Phagophore-organelle membrane contact site

A phagophore-organelle membrane contact site is the zone of apposition through which a growing phagophore (isolation membrane) is physically held against a donor or anchor organelle while the autophagosome is built. Canonically this is the phagophore-endoplasmic reticulum membrane contact site: a bridging assembly in which an ATG2-family rod spans the ~10-20 nm gap between the ER and the phagophore rim, an Atg18/WIPI4-family beta-propeller clamps the ATG2 tip onto phosphatidylinositol 3-phosphate (PI3P) on the phagophore, and lipid scramblases work on both sides - VMP1 and TMEM41B in the donor ER membrane, and the ATG9 trimer at the phagophore rim - so that glycerophospholipids delivered by ATG2 into one leaflet are equilibrated across the bilayer. The site is nucleated by the Atg1/ULK1 kinase complex together with class III PI3K-derived PI3P, operates as a lipid conduit that drives phagophore expansion, and is taken apart when contacts are dissolved and the phagophore is sealed. Related contact sites use the same bridging logic with a different partner organelle: PI3P-rich endosomes can serve as an alternative ATG2 lipid donor, and in budding yeast Vac8 anchors the phagophore assembly site to the vacuole, giving a positional rather than lipid-donating attachment. This module models the site as a cellular component with an assembly step, a composition, a lipid flux function, and a disassembly step.

MODULE:phagophore_organelle_contact_siteDRAFTCONCRETECellular Componentmodules/phagophore_organelle_contact_site.yaml
organelle membrane contact siteGO:0044232 phagophore assembly siteGO:0000407 autophagosome assemblyGO:0000045
PMID:37465355
The Organization and Function of the Phagophore-ER Membrane Contact Sites.
Frames the phagophore-ER interface as a bona fide membrane contact site organized by the ATG9 scramblase, ATG2 lipid transfer, and Atg18/WIPI4 beta-propeller families - the boundary this module models.
The phagophore establishes membrane-contact sites (MCSs) with the endoplasmic reticulum (ER)
PMID:19898463
A subdomain of the endoplasmic reticulum forms a cradle for autophagosome formation.
Electron tomography establishes the contact site morphologically: an ER subdomain cradles the isolation membrane and the two membranes are interconnected.
Electron tomography revealed that the ER-IM complex appears as a subdomain of the ER that formed a cradle encircling the IM, and showed that both ER and isolation membranes are interconnected.
PMID:18725538
Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum.
Defines the PI3P-enriched, ER-connected omegasome as the platform on which the contact site and the phagophore form.
provides a membrane platform for accumulation of autophagosomal proteins, expansion of autophagosomal membranes, and emergence of fully formed autophagosomes

Boundary decisions. The module core is the bridging machinery that physically holds the phagophore against a partner organelle and moves lipid across that gap: ATG2, Atg18/WIPI4, ATG9, and the donor-membrane scramblases VMP1 and TMEM41B. Nucleation (Atg1/ULK1 complex, class III PI3K, PI3P, omegasome markers) is retained as an explicit assembly part because the site does not exist without it, and disassembly (VMP1/SERCA-dependent contact dissolution, ESCRT-III-dependent sealing) is retained because the site is inherently transient. Deliberately excluded as neighbouring modules: the ATG8/LC3 conjugation cascade (ATG7, ATG3, ATG12-ATG5-ATG16L1) even though WIPI2 recruits it at the same place and time; cargo receptors and selective-autophagy adaptors; ATG9 vesicle trafficking to and from the site; and autophagosome- lysosome/vacuole fusion. Sibling module. MODULE:phagophore_assembly_site models the PAS (GO:0000407) - the Atg-protein condensate that organizes the machinery and at which this contact site is built. The two are deliberately separate objects: the PAS is the hub, this module is the junction. The nucleation part here overlaps the PAS module by design, because a contact site that is never nucleated is not a module; the PAS module owns the scaffolding, condensate, and turnover biology and does not duplicate the ATG2/WIPI4/ATG9 mechanics modeled here. There is no GO cellular-component term for the ER-phagophore contact site, so the module node is grounded on the parent GO:0044232 organelle membrane contact site plus GO:0000407 phagophore assembly site; only the yeast vacuole variant has a dedicated term (GO:0120095). This is recorded as an ontology knowledge gap rather than papered over with an approximate term. Family-level roles carry PANTHER/PAINT ancestral nodes taken verbatim from the local IBD slices (PTHR13190/PTN000324023 for ATG2, PTHR13038/PTN000315580 for ATG9, PTHR11227/PTN000132136 for the Atg18/WIPI propellers). VMP1 and TMEM41B have no local PANTHER slice, so they are grounded by representative members only.

