the TRADD:TRAF2:RIPK1:FADD:CASP8 complex, thereby inhibiting both apoptosis and necroptosis (Pop C et al. 2011; Oberst A et al. 2011; Hughes MA et al. 2009; Lalaoui N et al 2020). Processing of FLIP(L) also occurs at the DISC and depends on CASP8 activity (zymogen and mature form). Upon activation FLIP(L) is cleaved to generate N\u2011terminal FLIP(p43) and C\u2011terminal FLIP(p12) (Irmler M et al. 1997; Chang DW et al. 2002; Yu JW et al. 2009; Pop C et al. 2011). FLIP(S) is a truncated version of procaspase\u20118 containing tandem DEDs only. FLIP(S) acts purely as an antagonist of CASP8 activity inhibiting apoptosis. FLIP(S) has also been proposed to induce necroptosis in conditions when RIPK1 is deubiquitylated and when FLIP(L) is absent (Feoktistova M et al. 2011). Important to note that the latest statement has been shown in the context of the TLR3 signalling pathway.",
"cellular_location": "cytosol",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q14790-1",
"Q13546-1"
],
"evidence": [
{
"id": "R-HSA-9697747",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9697747"
}
]
},
{
"id": "R-HSA-9697750",
"name": "RIPK1 is cleaved by CASP8:FLIP(L)",
"equation": "",
"summary": "Receptor-interacting serine/threonine-protein kinase 1 (RIPK1) can be a part of cell death and survival signaling complexes. Whether RIPK1 functions in apoptosis, necroptosis or NFkB signaling is dependent on autocrine/paracrine signals, on the cellular context and tightly regulated by posttranslational modifications of RIP1 itself. Following ligation of TNFR1, RIPK1 is recruited to the TNFR1:TRADD:TRAF2 complex where it is ubiquitinated by BIRC2/3 (also known as inhibitor of apoptosis proteins cIAP1/2) and LUBAC. Polyubiquitination of RIPK1 is required for recruitment of signaling molecules/complexes such as the IKK complex and TAK1 complex. IKKs and TAK1 phosphorylate RIPK1 to limit its cytotoxic activity and activate NFkappaB and MAPK pathways, resulting in expression of both pro-inflammatory cytokines and pro-survival genes including FADD-like interleukin-1 beta converting enzyme (FLICE)-inhibitory protein (cFLIP, encoded by the CFLAR gene) (Ea CK et al. 2006). Conversely, deubiquitination of RIPK1, mediated by BIRC2/3 (cIAP) inhibition or the deubiquitylases A20 or CYLD, switches the pro-survival function of RIPK1 to caspase-mediated pro-apoptotic signaling (Fujikura D et al. 2012; Moquin DM et al. 2013). The TRADD:TRAF2:RIPK1 complex detaches from TNFR1 and recruits FADD and procaspase-8 (CASP8). CASP8 in human and rodent cells facilitates the cleavage of kinases RIPK1 and RIPK3 and prevents RIPK1/RIPK3-dependent necroptosis (Lin Y et al. 1999; Hopkins-Donaldson S et al. 2000; Meng H et al. 2018; Newton K et al. 2019; Zhang X et al. 2019; Tao P et al. 2020; Lalaoui N et al. 2020). The balance between caspase-dependent apoptosis and RIPK-dependent necroptosis was found to depend on the levels of CASP8 and cFLIP (CFLAR) (reviewed in Tummers B & Green DR 2017). In the presence of cFLIP, both CASP8 and FLIP are recruited to the TRADD:TRAF2:RIPK1:FADD complex. cFLIP exists in two main isoforms: long FLIP(L) and short FLIP(S) forms. The heterodimers of FLIP(L):CASP8 inhibit CASP8 activity limiting the cleavage of CASP3/7 but allowing the cleavage of RIPK1 to cause the dissociation of the TRADD:TRAF2:RIPK1:FADD:CASP8 complex, thereby inhibiting both apoptosis and necroptosis (Pop C et al. 2011; Oberst A et al. 2011; Hughes MA et al. 2009; Lalaoui N et al 2020). FLIP(S) has also been proposed to induce necroptosis in conditions when RIPK1 is deubiquitylated and when FLIP(L) is absent (Feoktistova M et al. 2011). Note that the latest statement has been proven in the context of the TLR3 signalling pathway. ; ;",
"cellular_location": "cytosol",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q14790-1",
"Q13546-1"
],
"evidence": [
{
"id": "R-HSA-9697750",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9697750"
}
]
},
{
"id": "R-HSA-9705145",
"name": "TBK1, IKBKE form homodimers",
"equation": "",
"summary": "TBK1 (tumor necrosis factor (TNF) receptor-associated factor (TRAF) family member-associated NF-\u03baB activator (TANK)-binding kinase 1) and its close homolog inhibitor-kappa-B kinase (IKK) epsilon (IKK\u03b5 or IKBKE) are serine/threonine-protein kinases that trigger phosphorylation of interferon regulatory factor 3 (IRF3) and IRF7 and subsequent expression of type I interferons (IFNs; IFN-\u03b1/\u03b2). Type I IFNs can induce the expression of numerous antiviral genes called interferon-stimulated genes (ISGs). Structural studies revealed a dimeric assembly of TBK1 stabilized by an extensive network of interactions among its kinase, ubiquitin-like (ULD) and scaffold/dimerization (SDD) domains (Larabi A et al. 2013; Tu D et al. 2013). IKBKE was also reported to form dimers (Nakatsu Y et al. 2014). Even though the contacts that stabilize the TBK1 dimer are largely conserved in IKK\u03b5 (IKBKE), studies reported differences in activation mechanisms between TBK1 and IKBKE (Larabi A et al. 2013; Tu D et al. 2013; Nakatsu Y et al. 2014). While the C-terminal region was required for dimerization of IKBKE and downstream signaling, a C-terminally truncated fragment of TBK1 formed a dimer both in vitro and in vivo and was able to induce IRF3 phosphorylation (Nakatsu Y et al. 2014). Mutants that interfere with TBK1 dimerization showed significantly reduced trans-autophosphorylation upon expression in human embryonic kidney 293 (HEK293) cells (Larabi A et al. 2013). An intact TBK1 dimer was modified by K63-linked polyubiquitination on lysine 30 and lysine 401, and these modifications were required for TBK1 activation in HEK293 cells (Tu D et al. 2013). Similar findings were reported for IKBKE (Zhou AY et al. 2013). Further, interferon-\u03b2 expression was ablated in TBK1-/- mouse embryo fibroblasts (MEFs) cells reconstituted with dimerization defective TBK1 mutants (Tu D et al. 2013). Structural studies suggest that TBK1 dimerization is required for kinase activation via transautophosphorylation at Ser172 of dimeric TBK1 (Larabi A et al. 2013; Tu D et al. 2013; Ma X et al. 2012). However, dimerization of TBK1 was not required for TBK1 downstream activity once the activation loop was phosphorylated (Ma X et al. 2012; Larabi A et al. 2013). These observations are supported by findings that amyotrophic lateral sclerosis (ALS)-associated TBK1 mutations in ULD or SDD displayed defects in dimerization of TBK1 without losing kinase activity (Ye J et al. 2019). The Reactome event shows homodimer formation of TBK1 and/or IKBKE in the RIG-I-like receptors (RLRs):mitochondrial antiviral-signaling protein (MAVS) signaling pathway.
",
"cellular_location": "mitochondrial outer membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q12933-1",
"Q14164-1",
"Q9UHD2-1",
"Q9Y4K3-1",
"Q8IUD6-1",
"Q9BYX4-1",
"Q14258-1",
"O95786-1",
"Q9C037-1"
],
"evidence": [
{
"id": "R-HSA-9705145",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9705145"
}
]
},
{
"id": "R-HSA-9705323",
"name": "Phosphorylation of TBK1/IKBKE",
"equation": "",
"summary": "Viral nucleic acids are sensed by cellular pattern-recognition receptors (PRRs), such as RIG-I-like receptors (RLR). RLRs activate the adaptor protein called mitochondrial antiviral-signaling protein (MAVS). MAVS recruits TBK1 (tumor necrosis factor (TNF) receptor-associated factor (TRAF) family member-associated NF-\u03baB activator (TANK)-binding kinase 1) and/or its close homolog inhibitor-kappa-B kinase (IKK) epsilon (IKK\u03b5 or IKBKE) via TRAFs (Fitzgerald KA et al. 2003; Fang R et al. 2017). The enzymatic activity of TBK1/IKBKE is initiated by phosphorylation at Ser172 located in the T loop of the TBK1 and IKK\u03b5 kinase domains, which is essential for the enhancement of kinase activity (Shimada T et al. 1999; Kishore N et al. 2002; Ma X et al. 2012; Gu L et al. 2013). TBK1 forms a homodimer (Larabi A et al. 2013; Tu D et al. 2013) and structural studies suggest that dimerization of TBK1 precludes autophosphorylation and activation in cis (Larabi A et al. 2013). IKBKE is also a dimer (Nakatsu Y et al. 2014). Other kinases such as IKKs were also implicated in TBK1/IKBKE activation (Fang R et al. 2017). Further, K63-linked polyubiquitination on Lys30 and Lys401 enhanced TBK1/IKBKE activation in HEK293 cells (Tu D et al. 2013; Zhou AY et al. 2013).
Activated TBK1 and IKBKE in turn trigger phosphorylation of interferon regulatory factor 3 (IRF3) and IRF7 and subsequent expression of type I interferons (IFNs; IFN-\u03b1/\u03b2). Type I IFNs can induce the expression of numerous antiviral genes called interferon-stimulated genes (ISGs).
Many viruses have evolved numerous mechanisms to evade antiviral action of type I IFNs by acting at the level of the TBK1/IKBKE kinases. For example, nonstructural protein 13 (nsp13) of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) binds and blocks TBK1 phosphorylation, while nsp6 binds TBK1 to suppress TBK1-mediated phosphorylation of IRF3 (Xia H et al. 2020). SARS-CoV-2 membrane protein M interacts with MAVS and TBK1 thus preventing the formation of MAVS signalosome (Zheng Y et al. 2020).", "cellular_location": "mitochondrial outer membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q12933-1", "Q14164-1", "Q9UHD2-1", "Q9Y4K3-1", "Q8IUD6-1", "Q9BYX4-1", "Q14258-1", "O95786-1", "Q9C037-1" ], "evidence": [ { "id": "R-HSA-9705323", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9705323" } ] }, { "id": "R-HSA-9750946", "name": "TRAF2,6 ubiquitinates NLRC5", "equation": "", "summary": "NOD-like receptor C5 (NLRC5) functions as negative regulator of the NF-kappa B signaling pathway by targeting the I-kappa-B-kinase (IKK) complex (Cui J et al. 2010). The IKK complex consists of two catalytic subunits, IKBKA (KK\u03b1 or CHUK) and IKBKB (IKK\u03b2), associated with a regulatory subunit IKBKG (NEMO). NLRC5 directly binds to CHUK and IKBKB inhibiting their phosphorylation and interaction with IKBKG (Cui J et al. 2010). The dynamics of NLRC5 interaction with IKBKB/CHUK is regulated by TRAF2 or TRAF6-dependent ubiquitination of NLRC5 (Meng Q et al. 2015). Active TRAF2/6 catalyzed K63-linked polyubiquitination of NLRC5 at K1178 in human and mouse cells in response to LPS stimulation. The ubiquitinated NLRC5 (K63-polyUb-NLRC5) blocked NLRC5 interaction with IKBKB/CHUK thereby resulting in a decreased inhibitory function of NLRC5. The TRAF2/TRAF6-mediated ubiquitination of NLRC5 was reversely regulated by USP14 (Meng Q et al. 2015).;", "cellular_location": "cytosol", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q12933-1", "O15111-1", "Q9Y4K3-1", "O14920-1" ], "evidence": [ { "id": "R-HSA-9750946", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9750946" } ] }, { "id": "R-HSA-9793679", "name": "LUBAC ubiquitinates RIPK1 at K627", "equation": "", "summary": "Ligation of TNF-\u03b1 to TNF receptor 1 (TNFR1) induces the formation of the TNFR1 signaling complex composed of TNFR1, TRADD (TNFR1-associated death domain), TRAF2 (TNF receptor associated factor-2), RIPK1 (receptor-interacting serin/threonine protein kinase 1), and E3 ubiquitin ligases BIRC2, BIRC3 (cIAP1/2, cellular inhibitor of apoptosis) and LUBAC (linear ubiquitin chain assembly complex) (Micheau O and Tschopp J 2003). The conjugation of K63-linked ubiquitin (Ub) chains by BIRC2/3 to RIPK1 allows further recruitment and activation of the TAK1 (also known as MAP3K7) complex and I\u03baB kinase (IKK) complex which in turn drives activation of NF-kappa-B (Ea CK et al. 2006; Haas et al. 2009). The catalytic activity of LUBAC, composed of HOIL-1L, HOIP, and SHARPIN, specifically generates Met1-linked (also known as linear) polyUb chains (Kirisako T et al. 2006; Walczak H et al. 2012; Rittinger K & Ikeda F 2017; Fuseya Y & Iwai K 2021). UBE2L3 functions as E2-conjugating enzyme for LUBAC (Lewis MJ et al. 2015; Fu B et al. 2014). LUBAC was shown to catalyze Met1-linked ubiquitination of RIPK1 at K627 upon co-expression of Flag-RIPK1 with Myc-tagged components of LUBAC (HOIP, HOIL1, and SHARPIN) in human embryonic kidney 293T (HEK293T) cells (Tu H et al. 2021). Linear ubiquitination of mouse Ripk1 on K612 (K627 in human) inhibited TNF-\u03b1\u2013induced apoptosis and necroptosis in mouse embryonic fibroblast (MEF) cells. Mutagenesis analysis further confirmed the importance of the K627 (K612 in mouse) ubiquitination site of RIPK1 in the TNFR1 signaling pathway (Li X et al. 2020). Further, LUBAC is known to ubiquitinate IKBKG (NEMO), a regulatory component of the IKK complex. LUBAC-mediated IKBKG ubiquitination enhanced IKBKG interaction with the TNFR1 signaling complex and stabilized this protein complex to promote activation of NF-kappa-B (Haas TL et al. 2009). Importantly, deletion of the LUBAC component SHARPIN in mice or mutation of HOIL-1 in humans, lead to hyperinflammatory phenotypes, indicating key roles of LUBAC and linear Ub chains in the response to infection and inflammation (Gerlach B et al. 2011; Ikeda F et al. 2011; Tokunaga F et al. 2011; Boisson B et al. 2012). The data suggest that LUBAC-mediated linear ubiquitylation of RIPK1 limits TNF-\u03b1\u2013induced cell death.
