identifier: METPO:1000333
label: NaCl optimum
definition: A salinity phenotype with numerical limits that supports the most efficient
  growth and reproduction of an organism.
definition_source: DOI:10.1093/femsre/fuy009
trait_category: ENVIRONMENT
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000532
- METPO:1000536
created_by: Luke Wang
evidence:
- reference: DOI:10.1093/femsre/fuy009
  snippet: optimal NaCl
  notes: Osmoadaptation review supports the NaCl concentration at which growth rate
    is maximal 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 balance at the optimal NaCl as the
    mechanistic basis of the NaCl-optimum phenotype.
causal_graphs:
- graph_id: nacl_optimum_balanced_osmoadaptation
  title: NaCl-optimum balanced osmoadaptation
  description: DOI-backed graph linking ambient NaCl, osmotic balance via compatible
    solutes and ion homeostasis, and maximal growth rate to the NaCl-optimum phenotype.
  nodes:
  - node_id: nacl_optimum_trait
    label: NaCl optimum
    node_type: TRAIT
    grounding: METPO:1000333
    description: NaCl concentration at which growth rate is maximal.
  - node_id: ambient_nacl
    label: ambient NaCl concentration
    node_type: ENVIRONMENTAL_FACTOR
    description: Ambient NaCl level imposed on the cell.
  - node_id: osmotic_balance
    label: osmotic balance
    node_type: BIOLOGICAL_PROCESS
    description: Steady-state matching of intracellular osmotic activity to the external
      salt concentration.
  - node_id: compatible_solutes
    label: compatible solutes
    node_type: CHEMICAL
    description: Organic osmolytes (ectoine, glycine betaine) maintaining cytoplasmic
      osmotic activity.
    grounding: CHEBI:25728
  - node_id: na_h_antiporters
    label: Na+/H+ antiporters
    node_type: GENE_OR_PROTEIN
    description: Membrane antiporters extruding Na+ in exchange for H+ to maintain
      ion homeostasis.
  - node_id: maximal_growth_rate
    label: maximal growth rate
    node_type: BIOLOGICAL_PROCESS
    description: Peak specific growth rate achieved at the optimal NaCl.
  - node_id: osmotic_stress
    label: osmotic stress
    node_type: BIOLOGICAL_PROCESS
    description: Cellular stress imposed by an external salt concentration that perturbs
      water activity.
    grounding: GO:0006970
  - node_id: salt_in_strategy
    label: salt-in strategy
    node_type: BIOLOGICAL_PROCESS
    description: Osmoadaptive strategy of accumulating molar inorganic ions (notably
      KCl) in the cytoplasm.
    grounding: METPO:1007720
  - node_id: intracellular_k_accumulation
    label: intracellular K+ accumulation
    node_type: BIOLOGICAL_PROCESS
    description: Accumulation of molar concentrations of potassium ions to balance
      external salt.
  - node_id: acidic_proteome
    label: acidic proteome
    node_type: QUALITY
    description: Highly acidic proteome adapted to function at high intracellular
      salt concentrations.
  - node_id: protein_stability_high_salt
    label: protein stability at high salt
    node_type: BIOLOGICAL_PROCESS
    description: Maintenance of protein folding and enzymatic function under near-saturating
      intracellular salt.
  - node_id: compatible_solute_accumulation
    label: compatible-solute accumulation
    node_type: BIOLOGICAL_PROCESS
    description: Accumulation of organic compatible solutes that do not interfere
      with enzymatic activity.
  - node_id: compatible_solute_uptake
    label: compatible solute uptake
    node_type: BIOLOGICAL_PROCESS
    description: Import of compatible solutes from the medium, energetically favored
      over de novo synthesis.
  - node_id: lower_energetic_cost
    label: lower energetic cost than de novo synthesis
    node_type: QUALITY
    description: Reduced metabolic energy expenditure relative to synthesizing compatible
      solutes de novo.
  - node_id: na_antiport_activity
    label: Na+/H+ antiport activity
    node_type: MOLECULAR_FUNCTION
    description: Antiporter-mediated Na+ extrusion lowering cytoplasmic Na+ to prevent
      toxicity.