11Nodes
7Parts
1Variant Sets
3Variants
17Annotons
7Connections

Derived QC

Recommended-field compliance

33.3% recommended fields populated
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Module deep research

✗ none found

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

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

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.

  • contact_site_nucleation → contact_site_composition [NOT_CHECKED]
    Not a metabolic chain; these steps are linked by protein recruitment, not by a shared small-molecule intermediate.
  • lipid_flux_through_site → contact_site_disassembly [NOT_CHECKED]
    Temporal ordering of membrane events, not a reaction chain with a shared intermediate.

Gene-review completeness (13/25 grounded genes reviewed)

4 complete review(s) · 8 with deep research · 12 missing review · 5 reviewed but lacking deep research

Gene Review Complete Deep research
ANKFY1 Q9P2R3 ✓ 36/38 ✓
ATG14 Q6ZNE5 ✓ 92/95 ✓
ATG2A Q2TAZ0 ✓ 30/31 ✓
ATG2B Q96BY7 ✓ ✓ ✓
ATG9A Q7Z3C6 ✓ ✓ ✗
BECN1 Q14457 ✓ 189/191 ✓
CHMP2A O43633 ✓ ✓ ✓
ATG13 O75143 ✗ — —
Vac8 (S. cerevisiae) P39968 ✗ — —
Atg18 (S. cerevisiae) P43601 ✗ — —
Atg2 (S. cerevisiae) P53855 ✗ — —
PIK3C3 Q8NEB9 ✓ 108/119 ✓
PIK3R4 Q99570 ✓ 64/66 ✗
Atg13 (S. cerevisiae) Q06628 ✗ — —
Atg9 (S. cerevisiae) Q12142 ✗ — —
TMEM41B Q5BJD5 ✗ — —
RB1CC1 (FIP200) Q8TDY2 ✗ — —
NRBF2 Q96F24 ✗ — —
ATG101 Q9BSB4 ✗ — —
ZFYVE1 (DFCP1) Q9HBF4 ✗ — —
WDR45/WIPI4 (human) Q9Y484 ✗ — —
ULK1 O75385 ✓ 137/139 ✗
VMP1 Q96GC9 ✓ ✓ ✓
VPS4A Q9UN37 ✓ 139/141 ✗
WIPI2 Q9Y4P8 ✓ 43/45 ✗

Details

Context
eukaryotes
phagophoreGO:0061908 endoplasmic reticulum membraneGO:0005789 phagophore assembly site membraneGO:0034045
macroautophagy-inducing conditionsGO:0016236
Phagophore-organelle membrane contact siteCellular Componentphagophore_organelle_contact_site

A transient bridging assembly that holds the rim of a growing phagophore against a partner organelle membrane. In its canonical form the partner is the ER and the site is a lipid conduit; the same architecture is reused with endosomes as an alternative lipid donor, and a related, non-donating attachment anchors the phagophore assembly site to the yeast vacuole.

organelle membrane contact siteGO:0044232 phagophore assembly siteGO:0000407 autophagosome assemblyGO:0000045
Context
eukaryotes
phagophoreGO:0061908 endoplasmic reticulum membraneGO:0005789 phagophore assembly site membraneGO:0034045
macroautophagy-inducing conditionsGO:0016236

Connections

PI3P written at the nucleation platform is the address that recruits the Atg18/WIPI propellers and, through them, the ATG2 bridge.
The assembled three-face architecture is what makes directional lipid flux possible; neither tethering nor scrambling suffices alone.
atg9_rim_scramblase -> atg2_tether Positively Regulates
Atg9 binding confines Atg2 to the growing phagophore extremities; disrupting the Atg2-Atg9 interaction gives an aberrant distribution of Atg2 and of ER contact sites on forming phagophores.
PMID:29848619
Atg2-Atg9 binding is required for Atg2 confinement to the phagophore rim.
Its interaction with Atg9, however, is key for Atg2 confinement to the growing phagophore extremities and subsequent association of Atg18.
wipi4_atg18_clamp -> atg2_tether Positively Regulates
The PI3P-bound propeller stabilizes the ATG2 tip on the phagophore, orienting the tether and accelerating transfer.
Expansion is followed by contact dissolution and sealing of the rim.
VMP1, acting through SERCA, limits the lifetime of the contact; without it isolation membranes remain stably associated with the ER.
Sealing removes the open phagophore rim, ending lipid delivery through the site.
Part 1: PI3P-dependent nucleation and recruitment of the contact site
Nucleation of the phagophore-organelle contact siteBiological Processcontact_site_nucleation

