Metazoan autophagosome biogenesis and maturation

In animals, macroautophagy builds a double-membrane autophagosome around cytoplasmic cargo and delivers it to lysosomes. The core steps are shared with yeast, but several are wired differently. An initiation complex of the Atg1/ULK kinase, ATG13 and ATG101 marks the site of formation, which in animals lies on endoplasmic reticulum (ER) subdomains called omegasomes. The class III phosphatidylinositol 3-kinase complex I (VPS34, the pseudokinase VPS15, Beclin 1 and ATG14) makes phosphatidylinositol 3-phosphate (PI3P) on this membrane. Two kinds of WD40 PROPPIN read PI3P. WIPI1/2-type proteins recruit the conjugation machinery, and WIPI3/4-type proteins partner the ATG2 rod in an ATG2-ATG18 complex. ATG2 carries lipids from the ER to the growing phagophore, and the ATG9 scramblase spreads them between the two leaflets. Atg8-family proteins are primed by ATG4 and conjugated to phosphatidylethanolamine by the E1 ATG7, the E2 ATG3 and the E3-like ATG12-ATG5-ATG16 complex, with ATG16 setting where conjugation happens. Animals have two Atg8 subfamilies, GABARAP-type and LC3-type, and the stage at which each acts differs between lineages: in nematodes the GABARAP-type protein acts early and the LC3-type protein late, whereas in mammalian cells the GABARAP subfamily dominates autophagosome-lysosome fusion. Cargo receptors such as p62/SQSTM1 link ubiquitinated cargo to Atg8-family proteins. Fusion with late endosomes and lysosomes needs EPG5, a metazoan-specific RAB7 effector that binds Atg8-family proteins and SNAREs and makes sure autophagosomes fuse with the correct partner.

MODULE:metazoan_autophagosome_biogenesisDRAFTCONCRETEBiological Processmodules/metazoan_autophagosome_biogenesis.yaml
macroautophagyGO:0016236
PMID:20550938
C. elegans screen identifies autophagy genes specific to multicellular organisms.
Genetic screens in C. elegans define metazoan-specific autophagy genes (epg-2 to epg-5) acting at discrete steps, including EPG-5 in formation of degradative autolysosomes.
Genetic analysis reveals that epg-2, -3, -4, and -5 define discrete genetic steps of the autophagy pathway.
PMID:21802374
The WD40 repeat PtdIns(3)P-binding protein EPG-6 regulates progression of omegasomes to autophagosomes.
Hierarchical analysis of worm autophagy genes in aggregate degradation: the UNC-51 complex, EPG-8/Atg14 and lipidated LGG-1 binding to aggregates are required for omegasome formation; the two PI3P effectors EPG-6 and ATG-18 act differently.
We also established the hierarchical relationship of autophagy genes in degradation of protein aggregates and revealed that the UNC-51/Atg1 complex, EPG-8/Atg14, and binding of lipidated LGG-1 to protein aggregates are required for omegasome formation.
PMID:24374177
The C. elegans LC3 acts downstream of GABARAP to degrade autophagosomes by interacting with the HOPS subunit VPS39.
Sequential requirement of LGG-1, LGG-2, RAB-7 and HOPS in generating autolysosomes in C. elegans.
Genetic analyses sustain a sequential implication of LGG-1, LGG-2, RAB-7, and HOPS complex to generate autolysosomes.
PMID:27864321
Atg8 family LC3/GABARAP proteins are crucial for autophagosome-lysosome fusion but not autophagosome formation during PINK1/Parkin mitophagy and starvation.
In human cells lacking all six Atg8 proteins, autophagosomes still form but are smaller, and fusion with lysosomes fails.
Although neither GABARAPs nor LC3s are required for autophagosome biogenesis, loss of all Atg8s yields smaller autophagosomes and a slowed initial rate of autophagosome formation.
file:modules/phagophore_assembly_site.yaml
Phagophore assembly site (PAS) module (budding yeast)
The yeast module that models the Atg17-Atg29-Atg31 scaffold and Atg1-complex condensate, Atg9 vesicles, PI3K complex I, Atg2-Atg18 and the Atg8 conjugation system at the PAS. This module is its metazoan counterpart.
file:modules/phagophore_organelle_contact_site.yaml
Phagophore-organelle membrane contact site module
Models the ER-phagophore bridge (ATG2 rod, WIPI4 clamp, VMP1/TMEM41B and ATG9 scramblases) in structural detail; this module includes ATG2 and ATG9 only as the lipid-supply step.

Boundary. Bulk and selective macroautophagy in animals, from the initiation complex to fusion of the autophagosome with late endosomes and lysosomes. Eight parts in pathway order: ULK1 initiation complex, PI3KC3-C1 nucleation, PI3P effectors, lipid supply (ATG2, ATG9), Atg8 conjugation, Atg8-family membrane proteins (with a lineage variant set for the stage at which each subfamily acts), optional cargo recruitment (SQSTM1/SQST-1), and EPG5-dependent fusion. Upstream regulation by mTOR and AMPK, transcriptional induction by TFEB/HLH-30, lysosomal degradation itself, and the PI3KC3-C2 endocytic complex are outside the boundary. HLH-30 and the LIPL-4 lipid branch are modelled in MODULE:c_elegans_lysosomal_lipid_signaling. Mitochondrion-specific receptors are modelled in MODULE:mitophagy. Context taxon. Metazoa. The boundary is drawn around steps that are shared by nematodes and mammals and that differ from budding yeast: ATG101 in the initiation complex (absent from Saccharomyces cerevisiae), the omegasome/ER origin, the split of Atg8 into GABARAP and LC3 subfamilies, and EPG5 at fusion (no yeast ortholog). Representative members are the C. elegans protein (where the genetics of the metazoan-specific steps was worked out) and the human ortholog, each with a gene review. Human ATG101, ATG3, ATG4B and WDR45 (WIPI4) have no gene review here, so those roles are represented by the worm protein only. Relation to MODULE:phagophore_assembly_site. That module is yeast-centred and models the Atg17-Atg29-Atg31 scaffold, which animals lack (FIP200 takes its place in mammals), and the condensate biophysics of the PAS. This module models the same conserved activities at the level of families, and adds the metazoan-specific steps. MODULE:phagophore_organelle_contact_site models the ATG2 bridge and scramblases structurally; here they appear only as the lipid-supply part. Members noted but not modelled as annotons. ATG14 (worm EPG-8, a divergent homolog; human ATG14 Q6ZNE5), ATG12 (worm LGG-3), FIP200/RB1CC1, VMP1 (EPG-3), EI24 (EPG-4), ATG-16.1, ATG-4.2, VPS-39/HOPS, RAB7, STX17-SNAP29 and the worm scaffold EPG-7. ATG-4.2 acts mainly at the delipidation/maturation stage (PMID:22767594) and would be a separate annoton if modelled. BEC-1 also acts in the PI3KC3-C2 complex in endosome-to-Golgi retrograde transport and phagosome maturation (PMID:21183797). ATG-18, EPG-5 and LGG-1 also act in phagocytes to degrade apoptotic corpses (PMID:22451698). These roles are noted in the gene reviews and are outside this module. Lipidation nuance. In C. elegans, LGG-1 cleavage, not PE conjugation, is essential for autophagosome initiation (PMID:37395461), and in human cells autophagosomes still form without any Atg8 protein (PMID:27864321). The Atg8-family annotons keep phosphatidylethanolamine binding as their MF to match the gene review core functions, and this caveat is recorded as a knowledge gap. Lipidation process term. The E1, E2 and E3-like annotons (atg7_e1, atg3_e2, atg5_e3) carry C-terminal protein lipidation (GO:0006501) as their process, not the precomposed GO:0061739 protein lipidation involved in autophagosome assembly: this module supplies the autophagosome-assembly context, and their molecular functions name the Atg8-family substrate (projects/INVOLVED_IN_PRECOMPOSITION.md). The atg8_conjugation node keeps GO:0061739 as its concept, because a node concept maps the step to its exact GO class rather than annotating a gene. If GO obsoletes GO:0061739, the concept becomes GO:0006501, and the node description already names the Atg8-family substrate.

