atg1

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005737 cytoplasm	IBA GO_REF:0000033	ACCEPT	Summary: Cytoplasmic localization is correct and directly supported by experimental evidence in Dictyostelium; Atg1-GFP shows a general cytoplasmic distribution. Reason: Atg1 acts predominantly in the cytoplasm, consistent with direct localization data and with its role as the cytoplasmic autophagy-initiating kinase. Supporting Evidence: PMID:26246495 Atg1 fused to GFP has been shown previously to have a general cytoplasmic pattern in Dictyostelium cells with no specific puncta localization
GO:0000045 autophagosome assembly	IBA GO_REF:0000033	ACCEPT	Summary: Atg1 is the upstream kinase that initiates autophagosome formation, a core conserved function directly demonstrated in Dictyostelium. Reason: Kinase-dead Atg1 blocks functional autophagosome formation and Atg1 is required for macroautophagy, making autophagosome assembly a core function. Supporting Evidence: PMID:17031001 In cells expressing dominant-negative DdAtg1, autophagosomes are formed and accumulate but seem not to be functional
GO:0000423 mitophagy	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: Mitophagy is a conserved ULK1/Atg1 selective-autophagy function, but direct evidence in Dictyostelium is lacking; the one study of Atg1 and mitochondria concluded an ancillary role in energy balance rather than direct organelle turnover. Reason: The IBA transfer of mitophagy from ULK1 orthologs is plausible but not demonstrated for Dictyostelium Atg1, where mitochondrial effects appear indirect; retained as non-core pending direct evidence. Supporting Evidence: PMID:39056773 Atg1's effects on energy homeostasis indicate a peripheral ancillary role in the mitochondrial signalling network, with effects on energy balance rather than direct effects on electron transport chain function
GO:0010506 regulation of autophagy	IBA GO_REF:0000033	ACCEPT	Summary: Atg1 is the induction-regulating kinase of the autophagy pathway, a core conserved function. Reason: As the catalytic subunit of the Atg1 complex, Atg1 controls the induction of autophagy, consistent with this annotation. Supporting Evidence: PMID:26246495 The first steps of induction and nucleation are controlled by the serine/threonine kinase Atg1/ULK1 and the class III PI3 K VPS34
GO:0042594 response to starvation	IBA GO_REF:0000033	ACCEPT	Summary: Atg1-dependent autophagy is induced by and required for survival during starvation, well supported in Dictyostelium. Reason: atg1 mutants show reduced survival during nitrogen starvation, directly linking Atg1 to the starvation response. Supporting Evidence: PMID:14736886 reduced survival during nitrogen starvation
GO:0061709 reticulophagy	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: Reticulophagy (ER-phagy) is a conserved selective-autophagy branch inferred from orthologs, but has not been demonstrated for Dictyostelium Atg1. Reason: No direct evidence for ER-selective autophagy by Dictyostelium Atg1; retained as a non-core phylogenetic inference.
GO:0000407 phagophore assembly site	IBA GO_REF:0000033	ACCEPT	Summary: Atg1 acts at the phagophore assembly site (preautophagosomal structure), where it initiates autophagosome formation. Reason: Kinase-dead Atg1 colocalizes with the Atg8 marker of preautophagosomal structures, supporting activity at this site. Supporting Evidence: PMID:17031001 colocalizes with red fluorescent protein (RFP)-tagged DdAtg8, a marker of
GO:0005776 autophagosome	IBA GO_REF:0000033	ACCEPT	Summary: Atg1 localizes to preautophagosomal structures and autophagosomes as shown by colocalization with the Atg8 marker. Reason: Direct colocalization of Atg1 with RFP-Atg8-labeled autophagosomes supports this localization annotation. Supporting Evidence: PMID:17031001 a marker of preautophagosomal structures and autophagosomes
GO:0004674 protein serine/threonine kinase activity	IBA GO_REF:0000033	ACCEPT	Summary: Atg1 is a serine/threonine protein kinase; this is the core molecular function. Reason: The conserved kinase domain and demonstrated kinase-dependent (dominant-negative kinase-dead) function establish Ser/Thr kinase activity as the core molecular function. Supporting Evidence: PMID:17031001 Kinase-negative DdAtg1 acts in a
GO:0034045 phagophore assembly site membrane	IBA GO_REF:0000033	ACCEPT	Summary: Atg1 associates with the phagophore assembly site (preautophagosomal structure) membrane as a peripheral membrane protein. Reason: Consistent with UniProt subcellular location (preautophagosomal structure membrane, peripheral) and with Atg1 activity at the PAS. Supporting Evidence: PMID:17031001 a marker of preautophagosomal structures and autophagosomes
GO:0005829 cytosol	IBA GO_REF:0000033	ACCEPT	Summary: Consistent with the observed diffuse cytoplasmic/cytosolic distribution of Atg1. Reason: Atg1-GFP shows a general cytoplasmic pattern, consistent with a cytosolic pool. Supporting Evidence: PMID:26246495 Atg1 fused to GFP has been shown previously to have a general cytoplasmic pattern in Dictyostelium cells with no specific puncta localization
GO:0034727 piecemeal microautophagy of the nucleus	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: A yeast-derived selective microautophagy process; not demonstrated for Dictyostelium Atg1. Reason: No direct evidence in Dictyostelium; retained as a non-core phylogenetic inference from fungal orthologs.
GO:0004672 protein kinase activity	IEA GO_REF:0000002	ACCEPT	Summary: General protein kinase activity, a correct parent term of the specific Ser/Thr kinase activity. Reason: Correct but less specific than protein serine/threonine kinase activity; the more specific term is captured elsewhere. Supporting Evidence: PMID:17031001 these domains are essential for autophagy and development
GO:0004674 protein serine/threonine kinase activity	IEA GO_REF:0000120	ACCEPT	Summary: Core molecular function, correctly assigned by automated methods. Reason: Atg1 belongs to the APG1/unc-51/ULK1 Ser/Thr kinase subfamily; this is the core molecular function. Supporting Evidence: PMID:26246495 the serine/threonine kinase Atg1/ULK1
GO:0005524 ATP binding	IEA GO_REF:0000002	ACCEPT	Summary: ATP binding is required for kinase catalysis and is supported by the conserved ATP-binding motif in the kinase domain. Reason: The protein has a canonical protein kinase ATP-binding site; ATP binding is intrinsic to its catalytic function. Supporting Evidence: PMID:26246495 the serine/threonine kinase Atg1/ULK1
GO:0005737 cytoplasm	IEA GO_REF:0000044	ACCEPT	Summary: Cytoplasmic localization from UniProt subcellular location mapping; correct. Reason: Consistent with direct experimental evidence for cytoplasmic localization. Supporting Evidence: PMID:26246495 Atg1 fused to GFP has been shown previously to have a general cytoplasmic pattern in Dictyostelium cells with no specific puncta localization
GO:0034045 phagophore assembly site membrane	IEA GO_REF:0000044	ACCEPT	Summary: Preautophagosomal structure membrane localization from UniProt; consistent with Atg1 activity at the PAS. Reason: Matches UniProt subcellular location (preautophagosomal structure membrane) and Atg1's role at the phagophore assembly site. Supporting Evidence: PMID:17031001 a marker of preautophagosomal structures and autophagosomes
GO:0106310 protein serine kinase activity	IEA GO_REF:0000116	ACCEPT	Summary: Serine kinase activity assigned via Rhea reaction mapping; consistent with the Ser/Thr kinase activity of Atg1. Reason: Correct reflection of the phosphotransferase reaction catalyzed by this Ser/Thr kinase. Supporting Evidence: PMID:26246495 the serine/threonine kinase Atg1/ULK1
GO:0071692 protein localization to extracellular region	IMP PMID:38986731 Trafficking of adhesion and aggregation-modulating proteins ...	KEEP AS NON CORE	Summary: atg1 (with atg9) modulates the intracellular and extracellular amounts of the adhesion protein CadA and the secreted counting factor CtnA during aggregation, an autophagy-dependent secretion role. Reason: The effect on extracellular protein levels is a downstream consequence of Atg1-dependent autophagy and unconventional secretion, not a core molecular function; retained as a non-core process. Supporting Evidence: PMID:38986731 The intracellular and extracellular amounts of CadA are modulated by autophagy genes
GO:0005737 cytoplasm	ISS GO_REF:0000024	ACCEPT	Summary: Cytoplasmic localization inferred from orthologs; consistent with direct Dictyostelium data. Reason: Supported by direct experimental localization of Atg1 to the cytoplasm. Supporting Evidence: PMID:26246495 Atg1 fused to GFP has been shown previously to have a general cytoplasmic pattern in Dictyostelium cells with no specific puncta localization
GO:0034045 phagophore assembly site membrane	ISS GO_REF:0000024	ACCEPT	Summary: PAS membrane localization inferred from orthologs; consistent with Atg1 activity at the phagophore assembly site. Reason: Matches UniProt subcellular location and Atg1's autophagy-initiating role. Supporting Evidence: PMID:17031001 a marker of preautophagosomal structures and autophagosomes