The Atg1/ULK1 kinase complex and the class III PI3K complex I act on an ER subdomain to generate a PI3P-enriched platform (the omegasome in mammals, the PAS in yeast). PI3P is the address that recruits the Atg18/WIPI beta-propellers, and through them ATG2, establishing the apposition between the nascent phagophore and the ER.

omegasomeGO:1990462 protein localization to phagophore assembly siteGO:0034497

Annotons

Atg1/ULK1 kinase complex initiation of the site
ulk1_atg1_initiation_complex
Participant: Protein Complex: Atg1/ULK1 kinase complex
Protein Complex:
Atg1/ULK1 kinase complexGO:1990316 Autophagy-initiating serine/threonine kinase complex. Human subunits are given as representative members; the yeast counterpart is Atg1-Atg13-Atg17-Atg29-Atg31.
Active units:
ULK1 catalytic subunit
Participant: Gene Product: ULK1
Gene Product:
ULK1UniProtKB:O75385
Role: initiating protein serine/threonine kinase
Function:
protein serine/threonine kinase activityGO:0004674
ATG13 subunit
Participant: Gene Product: ATG13
Gene Product:
ATG13UniProtKB:O75143
Role: scaffolding/adaptor subunit; in yeast the equivalent subunit is the receptor through which Vac8 anchors the PAS to the vacuole
RB1CC1/FIP200 subunit
Participant: Gene Product: RB1CC1 (FIP200)
Gene Product:
RB1CC1 (FIP200)UniProtKB:Q8TDY2
Role: scaffold subunit; cooperates with WIPI2 in forming ER-isolation membrane contacts
ATG101 subunit
Participant: Gene Product: ATG101
Gene Product:
ATG101UniProtKB:Q9BSB4
Role: ATG13-stabilizing subunit

Function

protein serine/threonine kinase activityGO:0004674

Processes

autophagosome assemblyGO:0000045

Locations

phagophore assembly siteGO:0000407
PMID:28890335
WIPI2 acting with the ULK1/FIP200 complex and PI(3)P contributes to formation of the ER-isolation membrane contact.
Interaction of WIPI2 with the ULK1/FIP200 complex and PI(3)P contributes to the formation of ER-IM contacts
Class III PI3K complex I generation of PI3P at the site
pi3kc3_c1_pi3p_synthesis
Participant: Protein Complex: phosphatidylinositol 3-kinase complex, class III, type I
Protein Complex:
phosphatidylinositol 3-kinase complex, class III, type IGO:0034271 Autophagy-specific PI3KC3-C1 (VPS34-VPS15-Beclin1-ATG14, with NRBF2), which writes the PI3P that defines the site.
Active units:
PIK3C3/VPS34 catalytic subunit
Participant: Gene Product: PIK3C3 (VPS34)
Gene Product:
PIK3C3 (VPS34)UniProtKB:Q8NEB9
Role: PI3P-generating lipid kinase
Function:
1-phosphatidylinositol-3-kinase activityGO:0016303
PIK3R4/VPS15 subunit
Participant: Gene Product: PIK3R4 (VPS15)
Gene Product:
PIK3R4 (VPS15)UniProtKB:Q99570
Role: membrane-anchoring regulatory subunit
BECN1 subunit
Participant: Gene Product: BECN1
Gene Product:
BECN1UniProtKB:Q14457
Role: scaffold subunit
ATG14 subunit
Participant: Gene Product: ATG14
Gene Product:
ATG14UniProtKB:Q6ZNE5
Role: targeting subunit that directs the complex to the autophagy site
NRBF2 subunit
Participant: Gene Product: NRBF2
Gene Product:
NRBF2UniProtKB:Q96F24
Role: accessory subunit modulating complex I activity

Function

1-phosphatidylinositol-3-kinase activityGO:0016303
Substrates: 1-phosphatidyl-1D-myo-inositol
Products: 1-phosphatidyl-1D-myo-inositol 3-phosphate (PI3P)

Processes

autophagosome assemblyGO:0000045

Locations

omegasomeGO:1990462
PMID:18725538
A Vps34/Beclin-dependent, PI3P-enriched compartment in dynamic equilibrium with the ER is the platform on which autophagosomal membranes expand.
provides a membrane platform for accumulation of autophagosomal proteins, expansion of autophagosomal membranes, and emergence of fully formed autophagosomes
DFCP1/ZFYVE1 marking of the omegasome platform
dfcp1_omegasome_marker
Participant: Gene Product: ZFYVE1 (DFCP1)
Gene Product:
ZFYVE1 (DFCP1)UniProtKB:Q9HBF4

Function

phosphatidylinositol-3-phosphate bindingGO:0032266

Locations

omegasomeGO:1990462

PI3P- and ER-binding marker whose starvation-induced translocation defined the omegasome. Included as the operational marker of the platform on which the contact site forms; it is not part of the bridging machinery.

