identifier: METPO:1004003
label: plant pathogen
definition: A pathogen that infects organisms in the kingdom Viridiplantae.
definition_source: DOI:10.1146/annurev.phyto.43.040204.135923
trait_category: ECOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1004000
evidence:
- reference: DOI:10.1146/annurev.phyto.43.040204.135923
  snippet: type III secretion
  notes: Plant-pathology review supports type III secretion of effectors as the central
    mechanism by which bacterial plant pathogens manipulate plant cells.
- reference: DOI:10.1146/annurev.micro.55.1.535
  snippet: cell-wall-degrading enzymes
  notes: Plant-pathogen review supports secreted plant-cell-wall-degrading enzymes
    as essential virulence factors of bacterial phytopathogens.
canonical_examples:
- taxon_id: NCBITaxon:317
  taxon_label: Pseudomonas syringae
  note: "Model bacterial plant pathogen (Type III secretion, effector biology). Agrobacterium tumefaciens is the classic crown-gall/genetic-tool exemplar."
  reference: PMID:29479077
causal_graphs:
- graph_id: plant_pathogen_t3ss_effector_program
  title: Plant-pathogen T3SS-effector and wall-degradation program
  description: DOI-backed graph linking plant-cell-wall degradation, type III secretion
    of effectors, suppression of plant immunity, and plant tissue colonization to
    the plant-pathogen phenotype.
  nodes:
  - node_id: plant_pathogen_trait
    label: plant pathogen
    node_type: TRAIT
    grounding: METPO:1004003
    description: Pathogen of plant hosts.
  - node_id: cwd_enzymes
    label: plant-cell-wall-degrading enzymes
    node_type: GENE_OR_PROTEIN
    description: Secreted enzymes (e.g., pectinases, cellulases) degrading the plant
      cell wall.
  - node_id: t3ss
    label: type III secretion system
    node_type: GENE_OR_PROTEIN
    description: Bacterial T3SS delivering effector proteins into plant cells.
  - node_id: t3ss_effectors
    label: T3SS effector proteins
    node_type: GENE_OR_PROTEIN
    description: Bacterial effector proteins translocated into plant cells by the
      T3SS.
  - node_id: plant_immune_suppression
    label: plant immune suppression
    node_type: BIOLOGICAL_PROCESS
    description: Suppression of plant innate immunity by translocated effectors.
  - node_id: plant_tissue_colonization
    label: plant tissue colonization
    node_type: BIOLOGICAL_PROCESS
    description: Establishment of microbial growth in plant tissues.
    grounding: GO:0140649
  - node_id: plant_disease
    label: plant disease
    node_type: BIOLOGICAL_PROCESS
    description: Pathology produced in a plant host.
  - node_id: quorum_sensing
    label: quorum sensing
    node_type: BIOLOGICAL_PROCESS
    description: Cell-density-dependent signaling (e.g., AHL, DSF) coordinating group
      behaviors in bacterial pathogens.
    grounding: GO:0009372
  - node_id: biofilm_formation
    label: biofilm formation
    node_type: BIOLOGICAL_PROCESS
    description: Formation of structured surface-attached microbial communities.
    grounding: GO:0042710
  - node_id: eps_production
    label: exopolysaccharide production
    node_type: BIOLOGICAL_PROCESS
    description: Biosynthesis of extracellular polysaccharides forming the biofilm
      matrix.
  - node_id: plant_cell_wall
    label: plant cell wall
    node_type: CELLULAR_LOCALIZATION
    description: Plant-type cell wall, the structural barrier degraded during host
      invasion.
    grounding: GO:0009505
  - node_id: apoplastic_effector_secretion
    label: ER-Golgi apoplastic effector secretion
    node_type: BIOLOGICAL_PROCESS
    description: Conventional ER-Golgi secretory pathway delivering apoplastic effectors
      in fungal/oomycete pathogens.
  - node_id: apoplastic_effectors
    label: apoplastic effectors
    node_type: GENE_OR_PROTEIN
    description: Secreted pathogen effector proteins acting in the host apoplast.
  edges:
  - subject: cwd_enzymes
    predicate: enables
    object: plant_tissue_colonization
    description: Plant-cell-wall-degrading enzymes enable bacterial spread within
      plant tissues.
    evidence:
    - reference: DOI:10.1146/annurev.micro.55.1.535
      snippet: cell-wall-degrading enzymes
      notes: Supports CWD enzymes as virulence factors in plant infection.
    predicate_id: RO:0002327
  - subject: t3ss
    predicate: delivers
    object: t3ss_effectors
    description: The T3SS translocates effector proteins from the bacterium into plant
      cells.
    evidence:
    - reference: DOI:10.1146/annurev.phyto.43.040204.135923
      snippet: type III secretion system
      notes: Supports the T3SS as the delivery system for bacterial effectors into
        plant cells.
