identifier: METPO:1000475 label: pH delta mid1 definition: A pH delta phenotype with a growth-supporting pH breadth of approximately 2–3 pH units, characteristic of organisms with moderate 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_2_3 synonym_type: RELATED_SYNONYM source: metpo.owl evidence: - reference: DOI:10.1038/nrmicro2549 snippet: pH homeostasis notes: pH-homeostasis review supports moderate pH-homeostasis flexibility as common among non-extreme microorganisms. causal_graphs: - graph_id: ph_delta_mid1_moderate_breadth title: pH-delta-mid1 moderate-breadth pH homeostasis description: DOI-backed graph linking moderate pH-homeostasis flexibility to a pH growth breadth of approximately 2–3 pH units. nodes: - node_id: ph_delta_mid1_trait label: pH delta mid1 node_type: TRAIT grounding: METPO:1000475 description: pH growth-supporting breadth approximately 2–3 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: moderate_ph_homeostasis label: moderate pH-homeostasis flexibility node_type: BIOLOGICAL_PROCESS description: Mid-range capacity to remodel proton extrusion and envelope buffering across a few pH units. - node_id: f0f1_atpase label: F0F1-ATPase node_type: GENE_OR_PROTEIN description: F0F1-ATP synthase/ATPase complex that can hydrolyze ATP to consume and export intracellular protons. - node_id: cytoplasmic_ph_homeostasis label: cytoplasmic pH homeostasis node_type: BIOLOGICAL_PROCESS description: Maintenance of near-neutral cytoplasmic pH under external pH stress. grounding: GO:0051453 - node_id: gln_glu_decarboxylation_pathway label: glutamine/glutamate decarboxylation pathway node_type: PATHWAY description: Coupled glutamine conversion and glutamate decarboxylation that consumes intracellular protons. - node_id: intracellular_proton label: intracellular proton (H+) node_type: CHEMICAL description: Cytoplasmic hydron whose concentration sets internal pH. - node_id: ybas_glutaminase label: YbaS glutaminase node_type: GENE_OR_PROTEIN description: Glutaminase converting glutamine to glutamate plus ammonia. - node_id: ammonia label: ammonia node_type: CHEMICAL description: Ammonia that neutralizes intracellular protons. grounding: CHEBI:16134 - node_id: membrane_saturated_fatty_acids label: membrane saturated fatty acid content node_type: QUALITY description: Increased proportion of saturated fatty acids in the membrane lipid bilayer. - node_id: proton_diffusion_across_membrane label: proton diffusion across membrane node_type: BIOLOGICAL_PROCESS description: Passive leakage of protons across the cytoplasmic membrane. - node_id: oxidative_phosphorylation label: oxidative phosphorylation / electron transport chain node_type: PATHWAY description: ETC activity (nuo, cyo, ndh, sdh) generating and maintaining the proton motive force. - node_id: proton_motive_force label: proton motive force node_type: BIOLOGICAL_PROCESS description: Transmembrane electrochemical proton gradient supporting acid-side pH homeostasis. edges: - subject: moderate_ph_homeostasis predicate: produces object: ph_delta_mid1_trait description: Moderate pH-homeostasis flexibility yields a 2–3 pH-unit pH-delta breadth. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: pH homeostasis notes: Supports moderate flexibility as the basis of an intermediate breadth. predicate_id: METPO:2000202 - subject: ph_delta_mid1_trait predicate: is a object: ph_delta description: pH delta mid1 is a quantitative bin of the pH-delta phenotype. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: external pH notes: Supports the 2–3 unit breadth as a value within the pH-delta distribution. predicate_id: rdfs:subClassOf - subject: f0f1_atpase predicate: contributes to object: cytoplasmic_ph_homeostasis description: Under acid stress F0F1-ATPase hydrolyzes ATP to consume/export intracellular H+, maintaining cytoplasmic pH. evidence: - reference: DOI:10.3390/microorganisms12091774 notes: F0F1-ATPase under acid stress hydrolyzes ATP to consume intracellular H+ to maintain homeostasis; broad pH-homeostasis mechanism. predicate_id: RO:0002326 - subject: gln_glu_decarboxylation_pathway predicate: consumes object: intracellular_proton description: Coupled glutamine conversion and glutamate decarboxylation consume two intracellular H+, enhancing acid resistance. evidence: - reference: DOI:10.3390/microorganisms12091774 notes: Glutamine conversion and glutamate decarboxylation can act together to consume two H+; pathway-level proton-consumption module. predicate_id: biolink:consumes - subject: ybas_glutaminase predicate: produces object: ammonia description: YbaS glutaminase converts glutamine to glutamate and releases ammonia, which neutralizes intracellular protons. evidence: - reference: DOI:10.3390/microorganisms12091774 notes: The glutaminase YbaS converts glutamine to glutamate and releases ammonia, which neutralizes intracellular protons. predicate_id: METPO:2000202 - subject: membrane_saturated_fatty_acids predicate: decreases object: proton_diffusion_across_membrane description: A higher proportion of saturated membrane fatty acids limits passive proton diffusion across the membrane. evidence: - reference: DOI:10.1128/aem.00569-24 notes: Conversion of unsaturated to saturated fatty acids limits proton diffusion; broadly plausible membrane-permeability mechanism. predicate_id: RO:0002212 - subject: oxidative_phosphorylation predicate: maintains object: proton_motive_force description: Upregulated oxidative phosphorylation/ETC increases proton export and maintains the proton motive force, helping resist cytoplasmic pH decreases. evidence: - reference: DOI:10.3390/microorganisms12081565 notes: Upregulation of oxidative phosphorylation genes increases proton export rate and maintains a proton motive force that helps cells resist cytoplasmic pH decreases under mild acid (pH 6.0) growth. - subject: proton_motive_force predicate: contributes to object: cytoplasmic_ph_homeostasis description: A maintained proton motive force supports cytoplasmic pH homeostasis under acid stress. evidence: - reference: DOI:10.3390/microorganisms12081565 notes: PMF generated/maintained by oxidative phosphorylation helps cells resist cytoplasmic pH decreases. predicate_id: RO:0002326 - subject: cytoplasmic_ph_homeostasis predicate: contributes to object: moderate_ph_homeostasis description: Cytoplasmic pH homeostasis modules collectively underlie moderate pH-homeostasis flexibility. evidence: - reference: DOI:10.3390/microorganisms12091774 notes: Proton-consumption and proton-export modules maintaining cytoplasmic pH underpin homeostatic flexibility across a few pH units. predicate_id: RO:0002326 curation_history: - timestamp: '2026-05-05T01:35:46.838958+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 moderate pH-homeostasis flexibility to the moderate-breadth pH-delta-mid1 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 (10 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:10Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 6 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326×3, biolink:consumes×1, METPO:2000202×1, RO:0002212×1). llm_assisted: true - timestamp: '2026-06-24T17:21:17Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0051453×1, CHEBI:16134×1). llm_assisted: true