identifier: METPO:1000334 label: NaCl range definition: A salinity phenotype with numerical limits that bounds the minimum and maximum NaCl concentrations supporting growth of an organism. definition_source: DOI:10.1093/femsre/fuy009 trait_category: ENVIRONMENT term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000532 - METPO:1000535 created_by: Anthea Guo evidence: - reference: DOI:10.1093/femsre/fuy009 snippet: salinity range notes: Osmoadaptation review supports the span of NaCl concentrations supporting growth as a standard halophily descriptor. - reference: DOI:10.1186/1746-1448-4-2 snippet: ways they cope with the high salt concentrations notes: Saline-Systems review supports osmotic-tolerance breadth as the basis of the NaCl-range phenotype. causal_graphs: - graph_id: nacl_range_tolerance_breadth title: NaCl-range osmotic-tolerance breadth description: DOI-backed graph linking ambient NaCl, osmoadaptive tolerance to low and high salt, and the bounded span of growth-supporting NaCl concentrations. nodes: - node_id: nacl_range_trait label: NaCl range node_type: TRAIT grounding: METPO:1000334 description: Span of NaCl concentrations supporting growth. - node_id: ambient_nacl label: ambient NaCl concentration node_type: ENVIRONMENTAL_FACTOR description: Ambient NaCl level imposed on the cell. - node_id: low_salt_tolerance label: low-salt tolerance node_type: BIOLOGICAL_PROCESS description: Capacity to maintain turgor and ion homeostasis at low ambient NaCl. - node_id: high_salt_tolerance label: high-salt tolerance node_type: BIOLOGICAL_PROCESS description: Capacity to maintain osmotic balance under elevated NaCl. - node_id: bounded_growth_window label: bounded growth window node_type: BIOLOGICAL_PROCESS description: Span of NaCl concentrations between the minimum and maximum that support growth. - node_id: c_di_amp label: cyclic di-AMP node_type: CHEMICAL description: Second messenger nucleotide that regulates K+ uptake and osmolyte transport. grounding: CHEBI:71578 - node_id: trk_ktr_k_influx label: Trk/Ktr potassium influx systems node_type: GENE_OR_PROTEIN description: Low-affinity potassium import systems (TrkAH, KtrAB, KtrCD) with c-di-AMP-binding gating subunits. - node_id: kima_kup_k_uptake label: KimA/Kup high-affinity K+ uptake transporters node_type: GENE_OR_PROTEIN description: High-affinity potassium uptake transporters (KimA, KupA/KupB) directly inhibited by c-di-AMP. - node_id: kdp_expression label: Kdp system / KdpFABC expression node_type: BIOLOGICAL_PROCESS description: Transcription of the kdpFABC high-affinity K+ uptake operon, regulated via KdpD. - node_id: opua_solute_importers label: OpuA-like compatible-solute importers node_type: GENE_OR_PROTEIN description: ABC-type compatible-solute importers (OpuA family) bound and regulated by c-di-AMP. edges: - subject: ambient_nacl predicate: defines object: bounded_growth_window description: Ambient NaCl defines the axis over which the growth window is bounded. evidence: - reference: DOI:10.1093/femsre/fuy009 snippet: salinity range notes: Supports NaCl as the axis bounding the growth window. predicate_id: METPO:2007500 - subject: low_salt_tolerance predicate: defines object: bounded_growth_window description: Tolerance to low salt sets the lower bound of the growth window. evidence: - reference: DOI:10.1186/1746-1448-4-2 snippet: cope with the high salt concentrations notes: Saline-Systems review frames halophily around salt-tolerance mechanisms that span both the lower and upper limits of growth-supporting salinity. predicate_id: METPO:2007500 - subject: high_salt_tolerance predicate: defines object: bounded_growth_window description: Tolerance to high salt sets the upper bound of the growth window. evidence: - reference: DOI:10.1093/femsre/fuy009 snippet: high salt concentrations notes: Supports tolerance to high salt as the upper-bound mechanism. predicate_id: METPO:2007500 - subject: bounded_growth_window predicate: manifests as object: nacl_range_trait description: The bounded growth window manifests the NaCl-range phenotype. evidence: - reference: DOI:10.1093/femsre/fuy009 snippet: salinity range notes: Supports the trait endpoint. predicate_id: METPO:2007400 - subject: c_di_amp predicate: inhibits object: trk_ktr_k_influx description: c-di-AMP binds gating subunits of Trk/Ktr systems, inhibiting potassium influx. evidence: - reference: DOI:10.1128/MMBR.00181-23 notes: TrkAH, KtrAB and KtrCD gating subunits bind c-di-AMP, inhibiting potassium influx (Foster et al. 2024, review across multiple bacteria). predicate_id: RO:0002212 - subject: c_di_amp predicate: inhibits object: kima_kup_k_uptake description: c-di-AMP directly inhibits high-affinity K+ uptake transporters KimA and Kup. evidence: - reference: DOI:10.1128/MMBR.00181-23 notes: High-affinity transporters (KimA, KupA/KupB) are inhibited directly by cyclic di-AMP, affecting K+ homeostasis underlying NaCl limits. predicate_id: RO:0002212 - subject: c_di_amp predicate: inhibits object: kdp_expression description: c-di-AMP binding to KdpD inhibits kdpFABC transcription. evidence: - reference: DOI:10.1128/MMBR.00181-23 notes: KdpD binding of cyclic di-AMP inhibits kdpFABC transcription (Foster et al. 2024 review). predicate_id: RO:0002212 - subject: c_di_amp predicate: regulates object: opua_solute_importers description: c-di-AMP binds and regulates OpuA-like compatible-solute importers. evidence: - reference: DOI:10.1128/MMBR.00181-23 notes: c-di-AMP binds OpuA-like ABC compatible-solute importers, linking the regulatory module to osmolyte accumulation. predicate_id: RO:0002211 - subject: c_di_amp predicate: reduces object: high_salt_tolerance description: Elevated c-di-AMP correlates with salt sensitivity and narrower NaCl tolerance. evidence: - reference: DOI:10.1128/MMBR.00181-23 notes: High cyclic di-AMP levels correlate with salt sensitivity, narrowing salt tolerance via suppressed K+ uptake (Foster et al. 2024 review). predicate_id: METPO:2000017 curation_history: - timestamp: '2026-05-05T01:35:46.816101+00:00' curator: seed_from_metpo action: SEEDED_FROM_METPO changes: imported from data/raw/metpo.owl (CLASS) llm_assisted: false - timestamp: '2026-05-12T10:00:00-07:00' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added DOI-backed causal graph linking ambient NaCl and low/high-salt tolerance to the bounded NaCl-range phenotype. llm_assisted: true - timestamp: '2026-05-23T21:30:06Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007400×1). llm_assisted: true - timestamp: '2026-05-24T07:37:39Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500×1). llm_assisted: true - timestamp: '2026-05-26T05:00:47Z' curator: claude action: RENAME_PREDICATE_LABELS changes: 'Renamed 2 causal-edge predicate label(s) to align with existing groundings: sets → defines ×2.' llm_assisted: true - timestamp: '2026-05-26T05:00:50Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2007500×2). llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 5 evidence-backed generic edges (5 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:10Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002212×3, RO:0002211×1, METPO:2000017×1). llm_assisted: true - timestamp: '2026-06-24T17:23:31Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:71578×1). llm_assisted: true