Phagosome maturation

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.

MODULE:phagosome_maturationDRAFTABSTRACTOrganelle Lifecyclemodules/phagosome_maturation.yaml
phagosome maturationGO:0090382
GO:0090382
phagosome maturation
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).
PMID:22560866
How nascent phagosomes mature to become phagolysosomes.
Maturation is an ordered series of fusions that ends in a degradative phagolysosome.
Maturation entails orderly sequential fusion of the phagosomal vacuole with specialized endocytic and secretory compartments.
PMID:18351800
Phagocytic receptor CED-1 initiates a signaling pathway for degrading engulfed apoptotic cells.
Time-lapse imaging in C. elegans gives the order of events on the phagosome that the parts of this module follow.
sequential enrichment on phagocytic membranes of phagocytic receptor cell death abnormal 1
PMID:30730983
PIKfyve/Fab1 is required for efficient V-ATPase and hydrolase delivery to phagosomes, phagosomal killing, and restriction of Legionella infection.
Dictyostelium is used as a model phagocyte for phagosome maturation, so the module applies to amoebae as well as animals.
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.
file:modules/phagocytic_engulfment.yaml
Module: Phagocytic engulfment
Sibling module. It supplies the sealed nascent phagosome that this module matures.

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.

6Nodes
5Parts
0Variant Sets
0Variants
11Annotons
3Connections

Derived QC

Recommended-field compliance

44.4% recommended fields populated
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Module deep research

✗ none found

No MODULE:phagosome_maturation deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ representative grounding skipped for abstract module.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • early_phagosome_stage → rab5_to_rab7_conversion [NOT_CHECKED]
  • rab5_to_rab7_conversion → phagosome_lysosome_fusion [NOT_CHECKED]
  • phagosome_lysosome_fusion → phagosome_acidification [NOT_CHECKED]

