TraitMech

TraitMech › ENVIRONMENT

temperature range mid3

METPO:1000452 · CLASS · REVIEWED

A temperature range phenotype in which the growth-supporting ambient temperature range spans approximately 30–34 °C, characteristic of mesophilic physiology.

Trait evidence (1)

Temperature-range-mid3 upper-mesophile context

DOI-backed nonmechanistic graph annotating upper-mesophile growth-range context, the DesK/DesR membrane-order sensor, des expression, cooling-induced membrane rigidification, and homeoviscous liquid-crystalline membrane maintenance.

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-range-mid3 upper-mesophile context Interactive directed graph showing evidence-backed causal relationships for temperature range mid3.

Edge evidence

  • upper-mesophile adaptation confers temperature range mid3 METPO:2007700

    Upper-mesophile adaptation enables growth across 30–34 °C.

  • temperature range mid3 is a temperature range rdfs:subClassOf

    Temperature range mid3 is a quantitative bin of the temperature-range phenotype.

  • membrane order / fluidity state positively regulates DesK kinase-dominant state RO:0002213

    Increased membrane order (reduced fluidity) promotes the DesK kinase-dominant state; membrane physical state is the proximate signal.

    • DOI:10.1128/spectrum.03925-23 Upon temperature decrease, the membrane rigidifies and increases in thickness, resulting in activation of the kinase-dominant state of DesK Verified against the open Sidarta et al. introduction; the current Des model links temperature-decrease-driven membrane rigidification/thickening to the active kinase-dominant state.
  • phosphorylated DesR positively regulates des (acyl-lipid desaturase) RO:0002213

    DesR-P tetramerizes, binds the des promoter, and positively regulates des expression for lipid desaturation.

    • DOI:10.1128/spectrum.03925-23 activating expression of the des gene Verified against the open Sidarta et al. introduction; phosphorylated DesR tetramers bind Pdes and activate des transcription.
  • des (acyl-lipid desaturase) regulates membrane fatty acyl chains RO:0002211

    Des-mediated unsaturation regulates membrane fatty acyl chains, fluidizing the membrane and reducing bilayer thickness.

    • DOI:10.1128/spectrum.03925-23 desaturates the fatty acyl chains Verified against the open Sidarta et al. introduction; Des desaturates membrane-lipid fatty acyl chains as the effector of the DesK/DesR temperature-sensing system.
  • temperature decrease causes membrane rigidification and increased thickness biolink:causes

    A temperature decrease causes membrane rigidification and increased thickness, a physical trigger for homeoviscous adaptation.

    • DOI:10.1128/spectrum.03925-23 rigidification and concomitant thickening Verified against the open Sidarta et al. introduction; temperature decrease is described as causing cell-membrane rigidification and thickening.
  • homeoviscous adaptation contributes to liquid-crystalline membrane state RO:0002326

    Homeoviscous adaptation contributes to a functional liquid-crystalline membrane state at low temperature.

    • DOI:10.1007/s42770-023-01057-4 maintain the liquid crystalline phase Verified against the open Ramón et al. review; organisms in cold environments are described as adapting their membrane composition to maintain a liquid-crystalline state.
  • membrane rigidification and increased thickness associated with membrane order / fluidity state biolink:associated_with

    Cooling-induced membrane rigidification is associated with the ordered membrane state sensed by DesK.

    • DOI:10.1128/spectrum.03925-23 membrane rigidifies and increases in thickness Verified against the open Sidarta et al. introduction; this connector joins the cooling membrane signal to the DesK kinase-state branch.
  • membrane fatty acyl chains associated with homeoviscous adaptation biolink:associated_with

    Des-mediated fatty-acyl-chain unsaturation is associated with homeoviscous membrane adaptation.

    • DOI:10.1128/spectrum.03925-23 resulting in membrane fluidization and concomitant decrease of bilayer thickness Verified against the open Sidarta et al. introduction; this connector keeps des expression as membrane-fatty-acyl remodeling context.
  • DesK regulates phosphorylated DesR RO:0002211

    DesK regulates DesR phosphorylation in the core two-component signaling step linking membrane physical state to transcriptional response.

    • DOI:10.1128/spectrum.03925-23 phosphorylating or dephosphorylating DesR Verified against the open Sidarta et al. introduction; DesK is described as a membrane-associated histidine kinase that phosphorylates or dephosphorylates DesR in a temperature-dependent manner.

