identifier: traitmech:000116
label: proteolysis
definition: A biopolymer-degradation metabolism in which an organism secretes proteases
  to hydrolyze extracellular proteins and peptides into amino acids and short peptides
  for nutrition.
definition_source: DOI:10.1128/mmbr.62.3.597-635.1998
trait_category: METABOLISM
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- traitmech:000110
synonyms:
- synonym_text: proteolytic
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1128/mmbr.62.3.597-635.1998
- synonym_text: protein degradation
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1128/mmbr.62.3.597-635.1998
evidence:
- reference: DOI:10.1128/mmbr.62.3.597-635.1998
  notes: Rao et al. review microbial proteases, noting that secreted (extracellular)
    proteases play a major nutritional role through their depolymerizing activity.
- reference: DOI:10.1093/femsre/fuab046
  notes: Review of Bacillus proteases covers extracellular protease activities and
    their functions.
canonical_examples:
- taxon_id: NCBITaxon:1423
  taxon_label: Bacillus subtilis
  note: "Model secretor of extracellular proteases (subtilisin); paradigm for bacterial proteolysis."
  reference: PMID:34410368
causal_graphs:
- graph_id: proteolysis_extracellular_protease
  title: Proteolysis hydrolyzes extracellular proteins to amino acids
  description: Evidence-backed causal sketch linking secreted bacterial proteases
    to extracellular hydrolysis of proteins/peptides into amino acids and short peptides.
  nodes:
  - node_id: proteolysis_trait
    label: proteolysis
    node_type: TRAIT
    grounding: traitmech:000116
    description: Secreted-protease hydrolysis of extracellular proteins.
  - node_id: extracellular_protease
    label: secreted proteases
    node_type: GENE_OR_PROTEIN
    description: Extracellular microbial proteases acting on protein substrates.
  - node_id: amino_acids
    label: amino acids / short peptides
    node_type: CHEMICAL
    description: Assimilable nutrients released from protein hydrolysis.
  - node_id: peptides
    label: peptides / oligopeptides
    node_type: CHEMICAL
    description: Oligopeptides (~4-30 aa) released by extracellular protease cleavage
      of proteins.
  - node_id: peptide_transport_systems
    label: peptide transport systems (Opp/DtpT/Dpp)
    node_type: GENE_OR_PROTEIN
    description: Membrane transporters (oligopeptide permease Opp, DtpT, ABC transporter
      Dpp) importing peptides short enough for uptake.
  - node_id: intracellular_peptidases
    label: intracellular peptidases
    node_type: GENE_OR_PROTEIN
    description: Cytoplasmic exo-/endo-peptidases that further hydrolyze imported
      peptides to free amino acids.
  - node_id: large_proteins
    label: large extracellular proteins
    node_type: CHEMICAL
    description: Intact extracellular proteins too large for direct uptake by prokaryotic
      transporters.
  - node_id: substrate_stoichiometry
    label: substrate source / concentration / C:N stoichiometry
    node_type: ENVIRONMENTAL_FACTOR
    description: Environmental substrate characteristics that filter expression of
      secreted extracellular proteases.
  edges:
  - subject: extracellular_protease
    predicate: enables
    object: proteolysis_trait
    description: Secreted proteases drive extracellular protein hydrolysis.
    evidence:
    - reference: DOI:10.1128/mmbr.62.3.597-635.1998
      notes: Rao et al. review microbial proteases and their depolymerizing nutritional
        role.
    predicate_id: RO:0002327
  - subject: proteolysis_trait
    predicate: produces
    object: amino_acids
    description: Protein hydrolysis releases amino acids and short peptides.
    evidence:
    - reference: DOI:10.1093/femsre/fuab046
      notes: Bacillus protease review covers extracellular protease activities.
    predicate_id: METPO:2000202
  - subject: proteolysis_trait
    predicate: produces
    object: peptides
    description: Extracellular protein hydrolysis yields oligopeptides (~4-30 aa).
    evidence:
    - reference: DOI:10.1186/s43014-023-00165-w
      notes: '"protein to oligopeptides" / "producing peptides of roughly 4-30 amino
        acids"; extracellular proteolytic enzymes produce peptides.'
    predicate_id: METPO:2000202
  - subject: peptide_transport_systems
    predicate: imports
    object: peptides
    description: Peptide transporters import peptides short enough for uptake.
    evidence:
    - reference: DOI:10.1186/s43014-023-00165-w
      notes: 'Peptides "taken up by dedicated transporters: oligopeptide permease
        (Opp, an ATP-driven system)", DtpT and ABC transporter Dpp.'
    predicate_id: METPO:2000208
  - subject: intracellular_peptidases
    predicate: hydrolyzes
    object: peptides
    description: Intracellular peptidases further hydrolyze imported peptides.
    evidence:
    - reference: DOI:10.1186/s43014-023-00165-w
      notes: '"Inside the cell, multiple peptidases... further hydrolyze peptides".'
    predicate_id: METPO:2000013
  - subject: intracellular_peptidases
    predicate: produces
    object: amino_acids
    description: Intracellular peptidases produce free amino acids used for growth.
    evidence:
    - reference: DOI:10.1186/s43014-023-00165-w
      notes: '"further hydrolyze peptides to free amino acids used for growth".'
    predicate_id: METPO:2000202
  - subject: large_proteins
    predicate: necessitates
    object: proteolysis_trait
    description: Proteins too large for direct uptake necessitate extracellular hydrolysis.
    evidence:
    - reference: DOI:10.1128/spectrum.03036-23
      notes: '"proteins are too large for direct uptake by prokaryotic transporter
        systems... explaining the need for extracellular cleavage".'
  - subject: substrate_stoichiometry
    predicate: controls expression of
    object: extracellular_protease
    description: Substrate source/concentration/C:N stoichiometry filters expression
      of secreted proteases.
    evidence:
    - reference: DOI:10.1128/spectrum.03036-23
      notes: '"the substrate''s source, concentration and stoichiometry impose strong
        filtering on the expression of extracellular enzymes".'
curation_history:
- timestamp: '2026-06-08T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate METABOLISM trait (proteolysis / extracellular protein
    degradation); leftover round, sub-variant of biopolymer degradation.
  llm_assisted: true
- timestamp: '2026-06-10T14:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (extracellular protease / amino-acid
    release) with RO/METPO predicate groundings; promoted PROPOSED to REVIEWED.
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 6 evidence-backed generic edges (5 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:12Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000202×2, METPO:2000208×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:38Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000013×1).
  llm_assisted: true