id: MODULE:p53_signaling title: p53 signaling — stress-kinase stabilisation of p53 (ATM/ATR, CHK2/CHK1), MDM2-MDM4 ubiquitin-ligase negative feedback, ARF inhibition of MDM2, acetylation control, and p53 tetramer transactivation of target genes; TP53/MDM2/MDM4/CDKN2A(ARF)/ATM/ATR/CHEK2/CHEK1/EP300/CREBBP/KAT5/SIRT1 description: >- The tumour suppressor p53 (TP53) is a sequence-specific transcription factor that is kept at low levels in unstressed cells by the RING E3 ubiquitin ligase MDM2. MDM2 binds the N-terminal transactivation domain of p53, which both conceals the domain from the transcription machinery and positions p53 for polyubiquitylation and proteasomal degradation. The MDM2 paralog MDM4 (MDMX) has no ligase activity of its own toward p53 but heterodimerises with MDM2 through the RING domain, stimulating MDM2 E3 activity, and also binds and inhibits the p53 transactivation domain. Because the MDM2 gene is itself a p53 target, the circuit is a negative feedback loop. Stress releases p53 from this loop in two main ways. DNA damage activates the PI3K-like kinases ATM (double-strand breaks) and ATR (replication stress and UV damage), which phosphorylate p53 on Ser15 and MDM2, and activate the effector kinases CHK2 and CHK1, which phosphorylate p53 on Ser20 in the MDM2-binding region; these modifications weaken the p53-MDM2 interaction and stabilise p53. Oncogenic signalling induces the ARF product of the CDKN2A locus, which binds MDM2, inhibits its E3 activity and sequesters it in the nucleolus. Stabilised p53 binds its response elements as a tetramer and recruits the coactivator acetyltransferases p300 and CBP, which acetylate the p53 C-terminal domain as well as promoter histones; KAT5 (TIP60) acetylates p53 Lys120 in the DNA-binding domain, a mark needed for induction of pro-apoptotic targets, and the NAD-dependent deacetylase SIRT1 removes p53 acetylation and dampens its activity. The transcriptional outputs, such as CDKN1A (p21), BBC3 (PUMA), PMAIP1 (NOXA) and BAX, then execute cell-cycle arrest, apoptosis or senescence through modules downstream of this circuit. status: DRAFT scope: CONCRETE evidence: - source_id: PW:0000718 title: p53 signaling pathway statement: >- The module boundary follows the RGD Pathway Ontology term and its diagram. The diagram draws Mdm2 and Mdm4 associated with and negatively affecting Tp53, Mdm2 associated with Mdm4, Tp53 positively affecting Mdm2 (the feedback loop), the ATM signaling pathway positively affecting "p53, Mdm2 phosphorylation", "p53, Mdm2 acetylation" positively affecting Tp53 and negatively affecting Mdm2, endogenous and exogenous stress positively affecting Tp53, and Tp53 positively affecting "p53 targets", cell cycle arrest, senescence, the intrinsic apoptotic pathway and RNA polymerase II transcription. Derived through projects/RGD_PATHWAY_ONTOLOGY (pathways/PW_0000718.yaml). - source_id: file:projects/RGD_PATHWAY_ONTOLOGY/pathways/PW_0000718.yaml title: RGD PW:0000718 pathway description statement: RGD's description of the MDM2-p53 negative feedback loop at the core of the module. supporting_text: In the unstressed state, Mdm2 binds to and sterically blocks the transactivation domain of p53, it also acts as an E3 ubiquitin ligase for p53 and itself. Mdm2 is a target of p53, hence the negative feedback loop it provides. - source_id: GO:0072331 title: signal transduction by p53 class mediator statement: >- The curated skos:closeMatch GO process for PW:0000718 in projects/RGD_PATHWAY_ONTOLOGY/data/module_seeds.yaml, used as the module concept. - source_id: gomodel:680ad14200006012 title: Negative regulation of signal transduction by p53 by RAD54B (Human) statement: >- Human GO-CAM in which MDM4 enzyme activator activity directly positively regulates MDM2 ubiquitin protein ligase activity, which directly negatively regulates TP53 (promoter-specific chromatin binding, part of signal transduction by p53 class mediator), in the nucleoplasm. It grounds the MDM2-MDM4 part of the module. - source_id: gomodel:646ff70100000239 title: Negative regulation of signal transduction by p53 class mediator by MORN3. (Human) statement: >- Human GO-CAM in which MDM2 ubiquitin protein ligase activity and SIRT1 NAD-dependent protein lysine deacetylase activity both act on the TP53 DNA-binding transcription factor activity, part of signal transduction by p53 class mediator. It grounds the SIRT1 deacetylation part. - source_id: PMID:8319905 title: The p53-mdm-2 autoregulatory feedback loop. statement: MDM2 is a p53 target gene whose product inhibits p53, forming the feedback loop. supporting_text: This creates a feedback loop that regulates both the activity of the p53 protein and