GSDMD (Gasdermin-D) is the terminal executioner of pyroptosis, a lytic, pro-inflammatory form of programmed cell death. The full-length protein is autoinhibited: an N-terminal pore-forming domain is held inactive by an intramolecular interaction with its C-terminal repressor domain. Inflammatory caspases cleave the interdomain linker β CASP1 at Asp275 in the canonical inflammasome pathway, and CASP4/CASP5 in the non-canonical pathway triggered by cytosolic lipopolysaccharide (CASP8 cleaves it in the Yersinia/TAK1-inactivation context) β releasing the N-terminal fragment (GSDMD-NT). GSDMD-NT translocates to the plasma membrane, where it binds acidic inner-leaflet phospholipids (monophosphorylated and bisphosphorylated phosphatidylinositols, phosphatidic acid, phosphatidylserine) and cardiolipin, oligomerizes, and inserts to form large ring-shaped transmembrane pores of 10-15 nm inner diameter. These pores conduct mature interleukin-1 family cytokines (IL-1Ξ² and IL-18) out of the cell and drive pyroptosis; terminal membrane rupture is executed downstream by NINJ1. Because its lipid specificity restricts pore formation to the inner leaflet, GSDMD-NT released from dying cells is directly bactericidal against Gram-negative and Gram-positive bacteria while sparing neighboring host cells. GSDMD activity is tuned by cleavage site choice (CASP3/CASP7 cleavage at Asp87 inactivates it) and by post-translational modifications including palmitoylation, succination, and O-GlcNAcylation of Cys191. A minor CASP3/CASP7-generated p13 fragment additionally acts in the nucleus, and the protein is targeted by several microbial evasion mechanisms.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0042742 defense response to bacterium | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic (IBA) inference that GSDMD participates in antibacterial defense; consistent with the direct bactericidal activity of secreted/intracellular GSDMD-NT against bacteria. Reason: GSDMD-NT binds bacterial membrane lipids (cardiolipin) and is directly microbicidal, and GSDMD drives pyroptosis of infected cells; the IBA is well grounded in gasdermin-family experimental data (PMID:27281216). Supporting Evidence: PMID:27281216 exhibit membrane-disrupting cytotoxicity in mammalian cells and artificially transformed bacteria |
| GO:0070269 pyroptotic inflammatory response | IBA GO_REF:0000033 | ACCEPT | Summary: IBA inference that GSDMD mediates the pyroptotic inflammatory response; this is the defining biology of the gene. Reason: GSDMD is the terminal executioner of pyroptosis, forming the plasma-membrane pore that releases IL-1 family cytokines; core process, strongly supported experimentally (PMID:27281216, PMID:33883744). Supporting Evidence: PMID:33883744 enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0005546 phosphatidylinositol-4,5-bisphosphate binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA inference that GSDMD binds phosphatidylinositol-4,5-bisphosphate; a real inner-leaflet membrane-targeting activity of GSDMD-NT. Reason: GSDMD-NT binds bisphosphorylated phosphoinositides including PI(4,5)P2 as part of its inner-leaflet membrane targeting (UniProt FUNCTION; PMID:27281216). Supporting Evidence: PMID:27281216 GSDMD, GSDMA3 and GSDMA can bind membrane lipids, phosphoinositides |
| GO:0070273 phosphatidylinositol-4-phosphate binding | IBA GO_REF:0000033 | ACCEPT | Summary: IBA inference that GSDMD binds phosphatidylinositol-4-phosphate; a bona fide membrane-targeting lipid interaction of GSDMD-NT. Reason: GSDMD-NT binds monophosphorylated phosphoinositides such as PI4P on the inner leaflet, driving pore localization (UniProt FUNCTION; PMID:27281216). Supporting Evidence: PMID:27281216 GSDMD, GSDMA3 and GSDMA can bind membrane lipids, phosphoinositides |
| GO:0001786 phosphatidylserine binding | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA inference that GSDMD binds phosphatidylserine, an inner-leaflet acidic phospholipid; real but weaker than the phosphoinositide interactions. Reason: Genuine but minor. UniProt places phosphatidylserine and phosphatidic acid on identical footing - GSDMD-NT "strongly binds to inner leaflet lipids, including monophosphorylated phosphatidylinositols ... and more weakly to phosphatidic acid and phosphatidylserine" (UniProt FUNCTION). The phosphoinositides are the core targeting determinant, so PS binding is treated as non-core, consistently with GO:0070300 phosphatidic acid binding. The cached PMID:27281216 abstract does not itself mention phosphatidylserine, so no supporting quote is attached. |
