Gene Ontology annotation through association of InterPro records with GO terms
Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity
Annotation inferences using phylogenetic trees
Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt
Electronic Gene Ontology annotations created by ARBA machine learning models
Combined Automated Annotation using Multiple IEA Methods
ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe
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Provides subcellular localization data for Atg13 (cytoplasm/cytosol)
"Next, we determined the localization of 4,431 proteins"
Autophagy-deficient Schizosaccharomyces pombe mutants undergo partial sporulation during nitrogen starvation
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Demonstrates that atg13 is required for autophagy
"Using this marker, 13 Atg homologues were also found to be required for autophagy in fission yeast"
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Shows that autophagy-deficient mutants can partially sporulate when amino acids are provided
"In budding yeast, autophagy-deficient mutants are known to be sterile, whereas in fission yeast we found that up to 30 % of autophagy-defective cells with amino acid auxotrophy were able to recover sporulation when an excess of required amino acids was supplied"
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Indicates that autophagy supplies nitrogen for sporulation, explaining why atg13 affects sporulation indirectly
"fission yeast may store sufficient intracellular nitrogen to allow partial sporulation under nitrogen-limiting conditions, although the majority of the nitrogen source is supplied by autophagy"
Global analysis of fission yeast mating genes reveals new autophagy factors
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Confirms atg13 is required for macroautophagy
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Shows Atg13 localizes to the PAS
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Demonstrates atg13 deletion impairs Atg8 processing
Structure of the Atg101-Atg13 complex reveals essential roles of Atg101 in autophagy initiation
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Crystal structure of S. pombe Atg101-Atg13 HORMA heterodimer
"Here, we report the crystal structure of the fission yeast Atg101-Atg13 complex"
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Shows Atg13 HORMA has C-Mad2-like conformation
"Atg101 resembles O-Mad2 rather than the C-Mad2-like Atg13"
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Demonstrates Atg101 stabilizes Atg13 through HORMA-HORMA interaction
"Atg13 HORMA from higher eukaryotes possesses an inherently unstable fold, which is stabilized by Atg101 via interactions analogous to those between O-Mad2 and C-Mad2"
Atg20- and Atg24-family proteins promote organelle autophagy in fission yeast
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Demonstrates Atg13 is required for mitophagy in S. pombe
"in a distantly related fungal organism, the fission yeast Schizosaccharomyces pombe, autophagy of ER and mitochondria is induced by nitrogen starvation and is promoted by three Atg20- and Atg24-family proteins"
Conserved and unique features of the fission yeast core Atg1 complex
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Confirms Atg13 interacts with Atg1, Atg17, and Atg101
"Our pairwise coprecipitation experiments showed that while the interactions between Atg1, Atg13, and Atg17 are conserved, Atg101 does not bind Atg17"
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Shows Atg101 stabilizes Atg13 through HORMA domain interaction
"Atg101 interacts with the HORMA domain of Atg13 and this enhances the stability of both proteins"
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Demonstrates S. pombe Atg1 complex composition resembles mammalian ULK complex
"Although the human ULK complex mediates phagophore initiation similar to the budding yeast Saccharomyces cerevisiae Atg1 complex, this complex contains ATG101 but not Atg29 and Atg31"
Atg38-Atg8 interaction in fission yeast establishes a positive feedback loop to promote autophagy
Visual detection of binary, ternary and quaternary protein interactions in fission yeast using a Pil1 co-tethering assay
Deep research on Atg13 function in S. pombe
Atg1 kinase in fission yeast is activated by Atg11-mediated dimerization and cis-autophosphorylation
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In S. pombe, Atg1 kinase activity requires Atg11 (the FIP200/RB1CC1 ortholog) but does NOT require Atg13, Atg17, or Atg101. This is a key fission-yeast-specific divergence from the budding-yeast paradigm in which Atg13 binding activates Atg1.
"in the fission yeast
Schizosaccharomyces pombe, Atg1 kinase activity requires Atg11, the ortholog of
mammalian FIP200/RB1CC1, but does not require Atg13, Atg17, or Atg101."
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Atg1 activation is achieved by Atg11-mediated dimerization and cis-autophosphorylation, not by Atg13 binding.
"Dimerizing Atg1 is
the main role of Atg11, as it can be bypassed by artificially dimerizing Atg1."
Fission Yeast Autophagy Machinery
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The S. pombe Atg1 complex comprises Atg1, Atg13, Atg17, and Atg11, and (like the mammalian ULK1 complex) contains an Atg101 homolog but lacks Atg29/Atg31.
"pombe Atg1 complex has Atg1, Atg13, Atg17, and Atg11 subunits."
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Atg13 is described as the scaffold protein of the Atg1 complex.
"the Atg1 complex functioning in bulk autophagy is composed of Atg1 serine/threonine protein kinase, the scaffold protein Atg13"
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atg13 deletion mutants lose viability during nitrogen starvation and exhibit a mating defect, consistent with a requirement for autophagy in starvation survival and mating/sporulation.
"fission yeast atg1, atg8, and atg13 deletion mutants lose viability during nitrogen starvation and exhibit a mating defect"
Falcon deep research report on Atg13 (S. pombe) function for GO annotation
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Falcon synthesis classifies Atg13 in S. pombe primarily as a scaffold/adaptor protein within the Atg1 initiation machinery (not an enzyme), directly binding Atg1 and Atg17 to organize the initiation complex.
"it is primarily a **scaffold/adaptor protein** within the Atg1 initiation machinery. In fission yeast, Atg13 is described as a subunit of the Atg1 kinase complex and directly interacts with Atg1 and Atg17, supporting assembly/organization of the initiation complex"
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Atg13 has an N-terminal HORMA domain (residues 1-269) that binds Atg101, and a C-terminal region/CTD (residues 392-758) that mediates Atg1 and Atg17 binding; Atg13 helps anchor Atg1 to the Atg17 scaffold.
"An **N-terminal HORMA domain** (Atg13^HORMA; residues **1–269**) that binds Atg101"
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Atg101 binds the Atg13 HORMA domain to form an obligate heterodimer that strongly stabilizes Atg13; DSF melting temperatures were ~43C (Atg13 HORMA), ~48C (Atg101), and ~63C (heterodimer).
"an estimated melting temperature (T_m) of approximately **43°C** for Atg13^HORMA alone"
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Falcon synthesis (citing Pan et al. 2020) emphasizes that in S. pombe Atg13 is NOT required for Atg1 autophosphorylation; Atg11 rather than Atg13 is central for Atg1 kinase activation.
"Atg11** (FIP200 ortholog) rather than Atg13 is emphasized as required for normal Atg1 kinase activity"
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TORC1-dependent regulation of S. pombe Atg13 is proposed but residue-level phosphosite mapping remains incomplete; specific Atg13 phosphorylation sites are still unknown in the cited 2024 phosphoproteomic context.
"specific Atg13 residues remain unknown"
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Direct microscopy-based localization of S. pombe Atg13 was not found in the retrieved sources; PAS association is inferred from the complex role rather than directly demonstrated by imaging in the falcon-collected excerpts.
"the gathered excerpts do not provide a direct microscopy-based localization result for S. pombe Atg13 itself"