identifier: METPO:1000615
label: mesophilic
definition: A temperature preference in which growth is favored at intermediate temperatures,
  typically ~20–45 °C.
definition_source: DOI:10.1016/j.bpj.2013.06.029
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000613
evidence:
- reference: DOI:10.1016/j.bpj.2013.06.029
  snippet: Escherichia coli, a mesophilic bacterium
  notes: 'Organism example: Escherichia coli is described as mesophilic.'
- reference: DOI:10.1146/annurev-micro-091313-103612
  snippet: more unsaturated fatty acids
  notes: Membrane-adaptation review supports homoviscous membrane composition matched
    to ambient temperature as the basis of mesophile physiology.
canonical_examples:
- taxon_id: NCBITaxon:562
  taxon_label: Escherichia coli
  note: "Canonical mesophile and universal model organism (optimum ~37 C)."
  reference: DOI:10.1021/acsomega.2c04786
causal_graphs:
- graph_id: mesophilic_homoviscous_adaptation
  title: Mesophilic homoviscous and enzymatic adaptation mechanism
  description: DOI-backed graph linking mesophily to moderate ambient temperature,
    homoviscous membrane lipid composition, mesophile enzyme repertoire, and balanced
    growth at intermediate temperatures.
  nodes:
  - node_id: mesophilic_trait
    label: mesophilic
    node_type: TRAIT
    grounding: METPO:1000615
    description: Growth is favored at intermediate temperatures (~20–45 °C).
  - node_id: moderate_temperature
    label: moderate ambient temperature
    node_type: ENVIRONMENTAL_FACTOR
    description: Ambient temperature in the ~20–45 °C mesophilic range.
  - node_id: membrane_fluidity
    label: membrane fluidity
    node_type: QUALITY
    description: Physical state of the cytoplasmic membrane supporting transport and
      bioenergetics.
    grounding: METPO:1007505
  - node_id: homoviscous_lipid_composition
    label: homoviscous lipid composition
    node_type: CELLULAR_LOCALIZATION
    description: Lipid composition tuned to maintain target membrane fluidity at mesophilic
      temperatures.
  - node_id: mesophile_enzyme_repertoire
    label: mesophile enzyme repertoire
    node_type: GENE_OR_PROTEIN
    description: Enzymes with peak activity in the mesophile temperature range.
  - node_id: balanced_growth
    label: balanced mesophilic growth
    node_type: BIOLOGICAL_PROCESS
    description: Sustained growth rate at intermediate temperatures.
  - node_id: temperature_decrease
    label: temperature decrease
    node_type: ENVIRONMENTAL_FACTOR
    description: A downshift in ambient temperature within the mesophilic regime.
  - node_id: unsaturated_fatty_acids
    label: unsaturated fatty acids
    node_type: CHEMICAL
    description: Membrane acyl chains with cis double bonds that increase membrane
      fluidity.
    grounding: CHEBI:27208
  - node_id: cold_shock
    label: cold shock
    node_type: ENVIRONMENTAL_FACTOR
    description: Abrupt temperature downshift triggering the cold-shock response.
  - node_id: cspa
    label: CspA cold-shock protein
    node_type: GENE_OR_PROTEIN
    description: Major cold-shock RNA chaperone preventing inhibitory RNA secondary
      structure.
  - node_id: translation
    label: translation
    node_type: BIOLOGICAL_PROCESS
    description: Protein synthesis from mRNA, maintained during cold shock.
    grounding: GO:0006412
  - node_id: heat_shock
    label: heat shock
    node_type: ENVIRONMENTAL_FACTOR
    description: Temperature upshift triggering the heat-shock response.
  - node_id: rpoh_sigma32
    label: sigma-32 (RpoH)
    node_type: GENE_OR_PROTEIN
    description: Alternative sigma factor controlling the bacterial heat-shock regulon.
  - node_id: heat_shock_genes
    label: heat shock genes
    node_type: GENE_OR_PROTEIN
    description: Genes (e.g. chaperones, proteases) induced to mitigate heat stress.
  - node_id: dnak
    label: DnaK chaperone
    node_type: GENE_OR_PROTEIN
    description: Hsp70 chaperone that sequesters sigma-32, negatively regulating its
      activity.
  edges:
  - subject: moderate_temperature
    predicate: selects for
    object: mesophilic_trait
    description: Moderate ambient temperatures select for mesophilic physiology.
    evidence:
    - reference: DOI:10.1016/j.bpj.2013.06.029
      snippet: Escherichia coli, a mesophilic bacterium
      notes: Supports a representative mesophile thriving at moderate temperatures.
    predicate_id: METPO:2007401
  - subject: homoviscous_lipid_composition
    predicate: regulates
    object: membrane_fluidity
    description: Homoviscous lipid composition maintains target membrane fluidity
      at mesophilic temperatures.