Function consistency and core coverage

9 gene-function check(s) reflected in core functions · 0 conflict(s) · 19 evidence or coverage gap(s) (32 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
rab5_gtpase rab-5 (C. elegans)
UniProtKB:P91857
Family Representative 		GTPase activity
GO:0003924 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
rab5_gtpase Rab5 (D. melanogaster)
UniProtKB:Q9V3I2
Family Representative 		GTPase activity
GO:0003924 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
rab5_gtpase rab5A (D. discoideum)
UniProtKB:Q86JP3
Family Representative 		GTPase activity
GO:0003924 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
rab5_gtpase VPS21 (S. cerevisiae)
UniProtKB:P36017
Family Representative 		GTPase activity
GO:0003924 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
vps34_class_iii_pi3k PIK3C3 (human)
UniProtKB:Q8NEB9
Family Representative 		1-phosphatidylinositol-3-kinase activity
GO:0016303 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
vps34_class_iii_pi3k vps-34 (C. elegans)
UniProtKB:Q9TXI7
Family Representative 		1-phosphatidylinositol-3-kinase activity
GO:0016303 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
vps34_class_iii_pi3k pikE (D. discoideum)
UniProtKB:P54676
Family Representative 		1-phosphatidylinositol-3-kinase activity
GO:0016303 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
vps34_class_iii_pi3k VPS34 (S. cerevisiae)
UniProtKB:P22543
Family Representative 		1-phosphatidylinositol-3-kinase activity
GO:0016303 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dyn1_phagosomal_dynamin dyn-1 (C. elegans)
UniProtKB:P39055
Family Representative 		GTPase activity
GO:0003924 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
dyn1_phagosomal_dynamin dymA (D. discoideum)
UniProtKB:Q94464
Family Representative 		GTPase activity
GO:0003924 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
mon1_ccz1_rab7_gef PROTEIN_COMPLEX
Gene 		guanyl-nucleotide exchange factor activity
GO:0005085 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
pikfyve_pi35p2 PIKfyve (D. discoideum)
UniProtKB:B0G126
Family Representative 		1-phosphatidylinositol-3-phosphate 5-kinase activity
GO:0000285 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
pikfyve_pi35p2 fab1 (D. melanogaster)
UniProtKB:O96838
Family Representative 		1-phosphatidylinositol-3-phosphate 5-kinase activity
GO:0000285 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
pikfyve_pi35p2 FAB1 (S. cerevisiae)
UniProtKB:P34756
Family Representative 		1-phosphatidylinositol-3-phosphate 5-kinase activity
GO:0000285 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
rab7_gtpase RAB7A (human)
UniProtKB:P51149
Family Representative 		GTPase activity
GO:0003924 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
rab7_gtpase rab-7 (C. elegans)
UniProtKB:Q23146
Family Representative 		GTPase activity
GO:0003924 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
rab7_gtpase Rab7 (D. melanogaster)
UniProtKB:O76742
Family Representative 		GTPase activity
GO:0003924 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
rab7_gtpase rab7A (D. discoideum)
UniProtKB:P36411
Family Representative 		GTPase activity
GO:0003924 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
rab7_gtpase YPT7 (S. cerevisiae)
UniProtKB:P32939
Family Representative 		GTPase activity
GO:0003924 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
rilp_rab7_effector RILP (human)
UniProtKB:Q96NA2
Family Representative 		protein-macromolecule adaptor activity
GO:0030674 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
rilp_rab7_effector Rilp (mouse)
UniProtKB:Q5ND29
Family Representative 		protein-macromolecule adaptor activity
GO:0030674 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
hops_tether PROTEIN_COMPLEX
Gene 		molecular adaptor activity
GO:0060090 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
v_atpase PROTEIN_COMPLEX
Gene 		proton-transporting ATPase activity, rotational mechanism
GO:0046961 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
nox2_oxidase CYBB (human)
UniProtKB:P04839
Family Representative 		superoxide-generating NAD(P)H oxidase activity
GO:0016175 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
nox2_oxidase Cybb (mouse)
UniProtKB:Q61093
Family Representative 		superoxide-generating NAD(P)H oxidase activity
GO:0016175 		Review Missing
No ai-review exists for this protein; its function and core-function coverage cannot yet be checked.
rab5_gtpase Rab5 GTPase
PANTHER:PTHR24073:SF858
Family 		GTPase activity
GO:0003924 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR24073:SF858.
vps34_class_iii_pi3k class III PI3K VPS34
PANTHER:PTHR10048:SF7
Family 		1-phosphatidylinositol-3-kinase activity
GO:0016303 		Family Supported
Family review supports GO:0016303 for PANTHER:PTHR10048:SF7. All three PI3K classes phosphorylate phosphatidylinositol at the 3-position: class III VPS34 (SF7, selected by the phosphoinositide_biosynthesis and phagosome_maturation modules, and its sole activity), the class II PI3Ks (SF28, SF29, SF30), and the class I catalytic subunits in vitro (SF107, SF33, SF34, SF35), whose PIK3CA and PIK3CD reviews keep the term. Not the type III PI4Ks. SF111 (C. elegans AGE-1, a class I catalytic subunit) is listed too; its review keeps the in vitro activity as non-core. For the class I subfamilies the scope records a measured in vitro activity, not the physiological one: in cells their main substrate is PI(4,5)P2. Read "safe" for those subfamilies with that caveat.
dyn1_phagosomal_dynamin dynamin
PANTHER:PTHR11566
Family 		GTPase activity
GO:0003924 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR11566.
pikfyve_pi35p2 PIKfyve/Fab1 phosphoinositide 5-kinase
PANTHER:PTHR45748:SF7
Family 		1-phosphatidylinositol-3-phosphate 5-kinase activity
GO:0000285 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR45748:SF7.
rab7_gtpase Rab7 GTPase
PANTHER:PTHR47981
Family 		GTPase activity
GO:0003924 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR47981.
rilp_rab7_effector RILP
PANTHER:PTHR21502:SF7
Family 		protein-macromolecule adaptor activity
GO:0030674 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR21502:SF7.
nox2_oxidase NOX2/CYBB NADPH oxidase
PANTHER:PTHR11972:SF60
Family 		superoxide-generating NAD(P)H oxidase activity
GO:0016175 		Family Function Unreviewed
The family review has no applicable adjudication supporting or excluding GO:0016175.

