ATG1 encodes the serine/threonine protein kinase Atg1 of budding yeast, the catalytic subunit of the Atg1 kinase complex (Atg1-Atg13-Atg17-Atg29-Atg31) that starts autophagosome formation. The 897-residue protein has an N-terminal protein kinase domain, a central region carrying an Atg8-interacting (AIM/LIR) motif, and C-terminal tandem MIT domains that bind Atg13. Under nutrient-rich conditions TORC1 and PKA keep the complex inactive. When nitrogen or other nutrients are limiting, dephosphorylated Atg13 bridges Atg1 to the Atg17 scaffold, kinase activity rises, and the complex assembles at the pre-autophagosomal structure (phagophore assembly site, PAS) next to the vacuole. There it tethers Atg9 vesicles and recruits downstream Atg proteins. Atg1 phosphorylates Atg9, which is needed to recruit Atg8 and Atg18 and to expand the isolation membrane. It also phosphorylates Atg4, which protects the Atg8-PE pool at the PAS, and it re-phosphorylates Atg13 to end autophagy during prolonged starvation. Atg1 also has kinase-independent scaffolding functions in autophagosome nucleation. Its AIM-mediated binding to Atg8 places it on the isolation membrane and autophagosome, where it promotes maturation and is itself delivered to the vacuole. Atg1 is needed for the constitutive cytoplasm-to-vacuole targeting (Cvt) pathway, for which its kinase activity is essential, and for bulk and selective forms of autophagy, including mitophagy, reticulophagy, piecemeal microautophagy of the nucleus and late nucleophagy. Loss of ATG1 lowers survival during starvation.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000045 autophagosome assembly | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000681272 (Atg1/ULK node); ATG1 itself is one of the experimental seeds of this IBD. Reason: ATG1 lies in PTHR24348 (APG1/unc-51/ULK1 subfamily) and seeds the PTN000681272 autophagosome assembly IBD; yeast experiments show Atg1 kinase acts early in autophagosome formation by driving outgrowth of autophagosomal membranes. Core function. Supporting Evidence: PMID:24440502 These findings show that the Atg1 kinase acts early in autophagy by regulating the outgrowth of autophagosomal membranes. file:yeast/ATG1/ATG1-uniprot.txt Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. APG1/unc-51/ULK1 subfamily. |
| GO:0000045 autophagosome assembly | IDA PMID:18725539 In vivo reconstitution of autophagy in Saccharomyces cerevis... | ACCEPT | Summary: In vivo reconstitution in a 24-ATG-deletion strain showed that Atg1 and Atg13 are needed for Atg17 assembly at the PAS under starvation, an initial step of autophagosome formation. Reason: Direct reconstitution evidence that Atg1 (with Atg13) is part of the initial protein assembly at the phagophore assembly site that builds autophagosomes. Supporting Evidence: PMID:18725539 When both Atg1 and Atg13 were expressed, Atg17-GFP puncta localized at perivacuolar sites under starvation conditions. |
| GO:0000045 autophagosome assembly | IMP PMID:22778255 The autophagy-related protein kinase Atg1 interacts with the... | ACCEPT | Summary: Mutating the Atg1 AIM/LIR (Atg8-binding motif) causes a significant autophagy defect without affecting Atg1's initiation functions, showing that Atg1 also acts on the isolation membrane to help it mature into an autophagosome. Reason: IMP evidence that Atg1 has a second, Atg8-dependent role in autophagosome formation, in addition to initiation. Supporting Evidence: PMID:22778255 We also show that mutations in the Atg1 AIM cause a significant defect in autophagy, without affecting the functions of Atg1 implicated in triggering autophagosome formation. PMID:22778255 We find that Atg1 contains an AIM and directly interacts with Atg8. |
| GO:0000045 autophagosome assembly | IMP PMID:9224897 Apg1p, a novel protein kinase required for the autophagic pr... | ACCEPT | Summary: The original APG1 cloning paper showed APG1 encodes a Ser/Thr kinase needed for autophagy; apg1 mutants do not form autophagosomes. Reason: The cached record is abstract-only, but the claim matches the independent aut3 (atg1) null phenotype, which lacks autophagic vesicle accumulation, and later mechanistic work. Defer to the curator. Supporting Evidence: PMID:9224897 Here we show that the APG1 gene, involved in the autophagic process in yeast, encodes a novel type of Ser/Thr protein kinase. PMID:9190802 They are unable to accumulate autophagic vesicles in the vacuole during starvation. |
| GO:0000045 autophagosome assembly | NAS PMID:18287526 Organization of the pre-autophagosomal structure responsible... | ACCEPT | Summary: NAS from a study showing that the Atg1 kinase complex is needed to recruit Atg proteins to the PAS and, with Atg17-Atg29-Atg31, to organise the PAS for autophagosome formation. Reason: The statement in the abstract supports Atg1 participating in autophagosome formation by organising the PAS. Supporting Evidence: PMID:18287526 The Atg1 kinase complex (Atg1-Atg13) is also essential for recruitment of Atg proteins to the PAS. PMID:18287526 Our results suggest that Atg1 complex and the autophagy-unique Atg proteins cooperatively organize the PAS in response to starvation signals. |
