identifier: METPO:1000688
label: coccobacillus shaped
definition: A cell shape intermediate between spherical cocci and elongated bacilli,
  typically appearing as short or plump rods.
definition_source: DOI:10.1128/JB.187.1.54-64.2005
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000666
synonyms:
- synonym_text: coccobacillus
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1128/JB.187.1.54-64.2005
  snippet: changes shape, from a rod to coccobacillus
  notes: Supports coccobacillus morphology as a short-rod state associated with cell-shape
    control in representative bacteria.
canonical_examples:
- taxon_id: NCBITaxon:727
  taxon_label: Haemophilus influenzae
  note: "Textbook coccobacillus (short oval rod); first free-living organism to have its genome sequenced."
  reference: PMID:7542800
causal_graphs:
- graph_id: coccobacillus_shaped_short_rod_morphogenesis
  title: Coccobacillus short-rod morphogenesis mechanism
  description: Evidence-backed causal sketch linking coccobacillus shape to peptidoglycan
    synthesis, MreB-associated elongation, septal growth, and reduced length-to-width
    ratio.
  nodes:
  - node_id: coccobacillus_shaped_trait
    label: coccobacillus shaped
    node_type: TRAIT
    grounding: METPO:1000688
    description: Short, plump rod morphology intermediate between coccus and bacillus.
  - node_id: mreB
    label: MreB
    node_type: GENE_OR_PROTEIN
    description: Actin-like bacterial cytoskeletal protein involved in cell-shape
      control.
    grounding: UniProtKB:A0A1B1UYY2
  - node_id: peptidoglycan_synthesis
    label: peptidoglycan synthesis
    node_type: BIOLOGICAL_PROCESS
    description: Cell-wall synthesis and remodeling process.
    grounding: GO:0009252
  - node_id: septal_growth
    label: septal growth
    node_type: BIOLOGICAL_PROCESS
    description: Division-associated cell-wall synthesis.
  - node_id: short_rod_geometry
    label: short-rod geometry
    node_type: BIOLOGICAL_PROCESS
    description: Cell geometry with reduced length-to-width ratio.
  - node_id: rodA_pbp3_elongasome
    label: RodA/PBP3 elongasome
    node_type: GENE_OR_PROTEIN
    description: SEDS/PBP pair RodA/PBP3 mediating lateral cell-wall elongation.
  - node_id: length_to_width_ratio
    label: cell length-to-width ratio
    node_type: QUALITY
    description: Geometric ratio of long to short cell axes that distinguishes rods
      from cocci.
  - node_id: gpsB
    label: GpsB
    node_type: GENE_OR_PROTEIN
    description: Cell-cycle regulator coordinating peptidoglycan synthase localization.
    grounding: UniProtKB:A0A060RK42
  - node_id: pbp2_localization
    label: PBP2 localization
    node_type: CELLULAR_LOCALIZATION
    description: Spatial distribution of penicillin-binding protein 2 between periphery
      and septum.
  - node_id: ftsZ_filament
    label: FtsZ filament properties
    node_type: GENE_OR_PROTEIN
    description: Divisome tubulin-homolog FtsZ filament conformation affecting cell-wall
      insertion geometry.
  - node_id: pbp2_elongasome
    label: PBP2 (elongasome transpeptidase)
    node_type: GENE_OR_PROTEIN
    description: Penicillin-binding protein 2, transpeptidase of the RodA-PBP2 elongasome
      supporting rod shape.
  edges:
  - subject: mreB
    predicate: controls
    object: peptidoglycan_synthesis
    description: MreB contributes to control of peptidoglycan synthetic complexes.
    evidence:
    - reference: DOI:10.1128/JB.187.1.54-64.2005
      snippet: control of the peptidoglycan synthetic complexes
      notes: Supports MreB involvement in shape-related PG synthesis.
    predicate_id: RO:0002211
  - subject: peptidoglycan_synthesis
    predicate: causes
    object: short_rod_geometry
    description: Wall synthesis patterns determine whether cells remain rod-like or
      become short coccobacilli.
    evidence:
    - reference: DOI:10.1128/JB.187.1.54-64.2005
      snippet: conditions causing changes in cell shape
      notes: Supports PG-associated shape changes to a coccobacillus state.
