identifier: METPO:1000676
label: helical shaped
definition: A cell shape in which an organism has a corkscrew-like helical cell body
  with curvature and twist along its long axis.
definition_source: DOI:10.1016/j.cell.2010.03.046
trait_category: MORPHOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000666
synonyms:
- synonym_text: helical-shaped
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
created_by: Jed Dongjin Kim-Ozaeta
evidence:
- reference: DOI:10.1016/j.cell.2010.03.046
  snippet: coordinated action of multiple proteins relaxes peptidoglycan crosslinking
  notes: Supports a mechanistic basis for helical bacterial cell curvature and twist
    in Helicobacter pylori.
canonical_examples:
- taxon_id: NCBITaxon:210
  taxon_label: Helicobacter pylori
  note: "Textbook helical bacterium; helical shape aids gastric mucus colonisation."
  reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC6597387/
causal_graphs:
- graph_id: helical_shaped_pg_relaxation
  title: Helical-shape peptidoglycan relaxation mechanism
  description: Evidence-backed causal sketch linking helical cell shape to H. pylori
    shape proteins, peptidoglycan crosslink relaxation, and curvature plus twist.
  nodes:
  - node_id: helical_shaped_trait
    label: helical shaped
    node_type: TRAIT
    grounding: METPO:1000676
    description: Corkscrew-like bacterial morphology with curvature and twist.
  - node_id: csd_shape_proteins
    label: Csd shape proteins
    node_type: GENE_OR_PROTEIN
    description: H. pylori Csd1-Csd3 peptidoglycan endopeptidase homologs.
  - node_id: ccmA
    label: CcmA
    node_type: GENE_OR_PROTEIN
    description: Bactofilin-like protein implicated in H. pylori helical shape.
    grounding: UniProtKB:E0X6H3
  - node_id: peptidoglycan_crosslink_relaxation
    label: peptidoglycan crosslink relaxation
    node_type: BIOLOGICAL_PROCESS
    description: Local reduction or remodeling of peptidoglycan crosslinks.
  - node_id: helical_curvature_twist
    label: helical curvature and twist
    node_type: BIOLOGICAL_PROCESS
    description: Cell-wall geometry that produces a helical cell body.
  - node_id: pg_dl_carboxypeptidase_activity
    label: peptidoglycan DL-carboxypeptidase activity
    node_type: MOLECULAR_FUNCTION
    description: Enzymatic cleavage of monomeric tripeptides to dipeptides in the
      peptidoglycan stem.
  - node_id: pg_stem_peptide_trimming
    label: peptidoglycan stem peptide trimming
    node_type: BIOLOGICAL_PROCESS
    description: Conversion of monomeric tripeptides to dipeptides, altering peptidoglycan
      stem composition.
  - node_id: pg_modifying_enzyme_loss
    label: loss of peptidoglycan-modifying enzyme
    node_type: STATE
    description: Absence or inactivation of a peptidoglycan-remodeling enzyme required
      for helical shape.
  - node_id: rod_shaped_morphology
    label: rod-shaped morphology
    node_type: QUALITY
    description: Straight rod cell shape resulting from loss of helical curvature.
  - node_id: pg_crosslink_hydrolysis
    label: localized peptidoglycan crosslink hydrolysis
    node_type: BIOLOGICAL_PROCESS
    description: Localized hydrolysis/relaxation of peptidoglycan crosslinks generating
      helical geometry.
  edges:
  - subject: csd_shape_proteins
    predicate: promotes
    object: peptidoglycan_crosslink_relaxation
    description: Csd peptidoglycan endopeptidase homologs contribute to reduced crosslinking
      in helical-shape generation.
    evidence:
    - reference: DOI:10.1016/j.cell.2010.03.046
      snippet: three LytM peptidoglycan endopeptidase homologs
      notes: Supports Csd proteins as required genes in the H. pylori helical shape
        pathway.
    predicate_id: RO:0002213
  - subject: ccmA
    predicate: contributes to
    object: peptidoglycan_crosslink_relaxation
    description: CcmA contributes to the shape-generating pathway for helical morphology.