| GO:0000407 phagophore assembly site | IBA GO_REF:0000033 | ACCEPT | Summary: IBA to phagophore assembly site from PTN000681272; ATG1 is one of the experimental seeds. Reason: Atg1 localises to the PAS in yeast by several independent IDA studies; the IBA reflects conserved PAS localisation of Atg1/ULK proteins. Supporting Evidence: PMID:11689437 This pre-autophagosomal structure, containing at least five Apg proteins, i.e. Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p, is localized in the vicinity of the vacuole. |
| GO:0000407 phagophore assembly site | IDA PMID:11689437 The pre-autophagosomal structure organized by concerted func... | ACCEPT | Summary: Atg1 (Apg1p) was one of the five founding proteins that define the pre-autophagosomal structure next to the vacuole. Reason: Direct localisation evidence. Supporting Evidence: PMID:11689437 This pre-autophagosomal structure, containing at least five Apg proteins, i.e. Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p, is localized in the vicinity of the vacuole. |
| GO:0000407 phagophore assembly site | IDA PMID:15659643 Atg11 links cargo to the vesicle-forming machinery in the cy... | ACCEPT | Summary: GFP-Atg1 forms a PAS dot whose formation depends on Atg11 domains that target cargo to the PAS (Cvt conditions). Reason: Direct localisation evidence of Atg1 at the PAS. Supporting Evidence: PMID:15659643 possessed a punctate GFP-Atg1 dot, which was comparable with the level seen with wild-type Atg11 |
| GO:0000407 phagophore assembly site | IDA PMID:18497569 Localization of autophagy-related proteins in yeast using a ... | ACCEPT | Summary: Systematic Atg-vYFP localisation during rapamycin-induced autophagy; Atg1 was among the fusions localised. Reason: The cached record is abstract-only, so the Atg1-specific image cannot be checked here. PAS localisation of Atg1 is well established (PMID:11689437), so the annotation is accepted, deferring to the curator. Supporting Evidence: PMID:18497569 we localized these Atgp-vYFP chimeras during rapamycin-induced autophagy PMID:11689437 This pre-autophagosomal structure, containing at least five Apg proteins, i.e. Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p, is localized in the vicinity of the vacuole. |
| GO:0000421 autophagosome membrane | IDA PMID:22885598 Binding of the Atg1/ULK1 kinase to the ubiquitin-like protei... | ACCEPT | Summary: Atg1 is targeted to autophagosomes by LIR-dependent binding to Atg8, and is then carried into the vacuole. Reason: Direct evidence that Atg1 associates with autophagosomal membranes through Atg8, which UniProt also curates. Supporting Evidence: PMID:22885598 Atg8 targets Atg1/ULK1 to autophagosomes, where it may promote autophagosome maturation and/or fusion with vacuoles/lysosomes. file:yeast/ATG1/ATG1-uniprot.txt The LIR motif is required for the interaction with ATG8 and for the association of ATG1 with autophagosomes. |
| GO:0000422 autophagy of mitochondrion | IMP PMID:19793921 A genomic screen for yeast mutants defective in selective mi... | MODIFY | Summary: atg1 deletion reduces mitoPho8Delta60 mitophagy activity to background. Reason: The term is correct but general. The mitochondrial degradation measured here is the starvation/post-log-phase macroautophagic pathway, which corresponds to GO:0000423 mitophagy (is_a GO:0000422) and is also asserted by IBA. Atg1 acts here through its core autophagosome-formation role, so this is non-core. Proposed replacements: mitophagy Supporting Evidence: PMID:19793921 In the atg1 Ξ strain, the alkaline phosphatase activities during both starvation conditions represent the background level. |
| GO:0000423 mitophagy | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA to mitophagy from PTN000681273. ATG1 is not a seed for this IBD, but yeast data independently show that atg1 deletion abolishes mitophagy. Reason: Correct: mitophagy needs the core Atg1-dependent autophagosome machinery. It is a cargo-specific use of the core function, not a distinct Atg1 activity. Supporting Evidence: PMID:19793921 In the atg1 Ξ strain, the alkaline phosphatase activities during both starvation conditions represent the background level. |
| GO:0004672 protein kinase activity | HDA PMID:16319894 Global analysis of protein phosphorylation in yeast. | MODIFY | Summary: Proteome-chip in vitro phosphorylation screen including Atg1. Reason: Atg1 is a protein kinase, but the more specific protein serine/threonine kinase activity (GO:0004674), which the gene already carries by IDA, is supported by direct substrate phosphorylation of Ser and Thr residues (PMID:24440502). Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:24440502 The multimembrane-spanning protein Atg9 is a direct target of this kinase essential for autophagy. PMID:24440502 Whereas the wild-type protein was active, the kinase-dead Atg1 D211A mutant did not show in vitro autophosphorylation activity |