PMID:18725538
DFCP1 translocates in a Vps34/Beclin- and PI3P-dependent manner to the ER-connected omegasome.
Translocation is dependent on Vps34 and beclin function.
WIPI2 PI3P effector at the nascent site
wipi2_pi3p_effector
Participant: Gene Product: WIPI2
Gene Product:
WIPI2UniProtKB:Q9Y4P8

Function

phosphatidylinositol-3-phosphate bindingGO:0032266

Processes

autophagosome assemblyGO:0000045

Locations

phagophore assembly siteGO:0000407

PI3P effector that, together with the ULK1/FIP200 complex, contributes to formation of the ER-isolation membrane contact. WIPI2 also recruits the ATG12-ATG5-ATG16L1 lipidation machinery, but that cascade is a neighbouring module and is not modeled here.

PMID:28890335
WIPI2, the ULK1/FIP200 complex, and PI(3)P together contribute to ER-isolation membrane contact formation.
Interaction of WIPI2 with the ULK1/FIP200 complex and PI(3)P contributes to the formation of ER-IM contacts
PMID:24954904
WIPI2b is the PI3P effector that couples the site to LC3 conjugation.
WIPI2b is a PtdIns(3)P effector upstream of Atg16L1 and is required for LC3 conjugation and starvation-induced autophagy through recruitment of the Atg12-5-16L1 complex
Part 2: composition of the assembled contact site
Composition of the phagophore-organelle contact siteCellular Componentcontact_site_composition

The assembled site has three functional faces: the donor organelle membrane, which must supply lipid from both leaflets; the bridge, an ATG2 rod clamped to the phagophore by an Atg18/WIPI propeller; and the phagophore rim, where the ATG9 trimer equilibrates newly delivered lipid across the bilayer. Losing any one face blocks phagophore expansion.

organelle membrane contact siteGO:0044232
Part 1: donor organelle membrane face
Donor membrane face of the contact siteCellular Componentdonor_membrane_face

The partner-organelle side of the contact, canonically the ER membrane. Bulk lipid leaves the ER cytosolic leaflet through the ATG2 bridge; the ER-resident scramblases VMP1 and TMEM41B maintain transbilayer lipid distribution in the donor membrane and are required for normal autophagosome, lipid droplet, and lipoprotein formation.

endoplasmic reticulum membraneGO:0005789

Annotons

VMP1 ER phospholipid scramblase
vmp1_er_scramblase
Participant: Gene Product: VMP1
Gene Product:
VMP1UniProtKB:Q96GC9 Metazoan-specific member of the TMEM41/VMP1 (DedA-like) superfamily; absent from S. cerevisiae, which is why the yeast contact site is modeled without it.

Function

phospholipid scramblase activityGO:0017128

Locations

endoplasmic reticulum membraneGO:0005789

Dual role at this site: an ER scramblase in the donor membrane, and the factor that limits the lifetime of the contact (see the disassembly part).

PMID:33929485
VMP1 is a phospholipid scramblase of the ER membrane.
we show that TMEM41B and VMP1 are phospholipid scramblases whose deficiency impairs the normal cellular distribution of cholesterol and phosphatidylserine
TMEM41B ER phospholipid scramblase
tmem41b_er_scramblase
Participant: Gene Product: TMEM41B
Gene Product:
TMEM41BUniProtKB:Q5BJD5

Function

phospholipid scramblase activityGO:0017128

Locations

endoplasmic reticulum membraneGO:0005789

VMP1 paralogue in the same superfamily; required for autophagosome formation and for normal cholesterol and phosphatidylserine distribution.

PMID:33929485
TMEM41B is an ER phospholipid scramblase acting with VMP1.
TMEM41B and VMP1 are integral membrane proteins of the endoplasmic reticulum (ER) and regulate the formation of autophagosomes, lipid droplets (LDs), and lipoproteins.
Part 2: bridging tether between the two membranes
ATG2-Atg18/WIPI bridging tetherMolecular Functionlipid_transfer_bridge

The physical bridge. ATG2 is a rod-shaped protein with a hydrophobic groove running its length and a membrane-binding region at each tip: the N-terminal region associates with the ER, and a C-terminal amphipathic helix in the CLR region attaches to the phagophore. An Atg18/WIPI4-family beta-propeller binds one tip and clamps it onto PI3P, which is what makes the tether directional - PI3P-containing membrane on one side, PI3P-free membrane on the other.

