ATG-16.2 is one of two C. elegans orthologs of yeast Atg16 and mammalian ATG16L1. It has an N-terminal ATG-5-binding region, a central coiled-coil that mediates self-association and association with ATG-16.1, and seven C-terminal WD40 repeats. Through ATG-5 it forms part of the LGG-3/ATG12-ATG-5-ATG-16 complex, and it specifies the membrane sites at which lipidated LGG-1 assembles into puncta: in atg-16.2; atg-16.1 double mutants lipidated LGG-1 accumulates but LGG-1 puncta are absent, and ATG-16.2 targeted to the plasma membrane nucleates ectopic LGG-1 puncta. ATG-16.2 makes the larger contribution of the two paralogs to aggrephagy in the embryo, its WD40 repeats are dispensable for this role, and it also binds LGG-2. It is broadly expressed in neurons, muscles and intestine, and it is required for the late-larval expansion of germline stem cell progenitors.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000045 autophagosome assembly | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that ATG-16.2 participates in autophagosome assembly. Reason: Core process; directly supported by C. elegans genetics showing ATG-16 is required for LGG-1 puncta formation (PMID:24185444). Supporting Evidence: PMID:24185444 In atg-16.2; atg-16.1 double mutants, the lipidated form of LGG-1 accumulates, but LGG-1 puncta are completely absent. |
| GO:0000045 autophagosome assembly | IEA GO_REF:0000120 | ACCEPT | Summary: Combined automated annotation (ATG16 InterPro family, ARBA) to autophagosome assembly. Reason: Correct; consistent with experimental data. |
| GO:0000045 autophagosome assembly | IMP PMID:24185444 The two C. elegans ATG-16 homologs have partially redundant ... | ACCEPT | Summary: atg-16.2 mutants have fewer and weaker LGG-1 puncta, and double mutants with atg-16.1 lack LGG-1 puncta entirely. Reason: Direct loss-of-function evidence for the core process. Supporting Evidence: PMID:24185444 LGG-1 puncta are markedly fewer in number and weaker in intensity in atg-16.2 mutants |
| GO:0000045 autophagosome assembly | NAS PMID:24185444 The two C. elegans ATG-16 homologs have partially redundant ... | ACCEPT | Summary: Author statement; redundant with the IMP row. Reason: Correct. Supporting Evidence: PMID:24185444 As in other systems, ATG-16 is required for formation of LGG-1 puncta. |
| GO:0000421 autophagosome membrane | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic inference that ATG-16.2 is active at the autophagosome membrane. Reason: Atg16 orthologs act on the forming phagophore and largely dissociate before or at autophagosome closure, so the phagophore membrane is the precise location. Retained as non-core rather than removed because GO autophagosome membrane is broad. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000459085 SUPPORTS TRANSFER ATG16 clade node seeded by mammalian ATG16L1; location is approximately right but less precise than phagophore membrane. |
| GO:0005515 protein binding | IPI PMID:24185444 The two C. elegans ATG-16 homologs have partially redundant ... | REMOVE | Summary: Pull-down interactions of ATG-16.2 with ATG-16.1 (Q19124) and ATG-5 (Q3V5I7). Reason: The interactions are real (removal does not mean they are false) but protein binding is uninformative. ATG-5 binding defines membership of the Atg12-Atg5-Atg16 complex (GO:0034274, annotated separately), and ATG-16 self/hetero-association reflects coiled-coil oligomerization of that complex. Supporting Evidence: PMID:24185444 ATG-16.1 and ATG-16.2 interact with themselves and each other and also directly associate with ATG-5. |
| GO:0005515 protein binding | IPI PMID:24185444 The two C. elegans ATG-16 homologs have partially redundant ... | REMOVE | Summary: Pull-down interactions of ATG-16.2 with ATG-16.1 (Q19124) and ATG-5 (Q3V5I7). Reason: The interactions are real (removal does not mean they are false) but protein binding is uninformative. ATG-5 binding defines membership of the Atg12-Atg5-Atg16 complex (GO:0034274, annotated separately), and ATG-16 self/hetero-association reflects coiled-coil oligomerization of that complex. Supporting Evidence: PMID:24185444 ATG-16.1 and ATG-16.2 interact with themselves and each other and also directly associate with ATG-5. |
| GO:0005737 cytoplasm | IDA PMID:24185444 The two C. elegans ATG-16 homologs have partially redundant ... | ACCEPT | Summary: ATG-16.2 reporter is cytoplasmic. Reason: Experimental localization consistent with a soluble autophagy complex subunit. Supporting Evidence: file:worm/atg-16.2/atg-16.2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0005737 cytoplasm | IEA GO_REF:0000120 | ACCEPT | Summary: Combined automated annotation to cytoplasm. Reason: Correct. |