    evidence:
    - reference: DOI:10.1146/annurev-micro-091313-103612
      snippet: more unsaturated fatty acids
      notes: Supports homoviscous adaptation as the mechanism setting membrane fluidity.
    predicate_id: RO:0002211
  - subject: mesophile_enzyme_repertoire
    predicate: enables
    object: balanced_growth
    description: Mesophile enzyme repertoire enables balanced growth at intermediate
      temperatures.
    evidence:
    - reference: DOI:10.1016/s0300-9629(97)00003-0
      snippet: energy transducing enzymes
      notes: Supports temperature-tuned enzyme repertoires as the basis of adapted
        growth.
    predicate_id: RO:0002327
  - subject: balanced_growth
    predicate: manifests as
    object: mesophilic_trait
    description: Balanced growth at moderate temperatures manifests the mesophilic
      trait.
    evidence:
    - reference: DOI:10.1016/j.bpj.2013.06.029
      snippet: Escherichia coli, a mesophilic bacterium
      notes: Supports the trait endpoint in a representative organism.
    predicate_id: METPO:2007400
  - subject: temperature_decrease
    predicate: increases
    object: unsaturated_fatty_acids
    description: Temperature downshift increases membrane unsaturated fatty acid content
      (homeoviscous adaptation).
    evidence:
    - reference: DOI:10.1007/s42770-023-01057-4
      notes: Low-temperature adaptation includes increased unsaturation of membrane
        acyl chains; broad bacterial homeoviscous adaptation.
    predicate_id: RO:0002213
  - subject: cold_shock
    predicate: induces
    object: cspa
    description: Cold shock induces the cold-shock protein CspA.
    evidence:
    - reference: DOI:10.1007/s12275-023-00031-x
      notes: Cold shock responses include induction of Csp proteins, notably CspA
        (~15% of protein synthesis after cold shock).
  - subject: cspa
    predicate: promotes
    object: translation
    description: CspA acts as an RNA chaperone preventing RNA secondary structure,
      promoting translation during cold shock.
    evidence:
    - reference: DOI:10.1007/s12275-023-00031-x
      notes: CspA binds/unwinds RNA to promote single-strandedness and translation
        during cold shock.
    predicate_id: RO:0002213
  - subject: heat_shock
    predicate: induces
    object: rpoh_sigma32
    description: Heat shock induces synthesis of sigma-32 (RpoH).
    evidence:
    - reference: DOI:10.1007/s12275-023-00031-x
      notes: Heat-induced synthesis of sigma-32 (rpoH); canonical bacterial heat-shock
        regulation relevant to mesophiles near the upper temperature range.
  - subject: rpoh_sigma32
    predicate: activates expression of
    object: heat_shock_genes
    description: Sigma-32 (RpoH) activates expression of heat-shock genes.
    evidence:
    - reference: DOI:10.1007/s12275-023-00031-x
      notes: Heat shock regulation centers on sigma factor RpoH (sigma-32) directing
        heat-shock gene expression.
  - subject: dnak
    predicate: negatively regulates
    object: rpoh_sigma32
    description: DnaK chaperone sequesters sigma-32, negatively regulating its activity.
    evidence:
    - reference: DOI:10.1007/s12275-023-00031-x
      notes: RpoH is controlled by DnaK chaperone sequestration; canonical negative
        regulation in Gram-negative bacteria.
curation_history:
- timestamp: '2026-05-05T01:35:46.857659+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 Escherichia coli organism example with PMID-backed evidence.
  llm_assisted: true
- timestamp: '2026-05-13T11:30:00-07:00'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added DOI-backed causal graph linking moderate ambient temperature, homoviscous
    membrane composition, mesophile enzyme repertoire, and balanced growth to the
    mesophilic trait.
  llm_assisted: true
- timestamp: '2026-05-13T22:45:00-07:00'
  curator: codex
  action: IMPROVED_CAUSAL_GRAPH_EVIDENCE
  changes: Replaced Escherichia coli mesophile PMID fallback with the article DOI
    in definition, record evidence, and CausalEdge evidence.
  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: '2026-05-23T21:30:06Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2007401×1, 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:
    maintains → regulates ×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:0002211×1).
  llm_assisted: true
- timestamp: '2026-05-24T04:41:03Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (METPO:1007505×1).
  llm_assisted: true
- timestamp: '2026-05-26T02:30:12Z'
  curator: claude
  action: RETYPE_CAUSAL_NODES
  changes: 'Re-typed 1 causal-node node_type field(s) to align with CausalNodeTypeEnum
    semantics: membrane fluidity: BIOLOGICAL_PROCESS → QUALITY ×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 (9 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:10Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002213×2).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:30Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:27208×1, GO:0006412×1).
  llm_assisted: true