Gene-review completeness (19/52 grounded genes reviewed)

14 complete review(s) · 17 with deep research · 33 missing review · 2 reviewed but lacking deep research

Gene Review Complete Deep research
ATP6V1A P38606 ✓ ✓ ✓
PIKfyve (D. discoideum) B0G126 ✗ — —
Ccz1 Q9VZL5 ✓ ✓ ✓
dyn-1 P39055 ✓ 45/47 ✓
FAB1 P34756 ✓ ✓ ✓
LAMP1 P11279 ✓ ✓ ✗
Lamp1 P11438 ✓ 121/124 ✓
LAMP2 P13473 ✓ ✓ ✗
MON1 P53129 ✓ ✓ ✓
Mon1 Q9VR38 ✓ 18/19 ✓
Rab7 (D. melanogaster) O76742 ✗ — —
fab1 (D. melanogaster) O96838 ✗ — —
CYBB (human) P04839 ✗ — —
Lamp2 (mouse) P17047 ✗ — —
VPH1 (S. cerevisiae) P32563 ✗ — —
VPS21 (S. cerevisiae) P36017 ✗ — —
rab7A (D. discoideum) P36411 ✗ — —
CCZ1 (S. cerevisiae) P38273 ✗ — —
VPS41 (S. cerevisiae) P38959 ✗ — —
VPS41 (human) P49754 ✗ — —
vatA (D. discoideum) P54647 ✗ — —
pikE (D. discoideum) P54676 ✗ — —
CCZ1 (human) P86791 ✗ — —
PIK3C3 Q8NEB9 ✓ 108/119 ✓
VAM6 (S. cerevisiae) Q07468 ✗ — —
vps-41 (C. elegans) Q19954 ✗ — —
vps-39 (C. elegans) Q1ZXS5 ✗ — —
vatM (D. discoideum) Q54E04 ✗ — —
DDB_G0288589 (D. discoideum) Q54IQ5 ✗ — —
vps41 (D. discoideum) Q54LI4 ✗ — —
mon1 (D. discoideum) Q54TG0 ✗ — —
Rilp (mouse) Q5ND29 ✗ — —
Cybb (mouse) Q61093 ✗ — —
lt (D. melanogaster) Q7PL76 ✗ — —
rab5A (D. discoideum) Q86JP3 ✗ — —
MON1A (human) Q86VX9 ✗ — —
dymA (D. discoideum) Q94464 ✗ — —
VPS39 (human) Q96JC1 ✗ — —
RILP (human) Q96NA2 ✗ — —
sand-1 (C. elegans) Q9BI89 ✗ — —
Rab5 (D. melanogaster) Q9V3I2 ✗ — —
Vps39 (D. melanogaster) Q9VEA2 ✗ — —
ccz-1 (C. elegans) Q9XVL8 ✗ — —
rab-5 P91857 ✓ 32/35 ✓
rab-7 Q23146 ✓ ✓ ✓
RAB7A P51149 ✓ ✓ ✓
unc-32 P30628 ✓ ✓ ✓
vha-13 Q9XW92 ✓ ✓ ✓
VMA1 P17255 ✓ ✓ ✓
vps-34 Q9TXI7 ✓ ✓ ✓
VPS34 P22543 ✓ ✓ ✓
YPT7 P32939 ✓ ✓ ✓

Details

Context
EukaryotaNCBITaxon:2759
phagocyteCL:0000234
phagocytic vesicleGO:0045335
Phagosome maturationOrganelle Lifecyclephagosome_maturation
phagosome maturationGO:0090382
Context
EukaryotaNCBITaxon:2759
phagocyteCL:0000234
phagocytic vesicleGO:0045335

Connections

GTP-Rab5 on the early phagosome recruits the Mon1-Ccz1 complex, and VPS34-made PI(3)P is the substrate for PIKfyve.
Rab7 activation by Mon1-Ccz1 and PIKfyve-dependent Rab7 acquisition are needed for fusion with late endosomes and lysosomes.
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.
Part 1: early phagosome (Rab5/PI(3)P stage)
Early phagosome Rab5 and PI(3)P stageBiological Processearly_phagosome_stage

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

RAB5 GTPase on early phagosomes
rab5_gtpase
Participant: Family: Rab5 GTPase
Family:
Rab5 GTPasePANTHER:PTHR24073:SF858
Representative Members: rab-5 (C. elegans)UniProtKB:P91857 Rab5 (D. melanogaster)UniProtKB:Q9V3I2 rab5A (D. discoideum)UniProtKB:Q86JP3 VPS21 (S. cerevisiae)UniProtKB:P36017

Function

GTPase activityGO:0003924

Locations

phagocytic vesicle membraneGO:0030670

Marks the early phagosome. In its GTP-bound form it recruits VPS34 and the Mon1-Ccz1 complex.