11Nodes
8Parts
1Variant Sets
2Variants
21Annotons
9Connections

Derived QC

Recommended-field compliance

65.2% recommended fields populated
  • knowledge_gaps[0] · boundary (0/1)
  • knowledge_gaps[0].provenance[0] · reference_section_type (0/1)
  • knowledge_gaps[0].provenance[1] · reference_section_type (0/1)
  • knowledge_gaps[1] · boundary (0/1)
  • knowledge_gaps[1].provenance[0] · reference_section_type (0/1)
  • knowledge_gaps[1].provenance[1] · reference_section_type (0/1)
  • knowledge_gaps[2] · boundary (0/1)
  • knowledge_gaps[2].provenance[0] · reference_section_type (0/1)

Module deep research

✗ none found

No MODULE:metazoan_autophagosome_biogenesis 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.

  • ulk1_initiation → pi3k_nucleation [NOT_CHECKED]
  • pi3p_effector → lipid_supply [NOT_CHECKED]
  • pi3p_effector → atg8_conjugation [NOT_CHECKED]
  • atg8_family → maturation_fusion [NOT_CHECKED]

Function consistency and core coverage

28 gene-function check(s) reflected in core functions · 0 conflict(s) · 25 evidence or coverage gap(s) (55 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
ulk_kinase UNC-51 (C. elegans)
UniProtKB:Q23023
Family Representative 		protein serine/threonine kinase activity
GO:0004674 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
ulk_kinase ULK1 (human)
UniProtKB:O75385
Family Representative 		protein serine/threonine kinase activity
GO:0004674 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg13_regulator ATG-13/EPG-1 (C. elegans)
UniProtKB:P34379
Family Representative 		protein kinase regulator activity
GO:0019887 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg13_regulator ATG13 (human)
UniProtKB:O75143
Family Representative 		protein kinase regulator activity
GO:0019887 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg101_subunit EPG-9 (C. elegans)
UniProtKB:Q95XH2
Family Representative 		protein kinase binding
GO:0019901 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
vps34_kinase VPS-34/LET-512 (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_kinase PIK3C3/VPS34 (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).
vps15_pseudokinase VPS-15 (C. elegans)
UniProtKB:Q23669
Family Representative 		1-phosphatidylinositol-3-kinase activity
GO:0016303 		Contributes Only
The review records contribution to this activity, not independent enabling. Check whether the module participant should be a complex.
vps15_pseudokinase PIK3R4/VPS15 (human)
UniProtKB:Q99570
Family Representative 		1-phosphatidylinositol-3-kinase activity
GO:0016303 		Contributes Only
The review records contribution to this activity, not independent enabling. Check whether the module participant should be a complex.
beclin_scaffold BEC-1 (C. elegans)
UniProtKB:Q22592
Family Representative 		protein-macromolecule adaptor activity
GO:0030674 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
beclin_scaffold BECN1 (human)
UniProtKB:Q14457
Family Representative 		protein-macromolecule adaptor activity
GO:0030674 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
wipi12_pi3p_binding ATG-18 (C. elegans)
UniProtKB:O16466
Family Representative 		phosphatidylinositol-3-phosphate binding
GO:0032266 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
wipi12_pi3p_binding WIPI2 (human)
UniProtKB:Q9Y4P8
Family Representative 		phosphatidylinositol-3-phosphate binding
GO:0032266 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
wipi34_pi3p_binding EPG-6 (C. elegans)
UniProtKB:Q86MP3
Family Representative 		phosphatidylinositol-3-phosphate binding
GO:0032266 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg2_lipid_transfer ATG-2 (C. elegans)
UniProtKB:Q21480
Family Representative 		lipid transfer activity
GO:0120013 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg2_lipid_transfer ATG2A (human)
UniProtKB:Q2TAZ0
Family Representative 		lipid transfer activity
GO:0120013 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg9_scramblase ATG-9 (C. elegans)
UniProtKB:Q9TXN6
Family Representative 		phospholipid scramblase activity
GO:0017128 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg9_scramblase ATG9A (human)
UniProtKB:Q7Z3C6
Family Representative 		phospholipid scramblase activity
GO:0017128 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg4_priming ATG-4.1 (C. elegans)
UniProtKB:K8ESC5
Family Representative 		cysteine-type endopeptidase activity
GO:0004197 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg7_e1 ATG-7 (C. elegans)
UniProtKB:G5EBK4
Family Representative 		Atg8 activating enzyme activity
GO:0019779 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg7_e1 ATG7 (human)
UniProtKB:O95352
Family Representative 		Atg8 activating enzyme activity
GO:0019779 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg3_e2 ATG-3 (C. elegans)
UniProtKB:Q9N369
Family Representative 		Atg8-family conjugating enzyme activity
GO:0141046 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg5_e3 ATG-5 (C. elegans)
UniProtKB:Q3V5I7
Family Representative 		Atg8-family ligase activity
GO:0019776 		Contributes Only
The review records contribution to this activity, not independent enabling. Check whether the module participant should be a complex.
atg5_e3 ATG5 (human)
UniProtKB:Q9H1Y0
Family Representative 		Atg8-family ligase activity
GO:0019776 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg16_site ATG-16.2 (C. elegans)
UniProtKB:Q09406
Family Representative 		protein-membrane adaptor activity
GO:0043495 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
atg16_site ATG16L1 (human)
UniProtKB:Q676U5
Family Representative 		protein-membrane adaptor activity
GO:0043495 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
lgg1_early LGG-1 (C. elegans)
UniProtKB:Q09490
Family Representative 		phosphatidylethanolamine binding
GO:0008429 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
lgg2_late LGG-2 (C. elegans)
UniProtKB:Q23536
Family Representative 		phosphatidylethanolamine binding
GO:0008429 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
lc3_elongation MAP1LC3B (human)
UniProtKB:Q9GZQ8
Family Representative 		phosphatidylethanolamine binding
GO:0008429 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
gabarap_fusion GABARAP (human)
UniProtKB:O95166
Family Representative 		phosphatidylethanolamine binding
GO:0008429 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
sqstm1_receptor SQST-1 (C. elegans)
UniProtKB:Q22436
Family Representative 		autophagy cargo adaptor activity
GO:0160247 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
sqstm1_receptor SQSTM1/p62 (human)
UniProtKB:Q13501
Family Representative 		autophagy cargo adaptor activity
GO:0160247 		Function Unreviewed
No retained annotation or core molecular function supports this GO assertion. Missing or broader evidence is a coverage gap, not proof the activity is absent.
epg5_tether EPG-5 (C. elegans)
UniProtKB:Q18892
Family Representative 		vesicle membrane tethering activity
GO:7770062 		Function Unreviewed
No retained annotation or core molecular function supports this GO assertion. Missing or broader evidence is a coverage gap, not proof the activity is absent.
epg5_tether EPG5 (human)
UniProtKB:Q9HCE0
Family Representative 		vesicle membrane tethering activity
GO:7770062 		Function Unreviewed
No retained annotation or core molecular function supports this GO assertion. Missing or broader evidence is a coverage gap, not proof the activity is absent.
ulk_kinase Atg1/ULK1 kinases
PANTHER:PTHR24348
Family 		protein serine/threonine kinase activity
GO:0004674 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR24348.
atg13_regulator ATG13 proteins
PANTHER:PTHR13430
Family 		protein kinase regulator activity
GO:0019887 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR13430.
atg101_subunit ATG101 proteins
PANTHER:PTHR13292
Family 		protein kinase binding
GO:0019901 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR13292.
vps34_kinase VPS34 class III PI3K catalytic subunits
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.
vps15_pseudokinase VPS15/PIK3R4 proteins
PANTHER:PTHR17583
Family 		1-phosphatidylinositol-3-kinase activity
GO:0016303 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR17583.
beclin_scaffold Beclin 1 proteins
PANTHER:PTHR12768
Family 		protein-macromolecule adaptor activity
GO:0030674 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR12768.
wipi12_pi3p_binding WIPI1/2-type PROPPINs (Atg18 clade)
PANTHER:PTHR11227
Family 		phosphatidylinositol-3-phosphate binding
GO:0032266 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR11227.
wipi34_pi3p_binding WIPI3/4-type PROPPINs (EPG-6/WDR45 clade)
PANTHER:PTHR11227:SF29
Family 		phosphatidylinositol-3-phosphate binding
GO:0032266 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR11227:SF29.
atg2_lipid_transfer ATG2 proteins
PANTHER:PTHR13190
Family 		lipid transfer activity
GO:0120013 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR13190.
atg9_scramblase ATG9 proteins
PANTHER:PTHR13038
Family 		phospholipid scramblase activity
GO:0017128 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR13038.
atg4_priming ATG4 cysteine proteases
PANTHER:PTHR22624
Family 		cysteine-type endopeptidase activity
GO:0004197 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR22624.
atg7_e1 ATG7 proteins
PANTHER:PTHR10953:SF3
Family 		Atg8 activating enzyme activity
GO:0019779 		Family Supported
Family review supports GO:0019779 for PANTHER:PTHR10953:SF3. ATG8-family activation is the second activity of the ATG7 subfamily SF3.
atg3_e2 ATG3 proteins
PANTHER:PTHR12866
Family 		Atg8-family conjugating enzyme activity
GO:0141046 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR12866.
atg5_e3 ATG5 proteins
PANTHER:PTHR13040
Family 		Atg8-family ligase activity
GO:0019776 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR13040.
atg16_site ATG16 proteins
PANTHER:PTHR19878
Family 		protein-membrane adaptor activity
GO:0043495 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR19878.
lgg1_early GABARAP-subfamily Atg8 proteins
PANTHER:PTHR10969
Family 		phosphatidylethanolamine binding
GO:0008429 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR10969.
lgg2_late LC3-subfamily Atg8 proteins
PANTHER:PTHR10969
Family 		phosphatidylethanolamine binding
GO:0008429 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR10969.
lc3_elongation LC3-subfamily Atg8 proteins
PANTHER:PTHR10969
Family 		phosphatidylethanolamine binding
GO:0008429 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR10969.
gabarap_fusion GABARAP-subfamily Atg8 proteins
PANTHER:PTHR10969
Family 		phosphatidylethanolamine binding
GO:0008429 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR10969.
sqstm1_receptor p62/sequestosome 1 proteins
PANTHER:PTHR15090
Family 		autophagy cargo adaptor activity
GO:0160247 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR15090.
epg5_tether EPG5 proteins
PANTHER:PTHR31139
Family 		vesicle membrane tethering activity
GO:7770062 		Family Review Missing
No supported structured family review is available for PANTHER:PTHR31139.

