identifier: METPO:1000666
label: cell shape
definition: A phenotype that describes the characteristic three-dimensional morphological
  form of a microbial cell, determined by cell wall structure, cytoskeletal elements,
  and environmental factors.
definition_source: DOI:10.1038/nrmicro1205
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000059
synonyms:
- synonym_text: Morphology.cell morphology.cell shape
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: cell_shape
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
created_by: Luke Wang
evidence:
- reference: DOI:10.1038/nrmicro1205
  snippet: bacterial cell wall ... primary role in maintaining cell shape
  notes: Supports bacterial cell shape as determined by cell wall and cytoskeletal
    elements.
causal_graphs:
- graph_id: cell_shape_peptidoglycan_cytoskeleton
  title: Bacterial cell-shape morphogenesis mechanism
  description: Evidence-backed causal sketch linking cell shape to peptidoglycan synthesis,
    PBPs, MreB, FtsZ, crescentin, and localized wall growth.
  nodes:
  - node_id: cell_shape_trait
    label: cell shape
    node_type: TRAIT
    grounding: METPO:1000666
    description: Characteristic three-dimensional microbial cell morphology.
  - node_id: peptidoglycan_cell_wall
    label: peptidoglycan cell wall
    node_type: CELLULAR_LOCALIZATION
    grounding: GO:0009274
    description: Cell-wall polymer network maintaining bacterial shape.
  - node_id: peptidoglycan_synthesis
    label: peptidoglycan synthesis
    node_type: BIOLOGICAL_PROCESS
    description: Biosynthesis and remodeling of the bacterial cell wall.
    grounding: GO:0009252
  - node_id: penicillin_binding_proteins
    label: penicillin-binding proteins
    node_type: GENE_OR_PROTEIN
    description: Enzymes that synthesize and remodel peptidoglycan.
  - node_id: mreB
    label: MreB
    node_type: GENE_OR_PROTEIN
    description: Actin-like bacterial cytoskeletal protein involved in rod-shape determination.
    grounding: UniProtKB:A0A1B1UYY2
  - node_id: ftsZ
    label: FtsZ
    node_type: GENE_OR_PROTEIN
    description: Tubulin-like bacterial cell-division protein.
    grounding: UniProtKB:C0LUM8
  - node_id: crescentin
    label: crescentin
    node_type: GENE_OR_PROTEIN
    description: Intermediate-filament-like protein required for curved rod shape
      in Caulobacter.
    grounding: UniProtKB:A0A2N9AY16
  - node_id: rod_complex
    label: Rod complex (elongasome)
    node_type: PATHWAY
    description: Elongasome machinery that directs lateral peptidoglycan synthesis
      and architecture.
  - node_id: peptidoglycan_architecture
    label: peptidoglycan architecture
    node_type: CELLULAR_LOCALIZATION
    description: Spatial organization and dense structure of the peptidoglycan wall.
  - node_id: rod_shape
    label: rod shape
    node_type: QUALITY
    description: Rod (bacillus) cell-shape outcome.
  - node_id: a22_inhibitor
    label: A22 (MreB inhibitor)
    node_type: CHEMICAL
    description: Small-molecule inhibitor that reduces MreB filament assembly.
  - node_id: cardiolipin_lipid_order
    label: cardiolipin / increased lipid order
    node_type: CHEMICAL
    description: Membrane lipid composition state with increased lipid order.
  - node_id: flotillins
    label: flotillins
    node_type: GENE_OR_PROTEIN
    description: Membrane microdomain scaffolding proteins.
  - node_id: cell_wall_synthesis
    label: cell wall synthesis
    node_type: BIOLOGICAL_PROCESS
    description: Synthesis of the bacterial cell wall.
  edges:
  - subject: peptidoglycan_cell_wall
    predicate: regulates
    object: cell_shape_trait
    description: The peptidoglycan wall has a primary role in maintaining bacterial
      cell shape.
    evidence:
    - reference: DOI:10.1038/nrmicro1205
      snippet: primary role in maintaining cell shape
      notes: Review supports peptidoglycan wall as central to cell shape.
    predicate_id: RO:0002211
  - subject: penicillin_binding_proteins
    predicate: catalyzes
    object: peptidoglycan_synthesis
    description: PBPs synthesize and remodel peptidoglycan during growth and division.
    evidence:
    - reference: DOI:10.1038/nrmicro1205
      snippet: carry out the reactions for synthesis and remodelling
      notes: Supports PBPs in peptidoglycan synthesis/remodeling.