This Reactome event describes LUBAC-mediated Met1-linked polyubiquitination (M1polyUb) of RIPK1 at K627 within the TNFR1 signaling complex.", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q96EP0-1", "Q9BYM8-1", "Q12933-1", "P98170-1", "Q13546-1", "P68036-1", "Q13490-1", "Q13489-1" ], "evidence": [ { "id": "R-HSA-9793679", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9793679" } ] }, { "id": "R-HSA-9793680", "name": "OPTN binds polyUb-RIPK1 within the TNFR1 complex", "equation": "", "summary": "Optineurin (OPTN, also called FIP2 and NRP), is a multifunctional adaptor protein that contains several domains including two coiled-coil domains, a leucine zipper (LZ) domain, an LC3-interacting region (LIR), a ubiquitin-binding domain (UBD), and a zinc finger (ZF) domain. OPTN has been implicated in regulating various signaling pathways including NF-kappa-B activation, TBK1-mediated type I interferon production, programmed cell death, and autophagy (reviewed in Markovinovic A et al. 2017; Slowicka K & van Loo G 2018; Toth RP & Atkin JD 2018). OPTN has been identified as a negative regulator of the tumor necrosis factor \u03b1 (TNF- \u03b1)-induced signaling pathway that targets several downstream components including receptor-interacting serine/threonine protein kinase 1 (RIPK1), caspase 8 (CASP8) and ubiquitin (Ub) carboxyl-terminal hydrolase CYLD (Zhu G et al. 2007; Nagabhushana A et al. 2011; Nakazawa S et al. 2016). TNF-\u03b1 binding to TNF receptor 1 (TNFR1) results in the sequential formation of several signaling complexes that trigger inflammatory responses and cell survival or cell death (Walczak H 2011; Ofengeim D & Yuan J 2013). The rapidly forming complex-I (TNFR1 signaling complex) is assembled at the receptor\u2019s cytoplasmic tail. The components of this complex, including RIPK1, are rapidly conjugated with Ub chains by various E3 ligases (Micheau O and Tschopp J 2003; Yuan J et al. 2019). The ubiquitination status (K63-, M1-linked or Ub-free) of RIPK1 determines cell fate downstream of the TNFR1 signaling complex. OPTN has been shown to associate with TNFR1 and RIPK1 by coimmunoprecipitation in a TNF-\u03b1-stimulated mouse embryonic fibroblasts (MEF) (Zhu G et al. 2007) and human epithelial carcinoma KB cell line (a subclone of HeLa cells) (Klingseisen L et al. 2012) suggesting that OPTN is recruited to the TNFR1 complex. In OPTN-deficient HeLa cells, IP assays show enhanced association of TNFR1 with ubiquitinated RIPK1 and two subunits of linear ubiquitin chain assembly complex (LUBAC), HOIL-1L and SHARPIN Nakazawa S et al. 2016). In contrast, overexpression of OPTN suppresses these associations within the TNFR1 signaling complex suggesting that OPTN binding downregulates the TNFR1 complex activity (Nakazawa S et al. 2016). Further, endogenous OPTN immunoprecipitates with polyubiquitinated RIPK1 in TNF-\u03b1-stimulated HeLa cells (Zhu G et al. 2007; Nakazawa S et al. 2016) and with anti-linear Ub antibody in TNF-\u03b1-stimulated HEK293T cells (Nakazawa S et al. 2016). In vitro pull-down assays show that maltose-binding protein (MBP)-fused OPTN (Nakazawa S et al. 2016) or glutathione S-transferase (GST)-fused OPTN (Gleason CE et al. 2011) can be copurified with M1- and K63-linked polyubiquitin, but not K48-linked polyubiquitin. Structural studies further confirm that OPTN functions through its ability to bind polyubiquitinated proteins showing that the UBD of OPTN preferentially recognizes linear M1-linked Ub chains (Nakazawa S et al. 2016; Li F et al. 2018). A surface plasmon resonance (SPR) analysis has revealed that OPTN binds to M1-linked Ub with the micromolar affinity (Nakazawa S et al. 2016). These findings suggest that the Ub-binding activity of OPTN downregulates the TNF-\u03b1-induced signaling pathway by targeting RIPK1 function within the TNFR1 signaling complex (Zhu G et al. 2007; Nakazawa S et al. 2016). However, the precise role of OPTN downstream of TNFR1 remains unclear. TNF-\u03b1 was found to induce OPTN expression in an NF-kappa-B-dependent manner in human lung adenocarcinoma A549 cells and HeLa cells (Sudhakar C et al. 2009). OPTN was shown to suppress activation of NF-kappa-B in TNF-\u03b1-stimulated HeLa cells (Sudhakar C et al. 2009; Nakazawa S et al. 2016) and human embryonic kidney 293T (HEK293T) cells (Munitic I et al. 2013). In addition, increased NF-kappa-B activity has been observed in OPTN-deficient mouse microglial BV2 cells, neuroblastoma Neuro2a cells and hybrid NSC-34 cells produced by fusing neuroblastoma and spinal-cord motor neurons (Akizuki M et al. 2013; Maruyama H et al. 2010; Cao LL et al. 2021). Further, the UBD-disrupting mutant OPTN D474N as well as amyotrophic lateral sclerosis (ALS)-associated mutation OPTN E478G, prevent binding of OPTN to polyUb (Gleason CE et al. 2011; Nakazawa S et al. 2016) and fail to suppress TNF-alpha-mediated NF-kappa-B activation in human and mouse cells (Zhu G et al. 2007; Sudhakar C et al. 2009; Maruyama H et al. 2010; Nakazawa S et al. 2016). Elevated expression of RIPK1 and downregulated expression of OPTN has been detected in the brains of Alzheimer's disease (AD) patients and the APP/PS1 mouse model of AD (Cao LL et al. 2021). Intracerebroventricular injection of adeno-associated virus (AAV) vector encoding OPTN to APP/PS1 mice reduces neuroinflammation in microglial cells and astrocytes via RIPK-dependent NF-kappa-B pathways (Cao LL et al. 2021). Although OPTN is believed to downregulate TNF-induced inflammation, in ex vivo studies in various primary cells, including bone marrow-derived macrophages, microglia and MEFs isolated from OPTN-deficient or OPTN-insufficient mice (carrying point mutation D477N or C-terminal truncation, which cannot bind polyubiquitin), OPTN had no effect on NF-kappa-B signaling, suggesting that the mechanism of OPTN-mediated regulation is indirect and/or depends on the NF-kappa-B-mediated upregulation of OPTN expression (Sudhakar C et al. 2009; Gleason CE et al. 2011; Munitic I et al. 2013; Slowicka K et al. 2016; Markovinovic A et al. 2018; reviewed in Slowicka K & van Loo G 2018; Prescott JA et al. 2021). Further, ectopic overexpression of OPTN results in decreased protein levels of RIPK1 without affecting the mRNA levels of RIPK1 in BV2 cells, suggesting that OPTN may regulate RIPK1 activity by enhancing RIPK1 degradation (Cao LL et al. 2021). Moreover, OPTN-deficient mice developed neuropathology resembling one aspect of ALS namely dysmyelination, and this neuropathy was associated with RIPK1-dependent induction of necroptosis in the spinal cord and was linked to decreased K48-ubiquitination and turnover of RIPK1 (Ito Y et al 2016). However, dysmyelination was not confirmed in a follow-up study (Dermentzaki G et al. 2019), which showed that unmanipulated Optn-deficient mice had no phenotype and that OPTN-deficiency had an effect on RIPK1 in vitro but not in vivo. The same study did not find any significant changes in RIPK1 levels in motor cortex samples from patients with ALS (Dermentzaki et al. 2019). Further research is needed to clarify the role of RIPK1-induced necroptosis in the pathogenesis of ALS (Ito Y et al 2016; Dermentzaki et al. 2019). Moreover, as an autophagy receptor, OPTN binds polyubiquitinated cargos through its UBD and delivers them to autophagosomes via LIR-mediated interaction with microtubule-associated protein 1A/1B (MAP1LC3 or LC3), a key initiator of autophagy. The autophagy receptor function of OPTN is enhanced by TANK-binding kinase 1 (TBK1)-mediated phosphorylation of OPTN (Li F et al. 2018). The N-terminal coiled-coil domain of OPTN directly interacts with the C-terminal domain of TBK1 to form a stable complex (Li F et al. 2018). Both OPTN and TBK1 have been shown to associate with the components of the TNFR1 signaling complex in the M1 (or K63)-linked polyUb-dependent manner to alter RIPK1 function (Zhu G et al. 2007; Nakazawa S et al. 2016; Lafont E et al. 2018; Xu D et al. 2018; Taft J et al. 2021). Notably, TBK1-mediated phosphorylation of OPTN on S473 has been shown to broaden the binding specificity of OPTN to other polyubiquitin chains including K48-linked polyUb (Li F et al. 2018). Similar to OPTN, TBK1 deficiency, which is embryonically lethal (Bonnard M et al. 2000), results in the TNF-\u03b1-stimulated hyperactivation of RIPK1 kinase activity leading to necroptosis in vitro and in vivo (Xu D et al. 2018; Taft J et al. 2021). Mutations of TBK1 that cannot bind OPTN have been linked to ALS and a related neurodegenerative diasease, frontotemporal dementia (FTD) (Freischmidt A et al. 2015; Cirulli ET et al. 2015). Further, TBK1 deficiency shows limited effect on TNF-induced gene expression in human A549 and mouse embryonic fibroblasts (MEF) (Lafont E et al. 2018). Thus, OPTN may participate in the crosstalk between TNF-\u03b1-induced cell death signaling and cytoprotective autophagy by targeting RIPK1-containing complexes for autophagic degradation. Besides RIPK1, OPTN may control the TNF-\u03b1-induced signaling by binding CYLD (Nagabhushana A et al. 2011) and pro-CASP8 (Nakazawa S et al. 2016). In addition, the OPTN:TBK1 axis regulates host immune responses downstream of pattern-recognition receptors (PRR) such as Toll-like receptor 3 (TLR3) or retinoic-acid-inducible protein 1 (RIG-I, also known as DDX58) (Meena NP et al. 2016; Pourcelot M et al. 2016; Markovinovic A et al. 2018; O\u2019Loughlin T et al. 2020). OPTN has been shown to translocate to Golgi-proximal foci in human retinal pigment epithelium (RPE) cells in response to TLR3 ligand (poly(I:C)) and DDX58 ligand (pppRNA) (O\u2019Loughlin T et al. 2020). OPTN-interacting proteins, including TBK1, CYLD and components of the LUBAC complex, have been identified in these foci, suggesting that OPTN inhibits the PRR-mediated innate immune response through sequestering key components of NF-kappa-B and TBK1:IRF3 signaling pathways in the perinuclear compartment (O\u2019Loughlin T et al. 2020).
