TraitMech

TraitMech › ENVIRONMENT

temperature optimum mid4

METPO:1000446 · CLASS · REVIEWED

A temperature optimum phenotype with the best-growth ambient temperature between approximately 34 and 40 °C, characteristic of warm-mesophilic physiology (including many mammalian host-associated bacteria).

Trait evidence (1)

Temperature-optimum-mid4 warm-mesophile setpoint

DOI-backed graph linking warm-mesophile membrane and enzyme adaptation to a temperature optimum between 34 and 40 °C.

NONMECHANISTIC · This record is a quantitative measurement, interval, or bin in the environmental phenotype hierarchy; a token protein example would misrepresent the measured value as one inherited molecular mechanism.

Temperature-optimum-mid4 warm-mesophile setpoint Interactive directed graph showing evidence-backed causal relationships for temperature optimum mid4.

Edge evidence

  • warm host-associated environment engages warm-mesophile adaptation

    Warm host-associated environments engage warm-mesophile adaptation.

  • warm-mesophile adaptation confers temperature optimum mid4 METPO:2007700

    Warm-mesophile adaptation yields a 34–40 °C optimum.

  • temperature optimum mid4 is a temperature optimum rdfs:subClassOf

    Temperature optimum mid4 is a quantitative bin of the temperature-optimum phenotype.

    • DOI:10.1016/s0300-9629(97)00003-0 adapted to environments of high temperature Supports the 34–40 °C optimum as a value within the temperature-optimum distribution.
  • temperature downshift increases unsaturated fatty acid proportion RO:0002213

    Temperature downshift increases the proportion of unsaturated fatty acids (homeoviscous adaptation).

  • unsaturated fatty acid proportion maintains membrane fluidity homeostasis

    Increased unsaturated fatty acids maintain membrane fluidity homeostasis.

  • membrane fluidity homeostasis induces unsaturated fatty acid biosynthesis response

    Sensed decreases in membrane fluidity induce the unsaturated fatty acid biosynthesis response.

  • RNA thermometer hairpin occludes Shine-Dalgarno / AUG ribosome binding site

    RNA thermometer hairpins occlude the Shine-Dalgarno/AUG region, repressing translation at low temperature.

  • temperature upshift / heat shock melts RNA thermometer hairpin

    Temperature upshift / heat shock melts RNA thermometer structures.

  • RNA thermometer hairpin enables ribosome binding and translation initiation RO:0002327

    Melting of the RNA thermometer exposes the ribosome binding site and enables translation initiation.

  • DnaK chaperone negatively regulates RpoH (sigma-32) heat-shock sigma factor RO:0002212

    DnaK binds and retains RpoH, negatively regulating the heat-shock sigma factor.

  • FtsH protease controls abundance of RpoH (sigma-32) heat-shock sigma factor

    FtsH protease controls RpoH protein levels.

Provenance

Identifier source
METPO (2026-06-12)
Definition source
DOI:10.1146/annurev-micro-091313-103612

Parent traits (1)

Synonyms (3)

  • Mesophilie EXACT_SYNONYM · metpo.owl
  • TO_34_to_40 RELATED_SYNONYM · metpo.owl
  • mesophilic EXACT_SYNONYM · https://w3id.org/metpo/releases/2026-06-12/metpo.owl

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000446 [-0.375, -2.796, -0.478, +0.320, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Deep research

Generated by just research-trait; source: research/traits/environment/temperature_optimum_mid4-deep-research-falcon.md

Unreviewed literature output — not curated TraitMech content Ontology identifiers suggested below have not been resolved against their ontologies, and some are known to be wrong. Check any CURIE against the source before using it. 
# Microbial Trait Causal Graph Curation Report:
**Temperature Optimum Mid4 (METPO:1000446)**

---

## 1. Trait Scope Summary

METPO:1000446 (temperature optimum mid4) denotes a **warm-mesophilic growth phenotype** with optimal growth temperature between approximately **34 and 40 °C** (engqvist2018correlatingenzymeannotations pages 1-2). This range captures many host-associated bacteria adapted to mammalian body temperatures, including the model organism *Escherichia coli* (Topt=37 °C) (blaby2012experimentalevolutionof pages 1-2). The trait represents the **assay-derived temperature yielding maximal exponential-phase growth rate** rather than maximum survival temperature or broad growth range (blaby2012experimentalevolutionof pages 1-2, murata2011molecularstrategyfor pages 1-2).

Literature boundaries between psychrophiles (<15 °C), mesophiles (15–50 °C), thermophiles (>50 °C), and intermediate categories remain inconsistent (engqvist2018correlatingenzymeannotations pages 1-2); METPO:1000446 should therefore be curated as an **assay-observable setpoint** rather than a categorical mesophily designation. A recent large-scale analysis of 21,498 microbes demonstrated a Pearson correlation of up to 0.89 between optimal growth temperature and mean enzyme optima, validating the physiological relevance of this trait (engqvist2018correlatingenzymeannotations pages 1-2).