| GO:0004672 protein kinase activity | IEA GO_REF:0000002 | MODIFY | Summary: InterPro Ser/Thr kinase active-site mapping to protein kinase activity. Reason: Correct but general; refine to GO:0004674 protein serine/threonine kinase activity, which experiments support. Proposed replacements: protein serine/threonine kinase activity Supporting Evidence: PMID:24440502 The multimembrane-spanning protein Atg9 is a direct target of this kinase essential for autophagy. |
| GO:0004674 protein serine/threonine kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA to protein serine/threonine kinase activity from PTN002805221; ATG1 is one of the experimental seeds. Reason: Core catalytic activity, directly shown in yeast. Supporting Evidence: PMID:24440502 The multimembrane-spanning protein Atg9 is a direct target of this kinase essential for autophagy. PMID:24440502 Whereas the wild-type protein was active, the kinase-dead Atg1 D211A mutant did not show in vitro autophosphorylation activity |
| GO:0004674 protein serine/threonine kinase activity | IDA PMID:22885598 Binding of the Atg1/ULK1 kinase to the ubiquitin-like protei... | ACCEPT | Summary: Atg1 kinase activity measured in a study of Atg13 and Atg8 binding; Atg13 binding is needed for full kinase activity. Reason: Direct kinase assays on yeast Atg1. Supporting Evidence: PMID:22885598 while the interaction of Atg13 and Atg1 was important for full kinase activity |
| GO:0004674 protein serine/threonine kinase activity | IDA PMID:24440502 Early steps in autophagy depend on direct phosphorylation of... | ACCEPT | Summary: Purified Atg1 autophosphorylates (lost in D211A kinase-dead) and directly phosphorylates Atg9 and other Atg proteins found by consensus peptide arrays. Reason: Definitive biochemical evidence of Ser/Thr kinase activity. Supporting Evidence: PMID:24440502 Whereas the wild-type protein was active, the kinase-dead Atg1 D211A mutant did not show in vitro autophosphorylation activity PMID:24440502 The multimembrane-spanning protein Atg9 is a direct target of this kinase essential for autophagy. |
| GO:0004674 protein serine/threonine kinase activity | IDA PMID:25921291 Dynamic phosphoproteomics reveals TORC1-dependent regulation... | ACCEPT | Summary: Dynamic phosphoproteomics after TORC1 perturbation used to infer kinase-substrate relationships, including Atg1 targets. Reason: The cached record is abstract-only, so the Atg1-specific data cannot be checked. The activity itself is established beyond doubt (PMID:24440502), so the annotation is accepted, deferring to the curator. Supporting Evidence: PMID:24440502 The multimembrane-spanning protein Atg9 is a direct target of this kinase essential for autophagy. |
| GO:0004674 protein serine/threonine kinase activity | IDA PMID:28821724 Atg4 proteolytic activity can be inhibited by Atg1 phosphory... | ACCEPT | Summary: Atg1 phosphorylates the protease Atg4, which inhibits it at the site of autophagosome biogenesis. Reason: Direct substrate phosphorylation (UniProt curates the Ser phosphorylation reaction from this paper). Supporting Evidence: PMID:28821724 Here we show that phosphorylation by Atg1 inhibits Atg4 function, an event that appears to exclusively occur at the site of autophagosome biogenesis. |
| GO:0004674 protein serine/threonine kinase activity | IDA PMID:33536246 Vacuolar protein Tag1 and Atg1-Atg13 regulate autophagy term... | ACCEPT | Summary: Atg1 re-phosphorylates Atg13 during prolonged nitrogen starvation to terminate autophagy. Reason: Identifies Atg13 as an Atg1 substrate in vivo. Supporting Evidence: PMID:33536246 termination is mediated by re-phosphorylation of Atg13 by the Atg1 protein kinase |
| GO:0004674 protein serine/threonine kinase activity | IDA PMID:9224897 Apg1p, a novel protein kinase required for the autophagic pr... | ACCEPT | Summary: APG1 cloning; identified as a Ser/Thr protein kinase. Reason: The abstract states the activity, and later biochemistry confirms it. Supporting Evidence: PMID:9224897 Here we show that the APG1 gene, involved in the autophagic process in yeast, encodes a novel type of Ser/Thr protein kinase. PMID:24440502 Whereas the wild-type protein was active, the kinase-dead Atg1 D211A mutant did not show in vitro autophosphorylation activity |
| GO:0004674 protein serine/threonine kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (InterPro Atg1-like/tMIT, EC 2.7.11.1) to Ser/Thr kinase activity. Reason: Agrees with the experimental data. Supporting Evidence: PMID:24440502 Whereas the wild-type protein was active, the kinase-dead Atg1 D211A mutant did not show in vitro autophosphorylation activity |
| GO:0004674 protein serine/threonine kinase activity | IMP PMID:9224897 Apg1p, a novel protein kinase required for the autophagic pr... | ACCEPT | Summary: IMP for kinase activity from the APG1 cloning paper (presumably kinase-domain mutant analysis). Reason: Abstract-only record, but the activity is fully established; defer to the curator. Supporting Evidence: PMID:9224897 Here we show that the APG1 gene, involved in the autophagic process in yeast, encodes a novel type of Ser/Thr protein kinase. |
