Atg16 is a core autophagy protein that functions as an essential structural component of the Atg12-Atg5-Atg16 complex (E3-like ligase), which promotes the conjugation of Atg8 to phosphatidylethanolamine (PE) during autophagosome biogenesis. The protein contains an N-terminal Atg5-binding domain and a C-terminal coiled-coil domain required for homodimerization. In S. pombe, Atg16 localizes to the phagophore assembly site (PAS) in a manner dependent on Atg18a and is required for efficient macroautophagy.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: IEA annotation derived from UniProtKB-SubCell mapping. Atg16 is predominantly cytosolic in vegetative cells, with a fraction localizing to the PAS upon autophagy induction. High-throughput localization data from PMID:16823372 confirms cytoplasmic localization. Reason: Cytoplasmic localization is consistent with the known biology of Atg16. The protein exists in the cytoplasm and is recruited to the PAS upon autophagy induction. This annotation correctly captures the baseline localization. Supporting Evidence: PMID:16823372 we determined the localization of 4,431 proteins, corresponding to approximately 90% of the fission yeast proteome |
| GO:0006914 autophagy | IEA GO_REF:0000043 | MODIFY | Summary: IEA annotation based on UniProtKB keyword mapping from the Autophagy keyword. Atg16 is a core autophagy protein essential for autophagosome biogenesis. Direct experimental evidence supports its role in macroautophagy [PMID:23950735]. Reason: While not incorrect, this annotation is too general. More specific experimental evidence (IMP from PMID:23950735) supports a role in macroautophagy (GO:0016236), which is the correct specific term for this protein. The IEA should be retained but the more specific macroautophagy term (already annotated with IMP) better captures the function. Proposed replacements: macroautophagy Supporting Evidence: PMID:23950735 we obtained a comprehensive catalog of autophagy genes in this highly tractable organism, including genes encoding three heretofore unidentified core Atg proteins, Atg10, Atg14, and Atg16 file:SCHPO/atg16/atg16-deep-research-falcon.md **atg16ฮ** cells are defective in CFP-Atg8 processing under nitrogen starvation |
| GO:0015031 protein transport | IEA GO_REF:0000043 | MARK AS OVER ANNOTATED | Summary: IEA annotation based on UniProtKB keyword mapping from the Protein Transport keyword. This appears to be an indirect annotation reflecting that autophagy involves protein transport to the vacuole/lysosome. Reason: Atg16 does not directly function as a protein transporter. Its role is as a scaffold/E3-like ligase component in the Atg12-Atg5-Atg16 complex that promotes Atg8 lipidation. The protein transport annotation is too generic and does not capture the specific molecular function. Autophagy does involve protein transport to the vacuole, but this is not Atg16's specific function. Supporting Evidence: PMID:23950735 Atg18a uniquely required for the targeting of the Atg12-Atg5ยทAtg16 complex file:SCHPO/atg16/atg16-deep-research-falcon.md Atg16 is the scaffold subunit of the **Atg12โAtg5โAtg16** complex, which functions as the **E3-like factor for Atg8 conjugation to phosphatidylethanolamine (PE)** and helps determine where Atg8 lipidation occurs on autophagic membranes. |
| GO:0034045 phagophore assembly site membrane | IEA GO_REF:0000044 | MODIFY | Summary: IEA annotation based on UniProtKB subcellular location mapping. UniProt notes that Atg16 localizes to the PAS membrane as a peripheral membrane protein. Direct experimental evidence from PMID:23950735 and PMID:31941401 confirms PAS localization. Reason: This annotation is accurate and consistent with experimental evidence showing Atg16 localizes to the PAS upon autophagy induction. The protein is known to function at the PAS membrane during autophagosome biogenesis. [2026-08 re-review against GO issue #29437] The supporting evidence quoted here describes PAS puncta / PAS accumulation, not a membrane. GO:0034045 asserts, via bounding_layer_of, that a membrane bounds the phagophore assembly site; the PAS is a liquid-like protein condensate with no bounding bilayer (PMID:32025038), and the term additionally carries 'phagophore' and 'isolation membrane' as synonyms of the distinct term GO:0061908. This annotation derives solely from the UniProt SL-0221 subcellular location via GO_REF:0000044, which is the propagation source rather than independent evidence. Generalize to the structure the cited experiments actually show. Proposed replacements: phagophore assembly site Supporting Evidence: PMID:23950735 atg18aฮ abolished the starvation-induced puncta formation by Atg5 and Atg16 PMID:31941401 PAS accumulation of Atg2, Atg18b, Atg24b, Atg5, Atg16, and Atg8 reduced by the Atg38 AIM mutation was recovered by expressing 3รEEEWEEL-Atg14 or Atg14-3รEEEWEEL file:SCHPO/atg16/atg16-deep-research-falcon.md Atg16 localizes to the **PAS (phagophore assembly site / pre-autophagosomal structure)** during starvation and colocalizes with **CFP-Atg8** |
