identifier: METPO:1000667
label: bacillus shaped
definition: A cell shape characterized by an elongated, rod cylindrical morphology
  with relatively parallel sides and rounded ends.
definition_source: DOI:10.1146/annurev-cellbio-010521-010834
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000666
synonyms:
- synonym_text: bacillus
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
created_by: Anthea Guo
evidence:
- reference: DOI:10.1146/annurev-cellbio-010521-010834
  snippet: bacterial rod shape formation
  notes: Supports bacillus shape as a rod-like bacterial morphogenesis phenotype.
canonical_examples:
- taxon_id: NCBITaxon:1423
  taxon_label: Bacillus subtilis
  note: "The namesake bacillus (straight rod); model Gram-positive rod-shaped bacterium."
  reference: PMID:9384377
causal_graphs:
- graph_id: bacillus_shaped_rod_elongation
  title: Bacillus-shape rod elongation mechanism
  description: Evidence-backed causal sketch linking bacillus morphology to MreB-organized
    Rod complexes, lateral peptidoglycan insertion, and FtsZ-coupled division.
  nodes:
  - node_id: bacillus_shaped_trait
    label: bacillus shaped
    node_type: TRAIT
    grounding: METPO:1000667
    description: Elongated cylindrical rod-like bacterial morphology.
  - node_id: mreB
    label: MreB
    node_type: GENE_OR_PROTEIN
    description: Actin-like protein involved in rod-shape maintenance.
    grounding: UniProtKB:A0A1B1UYY2
  - node_id: rod_complex
    label: Rod complex
    node_type: GENE_OR_PROTEIN
    description: MreB-associated cell-wall elongation machinery.
  - node_id: peptidoglycan_synthesis
    label: peptidoglycan synthesis
    node_type: BIOLOGICAL_PROCESS
    description: Cell-wall synthesis and remodeling.
    grounding: GO:0009252
  - node_id: lateral_cell_wall_elongation
    label: lateral cell-wall elongation
    node_type: BIOLOGICAL_PROCESS
    description: Sidewall growth that lengthens rod-shaped cells.
  - node_id: ftsZ
    label: FtsZ
    node_type: GENE_OR_PROTEIN
    description: Division-ring protein coordinating septal growth.
    grounding: UniProtKB:C0LUM8
  - node_id: peptidoglycan_cell_wall
    label: peptidoglycan cell wall
    node_type: CELLULAR_LOCALIZATION
    description: Peptidoglycan sacculus that protects against osmotic lysis and determines
      cell shape.
  - node_id: rodA_pbp2_synthase
    label: RodA-PBP2 synthase (Rod complex)
    node_type: GENE_OR_PROTEIN
    description: Essential elongasome peptidoglycan synthase responsible for bacterial
      elongation.
  - node_id: bacterial_elongation
    label: bacterial cell elongation
    node_type: BIOLOGICAL_PROCESS
    description: Lengthwise growth of the rod-shaped cell driven by elongasome synthesis.
  - node_id: circumferential_glycan_insertion
    label: circumferential glycan strand insertion
    node_type: BIOLOGICAL_PROCESS
    description: Elongasome-mediated insertion of long glycan strands as barrel-hoop-like
      reinforcing structures.
  - node_id: moenomycin
    label: moenomycin
    node_type: CHEMICAL
    description: Antibiotic that inhibits class A penicillin-binding proteins (PG
      glycosyltransferases).
    grounding: CHEBI:28908
  - node_id: class_a_pbps
    label: class A penicillin-binding proteins
    node_type: GENE_OR_PROTEIN
    description: Class A PBPs (aPBPs), a family of peptidoglycan synthases.
  - node_id: rodZ
    label: RodZ
    node_type: GENE_OR_PROTEIN
    description: Membrane protein broadly implicated in rod-shape maintenance.
    grounding: UniProtKB:H1XNL6
  - node_id: spherical_morphology
    label: spherical cell morphology
    node_type: TRAIT
    description: Coccus-like spherical cell shape, the phenotype arising from loss
      of rod-shape determinants.
  edges:
  - subject: mreB
    predicate: enables
    object: rod_complex
    description: MreB organizes rod-shape elongation machinery.
    evidence:
    - reference: DOI:10.1146/annurev-cellbio-010521-010834
      snippet: MreB filaments interact with Rod complexes
      notes: Supports MreB-Rod complex interaction in rod-shape regulation.