the expression of the mdm-2 gene. notes: >- Derived from the RGD Pathway Ontology diagram PW:0000718 (p53 signaling pathway) through the RGD_PATHWAY_ONTOLOGY project's diagram->module route (seed in projects/RGD_PATHWAY_ONTOLOGY/data/module_seeds.yaml, tier related_module_only). The seed's only existing related module was c_elegans_core_apoptosis, matched because it uses a descendant of the mapped GO term; it models CEP-1-dependent germline apoptosis in C. elegans and is not a human p53 circuit, so it is neither referenced nor duplicated here. The seed's best-overlap GO-CAM (gomodel:65a1f4f800001246, lactylation of MRE11 by CREBBP and of NBN by KAT5 in homologous recombination) shares only DNA-repair genes with the pathway and is not linked. The diagram draws only three genes (Mdm2, Mdm4, Tp53); RGD curates 40 human genes to PW:0000718: ABL1 ATM BRCA1 CHEK1 CHEK2 COP1 CREBBP ETS1 HDAC1 KAT2A KAT2B KAT5 KAT8 MDM2 MDM4 MRE11 MUC1 NFYA NFYB NFYC PIN1 POU4F1 POU4F2 PPP1R13B PPP1R13L RCHY1 SETD7 SIRT1 SMYD2 SREBF2 TP53 TP53BP2 TP63 TP73 USP7 VDR YBX1 ZNF385A ZNF420 ZNHIT1. Nine are modelled as participants (TP53, MDM2, MDM4, ATM, CHEK1, CHEK2, CREBBP, KAT5, SIRT1). Three gene products not on the RGD list are added because the circuit cannot be drawn without them: ATR (the replication-stress kinase upstream of CHK1), ARF (the CDKN2A alternative-reading-frame product, the oncogenic-stress inhibitor of MDM2), and EP300 as the paralog shown by Gu and Roeder to acetylate p53 (grouped with CREBBP in one family annoton). Molecular functions come from each protein's experimental GO annotations in QuickGO (November 2026): TP53 GO:0001228 (IDA), MDM2 GO:0061630 (IDA/IMP/EXP), MDM4 GO:0008047 (IDA, with extension has_input MDM2 and directly positively regulates ubiquitin protein ligase activity), ARF GO:1990948 (IDA), ATM, ATR and CHEK2 GO:0004674 (IDA), CHEK1 GO:0106310 (EXP/IDA), KAT5 and p300/CBP GO:0061733 (IDA), SIRT1 GO:0034979 (IDA). Gene reviews exist for TP53, CDKN2A (p16 entry P42771) and CDKN2A__Q8N726 (ARF), ATM, CHEK1, CHEK2, CREBBP, EP300, SIRT1, COP1 and ABL1. Substrate versus participant (CLAUDE.md). p53 target genes are transcriptional outputs of the circuit, not participants in it. CDKN1A, BAX, BBC3 (PUMA), PMAIP1 (NOXA) and GADD45A are therefore not annotons; their products act in downstream modules referenced as optional output parts (bcl2_family_momp_control#bh3_only_activation for the BH3-only proteins and BAX; g1_s_transition#g1s_cdk_activation for p21 inhibition of G1/S cyclin-CDK). The comparator check agrees with this convention: in human GOA, BBC3, BAX and GADD45A carry no annotation to GO:0072331 or its descendants, and CDKN1A carries only IEA/TAS rows to GO:0030330, whereas the circuit components MDM2 (IMP), KAT5 (IDA) and SIRT1 (IMP, GO:0042771) carry experimental ones. PMAIP1 carries GO:0072332 (IMP), which is the apoptotic output process rather than the p53 signal itself. MDM2 is the exception the rule allows: it is a p53 target, but its product does work in the circuit (E3 ligase activity on p53), so it is a participant, and the p53 -> MDM2 transcriptional edge closes the feedback loop. p53 itself is a substrate of every enzyme in parts 2-4 and 6-7, but it is also the pathway's transcription factor, so it is the central participant. Two human GO-CAMs do model target-gene products as downstream activities (BAX channel activity in gomodel:69b3372b00001963; CDKN1A CDK inhibitor activity in gomodel:69d8496c00000318, p21 induction via HIPK2); that is consistent with treating them as outputs causally downstream of the p53 activity. Boundary decisions. (1) ATM activation at double-strand breaks is not re-modelled: part 1 is a module_ref to atm_dsb_signaling#atm_activation and is optional, because p53 also responds to ATR-dependent and ARF-dependent stress. Only ATM's own action on p53 and MDM2 is an annoton here. MRE11 and BRCA1, on the RGD list, belong to that module. ATR activation (ATRIP, TOPBP1, 9-1-1) is out of scope; no human ATR module exists (dmel_atr_atrip_complex and dmel_9_1_1_checkpoint_clamp are fly modules). (2) Ribosomal-protein inhibition of MDM2 (RPL5, RPL11, nucleolar stress) is named in the ARF part description but not modelled. (3) Further p53 ubiquitin-system components on the RGD list are not modelled: COP1 and RCHY1 (Pirh2) are additional p53 E3 ligases (RCHY1 is itself p53-induced, a second feedback loop), and USP7 (HAUSP) deubiquitinates both p53 (PMID:11923872) and MDM2, so its net effect is context dependent. They are candidates for a later extension of part 3. (4) Other p53 modifiers on the RGD list are not modelled to keep the core circuit legible: KAT2A and KAT2B (PCAF; Lys320 