identifier: METPO:1000687
label: branched shaped
definition: A cell shape in which an organism forms lateral branches from filamentous
  or hyphal cells.
definition_source: DOI:10.1016/j.mib.2012.10.012
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000666
synonyms:
- synonym_text: branced
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
- synonym_text: branched
  synonym_type: RELATED_SYNONYM
  source: corrected-from-metpo.owl
evidence:
- reference: DOI:10.1016/j.mib.2012.10.012
  snippet: Streptomyces grow by tip extension and through the initiation of new branches
  notes: Supports branched morphology as a Streptomyces hyphal growth phenotype.
canonical_examples:
- taxon_id: NCBITaxon:1681
  taxon_label: Bifidobacterium bifidum
  note: "Y-shaped / branched (bifid) cell morphology; model gut commensal actinobacterium."
  reference: PMID:20805404
causal_graphs:
- graph_id: branched_shaped_streptomyces_branching
  title: Branched-shape Streptomyces branch-site mechanism
  description: Evidence-backed causal sketch linking branched morphology to DivIVA
    foci, branch-site selection, polarisome behavior, local peptidoglycan assembly,
    and lateral branch outgrowth.
  nodes:
  - node_id: branched_shaped_trait
    label: branched shaped
    node_type: TRAIT
    grounding: METPO:1000687
    description: Filamentous bacterial morphology with lateral branches.
  - node_id: divIVA_foci
    label: DivIVA foci
    node_type: GENE_OR_PROTEIN
    description: DivIVA assemblies marking future Streptomyces branch sites.
  - node_id: branch_site_selection
    label: branch-site selection
    node_type: BIOLOGICAL_PROCESS
    description: Selection of a new site for lateral branch outgrowth.
  - node_id: polarisome_behavior
    label: polarisome behavior
    node_type: BIOLOGICAL_PROCESS
    description: Dynamics of the polar growth machinery that controls branch growth.
  - node_id: local_cell_wall_assembly
    label: local cell-wall assembly
    node_type: BIOLOGICAL_PROCESS
    description: Peptidoglycan assembly at a new growth zone.
  - node_id: lateral_branch_outgrowth
    label: lateral branch outgrowth
    node_type: BIOLOGICAL_PROCESS
    description: Emergence and extension of a new hyphal branch.
  - node_id: polarisome_splitting
    label: DivIVA polarisome splitting
    node_type: BIOLOGICAL_PROCESS
    description: Splitting of polarisomes at growing tips generating daughter polarisomes.
  - node_id: divIVA_scy_filp_polarisome
    label: DivIVA/Scy/FilP polarisome
    node_type: GENE_OR_PROTEIN
    description: Apical polarisome complex of DivIVA with Scy and FilP.
  - node_id: pg_enzyme_localization
    label: localization of peptidoglycan synthases and hydrolases to the apex
    node_type: BIOLOGICAL_PROCESS
    description: Recruitment of cell-wall synthesis enzymes to the growing pole.
  - node_id: afsk_divIVA_phosphorylation
    label: AfsK-mediated DivIVA phosphorylation
    node_type: BIOLOGICAL_PROCESS
    description: AfsK kinase phosphorylation of DivIVA driving new polarisome formation.
  - node_id: multiple_polarisomes_hyperbranching
    label: multiple new polarisomes and hyperbranching
    node_type: STATE
    description: Formation of extra polarisomes producing a hyperbranching phenotype.
  - node_id: sppa_divIVA_dephosphorylation
    label: SppA dephosphorylation of DivIVA
    node_type: BIOLOGICAL_PROCESS
    description: SppA phosphatase reversal of DivIVA phosphorylation opposing hyperbranching.
  - node_id: cell_wall_stress
    label: cell-wall stress (bacitracin/vancomycin)
    node_type: ENVIRONMENTAL_FACTOR
    description: Antibiotic-induced cell-wall stress signaling.
  - node_id: stlp_membrane_microdomains
    label: StlP membrane microdomain formation
    node_type: BIOLOGICAL_PROCESS
    description: Stomatin-like protein StlP organizing membrane microdomains governing
      polar growth.
  - node_id: proper_polar_growth_branch_spacing
    label: proper polar growth and normal branch spacing
    node_type: STATE
    description: Regulated polar growth yielding normal tip-to-branch distance.
  edges:
  - subject: divIVA_foci
    predicate: marks
    object: branch_site_selection
    description: DivIVA foci mark sites where lateral branches will emerge.
    evidence:
    - reference: DOI:10.1371/journal.pgen.1002423
      snippet: mark sites of future branch outgrowth
      notes: Supports DivIVA foci as branch-site markers.