GO:0106310 protein serine kinase activity	ISS GO_REF:0000024	ACCEPT	Summary: Serine kinase activity inferred from sequence similarity; consistent with the core Ser/Thr kinase function. Reason: Correct reflection of Atg1 kinase activity. Supporting Evidence: PMID:26246495 the serine/threonine kinase Atg1/ULK1
GO:0000902 cell morphogenesis	IMP PMID:39056773 The Multifaceted Interactions of Dictyostelium Atg1 with Mit...	KEEP AS NON CORE	Summary: atg1 null cells are consistently smaller and show altered nuclear division; this reflects effects on cell size/division rather than a dedicated morphogenetic program. Reason: The cell-size phenotype is a pleiotropic consequence of altered autophagy and growth/energy homeostasis, not a core function; retained as non-core. Supporting Evidence: PMID:39056773 the null mutant exhibited consistently smaller average cell sizes when grown axenically
GO:0009267 cellular response to starvation	IDA PMID:39056773 The Multifaceted Interactions of Dictyostelium Atg1 with Mit...	KEEP AS NON CORE	Summary: Atg1 increases tolerance of Dictyostelium to starvation, consistent with its role in starvation-induced autophagy. Reason: A genuine, experimentally supported role, but downstream of the core kinase/autophagy function; retained as non-core. Supporting Evidence: PMID:39056773 Atg1 increases the tolerance of D. discoideum to starvation and cAMP treatment
GO:0030587 sorocarp development	IDA PMID:39056773 The Multifaceted Interactions of Dictyostelium Atg1 with Mit...	KEEP AS NON CORE	Summary: Altered atg1 expression produces smaller fruiting bodies and multi-tipped aggregates, confirming a role in multicellular (sorocarp) development. Reason: A pleiotropic developmental role that follows from Atg1-dependent autophagy during starvation-induced development; retained as non-core. Supporting Evidence: PMID:39056773 both atg1 antisense inhibition and overexpression resulted in smaller fruiting bodies
GO:0048548 regulation of pinocytosis	IMP PMID:39056773 The Multifaceted Interactions of Dictyostelium Atg1 with Mit...	KEEP AS NON CORE	Summary: Atg1 positively regulates macropinocytosis; the null mutant has a macropinocytic defect and uptake correlates with atg1 expression. Reason: A real, experimentally supported regulatory effect on macropinocytic uptake, but a downstream/pleiotropic role rather than a core function. Supporting Evidence: PMID:39056773 the atg1 null mutant displayed a macropinocytic defect
GO:0010629 negative regulation of gene expression	IDA PMID:39056773 The Multifaceted Interactions of Dictyostelium Atg1 with Mit...	KEEP AS NON CORE	Summary: Overexpression data suggest Atg1 negatively regulates the prestalk marker ecmA; the effect on individual genes was modest. Reason: A downstream developmental gene-expression effect, supported but not a core molecular function; retained as non-core. Supporting Evidence: PMID:39056773 This suggests that Atg1 negatively regulates prestalk gene (ecmA) expression
GO:0009617 response to bacterium	IMP PMID:22575510 Lipopolysaccharide induction of autophagy is associated with...	KEEP AS NON CORE	Summary: atg1 is required for LPS-enhanced clearance of phagocytosed bacteria, linking Atg1-dependent autophagy to the antibacterial response. Reason: A genuine cell-autonomous defense role mediated by autophagy, but downstream of the core kinase/autophagy function; retained as non-core. Supporting Evidence: PMID:22575510 LPS pre-treatment did not enhance clearance of phagocytized S. aureus in cells deficient for either atg1 or atg9
GO:0031152 aggregation involved in sorocarp development	IMP PMID:39056773 The Multifaceted Interactions of Dictyostelium Atg1 with Mit...	KEEP AS NON CORE	Summary: atg1-null cells are unable to aggregate, a hallmark of severe autophagy impairment in Dictyostelium development. Reason: An experimentally established developmental phenotype downstream of Atg1-dependent autophagy; retained as non-core. Supporting Evidence: PMID:26246495 Amoebas in which Atg1 has been knocked out are unable to aggregate
GO:0043327 chemotaxis to cAMP	IMP PMID:39056773 The Multifaceted Interactions of Dictyostelium Atg1 with Mit...	UNDECIDED	Summary: This study measured cAMP/starvation survival and aggregation timing but did not directly assay chemotaxis to cAMP; a direct chemotaxis role for Atg1 cannot be verified from the available text. Reason: The cited paper does not present a direct chemotaxis assay, and antisense inhibition had no pronounced effect on aggregation; the supporting evidence for a specific chemotaxis-to-cAMP function cannot be verified.
GO:0043457 regulation of cellular respiration	IDA PMID:39056773 The Multifaceted Interactions of Dictyostelium Atg1 with Mit...	KEEP AS NON CORE	Summary: Knockout of atg1 alters mitochondrial and non-mitochondrial respiration, supporting a role in modulating cellular respiration. Reason: An experimentally supported but indirect/peripheral effect on energy homeostasis, not a core molecular function; retained as non-core. Supporting Evidence: PMID:39056773 knocking out atg1 caused reductions in basal mitochondrial and non-mitochondrial respiration
GO:0043653 mitochondrial fragmentation involved in apoptotic process	IDA PMID:39056773 The Multifaceted Interactions of Dictyostelium Atg1 with Mit...	UNDECIDED	Summary: The cited study characterized mitochondrial membrane mass, potential, ROS and respiration but did not demonstrate mitochondrial fragmentation as part of an apoptotic process; Dictyostelium cell death is characteristically non-apoptotic. Reason: The specific term (apoptotic mitochondrial fragmentation) is not supported by the available text and apoptosis is not an established Dictyostelium cell-death mode; the basis for this annotation cannot be verified.
GO:0044351 macropinocytosis	IDA PMID:39056773 The Multifaceted Interactions of Dictyostelium Atg1 with Mit...	KEEP AS NON CORE	Summary: atg1-null cells display a macropinocytic defect and macropinocytic uptake correlates positively with atg1 expression. Reason: A genuine effect on macropinocytosis, but a downstream/pleiotropic role rather than a core molecular function; retained as non-core. Supporting Evidence: PMID:39056773 macropinocytic uptake rates were positively correlated with the atg1 expression index
GO:0004672 protein kinase activity	IDA PMID:17031001 Function of the Dictyostelium discoideum Atg1 kinase during ...	ACCEPT	Summary: Direct evidence that the Atg1 kinase domain is essential for function; kinase-dead Atg1 acts as a dominant negative. Reason: The kinase domain is essential for autophagy and development, and a kinase-negative mutant is dominant-negative, directly demonstrating catalytic protein kinase function. Supporting Evidence: PMID:17031001 these domains are essential for autophagy and development
GO:0016236 macroautophagy	IMP PMID:17031001 Function of the Dictyostelium discoideum Atg1 kinase during ...	ACCEPT	Summary: Atg1 kinase and its conserved C-terminal domain are essential for macroautophagy in Dictyostelium, a core function. Reason: Kinase-dead Atg1 blocks functional autophagy and the domains are essential for autophagy; macroautophagy is a core biological process for Atg1. Supporting Evidence: PMID:17031001 In cells expressing dominant-negative DdAtg1, autophagosomes are formed and accumulate but seem not to be functional
GO:0048102 autophagic cell death	IMP PMID:15358773 Autophagy gene disruption reveals a non-vacuolar cell death ...	KEEP AS NON CORE	Summary: atg1 disruption blocks autophagy and vacuolization in the developmental vacuolar cell death model, showing Atg1 is required for autophagic (vacuolar) cell death. Reason: An experimentally supported developmental cell-death role that is downstream of Atg1-dependent autophagy; retained as non-core. Supporting Evidence: PMID:15358773 led in atg1 mutant cells to impaired autophagy and to no vacuolization
GO:0008047 enzyme activator activity	IDA PMID:26246495 Dissecting the function of Atg1 complex in Dictyostelium aut...	KEEP AS NON CORE	Summary: Atg1 positively regulates the activity of the pentose-phosphate-pathway enzyme transketolase (TKT), with which it physically interacts; TKT activity rises with Atg1 overexpression and falls in atg1-null or kinase-dead conditions. Reason: Atg1 acts as a positive regulator of TKT activity (likely via its kinase function), but this enzyme-activation role is a specialized regulatory link rather than the core evolved molecular function; retained as non-core. Supporting Evidence: PMID:26246495 There is an increase in activity in cells overexpressing Atg1. By contrast, TKT activity decreases in cells in which atg1 has been deleted
GO:0097300 programmed necrotic cell death	IDA PMID:17150370 From autophagic to necrotic cell death in Dictyostelium.	UNDECIDED	Summary: This review describes that disrupting atg1 reveals a non-vacuolar (necrotic-like) cell death pathway; necrotic death occurs in the absence of Atg1 rather than requiring it, so a positive involvement of Atg1 in necrotic death is not clearly supported. Reason: The relationship between Atg1 and necrotic cell death is indirect (necrosis is unmasked when autophagic death is blocked); the supporting text is from a review and does not establish that Atg1 is involved_in programmed necrotic death.