Annotons

ATG2-family ER-phagophore membrane tether
atg2_tether
Participant: Family: ATG2 family
Family:
ATG2 familyPANTHER:PTHR13190 Chorein/VPS13-like rod proteins dedicated to autophagy; two paralogues (ATG2A, ATG2B) in mammals, a single Atg2 in yeasts and plants.
Representative Members: ATG2A (human)UniProtKB:Q2TAZ0 ATG2B (human)UniProtKB:Q96BY7 Atg2 (S. cerevisiae)UniProtKB:P53855

Function

endoplasmic reticulum-organelle membrane tether activityGO:0170009 Tethering half of the ATG2 role; the lipid transfer it also performs is modeled in the lipid flux part.
Targets: phagophoreGO:0061908

Processes

autophagosome assemblyGO:0000045

Locations

organelle membrane contact siteGO:0044232
PMID:30254161
Atg2 has membrane-binding regions at both ends and acts as a tether.
we show that Atg2 has two membrane-binding domains in the N- and C-terminal regions and acts as a membrane tether during autophagosome formation
PMID:30911189
Atg2 physically links the expanding isolation membrane edge to the ER.
Atg2 physically links the edge of the expanding IM with the endoplasmic reticulum (ER), a role that is essential for autophagosome formation.
PMID:30185561
EM and cross-linking show ATG2A bridges two membranes through its tips.
ATG2A is a rod-shaped protein that can bridge neighboring vesicles through interactions at each of its tips.
ATG2 C-terminal CLR amphipathic helix anchoring to the phagophore
atg2_clr_rim_anchor
Participant: Domain: ATG2 C-terminal localization region (CLR) amphipathic helix
Domain:
ATG2 C-terminal localization region (CLR) amphipathic helix Conserved short amphipathic-helix region at the ATG2 C-terminus, not registered in Pfam, that carries the membrane-binding site through which ATG2 attaches to the phagophore and that facilitates Atg18 binding to PI3P.

The molecular attachment point after which this module is named: the physical grip of the bridge on the phagophore rim.

PMID:37465355
The phagophore-attaching membrane-binding site of ATG2 lies in the CLR region.
The membrane binding site responsible of the attachment with the phagophore is within the CLR domain
PMID:30254161
The C-terminal amphipathic helix binds membrane and promotes Atg18 binding to PI3P, targeting the complex to the PAS.
An amphipathic helix in the C-terminal region binds to membranes and facilitates Atg18 binding to PI3P to target the Atg2-Atg18 complex to the PAS.
Atg18/WIPI4-family PI3P clamp on the ATG2 tip
wipi4_atg18_clamp
Participant: Family: Atg18/WIPI PROPPIN family
Family:
Atg18/WIPI PROPPIN familyPANTHER:PTHR11227 Seven-bladed beta-propellers that bind PI3P (PROPPINs). WIPI4/WDR45 is the ATG2 partner in mammals; Atg18 plays the equivalent role in yeast. WIPI2, in the same family, acts earlier at nucleation and is modeled separately.
Representative Members: WDR45/WIPI4 (human)UniProtKB:Q9Y484 Atg18 (S. cerevisiae)UniProtKB:P43601

Function

phosphatidylinositol-3-phosphate bindingGO:0032266

Locations

phagophoreGO:0061908

Binds one tip of the ATG2 rod and holds it on the PI3P-rich phagophore membrane, giving the bridge its orientation and raising the efficiency of transfer.

PMID:31271352
WIPI4 stabilizes ATG2A on PI3P membranes and thereby promotes tethering and transfer to a PI3P-free membrane.
The PI3P effectors WIPI4 and WIPI1 associate ATG2A stably to PI3P-containing vesicles, thereby facilitating ATG2A-mediated tethering and lipid transfer between PI3P-containing vesicles and PI3P-free vesicles.
PMID:30185561
WIPI4 binds one ATG2A tip, letting the complex tether a PI3P vesicle to a PI3P-free vesicle.
WIPI4 binds to one of the tips, enabling the ATG2A-WIPI4 complex to tether a PI3P-containing vesicle to another PI3P-free vesicle.
Part 3: phagophore rim face
Phagophore rim face of the contact siteCellular Componentphagophore_rim_face