Gene-review completeness (34/34 grounded genes reviewed)

24 complete review(s) · 23 with deep research · 0 missing review · 11 reviewed but lacking deep research

Gene Review Complete Deep research
atg-13 P34379 ✓ ✓ ✓
atg-16.2 Q09406 ✓ ✓ ✓
atg-18 O16466 ✓ ✓ ✓
atg-2 Q21480 ✓ ✓ ✓
atg-3 Q9N369 ✓ ✓ ✓
atg-4.1 K8ESC5 ✓ ✓ ✓
atg-5 Q3V5I7 ✓ ✓ ✓
atg-7 G5EBK4 ✓ ✓ ✓
atg-9 Q9TXN6 ✓ ✓ ✗
ATG13 O75143 ✓ ✓ ✗
ATG16L1 Q676U5 ✓ ✓ ✗
ATG2A Q2TAZ0 ✓ 30/31 ✓
ATG5 Q9H1Y0 ✓ 88/90 ✓
ATG7 O95352 ✓ ✓ ✓
ATG9A Q7Z3C6 ✓ ✓ ✗
bec-1 Q22592 ✓ ✓ ✓
BECN1 Q14457 ✓ 189/191 ✓
epg-5 Q18892 ✓ ✓ ✓
epg-6 Q86MP3 ✓ ✓ ✓
epg-9 Q95XH2 ✓ ✓ ✓
EPG5 Q9HCE0 ✓ 14/16 ✗
GABARAP O95166 ✓ ✓ ✗
lgg-1 Q09490 ✓ 48/49 ✓
lgg-2 Q23536 ✓ ✓ ✓
MAP1LC3B Q9GZQ8 ✓ ✓ ✗
PIK3C3 Q8NEB9 ✓ 108/119 ✓
PIK3R4 Q99570 ✓ 64/66 ✗
sqst-1 Q22436 ✓ 13/14 ✓
SQSTM1 Q13501 ✓ ✓ ✓
ULK1 O75385 ✓ 137/139 ✗
unc-51 Q23023 ✓ ✓ ✓
vps-15 Q23669 ✓ ✓ ✗
vps-34 Q9TXI7 ✓ ✓ ✓
WIPI2 Q9Y4P8 ✓ 43/45 ✗

Details

Context
MetazoaNCBITaxon:33208
cytoplasmGO:0005737
Metazoan autophagosome biogenesis and maturationBiological Processmetazoan_autophagosome_biogenesis

ULK1-complex initiation, PI3KC3-C1 nucleation, PI3P effector recruitment, ATG2/ATG9 lipid supply, Atg8 conjugation and membrane anchoring, cargo recruitment and EPG5-dependent fusion of autophagosomes with lysosomes in animals.

