identifier: METPO:1000668
label: coccus shaped
definition: A cell shape in which an organism has a spherical or nearly spherical
  morphology, with roughly equal dimensions in all directions.
definition_source: DOI:10.1038/nrmicro3088
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000666
synonyms:
- synonym_text: coccus
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: coccus-shaped
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
created_by: Jed Dongjin Kim-Ozaeta
evidence:
- reference: DOI:10.1038/nrmicro3088
  snippet: spherical cocci synthesize peptidoglycan only at the division septum
  notes: Supports coccus shape as a spherical morphology with septal wall growth rather
    than lateral elongation.
- reference: PMID:19747126
  snippet: Staphylococcus aureus is a facultative, Gram-positive coccus
  notes: 'Organism example: Staphylococcus aureus is described as coccus-shaped.'
canonical_examples:
- taxon_id: NCBITaxon:1280
  taxon_label: Staphylococcus aureus
  note: "Textbook spherical coccus (grape-like clusters); a model Gram-positive, second only to E. coli in study volume."
  reference: https://journals.asm.org/doi/10.1128/jb.00106-25
causal_graphs:
- graph_id: coccus_shaped_septal_growth
  title: Coccus-shape septal growth mechanism
  description: Evidence-backed causal sketch linking spherical coccus morphology to
    septal peptidoglycan synthesis, FtsZ-directed division, and reduced reliance on
    lateral elongation systems.
  nodes:
  - node_id: coccus_shaped_trait
    label: coccus shaped
    node_type: TRAIT
    grounding: METPO:1000668
    description: Spherical or nearly spherical bacterial cell morphology.
  - node_id: septal_peptidoglycan_synthesis
    label: septal peptidoglycan synthesis
    node_type: BIOLOGICAL_PROCESS
    description: Cell-wall synthesis localized to the division septum.
  - node_id: ftsZ_division_ring
    label: FtsZ division ring
    node_type: GENE_OR_PROTEIN
    description: Tubulin-like division scaffold that recruits septal synthesis machinery.
  - node_id: penicillin_binding_proteins
    label: penicillin-binding proteins
    node_type: GENE_OR_PROTEIN
    description: Cell-wall synthesis enzymes recruited to division sites.
  - node_id: lateral_elongation
    label: lateral cell-wall elongation
    node_type: BIOLOGICAL_PROCESS
    description: Sidewall growth mode common in rod-shaped bacteria.
  - node_id: peripheral_peptidoglycan_synthesis
    label: peripheral peptidoglycan synthesis
    node_type: BIOLOGICAL_PROCESS
    description: Cell-wall synthesis at the cell periphery/mid-cell that drives longitudinal
      elongation toward ovoid morphology.
  - node_id: divisome_complex
    label: divisome complex
    node_type: GENE_OR_PROTEIN
    description: Multiprotein cell-division machinery coordinating septal peptidoglycan
      synthesis in cocci.
  - node_id: orthogonal_division_planes
    label: orthogonal division planes
    node_type: BIOLOGICAL_PROCESS
    description: Alternating cell division in two or three orthogonal planes characteristic
      of spherical cocci.
  - node_id: ovoid_shape
    label: ovococcal/ovoid shape
    node_type: QUALITY
    description: Slightly elongated ovoid cell morphology produced by mid-cell peripheral
      peptidoglycan synthesis.
  edges:
  - subject: ftsZ_division_ring
    predicate: recruits
    object: penicillin_binding_proteins
    description: FtsZ-associated division machinery recruits cell-wall enzymes for
      septal synthesis in cocci.
    evidence:
    - reference: DOI:10.1038/nrmicro3088
      snippet: one type of cell wall synthesis machinery
      notes: Review describes coccal growth as relying on division-septum wall synthesis
        machinery.