PMID:18425118
A pathway for phagosome maturation during engulfment of apoptotic cells.
In C. elegans, RAB-5 is needed for corpse degradation and for VPS-34 activity on phagosomes.
suggesting that RAB-5 is required for VPS-34 activity
PMID:20305638
Identification of two evolutionarily conserved genes regulating processing of engulfed apoptotic cells.
Phagosomes in sand-1 or ccz-1 mutants still recruit RAB-5 but do not reach the RAB-7 stage.
the phagosomes recruit the small GTPase RAB-5 but fail to progress to the subsequent RAB-7(+) stage
PMID:41852341
PIKfyve is required for efficient phagosomal Rab7 acquisition and the delivery and fusion of early macropinosomes to phagosomes.
In Dictyostelium, Rab5A is recruited to new phagosomes and then removed.
RFP–Rab5A was further recruited to phagosomes following internalisation before its removal in the following minutes.
VPS34 class III PI3K
vps34_class_iii_pi3k
Participant: Family: class III PI3K VPS34
Family:
class III PI3K VPS34PANTHER:PTHR10048:SF7
Representative Members: PIK3C3 (human)UniProtKB:Q8NEB9 vps-34 (C. elegans)UniProtKB:Q9TXI7 pikE (D. discoideum)UniProtKB:P54676 VPS34 (S. cerevisiae)UniProtKB:P22543

Function

1-phosphatidylinositol-3-kinase activityGO:0016303

Locations

phagocytic vesicle membraneGO:0030670

Makes PI(3)P on the sealed phagosome. PI(3)P recruits FYVE/PX effectors and is needed for phagolysosome formation.

PMID:11581283
Distinct roles of class I and class III phosphatidylinositol 3-kinases in phagosome formation and maturation.
VPS34 makes phagosomal PI(3)P and is essential for phagolysosome formation.
The class III PI 3-kinase VPS34 was found to be responsible for PI(3)P synthesis and essential for phagolysosome formation.
PMID:18425118
A pathway for phagosome maturation during engulfment of apoptotic cells.
In C. elegans, loss of vps-34 or dyn-1 leaves engulfed corpses undegraded in phagosomes that fail to recruit RAB-5.
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.
file:genes/human/PIK3C3/PIK3C3-ai-review.yaml
PIK3C3 gene review
The PIK3C3 review gives 1-phosphatidylinositol-3-kinase activity (GO:0016303) as the core MF.

The Dictyostelium VPS34 ortholog pikE is listed as a family member only; no phagosome loss-of-function study of pikE was found.

Dynamin on nascent phagosomes
dyn1_phagosomal_dynamin
Participant: Family: dynamin
Family:
dynaminPANTHER:PTHR11566
Representative Members: dyn-1 (C. elegans)UniProtKB:P39055 dymA (D. discoideum)UniProtKB:Q94464

Function

GTPase activityGO:0003924

Processes

phagosome maturationGO:0090382

Locations

phagocytic vesicle membraneGO:0030670

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.

PMID:18351800
Phagocytic receptor CED-1 initiates a signaling pathway for degrading engulfed apoptotic cells.
The CED-1, CED-6 and DYN-1 route controls PI(3)P and RAB-7 enrichment and phagolysosome formation.
controls the rate of enrichment of PI(3)P and RAB-7 on phagosomal surfaces and the formation of phagolysosomes
PMID:22008230
Dynamin A, Myosin IB and Abp1 couple phagosome maturation to F-actin binding.
In Dictyostelium, dymA knockout impairs phagosome acidification.
Knockout of dymA impairs phagosome acidification
PMID:27170354
Dictyostelium EHD associates with Dynamin and participates in phagosome maturation.
dymA and EHD knockouts have separate phagosome maturation defects.
DymA and EHD play non-redundant and independent functions in phagosome maturation
file:genes/worm/dyn-1/dyn-1-ai-review.yaml
dyn-1 gene review
The dyn-1 review gives GTPase activity in phagosome maturation involved in apoptotic cell clearance (GO:0090386) as a core function.
Part 2: Rab5-to-Rab7 conversion
Mon1-Ccz1-mediated Rab5-to-Rab7 conversionRegulatory Steprab5_to_rab7_conversion