GO:0005515 protein binding	IPI PMID:31680241 AMPKα promotes basal autophagy induction in Dictyostelium di...	KEEP AS NON CORE	Summary: Co-immunoprecipitation shows an AMPK-ATG1 interaction conserved in basal autophagy. Bare 'protein binding' is uninformative; the meaningful content is the specific interaction with AMPK. Reason: Per curation guidance, generic protein binding is not retained as a core function; the AMPK interaction is captured here as a non-core regulatory partnership. Supporting Evidence: PMID:31680241 Co-immunoprecipitation studies show conservation of the AMPK-ATG1
GO:0050830 defense response to Gram-positive bacterium	IDA PMID:28414774 Mycobacterium marinum antagonistically induces an autophagic...	UNDECIDED	Summary: This study focuses on the ESX-1/TORC1-dependent manipulation of autophagy by Mycobacterium marinum; a specific, verifiable role for Atg1 in defense against a Gram-positive bacterium is not evident from the available text. Reason: The cached text does not establish an Atg1-specific defense role against Gram-positive bacteria; the annotation cannot be verified from the available evidence.
GO:1905037 autophagosome organization	IMP PMID:28414774 Mycobacterium marinum antagonistically induces an autophagic...	KEEP AS NON CORE	Summary: Atg1 is required for autophagosome formation/organization, an essentially core autophagy function; autophagosomes formed without functional Atg1 are aberrant. Reason: Autophagosome organization is closely tied to Atg1's core autophagy-initiating role; captured here as a non-core process-level annotation with the core function recorded under macroautophagy/autophagosome assembly. Supporting Evidence: PMID:17031001 In cells expressing dominant-negative DdAtg1, autophagosomes are formed and accumulate but seem not to be functional
GO:0005515 protein binding	IPI PMID:26246495 Dissecting the function of Atg1 complex in Dictyostelium aut...	KEEP AS NON CORE	Summary: Yeast two-hybrid and pull-down show Atg1 interacts with Atg13 and with the pentose-phosphate enzyme transketolase (TKT). Bare 'protein binding' is uninformative; the specific partners are the meaningful content. Reason: Per curation guidance, generic protein binding is not retained as core; the Atg13 and TKT interactions are better represented via the Atg1 complex membership and the enzyme-activator annotation. Supporting Evidence: PMID:26246495 TKT–HA is efficiently pulled down by GFP-Atg1
GO:1990316 Atg1/ULK1 kinase complex	IDA PMID:26246495 Dissecting the function of Atg1 complex in Dictyostelium aut...	ACCEPT	Summary: Atg1 is the catalytic subunit of the conserved Atg1-Atg13-Atg101 kinase complex in Dictyostelium, confirmed by yeast two-hybrid and pull-down. Reason: Direct evidence establishes the Atg1-Atg13-Atg101 core complex, making Atg1/ULK1 kinase complex membership a core annotation. Supporting Evidence: PMID:26246495 The core of this assembly of proteins is formed by Atg1-Atg13-Atg101, which seems to be conserved
GO:0001878 response to yeast	IMP PMID:27818653 Dictyostelium discoideum as a Novel Host System to Study the...	KEEP AS NON CORE	Summary: atg1-null cells show altered (increased) ability to predate yeast, implicating Atg1-dependent autophagy in the amoeba's interaction with yeast. Reason: A downstream, autophagy-mediated host-microbe interaction phenotype; retained as non-core. Supporting Evidence: PMID:27818653 mutants increase (atg1-, kil1-, kil2-) or decrease (atg6-) the ability of the
GO:0035891 exit from host cell	IMP PMID:25646440 The autophagic machinery ensures nonlytic transmission of my...	KEEP AS NON CORE	Summary: The autophagic machinery is required for nonlytic cell-to-cell transmission (ejection) of mycobacteria; impairing autophagy blocks transmission. Reason: A specialized host-pathogen role mediated by Atg1-dependent autophagy; retained as non-core. Supporting Evidence: PMID:25646440 If autophagy is impaired, cell-to-cell transmission is
GO:0042742 defense response to bacterium	IMP PMID:25646440 The autophagic machinery ensures nonlytic transmission of my...	KEEP AS NON CORE	Summary: Atg1-dependent autophagy contributes to control of intracellular mycobacteria; autophagy impairment compromises the host and permits transmission. Reason: A cell-autonomous antibacterial defense role mediated by autophagy; downstream of the core function and retained as non-core. Supporting Evidence: PMID:25646440 If autophagy is impaired, cell-to-cell transmission is inhibited, the host plasma membrane becomes compromised and the host cells die
GO:0030587 sorocarp development	IMP PMID:14736886 Dictyostelium macroautophagy mutants vary in the severity of...	KEEP AS NON CORE	Summary: atg1 mutation causes severe developmental defects; the atg1-1 mutant fails to aggregate on bacterial lawns and arrests as loose mounds. Reason: A well-established developmental requirement downstream of Atg1-dependent autophagy; retained as non-core. Supporting Evidence: PMID:14736886 does not aggregate on bacterial lawns
GO:0031288 sorocarp morphogenesis	IMP PMID:14736886 Dictyostelium macroautophagy mutants vary in the severity of...	KEEP AS NON CORE	Summary: atg1 mutants produce aberrant fruiting-body morphology, reflecting a requirement for Atg1 in sorocarp morphogenesis. Reason: A developmental morphogenesis phenotype downstream of Atg1-dependent autophagy; retained as non-core. Supporting Evidence: PMID:14736886 Mutations in the three genes produce aberrant development
GO:0004674 protein serine/threonine kinase activity	ISS PMID:14736886 Dictyostelium macroautophagy mutants vary in the severity of...	ACCEPT	Summary: Ser/Thr kinase activity inferred from the conserved kinase domain; the core molecular function. Reason: Consistent with the kinase-domain-dependent function directly demonstrated in Dictyostelium. Supporting Evidence: PMID:26246495 the serine/threonine kinase Atg1/ULK1
GO:0005737 cytoplasm	IDA PMID:14736886 Dictyostelium macroautophagy mutants vary in the severity of...	ACCEPT	Summary: Cytoplasmic localization; consistent with the diffuse cytoplasmic distribution of Atg1 reported across studies. Reason: Cytoplasmic localization of Atg1 is well established by direct evidence. Supporting Evidence: PMID:26246495 Atg1 fused to GFP has been shown previously to have a general cytoplasmic pattern in Dictyostelium cells with no specific puncta localization
GO:0006995 cellular response to nitrogen starvation	IMP PMID:14736886 Dictyostelium macroautophagy mutants vary in the severity of...	KEEP AS NON CORE	Summary: atg1 mutants show reduced survival during nitrogen starvation, linking Atg1 to the nitrogen-starvation response. Reason: A supported starvation-response phenotype downstream of Atg1-dependent autophagy; retained as non-core. Supporting Evidence: PMID:14736886 reduced survival during nitrogen starvation
GO:0016236 macroautophagy	IMP PMID:14736886 Dictyostelium macroautophagy mutants vary in the severity of...	ACCEPT	Summary: atg1 is required for macroautophagy in Dictyostelium, a core function. Reason: Direct genetic evidence that Atg1 is required for macroautophagy; a core biological process. Supporting Evidence: PMID:14736886 genes are required for macroautophagy in Dictyostelium
GO:0030435 sporulation resulting in formation of a cellular spore	IMP PMID:14736886 Dictyostelium macroautophagy mutants vary in the severity of...	KEEP AS NON CORE	Summary: Because Atg1 is required for normal fruiting-body development, spore formation is impaired in atg1 mutants; this is a downstream developmental consequence. Reason: A developmental sporulation phenotype downstream of Atg1-dependent autophagy; retained as non-core. Supporting Evidence: PMID:14736886 Mutations in the three genes produce aberrant development

📄 View Raw YAML

id: Q86CS2
gene_symbol: atg1
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:44689
  label: Dictyostelium discoideum
description: >-
  atg1 encodes the Dictyostelium discoideum ortholog of the Atg1/ULK1
  serine/threonine protein kinase, the most upstream component of the
  macroautophagy induction machinery. The protein has an N-terminal protein
  kinase domain (residues ~7-266) followed by an asparagine/glutamine-rich
  low-complexity region and a conserved C-terminal domain required for its
  localization to forming autophagosomes. Atg1 is the catalytic subunit of the
  Atg1 kinase complex (with Atg13 and Atg101), and its kinase activity initiates
  phagophore/autophagosome formation. Because Dictyostelium undergoes
  starvation-induced multicellular development that depends on autophagy for
  nutrient mobilization, Atg1 is essential for aggregation and for normal
  fruiting-body (sorocarp) formation, and it is required for the vacuolar
  (autophagic) cell death of terminally differentiating cells. Atg1-dependent
  autophagy also contributes to cell-autonomous defense against ingested
  bacteria and yeasts and to nutrient and energy homeostasis, and the kinase
  additionally influences macropinocytosis, cell size and nuclear division, gene
  expression, and mitochondrial energy balance. Atg1 localizes predominantly to
  the cytoplasm and cytosol, with a pool at the preautophagosomal structure
  (phagophore assembly site) membrane.