acetylation, in the p21 induction GO-CAM gomodel:69c59f8a00000219), KAT8 (MOF; Lys120, redundant with KAT5 and named in the KAT5 annoton), SETD7 (Lys372 methylation), SMYD2 (repressive Lys370 methylation), HDAC1 (deacetylation with NuRD/MTA2), PIN1 (phosphorylation-dependent prolyl isomerisation) and ABL1 (damage-induced phosphorylation of MDM2 and MDM4). (5) The ASPP proteins PPP1R13B (ASPP1), TP53BP2 (ASPP2) and PPP1R13L (iASPP) modulate p53 promoter selection toward or away from apoptotic targets; they are context regulators of target choice, not part of the stabilisation circuit. (6) Gene products that bind p53 or its target promoters as transcriptional partners or regulators of TP53 expression (NFYA, NFYB, NFYC, ETS1, YBX1, VDR, SREBF2, POU4F1, POU4F2, MUC1, ZNF385A, ZNF420/Apak, ZNHIT1) are peripheral and not modelled. (7) The p53 paralogs TP63 and TP73 share response elements but have their own developmental and DNA-damage roles; they are not variants of this human p53 module. (8) Repression of RNA polymerase I and III transcription, non-coding RNA targets and regulators, and p53 transcription-independent mitochondrial apoptosis are drawn or described by RGD but left out. (9) The RGD diagram links PW:0000104 (intrinsic apoptotic pathway), PW:0000127 and PW:0001274 (RNA polymerase II transcription and its initiation) and PW:0001361 (ATM signaling pathway). These are mentioned here, reached through module_ref or as context, and are not listed as evidence sources; PW:0001361 is the evidence source of atm_dsb_signaling. (10) The module concept is GO:0072331 (the curated closeMatch), not its DNA-damage child GO:0030330, because ARF-driven activation is not a DNA damage response. GO-CAM and GOA observations for upstream review. In human GOA, CHEK1's experimental MF rows use GO:0106310 protein serine kinase activity while CHEK2, ATM and ATR use GO:0004674; both are correct for serine kinases, but the split is a curation inconsistency rather than a biological difference. The MDM4 enzyme activator annotation (GO:0008047) rests on PMID:25384516, a paper about RAD54B as a scaffold for the MDM2-MDMX ligase, rather than on the primary MDM2-MDMX heterodimer studies. The ARF GO:1990948 IDA comes from PMID:18560357 (a ribosomal protein L5/L11 study) rather than from the original ARF-MDM2 papers. The p53 GO-CAM activities are typed inconsistently across models (GO:0003700, GO:0000981, GO:0001228 and GO:1990841 for the same p53 role). TP53 and CHEK1 gene reviews do not list GO:0001228 or GO:0106310 in core_functions (module validator conformance warnings). PANTHER family ids and PTNs are deliberately not asserted. module: id: p53_signaling label: p53 signaling (MDM2-MDM4 feedback, stress-kinase and ARF release, p53 transactivation) module_type: SIGNALING_PATHWAY concepts: - preferred_term: signal transduction by p53 class mediator term: id: GO:0072331 label: signal transduction by p53 class mediator description: >- The GO process mapped (skos:closeMatch) to PW:0000718: the intracellular cascade in which a p53-family protein relays a stress signal and regulates transcription. context: taxa: - preferred_term: Homo sapiens term: id: NCBITaxon:9606 label: Homo sapiens cellular_components: - preferred_term: nucleoplasm term: id: GO:0005654 label: nucleoplasm parts: - order: 1 optional: true role: DNA double-strand break input through ATM activation node: id: atm_dsb_input label: MRN recruitment and activation of ATM at DNA double-strand breaks description: >- Included by reference to the ATM activation step of the ATM DSB signalling module (MRN sensing, ATM monomerisation and Ser1981 autophosphorylation, KAT5 acetylation of ATM). Optional because p53 is also released by stresses that do not act through ATM (ATR-dependent replication and UV stress, and ARF-dependent oncogenic stress, parts 2 and 4). module_ref: atm_dsb_signaling#atm_activation - order: 2 role: stress-kinase phosphorylation of p53 and MDM2 node: id: p53_stabilizing_phosphorylation label: ATM/ATR and CHK2/CHK1 phosphorylation of p53 (Ser15, Ser20) and MDM2 module_type: REGULATORY_STEP description: >- The DNA damage kinases phosphorylate the p53 N-terminus: ATM (and ATR) on Ser15, CHK2 and CHK1 on Ser20 in the MDM2-binding region. ATM also phosphorylates MDM2. These modifications weaken the p53-MDM2 interaction, stabilise p53 and favour coactivator binding. annotons: - id: atm_p53_kinase label: ATM phosphorylation of p53 Ser15 and of MDM2 participant: selector_type: GENE_PRODUCT gene_product: preferred_term: ATM term: id: UniProtKB:Q13315 label: Serine-protein kinase ATM function: preferred_term: protein serine/threonine kinase activity term: id: GO:0004674 