identifier: traitmech:000064
label: S-layer
definition: A morphology trait in which the cell surface is coated by a crystalline,
  two-dimensional array of self-assembling proteinaceous (glyco)protein subunits (a
  surface layer), found in many bacteria and most archaea.
definition_source: DOI:10.1038/nrmicro3213
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000059
synonyms:
- synonym_text: surface layer
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1038/nrmicro3213
evidence:
- reference: DOI:10.1038/nrmicro3213
  notes: Fagan & Fairweather describe the S-layer as a self-assembled, regularly spaced
    two-dimensional protein array coating the cell surface.
- reference: DOI:10.1038/s41579-025-01258-8
  notes: Review of assembly, architecture and functional roles of microbial surface
    layers supports the S-layer as a defined cell-surface structure.
canonical_examples:
- taxon_id: NCBITaxon:1422
  taxon_label: Geobacillus stearothermophilus
  note: "Long-standing model for crystalline bacterial surface-layer (S-layer) structure and assembly."
  reference: DOI:10.1111/1574-6976.12063
causal_graphs:
- graph_id: s_layer_2d_protein_array
  title: S-layer crystalline (glyco)protein surface array
  description: Evidence-backed causal sketch linking self-assembly of (glyco)protein
    subunits into a regular 2D array to the S-layer surface coating.
  nodes:
  - node_id: s_layer_trait
    label: S-layer
    node_type: TRAIT
    grounding: traitmech:000064
    description: Crystalline 2D (glyco)protein array coating the cell surface.
  - node_id: s_layer_subunits
    label: S-layer (glyco)protein subunits
    node_type: GENE_OR_PROTEIN
    description: Self-assembling proteinaceous building blocks of the S-layer.
  - node_id: s_layer_assembly
    label: S-layer assembly
    node_type: BIOLOGICAL_PROCESS
    description: Self-assembly of S-layer subunits into a regularly spaced 2D array.
  - node_id: s_layer_2d_lattice
    label: 2D paracrystalline S-layer lattice
    node_type: CELLULAR_LOCALIZATION
    description: Regularly spaced two-dimensional paracrystalline lattice formed by
      self-assembled S-layer proteins coating the cell surface.
  edges:
  - subject: s_layer_subunits
    predicate: enables
    object: s_layer_assembly
    description: Self-assembling (glyco)protein subunits build the S-layer array.
    evidence:
    - reference: DOI:10.1038/nrmicro3213
      notes: Fagan & Fairweather describe self-assembled (glyco)protein arrays forming
        the S-layer.
    predicate_id: RO:0002327
  - subject: s_layer_assembly
    predicate: enables
    object: s_layer_trait
    description: Completed 2D assembly realizes the S-layer surface coating.
    evidence:
    - reference: DOI:10.1038/s41579-025-01258-8
      notes: Review of assembly, architecture, and functional roles of microbial surface
        layers.
    predicate_id: RO:0002327
  - subject: s_layer_subunits
    predicate: self-assembles into
    object: s_layer_2d_lattice
    description: S-layer proteins self-assemble into a 2D paracrystalline lattice;
      N-terminal regions mediate self-assembly into the layer.
    evidence:
    - reference: DOI:10.1073/pnas.2401686121
      notes: S-layers are self-assembling, crystalline surface proteins; the N-terminal
        region mediates self-assembly into the layer (curation-safe at class level).
curation_history:
- timestamp: '2026-06-03T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate MORPHOLOGY trait (S-layer) 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 (S-layer 2D protein array assembly)
    with RO predicate groundings; promoted PROPOSED to REVIEWED.
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 1 evidence-backed generic edges (1 new nodes) from the deep-research
    report.
  llm_assisted: true