  - subject: penicillin_binding_proteins
    predicate: catalyzes
    object: septal_peptidoglycan_synthesis
    description: PBPs catalyze peptidoglycan assembly at the septum.
    evidence:
    - reference: DOI:10.1038/nrmicro3088
      snippet: catalysed by one type of cell wall synthesis machinery
      notes: Supports wall-synthesis enzymes as the proximal machinery for septal
        peptidoglycan synthesis in spherical cocci.
    predicate_id: biolink:catalyzes
  - subject: septal_peptidoglycan_synthesis
    predicate: regulates
    object: coccus_shaped_trait
    description: Septum-centered peptidoglycan synthesis supports spherical coccus
      morphology.
    evidence:
    - reference: DOI:10.1038/nrmicro3088
      snippet: synthesize peptidoglycan only at the division septum
      notes: Supports septal-only wall synthesis as a mechanism for spherical coccal
        growth.
    predicate_id: RO:0002211
  - subject: lateral_elongation
    predicate: reduced in
    object: coccus_shaped_trait
    description: Cocci lack the sustained lateral elongation mode that produces rod
      morphology.
    evidence:
    - reference: DOI:10.1038/nrmicro3088
      snippet: round, rod-shaped, curved and spiral cells
      notes: Review contrasts mechanisms for cocci with rod-shaped lateral growth;
        edge is retained as a broad mechanistic distinction rather than a universal
        gene-loss claim.
  - subject: peripheral_peptidoglycan_synthesis
    predicate: negatively associated with
    object: coccus_shaped_trait
    description: Peripheral/mid-cell wall synthesis drives elongation away from true
      spherical coccus morphology.
    evidence:
    - reference: DOI:10.1038/nrmicro3088
      notes: 'Pinho 2013: ovococci perform both septal and peripheral peptidoglycan
        synthesis; peripheral synthesis drives slight longitudinal elongation and
        the ovoid shape, distinguishing it from true cocci.'
  - subject: divisome_complex
    predicate: mediates
    object: septal_peptidoglycan_synthesis
    description: Divisome-centered machinery mediates peptidoglycan synthesis at the
      septum in cocci.
    evidence:
    - reference: DOI:10.1042/BSR20221664
      notes: 'Battaje 2023: in cocci, peptidoglycan synthesis takes place mostly at
        the site of division, i.e. the septum coordinated by FtsZ via the divisome
        complex.'
  - subject: ftsZ_division_ring
    predicate: coordinates
    object: septal_peptidoglycan_synthesis
    description: FtsZ coordinates septal peptidoglycan synthesis, linking the cytoskeletal
      ring to coccal septal growth.
    evidence:
    - reference: DOI:10.1042/BSR20221664
      notes: 'Battaje 2023: peptidoglycan synthesis takes place mostly at the septum
        coordinated by FtsZ; broad across bacteria, especially cocci.'
  - subject: coccus_shaped_trait
    predicate: associated with
    object: orthogonal_division_planes
    description: Spherical cocci alternate division in two or three orthogonal planes.
    evidence:
    - reference: DOI:10.1038/nrmicro3088
      notes: 'Pinho 2013: spherical cocci can alternate division in two or three orthogonal
        planes; a morphology-associated arrangement behavior.'
    predicate_id: biolink:associated_with
  - subject: peripheral_peptidoglycan_synthesis
    predicate: produces
    object: ovoid_shape
    description: Peripheral synthesis between equatorial rings produces ovococcal/ovoid
      shape, a boundary contrast to true cocci.
    evidence:
    - reference: DOI:10.1038/nrmicro3088
      notes: 'Pinho 2013: peripheral synthesis occurring at mid-cell, between the
        equatorial rings, drives slight longitudinal elongation and the ovoid shape.'
    predicate_id: METPO:2000202
curation_history:
- timestamp: '2026-05-05T01:35:46.886046+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-06T14:40:41-07:00'
  curator: codex
  action: CURATED_WITH_ORGANISM_EXAMPLE
  changes: Added Staphylococcus aureus organism example with PMID-backed evidence.
  llm_assisted: true
- timestamp: '2026-05-11T18:00:00-07:00'
  curator: codex
  action: CURATED_WITH_LITERATURE
  changes: Replaced PMID definition source with DOI-backed coccoid growth review and
    added causal graph for FtsZ-associated septal peptidoglycan synthesis and spherical
    morphology.
  llm_assisted: true
- timestamp: '2026-05-20T05:49:24Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:catalyzes×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:13:19Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
    maintains → regulates ×1.'
  llm_assisted: true
- timestamp: '2026-05-24T04:13:21Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002211×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (4 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
    (biolink:associated_with×1, METPO:2000202×1).
  llm_assisted: true