label: protein serine/threonine kinase activity targets: - preferred_term: TP53 (Ser15) term: id: UniProtKB:P04637 label: Cellular tumor antigen p53 - preferred_term: MDM2 term: id: UniProtKB:Q00987 label: E3 ubiquitin-protein ligase Mdm2 locations: - preferred_term: nucleoplasm term: id: GO:0005654 label: nucleoplasm role_description: >- Activated by double-strand breaks (part 1); phosphorylates p53 Ser15 directly and also phosphorylates and activates CHK2, and phosphorylates MDM2, so it acts on both partners of the feedback loop. evidence: - source_id: PMID:9843217 statement: Recombinant ATM phosphorylates p53 on Ser15, and ATM is required for IR-induced Ser15 phosphorylation. supporting_text: Recombinant ATM protein phosphorylates p53 on serine 15 near the N terminus. - source_id: PMID:9733515 statement: Endogenous ATM phosphorylates p53 Ser15, and ionizing radiation enhances this activity. supporting_text: Immunoprecipitated ATM had intrinsic protein kinase activity and phosphorylated p53 on serine-15 in a manganese-dependent manner. - source_id: PMID:10611322 statement: ATM phosphorylates MDM2 directly after DNA strand breaks. supporting_text: Furthermore, MDM2 is directly phosphorylated by ATM in vitro. - id: atr_p53_kinase label: ATR phosphorylation of p53 Ser15 participant: selector_type: GENE_PRODUCT gene_product: preferred_term: ATR term: id: UniProtKB:Q13535 label: Serine/threonine-protein kinase ATR function: preferred_term: protein serine/threonine kinase activity term: id: GO:0004674 label: protein serine/threonine kinase activity targets: - preferred_term: TP53 (Ser15, Ser37) term: id: UniProtKB:P04637 label: Cellular tumor antigen p53 locations: - preferred_term: nucleoplasm term: id: GO:0005654 label: nucleoplasm role_description: >- The replication-stress and UV arm. ATR phosphorylates p53 Ser15 (and Ser37) and activates CHK1. ATR activation (ATRIP, TOPBP1, 9-1-1 clamp) is not modelled here. evidence: - source_id: PMID:9925639 statement: ATR phosphorylates p53 in vitro and catalytically inactive ATR blocks damage-induced Ser15 phosphorylation. supporting_text: ATR phosphorylated p53 at Ser-15 and Ser-37 in vitro, suggesting that p53 is a target for phosphorylation by ATR in DNA-damaged cells. - id: chek2_p53_kinase label: CHK2 phosphorylation of p53 Ser20 participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CHEK2 (CHK2) term: id: UniProtKB:O96017 label: Serine/threonine-protein kinase Chk2 function: preferred_term: protein serine/threonine kinase activity term: id: GO:0004674 label: protein serine/threonine kinase activity targets: - preferred_term: TP53 (Ser20) term: id: UniProtKB:P04637 label: Cellular tumor antigen p53 locations: - preferred_term: nucleoplasm term: id: GO:0005654 label: nucleoplasm role_description: >- ATM-activated effector kinase. Ser20 phosphorylation lies in the MDM2-binding region of the transactivation domain and dissociates p53-MDM2 complexes. evidence: - source_id: PMID:10673500 statement: CHK2 phosphorylates p53 Ser20 and dissociates p53-MDM2 complexes in vitro; dominant-negative CHK2 blocks p53 stabilization. supporting_text: In vitro, Chk2/hCds1 phosphorylated p53 on Ser-20 and dissociated preformed complexes of p53 with Mdm2, a protein that targets p53 for degradation. - source_id: PMID:10710310 statement: Chk2-deficient cells fail to stabilise p53 after irradiation. supporting_text: Chk2-/- cells were defective for p53 stabilization and for induction of p53-dependent transcripts such as p21 in response to gamma irradiation. - id: chek1_p53_kinase label: CHK1 phosphorylation of p53 Ser20 participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CHEK1 (CHK1) term: id: UniProtKB:O14757 label: Serine/threonine-protein kinase Chk1 function: preferred_term: protein serine kinase activity term: id: GO:0106310 label: protein serine kinase activity targets: - preferred_term: TP53 (Ser20) term: id: UniProtKB:P04637 label: Cellular tumor antigen p53 locations: - preferred_term: nucleoplasm term: id: GO:0005654 label: nucleoplasm role_description: >- ATR-activated effector kinase; phosphorylates tetrameric p53 at Ser20 and other inducible N- and C-terminal sites. evidence: - source_id: PMID:10673501 statement: Recombinant CHK1, but not a kinase-dead mutant, phosphorylates p53 Ser20. supporting_text: We confirmed that recombinant hCHK1, but not a kinase-defective version of hCHK1, can phosphorylate p53 in vitro at S20. - order: 3 role: MDM2-MDM4 ubiquitin-ligase negative feedback on p53 node: id: mdm2_mdm4_feedback label: MDM2 E3 ubiquitin ligase activity on p53, stimulated by MDM4 module_type: REGULATORY_STEP description: >- MDM2 binds the p53 transactivation domain