macroautophagyGO:0016236
Context
MetazoaNCBITaxon:33208
cytoplasmGO:0005737

Connections

The ULK1 complex acts upstream of PI3KC3-C1 recruitment; in C. elegans the UNC-51 complex is needed for omegasome formation.
pi3k_nucleation -> pi3p_effector Provides Input For
PI3P made by VPS34 in PI3KC3-C1 is the lipid that WIPI proteins bind.
WIPI3/4-type proteins hold ATG2 at the PI3P-positive phagophore edge.
WIPI2 recruits ATG16L1 and so the E3-like complex to the phagophore. In C. elegans, atg-16.2 is placed genetically upstream of atg-2, epg-6 and atg-18, so the order is not strictly linear.
atg8_conjugation -> atg8_family Provides Input For
The conjugation system attaches Atg8-family proteins to phosphatidylethanolamine on the phagophore.
cargo_recruitment -> atg8_family Provides Input For
Cargo receptors bind Atg8-family proteins through LIR motifs and bring cargo into the forming autophagosome.
Atg8-family proteins on the closed autophagosome are needed for fusion; EPG5 binds them on the autophagosome.
PMID:27864321
Atg8 family LC3/GABARAP proteins are crucial for autophagosome-lysosome fusion but not autophagosome formation during PINK1/Parkin mitophagy and starvation.
Atg8 proteins are dispensable for autophagosome formation but essential for fusion.
We show that Atg8s are dispensable for autophagosome formation and selective engulfment of mitochondria, but essential for autophagosome-lysosome fusion.
Part 1: initiation by the Atg1/ULK1 kinase complex
ULK1-ATG13-ATG101 initiation complexProtein Complexulk1_initiation

The Atg1/ULK1 kinase, ATG13 and ATG101 form the most upstream autophagy-specific complex. ATG13 binds the kinase and links it to the scaffold FIP200 in mammals; ATG101 binds ATG13. ATG101 is present in animals but absent from budding yeast. In C. elegans the complex is UNC-51, ATG-13 (EPG-1) and EPG-9.

Atg1/ULK1 kinase complexGO:1990316

Annotons

Atg1/ULK1 serine/threonine kinase
ulk_kinase
Participant: Family: Atg1/ULK1 kinases
Family:
Atg1/ULK1 kinasesPANTHER:PTHR24348
Representative Members: UNC-51 (C. elegans)UniProtKB:Q23023 ULK1 (human)UniProtKB:O75385

Function

protein serine/threonine kinase activityGO:0004674 Autophagy role only. UNC-51 also acts in axon guidance, which is outside this module (unc-51 gene review).

Processes

autophagosome assemblyGO:0000045

Locations

phagophore assembly siteGO:0000407

Initiating kinase that phosphorylates downstream autophagy proteins once mTOR inhibition is relieved.

PMID:19225151
ULK-Atg13-FIP200 complexes mediate mTOR signaling to the autophagy machinery.
Human ATG13 links ULK1/2 to FIP200 and activates ULK.
The mammalian Atg13 binds both ULK1 and ULK2 and mediates the interaction of the ULK proteins with FIP200.
PMID:19377305
epg-1 functions in autophagy-regulated processes and may encode a highly divergent Atg13 homolog in C. elegans.
The worm Atg13 homolog EPG-1 binds UNC-51.
epg-1 displays a similar expression pattern to, and directly interacts with, the C. elegans Atg1 homolog UNC-51
ATG13 kinase regulatory subunit
atg13_regulator
Participant: Family: ATG13 proteins
Family:
ATG13 proteinsPANTHER:PTHR13430
Representative Members: ATG-13/EPG-1 (C. elegans)UniProtKB:P34379 ATG13 (human)UniProtKB:O75143

Function

protein kinase regulator activityGO:0019887 Stabilises and activates the ULK kinase. ATG13 is a subunit of the ULK1 complex, not of the PI3K complex.

Processes

autophagosome assemblyGO:0000045

Locations

phagophore assembly siteGO:0000407

Regulatory subunit that binds the kinase and the other complex subunits (FIP200 in mammals, ATG101).

PMID:19225151
ULK-Atg13-FIP200 complexes mediate mTOR signaling to the autophagy machinery.
ATG13 binding stabilises and activates ULK and is needed for autophagosome formation.
The binding of Atg13 stabilizes and activates ULK and facilitates the phosphorylation of FIP200 by ULK, whereas knockdown of Atg13 inhibits autophagosome formation.
PMID:19377305
epg-1 functions in autophagy-regulated processes and may encode a highly divergent Atg13 homolog in C. elegans.
EPG-1 is a divergent worm Atg13 that binds UNC-51.
suggesting that epg-1 encodes a divergent functional homolog of Atg13 in C. elegans
ATG101 subunit
atg101_subunit
Participant: Family: ATG101 proteins
Family:
ATG101 proteinsPANTHER:PTHR13292
Representative Members: EPG-9 (C. elegans)UniProtKB:Q95XH2

Function

protein kinase bindingGO:0019901 As in the epg-9 gene review core function; EPG-9 binds ATG-13 within the kinase complex.

Processes

autophagosome assemblyGO:0000045

Locations

phagophore assembly siteGO:0000407

Animal-specific subunit (absent from budding yeast) that binds ATG13; its loss phenocopies loss of the kinase.

PMID:22885670
The C. elegans ATG101 homolog EPG-9 directly interacts with EPG-1/Atg13 and is essential for autophagy.
EPG-9 binds EPG-1/Atg13 and its mutants resemble unc-51 and epg-1 mutants.
epg-9 mutants exhibit autophagy phenotypes characteristic of those associated with loss of function of unc-51/Atg1 and epg-1/Atg13. epg-9 encodes a protein with significant homology to mammalian ATG101. EPG-9 directly interacts with EPG-1/Atg13.
Part 2: autophagic membrane nucleation by the class III PI3K complex I
PI3KC3-C1 nucleation (VPS34, VPS15, Beclin 1)Protein Complexpi3k_nucleation

The class III PI3K complex I (VPS34, VPS15, Beclin 1 and ATG14) makes PI3P on ER-associated omegasomes and phagophores. VPS34 is the catalytic subunit; VPS15 is a pseudokinase that contributes to the activity of the complex; Beclin 1 is the scaffold. ATG14 (EPG-8 in C. elegans, a divergent homolog that binds BEC-1) directs the complex to autophagy. A second complex with UVRAG instead of ATG14 (PI3KC3-C2) acts in endocytic trafficking and is outside this module.

phosphatidylinositol 3-kinase complex, class III, type IGO:0034271

Annotons

VPS34 phosphatidylinositol 3-kinase
vps34_kinase
Participant: Family: VPS34 class III PI3K catalytic subunits
Family:
VPS34 class III PI3K catalytic subunitsPANTHER:PTHR10048:SF7
Representative Members: VPS-34/LET-512 (C. elegans)UniProtKB:Q9TXI7 PIK3C3/VPS34 (human)UniProtKB:Q8NEB9

Function

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

Processes

phosphatidylinositol-3-phosphate biosynthetic processGO:0036092 autophagosome assemblyGO:0000045

Locations

phagophore assembly siteGO:0000407

Catalytic subunit that makes PI3P at the site of autophagosome formation. Its activity depends on Beclin 1.