---

## 2. Candidate Causal Graph Entities

### 2.1 Membrane and Lipid Entities
- **Membrane fluidity** (no CURIE; physiological property)
- **Phospholipid saturation ratio** (saturated/unsaturated)
- **Saturated fatty acids** (C16:0, C18:0 acyl-ACP)
- **Unsaturated fatty acids** (C16:1, C18:1 acyl-ACP)
- **FabI** (β-keto-acyl-ACP reductase; label-only or EC:1.3.1.10)
- **FabB** (β-keto-acyl-ACP synthase I; label-only or EC:2.3.1.179)
- **FabA** (β-hydroxydecanoyl-ACP dehydrase/isomerase; label-only or EC:4.2.1.59)
- **PlsB** (glycerol-3-phosphate acyltransferase; EC:2.3.1.15)
- **PlsC** (1-acylglycerol-3-phosphate acyltransferase; EC:2.3.1.51)

### 2.2 Chaperones and Protein Quality Control
- **DnaK** (chaperone Hsp70; label-only or UniProt:P0A6Y8 for *E. coli*)
- **DnaJ** (chaperone Hsp40 co-chaperone; label-only or UniProt:P08622 for *E. coli*)
- **GroEL** / **GroES** (chaperonins; label-only)
- **ClpXP**, **Lon**, **FtsH** (ATP-dependent proteases; label-only)

### 2.3 Heat-Shock Sigma Factors
- **RpoH** (σ32, heat-shock sigma factor; label-only)
- **RpoE** (σ24, envelope-stress sigma factor; label-only)

### 2.4 tRNA and Translation
- **tRNA modification enzymes** (e.g., tRNA-Gln, tRNA-His modifications; functional category)
- **Ribosomal proteins** (downregulated at critical high temperature; GO:0005840 for ribosome)
- **Translation** (GO:0006412)

### 2.5 Outer Membrane and Cell Envelope
- **Outer-membrane organization** (functional category)
- **Lipopolysaccharide biosynthesis** (early glycosyltransferases; label-only or GO:0009103)
- **DegP** (periplasmic protease; label-only)

### 2.6 Oxidative Stress and Energy
- **Oxidative stress resistance** (functional category; GO:0006979)
- **Catalase**, **superoxide dismutase** (label-only or EC:1.11.1.6, EC:1.15.1.1)
- **DNA double-strand break repair** (label-only or GO:0006302)
- **ATP homeostasis** (functional category)

### 2.7 Environmental and Experimental Factors
- **Ambient temperature** (ENVO:01000152 or similar; environmental factor)
- **Mammalian host environment** (37 °C; ENVO context)

---

## 3. Evidence-Backed Candidate Edges

Showing the first 60 of 267 lines of findings; the linked file also carries the run's front matter and the prompt it was given — read the full report.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

  • Escherichia coli K-12 NCBITaxon:83333 DOI:10.1128/AEM.05773-11 Wild-type E. coli K-12 in the thermal-evolution study had a 37 degrees C growth optimum before the glpF-associated shift, wholly inside the approximately 34-40-degree bin.

Curation history

  1. · SEEDED_FROM_METPO · seed_from_metpo

    imported from data/raw/metpo.owl (CLASS)

  2. · CURATED_CAUSAL_GRAPH · claude

    Added DOI-backed definition and causal graph linking warm-mesophile adaptation to the temperature-optimum-mid4 bin.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1, rdfs:subClassOf×1).

  4. · ENRICH_CAUSAL_GRAPH · claude

    Added 8 evidence-backed generic edges (11 new nodes) from the deep-research report.

  5. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002213×1, RO:0002327×1).

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A0D7UY21×1).

  7. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212×1).

  8. · MIGRATE_MICROBE_DOMAIN_EDGES · claude

    Re-grounded 1 causal edge(s) off microbe-domain METPO predicates (1 to confers), issue 301. The previous predicates are transitively rdfs:subPropertyOf METPO:2000001, whose rdfs:domain is METPO:1000525 (microbe), so a causal-graph subject entailed that the subject IS a microbe; CausalNodeTypeEnum has no organism member, so no such edge could ever satisfy the domain. Edge directions are unchanged - this pass only relabels and re-grounds. RO:0002234 (has output) is used where the subject is an activity, since biolink gives it the domain 'biological process or activity'; the METPO replacements are proposed in proposals/metpo_traitmech_v8 and v9 and are placeholder ids until METPO mints them.

  9. · REVIEW_UNIPROT_INSTANCE_GROUNDINGS · codex

    Reviewed 1 organism-specific UniProtKB grounding(s): replaced 1 with taxon-agnostic GO/InterPro terms and retracted 0 to label-only where no exact semantic term was supported (docs/GROUNDING_POLICY.md).

  10. · REVIEW_GRAPH_PROTEIN_TAXON · claude

    Backfilled provenance (review issue 517) for the codex protein-taxon review tranche of 2026-08-24/25, which shipped without a per-record event. In this record the tranche: set graph scope temperature_optimum_mid4_warm_mesophile=NONMECHANISTIC with scope_notes; marked 2 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (dnak_chaperone, rpoh_sigma_factor); retyped 2 node(s) (rna_thermometer->RNA, shine_dalgarno_sequence->GENETIC_ELEMENT).

  11. · ADD_EXACT_ONTOLOGY_MATCH · codex

    Ontology exact-match review (2026-08-25): declared exact synonym(s): 'mesophilic'. Evidence is predicate-scoped in the versioned ontology snapshots; OAK cross-checked direct data, and OLS4 spot-checked release deltas and disputed hits.

  12. · ADD_CANONICAL_EXAMPLES · codex

    Resolved issue #444 after the #591 source/bin policy with 1 direct source-backed canonical example(s): Escherichia coli K-12 (NCBITaxon:83333; DOI:10.1128/AEM.05773-11). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.