This Reactome event shows OPTN association with ubiquitinated RIPK1 within the TNFR1 signaling complex.", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q96EP0-1", "Q9BYM8-1", "Q12933-1", "P98170-1", "Q13546-1", "Q13490-1", "Q13489-1", "Q9NQC7-1" ], "evidence": [ { "id": "R-HSA-9793680", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9793680" } ] }, { "id": "R-HSA-9796342", "name": "MIB2 binds RIPK1 within TNF-:TNFR1:TRADD:RIPK1:TRAF2", "equation": "", "summary": "Ligation of TNF-\u03b1 to TNF receptor 1 (TNFR1) results in the sequential formation of several signaling complexes (Walczak H 2011). The rapidly forming complex-I (TNFR1 signaling complex) is assembled at the receptor\u2019s cytoplasmic tail and consists of TNFR1, TRADD (TNFR1-associated death domain), TRAF2 (TNF receptor associated factor-2), RIPK1 (receptor-interacting serine/threonine protein kinase 1), and E3 ubiquitin (Ub) ligases BIRC2, BIRC3 (cIAP1/2, cellular inhibitor of apoptosis) and LUBAC (linear ubiquitin chain assembly complex) (Micheau O and Tschopp J 2003; Yuan J et al. 2019). Within this complex, RIPK1 and other proteins are rapidly conjugated with Ub chains by various E3 ligases. The ubiquitination status of RIPK1 determines cell fate downstream of the TNFR1 signaling complex. The conjugation of K63-linked Ub chains by BIRC2/3 or Met1-linked Ub chains by LUBAC, have been shown to promote RIPK1-dependent pro-survival NF-kappa-B signaling while inhibiting RIPK1-mediated apoptosis and necroptosis (Micheau O and Tschopp J 2003; Yuan J et al. 2019). Deubiquitinating enzymes, such as Ub carboxyl-terminal hydrolase CYLD, remove Ub chains from RIPK1 leading to the formation of the cytosolic complex IIa, TRADD:TRAF2:RIPK1:FADD:caspase-8 (CASP8), which activates apoptosis. In addition, RIPK1 also interacts with RIPK3 and MLKL to form the cytosolic complex IIb, which activates necroptosis (Micheau O and Tschopp J 2003; Yuan J et al. 2019). In these cell death-inducing complexes, RIPK1 activity is also regulated by ubiquitination (Amin P et al. 2018; de Almagro M et al. 2015). Besides, a RING-type E3 Ub ligase mind bomb-2 (MIB2) is also recruited to the TNFR1 signaling complex-I, where it conjugates inhibitory Ub chains to RIPK1 (Feltham R et al. 2018; Nakabayashi O et al. 2021). Studies in TNF-\u03b1-stimulated epithelial cells including human breast carcinoma MDA-MB-231, fibrosarcoma HT1080, and renal adenocarcinoma 786-0 cell lines showed that endogenous MIB2 is recruited to the TNFR1 complex in a time-dependent manner, peaking at 15 min (Feltham R et al 2018). Similar results were obtained in HeLa cells (Nakabayashi O et al. 2021). Endogenous MIB2 co-immunoprecipitated with ubiquitylated RIPK1 and other components of complex-I such as TRADD, TNFR1, and SHARPIN in TNF-treated MDA-MB-231 and 786-0 cells (Feltham R et al. 2018). RIPK1 is thought to mediate the recruitment of MIB2 to the TNFR1 complex (Feltham R et al. 2018). Co-immunoprecipitation analysis showed interaction between MIB2 and RIPK1 upon co-expression of tagged proteins in human embryonic kidney 293T (HEK293T) cells (Feltham R et al. 2018). In vitro-synthesized MIB2 co-purified RIPK1 from cellular extract of MDA-MB-231 cells upon TNF/Smac mimetic-164/zVAD-fm-induced cell death. Mutagenesis studies using overexpressed proteins revealed that the N-terminal MZM region of MIB2, which contains two Mib-HERC2 domains and a ZZ-type zinc finger motif (ZZ domain), interacted with the linker region of RIPK1 in HEK293T cells (Feltham R et al. 2018). Further, mutant MIB2 carrying mutation of the coordinating Cys residue of the ZZ domain within the MZM region did not interact with RIPK1 (Feltham R et al. 2018). When compared to wild-type (wt) MIB2, mutant MIB2 lacking the functional ZZ domain required for RIPK1 binding, failed to suppress TNF-induced CASP8 activation and cell death in MIB2-deficient MDA-MB-231 cells reconstituted with either wt MIB2 or mutant MIB2 (Feltham R et al. 2018). Structural and biochemical studies of MIB1, a paralogue of MIB2, further support the essential role of the MZM region in a substrate recognition (McMillan BJ et al. 2015; Guo B et al. 2016). MIB1 also interacted with RIPK1 in overexpression experiments using HEK293T cells (not shown here). However, RIPK1 was less efficiently ubiquitinated by MIB1 than by MIB2 (Feltham R et al. 2018). Upon TNF stimulation, recruited MIB2 conjugates different types of polyUb chains to RIPK1 targeting multiple lysine (K) residues (Feltham R et al. 2018). MIB2-mediated ubiquitination of K377 is thought to suppress auto-phosphorylation of RIPK1 at S166. Auto-phosphorylated RIPK1 provides a platform to form downstream death-inducing signalling complexes-IIa and IIb, causing apoptosis or necroptosis respectively (Laurien L et al. 2020; Chen X et al. 2022). MIB2-mediated ubiquitination of K604 and K634 within the death-domain (DD) of RIPK1 is predicted to affect both DD-mediated homotypic as well as heterotypic interactions of RIPK1 (Feltham R et al. 2018). MIB2 deficiency enhanced TNF-induced phosphorylation of RIPK1 at S166 in HeLa cells (Nakabayashi O et al. 2021). Depletion of MIB2 sensitized 786-0 cells to TNF-Induced and RIPK1-dependent cell death (Feltham R et al. 2018). Further, MIB2 deficiency had no effect on TNF-\u03b1-induced NF-kappa-B signaling pathway in human colorectal carcinoma HCT116 cells, HeLa cells (Nakabayashi O et al. 2021), MDA-MB-231, 786-0 and HEK293T cells (Feltham R et al. 2018) suggesting that the E3 Ub ligase activity of MIB2 protects cells from TNF-induced cell death without affecting the NF-kappa-B-mediated signaling.
Besides RIPK1, MIB2 was found to interact with other components downstream of the TNFR1 signaling complex. MIB2-mediated K48-linked ubiquitination of CYLD targets CYLD for proteasomal degradation thus preventing CYLD-mediated deubiquitination of RIPK1 and RIPK1-dependent cell death (Uematsu A et al. 2019). In addition, MIB2 binds cellular FLICE-like inhibitory protein long (FLIP(L) encoded by the CFLAR gene) in a RIPK1-independent manner (Nakabayashi O et al. 2021). As a homolog of caspase-8 (CASP8), CFLAR controls the pro-apoptotic function of CASP8 within the complex-IIa, TRADD:FADD:TRAF2:RIPK1:CASP8. The MIB2:CFLAR interaction increased stability of CFLAR (FLIP(L)) thereby attenuating TNF-\u03b1\u2013induced apoptosis (Nakabayashi O et al. 2021). Thus, MIB2 is thought to suppress both RIPK1 kinase activity-dependent and -independent cell death, through ubiquitination of RIPK1 and cFLIPL, respectively (Nakabayashi O et al. 2021). Together, these data suggest that the E3 ligase activity of MIB2 suppresses the TNF-induced cell death by attaching polyUb chains to RIPK1, CFLAR and CYLD (Feltham R et al. 2018; Uematsu A et al. 2019; Nakabayashi O et al. 2021).
This Reactome event describes MIB2 binding to RIPK1 within the TNF-\u03b1:TNFR1:TRADD:RIPK1:TRAF2 complex.", "cellular_location": "cytosol", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q96AX9-1", "Q12933-1", "Q13546-1", "P51668-1" ], "evidence": [ { "id": "R-HSA-9796342", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9796342" } ] }, { "id": "R-HSA-9796346", "name": "MIB2 ubiquitinates RIPK1 at K377, K604, K634", "equation": "", "summary": "Ligation of TNF-\u03b1 to TNF receptor 1 (TNFR1) results in the sequential formation of several signaling complexes (Walczak H 2011). The rapidly forming complex-I (TNFR1 signaling complex) is assembled at the receptor\u2019s cytoplasmic tail and consists of TNFR1, TRADD (TNFR1-associated death domain), TRAF2 (TNF receptor associated factor-2), RIPK1 (receptor-interacting serine/threonine protein kinase 1), and E3 ubiquitin (Ub) ligases BIRC2, BIRC3 (cIAP1/2, cellular inhibitor of apoptosis) and LUBAC (linear ubiquitin chain assembly complex) (Micheau O and Tschopp J 2003; Yuan J et al. 2019). Within this complex, RIPK1 and other proteins are rapidly conjugated with Ub chains by various E3 ligases (Walczak H 2011). The ubiquitination status of RIPK1 determines cell fate downstream of the TNFR1 signaling complex. The conjugation of K63-linked Ub chains by BIRC2/3 or Met1-linked Ub chains by LUBAC, have been shown to promote RIPK1-dependent pro-survival NF-kappa-B signaling while inhibiting RIPK1-mediated apoptosis and necroptosis (Micheau O and Tschopp J 2003; Yuan J et al. 2019). Deubiquitinating enzymes, such as Ub carboxyl-terminal hydrolase CYLD, remove Ub chains from RIPK1 leading to the formation of the cytosolic complex IIa, TRADD:TRAF2:RIPK1:FADD:caspase-8 (CASP8), which activates apoptosis. In addition, RIPK1 also interacts with RIPK3 and MLKL to form the cytosolic complex IIb, which activates necroptosis (Micheau O and Tschopp J 2003; Yuan J et al. 2019). In these cell death-inducing complexes, RIPK1 activity is also regulated by ubiquitination (Amin P et al. 2018; de Almagro M et al. 2015). Besides, a RING-type E3 Ub ligase mind bomb-2 (MIB2) is also recruited to the TNFR1 signaling complex-I, where it conjugates inhibitory Ub chains to RIPK1 (Feltham R et al. 2018; Nakabayashi O et al. 2021). Studies in TNF-\u03b1-stimulated epithelial cells including human breast carcinoma MDA-MB-231, fibrosarcoma HT1080, and renal adenocarcinoma 786-0 cell lines showed that endogenous MIB2 is recruited to the TNFR1 complex in a time-dependent manner, peaking at 15 min (Feltham R et al 2018). Similar results were obtained in HeLa cells (Nakabayashi O et al. 2021). RIPK1 is thought to mediate the recruitment of MIB2 to the TNFR1 complex (Feltham R et al. 2018). Upon TNF stimulation, recruited MIB2 conjugates different types of polyUb chains to RIPK1 targeting multiple lysine (K) residues (Feltham R et al. 2018). MIB2-mediated ubiquitination of K377 is thought to suppress auto-phosphorylation of RIPK1 at S166. Autophosphorylated RIPK1 provides a platform to form downstream death-inducing signaling complexes-IIa and IIb, causing apoptosis or necroptosis respectively (Laurien L et al. 2020; Chen X et al. 2022). Ubiquitination of RIPK1 at K377 is also mediated by BIRC2/3. Further, MIB2-mediated ubiquitination of K604 and K634 within the death-domain (DD) of RIPK1 is predicted to affect both DD-mediated homotypic as well as heterotypic interactions of RIPK1 (Feltham R et al. 2018). MIB2 deficiency enhanced TNF-induced phosphorylation of RIPK1 at S166 in HeLa cells (Nakabayashi O et al. 2021). Depletion of MIB2 sensitized 786-0 cells to TNF-Induced and RIPK1-dependent cell death (Feltham R et al. 2018). Further, MIB2 deficiency had no effect on TNF\u03b1-induced NF-kappa-B signaling pathway in human colorectal carcinoma HCT116 cells, HeLa cells (Nakabayashi O et al. 2021), MDA-MB-231, 786-0 and HEK293T cells (Feltham R et al. 2018) suggesting that the E3 Ub ligase activity of MIB2 protects cells from TNF-induced cell death without affecting the NF-kappa-B-mediated signaling.
Besides RIPK1, MIB2 was found to interact with other components downstream of the TNFR1 signaling complex. MIB2-mediated K48-linked ubiquitination of CYLD targets CYLD for proteasomal degradation thus preventing CYLD-mediated deubiquitination of RIPK1 and RIPK1-dependent cell death (Uematsu A et al. 2019). In addition, MIB2 binds cellular FLICE-like inhibitory protein long (FLIP(L) encoded by the CFLAR gene) in a RIPK1-independent manner (Nakabayashi O et al. 2021). As a homolog of caspase-8 (CASP8), CFLAR controls the pro-apoptotic function of CASP8 within the complex-IIa, TRADD:FADD:TRAF2:RIPK1:CASP8. The MIB2:CFLAR interaction increased stability of CFLAR (FLIP(L)) thereby attenuating TNF-\u03b1\u2013induced apoptosis (Nakabayashi O et al. 2021). Thus, MIB2 is thought to suppress both RIPK1 kinase activity-dependent and -independent cell death, through ubiquitination of RIPK1 and FLIP(L), respectively (Nakabayashi O et al. 2021). Together, these data suggest that the E3 ligase activity of MIB2 suppresses the TNF-induced cell death by attaching polyUb chains to RIPK1, CFLAR and CYLD (Feltham R et al. 2018; Uematsu A et al. 2019; Nakabayashi O et al. 2021).
This Reactome event describes MIB2-mediated polyubiquitination of RIPK1 at K377, K604 and K634 within the TNF\u03b1:TNFR1:TRADD:RIPK1:TRAF2 complex.", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q96AX9-1", "Q12933-1", "Q13546-1", "P51668-1" ], "evidence": [ { "id": "R-HSA-9796346", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9796346" } ] }, { "id": "R-HSA-9796379", "name": "CYLD:SPATA2:LUBAC binds TNFR1 signaling complex", "equation": "", "summary": "The N-terminal methionine-linked ubiquitin (Met1-Ub) chains, or linear Ub chains, are conjugated to target proteins by the linear ubiquitin chain assembly complex (LUBAC) composed of HOIL-1L, HOIP, and SHARPIN (Kirisako T et al. 2006; Walczak H et al. 2012). LUBAC and linear polyubiquitination has been implicated in the regulation of innate immunity and cell death (Tokunaga F et al. 2011; Gerlach B et al. 2011). LUBAC activity is regulated by deubiquitinases (DUBs) such as OTULIN and CYLD, which hydrolyze Ub chains to reverse the modification of target proteins (Takiuchi T et al. 2014). OTULIN and CYLD associate with HOIP, the catalytic subunit of LUBAC, to cleave Ub chains in a linkage-specific fashion. OTULIN exclusively hydrolyzes Met1-Ub, while CYLD disassembles both Met1-Ub and Lys63-Ub (Fiil BK et al. 2013; Harhaj EW and Dixit VM 2012; Hrdinka M et al. 2016; Sato Y 2022). The CYLD interaction with LUBAC is facilitated by spermatogenesis-associated protein 2 (SPATA2) (Elliott PR et al. 2016; Kupka S et al. 2016; Schlicher L et al. 2016; Wagner SA et al. 2016). Genome-wide siRNA screen identified SPATA2 as a gene involved in mediating necroptosis (Hitomi J et al. 2008). Structural and biochemical studies revealed that the N-terminal PNGase/UBA or UBX (PUB) domain of SPATA2 interacts with the Ub-specific protease (USP) domain of CYLD, whereas the C-terminal PUB-interacting motif (PIM) of SPATA2 binds the PUB domain of HOIP (reviewed in Schlicher L et al. 2017; Elliott PR et al. 2016; Kupka S et al. 2016; Schlicher L et al. 2016). Under steady-state conditions, SPATA2 was found to bridge CYLD and LUBAC forming the trimeric CYLD:SPATA2:LUBAC complex (Wagner SA et al. 2016; Elliott PR et al. 2016; reviewed in Schlicher L et al. 2017). In TNF\u03b1-stimulated human and mouse cells, CYLD:SPATA2:LUBAC is rapidly recruited into the TNFR1 signaling complex (Wagner SA et al. 2016; Elliott PR et al. 2016; Kupka S et al. 2016; Schlicher L et al. 2016; Wei R et al. 2017; reviewed in Schlicher L et al. 2017). Knockdown of SPATA2 selectively abolished CYLD interaction with the TNFR1 complex, without abolishing binding of LUBAC components (Wagner SA et al. 2016). Within the TNFR1 signaling complex, SPATA2 promotes the deubiquitinase activity of CYLD resulting in CYLD-mediated removal of Met1- and K63-linked polyubiquitin chains from specific substrates such as RIPK1 (Wei R et al. 2017). SPATA2 deficiency increased the Met1-linked ubiquitination of RIPK1, which resulted in inhibition of RIPK1 kinase activity and RIPK1-mediated cell death in mouse cells (Wei R et al. 2017). SPATA2 deficiency promoted the production of proinflammatory cytokines in TNF\u03b1-treated mice in vivo (Wei R et al. 2017). Further, SPATA2 deficiency protected against TNF-induced cell death in human and mouse cells (Wagner SA et al. 2016; Kupka S et al. 2016; Schlicher L et al. 2016; Wei R et al. 2017). These data suggest that SPATA2 regulates inflammatory signaling and cell death program via linking CYLD and LUBAC to limit LUBAC-mediated Met1-Ub.