PMID:11927551
Membrane transport in Caenorhabditis elegans: an essential role for VPS34 at the nuclear membrane.
Immunopurified worm VPS-34 phosphorylates PtdIns to PtdIns 3-P.
The anti- Ce VPS34 immunoprecipitate displayed a lipid kinase activity towards PtdIns, yielding PtdIns 3-P as a product.
PMID:16111945
Inactivation of the autophagy gene bec-1 triggers apoptotic cell death in C. elegans.
BEC-1 is needed for the function of the class III PI3K LET-512/VPS-34, which is required for autophagy.
We demonstrate that BEC-1 is necessary for the function of the class III PI3 kinase LET-512/Vps34, an essential protein required for autophagy, membrane trafficking, and endocytosis.
VPS15 pseudokinase regulatory subunit
vps15_pseudokinase
Participant: Family: VPS15/PIK3R4 proteins
Family:
VPS15/PIK3R4 proteinsPANTHER:PTHR17583
Representative Members: VPS-15 (C. elegans)UniProtKB:Q23669 PIK3R4/VPS15 (human)UniProtKB:Q99570

Function

1-phosphatidylinositol-3-kinase activityGO:0016303 contributes_to: VPS15 is a pseudokinase that does not itself phosphorylate lipids. It binds VPS34, raises its activity and regulates the complex, so the worm and human gene reviews record it as contributing to the catalytic activity of the complex.

Processes

autophagosome assemblyGO:0000045

Locations

phagophore assembly siteGO:0000407

Pseudokinase subunit that stabilises VPS34 and controls the activity of the complex on membranes.

PMID:8999962
Characterization of p150, an adaptor protein for the human phosphatidylinositol (PtdIns) 3-kinase. Substrate presentation by phosphatidylinositol transfer protein to the p150.Ptdins 3-kinase complex.
Human p150/VPS15 binds VPS34 and raises its lipid kinase activity.
Recombinant p150 associated with PtdIns 3-kinase in vitro in a stable manner
PMID:26783301
Negative regulation of phosphatidylinositol 3-phosphate levels in early-to-late endosome conversion.
In C. elegans the class III PI3K complex is VPS-34, BEC-1 and VPS-15.
the class III PI3K complex, which is composed of VPS-34, BEC-1, and VPS-15/p150
Beclin 1 class III PI3K complex adaptor
beclin_scaffold
Participant: Family: Beclin 1 proteins
Family:
Beclin 1 proteinsPANTHER:PTHR12768
Representative Members: BEC-1 (C. elegans)UniProtKB:Q22592 BECN1 (human)UniProtKB:Q14457

Function

protein-macromolecule adaptor activityGO:0030674 Links VPS34-VPS15 to the autophagy-specific subunit ATG14 (EPG-8 in C. elegans). Beclin 1 also binds BCL-2 family proteins (CED-9 in C. elegans), which is outside this module.

Processes

autophagosome assemblyGO:0000045

Locations

phagophore assembly siteGO:0000407

Non-catalytic scaffold that holds together the autophagy-specific class III PI3K complex.

PMID:21116129
The coiled-coil domain protein EPG-8 plays an essential role in the autophagy pathway in C. elegans.
EPG-8, a divergent Atg14 homolog, binds BEC-1 directly.
EPG-8 directly interacts with the C. elegans Beclin 1 homolog, BEC-1. Our study demonstrates that epg-8 may function as a highly divergent homolog of the yeast autophagy gene Atg14.
PMID:12958363
Autophagy genes are essential for dauer development and life-span extension in C. elegans.
bec-1 is the worm ortholog of APG6/VPS30/beclin 1 and is required for dauer morphogenesis and lifespan extension.
bec-1, the C. elegans ortholog of the yeast and mammalian autophagy gene APG6/VPS30/beclin1, is essential for normal dauer morphogenesis and life-span extension
Part 3: PI3P effector recruitment to early autophagic membranes
WIPI/PROPPIN PI3P effectorsMolecular Functionpi3p_effector

Two kinds of WD40 PROPPIN bind PI3P through an FRRG motif. WIPI1/2 type proteins (C. elegans ATG-18, human WIPI2) recruit the ATG12-ATG5-ATG16 complex and act in autophagosome formation. WIPI3/4-type proteins (C. elegans EPG-6, human WDR45/WIPI4) bind ATG2 and form the ATG2-ATG18 complex that moves omegasomes forward to autophagosomes. Both kinds belong to one PANTHER family; the split is a subfamily (paralog) split.

Annotons

WIPI1/2-type PI3P effector
wipi12_pi3p_binding
Participant: Family: WIPI1/2-type PROPPINs (Atg18 clade)
Family:
WIPI1/2-type PROPPINs (Atg18 clade)PANTHER:PTHR11227 The PANTHER family also contains the WIPI3/4-type paralogs; only the WIPI1/2 clade fills this role.
Representative Members: ATG-18 (C. elegans)UniProtKB:O16466 WIPI2 (human)UniProtKB:Q9Y4P8

Function

phosphatidylinositol-3-phosphate bindingGO:0032266 WIPI2 also acts as an adaptor that recruits ATG16L1 (human WIPI2 gene review); PI3P binding is the activity shared with ATG-18.

Processes

autophagosome assemblyGO:0000045

Locations

phagophore assembly siteGO:0000407

Reads PI3P made by PI3KC3-C1 and recruits the Atg8 conjugation machinery.

PMID:20505359
Mammalian Atg18 (WIPI2) localizes to omegasome-anchored phagophores and positively regulates LC3 lipidation.
WIPI2 is a PI3P effector needed to form LC3-positive autophagosomes.
WIPI2 is recruited to early autophagosomal structures along with Atg16L and ULK1 and is required for the formation of LC3-positive autophagosomes.
PMID:21802374
The WD40 repeat PtdIns(3)P-binding protein EPG-6 regulates progression of omegasomes to autophagosomes.
ATG-18 is a PI3P effector with a role in autophagosome formation that differs from EPG-6.
Another WD40 repeat PtdIns(3)P effector, ATG-18, plays a distinct role in autophagosome formation.
PMID:22451698
Autophagy genes function sequentially to promote apoptotic cell corpse degradation in the engulfing cell.
The FRRG motif of ATG-18 is its PI3P binding site.
FRRG (amino acids 227–230) in ATG-18 was identified as the PI(3)P binding site
WIPI3/4-type PI3P effector, partner of ATG2
wipi34_pi3p_binding
Participant: Family: WIPI3/4-type PROPPINs (EPG-6/WDR45 clade)
Family:
WIPI3/4-type PROPPINs (EPG-6/WDR45 clade)PANTHER:PTHR11227:SF29 PANTHER places EPG-6 in the WIPI4 subfamily. Human WDR45 (WIPI4) has no gene review here; the worm protein is the representative.
Representative Members: EPG-6 (C. elegans)UniProtKB:Q86MP3

Function

phosphatidylinositol-3-phosphate bindingGO:0032266 Acts within the ATG2-ATG18 complex (GO:0062079), where it holds the ATG2 tip on PI3P-containing membranes (epg-6 gene review).

Processes

autophagosome assemblyGO:0000045

Locations

phagophoreGO:0061908

Binds ATG2 and PI3P and moves omegasomes forward to autophagosomes.

