identifier: METPO:1000885
label: cell length medium
definition: A cell-length phenotype in which the longer cell dimension lies approximately
  between 2 and 3 micrometers.
definition_source: DOI:10.1126/science.aaa1313
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000881
synonyms:
- synonym_text: L_2_3
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1126/science.aaa1313
  snippet: cell size scales with growth rate
  notes: Growth-rate-dependent size law supports medium cell length as a typical outcome
    at moderate growth rates.
causal_graphs:
- graph_id: cell_length_medium_growth_rate
  title: Medium cell-length under moderate growth
  description: DOI-backed graph linking moderate elongation rate and the growth-rate
    size law to a medium cell-length range (2–3 μm).
  nodes:
  - node_id: cell_length_medium_trait
    label: cell length medium
    node_type: TRAIT
    grounding: METPO:1000885
    description: Cell length approximately 2–3 μm.
  - node_id: cell_length_trait
    label: cell length
    node_type: TRAIT
    grounding: METPO:1000881
    description: Regulated longer cellular dimension.
  - node_id: moderate_growth_rate
    label: moderate growth rate
    node_type: BIOLOGICAL_PROCESS
    description: Moderate exponential growth rate typical of common bacterial culture.
  - node_id: growth_rate_size_law
    label: growth-rate size law
    node_type: BIOLOGICAL_PROCESS
    description: Empirical scaling of average cell size with growth rate.
  - node_id: rod_complex
    label: Rod complex (elongasome)
    node_type: PATHWAY
    description: Elongasome machinery (MreB/MreC/MreD/RodA/PBP2) directing lateral
      peptidoglycan synthesis.
  - node_id: rodA_pbp2_complex
    label: RodA-PBP2 complex
    node_type: GENE_OR_PROTEIN
    description: SEDS glycosyltransferase RodA paired with transpeptidase PBP2, the
      core PG-synthesizing pair of the elongasome.
  - node_id: pg_insertion_elongation
    label: peptidoglycan insertion during elongation
    node_type: BIOLOGICAL_PROCESS
    description: Insertion of new peptidoglycan along the cell cylinder driving elongation.
  - node_id: mreC_mreD_balance
    label: MreC/MreD balance
    node_type: GENE_OR_PROTEIN
    description: Relative levels of MreC and MreD that tune elongasome transpeptidase
      activity.
  - node_id: pbp2_activity
    label: PBP2 transpeptidase activity
    node_type: MOLECULAR_FUNCTION
    description: Essential elongation transpeptidase activity of penicillin-binding
      protein 2.
  - node_id: pg_density
    label: peptidoglycan density / mechanical strength
    node_type: QUALITY
    description: Density and mechanical integrity of the peptidoglycan sacculus.
  - node_id: rod_shape
    label: rod shape
    node_type: TRAIT
    description: Elongated cylindrical (rod) cell morphology.
  - node_id: membrane_synthesis
    label: membrane synthesis
    node_type: BIOLOGICAL_PROCESS
    description: Synthesis of membrane lipids (fatty acid/phospholipid synthesis).
  - node_id: envelope_balance_state
    label: PG-membrane envelope balance
    node_type: STATE
    description: Balanced synthesis of peptidoglycan cell wall and cell membrane required
      for normal growth and shape.
  edges:
  - subject: moderate_growth_rate
    predicate: feeds into
    object: growth_rate_size_law
    description: Moderate exponential growth rates engage the growth-rate size law.
    evidence:
    - reference: DOI:10.1126/science.aaa1313
      snippet: cell size scales with growth rate
      notes: Supports growth rate as the input to the size-scaling relationship.
  - subject: growth_rate_size_law
    predicate: produces
    object: cell_length_medium_trait
    description: At moderate growth rates the size law produces medium cell length.
    evidence:
    - reference: DOI:10.1126/science.aaa1313
      snippet: cell size scales with growth rate
      notes: Supports medium length as the expected size at moderate growth rates.
    predicate_id: METPO:2000202
  - subject: cell_length_medium_trait
    predicate: is a
    object: cell_length_trait
    description: Medium cell length is a quantitative bin of the cell-length phenotype.
    evidence:
    - reference: DOI:10.1016/j.cub.2014.07.022
      snippet: cell size is tightly controlled
      notes: Supports medium length as a value within the regulated cell-length distribution.
    predicate_id: rdfs:subClassOf
  - subject: rodA_pbp2_complex
    predicate: enables
    object: pg_insertion_elongation
    description: RodA glycosyltransferase and PBP2 transpeptidase together enable
      peptidoglycan insertion that drives elongation.
    evidence:
    - reference: DOI:10.1002/mbo3.1385
      notes: RodA is a glycosyltransferase and PBP2 a transpeptidase required for
        cell elongation; Rod-complex rotation supports even PG insertion along the
        cylinder (broadly curatable general rod-bacterium mechanism).
    predicate_id: RO:0002327
  - subject: mreC_mreD_balance
    predicate: modulates
    object: pbp2_activity
    description: The balance between MreC and MreD modulates PBP2, the essential elongation
      transpeptidase.
    evidence:
    - reference: DOI:10.1002/mbo3.1385
      notes: '"the balance between MreC and MreD modulates PBP2 activity" - mechanistic
        edge for elongation control.'
    predicate_id: RO:0002211
  - subject: rod_complex
    predicate: increases
    object: pg_density
    description: An intact Rod complex builds dense peptidoglycan; loss yields PG
      with large holes and reduced mechanical strength.
    evidence:
    - reference: DOI:10.1002/mbo3.1385
      notes: '"The Rod complex may be a determinant not only for the whole shape of
        peptidoglycan but also for its highly dense structure."'
    predicate_id: RO:0002213
  - subject: pg_density
    predicate: maintains
    object: rod_shape
    description: Dense peptidoglycan produced by the elongation machinery maintains
      rod shape, the morphology context for medium cell length.
    evidence:
    - reference: DOI:10.1002/mbo3.1385
      notes: '"PG determines bacterial cell shape" - elongation machinery and dense
        PG determine whole-cell rod shape.'
  - subject: membrane_synthesis
    predicate: balances with PG synthesis to maintain
    object: envelope_balance_state
    description: Balanced membrane and peptidoglycan synthesis is critical; reducing
      membrane synthesis restores balance when PG capacity is limited.
    evidence:
    - reference: DOI:10.1128/mbio.00475-23
      notes: '"Balanced synthesis of the peptidoglycan cell wall and the cell membrane
        is critical" - broader envelope-balance mechanism affecting elongation and
        shape.'
curation_history:
- timestamp: '2026-05-05T01:35:46.920338+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 moderate growth rate and the growth-rate
    size law to medium cell length (2–3 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 5 evidence-backed generic edges (9 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:0002327×1, RO:0002211×1, RO:0002213×1).
  llm_assisted: true