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

Mon1-Ccz1 Rab7 GEF complex
mon1_ccz1_rab7_gef
Participant: Protein Complex: Mon1-Ccz1 complex
Protein Complex:
Mon1-Ccz1 complexGO:0035658
Active units:
MON1/SAND-1
Participant: Family: MON1/SAND-1
Family:
MON1/SAND-1PANTHER:PTHR13027
Representative Members: MON1A (human)UniProtKB:Q86VX9 sand-1 (C. elegans)UniProtKB:Q9BI89 Mon1 (D. melanogaster)UniProtKB:Q9VR38 mon1 (D. discoideum)UniProtKB:Q54TG0 MON1 (S. cerevisiae)UniProtKB:P53129
Role: Rab5 effector subunit of the Rab7 GEF
CCZ1/CCZ-1
Participant: Family: CCZ1/CCZ-1
Family:
CCZ1/CCZ-1PANTHER:PTHR13056:SF0
Representative Members: CCZ1 (human)UniProtKB:P86791 ccz-1 (C. elegans)UniProtKB:Q9XVL8 Ccz1 (D. melanogaster)UniProtKB:Q9VZL5 DDB_G0288589 (D. discoideum)UniProtKB:Q54IQ5 CCZ1 (S. cerevisiae)UniProtKB:P38273
Role: GEF subunit partner

Function

guanyl-nucleotide exchange factor activityGO:0005085
Targets: RAB7

Locations

phagocytic vesicle membraneGO:0030670

A Rab5 effector that binds and activates Rab7, linking the Rab5 stage to the Rab7 stage.

PMID:20305638
Identification of two evolutionarily conserved genes regulating processing of engulfed apoptotic cells.
Mon1 binds GTP-Rab5, and the Mon1-Ccz1 complex binds Rab7 and affects its activation.
a Mon1-Ccz1 complex (but not either protein alone) could bind Rab7 and could also influence Rab7 activation

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.

PIKfyve makes PI(3,5)P2 on maturing phagosomes
pikfyve_pi35p2
Participant: Family: PIKfyve/Fab1 phosphoinositide 5-kinase
Family:
PIKfyve/Fab1 phosphoinositide 5-kinasePANTHER:PTHR45748:SF7
Representative Members: PIKfyve (D. discoideum)UniProtKB:B0G126 fab1 (D. melanogaster)UniProtKB:O96838 FAB1 (S. cerevisiae)UniProtKB:P34756

Function

1-phosphatidylinositol-3-phosphate 5-kinase activityGO:0000285

Locations

phagocytic vesicle membraneGO:0030670

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.

PMID:30730983
PIKfyve/Fab1 is required for efficient V-ATPase and hydrolase delivery to phagosomes, phagosomal killing, and restriction of Legionella infection.
In Dictyostelium, PIKfyve knockout blocks V-ATPase and protease delivery to phagosomes and their acidification.
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.
PMID:41852341
PIKfyve is required for efficient phagosomal Rab7 acquisition and the delivery and fusion of early macropinosomes to phagosomes.
In Dictyostelium, loss of PIKfyve leaves Rab5 dynamics intact but reduces Rab7 acquisition by fusion.
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
PMID:30730983
PIKfyve/Fab1 is required for efficient V-ATPase and hydrolase delivery to phagosomes, phagosomal killing, and restriction of Legionella infection.
PIKfyve inhibitors also impair phagosome maturation in mammalian macrophages and neutrophils.
has allowed researchers to demonstrate the importance of PI(3)P to PI(3,5)P2 conversion for phagosomal maturation in macrophages and neutrophils
Part 3: phagosome-lysosome fusion
Rab7-dependent phagosome-lysosome fusionBiological Processphagosome_lysosome_fusion

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.

phagosome-lysosome fusionGO:0090385

Annotons

RAB7 GTPase on late phagosomes
rab7_gtpase
Participant: Family: Rab7 GTPase
Family:
Rab7 GTPasePANTHER:PTHR47981
Representative Members: RAB7A (human)UniProtKB:P51149 rab-7 (C. elegans)UniProtKB:Q23146 Rab7 (D. melanogaster)UniProtKB:O76742 rab7A (D. discoideum)UniProtKB:P36411 YPT7 (S. cerevisiae)UniProtKB:P32939

Function

GTPase activityGO:0003924

Processes

phagosome-lysosome fusionGO:0090385

Locations

phagocytic vesicle membraneGO:0030670

Its recruitment comes before, and is needed for, phagosome fusion with late endosomes and lysosomes and delivery of lysosomal membrane proteins and hydrolases.