| GO:0072559 NLRP3 inflammasome complex | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA inference placing GSDMD as part_of the NLRP3 inflammasome complex; GSDMD is a downstream substrate/effector recruited at the inflammasome rather than a stable structural subunit. Reason: GSDMD is cleaved by inflammasome-activated caspase-1 but is not a stoichiometric component of the NLRP3 sensor/adaptor/caspase platform. A part_of qualifier asserts structural membership, which overshoots a substrate/recruitment relationship, so this is an over-annotation rather than a peripheral truth. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION COMPARTMENT OR COMPLEX MISMATCH Sources checked: MGI:MGI:1916396 SUPPORTS SOURCE BUT NOT TARGET The dispute is not with the node placement. Gasdermin-D's association with the NLRP3 inflammasome is genuinely conserved across the clade, so the IBD is soundly placed and the transfer to human GSDMD is correct as far as the biology goes. What is wrong is the term/qualifier chosen to express it. PANTHER:PTN000419163 SUPPORTS SOURCE BUT NOT TARGET Ancestral node for the gasdermin family. Inheriting "acts at the inflammasome" does not license part_of a complex whose subunits are the sensor, ASC and caspase-1; a regulatory/substrate relation term would carry the same inherited claim without asserting stoichiometric membership. |
| GO:0005576 extracellular region | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: IEA localization to the extracellular region; consistent with secretion of the GSDMD-NT fragment, which is released and is bactericidal. Reason: GSDMD-NT can be secreted/released to the extracellular space (UniProt SUBCELLULAR LOCATION, Secreted), but the extracellular pool is secondary to the plasma-membrane pore; keep as non-core. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: IEA nuclear localization; reflects the p13 CASP3/7 cleavage fragment that acts as a STAT1 transcription coactivator (by similarity, mouse). Reason: A minor p13 fragment translocates to the nucleus as a transcription coactivator (UniProt, by similarity to mouse Q9D8T2); real but fragment-specific and secondary to the pore-forming function, so non-core. |
| GO:0005829 cytosol | IEA GO_REF:0000120 | ACCEPT | Summary: IEA localization to cytosol; correct location of the autoinhibited full-length GSDMD precursor. Reason: Full-length GSDMD resides in the cytosol prior to caspase cleavage (UniProt SUBCELLULAR LOCATION: Cytoplasm, cytosol). |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: IEA localization to the plasma membrane; correct location of the active GSDMD-NT pore. Reason: Cleaved GSDMD-NT translocates to and forms pores in the plasma membrane (UniProt; PMID:27281216, PMID:33883744). Supporting Evidence: PMID:27281216 Gasdermin-N moved to the plasma membrane |
| GO:0031966 mitochondrial membrane | IEA GO_REF:0000120 | KEEP AS NON CORE | Summary: IEA localization to the mitochondrial membrane; GSDMD-NT can permeabilize mitochondria (by similarity), a secondary activity. Reason: GSDMD-NT also forms pores in the mitochondrial membrane releasing mtDNA (UniProt, by similarity); real but secondary to the plasma-membrane pore, so non-core. |
| GO:0055085 transmembrane transport | IEA GO_REF:0000108 | ACCEPT | Summary: IEA (inter-ontology inference) that GSDMD is involved in transmembrane transport; the GSDMD pore is a large non-selective conduit for cargo across the membrane. Reason: The GSDMD-NT pore mediates transmembrane passage of IL-1 family cytokines and other cargo; this is a logical consequence of its wide-pore channel activity (PMID:33883744). Supporting Evidence: PMID:33883744 enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0061702 canonical inflammasome complex | IEA GO_REF:0000044 | MARK AS OVER ANNOTATED | Summary: IEA placement as part_of the canonical inflammasome complex; GSDMD is the caspase-1 substrate/effector at the inflammasome rather than a core structural subunit. Reason: GSDMD is recruited and cleaved by the canonical inflammasome but is not a stoichiometric component of the sensor/ASC/caspase-1 platform; the part_of structural claim overshoots a substrate relationship. |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | MARK AS OVER ANNOTATED | Summary: Generic 'protein binding' from a high-throughput human interactome map; uninformative about GSDMD's molecular function. Reason: Per project guidelines the bare 'protein binding' (GO:0005515) term conveys no specific function and derives from a proteome-scale Y2H screen (PMID:25416956); should be superseded by specific MF terms where a real partner is characterized. |
| GO:0005515 protein binding | IPI PMID:31515488 Extensive disruption of protein interactions by genetic vari... | MARK AS OVER ANNOTATED | Summary: Generic 'protein binding' from an interactome/variant-perturbation screen; uninformative. Reason: Bare 'protein binding' (GO:0005515) from a systematic interaction dataset (PMID:31515488) does not describe a specific molecular function; over-annotation per project guidelines. |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Generic 'protein binding' from the HuRI reference binary interactome; uninformative. Reason: Bare 'protein binding' (GO:0005515) from a reference interactome map (PMID:32296183) adds no specific functional information; over-annotation per project guidelines. |
