identifier: traitmech:000063
label: capsule
definition: A morphology trait in which the cell is surrounded by a well-organized
  layer of polysaccharide (or rarely polypeptide) external to the cell envelope, mediating
  adhesion, desiccation resistance, and immune evasion.
definition_source: DOI:10.1146/annurev.micro.50.1.285
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000059
synonyms:
- synonym_text: capsulated
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1146/annurev.micro.50.1.285
- synonym_text: capsular polysaccharide
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1146/annurev.biochem.75.103004.142545
evidence:
- reference: DOI:10.1146/annurev.micro.50.1.285
  notes: Roberts, "The biochemistry and genetics of capsular polysaccharide production
    in bacteria", treats the capsule as an organized external polysaccharide layer.
- reference: DOI:10.1146/annurev.biochem.75.103004.142545
  notes: Whitfield reviews biosynthesis and assembly of capsular polysaccharides in
    Escherichia coli.
canonical_examples:
- taxon_id: NCBITaxon:573
  taxon_label: Klebsiella pneumoniae
  note: "Textbook polysaccharide-capsule producer; capsule is a defining virulence factor."
  reference: PMID:27715471
causal_graphs:
- graph_id: capsule_polysaccharide_protection
  title: Capsule polysaccharide layer mediates adhesion and immune evasion
  description: Evidence-backed causal sketch linking capsular polysaccharide biosynthesis
    to a surface polysaccharide layer that mediates adhesion, desiccation resistance,
    and immune evasion.
  nodes:
  - node_id: capsule_trait
    label: capsule
    node_type: TRAIT
    grounding: traitmech:000063
    description: Possession of a well-organized external polysaccharide layer.
  - node_id: capsular_polysaccharide
    label: capsular polysaccharide
    node_type: CHEMICAL
    description: High-MW (often acidic) polysaccharide attached external to the cell
      envelope.
    grounding: CHEBI:3379
  - node_id: capsule_assembly
    label: capsular polysaccharide assembly
    node_type: BIOLOGICAL_PROCESS
    description: Synthesis, export, and surface assembly of capsule polymers.
  - node_id: immune_evasion
    label: host immune evasion
    node_type: QUALITY
    description: Reduced recognition and clearance by host innate immunity.
  - node_id: wzx_flippase
    label: Wzx flippase
    node_type: GENE_OR_PROTEIN
    description: Inner-membrane flippase that translocates lipid-linked capsule repeat
      units across the inner membrane in the Wzx/Wzy-dependent pathway.
    grounding: UniProtKB:A0A0G3EZQ9
  - node_id: lipid_linked_repeat_unit
    label: lipid-linked capsule repeat unit
    node_type: CHEMICAL
    description: Undecaprenyl-linked oligosaccharide repeat unit assembled on the
      cytoplasmic face of the inner membrane.
  - node_id: wzy_polymerase
    label: Wzy polymerase
    node_type: GENE_OR_PROTEIN
    description: Polymerase that links capsule repeat units into a growing polysaccharide
      chain in the Wzx/Wzy-dependent pathway.
  - node_id: wzb_phosphatase_cycle
    label: Wzb phosphatase cycle
    node_type: BIOLOGICAL_PROCESS
    description: Wzb-catalyzed phosphorylation/dephosphorylation cycle of the Wzc
      tyrosine autokinase regulating capsule assembly.
  - node_id: wzc_capsule_assembly
    label: Wzc-regulated capsule assembly
    node_type: BIOLOGICAL_PROCESS
    description: Capsule polymerization and export controlled by the Wzc polysaccharide
      copolymerase/tyrosine autokinase.
  - node_id: wza_export_protein
    label: Wza outer-membrane export protein
    node_type: GENE_OR_PROTEIN
    description: Outer-membrane polysaccharide export protein that translocates capsule
      polymer across the outer membrane.