| GO:0005737 cytoplasm | NAS PMID:24185444 The two C. elegans ATG-16 homologs have partially redundant ... | ACCEPT | Summary: Author statement of cytoplasmic localization. Reason: Correct; redundant with IDA. Supporting Evidence: file:worm/atg-16.2/atg-16.2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm |
| GO:0005886 plasma membrane | EXP PMID:24185444 The two C. elegans ATG-16 homologs have partially redundant ... | MARK AS OVER ANNOTATED | Summary: Plasma membrane localization. The abstract describes ATG-16.2 deliberately targeted to the plasma membrane as an ectopic nucleation site for LGG-1 puncta. Reason: The only plasma-membrane observation visible in the cached text (abstract, introduction and discussion; Results not cached) is ectopic, engineered targeting used to show that membrane-tethered ATG-16.2 can specify LGG-1 puncta sites. That is strong evidence for ATG-16.2 function but not for a native plasma-membrane location. Not removed because the curator may have seen additional data in the Results. Supporting Evidence: PMID:24185444 ATG-16.2 ectopically expressed on the plasma membrane provides novel sites of LGG-1 puncta formation. |
| GO:0005886 plasma membrane | IEA GO_REF:0000044 | MARK AS OVER ANNOTATED | Summary: UniProt SubCell (cell membrane) mapping, derived from the same paper. Reason: Derived from the same ectopic-targeting observation as the EXP row; the native location is cytoplasm and the forming phagophore. Supporting Evidence: PMID:24185444 ATG-16.2 ectopically expressed on the plasma membrane provides novel sites of LGG-1 puncta formation. |
| GO:0006914 autophagy | NAS PMID:24185444 The two C. elegans ATG-16 homologs have partially redundant ... | ACCEPT | Summary: Author statement; ATG-16.2 functions in autophagy. Reason: Correct, general. Supporting Evidence: PMID:24185444 We showed that atg-16.2 mutants exhibit a stronger autophagic defect than atg-16.1 mutants. |
| GO:0016236 macroautophagy | NAS PMID:24185444 The two C. elegans ATG-16 homologs have partially redundant ... | ACCEPT | Summary: Author statement; ATG-16.2 functions in macroautophagy. Reason: Correct. Supporting Evidence: PMID:24185444 We showed that atg-16.2 mutants exhibit a stronger autophagic defect than atg-16.1 mutants. |
| GO:0034045 obsolete phagophore assembly site membrane | IBA GO_REF:0000033 | MODIFY | Summary: Phylogenetic inference to phagophore assembly site membrane, now obsolete in GO (QuickGO replaced_by GO:7770114 phagophore membrane). Reason: The intended location, the forming phagophore membrane where ATG16 specifies LGG-1 lipidation sites, is correct; update to the replacement term. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000459085 SUPPORTS TRANSFER ATG16 clade node; inference sound, only the GO term has been obsoleted. Proposed replacements: phagophore membrane |
| GO:0034045 obsolete phagophore assembly site membrane | NAS PMID:24185444 The two C. elegans ATG-16 homologs have partially redundant ... | MODIFY | Summary: Author statement mapped to the now-obsolete PAS membrane term. Reason: Update to the GO replacement term phagophore membrane. Proposed replacements: phagophore membrane |
| GO:0034274 Atg12-Atg5-Atg16 complex | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference that ATG-16.2 is part of the Atg12-Atg5-Atg16 complex. Reason: Core complex membership, supported by direct binding of ATG-16.2 to ATG-5 in C. elegans. Supporting Evidence: PMID:24185444 ATG-16.1 and ATG-16.2 interact with themselves and each other and also directly associate with ATG-5. |
| GO:0034274 Atg12-Atg5-Atg16 complex | NAS PMID:24185444 The two C. elegans ATG-16 homologs have partially redundant ... | ACCEPT | Summary: Author statement of complex membership. Reason: Correct. Supporting Evidence: PMID:24185444 ATG-16.1 and ATG-16.2 interact with themselves and each other and also directly associate with ATG-5. |
| GO:0035973 aggrephagy | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA annotation to aggrephagy. Reason: Correct; supported by experimental rows from PMID:24185444. |