| GO:0005515 protein binding | IPI PMID:34296442 SARS-CoV-2 nucleocapsid suppresses host pyroptosis by blocki... | MARK AS OVER ANNOTATED | Summary: Generic 'protein binding' from a study of SARS-CoV-2 nucleocapsid binding GSDMD to block its cleavage; the interaction is real (viral N protein) but the term itself is uninformative. Reason: Although PMID:34296442 documents a specific SARS-CoV-2 nucleocapsid-GSDMD interaction that suppresses pyroptosis, the bare 'protein binding' (GO:0005515) term does not capture this; over-annotated as an MF and better represented by a specific descriptor if desired. |
| GO:0001786 phosphatidylserine binding | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA (ortholog transfer) phosphatidylserine binding; duplicates the weak PS-binding activity of GSDMD-NT. Reason: GSDMD-NT binds phosphatidylserine "more weakly" than the phosphoinositides (UniProt FUNCTION), on the same footing as phosphatidic acid; genuine but a minor contributor to inner-leaflet targeting, so non-core. The cached PMID:27281216 abstract does not mention phosphatidylserine, so no supporting quote is attached. |
| GO:0005546 phosphatidylinositol-4,5-bisphosphate binding | IEA GO_REF:0000107 | ACCEPT | Summary: IEA PI(4,5)P2 binding; duplicates the supported bisphosphoinositide-binding activity of GSDMD-NT. Reason: GSDMD-NT binds PI(4,5)P2 as part of inner-leaflet membrane targeting (UniProt; PMID:27281216). Supporting Evidence: PMID:27281216 GSDMD, GSDMA3 and GSDMA can bind membrane lipids, phosphoinositides |
| GO:0009306 protein secretion | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA involvement in protein secretion; the GSDMD pore is the conduit for unconventional secretion of IL-1 family cytokines. Reason: GSDMD pores conduct IL-1beta/IL-18 out of the cell, a plausible generalization to 'protein secretion' (PMID:33883744); retain but as non-core relative to the specific pore/pyroptosis terms. Supporting Evidence: PMID:33883744 enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0022829 wide pore channel activity | IEA GO_REF:0000107 | ACCEPT | Summary: IEA (ortholog transfer) of wide pore channel activity; this is the defining molecular function of GSDMD, directly demonstrated experimentally. Reason: GSDMD-NT forms large (10-15 nm inner diameter) transmembrane pores; the IEA duplicates the IDA-supported core MF (PMID:33883744, PMID:35794369). Supporting Evidence: PMID:33883744 Cleaved GSDMD forms transmembrane pores to enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0032731 positive regulation of interleukin-1 beta production | IEA GO_REF:0000107 | ACCEPT | Summary: IEA positive regulation of IL-1beta production; GSDMD pores mediate release of mature IL-1beta. Reason: GSDMD pore formation drives IL-1beta release and thereby promotes IL-1beta production/output in the inflammatory response (PMID:33883744). Supporting Evidence: PMID:33883744 enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0046931 pore complex assembly | IEA GO_REF:0000107 | ACCEPT | Summary: IEA involvement in pore complex assembly; GSDMD-NT oligomerizes to assemble the transmembrane pore. Reason: GSDMD-NT homooligomerizes into a ring-shaped transmembrane pore complex; central to its mechanism (PMID:33883744). Supporting Evidence: PMID:33883744 Cleaved GSDMD forms transmembrane pores to enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0050729 positive regulation of inflammatory response | IEA GO_REF:0000107 | ACCEPT | Summary: IEA positive regulation of the inflammatory response; consequence of GSDMD-driven cytokine release and pyroptosis. Reason: GSDMD pore formation drives release of pro-inflammatory IL-1 cytokines and pyroptosis, amplifying inflammation (PMID:33883744). Supporting Evidence: PMID:33883744 enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0050829 defense response to Gram-negative bacterium | IEA GO_REF:0000107 | ACCEPT | Summary: IEA defense response to Gram-negative bacterium; GSDMD-NT kills Gram-negative bacteria and executes pyroptosis in the non-canonical (cytosolic LPS) pathway. Reason: Secreted/intracellular GSDMD-NT is directly bactericidal against Gram-negative bacteria and GSDMD executes pyroptosis downstream of cytosolic-LPS sensing (PMID:27281216). Supporting Evidence: PMID:27281216 exhibit membrane-disrupting cytotoxicity in mammalian cells and artificially transformed bacteria |
| GO:0050830 defense response to Gram-positive bacterium | IEA GO_REF:0000107 | ACCEPT | Summary: IEA defense response to Gram-positive bacterium; GSDMD-NT has direct bactericidal activity against Gram-positive bacteria. Reason: GSDMD-NT binds and kills both Gram-negative and Gram-positive bacteria (UniProt; PMID:27281216). Supporting Evidence: PMID:27281216 exhibit membrane-disrupting cytotoxicity in mammalian cells and artificially transformed bacteria |