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
  • TR_30_to_34 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:1000452 [-1.351, +1.368, -2.814, +2.551, …]

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_range_mid3-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. 
# Curation report: microbial **temperature range mid3**

## Executive conclusion

**Target trait:** **temperature range mid3**
**Identifier:** **METPO:1000452**
**Category/kind:** ENVIRONMENT / CLASS
**Definition supplied for curation:** a growth-supporting ambient-temperature range spanning approximately **30–34 °C**, characteristic of mesophilic physiology.
**Parent:** **METPO:1000306**
**Synonyms:** *Mesophilie*; *TR_30_to_34*.

The most defensible causal backbone is **ambient temperature → membrane physical state → membrane-fluidity sensing → fatty-acid remodeling → membrane fluidity compatible with growth**. In *Bacillus subtilis*, the DesK–DesR–des pathway supplies unusually strong molecular evidence for this chain. Recent 2024 lipidomics confirms extensive, but strain-dependent, remodeling of unsaturated fatty acids in *Acinetobacter baumannii*. Chaperone and proteostasis mechanisms are biologically relevant to thermal tolerance, but the retrieved 2024 intervention studies measured survival after severe heat shock rather than sustained growth across a 30–34 °C interval; these edges should therefore remain provisional for this trait. No retrieved study directly demonstrates that a particular molecular perturbation creates the **exact 30–34 °C growth-range breadth**.

## 1. Trait scope and boundary conditions

### 1.1 What the phenotype represents

For TraitMech, **METPO:1000452 should be modeled as an assay-observed thermal niche breadth**, not as a molecular stress response. A positive assignment requires net population growth over a temperature interval whose span falls approximately in the 30–34 °C bin. Suitable endpoints include repeated cell division, increase in viable biomass, specific growth rate, or another validated measure of sustained reproduction.

The phenotype should ideally be represented using cardinal-temperature observations:

- **TMIN:** lowest temperature permitting detectable sustained growth;
- **TOPT:** temperature giving the maximum growth rate under the assay conditions;
- **TMAX:** highest temperature permitting sustained growth;
- **growth-range breadth:** approximately `TMAX − TMIN`, subject to the temperatures actually tested.

A recent adaptive-evolution study explicitly uses TMIN, TMAX, and TOPT to characterize microbial growth profiles and defines mesophiles broadly by **TOPT 20–45 °C**. This broad mesophile definition is not equivalent to a 30–34 °C-wide growth range (lehmann2023adaptivelaboratoryevolution pages 1-2).

### 1.2 Distinctions from neighboring phenotypes

1. **Not temperature optimum.** A microorganism may have TOPT near 30–34 °C but possess a much narrower or wider growth range. Conversely, a 30–34 °C-wide range does not determine where TOPT lies.
2. **Not growth at 30–34 °C.** The supplied definition concerns the *span* of temperatures supporting growth, not merely growth at temperatures numerically between 30 and 34 °C.
3. **Not heat- or cold-shock survival.** Retention of viability after 30 minutes at 55 °C or five days at 52 °C does not establish reproduction at those temperatures or a 30–34 °C growth breadth (liang2024interactionsbetweenchaperone pages 8-10, sato2024effectsofsmall pages 10-11).
4. **Not generic mesophily.** Mesophily is commonly classified by TOPT, whereas this METPO class is a quantitative range bin (lehmann2023adaptivelaboratoryevolution pages 1-2).
5. **Assay dependence is intrinsic.** Medium, pH, oxygen, inoculum history, acclimation, incubation time, and temperature sampling density can alter observed TMIN and TMAX. A coarse temperature grid can over- or underestimate range breadth.

**Recommended graph interpretation:** mechanisms below should be treated as contributors that preserve growth across moderately changing temperatures, not as sufficient determinants of the exact bin.

## 2. Candidate nodes grouped by type

### Trait and experimental nodes

- **temperature range mid3 — METPO:1000452**
- Ambient growth temperature
- Decreased ambient temperature
- Increased ambient temperature
- Temperature shift / cold shock / heat shock
- Sustained growth rate
- TMIN, TOPT, TMAX
- Growth-supporting temperature-range breadth
- Culture medium, oxygen status, pH, acclimation time, and assay duration

### Cellular structures, physical states, and processes

- Cytoplasmic membrane — candidate **GO:0005886**
- Membrane lipid bilayer
- Membrane fluidity
- Membrane lipid order
- Liquid-crystalline membrane state
- Gel-state membrane

Showing the first 60 of 268 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.

