identifier: METPO:1000477 label: pH delta mid3 definition: A pH delta phenotype with a growth-supporting pH breadth of approximately 4–5 pH units, characteristic of organisms with wide pH-tolerance breadth. definition_source: DOI:10.1038/nrmicro2549 trait_category: ENVIRONMENT term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000232 synonyms: - synonym_text: pHd_4_5 synonym_type: RELATED_SYNONYM source: metpo.owl evidence: - reference: DOI:10.1038/nrmicro2549 snippet: pH homeostasis notes: pH-homeostasis review supports wide pH-homeostasis flexibility as the basis of euryphilic pH-tolerance. causal_graphs: - graph_id: ph_delta_mid3_wide_breadth title: pH-delta-mid3 wide-breadth pH homeostasis description: DOI-backed graph linking wide pH-homeostasis flexibility to a pH growth breadth of approximately 4–5 pH units. nodes: - node_id: ph_delta_mid3_trait label: pH delta mid3 node_type: TRAIT grounding: METPO:1000477 description: pH growth-supporting breadth approximately 4–5 pH units. - node_id: ph_delta label: pH delta node_type: TRAIT grounding: METPO:1000232 description: Breadth of the growth-supporting external pH range. - node_id: wide_ph_homeostasis label: wide pH-homeostasis flexibility node_type: BIOLOGICAL_PROCESS description: Strong cross-axis pH-homeostasis capacity allowing growth across a wide range of external pH. - node_id: external_alkaline_ph label: external alkaline pH node_type: ENVIRONMENTAL_FACTOR description: High external pH challenging cytoplasmic pH homeostasis. - node_id: na_h_antiport label: electrogenic Na+/H+ antiport node_type: BIOLOGICAL_PROCESS description: Sodium:proton antiport supporting cytoplasmic pH homeostasis at alkaline pH. - node_id: pmf_regulation label: regulation of membrane potential and pH gradient node_type: BIOLOGICAL_PROCESS description: Regulation of the proton motive force components Delta-psi and Delta-pH. - node_id: cytoplasmic_ph_maintenance label: cytoplasmic pH maintenance node_type: BIOLOGICAL_PROCESS description: Maintenance of cytoplasmic pH within a viable range across external pH changes. - node_id: proton_pumping_respiratory_complexes label: proton-pumping respiratory complexes node_type: GENE_OR_PROTEIN description: Respiratory-chain primary proton pumps that build the proton motive force. - node_id: proton_motive_force label: proton motive force node_type: BIOLOGICAL_PROCESS description: Electrochemical proton gradient (PMF) used for transport and pH regulation. - node_id: f0f1_atpase label: F0F1-ATPase node_type: GENE_OR_PROTEIN description: Proton-translocating ATP synthase/ATPase that can extrude protons under acid stress. - node_id: phosphate_buffering label: cytoplasmic phosphate buffering capacity node_type: QUALITY description: Physicochemical buffering of intracellular pH by cytoplasmic phosphate. - node_id: intracellular_ph_stability label: intracellular pH stability node_type: STATE description: Stabilized intracellular pH within a narrow viable range. - node_id: aa_decarboxylation label: amino-acid decarboxylation pathways node_type: PATHWAY description: Decarboxylation pathways that consume protons and store energy as PMF. - node_id: membrane_lipid_remodeling label: membrane lipid composition shifts node_type: BIOLOGICAL_PROCESS description: Adjustments of membrane lipid composition altering envelope properties. - node_id: proton_permeability label: membrane proton permeability node_type: QUALITY description: Permeability of the cell membrane to protons. edges: - subject: wide_ph_homeostasis predicate: produces object: ph_delta_mid3_trait description: Wide pH-homeostasis flexibility yields a 4–5 pH-unit pH-delta breadth. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: pH homeostasis notes: Supports wide pH-homeostasis flexibility as the basis of a wide breadth. predicate_id: METPO:2000202 - subject: ph_delta_mid3_trait predicate: is a object: ph_delta description: pH delta mid3 is a quantitative bin of the pH-delta phenotype. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: external pH notes: Supports the 4–5 unit breadth as a value within the pH-delta distribution. predicate_id: rdfs:subClassOf - subject: external_alkaline_ph predicate: increases reliance on object: na_h_antiport description: High external pH increases reliance on electrogenic Na+/H+ antiport for cytoplasmic pH homeostasis. evidence: - reference: DOI:10.1038/nrmicro2549 notes: Multiple Na+/H+ and K+/H+ antiporters are critical for alkaline homeostasis, driven by membrane potential. - subject: pmf_regulation predicate: supports object: cytoplasmic_ph_maintenance description: Regulation of Delta-psi and Delta-pH supports maintenance of cytoplasmic pH across external pH changes. evidence: - reference: DOI:10.1038/nrmicro2549 notes: PMF (Delta-pH and Delta-psi) is central to pH homeostasis; neutralophiles keep cytoplasmic pH near 7.5 across external pH ~5.5-9.0. - subject: proton_pumping_respiratory_complexes predicate: contribute to object: proton_motive_force description: Proton-pumping respiratory complexes contribute to the PMF used for pH homeostasis. evidence: - reference: DOI:10.1038/nrmicro2549 notes: Cells use primary proton pumps including respiratory-chain pumps to create PMF for transport and pH regulation. - subject: f0f1_atpase predicate: contributes to object: cytoplasmic_ph_maintenance description: F0F1-ATPase can extrude protons and contributes to pH homeostasis under acid stress. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: F1Fo-ATPase hydrolytic activity can drive H+ extrusion; key regulator in low-pH contexts. predicate_id: RO:0002326 - subject: phosphate_buffering predicate: stabilizes object: intracellular_ph_stability description: Cytoplasmic phosphate buffering capacity stabilizes intracellular pH. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: At pH ~7.2 only ~10 free protons present; cytoplasmic phosphate buffering (~100 mM) makes buffering essential. - subject: aa_decarboxylation predicate: contributes to object: proton_motive_force description: Amino-acid decarboxylation pathways consume protons and contribute to PMF and intracellular pH control. evidence: - reference: DOI:10.1093/femsre/fuad033 notes: Decarboxylation releases ~20 kJ/mol that can be stored as PMF; decarboxylation pathways are key pH regulators. predicate_id: RO:0002326 - subject: membrane_lipid_remodeling predicate: reduces object: proton_permeability description: Membrane lipid composition shifts reduce proton permeability. evidence: - reference: DOI:10.3389/fmicb.2022.1034164 notes: Membrane composition adjustments limit proton permeability and alter phospholipid headgroups under high pH. predicate_id: METPO:2000017 curation_history: - timestamp: '2026-05-05T01:35:46.839862+00:00' curator: seed_from_metpo action: SEEDED_FROM_METPO changes: imported from data/raw/metpo.owl (CLASS) llm_assisted: false - timestamp: '2026-05-13T10:00:00-07:00' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added DOI-backed definition and causal graph linking wide pH-homeostasis flexibility to the wide-breadth pH-delta-mid3 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: '2026-06-23T00:00:00Z' 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: '2026-06-24T17:21:10Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326×2, METPO:2000017×1). llm_assisted: true