| GO:0051260 protein homooligomerization | IEA GO_REF:0000107 | ACCEPT | Summary: IEA protein homooligomerization; GSDMD-NT oligomerizes into a 31-34-subunit ring, essential for pore formation. Reason: GSDMD-NT homooligomerizes within the membrane to form the pore (UniProt SUBUNIT; PMID:33883744); core to the mechanism. Supporting Evidence: PMID:33883744 Cleaved GSDMD forms transmembrane pores to enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0070269 pyroptotic inflammatory response | IEA GO_REF:0000107 | ACCEPT | Summary: IEA pyroptotic inflammatory response; duplicates the core pyroptosis process of GSDMD. Reason: GSDMD is the executioner of pyroptosis and the associated inflammatory response (PMID:33883744); core process. Supporting Evidence: PMID:33883744 enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0070273 phosphatidylinositol-4-phosphate binding | IEA GO_REF:0000107 | ACCEPT | Summary: IEA PI4P binding; duplicates the supported monophosphoinositide-binding activity of GSDMD-NT. Reason: GSDMD-NT binds PI4P for inner-leaflet targeting (UniProt; PMID:27281216). Supporting Evidence: PMID:27281216 GSDMD, GSDMA3 and GSDMA can bind membrane lipids, phosphoinositides |
| GO:0070300 phosphatidic acid binding | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: IEA phosphatidic acid binding; a real but weaker lipid interaction of GSDMD-NT. Reason: GSDMD-NT binds phosphatidic acid more weakly than phosphoinositides (UniProt FUNCTION); genuine but a minor contributor to membrane targeting, so non-core. |
| GO:0072559 NLRP3 inflammasome complex | IEA GO_REF:0000107 | MARK AS OVER ANNOTATED | Summary: IEA placement as part_of the NLRP3 inflammasome complex; recruitment/substrate relationship rather than a core structural subunit. Reason: GSDMD is the effector substrate cleaved at the NLRP3 inflammasome, not a stoichiometric subunit of the sensor complex; the part_of structural claim overshoots the evidence. |
| GO:0141201 pyroptotic cell death | IEA GO_REF:0000107 | ACCEPT | Summary: IEA pyroptotic cell death; the core lytic cell-death process executed by GSDMD. Reason: GSDMD-NT pores drive pyroptotic cell death (PMID:33883744); core process. Supporting Evidence: PMID:33883744 enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:1901612 cardiolipin binding | IEA GO_REF:0000107 | ACCEPT | Summary: IEA cardiolipin binding; a key lipid interaction underlying GSDMD-NT bactericidal activity and mitochondrial targeting. Reason: GSDMD-NT binds cardiolipin (present on bacterial and mitochondrial membranes), explaining its microbicidal activity (UniProt; PMID:27281216). Supporting Evidence: PMID:27281216 GSDMD, GSDMA3 and GSDMA can bind membrane lipids, phosphoinositides |
| GO:0005654 nucleoplasm | IDA GO_REF:0000052 | KEEP AS NON CORE | Summary: IDA nucleoplasm localization from an immunofluorescence dataset; consistent with the nuclear p13 fragment but secondary to core function. Reason: Nuclear/nucleoplasm signal reflects the minor p13 transcription-coactivator fragment (UniProt, by similarity); real but fragment-specific and not the core pore-forming function, so non-core. |
| GO:0005886 plasma membrane | IDA PMID:33883744 Gasdermin D pore structure reveals preferential release of m... | ACCEPT | Summary: IDA that GSDMD is active at the plasma membrane; the site of pore assembly, from the cryo-EM pore study. Reason: The GSDMD-NT pore assembles in and acts at the plasma membrane (PMID:33883744); correct active-location assignment. Supporting Evidence: PMID:33883744 Cleaved GSDMD forms transmembrane pores to enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0022829 wide pore channel activity | IDA PMID:33883744 Gasdermin D pore structure reveals preferential release of m... | ACCEPT | Summary: IDA of wide pore channel activity from the cryo-EM GSDMD pore structure; the defining core molecular function. Reason: Cryo-EM shows GSDMD-NT forms a large transmembrane channel that conducts IL-1 cargo (PMID:33883744); core MF. Two sourced pore diameters coexist and are not in conflict: the cryo-EM 33-subunit GSDMD pore has an inner diameter of ~215 A (21.5 nm), while UniProt's 10-15 nm figure comes from the earlier liposome/AFM gasdermin-N measurements of PMID:27281216. Either way the conduit is wide and non-selective. Supporting Evidence: PMID:33883744 Cleaved GSDMD forms transmembrane pores to enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0050729 positive regulation of inflammatory response | IDA PMID:33883744 Gasdermin D pore structure reveals preferential release of m... | ACCEPT | Summary: IDA positive regulation of inflammatory response tied to GSDMD pore-mediated IL-1 release. Reason: The GSDMD pore preferentially releases mature IL-1, promoting the inflammatory response (PMID:33883744). Supporting Evidence: PMID:33883744 enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0141201 pyroptotic cell death | IDA PMID:33883744 Gasdermin D pore structure reveals preferential release of m... | ACCEPT | Summary: IDA pyroptotic cell death from the GSDMD pore structure/function study; core process. Reason: Cleaved GSDMD forms transmembrane pores that drive cell lysis through pyroptosis (PMID:33883744). Supporting Evidence: PMID:33883744 enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0005576 extracellular region | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS localization to the extracellular region; consistent with secreted GSDMD-NT. Reason: GSDMD-NT can be secreted and is bactericidal extracellularly (UniProt, Secreted); secondary to the plasma-membrane pore, so non-core. |
| GO:0005634 nucleus | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS nuclear localization; reflects the p13 transcription-coactivator fragment (by similarity). Reason: Nuclear localization is due to the minor p13 fragment acting as a STAT1 coactivator (UniProt, by similarity to mouse); fragment-specific and secondary, so non-core. |
| GO:0005886 plasma membrane | EXP PMID:27281216 Pore-forming activity and structural autoinhibition of the g... | ACCEPT | Summary: EXP plasma membrane localization directly observed for gasdermin-N during pyroptosis; the pore site. Reason: Gasdermin-N (GSDMD-NT) moves to the plasma membrane during pyroptosis where it forms pores (PMID:27281216). Supporting Evidence: PMID:27281216 Gasdermin-N moved to the plasma membrane |
| GO:0005886 plasma membrane | EXP PMID:38530158 The palmitoylation of gasdermin D directs its membrane trans... | ACCEPT | Summary: EXP plasma membrane localization from the study showing palmitoylation directs GSDMD membrane translocation and pore formation. Reason: Palmitoylation at Cys191 directs GSDMD translocation to the plasma membrane and pore formation (PMID:38530158); correct active location. |
| GO:0005886 plasma membrane | EXP PMID:38599239 ROS-dependent S-palmitoylation activates cleaved and intact ... | ACCEPT | Summary: EXP plasma membrane localization from the study of ROS-dependent S-palmitoylation activating GSDMD. Reason: S-palmitoylation promotes GSDMD membrane localization/activation at the plasma membrane (PMID:38599239); consistent with the pore site. |
| GO:0031966 mitochondrial membrane | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS mitochondrial membrane localization; GSDMD-NT can permeabilize mitochondria (by similarity), a secondary activity. Reason: GSDMD-NT also targets the mitochondrial membrane to release mtDNA (UniProt, by similarity); real but secondary to the plasma-membrane pore. |
| GO:0061702 canonical inflammasome complex | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: ISS placement as part_of the canonical inflammasome complex; substrate/effector recruitment rather than a core structural subunit. Reason: GSDMD is the caspase-1 substrate at the canonical inflammasome, not a stoichiometric subunit; the part_of structural claim overshoots the evidence. |
| GO:0022829 wide pore channel activity | IDA PMID:35794369 Allergen protease-activated stress granule assembly and gasd... | ACCEPT | Summary: IDA of wide pore channel activity from the allergen-protease p40-fragment study; independent experimental support for the core pore MF. Reason: A caspase-independent N-terminal GSDMD fragment (p40 in mouse, the corresponding GSDMD1-290/p35 fragment in human cells) forms membrane pores that release cytosolic IL-33, independently confirming GSDMD wide-pore channel activity (PMID:35794369); core MF. Supporting Evidence: PMID:35794369 generated p40 NT-Gsdmd, which promoted the cytosolic IL-33 to cross the membrane into the extracellular space |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9716258 | ACCEPT | Summary: TAS cytosol localization from a Reactome reaction (GSDMD cleavage/oligomerization/lipid-binding step); correct location of the GSDMD precursor. Reason: Full-length GSDMD and its cleavage/activation reactions occur in the cytosol (Reactome R-HSA-9716258; UniProt SUBCELLULAR LOCATION: cytosol). |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9693324 | ACCEPT | Summary: TAS cytosol localization from a Reactome reaction (GSDMD cleavage/oligomerization/lipid-binding step); correct location of the GSDMD precursor. Reason: Full-length GSDMD and its cleavage/activation reactions occur in the cytosol (Reactome R-HSA-9693324; UniProt SUBCELLULAR LOCATION: cytosol). |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9710106 | ACCEPT | Summary: TAS cytosol localization from a Reactome reaction (GSDMD cleavage/oligomerization/lipid-binding step); correct location of the GSDMD precursor. Reason: Full-length GSDMD and its cleavage/activation reactions occur in the cytosol (Reactome R-HSA-9710106; UniProt SUBCELLULAR LOCATION: cytosol). |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9686088 | ACCEPT | Summary: TAS cytosol localization from a Reactome reaction (GSDMD cleavage/oligomerization/lipid-binding step); correct location of the GSDMD precursor. Reason: Full-length GSDMD and its cleavage/activation reactions occur in the cytosol (Reactome R-HSA-9686088; UniProt SUBCELLULAR LOCATION: cytosol). |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9647619 | ACCEPT | Summary: TAS cytosol localization from a Reactome reaction (GSDMD cleavage/oligomerization/lipid-binding step); correct location of the GSDMD precursor. Reason: Full-length GSDMD and its cleavage/activation reactions occur in the cytosol (Reactome R-HSA-9647619; UniProt SUBCELLULAR LOCATION: cytosol). |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9647631 | ACCEPT | Summary: TAS cytosol localization from a Reactome reaction (GSDMD cleavage/oligomerization/lipid-binding step); correct location of the GSDMD precursor. Reason: Full-length GSDMD and its cleavage/activation reactions occur in the cytosol (Reactome R-HSA-9647631; UniProt SUBCELLULAR LOCATION: cytosol). |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9647643 | ACCEPT | Summary: TAS cytosol localization from a Reactome reaction (GSDMD cleavage/oligomerization/lipid-binding step); correct location of the GSDMD precursor. Reason: Full-length GSDMD and its cleavage/activation reactions occur in the cytosol (Reactome R-HSA-9647643; UniProt SUBCELLULAR LOCATION: cytosol). |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9647645 | ACCEPT | Summary: TAS cytosol localization from a Reactome reaction (GSDMD cleavage/oligomerization/lipid-binding step); correct location of the GSDMD precursor. Reason: Full-length GSDMD and its cleavage/activation reactions occur in the cytosol (Reactome R-HSA-9647645; UniProt SUBCELLULAR LOCATION: cytosol). |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9647680 | ACCEPT | Summary: TAS cytosol localization from a Reactome reaction (GSDMD cleavage/oligomerization/lipid-binding step); correct location of the GSDMD precursor. Reason: Full-length GSDMD and its cleavage/activation reactions occur in the cytosol (Reactome R-HSA-9647680; UniProt SUBCELLULAR LOCATION: cytosol). |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9710353 | ACCEPT | Summary: TAS cytosol localization from a Reactome reaction (GSDMD cleavage/oligomerization/lipid-binding step); correct location of the GSDMD precursor. Reason: Full-length GSDMD and its cleavage/activation reactions occur in the cytosol (Reactome R-HSA-9710353; UniProt SUBCELLULAR LOCATION: cytosol). |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9947997 | ACCEPT | Summary: TAS cytosol localization from a Reactome reaction (GSDMD cleavage/oligomerization/lipid-binding step); correct location of the GSDMD precursor. Reason: Full-length GSDMD and its cleavage/activation reactions occur in the cytosol (Reactome R-HSA-9947997; UniProt SUBCELLULAR LOCATION: cytosol). |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9948146 | ACCEPT | Summary: TAS cytosol localization from a Reactome reaction (GSDMD cleavage/oligomerization/lipid-binding step); correct location of the GSDMD precursor. Reason: Full-length GSDMD and its cleavage/activation reactions occur in the cytosol (Reactome R-HSA-9948146; UniProt SUBCELLULAR LOCATION: cytosol). |
| GO:0001786 phosphatidylserine binding | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS phosphatidylserine binding; duplicates the weak PS-binding activity of GSDMD-NT. Reason: GSDMD-NT binds phosphatidylserine "more weakly" than the phosphoinositides (UniProt FUNCTION), on the same footing as phosphatidic acid; genuine but a minor contributor to inner-leaflet targeting, so non-core. The cached PMID:27281216 abstract does not mention phosphatidylserine, so no supporting quote is attached. |
| GO:0005829 cytosol | ISS GO_REF:0000024 | ACCEPT | Summary: ISS cytosol localization; correct location of the full-length GSDMD precursor. Reason: Full-length GSDMD resides in the cytosol before caspase cleavage (UniProt). |
| GO:0005886 plasma membrane | ISS GO_REF:0000024 | ACCEPT | Summary: ISS plasma membrane localization; correct location of the active GSDMD-NT pore. Reason: GSDMD-NT forms pores in the plasma membrane (UniProt; PMID:27281216, PMID:33883744). Supporting Evidence: PMID:27281216 Gasdermin-N moved to the plasma membrane |
| GO:0046931 pore complex assembly | ISS GO_REF:0000024 | ACCEPT | Summary: ISS involvement in pore complex assembly; GSDMD-NT oligomerizes to build the transmembrane pore. Reason: GSDMD-NT assembles into a ring-shaped transmembrane pore complex (PMID:33883744); core mechanism. Supporting Evidence: PMID:33883744 Cleaved GSDMD forms transmembrane pores to enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0050829 defense response to Gram-negative bacterium | ISS GO_REF:0000024 | ACCEPT | Summary: ISS defense response to Gram-negative bacterium; GSDMD-NT is directly bactericidal and executes non-canonical pyroptosis. Reason: GSDMD-NT kills Gram-negative bacteria and mediates pyroptosis downstream of cytosolic LPS sensing (PMID:27281216). Supporting Evidence: PMID:27281216 exhibit membrane-disrupting cytotoxicity in mammalian cells and artificially transformed bacteria |