existing_annotations:
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: Cytoplasmic localization is correct and directly supported by experimental
      evidence in Dictyostelium; Atg1-GFP shows a general cytoplasmic distribution.
    action: ACCEPT
    reason: Atg1 acts predominantly in the cytoplasm, consistent with direct localization
      data and with its role as the cytoplasmic autophagy-initiating kinase.
    supported_by:
    - reference_id: PMID:26246495
      supporting_text: Atg1 fused to GFP has been shown previously to have a general
        cytoplasmic pattern in Dictyostelium cells with no specific puncta localization
- term:
    id: GO:0000045
    label: autophagosome assembly
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: Atg1 is the upstream kinase that initiates autophagosome formation, a
      core conserved function directly demonstrated in Dictyostelium.
    action: ACCEPT
    reason: Kinase-dead Atg1 blocks functional autophagosome formation and Atg1 is
      required for macroautophagy, making autophagosome assembly a core function.
    supported_by:
    - reference_id: PMID:17031001
      supporting_text: In cells expressing dominant-negative DdAtg1, autophagosomes
        are formed and accumulate but seem not to be functional
- term:
    id: GO:0000423
    label: mitophagy
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: Mitophagy is a conserved ULK1/Atg1 selective-autophagy function, but
      direct evidence in Dictyostelium is lacking; the one study of Atg1 and mitochondria
      concluded an ancillary role in energy balance rather than direct organelle turnover.
    action: KEEP_AS_NON_CORE
    reason: The IBA transfer of mitophagy from ULK1 orthologs is plausible but not
      demonstrated for Dictyostelium Atg1, where mitochondrial effects appear indirect;
      retained as non-core pending direct evidence.
    supported_by:
    - reference_id: PMID:39056773
      supporting_text: Atg1's effects on energy homeostasis indicate a peripheral
        ancillary role in the mitochondrial signalling network, with effects on energy
        balance rather than direct effects on electron transport chain function
- term:
    id: GO:0010506
    label: regulation of autophagy
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: Atg1 is the induction-regulating kinase of the autophagy pathway, a core
      conserved function.
    action: ACCEPT
    reason: As the catalytic subunit of the Atg1 complex, Atg1 controls the induction
      of autophagy, consistent with this annotation.
    supported_by:
    - reference_id: PMID:26246495
      supporting_text: The first steps of induction and nucleation are controlled
        by the serine/threonine kinase Atg1/ULK1 and the class III PI3 K VPS34
- term:
    id: GO:0042594
    label: response to starvation
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: Atg1-dependent autophagy is induced by and required for survival during
      starvation, well supported in Dictyostelium.
    action: ACCEPT
    reason: atg1 mutants show reduced survival during nitrogen starvation, directly
      linking Atg1 to the starvation response.
    supported_by:
    - reference_id: PMID:14736886
      supporting_text: reduced survival during nitrogen starvation
- term:
    id: GO:0061709
    label: reticulophagy
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: Reticulophagy (ER-phagy) is a conserved selective-autophagy branch inferred
      from orthologs, but has not been demonstrated for Dictyostelium Atg1.
    action: KEEP_AS_NON_CORE
    reason: No direct evidence for ER-selective autophagy by Dictyostelium Atg1; retained
      as a non-core phylogenetic inference.
- term:
    id: GO:0000407
    label: phagophore assembly site
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: Atg1 acts at the phagophore assembly site (preautophagosomal structure),
      where it initiates autophagosome formation.
    action: ACCEPT
    reason: Kinase-dead Atg1 colocalizes with the Atg8 marker of preautophagosomal
      structures, supporting activity at this site.
    supported_by:
    - reference_id: PMID:17031001
      supporting_text: colocalizes with red fluorescent protein (RFP)-tagged DdAtg8,
        a marker of
- term:
    id: GO:0005776
    label: autophagosome
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: Atg1 localizes to preautophagosomal structures and autophagosomes as
      shown by colocalization with the Atg8 marker.
    action: ACCEPT
    reason: Direct colocalization of Atg1 with RFP-Atg8-labeled autophagosomes supports
      this localization annotation.
    supported_by:
    - reference_id: PMID:17031001
      supporting_text: a marker of preautophagosomal structures and autophagosomes
- term:
    id: GO:0004674
    label: protein serine/threonine kinase activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: Atg1 is a serine/threonine protein kinase; this is the core molecular
      function.
    action: ACCEPT
    reason: The conserved kinase domain and demonstrated kinase-dependent (dominant-negative
      kinase-dead) function establish Ser/Thr kinase activity as the core molecular
      function.
    supported_by:
    - reference_id: PMID:17031001
      supporting_text: Kinase-negative DdAtg1 acts in a
- term:
    id: GO:0034045
    label: phagophore assembly site membrane
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: Atg1 associates with the phagophore assembly site (preautophagosomal
      structure) membrane as a peripheral membrane protein.
    action: ACCEPT
    reason: Consistent with UniProt subcellular location (preautophagosomal structure
      membrane, peripheral) and with Atg1 activity at the PAS.
    supported_by:
    - reference_id: PMID:17031001
      supporting_text: a marker of preautophagosomal structures and autophagosomes
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: is_active_in
  review:
    summary: Consistent with the observed diffuse cytoplasmic/cytosolic distribution
      of Atg1.
    action: ACCEPT
    reason: Atg1-GFP shows a general cytoplasmic pattern, consistent with a cytosolic
      pool.
    supported_by:
    - reference_id: PMID:26246495
      supporting_text: Atg1 fused to GFP has been shown previously to have a general
        cytoplasmic pattern in Dictyostelium cells with no specific puncta localization
- term:
    id: GO:0034727
    label: piecemeal microautophagy of the nucleus
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: A yeast-derived selective microautophagy process; not demonstrated for
      Dictyostelium Atg1.
    action: KEEP_AS_NON_CORE
    reason: No direct evidence in Dictyostelium; retained as a non-core phylogenetic
      inference from fungal orthologs.