This Reactome event shows the recruitment of the CYLD:SPATA2:LUBAC complex to the TNFR1 signaling complex. ; ;", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q96EP0-1", "Q9BYM8-1", "Q12933-1", "P98170-1", "Q13546-1", "Q13490-1", "Q13489-1", "Q9NQC7-1" ], "evidence": [ { "id": "R-HSA-9796379", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9796379" } ] }, { "id": "R-HSA-9815501", "name": "MAPKAPK2 phosphorylates RIPK1 at S320", "equation": "", "summary": "Binding of TNF\u03b1 to TNF receptor 1 (TNFR1) induces the sequential formation of several signaling complexes, namely complex I and complex IIa/b (Micheau O and Tschopp J 2003; Walczak H 2011; Yuan J et al. 2019). These complexes support either cell survival (complex I) or cell death (complex II). The dynamic assembly of these complexes is tightly regulated by proteolysis, ubiquitination and phosphorylation of receptor-interacting serine/threonine protein kinase 1 (RIPK1) and other components of the TNF\u03b1 signaling pathway (reviewed in Yuan J et al. 2019; Varfolomeev E & Vucic D 2022). RIPK1 functions as a key regulator of both cell survival and cell death (reviewed in Ju E et al. 2022). Deubiquitination of RIPK1 leads to the activation of RIPK1 kinase activity, which promotes autophosphorylation of RIPK1 and RIPK1 kinase-dependent cell death (reviewed in Ju E et al. 2022). The kinase activity of RIPK1 is regulated by phosphorylation (Lafont E et al. 2018; Dondelinger Y et al. 2019; reviewed in Delanghe T et al. 2020; Ju E et al. 2022). The components of I-kappa-B kinase complex, namely inhibitor of nuclear factor kappa B subunit \u03b1 (IKK\u03b1 or CHUK) and subunit \u03b2 (IKK\u03b2 or IKBKB), can directly phosphorylate RIPK1 within the membrane-bound TNFR1 signaling complex (complex I) (Dondelinger Y et al. 2019; Delanghe T et al. 2020). In addition, TANK binding kinase 1 (TBK1) and IKK\u03b5 (IKBKE) are recruited to complex I to phosphorylate RIPK1 independently from IKK\u03b1/IKK\u03b2. These phosphorylation events suppress activation of RIPK1 within complex I, preventing subsequent formation of the death-inducing complex II (Lafont E et al. 2018; reviewed in Delanghe T et al. 2020). In the cytosol, RIPK1 is phosphorylated by MAPK-activated protein kinase 2 (MAPKAPK2 or MK2) (Jaco I et al. 2017; Dondelinger Y et al. 2017; Menon MB et al. 2017). MAPKAPK2 (MK2) deficiency sensitized human and mouse cells to TNF-induced RIPK1-dependent cell death (Jaco I et al. 2017; Dondelinger Y et al. 2017; Menon MB et al. 2017; Chen IT et al. 2021). In the mouse model of TNF\u03b1-induced systemic inflammation, MAPKAPK2 (MK2)-deficient mice exhibited significantly increased inflammatory response, cellular damage and mortality compared to wild type controls following treatment with TNF\u03b1 (Vandendriessche B et al. 2014; Dondelinger Y et al. 2017). Mass spectrometry (MS)-based phosphoproteomics using mouse LPS-treated bone marrow-derived macrophage (BMDM) and stress-stimulated embryonic fibroblasts (MEF) identified RIPK1 as a direct substrate of MAPKAPK2 (Menon MB et al. 2017). Immunoblotting and mutagenesis analysis further confirmed MAPKAPK2 (MK2)-dependent phosphorylation of RIPK1 in TNF-stimulated mouse and human cells (Jaco I et al. 2017; Dondelinger Y et al. 2017; Menon MB et al. 2017). MAPKAPK2-mediated phosphorylation of RIPK1 inhibited the ability of RIPK1 to bind to FADD in mouse cells (Jaco I et al. 2017; Dondelinger Y et al. 2017; Menon MB et al. 2017). MAPKAPK2 was shown to phosphorylate mouse RIPK1 at serine 321 (S321) and S336 (equivalent to S320 and S335 in human RIPK1) (Jaco I et al. 2017; Dondelinger Y et al. 2017; Menon MB et al. 2017). Other protein kinases such as transforming growth factor \u03b2-activated kinase 1 (TAK1) or IKK\u03b1/IKK\u03b2 may also regulate phosphorylation of RIPK1 at these phospho-acceptor sites (Krishnan RK et al. 2015; Mohideen F et al. 2017; Geng J et al. 2017). Functional analysis revealed that phosphorylation of human RIPK1 at S320 negatively regulates RIPK1 autophosphorylation at S166, which is essential for the RIPK1 kinase activity and subsequent induction of cell death signaling (Mohideen F et al. 2017; Du J et al. 2021). While phosphorylation of RIPK1 at S320 had no effect on TNF\u03b1-induced NF-\u03baappa-B signaling, it limited RIPK1 kinase activation and association with FADD and CASP8 in human cells (Mohideen F et al. 2017). Similar results were obtained for S321/S336 of mouse RIPK1 (Geng J et al. 2017; Dondelinger Y et al. 2017; Menon MB et al. 2017; Jaco I et al. 2017). These data suggest that MAPKAPK2-mediated phosphorylation of RIPK1 at S320 limits TNF\u03b1-induced RIPK1-dependent cell death. Besides TNFR1, MAPKAPK2 regulates RIPK1 activity downstream of Toll-like receptor 4 (TLR4) upon LPS stimulation (Jaco I et al. 2017; Menon MB et al 2017). Moreover, MAPKAPK2 controls inflammation by regulating expression of inflammatory cytokines such as TNF\u03b1, IL-1\u03b2 and IL-6 (reviewed in Morgan D et al. 2022).
Upon TNFa stimulation, MAPKAPK2 (MK2) is activated by p38 MAPK downstream of TAK1, which is recruited to and activated in the TNFR1 signaling complex (Jaco I et al. 2017). Activated TAK1 mediates TNF-induced NF-kappa-B and MAPK signaling pathways. Pathogenic bacteria developed strategies to suppress host immune responses by blocking activation of NF-kappa-B and MAPK signaling pathways (Philip NH et al. 2014; He C et al. 2017; Orning P et al. 2018; Malireddi RKS et al. 2020). For example, the cytotoxicity of pathogenic Yersinia species is caused by Yersinia outer protein YopJ secreted in Y. pestis and Y. pseudotuberculosis and YopP secreted by Y. enterocolitica. The acetyltransferase activity of YopJ/P catalyses O-acetylation of specific serine and/or threonine residues in the activation loop of protein kinases. YopJ/P-mediated acetylation of TAK1 suppresses the catalytic activity of TAK1 and thus preventing production of pro-inflammatory cytokines in human and mouse cells (Thiefes A et al. 2006; Paquette N et al. 2012). Further, YopP was shown to suppress TAK1/p38 MAPK/MK2 signaling while inducing activation of RIPK1 in Y. enterocolitica-infected mouse J774A.1 macrophages (Menon MB et al. 2017). These data suggest that Yersinia-mediated inactivation of TAK1 leads to induction of RIPK1-dependent cell death, which contributes to host defense against pathogens (Weng D et al. 2014; Philip NH et al. 2014; Menon MB et al. 2017; Peterson LW et al. 2017; Orning P et al. 2018).
This Reactome event shows MAPKAPK2 (MK2)-mediated phosphorylation of cytosolic RIPK1 at S320 in response to TNF\u03b1 stimulation.", "cellular_location": "cytosol", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "P49137-1", "Q12933-1", "Q13546-1" ], "evidence": [ { "id": "R-HSA-9815501", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9815501" } ] }, { "id": "R-HSA-9817362", "name": "SPATA2:CYLD-bound LUBAC ubiquitinates RIPK1 at K627 within the TNFR1 signaling complex", "equation": "", "summary": "TNF-\u03b1 ligation to TNF receptor 1 (TNFR1) induces the formation of the TNFR1 signaling complex composed of TNFR1, TRADD (TNFR1-associated death domain), TRAF2 (TNF receptor associated factor-2), RIPK1 (receptor-interacting serin/threonine protein kinase 1), and E3 ubiquitin ligases BIRC2, BIRC3 (cIAP1/2, cellular inhibitor of apoptosis) and LUBAC (linear ubiquitin chain assembly complex) (Micheau O and Tschopp J 2003). The conjugation of K63-linked ubiquitin (Ub) chains by BIRC2/3 to RIPK1 allows further recruitment and activation of the TAK1 (also known as MAP3K7) complex and I\u03baB kinase (IKK) complex which in turn drives activation of NF-kappa-B (Ea CK et al. 2006; Haas et al. 2009). The catalytic activity of LUBAC, composed of HOIL-1L, HOIP, and SHARPIN, specifically generates the N-terminal methionine-linked ubiquitin (Met1-Ub) chains (also known as linear Ub chains) (Kirisako T et al. 2006; Walczak H et al. 2012; Rittinger K & Ikeda F 2017; Fuseya Y & Iwai K 2021). UBE2L3 functions as E2-conjugating enzyme for LUBAC (Lewis MJ et al. 2015; Fu B et al. 2014). LUBAC was shown to catalyze Met1-linked ubiquitination of RIPK1 at K627 upon co-expression of Flag-RIPK1 with Myc-tagged components of LUBAC (HOIP, HOIL1, and SHARPIN) in human embryonic kidney 293T (HEK293T) cells (Tu H et al. 2021). Linear ubiquitination of mouse Ripk1 on K612 (K627 in human) inhibited TNF-\u03b1\u2013induced apoptosis and necroptosis in mouse embryonic fibroblast (MEF) cells. Mutagenesis analysis further confirmed the importance of the K627 (K612 in mouse) ubiquitination site of RIPK1 in the TNFR1 signaling pathway (Li X et al. 2020). Further, LUBAC is known to ubiquitinate IKBKG (NEMO), a regulatory component of the IKK complex. LUBAC-mediated IKBKG ubiquitination enhanced IKBKG interaction with the TNFR1 signaling complex and stabilized this protein complex to promote activation of NF-kappa-B (Haas TL et al. 2009). Importantly, deletion of the LUBAC component SHARPIN in mice or mutation of HOIL-1 in humans, leads to hyperinflammatory phenotypes, indicating key roles of LUBAC and linear Ub chains in the response to infection and inflammation (Gerlach B et al. 2011; Ikeda F et al. 2011; Tokunaga F et al. 2011; Boisson B et al. 2012). The data suggest that LUBAC-mediated linear ubiquitylation of RIPK1 limits TNF-\u03b1\u2013induced cell death. LUBAC activity is regulated by deubiquitinases (DUBs) such as OTULIN and CYLD, which hydrolyze Ub chains to reverse the modification of target proteins (Takiuchi T et al. 2014). OTULIN and CYLD associate with HOIP, the catalytic subunit of LUBAC, to cleave Ub chains in a linkage-specific fashion. OTULIN exclusively hydrolyzes Met1-Ub, while CYLD disassembles both Met1-Ub and Lys63-Ub (Fiil BK et al. 2013; Harhaj EW and Dixit VM 2012; Hrdinka M et al. 2016; Sato Y 2022). The CYLD interaction with LUBAC is facilitated by spermatogenesis-associated protein 2 (SPATA2) (Elliott PR et al. 2016; Kupka S et al. 2016; Schlicher L et al. 2016; Wagner SA et al. 2016). The CYLD:SPATA2:LUBAC complex is rapidly recruited into the TNFR1 signaling complex to regulate ubiquitination/deubiquitination downstream of TNFR1 (Wagner SA et al. 2016; Elliott PR et al. 2016; Kupka S et al. 2016; Schlicher L et al. 2016; Wei R et al. 2017; reviewed in Schlicher L et al. 2017).
