identifier: METPO:1000616
label: thermophilic
definition: A temperature preference in which growth is favored at elevated temperatures,
  typically ≥45 °C.
definition_source: DOI:10.1016/s0300-9629(97)00003-0
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000613
evidence:
- reference: DOI:10.1016/s0300-9629(97)00003-0
  snippet: adapted to environments of high temperature
  notes: Supports thermophilic growth as adaptation to elevated temperature.
- reference: PMID:24058645
  snippet: Geobacillus stearothermophilus is a gram-positive, thermophilic bacterium
  notes: 'Organism example: Geobacillus stearothermophilus is described as thermophilic.'
canonical_examples:
- taxon_id: NCBITaxon:274
  taxon_label: Thermus thermophilus
  note: "Model thermophile (~65-72 C); Taq relative and structural-biology workhorse."
  reference: DOI:10.1007/s00792-009-0226-6
causal_graphs:
- graph_id: thermophilic_heat_adaptation
  title: Thermophilic heat-adaptation mechanism
  description: Evidence-backed causal sketch linking thermophily to elevated temperature,
    membrane lipid adaptation, thermostable proteins, and energy transduction constraints.
  nodes:
  - node_id: thermophilic_trait
    label: thermophilic
    node_type: TRAIT
    grounding: METPO:1000616
    description: Growth is favored at elevated temperatures.
  - node_id: high_temperature
    label: high temperature
    node_type: ENVIRONMENTAL_FACTOR
    description: Elevated-temperature growth condition.
    grounding: PATO:0001305
  - node_id: membrane_lipid_composition
    label: membrane lipid composition
    node_type: CELLULAR_LOCALIZATION
    description: Membrane lipid features altered during high-temperature adaptation.
  - node_id: membrane_proton_permeability
    label: membrane proton permeability
    node_type: BIOLOGICAL_PROCESS
    description: Proton leakiness of the cytoplasmic membrane at elevated temperature.
  - node_id: thermostable_proteins
    label: thermostable proteins
    node_type: GENE_OR_PROTEIN
    description: Proteins with increased resistance to thermal denaturation.
  - node_id: energy_transducing_enzymes
    label: energy-transducing enzymes
    node_type: GENE_OR_PROTEIN
    description: Enzymes involved in membrane bioenergetics at elevated temperature.
  - node_id: reverse_gyrase
    label: reverse gyrase
    node_type: GENE_OR_PROTEIN
    description: ATP-dependent topoisomerase that introduces positive DNA supercoils,
      characteristic of thermophiles.
    grounding: UniProtKB:A0A088E825
  - node_id: positive_dna_supercoiling
    label: positive DNA supercoiling
    node_type: BIOLOGICAL_PROCESS
    description: Introduction of positive supercoils into genomic DNA.
  - node_id: dna_melting
    label: DNA melting
    node_type: BIOLOGICAL_PROCESS
    description: Thermal denaturation/strand separation of DNA at elevated temperature.
  - node_id: genome_integrity
    label: genome integrity maintenance
    node_type: BIOLOGICAL_PROCESS
    description: Maintenance of genome integrity including DNA repair under thermal
      stress.
  - node_id: group_ii_chaperonin
    label: group II chaperonin (thermosome)
    node_type: GENE_OR_PROTEIN
    description: HSP60-type group II chaperonin that refolds denatured proteins in
      an ATP-dependent manner.
  - node_id: denatured_proteins
    label: denatured proteins
    node_type: GENE_OR_PROTEIN
    description: Proteins unfolded or denatured during thermal stress.
  - node_id: cyclopentane_ring_number
    label: tetraether lipid cyclopentane ring number
    node_type: QUALITY
    description: Number of cyclopentane rings in archaeal tetraether membrane lipids.
  - node_id: membrane_rigidity
    label: membrane rigidity
    node_type: QUALITY
    description: Membrane condensation, packing tightness, and rigidity.
  edges:
  - subject: high_temperature
    predicate: selects for
    object: thermophilic_trait
    description: High-temperature environments select for thermophilic growth capacity.
    evidence:
    - reference: DOI:10.1016/s0300-9629(97)00003-0
      snippet: adapted to environments of high temperature
      notes: Review supports thermophile adaptation to high-temperature environments.
    predicate_id: METPO:2007401
  - subject: high_temperature
    predicate: increases
    object: membrane_proton_permeability
    description: Elevated temperature increases proton permeability of the cytoplasmic
      membrane.