- term:
    id: GO:0004672
    label: protein kinase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: General protein kinase activity, a correct parent term of the specific
      Ser/Thr kinase activity.
    action: ACCEPT
    reason: Correct but less specific than protein serine/threonine kinase activity;
      the more specific term is captured elsewhere.
    supported_by:
    - reference_id: PMID:17031001
      supporting_text: these domains
        are essential for autophagy and development
- term:
    id: GO:0004674
    label: protein serine/threonine kinase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: Core molecular function, correctly assigned by automated methods.
    action: ACCEPT
    reason: Atg1 belongs to the APG1/unc-51/ULK1 Ser/Thr kinase subfamily; this is
      the core molecular function.
    supported_by:
    - reference_id: PMID:26246495
      supporting_text: the serine/threonine kinase Atg1/ULK1
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: enables
  review:
    summary: ATP binding is required for kinase catalysis and is supported by the conserved
      ATP-binding motif in the kinase domain.
    action: ACCEPT
    reason: The protein has a canonical protein kinase ATP-binding site; ATP binding
      is intrinsic to its catalytic function.
    supported_by:
    - reference_id: PMID:26246495
      supporting_text: the serine/threonine kinase Atg1/ULK1
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: Cytoplasmic localization from UniProt subcellular location mapping; correct.
    action: ACCEPT
    reason: Consistent with direct experimental evidence for cytoplasmic localization.
    supported_by:
    - reference_id: PMID:26246495
      supporting_text: Atg1 fused to GFP has been shown previously to have a general
        cytoplasmic pattern in Dictyostelium cells with no specific puncta localization
- term:
    id: GO:0034045
    label: phagophore assembly site membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000044
  qualifier: located_in
  review:
    summary: Preautophagosomal structure membrane localization from UniProt; consistent
      with Atg1 activity at the PAS.
    action: ACCEPT
    reason: Matches UniProt subcellular location (preautophagosomal structure membrane)
      and Atg1's role at the phagophore assembly site.
    supported_by:
    - reference_id: PMID:17031001
      supporting_text: a marker of preautophagosomal structures and autophagosomes
- term:
    id: GO:0106310
    label: protein serine kinase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000116
  qualifier: enables
  review:
    summary: Serine kinase activity assigned via Rhea reaction mapping; consistent
      with the Ser/Thr kinase activity of Atg1.
    action: ACCEPT
    reason: Correct reflection of the phosphotransferase reaction catalyzed by this
      Ser/Thr kinase.
    supported_by:
    - reference_id: PMID:26246495
      supporting_text: the serine/threonine kinase Atg1/ULK1
- term:
    id: GO:0071692
    label: protein localization to extracellular region
  evidence_type: IMP
  original_reference_id: PMID:38986731
  qualifier: involved_in
  review:
    summary: atg1 (with atg9) modulates the intracellular and extracellular amounts
      of the adhesion protein CadA and the secreted counting factor CtnA during aggregation,
      an autophagy-dependent secretion role.
    action: KEEP_AS_NON_CORE
    reason: The effect on extracellular protein levels is a downstream consequence
      of Atg1-dependent autophagy and unconventional secretion, not a core molecular
      function; retained as a non-core process.
    supported_by:
    - reference_id: PMID:38986731
      supporting_text: The intracellular and extracellular amounts of CadA are modulated
        by autophagy genes
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: located_in
  review:
    summary: Cytoplasmic localization inferred from orthologs; consistent with direct
      Dictyostelium data.
    action: ACCEPT
    reason: Supported by direct experimental localization of Atg1 to the cytoplasm.
    supported_by:
    - reference_id: PMID:26246495
      supporting_text: Atg1 fused to GFP has been shown previously to have a general
        cytoplasmic pattern in Dictyostelium cells with no specific puncta localization
- term:
    id: GO:0034045
    label: phagophore assembly site membrane
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: located_in
  review:
    summary: PAS membrane localization inferred from orthologs; consistent with Atg1
      activity at the phagophore assembly site.
    action: ACCEPT
    reason: Matches UniProt subcellular location and Atg1's autophagy-initiating role.
    supported_by:
    - reference_id: PMID:17031001
      supporting_text: a marker of preautophagosomal structures and autophagosomes
- term:
    id: GO:0106310
    label: protein serine kinase activity
  evidence_type: ISS
  original_reference_id: GO_REF:0000024
  qualifier: enables
  review:
    summary: Serine kinase activity inferred from sequence similarity; consistent with
      the core Ser/Thr kinase function.
    action: ACCEPT
    reason: Correct reflection of Atg1 kinase activity.
    supported_by:
    - reference_id: PMID:26246495
      supporting_text: the serine/threonine kinase Atg1/ULK1
- term:
    id: GO:0000902
    label: cell morphogenesis
  evidence_type: IMP
  original_reference_id: PMID:39056773
  qualifier: involved_in
  review:
    summary: atg1 null cells are consistently smaller and show altered nuclear division;
      this reflects effects on cell size/division rather than a dedicated morphogenetic
      program.
    action: KEEP_AS_NON_CORE
    reason: The cell-size phenotype is a pleiotropic consequence of altered autophagy
      and growth/energy homeostasis, not a core function; retained as non-core.
    supported_by:
    - reference_id: PMID:39056773
      supporting_text: the null mutant exhibited consistently smaller average cell
        sizes when grown axenically
- term:
    id: GO:0009267
    label: cellular response to starvation
  evidence_type: IDA
  original_reference_id: PMID:39056773
  qualifier: involved_in
  review:
    summary: Atg1 increases tolerance of Dictyostelium to starvation, consistent with
      its role in starvation-induced autophagy.
    action: KEEP_AS_NON_CORE
    reason: A genuine, experimentally supported role, but downstream of the core kinase/autophagy
      function; retained as non-core.
    supported_by:
    - reference_id: PMID:39056773
      supporting_text: Atg1 increases the tolerance of D. discoideum to starvation
        and cAMP treatment
- term:
    id: GO:0030587
    label: sorocarp development
  evidence_type: IDA
  original_reference_id: PMID:39056773
  qualifier: involved_in
  review:
    summary: Altered atg1 expression produces smaller fruiting bodies and multi-tipped
      aggregates, confirming a role in multicellular (sorocarp) development.
    action: KEEP_AS_NON_CORE
    reason: A pleiotropic developmental role that follows from Atg1-dependent autophagy
      during starvation-induced development; retained as non-core.
    supported_by:
    - reference_id: PMID:39056773
      supporting_text: both atg1 antisense inhibition and overexpression resulted in
        smaller fruiting bodies
- term:
    id: GO:0048548
    label: regulation of pinocytosis
  evidence_type: IMP
  original_reference_id: PMID:39056773
  qualifier: involved_in
  review:
    summary: Atg1 positively regulates macropinocytosis; the null mutant has a macropinocytic
      defect and uptake correlates with atg1 expression.
    action: KEEP_AS_NON_CORE
    reason: A real, experimentally supported regulatory effect on macropinocytic uptake,
      but a downstream/pleiotropic role rather than a core function.
    supported_by:
    - reference_id: PMID:39056773
      supporting_text: the atg1 null mutant displayed a macropinocytic defect
- term:
    id: GO:0010629
    label: negative regulation of gene expression
  evidence_type: IDA
  original_reference_id: PMID:39056773
  qualifier: involved_in
  review:
    summary: Overexpression data suggest Atg1 negatively regulates the prestalk marker
      ecmA; the effect on individual genes was modest.
    action: KEEP_AS_NON_CORE
    reason: A downstream developmental gene-expression effect, supported but not a
      core molecular function; retained as non-core.
    supported_by:
    - reference_id: PMID:39056773
      supporting_text: This suggests that Atg1 negatively regulates prestalk gene (ecmA)
        expression
- term:
    id: GO:0009617
    label: response to bacterium
  evidence_type: IMP
  original_reference_id: PMID:22575510
  qualifier: involved_in
  review:
    summary: atg1 is required for LPS-enhanced clearance of phagocytosed bacteria,
      linking Atg1-dependent autophagy to the antibacterial response.
    action: KEEP_AS_NON_CORE
    reason: A genuine cell-autonomous defense role mediated by autophagy, but downstream
      of the core kinase/autophagy function; retained as non-core.
    supported_by:
    - reference_id: PMID:22575510
      supporting_text: LPS pre-treatment did not enhance clearance of phagocytized
        S. aureus in cells deficient for either atg1 or atg9
- term:
    id: GO:0031152
    label: aggregation involved in sorocarp development
  evidence_type: IMP
  original_reference_id: PMID:39056773
  qualifier: involved_in
  review:
    summary: atg1-null cells are unable to aggregate, a hallmark of severe autophagy
      impairment in Dictyostelium development.
    action: KEEP_AS_NON_CORE
    reason: An experimentally established developmental phenotype downstream of Atg1-dependent
      autophagy; retained as non-core.
    supported_by:
    - reference_id: PMID:26246495
      supporting_text: Amoebas in which Atg1 has been knocked out are unable to aggregate
- term:
    id: GO:0043327
    label: chemotaxis to cAMP
  evidence_type: IMP
  original_reference_id: PMID:39056773
  qualifier: involved_in
  review:
    summary: This study measured cAMP/starvation survival and aggregation timing but
      did not directly assay chemotaxis to cAMP; a direct chemotaxis role for Atg1
      cannot be verified from the available text.
    action: UNDECIDED
    reason: The cited paper does not present a direct chemotaxis assay, and antisense
      inhibition had no pronounced effect on aggregation; the supporting evidence for
      a specific chemotaxis-to-cAMP function cannot be verified.
