id: MODULE:phagosome_maturation title: Phagosome maturation description: >- Phagosome maturation turns the nascent phagosome, which has no microbicidal or degradative activity, into a phagolysosome. It does so through an ordered series of fusion and fission events with endocytic and lysosomal compartments. The sealed phagosome first recruits active Rab5, and the class III PI3K VPS34 makes PI(3)P on its membrane. PIKfyve converts part of this PI(3)P to PI(3,5)P2. The Mon1-Ccz1 complex, a Rab5 effector and Rab7 GEF, then hands the vacuole over to Rab7. Rab7 and the HOPS tethering complex drive fusion with late endosomes and lysosomes, and the V-ATPase delivered by these fusions acidifies the lumen. This core machinery is shared by eukaryotes and works the same way in amoebae that eat bacteria, in nematode and fly cells that clear apoptotic corpses, and in mammalian macrophages. Animals add lineage-specific parts: the Rab7 effector RILP and LAMP membrane proteins. In vertebrate professional phagocytes, the NOX2 NADPH oxidase also assembles on the phagosomal membrane and produces superoxide into the lumen. status: DRAFT scope: ABSTRACT references: - id: PMID:22560866 title: How nascent phagosomes mature to become phagolysosomes. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- PubMed-verified review (Fairn & Grinstein 2012). Supports the module boundary and the sequential-fusion model. - id: PMID:18813294 title: "Phagosome maturation: going through the acid test." reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- PubMed-verified review (Kinchen & Ravichandran 2008); full text cached. Source for V-ATPase delivery and for HOPS acting downstream of RAB-7 recruitment in C. elegans. - id: PMID:18425118 title: A pathway for phagosome maturation during engulfment of apoptotic cells. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Europe PMC-verified; full text cached (Kinchen et al. 2008). C. elegans RNAi and mutants: RAB-5 then RAB-7 on corpse phagosomes, VPS-34 and DYN-1 needed for RAB-5 recruitment, HOPS knockdown arrests phagosomes at the RAB-7 stage. - 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. VPS34 makes PI(3)P on the sealed phagosome and is required for phagolysosome formation. - id: PMID:20305638 title: Identification of two evolutionarily conserved genes regulating processing of engulfed apoptotic cells. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- PubMed-verified; full text cached. SAND-1/Mon1 and CCZ-1 are needed for the RAB-5 to RAB-7 transition on apoptotic-cell phagosomes in worms and mammals. - id: PMID:18351800 title: Phagocytic receptor CED-1 initiates a signaling pathway for degrading engulfed apoptotic cells. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- PubMed-verified; full text cached. Gives the order CED-1, DYN-1, PI(3)P, RAB-7 on C. elegans phagosomes, and shows that RAB-7 is needed for lysosome recruitment and fusion. - id: PMID:12944476 title: "Phagosomes fuse with late endosomes and/or lysosomes by extension of membrane protrusions along microtubules: role of Rab7 and RILP." reference_review: relevance: HIGH correctness: VERIFIED review_notes: PubMed-verified; Rab7 and its effector RILP are needed for phagosome fusion with late endosomes and lysosomes. - id: PMID:17245426 title: LAMP proteins are required for fusion of lysosomes with phagosomes. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- PubMed-verified. LAMP-1/LAMP-2 double deficiency in mouse cells stops maturation after the Rab5/PI(3)P stage. The molecular basis is attributed to impaired motility rather than to a defined activity. - id: PMID:7719350 title: Mouse model of X-linked chronic granulomatous disease, an inherited defect in phagocyte superoxide production. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- PubMed-verified. gp91phox (CYBB/NOX2) null mice lack phagocyte superoxide production and are more susceptible to infection. - id: PMID:11559753 title: Rab7 regulates phagosome maturation in Dictyostelium. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Europe PMC-verified; abstract only (Rupper et al. 2001). Dominant negative Rab7 in Dictyostelium blocks delivery of lysosomal membrane proteins and hydrolases to phagosomes. - id: PMID:30730983 title: PIKfyve/Fab1 is required for efficient V-ATPase and hydrolase delivery to phagosomes, phagosomal killing, and restriction of Legionella infection. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Europe PMC-verified; full text cached (Buckley et al. 2019). PIKfyve knockout in Dictyostelium (DDB_G0279149) blocks V-ATPase and protease delivery to phagosomes and phagosome acidification. - id: PMID:41852341 title: PIKfyve is required for efficient phagosomal Rab7 acquisition and the delivery and fusion of early macropinosomes to phagosomes. reference_review: relevance: HIGH correctness: VERIFIED review_notes: >- Europe PMC-verified; full text cached (Vines et al. 2026). In Dictyostelium, Rab5A comes and goes normally on phagosomes of PIKfyve knockouts, but Rab7 acquisition by fusion fails. - id: PMID:22008230 title: Dynamin A, Myosin IB and Abp1 couple phagosome maturation to F-actin binding. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Europe PMC-verified; abstract only (Gopaldass et al. 2012). dymA knockout in Dictyostelium impairs phagosome acidification. - id: PMID:27170354 title: Dictyostelium EHD associates with Dynamin and participates in phagosome maturation. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Europe PMC-verified; abstract only (Gueho et al. 2016). dymA and ehd knockouts have independent phagosome maturation defects. - id: PMID:11956322 title: Altered expression of the 100 kDa subunit of the Dictyostelium vacuolar proton pump impairs enzyme assembly, endocytic function and cytosolic pH regulation. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Europe PMC-verified; abstract only (Liu et al. 2002). Lowering VatM (V0 subunit a) mislocalises the V1 A subunit and slows phagocytosis and endosomal transit. Phagosome acidification was not measured directly. - id: PMID:20052281 title: Retrieval of the vacuolar H-ATPase from phagosomes revealed by live cell imaging. reference_review: relevance: MEDIUM correctness: VERIFIED review_notes: >- Europe PMC-verified; full text cached (Clarke et al. 2010). VatM-GFP imaging of V-ATPase delivery to and retrieval from Dictyostelium phagosomes. - id: PMID:21606208 title: Actin polymerization driven by WASH causes V-ATPase retrieval and vesicle neutralization before exocytosis. reference_review: relevance: LOW correctness: VERIFIED review_notes: >- Europe PMC-verified; full text cached (Carnell et al. 2011). WASH retrieves V-ATPase from Dictyostelium phagosomes before exocytosis. Cited only to mark the module boundary; this step belongs to phagosome resolution and is not modelled here. evidence: - source_id: GO:0090382 title: phagosome maturation statement: >- The module is grounded in the GO process for phagosome maturation. Its fusion and acidification parts are grounded in the child processes phagosome-lysosome fusion (GO:0090385) and phagosome acidification (GO:0090383). - source_id: PMID:22560866 title: How nascent phagosomes mature to become phagolysosomes. statement: Maturation is an ordered series of fusions that ends in a degradative phagolysosome. supporting_text: Maturation entails orderly sequential fusion of the phagosomal vacuole with specialized endocytic and secretory compartments. - source_id: PMID:18351800 title: Phagocytic receptor CED-1 initiates a signaling pathway for degrading engulfed apoptotic cells. statement: >- Time-lapse imaging in C. elegans gives the order of events on the phagosome that the parts of this module follow. supporting_text: sequential enrichment on phagocytic membranes of phagocytic receptor cell death abnormal 1 - source_id: PMID:30730983 title: PIKfyve/Fab1 is required for efficient V-ATPase and hydrolase delivery to phagosomes, phagosomal killing, and restriction of Legionella infection. statement: >- Dictyostelium is used as a model phagocyte for phagosome maturation, so the module applies to amoebae as well as animals. supporting_text: >- Here, we analyse the role of the phosphoinositide (PI) 5-kinase PIKfyve in phagosome maturation and killing, using the amoeba and model phagocyte Dictyostelium discoideum. - source_id: file:modules/phagocytic_engulfment.yaml title: "Module: Phagocytic engulfment" statement: Sibling module. It supplies the sealed nascent phagosome that this module matures. notes: >- Boundary: this module starts with the sealed nascent phagosome and ends with a degradative phagolysosome. Excluded: particle recognition and engulfment (MODULE:phagocytic_engulfment); hydrolases and cargo export (MODULE:phagolysosomal_cargo_degradation); MHC class II antigen processing on phagosomes; LC3-associated phagocytosis; pathogen subversion of maturation; and phagosome resolution. Resolution includes the WASH-driven retrieval of V-ATPase and reneutralisation before exocytosis in Dictyostelium (PMID:21606208), and the vacuolin and LvsB steps of the amoebal post-lysosomal stage. Taxon scope: the core parts (Rab5, VPS34, dynamin, PIKfyve, Mon1-Ccz1, Rab7, HOPS, V-ATPase) are grounded on PANTHER families with members from mammals, C. elegans, Drosophila, Dictyostelium and, for orientation, the yeast vacuole homologs. Loss-of-function evidence comes from mouse and human cells, C. elegans and Dictyostelium. RILP and LAMP-1/LAMP-2 are animal-specific annotons and NOX2 is an optional vertebrate part. Family grounding follows PANTHER's own classification files. Where it differs from the UniProt PANTHER cross-reference the difference is noted on the family. RAB5 was previously left as a human gene product because its UniProt cross-reference (PTHR47978) has no PANTHER name; PANTHER's classification puts the Rab5 orthologs in PTHR24073. module: id: phagosome_maturation label: Phagosome maturation module_type: ORGANELLE_LIFECYCLE concepts: - preferred_term: phagosome maturation term: id: GO:0090382 label: phagosome maturation context: taxa: - preferred_term: Eukaryota term: id: NCBITaxon:2759 label: Eukaryota notes: >- The Rab5/Rab7, VPS34, PIKfyve, Mon1-Ccz1, HOPS and V-ATPase machinery is found across eukaryotes, and phagosome maturation with these parts is shown in Dictyostelium as well as in animals. RILP and LAMPs are animal-specific, and NOX2 is specific to vertebrate professional phagocytes. cell_types: - preferred_term: phagocyte term: id: CL:0000234 label: phagocyte cellular_components: - preferred_term: phagocytic vesicle term: id: GO:0045335 label: phagocytic vesicle parts: - order: 1 role: early phagosome (Rab5/PI(3)P stage) node: id: early_phagosome_stage label: Early phagosome Rab5 and PI(3)P stage module_type: BIOLOGICAL_PROCESS description: >- Soon after sealing, the phagosome acquires active Rab5. Rab5 recruits the class III PI3K VPS34, which makes a short-lived PI(3)P pool on the phagosomal membrane. Dynamin is also enriched on nascent phagosomes: in C. elegans DYN-1 sets how quickly PI(3)P and RAB-7 appear, and in Dictyostelium dynamin A is needed for normal acidification. annotons: - id: rab5_gtpase label: RAB5 GTPase on early phagosomes participant: selector_type: FAMILY family: preferred_term: Rab5 GTPase term: id: PANTHER:PTHR24073:SF858 label: DRAB5 representative_members: - preferred_term: rab-5 (C. elegans) term: id: UniProtKB:P91857 label: small monomeric GTPase - preferred_term: Rab5 (D. melanogaster) term: id: UniProtKB:Q9V3I2 label: Ras-related protein Rab5 - preferred_term: rab5A (D. discoideum) term: id: UniProtKB:Q86JP3 label: Ras-related protein Rab-5A - preferred_term: VPS21 (S. cerevisiae) term: id: UniProtKB:P36017 label: Vacuolar protein sorting-associated protein 21 ancestral_nodes: - preferred_term: PAINT node PTN000634566 for Rab5 term: id: PANTHER:PTN000634566 label: PTN000634566 description: >- Eukaryote-level PAINT IBD node (taxon:2759) in PTHR24073 propagating C:GO:0005768 endosome. Human RAB5A (UniProtKB:P20339), C. elegans rab-5 (WB:WBGene00004268), Drosophila Rab5 (FB:FBgn0014010), Dictyostelium rab5A (dictyBase:DDB_G0271984) and yeast VPS21 (SGD:S000005615) are among the seeds, so the node spans the vertebrate RAB5 subfamilies and SF858. