identifier: METPO:1000681
label: rod shaped
definition: A cell shape in which an organism has an elongated, cylindrical morphology
  with relatively straight sides and rounded or flat 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: S_rod
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: rod-shaped
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
created_by: Luke Wang
evidence:
- reference: DOI:10.1146/annurev-cellbio-010521-010834
  snippet: bacterial rod shape formation
  notes: Supports rod shape as an actively regulated bacterial morphogenesis phenotype.
- reference: PMID:7575501
  snippet: why E. coli is rod-shaped
  notes: 'Organism example: Escherichia coli is described as rod-shaped.'
canonical_examples:
- taxon_id: NCBITaxon:562
  taxon_label: Escherichia coli
  note: "Textbook rod (bacillus); the universal Gram-negative model bacterium."
  reference: PMID:21501250
causal_graphs:
- graph_id: rod_shaped_mreB_peptidoglycan
  title: Rod-shape MreB and peptidoglycan mechanism
  description: Evidence-backed causal sketch linking rod shape to MreB-guided peptidoglycan
    synthesis, Rod complex activity, cell-wall elongation, and FtsZ division coupling.
  nodes:
  - node_id: rod_shaped_trait
    label: rod shaped
    node_type: TRAIT
    grounding: METPO:1000681
    description: Elongated cylindrical 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: Cell-wall elongation machinery associated with MreB in rod-shaped
      bacteria.
  - node_id: peptidoglycan_synthesis
    label: peptidoglycan synthesis
    node_type: BIOLOGICAL_PROCESS
    description: Cell-wall synthesis and remodeling process.
    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: rodA_pbp2_complex
    label: RodA-PBP2 complex
    node_type: GENE_OR_PROTEIN
    description: Elongation synthase complex (RodA glycosyltransferase + PBP2 transpeptidase)
      of the Rod system.
  - node_id: pbp2_structural_opening
    label: PBP2 structural opening
    node_type: MOLECULAR_FUNCTION
    description: Open/active conformational state of PBP2 that allosterically activates
      the elongation synthase.
  - node_id: rodA_polymerization
    label: RodA polymerization activity
    node_type: MOLECULAR_FUNCTION
    description: Glycan-strand polymerizing (glycosyltransferase) activity of RodA.
  - node_id: pg_crosslinking
    label: peptidoglycan crosslinking
    node_type: BIOLOGICAL_PROCESS
    description: Transpeptidation crosslinking of peptidoglycan strands during sidewall
      synthesis.
  - node_id: mreC
    label: MreC
    node_type: GENE_OR_PROTEIN
    description: Periplasmic Rod-system component that activates PBP2 by promoting
      its open conformation.
    grounding: UniProtKB:A0A1L9R356
  - node_id: elongasome_processivity
    label: elongasome processivity
    node_type: BIOLOGICAL_PROCESS
    description: Processive circumferential movement of MreB-associated elongasomes
      during sidewall synthesis.
  - node_id: sidewall_reinforcement
    label: rod-shaped sidewall reinforcement
    node_type: BIOLOGICAL_PROCESS
    description: Mechanical reinforcement of the cylindrical sidewall via long circumferential
      glycan hoops.
  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 elongates rod-shaped cells.
    evidence:
    - reference: DOI:10.1038/nrmicro2677
      snippet: elongation mode of peptidoglycan synthesis
      notes: Supports peptidoglycan synthesis in cell elongation.
    predicate_id: METPO:2000202
  - subject: lateral_cell_wall_elongation
    predicate: regulates
    object: rod_shaped_trait
    description: Lateral wall elongation preserves the cylindrical 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 morphology.
    evidence:
    - reference: DOI:10.1038/nrmicro1205
      snippet: FtsZ collaborates with penicillin binding proteins
      notes: Supports FtsZ-PBP collaboration in bacterial cell-shape generation.
  - subject: rodA_pbp2_complex
    predicate: positively regulates
    object: rod_shaped_trait
    description: The active elongation synthase complex supports proper rod-shaped
      morphology during growth.
    evidence:
    - reference: DOI:10.1038/s41467-023-39037-9
      notes: Structural opening couples RodA glycan polymerization and PBP2 crosslinking,
        a coupling essential in vivo for rod-shaped growth.
  - subject: pbp2_structural_opening
    predicate: activates
    object: rodA_polymerization
    description: Conformational opening of PBP2 allosterically stimulates RodA polymerization.
    evidence:
    - reference: DOI:10.1038/s41467-023-39037-9
      notes: Structural opening promotes RodA polymerization activity.
    predicate_id: RO:0002213
  - subject: pbp2_structural_opening
    predicate: enables
    object: pg_crosslinking
    description: The open state elevates the PBP2 TP domain toward the PG layer, enabling
      crosslinking.
    evidence:
    - reference: DOI:10.1038/s41467-023-39037-9
      notes: Opening of PBP2 elevates the TP domain, facilitating crosslinking.
    predicate_id: RO:0002327
  - subject: mreC
    predicate: activates
    object: rodA_pbp2_complex
    description: MreC binds the PBP2 pedestal domain and biases RodA-PBP2 into the
      open, catalytically active conformation.
    evidence:
    - reference: DOI:10.1038/s41467-023-39037-9
      notes: MreC is implicated as an activator that promotes the open, catalytically
        active conformation of PBP2.
    predicate_id: RO:0002213
  - subject: rodA_polymerization
    predicate: regulates
    object: elongasome_processivity
    description: RodA abundance/activity tunes processive dynamics of MreB-associated
      elongasomes.
    evidence:
    - reference: DOI:10.1038/s41467-024-49785-x
      notes: RodA abundance regulates elongasome processivity, reversal frequency,
        and pausing.
    predicate_id: RO:0002211
  - subject: elongasome_processivity
    predicate: contributes to
    object: sidewall_reinforcement
    description: Processive circumferential synthesis lays long glycan hoops that
      mechanically reinforce the cylinder.
    evidence:
    - reference: DOI:10.1038/s41467-024-49785-x
      notes: Long glycan strands act as barrel-hoop-like reinforcing structures of
        the rod sidewall.
    predicate_id: RO:0002326
curation_history:
- timestamp: '2026-05-05T01:35:46.893421+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-06T14:40:41-07:00'
  curator: codex
  action: CURATED_WITH_ORGANISM_EXAMPLE
  changes: Added Escherichia coli organism example with PMID-backed evidence.
  llm_assisted: true
- timestamp: '2026-05-11T00:00:00-07:00'
  curator: codex
  action: CURATED_WITH_LITERATURE
  changes: Replaced PMID definition source with DOI-backed rod-shape source and added
    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: '2026-05-24T04:13:22Z'
  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: '2026-05-24T04:38:01Z'
  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: '2026-05-24T05:05:15Z'
  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: '2026-05-26T05:00:51Z'
  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 6 evidence-backed generic edges (7 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:14Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002213×2, RO:0002327×1, RO:0002211×1, RO:0002326×1).
  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:A0A1L9R356×1).
  llm_assisted: true