    predicate_id: biolink:causes
  - subject: septal_growth
    predicate: contributes to
    object: short_rod_geometry
    description: Division-associated septal growth contributes to the short-rod intermediate
      geometry.
    evidence:
    - reference: DOI:10.1128/JB.187.1.54-64.2005
      snippet: role at mid-cell ... in early septation
      notes: Supports a septation-linked role for MreB in representative coccobacillus-forming
        cells.
    predicate_id: RO:0002326
  - subject: short_rod_geometry
    predicate: produces
    object: coccobacillus_shaped_trait
    description: Short-rod geometry produces the coccobacillus-shaped trait.
    evidence:
    - reference: DOI:10.1128/JB.187.1.54-64.2005
      snippet: from a rod to coccobacillus
      notes: Supports the trait endpoint as a short-rod morphology.
    predicate_id: METPO:2000202
  - subject: rodA_pbp3_elongasome
    predicate: increases
    object: length_to_width_ratio
    description: Elongasome-driven lateral wall synthesis increases the long-to-short
      axis ratio, opposing a coccoid shape.
    evidence:
    - reference: DOI:10.1128/mBio.03235-23
      notes: This elongation depends on the SEDS/PBP pair RodA/PBP3 and is seen as
        an increased ratio of long to short cell axes.
    predicate_id: RO:0002213
  - subject: length_to_width_ratio
    predicate: determines
    object: short_rod_geometry
    description: A reduced but non-coccoid length-to-width ratio defines the short-rod
      geometry of coccobacilli.
    evidence:
    - reference: DOI:10.1128/mBio.03235-23
      notes: Long-to-short cell axis ratio quantifies the elongation state intermediate
        between coccus and rod.
  - subject: gpsB
    predicate: regulates
    object: pbp2_localization
    description: GpsB regulates the localization of PBP2 between cell periphery and
      division septum.
    evidence:
    - reference: DOI:10.1128/mBio.03235-23
      notes: a gpsB mutant shows the strongest morphological phenotype, driven by
        partial delocalization of PBP2 and PBP4 away from the division septum.
    predicate_id: RO:0002211
  - subject: pbp2_localization
    predicate: controls
    object: peptidoglycan_synthesis
    description: Spatial localization of PBP2 controls where peptidoglycan insertion
      and crosslinking occur, biasing cells toward elongation or rounding.
    evidence:
    - reference: DOI:10.1128/mBio.03235-23
      notes: Increased PBP2/PBP4 at the cell periphery raises peptidoglycan insertion
        and crosslinking throughout the cell, impairing elongation.
    predicate_id: RO:0002211
  - subject: ftsZ_filament
    predicate: directs
    object: peptidoglycan_synthesis
    description: FtsZ filament geometry directs asymmetric, helical patterns of cell-wall
      insertion.
    evidence:
    - reference: DOI:10.1128/mBio.00908-16
      notes: altered FtsZ filaments direct asymmetric, helical cell-wall insertion,
        generating elongation; this helical pattern of wall insertion leads to elongation.
    predicate_id: RO:0002211
  - subject: pbp2_elongasome
    predicate: required for
    object: short_rod_geometry
    description: PBP2 transpeptidase activity within the RodA-PBP2 elongasome is required
      to maintain non-spherical rod/short-rod geometry.
    evidence:
    - reference: DOI:10.1073/pnas.2215237120
      notes: Loss of RodA-PBP2 elongasome activity drives a rod-to-sphere transition;
        PBP2 transpeptidase activity is required for rod-shape maintenance.
curation_history:
- timestamp: '2026-05-05T01:35:46.897227+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-11T20:05:00-07:00'
  curator: codex
  action: CURATED_WITH_LITERATURE
  changes: Added DOI-backed definition and causal graph for MreB, peptidoglycan synthesis,
    septal growth, and short-rod coccobacillus geometry.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:31Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002326×1, METPO:2000202×1).
  llm_assisted: true
- timestamp: '2026-05-23T21:30:07Z'
  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: '2026-05-24T04:13:19Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
    shapes → causes ×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
    (biolink:causes×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:38:00Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0009252×1).
  llm_assisted: true
- timestamp: '2026-05-24T05:05:14Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A1B1UYY2×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 6 evidence-backed generic edges (6 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:13Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002211×3, RO:0002213×1).
  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:A0A060RK42×1).
  llm_assisted: true