id: MODULE:phagocytic_engulfment title: Phagocytic engulfment description: >- Phagocytic engulfment is the receptor-driven internalization of a large particle (a microbe, an opsonized target, or an apoptotic cell) into a plasma-membrane-derived vacuole, the nascent phagosome. A cell-surface receptor recognizes the particle, either directly (beta-glucan, phosphatidylserine) or through a bound opsonin or bridging ligand (IgG, iC3b, GAS6). Receptor engagement then activates Rho-family GTPases, Rac and Cdc42 for Fc-gamma and apoptotic-cell receptors and RhoA for complement receptor 3. The GTPases drive Arp2/3-dependent actin polymerization that extends pseudopods around the particle. Class I PI3K activity and dynamin are then needed to complete pseudopod extension and close the phagocytic cup. The Rac-to-actin core is shared by animal phagocytes and phagotrophic amoebae. In Dictyostelium, Rac GTPases, the SCAR/WAVE nucleation-promoting factor and the Arp2/3 complex build the phagocytic cup, and PI(3,4,5)P3 forms at the site of engulfment. The receptors differ between lineages. Amoebae recognize bacteria with receptors such as the GPCR fAR1 and the adhesion protein SibA. Animals use the CED-1/Draper/MEGF10 receptor family and its CED-6/GULP adaptor, and the CRK/DOCK180/ELMO Rac GEF (CED-2/CED-5/CED-12 in C. elegans). Vertebrates add opsonin receptors for IgG and complement and lectin receptors such as Dectin-1. status: DRAFT references: - id: PMID:23420848 title: "Phosphatidylserine recognition and induction of apoptotic cell clearance by Drosophila engulfment receptor Draper." reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- PubMed-verified; abstract cached. Draper extracellular region binds phosphatidylserine (solid-phase and SPR assays). Cited in the CED-1/MEGF10 ligand knowledge gap. - id: PMID:25319336 title: "Phagocytosis: receptors, signal integration, and the cytoskeleton." reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- PubMed-verified review (Freeman & Grinstein 2014). Supports the receptor repertoire and the staged actin-remodeling framework used to order parts 2-4 of this module. - id: PMID:21910624 title: The cell biology of phagocytosis. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- PubMed-verified review (Flannagan, Jaumouille & Grinstein 2012). Supports the module boundary: phagosome formation here, maturation in MODULE:phagosome_maturation. - id: PMID:9831565 title: Identification of two distinct mechanisms of phagocytosis controlled by different Rho GTPases. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- PubMed-verified. Defines the Rac/Cdc42 (Fc-gamma receptor, type I) versus RhoA (CR3, type II) split that is modelled as the Rho-GTPase variant set. - id: PMID:9314552 title: A critical role for Syk in signal transduction and phagocytosis mediated by Fcgamma receptors on macrophages. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- PubMed-verified; full text cached. Syk-deficient macrophages form actin cups but fail to internalize IgG-coated particles, and PI3K inhibitors arrest at the same stage. - id: PMID:10783245 title: Involvement of the Arp2/3 complex in phagocytosis mediated by FcgammaR or CR3. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- PubMed-verified (May et al. 2000). The cached record has no abstract, so it is cited by title only for Arp2/3 involvement in both FcgammaR and CR3 uptake. - id: PMID:10601359 title: Dynamin 2 is required for phagocytosis in macrophages. reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; full text cached. Dominant-negative dynamin 2 arrests membrane extension around the particle. - id: PMID:11581283 title: Distinct roles of class I and class III phosphatidylinositol 3-kinases in phagosome formation and maturation. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- PubMed-verified; full text cached. Class I PI3K is required for optimal phagocytosis but not for maturation. This separates the class I PI3K step here from the class III (VPS34) step in MODULE:phagosome_maturation. - id: PMID:12163569 title: Dectin-1 is a major beta-glucan receptor on macrophages. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: PubMed-verified; grounds the non-opsonic beta-glucan receptor variant. - id: PMID:17960135 title: Identification of Tim4 as a phosphatidylserine receptor. reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; grounds TIMD4 as a phosphatidylserine-recognizing engulfment receptor. - id: PMID:11163239 title: CED-1 is a transmembrane receptor that mediates cell corpse engulfment in C. elegans. reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; CED-1 is the engulfment receptor of the CED-1/CED-6/CED-7 route. - id: PMID:9635426 title: Candidate adaptor protein CED-6 promotes the engulfment of apoptotic cells in C. elegans. reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; CED-6 is a PTB-domain adaptor that acts in engulfing cells. - id: PMID:9635425 title: The C. elegans cell corpse engulfment gene ced-7 encodes a protein similar to ABC transporters. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- PubMed-verified. CED-7 acts in both dying and engulfing cells. Its mechanism is a proposal in the paper, so it is recorded as a knowledge gap and not as an annoton. - id: PMID:9548255 title: C. elegans phagocytosis and cell-migration protein CED-5 is similar to human DOCK180. reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; establishes CED-5 as the DOCK180 ortholog. - id: PMID:10707082 title: CED-2/CrkII and CED-10/Rac control phagocytosis and cell migration in Caenorhabditis elegans. reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; places CED-2/CrkII and CED-5 upstream of CED-10/Rac in engulfing cells. - id: PMID:11595183 title: CED-12/ELMO, a novel member of the CrkII/Dock180/Rac pathway, is required for phagocytosis and cell migration. reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; CED-12/ELMO binds CED-5/Dock180 to form the Rac-activating complex. - id: PMID:12134158 title: Unconventional Rac-GEF activity is mediated through the Dock180-ELMO complex. reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; shows that the GEF (Docker/DHR-2) activity lies in Dock180 and needs ELMO. - id: PMID:15744306 title: Two pathways converge at CED-10 to mediate actin rearrangement and corpse removal in C. elegans. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- PubMed-verified. Both C. elegans engulfment routes converge on CED-10/Rac. Also the source for the open question of how CED-1/CED-6 signalling reaches actin. - id: PMID:27170117 title: Megf10 Is a Receptor for C1Q That Mediates Clearance of Apoptotic Cells by Astrocytes. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- PubMed-verified. Megf10 binds C1q with high affinity and confers apoptotic-cell phagocytosis. Grounds the MF of the CED-1/MEGF10 annoton. - id: PMID:20526330 title: Caenorhabditis elegans transthyretin-like protein TTR-52 mediates recognition of apoptotic cells by the CED-1 phagocyte receptor. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Full text cached. TTR-52 binds both phosphatidylserine and the CED-1 extracellular domain and is needed for CED-1 clustering. Grounds the TTR-52 bridging annoton. - id: PMID:29799847 title: A G-protein-coupled chemoattractant receptor recognizes lipopolysaccharide for bacterial phagocytosis. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Europe PMC-verified (Pan et al. 2018, PLoS Biol); full text cached. far1-null Dictyostelium cells are defective in phagocytosis of Klebsiella, and the fAR1 Venus-flytrap domain binds LPS. Grounds the amoebal receptor variant. - id: PMID:16699495 title: An adhesion molecule in free-living Dictyostelium amoebae with integrin beta features. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Europe PMC-verified (Cornillon et al. 2006, EMBO Rep); abstract only. sibA inactivation reduces adhesion to phagocytic particles. - id: PMID:10944536 title: Phg1p is a nine-transmembrane protein superfamily member involved in dictyostelium adhesion and phagocytosis. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Europe PMC-verified (Cornillon et al. 2000, JBC); abstract only. phg1 mutants fail to adhere to particles. Cited for the TM9/Phg1 note, not as an annoton. - id: PMID:22219373 title: TM9/Phg1 and SadA proteins control surface expression and stability of SibA adhesion molecules in Dictyostelium. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Europe PMC-verified (Froquet et al. 2012, MBoC); full text cached. Phg1A acts by setting SibA surface levels, which is why Phg1/TM9 is not modelled as a recognition annoton. - id: PMID:18796536 title: TM9SF4 is required for Drosophila cellular immunity via cell adhesion and phagocytosis. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Europe PMC-verified (Bergeret et al. 2008, J Cell Sci); abstract only. Shows that the Phg1/TM9SF4 requirement for phagocytosis is shared by Drosophila hemocytes. - id: PMID:11683394 title: The WASp-like protein scar regulates macropinocytosis, phagocytosis and endosomal membrane flow in Dictyostelium. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Europe PMC-verified (Seastone et al. 2001, J Cell Sci); abstract only. scar-null Dictyostelium cells have reduced phagocytosis. - id: PMID:12919849 title: Identification of cytoskeletal regulatory proteins required for efficient phagocytosis in Drosophila. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Europe PMC-verified (Pearson et al. 2003, Microbes Infect); abstract only. D-SCAR loss reduces phagocytosis of bacteria by Drosophila hemocytes and S2 cells. - id: PMID:36897976 title: Convergence of Ras- and Rac-regulated formin pathways is pivotal for phagosome formation and particle uptake in Dictyostelium. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Europe PMC-verified (Koerber et al. 2023, PNAS); full text cached. Its introduction summarizes the SCAR/WAVE and Arp2/3 machinery at the cup rim. Its formin results (ForB, ForG at the cup base) are noted but not modelled. - id: PMID:10825297 title: Rac1 GTPases control filopodia formation, cell motility, endocytosis, cytokinesis and development in Dictyostelium. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Europe PMC-verified (Dumontier et al. 2000, J Cell Sci); abstract only. Constitutively active Rac1 mutants act as dominant negatives and impair phagocytosis. - id: PMID:16950926 title: RacG regulates morphology, phagocytosis, and chemotaxis. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Europe PMC-verified (Somesh et al. 2006, Eukaryot Cell); full text cached. RacG localizes to the phagocytic cup rim and stimulates Arp2/3-dependent actin polymerization. The knockout phenotype is mild. - id: PMID:11807934 title: Dynamics of the Dictyostelium Arp2/3 complex in endocytosis, cytokinesis, and chemotaxis. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Europe PMC-verified (Insall et al. 2001, Cell Motil Cytoskeleton); abstract only. Localization evidence: Arp2/3 is recruited to sites of phagocytosis. - id: PMID:15572406 title: In vivo analysis of 3-phosphoinositide dynamics during Dictyostelium phagocytosis and chemotaxis. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Europe PMC-verified (Dormann et al. 2004, J Cell Sci); abstract only. PI(3,4,5)P3 forms transiently at amoebal engulfment sites. This is localization of the PI3K product, not a loss-of-function result. - id: PMID:18432193 title: Draper-dependent glial phagocytic activity is mediated by Src and Syk family kinase signalling. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Europe PMC-verified (Ziegenfuss et al. 2008, Nature); abstract only. Shark binds the Draper ITAM and is essential for Draper-mediated glial engulfment. - id: PMID:18854143 title: An Elmo-like protein associated with myosin II restricts spurious F-actin events to coordinate phagocytosis and chemotaxis. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Europe PMC-verified (Isik et al. 2008, Dev Cell); abstract only. Dictyostelium ElmoA restrains phagocytosis, so it is not used as an exemplar of the Rac-activating ELMO role. - id: PMID:19037099 title: Dictyostelium Dock180-related RacGEFs regulate the actin cytoskeleton during cell motility. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Europe PMC-verified (Para et al. 2009, MBoC); full text cached. An ELMO-DockD complex acts on Rac in amoebal motility. Phagocytosis was not the readout. - id: PMID:9880338 title: Disruption of a dynamin homologue affects endocytosis, organelle morphology, and cytokinesis in Dictyostelium discoideum. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Europe PMC-verified (Wienke et al. 1999, MBoC); abstract only. Dictyostelium dynamin A acts on endo-lysosomal membranes and not at the plasma membrane, so amoebal dynamin is not used for cup closure. evidence: - source_id: GO:0006911 title: phagocytosis, engulfment statement: >- The module is grounded in the GO process for internalizing a particle by surrounding it with plasma membrane. Recognition (GO:0006910) is modelled as the first part. Phagosome maturation (GO:0090382) is a separate module. - source_id: PMID:25319336 title: "Phagocytosis: receptors, signal integration, and the cytoskeleton." statement: >- Receptor diversity and staged actin remodeling (cortical disruption, then polymerization for pseudopod extension, then termination for closure) set the part order of this module. supporting_text: the actin polymerization that propels pseudopod extension - source_id: PMID:15744306 title: Two pathways converge at CED-10 to mediate actin rearrangement and corpse removal in C. elegans. statement: >- The two partially redundant C. elegans engulfment routes share a Rac output. This supports treating receptor classes as alternative entry points into a shared Rho-GTPase/actin core. supporting_text: two conserved, partially redundant genetic pathways regulate this process - source_id: PMID:36897976 title: Convergence of Ras- and Rac-regulated formin pathways is pivotal for phagosome formation and particle uptake in Dictyostelium. statement: >- In Dictyostelium, as in animal phagocytes, Arp2/3 activity downstream of SCAR/WAVE and Rho-family GTPases builds the protruding rim of the phagocytic cup, and loss of SCAR reduces phagocytosis. This supports a eukaryote-wide context for the Rac-to-actin core of the module. supporting_text: actin assembly at the tips of macroendocytic cups is initiated by the actin-related protein (Arp) 2/3 complex downstream of the SCAR (suppressor of cAMP receptor)/WAVE (Wiskott-Aldrich syndrome protein family verprolin homologs) complex (also known as the WAVE regulatory complex, WRC) activation and Rho family GTPase signaling - source_id: PMID:29799847 title: A G-protein-coupled chemoattractant receptor recognizes lipopolysaccharide for bacterial phagocytosis. statement: >- Dictyostelium lacks Fc-gamma and complement receptors and uses its own receptors to recognize bacteria. Receptor classes are therefore modelled as lineage-specific variants feeding a shared core. supporting_text: as typical phagocytic receptors, such as complement receptors or Fcγ receptors, have not been found in Dictyostelium, it remains mysterious how these cells recognize bacteria - source_id: file:modules/fc_gamma_receptor_signaling.yaml title: "Module: Fc-gamma receptor signaling pathway" statement: >- The Fc-gamma receptor recognition variant here covers only the engulfment role. MODULE:fc_gamma_receptor_signaling models the full ITAM/SYK/BTK signaling pathway, including the PLC-gamma and inflammatory branches. - source_id: file:modules/phagosome_maturation.yaml title: "Module: Phagosome maturation" statement: >- Sibling module. The sealed nascent phagosome produced here is the input to phagosome maturation. notes: >- Boundary: this module runs from particle recognition to closure of the phagocytic cup. It does not include phagosome maturation (the Rab5-to-Rab7 transition, lysosome fusion, acidification and the NADPH oxidase), which is in MODULE:phagosome_maturation. Also excluded: generation of "eat-me" signals on the target (for example XKR8-mediated phosphatidylserine exposure, GO:0070782), find-me chemotaxis, "don't-eat-me" checkpoints (CD47-SIRPA), and the inflammatory and transcriptional outputs of phagocytic receptors. LC3-associated phagocytosis (RUBCN, NOX2, ATG16L1 WD40 domain) is a related route that has not been modelled here. Taxon scope. The context is Eukaryota because the core that turns receptor signals into a phagocytic cup is shared by animals and phagotrophic amoebae. Dictyostelium needs Rac GTPases (PMID:10825297), the SCAR/WAVE nucleation-promoting factor (PMID:11683394) and the Arp2/3 complex (PMID:11807934, PMID:36897976) to engulf particles, and makes PI(3,4,5)P3 at engulfment sites (PMID:15572406). Each lineage-specific part carries its own taxon context. The Fc-gamma receptor, CR3 and Dectin-1 variants are vertebrate-only. TIMD4, GAS6 and MERTK in the apoptotic-cell variant are vertebrate-only, while the CED-1/Draper/MEGF10 receptor, CED-6/GULP and the Draper-Shark kinase link are bilaterian. The fAR1/SibA variant is shown only in Dictyostelium. Three core annotons have evidence from animals only. (1) The CRK/DOCK180/ELMO Rac GEF. PAINT places DOCK GEF activity at a eukaryote-level node, and Dictyostelium has an ELMO-DockD complex that acts on Rac during motility (PMID:19037099). But the best-studied amoebal ELMO, ElmoA, restrains phagocytosis rather than promoting it (PMID:18854143), and no amoebal CRK ortholog is known. (2) Class I PI3K at cup closure. In Dictyostelium, class I PI3K products appear at engulfment sites, but a loss-of-function phagocytosis defect for pikA/pikB was not found in the literature reviewed here. (3) Dynamin at cup closure. Dictyostelium dynamin A acts on endo-lysosomal membranes and not at the plasma membrane (PMID:9880338), so only mammalian dynamin 2 evidence supports this step. Receptor variants are alternatives (ONE_OR_MORE). A professional phagocyte usually uses several at once, and opsonic and non-opsonic routes can cooperate. The apoptotic-cell variant combines vertebrate receptors (TIMD4, the GAS6-MERTK bridge) with the CED-1/Draper/MEGF10 receptor family, its CED-6/GULP adaptor and the Syk-like kinase Shark. The CED-1/MEGF10 receptor is grounded on PTHR24035, the family PANTHER's own classification and PAINT use (ced-1 and Draper in SF109, MEGF10 in SF136). The UniProt/InterPro cross-references name PTHR24043 and PTHR24052 instead; see projects/PANTHER_FAMILY_ASSIGNMENT_DISCREPANCIES.md. PANTHER also places Dictyostelium SibA in SF109 (PROTEIN DRAPER), and SibA is a seed of the PAINT node PTN009076277 that carries scavenger