| GO:0005515 protein binding | IPI PMID:10688190 A comprehensive analysis of protein-protein interactions in ... | REMOVE | Summary: Large-scale two-hybrid interaction with Atg13 (Q06628). Reason: Generic protein binding is uninformative and is removed under the repository's GO:0005515 policy; this does not dispute the reported interaction. The Atg1-Atg13 association is captured by Atg1/ULK1 kinase complex (GO:1990316). Supporting Evidence: PMID:24793651 Atg13 also binds Atg17, using a short region, thereby bridging Atg1 and Atg17 and leading to Atg1-complex formation. |
| GO:0005515 protein binding | IPI PMID:11309418 Cvt9/Gsa9 functions in sequestering selective cytosolic carg... | REMOVE | Summary: Interaction with Atg11/Cvt9 (Q12527), the selective-autophagy scaffold. Reason: Generic protein binding is uninformative and is removed under the repository's GO:0005515 policy; this does not dispute the reported interaction. No more specific MF is supported for Atg1 from this interaction. Supporting Evidence: PMID:11309418 Cvt9 oligomers peripherally associate with a novel, perivacuolar membrane compartment and interact with Apg1 |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | REMOVE | Summary: Affinity-purification/MS interaction with Atg13. Reason: Generic protein binding is uninformative and is removed under the repository's GO:0005515 policy; this does not dispute the reported interaction. Captured by GO:1990316. Supporting Evidence: PMID:24793651 Atg13 also binds Atg17, using a short region, thereby bridging Atg1 and Atg17 and leading to Atg1-complex formation. |
| GO:0005515 protein binding | IPI PMID:19805182 The Tor and PKA signaling pathways independently target the ... | REMOVE | Summary: Atg1-Atg13 interaction in a PKA/Tor regulation study. Reason: Generic protein binding is uninformative and is removed under the repository's GO:0005515 policy; this does not dispute the reported interaction. Captured by GO:1990316. Supporting Evidence: PMID:19805182 the Atg1/Atg13 kinase complex is a key site of signal integration within this degradative pathway |
| GO:0005515 protein binding | IPI PMID:20489023 A global protein kinase and phosphatase interaction network ... | REMOVE | Summary: Kinase interaction network AP-MS: Atg13. Reason: Generic protein binding is uninformative and is removed under the repository's GO:0005515 policy; this does not dispute the reported interaction. Captured by GO:1990316. Supporting Evidence: PMID:24793651 Atg13 also binds Atg17, using a short region, thereby bridging Atg1 and Atg17 and leading to Atg1-complex formation. |
| GO:0005515 protein binding | IPI PMID:20489023 A global protein kinase and phosphatase interaction network ... | REMOVE | Summary: Kinase interaction network AP-MS: Atg11. Reason: Generic protein binding is uninformative and is removed under the repository's GO:0005515 policy; this does not dispute the reported interaction. Supporting Evidence: PMID:20489023 We identified a kinase and phosphatase interaction (KPI) network of 1844 interactions in budding yeast by mass spectrometric analysis of protein complexes. |
| GO:0005515 protein binding | IPI PMID:22885598 Binding of the Atg1/ULK1 kinase to the ubiquitin-like protei... | MODIFY | Summary: Direct LIR-dependent binding of Atg1 to the ubiquitin-like protein Atg8 (P38182), which targets Atg1 to autophagosomes. Reason: The paper supports a more informative MF: direct, motif-dependent binding to the ubiquitin-like protein Atg8, which has a functional consequence (targeting to autophagosomes). GO has no Atg8-family-specific binding term, so ubiquitin-like protein binding (GO:0032182) is used. Proposed replacements: ubiquitin-like protein binding Supporting Evidence: PMID:22885598 We identify Atg8 as a novel regulator of Atg1/ULK1, which directly binds Atg1/ULK1 in a LC3-interaction region (LIR)-dependent manner. PMID:22778255 We find that Atg1 contains an AIM and directly interacts with Atg8. |
| GO:0005515 protein binding | IPI PMID:22885598 Binding of the Atg1/ULK1 kinase to the ubiquitin-like protei... | REMOVE | Summary: Direct Atg1-Atg13 binding, needed for full kinase activity. Reason: Generic protein binding is uninformative and is removed under the repository's GO:0005515 policy; this does not dispute the reported interaction. Its functional meaning is captured by Atg1/ULK1 kinase complex membership and by the kinase activity rows. Supporting Evidence: PMID:22885598 while the interaction of Atg13 and Atg1 was important for full kinase activity |
| GO:0005515 protein binding | IPI PMID:22885598 Binding of the Atg1/ULK1 kinase to the ubiquitin-like protei... | REMOVE | Summary: Atg1-Atg11 interaction. Reason: Generic protein binding is uninformative and is removed under the repository's GO:0005515 policy; this does not dispute the reported interaction. |
| GO:0005515 protein binding | IPI PMID:24793651 Structural basis of starvation-induced assembly of the autop... | REMOVE | Summary: Crystal structure: Atg13 binds the tandem MIT domains of Atg1. Reason: Generic protein binding is uninformative and is removed under the repository's GO:0005515 policy; this does not dispute the reported interaction. The structural finding is captured by GO:1990316. Supporting Evidence: PMID:24793651 Atg13 also binds Atg17, using a short region, thereby bridging Atg1 and Atg17 and leading to Atg1-complex formation. |