The acceptor side. ATG9 concentrates with ATG2 at the open, expanding edge of the phagophore, where it scrambles the newly arrived phospholipids from the cytosolic to the lumenal leaflet. Without this, lipid delivered by ATG2 would accumulate in one leaflet and expansion would stall. ATG9 binding is also what confines ATG2 to the rim and permits the contact site to form at all.

phagophoreGO:0061908

Annotons

ATG9-family lipid scramblase at the phagophore rim
atg9_rim_scramblase
Participant: Family: ATG9 family
Family:
ATG9 familyPANTHER:PTHR13038 The only transmembrane protein of the core autophagy machinery; a homotrimer with a solvated central pore.
Representative Members: ATG9A (human)UniProtKB:Q7Z3C6 Atg9 (S. cerevisiae)UniProtKB:Q12142

Function

phospholipid scramblase activityGO:0017128

Processes

autophagosome assemblyGO:0000045

Locations

phagophoreGO:0061908
PMID:33106658
Atg9 sits with Atg2 at the expanding isolation-membrane edge and scrambles phospholipids.
Atg9 colocalizes with Atg2 at the expanding edge of the isolation membrane (IM), where Atg2 receives phospholipids from the endoplasmic reticulum (ER).
PMID:33106659
Pore mutations that reduce ATG9A scrambling produce markedly smaller autophagosomes.
Mutations in the pore reduce scrambling activity and yield markedly smaller autophagosomes, indicating that lipid scrambling by ATG9A is essential for membrane expansion.
PMID:29848619
Atg9 binding confines Atg2 to the growing phagophore extremities and is required to establish phagophore-ER contact sites.
Assembly of the Atg9-Atg2-Atg18 complex is important to establish phagophore-endoplasmic reticulum (ER) contact sites.
Part 3: lipid flux through the assembled site
Lipid flux through the contact siteTransport Steplipid_flux_through_site

The reason the site exists. Once assembled, the ATG2-WIPI4-ATG9 unit moves glycerophospholipids from the donor membrane into the phagophore faster than either tethering or scrambling could achieve alone: ATG2 extracts lipids into its hydrophobic groove and unloads them into the acceptor cytosolic leaflet, and ATG9 redistributes them across the bilayer. Net flux drives phagophore expansion.

intermembrane lipid transferGO:0120009

Annotons

ATG2-WIPI4-ATG9 lipid conduit
atg2_wipi4_atg9_conduit
Participant: Protein Complex: ATG2-WIPI4-ATG9 lipid transfer and equilibration unit
Protein Complex:
ATG2-WIPI4-ATG9 lipid transfer and equilibration unit Functional unit spanning the contact: the ATG2 rod clamped by an Atg18/WIPI propeller and docked onto the ATG9 trimer at the phagophore rim. No GO complex term exists for this assembly.
Active units:
ATG2 lipid transfer rod
Participant: Family: ATG2 family
Family:
ATG2 familyPANTHER:PTHR13190
Representative Members: ATG2A (human)UniProtKB:Q2TAZ0
Role: extracts lipid from the donor membrane and unloads it into the phagophore
Function:
lipid transfer activityGO:0120013
Atg18/WIPI4 propeller
Participant: Family: Atg18/WIPI PROPPIN family
Family:
Atg18/WIPI PROPPIN familyPANTHER:PTHR11227
Representative Members: WDR45/WIPI4 (human)UniProtKB:Q9Y484
Role: holds the transferring tip on PI3P, increasing transfer efficiency
ATG9 scramblase
Participant: Family: ATG9 family
Family:
ATG9 familyPANTHER:PTHR13038
Representative Members: ATG9A (human)UniProtKB:Q7Z3C6
Role: equilibrates delivered lipid between the two phagophore leaflets

Function

lipid transfer activityGO:0120013
Substrates: glycerophospholipids of the donor membrane
Source location: endoplasmic reticulum membraneGO:0005789
Destination location: phagophoreGO:0061908