receptor activity for CED-1 and MEGF10. SibA is nevertheless modelled as a separate amoebal gene product, because its assayed role is adhesion to particles and no ligand-binding activity has been shown. Whether it shares an ancestral engulfment-receptor function with CED-1 is recorded as a knowledge gap. Not modelled as annotons. TM9/Phg1 nonaspanins (Dictyostelium Phg1A, Drosophila TM9SF4) are needed for adhesion to particles and phagocytosis in both lineages (PMID:10944536, PMID:18796536). Phg1A acts by setting the surface level of SibA (PMID:22219373), so it supports recognition rather than carrying it out. Formins (Dictyostelium ForB and ForG) build linear actin at the cup base (PMID:36897976) and could be added as a further actin annoton. The worm DYN-1 gene review places DYN-1's engulfment-cell role at phagosome maturation (GO:0090386). Mammalian dynamin 2 also acts earlier, at pseudopod extension. The dynamin family therefore appears in this module for cup closure (DNM2 evidence) and again in MODULE:phagosome_maturation (DYN-1 evidence). module: id: phagocytic_engulfment label: Phagocytic engulfment module_type: BIOLOGICAL_PROCESS concepts: - preferred_term: phagocytosis, engulfment term: id: GO:0006911 label: phagocytosis, engulfment context: taxa: - preferred_term: Eukaryota term: id: NCBITaxon:2759 label: Eukaryota notes: >- The Rac-to-Arp2/3 core of cup formation is shared by animal phagocytes and phagotrophic amoebae such as Dictyostelium. Receptor variants and some core annotons are narrower; each lineage-specific variant states its own taxon context, and the module notes list the core annotons that have evidence from animals only. cell_types: - preferred_term: phagocyte term: id: CL:0000234 label: phagocyte notes: >- Includes professional phagocytes (macrophages, neutrophils, dendritic cells, insect hemocytes), non-professional engulfing cells such as the C. elegans hypodermal and gonadal sheath cells that clear apoptotic corpses, and free-living amoebae that feed on bacteria. cellular_components: - preferred_term: phagocytic cup term: id: GO:0001891 label: phagocytic cup parts: - order: 1 role: particle recognition node: id: particle_recognition label: Particle recognition by phagocytic receptors module_type: BIOLOGICAL_PROCESS description: >- A cell-surface receptor binds the particle, either directly or through an opsonin or bridging molecule. The receptors cluster and signal across the plasma membrane. concepts: - preferred_term: phagocytosis, recognition term: id: GO:0006910 label: phagocytosis, recognition variant_sets: - id: phagocytic_receptor_class label: Phagocytic receptor class axis: receptor class and target ligand selection: ONE_OR_MORE notes: >- The receptor class decides which Rho GTPase program is used downstream (see Rho-family GTPase activation) and whether uptake is inflammatory. For example, IgG-dependent uptake triggers a respiratory burst and complement-dependent uptake does not (PMID:9831565). Receptor classes are lineage-specific, and each variant carries its own taxon context. variants: - id: fc_gamma_receptor_recognition label: Fc-gamma receptor recognition of IgG-opsonized particles module_type: SIGNALING_PATHWAY description: >- Activating Fc-gamma receptors bind IgG-coated particles. ITAM phosphorylation recruits SYK, which is required for internalization after actin cups have formed. context: taxa: - preferred_term: Vertebrata term: id: NCBITaxon:7742 label: Vertebrata notes: >- Lineage-specific variant. IgG-dependent uptake is a vertebrate adaptive-immune mechanism, so the participants are human gene products, not families. concepts: - preferred_term: Fc-gamma receptor signaling pathway involved in phagocytosis term: id: GO:0038096 label: Fc-gamma receptor signaling pathway involved in phagocytosis annotons: - id: fcgr2a_igg_receptor label: FCGR2A IgG receptor participant: selector_type: GENE_PRODUCT gene_product: preferred_term: FCGR2A term: id: UniProtKB:P12318 label: Low affinity immunoglobulin gamma Fc region receptor II-a function: preferred_term: IgG receptor activity term: id: GO:0019770 label: IgG receptor activity locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Representative activating Fc-gamma receptor with an ITAM in its own cytoplasmic tail. It binds the Fc region of IgG on opsonized particles and starts phagocytic signaling when clustered. - id: syk_fcgr_kinase label: SYK kinase downstream of Fc-gamma receptors participant: selector_type: GENE_PRODUCT gene_product: preferred_term: SYK term: id: UniProtKB:P43405 label: Tyrosine-protein kinase SYK function: preferred_term: non-membrane spanning protein tyrosine kinase activity term: id: GO:0004715 label: non-membrane spanning protein tyrosine kinase activity locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Binds phosphorylated receptor ITAMs and phosphorylates downstream substrates. It is needed to go from actin-cup formation to internalization of IgG-opsonized particles, but not for uptake of latex beads or E. coli. evidence: - source_id: PMID:9314552 title: A critical role for Syk in signal transduction and phagocytosis mediated by Fcgamma receptors on macrophages. statement: Syk-deficient macrophages make actin cups but do not internalize Fc-gamma receptor-bound particles. supporting_text: Syk is required for FcγR-induced phagocytosis, but not for phagocytosis of latex beads or microorganisms. evidence: - source_id: file:modules/fc_gamma_receptor_signaling.yaml title: "Module: Fc-gamma receptor signaling pathway" statement: The wider Fc-gamma receptor signaling pathway is modelled in its own module. - id: complement_receptor_3_recognition label: Complement receptor 3 recognition of iC3b-opsonized particles module_type: BIOLOGICAL_PROCESS description: >- The integrin alphaM-beta2 heterodimer (CR3, Mac-1) binds iC3b on complement-opsonized particles. Uptake is RhoA-dependent ("type II") and is not accompanied by a respiratory burst. context: taxa: - preferred_term: Vertebrata term: id: NCBITaxon:7742 label: Vertebrata notes: >- Lineage-specific variant. The iC3b opsonin and the leukocyte beta-2 integrin CR3 are vertebrate-specific. annotons: - id: cr3_ic3b_receptor label: CR3 (integrin alphaM-beta2) iC3b receptor participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: complement receptor 3 (integrin alphaM-beta2) term: id: GO:0034688 label: integrin alphaM-beta2 complex active_units: - id: itgam_unit label: ITGAM (CD11b) alpha subunit role: ligand-binding alpha chain participant: selector_type: GENE_PRODUCT gene_product: preferred_term: ITGAM term: id: UniProtKB:P11215 label: Integrin alpha-M - id: itgb2_unit label: ITGB2 (CD18) beta subunit role: signaling beta chain participant: selector_type: GENE_PRODUCT gene_product: preferred_term: ITGB2 term: id: UniProtKB:P05107 label: Integrin beta-2 function: preferred_term: complement component iC3b receptor activity term: id: GO:0001858 label: complement component iC3b receptor activity locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Binds iC3b on complement-opsonized particles and drives RhoA-dependent phagocytosis. evidence: - source_id: PMID:9831565 title: Identification of two distinct mechanisms of phagocytosis controlled by different Rho GTPases. statement: Complement receptor phagocytosis is a distinct, Rho-mediated mechanism. supporting_text: type II, used by the complement receptor, is mediated by Rho - id: beta_glucan_recognition label: Dectin-1 recognition of beta-glucan particles module_type: BIOLOGICAL_PROCESS description: >- Non-opsonic recognition of fungal cell-wall beta-glucans by the C-type lectin receptor Dectin-1 (CLEC7A). context: taxa: - preferred_term: Vertebrata term: id: NCBITaxon:7742 label: Vertebrata notes: Lineage-specific variant. Dectin-1 is a vertebrate myeloid C-type lectin receptor. annotons: - id: clec7a_beta_glucan_receptor label: Dectin-1 beta-glucan receptor participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CLEC7A term: id: UniProtKB:Q9BXN2 label: C-type lectin domain family 7 member A function: preferred_term: pattern recognition receptor activity term: id: GO:0038187 label: pattern recognition receptor activity targets: - preferred_term: (1->3)-beta-D-glucan locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Main macrophage receptor for non-opsonic beta-glucan particles such as zymosan. evidence: - source_id: PMID:12163569 title: Dectin-1 is a major beta-glucan receptor on macrophages. statement: Dectin-1 mediates beta-glucan-dependent, non-opsonic zymosan recognition by primary macrophages. supporting_text: Dectin-1 was almost exclusively responsible for the beta-glucan-dependent, nonopsonic recognition of zymosan - id: apoptotic_cell_recognition label: Apoptotic-cell recognition (efferocytic receptors) module_type: BIOLOGICAL_PROCESS description: >- Recognition of apoptotic cells, mainly through exposed phosphatidylserine. Recognition can be direct (TIMD4) or through a bridging ligand (GAS6 to MERTK, TTR-52 to CED-1). The CED-1/Draper/MEGF10 receptor family and its PTB-domain adaptor CED-6/GULP form a conserved receptor-adaptor unit. In Drosophila, Draper also signals through its ITAM to the Syk-family kinase Shark. context: taxa: - preferred_term: Bilateria term: id: NCBITaxon:33213 label: Bilateria notes: >- Lineage-specific variant. The CED-1/Draper/MEGF10 and CED-6/GULP families act in