    predicate_id: biolink:catalyzes
  - subject: peptidoglycan_synthesis
    predicate: causes
    object: cell_shape_trait
    description: Spatial regulation of wall synthesis determines growth morphology.
    evidence:
    - reference: DOI:10.1038/nrmicro2677
      snippet: peptidoglycan synthesis to bacterial growth and morphology
      notes: Review supports regulated peptidoglycan synthesis as a determinant of
        morphology.
    predicate_id: biolink:causes
  - subject: mreB
    predicate: positions
    object: peptidoglycan_synthesis
    description: MreB helps organize or position peptidoglycan synthesis machinery.
    evidence:
    - reference: DOI:10.1038/nrmicro2677
      snippet: positions peptidoglycan biosynthesis machineries
      notes: Supports MreB in spatial organization of cell-wall synthesis.
  - subject: ftsZ
    predicate: regulates
    object: cell_shape_trait
    description: FtsZ controls division-associated shape generation and septal wall
      synthesis.
    evidence:
    - reference: DOI:10.1038/nrmicro1205
      snippet: FtsZ is essential for cell division
      notes: Supports FtsZ as a shape-related cytoskeletal protein through cell division.
    predicate_id: RO:0002211
  - subject: crescentin
    predicate: contributes to
    object: cell_shape_trait
    description: Crescentin contributes to curved-rod cell shape in representative
      bacteria.
    evidence:
    - reference: DOI:10.1038/nrmicro1205
      snippet: crescentin is required for the curved-rod shape
      notes: Supports crescentin as a cell-shape determinant in Caulobacter.
    predicate_id: RO:0002326
  - subject: rod_complex
    predicate: shapes
    object: peptidoglycan_architecture
    description: The rod complex (elongasome) determines the overall shape and dense
      architecture of peptidoglycan.
    evidence:
    - reference: DOI:10.1002/mbo3.1385
      notes: Rod complex may be a determinant for the whole shape of peptidoglycan
        and its highly dense structure.
  - subject: peptidoglycan_architecture
    predicate: regulates
    object: cell_shape_trait
    description: Peptidoglycan wall architecture underlies cell shape.
    evidence:
    - reference: DOI:10.1002/mbo3.1385
      notes: Peptidoglycan determines cell shape (broad bacterial claim).
    predicate_id: RO:0002211
  - subject: mreB
    predicate: organizes
    object: rod_shape
    description: MreB coordinates with PG synthases to organize cell-wall synthesis
      for rod shape.
    evidence:
    - reference: DOI:10.1042/bsr20221664
      notes: MreB coordinates with PG synthases and is linked to rod shape.
  - subject: a22_inhibitor
    predicate: disrupts
    object: rod_shape
    description: A22 reduces MreB filaments, causing loss of rod shape and lysis.
    evidence:
    - reference: DOI:10.1128/jb.00433-22
      notes: A22 reduces MreB filaments leading to loss of rod shape and lysis.
  - subject: cardiolipin_lipid_order
    predicate: inhibits
    object: mreB
    description: Increased lipid order or cardiolipin interferes with MreB assembly.
    evidence:
    - reference: DOI:10.1128/jb.00433-22
      notes: Increased lipid order or cardiolipin interferes with MreB assembly.
    predicate_id: RO:0002212
  - subject: flotillins
    predicate: promotes
    object: cell_wall_synthesis
    description: Flotillins promote MreB activity and cell-wall synthesis via membrane
      organization.
    evidence:
    - reference: DOI:10.1128/jb.00433-22
      notes: Absence of flotillins downregulates MreB activity and cell wall synthesis.
    predicate_id: RO:0002213
curation_history:
- timestamp: '2026-05-05T01:35:46.884864+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-11T00:00:00-07:00'
  curator: codex
  action: CURATED_WITH_LITERATURE
  changes: Reviewed cell shape trait and added DOI-backed causal graph for peptidoglycan
    cell wall, PBPs, MreB, FtsZ, crescentin, and localized wall growth.
  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:0002211×1, RO:0002326×1).
  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: '2026-05-24T04:38:00Z'
  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 3 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A1B1UYY2×1, UniProtKB:C0LUM8×1, UniProtKB:A0A2N9AY16×1).
  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:
    determines → causes ×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
    (biolink:causes×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 6 evidence-backed generic edges (7 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:13Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002211×1, RO:0002212×1, RO:0002213×1).
  llm_assisted: true