Processes

intermembrane lipid transferGO:0120009 autophagosome assemblyGO:0000045

Locations

organelle membrane contact siteGO:0044232
PMID:30952800
ATG2 is a lipid-transfer protein operating at the ER-autophagosome interface.
the autophagy protein, ATG2, without a clear function since its discovery over 20 yr ago, is in fact a lipid-transfer protein likely operating at the ER-autophagosome interface
PMID:31271352
ATG2A extracts and unloads lipids, and does so more efficiently between tethered membranes.
ATG2A can extract lipids from membrane vesicles and unload them to other vesicles. Lipid transfer by ATG2A is more efficient between tethered vesicles than between untethered vesicles.
PMID:30185561
ATG2 localizes to the PI3P-enriched ER-phagophore junction and is required for phagophore expansion.
Expansion of the precursor membrane phagophore requires autophagy-related 2 (ATG2), which localizes to the PI3P-enriched ER-phagophore junction.
Part 4: dissolution of the contact and sealing of the phagophore
Disassembly of the phagophore-organelle contact siteRegulatory Stepcontact_site_disassembly

The site is obligatorily transient. Two events dismantle it. First, the ER-isolation membrane contact must be actively dissolved: VMP1 promotes SERCA activity and thereby limits contact formation, and cells lacking VMP1 accumulate isolation membranes stably stuck to the ER with autophagosome formation blocked. Second, ESCRT-III-mediated abscission at the rim seals the phagophore into a closed double-membrane autophagosome, removing the open edge on which the bridging machinery acts. Whether the bridging proteins leave before, during, or after sealing is not established (see knowledge gaps).

Annotons

VMP1-SERCA control of contact lifetime
vmp1_serca_contact_dissolution
Participant: Gene Product: VMP1
Gene Product:
VMP1UniProtKB:Q96GC9

Function

SERCA-activating control of ER contact-site lifetime VMP1 binds SERCA and prevents assembly of the inhibitory SERCA/PLN/SLN complex, raising calcium-pump activity and limiting the persistence of ER-isolation membrane contacts. No GO molecular-function term captures this activator role, so only a preferred term is given.
Targets: SERCA (sarco/endoplasmic reticulum calcium ATPase)

Processes

positive regulation of ATPase-coupled calcium transmembrane transporter activityGO:1901896

Locations

endoplasmic reticulum membraneGO:0005789
PMID:28890335
VMP1 loss stabilizes ER-isolation membrane contacts and blocks autophagosome formation.
Loss of VMP1 causes stable association of IMs with the ER, thus blocking autophagosome formation.
PMID:28890335
VMP1 acts on contact formation by promoting SERCA activity, binding SERCA and preventing assembly of its inhibitory complex.
VMP1 interacts with SERCA and prevents formation of the SERCA/PLN/SLN inhibitory complex.
ESCRT-III sealing of the phagophore rim
escrt_iii_rim_sealing
Participant: Protein Complex: ESCRT III complex
Protein Complex:
ESCRT III complexGO:0000815 Membrane-remodeling polymer recruited to the phagophore to separate the inner and outer autophagosomal membranes.
Active units:
CHMP2A subunit
Participant: Gene Product: CHMP2A
Gene Product:
CHMP2AUniProtKB:O43633
Role: ESCRT-III subunit required for phagophore closure

Processes

autophagosome assemblyGO:0000045

Locations

phagophoreGO:0061908

Terminates the contact site by abolishing the open rim that the ATG2/ATG9 machinery works on.

PMID:30030437
CHMP2A is a critical regulator of phagophore closure.
we identify the endosomal sorting complexes required for transport (ESCRT)-III component CHMP2A as a critical regulator of phagophore closure
PMID:30030437
CHMP2A separates the inner and outer autophagosomal membranes.
During autophagy, CHMP2A translocates to the phagophore and regulates the separation of the inner and outer autophagosomal membranes to form double-membrane autophagosomes.
VPS4 AAA-ATPase-driven abscission
vps4_atpase_abscission
Participant: Gene Product: VPS4A
Gene Product:
VPS4AUniProtKB:Q9UN37

Function

ATP hydrolysis activityGO:0016887

Processes

autophagosome assemblyGO:0000045

AAA-ATPase that remodels and disassembles the ESCRT-III polymer; its inhibition impairs autophagosome completion.

PMID:30030437
Inhibiting VPS4 ATPase activity impairs autophagosome completion.
Consistently, inhibition of the AAA-ATPase VPS4 activity impairs autophagosome completion.
Variant set: Partner organelle and attachment mode by partner organelle / taxon (One Or More)

The first two variants are lipid-donating contacts built on the same ATG2 bridge; the third is a positional anchor that supplies no lipid and uses an entirely different tether. They are alternatives in the sense of which partner a given phagophore is attached to, and can co-occur.