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of endosome location from PAINT node PTN000634566 in PTHR24073. notes: >- PANTHER's classification puts the invertebrate, amoebal and yeast Rab5 orthologs in PTHR24073:SF858 and the vertebrate paralogs in sister subfamilies (RAB5A SF1129, RAB5B SF555, RAB5C SF366), so human RAB5A (UniProtKB:P20339) is not listed as a member. UniProt cross-references all of these to PTHR47978, which has no PANTHER name. function: preferred_term: GTPase activity term: id: GO:0003924 label: GTPase activity locations: - preferred_term: phagocytic vesicle membrane term: id: GO:0030670 label: phagocytic vesicle membrane role_description: >- Marks the early phagosome. In its GTP-bound form it recruits VPS34 and the Mon1-Ccz1 complex. evidence: - source_id: PMID:18425118 title: A pathway for phagosome maturation during engulfment of apoptotic cells. statement: In C. elegans, RAB-5 is needed for corpse degradation and for VPS-34 activity on phagosomes. supporting_text: suggesting that RAB-5 is required for VPS-34 activity - source_id: PMID:20305638 title: Identification of two evolutionarily conserved genes regulating processing of engulfed apoptotic cells. statement: Phagosomes in sand-1 or ccz-1 mutants still recruit RAB-5 but do not reach the RAB-7 stage. supporting_text: the phagosomes recruit the small GTPase RAB-5 but fail to progress to the subsequent RAB-7(+) stage - source_id: PMID:41852341 title: PIKfyve is required for efficient phagosomal Rab7 acquisition and the delivery and fusion of early macropinosomes to phagosomes. statement: In Dictyostelium, Rab5A is recruited to new phagosomes and then removed. supporting_text: RFP–Rab5A was further recruited to phagosomes following internalisation before its removal in the following minutes. - id: vps34_class_iii_pi3k label: VPS34 class III PI3K participant: selector_type: FAMILY family: preferred_term: class III PI3K VPS34 term: id: PANTHER:PTHR10048:SF7 label: PHOSPHATIDYLINOSITOL 3-KINASE CATALYTIC SUBUNIT TYPE 3 representative_members: - preferred_term: PIK3C3 (human) term: id: UniProtKB:Q8NEB9 label: Phosphatidylinositol 3-kinase catalytic subunit type 3 - preferred_term: vps-34 (C. elegans) term: id: UniProtKB:Q9TXI7 label: Phosphatidylinositol 3-kinase catalytic subunit type 3 - preferred_term: pikE (D. discoideum) term: id: UniProtKB:P54676 label: Phosphatidylinositol 3-kinase VPS34-like - preferred_term: VPS34 (S. cerevisiae) term: id: UniProtKB:P22543 label: Phosphatidylinositol 3-kinase VPS34 ancestral_nodes: - preferred_term: PAINT node PTN000005955 for VPS34 term: id: PANTHER:PTN000005955 label: PTN000005955 description: >- Local PAINT IBD node in PTHR10048 (taxon:2759) propagating F:GO:0016303 1-phosphatidylinositol-3-kinase activity. PIK3C3 (Q8NEB9), C. elegans vps-34 (WB:WBGene00006932), Drosophila Pi3K59F (FB:FBgn0015277) and yeast VPS34 (SGD:S000004230) are among the seeds. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of 1-phosphatidylinositol-3-kinase activity from PAINT node PTN000005955 in PTHR10048. function: preferred_term: 1-phosphatidylinositol-3-kinase activity term: id: GO:0016303 label: 1-phosphatidylinositol-3-kinase activity locations: - preferred_term: phagocytic vesicle membrane term: id: GO:0030670 label: phagocytic vesicle membrane role_description: >- Makes PI(3)P on the sealed phagosome. PI(3)P recruits FYVE/PX effectors and is needed for phagolysosome formation. evidence: - source_id: PMID:11581283 title: Distinct roles of class I and class III phosphatidylinositol 3-kinases in phagosome formation and maturation. statement: VPS34 makes phagosomal PI(3)P and is essential for phagolysosome formation. supporting_text: The class III PI 3-kinase VPS34 was found to be responsible for PI(3)P synthesis and essential for phagolysosome formation. - source_id: PMID:18425118 title: A pathway for phagosome maturation during engulfment of apoptotic cells. statement: In C. elegans, loss of vps-34 or dyn-1 leaves engulfed corpses undegraded in phagosomes that fail to recruit RAB-5. supporting_text: In-depth analysis of two candidate genes, vps-34 and dyn-1/dynamin, showed accumulation of internalized, but undegraded corpses within abnormal phagosomes that are defective in RAB-5 recruitment. - source_id: file:genes/human/PIK3C3/PIK3C3-ai-review.yaml title: PIK3C3 gene review statement: The PIK3C3 review gives 1-phosphatidylinositol-3-kinase activity (GO:0016303) as the core MF. notes: >- The Dictyostelium VPS34 ortholog pikE is listed as a family member only; no phagosome loss-of-function study of pikE was found. - id: dyn1_phagosomal_dynamin label: Dynamin on nascent phagosomes participant: selector_type: FAMILY family: preferred_term: dynamin term: id: PANTHER:PTHR11566 label: DYNAMIN representative_members: - preferred_term: dyn-1 (C. elegans) term: id: UniProtKB:P39055 label: Dynamin - preferred_term: dymA (D. discoideum) term: id: UniProtKB:Q94464 label: Dynamin-A ancestral_nodes: - preferred_term: PAINT node PTN000170013 for dynamin term: id: PANTHER:PTN000170013 label: PTN000170013 description: >- Local PAINT IBD node in PTHR11566 propagating F:GO:0003924 GTPase activity. Human DNM2 (UniProtKB:P50570), C. elegans dyn-1 (WB:WBGene00001130) and Dictyostelium dymA (dictyBase:DDB_G0277849) are among the seeds. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of GTPase activity from PAINT node PTN000170013 in PTHR11566. notes: >- The two members sit in different subfamilies: dyn-1 in PTHR11566:SF212 (classical dynamin) and dymA in PTHR11566:SF21 (dynamin-related protein 1 group), so the family is used. function: preferred_term: GTPase activity term: id: GO:0003924 label: GTPase activity processes: - preferred_term: phagosome maturation term: id: GO:0090382 label: phagosome maturation locations: - preferred_term: phagocytic vesicle membrane term: id: GO:0030670 label: phagocytic vesicle membrane role_description: >- Recruited to nascent phagosomes. In C. elegans DYN-1 acts downstream of CED-1/CED-6 and controls how fast PI(3)P and RAB-7 build up on phagosomes containing apoptotic cells. In Dictyostelium dynamin A is needed for normal phagosome acidification. evidence: - source_id: PMID:18351800 title: Phagocytic receptor CED-1 initiates a signaling pathway for degrading engulfed apoptotic cells. statement: The CED-1, CED-6 and DYN-1 route controls PI(3)P and RAB-7 enrichment and phagolysosome formation. supporting_text: controls the rate of enrichment of PI(3)P and RAB-7 on phagosomal surfaces and the formation of phagolysosomes - source_id: PMID:22008230 title: Dynamin A, Myosin IB and Abp1 couple phagosome maturation to F-actin binding. statement: In Dictyostelium, dymA knockout impairs phagosome acidification. supporting_text: Knockout of dymA impairs phagosome acidification - source_id: PMID:27170354 title: Dictyostelium EHD associates with Dynamin and participates in phagosome maturation. statement: dymA and EHD