  - subject: branch_site_selection
    predicate: controls
    object: polarisome_behavior
    description: Branch-site selection controls where new polar growth machinery is
      established.
    evidence:
    - reference: DOI:10.1016/j.mib.2012.10.012
      snippet: principal mechanism of branch site selection
      notes: Supports branch-site selection as a regulated mechanism.
    predicate_id: RO:0002211
  - subject: polarisome_behavior
    predicate: directs
    object: local_cell_wall_assembly
    description: Polarisome behavior directs local wall assembly at the branch site.
    evidence:
    - reference: DOI:10.1016/j.mib.2012.10.012
      snippet: modulate polar growth and hyphal branching
      notes: Supports polarisome modulation of polar growth and branching.
    predicate_id: RO:0002211
  - subject: local_cell_wall_assembly
    predicate: regulates
    object: lateral_branch_outgrowth
    description: Local wall assembly drives emergence of the lateral branch.
    evidence:
    - reference: DOI:10.1016/j.mib.2012.10.012
      snippet: apical growth requires the localization of the machinery
      notes: Supports localized wall-building machinery as needed for apical branch
        outgrowth.
    predicate_id: RO:0002211
  - subject: lateral_branch_outgrowth
    predicate: manifests as
    object: branched_shaped_trait
    description: Lateral branch outgrowth manifests the branched-shape phenotype.
    evidence:
    - reference: DOI:10.1016/j.mib.2012.10.012
      snippet: initiation of new branches
      notes: Supports branched morphology as a Streptomyces growth phenotype.
    predicate_id: METPO:2007400
  - subject: polarisome_splitting
    predicate: causes
    object: lateral_branch_outgrowth
    description: Polarisome splitting at growing tips generates daughter polarisomes
      that coordinate new lateral branch emergence.
    evidence:
    - reference: DOI:10.1093/femsml/uqad020
      notes: Splitting of polarisomes at growing tips generates daughter polarisomes
        that coordinate emergence of new lateral branches upon reaching a critical
        size.
    predicate_id: biolink:causes
  - subject: divIVA_scy_filp_polarisome
    predicate: localizes
    object: pg_enzyme_localization
    description: The DivIVA/Scy/FilP polarisome localizes peptidoglycan synthases
      and hydrolases to the apex.
    evidence:
    - reference: DOI:10.1128/mbio.01492-24
      notes: The polarisome composed of DivIVA with Scy and FilP localizes cell-wall
        enzymes to one pole, linking polarity establishment to branching.
  - subject: afsk_divIVA_phosphorylation
    predicate: stimulates
    object: multiple_polarisomes_hyperbranching
    description: AfsK-mediated DivIVA phosphorylation disassembles the apical polarisome
      and stimulates multiple new polarisomes.
    evidence:
    - reference: DOI:10.1093/femsml/uqad020
      notes: Constitutive AfsK activity/high DivIVA phosphorylation disassembles the
        apical polarisome and stimulates multiple new polarisomes, producing a hyperbranching
        phenotype.
  - subject: sppa_divIVA_dephosphorylation
    predicate: opposes
    object: multiple_polarisomes_hyperbranching
    description: SppA dephosphorylation of DivIVA opposes AfsK-driven hyperbranching,
      defining a reversible branching-control circuit.
    evidence:
    - reference: DOI:10.1093/femsml/uqad020
      notes: AfsK phosphorylates DivIVA in response to bacitracin/vancomycin stress,
        while SppA dephosphorylates DivIVA, defining a reversible branching-control
        circuit.
  - subject: cell_wall_stress
    predicate: activates
    object: afsk_divIVA_phosphorylation
    description: Cell-wall stress activates AfsK-dependent DivIVA phosphorylation.
    evidence:
    - reference: DOI:10.1093/femsml/uqad020
      notes: AfsK phosphorylates DivIVA in response to cell-wall stress (e.g., bacitracin,
        vancomycin).
    predicate_id: RO:0002213
  - subject: stlp_membrane_microdomains
    predicate: enables
    object: proper_polar_growth_branch_spacing
    description: StlP membrane microdomain formation enables proper polar growth and
      normal branch spacing.
    evidence:
    - reference: DOI:10.1038/s41467-025-58093-x
      notes: Loss of StlP leads to branching of filaments; constitutive stlP expression
        notably reduces lateral branching and increases tip-to-branch distance.
    predicate_id: RO:0002327
curation_history:
- timestamp: '2026-05-05T01:35:46.896783+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-11T21:00:00-07:00'
  curator: codex
  action: CURATED_WITH_LITERATURE
  changes: Added DOI-backed definition and causal graph for DivIVA foci, branch-site
    selection, polarisome behavior, local cell-wall assembly, and lateral branch outgrowth.
  llm_assisted: true
- timestamp: '2026-05-23T21:30:07Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002211×2, METPO:2007400×1).
  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:
    drives → 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: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 6 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
    (biolink:causes×1, RO:0002213×1, RO:0002327×1).
  llm_assisted: true