identifier: METPO:1003000 label: pH growth preference definition: A phenotype that describes how the rate and extent of population growth are affected by environmental pH. definition_source: DOI:10.1038/nrmicro2549 trait_category: ENVIRONMENT term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000059 evidence: - reference: DOI:10.1038/nrmicro2549 snippet: external pH values that are outside the cytoplasmic pH range notes: Supports environmental pH as a growth-relevant condition requiring pH homeostasis. causal_graphs: - graph_id: ph_growth_preference_homeostasis title: Environmental pH control of growth preference description: Evidence-backed causal sketch linking environmental pH, pH sensing, and cytoplasmic pH homeostasis to growth preference phenotypes. nodes: - node_id: ph_growth_preference_trait label: pH growth preference node_type: TRAIT grounding: METPO:1003000 description: Growth-rate and growth-extent phenotype shaped by environmental pH. - node_id: environmental_ph label: environmental pH node_type: ENVIRONMENTAL_FACTOR description: Acidity or alkalinity of the growth environment. - node_id: acidic_external_ph label: acidic external pH node_type: ENVIRONMENTAL_FACTOR description: External pH below the cytoplasmic pH range compatible with growth. grounding: PATO:0001429 - node_id: alkaline_external_ph label: alkaline external pH node_type: ENVIRONMENTAL_FACTOR description: External pH above the cytoplasmic pH range compatible with growth. grounding: PATO:0001430 - node_id: ph_sensing label: pH sensing node_type: MOLECULAR_FUNCTION description: Detection of external or envelope pH change by regulatory proteins and transporters. - node_id: cytoplasmic_ph_homeostasis label: cytoplasmic pH homeostasis node_type: BIOLOGICAL_PROCESS description: Maintenance of intracellular pH within a range compatible with growth. grounding: GO:0051453 - node_id: f1f0_atpase label: proton-translocating F1F0-ATPase node_type: GENE_OR_PROTEIN description: F-type ATP synthase/ATPase that translocates protons across the membrane, contributing to pH homeostasis. - node_id: amino_acid_decarboxylase_systems label: amino-acid decarboxylase systems node_type: PATHWAY description: Inducible decarboxylase systems (e.g. GAD, arginine/agmatine) that consume cytoplasmic protons. - node_id: amino_acid_decarboxylation label: amino-acid decarboxylation node_type: BIOLOGICAL_PROCESS description: Decarboxylation of amino acids that consumes protons and raises cytoplasmic alkalinity. - node_id: na_h_antiport label: Na+/H+ antiport node_type: MOLECULAR_FUNCTION description: Sodium/proton antiporter activity (e.g. Mrp system) coupling Na+ efflux to H+ import. - node_id: proton_consuming_reaction_genes label: proton-consuming reaction genes node_type: GENE_OR_PROTEIN description: Gene families for proton-consuming reactions (decarboxylases, deaminases). - node_id: na_h_antiporter_genes label: Na+/H+ antiporter genes node_type: GENE_OR_PROTEIN description: Na+/H+ antiporter gene families (e.g. Mrp/Mnh/Nha) associated with pH preference. edges: - subject: environmental_ph predicate: regulates object: ph_growth_preference_trait description: Environmental pH determines which pH conditions support growth. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: tolerate or grow at external pH values notes: Review frames pH growth as a response to external pH outside the cytoplasmic range. predicate_id: RO:0002211 - subject: acidic_external_ph predicate: challenges object: cytoplasmic_ph_homeostasis description: Acidic environments impose inward proton stress that must be managed for growth. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: acid challenge conditions include increased expression and activity notes: Supports active mechanisms under acid challenge. predicate_id: METPO:2007406 - subject: alkaline_external_ph predicate: challenges object: cytoplasmic_ph_homeostasis description: Alkaline environments require active proton accumulation or generation to maintain cytoplasmic pH. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: active proton accumulation or generation in the cytoplasm notes: Supports alkaline-pH homeostasis as a growth-enabling process. predicate_id: METPO:2007406 - subject: ph_sensing predicate: regulates object: cytoplasmic_ph_homeostasis description: pH-sensing and signalling systems regulate homeostasis responses to acid or alkali. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: pH-sensing and signalling capabilities notes: Supports regulatory sensing as part of homeostasis. predicate_id: RO:0002211 - subject: cytoplasmic_ph_homeostasis predicate: enables object: ph_growth_preference_trait description: Growth at preferred pH depends on maintaining intracellular pH compatible with cellular processes. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: robust mechanisms for cytoplasmic pH homeostasis notes: Supports cytoplasmic pH homeostasis as central to growth under pH stress. predicate_id: RO:0002327 - subject: f1f0_atpase predicate: contributes to object: cytoplasmic_ph_homeostasis description: The proton-translocating F1F0-ATPase mediates pH homeostasis supporting growth under low pH. evidence: - reference: DOI:10.1093/femsre/fuad062 notes: pH homeostasis mediated by the proton-translocating F1F0-ATPase; general across taxa. predicate_id: RO:0002326 - subject: acidic_external_ph predicate: induces object: amino_acid_decarboxylase_systems description: Low external pH induces amino-acid decarboxylase systems that consume protons. evidence: - reference: DOI:10.1093/femsre/fuad062 notes: amino-acid decarboxylase systems (GAD, agmatine/arginine decarboxylation) that consume protons and raise cytoplasmic alkalinity. - subject: amino_acid_decarboxylase_systems predicate: enables object: amino_acid_decarboxylation description: Decarboxylase systems carry out amino-acid decarboxylation. evidence: - reference: DOI:10.1093/femsre/fuad062 notes: amino-acid decarboxylase systems that consume protons and raise cytoplasmic alkalinity. predicate_id: RO:0002327 - subject: amino_acid_decarboxylation predicate: contributes to object: cytoplasmic_ph_homeostasis description: Amino-acid decarboxylation consumes protons and raises cytoplasmic alkalinity, aiding pH homeostasis. evidence: - reference: DOI:10.1093/femsre/fuad062 notes: consume protons and raise cytoplasmic alkalinity. predicate_id: RO:0002326 - subject: na_h_antiport predicate: contributes to object: cytoplasmic_ph_homeostasis description: Na+/H+ antiport (notably the Mrp system) is the major mechanism for alkaline pH homeostasis. evidence: - reference: DOI:10.1038/nrmicro2549 notes: Na+/H+ antiporters (notably the multicomponent Mrp system) are the major mechanism for alkaliphile pH homeostasis. predicate_id: RO:0002326 - subject: proton_consuming_reaction_genes predicate: associated with object: acidic_external_ph description: Genes for proton-consuming reactions (decarboxylases/deaminases) are consistently associated with lower pH preference. evidence: - reference: DOI:10.1126/sciadv.adf8998 notes: proton-consuming reactions (decarboxylases, deaminases) consistently associated with pH preference across environments. predicate_id: biolink:associated_with - subject: na_h_antiporter_genes predicate: associated with object: alkaline_external_ph description: Na+/H+ antiporter genes (PhaGF/MnhG/MrpF/YufB) are associated with higher pH preference. evidence: - reference: DOI:10.1126/sciadv.adf8998 notes: Na+/H+ antiporters PhaGF, MnhG, MrpF, YufB associated with higher pH preference. predicate_id: biolink:associated_with curation_history: - timestamp: '2026-05-05T01:35:46.936639+00:00' curator: seed_from_metpo action: SEEDED_FROM_METPO changes: imported from data/raw/metpo.owl (CLASS) llm_assisted: false - timestamp: '2026-05-11T00:00:00-07:00' curator: codex action: CURATED_WITH_LITERATURE changes: Reviewed pH growth preference trait and added DOI-backed evidence and causal graph for pH sensing and cytoplasmic pH homeostasis. 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 (RO:0002211×1, 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:2007406×2). llm_assisted: true - timestamp: '2026-05-24T04:38:00Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0030641×1). llm_assisted: true - timestamp: '2026-05-24T08:14:32Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv (PATO:0001428×1, PATO:0001429×1). llm_assisted: true - timestamp: '2026-05-26T05:00:47Z' curator: claude action: RENAME_PREDICATE_LABELS changes: 'Renamed 1 causal-edge predicate label(s) to align with existing groundings: influences → regulates ×1.' llm_assisted: true - timestamp: '2026-05-26T05:00:50Z' 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: '2026-06-15T07:20:36Z' curator: claude action: FIX_NODE_GROUNDING_CURIE changes: Overwrote 1 causal-node grounding(s) (obsolete/wrong GO -> corrected, verified vs OAK). llm_assisted: true - timestamp: '2026-06-15T07:21:43Z' curator: claude action: FIX_NODE_GROUNDING_CURIE changes: Overwrote 2 pH causal-node grounding(s) to corrected PATO CURIEs (phase-2; verified vs OAK). llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 7 evidence-backed generic edges (6 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:associated_with×2, RO:0002327×1). llm_assisted: true