knockouts have separate phagosome maturation defects. supporting_text: DymA and EHD play non-redundant and independent functions in phagosome maturation - source_id: file:genes/worm/dyn-1/dyn-1-ai-review.yaml title: dyn-1 gene review statement: >- The dyn-1 review gives GTPase activity in phagosome maturation involved in apoptotic cell clearance (GO:0090386) as a core function. - order: 2 role: Rab5-to-Rab7 conversion node: id: rab5_to_rab7_conversion label: Mon1-Ccz1-mediated Rab5-to-Rab7 conversion module_type: REGULATORY_STEP description: >- The Mon1-Ccz1 complex binds GTP-Rab5 and activates Rab7. This hands the phagosome over from the Rab5 to the Rab7 stage. In sand-1 or ccz-1 mutant worms, engulfed corpses stay in RAB-5-positive phagosomes. PIKfyve, which makes PI(3,5)P2 from PI(3)P, is also needed for phagosomes to acquire Rab7: in Dictyostelium PIKfyve knockouts Rab5 dynamics are normal but little Rab7 or V-ATPase arrives. annotons: - id: mon1_ccz1_rab7_gef label: Mon1-Ccz1 Rab7 GEF complex participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: Mon1-Ccz1 complex term: id: GO:0035658 label: Mon1-Ccz1 complex active_units: - id: mon1_unit label: MON1/SAND-1 role: Rab5 effector subunit of the Rab7 GEF participant: selector_type: FAMILY family: preferred_term: MON1/SAND-1 term: id: PANTHER:PTHR13027 label: SAND PROTEIN-RELATED representative_members: - preferred_term: MON1A (human) term: id: UniProtKB:Q86VX9 label: Vacuolar fusion protein MON1 homolog A - preferred_term: sand-1 (C. elegans) term: id: UniProtKB:Q9BI89 label: Vacuolar fusion protein MON1 homolog - preferred_term: Mon1 (D. melanogaster) term: id: UniProtKB:Q9VR38 label: Vacuolar fusion protein MON1 homolog - preferred_term: mon1 (D. discoideum) term: id: UniProtKB:Q54TG0 label: DUF254 family protein - preferred_term: MON1 (S. cerevisiae) term: id: UniProtKB:P53129 label: Vacuolar fusion protein MON1 ancestral_nodes: - preferred_term: PAINT node PTN000315021 for MON1 term: id: PANTHER:PTN000315021 label: PTN000315021 description: >- Eukaryote-level PAINT IBD node (taxon:2759) in PTHR13027 propagating F:GO:0005085 guanyl-nucleotide exchange factor activity. Drosophila Mon1 (FB:FBgn0031640) and yeast MON1 (SGD:S000003092) are the seeds. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of guanyl-nucleotide exchange factor activity from PAINT node PTN000315021 in PTHR13027. notes: >- Human MON1A is in PTHR13027:SF14 and the other members in SF7, so the family is used. - id: ccz1_unit label: CCZ1/CCZ-1 role: GEF subunit partner participant: selector_type: FAMILY family: preferred_term: CCZ1/CCZ-1 term: id: PANTHER:PTHR13056:SF0 label: VACUOLAR FUSION PROTEIN CCZ1 HOMOLOG-RELATED representative_members: - preferred_term: CCZ1 (human) term: id: UniProtKB:P86791 label: Vacuolar fusion protein CCZ1 homolog - preferred_term: ccz-1 (C. elegans) term: id: UniProtKB:Q9XVL8 label: Vacuolar fusion protein CCZ1 homolog - preferred_term: Ccz1 (D. melanogaster) term: id: UniProtKB:Q9VZL5 label: Vacuolar fusion protein CCZ1 homolog - preferred_term: DDB_G0288589 (D. discoideum) term: id: UniProtKB:Q54IQ5 label: Vacuolar fusion protein CCZ1 homolog - preferred_term: CCZ1 (S. cerevisiae) term: id: UniProtKB:P38273 label: Vacuolar fusion protein CCZ1 ancestral_nodes: - preferred_term: PAINT node PTN000316458 for CCZ1 term: id: PANTHER:PTN000316458 label: PTN000316458 description: >- Eukaryote-level PAINT IBD node (taxon:2759) in PTHR13056 propagating C:GO:0035658 Mon1-Ccz1 complex and F:GO:0005085 guanyl-nucleotide exchange factor activity. Human CCZ1 (P86791), C. elegans ccz-1 (WB:WBGene00010283), Drosophila Ccz1 (FB:FBgn0035470) and yeast CCZ1 (SGD:S000000335) are among the complex seeds. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of Mon1-Ccz1 complex and guanyl-nucleotide exchange factor activity from PAINT node PTN000316458 in PTHR13056. function: preferred_term: guanyl-nucleotide exchange factor activity term: id: GO:0005085 label: guanyl-nucleotide exchange factor activity targets: - preferred_term: RAB7 locations: - preferred_term: phagocytic vesicle membrane term: id: GO:0030670 label: phagocytic vesicle membrane role_description: >- A Rab5 effector that binds and activates Rab7, linking the Rab5 stage to the Rab7 stage. evidence: - source_id: PMID:20305638 title: Identification of two evolutionarily conserved genes regulating processing of engulfed apoptotic cells. statement: Mon1 binds GTP-Rab5, and the Mon1-Ccz1 complex binds Rab7 and affects its activation. supporting_text: a Mon1-Ccz1 complex (but not either protein alone) could bind Rab7 and could also influence Rab7 activation notes: >- The phagosome paper shows that Mon1-Ccz1 binds Rab7 and affects its activation. Direct GEF catalysis was established for the orthologous yeast and fly complexes, which seed the eukaryote-level GEF nodes PTN000315021 and PTN000316458. The Dictyostelium orthologs are listed as family members only; no amoebal loss-of-function study was found. - id: pikfyve_pi35p2 label: PIKfyve makes PI(3,5)P2 on maturing phagosomes participant: selector_type: FAMILY family: preferred_term: PIKfyve/Fab1 phosphoinositide 5-kinase term: id: PANTHER:PTHR45748:SF7 label: 1-PHOSPHATIDYLINOSITOL 3-PHOSPHATE 5-KINASE-RELATED representative_members: - preferred_term: PIKfyve (D. discoideum) term: id: UniProtKB:B0G126 label: 1-phosphatidylinositol 3-phosphate 5-kinase - preferred_term: fab1 (D. melanogaster) term: id: UniProtKB:O96838 label: Putative 1-phosphatidylinositol 3-phosphate 5-kinase - preferred_term: FAB1 (S. cerevisiae) term: id: UniProtKB:P34756 label: 1-phosphatidylinositol 3-phosphate 5-kinase FAB1 ancestral_nodes: - preferred_term: PAINT node PTN000144086 for PIKfyve/Fab1 term: id: PANTHER:PTN000144086 label: PTN000144086 description: >- Eukaryote-level PAINT IBD node (taxon:2759) in PTHR45748 propagating F:GO:0000285 1-phosphatidylinositol-3-phosphate 5-kinase activity (seeds include yeast FAB1 SGD:S000001915 and Drosophila fab1 FB:FBgn0028741) and P:GO:0007033 vacuole organization (seeds include Dictyostelium PIKfyve dictyBase:DDB_G0279149). evidence: - source_id: GO_REF:0000033 statement: IBD propagation of 1-phosphatidylinositol-3-phosphate 5-kinase activity from PAINT node PTN000144086 in PTHR45748. notes: >- PANTHER puts mammalian PIKFYVE (human Q9Y2I7, mouse Q9Z1T6) in a separate family, PTHR46715:SF1, so it is not listed as a member here. PTHR45748:SF7 