identifier: METPO:1000447
label: temperature optimum high
definition: A temperature optimum phenotype with the best-growth ambient temperature
  above approximately 40 °C, characteristic of thermophilic physiology.
definition_source: DOI:10.1016/s0300-9629(97)00003-0
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000304
synonyms:
- synonym_text: Thermophile
  synonym_type: EXACT_SYNONYM
  source: metpo.owl
- synonym_text: TO_>40
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1016/s0300-9629(97)00003-0
  snippet: adapted to environments of high temperature
  notes: Thermophile-adaptation review supports the >40 °C optimum as the thermophile
    category.
- reference: DOI:10.1128/MMBR.65.1.1-43.2001
  snippet: resistant to irreversible inactivation at high temperatures
  notes: Thermostable-protein review supports thermostable proteins as the mechanism
    enabling thermophile optima.
causal_graphs:
- graph_id: temperature_optimum_high_thermophile_setpoint
  title: Temperature-optimum-high thermophile setpoint
  description: DOI-backed graph linking thermophile membrane and protein thermostability
    adaptation to a temperature optimum above 40 °C.
  nodes:
  - node_id: temperature_optimum_high_trait
    label: temperature optimum high
    node_type: TRAIT
    grounding: METPO:1000447
    description: Temperature optimum above ~40 °C.
  - node_id: temperature_optimum
    label: temperature optimum
    node_type: TRAIT
    grounding: METPO:1000304
    description: Ambient temperature supporting maximal growth.
  - node_id: hot_environment
    label: hot environment
    node_type: ENVIRONMENTAL_FACTOR
    description: Habitat ambient temperature above ~40 °C, typical of hot springs
      and compost.
  - node_id: thermophile_thermostability
    label: thermophile protein thermostability
    node_type: BIOLOGICAL_PROCESS
    description: Heat-stable membrane lipids and proteins that retain function at
      elevated temperatures.
  - node_id: reverse_gyrase
    label: reverse gyrase
    node_type: GENE_OR_PROTEIN
    description: Thermophile topoisomerase that introduces positive supercoils into
      DNA.
    grounding: UniProtKB:A0A088E825
  - node_id: positive_dna_supercoiling
    label: positive DNA supercoiling
    node_type: BIOLOGICAL_PROCESS
    description: Positive supercoiling of DNA, a hallmark topological state in thermophiles.
  - node_id: dna_melting_high_temperature
    label: DNA melting at high temperature
    node_type: BIOLOGICAL_PROCESS
    description: Thermal denaturation (strand separation) of DNA at elevated temperature.
  - node_id: nucleoid_associated_proteins
    label: nucleoid-associated proteins
    node_type: GENE_OR_PROTEIN
    description: Proteins that organize the nucleoid and enhance DNA thermostability.
  - node_id: genome_thermostability
    label: genome thermostability
    node_type: QUALITY
    description: Resistance of the genome to heat-induced denaturation.
  - node_id: small_heat_shock_proteins
    label: small heat shock proteins
    node_type: GENE_OR_PROTEIN
    description: Chaperones that bind denaturing proteins to prevent aggregation under
      heat stress.
  - node_id: protein_aggregation_heat
    label: heat-induced protein aggregation
    node_type: BIOLOGICAL_PROCESS
    description: Aggregation of denatured proteins under elevated temperature.
  - node_id: thermosome
    label: thermosome (group II chaperonin)
    node_type: GENE_OR_PROTEIN
    description: Group II chaperonin that refolds denatured proteins in an ATP-dependent
      manner.
  - node_id: denatured_protein_refolding
    label: refolding of denatured proteins
    node_type: BIOLOGICAL_PROCESS
    description: ATP-dependent refolding of heat-denatured proteins.
  - node_id: membrane_lipid_composition
    label: altered membrane lipid composition
    node_type: BIOLOGICAL_PROCESS
    description: Remodeling of cytoplasmic membrane lipids in response to high temperature.
  - node_id: membrane_thermostability
    label: cytoplasmic membrane thermostability
    node_type: QUALITY
    description: Stabilization of the cytoplasmic membrane at high temperature.