ER-phagophore contact site (canonical)Cellular Componenter_phagophore_contact

The default and best-characterized realization. The ER cradles the isolation membrane as a continuous subdomain, ATG2 bridges the gap, and the ER is the principal lipid donor. GO has no cellular-component term for this structure.

endoplasmic reticulum membraneGO:0005789
PMID:19898463
The ER forms a cradle encircling the isolation membrane, with the two membranes interconnected.
Electron tomography revealed that the ER-IM complex appears as a subdomain of the ER that formed a cradle encircling the IM, and showed that both ER and isolation membranes are interconnected.
PMID:19855179
3D tomography reveals connections between the phagophore and endoplasmic reticulum.
Independent electron tomography showing direct connections between the phagophore and the ER. Cached abstract-only, so no verbatim quote is asserted.

Annotons

ATG2 N-terminal region association with the ER
atg2_n_terminal_er_association
Participant: Family: ATG2 family
Family:
ATG2 familyPANTHER:PTHR13190
Representative Members: ATG2A (human)UniProtKB:Q2TAZ0 Atg2 (S. cerevisiae)UniProtKB:P53855

Function

endoplasmic reticulum-organelle membrane tether activityGO:0170009

Locations

endoplasmic reticulum membraneGO:0005789

The ER-specific half of the bridge. The N-terminal membrane-binding region is dispensable for targeting the Atg2-Atg18 complex to the PAS but is what engages the ER, so it is the feature that makes this variant an ER contact rather than an endosomal one.

PMID:30254161
The N-terminal region of Atg2 associates with the ER and is required for isolation membrane formation at the PAS.
Our data suggest that this region associates with the endoplasmic reticulum (ER) and is responsible for the formation of the isolation membrane at the PAS.
Endosome-phagophore contact site (alternative lipid donor)Cellular Componentendosome_phagophore_contact

PI3P-rich endosomes can substitute as the ATG2 lipid source. ANKFY1, an endosomal FYVE-domain protein, binds PI3P and ATG2A and enhances ATG2A-mediated transfer; its depletion phenocopies ATG2A/B loss. Reported by a single laboratory, so modeled as an alternative route rather than as core composition.

recycling endosomeGO:0055037

Annotons

ANKFY1 recruitment of ATG2A to PI3P-rich endosomes
ankfy1_endosome_bridge
Participant: Gene Product: ANKFY1
Gene Product:
ANKFY1UniProtKB:Q9P2R3

Function

phosphatidylinositol-3-phosphate bindingGO:0032266

FYVE-domain endosomal protein that recruits ATG2A to endosomal PI3P and enhances ATG2A-mediated lipid transfer.

PMID:38622126
ANKFY1 recruits ATG2A to PI3P-rich endosomes and promotes transfer to phagophores.
we propose that ANKFY1 recruits ATG2A to PI3P-enriched endosomes and promotes ATG2A-mediated lipid transfer from endosomes to phagophores
Vacuole-phagophore anchor (budding yeast)Cellular Componentvacuole_phagophore_anchor

In S. cerevisiae the PAS is always made next to the vacuole. Vac8, an armadillo-repeat protein of the vacuolar membrane, tethers the PAS through the Atg1-complex subunit Atg13 and holds it there for the whole of autophagosome biogenesis. This attachment is positional - it confines where the phagophore is built and couples formation to subsequent fusion - and is not a lipid-donating contact. It is the one phagophore contact site with a dedicated GO term.

vacuole-isolation membrane contact siteGO:0120095
Context
Saccharomyces cerevisiae

Annotons

Vac8 vacuolar tether for the phagophore assembly site
vac8_vacuolar_tether
Participant: Gene Product: Vac8 (S. cerevisiae)
Gene Product:
Vac8 (S. cerevisiae)UniProtKB:P39968

Function

vacuolar membrane tether for the phagophore assembly site Armadillo-repeat tether anchoring the PAS to the vacuolar membrane via Atg13. GO's tether-activity terms are all ER-centric (e.g. GO:0170009), so no exact term is asserted.
Targets: Atg13 (S. cerevisiae)UniProtKB:Q06628

Locations

vacuolar membraneGO:0005774 vacuole-isolation membrane contact siteGO:0120095
PMID:31649143
Vac8 is the vacuolar tether that anchors the PAS via Atg13 throughout autophagosome biogenesis.
We show that Vac8 constitutes a vacuolar tether that stably anchors the PAS to the vacuole throughout autophagosome biogenesis via the PAS component Atg13.
PMID:31649143
The Vac8-dependent connection creates a confined space for autophagosome biogenesis between ER and vacuole.
the stable PAS-vacuole connection established by Vac8 creates a confined space for autophagosome biogenesis between the ER and the vacuole