- term:
    id: GO:0043457
    label: regulation of cellular respiration
  evidence_type: IDA
  original_reference_id: PMID:39056773
  qualifier: involved_in
  review:
    summary: Knockout of atg1 alters mitochondrial and non-mitochondrial respiration,
      supporting a role in modulating cellular respiration.
    action: KEEP_AS_NON_CORE
    reason: An experimentally supported but indirect/peripheral effect on energy homeostasis,
      not a core molecular function; retained as non-core.
    supported_by:
    - reference_id: PMID:39056773
      supporting_text: knocking out atg1 caused reductions in basal mitochondrial and
        non-mitochondrial respiration
- term:
    id: GO:0043653
    label: mitochondrial fragmentation involved in apoptotic process
  evidence_type: IDA
  original_reference_id: PMID:39056773
  qualifier: involved_in
  review:
    summary: The cited study characterized mitochondrial membrane mass, potential,
      ROS and respiration but did not demonstrate mitochondrial fragmentation as part
      of an apoptotic process; Dictyostelium cell death is characteristically non-apoptotic.
    action: UNDECIDED
    reason: The specific term (apoptotic mitochondrial fragmentation) is not supported
      by the available text and apoptosis is not an established Dictyostelium cell-death
      mode; the basis for this annotation cannot be verified.
- term:
    id: GO:0044351
    label: macropinocytosis
  evidence_type: IDA
  original_reference_id: PMID:39056773
  qualifier: involved_in
  review:
    summary: atg1-null cells display a macropinocytic defect and macropinocytic uptake
      correlates positively with atg1 expression.
    action: KEEP_AS_NON_CORE
    reason: A genuine effect on macropinocytosis, but a downstream/pleiotropic role
      rather than a core molecular function; retained as non-core.
    supported_by:
    - reference_id: PMID:39056773
      supporting_text: macropinocytic uptake rates were positively correlated with
        the atg1 expression index
- term:
    id: GO:0004672
    label: protein kinase activity
  evidence_type: IDA
  original_reference_id: PMID:17031001
  qualifier: enables
  review:
    summary: Direct evidence that the Atg1 kinase domain is essential for function;
      kinase-dead Atg1 acts as a dominant negative.
    action: ACCEPT
    reason: The kinase domain is essential for autophagy and development, and a kinase-negative
      mutant is dominant-negative, directly demonstrating catalytic protein kinase
      function.
    supported_by:
    - reference_id: PMID:17031001
      supporting_text: these domains
        are essential for autophagy and development
- term:
    id: GO:0016236
    label: macroautophagy
  evidence_type: IMP
  original_reference_id: PMID:17031001
  qualifier: involved_in
  review:
    summary: Atg1 kinase and its conserved C-terminal domain are essential for macroautophagy
      in Dictyostelium, a core function.
    action: ACCEPT
    reason: Kinase-dead Atg1 blocks functional autophagy and the domains are essential
      for autophagy; macroautophagy is a core biological process for Atg1.
    supported_by:
    - reference_id: PMID:17031001
      supporting_text: In cells expressing dominant-negative DdAtg1, autophagosomes
        are formed and accumulate but seem not to be functional
- term:
    id: GO:0048102
    label: autophagic cell death
  evidence_type: IMP
  original_reference_id: PMID:15358773
  qualifier: involved_in
  review:
    summary: atg1 disruption blocks autophagy and vacuolization in the developmental
      vacuolar cell death model, showing Atg1 is required for autophagic (vacuolar)
      cell death.
    action: KEEP_AS_NON_CORE
    reason: An experimentally supported developmental cell-death role that is downstream
      of Atg1-dependent autophagy; retained as non-core.
    supported_by:
    - reference_id: PMID:15358773
      supporting_text: led in atg1 mutant cells to impaired autophagy and to no vacuolization
- term:
    id: GO:0008047
    label: enzyme activator activity
  evidence_type: IDA
  original_reference_id: PMID:26246495
  qualifier: enables
  review:
    summary: Atg1 positively regulates the activity of the pentose-phosphate-pathway
      enzyme transketolase (TKT), with which it physically interacts; TKT activity
      rises with Atg1 overexpression and falls in atg1-null or kinase-dead conditions.
    action: KEEP_AS_NON_CORE
    reason: Atg1 acts as a positive regulator of TKT activity (likely via its kinase
      function), but this enzyme-activation role is a specialized regulatory link rather
      than the core evolved molecular function; retained as non-core.
    supported_by:
    - reference_id: PMID:26246495
      supporting_text: There is an increase in activity in cells overexpressing Atg1.
        By contrast, TKT activity decreases in cells in which atg1 has been deleted
- term:
    id: GO:0097300
    label: programmed necrotic cell death
  evidence_type: IDA
  original_reference_id: PMID:17150370
  qualifier: involved_in
  review:
    summary: This review describes that disrupting atg1 reveals a non-vacuolar (necrotic-like)
      cell death pathway; necrotic death occurs in the absence of Atg1 rather than
      requiring it, so a positive involvement of Atg1 in necrotic death is not clearly
      supported.
    action: UNDECIDED
    reason: The relationship between Atg1 and necrotic cell death is indirect (necrosis
      is unmasked when autophagic death is blocked); the supporting text is from a
      review and does not establish that Atg1 is involved_in programmed necrotic death.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:31680241
  qualifier: enables
  review:
    summary: Co-immunoprecipitation shows an AMPK-ATG1 interaction conserved in basal
      autophagy. Bare 'protein binding' is uninformative; the meaningful content is
      the specific interaction with AMPK.
    action: KEEP_AS_NON_CORE
    reason: Per curation guidance, generic protein binding is not retained as a core
      function; the AMPK interaction is captured here as a non-core regulatory partnership.
    supported_by:
    - reference_id: PMID:31680241
      supporting_text: Co-immunoprecipitation studies show conservation of the AMPK-ATG1
- term:
    id: GO:0050830
    label: defense response to Gram-positive bacterium
  evidence_type: IDA
  original_reference_id: PMID:28414774
  qualifier: involved_in
  review:
    summary: This study focuses on the ESX-1/TORC1-dependent manipulation of autophagy
      by Mycobacterium marinum; a specific, verifiable role for Atg1 in defense against
      a Gram-positive bacterium is not evident from the available text.
    action: UNDECIDED
    reason: The cached text does not establish an Atg1-specific defense role against
      Gram-positive bacteria; the annotation cannot be verified from the available
      evidence.
- term:
    id: GO:1905037
    label: autophagosome organization
  evidence_type: IMP
  original_reference_id: PMID:28414774
  qualifier: acts_upstream_of_or_within
  review:
    summary: Atg1 is required for autophagosome formation/organization, an essentially
      core autophagy function; autophagosomes formed without functional Atg1 are aberrant.
    action: KEEP_AS_NON_CORE
    reason: Autophagosome organization is closely tied to Atg1's core autophagy-initiating
      role; captured here as a non-core process-level annotation with the core function
      recorded under macroautophagy/autophagosome assembly.
    supported_by:
    - reference_id: PMID:17031001
      supporting_text: In cells expressing dominant-negative DdAtg1, autophagosomes
        are formed and accumulate but seem not to be functional
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:26246495
  qualifier: enables
  review:
    summary: Yeast two-hybrid and pull-down show Atg1 interacts with Atg13 and with
      the pentose-phosphate enzyme transketolase (TKT). Bare 'protein binding' is uninformative;
      the specific partners are the meaningful content.
    action: KEEP_AS_NON_CORE
    reason: Per curation guidance, generic protein binding is not retained as core;
      the Atg13 and TKT interactions are better represented via the Atg1 complex membership
      and the enzyme-activator annotation.