and polyubiquitylates p53 for proteasomal degradation; MDM4 binds both p53 and MDM2 and stimulates MDM2 E3 activity. MDM2 is transcriptionally induced by p53, closing the negative feedback loop. annotons: - id: mdm2_p53_ligase label: MDM2 ubiquitin protein ligase activity toward p53 participant: selector_type: GENE_PRODUCT gene_product: preferred_term: MDM2 term: id: UniProtKB:Q00987 label: E3 ubiquitin-protein ligase Mdm2 function: preferred_term: ubiquitin protein ligase activity term: id: GO:0061630 label: ubiquitin protein ligase activity targets: - preferred_term: TP53 term: id: UniProtKB:P04637 label: Cellular tumor antigen p53 processes: - preferred_term: negative regulation of signal transduction by p53 class mediator term: id: GO:1901797 label: negative regulation of signal transduction by p53 class mediator locations: - preferred_term: nucleoplasm term: id: GO:0005654 label: nucleoplasm role_description: >- Both a component of the circuit and a p53 transcriptional target: MDM2 occludes the p53 transactivation domain (Phe19, Trp23, Leu26 insert into the MDM2 N-terminal cleft) and is the principal p53 E3 ligase. evidence: - source_id: PMID:9450543 statement: MDM2 polyubiquitylates p53 with E1 and UbcH5 in vitro. supporting_text: p53 was polyubiquitinated in the presence of E1, UbcH5 as E2 and MDM2 oncoprotein. - source_id: PMID:9153395 statement: MDM2 promotes rapid degradation of p53 and terminates the p53 signal. supporting_text: We now report that Mdm2 also promotes the rapid degradation of p53 under conditions in which p53 is otherwise stabilized. - source_id: PMID:9153396 statement: Endogenous MDM2 levels regulate p53 stability through proteasome-dependent degradation. supporting_text: Endogenous levels of Mdm2 are sufficient to regulate p53 stability, and overexpression of Mdm2 can reduce the amount of endogenous p53. - source_id: PMID:8875929 statement: MDM2 conceals the p53 transactivation domain. supporting_text: These same p53 residues are also involved in transactivation, supporting the hypothesis that MDM2 inactivates p53 by concealing its transactivation domain. gocam_associations: - model: gomodel:680ad14200006012 activity: gomodel:680ad14200006012/680ad14200006066 title: MDM2 ubiquitin protein ligase activity (GO:0061630), directly negatively regulates TP53, Negative regulation of signal transduction by p53 by RAD54B (Human) - model: gomodel:646ff70100000239 activity: gomodel:646ff70100000239/646ff70100000245 title: MDM2 ubiquitin protein ligase activity (GO:0061630), Negative regulation of signal transduction by p53 class mediator by MORN3 (Human) - model: gomodel:69b3372b00001963 activity: gomodel:69b3372b00001963/69b3372b00001964 title: MDM2 ubiquitin protein ligase activity (GO:0061630), MDM2-UBE4B cooperation to ubiquitinate P53 (Human) - id: mdm4_mdm2_activator label: MDM4 (MDMX) stimulation of MDM2 E3 activity participant: selector_type: GENE_PRODUCT gene_product: preferred_term: MDM4 (MDMX) term: id: UniProtKB:O15151 label: Protein Mdm4 function: preferred_term: enzyme activator activity term: id: GO:0008047 label: enzyme activator activity targets: - preferred_term: MDM2 term: id: UniProtKB:Q00987 label: E3 ubiquitin-protein ligase Mdm2 processes: - preferred_term: negative regulation of signal transduction by p53 class mediator term: id: GO:1901797 label: negative regulation of signal transduction by p53 class mediator locations: - preferred_term: nucleoplasm term: id: GO:0005654 label: nucleoplasm role_description: >- MDM2 paralog without effective p53 E3 activity of its own. It binds the p53 transactivation domain and inhibits transactivation, and as the MDM2-MDM4 RING heterodimer it stimulates MDM2-mediated p53 ubiquitylation. Unlike MDM2 it is not induced by p53. evidence: - source_id: PMID:8895579 statement: MDMX binds p53 and inhibits the p53 transactivation domain, but, unlike MDM2, is not transcriptionally induced by damage. supporting_text: This interaction probably occurs with the N-terminal part of p53, because the activity of the transcription activation domain of p53 was inhibited by co-transfection of MDMX. - source_id: PMID:25384516 statement: MDM2-MDMX act as a ubiquitin-ligase complex for p53 degradation (the source of the MDM4 enzyme activator IDA annotation). supporting_text: We find that Rad54B functions as a scaffold for p53 degradation via its direct interaction with the MDM2-MDMX ubiquitin-ligase complex. gocam_associations: - model: gomodel:680ad14200006012 activity: gomodel:680ad14200006012/680ad14200006096 title: MDM4 enzyme activator activity (GO:0008047), directly positively regulates MDM2, Negative regulation of signal transduction by p53 by RAD54B (Human) - order: 4 role: ARF inhibition and nucleolar sequestration of MDM2 node: id: arf_mdm2_inhibition label: ARF (CDKN2A) inhibition of MDM2 E3 activity module_type: REGULATORY_STEP description: >- ARF, the alternative-reading-frame product of the CDKN2A locus, accumulates under oncogenic stress (an upstream input not modelled here). ARF binds MDM2, inhibits its ubiquitin ligase activity, promotes MDM2 degradation and holds it in the nucleolus, stabilising p53 without DNA damage signalling. Ribosomal proteins RPL5 and RPL11 inhibit MDM2 in a similar way during nucleolar stress (not modelled). annotons: - id: arf_mdm2_inhibitor label: ARF ubiquitin ligase inhibitor activity on MDM2 participant: selector_type: GENE_PRODUCT gene_product: preferred_term: ARF (p14ARF; CDKN2A alternative reading frame product) term: id: UniProtKB:Q8N726 label: Tumor suppressor ARF function: preferred_term: ubiquitin ligase inhibitor activity term: id: GO:1990948 label: ubiquitin ligase inhibitor activity targets: - preferred_term: MDM2 term: id: UniProtKB:Q00987 label: E3 ubiquitin-protein ligase Mdm2 locations: - preferred_term: nucleolus term: id: GO:0005730 label: nucleolus role_description: >- The exon 1beta-encoded N-terminal domain of ARF binds a central/C-terminal region of MDM2. ARF is a distinct protein (UniProtKB:Q8N726) from the CDK4/6 inhibitor p16INK4a encoded by the same gene. evidence: - source_id: PMID:9529249 statement: ARF binds MDM2, promotes its degradation and stabilises p53. supporting_text: We show here that ARF binds to MDM2 and promotes the rapid degradation of MDM2. - source_id: PMID:9529248 statement: p19Arf binds MDM2 and blocks MDM2-induced p53 degradation and transactivational silencing. supporting_text: p19Arf functions mechanistically to prevent MDM2's neutralization of p53 - source_id: PMID:18560357 statement: p14ARF inhibits MDM2 E3 activity (the source of the ARF ubiquitin ligase inhibitor IDA annotation). supporting_text: We found that when overexpressed alone, L11 is much less potent in inhibiting MDM2 than p14(ARF). - source_id: file:genes/human/CDKN2A__Q8N726/CDKN2A__Q8N726-uniprot.txt statement: UniProt records experimentally supported nucleolar and nucleoplasmic location for ARF. supporting_text: 'SUBCELLULAR LOCATION: Nucleus, nucleolus {ECO:0000269|PubMed:16173922,' - order: 5 role: p53 tetramer sequence-specific transactivation node: id: p53_transactivation label: p53 tetramer DNA-binding transcription activator activity at response elements module_type: REGULATORY_STEP description: >- Stabilised p53 binds its response elements as a tetramer (dimer of dimers) through the zinc-coordinating DNA-binding domain and activates RNA polymerase II transcription of target genes, including MDM2 itself. annotons: - id: tp53_transcription_activator label: TP53 DNA-binding transcription activator activity, RNA polymerase II-specific participant: selector_type: GENE_PRODUCT gene_product: preferred_term: TP53 (p53) term: id: UniProtKB:P04637 label: Cellular tumor antigen p53 function: preferred_term: DNA-binding transcription activator activity, RNA polymerase II-specific term: id: GO:0001228 label: DNA-binding transcription activator activity, RNA polymerase II-specific processes: - preferred_term: signal transduction by p53 class mediator term: id: GO:0072331 label: signal transduction by p53 class mediator locations: - preferred_term: chromatin term: id: GO:0000785 label: chromatin role_description: >- The pathway's transcription factor. Its targets are outputs of the module, not participants, except MDM2 (part 3), whose product feeds back on p53. evidence: - source_id: PMID:8319905 statement: p53 binds a response element in the MDM2 gene and regulates its transcription. supporting_text: The mdm-2 gene is shown here to contain a p53 DNA-binding site and a genetically responsive element such that expression of the mdm-2 gene can be regulated by the level of wild-type p53 protein. - source_id: PMID:12609999 statement: p53 binds the p21 promoter response elements and needs its activation domains and p300/CBP to induce p21 (one of the GO:0001228 IDA sources). supporting_text: We found that like wild-type p53, these p53 mutants are capable of binding to the p53 response elements in the p21 promoter. gocam_associations: - model: gomodel:69d8496c00003152 activity: gomodel:69d8496c00003152/69d8496c00003296 title: TP53 DNA-binding transcription activator activity, RNA polymerase II-specific (GO:0001228), FBXO42-mediated degradation of p53 via CUL1/RBX1 (Human) - model: gomodel:69b3372b00001963 activity: gomodel:69b3372b00001963/69b3372b00001985 title: TP53 DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), part