This Reactome event describes LUBAC-mediated Met1-linked polyubiquitination (M1polyUb) of RIPK1 at K627 within the TNFR1 signaling complex.", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q96EP0-1", "Q9BYM8-1", "Q12933-1", "P98170-1", "Q13546-1", "P68036-1", "Q13490-1", "Q13489-1", "Q9NQC7-1" ], "evidence": [ { "id": "R-HSA-9817362", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9817362" } ] }, { "id": "R-HSA-9817397", "name": "TBK1, IKBKE phosphorylate RIPK1 at T189", "equation": "", "summary": "Binding of TNF\u03b1 to TNF receptor 1 (TNFR1) induces either cell survival or cell death through the sequential formation of several signaling complexes, namely complex-I, IIa and IIb (Micheau O and Tschopp J 2003; Walczak H 2011). The dynamic assembly of these complexes is tightly regulated by proteolysis, ubiquitination, deubiquitination and phosphorylation of receptor-interacting serine/threonine protein kinase 1 (RIPK1) and other components of the TNF\u03b1 signaling pathway. The rapidly forming complex-I (the TNFR1 signaling complex) is assembled at the receptor\u2019s cytoplasmic tail and consists of TNFR1, TNFR1-associated death domain (TRADD), TNF receptor associated factor-2 (TRAF2) and RIPK1 (Micheau O and Tschopp J 2003). The activated TNFR1 signaling complex (complex-I) recruits several E3 ubiquitin (Ub) ligases, such as cIAP1/2 cellular inhibitor of apoptosis (BIRC2, BIRC3), mind bomb 2 (MIB2) or linear ubiquitin chain assembly complex (LUBAC) (Micheau O and Tschopp J 2003; Feltham R et al. 2018; Yuan J et al. 2019). K63-linked ubiquitination by BIRC2, BIRC3 and MIB2 as well as LUBAC-mediated Met1-linked linear ubiquitination of RIPK1 and other complex components stabilize the membrane-bound pro-survival TNFR1 signaling complex, while suppressing the formation of the cytosolic death-inducing complex IIa (TRADD:TRAF2:RIPK1:FADD:CASP8) and IIb (RIPK1:RIPK3:MLKL). The catalytic activity of LUBAC also enables recruitment of TRAF-associated NF-\u03baB activator (TANK) binding kinase 1 (TBK1) and inhibitor-kappa-B kinase (IKK) epsilon (IKK\u03b5 or IKBKE) to the TNFR1 signaling complex (Lafont E et al. 2018; Xu D et al. 2018). LUBAC is composed of the HOIP, HOIL-1L, and SHARPIN subunits. HOIP deficiency strongly diminished recruitment of TBK1 or IKBKE to the complex-I in human cervical carcinoma epithelial HeLa cells and lung carcinoma epithelial A549 cells (Lafont E et al. 2018). Western blot analysis revealed that TBK1 and IKBKE are recruited to and strongly phosphorylated within the TNFR1 complex in various TNF\u03b1-stimulated human cell lines including A549, keratinocyte HaCaT, monocytic U937 and THP-1 cells (Lafont E et al. 2018). Similarly, TBK1 was found to associate with components of the complex-I in the LUBAC-dependent manner in mouse cells (Xu D et al. 2018). IKBKE, but not TBK1, was detected within the TNFR1 complex in human telomerase reverse transcriptase (TERT)-immortalized dermal fibroblasts derived from patients with TBK1 deficiency as a result of loss-of-function mutation at W619* (Taft J et al. 2021). The enzymatic activity of TBK1/IKBKE is initiated by phosphorylation at S172 located in the T loop of the TBK1 and IKK\u03b5 kinase domains (Shimada T et al. 1999; Kishore N et al. 2002; Gu L et al. 2013). Activated TBK1 and IKBKE are known to trigger phosphorylation of interferon regulatory factor 3 (IRF3) and IRF7 and subsequent expression of type I interferons (IFNs; IFN-\u03b1/\u03b2) downstream of pattern recognition receptors, such as Toll-like receptors 3 and 4 (TLR3, TLR4), cGAS/STING and RIG-I-like receptors (Fitzgerald KA et al. 2003; Fang R et al. 2017). While TBK1 or IKBKE showed limited effect on TNF-induced gene expression in human A549 and mouse embryonic fibroblasts (MEF) (Lafont E et al. 2018), both kinases prevented TNF\u03b1-induced cell death by suppressing RIPK1 activation in human and mouse cells (Lafont E et al. 2018; Xu D et al. 2018; Taft J et al. 2021). Mechanistically, TBK1 and/or IKBKE directly phosphorylate RIPK1 within the TNFR1 signaling complex to prevent RIPK1 kinase-dependent cell death signaling downstream of TNFR1 (Lafont E et al. 2018; Xu D et al. 2018). Mass spectrometry analysis suggests that human RIPK1 is phosphorylated by TBK1 at T189 (Xu D et al. 2018). Using a phospho-specific antibody, T189 of RIPK1 was detected as a phosphorylation site upon incubation with TBK1 in in vitro kinase assay and upon co-expression of tagged proteins in human embryonic kidney HEK293T cells. This phosphorylation was inhibited by TBK1/IKBKE inhibitor MRT67307 (Xu D et al. 2018). Phosphorylation of endogenous RIPK1 at T189 was detected in TNF-stimulated Jurkat cells (Xu D et al. 2018). Others reported that TBK1 or IKBKE phosphorylate RIPK1 at multiple residues (Lafont E et al. 2018). Further, TBK1 or IKBKE deficiency enhanced TNF-induced autophosphorylation of RIPK1, association of RIPK3 with caspase-8:FADD and levels of phosphorylated MLKL in human A549 and HeLa cells (Lafont E et al. 2018). Similar findings were reported for mouse cells (Lafont E et al. 2018; Xu D et al. 2018). In vivo studies showed that the embryonic lethality of Tbk1\u2212/\u2212 mice was caused by TNF\u03b1-stimulated hyperactivation of RIPK1 kinase activity (Xu D et al. 2018). Moreover, chronic systemic autoinflammation in patients carrying homozygous loss-of-function mutations in TBK1 (W619*, R440* and Y212D) is associated with enhanced TNF\u03b1-induced RIPK1-dependent cell death (Taft J et al. 2021). In addition, TBK1-mediated phosphorylation of CYLD may also control the TNFR1 signaling pathway by regulating the ubiquitination status of RIPK1 (Xu X et al. 2020; Taft J et al. 2021). These data suggest that TBK1 and IKBKE downregulate RIPK1 auto-phosphorylation within the complex-I, thereby preventing TNF\u03b1- induced RIPK1-kinase-activity-dependent cell death.
This Reactome event describes TBK1/IKBKE-mediated phosphorylation of RIPK1 at T189 within the TNFR1 signaling complex.", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q96EP0-1", "Q9BYM8-1", "Q12933-1", "Q14164-1", "Q9UHD2-1", "P98170-1", "Q13546-1", "Q13490-1", "Q13489-1", "Q9NQC7-1" ], "evidence": [ { "id": "R-HSA-9817397", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9817397" } ] }, { "id": "R-HSA-9817400", "name": "CYLD hydrolyses K63polyUb on RIPK1 within the TNFR1 complex", "equation": "", "summary": "Binding of TNF\u03b1 to TNF receptor 1 (TNFR1) induces the sequential formation of several signaling complexes, namely complex I and complex IIa/b (Walczak H 2011; Yuan J et al. 2019). These complexes support either cell survival (complex I) or cell death (complex II). The assembly of these complexes is tightly regulated by proteolysis, ubiquitination and phosphorylation of receptor-interacting serine/threonine protein kinase 1 (RIPK1) and other components of the TNF\u03b1 signaling pathway (reviewed in Yuan J et al. 2019; Varfolomeev E & Vucic D 2022). RIPK1 functions as a key regulator of both cell survival and cell death (reviewed in Ju E et al. 2022). Enzymatically inactive polyubiquitin-bound RIPK1 serves as a scaffold in the TNFR1 signaling complex (complex I) to recruit TAK1 kinase complex and I-kappa-B kinase (IKK) complex contributing to activation of mitogen-activated protein kinase (MAPK) and NF-kappa-B signaling pathways, which regulate expression of pro-survival and inflammatory genes. Deubiquitination of RIPK1 leads to the activation of RIPK1 kinase activity, which promotes RIPK1 kinase-dependent cell death (reviewed in Ju E et al. 2022). Several deubiquitinating enzymes, such as tumor necrosis factor alpha-induced protein 3 (TNFAIP3, known as Zn finger protein A20) or ubiquitin (Ub) carboxyl-terminal hydrolase CYLD, have been implicated in the regulation of RIPK1 activity. CYLD disassembles both Met1- and Lys63-polyUb chains (Fiil BK et al. 2013; Harhaj EW and Dixit VM 2012; Hrdinka M et al. 2016; Sato Y 2022). Upon TNF\u03b1 stimulation, CYLD is recruited to the TNFR1 signaling complex along with the linear ubiquitin chain assembly complex (LUBAC). Interaction of CYLD with LUBAC is facilitated by spermatogenesis-associated protein 2 (SPATA2) (Elliott PR et al. 2016; Kupka S et al. 2016; Schlicher L et al. 2016; Wagner SA et al. 2016). The CYLD:SPATA2:LUBAC complex is rapidly recruited into the TNFR1 signaling complex to regulate ubiquitination/deubiquitination downstream of TNFR1 (Wagner SA et al. 2016; Elliott PR et al. 2016; Kupka S et al. 2016; Schlicher L et al. 2016; Wei R et al. 2017; reviewed in Schlicher L et al. 2017).
This Reactome event describes CYLD-mediated cleavage of K63-linked polyubiquitin chains on RIPK1 within the TNFR1 signaling complex. The deubiquitinase activity of CYLD attenuates TNF\u03b1-induced NF-kappa-B and MAPK signaling, but promotes cell death.
",
"cellular_location": "cytosol, plasma membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q96EP0-1",
"Q9BYM8-1",
"Q12933-1",
"P98170-1",
"Q13546-1",
"Q13490-1",
"Q13489-1",
"Q9NQC7-1"
],
"evidence": [
{
"id": "R-HSA-9817400",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9817400"
}
]
},
{
"id": "R-HSA-9817411",
"name": "TBK1, IKBKE binds Met1-polyUb within the TNFR1 complex",
"equation": "",
"summary": "The catalytic activity of linear ubiquitin chain assembly complex (LUBAC) enables recruitment of TRAF-associated NF-\u03baB activator (TANK) binding kinase 1 (TBK1) and inhibitor-kappa-B kinase (IKK) epsilon (IKK\u03b5 or IKBKE) to the TNFR1 signaling complex, also known as complex-I (Lafont E et al. 2018; Xu D et al. 2018). LUBAC, composed of the HOIP, HOIL-1L, and SHARPIN subunits, generates linear Met1-linked polyubiquitin chains. HOIP deficiency strongly diminished recruitment of TBK1 or IKBKE to the complex-I in human epithelial cervical carcinoma HeLa cells and lung carcinoma A549 cells (Lafont E et al. 2018). Western blot analysis revealed that TBK1 and IKBKE are recruited to and strongly phosphorylated within the TNFR1 complex in various TNF\u03b1-stimulated human cell lines including A549, keratinocyte HaCaT, monocytic U937 and THP-1 cells (Lafont E et al. 2018). Similarly, TBK1 was found to associate with components of the complex-I in the LUBAC-dependent manner in mouse cells (Xu D et al. 2018). IKBKE, but not TBK1, was detected within the TNFR1 complex in human telomerase reverse transcriptase (TERT)-immortalized dermal fibroblasts derived from patients with TBK1 deficiency as a result of loss-of-function mutation at W619* (Taft J et al. 2021). The enzymatic activity of TBK1/IKBKE is initiated by phosphorylation at S172 located in the T loop of the TBK1 and IKK\u03b5 kinase domains (Shimada T et al. 1999; Kishore N et al. 2002; Gu L et al. 2013). Activated TBK1 and IKBKE are known to trigger phosphorylation of interferon regulatory factor 3 (IRF3) and IRF7 and subsequent expression of type I interferons (IFNs; IFN-\u03b1/\u03b2) downstream of pattern recognition receptors, such as Toll-like receptors 3 and 4 (TLR3, TLR4), cGAS/STING and RIG-I-like receptors (Fitzgerald KA et al. 2003; Fang R et al. 2017). While TBK1 or IKBKE showed limited effect on TNF\u03b1-induced gene expression in human A549 and mouse embryonic fibroblasts (MEF) (Lafont E et al. 2018), both kinases prevented TNF\u03b1-induced cell death by suppressing RIPK1 activation in human and mouse cells (Lafont E et al. 2018; Xu D et al. 2018; Taft J et al. 2021). TBK1 and/or IKBKE directly phosphorylate RIPK1 within the TNFR1 signaling complex to prevent RIPK1 kinase-dependent cell death downstream of TNFR1 (Lafont E et al. 2018; Xu D et al. 2018). TBK1 or IKBKE deficiency enhanced TNF-induced autophosphorylation of RIPK1, association of RIPK3 with caspase-8:FADD and phosphorylation of MLKL in human A549 and HeLa cells (Lafont E et al. 2018). Similar findings were reported for mouse cells (Lafont E et al. 2018; Xu D et al. 2018). In vivo studies showed that the embryonic lethality of Tbk1\u2212/\u2212 mice was caused by TNF\u03b1-stimulated hyperactivation of RIPK1 kinase activity (Xu D et al. 2018). Furthermore, chronic systemic autoinflammation in patients carrying homozygous loss-of-function mutations in TBK1 (W619*, R440* and Y212D) is associated with the enhanced TNF\u03b1-induced RIPK1-dependent cell death (Taft J et al. 2021). In addition, TBK1-mediated phosphorylation of CYLD may also control the TNFR1 signaling pathway by regulating the ubiquitination status of RIPK1 (Xu X et al. 2020; Taft J et al. 2021). These data suggest that TBK1 and IKBKE downregulate RIPK1 auto-phosphorylation within the complex-I, thereby preventing TNF\u03b1- induced RIPK1-kinase-activity-dependent cell death.