holds the amoebal, fungal, insect, nematode and Xenopus orthologs. function: preferred_term: 1-phosphatidylinositol-3-phosphate 5-kinase activity term: id: GO:0000285 label: 1-phosphatidylinositol-3-phosphate 5-kinase activity locations: - preferred_term: phagocytic vesicle membrane term: id: GO:0030670 label: phagocytic vesicle membrane role_description: >- Converts phagosomal PI(3)P to PI(3,5)P2. Without it, phagosomes acquire Rab5 normally but do not fuse with the Rab7- and V-ATPase-positive endosomes, so they acquire little Rab7, fail to acidify and digest poorly. evidence: - source_id: PMID:30730983 title: PIKfyve/Fab1 is required for efficient V-ATPase and hydrolase delivery to phagosomes, phagosomal killing, and restriction of Legionella infection. statement: In Dictyostelium, PIKfyve knockout blocks V-ATPase and protease delivery to phagosomes and their acidification. supporting_text: Disruption of PIKfyve inhibited delivery of both the vacuolar V-ATPase and proteases, dramatically reducing the ability of cells to acidify newly formed phagosomes and digest their contents. - source_id: PMID:41852341 title: PIKfyve is required for efficient phagosomal Rab7 acquisition and the delivery and fusion of early macropinosomes to phagosomes. statement: In Dictyostelium, loss of PIKfyve leaves Rab5 dynamics intact but reduces Rab7 acquisition by fusion. supporting_text: although early Rab5 dynamics are unaffected, loss of PIKfyve reduces phagosomal Rab7 acquisition by preventing fusion with a pool of Rab7 and V-ATPase positive endosomes - source_id: PMID:30730983 title: PIKfyve/Fab1 is required for efficient V-ATPase and hydrolase delivery to phagosomes, phagosomal killing, and restriction of Legionella infection. statement: PIKfyve inhibitors also impair phagosome maturation in mammalian macrophages and neutrophils. supporting_text: has allowed researchers to demonstrate the importance of PI(3)P to PI(3,5)P2 conversion for phagosomal maturation in macrophages and neutrophils - order: 3 role: phagosome-lysosome fusion node: id: phagosome_lysosome_fusion label: Rab7-dependent phagosome-lysosome fusion module_type: BIOLOGICAL_PROCESS description: >- Active Rab7 and the HOPS tethering complex drive fusion of the phagosome with late endosomes and lysosomes. In C. elegans, HOPS acts downstream of RAB-7 recruitment. In animals, Rab7 also recruits RILP and the dynein-dynactin motor, which move the phagosome toward the cell center and extend tubules toward late endocytic compartments, and LAMP-1/LAMP-2 are needed for Rab7 recruitment and fusion. concepts: - preferred_term: phagosome-lysosome fusion term: id: GO:0090385 label: phagosome-lysosome fusion annotons: - id: rab7_gtpase label: RAB7 GTPase on late phagosomes participant: selector_type: FAMILY family: preferred_term: Rab7 GTPase term: id: PANTHER:PTHR47981 label: RAB FAMILY representative_members: - preferred_term: RAB7A (human) term: id: UniProtKB:P51149 label: Ras-related protein Rab-7a - preferred_term: rab-7 (C. elegans) term: id: UniProtKB:Q23146 label: Ras-related protein Rab-7a - preferred_term: Rab7 (D. melanogaster) term: id: UniProtKB:O76742 label: Ras-related protein Rab7 - preferred_term: rab7A (D. discoideum) term: id: UniProtKB:P36411 label: Ras-related protein Rab-7a - preferred_term: YPT7 (S. cerevisiae) term: id: UniProtKB:P32939 label: Ypt/Rab-type GTPase YPT7 ancestral_nodes: - preferred_term: PAINT node PTN000635769 for RAB7 term: id: PANTHER:PTN000635769 label: PTN000635769 description: >- Local PAINT IBD node in PTHR47981 propagating P:GO:0090385 phagosome-lysosome fusion (seed UniProtKB:P51149), plus C:GO:0005764 lysosome and C:GO:0005770 late endosome. Dictyostelium rab7A (dictyBase:DDB_G0269236) is among the lysosome seeds. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of phagosome-lysosome fusion from PAINT node PTN000635769 in PTHR47981. - preferred_term: PAINT node PTN001939797 for RAB7 term: id: PANTHER:PTN001939797 label: PTN001939797 description: >- Local PAINT IBD node in PTHR47981 (taxon:2759) propagating F:GO:0003925 G protein activity, P:GO:0007033 vacuole organization and C:GO:0005773 vacuole. P51149, C. elegans rab-7 (WB:WBGene00004271), yeast YPT7 (SGD:S000004460) and Dictyostelium rab7A (dictyBase:DDB_G0269236) are among the seeds. evidence: - source_id: GO_REF:0000033 statement: IBD propagation from PAINT node PTN001939797 in PTHR47981. notes: >- Human RAB7A is in PTHR47981:SF13 and the other members in SF20, so the family is used. function: preferred_term: GTPase activity term: id: GO:0003924 label: GTPase activity processes: - preferred_term: phagosome-lysosome fusion term: id: GO:0090385 label: phagosome-lysosome fusion locations: - preferred_term: phagocytic vesicle membrane term: id: GO:0030670 label: phagocytic vesicle membrane role_description: >- Its recruitment comes before, and is needed for, phagosome fusion with late endosomes and lysosomes and delivery of lysosomal membrane proteins and hydrolases. evidence: - source_id: PMID:12944476 title: "Phagosomes fuse with late endosomes and/or lysosomes by extension of membrane protrusions along microtubules: role of Rab7 and RILP." statement: Rab7 recruitment comes before, and is needed for, phagosome fusion with late endosomes and lysosomes. supporting_text: Rab7 recruitment to phagosomes was found to precede and to be essential for their fusion with late endosomes and/or lysosomes - source_id: PMID:18351800 title: Phagocytic receptor CED-1 initiates a signaling pathway for degrading engulfed apoptotic cells. statement: RAB-7 promotes lysosome recruitment and fusion to apoptotic-cell phagosomes in C. elegans. supporting_text: We further identified an essential role of RAB-7 in promoting the recruitment and fusion of lysosomes to phagosomes. - source_id: PMID:18425118 title: A pathway for phagosome maturation during engulfment of apoptotic cells. statement: In C. elegans, rab-7 knockdown arrests corpse phagosomes at the RAB-5 stage. supporting_text: in rab-7(RNAi) worms, phagosomes containing apoptotic germ cells were arrested at the RAB-5-positive stage - source_id: PMID:11559753 title: Rab7 regulates phagosome maturation in Dictyostelium. statement: In Dictyostelium, dominant negative Rab7 blocks delivery of a lysosomal membrane protein and a glycosidase to phagosomes. supporting_text: LBC phagosomes isolated from cells overexpressing dominant negative (DN) Rab7 contained very low levels of LmpA (lysosomal integral membrane protein) and alpha-mannosidase was not detectable. - source_id: file:genes/human/RAB7A/RAB7A-ai-review.yaml title: RAB7A gene review statement: The RAB7A review gives GTPase activity (GO:0003924) as the core MF. - id: rilp_rab7_effector label: RILP Rab7 effector (vertebrate) participant: selector_type: FAMILY family: preferred_term: RILP term: id: PANTHER:PTHR21502:SF7 label: RAB-INTERACTING LYSOSOMAL PROTEIN representative_members: - preferred_term: RILP (human) term: id: UniProtKB:Q96NA2 label: Rab-interacting lysosomal protein - preferred_term: Rilp (mouse) term: id: UniProtKB:Q5ND29 label: Rab-interacting lysosomal protein function: preferred_term: protein-macromolecule adaptor activity term: id: GO:0030674 label: protein-macromolecule adaptor activity locations: - preferred_term: phagocytic vesicle membrane term: id: GO:0030670 label: phagocytic vesicle membrane role_description: >- Bridges active Rab7 on the phagosome to the dynein-dynactin motor. This drives centripetal movement and the extension of tubules toward late endocytic compartments. evidence: - source_id: PMID:12944476 title: "Phagosomes fuse with late endosomes and/or lysosomes by extension of membrane protrusions along microtubules: role of Rab7 and RILP." statement: RILP bridges Rab7-positive phagosomes to dynein-dynactin. supporting_text: which in turn bridges phagosomes with dynein-dynactin notes: >- Animal-specific. In the local PANTHER files the RILP subfamily (PTHR21502:SF7) has only vertebrate members, and the wider family is named for DZIP1. Phagosomes in amoebae, nematodes and flies are not known to use a RILP ortholog, so this annoton applies to vertebrates. How Rab7 couples phagosomes to motors elsewhere is not modelled. - id: hops_tether label: HOPS tethering complex participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: HOPS complex term: id: GO:0030897 label: HOPS complex active_units: - id: vps41_unit label: VPS41 role: Rab7-interacting HOPS-specific subunit participant: selector_type: FAMILY family: preferred_term: VPS41 term: id: PANTHER:PTHR12616:SF1 label: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 41 HOMOLOG representative_members: - preferred_term: VPS41 (human) term: id: UniProtKB:P49754 label: Vacuolar protein sorting-associated protein 41 homolog - preferred_term: vps-41 (C. elegans) term: id: UniProtKB:Q19954 label: Vacuolar protein sorting-associated protein 41 homolog - preferred_term: lt (D. melanogaster) term: id: UniProtKB:Q7PL76 label: Vacuolar protein sorting-associated protein 41 homolog - preferred_term: vps41 (D. discoideum) term: id: UniProtKB:Q54LI4 label: RING zinc finger-containing protein - preferred_term: VPS41 (S. cerevisiae) term: id: UniProtKB:P38959 label: Vacuolar protein sorting-associated protein 41 ancestral_nodes: - preferred_term: PAINT node PTN000289375 for VPS41 term: id: PANTHER:PTN000289375 label: PTN000289375 description: >- Eukaryote-level PAINT IBD node (taxon:2759) in PTHR12616 propagating C:GO:0030897 HOPS complex and P:GO:0007034 vacuolar transport. Human VPS41 (P49754) is among the seeds. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of HOPS complex from PAINT node PTN000289375 in PTHR12616. - id: vps39_unit label: VPS39 role: HOPS-specific subunit participant: selector_type: FAMILY family: preferred_term: VPS39/VAM6 term: id: PANTHER:PTHR12894:SF49 label: VAM6_VPS39-LIKE PROTEIN representative_members: - preferred_term: VPS39 (human) term: id: UniProtKB:Q96JC1 label: Vam6/Vps39-like protein - preferred_term: vps-39 (C. elegans) term: id: UniProtKB:Q1ZXS5 label: Vacuolar protein sorting-associated protein 39 homolog - preferred_term: Vps39 (D. melanogaster) term: id: UniProtKB:Q9VEA2 label: Vacuolar protein sorting-associated protein 39 homolog - preferred_term: VAM6 (S. cerevisiae) term: id: UniProtKB:Q07468 label: Vacuolar morphogenesis protein 6 ancestral_nodes: - preferred_term: PAINT node PTN000307050 for VPS39 term: id: PANTHER:PTN000307050 label: PTN000307050 description: >- Opisthokont-level PAINT IBD node (taxon:33154) in PTHR12894 propagating C:GO:0030897 HOPS complex. Human VPS39 (Q96JC1) is among the seeds. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of HOPS complex from PAINT node PTN000307050 in PTHR12894. notes: >- The Dictyostelium vps39 gene product (UniProtKB:B0G127) is classified in PTHR12894:SF33, not SF49, and the wider family (CNH DOMAIN CONTAINING) also holds unrelated CNH-domain proteins, so it is not listed. function: preferred_term: molecular adaptor activity term: id: GO:0060090 label: molecular adaptor activity locations: - preferred_term: phagocytic vesicle membrane term: id: GO:0030670 label: phagocytic vesicle membrane role_description: >- Multisubunit tether that bridges Rab7-positive membranes and promotes SNARE-mediated fusion with lysosomes. evidence: - source_id: PMID:18425118 title: A pathway for phagosome maturation during engulfment of apoptotic cells. statement: In C. elegans, knockdown of HOPS subunits arrests corpse phagosomes at the RAB-7 stage. supporting_text: Here, we show that knockdown of vps-11, vps-16, vps-18, vps-33, vps-39 and vps-41 result in phagosome arrest at the RAB-7(+) stage. - source_id: PMID:18813294 title: "Phagosome maturation: going through the acid test." statement: Genetic studies in C. elegans place HOPS downstream of RAB-7 recruitment on phagosomes. supporting_text: genetic studies in the nematode suggest that this complex instead functions downstream of RAB-7 recruitment during phagosome maturation gocam_associations: - model: gomodel:67b1629100003158 title: RAB39A and RAB2A-induced HOPS-mediated autophagosome-lysosome fusion (Human) description: >- This GO-CAM models HOPS with molecular adaptor activity for autophagosome-lysosome fusion. The same MF is used here for the equivalent phagosome-lysosome fusion step. notes: >- GO has no HOPS-specific tethering MF in common use. Molecular adaptor activity (GO:0060090) follows the GO-CAM convention for this complex. The phagosome evidence is from C. elegans; HOPS has not been tested on Dictyostelium phagosomes. - id: lamp_proteins label: LAMP-1/LAMP-2 (animal) participant: selector_type: FAMILY family: preferred_term: LAMP-1 and LAMP-2 (redundant) term: id: PANTHER:PTHR11506 label: LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN representative_members: - preferred_term: LAMP1 (human) term: id: UniProtKB:P11279 label: Lysosome-associated membrane glycoprotein 1 - preferred_term: LAMP2 (human) term: id: UniProtKB:P13473 label: Lysosome-associated membrane glycoprotein 2 - preferred_term: Lamp1 (mouse) term: id: UniProtKB:P11438 label: Lysosome-associated membrane glycoprotein 1 - preferred_term: Lamp2 (mouse) term: id: UniProtKB:P17047 label: Lysosome-associated membrane glycoprotein 2 ancestral_nodes: - preferred_term: PAINT node PTN000897064 for LAMP term: id: PANTHER:PTN000897064 label: PTN000897064 description: >- Local PAINT IBD node in PTHR11506 propagating C:GO:0005765 lysosomal membrane. Human LAMP1 (P11279) and LAMP2 (P13473) are among the seeds. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of lysosomal membrane from PAINT node PTN000897064 in PTHR11506. notes: >- LAMP1 (PTHR11506:SF27) and LAMP2 (SF6) are in different subfamilies, so the family is used. The family also holds LAMP3, LAMP5, CD68 and invertebrate LAMPs, which have not been tested in phagosome maturation. locations: - preferred_term: lysosomal membrane term: id: GO:0005765 label: lysosomal membrane role_description: >- Lysosomal membrane glycoproteins delivered to phagosomes. Losing both LAMP-1 and LAMP-2 stops maturation before Rab7 recruitment and lysosome fusion. No molecular function is asserted (see knowledge gaps). evidence: - source_id: PMID:17245426 title: LAMP proteins are required for fusion of lysosomes with phagosomes. statement: LAMP-1/LAMP-2 double-deficient mouse phagosomes acquire Rab5 and PI(3)P but do not recruit Rab7 or fuse with lysosomes. supporting_text: failed to recruit Rab7 and did not fuse with lysosomes notes: >- Animal-specific. The evidence is from mouse cells. Amoebae have lysosomal membrane proteins such as LmpA, but these are not LAMP family members. - order: 4 role: phagosome acidification node: id: phagosome_acidification label: V-ATPase-driven phagosome acidification module_type: TRANSPORT_STEP description: >- The plasma membrane that forms the phagosome has no V-ATPase. The pump is delivered by fusion with endosomes as the phagosome matures and pumps protons into the lumen. The low pH activates delivered acid hydrolases and is needed for degradation. concepts: - preferred_term: phagosome acidification term: id: GO:0090383 label: phagosome acidification annotons: - id: v_atpase label: V-type proton ATPase participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: V-ATPase term: id: GO:0033176 label: proton-transporting V-type ATPase complex active_units: - id: atp6v1a_unit label: V1 catalytic subunit A role: ATP-hydrolyzing catalytic subunit of V1 participant: selector_type: FAMILY family: preferred_term: V-ATPase catalytic subunit A term: id: PANTHER:PTHR43607 label: V-TYPE PROTON ATPASE CATALYTIC SUBUNIT A representative_members: - preferred_term: ATP6V1A (human) term: id: UniProtKB:P38606 label: V-type proton ATPase catalytic subunit A - preferred_term: vha-13 (C. elegans) term: id: UniProtKB:Q9XW92 label: V-type proton ATPase catalytic subunit A - preferred_term: vatA (D. discoideum) term: id: UniProtKB:P54647 label: V-type proton ATPase catalytic subunit A - preferred_term: VMA1 (S. cerevisiae) term: id: UniProtKB:P17255 label: V-type proton ATPase catalytic subunit A ancestral_nodes: - preferred_term: PAINT node PTN000389802 for V1 subunit A term: id: PANTHER:PTN000389802 label: PTN000389802 description: >- Eukaryote-level PAINT IBD node (taxon:2759) in PTHR43607 propagating C:GO:0000221 vacuolar proton-transporting V-type ATPase, V1 domain. Human ATP6V1A (P38606) is among the seeds. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of V1 domain location from PAINT node PTN000389802 in PTHR43607. notes: >- Human ATP6V1A is in PTHR43607:SF9 and the other members in SF1, so the family is used. - id: v0a_unit label: V0 subunit a role: proton-translocating transmembrane subunit of V0 participant: selector_type: FAMILY family: preferred_term: V-ATPase subunit a, vacuolar/lysosomal type term: id: PANTHER:PTHR11629:SF63 label: V-TYPE PROTON ATPASE SUBUNIT A representative_members: - preferred_term: vatM (D. discoideum) term: id: UniProtKB:Q54E04 label: Vacuolar proton translocating ATPase 100 kDa subunit - preferred_term: unc-32 (C. elegans) term: id: UniProtKB:P30628 label: V-type proton ATPase 116 kDa subunit a 1 - preferred_term: VPH1 (S. cerevisiae) term: id: UniProtKB:P32563 label: V-type proton ATPase subunit a, vacuolar isoform ancestral_nodes: - preferred_term: PAINT node PTN000179505 for V0 subunit a term: id: PANTHER:PTN000179505 label: PTN000179505 description: >- Local PAINT IBD node in PTHR11629 propagating F:GO:0046961 proton-transporting ATPase activity, rotational mechanism. Dictyostelium vatM (dictyBase:DDB_G0291858) and yeast VPH1 and STV1 are among the seeds. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of proton-transporting ATPase activity, rotational mechanism from PAINT node PTN000179505 in PTHR11629. notes: >- The mammalian a isoforms (ATP6V0A1 SF68, ATP6V0A2 SF22, TCIRG1 SF21, ATP6V0A4 SF26) are in other PTHR11629 subfamilies, and which of them serves the phagosome is not resolved here, so none is listed. function: preferred_term: proton-transporting ATPase activity, rotational mechanism term: id: GO:0046961 label: proton-transporting ATPase activity, rotational mechanism processes: - preferred_term: phagosome acidification term: id: GO:0090383 label: phagosome acidification locations: - preferred_term: phagocytic vesicle membrane term: id: GO:0030670 label: phagocytic vesicle membrane role_description: >- Couples ATP hydrolysis in the V1 domain to proton transport by the V0 domain, acidifying the phagosome lumen. evidence: - source_id: PMID:18813294 title: "Phagosome maturation: going through the acid test." statement: V-ATPases are proton pumps delivered to the phagosome during maturation. supporting_text: V-type (vacuolar) ATPases, proton pumps driven by the hydrolysis of ATP40, are trafficked to the phagosome at relatively late stages - source_id: PMID:20052281 title: Retrieval of the vacuolar H-ATPase from phagosomes revealed by live cell imaging. statement: In Dictyostelium, the V-ATPase reaches the phagosome by fusion with endosomes that carry it. supporting_text: The enzyme is not present in the plasma membrane from which a phagosome is formed, but is rapidly delivered by fusion with endosomes