  • Bacillus nakamurai NCBITaxon:1793963 DOI:10.1099/ijsem.0.001135 Bacillus nakamurai NRRL B-41091T grew from 17 to 50 degrees C in its primary species description, a directly reported 33-degree breadth within the approximately 30-34-degree range-width 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 upper-mesophile adaptation to the temperature-range-mid3 bin.

  3. · GROUND_CAUSAL_PREDICATES · claude

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

  4. · ENRICH_CAUSAL_GRAPH · claude

    Added 6 evidence-backed generic edges (11 new nodes) from the deep-research report.

  5. · GROUND_CAUSAL_PREDICATES · claude

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

  6. · GROUND_CAUSAL_NODES · claude

    Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A067Z5N7×1, UniProtKB:A0A067Z2X2×1).

  7. · RETRACT_DEAD_UNIPROT_GROUNDINGS · claude

    Retracted 2 UniProtKB grounding(s) whose accessions are deleted from UniProt; nodes demoted to label-only pending re-grounding (docs/GROUNDING_POLICY.md)

  8. · MIGRATE_ENABLES_TRAIT_EDGES · claude

    Migrated 1 causal edge(s) off enables/RO:0002327 with a TRAIT object (1 to confers), issue 302. RO:0002327 has range 'biological process or activity', which a trait (a disposition) cannot satisfy, so the previous form entailed trait is-a BiologicalProcessOrActivity. The replacements are proposed in proposals/metpo_traitmech_v8 and are placeholder ids until METPO mints them.

  9. · NORMALISE_NODE_TYPE · codex

    Tranche 5 of issue 356 settles the process/quality families and merges ids that meant the same sense: membrane_rigidity is QUALITY. Membrane rigidity is a physical attribute of the bilayer and therefore a QUALITY under the schema's membrane-fluidity example.

  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_range_mid3_upper_mesophile=NONMECHANISTIC with scope_notes; marked 3 GENE_OR_PROTEIN node(s) REVIEWED_LABEL_ONLY with grounding_notes (desk, desr, des_gene).

  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): Bacillus nakamurai (NCBITaxon:1793963; DOI:10.1099/ijsem.0.001135). The note retains the measured value or scopes broad-class examples to the cited branch; no paid research was used.

  13. · REVIEW_CAUSAL_EVIDENCE · codex

    Reviewed the temperature_range_mid3_upper_mesophile graph for issue #183: added snippets to 6 edge-level evidence items and grounded the DesK/DesR thermosensing predicates to RO:0002213, RO:0002211, or RO:0002326. No paid research service was called.

  14. · CONNECT_CAUSAL_GRAPH_COMPONENTS · codex

    Resolved issue #183 graph fragmentation (5 components to 1) by adding 4 source- and verbatim-snippet-backed association connectors among DesK/DesR membrane-order sensing, des expression, cooling-induced membrane rigidification, and homeoviscous liquid-crystalline membrane branches. No paid research service was called.

  15. · ADVERSARIAL_REVIEW_REPAIR · codex

    Addressed PR #664 adversarial review: replaced copied nonmechanistic bridge snippets with independent exact source snippets while preserving the existing connector edge scope.

  16. · ADVERSARIAL_REVIEW_REPAIR · codex

    Addressed PR #664 adversarial review issue #693: replaced weak DesK/DesR connector edges by routing DesK directly to phosphorylated DesR, removed the redundant unphosphorylated DesR node, and updated the original connector history.

  17. · ADVERSARIAL_REVIEW_REPAIR · codex

    Addressed PR #664 adversarial review issues #696, #698, and #699: strengthened the DesK kinase-state snippet and removed weak association connectors to DesK and upper-mesophile adaptation.

  18. · ADVERSARIAL_REVIEW_REPAIR · codex

    Addressed PR #664 adversarial review issue #702: appended corrective issue-183 provenance after evidence-weak connectors were pruned; this NONMECHANISTIC graph intentionally ships with 3 disconnected components until independent trait-specific connectors are curated.

  19. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (METPO:1016200×1).