| GO:0051321 meiotic cell cycle | IEA GO_REF:0000043 | REMOVE | Summary: IEA annotation based on UniProtKB keyword mapping from the Meiosis keyword. The Meiosis keyword was assigned to atg16 based on PMID:16169489, a high-throughput knockout screen that identified genes affecting meiotic chromosome segregation. However, this is a classic case of over-annotation: autophagy is upregulated during meiosis/sporulation in yeast, and loss of autophagy genes affects meiotic processes indirectly rather than through direct involvement in the meiotic cell cycle machinery. Reason: This annotation represents an over-annotation resulting from the indirect effects of autophagy defects on meiosis. Atg16 is a core autophagy protein, not a meiotic cell cycle regulator. The screen in PMID:16169489 identified atg16 because autophagy is required during nutrient starvation that triggers meiosis/sporulation in fission yeast. The meiotic defects observed in atg16 mutants are secondary consequences of impaired autophagy, not evidence that Atg16 directly participates in meiotic cell cycle regulation. ATG genes are autophagy machinery components, and this keyword assignment conflates upstream/downstream relationships. The protein's core function is in autophagosome biogenesis, not meiotic regulation. Supporting Evidence: file:SCHPO/atg16/atg16-deep-research-perplexity.md The atg16 gene in Schizosaccharomyces pombe encodes autophagy protein 16, a conserved component of the autophagy machinery |
| GO:0000407 phagophore assembly site | IDA PMID:31941401 Atg38-Atg8 interaction in fission yeast establishes a positi... | ACCEPT | Summary: IDA annotation showing Atg16 localizes to the phagophore assembly site (PAS). This study by Yu et al. (2020) demonstrated that the Atg38-Atg8 interaction affects PAS accumulation of multiple Atg proteins including Atg16. The study showed that PAS accumulation of Atg16 was reduced by the Atg38 AIM mutation and could be recovered by artificial Atg14-Atg8 interaction constructs. Reason: Direct experimental evidence from fluorescence microscopy demonstrates Atg16 localizes to the PAS. This is a core localization for Atg16 function in autophagosome biogenesis. Supporting Evidence: PMID:31941401 PAS accumulation of Atg2, Atg18b, Atg24b, Atg5, Atg16, and Atg8 reduced by the Atg38 AIM mutation was recovered by expressing 3รEEEWEEL-Atg14 or Atg14-3รEEEWEEL |
| GO:0000407 phagophore assembly site | IDA PMID:23950735 Global analysis of fission yeast mating genes reveals new au... | ACCEPT | Summary: IDA annotation showing Atg16 localizes to the PAS. The study by Sun et al. 2013 systematically examined subcellular localization of fission yeast autophagy factors and showed that Atg16 forms cytoplasmic puncta that colocalize with Atg8 at the PAS upon starvation induction. The study also showed that Atg18a is required for Atg16 recruitment to the PAS. Reason: This is the primary experimental study demonstrating PAS localization of Atg16 in S. pombe. The evidence includes colocalization with Atg8 puncta and demonstration that recruitment requires the PI3P-binding protein Atg18a. Supporting Evidence: PMID:23950735 Fifteen Atg proteins colocalized with CFP-Atg8 at cytoplasmic puncta induced by starvation PMID:23950735 atg18aฮ abolished the starvation-induced puncta formation by Atg5 and Atg16 PMID:23950735 Atg18a may serve as a binding platform for the recruitment of the Atg12โAtg5ยทAtg16 complex to PAS file:SCHPO/atg16/atg16-deep-research-falcon.md Atg18a is uniquely required to target the Atg12โAtg5ยทAtg16 complex to the PAS |
| GO:0016236 macroautophagy | IMP PMID:23950735 Global analysis of fission yeast mating genes reveals new au... | ACCEPT | Summary: IMP annotation showing Atg16 is involved in macroautophagy. The study identified atg16 as a core autophagy gene through genome-wide screening. Deletion of atg16 causes defects in CFP-Atg8 processing, a standard assay for autophagy function. The study demonstrated that Atg16 is part of the Atg12-Atg5-Atg16 complex required for autophagosome biogenesis. Reason: This is the core biological process annotation for Atg16. Direct genetic evidence shows that atg16 deletion impairs autophagy, and the protein functions in the conserved Atg12-Atg5-Atg16 complex that promotes Atg8 lipidation. This is the primary function of Atg16. Supporting Evidence: PMID:23950735 we obtained a comprehensive catalog of autophagy genes in this highly tractable organism, including genes encoding three heretofore unidentified core Atg proteins, Atg10, Atg14, and Atg16 PMID:23950735 SPBC405.05 is currently annotated as a sequence orphan. We found that it shares homology with S. cerevisiae Atg16 in both the N-terminal Atg5-binding domain and the C-terminal coiled-coil domain PMID:23950735 S. pombe SPBC405.05/Atg16 protein interacts with Atg5 both in the presence and in the absence of Atg12 file:SCHPO/atg16/atg16-deep-research-falcon.md **atg16ฮ** cells are defective in CFP-Atg8 processing under nitrogen starvation |