| GO:0035973 aggrephagy | IGI PMID:24185444 The two C. elegans ATG-16 homologs have partially redundant ... | ACCEPT | Summary: atg-16.2; atg-16.1 double mutants have a much more severe aggrephagy defect than either single mutant. Reason: Genetic interaction showing partially redundant function of the two paralogs in aggrephagy. Supporting Evidence: PMID:24185444 the two ATG-16 homologs have partially redundant yet distinct functions in the aggrephagy pathway |
| GO:0035973 aggrephagy | IMP PMID:24185444 The two C. elegans ATG-16 homologs have partially redundant ... | ACCEPT | Summary: atg-16.2 single mutants are defective in degradation of protein aggregates; the WD repeats are dispensable for this role. Reason: Direct loss-of-function evidence; aggrephagy is the main physiological readout in the embryo. Supporting Evidence: PMID:24185444 the C-terminal WD repeats are dispensable for the role of atg-16.2 in aggrephagy |
| GO:0036093 germ cell proliferation | IMP PMID:28285998 A Non-Cell-Autonomous Role of BEC-1/BECN1/Beclin1 in Coordin... | KEEP AS NON CORE | Summary: Ames et al. found atg-16.2 is required for the late-larval expansion of germline stem cell progenitors, acting through DAF-16/FOXO. Reason: A developmental requirement downstream of (or alongside) autophagy, acting via insulin/DAF-16 signalling; not the core function of ATG-16.2. Supporting Evidence: PMID:28285998 atg-16.2/ATG16L, atg-18/WIPI1/2, and atg-7/ATG7 are required for the late larval expansion of germline stem cell progenitors |
| GO:0042078 germ-line stem cell division | IMP PMID:28285998 A Non-Cell-Autonomous Role of BEC-1/BECN1/Beclin1 in Coordin... | KEEP AS NON CORE | Summary: ATG-16.2 promotes cell-cycle progression of germline stem cells. Reason: Abstract supports a role in germline stem cell cell-cycle progression; a pleiotropic developmental phenotype rather than a core function. Supporting Evidence: PMID:28285998 ATG-16.2/ATG16L all promote cell-cycle progression and are negatively regulated by the phosphatase and tensin homolog DAF-18/PTEN |
| GO:0043495 protein-membrane adaptor activity | IBA GO_REF:0000033 | ACCEPT | Summary: Phylogenetic inference of protein-membrane adaptor activity, from human ATG16L1, which links the ATG12-ATG5 conjugate to membranes. Reason: Consistent with C. elegans data: ATG-16 is dispensable for LGG-1 lipidation per se but is required to localize it into puncta, and membrane-tethered ATG-16.2 is sufficient to nucleate ectopic LGG-1 puncta, i.e. ATG-16.2 links the conjugation machinery to a membrane site. Supporting Evidence: PMID:24185444 In atg-16.2; atg-16.1 double mutants, LGG-1-II accumulates but LGG-1 puncta are completely absent, whereas forced expression of plasma membrane-localized ATG-16.2 is sufficient to nucleate ectopic LGG-1 puncta. |
| GO:0050830 defense response to Gram-positive bacterium | IEP PMID:24882217 Innate host defense requires TFEB-mediated transcription of ... | KEEP AS NON CORE | Summary: Visvikis et al. found that HLH-30/TFEB drives induction of antimicrobial and autophagy genes after S. aureus infection; atg-16.2 expression is induced. Reason: Expression-pattern evidence only; it shows atg-16.2 is induced by infection, not that ATG-16.2 itself executes a defense step. The abstract reports that autophagy genes are needed for host tolerance of infection, so a non-core role is plausible. Supporting Evidence: PMID:24882217 drove the expression of close to 80% of the host response, including antimicrobial and autophagy genes that were essential for host tolerance of infection |
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Download this section (compressed HTML)Q: How does ATG-16.2 find its membrane sites in C. elegans: does it bind an EPG-6 or ATG-18 WIPI-like protein, as ATG16L1 binds WIPI2, or membranes directly?
Q: Why does LGG-1 lipidation increase rather than decrease in atg-16.2; atg-16.1 double mutants, unlike in yeast and mouse Atg16 mutants?
Q: What do the WD40 repeats of ATG-16.2 do, given that they are dispensable for aggrephagy, and is its binding to LGG-2 through them functionally important?
Experiment: Map the membrane-recruitment determinant of ATG-16.2 with truncations and point mutants in the coiled-coil and linker regions, and test their binding to EPG-6/ATG-18 and liposomes alongside rescue of LGG-1 puncta in atg-16.2; atg-16.1 double mutants.
Type: genetics and biochemistry
atg-16.2 encodes a divergent ortholog of the autophagic budding yeast protein Atg16p, and of human ATG16L1 (OMIM:610767, associated with Crohndisease) and ATG16L2; ATG-16.2 is paralogous to ATG-16.1; ATG-16.2 hasno obvious function in mass RNAi assays.
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