  - subject: t3ss_effectors
    predicate: suppresses
    object: plant_immune_suppression
    description: Translocated T3SS effectors suppress plant innate immunity.
    evidence:
    - reference: DOI:10.1146/annurev.phyto.43.040204.135923
      snippet: effector proteins
      notes: Supports T3SS-delivered effector proteins as the plant-immunity-suppressing
        factors.
    predicate_id: RO:0002212
  - subject: plant_immune_suppression
    predicate: enables
    object: plant_tissue_colonization
    description: Immune suppression supports sustained colonization of plant tissues.
    evidence:
    - reference: DOI:10.1146/annurev.phyto.43.040204.135923
      snippet: plant pathogen
      notes: Supports immune-suppression-driven colonization as a hallmark of plant-pathogen
        infection biology.
    predicate_id: RO:0002327
  - subject: plant_tissue_colonization
    predicate: causes
    object: plant_disease
    description: Established colonization of plant tissues causes plant disease.
    evidence:
    - reference: DOI:10.1146/annurev.micro.55.1.535
      snippet: cell-wall-degrading enzymes
      notes: Supports colonization-to-disease progression in plant pathogens.
    predicate_id: biolink:causes
  - subject: plant_disease
    predicate: manifests as
    object: plant_pathogen_trait
    description: Plant disease manifests the plant-pathogen trait.
    evidence:
    - reference: DOI:10.1146/annurev.phyto.43.040204.135923
      snippet: type III secretion
      notes: Supports the trait endpoint.
    predicate_id: METPO:2007400
  - subject: quorum_sensing
    predicate: positively regulates
    object: biofilm_formation
    description: Quorum sensing is required for cooperative biofilm formation in plant-pathogenic
      bacteria.
    evidence:
    - reference: DOI:10.3390/plants12112207
      notes: QS is required for cooperative biofilm formation and regulates toxins,
        enzymes, EPS, and virulence factors.
  - subject: quorum_sensing
    predicate: positively regulates
    object: eps_production
    description: Quorum sensing and c-di-GMP signaling positively regulate exopolysaccharide
      biosynthesis.
    evidence:
    - reference: DOI:10.3390/plants12112207
      notes: EPS such as amylovoran, levan, xanthan, stewartan, and cellulose are
        often regulated by intracellular c-di-GMP and QS.
  - subject: eps_production
    predicate: enables
    object: biofilm_formation
    description: Exopolysaccharide production builds the biofilm matrix enabling biofilm
      formation.
    evidence:
    - reference: DOI:10.3390/plants12112207
      notes: EPS form the matrix of cooperative biofilms in plant-pathogenic bacteria.
    predicate_id: RO:0002327
  - subject: cwd_enzymes
    predicate: degrades
    object: plant_cell_wall
    description: Secreted cell-wall-degrading enzymes degrade the plant cell wall.
    evidence:
    - reference: DOI:10.21608/mb.2024.307263.1134
      notes: Secretion of cell-wall-degrading enzymes (pectinase, chitinase, cellulase,
        protease) that enable invasion and colonization.
    predicate_id: METPO:2000007
  - subject: apoplastic_effector_secretion
    predicate: delivers
    object: apoplastic_effectors
    description: The conventional ER-Golgi secretory pathway delivers apoplastic effectors.
    evidence:
    - reference: DOI:10.1094/MPMI-12-23-0212-CR
      notes: Apoplastic effectors are secreted via the conventional endoplasmic reticulum
        (ER)-Golgi pathway.
  - subject: apoplastic_effectors
    predicate: suppresses
    object: plant_immune_suppression
    description: Secreted apoplastic effectors contribute to suppression of plant
      immunity during infection.
    evidence:
    - reference: DOI:10.1094/MPMI-12-23-0212-CR
      notes: Apoplastic effectors delivered to the host act to subvert plant defenses
        and permit infection.
    predicate_id: RO:0002212
curation_history:
- timestamp: '2026-05-05T01:35:46.949239+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-11T23:15:00-07:00'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph linking plant-cell-wall-degrading enzymes,
    T3SS effector delivery, immune suppression, plant tissue colonization, and disease
    to the plant-pathogen trait.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:29Z'
  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: '2026-05-20T05:49:23Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:causes×1).
  llm_assisted: true
- timestamp: '2026-05-23T21:30:06Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007400×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:13:18Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings:
    supports → enables ×1.'
  llm_assisted: true
- timestamp: '2026-05-24T04:13:20Z'
  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: '2026-06-13T21:03:25Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002212×1).
  llm_assisted: true
- timestamp: '2026-06-17T04:09:43Z'
  curator: claude
  action: REMOVE_REDUNDANT_SYNONYM
  changes: Removed 1 synonym(s) whose text duplicated the label (seeder redundancy;
    no information lost).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 6 evidence-backed generic edges (6 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:09Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×1, RO:0002212×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:29Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 4 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0140649×1, GO:0009372×1, GO:0042710×1, GO:0009505×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:36Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000007×1).
  llm_assisted: true