This Reactome event describes TBK1/IKBKE recruitment to and activation within the TNFR1 signaling complex.", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q96EP0-1", "Q9BYM8-1", "Q12933-1", "Q14164-1", "Q9UHD2-1", "P98170-1", "Q13546-1", "Q13490-1", "Q13489-1", "Q9NQC7-1" ], "evidence": [ { "id": "R-HSA-9817411", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9817411" } ] }, { "id": "R-HSA-9818789", "name": "CHUK, IKBKB phosphorylate RIPK1 at S25", "equation": "", "summary": "Binding of TNF\u03b1 to TNF receptor 1 (TNFR1) induces the sequential formation of several signaling complexes, namely complex I and complex IIa/b (Walczak H 2011; Yuan J et al. 2019). These complexes support either cell survival (complex I) or cell death (complex II). The dynamic assembly of these complexes is tightly regulated by proteolysis, ubiquitination and phosphorylation of receptor-interacting serine/threonine protein kinase 1 (RIPK1) and other components of the TNF\u03b1 signaling pathway (reviewed in Yuan J et al. 2019; Varfolomeev E & Vucic D 2022). RIPK1 functions as a key regulator of both cell survival and cell death (reviewed in Ju E et al. 2022). Enzymatically inactive polyubiquitin-bound RIPK1 serves as a scaffold in the TNFR1 signaling complex (complex I) to recruit TAK1 kinase complex and I-kappa-B kinase (IKK) complex contributing to activation of mitogen-activated protein kinase (MAPK) and NF-kappa-B signaling pathways, which regulate expression of pro-survival and inflammatory genes. Deubiquitination of RIPK1 leads to the activation of RIPK1 kinase activity, which promotes autophosphorylation of RIPK1 and RIPK1 kinase-dependent cell death (reviewed in Ju E et al. 2022). The kinase activity of RIPK1 is regulated by phosphorylation (Lafont E et al. 2018; Dondelinger Y et al. 2019; reviewed in Delanghe T et al. 2020; Ju E et al. 2022). The components of I-kappa-B kinase complex, namely inhibitor of nuclear factor kappa B subunit \u03b1 (IKK\u03b1 or CHUK) and subunit \u03b2 (IKK\u03b2 or IKBKB), can directly phosphorylate RIPK1 within the membrane-bound TNFR1 signaling complex (complex I) (Dondelinger Y et al. 2015, 2019). IKK phosphorylates S25 in the kinase domain of RIPK1 to block ATP binding, preventing RIPK1 kinase activation and cell death (Dondelinger Y et al. 2019). Expression of phospho-mimetic S25D RIPK1 mutant prevented TNF-induced cell death in RIPK1-null human Jurkat cells and mouse embryonic fibroblasts (MEF). Autophosphorylation of RIPK1 on S166 and activation of RIPK1 kinase were inhibited in mouse bone marrow-derived macrophages (BMDMs) and MEFs isolated from mice carrying S25D RIPK1 mutant (Dondelinger Y et al. 2019; Puylaert P et al. 2022). Inhibition of IKK activity by Yersinia infection or by SHARPIN gene mutations results in defective phosphorylation of RIPK1 at S25 by IKK\u03b1/\u03b2 (Dondelinger Y et al. 2019). Restoring S25 phosphorylation with S25D RIPK1 prevented TNF-induced RIPK1 kinase-dependent cell death in Yersinia-infected BMDMs. Further, mimicking S25 phosphorylation impaired host immune response to Yersinia infection in vivo in bone marrow chimeric mice, suggesting that RIPK1 kinase-dependent cell death contributes to immune defense in response to pathogens. Similarly, S25D RIPK1 suppressed TNF-induced cell death in mouse dermal fibroblasts (MDFs) isolated from SHARPIN-deficient mice. These data suggest that IKK\u03b1/\u03b2-mediated phosphorylation of RIPK1 at S25 downregulates RIPK1 auto-phosphorylation downstream of TNFR1, thereby preventing TNF\u03b1-induced RIPK1 kinase-dependent cell death (Dondelinger Y et al. 2019).
This Reactome event describes IKK mediated phosphorylation of RIPK1 at S25 within the TNFR1 signaling complex.; ; ;", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q96EP0-1", "Q9BYM8-1", "Q12933-1", "O15111-1", "P98170-1", "Q13546-1", "O14920-1", "Q13490-1", "Q13489-1", "Q9NQC7-1" ], "evidence": [ { "id": "R-HSA-9818789", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9818789" } ] }, { "id": "R-HSA-9818975", "name": "CYLD hydrolyses M1polyUb on RIPK1 within the TNFR1 complex", "equation": "", "summary": "Binding of TNF\u03b1 to TNF receptor 1 (TNFR1) induces the sequential formation of several signaling complexes, namely complex I and complex IIa/b (Walczak H 2011; Yuan J et al. 2019). These complexes support either cell survival (complex I) or cell death (complex II). The assembly of these complexes is tightly regulated by proteolysis, ubiquitination and phosphorylation of receptor-interacting serine/threonine protein kinase 1 (RIPK1) and other components of the TNF\u03b1 signaling pathway (reviewed in Yuan J et al. 2019; Varfolomeev E & Vucic D 2022). RIPK1 functions as a key regulator of both cell survival and cell death (reviewed in Ju E et al. 2022). Enzymatically inactive polyubiquitin-bound RIPK1 serves as a scaffold in the TNFR1 signaling complex (complex I) to recruit TAK1 kinase complex and I-kappa-B kinase (IKK) complex contributing to activation of mitogen-activated protein kinase (MAPK) and NF-kappa-B signaling pathways, which regulate expression of pro-survival and inflammatory genes. Deubiquitination of RIPK1 leads to the activation of RIPK1 kinase activity, which promotes RIPK1 kinase-dependent cell death (reviewed in Ju E et al. 2022). Several deubiquitinating enzymes, such as tumor necrosis factor alpha-induced protein 3 (TNFAIP3, known as Zn finger protein A20) or ubiquitin (Ub) carboxyl-terminal hydrolase CYLD, have been implicated in the regulation of RIPK1 activity. CYLD disassembles both Met1- and Lys63-polyUb chains (Fiil BK et al. 2013; Harhaj EW and Dixit VM 2012; Hrdinka M et al. 2016; Sato Y 2022). Upon TNF\u03b1 stimulation, CYLD is recruited to the TNFR1 signaling complex along with the linear ubiquitin chain assembly complex (LUBAC). Interaction of CYLD with LUBAC is facilitated by spermatogenesis-associated protein 2 (SPATA2) (Elliott PR et al. 2016; Kupka S et al. 2016; Schlicher L et al. 2016; Wagner SA et al. 2016). The CYLD:SPATA2:LUBAC complex is rapidly recruited into the TNFR1 signaling complex to regulate ubiquitination/deubiquitination downstream of TNFR1 (Wagner SA et al. 2016; Elliott PR et al. 2016; Kupka S et al. 2016; Schlicher L et al. 2016; Wei R et al. 2017; reviewed in Schlicher L et al. 2017).
This Reactome event describes CYLD-mediated cleavage of Met1-linked polyubiquitin chains on RIPK1 within the TNFR1 signaling complex. The deubiquitinase activity of CYLD attenuates TNF\u03b1-induced NF-kappa-B and MAPK signaling, but promotes cell death.
",
"cellular_location": "cytosol, plasma membrane",
"input_participant_list": [],
"output_participant_list": [],
"enzyme_list": [
"Q96EP0-1",
"Q9BYM8-1",
"Q12933-1",
"P98170-1",
"Q13546-1",
"Q13490-1",
"Q13489-1",
"Q9NQC7-1"
],
"evidence": [
{
"id": "R-HSA-9818975",
"database": "Reactome",
"url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9818975"
}
]
},
{
"id": "R-HSA-9819106",
"name": "ULK1 phosphorylates RIPK1 at S357",
"equation": "",
"summary": "Autophagy controls programmed cell death through different cross-talk signals (Bray K et al. 2012; Goodall ML et al. 2016; Lim J et al 2019; Wu W et al. 2020). For instance, serine/threonine kinase Unc-51-like kinase-1 (ULK1), an essential initiator of the autophagy response, regulates the tumor necrosis factor \u03b1 (TNF\u03b1)-induced signaling pathway (Wu W et al. 2020; reviewed in Zou L et al. 2022). TNF\u03b1 binds TNF receptor 1 (TNFR1) inducing the sequential formation of several signaling complexes, namely complex I and complex IIa/b (Micheau O and Tschopp J 2003; Walczak H 2011; Yuan J et al. 2019). These complexes support either cell survival (complex I) or cell death (complex II). Receptor-interacting serine/threonine protein kinase 1 (RIPK1) functions as a key regulator of the TNF:TNFR1 signaling pathway (reviewed in Ju E et al. 2022). The RIPK1 activity is tightly regulated by proteolysis, ubiquitination and phosphorylation (reviewed in Delanghe T et al. 2020; Ju E et al. 2022). RIPK1 was identified as a substrate of ULK1 (Wu W et al. 2020). ULK1 deficiency enhanced autophosphorylation of RIPK1 at S166 and association of RIPK1 with FADD in TNF-stimulated mouse fibroblast L929 and MEF cells (Wu W et al. 2020). Co-immunoprecipitation assay showed that ULK1 associated with RIPK1 upon co-expression of tagged proteins in human embryonic kidney 293 (HEK293) cells (Wu W et al. 2020). The interaction between endogenous ULK1 and RIPK1 was detected in TNF-stimulated L929 cells. The kinase activity of ULK1 was found to phosphorylate RIPK1 at S357 in HEK293 (Wu W et al. 2020). The ULK1-mediated phosphorylation of RIPK1 occurred preferentially in the cytosol preventing the formation of complex II (Wu W et al. 2020). These data suggest that ULK1 exerts a cytoprotective function by suppressing RIPK1-mediated cell death.
This Reactome event describes ULK1-mediated phosphorylation of RIPK1 at S357 within the cytosolic TRAF2:TRADD:RIPK1 complex.", "cellular_location": "cytosol", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q12933-1", "O75385-1", "Q13546-1" ], "evidence": [ { "id": "R-HSA-9819106", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9819106" } ] }, { "id": "R-HSA-9824874", "name": "OPTN recruits CYLD to the TNFR1 complex", "equation": "", "summary": "Optineurin (OPTN) is a multifunctional, ubiquitin-binding adaptor protein which exhibits a high homology with IKBKG (NEMO, the regulatory subunit of the IkB kinase complex). OPTN has been implicated in regulating of various signaling pathways including NF-kappa-B activation, TBK1-mediated type I interferon production, programmed cell death, and autophagy (reviewed in Markovinovic A et al. 2017; Slowicka K & van Loo G 2018; Toth RP & Atkin JD 2018). In human and mouse cells, OPTN was identified as a negative regulator of the tumor necrosis factor \u03b1 (TNF-\u03b1)-induced signaling pathway by targeting several downstream components including receptor-interacting serine/threonine protein kinase 1 (RIPK1), caspase 8 (CASP8), and ubiquitin (Ub) carboxyl-terminal hydrolase CYLD (Zhu G et al. 2007; Nagabhushana A et al. 2011; Nakazawa S et al. 2016). Direct association of OPTN with TNFR1 and RIPK1 was detected in TNF-\u03b1-stimulated human epithelial carcinoma KB cells and HeLa cells by coimmunoprecipitation suggesting that OPTN is recruited to the TNFR1 complex (Zhu G et al. 2007; Klingseisen L et al. 2012; Nakazawa S et al. 2016). Structural and biochemical studies showed that OPTN functions through its ability to bind ubiquitinated proteins such as RIPK1, and the UBAN domain of OPTN preferentially recognizes linear polyUb chains (Gleason CE et al. 2011; Nakazawa S et al. 2016; Li F et al. 2018). Although the highest affinity is seen for M1-linked polyUb chains, TBK1-mediated phosphorylation of OPTN on S473 has been shown to broaden its specificity to include K63- and K48-linked polyUb chains (Li F et al. 2018). The Ub-binding activity of OPTN is thought to downregulate the TNF-\u03b1 mediated NF-kappa-B activation (Zhu G et al. 2007; Maruyama H et al. 2010; Nakazawa S et al. 2016) by suppressing a scaffold function of RIPK1 within the TNFR1 signaling complex (Zhu G et al. 2007; Nakazawa S et al. 2016). In addition, OPTN interacts with deubiquitinase CYLD, which acts as a negative regulator of the TNFR1-induced gene expression by hydrolyzing K63-, M1-linked polyUb chains of RIPK1. CoIP assay detected interaction of OPTN with CYLD upon co-expression of tagged proteins in HeLa cells (Nagabhushana A et al. 2011). Defective binding of the glaucoma-associated OPTN H486R variant to CYLD prevented CYLD-mediated inhibition of TNF\u03b1-induced NF-kappa-B activity upon co-expression of OPTN and CYLD in HeLa cells. A catalytically inactive CYLD variant co-immunoprecipitated polyUb-RIPK1 along with OPTN in HeLa cells. Further, OPTN knockdown prevented RIPK1 deubiquitination by overexpressed CYLD in TNF-\u03b1-induced HeLa cells (Nagabhushana A et al. 2011). The data suggest that OPTN directly interacts with CYLD and RIPK1 to mediate deubiquitination of RIPK1 by CYLD within the TNFR1 signaling complex thus suppressing the NF-kappa-B signaling pathway. However, the OPTN regulatory function on NF-kappa-B signaling observed in vitro has not been confirmed in vivo suggesting that the mechanism of OPTN-mediated regulation is indirect and/or depends on the NF-kappa-B-mediated upregulation of OPTN (Sudhakar C et al. 2009; Gleason CE et al. 2011; Munitic I et al. 2013; Slowicka K et al. 2016; Markovinovic A et al. 2018).
