identifier: traitmech:000079
label: oxidative stress response
definition: A stress response that defends the cell against reactive oxygen species
  (e.g. superoxide and hydrogen peroxide) through detoxifying enzymes, regulators,
  and damage-repair systems.
definition_source: DOI:10.1038/nrmicro3032
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- traitmech:000078
evidence:
- reference: DOI:10.1038/nrmicro3032
  notes: Imlay reviews the molecular mechanisms and physiological consequences of
    oxidative stress and the cellular defenses against reactive oxygen species.
- reference: DOI:10.1007/s00018-003-3206-5
  notes: Chelikani, Fita & Loewen support catalases as core enzymes of the oxidative-stress
    defense.
canonical_examples:
- taxon_id: NCBITaxon:562
  taxon_label: Escherichia coli
  note: "Paradigm of the bacterial oxidative-stress response (OxyR and SoxRS regulons)."
  reference: PMID:22381957
causal_graphs:
- graph_id: oxidative_stress_response_ros_defense
  title: Defense against reactive oxygen species
  description: Evidence-backed causal sketch linking reactive oxygen species to an
    induced oxidative-stress defense.
  nodes:
  - node_id: oxidative_stress_response_trait
    label: oxidative stress response
    node_type: TRAIT
    grounding: traitmech:000079
    description: Capacity to defend against reactive oxygen species.
  - node_id: hydrogen_peroxide
    label: hydrogen peroxide
    node_type: CHEMICAL
    grounding: CHEBI:16240
    description: Representative reactive oxygen species.
  - node_id: oxidative_stress_process
    label: response to oxidative stress
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0006979
    description: Defense response to reactive oxygen species.
  - node_id: oxyr_regulator
    label: OxyR transcriptional regulator
    node_type: GENE_OR_PROTEIN
    description: Widely conserved bacterial transcription factor that activates oxidative-stress
      defense genes.
  - node_id: rpos_sigma_factor
    label: RpoS (sigma-S) general stress sigma factor
    node_type: GENE_OR_PROTEIN
    description: Global stress sigma factor controlling a stress regulon that includes
      oxidative-stress defenses.
  - node_id: thioredoxin_system
    label: thioredoxin system
    node_type: PATHWAY
    description: Thiol-disulfide redox repair system supporting survival under oxidative/oxidant
      stress.
  edges:
  - subject: hydrogen_peroxide
    predicate: causes
    object: oxidative_stress_process
    description: Reactive oxygen species trigger the oxidative-stress response.
    evidence:
    - reference: DOI:10.1038/nrmicro3032
      notes: Imlay reviews ROS damage and induced defenses.
    predicate_id: biolink:causes
  - subject: oxidative_stress_process
    predicate: enables
    object: oxidative_stress_response_trait
    description: The induced defense realizes the oxidative-stress-response trait.
    evidence:
    - reference: DOI:10.1007/s00018-003-3206-5
      notes: Chelikani et al. support catalases as core oxidative-stress enzymes.
    predicate_id: RO:0002327
  - subject: oxyr_regulator
    predicate: positively regulates
    object: oxidative_stress_process
    description: OxyR activates transcription of genes that defend the cell against
      oxidative stress.
    evidence:
    - reference: DOI:10.1099/mic.0.001481
      notes: OxyR is widely conserved in bacteria and activates transcription of a
        set of genes that influence cellular defence against oxidative stress.
  - subject: rpos_sigma_factor
    predicate: positively regulates
    object: oxidative_stress_process
    description: The general stress sigma factor RpoS controls oxidative-stress defense
      outputs; its loss increases sensitivity to oxidative stress.
    evidence:
    - reference: DOI:10.1128/mmbr.00151-22
      notes: Cells devoid of RpoS are sensitive to oxidative stress; the RpoS regulon
        includes oxidative-stress genes (dps, catalases, sodA, osmC).
  - subject: thioredoxin_system
    predicate: contributes to
    object: oxidative_stress_process
    description: Thioredoxin thiol-repair systems support survival under oxidative/oxidant
      stress, including in anaerobes and spores.
    evidence:
    - reference: DOI:10.1371/journal.ppat.1012001
      notes: Multiple thioredoxin systems are involved in the response to oxidative
        stresses, broadening thiol-repair scope beyond classic aerobes.
    predicate_id: RO:0002326
curation_history:
- timestamp: '2026-06-04T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate PHYSIOLOGY trait (oxidative stress response); sub-variant
    of stress response.
  llm_assisted: true
- timestamp: '2026-06-08T13:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (ROS defense) with GO/CHEBI node groundings
    and biolink/RO predicate groundings; promoted PROPOSED to REVIEWED.
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 3 evidence-backed generic edges (3 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:15Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002326×1).
  llm_assisted: true