identifier: traitmech:000118
label: staphylococcus arrangement
definition: A cell arrangement in which dividing cocci form irregular three-dimensional
  grape-like clusters because division planes occur in multiple, non-orthogonal orientations
  and daughter cells remain attached.
definition_source: DOI:10.1128/MMBR.00001-06
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000666
synonyms:
- synonym_text: cluster-forming cocci
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1128/MMBR.00001-06
evidence:
- reference: DOI:10.1128/MMBR.00001-06
  notes: Young's review treats clustered coccal arrangement as a division-plane- determined
    heritable morphology.
- reference: DOI:10.1038/ncomms4842
  notes: Division-plane orientation and daughter-cell separation govern formation
    of three-dimensional coccal clusters.
canonical_examples:
- taxon_id: NCBITaxon:1280
  taxon_label: Staphylococcus aureus
  note: "Namesake of the staphylococcal arrangement (grape-like irregular clusters from division in multiple planes)."
  reference: PMID:845124
causal_graphs:
- graph_id: staphylococcus_irregular_division_cluster
  title: Staphylococcus arrangement via multi-plane non-orthogonal division
  description: Evidence-backed causal sketch linking non-orthogonal multi-plane division
    and incomplete daughter-cell separation to irregular grape-like coccal clusters.
  nodes:
  - node_id: staphylococcus_trait
    label: staphylococcus arrangement
    node_type: TRAIT
    grounding: traitmech:000118
    description: Cocci forming irregular three-dimensional grape-like clusters.
  - node_id: cell_division
    label: cell division
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0051301
    description: Bacterial binary fission.
  - node_id: multiplane_nonorthogonal_division
    label: multi-plane non-orthogonal division
    node_type: QUALITY
    description: Successive division planes oriented in multiple non-orthogonal directions.
  - node_id: facz
    label: FacZ
    node_type: GENE_OR_PROTEIN
    description: S. aureus division-site placement factor that prevents aberrant Z-ring
      placement.
  - node_id: gpsb
    label: GpsB
    node_type: GENE_OR_PROTEIN
    description: Conserved cell-division regulator that promotes lateral interactions
      between FtsZ filaments.
    grounding: UniProtKB:A0A060RK42
  - node_id: ftsz
    label: FtsZ
    node_type: GENE_OR_PROTEIN
    description: Tubulin-like central divisome protein forming the cytokinetic Z-ring.
    grounding: UniProtKB:C0LUM8
  - node_id: ftsz_ring
    label: FtsZ Z-ring
    node_type: CELLULAR_LOCALIZATION
    description: Dynamic treadmilling FtsZ polymer ring that establishes the division
      site.
  - node_id: divisome_pg_synthesis
    label: divisome peptidoglycan synthesis at division site
    node_type: BIOLOGICAL_PROCESS
    description: Septal peptidoglycan synthesis machinery organized at the division
      site.
  edges:
  - subject: multiplane_nonorthogonal_division
    predicate: causes
    object: staphylococcus_trait
    description: Multi-plane non-orthogonal division with incomplete separation generates
      3D coccal clusters.
    evidence:
    - reference: DOI:10.1038/ncomms4842
      notes: Division-plane orientation and daughter-cell separation govern formation
        of three-dimensional coccal clusters.
    predicate_id: biolink:causes
  - subject: cell_division
    predicate: enables
    object: staphylococcus_trait
    description: Bacterial cell division underlies coccal cluster formation.
    evidence:
    - reference: DOI:10.1128/MMBR.00001-06
      notes: Young treats clustered coccal arrangement as a division-plane- determined
        heritable morphology.
    predicate_id: RO:0002327
  - subject: facz
    predicate: prevents aberrant placement of
    object: ftsz_ring
    description: FacZ prevents aberrant membrane invaginations and multiple/mispositioned
      FtsZ cytokinetic rings.
    evidence:
    - reference: DOI:10.1038/s41564-024-01607-y
      notes: '"Inactivation of FacZ produced aberrant membrane invaginations and multiple
        FtsZ cytokinetic rings"; peer-reviewed S. aureus phenotype.'
  - subject: facz
    predicate: interacts with
    object: gpsb
    description: FacZ directly interacts with the division regulator GpsB.
    evidence:
    - reference: DOI:10.1038/s41564-024-01607-y
      notes: '"FacZ interacts directly with GpsB both in vitro and in vivo"; direct
        biochemical and cellular interaction.'
    predicate_id: biolink:interacts_with
  - subject: facz
    predicate: antagonizes
    object: gpsb
    description: FacZ antagonizes GpsB to prevent spurious Z-ring formation and aberrant
      envelope invaginations.
    evidence:
    - reference: DOI:10.1038/s41564-024-01607-y
      notes: Authors propose FacZ antagonizes GpsB to prevent spurious Z-ring formation;
        peer-reviewed proposed model.
  - subject: gpsb
    predicate: promotes lateral interactions between
    object: ftsz
    description: GpsB promotes lateral interactions between FtsZ filaments.
    evidence:
    - reference: DOI:10.1038/s41564-024-01607-y
      notes: '"GpsB itself interacts with FtsZ and promotes lateral interactions between
        FtsZ filaments."'
  - subject: ftsz_ring
    predicate: organizes
    object: divisome_pg_synthesis
    description: Treadmilling FtsZ Z-ring organizes the divisome peptidoglycan synthesis
      machinery at the division site.
    evidence:
    - reference: DOI:10.1038/s41564-024-01607-y
      notes: '"the septum is built by the divisome organized by treadmilling FtsZ
        polymers that form a dynamic Z-ring to establish the division site."'
curation_history:
- timestamp: '2026-06-08T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate MORPHOLOGY trait (staphylococcus / cluster arrangement);
    leftover round, cell-arrangement sibling of diplococcus shaped.
  llm_assisted: true
- timestamp: '2026-06-09T15:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (multi-plane non-orthogonal division
    → cluster) with GO node grounding and RO/biolink predicate groundings; promoted
    PROPOSED to REVIEWED.
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (5 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:14Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:interacts_with×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:19Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:C0LUM8×1).
  llm_assisted: true
- timestamp: '2026-06-26T07:15:20Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A060RK42×1).
  llm_assisted: true