identifier: METPO:1000890
label: cell width large
definition: A cell-width phenotype in which the shorter cell dimension exceeds approximately
  0.9 micrometers.
definition_source: DOI:10.1146/annurev-cellbio-101011-155745
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000882
synonyms:
- synonym_text: W_>0.9
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1146/annurev-cellbio-101011-155745
  snippet: MreB-directed peptidoglycan synthesis
  notes: Supports MreB/Rod-complex activity as the control point governing wide rod
    radii.
- reference: DOI:10.1126/science.aaa1313
  snippet: cell size scales with growth rate
  notes: Growth-rate-dependent size law supports widening of cells at fast growth
    rates or under nutrient-rich conditions.
causal_graphs:
- graph_id: cell_width_large_setpoint_increase
  title: Large cell-width by elevated wall-radius set-point
  description: DOI-backed graph linking nutrient-rich growth conditions and an elevated
    MreB-driven wall-radius set-point to wide rods (>0.9 μm).
  nodes:
  - node_id: cell_width_large_trait
    label: cell width large
    node_type: TRAIT
    grounding: METPO:1000890
    description: Cell width exceeding approximately 0.9 μm.
  - node_id: cell_width_trait
    label: cell width
    node_type: TRAIT
    grounding: METPO:1000882
    description: Regulated shorter cellular dimension.
  - node_id: rich_growth_conditions
    label: rich growth conditions
    node_type: ENVIRONMENTAL_FACTOR
    description: Nutrient-rich conditions promoting fast growth and larger cells.
  - node_id: rod_complex_pg
    label: Rod-complex peptidoglycan synthesis
    node_type: BIOLOGICAL_PROCESS
    description: MreB-organized lateral peptidoglycan assembly.
  - node_id: roda_pbp2_complex
    label: RodA-PBP2 elongasome complex
    node_type: GENE_OR_PROTEIN
    description: SEDS-bPBP synthase pair driving lateral (sidewall) peptidoglycan
      synthesis.
  - node_id: roda_pbp2_activation
    label: RodA-PBP2 allosteric activation
    node_type: BIOLOGICAL_PROCESS
    description: Structural opening coupling peptidoglycan polymerization and crosslinking.
  - node_id: pg_polymerization_crosslinking
    label: peptidoglycan polymerization and crosslinking
    node_type: BIOLOGICAL_PROCESS
    description: Glycan-chain polymerization and transpeptidase crosslinking during
      elongation.
  - node_id: sidewall_pg_insertion
    label: lateral sidewall peptidoglycan insertion
    node_type: BIOLOGICAL_PROCESS
    description: Insertion of new peptidoglycan at dispersed lateral cell-wall sites.
  - node_id: mreb_filaments
    label: MreB cytoskeletal filaments
    node_type: GENE_OR_PROTEIN
    description: Actin-like filaments guiding circumferential peptidoglycan insertion.
  - node_id: circumferential_pg_insertion
    label: circumferential peptidoglycan insertion
    node_type: BIOLOGICAL_PROCESS
    description: Peptidoglycan insertion oriented perpendicular to the long cell axis.
  - node_id: rod_complex_rotation
    label: Rod-complex circumferential rotation
    node_type: BIOLOGICAL_PROCESS
    description: Rotation of the Rod complex perpendicular to the long cell axis.
  - node_id: even_pg_distribution
    label: even peptidoglycan distribution
    node_type: QUALITY
    description: Evenly distributed insertion of peptidoglycan in the cell-surface
      layer.
  - node_id: mrec_mred_balance
    label: MreC-MreD balance
    node_type: GENE_OR_PROTEIN
    description: Stoichiometric balance of MreC and MreD accessory regulators.
  - node_id: pbp2_activity
    label: PBP2 transpeptidase activity
    node_type: MOLECULAR_FUNCTION
    description: Peptidoglycan crosslinking activity of the bifunctional PBP2 synthase.
  - node_id: lipid_ii
    label: Lipid II
    node_type: CHEMICAL
    description: Disaccharide-pentapeptide lipid-linked peptidoglycan precursor.
    grounding: CHEBI:27692
  edges:
  - subject: rich_growth_conditions
    predicate: shifts
    object: rod_complex_pg
    description: Rich growth conditions shift Rod-complex activity toward a larger
      radius set-point.
    evidence:
    - reference: DOI:10.1126/science.aaa1313
      snippet: cell size scales with growth rate
      notes: Supports growth-rate-dependent enlargement of cell radius.