PMID:12944476
Phagosomes fuse with late endosomes and/or lysosomes by extension of membrane protrusions along microtubules: role of Rab7 and RILP.
Rab7 recruitment comes before, and is needed for, phagosome fusion with late endosomes and lysosomes.
Rab7 recruitment to phagosomes was found to precede and to be essential for their fusion with late endosomes and/or lysosomes
PMID:18351800
Phagocytic receptor CED-1 initiates a signaling pathway for degrading engulfed apoptotic cells.
RAB-7 promotes lysosome recruitment and fusion to apoptotic-cell phagosomes in C. elegans.
We further identified an essential role of RAB-7 in promoting the recruitment and fusion of lysosomes to phagosomes.
PMID:18425118
A pathway for phagosome maturation during engulfment of apoptotic cells.
In C. elegans, rab-7 knockdown arrests corpse phagosomes at the RAB-5 stage.
in rab-7(RNAi) worms, phagosomes containing apoptotic germ cells were arrested at the RAB-5-positive stage
PMID:11559753
Rab7 regulates phagosome maturation in Dictyostelium.
In Dictyostelium, dominant negative Rab7 blocks delivery of a lysosomal membrane protein and a glycosidase to phagosomes.
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.
file:genes/human/RAB7A/RAB7A-ai-review.yaml
RAB7A gene review
The RAB7A review gives GTPase activity (GO:0003924) as the core MF.
RILP Rab7 effector (vertebrate)
rilp_rab7_effector
Participant: Family: RILP
Family:
RILPPANTHER:PTHR21502:SF7
Representative Members: RILP (human)UniProtKB:Q96NA2 Rilp (mouse)UniProtKB:Q5ND29

Function

protein-macromolecule adaptor activityGO:0030674

Locations

phagocytic vesicle membraneGO:0030670

Bridges active Rab7 on the phagosome to the dynein-dynactin motor. This drives centripetal movement and the extension of tubules toward late endocytic compartments.

PMID:12944476
Phagosomes fuse with late endosomes and/or lysosomes by extension of membrane protrusions along microtubules: role of Rab7 and RILP.
RILP bridges Rab7-positive phagosomes to dynein-dynactin.
which in turn bridges phagosomes with dynein-dynactin

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.

HOPS tethering complex
hops_tether
Participant: Protein Complex: HOPS complex
Protein Complex:
HOPS complexGO:0030897
Active units:
VPS41
Participant: Family: VPS41
Family:
VPS41PANTHER:PTHR12616:SF1
Representative Members: VPS41 (human)UniProtKB:P49754 vps-41 (C. elegans)UniProtKB:Q19954 lt (D. melanogaster)UniProtKB:Q7PL76 vps41 (D. discoideum)UniProtKB:Q54LI4 VPS41 (S. cerevisiae)UniProtKB:P38959
Role: Rab7-interacting HOPS-specific subunit
VPS39
Participant: Family: VPS39/VAM6
Family:
VPS39/VAM6PANTHER:PTHR12894:SF49
Representative Members: VPS39 (human)UniProtKB:Q96JC1 vps-39 (C. elegans)UniProtKB:Q1ZXS5 Vps39 (D. melanogaster)UniProtKB:Q9VEA2 VAM6 (S. cerevisiae)UniProtKB:Q07468
Role: HOPS-specific subunit

Function

molecular adaptor activityGO:0060090

Locations

phagocytic vesicle membraneGO:0030670

Multisubunit tether that bridges Rab7-positive membranes and promotes SNARE-mediated fusion with lysosomes.

PMID:18425118
A pathway for phagosome maturation during engulfment of apoptotic cells.
In C. elegans, knockdown of HOPS subunits arrests corpse phagosomes at the RAB-7 stage.
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.
PMID:18813294
Phagosome maturation: going through the acid test.
Genetic studies in C. elegans place HOPS downstream of RAB-7 recruitment on phagosomes.
genetic studies in the nematode suggest that this complex instead functions downstream of RAB-7 recruitment during phagosome maturation

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.

LAMP-1/LAMP-2 (animal)
lamp_proteins
Participant: Family: LAMP-1 and LAMP-2 (redundant)
Family:
LAMP-1 and LAMP-2 (redundant)PANTHER:PTHR11506
Representative Members: LAMP1 (human)UniProtKB:P11279 LAMP2 (human)UniProtKB:P13473 Lamp1 (mouse)UniProtKB:P11438 Lamp2 (mouse)UniProtKB:P17047

Locations

lysosomal membraneGO:0005765

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).