  - node_id: aa_composition_thermostability
    label: hydrophobic and charged amino acid enrichment
    node_type: BIOLOGICAL_PROCESS
    description: Enrichment of hydrophobic and charged residues in thermophile proteins.
  edges:
  - subject: hot_environment
    predicate: selects for
    object: thermophile_thermostability
    description: Hot environments select for thermophile thermostable machinery.
    evidence:
    - reference: DOI:10.1016/s0300-9629(97)00003-0
      snippet: adapted to environments of high temperature
      notes: Supports hot environments as the context for thermophile optima.
    predicate_id: METPO:2007401
  - subject: thermophile_thermostability
    predicate: produces
    object: temperature_optimum_high_trait
    description: Thermophile thermostability yields a >40 °C optimum.
    evidence:
    - reference: DOI:10.1128/MMBR.65.1.1-43.2001
      snippet: resistant to irreversible inactivation at high temperatures
      notes: Supports thermostability as the mechanism producing thermophile optima.
    predicate_id: METPO:2000202
  - subject: temperature_optimum_high_trait
    predicate: is a
    object: temperature_optimum
    description: Temperature optimum high is a quantitative bin of the temperature-optimum
      phenotype.
    evidence:
    - reference: DOI:10.1016/s0300-9629(97)00003-0
      snippet: adapted to environments of high temperature
      notes: Supports the >40 °C optimum as a value within the temperature-optimum
        distribution.
    predicate_id: rdfs:subClassOf
  - subject: reverse_gyrase
    predicate: positively regulates
    object: positive_dna_supercoiling
    description: Reverse gyrase introduces positive supercoils into DNA, a thermophile
      hallmark.
    evidence:
    - reference: DOI:10.1264/jsme2.me23087
      notes: Reverse gyrase introduces positive supercoils into DNA and is a hallmark
        of many thermophiles.
  - subject: positive_dna_supercoiling
    predicate: reduces
    object: dna_melting_high_temperature
    description: Positive supercoiling limits DNA melting and prevents thermal denaturation.
    evidence:
    - reference: DOI:10.1264/jsme2.me23087
      notes: Reverse gyrase / positive supercoiling proposed to limit DNA melting
        and prevent thermal denaturation.
    predicate_id: METPO:2000017
  - subject: nucleoid_associated_proteins
    predicate: increases
    object: genome_thermostability
    description: Nucleoid-associated proteins enhance DNA/genome thermostability.
    evidence:
    - reference: DOI:10.1264/jsme2.me23087
      notes: NAPs affect 3D genome organization and enhance DNA thermostability; abundance
        correlates with growth temperature.
    predicate_id: RO:0002213
  - subject: small_heat_shock_proteins
    predicate: prevents
    object: protein_aggregation_heat
    description: Small heat shock proteins bind denaturing proteins to prevent heat-induced
      aggregation.
    evidence:
    - reference: DOI:10.1128/mbio.03593-22
      notes: Small HSPs bind denaturing proteins and protect them from aggregation
        under heat stress.
    predicate_id: RO:0002212
  - subject: thermosome
    predicate: refolds
    object: denatured_protein_refolding
    description: Thermosome refolds denatured proteins in an ATP-dependent manner.
    evidence:
    - reference: DOI:10.1128/mbio.03593-22
      notes: Thermosome refolds denatured proteins in an ATP-dependent manner.
  - subject: membrane_lipid_composition
    predicate: stabilizes
    object: membrane_thermostability
    description: Altered membrane lipid composition stabilizes the cytoplasmic membrane
      at high temperature.
    evidence:
    - reference: DOI:10.1128/mbio.03593-22
      notes: Heat shock leads to an altered lipid composition of the cytoplasmic membrane;
        unique membrane composition is a recognized thermophile adaptation.
  - subject: aa_composition_thermostability
    predicate: increases
    object: thermophile_thermostability
    description: Enrichment in hydrophobic and charged amino acids increases protein
      thermostability.
    evidence:
    - reference: DOI:10.1128/mbio.02174-23
      notes: Thermophiles show enrichment in hydrophobic and charged amino acids contributing
        to intrinsic protein thermostability.
    predicate_id: RO:0002213
curation_history:
- timestamp: '2026-05-05T01:35:46.822120+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-13T11:00:00-07:00'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added DOI-backed definition and causal graph linking thermophile thermostability
    to the temperature-optimum-high bin.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:30Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000202×1, rdfs:subClassOf×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: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 7 evidence-backed generic edges (12 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:11Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002213×2, METPO:2000017×1, RO:0002212×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:21:17Z'
  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