identifier: traitmech:000647
label: autophagic glycogen degradation
definition: An autophagy phenotype in which a microbial cell degrades intracellular
  glycogen by delivering it to lysosomal or vacuolar compartments.
definition_source: DOI:10.4161/auto.6.4.11736
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: PROPOSED
parent_traits:
- traitmech:000638
evidence:
- reference: DOI:10.4161/auto.6.4.11736
  snippet: Our results indicate that autophagy and Sga1 act cooperatively in vacuolar
    glycogen breakdown
  notes: PMID:20383057. DOI-matched scientific abstract directly read in Europe PMC
    metadata. Supports autophagy-associated vacuolar glycogen hydrolysis in Magnaporthe
    oryzae during asexual development. The reported breakdown supports conidia formation
    but is dispensable for pathogenicity. Cytoplasmic retargeting of GFP-Sga1 is an
    engineered rescue, not a natural vacuolar-flux exemplar. Full Methods, actual
    figures and independent strain provenance were not inspected.
- reference: DOI:10.3390/cells13060467
  snippet: vacuolar delivery of Glg1-GFP and its processing to free GFP were strictly
    dependent on autophagic machinery and vacuolar proteolysis.
  notes: PMID:38534311, PMC10969688. Scientific abstract, XML Methods 2.1, Results
    3.2-3.4 and Discussion were read. The authors conclude nonselective glycogen autophagy
    in nitrogen-starved Komagataella phaffii using glycogen-bound, nonbinding and
    cytosolic reporters. Atg11 independence alone is not the selectivity argument.
    TCA extraction under-recovers the bound reporter; raw free-GFP/total-fusion ratios
    are unreliable. Reporter proteolysis is not a direct polymer-hydrolysis assay.
    Actual panels and independent strain provenance remain uninspected.
- reference: DOI:10.3390/ijms252111772
  snippet: The K. phaffii Gsy1-GFP marked the GGs and reported on their autophagic
    degradation during nitrogen starvation, as expected.
  notes: PMID:39519320, PMC11546884. DOI-matched scientific abstract and XML Results
    2.2-2.3 and Discussion were read. GGs means glycogen granules. This follow-up
    uses Gsy1 and CBM20 reporters to support neutral cargo behavior in nitrogen-starved
    K. phaffii; it is not independent-laboratory replication. Early Gsy1-GFP dot disappearance
    is autophagy-independent and is not positive flux evidence. A human STBD1 domain
    used as a reporter does not establish a native human mechanism in yeast. Complete
    Methods, actual panels and strain provenance were not inspected.
- reference: DOI:10.1016/j.isci.2024.109810
  snippet: glycophagy may play a role in the suppression of glycogen consumption,
    rather than enhancing degradation.
  notes: 'PMID:38832010, PMC11145338. Exact XML Results sec2.7 span, not an abstract
    quote. Scientific Summary, Results, Discussion, Limitations and selected yeast,
    GFP-cleavage and glycogen-assay Methods were read. Boundary evidence: Atg45-dependent
    vacuolar delivery during Saccharomyces cerevisiae sporulation can preserve glycogen.
    Do not score that delivery alone as degradation. Receptor recruitment and prolonged-starvation
    reporter turnover do not make storage and hydrolysis interchangeable. Actual panels,
    supplements and independent strain provenance remain unread.'
discussions:
- discussion_id: autophagic-glycogen-degradation-scope
  prompt: Distinguish degradation from broader glycophagy usage.
  kind: CURATION_TODO
  status: OPEN
  rationale: The explicit degradative endpoint narrows autophagy traitmech:000638
    without changing that parent's identity. This is intracellular cargo recycling,
    not growth on glycogen, extracellular amylolysis, granule possession or a gene
    inventory. The Cells paper introduces glycophagy as selective but reports nonselective
    K. phaffii turnover; the iScience paper also uses glycophagy for vacuolar preservation
    during sporulation. Those source-attributed usages are not exact synonyms of this
    endpoint-defined record. GO:0061723 was directly resolved at https://www.ebi.ac.uk/QuickGO/services/ontology/go/terms/GO%3A0061723
    as a nonobsolete biological process for selective glycogen degradation by macroautophagy.
    It is narrower on selectivity and route, and is not an exact organismal phenotype.
    Omit exact xrefs and synonyms. Broader delivery/storage and selective subtype
    relationships require human review, not silent normalization of conflicting terminology.
  posed_by: codex
  posed_date: '2026-10-06'
- discussion_id: autophagic-glycogen-degradation-assays-and-exemplars
  prompt: Resolve polymer turnover, natural exemplars and mechanisms.
  kind: KNOWLEDGE_GAP
  status: OPEN
  rationale: Keep glycogen-bound reporter cleavage, vacuolar localization, glycogen
    content and polymer hydrolysis as distinct readouts. Do not impose universal Sga1,
    Atg45, Atg11, starvation, sporulation, selectivity or a macroautophagic route.
    Yeast species and nutrient conditions can differ. The Atg45 storage result is
    a boundary, not positive evidence of this endpoint. Canonical examples remain
    unset pending independent natural-strain provenance and direct endpoint support;
    reporter and deletion strains are qualified evidence, not natural exemplars. Protein
    graphs require native taxon-paired accessions and functional evidence. Human disease
    models and an Aspergillus enzyme used as an assay reagent are not microbial observations
    of this trait. Inspect actual panels before protein-level curation.
  posed_by: codex
  posed_date: '2026-10-06'
curation_history:
- timestamp: '2026-10-06T17:24:49Z'
  curator: codex
  action: MINTED_TRAITMECH_ID
  changes: Added autophagic glycogen degradation with four DOI-backed source-matched
    snippets and explicit storage, selectivity and reporter limits. Fresh ignored-and-hidden
    searches, seed and METPO inventories found no exact record. Reserved METPO:1060000
    in v523 with unchanged corrected autophagy parent context. Deferred broad glycophagy
    equivalence, natural exemplars and protein mechanisms.
  llm_assisted: true