PMID:17245426
LAMP proteins are required for fusion of lysosomes with phagosomes.
LAMP-1/LAMP-2 double-deficient mouse phagosomes acquire Rab5 and PI(3)P but do not recruit Rab7 or fuse with lysosomes.
failed to recruit Rab7 and did not fuse with lysosomes

Animal-specific. The evidence is from mouse cells. Amoebae have lysosomal membrane proteins such as LmpA, but these are not LAMP family members.

Part 4: phagosome acidification
V-ATPase-driven phagosome acidificationTransport Stepphagosome_acidification

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.

phagosome acidificationGO:0090383

Annotons

V-type proton ATPase
v_atpase
Participant: Protein Complex: V-ATPase
Protein Complex:
V-ATPaseGO:0033176
Active units:
V1 catalytic subunit A
Participant: Family: V-ATPase catalytic subunit A
Family:
V-ATPase catalytic subunit APANTHER:PTHR43607
Representative Members: ATP6V1A (human)UniProtKB:P38606 vha-13 (C. elegans)UniProtKB:Q9XW92 vatA (D. discoideum)UniProtKB:P54647 VMA1 (S. cerevisiae)UniProtKB:P17255
Role: ATP-hydrolyzing catalytic subunit of V1
V0 subunit a
Participant: Family: V-ATPase subunit a, vacuolar/lysosomal type
Family:
V-ATPase subunit a, vacuolar/lysosomal typePANTHER:PTHR11629:SF63
Representative Members: vatM (D. discoideum)UniProtKB:Q54E04 unc-32 (C. elegans)UniProtKB:P30628 VPH1 (S. cerevisiae)UniProtKB:P32563
Role: proton-translocating transmembrane subunit of V0

Function

proton-transporting ATPase activity, rotational mechanismGO:0046961

Processes

phagosome acidificationGO:0090383

Locations

phagocytic vesicle membraneGO:0030670

Couples ATP hydrolysis in the V1 domain to proton transport by the V0 domain, acidifying the phagosome lumen.

PMID:18813294
Phagosome maturation: going through the acid test.
V-ATPases are proton pumps delivered to the phagosome during maturation.
V-type (vacuolar) ATPases, proton pumps driven by the hydrolysis of ATP40, are trafficked to the phagosome at relatively late stages
PMID:20052281
Retrieval of the vacuolar H-ATPase from phagosomes revealed by live cell imaging.
In Dictyostelium, the V-ATPase reaches the phagosome by fusion with endosomes that carry it.
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.
PMID:11956322
Altered expression of the 100 kDa subunit of the Dictyostelium vacuolar proton pump impairs enzyme assembly, endocytic function and cytosolic pH regulation.
Lowering Dictyostelium VatM mislocalises the V1 A subunit, showing that subunit a is needed to assemble the pump.
the A subunit, a component of the peripheral catalytic domain of the V-ATPase, became mislocalized
file:genes/human/ATP6V1A/ATP6V1A-ai-review.yaml
ATP6V1A gene review
The ATP6V1A review gives proton-transporting ATPase activity, rotational mechanism (GO:0046961) as the core MF.
Part 5: phagosomal superoxide production (optional)
NOX2 phagosomal superoxide productionBiological Processphagosomal_nox2_burst

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
VertebrataNCBITaxon:7742
neutrophilCL:0000775 macrophageCL:0000235

Annotons

NOX2 (gp91phox) NADPH oxidase
nox2_oxidase
Participant: Family: NOX2/CYBB NADPH oxidase
Family:
NOX2/CYBB NADPH oxidasePANTHER:PTHR11972:SF60
Representative Members: CYBB (human)UniProtKB:P04839 Cybb (mouse)UniProtKB:Q61093

Function

superoxide-generating NAD(P)H oxidase activityGO:0016175

Locations

phagocytic vesicle membraneGO:0030670

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.

PMID:7719350
Mouse model of X-linked chronic granulomatous disease, an inherited defect in phagocyte superoxide production.
CYBB-null mice lack phagocyte superoxide production.
Affected hemizygous male mice lacked phagocyte superoxide production

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.