  - subject: rod_complex_pg
    predicate: produces
    object: cell_width_large_trait
    description: Elevated Rod-complex activity yields a wide rod radius.
    evidence:
    - reference: DOI:10.1146/annurev-cellbio-101011-155745
      snippet: MreB-directed peptidoglycan synthesis
      notes: Supports lateral PG synthesis as the producer of the wide cell radius.
    predicate_id: METPO:2000202
  - subject: cell_width_large_trait
    predicate: is a
    object: cell_width_trait
    description: Large cell width is a quantitative bin of the cell-width phenotype.
    evidence:
    - reference: DOI:10.1146/annurev-cellbio-101011-155745
      snippet: MreB-directed peptidoglycan synthesis
      notes: Supports large width as a value within the regulated cell-width distribution.
    predicate_id: rdfs:subClassOf
  - subject: roda_pbp2_activation
    predicate: positively regulates
    object: pg_polymerization_crosslinking
    description: Allosteric structural opening of RodA-PBP2 activates coupled PG polymerization
      and crosslinking.
    evidence:
    - reference: DOI:10.1038/s41467-023-39037-9
      notes: '"Structural opening couples the activation of polymerization and crosslinking
        and is essential in vivo."'
  - subject: roda_pbp2_complex
    predicate: mediates
    object: sidewall_pg_insertion
    description: Activated RodA-PBP2 elongasome synthesizes and inserts new PG at
      lateral wall sites.
    evidence:
    - reference: DOI:10.1073/pnas.2215237120
      notes: '"The elongasome... synthesizing and inserting new PG material at dispersed
        sites in the lateral cell wall."'
  - subject: sidewall_pg_insertion
    predicate: contributes to
    object: rod_complex_pg
    description: Lateral sidewall PG insertion is the Rod-complex-driven wall-elongation
      process that sets rod radius.
    evidence:
    - reference: DOI:10.1146/annurev-cellbio-101011-155745
      notes: Lateral PG insertion is the MreB/Rod-complex activity governing rod radius.
    predicate_id: RO:0002326
  - subject: mreb_filaments
    predicate: orients
    object: circumferential_pg_insertion
    description: MreB filaments orient peptidoglycan insertion perpendicular to the
      long cell axis, controlling rod radius.
    evidence:
    - reference: DOI:10.1073/pnas.2301987120
      notes: '"MreB filaments are thought to orient it orthogonally to the long cell
        axis" guiding PG insertion perpendicular to the long axis.'
  - subject: rod_complex_rotation
    predicate: enables
    object: even_pg_distribution
    description: Rotation of the Rod complex around the circumference enables evenly
      distributed PG insertion.
    evidence:
    - reference: DOI:10.1002/mbo3.1385
      notes: '"the Rod complex rotates perpendicularly to the long axis of the cell...
        allowing the insertion of peptidoglycan... in an evenly distributed manner."'
    predicate_id: RO:0002327
  - subject: mrec_mred_balance
    predicate: regulates
    object: pbp2_activity
    description: The balance between MreC and MreD determines PBP2 synthase activity.
    evidence:
    - reference: DOI:10.1002/mbo3.1385
      notes: '"the balance between MreC and MreD determines the activity of PBP2"'
    predicate_id: RO:0002211
  - subject: lipid_ii
    predicate: required for
    object: pg_polymerization_crosslinking
    description: Lipid II is the substrate required for peptidoglycan polymerization
      by Rod/elongasome synthases.
    evidence:
    - reference: DOI:10.3390/biom13050720
      notes: '"GTases and TPases utilize the disaccharide pentapeptide of Lipid-II
        as a substrate for PG polymerization and synthesis of the PG layer."'
curation_history:
- timestamp: '2026-05-05T01:35:46.922624+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-11T22:30:00-07:00'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph linking rich growth conditions and elevated
    Rod-complex activity to large cell width (>0.9 μm).
  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
    (METPO:2000202×1, rdfs:subClassOf×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 7 evidence-backed generic edges (11 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:0002326×1, RO:0002327×1, RO:0002211×1).
  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:27692×1).
  llm_assisted: true