PMID:21802374
The WD40 repeat PtdIns(3)P-binding protein EPG-6 regulates progression of omegasomes to autophagosomes.
EPG-6 binds PI3P and ATG-2 and is needed for omegasomes to become autophagosomes.
EPG-6 directly interacts with ATG-2. epg-6 and atg-2 regulate progression of omegasomes to autophagosomes, and their loss of function causes accumulation of enlarged early autophagic structures.
Part 4: lipid supply for phagophore expansion
ATG2 lipid transfer and ATG9 scramblingMolecular Functionlipid_supply

ATG2, held at the phagophore edge by WIPI3/4-type proteins, carries bulk glycerophospholipids from the ER to the growing phagophore. The ATG9 trimer scrambles lipids between leaflets so that the membrane can grow. The structure of this bridge is modelled in MODULE:phagophore_organelle_contact_site.

ATG2-ATG18 complexGO:0062079

Annotons

ATG2 bridge-like lipid transfer protein
atg2_lipid_transfer
Participant: Family: ATG2 proteins
Family:
ATG2 proteinsPANTHER:PTHR13190
Representative Members: ATG-2 (C. elegans)UniProtKB:Q21480 ATG2A (human)UniProtKB:Q2TAZ0

Function

lipid transfer activityGO:0120013
Source location: endoplasmic reticulum membrane
Destination location: phagophore

Processes

autophagosome assemblyGO:0000045

Locations

phagophoreGO:0061908

Rod-shaped protein that tethers the ER to the phagophore edge and moves lipids along its hydrophobic groove.

PMID:30952800
ATG2 transports lipids to promote autophagosome biogenesis.
Human ATG2A binds many glycerophospholipids and transfers them in vitro.
ATG2A can bind tens of glycerophospholipids at once and transfers lipids robustly in vitro
PMID:21802374
The WD40 repeat PtdIns(3)P-binding protein EPG-6 regulates progression of omegasomes to autophagosomes.
In C. elegans, ATG-2 binds EPG-6 and both are needed for omegasome progression.
EPG-6 directly interacts with ATG-2.
ATG9 phospholipid scramblase
atg9_scramblase
Participant: Family: ATG9 proteins
Family:
ATG9 proteinsPANTHER:PTHR13038
Representative Members: ATG-9 (C. elegans)UniProtKB:Q9TXN6 ATG9A (human)UniProtKB:Q7Z3C6

Function

phospholipid scramblase activityGO:0017128

Processes

autophagosome assemblyGO:0000045

Locations

phagophore assembly siteGO:0000407

Trimeric membrane protein in small vesicles that seeds the phagophore and equilibrates lipids delivered by ATG2 between leaflets.

PMID:33106659
Structure, lipid scrambling activity and role in autophagosome formation of ATG9A.
Human ATG9A scrambles lipids, and this is needed for autophagosome expansion.
Mutations in the pore reduce scrambling activity and yield markedly smaller autophagosomes, indicating that lipid scrambling by ATG9A is essential for membrane expansion.
PMID:33106658
Atg9 is a lipid scramblase that mediates autophagosomal membrane expansion.
Yeast and human Atg9 are lipid scramblases.
Here we report that yeast and human Atg9 are lipid scramblases that translocate phospholipids between outer and inner leaflets of liposomes in vitro
Part 5: Atg8-family priming and conjugation to phosphatidylethanolamine
ATG4 priming and ATG7-ATG3-ATG12-ATG5-ATG16 conjugationBiological Processatg8_conjugation

ATG4 cleaves the Atg8-family precursor to expose the C-terminal glycine. ATG7 (E1) activates it, ATG3 (E2) carries it, and the ATG12-ATG5-ATG16 complex (E3-like) transfers it to phosphatidylethanolamine on the phagophore. ATG16 decides where conjugation happens. In C. elegans, ATG-4.1 does most precursor processing and ATG-4.2 mainly delipidation, and the two ATG-16 paralogs are partly redundant.

protein lipidation involved in autophagosome assemblyGO:0061739 Atg12-Atg5-Atg16 complexGO:0034274

Annotons

ATG4 Atg8-family priming protease
atg4_priming
Participant: Family: ATG4 cysteine proteases
Family:
ATG4 cysteine proteasesPANTHER:PTHR22624 Human ATG4B has no gene review here; the worm priming paralog ATG-4.1 is the representative.
Representative Members: ATG-4.1 (C. elegans)UniProtKB:K8ESC5

Function

cysteine-type endopeptidase activityGO:0004197 Priming cleavage of the Atg8-family precursor. Delipidation (GO:0019786) is a separate, later activity, done mainly by ATG-4.2 in C. elegans.

Processes

autophagosome assemblyGO:0000045

Locations

cytoplasmGO:0005737

Exposes the C-terminal glycine of LGG-1/Atg8 for conjugation.

PMID:22767594
Differential function of the two Atg4 homologues in the aggrephagy pathway in Caenorhabditis elegans.
ATG-4.1 processes LGG-1 precursors much more efficiently than ATG-4.2.
In vitro enzymatic analysis revealed that ATG-4.1 processes LGG-1 precursors about 100-fold more efficiently than ATG-4.2.
ATG7 E1-like activating enzyme
atg7_e1
Participant: Family: ATG7 proteins
Family:
ATG7 proteinsPANTHER:PTHR10953:SF3
Representative Members: ATG-7 (C. elegans)UniProtKB:G5EBK4 ATG7 (human)UniProtKB:O95352

Function

Atg8 activating enzyme activityGO:0019779 ATG7 also activates ATG12 (GO:0019778) to make the ATG12-ATG5 conjugate.

Processes

C-terminal protein lipidationGO:0006501

Locations

cytoplasmGO:0005737

E1-like enzyme that activates Atg8-family proteins and ATG12.

PMID:27046254
Small differences make a big impact: Structural insights into the differential function of the 2 Atg8 homologs in C. elegans.
In C. elegans, ATG-7 and ATG-3 lipidate LGG-1 and LGG-2.
Lipidation of LGG-1 and LGG-2 is mediated by 2 enzymes, ATG-7 and ATG-3.
PMID:15355958
Human light chain 3/MAP1LC3B is cleaved at its carboxyl-terminal Met121 to expose Gly120 for lipidation and targeting to autophagosomal membranes.
Human Atg7 and Atg3 conjugate MAP1LC3B to phospholipid.
Human light chain 3/MAP1LC3B, an autophagosomal ortholog of yeast Atg8, is conjugated to phospholipid (PL) via ubiquitylation-like reactions mediated by human Atg7 and Atg3.
ATG3 E2-like conjugating enzyme
atg3_e2
Participant: Family: ATG3 proteins
Family:
ATG3 proteinsPANTHER:PTHR12866 Human ATG3 has no gene review here; the worm protein is the representative.
Representative Members: ATG-3 (C. elegans)UniProtKB:Q9N369

Function

Atg8-family conjugating enzyme activityGO:0141046

Processes

C-terminal protein lipidationGO:0006501

Locations

cytoplasmGO:0005737

E2-like enzyme that receives Atg8-family proteins from ATG7 and transfers them to phosphatidylethanolamine.