| GO:0005515 protein binding | IPI PMID:24968893 Hrr25 kinase promotes selective autophagy by phosphorylating... | REMOVE | Summary: Atg1 interaction with the Cvt cargo receptor Atg19 (P35193) in an Hrr25 study. Reason: Generic protein binding is uninformative and is removed under the repository's GO:0005515 policy; this does not dispute the reported interaction. Supporting Evidence: PMID:24968893 Selective autophagy is mediated by cargo receptors, which link the cargo to the scaffold protein Atg11 and to Atg8 family proteins on the forming autophagosomal membrane. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro kinase domain/ATP-binding signature to ATP binding. Reason: Correct: Atg1 is an active ATP-dependent kinase. ATP binding is part of the catalytic activity rather than a separate function. Supporting Evidence: PMID:24440502 Whereas the wild-type protein was active, the kinase-dead Atg1 D211A mutant did not show in vitro autophosphorylation activity |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: IBA to cytoplasm from PTN002805221; ATG1 is an experimental seed. Reason: Atg1 is cytosolic and is recruited to the PAS. Supporting Evidence: PMID:9190802 By using a fusion of Aut3p with green-fluorescent protein, Aut3p was localized to the cytosol. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt SubCell mapping to cytoplasm. Reason: Consistent with cytosolic localisation. Supporting Evidence: PMID:9190802 By using a fusion of Aut3p with green-fluorescent protein, Aut3p was localized to the cytosol. |
| GO:0005776 autophagosome | IBA GO_REF:0000033 | ACCEPT | Summary: IBA to autophagosome from PTN000681272; ATG1 is a seed. Reason: Atg8-dependent association with autophagosomes, and subsequent vacuolar delivery of Atg1, are shown in yeast. Supporting Evidence: PMID:22885598 Atg8 targets Atg1/ULK1 to autophagosomes, where it may promote autophagosome maturation and/or fusion with vacuoles/lysosomes. PMID:22778255 These results suggest that Atg1 associates with the isolation membrane by binding to Atg8, resulting in its incorporation into the autophagosome. |
| GO:0005829 cytosol | HDA PMID:26928762 One library to make them all: streamlining the creation of y... | ACCEPT | Summary: High-throughput SWAT N-terminal GFP localisation; cytosol. Reason: Consistent with low-throughput GFP localisation to the cytosol. Supporting Evidence: PMID:9190802 By using a fusion of Aut3p with green-fluorescent protein, Aut3p was localized to the cytosol. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: IBA to cytosol from PTN000681272; ATG1 is a seed. Reason: Consistent with yeast data. Supporting Evidence: PMID:9190802 By using a fusion of Aut3p with green-fluorescent protein, Aut3p was localized to the cytosol. |
| GO:0005829 cytosol | IDA PMID:9190802 AUT3, a serine/threonine kinase gene, is essential for autop... | ACCEPT | Summary: Aut3p-GFP localised to the cytosol. Reason: Direct localisation. Supporting Evidence: PMID:9190802 By using a fusion of Aut3p with green-fluorescent protein, Aut3p was localized to the cytosol. |
| GO:0006914 autophagy | IMP PMID:23382696 The role of autophagy in genome stability through suppressio... | MODIFY | Summary: Delta-atg1 used as an autophagy-deficient strain in a study linking starvation-induced autophagy to recovery from G2/M delay and genome stability. Reason: Correct but general. The autophagy at issue is starvation-induced bulk macroautophagy, so refine to GO:0016236 macroautophagy. The cell-cycle/genome-stability outcome is a downstream consequence of losing nutrient recycling and is not annotated as Atg1 process participation. Proposed replacements: macroautophagy Supporting Evidence: PMID:23382696 budding yeast cells can be efficiently returned to the G1 phase under starvation conditions in an autophagy-dependent manner |
| GO:0006995 cellular response to nitrogen starvation | IDA PMID:18725539 In vivo reconstitution of autophagy in Saccharomyces cerevis... | KEEP AS NON CORE | Summary: Reconstitution: Atg1 and Atg13 needed for Atg17 PAS puncta under nitrogen starvation. Reason: Atg1 is part of the cell's autophagic response to nitrogen starvation, and its kinase activity is raised by starvation. The response-level term is true but broader than the core function. Supporting Evidence: PMID:18725539 When both Atg1 and Atg13 were expressed, Atg17-GFP puncta localized at perivacuolar sites under starvation conditions. PMID:10995454 Here, we show that the protein kinase activity of Apg1 is enhanced by starvation or rapamycin treatment. |
| GO:0006995 cellular response to nitrogen starvation | IMP PMID:33536246 Vacuolar protein Tag1 and Atg1-Atg13 regulate autophagy term... | KEEP AS NON CORE | Summary: Atg1 re-phosphorylates Atg13 to end autophagy during persistent nitrogen starvation. Reason: Atg1 kinase activity directly shapes the time course of the nitrogen-starvation response. Non-core response-level term. Supporting Evidence: PMID:33536246 termination is mediated by re-phosphorylation of Atg13 by the Atg1 protein kinase |