| GO:0050830 defense response to Gram-positive bacterium | ISS GO_REF:0000024 | ACCEPT | Summary: ISS defense response to Gram-positive bacterium; GSDMD-NT is directly bactericidal against Gram-positive bacteria. Reason: GSDMD-NT binds and kills both Gram-negative and Gram-positive bacteria (UniProt; PMID:27281216). Supporting Evidence: PMID:27281216 exhibit membrane-disrupting cytotoxicity in mammalian cells and artificially transformed bacteria |
| GO:0051260 protein homooligomerization | ISS GO_REF:0000024 | ACCEPT | Summary: ISS protein homooligomerization; GSDMD-NT oligomerizes into the pore ring. Reason: GSDMD-NT homooligomerizes to form the transmembrane pore (UniProt SUBUNIT; PMID:33883744); core mechanism. Supporting Evidence: PMID:33883744 Cleaved GSDMD forms transmembrane pores to enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0070300 phosphatidic acid binding | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: ISS phosphatidic acid binding; a real but weaker lipid interaction of GSDMD-NT. Reason: GSDMD-NT binds phosphatidic acid more weakly than phosphoinositides (UniProt FUNCTION); minor contributor, so non-core. |
| GO:1901612 cardiolipin binding | ISS GO_REF:0000024 | ACCEPT | Summary: ISS cardiolipin binding; underlies GSDMD-NT bactericidal and mitochondrial-targeting activities. Reason: GSDMD-NT binds cardiolipin on bacterial/mitochondrial membranes (UniProt; PMID:27281216). Supporting Evidence: PMID:27281216 GSDMD, GSDMA3 and GSDMA can bind membrane lipids, phosphoinositides |
| GO:0005576 extracellular region | TAS Reactome:R-HSA-6798745 | KEEP AS NON CORE | Summary: TAS extracellular region from a neutrophil tertiary-granule exocytosis pathway; the route asserted is granule-proteomic, but the extracellular location itself is independently supported. Reason: The Reactome route (R-HSA-6798745, tertiary-granule exocytosis) rests on bulk granule proteomics, but unlike the granule-lumen terms the extracellular location is independently curated: GSDMD-NT is released and acts extracellularly (UniProt SUBCELLULAR LOCATION: Secreted). The compartment claim therefore stands; it is secondary to the plasma-membrane pore, so non-core rather than over-annotated. |
| GO:0005576 extracellular region | TAS Reactome:R-HSA-6798749 | KEEP AS NON CORE | Summary: TAS extracellular region from a neutrophil specific-granule exocytosis pathway; the route asserted is granule-proteomic, but the extracellular location itself is independently supported. Reason: The Reactome route (R-HSA-6798749, specific-granule exocytosis) rests on bulk granule proteomics, but the extracellular location is independently curated (UniProt SUBCELLULAR LOCATION: Secreted) and underlies the bactericidal activity of released GSDMD-NT. Secondary to the plasma-membrane pore, so non-core rather than over-annotated. |
| GO:0005576 extracellular region | TAS Reactome:R-HSA-6800434 | KEEP AS NON CORE | Summary: TAS extracellular region from a neutrophil ficolin-1-rich-granule exocytosis pathway; the route asserted is granule-proteomic, but the extracellular location itself is independently supported. Reason: The Reactome route (R-HSA-6800434, ficolin-1-rich-granule exocytosis) rests on bulk granule proteomics, but the extracellular location is independently curated (UniProt SUBCELLULAR LOCATION: Secreted). Secondary to the plasma-membrane pore, so non-core rather than over-annotated. |
| GO:0005829 cytosol | TAS Reactome:R-HSA-9710294 | ACCEPT | Summary: TAS cytosol localization from the Reactome GSDMD-expression reaction; correct location of the precursor. Reason: Newly expressed full-length GSDMD localizes to the cytosol (Reactome R-HSA-9710294; UniProt). |
| GO:0035580 specific granule lumen | TAS Reactome:R-HSA-6798749 | MARK AS OVER ANNOTATED | Summary: TAS specific granule lumen localization from neutrophil granule proteomics; bulk-proteomic assignment that places a cytosolic protein inside a granule lumen. Reason: Assignment derives from bulk neutrophil specific-granule proteomics (Reactome R-HSA-6798749). GSDMD is a cytosolic protein (UniProt SUBCELLULAR LOCATION: Cytoplasm, cytosol) with no signal peptide, so a granule *lumen* (topologically extracytosolic) assignment is a compartment mismatch rather than a peripheral truth; over-annotated. |