PMID:27046254
Small differences make a big impact: Structural insights into the differential function of the 2 Atg8 homologs in C. elegans.
In C. elegans, ATG-7 and ATG-3 lipidate LGG-1 and LGG-2.
Lipidation of LGG-1 and LGG-2 is mediated by 2 enzymes, ATG-7 and ATG-3.
ATG5 subunit of the E3-like ATG12-ATG5-ATG16 complex
atg5_e3
Participant: Family: ATG5 proteins
Family:
ATG5 proteinsPANTHER:PTHR13040
Representative Members: ATG-5 (C. elegans)UniProtKB:Q3V5I7 ATG5 (human)UniProtKB:Q9H1Y0

Function

Atg8-family ligase activityGO:0019776 contributes_to: the E3-like activity belongs to the ATG12-ATG5-ATG16 complex as a whole, with ATG5 carrying the ATG12 conjugate.

Processes

C-terminal protein lipidationGO:0006501

Locations

phagophoreGO:0061908

Carries ATG12 and binds ATG16 within the complex that stimulates ATG3 to transfer Atg8-family proteins to the membrane.

PMID:24185444
The two C. elegans ATG-16 homologs have partially redundant functions in the basal autophagy pathway.
Worm ATG-16 proteins bind ATG-5 directly.
ATG-16.1 and ATG-16.2 interact with themselves and each other and also directly associate with ATG-5.
ATG16 membrane-targeting subunit
atg16_site
Participant: Family: ATG16 proteins
Family:
ATG16 proteinsPANTHER:PTHR19878
Representative Members: ATG-16.2 (C. elegans)UniProtKB:Q09406 ATG16L1 (human)UniProtKB:Q676U5

Function

protein-membrane adaptor activityGO:0043495 ATG16 specifies the membrane on which Atg8-family proteins assemble rather than being needed for lipidation itself: in atg-16.1; atg-16.2 double mutants lipidated LGG-1 accumulates but LGG-1 puncta are absent.

Processes

autophagosome assemblyGO:0000045

Locations

phagophoreGO:0061908

Targets the ATG12-ATG5 conjugate to the right membrane and so sets the site of Atg8-family assembly.

PMID:24185444
The two C. elegans ATG-16 homologs have partially redundant functions in the basal autophagy pathway.
Without both ATG-16 paralogs, lipidated LGG-1 accumulates but puncta do not form; ATG-16.2 on the plasma membrane makes ectopic LGG-1 puncta.
In atg-16.2; atg-16.1 double mutants, the lipidated form of LGG-1 accumulates, but LGG-1 puncta are completely absent. ATG-16.2 ectopically expressed on the plasma membrane provides novel sites of LGG-1 puncta formation.
Part 6: Atg8-family proteins on the autophagic membrane
GABARAP-type and LC3-type Atg8 proteinsMolecular Functionatg8_family

Animal Atg8 proteins fall into GABARAP and LC3 subfamilies (one each in C. elegans, LGG-1 and LGG-2; three each in human). Both are conjugated to phosphatidylethanolamine and bind LIR-containing receptors and autophagy proteins. Both subfamilies are in one PANTHER family. The stage at which each subfamily acts differs between lineages and is modelled as a variant set. Human cells lacking all six Atg8 proteins still make autophagosomes, which are smaller, but fail to fuse them with lysosomes.

Variant set: Stage assignment of GABARAP-type and LC3-type Atg8 proteins by taxon / sequence lineage (Exactly One)

Both subfamilies are present in every variant; what differs is the step each subfamily is mainly needed for. The nematode and mammalian assignments are close to opposite for the GABARAP-type protein in early biogenesis.

Nematode staging (GABARAP-type early, LC3-type late)Molecular Functionnematode_atg8_staging

In C. elegans, LGG-1 (GABARAP-type) is processed and lipidated first, is needed for autophagosome formation, and is needed for LGG-2 (LC3-type) to reach autophagosomes. LGG-2 then drives maturation and tethering to lysosomes through the HOPS subunit VPS-39.

Annotons

GABARAP-type LGG-1 in autophagosome formation
lgg1_early
Participant: Family: GABARAP-subfamily Atg8 proteins
Family:
GABARAP-subfamily Atg8 proteinsPANTHER:PTHR10969 PANTHER family covers both subfamilies; this role is the GABARAP clade. Worm and human GABARAP-type proteins sit in different PANTHER subfamilies, so the role is grounded on the family.
Representative Members: LGG-1 (C. elegans)UniProtKB:Q09490

Function

phosphatidylethanolamine bindingGO:0008429 Covalent PE conjugation, as in the lgg-1 gene review core function. The cleaved, non-lipidated form is enough for autophagosome initiation, so PE conjugation mainly helps recognise cargo and degrade autophagosomes (PMID:37395461).

Processes

autophagosome assemblyGO:0000045

Locations

autophagosome membraneGO:0000421

Marks the growing autophagic membrane and acts upstream of LGG-2.

PMID:37395461
LGG-1/GABARAP lipidation is not required for autophagy and development in Caenorhabditis elegans.
Cleavage of LGG-1 into form I is essential for autophagosome initiation; lipidated form II helps recognise cargo and degrade autophagosomes.
The cleavage of LGG-1 into form I is essential for autophagosome initiation and biogenesis while form II is involved in cargo recognition and autophagosome degradation.
PMID:20523114
The autophagosomal protein LGG-2 acts synergistically with LGG-1 in dauer formation and longevity in C. elegans.
LGG-1, but not LGG-2, functionally complements yeast atg8.
LGG-1 but not LGG-2 is able to functionally complement the atg8 mutant yeast.
PMID:26687600
Structural Basis of the Differential Function of the Two C. elegans Atg8 Homologs, LGG-1 and LGG-2, in Autophagy.
LGG-1 is essential for aggregate degradation, while LGG-2 has cargo- and stage-specific roles.
lgg-1 is essential for degradation of protein aggregates, while lgg-2 has cargo-specific and developmental-stage-specific roles in aggregate degradation.
LC3-type LGG-2 in autophagosome maturation
lgg2_late
Participant: Family: LC3-subfamily Atg8 proteins
Family:
LC3-subfamily Atg8 proteinsPANTHER:PTHR10969 PANTHER family covers both subfamilies; this role is the LC3 clade. LGG-2 has its own PANTHER subfamily, separate from human LC3B, so the role is grounded on the family.
Representative Members: LGG-2 (C. elegans)UniProtKB:Q23536

Function

phosphatidylethanolamine bindingGO:0008429 C-terminal glycine PE conjugation, which LGG-2 needs to localise to autophagosomes (lgg-2 gene review core function).

Processes

autophagosome maturationGO:0097352 autophagosome-lysosome fusionGO:0061909

Locations

autophagosome membraneGO:0000421

Acts after LGG-1 and helps tether autophagosomes to lysosomes through VPS-39.

PMID:24374177
The C. elegans LC3 acts downstream of GABARAP to degrade autophagosomes by interacting with the HOPS subunit VPS39.
LGG-1 is needed for LGG-2 localisation; LGG-2 controls maturation and binds VPS-39.
LGG-1 acts upstream of LGG-2 to allow its localization to autophagosomes. LGG-2 controls the maturation of LGG-1-positive autophagosomes and facilitates the tethering with the lysosomes through a direct interaction with the VPS-39 HOPS complex subunit.
PMID:20523114
The autophagosomal protein LGG-2 acts synergistically with LGG-1 in dauer formation and longevity in C. elegans.
The C-terminal glycine of LGG-2 is needed for its modification and autophagosome localisation.
The C-terminal glycine residue of LGG-2 is essential for post-translational modification and localization to the autophagosomes.