    predicate_id: RO:0002327
  - subject: rod_complex
    predicate: directs
    object: peptidoglycan_synthesis
    description: Rod complexes direct sidewall peptidoglycan synthesis.
    evidence:
    - reference: DOI:10.1146/annurev-cellbio-010521-010834
      snippet: Rod complexes drive cell wall insertion
      notes: Supports Rod complex contribution to wall insertion.
    predicate_id: RO:0002211
  - subject: peptidoglycan_synthesis
    predicate: produces
    object: lateral_cell_wall_elongation
    description: Directed peptidoglycan synthesis supports cylindrical elongation.
    evidence:
    - reference: DOI:10.1038/nrmicro2677
      snippet: peptidoglycan synthesis to bacterial growth and morphology
      notes: Supports regulated peptidoglycan synthesis as a determinant of bacterial
        morphology.
    predicate_id: METPO:2000202
  - subject: lateral_cell_wall_elongation
    predicate: regulates
    object: bacillus_shaped_trait
    description: Lateral wall elongation maintains bacillus-like rod morphology.
    evidence:
    - reference: DOI:10.1016/j.tim.2011.11.004
      snippet: restores its rod shape
      notes: Supports MreB-associated cell-wall synthesis as important for rod shape
        restoration and maintenance.
    predicate_id: RO:0002211
  - subject: ftsZ
    predicate: coordinates with
    object: peptidoglycan_synthesis
    description: FtsZ coordinates division-associated peptidoglycan synthesis with
      rod-cell growth.
    evidence:
    - reference: DOI:10.1038/nrmicro1205
      snippet: FtsZ collaborates with penicillin binding proteins
      notes: Supports FtsZ-PBP collaboration in bacterial cell-shape generation.
  - subject: peptidoglycan_cell_wall
    predicate: determines
    object: bacillus_shaped_trait
    description: The peptidoglycan cell wall protects against osmotic lysis and determines
      cell shape.
    evidence:
    - reference: DOI:10.1038/s41467-023-39037-9
      notes: PG protects bacteria against osmotic lysis and determines cell shape.
  - subject: rodA_pbp2_synthase
    predicate: required for
    object: bacterial_elongation
    description: RodA-PBP2 is the essential synthase responsible for bacterial elongation.
    evidence:
    - reference: DOI:10.1038/s41467-023-39037-9
      notes: RodA-PBP2 is an essential synthase responsible for bacterial elongation.
  - subject: circumferential_glycan_insertion
    predicate: gives rise to
    object: bacillus_shaped_trait
    description: Elongasome inserts long glycan strands as barrel-hoop reinforcement,
      giving rise to a rod-shaped cell.
    evidence:
    - reference: DOI:10.1038/s41467-024-49785-x
      notes: Inserts long glycan strands acting as barrel-hoop-like reinforcing structures,
        thereby giving rise to a rod-shaped cell.
  - subject: moenomycin
    predicate: inhibits
    object: class_a_pbps
    description: Moenomycin inhibits class A penicillin-binding proteins, a family
      of PG synthases.
    evidence:
    - reference: DOI:10.1038/s41467-023-41082-3
      notes: Moenomycin inhibits a family of PG synthases known as Class-A penicillin-binding
        proteins.
    predicate_id: RO:0002212
  - subject: rodZ
    predicate: causally upstream of, negative effect
    object: spherical_morphology
    description: Loss of RodZ causes cells to become spherical, indicating RodZ maintains
      rod shape.
    evidence:
    - reference: DOI:10.3389/fmicb.2024.1400434
      notes: ' delta-rodZ cells were spherical (WT cells are rod-shaped); RodZ broadly
        implicated in rod maintenance.'
curation_history:
- timestamp: '2026-05-05T01:35:46.885522+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-11T18:00:00-07:00'
  curator: codex
  action: CURATED_WITH_LITERATURE
  changes: Reviewed bacillus shape as rod-like morphology and added DOI-backed causal
    graph for MreB, Rod complex, peptidoglycan synthesis, lateral wall elongation,
    and FtsZ coupling.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:31Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (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:
    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: '2026-05-24T04:38:00Z'
  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 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A1B1UYY2×1, UniProtKB:C0LUM8×1).
  llm_assisted: true
- timestamp: '2026-05-26T05:00:48Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
    organizes → enables ×1.'
  llm_assisted: true
- timestamp: '2026-05-26T05:00:50Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (8 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:12Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002212×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:33Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:28908×1).
  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:H1XNL6×1).
  llm_assisted: true