of intrinsic apoptotic signaling pathway by p53 class mediator, MDM2-UBE4B cooperation to ubiquitinate P53 (Human) - model: gomodel:680ad14200006012 activity: gomodel:680ad14200006012/680ad14200006105 title: TP53 promoter-specific chromatin binding (GO:1990841), part of signal transduction by p53 class mediator, Negative regulation of signal transduction by p53 by RAD54B (Human) - model: gomodel:646ff70100000239 activity: gomodel:646ff70100000239/646ff70100000261 title: TP53 DNA-binding transcription factor activity (GO:0003700), part of signal transduction by p53 class mediator, Negative regulation of signal transduction by p53 class mediator by MORN3 (Human) - order: 6 role: coactivator acetylation of p53 node: id: p53_acetylation label: p300/CBP and KAT5 acetylation of p53 module_type: REGULATORY_STEP description: >- p53 recruits the coactivator acetyltransferases p300 and CBP, which acetylate its C-terminal regulatory domain (stimulating sequence-specific DNA binding and competing with MDM2-directed ubiquitylation of the same lysines) as well as promoter histones. KAT5 (TIP60) acetylates Lys120 in the DNA-binding domain, a mark required for p53-dependent apoptosis but not for growth arrest. annotons: - id: p300_cbp_p53_acetylation label: p300/CBP protein-lysine acetyltransferase activity on the p53 C-terminus participant: selector_type: FAMILY family: preferred_term: p300/CBP coactivator acetyltransferases description: >- The two paralogous KAT3 coactivators. Gu and Roeder showed the activity with p300; CBP (on the RGD list) is its functionally overlapping paralog. No PANTHER id is asserted. representative_members: - preferred_term: EP300 (p300) term: id: UniProtKB:Q09472 label: Histone acetyltransferase p300 - preferred_term: CREBBP (CBP) term: id: UniProtKB:Q92793 label: Histone lysine acetyltransferase CREBBP function: preferred_term: protein-lysine-acetyltransferase activity term: id: GO:0061733 label: protein-lysine-acetyltransferase activity targets: - preferred_term: TP53 (C-terminal lysines) term: id: UniProtKB:P04637 label: Cellular tumor antigen p53 locations: - preferred_term: chromatin term: id: GO:0000785 label: chromatin role_description: >- Coactivators recruited by the p53 transactivation domain. Their histone acetyltransferase activity at target promoters is part of transactivation itself; here the module records their acetylation of p53. evidence: - source_id: PMID:9288740 statement: p300 acetylates the p53 C-terminal domain, stimulating sequence-specific DNA binding. supporting_text: Furthermore, the acetylation of p53 can dramatically stimulate its sequence-specific DNA-binding activity, possibly as a result of an acetylation-induced conformational change. - id: kat5_p53_k120_acetylation label: KAT5 (TIP60) acetylation of p53 Lys120 participant: selector_type: GENE_PRODUCT gene_product: preferred_term: KAT5 (TIP60) term: id: UniProtKB:Q92993 label: Histone acetyltransferase KAT5 function: preferred_term: protein-lysine-acetyltransferase activity term: id: GO:0061733 label: protein-lysine-acetyltransferase activity targets: - preferred_term: TP53 (Lys120) term: id: UniProtKB:P04637 label: Cellular tumor antigen p53 processes: - preferred_term: intrinsic apoptotic signaling pathway by p53 class mediator term: id: GO:0072332 label: intrinsic apoptotic signaling pathway by p53 class mediator locations: - preferred_term: nucleoplasm term: id: GO:0005654 label: nucleoplasm role_description: >- Biases p53 output toward apoptosis; KAT8 (MOF), also on the RGD list, acetylates the same residue. evidence: - source_id: PMID:17189186 statement: TIP60 acetylates p53 Lys120, which is needed for apoptosis but not growth arrest. supporting_text: Here, we show that Tip60 is required for both cell growth arrest and apoptosis mediated by p53 and also induces its acetylation specifically at lysine 120 (K120) within the DNA-binding domain. - order: 7 role: SIRT1 deacetylation of p53 node: id: p53_deacetylation label: SIRT1 NAD-dependent deacetylation of p53 module_type: REGULATORY_STEP description: >- SIRT1 removes the activating acetylation of p53 Lys382, reducing p53 transcriptional activity; it opposes part 6. annotons: - id: sirt1_p53_deacetylase label: SIRT1 NAD-dependent protein lysine deacetylase activity on p53 participant: selector_type: GENE_PRODUCT gene_product: preferred_term: SIRT1 term: id: UniProtKB:Q96EB6 label: NAD-dependent protein deacetylase sirtuin-1 function: preferred_term: NAD-dependent protein lysine deacetylase activity term: id: GO:0034979 label: NAD-dependent protein lysine deacetylase activity targets: - preferred_term: TP53 (Lys382) term: id: UniProtKB:P04637 label: Cellular