| GO:0010506 regulation of autophagy | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA to regulation of autophagy from PTN000681272 (seeds are metazoan; ATG1 is not a seed). Reason: Yeast data independently support a regulatory role: Atg1 phosphorylation inhibits Atg4 deconjugation, Atg1 re-phosphorylates Atg13 to end autophagy, and Atg8 binding couples Atg1 activity to flux. Atg1 is mainly a core component, so the regulatory term is non-core. Supporting Evidence: PMID:28821724 Here we show that phosphorylation by Atg1 inhibits Atg4 function, an event that appears to exclusively occur at the site of autophagosome biogenesis. PMID:33536246 termination is mediated by re-phosphorylation of Atg13 by the Atg1 protein kinase PMID:22885598 Atg8 binding triggers vacuolar degradation of the Atg1-Atg13 complex in yeast, thereby coupling Atg1 activity to autophagic flux |
| GO:0016236 macroautophagy | IMP PMID:32788210 Potassium starvation induces autophagy in yeast. | ACCEPT | Summary: Potassium-starvation-induced autophagy requires Atg1. Reason: Atg1 is required for, and acts in, macroautophagy. Core process. Supporting Evidence: PMID:32788210 We found that potassium-dependent autophagy requires the core pathway kinases Atg1, Atg5, and Vps34 |
| GO:0018105 peptidyl-serine phosphorylation | IMP PMID:33536246 Vacuolar protein Tag1 and Atg1-Atg13 regulate autophagy term... | KEEP AS NON CORE | Summary: Atg1-dependent re-phosphorylation of Atg13 serines during persistent starvation. Reason: Peptidyl-serine phosphorylation is the process view of the kinase activity on Atg13. Correct, but it restates the MF. Supporting Evidence: PMID:33536246 termination is mediated by re-phosphorylation of Atg13 by the Atg1 protein kinase |
| GO:0032258 cytoplasm to vacuole targeting by the Cvt pathway | IMP PMID:10995454 Tor-mediated induction of autophagy via an Apg1 protein kina... | ACCEPT | Summary: Atg1 kinase complex studies show Atg1 is required for both autophagy and the Cvt pathway, with Atg13 binding needed only for autophagy. Reason: Atg1 is required for Cvt vesicle formation. The Cvt pathway is restricted to a fungal clade; this is a yeast-specific core use of Atg1. Supporting Evidence: PMID:10995454 suggesting that the Apg1 complex plays an important role in switching between two distinct vesicular transport systems in a nutrient-dependent manner |
| GO:0032258 cytoplasm to vacuole targeting by the Cvt pathway | IMP PMID:12589048 Chemical genetic analysis of Apg1 reveals a non-kinase role ... | ACCEPT | Summary: Analog-sensitive Atg1 shows that kinase activity is needed for Cvt trafficking of prApe1. Reason: Direct IMP evidence; the kinase activity is specifically needed for the Cvt pathway. Supporting Evidence: PMID:12589048 we find that Apg1 kinase activity is required only for Cvt trafficking of aminopeptidase I but not for import via autophagy |
| GO:0034045 obsolete phagophore assembly site membrane | IBA GO_REF:0000033 | MODIFY | Summary: IBA to GO:0034045 (phagophore assembly site membrane) from PTN000681273. QuickGO lists this term as obsolete, recommending phagophore membrane, phagophore assembly site or phagophore depending on the evidence. Reason: Atg1 is a peripheral protein at the PAS and on the isolation membrane (phagophore). Both locations are already IDA-supported for ATG1 (GO:0000407, GO:0061908), so the annotation is moved to those terms. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000681273 Β· PTN000681273 SUPPORTS TRANSFER Node-level PAS-membrane localisation is biologically right for ATG1, but QuickGO reports GO:0034045 as obsoleted; the claim is carried by GO:0000407 and GO:0061908, both IDA-supported in yeast. Proposed replacements: phagophore assembly site phagophore Supporting Evidence: PMID:23549786 By contrast, Atg1, Atg8 and the Atg16-Atg12-Atg5 complex were present at both the VICS and the cup-shaped IM. PMID:11689437 This pre-autophagosomal structure, containing at least five Apg proteins, i.e. Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p, is localized in the vicinity of the vacuole. |
| GO:0034045 obsolete phagophore assembly site membrane | IEA GO_REF:0000044 | MODIFY | Summary: UniProt SubCell 'Preautophagosomal structure membrane' mapped to GO:0034045, which QuickGO reports as obsolete. Reason: As for the IBA row: replace with phagophore assembly site and phagophore, both directly supported in yeast. Proposed replacements: phagophore assembly site phagophore Supporting Evidence: file:yeast/ATG1/ATG1-uniprot.txt Localizes to both the isolation membrane (IM) and the vacuole-isolation membrane contact site (VICS) during IM expansion. |
| GO:0034727 piecemeal microautophagy of the nucleus | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA to piecemeal microautophagy of the nucleus from PTN000681273; ATG1 is the sole seed. Reason: Supported by yeast PMN assays (atg1 null blocks release of PMN vesicles). PMN uses core Atg machinery, so the term is non-core. Supporting Evidence: PMID:18701704 The absence of intravacuolar NLS-mcherry containing vesicles in atg1Ξ atg15Ξ double mutant cells confirmed that their biogenesis depends on the autophagic machinery |