| GO:0019776 Atg8-family ligase activity | ISO GO_REF:0000024 | ACCEPT | Summary: ISO annotation transferred from S. cerevisiae Atg16 (SGD:S000004769). The Atg12-Atg5-Atg16 complex functions as an E3-like ubiquitin ligase that promotes the conjugation of Atg8 to phosphatidylethanolamine. This activity is well characterized in budding yeast and mammals and is conserved in S. pombe. Reason: This molecular function annotation is appropriate for Atg16. The protein is part of the Atg12-Atg5-Atg16 complex that acts as an E3-like enzyme for Atg8 lipidation. The deep research document confirms this is a well-conserved function. The "contributes_to" qualifier is appropriate since Atg16 is one component of a multi-subunit complex. Supporting Evidence: file:SCHPO/atg16/atg16-deep-research-perplexity.md The ATG12โATG5โATG16 complex represents one of the most critical assemblies in the autophagy pathway, functioning as a specialized E3-like ubiquitin ligase file:SCHPO/atg16/atg16-deep-research-falcon.md Atg16 is the scaffold subunit of the **Atg12โAtg5โAtg16** complex, which functions as the **E3-like factor for Atg8 conjugation to phosphatidylethanolamine (PE)** and helps determine where Atg8 lipidation occurs on autophagic membranes. |
| GO:0005737 cytoplasm | HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ... | ACCEPT | Summary: HDA (High-throughput Direct Assay) annotation from a large-scale protein localization study. Matsuyama et al. performed ORFeome cloning and global analysis of protein localization in S. pombe using fluorescent protein tagging. Reason: This annotation is supported by systematic localization data. Atg16 is predominantly cytoplasmic in unstressed cells, consistent with its known biology as an autophagy protein that is recruited to the PAS upon autophagy induction. Supporting Evidence: PMID:16823372 we determined the localization of 4,431 proteins, corresponding to approximately 90% of the fission yeast proteome |
| GO:0005829 cytosol | HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ... | ACCEPT | Summary: HDA annotation from the same large-scale localization study (PMID:16823372). The cytosol annotation is more specific than cytoplasm and indicates the protein is soluble rather than membrane-associated under basal conditions. Reason: Cytosolic localization is consistent with Atg16 being a soluble protein that is recruited to the PAS membrane upon autophagy induction. The protein does not have transmembrane domains and functions as a peripheral membrane protein when localized to the PAS. Supporting Evidence: PMID:16823372 we determined the localization of 4,431 proteins, corresponding to approximately 90% of the fission yeast proteome |
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Download this section (compressed HTML)Q: What is the precise stoichiometry of the Atg12-Atg5-Atg16 complex in S. pombe? While the budding yeast and mammalian complexes have been well characterized structurally, the S. pombe complex stoichiometry has not been directly determined.
Q: Does S. pombe Atg16 have membrane-binding activity via an amphipathic helix like S. cerevisiae Atg16? The membrane-binding capability of Atg16 via an amphipathic helix has been characterized in budding yeast but not specifically confirmed in fission yeast.
Experiment: Structure determination of S. pombe Atg12-Atg5-Atg16 complex to confirm conserved structural features and enable comparison with budding yeast and mammalian complexes.
Hypothesis: The S. pombe Atg12-Atg5-Atg16 complex shares the same structural organization as the budding yeast and mammalian complexes.
Experiment: Direct measurement of Atg8-PE conjugation activity with purified S. pombe Atg12-Atg5-Atg16 complex to provide direct biochemical evidence for the E3-like ligase activity in the fission yeast system.
Hypothesis: The S. pombe Atg12-Atg5-Atg16 complex has E3-like ligase activity that promotes Atg8 lipidation in vitro.
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