tumor antigen p53 processes: - preferred_term: negative regulation of signal transduction by p53 class mediator term: id: GO:1901797 label: negative regulation of signal transduction by p53 class mediator locations: - preferred_term: nucleoplasm term: id: GO:0005654 label: nucleoplasm role_description: >- A pleiotropic NAD-dependent deacetylase; only its action on p53 belongs to this module. evidence: - source_id: PMID:11672523 statement: SIRT1 binds and deacetylates p53 Lys382 and reduces p53 transcriptional activity. supporting_text: Expression of wild-type hSir2 in human cells reduces the transcriptional activity of p53. - source_id: PMID:11672522 statement: Sir2alpha deacetylation negatively controls p53. gocam_associations: - model: gomodel:646ff70100000239 activity: gomodel:646ff70100000239/646ff70100000253 title: SIRT1 NAD-dependent protein lysine deacetylase activity (GO:0034979), part of negative regulation of signal transduction by p53 class mediator, MORN3 model (Human) - order: 8 optional: true role: pro-apoptotic output through BH3-only targets node: id: p53_apoptotic_output label: BH3-only activation and derepression (PUMA/BBC3, NOXA/PMAIP1) description: >- Included by reference to the BH3-only step of the BCL2-family MOMP control module. p53 transactivates BBC3 (PUMA), PMAIP1 (NOXA) and BAX; their products act there, not in this module. Optional because the output chosen depends on cell type and stimulus. module_ref: bcl2_family_momp_control#bh3_only_activation - order: 9 optional: true role: G1 arrest output through p21 inhibition of G1/S CDK node: id: p53_g1_arrest_output label: G1/S cyclin-CDK activation (inhibited by p53-induced p21/CDKN1A) description: >- Included by reference to the G1/S cyclin-CDK activation step of the G1/S transition module. p53-induced CDKN1A (p21) inhibits cyclin E-CDK2, arresting cells in G1. p21 is a p53 transcriptional output and is modelled neither here nor (yet) as a CKI annoton there. module_ref: g1_s_transition#g1s_cdk_activation connections: - source: atm_dsb_input target: p53_stabilizing_phosphorylation connection_type: POSITIVELY_REGULATES description: Activated ATM phosphorylates p53 and MDM2 directly and activates CHK2. - source: p53_stabilizing_phosphorylation target: mdm2_mdm4_feedback connection_type: NEGATIVELY_REGULATES description: >- Ser15/Ser20 phosphorylation of p53 and ATM phosphorylation of MDM2 weaken the p53-MDM2 interaction and p53 ubiquitylation. - source: p53_stabilizing_phosphorylation target: p53_transactivation connection_type: POSITIVELY_REGULATES description: N-terminal phosphorylation stabilises p53 and favours coactivator binding. - source: arf_mdm2_inhibition target: mdm2_mdm4_feedback connection_type: NEGATIVELY_REGULATES description: ARF inhibits MDM2 E3 activity and sequesters MDM2 in the nucleolus. - source: mdm2_mdm4_feedback target: p53_transactivation connection_type: NEGATIVELY_REGULATES description: MDM2 (stimulated by MDM4) ubiquitylates p53 for degradation and occludes its transactivation domain. - source: p53_transactivation target: mdm2_mdm4_feedback connection_type: POSITIVELY_REGULATES description: p53 transactivates the MDM2 gene, closing the negative feedback loop. - source: p53_acetylation target: p53_transactivation connection_type: POSITIVELY_REGULATES description: C-terminal acetylation stimulates sequence-specific DNA binding; K120 acetylation favours apoptotic targets. - source: p53_deacetylation target: p53_transactivation connection_type: NEGATIVELY_REGULATES description: SIRT1 removes activating acetylation and reduces p53 transcriptional activity. - source: p53_transactivation target: p53_apoptotic_output connection_type: POSITIVELY_REGULATES description: Transcriptional induction of BBC3 (PUMA), PMAIP1 (NOXA) and BAX. - source: p53_transactivation target: p53_g1_arrest_output connection_type: NEGATIVELY_REGULATES description: Transcriptional induction of CDKN1A (p21), which inhibits G1/S cyclin-CDK. knowledge_gaps: - gap_statement: >- How p53 chooses between cell-cycle arrest, senescence and apoptosis target programs is not resolved: the relative weight of response-element affinity, Lys120 acetylation, ASPP cofactors, p53 protein level and pulsatile versus sustained p53 dynamics in setting the outcome in a given cell type remains unknown. gap_kind: - BIOLOGY - gap_statement: >- The division of labour between MDM2 and MDM4 in vivo is incompletely understood, including how much p53 control depends on the MDM2-MDM4 RING heterodimer as an E3 versus MDM4 occlusion of the transactivation domain, and how damage-induced phosphorylation of MDM2 and MDM4 by ATM and ABL1 redistributes their activities. gap_kind: - BIOLOGY