identifier: METPO:1000481
label: NaCl delta mid2
definition: A NaCl delta phenotype with a growth-supporting NaCl breadth of approximately
  3–8% (w/v), characteristic of organisms with broad salinity tolerance.
definition_source: DOI:10.1093/femsre/fuy009
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000335
synonyms:
- synonym_text: Nad_3_8
  synonym_type: RELATED_SYNONYM
  source: metpo.owl
evidence:
- reference: DOI:10.1093/femsre/fuy009
  snippet: salinity range
  notes: Osmoadaptation review supports broad osmoadaptive breadths as the halotolerant
    / moderately euryhaline phenotype.
causal_graphs:
- graph_id: nacl_delta_mid2_broad_breadth
  title: NaCl-delta-mid2 broad-breadth osmoadaptation
  description: DOI-backed graph linking robust osmoadaptive flexibility to a 3–8%
    (w/v) NaCl growth breadth.
  nodes:
  - node_id: nacl_delta_mid2_trait
    label: NaCl delta mid2
    node_type: TRAIT
    grounding: METPO:1000481
    description: NaCl growth-supporting breadth approximately 3–8% w/v.
  - node_id: nacl_delta
    label: NaCl delta
    node_type: TRAIT
    grounding: METPO:1000335
    description: Breadth of the growth-supporting NaCl range.
  - node_id: robust_osmoadaptive_flexibility
    label: robust osmoadaptive flexibility
    node_type: BIOLOGICAL_PROCESS
    description: Strong osmolyte-remodeling capacity supporting growth across a broad
      salinity span.
  - node_id: cyclic_di_amp
    label: cyclic di-AMP
    node_type: CHEMICAL
    description: Second-messenger nucleotide acting as a master regulator of osmotic
      balance.
    grounding: CHEBI:71578
  - node_id: potassium_uptake_systems
    label: potassium uptake systems
    node_type: GENE_OR_PROTEIN
    description: K+ import transporters (KupA/KupB, KimA, Kdp).
  - node_id: cell_volume_regulation
    label: cell volume regulation
    node_type: BIOLOGICAL_PROCESS
    description: Regulation of cellular volume during osmotic stress.
  - node_id: osmolality
    label: osmolality
    node_type: ENVIRONMENTAL_FACTOR
    description: External solute concentration / osmotic pressure.
  - node_id: kdpfabc_complex
    label: KdpFABC complex
    node_type: GENE_OR_PROTEIN
    description: High-affinity potassium uptake P-type ATPase complex.
  - node_id: compatible_solute_transport
    label: compatible-solute accumulation/transport
    node_type: BIOLOGICAL_PROCESS
    description: Biosynthesis and uptake of compatible solutes/osmolytes.
  - node_id: osmoprotection
    label: osmoprotection
    node_type: BIOLOGICAL_PROCESS
    description: Response to osmotic stress conferring protection.
  - node_id: eps_matrix
    label: exopolysaccharide matrix
    node_type: CELLULAR_LOCALIZATION
    description: Extracellular polymeric substance matrix surrounding cells.
  - node_id: sodium_ion
    label: sodium ion
    node_type: CHEMICAL
    description: Na+ cation.
    grounding: CHEBI:29101
  - node_id: water_retention
    label: water retention / reduced pericellular Na+ toxicity
    node_type: BIOLOGICAL_PROCESS
    description: Retention of water and lowering of effective pericellular Na+.
  edges:
  - subject: robust_osmoadaptive_flexibility
    predicate: produces
    object: nacl_delta_mid2_trait
    description: Robust osmoadaptive flexibility yields a 3–8% NaCl-delta breadth.
    evidence:
    - reference: DOI:10.1093/femsre/fuy009
      snippet: salinity range
      notes: Supports robust osmoadaptive flexibility as the basis of a broad breadth.
    predicate_id: METPO:2000202
  - subject: nacl_delta_mid2_trait
    predicate: is a
    object: nacl_delta
    description: NaCl delta mid2 is a quantitative bin of the NaCl-delta phenotype.
    evidence:
    - reference: DOI:10.1093/femsre/fuy009
      snippet: salinity range
      notes: Supports the 3–8% breadth as a value within the NaCl-delta distribution.
    predicate_id: rdfs:subClassOf
  - subject: cyclic_di_amp
    predicate: inhibits
    object: potassium_uptake_systems
    description: c-di-AMP binding to transporters/riboswitches inhibits K+ import.
    evidence:
    - reference: DOI:10.1128/mmbr.00181-23
      notes: Binding of c-di-AMP to transporters and riboswitches inhibits potassium
        import (KupA/KupB, KimA, kdp operon).
    predicate_id: RO:0002212
  - subject: cyclic_di_amp
    predicate: modulates
    object: cell_volume_regulation
    description: c-di-AMP signaling acts as a master regulator of cell volume.
    evidence:
    - reference: DOI:10.1128/mmbr.00181-23
      notes: Review argues cyclic di-AMP is a master regulator of cell volume.
    predicate_id: RO:0002211
  - subject: osmolality
    predicate: upregulates
    object: kdpfabc_complex
    description: Elevated osmolality upregulates kdpFABC expression.
    evidence:
    - reference: DOI:10.1128/mmbr.00181-23
      notes: Osmolality upregulates kdpFABC expression (review-level, broadly useful).
  - subject: compatible_solute_transport
    predicate: causes
    object: osmoprotection
    description: Accumulation/transport of compatible solutes confers osmoprotection.
    evidence:
    - reference: DOI:10.1111/mec.16316
      notes: Compatible-solute biosynthesis/uptake and transporter genes -> osmotic
        protection.
    predicate_id: biolink:causes
  - subject: eps_matrix
    predicate: binds
    object: sodium_ion
    description: The EPS matrix binds Na+ cations.
    evidence:
    - reference: DOI:10.1093/femsre/fuaf020
      notes: The EPS matrix binds cations such as Na+ ions.
  - subject: eps_matrix
    predicate: promotes
    object: water_retention
    description: EPS matrix promotes water retention and reduces pericellular Na+
      toxicity.
    evidence:
    - reference: DOI:10.1093/femsre/fuaf020
      notes: Lowering effective pericellular Na+ and retaining water.
    predicate_id: RO:0002213
curation_history:
- timestamp: '2026-05-05T01:35:46.842087+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 definition and causal graph linking robust osmoadaptive
    flexibility to the broad-breadth NaCl-delta 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 6 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 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002212×1, RO:0002211×1, biolink:causes×1, RO:0002213×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:31Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:71578×1, CHEBI:29101×1).
  llm_assisted: true