    supported_by:
    - reference_id: PMID:26246495
      supporting_text: TKT–HA is efficiently pulled down by GFP-Atg1
- term:
    id: GO:1990316
    label: Atg1/ULK1 kinase complex
  evidence_type: IDA
  original_reference_id: PMID:26246495
  qualifier: part_of
  review:
    summary: Atg1 is the catalytic subunit of the conserved Atg1-Atg13-Atg101 kinase
      complex in Dictyostelium, confirmed by yeast two-hybrid and pull-down.
    action: ACCEPT
    reason: Direct evidence establishes the Atg1-Atg13-Atg101 core complex, making
      Atg1/ULK1 kinase complex membership a core annotation.
    supported_by:
    - reference_id: PMID:26246495
      supporting_text: The core of this assembly of proteins is formed by Atg1-Atg13-Atg101,
        which seems to be conserved
- term:
    id: GO:0001878
    label: response to yeast
  evidence_type: IMP
  original_reference_id: PMID:27818653
  qualifier: acts_upstream_of_or_within
  review:
    summary: atg1-null cells show altered (increased) ability to predate yeast, implicating
      Atg1-dependent autophagy in the amoeba's interaction with yeast.
    action: KEEP_AS_NON_CORE
    reason: A downstream, autophagy-mediated host-microbe interaction phenotype; retained
      as non-core.
    supported_by:
    - reference_id: PMID:27818653
      supporting_text: mutants increase (atg1-, kil1-, kil2-) or decrease (atg6-) the
        ability of the
- term:
    id: GO:0035891
    label: exit from host cell
  evidence_type: IMP
  original_reference_id: PMID:25646440
  qualifier: acts_upstream_of_or_within
  review:
    summary: The autophagic machinery is required for nonlytic cell-to-cell transmission
      (ejection) of mycobacteria; impairing autophagy blocks transmission.
    action: KEEP_AS_NON_CORE
    reason: A specialized host-pathogen role mediated by Atg1-dependent autophagy;
      retained as non-core.
    supported_by:
    - reference_id: PMID:25646440
      supporting_text: If autophagy is impaired, cell-to-cell transmission is
- term:
    id: GO:0042742
    label: defense response to bacterium
  evidence_type: IMP
  original_reference_id: PMID:25646440
  qualifier: acts_upstream_of_or_within
  review:
    summary: Atg1-dependent autophagy contributes to control of intracellular mycobacteria;
      autophagy impairment compromises the host and permits transmission.
    action: KEEP_AS_NON_CORE
    reason: A cell-autonomous antibacterial defense role mediated by autophagy; downstream
      of the core function and retained as non-core.
    supported_by:
    - reference_id: PMID:25646440
      supporting_text: If autophagy is impaired, cell-to-cell transmission is
        inhibited, the host plasma membrane becomes compromised and the host cells
        die
- term:
    id: GO:0030587
    label: sorocarp development
  evidence_type: IMP
  original_reference_id: PMID:14736886
  qualifier: acts_upstream_of_or_within
  review:
    summary: atg1 mutation causes severe developmental defects; the atg1-1 mutant fails
      to aggregate on bacterial lawns and arrests as loose mounds.
    action: KEEP_AS_NON_CORE
    reason: A well-established developmental requirement downstream of Atg1-dependent
      autophagy; retained as non-core.
    supported_by:
    - reference_id: PMID:14736886
      supporting_text: does not aggregate on bacterial lawns
- term:
    id: GO:0031288
    label: sorocarp morphogenesis
  evidence_type: IMP
  original_reference_id: PMID:14736886
  qualifier: acts_upstream_of_or_within
  review:
    summary: atg1 mutants produce aberrant fruiting-body morphology, reflecting a requirement
      for Atg1 in sorocarp morphogenesis.
    action: KEEP_AS_NON_CORE
    reason: A developmental morphogenesis phenotype downstream of Atg1-dependent autophagy;
      retained as non-core.
    supported_by:
    - reference_id: PMID:14736886
      supporting_text: Mutations in the three genes produce aberrant development
- term:
    id: GO:0004674
    label: protein serine/threonine kinase activity
  evidence_type: ISS
  original_reference_id: PMID:14736886
  qualifier: enables
  review:
    summary: Ser/Thr kinase activity inferred from the conserved kinase domain; the
      core molecular function.
    action: ACCEPT
    reason: Consistent with the kinase-domain-dependent function directly demonstrated
      in Dictyostelium.
    supported_by:
    - reference_id: PMID:26246495
      supporting_text: the serine/threonine kinase Atg1/ULK1
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: IDA
  original_reference_id: PMID:14736886
  qualifier: located_in
  review:
    summary: Cytoplasmic localization; consistent with the diffuse cytoplasmic distribution
      of Atg1 reported across studies.
    action: ACCEPT
    reason: Cytoplasmic localization of Atg1 is well established by direct evidence.
    supported_by:
    - reference_id: PMID:26246495
      supporting_text: Atg1 fused to GFP has been shown previously to have a general
        cytoplasmic pattern in Dictyostelium cells with no specific puncta localization
- term:
    id: GO:0006995
    label: cellular response to nitrogen starvation
  evidence_type: IMP
  original_reference_id: PMID:14736886
  qualifier: acts_upstream_of_or_within
  review:
    summary: atg1 mutants show reduced survival during nitrogen starvation, linking
      Atg1 to the nitrogen-starvation response.
    action: KEEP_AS_NON_CORE
    reason: A supported starvation-response phenotype downstream of Atg1-dependent
      autophagy; retained as non-core.
    supported_by:
    - reference_id: PMID:14736886
      supporting_text: reduced survival during nitrogen starvation
- term:
    id: GO:0016236
    label: macroautophagy
  evidence_type: IMP
  original_reference_id: PMID:14736886
  qualifier: acts_upstream_of_or_within
  review:
    summary: atg1 is required for macroautophagy in Dictyostelium, a core function.
    action: ACCEPT
    reason: Direct genetic evidence that Atg1 is required for macroautophagy; a core
      biological process.
    supported_by:
    - reference_id: PMID:14736886
      supporting_text: genes are required for macroautophagy in Dictyostelium
- term:
    id: GO:0030435
    label: sporulation resulting in formation of a cellular spore
  evidence_type: IMP
  original_reference_id: PMID:14736886
  qualifier: acts_upstream_of_or_within
  review:
    summary: Because Atg1 is required for normal fruiting-body development, spore formation
      is impaired in atg1 mutants; this is a downstream developmental consequence.
    action: KEEP_AS_NON_CORE
    reason: A developmental sporulation phenotype downstream of Atg1-dependent autophagy;
      retained as non-core.
    supported_by:
    - reference_id: PMID:14736886
      supporting_text: Mutations in the three genes produce aberrant development
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000024
  title: Manual transfer of experimentally-verified manual GO annotation data to orthologs
    by curator judgment of sequence similarity
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000044
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location
    vocabulary mapping, accompanied by conservative changes to GO terms applied by
    UniProt
  findings: []
- id: GO_REF:0000116
  title: Automatic Gene Ontology annotation based on Rhea mapping
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:14736886
  title: Dictyostelium macroautophagy mutants vary in the severity of their developmental
    defects.
  findings:
  - statement: atg1, atg6 and atg8 are all required for macroautophagy in Dictyostelium,
      and atg1 mutants show reduced survival during nitrogen starvation.
    supporting_text: genes are required for macroautophagy in Dictyostelium
  - statement: The atg1-1 mutant shows the most severe developmental defect, failing
      to aggregate on bacterial lawns and arresting as loose mounds.
    supporting_text: does not aggregate on bacterial lawns
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Primary characterization of the Dictyostelium atg1 knockout; establishes
      the requirement of Atg1 for macroautophagy, starvation survival, and multicellular
      development. Abstract-only in cache.
- id: PMID:15358773
  title: Autophagy gene disruption reveals a non-vacuolar cell death pathway in Dictyostelium.
  findings:
  - statement: Disruption of atg1 impairs autophagy and abolishes vacuolization in
      the developmental cell death model, though a non-vacuolar death still occurs.
    supporting_text: led in atg1 mutant cells to impaired autophagy and to no vacuolization
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Shows atg1 is required for autophagic vacuolization; also reveals
      an Atg1-independent non-vacuolar death pathway.