nematodes, insects and mammals, and the CED-6/GULP PAINT node is bilaterian. TIMD4, GAS6 and MERTK are vertebrate-only, and TTR-52 is a nematode protein; their annotons say so. concepts: - preferred_term: engulfment of apoptotic cell term: id: GO:0043652 label: engulfment of apoptotic cell annotons: - id: timd4_ps_receptor label: TIMD4 phosphatidylserine receptor participant: selector_type: GENE_PRODUCT gene_product: preferred_term: TIMD4 term: id: UniProtKB:Q96H15 label: T-cell immunoglobulin and mucin domain-containing protein 4 function: preferred_term: phosphatidylserine binding term: id: GO:0001786 label: phosphatidylserine binding locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Binds phosphatidylserine on apoptotic cells and tethers them to the phagocyte. It is a tethering receptor that works with signaling co-receptors. notes: Vertebrate-specific receptor, modelled as a human gene product. gocam_associations: - model: gomodel:68fac5ed00003572 activity: gomodel:68fac5ed00003572/68fac5ed00003599 title: XKR8 promotes phosphatidylserine exposure on apoptotic cell surface following activation by CASP3 (Human). description: TIMD4 is modelled with phosphatidylserine binding in apoptotic cell clearance. evidence: - source_id: PMID:17960135 title: Identification of Tim4 as a phosphatidylserine receptor. statement: An antibody that blocks phosphatidylserine-dependent engulfment of apoptotic cells recognizes Tim4. supporting_text: strongly inhibited the phosphatidylserine-dependent engulfment of apoptotic cells - id: gas6_ps_bridge label: GAS6 phosphatidylserine bridging ligand participant: selector_type: GENE_PRODUCT gene_product: preferred_term: GAS6 term: id: UniProtKB:Q14393 label: Growth arrest-specific protein 6 function: preferred_term: phosphatidylserine binding term: id: GO:0001786 label: phosphatidylserine binding locations: - preferred_term: extracellular region term: id: GO:0005576 label: extracellular region role_description: >- Secreted Gla-domain protein. It binds phosphatidylserine on apoptotic membranes and links them to TAM receptor tyrosine kinases such as MERTK. notes: Vertebrate-specific bridging ligand, modelled as a human gene product. evidence: - source_id: file:genes/human/GAS6/GAS6-ai-review.yaml title: GAS6 gene review statement: >- The GAS6 review core functions include phosphatidylserine binding (GO:0001786) for efferocytosis and TAM receptor ligand activity. - id: mertk_tam_receptor label: MERTK TAM receptor tyrosine kinase participant: selector_type: GENE_PRODUCT gene_product: preferred_term: MERTK term: id: UniProtKB:Q12866 label: Tyrosine-protein kinase Mer function: preferred_term: transmembrane receptor protein tyrosine kinase activity term: id: GO:0004714 label: transmembrane receptor protein tyrosine kinase activity locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Signaling receptor for GAS6/PROS1-bridged apoptotic cells. Ligand-induced kinase activity promotes cytoskeletal engulfment signaling. notes: >- Vertebrate-specific receptor, modelled as a human gene product. The primary MERTK efferocytosis paper (PMID:11346799, Scott et al. 2001) could not be cached (no abstract), so this annoton rests on the GAS6 review and on the TAM bridging model. - id: ttr52_ps_bridge label: TTR-52 phosphatidylserine bridging molecule (C. elegans) participant: selector_type: GENE_PRODUCT gene_product: preferred_term: ttr-52 term: id: UniProtKB:G5ED35 label: Transthyretin-like protein 52 function: preferred_term: protein-macromolecule adaptor activity term: id: GO:0030674 label: protein-macromolecule adaptor activity locations: - preferred_term: cell surface term: id: GO:0009986 label: cell surface role_description: >- Secreted transthyretin-like protein of the C. elegans CED-1 route. It binds phosphatidylserine on apoptotic cells and the EMI domain of CED-1, bridging the corpse to the engulfing cell. It plays the bridging role that GAS6 and C1q play upstream of mammalian receptors; it is modelled as a single gene product because no cross-species family for it has been established here. evidence: - source_id: PMID:20526330 title: Caenorhabditis elegans transthyretin-like protein TTR-52 mediates recognition of apoptotic cells by the CED-1 phagocyte receptor. statement: TTR-52 binds both phosphatidylserine and the CED-1 extracellular domain. supporting_text: TTR-52 recognizes surface-exposed phosphatidylserine (PtdSer) in vivo and binds to both PtdSer and the extracellular domain of CED-1 in vitro - source_id: file:genes/worm/ttr-52/ttr-52-ai-review.yaml title: ttr-52 gene review statement: >- The ttr-52 review gives protein-macromolecule adaptor activity (GO:0030674) in recognition of apoptotic cell as the core function. - id: ced1_megf10_engulfment_receptor label: CED-1/MEGF10 engulfment receptor participant: selector_type: FAMILY family: preferred_term: CED-1/Draper/MEGF10 engulfment receptor orthogroup description: >- Multiple-EGF-like-domain transmembrane receptors with NPxY/YxxL cytoplasmic motifs. Grounded on PANTHER's own classification (ced-1 and Draper in SF109, MEGF10 in SF136), not on the UniProt/InterPro cross-references, which name PTHR24043 and PTHR24052 (see projects/PANTHER_FAMILY_ASSIGNMENT_DISCREPANCIES.md). term: id: PANTHER:PTHR24035 label: MULTIPLE EPIDERMAL GROWTH FACTOR-LIKE DOMAINS PROTEIN representative_members: - preferred_term: ced-1 (C. elegans) term: id: UniProtKB:Q9XWD6 label: Cell death abnormality protein 1 - preferred_term: drpr (Drosophila) term: id: UniProtKB:Q9W0A0 label: Protein draper - preferred_term: MEGF10 (human) term: id: UniProtKB:Q96KG7 label: Multiple epidermal growth factor-like domains protein 10 ancestral_nodes: - preferred_term: PAINT node PTN002372116 for CED-1/Draper/MEGF10 term: id: PANTHER:PTN002372116 label: PTN002372116 description: >- Local PAINT IBD node in PTHR24035 propagating P:GO:0043652 engulfment of apoptotic cell. Seeds are FB:FBgn0027594 (drpr), MGI:2685177 (Megf10) and WB:WBGene00000415 (ced-1). evidence: - source_id: GO_REF:0000033 statement: IBD propagation of engulfment of apoptotic cell from PAINT node PTN002372116 in PTHR24035. - preferred_term: PAINT node PTN009076277 for CED-1/MEGF10 term: id: PANTHER:PTN009076277 label: PTN009076277 description: >- Local PAINT IBD node in PTHR24035 propagating F:GO:0005044 scavenger receptor activity (seeds UniProtKB:Q96KG7 and WB:WBGene00000415) and C:GO:0005886 plasma membrane. The plasma membrane seeds also include FB:FBgn0027594 (drpr) and dictyBase:DDB_G0287363 (Dictyostelium sibA), so the node sits above the amoebal SibA proteins. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of scavenger receptor activity from PAINT node PTN009076277 in PTHR24035. function: preferred_term: scavenger receptor activity term: id: GO:0005044 label: scavenger receptor activity processes: - preferred_term: engulfment of apoptotic cell term: id: GO:0043652 label: engulfment of apoptotic cell locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Clusters around cell corpses and signals through cytoplasmic tail motifs that bind PTB and SH2 domains. These motifs are needed for engulfment but not for clustering. evidence: - source_id: PMID:11163239 title: CED-1 is a transmembrane receptor that mediates cell corpse engulfment in C. elegans. statement: CED-1 is a cell-surface phagocytic receptor that recognizes cell corpses. supporting_text: CED-1 is a cell surface phagocytic receptor that recognizes cell corpses - source_id: PMID:27170117 title: Megf10 Is a Receptor for C1Q That Mediates Clearance of Apoptotic Cells by Astrocytes. statement: Megf10 binds the eat-me signal C1q, and its expression confers apoptotic-cell phagocytosis. supporting_text: Megf10 binds with high affinity to C1q, an eat-me signal for apoptotic cells - source_id: file:genes/worm/ced-1/ced-1-ai-review.yaml title: ced-1 gene review statement: >- The ced-1 review gives scavenger receptor activity (GO:0005044) in engulfment and recognition of apoptotic cells as the core function. - source_id: file:genes/human/MEGF10/MEGF10-ai-review.yaml title: MEGF10 gene review statement: >- The MEGF10 review gives scavenger receptor activity (GO:0005044) in engulfment of apoptotic cell, and C1q complex binding, as core functions. - id: ced6_gulp_adaptor label: CED-6/GULP engulfment adaptor participant: selector_type: FAMILY family: preferred_term: CED-6/GULP PTB-domain engulfment adaptor term: id: PANTHER:PTHR11232 label: PHOSPHOTYROSINE INTERACTION DOMAIN-CONTAINING FAMILY MEMBER representative_members: - preferred_term: ced-6 (C. elegans) term: id: UniProtKB:O76337 label: Cell death protein 6 - preferred_term: ced-6 (Drosophila) term: id: UniProtKB:Q7JUY7 label: PTB domain-containing adapter protein ced-6 - preferred_term: GULP1 (human) term: id: UniProtKB:Q9UBP9 label: PTB domain-containing engulfment adapter protein 1 ancestral_nodes: - preferred_term: PAINT node PTN000132688 for CED-6/GULP1 term: id: PANTHER:PTN000132688 label: PTN000132688 description: >- Local PAINT IBD node in PTHR11232 propagating P:GO:0006911 (phagocytosis, engulfment). Seeds are UniProtKB:Q9UBP9 (GULP1) and WB:WBGene00000420 (ced-6). Taxon scope Bilateria-level (taxon:33213). evidence: - source_id: GO_REF:0000033 statement: IBD propagation of phagocytosis, engulfment from PAINT node PTN000132688 in PTHR11232. function: preferred_term: signaling adaptor activity term: id: GO:0035591 label: signaling adaptor activity processes: - preferred_term: phagocytosis, engulfment term: id: GO:0006911 label: phagocytosis, engulfment locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- PTB-domain adaptor that binds the NPxY motif of CED-1/MEGF10 (and LRP1) tails and passes the signal on toward actin remodeling and dynamin recruitment. evidence: - source_id: PMID:9635426 title: Candidate adaptor protein CED-6 promotes the engulfment of apoptotic cells in C. elegans. statement: CED-6 is an adaptor in the engulfing cell that mediates recognition and engulfment of apoptotic cells. supporting_text: CED-6 is an adaptor molecule acting in a signal transduction pathway that specifically mediates the recognition and engulfment of apoptotic cells - source_id: file:genes/worm/ced-6/ced-6-ai-review.yaml title: ced-6 gene review statement: >- The ced-6 review gives signaling adaptor activity (GO:0035591) in engulfment of apoptotic cell as the core function, binding the CED-1 NPXY motif through its PTB domain. - id: shark_draper_kinase label: Shark Syk-family kinase downstream of Draper participant: selector_type: GENE_PRODUCT gene_product: preferred_term: Shark (Drosophila) term: id: UniProtKB:Q24145 label: Tyrosine-protein kinase Shark notes: >- Shark is the Drosophila kinase most similar to Syk and ZAP-70. PANTHER puts Shark (PTHR24418:SF372) and SYK (PTHR24418:SF231) in different subfamilies of a very large tyrosine kinase family, so no shared family selector is asserted. function: preferred_term: non-membrane spanning protein tyrosine kinase activity term: id: GO:0004715 label: non-membrane spanning protein tyrosine kinase activity locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Binds the ITAM in the Draper cytoplasmic tail, which the Src-family kinase Src42A phosphorylates, and is required for glia to engulf neuronal corpses and axon debris. This is the same ITAM-Src-Syk logic used by vertebrate Fc-gamma receptors. evidence: - source_id: PMID:18432193 title: Draper-dependent glial phagocytic activity is mediated by Src and Syk family kinase signalling. statement: Shark binds the Draper ITAM and is required for Draper-dependent glial engulfment. supporting_text: binds Draper through an immunoreceptor tyrosine-based activation motif (ITAM) in the Draper intracellular domain - source_id: PMID:18432193 title: Draper-dependent glial phagocytic activity is mediated by Src and Syk family kinase signalling. statement: Loss of Shark activity blocks Draper signalling in vivo. supporting_text: Shark activity is essential for Draper-mediated signalling events in vivo - id: amoebal_bacterial_recognition label: Bacterial recognition by amoebal receptors module_type: BIOLOGICAL_PROCESS description: >- Dictyostelium amoebae have no Fc-gamma or complement receptors. They recognize bacteria through the folate/LPS receptor fAR1, a G-protein-coupled receptor, and adhere to particles through the transmembrane protein SibA. Loss of either reduces uptake of particles or bacteria. context: taxa: - preferred_term: Dictyostelium discoideum term: id: NCBITaxon:44689 label: Dictyostelium discoideum notes: >- Lineage-specific variant. Both receptors were shown in D. discoideum; whether other amoebozoans use them is not established. annotons: - id: far1_lps_receptor label: fAR1 folate and LPS receptor participant: selector_type: GENE_PRODUCT gene_product: preferred_term: far1 (Dictyostelium) term: id: UniProtKB:Q54U89 label: Metabotropic glutamate receptor-like protein L notes: >- PANTHER places fAR1 in PTHR46924:SF1, a Dictyostelium metabotropic-glutamate-receptor-like family with no animal phagocytic receptor members, so it is modelled as a gene product. function: preferred_term: pattern recognition receptor activity term: id: GO:0038187 label: pattern recognition receptor activity targets: - preferred_term: lipopolysaccharide locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- G-protein-coupled receptor whose extracellular Venus-flytrap domain binds folate and bacterial LPS. Through its heterotrimeric G protein it reorganizes actin for both chemotaxis toward bacteria and their engulfment. evidence: - source_id: PMID:29799847 title: A G-protein-coupled chemoattractant receptor recognizes lipopolysaccharide for bacterial phagocytosis. statement: far1-null cells, and cells lacking its G proteins, are defective in phagocytosis of Klebsiella. supporting_text: Cells lacking fAR1 or its cognate G-proteins are defective in chemotaxis toward folate and phagocytosis of Klebsiella aerogenes - source_id: PMID:29799847 title: A G-protein-coupled chemoattractant receptor recognizes lipopolysaccharide for bacterial phagocytosis. statement: The fAR1 Venus-flytrap domain binds LPS. supporting_text: the extracellular Venus-Flytrap (VFT) domain of fAR1 acts as the binding site for both folate and LPS - id: siba_particle_adhesion label: SibA particle adhesion protein participant: selector_type: GENE_PRODUCT gene_product: preferred_term: sibA (Dictyostelium) term: id: UniProtKB:Q54KF7 label: Integrin beta-like protein A notes: >- PANTHER classifies SibA in PTHR24035:SF109 (PROTEIN DRAPER) with ced-1 and Draper, and SibA is a seed of PAINT node PTN009076277 in the CED-1/MEGF10 annoton. It is kept as a gene product here because its assayed function is adhesion, not ligand recognition. function: preferred_term: cell adhesion mediator activity term: id: GO:0098631 label: cell adhesion mediator activity locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Type I transmembrane protein with integrin-beta-like features whose cytoplasmic tail binds talin. It is needed for amoebae to adhere to phagocytic particles. Its surface level depends on the TM9 protein Phg1A. evidence: - source_id: PMID:16699495 title: An adhesion molecule in free-living Dictyostelium amoebae with integrin beta features. statement: sibA inactivation reduces adhesion to phagocytic particles. supporting_text: genetic inactivation of SIBA affects adhesion to phagocytic particles - source_id: PMID:22219373 title: TM9/Phg1 and SadA proteins control surface expression and stability of SibA adhesion molecules in Dictyostelium. statement: Phg1A controls how much SibA reaches the cell surface. supporting_text: genetic inactivation of the TM9 protein Phg1A dramatically decreases the surface levels of the SibA adhesion molecule - order: 2 role: Rho-family GTPase activation node: id: rho_gtpase_activation label: Rho-family GTPase activation at the phagocytic cup module_type: SIGNALING_PATHWAY description: >- Receptor signaling activates Rho-family GTPases at the site of particle contact. The receptor class decides which GTPases are used. variant_sets: - id: phagocytic_rho_gtpase_program label: Phagocytic Rho-GTPase program axis: Rho GTPase used (set by receptor class) selection: ONE_OR_MORE notes: >- Type I (Fc-gamma receptor; also apoptotic-cell receptors through DOCK1/ELMO1) uses Rac and Cdc42. Type II (CR3) uses RhoA (PMID:9831565). In C. elegans both corpse-engulfment routes converge on CED-10/Rac (PMID:15744306). In Dictyostelium, Rac1 and RacG act in phagocytosis (PMID:10825297, PMID:16950926), but the CRK/DOCK/ELMO route has not been shown to activate them during amoebal uptake. variants: - id: rac_cdc42_program label: Rac/Cdc42 program (type I) module_type: SIGNALING_PATHWAY description: >- The CRK adaptor recruits the DOCK180-ELMO bipartite GEF, which loads GTP onto Rac. Cdc42 and Rac then recruit WASP-family nucleation-promoting factors. The same unit (CED-2, CED-5, CED-12, CED-10) works in C. elegans corpse engulfment. annotons: - id: crk_ced2_adaptor label: CRK/CED-2 SH2-SH3 adaptor participant: selector_type: FAMILY family: preferred_term: CrkII/CED-2 SH2-SH3 adaptor orthogroup term: id: PANTHER:PTHR19969 label: SH2-SH3 ADAPTOR PROTEIN-RELATED representative_members: - preferred_term: CRK (human) term: id: UniProtKB:P46108 label: Adapter molecule crk - preferred_term: ced-2 (C. elegans) term: id: UniProtKB:Q9NHC3 label: Cell death abnormality protein 2 function: preferred_term: signaling adaptor activity term: id: GO:0035591 label: signaling adaptor activity locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- SH2-SH3 adaptor that binds phosphotyrosine signals through its SH2 domain and brings DOCK180/CED-5 in through its SH3 domain. notes: >- Phagocytic role shown in nematodes and mammals. No CRK ortholog with a phagocytic role is known in amoebae. evidence: - source_id: PMID:10707082 title: CED-2/CrkII and CED-10/Rac control phagocytosis and cell migration in Caenorhabditis elegans. statement: CED-2 binds CED-5 and acts upstream of CED-10 in engulfing cells. supporting_text: CED-2 and CED-5 physically interact - source_id: file:genes/worm/ced-2/ced-2-ai-review.yaml title: ced-2 gene review statement: >- The ced-2 review gives signaling adaptor activity (GO:0035591) in engulfment of apoptotic cell, Rac protein signal transduction and distal tip cell migration as core functions. - id: dock180_rac_gef label: DOCK180/CED-5 Rac guanine-nucleotide exchange factor participant: selector_type: FAMILY family: preferred_term: DOCK-A subfamily (DOCK180/CED-5/Myoblast city) term: id: PANTHER:PTHR45653 label: DEDICATOR OF CYTOKINESIS representative_members: - preferred_term: DOCK1 (human) term: id: UniProtKB:Q14185 label: Dedicator of cytokinesis protein 1 - preferred_term: ced-5 (C. elegans) term: id: UniProtKB:G5EEN3 label: CED-5 ancestral_nodes: - preferred_term: PAINT node PTN002902098 for DOCK-family GEFs term: id: PANTHER:PTN002902098 label: PTN002902098 description: >- Eukaryote-level (taxon:2759) local PAINT IBD node in PTHR45653 propagating F:GO:0005085 guanyl-nucleotide exchange factor activity. Seeds include UniProtKB:Q14185 (DOCK1) and FB:FBgn0015513 (Drosophila mbc). evidence: - source_id: GO_REF:0000033 statement: IBD propagation of guanyl-nucleotide exchange factor activity from PAINT node PTN002902098 in PTHR45653. function: preferred_term: guanyl-nucleotide exchange factor activity term: id: GO:0005085 label: guanyl-nucleotide exchange factor activity targets: - preferred_term: Rac1 / CED-10 locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Catalytic half of the bipartite DOCK180-ELMO GEF. Its DHR-2 (Docker) domain binds nucleotide-free Rac and loads it with GTP. notes: >- GEF activity is placed at a eukaryote-level PAINT node, and Dictyostelium DockD acts on Rac with an ELMO partner during motility (PMID:19037099). A phagocytic role for DOCK-A proteins is shown only in nematodes, insects and mammals. PANTHER puts ced-5 in SF10 (MYOBLAST CITY) and DOCK1 in SF1, so the family-level id is used. evidence: - source_id: PMID:12134158 title: Unconventional Rac-GEF activity is mediated through the Dock180-ELMO complex. statement: The Dock180 Docker domain mediates GTP loading of Rac, and a Dock180-ELMO1 interaction is required in cells. supporting_text: a Dock180 ELMO1 interaction is required - source_id: PMID:9548255 title: C. elegans phagocytosis and cell-migration protein CED-5 is similar to human DOCK180. statement: CED-5 is the C. elegans DOCK180 ortholog required for cell-corpse engulfment. supporting_text: encodes a protein that is similar to the human protein DOCK180 - source_id: file:genes/worm/ced-5/ced-5-ai-review.yaml title: ced-5 gene review statement: >- The ced-5 review gives guanyl-nucleotide exchange factor activity (GO:0005085) in engulfment of apoptotic cell and distal tip cell migration as core functions. - id: elmo_gef_adaptor label: ELMO/CED-12 GEF adaptor participant: selector_type: FAMILY family: preferred_term: ELMO/CED-12 family term: id: PANTHER:PTHR12771 label: ENGULFMENT AND CELL MOTILITY representative_members: - preferred_term: ELMO1 (human) term: id: UniProtKB:Q92556 label: Engulfment and cell motility protein 1 - preferred_term: ced-12 (C. elegans) term: id: UniProtKB:Q8STE5 label: Cell death abnormality protein 12 - preferred_term: Ced-12 (Drosophila) term: id: UniProtKB:Q9VKB2 label: Ced-12 function: preferred_term: guanyl-nucleotide exchange factor adaptor activity term: id: GO:0005091 label: guanyl-nucleotide exchange factor adaptor activity locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Binds DOCK180/CED-5 and is required for its Rac GEF activity in cells. ELMO is the non-catalytic partner of the bipartite GEF. notes: >- Phagocytic role shown in nematodes, insects and mammals. Dictyostelium ElmoA falls in the same PANTHER subfamily as worm and fly CED-12 (PTHR12771:SF56), but elmoA-null cells engulf faster (PMID:18854143), so ElmoA is not used as an exemplar. PANTHER's own files place worm CED-12 (Q8STE5) in SF56 although its UniProt entry has no PANTHER cross-reference. evidence: - source_id: PMID:11595183 title: CED-12/ELMO, a novel member of the CrkII/Dock180/Rac pathway, is required for phagocytosis and cell migration. statement: CED-12/ELMO binds CED-5/Dock180 and the complex stimulates Rac activation. supporting_text: this evolutionarily conserved complex stimulates a Rac-GEF - source_id: file:genes/DROME/Ced-12/Ced-12-ai-review.yaml title: Drosophila Ced-12 gene review statement: The Ced-12 review gives guanyl-nucleotide exchange factor adaptor activity (GO:0005091) as the core MF. - source_id: file:genes/worm/ced-12/ced-12-ai-review.yaml title: ced-12 gene review statement: >- The ced-12 review gives guanyl nucleotide exchange factor activator activity (GO:0160124) in engulfment of apoptotic cell and distal tip cell migration as core functions. This differs from the GEF adaptor term used here and in the Drosophila Ced-12 review; the two reviews have not yet been reconciled. - id: rac_cdc42_gtpase label: Rac/CED-10 and Cdc42 GTPases participant: selector_type: FAMILY family: preferred_term: Rac and Cdc42 Rho-family GTPases term: id: PANTHER:PTHR24072 label: RHO FAMILY GTPASE representative_members: - preferred_term: RAC1 (human) term: id: UniProtKB:P63000 label: Ras-related C3 botulinum toxin substrate 1 - preferred_term: ced-10 (C. elegans) term: id: UniProtKB:Q03206 label: Ras-related protein ced-10 - preferred_term: CDC42 (human) term: id: UniProtKB:P60953 label: Cell division control protein 42 homolog - preferred_term: rac1A (Dictyostelium) term: id: UniProtKB:P34144 label: Rho-related protein rac1A - preferred_term: racG (Dictyostelium) term: id: UniProtKB:Q9GPS0 label: Rho-related protein racG ancestral_nodes: - preferred_term: PAINT node PTN000632671 for Rho-family GTPases term: id: PANTHER:PTN000632671 label: PTN000632671 description: >- Local PAINT IBD node in PTHR24072 propagating F:GO:0003924 GTPase activity, F:GO:0005525, C:GO:0005886, P:GO:0007015 and P:GO:0007165. RAC1 (P63000) is among the seeds, and Dictyostelium rac1A (dictyBase:DDB_G0277869) seeds the GTP binding, plasma membrane and signal transduction annotations. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of GTPase activity from PAINT node PTN000632671 in PTHR24072. notes: >- PANTHER splits these members across subfamilies (RAC1 SF395, CDC42 SF136, ced-10 and rac1A SF359, racG SF272), so the family-level id is used. function: preferred_term: GTPase activity term: id: GO:0003924 label: GTPase activity locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: >- Molecular switches activated at the phagocytic cup. In the GTP form they recruit WASP-family and PAK effectors that drive actin polymerization. evidence: - source_id: PMID:9831565 title: Identification of two distinct mechanisms of phagocytosis controlled by different Rho GTPases. statement: Fc-gamma receptor (type I) phagocytosis requires Cdc42 and Rac. supporting_text: Type I, used by the immunoglobulin receptor, is mediated by Cdc42 and Rac - source_id: PMID:15744306 title: Two pathways converge at CED-10 to mediate actin rearrangement and corpse removal in C. elegans. statement: Both C. elegans engulfment routes converge on CED-10/Rac. supporting_text: CED-2, CED-5 and CED-12 (mammalian homologues CrkII, Dock180 and ELMO, respectively) function to activate CED-10 (Rac1) - source_id: PMID:10825297 title: Rac1 GTPases control filopodia formation, cell motility, endocytosis, cytokinesis and development in Dictyostelium. statement: >- In Dictyostelium, constitutively active Rac1 mutants act as dominant negatives and severely impair phagocytosis. supporting_text: these mutants were severely impaired in cell motility, colony growth, phagocytosis, pinocytosis, cytokinesis and development - source_id: PMID:16950926 title: RacG regulates morphology, phagocytosis, and chemotaxis. statement: >- Dictyostelium RacG concentrates at the rim of the forming phagocytic cup, and its overexpression increases uptake. supporting_text: RacG is enriched at the rim of the progressing phagocytic cup - id: rhoa_program label: RhoA program (type II, CR3) module_type: SIGNALING_PATHWAY description: >- Complement receptor 3 uptake depends on RhoA, which drives a different actin assembly: particles sink into the cell with few pseudopods. notes: >- Shown for the vertebrate CR3 route only. No RhoA-dependent uptake route has been described in amoebae. annotons: - id: rhoa_gtpase label: RhoA GTPase participant: selector_type: FAMILY family: preferred_term: RhoA subfamily term: id: PANTHER:PTHR24072:SF153 label: TRANSFORMING PROTEIN RHOA representative_members: - preferred_term: RHOA (human) term: id: UniProtKB:P61586 label: Transforming protein RhoA function: preferred_term: GTPase activity term: id: GO:0003924 label: GTPase activity locations: - preferred_term: plasma membrane term: id: GO:0005886 label: plasma membrane role_description: Rho-family switch needed for complement-receptor (type II) phagocytosis. evidence: - source_id: PMID:9831565 title: Identification of two distinct mechanisms of phagocytosis controlled by different Rho GTPases. statement: Complement receptor phagocytosis is mediated by Rho. supporting_text: type II, used by the complement receptor, is mediated by Rho - order: 3 role: actin polymerization for pseudopod extension node: id: phagocytic_actin_polymerization label: Arp2/3-dependent actin polymerization module_type: BIOLOGICAL_PROCESS description: >- Active Rho GTPases recruit WASP-family nucleation-promoting factors (SCAR/WAVE downstream of Rac, WASP/N-WASP downstream of Cdc42) that activate the Arp2/3 complex. Branched actin then pushes pseudopods around the particle. Arp2/3 is used by both Fc-gamma receptor and CR3 uptake (PMID:10783245) and is recruited to the phagocytic cup of Dictyostelium (PMID:11807934). concepts: - preferred_term: Arp2/3 complex-mediated actin nucleation term: id: GO:0034314 label: Arp2/3 complex-mediated actin nucleation annotons: - id: scar_wave_npf label: SCAR/WAVE nucleation-promoting factor participant: selector_type: FAMILY family: preferred_term: SCAR/WAVE nucleation-promoting