Connections

lgg1_early -> lgg2_late Precedes
LGG-1 is needed for LGG-2 to localise to autophagosomes.
Mammalian staging (LC3 in phagophore elongation, GABARAP at fusion)Molecular Functionmammalian_atg8_staging

In mammalian cells, the LC3 subfamily acts in elongation of the phagophore, and the GABARAP subfamily acts later. Gene knockouts show that the GABARAP subfamily recruits PLEKHM1 and governs autophagosome-lysosome fusion and PINK1/Parkin mitophagy, while the LC3 subfamily has a smaller role.

Annotons

LC3-subfamily Atg8 in phagophore elongation
lc3_elongation
Participant: Family: LC3-subfamily Atg8 proteins
Family:
LC3-subfamily Atg8 proteinsPANTHER:PTHR10969
Representative Members: MAP1LC3B (human)UniProtKB:Q9GZQ8

Function

phosphatidylethanolamine bindingGO:0008429 C-terminal Gly120 PE conjugation (MAP1LC3B gene review core function).

Processes

autophagosome assemblyGO:0000045

Locations

autophagosome membraneGO:0000421

Promotes elongation of the phagophore membrane.

PMID:20418806
LC3 and GATE-16/GABARAP subfamilies are both essential yet act differently in autophagosome biogenesis.
LC3s act in phagophore elongation and GABARAPs at a later maturation stage.
our results indicate that LC3s are involved in elongation of the phagophore membrane whereas the GABARAP/GATE-16 subfamily is essential for a later stage in autophagosome maturation.
PMID:15355958
Human light chain 3/MAP1LC3B is cleaved at its carboxyl-terminal Met121 to expose Gly120 for lipidation and targeting to autophagosomal membranes.
MAP1LC3B is cleaved to expose Gly120 for lipidation.
These results indicate that the carboxyl terminus of MAP1LC3B is cleaved to expose Gly(120) for further ubiquitylation-like reactions.
GABARAP-subfamily Atg8 at autophagosome-lysosome fusion
gabarap_fusion
Participant: Family: GABARAP-subfamily Atg8 proteins
Family:
GABARAP-subfamily Atg8 proteinsPANTHER:PTHR10969
Representative Members: GABARAP (human)UniProtKB:O95166

Function

phosphatidylethanolamine bindingGO:0008429 PE conjugation (GABARAP gene review core function).

Processes

autophagosome maturationGO:0097352 autophagosome-lysosome fusionGO:0061909

Locations

autophagosome membraneGO:0000421

Recruits PLEKHM1 and is the main Atg8 subfamily for autophagosome-lysosome fusion and PINK1/Parkin mitophagy.

PMID:27864321
Atg8 family LC3/GABARAP proteins are crucial for autophagosome-lysosome fusion but not autophagosome formation during PINK1/Parkin mitophagy and starvation.
The GABARAP subfamily governs autophagosome-lysosome fusion; the LC3 subfamily has a smaller role.
We find that the GABARAP subfamily promotes PLEKHM1 recruitment and governs autophagosome-lysosome fusion, whereas the LC3 subfamily plays a less prominent role in these processes.

Connections

LC3 acts in elongation before GABARAP-mediated maturation.
Part 7: selective cargo recruitment to Atg8-family-labelled membranes (optional)

Optional because p62/SQSTM1 is needed for selective aggregate degradation but not for bulk starvation-induced autophagy.

p62/SQSTM1 cargo receptorMolecular Functioncargo_recruitment

p62/SQSTM1 binds ubiquitinated cargo through its UBA domain and Atg8-family proteins through a LIR motif. In C. elegans the scaffold EPG-7 links SQST-1 aggregates to the autophagy machinery. Other receptors, such as worm SEPA-1 for P granules, follow the same logic.

Annotons

p62/SQSTM1 autophagy cargo receptor
sqstm1_receptor
Participant: Family: p62/sequestosome 1 proteins
Family:
p62/sequestosome 1 proteinsPANTHER:PTHR15090
Representative Members: SQST-1 (C. elegans)UniProtKB:Q22436 SQSTM1/p62 (human)UniProtKB:Q13501

Function

autophagy cargo adaptor activityGO:0160247 sqst-1 gene review core function. The human SQSTM1 review splits this into ubiquitin-modified protein reader activity and condensate scaffold activity.

Processes

aggrephagyGO:0035973

Locations

autophagosomeGO:0005776

Links ubiquitinated protein aggregates to Atg8-family-decorated autophagic membranes.

PMID:17580304
p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy.
Human p62 binds LC3 directly.
p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated
PMID:23530068
The scaffold protein EPG-7 links cargo-receptor complexes with the autophagic assembly machinery.
SQST-1 binds EPG-7; without EPG-7, SQST-1 aggregates do not associate properly with LGG-1 puncta.
SQST-1 directly interacts with EPG-7 and colocalizes with EPG-7 aggregates in autophagy mutants. Mutations in epg-7 impair association of SQST-1 aggregates with LGG-1/Atg8 puncta.
Part 8: autophagosome fusion with late endosomes/lysosomes
EPG5-dependent autophagosome-lysosome fusionBiological Processmaturation_fusion

EPG5 is a metazoan-specific RAB7 effector. It binds RAB7 and VAMP7/8 on late endosomes and lysosomes, and Atg8-family proteins and STX17-SNAP29 on autophagosomes. It stabilises the correct trans-SNARE complex so that autophagosomes fuse with the right partner. Without EPG5, non-degradative hybrid vesicles build up. HOPS tethering and the SNAREs themselves are context, not modelled here.

autophagosome-lysosome fusionGO:0061909

Annotons

EPG5 RAB7 effector tether
epg5_tether
Participant: Family: EPG5 proteins
Family:
EPG5 proteinsPANTHER:PTHR31139
Representative Members: EPG-5 (C. elegans)UniProtKB:Q18892 EPG5 (human)UniProtKB:Q9HCE0

Function

vesicle membrane tethering activityGO:7770062 Human EPG5 gene review core function. The worm epg-5 review records the parts of this activity as small GTPase (RAB-7) binding and SNARE binding.

Processes

autophagosome-lysosome fusionGO:0061909

Locations

late endosome membraneGO:0031902

Metazoan-specific tether that decides which membranes autophagosomes fuse with, so that degradative autolysosomes form.

PMID:27588602
The Vici Syndrome Protein EPG5 Is a Rab7 Effector that Determines the Fusion Specificity of Autophagosomes with Late Endosomes/Lysosomes.
EPG5 is recruited by Rab7 and VAMP7/8 and binds LC3/LGG-1 and STX17-SNAP29 on autophagosomes.
EPG5 is recruited to late endosomes/lysosomes by direct interaction with Rab7 and the late endosomal/lysosomal R-SNARE VAMP7/8. EPG5 also binds to LC3/LGG-1 (mammalian and C. elegans Atg8 homolog, respectively) and to assembled STX17-SNAP29 Qabc SNARE complexes on autophagosomes.
PMID:20550938
C. elegans screen identifies autophagy genes specific to multicellular organisms.
The mammalian EPG-5 homolog is needed to form degradative autolysosomes.
EI24 and mEPG5 are required for formation of degradative autolysosomes.