that already bear the V-ATPase in their membranes. - source_id: PMID:11956322 title: Altered expression of the 100 kDa subunit of the Dictyostelium vacuolar proton pump impairs enzyme assembly, endocytic function and cytosolic pH regulation. statement: Lowering Dictyostelium VatM mislocalises the V1 A subunit, showing that subunit a is needed to assemble the pump. supporting_text: the A subunit, a component of the peripheral catalytic domain of the V-ATPase, became mislocalized - source_id: file:genes/human/ATP6V1A/ATP6V1A-ai-review.yaml title: ATP6V1A gene review statement: The ATP6V1A review gives proton-transporting ATPase activity, rotational mechanism (GO:0046961) as the core MF. - order: 5 role: phagosomal superoxide production optional: true node: id: phagosomal_nox2_burst label: NOX2 phagosomal superoxide production module_type: BIOLOGICAL_PROCESS description: >- In vertebrate neutrophils and macrophages, the NOX2 NADPH oxidase assembles on the phagosomal membrane and moves electrons from cytosolic NADPH to oxygen in the lumen, making superoxide for microbial killing. Losing it causes chronic granulomatous disease. context: taxa: - preferred_term: Vertebrata term: id: NCBITaxon:7742 label: Vertebrata cell_types: - preferred_term: neutrophil term: id: CL:0000775 label: neutrophil - preferred_term: macrophage term: id: CL:0000235 label: macrophage annotons: - id: nox2_oxidase label: NOX2 (gp91phox) NADPH oxidase participant: selector_type: FAMILY family: preferred_term: NOX2/CYBB NADPH oxidase term: id: PANTHER:PTHR11972:SF60 label: CYTOCHROME B-245 HEAVY CHAIN representative_members: - preferred_term: CYBB (human) term: id: UniProtKB:P04839 label: NADPH oxidase 2 - preferred_term: Cybb (mouse) term: id: UniProtKB:Q61093 label: NADPH oxidase 2 ancestral_nodes: - preferred_term: PAINT node PTN000239643 for NADPH oxidases term: id: PANTHER:PTN000239643 label: PTN000239643 description: >- Local PAINT IBD node propagating F:GO:0016175 superoxide-generating NAD(P)H oxidase activity and C:GO:0043020 NADPH oxidase complex. CYBB (P04839) is among the seeds. evidence: - source_id: GO_REF:0000033 statement: IBD propagation of superoxide-generating NAD(P)H oxidase activity from PAINT node PTN000239643. function: preferred_term: superoxide-generating NAD(P)H oxidase activity term: id: GO:0016175 label: superoxide-generating NAD(P)H oxidase activity locations: - preferred_term: phagocytic vesicle membrane term: id: GO:0030670 label: phagocytic vesicle membrane role_description: >- Catalytic flavocytochrome b558 subunit of the phagocyte oxidase. It makes superoxide inside the phagosome once the cytosolic phox subunits and Rac have assembled with it. evidence: - source_id: PMID:7719350 title: Mouse model of X-linked chronic granulomatous disease, an inherited defect in phagocyte superoxide production. statement: CYBB-null mice lack phagocyte superoxide production. supporting_text: Affected hemizygous male mice lacked phagocyte superoxide production notes: >- Vertebrate-specific optional part. The CYBB subfamily (PTHR11972:SF60) has only vertebrate members in the local PANTHER files. Other eukaryotes, including Dictyostelium, have NADPH oxidases of the same family, but their role in phagosomal killing is not modelled here. connections: - source: early_phagosome_stage target: rab5_to_rab7_conversion connection_type: PRECEDES description: GTP-Rab5 on the early phagosome recruits the Mon1-Ccz1 complex, and VPS34-made PI(3)P is the substrate for PIKfyve. - source: rab5_to_rab7_conversion target: phagosome_lysosome_fusion connection_type: PRECEDES description: >- Rab7 activation by Mon1-Ccz1 and PIKfyve-dependent Rab7 acquisition are needed for fusion with late endosomes and lysosomes. - source: phagosome_lysosome_fusion target: phagosome_acidification connection_type: PRECEDES description: >- Most V-ATPase reaches the phagosome by fusion with late endocytic compartments, so full acidification depends on the fusion step. An earlier, smaller drop in pH is less well understood. knowledge_gaps: - gap_statement: >- The molecular activity by which LAMP-1/LAMP-2 enable Rab7 recruitment and phagosome-lysosome fusion is unknown. boundary: >- Phagosomes lacking both LAMPs reach the Rab5/PI(3)P stage but do not recruit Rab7 or fuse with lysosomes. The defect is attributed to impaired organelle motility along microtubules. gap_kind: - BIOLOGY dark_aspect: MF_DARK status: OPEN significance: >- LAMPs are needed for this step but cannot be given a molecular function, so the LAMP annoton has no function. resolution: >- Find the LAMP-dependent effector (for example a motor adaptor or a lipid or cholesterol transfer activity) that is missing from LAMP-null phagosomes. provenance: - reference_id: PMID:17245426 supporting_text: We attribute the deficiency to impaired organellar motility along microtubules. - gap_statement: >- The mechanism and molecular basis of early phagosome acidification, before V-ATPase is delivered by fusion, are not well understood. boundary: >- Most phagosomal acidification is done by V-ATPases delivered at later maturation stages. gap_kind: - BIOLOGY dark_aspect: BP_DARK status: OPEN significance: >- The acidification part covers only the V-ATPase component. An earlier contributor, if one exists, is not modelled. resolution: Measure phagosomal pH in the first minutes after sealing while V-ATPase is inhibited, and identify the transporters responsible. provenance: - reference_id: PMID:18813294 supporting_text: an `early' acidification step that results in a relatively small drop in pH and is not well understood - gap_statement: >- Which PI(3,5)P2 effector links PIKfyve activity to the fusion that delivers Rab7 and V-ATPase to the phagosome is unknown. boundary: >- PIKfyve loss leaves Rab5 dynamics intact but blocks fusion with Rab7- and V-ATPase-positive endosomes in Dictyostelium. gap_kind: - BIOLOGY dark_aspect: BP_DARK status: OPEN significance: >- The PIKfyve annoton has a defined activity, but the step it controls cannot yet be tied to a downstream effector in the fusion part. resolution: >- Screen Dictyostelium PI(3,5)P2-binding proteins for loss-of-function mutants that copy the PIKfyve-null failure to acquire Rab7 and V-ATPase. provenance: - reference_id: PMID:41852341 supporting_text: Disruption of PIKfyve results in severe defects in phagosomal maturation but the underlying mechanism remains unclear.