factors term: id: PANTHER:PTHR12902 label: WASP-1 representative_members: - preferred_term: WASF2 (human) term: id: UniProtKB:Q9Y6W5 label: Actin-binding protein WASF2 - preferred_term: WASF1 (human) term: id: UniProtKB:Q92558 label: Actin-binding protein WASF1 - preferred_term: SCAR (Drosophila) term: id: UniProtKB:F2FB81 label: Wiskott-Aldrich syndrome protein family member - preferred_term: scrA (Dictyostelium) term: id: UniProtKB:Q54NF8 label: Protein SCAR ancestral_nodes: - preferred_term: PAINT node PTN000307553 for SCAR/WAVE term: id: PANTHER:PTN000307553 label: PTN000307553 description: >- Eukaryote-level (taxon:2759) local PAINT IBD node in PTHR12902 propagating F:GO:0071933 Arp2/3 complex binding (seed UniProtKB:Q0IIJ3) and P:GO:0030036 actin cytoskeleton organization. The process seeds include dictyBase:DDB_G0285253 (scrA), FB:FBgn0041781 (SCAR), UniProtKB:Q92558 (WASF1) and WB:WBGene00006958 (wve-1). evidence: - source_id: GO_REF:0000033 statement: IBD propagation of Arp2/3 complex binding from PAINT node PTN000307553 in PTHR12902. notes: >- PANTHER puts WASF2 in SF6 and the fly, worm and amoebal SCAR proteins in SF1, so the family-level id is used. The PANTHER name WASP-1 is the official family label. function: preferred_term: Arp2/3 complex binding term: id: GO:0071933 label: Arp2/3 complex binding locations: - preferred_term: phagocytic cup term: id: GO:0001891 label: phagocytic cup role_description: >- Rac-activated nucleation-promoting factor, part of the WAVE regulatory complex. It collects at the protruding rim of the phagocytic cup and activates the Arp2/3 complex there. evidence: - source_id: PMID:11683394 title: The WASp-like protein scar regulates macropinocytosis, phagocytosis and endosomal membrane flow in Dictyostelium. statement: scar-null Dictyostelium cells have reduced rates of phagocytosis. supporting_text: Rates of fluid phase macropinocytosis and phagocytosis are significantly reduced in the scar- cell-line - source_id: PMID:12919849 title: Identification of cytoskeletal regulatory proteins required for efficient phagocytosis in Drosophila. statement: D-SCAR loss reduces phagocytosis of bacteria by Drosophila hemocytes and S2 cells. supporting_text: lack of D-SCAR significantly decreased phagocytosis of Escherichia coli and Staphylococcus aureus - source_id: PMID:36897976 title: Convergence of Ras- and Rac-regulated formin pathways is pivotal for phagosome formation and particle uptake in Dictyostelium. statement: SCAR collects as a ring along the cup edge, and its loss reduces F-actin at the cup rim. supporting_text: inactivation of SCAR in Dictyostelium, which accumulates in a ring-like fashion along the cup edge (17), diminishes F-actin at the protrusive cup rim - id: wasp_npf label: WASP/N-WASP nucleation-promoting factor participant: selector_type: FAMILY family: preferred_term: WASP/N-WASP nucleation-promoting factors notes: >- No PANTHER id is asserted. PANTHER's own files put WASL in PTHR13037:SF23 (family FORMIN) while UniProt names PTHR11202:SF36, and human WAS is absent from the PANTHER human classification file. representative_members: - preferred_term: WAS (human) term: id: UniProtKB:P42768 label: Actin nucleation-promoting factor WAS - preferred_term: WASL (human) term: id: UniProtKB:O00401 label: Actin nucleation-promoting factor WASL function: preferred_term: Arp2/3 complex binding term: id: GO:0071933 label: Arp2/3 complex binding locations: - preferred_term: phagocytic cup term: id: GO:0001891 label: phagocytic cup role_description: >- Cdc42-GTP binding releases autoinhibition. The C-terminal VCA region then binds and activates the Arp2/3 complex at the phagocytic cup. evidence: - source_id: PMID:12919849 title: Identification of cytoskeletal regulatory proteins required for efficient phagocytosis in Drosophila. statement: RNAi in Drosophila S2 cells shows that D-WASp also takes part in phagocytosis. supporting_text: RNA interference studies in S2 cells indicated that the D-SCAR homolog D-WASp also participates in phagocytosis notes: >- WASP is restricted to hematopoietic cells, and N-WASP is ubiquitous. Neither has a cached phagocytosis-specific primary paper here, so the mammalian side rests on the review literature (PMID:25319336) and on the Arp2/3 requirement (PMID:10783245). The SCAR/WAVE annoton above is the NPF with loss-of-function evidence in both amoebae and insects. - id: arp23_complex label: Arp2/3 complex participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: Arp2/3 complex term: id: GO:0005885 label: Arp2/3 protein complex active_units: - id: actr2_unit label: ARP2 role: actin-related nucleating subunit participant: selector_type: FAMILY family: preferred_term: ARP2 (actin-related protein 2) notes: >- No PANTHER id is asserted. ARP2 sits inside PTHR11937 (ACTIN), which also holds conventional actins, and PANTHER splits ARP2 across two subfamilies of the same name (human in SF409, amoebal and nematode in SF37). representative_members: - preferred_term: ACTR2 (human) term: id: UniProtKB:P61160 label: Actin-related protein 2 - preferred_term: arpB (Dictyostelium) term: id: UniProtKB:O96621 label: Actin-related protein 2 - id: actr3_unit label: ARP3 role: actin-related nucleating subunit participant: selector_type: FAMILY family: preferred_term: ARP3 (actin-related protein 3) notes: >- No PANTHER id is asserted, for the same reason as ARP2 (human in PTHR11937:SF175, amoebal and fly in SF31). representative_members: - preferred_term: ACTR3 (human) term: id: UniProtKB:P61158 label: Actin-related protein 3 - preferred_term: arpC (Dictyostelium) term: id: UniProtKB:P42528 label: Actin-related protein 3 function: preferred_term: actin filament binding term: id: GO:0051015 label: actin filament binding processes: - preferred_term: Arp2/3 complex-mediated actin nucleation term: id: GO:0034314 label: Arp2/3 complex-mediated actin nucleation locations: - preferred_term: phagocytic cup term: id: GO:0001891 label: phagocytic cup role_description: >- Binds the side of an existing filament and nucleates a branch, building the dendritic actin network that pushes pseudopods out. evidence: - source_id: PMID:10783245 title: Involvement of the Arp2/3 complex in phagocytosis mediated by FcgammaR or CR3. statement: The Arp2/3 complex is involved in both Fc-gamma receptor and CR3 phagocytosis (title-level citation; no abstract cached). - source_id: PMID:11807934 title: Dynamics of the Dictyostelium Arp2/3 complex in endocytosis, cytokinesis, and chemotaxis. statement: In Dictyostelium the Arp2/3 complex is recruited within seconds to sites of phagocytosis. supporting_text: in phagocytosis, macropinocytosis, and chemotaxis the complex is recruited within seconds to sites where actin polymerization is induced - source_id: PMID:16950926 title: RacG regulates morphology, phagocytosis, and chemotaxis. statement: In a Dictyostelium cell-free system, a phagocytic-cup Rac GTPase drives actin polymerization through Arp2/3. supporting_text: In a cell-free system, RacG stimulates actin polymerization through the Arp2/3 complex. - order: 4 role: phagocytic cup closure and internalization node: id: phagocytic_cup_closure label: Pseudopod extension completion and phagocytic cup closure module_type: BIOLOGICAL_PROCESS description: >- Class I PI3K turns over PI(4,5)P2 at the cup base, which ends actin polymerization. Dynamin is recruited to the forming phagosome. Both are needed for pseudopods to finish extending and for the cup to seal into a nascent phagosome. Blocking either arrests uptake at the same stage, after actin-cup formation. annotons: - id: class_i_pi3k label: Class I PI3K catalytic subunit participant: selector_type: FAMILY family: preferred_term: class I PI3K catalytic subunits notes: >- No PANTHER id is asserted. PTHR10048 (PHOSPHATIDYLINOSITOL KINASE) also contains PI4-kinases and the class III VPS34 that acts in phagosome maturation, and each class I isoform has its own subfamily. PIK3CD is the leukocyte-enriched member; PIK3CA and PIK3CB contribute depending on cell type. representative_members: - preferred_term: PIK3CD (human) term: id: UniProtKB:O00329 label: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit delta isoform - preferred_term: PIK3CA (human) term: id: UniProtKB:P42336 label: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform - preferred_term: PIK3CB (human) term: id: UniProtKB:P42338 label: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit beta isoform function: preferred_term: 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity term: id: GO:0046934 label: 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity locations: - preferred_term: phagocytic cup term: id: GO:0001891 label: phagocytic cup role_description: >- Makes PI(3,4,5)P3 in the nascent phagocytic cup. This is needed for optimal phagocytosis but not for later phagosome maturation. evidence: - source_id: PMID:11581283 title: Distinct roles of class I and class III phosphatidylinositol 3-kinases in phagosome formation and maturation. statement: Class I PI3K products appear in the nascent cup, and class I PI3K is required for optimal phagocytosis but not maturation. supporting_text: optimal phagocytosis, but not maturation, requires this type of enzyme - source_id: PMID:9314552 title: A critical role for Syk in signal transduction and phagocytosis mediated by Fcgamma receptors