Similar to mutations in the OPTN gene, CYLD mutations have been linked to the development of neurodegenerative diseases (Dobson-Stone C et al. 2020; Gu X et al. 2021; Xiao X et al. 2022). For example, the missense CYLD mutation M719V was identified in a family with autosomal dominant inheritance of frontotemporal dementia and amyotrophic lateral sclerosis (FTD-ALS) (Dobson-Stone C et al. 2020). When overexpressed in HEK293 cells, CYLD M719V has been shown to increase deubiquitinating activity of CYLD, leading to enhanced inhibition of the NF-kappa-B pathway, suggesting that this gain-of-function mechanism of action may contribute to the development of FTD-ALS (Dobson-Stone C et al. 2020).
This Reactome event shows CYLD association with OPTN bound to the TNFR1 signaling complex.", "cellular_location": "cytosol, plasma membrane", "input_participant_list": [], "output_participant_list": [], "enzyme_list": [ "Q96EP0-1", "Q9BYM8-1", "Q12933-1", "P98170-1", "Q13546-1", "Q13490-1", "Q13489-1", "Q9NQC7-1" ], "evidence": [ { "id": "R-HSA-9824874", "database": "Reactome", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9824874" } ] } ], "reaction_participants": [ { "participant_id": "R-HSA-450318", "participant_name": "p-S477,S479-IRF7 [cytosol]", "crossref": [ { "id": "Q92985", "database": "UniProt", "url": "" }, { "id": "ENST00000621391", "database": "Ensembl", "url": "" }, { "id": "Q92985", "database": "GeneCards", "url": "" }, { "id": "NP_004020.1", "database": "RefSeq", "url": "" }, { "id": "ENSP00000488591", "database": "Ensembl", "url": "" }, { "id": "ENST00000330243", "database": "Ensembl", "url": "" }, { "id": "ENSG00000185507", "database": "Ensembl", "url": "" }, { "id": "NP_001563.2", "database": "RefSeq", "url": "" }, { "id": "ENSG00000276561", "database": "Ensembl", "url": "" }, { "id": "Q92985", "database": "Pharos - Targets", "url": "" }, { "id": "XP_016873163.1", "database": "RefSeq", "url": "" }, { "id": "Q92985", "database": "PRO", "url": "" }, { "id": "ENSP00000329411", "database": "Ensembl", "url": "" }, { "id": "ENSP00000380697", "database": "Ensembl", "url": "" }, { "id": "ENST00000397566", "database": "Ensembl", "url": "" }, { "id": "ENSP00000331803", "database": "Ensembl", "url": "" }, { "id": "ENST00000633274", "database": "Ensembl", "url": "" }, { "id": "ENST00000348655", "database": "Ensembl", "url": "" }, { "id": "NP_004022.2", "database": "RefSeq", "url": "" }, { "id": "ENSP00000479615", "database": "Ensembl", "url": "" }, { "id": "ENSG00000185507-IRF7", "database": "HPA", "url": "" }, { "id": "ENSP00000488581", "database": "Ensembl", "url": "" }, { "id": "ENSP00000433903", "database": "Ensembl", "url": "" }, { "id": "ENST00000469048", "database": "Ensembl", "url": "" }, { "id": "2O61", "database": "PDB", "url": "" }, { "id": "ENSP00000480358", "database": "Ensembl", "url": "" }, { "id": "XP_005252963.1", "database": "RefSeq", "url": "" }, { "id": "ENSP00000488666", "database": "Ensembl", "url": "" }, { "id": "ENST00000533182", "database": "Ensembl", "url": "" }, { "id": "ENST00000633943", "database": "Ensembl", "url": "" }, { "id": "ENST00000525445", "database": "Ensembl", "url": "" }, { "id": "ENST00000632827", "database": "Ensembl", "url": "" }, { "id": "ENSP00000434607", "database": "Ensembl", "url": "" }, { "id": "ENSG00000185507", "database": "OpenTargets", "url": "" }, { "id": "HMDBP13795", "database": "HMDB Protein", "url": "" }, { "id": "ENSP00000488039", "database": "Ensembl", "url": "" }, { "id": "24630", "database": "Orphanet", "url": "" }, { "id": "ENST00000634105", "database": "Ensembl", "url": "" }, { "id": "ENST00000612534", "database": "Ensembl", "url": "" }, { "id": "ENSP00000434009", "database": "Ensembl", "url": "" } ] }, { "participant_id": "R-HSA-5668525", "participant_name": "K48polyUb-NIK [cytosol]", "crossref": [ { "id": "Q99558", "database": "UniProt", "url": "" }, { "id": "4IDV", "database": "PDB", "url": "" }, { "id": "6WPP", "database": "PDB", "url": "" }, { "id": "HMDBP01177", "database": "HMDB Protein", "url": "" }, { "id": "XP_011523743.1", "database": "RefSeq", "url": "" }, { "id": "6Z1Q", "database": "PDB", "url": "" }, { "id": "2074", "database": "Guide to Pharmacology - Targets", "url": "" }, { "id": "ENSP00000478552", "database": "Ensembl", "url": "" }, { "id": "ENST00000376926", "database": "Ensembl", "url": "" }, { "id": "M3K14_HUMAN", "database": "ZINC - Biogenic", "url": "" }, { "id": "ENST00000617331", "database": "Ensembl", "url": "" }, { "id": "23729", "database": "Orphanet", "url": "" }, { "id": "ENSG00000006062", "database": "Ensembl", "url": "" }, { "id": "ENSG00000006062", "database": "OpenTargets", "url": "" }, { "id": "Q99558", "database": "ZINC target", "url": "" }, { "id": "ENSP00000482657", "database": "Ensembl", "url": "" }, { "id": "ENSP00000480974", "database": "Ensembl", "url": "" }, { "id": "4G3D", "database": "PDB", "url": "" }, { "id": "M3K14_HUMAN", "database": "ZINC - Substances", "url": "" }, { "id": "ENSG00000006062-MAP3K14", "database": "HPA", "url": "" }, { "id": "M3K14_HUMAN", "database": "ZINC - Predictions - Purchasable", "url": "" }, { "id": "4IDT", "database": "PDB", "url": "" }, { "id": "NP_003945.2", "database": "RefSeq", "url": "" }, { "id": "ENST00000344686", "database": "Ensembl", "url": "" }, { "id": "Q99558", "database": "Pharos - Targets", "url": "" }, { "id": "Q99558", "database": "PRO", "url": "" }, { "id": "4DN5", "database": "PDB", "url": "" }, { "id": "6Z1T", "database": "PDB", "url": "" }, { "id": "Q99558", "database": "GeneCards", "url": "" } ] }, { "participant_id": "R-HSA-914241", "participant_name": "TRAF3 [cytosol]", "crossref": [ { "id": "Q13114", "database": "UniProt", "url": "" }, { "id": "2ECY", "database": "PDB", "url": "" }, { "id": "1L0A", "database": "PDB", "url": "" }, { "id": "1KZZ", "database": "PDB", "url": "" }, { "id": "NP_001186356.1", "database": "RefSeq", "url": "" }, { "id": "ENSG00000131323-TRAF3", "database": "HPA", "url": "" }, { "id": "2.3.2.27", "database": "IntEnz", "url": "" }, { "id": "NP_003291.2", "database": "RefSeq", "url": "" }, { "id": "1RF3", "database": "PDB", "url": "" }, { "id": "Q13114", "database": "PRO", "url": "" }, { "id": "1FLL", "database": "PDB", "url": "" }, { "id": "Q13114", "database": "Pharos - Targets", "url": "" }, { "id": "1FLK", "database": "PDB", "url": "" }, { "id": "XP_011535420.1", "database": "RefSeq", "url": "" }, { "id": "Q13114", "database": "GeneCards", "url": "" }, { "id": "20819", "database": "Orphanet", "url": "" }, { "id": "ENSP00000454207", "database": "Ensembl", "url": "" }, { "id": "ENST00000539721", "database": "Ensembl", "url": "" }, { "id": "XP_016877107.1", "database": "RefSeq", "url": "" }, { "id": "ENSP00000514678", "database": "Ensembl", "url": "" }, { "id": "XP_016877106.1", "database": "RefSeq", "url": "" }, { "id": "ENSP00000445998", "database": "Ensembl", "url": "" }, { "id": "ENST00000699894", "database": "Ensembl", "url": "" }, { "id": "ENST00000392745", "database": "Ensembl", "url": "" }, { "id": "ENST00000560371", "database": "Ensembl", "url": "" }, { "id": "1ZMS", "database": "PDB", "url": "" }, { "id": "ENSP00000376500", "database": "Ensembl", "url": "" }, { "id": "NP_663777.1", "database": "RefSeq", "url": "" }, { "id": "ENSG00000131323", "database": "Ensembl", "url": "" }, { "id": "NP_663778.1", "database": "RefSeq", "url": "" }, { "id": "2GKW", "database": "PDB", "url": "" }, { "id": "ENSG00000131323", "database": "OpenTargets", "url": "" } ] } ], "reaction_enzymes": [ { "uniprot_ac": "A5LHX3", "gene_name": "PSMB11", "activity": [ { "ec_number": "3.4.25.1", "activity": "Cleavage of peptide bonds with very broad specificity.", "evidence": [ { "id": "A5LHX3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/A5LHX3" } ] }, { "ec_number": "3.4.25.1", "activity": "", "evidence": [ { "id": "A5LHX3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/A5LHX3" } ] } ] }, { "uniprot_ac": "O00487", "gene_name": "PSMD14", "activity": [ { "ec_number": "3.4.19.-", "activity": "", "evidence": [ { "id": "O00487", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O00487" } ] } ] }, { "uniprot_ac": "O14920", "gene_name": "IKBKB", "activity": [ { "ec_number": "2.7.11.10", "activity": "ATP + L-seryl-[I-kappa-B protein] = ADP + H(+) + O-phospho-L-seryl-[I-kappa-B protein].", "evidence": [ { "id": "O14920", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O14920" } ] }, { "ec_number": "2.7.11.10", "activity": "", "evidence": [ { "id": "O14920", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O14920" } ] }, { "ec_number": "2.7.11.1", "activity": "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein].", "evidence": [ { "id": "O14920", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O14920" } ] } ] }, { "uniprot_ac": "O15111", "gene_name": "CHUK", "activity": [ { "ec_number": "2.7.11.10", "activity": "ATP + L-seryl-[I-kappa-B protein] = ADP + H(+) + O-phospho-L-seryl-[I-kappa-B protein].", "evidence": [ { "id": "O15111", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O15111" } ] }, { "ec_number": "2.7.11.10", "activity": "", "evidence": [ { "id": "O15111", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O15111" } ] } ] }, { "uniprot_ac": "O15294", "gene_name": "OGT", "activity": [ { "ec_number": "2.4.1.255", "activity": "L-threonyl-[protein] + UDP-N-acetyl-alpha-D-glucosamine = 3-O-(N-acetyl-beta-D-glucosaminyl)-L-threonyl-[protein] + H(+) + UDP.", "evidence": [ { "id": "O15294", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O15294" } ] }, { "ec_number": "2.4.1.255", "activity": "", "evidence": [ { "id": "O15294", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O15294" } ] } ] }, { "uniprot_ac": "O43318", "gene_name": "MAP3K7", "activity": [ { "ec_number": "2.7.11.25", "activity": "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein].", "evidence": [ { "id": "O43318", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O43318" } ] }, { "ec_number": "2.7.11.25", "activity": "", "evidence": [ { "id": "O43318", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O43318" } ] } ] }, { "uniprot_ac": "O75385", "gene_name": "ULK1", "activity": [ { "ec_number": "2.7.11.1", "activity": "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein].", "evidence": [ { "id": "O75385", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O75385" } ] }, { "ec_number": "2.7.11.1", "activity": "", "evidence": [ { "id": "O75385", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O75385" } ] } ] }, { "uniprot_ac": "O75604", "gene_name": "USP2", "activity": [ { "ec_number": "3.4.19.12", "activity": "Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).", "evidence": [ { "id": "O75604", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O75604" } ] }, { "ec_number": "3.4.19.12", "activity": "", "evidence": [ { "id": "O75604", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O75604" } ] } ] }, { "uniprot_ac": "O95786", "gene_name": "RIGI", "activity": [ { "ec_number": "3.6.4.13", "activity": "ATP + H2O = ADP + H(+) + phosphate.", "evidence": [ { "id": "O95786", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O95786" } ] }, { "ec_number": "3.6.4.13", "activity": "", "evidence": [ { "id": "O95786", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/O95786" } ] } ] }, { "uniprot_ac": "P21580", "gene_name": "TNFAIP3", "activity": [ { "ec_number": "3.4.19.12", "activity": "Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).", "evidence": [ { "id": "P21580", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P21580" } ] }, { "ec_number": "3.4.19.12", "activity": "", "evidence": [ { "id": "P21580", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P21580" } ] }, { "ec_number": "2.3.2.-", "activity": "", "evidence": [ { "id": "P21580", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P21580" } ] } ] }, { "uniprot_ac": "P28062", "gene_name": "PSMB8", "activity": [ { "ec_number": "3.4.25.1", "activity": "Cleavage of peptide bonds with very broad specificity.", "evidence": [ { "id": "P28062", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P28062" } ] }, { "ec_number": "3.4.25.1", "activity": "", "evidence": [ { "id": "P28062", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P28062" } ] } ] }, { "uniprot_ac": "P28065", "gene_name": "PSMB9", "activity": [ { "ec_number": "3.4.25.1", "activity": "Cleavage of peptide bonds with very broad specificity.", "evidence": [ { "id": "P28065", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P28065" } ] }, { "ec_number": "3.4.25.1", "activity": "", "evidence": [ { "id": "P28065", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P28065" } ] } ] }, { "uniprot_ac": "P28072", "gene_name": "PSMB6", "activity": [ { "ec_number": "3.4.25.1", "activity": "Cleavage of peptide bonds with very broad specificity.", "evidence": [ { "id": "P28072", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P28072" } ] }, { "ec_number": "3.4.25.1", "activity": "", "evidence": [ { "id": "P28072", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P28072" } ] } ] }, { "uniprot_ac": "P28074", "gene_name": "PSMB5", "activity": [ { "ec_number": "3.4.25.1", "activity": "Cleavage of peptide bonds with very broad specificity.", "evidence": [ { "id": "P28074", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P28074" } ] }, { "ec_number": "3.4.25.1", "activity": "", "evidence": [ { "id": "P28074", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P28074" } ] } ] }, { "uniprot_ac": "P40306", "gene_name": "PSMB10", "activity": [ { "ec_number": "3.4.25.1", "activity": "Cleavage of peptide bonds with very broad specificity.", "evidence": [ { "id": "P40306", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P40306" } ] }, { "ec_number": "3.4.25.1", "activity": "", "evidence": [ { "id": "P40306", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P40306" } ] } ] }, { "uniprot_ac": "P49137", "gene_name": "MAPKAPK2", "activity": [ { "ec_number": "2.7.11.1", "activity": "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein].", "evidence": [ { "id": "P49137", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P49137" } ] }, { "ec_number": "2.7.11.1", "activity": "", "evidence": [ { "id": "P49137", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P49137" } ] } ] }, { "uniprot_ac": "P51668", "gene_name": "UBE2D1", "activity": [ { "ec_number": "2.3.2.24", "activity": "S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E1 ubiquitin-activating enzyme]-L-cysteine + N(6)-monoubiquitinyl-[acceptor protein]-L-lysine.", "evidence": [ { "id": "P51668", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P51668" } ] }, { "ec_number": "2.3.2.23", "activity": "S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine.", "evidence": [ { "id": "P51668", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P51668" } ] }, { "ec_number": "2.3.2.23", "activity": "", "evidence": [ { "id": "P51668", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P51668" } ] } ] }, { "uniprot_ac": "P68036", "gene_name": "UBE2L3", "activity": [ { "ec_number": "2.3.2.23", "activity": "S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine.", "evidence": [ { "id": "P68036", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P68036" } ] }, { "ec_number": "2.3.2.23", "activity": "", "evidence": [ { "id": "P68036", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P68036" } ] } ] }, { "uniprot_ac": "P98170", "gene_name": "XIAP", "activity": [ { "ec_number": "2.3.2.27", "activity": "S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.", "evidence": [ { "id": "P98170", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P98170" } ] }, { "ec_number": "2.3.2.27", "activity": "", "evidence": [ { "id": "P98170", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/P98170" } ] } ] }, { "uniprot_ac": "Q12933", "gene_name": "TRAF2", "activity": [ { "ec_number": "2.3.2.27", "activity": "S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.", "evidence": [ { "id": "Q12933", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q12933" } ] }, { "ec_number": "2.3.2.27", "activity": "", "evidence": [ { "id": "Q12933", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q12933" } ] } ] }, { "uniprot_ac": "Q13107", "gene_name": "USP4", "activity": [ { "ec_number": "3.4.19.12", "activity": "Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).", "evidence": [ { "id": "Q13107", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q13107" } ] }, { "ec_number": "3.4.19.12", "activity": "", "evidence": [ { "id": "Q13107", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q13107" } ] } ] }, { "uniprot_ac": "Q13114", "gene_name": "TRAF3", "activity": [ { "ec_number": "2.3.2.27", "activity": "S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.", "evidence": [ { "id": "Q13114", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q13114" } ] }, { "ec_number": "2.3.2.27", "activity": "", "evidence": [ { "id": "Q13114", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q13114" } ] } ] }, { "uniprot_ac": "Q13233", "gene_name": "MAP3K1", "activity": [ { "ec_number": "2.3.2.27", "activity": "S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.", "evidence": [ { "id": "Q13233", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q13233" } ] }, { "ec_number": "2.7.11.25", "activity": "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein].", "evidence": [ { "id": "Q13233", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q13233" } ] }, { "ec_number": "2.7.11.25", "activity": "", "evidence": [ { "id": "Q13233", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q13233" } ] } ] }, { "uniprot_ac": "Q13489", "gene_name": "BIRC3", "activity": [ { "ec_number": "2.3.2.27", "activity": "S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.", "evidence": [ { "id": "Q13489", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q13489" } ] }, { "ec_number": "2.3.2.27", "activity": "", "evidence": [ { "id": "Q13489", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q13489" } ] } ] }, { "uniprot_ac": "Q13490", "gene_name": "BIRC2", "activity": [ { "ec_number": "2.3.2.27", "activity": "S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.", "evidence": [ { "id": "Q13490", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q13490" } ] }, { "ec_number": "2.3.2.27", "activity": "", "evidence": [ { "id": "Q13490", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q13490" } ] } ] }, { "uniprot_ac": "Q13546", "gene_name": "RIPK1", "activity": [ { "ec_number": "2.7.11.1", "activity": "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein].", "evidence": [ { "id": "Q13546", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q13546" } ] }, { "ec_number": "2.7.11.1", "activity": "", "evidence": [ { "id": "Q13546", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q13546" } ] } ] }, { "uniprot_ac": "Q14164", "gene_name": "IKBKE", "activity": [ { "ec_number": "2.7.11.10", "activity": "ATP + L-seryl-[I-kappa-B protein] = ADP + H(+) + O-phospho-L-seryl-[I-kappa-B protein].", "evidence": [ { "id": "Q14164", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q14164" } ] }, { "ec_number": "2.7.11.10", "activity": "", "evidence": [ { "id": "Q14164", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q14164" } ] } ] }, { "uniprot_ac": "Q14258", "gene_name": "TRIM25", "activity": [ { "ec_number": "2.3.2.27", "activity": "S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.", "evidence": [ { "id": "Q14258", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q14258" } ] }, { "ec_number": "6.3.2.n3", "activity": "ATP + [ISG15] + [protein]-lysine = AMP + diphosphate + [protein]-N-ISGyllysine.", "evidence": [ { "id": "Q14258", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q14258" } ] }, { "ec_number": "6.3.2.n3", "activity": "", "evidence": [ { "id": "Q14258", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q14258" } ] } ] }, { "uniprot_ac": "Q14790", "gene_name": "CASP8", "activity": [ { "ec_number": "3.4.22.61", "activity": "Strict requirement for Asp at position P1 and has a preferred cleavage sequence of (Leu/Asp/Val)-Glu-Thr-Asp-|-(Gly/Ser/Ala).", "evidence": [ { "id": "Q14790", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q14790" } ] }, { "ec_number": "3.4.22.61", "activity": "", "evidence": [ { "id": "Q14790", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q14790" } ] } ] }, { "uniprot_ac": "Q5VV17", "gene_name": "OTUD1", "activity": [ { "ec_number": "3.4.19.12", "activity": "Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).", "evidence": [ { "id": "Q5VV17", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q5VV17" } ] }, { "ec_number": "3.4.19.12", "activity": "", "evidence": [ { "id": "Q5VV17", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q5VV17" } ] } ] }, { "uniprot_ac": "Q6GQQ9", "gene_name": "OTUD7B", "activity": [ { "ec_number": "3.4.19.12", "activity": "Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).", "evidence": [ { "id": "Q6GQQ9", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q6GQQ9" } ] }, { "ec_number": "3.4.19.12", "activity": "", "evidence": [ { "id": "Q6GQQ9", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q6GQQ9" } ] } ] }, { "uniprot_ac": "Q86UV5", "gene_name": "USP48", "activity": [ { "ec_number": "3.4.19.12", "activity": "Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).", "evidence": [ { "id": "Q86UV5", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q86UV5" } ] }, { "ec_number": "3.4.19.12", "activity": "", "evidence": [ { "id": "Q86UV5", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q86UV5" } ] } ] }, { "uniprot_ac": "Q8IUD6", "gene_name": "RNF135", "activity": [ { "ec_number": "2.3.2.27", "activity": "S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.", "evidence": [ { "id": "Q8IUD6", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q8IUD6" } ] }, { "ec_number": "2.3.2.27", "activity": "", "evidence": [ { "id": "Q8IUD6", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q8IUD6" } ] } ] }, { "uniprot_ac": "Q96AX9", "gene_name": "MIB2", "activity": [ { "ec_number": "2.3.2.27", "activity": "S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.", "evidence": [ { "id": "Q96AX9", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q96AX9" } ] }, { "ec_number": "2.3.2.27", "activity": "", "evidence": [ { "id": "Q96AX9", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q96AX9" } ] } ] }, { "uniprot_ac": "Q96EP0", "gene_name": "RNF31", "activity": [ { "ec_number": "2.3.2.31", "activity": "[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-N(6)-ubiquitinyl-L-lysine.", "evidence": [ { "id": "Q96EP0", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q96EP0" } ] }, { "ec_number": "2.3.2.31", "activity": "", "evidence": [ { "id": "Q96EP0", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q96EP0" } ] } ] }, { "uniprot_ac": "Q99436", "gene_name": "PSMB7", "activity": [ { "ec_number": "3.4.25.1", "activity": "Cleavage of peptide bonds with very broad specificity.", "evidence": [ { "id": "Q99436", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q99436" } ] }, { "ec_number": "3.4.25.1", "activity": "", "evidence": [ { "id": "Q99436", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q99436" } ] } ] }, { "uniprot_ac": "Q99558", "gene_name": "MAP3K14", "activity": [ { "ec_number": "2.7.11.25", "activity": "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein].", "evidence": [ { "id": "Q99558", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q99558" } ] }, { "ec_number": "2.7.11.25", "activity": "", "evidence": [ { "id": "Q99558", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q99558" } ] } ] }, { "uniprot_ac": "Q9BYM8", "gene_name": "RBCK1", "activity": [ { "ec_number": "2.3.2.31", "activity": "[E2 ubiquitin-conjugating enzyme]-S-ubiquitinyl-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-N(6)-ubiquitinyl-L-lysine.", "evidence": [ { "id": "Q9BYM8", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9BYM8" } ] }, { "ec_number": "2.3.2.31", "activity": "", "evidence": [ { "id": "Q9BYM8", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9BYM8" } ] } ] }, { "uniprot_ac": "Q9BYX4", "gene_name": "IFIH1", "activity": [ { "ec_number": "3.6.4.13", "activity": "ATP + H2O = ADP + H(+) + phosphate.", "evidence": [ { "id": "Q9BYX4", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9BYX4" } ] }, { "ec_number": "3.6.4.13", "activity": "", "evidence": [ { "id": "Q9BYX4", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9BYX4" } ] } ] }, { "uniprot_ac": "Q9C037", "gene_name": "TRIM4", "activity": [ { "ec_number": "2.3.2.27", "activity": "S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.", "evidence": [ { "id": "Q9C037", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9C037" } ] }, { "ec_number": "2.3.2.27", "activity": "", "evidence": [ { "id": "Q9C037", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9C037" } ] } ] }, { "uniprot_ac": "Q9NQC7", "gene_name": "CYLD", "activity": [ { "ec_number": "3.4.19.12", "activity": "Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).", "evidence": [ { "id": "Q9NQC7", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9NQC7" } ] }, { "ec_number": "3.4.19.12", "activity": "", "evidence": [ { "id": "Q9NQC7", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9NQC7" } ] } ] }, { "uniprot_ac": "Q9UHD2", "gene_name": "TBK1", "activity": [ { "ec_number": "2.7.11.1", "activity": "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein].", "evidence": [ { "id": "Q9UHD2", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9UHD2" } ] }, { "ec_number": "2.7.11.1", "activity": "", "evidence": [ { "id": "Q9UHD2", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9UHD2" } ] } ] }, { "uniprot_ac": "Q9UK80", "gene_name": "USP21", "activity": [ { "ec_number": "3.4.19.12", "activity": "Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).", "evidence": [ { "id": "Q9UK80", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9UK80" } ] }, { "ec_number": "3.4.19.12", "activity": "", "evidence": [ { "id": "Q9UK80", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9UK80" } ] } ] }, { "uniprot_ac": "Q9UNE7", "gene_name": "STUB1", "activity": [ { "ec_number": "2.3.2.27", "activity": "S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.", "evidence": [ { "id": "Q9UNE7", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9UNE7" } ] }, { "ec_number": "2.3.2.27", "activity": "", "evidence": [ { "id": "Q9UNE7", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9UNE7" } ] } ] }, { "uniprot_ac": "Q9Y4K3", "gene_name": "TRAF6", "activity": [ { "ec_number": "2.3.2.27", "activity": "S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.", "evidence": [ { "id": "Q9Y4K3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9Y4K3" } ] }, { "ec_number": "2.3.2.27", "activity": "", "evidence": [ { "id": "Q9Y4K3", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9Y4K3" } ] } ] }, { "uniprot_ac": "Q9Y572", "gene_name": "RIPK3", "activity": [ { "ec_number": "2.7.11.1", "activity": "ATP + L-seryl-[protein] = ADP + H(+) + O-phospho-L-seryl-[protein].", "evidence": [ { "id": "Q9Y572", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9Y572" } ] }, { "ec_number": "2.7.11.1", "activity": "", "evidence": [ { "id": "Q9Y572", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprot/Q9Y572" } ] } ] } ], "biomarkers": [ { "assessed_biomarker_entity": "Tumor necrosis factor receptor-associated factor 2 (TRAF2)", "biomarker_id": "A0169", "evidence": [ { "id": "GLY_000625", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000625" }, { "id": "28855498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28855498" } ], "instances": [ { "best_biomarker_type": "prognostic", "status": "increased of TRAF2 level", "disease": { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "http://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, on chromosome 7", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "predisposing for prostate cancer", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, susceptibility to", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, susceptibility to", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "familial prostate carcinoma", "description": "Prostate carcinoma that has developed in relatives of patients with a history of prostate carcinoma." }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "familial prostate cancer", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", "name": "hereditary prostate cancer", "description": "" }, { "id": "MONDO:0023122", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0023122", 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