| GO:0034727 piecemeal microautophagy of the nucleus | IMP PMID:18701704 Piecemeal microautophagy of the nucleus requires the core ma... | KEEP AS NON CORE | Summary: PMN vesicle release into the vacuole needs Atg1 and other core ATG genes. Reason: Direct mutant evidence; a non-core selective autophagy type. Supporting Evidence: PMID:18701704 The absence of intravacuolar NLS-mcherry containing vesicles in atg1Ξ atg15Ξ double mutant cells confirmed that their biogenesis depends on the autophagic machinery |
| GO:0042594 response to starvation | IBA GO_REF:0000033 | MODIFY | Summary: IBA to response to starvation from PTN000681273; ATG1 is a seed. Reason: True but general. For ATG1 the starvations studied are nitrogen and potassium, both of which the gene carries directly. Refine to cellular response to nitrogen starvation (GO:0006995) and cellular response to potassium ion starvation (GO:0051365). The aut3 null also has reduced survival on starvation. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000681273 Β· PTN000681273 SUPPORTS TRANSFER ATG1 is among the experimental seeds; the node-level response to starvation term is correct and only refined to the nitrogen and potassium starvation responses shown in yeast. Proposed replacements: cellular response to nitrogen starvation cellular response to potassium ion starvation Supporting Evidence: PMID:9190802 aut3 null mutant cells are fully viable on rich media but show a reduced survival rate upon starvation. PMID:32788210 We found that potassium-dependent autophagy requires the core pathway kinases Atg1, Atg5, and Vps34 |
| GO:0042594 response to starvation | NAS PMID:18287526 Organization of the pre-autophagosomal structure responsible... | MODIFY | Summary: NAS: Atg1 complex organises the PAS in response to starvation signals. Reason: Same refinement as the IBA row: the starvation signals studied are nitrogen and potassium. Proposed replacements: cellular response to nitrogen starvation cellular response to potassium ion starvation Supporting Evidence: PMID:18287526 Our results suggest that Atg1 complex and the autophagy-unique Atg proteins cooperatively organize the PAS in response to starvation signals. |
| GO:0044804 nucleophagy | IMP PMID:22768199 A late form of nucleophagy in Saccharomyces cerevisiae. | KEEP AS NON CORE | Summary: Late nucleophagy (LN) of nucleoplasm reporter n-Rosella needs Atg1 (class II gene). Reason: Direct mutant evidence; a selective autophagy type driven by the core machinery. Supporting Evidence: PMID:22768199 a subset of the components of the core macroautophagic machinery is required for LN as it is efficiently inhibited in null mutants of several autophagy-related genes |
| GO:0051365 cellular response to potassium ion starvation | IMP PMID:32788210 Potassium starvation induces autophagy in yeast. | KEEP AS NON CORE | Summary: Atg1 required for autophagy induced by potassium starvation. Reason: True response-level term; Atg1 acts through macroautophagy. Supporting Evidence: PMID:32788210 We found that potassium-dependent autophagy requires the core pathway kinases Atg1, Atg5, and Vps34 |
| GO:0061709 reticulophagy | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA to reticulophagy from PTN000681273; ATG1 is a seed. Reason: Supported by yeast macro-ER-phagy data; a non-core selective autophagy type. Supporting Evidence: PMID:26181331 Like Atg11, deletion of the two core autophagy components, Atg1 and Atg8, result in an increase in the GFP-Snc1-PEM protein level |
| GO:0061709 reticulophagy | IMP PMID:26181331 A Role for Macro-ER-Phagy in ER Quality Control. | KEEP AS NON CORE | Summary: atg1 deletion blocks macro-ER-phagy of overexpressed GFP-Snc1-PEM. Reason: Direct mutant evidence; non-core. Supporting Evidence: PMID:26181331 Like Atg11, deletion of the two core autophagy components, Atg1 and Atg8, result in an increase in the GFP-Snc1-PEM protein level |
| GO:0061908 phagophore | IDA PMID:23549786 Fine mapping of autophagy-related proteins during autophagos... | ACCEPT | Summary: Atg1 localises to the cup-shaped isolation membrane (phagophore) as well as the VICS. Reason: Direct fine-mapping localisation. Supporting Evidence: PMID:23549786 By contrast, Atg1, Atg8 and the Atg16-Atg12-Atg5 complex were present at both the VICS and the cup-shaped IM. file:yeast/ATG1/ATG1-uniprot.txt Localizes to both the isolation membrane (IM) and the vacuole-isolation membrane contact site (VICS) during IM expansion. |
| GO:0106310 protein serine kinase activity | EXP PMID:24440502 Early steps in autophagy depend on direct phosphorylation of... | ACCEPT | Summary: Atg1 phosphorylates Atg9 on serine residues. Reason: Direct biochemistry. Supporting Evidence: PMID:24440502 The multimembrane-spanning protein Atg9 is a direct target of this kinase essential for autophagy. |