| GO:1904724 tertiary granule lumen | TAS Reactome:R-HSA-6798745 | MARK AS OVER ANNOTATED | Summary: TAS tertiary granule lumen localization from neutrophil granule proteomics; bulk-proteomic assignment that places a cytosolic protein inside a granule lumen. Reason: Assignment derives from bulk neutrophil tertiary-granule proteomics (Reactome R-HSA-6798745). GSDMD is a cytosolic protein (UniProt SUBCELLULAR LOCATION: Cytoplasm, cytosol) with no signal peptide, so a granule *lumen* assignment is a compartment mismatch rather than a peripheral truth; over-annotated. |
| GO:1904813 ficolin-1-rich granule lumen | TAS Reactome:R-HSA-6800434 | MARK AS OVER ANNOTATED | Summary: TAS ficolin-1-rich granule lumen localization from neutrophil granule proteomics; bulk-proteomic assignment that places a cytosolic protein inside a granule lumen. Reason: Assignment derives from bulk neutrophil ficolin-1-rich-granule proteomics (Reactome R-HSA-6800434). GSDMD is a cytosolic protein (UniProt SUBCELLULAR LOCATION: Cytoplasm, cytosol) with no signal peptide, so a granule *lumen* assignment is a compartment mismatch rather than a peripheral truth; over-annotated. |
| GO:0032731 positive regulation of interleukin-1 beta production | ISS GO_REF:0000024 | ACCEPT | Summary: ISS positive regulation of IL-1beta production; GSDMD pores mediate mature IL-1beta release. Reason: GSDMD pore formation drives IL-1beta release/output (PMID:33883744). Supporting Evidence: PMID:33883744 enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0070269 pyroptotic inflammatory response | ISS GO_REF:0000024 | ACCEPT | Summary: ISS pyroptotic inflammatory response; the core pyroptosis process of GSDMD. Reason: GSDMD executes pyroptosis and the associated inflammatory response (PMID:33883744); core process. Supporting Evidence: PMID:33883744 enable the release of IL-1 and to drive cell lysis through pyroptosis |
| GO:0072559 NLRP3 inflammasome complex | ISS GO_REF:0000024 | MARK AS OVER ANNOTATED | Summary: ISS placement as part_of the NLRP3 inflammasome complex; substrate/effector recruitment rather than a core structural subunit. Reason: GSDMD is recruited and cleaved at the NLRP3 inflammasome but is not a stoichiometric subunit; the part_of structural claim overshoots the evidence. |
Loading supporting contentβ¦
Download this section (compressed HTML)Q: What determines whether GSDMD pore formation leads to reversible membrane repair and cell survival versus NINJ1-mediated membrane rupture and pyroptotic death in a given cell type?
Q: How do the individual post-translational modifications of Cys191 (palmitoylation, succination, O-GlcNAcylation) and site-specific cleavage quantitatively tune GSDMD pore formation in vivo?
Q: What are the physiological roles and mechanisms of the minor GSDMD fragments (the nuclear p13 STAT1 coactivator and the allergen-protease-generated p40) relative to the canonical GSDMD-NT pore?
Q: Does a human orthologue of the mouse Gsdmd-Tmem106a trans-spliced chimeric mRNA exist, and if so does the GSDMD:TMEM106A protein act as a plasma-membrane cofactor that accelerates canonical GSDMD-NT pore formation and IL-1Ξ² release, as shown in mouse?
Experiment: Reconstitute GSDMD-NT pore formation in defined liposomes of varying lipid composition and measure conductance and cytokine (IL-1Ξ²/IL-18) passage to map the quantitative relationship between lipid specificity and pore properties.
Experiment: Use structure-guided GSDMD point mutants (cleavage-site, oligomerization, and lipid-binding interface variants) knocked in at the endogenous locus to dissect which activities are required for pyroptosis versus antibacterial defense in primary macrophages.
Experiment: Quantify the contribution of Cys191 modifications by combining chemical-genetic tools (e.g. the covalent Cys191 inhibitors) with mass spectrometry of the modified residue during inflammasome activation, correlating modification state with pore-forming capacity.
What is not known β curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The full complement of endogenous cofactors that tune GSDMD-NT pore assembly is not defined. A trans-spliced Gsdmd-Tmem106a chimeric protein was recently shown in mouse to localize to the plasma membrane and directly interact with canonical GSDMD N-termini to accelerate pore formation and IL-1Ξ² release, but whether an orthologous human chimera (or other such cofactors) operates is unknown.
OPEN BIOLOGY RESIDUAL_SUBGAP
What is known: The core pore-forming mechanism of canonical GSDMD-NT is textbook-solid (caspase cleavage, lipid binding, oligomerization, cryo-EM pore structure); the open question is the identity and human conservation of accessory cofactors that modulate pore kinetics.
Significance: Cofactor-accelerated pore formation would set the tempo of IL-1Ξ² release and the balance between host defense and immunopathology, and would be a potential intervention point in sepsis and autoinflammation.
Provenance (the field's own admissions):
Loading supporting contentβ¦
Download this section (compressed HTML)Loading supporting contentβ¦
Download this section (compressed HTML)