    evidence:
    - reference: DOI:10.1016/s0300-9629(97)00003-0
      snippet: proton permeability ... increase with the temperature
      notes: Supports membrane proton permeability as a high-temperature growth constraint.
    predicate_id: RO:0002213
  - subject: membrane_lipid_composition
    predicate: limits
    object: membrane_proton_permeability
    description: Lipid composition changes can reduce high-temperature membrane leakiness.
    evidence:
    - reference: DOI:10.1016/s0300-9629(97)00003-0
      snippet: changing the lipid composition
      notes: Supports lipid composition as an adaptation to membrane permeability.
    predicate_id: RO:0002212
  - subject: thermostable_proteins
    predicate: enables
    object: thermophilic_trait
    description: Thermostable proteins retain function during elevated-temperature
      growth.
    evidence:
    - reference: DOI:10.1128/MMBR.65.1.1-43.2001
      snippet: resistant to irreversible inactivation at high temperatures
      notes: Supports thermostability as a high-temperature enzyme feature.
    predicate_id: RO:0002327
  - subject: energy_transducing_enzymes
    predicate: enables
    object: thermophilic_trait
    description: Adapted energy-transducing enzymes support growth at elevated temperature.
    evidence:
    - reference: DOI:10.1016/s0300-9629(97)00003-0
      snippet: energy transducing enzymes
      notes: Review cites higher turnover rates and coupling-ion changes in high-temperature
        adaptation.
    predicate_id: RO:0002327
  - subject: reverse_gyrase
    predicate: introduces
    object: positive_dna_supercoiling
    description: Reverse gyrase introduces positive supercoils into thermophile DNA.
    evidence:
    - reference: DOI:10.1264/jsme2.me23087
      notes: 'Takemata 2024: "reverse gyrase introduces positive supercoils" (broadly
        accepted in thermophile genomics).'
  - subject: positive_dna_supercoiling
    predicate: limits
    object: dna_melting
    description: Positive DNA supercoiling limits thermal DNA melting, protecting
      genome integrity.
    evidence:
    - reference: DOI:10.1264/jsme2.me23087
      notes: 'Takemata 2024: "maintain the genome integrity of thermophiles by limiting
        DNA melting"; mechanism generalized across thermophiles.'
    predicate_id: RO:0002212
  - subject: reverse_gyrase
    predicate: mediates
    object: genome_integrity
    description: Reverse gyrase mediates DNA repair and genome-integrity maintenance
      in thermophiles.
    evidence:
    - reference: DOI:10.1264/jsme2.me23087
      notes: 'Takemata 2024: "maintain the genome integrity of thermophiles by ...
        mediating DNA repair".'
  - subject: group_ii_chaperonin
    predicate: refolds
    object: denatured_proteins
    description: The group II chaperonin (thermosome) refolds denatured proteins in
      an ATP-dependent manner.
    evidence:
    - reference: DOI:10.1128/mbio.03593-22
      notes: 'Baes 2023: "thermosome, which refolds proteins in an ATP-dependent manner".'
  - subject: cyclopentane_ring_number
    predicate: increases
    object: membrane_rigidity
    description: Increased cyclopentane ring number in tetraether lipids increases
      membrane condensation and rigidity.
    evidence:
    - reference: DOI:10.3389/frbis.2023.1338019
      notes: 'Chong 2024: "cyclopentane ring cyclization ... increase membrane condensation,
        packing tightness, rigidity".'
    predicate_id: RO:0002213
curation_history:
- timestamp: '2026-05-05T01:35:46.858214+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-06T14:58:45-07:00'
  curator: codex
  action: CURATED_WITH_ORGANISM_EXAMPLE
  changes: Added Geobacillus stearothermophilus organism example with PMID-backed
    evidence.
  llm_assisted: true
- timestamp: '2026-05-11T00:00:00-07:00'
  curator: codex
  action: CURATED_WITH_LITERATURE
  changes: Added DOI-backed thermophily causal graph for membrane permeability, lipid
    adaptation, thermostable proteins, and energy transduction.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:30Z'
  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: '2026-05-23T21:30:06Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007401×1).
  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: '2026-05-24T04:13:21Z'
  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: '2026-06-13T21:03:26Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002213×1, RO:0002212×1).
  llm_assisted: true
- timestamp: '2026-06-14T05:51:45Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (PATO:0001305×1).
  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 5 evidence-backed generic edges (8 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:11Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002212×1, RO:0002213×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:18Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (UniProtKB:A0A088E825×1).
  llm_assisted: true