    evidence:
    - reference: DOI:10.1016/j.cell.2010.03.046
      snippet: three LytM peptidoglycan endopeptidase homologs ... and a ccmA homolog
      notes: Supports CcmA as one of the proteins required for helical shape.
    predicate_id: RO:0002326
  - subject: peptidoglycan_crosslink_relaxation
    predicate: enables
    object: helical_curvature_twist
    description: Relaxed peptidoglycan crosslinking enables curvature and twist.
    evidence:
    - reference: DOI:10.1016/j.cell.2010.03.046
      snippet: relaxes peptidoglycan crosslinking, enabling helical cell curvature
        and twist
      notes: Direct evidence for PG crosslink relaxation causing helical geometry.
    predicate_id: RO:0002327
  - subject: helical_curvature_twist
    predicate: produces
    object: helical_shaped_trait
    description: Helical curvature and twist produce the helical-shaped trait.
    evidence:
    - reference: DOI:10.1016/j.cell.2010.03.046
      snippet: helical cell curvature and twist
      notes: Supports the morphology endpoint of the graph.
    predicate_id: METPO:2000202
  - subject: pg_dl_carboxypeptidase_activity
    predicate: causes
    object: pg_stem_peptide_trimming
    description: DL-carboxypeptidase activity trims monomeric tripeptides to dipeptides
      in the peptidoglycan stem.
    evidence:
    - reference: DOI:10.1371/journal.ppat.1002602
      notes: Pgp1 is a novel peptidoglycan DL-carboxypeptidase cleaving monomeric
        tripeptides to dipeptides.
    predicate_id: biolink:causes
  - subject: pg_stem_peptide_trimming
    predicate: promotes
    object: helical_shaped_trait
    description: Peptidoglycan stem peptide trimming supports generation of the helical
      cell shape.
    evidence:
    - reference: DOI:10.1371/journal.ppat.1002602
      notes: Pgp1 DL-carboxypeptidase activity on peptidoglycan stem peptides is required
        for helical cell shape.
    predicate_id: RO:0002213
  - subject: pg_modifying_enzyme_loss
    predicate: causes
    object: rod_shaped_morphology
    description: Loss of a peptidoglycan-modifying enzyme produces a straight rod-shaped
      morphology.
    evidence:
    - reference: DOI:10.1371/journal.ppat.1002602
      notes: Deletion of pgp1 resulted in a striking, rod-shaped morphology.
    predicate_id: biolink:causes
  - subject: rod_shaped_morphology
    predicate: negatively regulates
    object: helical_shaped_trait
    description: Rod-shaped morphology represents loss of the helical-shaped trait.
    evidence:
    - reference: DOI:10.1371/journal.ppat.1002602
      notes: pgp1 deletion converts helical cells to rod-shaped cells, i.e., loss
        of helical shape.
  - subject: pg_crosslink_hydrolysis
    predicate: enables
    object: helical_curvature_twist
    description: Localized peptidoglycan crosslink hydrolysis generates the curvature
      and twist underlying helical shape.
    evidence:
    - reference: DOI:10.1016/j.cell.2010.03.046
      notes: Coordinated action of multiple proteins relaxes peptidoglycan crosslinking,
        enabling helical cell curvature and twist.
    predicate_id: RO:0002327
curation_history:
- timestamp: '2026-05-05T01:35:46.890639+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-11T18:00:00-07:00'
  curator: codex
  action: CURATED_WITH_LITERATURE
  changes: Reviewed helical shape and added DOI-backed causal graph for Csd proteins,
    CcmA, peptidoglycan crosslink relaxation, and helical curvature.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:31Z'
  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, METPO:2000202×1).
  llm_assisted: true
- timestamp: '2026-05-24T05:05:14Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:E0X6H3×1).
  llm_assisted: true
- timestamp: '2026-06-13T21:03:26Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002213×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (5 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:13Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:causes×2, RO:0002213×1, RO:0002327×1).
  llm_assisted: true