on macrophages. statement: PI3K inhibitors block Fc-gamma receptor phagocytosis after actin-cup formation. supporting_text: inhibitors of phosphatidylinositol 3-kinase also blocked FcgammaR-mediated phagocytosis at this stage - source_id: file:genes/human/PIK3CD/PIK3CD-ai-review.yaml title: PIK3CD gene review statement: The PIK3CD review gives 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934) as the core MF. - source_id: PMID:15572406 title: In vivo analysis of 3-phosphoinositide dynamics during Dictyostelium phagocytosis and chemotaxis. statement: >- In Dictyostelium the class I PI3K product PI(3,4,5)P3 rises transiently at engulfment sites. This shows the same lipid step in amoebae but is not loss-of-function evidence. supporting_text: During phagocytosis and macropinocytosis PtdIns(3,4,5)P3 levels transiently increased at sites of engulfment notes: >- The requirement for class I PI3K at cup closure is shown in mammalian macrophages. Amoebal representatives are not listed because a phagocytosis defect in Dictyostelium pikA/pikB mutants was not found in the literature reviewed here. - id: dynamin_cup_closure label: Dynamin GTPase at the forming phagosome participant: selector_type: FAMILY family: preferred_term: dynamin-2 subfamily term: id: PANTHER:PTHR11566:SF23 label: DYNAMIN-2 representative_members: - preferred_term: DNM2 (human) term: id: UniProtKB:P50570 label: Dynamin-2 ancestral_nodes: - preferred_term: PAINT node PTN000170013 for dynamin-family GTPases term: id: PANTHER:PTN000170013 label: PTN000170013 description: >- Local PAINT IBD node in PTHR11566 propagating F:GO:0003924 GTPase activity. DNM2 (P50570) is among the seeds. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of GTPase activity from PAINT node PTN000170013 in PTHR11566. function: preferred_term: GTPase activity term: id: GO:0003924 label: GTPase activity locations: - preferred_term: phagocytic cup term: id: GO:0001891 label: phagocytic cup role_description: >- Collects on early phagosomes in a PI3K-dependent way. It is needed for membrane extension around the particle and is thought to help deliver focal membrane and seal the phagosome. evidence: - source_id: PMID:10601359 title: Dynamin 2 is required for phagocytosis in macrophages. statement: Dominant-negative dynamin 2 blocks internalization at the membrane-extension stage, and PI3K inhibition prevents dynamin recruitment. supporting_text: significantly inhibits particle internalization at the stage of membrane extension around the particle - source_id: PMID:9880338 title: Disruption of a dynamin homologue affects endocytosis, organelle morphology, and cytokinesis in Dictyostelium discoideum. statement: Dictyostelium dynamin A acts on endo-lysosomal membranes and not at the plasma membrane, which limits this step to the animal evidence. supporting_text: dynamin A is likely to function in membrane trafficking processes along the endo-lysosomal pathway of D. discoideum but not at the plasma membrane notes: >- Grounded on the vertebrate dynamin-2 subfamily because the evidence for a role at cup closure is from mammalian macrophages. Nematode DYN-1 acts mainly in phagosome maturation, and Dictyostelium dynamin A works on endo-lysosomal membranes rather than the plasma membrane. Whether any dynamin closes the phagocytic cup in amoebae is open. connections: - source: particle_recognition target: rho_gtpase_activation connection_type: CAUSES description: >- Clustered phagocytic receptors signal (through ITAM/SYK, CRK/DOCK/ELMO, or CED-6/GULP) to activate Rho-family GTPases at the contact site. - source: rho_gtpase_activation target: phagocytic_actin_polymerization connection_type: CAUSES description: GTP-bound Cdc42/Rac recruit and activate WASP-family NPFs and the Arp2/3 complex. - source: phagocytic_actin_polymerization target: phagocytic_cup_closure connection_type: PRECEDES description: >- Pseudopod extension comes before PI3K- and dynamin-dependent cup closure. SYK loss, PI3K inhibition and dominant-negative dynamin 2 all arrest uptake after actin-cup formation. knowledge_gaps: - gap_statement: >- The ligand that CED-1 recognizes on apoptotic cells, and so whether CED-1/MEGF10 has a direct ligand-binding molecular function, was not known when the C. elegans routes were defined. boundary: >- CED-1 is an engulfing-cell transmembrane receptor that clusters around corpses, and its tail motifs signal to CED-6. For mammalian MEGF10, high- affinity binding to the bridging eat-me signal C1q has been shown (PMID:27170117). The annoton now uses scavenger receptor activity, which the MEGF10 IDA and PAINT node PTN009076277 support. Drosophila Draper, a member of the same family, binds phosphatidylserine directly in solid-phase and surface plasmon resonance assays (PMID:23420848). Whether CED-1 and MEGF10 also bind phosphatidylserine directly is still open. gap_kind: - BIOLOGY dark_aspect: RESIDUAL_SUBGAP status: NARROWING significance: >- A direct phosphatidylserine-binding activity would show whether the receptor reads the eat-me signal itself or only through bridging molecules. resolution: >- Test direct binding of the CED-1 and MEGF10 ectodomains to phosphatidylserine with the solid-phase and surface plasmon resonance assays used for Draper. provenance: - reference_id: PMID:15744306 supporting_text: probably recognizes an unknown ligand on the apoptotic cell - reference_id: PMID:23420848 supporting_text: Draper is a phosphatidylserine-binding receptor for phagocytosis - gap_statement: >- How the CED-1/CED-6 route connects to actin remodeling, and which effectors sit between CED-6/GULP and the actin cytoskeleton, is unresolved. boundary: >- CED-1, CED-6 and CED-7 are needed for actin reorganization around the corpse, and the route converges with CED-2/5/12 on CED-10/Rac. gap_kind: - BIOLOGY dark_aspect: RESIDUAL_SUBGAP status: OPEN significance: Without this link there is no causal connection from the CED-6/GULP annoton to the Rho-GTPase part. resolution: Identify direct CED-6/GULP effectors and test whether they activate CED-10/Rac or act on actin independently. provenance: - reference_id: PMID:15744306 supporting_text: Molecular understanding of how the second pathway promotes engulfment of the apoptotic cell is lacking. - gap_statement: >- The molecular function of the ABC transporter CED-7 (ABCA1/ABCA7 in mammals) in engulfment is unknown, so it is not modelled as an annoton. boundary: >- CED-7 is a plasma-membrane ABC transporter that acts in both dying and engulfing cells and is needed for CED-1 to cluster around corpses. Genetically, with TTR-52 it promotes PS efflux from apoptotic cells in extracellular vesicles, but no transport assay has identified what the protein itself moves (see the ced-7 review). gap_kind: - BIOLOGY dark_aspect: MF_DARK status: OPEN significance: CED-7 is a core genetic component of the CED-1 route but has no assignable activity in this module. resolution: Find the CED-7 transport substrate and test whether its transport activity is needed for corpse recognition. provenance: - reference_id: PMID:9635425 supporting_text: We propose that CED-7 functions to translocate molecules that mediate homotypic adhesion - reference_id: PMID:22727702 supporting_text: CED-7 and TTR-52 may promote the efflux of PS from apoptotic cells through the generation of extracellular PS vesicles - gap_statement: >- It is not known whether the ELMO-DOCK Rac GEF takes part in phagocytosis by amoebae, or which GEF activates Rac at the amoebal phagocytic cup. boundary: >- DOCK GEF activity is placed at a eukaryote-level PAINT node, and Dictyostelium DockD binds an ELMO protein and acts on Rac in cell motility. The amoebal ELMO studied for phagocytosis, ElmoA, restrains uptake instead of promoting it. gap_kind: - BIOLOGY dark_aspect: RESIDUAL_SUBGAP status: OPEN significance: >- This decides whether the CRK/DOCK/ELMO arm of the module is eukaryote-wide or an animal addition to an older Rac-to-actin core. resolution: >- Measure particle uptake in Dictyostelium dock and elmo single and multiple mutants, and test which Rac GEFs are active at the phagocytic cup. provenance: - reference_id: PMID:18854143 supporting_text: Cells lacking ElmoA display an elevated rate of phagocytosis - reference_id: PMID:19037099 supporting_text: DdELMO1 is associated with DockD and that Rac1A and RacC are possible in vivo DockD substrates - gap_statement: >- Whether Dictyostelium SibA and the CED-1/Draper/MEGF10 receptors share an ancestral engulfment-receptor function is unknown. boundary: >- PANTHER classifies SibA in the same subfamily as ced-1 and Draper, and SibA is a seed of PAINT node PTN009076277, where it seeds the plasma membrane annotation; the scavenger receptor activity annotation there is seeded by CED-1 and MEGF10 only. SibA is needed for amoebae to adhere to phagocytic particles, but no ligand of SibA has been identified. gap_kind: - BIOLOGY dark_aspect: MF_DARK status: OPEN significance: >- A shared function would make the CED-1/Draper/MEGF10 receptor family a eukaryote-wide part of particle recognition rather than a bilaterian one. resolution: >- Identify what the SibA ectodomain binds on bacteria or beads, and test whether SibA rescues engulfment by ced-1 or drpr mutant cells. provenance: - reference_id: PMID:16699495 supporting_text: genetic inactivation of SIBA affects adhesion to phagocytic particles