  - node_id: kpsmt_abc_transporter
    label: KpsMT ABC transporter
    node_type: GENE_OR_PROTEIN
    description: ATP-binding cassette transporter that exports capsule polysaccharide
      chains across the inner membrane in the ABC-dependent pathway.
  edges:
  - subject: capsule_assembly
    predicate: produces
    object: capsular_polysaccharide
    description: Capsule biosynthesis synthesizes and exports the high-MW capsular
      polysaccharide.
    evidence:
    - reference: DOI:10.1146/annurev.biochem.75.103004.142545
      notes: Whitfield reviews biosynthesis, export, and surface assembly of the capsular
        polysaccharide polymer.
    predicate_id: biolink:produces
  - subject: capsule_assembly
    predicate: enables
    object: capsule_trait
    description: Surface assembly of capsule polymers realizes the capsulated phenotype.
    evidence:
    - reference: DOI:10.1146/annurev.biochem.75.103004.142545
      notes: Whitfield reviews biosynthesis and assembly of capsular polysaccharides.
    predicate_id: RO:0002327
  - subject: capsule_trait
    predicate: contributes to
    object: immune_evasion
    description: The capsule masks surface antigens and reduces phagocytic uptake.
    evidence:
    - reference: DOI:10.1146/annurev.micro.50.1.285
      notes: Roberts frames capsular polysaccharide as an immune-evasion and adhesion
        structure.
    predicate_id: RO:0002326
  - subject: wzx_flippase
    predicate: flips
    object: lipid_linked_repeat_unit
    description: Wzx flippase turns the completed lipid-linked repeat unit outward
      across the inner membrane.
    evidence:
    - reference: DOI:10.1038/s41522-024-00497-6
      notes: '"the complete repeat unit is turned outward by the Wzx flip enzyme";
        general Wzx/Wzy capsule biosynthesis, not taxon-specific.'
  - subject: wzy_polymerase
    predicate: polymerizes
    object: capsular_polysaccharide
    description: Wzy polymerase attaches the growing chain to new repeat units, building
      the capsular polysaccharide.
    evidence:
    - reference: DOI:10.1038/s41522-024-00497-6
      notes: '"the Wzy polymerase attaches the growing polymer chain to the newly
        formed repeat unit"; general Wzx/Wzy pathway.'
  - subject: wzb_phosphatase_cycle
    predicate: required for
    object: wzc_capsule_assembly
    description: The Wzb-catalyzed phosphorylation cycle of Wzc is a crucial step
      for capsule assembly.
    evidence:
    - reference: DOI:10.1038/s41522-024-00497-6
      notes: '"The phosphorylation cycle of Wzc, catalyzed by Wzb, is a crucial step.";
        general capsule biosynthesis.'
  - subject: wza_export_protein
    predicate: exports
    object: capsular_polysaccharide
    description: Wza translocates the assembled capsule polymer across the outer membrane.
    evidence:
    - reference: DOI:10.1038/s41522-024-00497-6
      notes: '"The polymer translocates across the outer membrane via Wza"; Wzx/Wzy-dependent
        pathway, broad mechanistic statement.'
    predicate_id: METPO:2000209
  - subject: kpsmt_abc_transporter
    predicate: exports
    object: capsular_polysaccharide
    description: The KpsMT ABC transporter exports capsule polysaccharide chains across
      the inner membrane in the ABC-dependent pathway.
    evidence:
    - reference: DOI:10.1038/s41522-024-00497-6
      notes: '"the ABC transporter (KpsMT) plays a pivotal role in exporting these
        chains"; general ABC-dependent capsule export.'
    predicate_id: METPO:2000209
curation_history:
- timestamp: '2026-06-03T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate MORPHOLOGY trait (capsule) from literature research
    to fill the cell-surface-structure gap.
  llm_assisted: true
- timestamp: '2026-06-09T15:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (capsule polysaccharide / immune evasion)
    with RO predicate groundings; promoted PROPOSED to REVIEWED.
  llm_assisted: true
- timestamp: '2026-06-14T06:55:38Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:3379×1).
  llm_assisted: true
- timestamp: '2026-06-16T00:00:00Z'
  curator: claude
  action: FIX_ORPHAN_NODE
  changes: Connected the previously-orphaned capsular_polysaccharide node via a 'produces'
    (biolink:produces) edge from capsule_assembly.
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (7 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:13Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000209×2).
  llm_assisted: true
- timestamp: '2026-06-26T07:15:19Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A0G3EZQ9×1).
  llm_assisted: true