| GO:0106310 protein serine kinase activity | EXP PMID:24905091 Atg1 kinase organizes autophagosome formation by phosphoryla... | ACCEPT | Summary: Commentary on Papinski et al. describing Atg1 phosphorylation of Atg9. Reason: Supports Atg1 serine kinase activity toward Atg9; the primary data are in PMID:24440502. Supporting Evidence: PMID:24905091 In our study, we determined the Saccharomyces cerevisiae Atg1 consensus phosphorylation sequence using a peptide array-based approach. PMID:24440502 The multimembrane-spanning protein Atg9 is a direct target of this kinase essential for autophagy. |
| GO:0106310 protein serine kinase activity | EXP PMID:28821724 Atg4 proteolytic activity can be inhibited by Atg1 phosphory... | ACCEPT | Summary: Atg1 phosphorylates Atg4 serine residues. Reason: Direct biochemistry. Supporting Evidence: PMID:28821724 Here we show that phosphorylation by Atg1 inhibits Atg4 function, an event that appears to exclusively occur at the site of autophagosome biogenesis. |
| GO:0106310 protein serine kinase activity | IEA GO_REF:0000116 | ACCEPT | Summary: Rhea-based IEA from the curated serine phosphorylation reaction. Reason: Agrees with the experimental data. Supporting Evidence: PMID:24440502 The multimembrane-spanning protein Atg9 is a direct target of this kinase essential for autophagy. |
| GO:0120095 vacuole-isolation membrane contact site | IDA PMID:23549786 Fine mapping of autophagy-related proteins during autophagos... | KEEP AS NON CORE | Summary: Atg1 present at the vacuole-isolation membrane contact site (VICS). Reason: Direct localisation, but a specialised sub-site; the PAS and phagophore capture the main location. Supporting Evidence: PMID:23549786 By contrast, Atg1, Atg8 and the Atg16-Atg12-Atg5 complex were present at both the VICS and the cup-shaped IM. |
| GO:1990316 Atg1/ULK1 kinase complex | IDA PMID:26753620 The Atg1-kinase complex tethers Atg9-vesicles to initiate au... | ACCEPT | Summary: In vitro reconstitution: assembled Atg1 complex becomes active and tethers Atg9 vesicles. Reason: Atg1 is the catalytic subunit of the Atg1 kinase complex. Supporting Evidence: PMID:26753620 We find that on assembly from its cytoplasmic subcomplexes, the Atg1-kinase complex becomes activated, enabling it to recruit and tether Atg9-vesicles. |
| GO:1990316 Atg1/ULK1 kinase complex | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA IEA to Atg1/ULK1 kinase complex. Reason: Agrees with experimental evidence (the ARBA prediction itself is not used as support). Supporting Evidence: PMID:15743910 Two-hybrid analyses and coimmunoprecipitation experiments demonstrated that Atg17 physically associates with Atg1-Atg13 complex, and this binding was enhanced under starvation conditions. PMID:24793651 Atg13 also binds Atg17, using a short region, thereby bridging Atg1 and Atg17 and leading to Atg1-complex formation. |
| GO:1990316 Atg1/ULK1 kinase complex | IPI PMID:15743910 Atg17 functions in cooperation with Atg1 and Atg13 in yeast ... | ACCEPT | Summary: Atg17 associates with the Atg1-Atg13 complex, enhanced by starvation. Reason: Direct evidence for complex membership. Supporting Evidence: PMID:15743910 Two-hybrid analyses and coimmunoprecipitation experiments demonstrated that Atg17 physically associates with Atg1-Atg13 complex, and this binding was enhanced under starvation conditions. |
| GO:1990316 Atg1/ULK1 kinase complex | NAS PMID:18287526 Organization of the pre-autophagosomal structure responsible... | ACCEPT | Summary: NAS: the Atg1 kinase complex (Atg1-Atg13) organises the PAS. Reason: Agrees with experimental evidence. Supporting Evidence: PMID:18287526 The Atg1 kinase complex (Atg1-Atg13) is also essential for recruitment of Atg proteins to the PAS. |
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Download this section (compressed HTML)Q: Which Atg1 functions in autophagosome nucleation are truly kinase-independent? Analog-sensitive Atg1 inhibition left autophagy-mediated import intact (PMID:12589048), but Atg9 phosphorylation by Atg1 is reported as essential for autophagy (PMID:24440502).
Q: GO has no term for binding to Atg8-family proteins, so ubiquitin-like protein binding (GO:0032182) is used for LIR/AIM-mediated Atg8 binding. Would an 'Atg8-family protein binding' term be useful for the many LIR-containing autophagy proteins?
Experiment: Use phospho-null and phosphomimetic alleles of the full set of in vivo Atg1 sites on Atg9, Atg4 and Atg13 in one strain, with analog-sensitive Atg1, to divide the Atg1-dependent steps of autophagosome formation into those that need catalysis and those that need only the scaffold.
Protein serine/threonine kinase; required for vesicle formation in autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; structurally required for phagophore assembly site formation; forms a complex with Atg13p and Atg17p during autophagy; required for re-phosphorylation of Atg13p during termination of autophagy, following prolonged nitrogen starvation; essential for cell cycle progression from G2/M to G1 under nitrogen starvation
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