- id: PMID:17031001
  title: Function of the Dictyostelium discoideum Atg1 kinase during autophagy and
    development.
  findings:
  - statement: The kinase domain and conserved C-terminal domain of DdAtg1 are essential
      for autophagy and development; a kinase-negative mutant is dominant-negative.
    supporting_text: these domains
      are essential for autophagy and development
  - statement: Kinase-negative DdAtg1 colocalizes with RFP-Atg8, a marker of preautophagosomal
      structures and autophagosomes.
    supporting_text: a marker of preautophagosomal structures and autophagosomes
  - statement: In dominant-negative Atg1 cells, autophagosomes form and accumulate
      but are non-functional.
    supporting_text: In cells expressing dominant-negative DdAtg1, autophagosomes
      are formed and accumulate but seem not to be functional
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Key functional study of DdAtg1 kinase and C-terminal domains and
      their role in autophagosome formation and localization.
- id: PMID:17150370
  title: From autophagic to necrotic cell death in Dictyostelium.
  findings: []
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Review of Dictyostelium cell death; the necrotic pathway is unmasked
      when autophagic death is blocked, so it does not establish a positive Atg1 role
      in necrosis.
- id: PMID:22575510
  title: Lipopolysaccharide induction of autophagy is associated with enhanced bactericidal
    activity in Dictyostelium discoideum.
  findings:
  - statement: LPS-enhanced clearance of phagocytosed S. aureus requires atg1 and
      atg9.
    supporting_text: LPS pre-treatment did not enhance clearance of phagocytized S.
      aureus in cells deficient for either atg1 or atg9
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Links Atg1-dependent autophagy to the antibacterial response.
- id: PMID:25646440
  title: The autophagic machinery ensures nonlytic transmission of mycobacteria.
  findings:
  - statement: Impairing autophagy blocks nonlytic cell-to-cell transmission of mycobacteria
      and compromises host membrane integrity.
    supporting_text: If autophagy is impaired, cell-to-cell transmission is
      inhibited, the host plasma membrane becomes compromised and the host cells die
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Autophagy machinery (including atg1) required for nonlytic mycobacterial
      egress/transmission.
- id: PMID:26246495
  title: Dissecting the function of Atg1 complex in Dictyostelium autophagy reveals
    a connection with the pentose phosphate pathway enzyme transketolase.
  findings:
  - statement: The Dictyostelium Atg1 complex core is Atg1-Atg13-Atg101, more similar
      to the mammalian than the yeast complex.
    supporting_text: The core of this assembly of proteins is formed by Atg1-Atg13-Atg101,
      which seems to be conserved
  - statement: Atg1 physically interacts with transketolase (TKT) and positively regulates
      its activity; TKT activity increases with Atg1 overexpression and decreases
      in atg1-null or kinase-dead cells.
    supporting_text: There is an increase in activity in cells overexpressing Atg1.
      By contrast, TKT activity decreases in cells in which atg1 has been deleted
  - statement: Atg1-GFP has a general cytoplasmic pattern with no specific puncta
      localization.
    supporting_text: Atg1 fused to GFP has been shown previously to have a general
      cytoplasmic pattern in Dictyostelium cells with no specific puncta localization
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Defines the Dictyostelium Atg1-Atg13-Atg101 complex and the Atg1-transketolase
      regulatory link; full text available.
- id: PMID:27818653
  title: Dictyostelium discoideum as a Novel Host System to Study the Interaction
    between Phagocytes and Yeasts.
  findings:
  - statement: atg1-null cells show altered ability to predate yeast, implicating
      autophagy in the amoeba-yeast interaction.
    supporting_text: mutants increase (atg1-, kil1-, kil2-) or decrease (atg6-) the
      ability of the
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Host-microbe interaction phenotype involving atg1.
- id: PMID:28414774
  title: Mycobacterium marinum antagonistically induces an autophagic response while
    repressing the autophagic flux in a TORC1- and ESX-1-dependent manner.
  findings: []
  reference_review:
    relevance: LOW
    correctness: UNVERIFIED
    review_notes: Focuses on ESX-1/TORC1 manipulation of autophagy by M. marinum;
      Atg1-specific role not verifiable from the cached text.
- id: PMID:31680241
  title: AMPKα promotes basal autophagy induction in Dictyostelium discoideum.
  findings:
  - statement: The AMPK-ATG1 axis is conserved in basal autophagy, shown by co-immunoprecipitation.
    supporting_text: Co-immunoprecipitation studies show conservation of the AMPK-ATG1
  reference_review:
    relevance: MEDIUM
    correctness: VERIFIED
    review_notes: Establishes an AMPK-Atg1 regulatory interaction in Dictyostelium
      basal autophagy. Abstract-only in cache.
- id: PMID:38986731
  title: Trafficking of adhesion and aggregation-modulating proteins during the early
    stages of Dictyostelium development.
  findings:
  - statement: Intracellular and extracellular amounts of the adhesion protein CadA
      are modulated by autophagy genes atg1 and atg9.
    supporting_text: The intracellular and extracellular amounts of CadA are modulated
      by autophagy genes
  reference_review:
    relevance: LOW
    correctness: VERIFIED
    review_notes: Links atg1 to trafficking/secretion of adhesion and aggregation
      proteins during aggregation. Abstract-only in cache.
- id: PMID:39056773
  title: The Multifaceted Interactions of Dictyostelium Atg1 with Mitochondrial Function,
    Endocytosis, Growth, and Development.
  findings:
  - statement: Atg1 positively regulates macropinocytosis; the null mutant has a macropinocytic
      defect and uptake correlates with atg1 expression.
    supporting_text: the atg1 null mutant displayed a macropinocytic defect
  - statement: Atg1 increases tolerance of Dictyostelium to starvation and cAMP treatment.
    supporting_text: Atg1 increases the tolerance of D. discoideum to starvation and
      cAMP treatment
  - statement: Altered atg1 expression yields smaller fruiting bodies and multi-tipped
      aggregates, and Atg1 has a peripheral role in mitochondrial signalling affecting
      respiration.
    supporting_text: knocking out atg1 caused reductions in basal mitochondrial and
      non-mitochondrial respiration
  reference_review:
    relevance: HIGH
    correctness: VERIFIED
    review_notes: Comprehensive phenotypic study of atg1 knockout, knockdown and overexpression
      across growth, endocytosis, development, and mitochondrial homeostasis; full
      text available.
core_functions:
- description: Atg1 is a serine/threonine protein kinase that acts as the catalytic
    subunit of the Atg1/ULK1 kinase complex (Atg1-Atg13-Atg101) to initiate macroautophagy,
    driving formation of the phagophore/autophagosome at the phagophore assembly site.
  molecular_function:
    id: GO:0004674
    label: protein serine/threonine kinase activity
  directly_involved_in:
  - id: GO:0016236
    label: macroautophagy
  - id: GO:0000045
    label: autophagosome assembly
  locations:
  - id: GO:0005737
    label: cytoplasm
  - id: GO:0000407
    label: phagophore assembly site
  - id: GO:0034045
    label: phagophore assembly site membrane
  in_complex:
    id: GO:1990316
    label: Atg1/ULK1 kinase complex
  supported_by:
  - reference_id: PMID:17031001
    supporting_text: these domains
      are essential for autophagy and development
  - reference_id: PMID:26246495
    supporting_text: The core of this assembly of proteins is formed by Atg1-Atg13-Atg101,
      which seems to be conserved
  - reference_id: PMID:14736886
    supporting_text: genes are required for macroautophagy in Dictyostelium
- description: Through its kinase activity and role in initiating autophagy, Atg1 regulates
    the induction of macroautophagy in response to nutrient/starvation status, making
    it essential for starvation-induced multicellular (sorocarp) development in Dictyostelium.
  molecular_function:
    id: GO:0004674
    label: protein serine/threonine kinase activity
  directly_involved_in:
  - id: GO:0010506
    label: regulation of autophagy
  - id: GO:0009267
    label: cellular response to starvation
  locations:
  - id: GO:0005737
    label: cytoplasm
  supported_by:
  - reference_id: PMID:26246495
    supporting_text: The first steps of induction and nucleation are controlled
      by the serine/threonine kinase Atg1/ULK1 and the class III PI3 K VPS34
  - reference_id: PMID:39056773
    supporting_text: Atg1 increases the tolerance of D. discoideum to starvation and
      cAMP treatment

Gene Description

Existing Annotations Review

Core Functions

Atg1 is a serine/threonine protein kinase that acts as the catalytic subunit of the Atg1/ULK1 kinase complex (Atg1-Atg13-Atg101) to initiate macroautophagy, driving formation of the phagophore/autophagosome at the phagophore assembly site.

Through its kinase activity and role in initiating autophagy, Atg1 regulates the induction of macroautophagy in response to nutrient/starvation status, making it essential for starvation-induced multicellular (sorocarp) development in Dictyostelium.

References

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