  - node_id: cytoplasmic_na_homeostasis
    label: cytoplasmic Na+ homeostasis
    node_type: BIOLOGICAL_PROCESS
    description: Maintenance of low cytoplasmic Na+ concentration to prevent ion toxicity.
  edges:
  - subject: ambient_nacl
    predicate: causes
    object: osmotic_balance
    description: External NaCl level engages the osmoadaptive balance machinery.
    evidence:
    - reference: DOI:10.1186/1746-1448-4-2
      snippet: cope with the high salt concentrations
      notes: Supports osmotic balance as the response to ambient NaCl.
    predicate_id: biolink:causes
  - subject: compatible_solutes
    predicate: regulates
    object: osmotic_balance
    description: Compatible-solute accumulation maintains osmotic balance at the optimal
      NaCl.
    evidence:
    - reference: DOI:10.1093/femsre/fuy009
      snippet: synthesize organic osmotic solutes
      notes: Supports compatible solutes as the osmoadaptive osmolyte.
    predicate_id: RO:0002211
  - subject: na_h_antiporters
    predicate: enables
    object: osmotic_balance
    description: Na+/H+ antiporters support ion homeostasis underlying osmotic balance.
    evidence:
    - reference: DOI:10.1093/femsre/fuy009
      snippet: Na+/H+ antiporters
      notes: Supports antiporter-driven Na+ extrusion as an osmoadaptive mechanism.
    predicate_id: RO:0002327
  - subject: osmotic_balance
    predicate: enables
    object: maximal_growth_rate
    description: Maintained osmotic balance enables peak growth at the optimal NaCl
      concentration.
    evidence:
    - reference: DOI:10.1186/1746-1448-4-2
      snippet: optimum
      notes: Supports peak growth at the optimal NaCl as the operational definition
        of NaCl optimum.
    predicate_id: RO:0002327
  - subject: maximal_growth_rate
    predicate: manifests as
    object: nacl_optimum_trait
    description: The NaCl concentration at which peak growth is achieved manifests
      the NaCl-optimum phenotype.
    evidence:
    - reference: DOI:10.1093/femsre/fuy009
      snippet: optimal NaCl
      notes: Supports the trait endpoint.
    predicate_id: METPO:2007400
  - subject: ambient_nacl
    predicate: induces
    object: osmotic_stress
    description: External NaCl concentration imposes osmotic stress that drives osmoadaptation.
    evidence:
    - reference: DOI:10.1186/1746-1448-4-2
      notes: Halophilic microorganisms use two strategies to balance their cytoplasm
        osmotically with their medium (broad review-level mechanism).
  - subject: salt_in_strategy
    predicate: increases
    object: intracellular_k_accumulation
    description: The salt-in strategy accumulates molar concentrations of KCl in the
      cytoplasm.
    evidence:
    - reference: DOI:10.1186/1746-1448-4-2
      notes: The first involves accumulation of molar concentrations of KCl; strong
        general mechanism across extreme halophiles.
    predicate_id: RO:0002213
  - subject: acidic_proteome
    predicate: enables
    object: protein_stability_high_salt
    description: An acidic proteome enables protein stability and enzymatic function
      at high intracellular salt.
    evidence:
    - reference: DOI:10.1186/1746-1448-4-2
      notes: The proteome of such organisms is highly acidic; requires adaptation
        of the intracellular enzymatic machinery at near-saturating salt.
    predicate_id: RO:0002327
  - subject: compatible_solute_accumulation
    predicate: regulates
    object: osmotic_balance
    description: Accumulation of organic compatible solutes maintains osmotic balance
      without interfering with enzyme activity.
    evidence:
    - reference: DOI:10.1186/1746-1448-4-2
      notes: Exclude salt from the cytoplasm and synthesize/accumulate organic compatible
        solutes that do not interfere with enzymatic activity; broad canonical mechanism.
    predicate_id: RO:0002211
  - subject: compatible_solute_uptake
    predicate: associated with
    object: lower_energetic_cost
    description: Uptake of compatible solutes from the medium is energetically favored
      over de novo synthesis.
    evidence:
    - reference: DOI:10.3389/fmicb.2022.846677
      notes: Uptake of compatible solute from the medium is preferred over de novo
        synthesis, reflecting an energetically favored mechanism.
    predicate_id: biolink:associated_with
  - subject: na_antiport_activity
    predicate: regulates
    object: cytoplasmic_na_homeostasis
    description: Na+/H+ antiport activity lowers cytoplasmic Na+ to maintain ion homeostasis
      and prevent toxicity.
    evidence:
    - reference: DOI:10.1128/aem.00145-24
      notes: Na+/H+ antiporters function to lower cytoplasmic Na+ to prevent toxicity
        and contribute to salt acclimation.
    predicate_id: RO:0002211
curation_history:
- timestamp: '2026-05-05T01:35:46.815612+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, osmotic balance via
    compatible solutes and Na+/H+ antiporters, and maximal growth rate to the NaCl-optimum
    phenotype.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:30Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002327×1).
  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: '2026-05-24T04:13:18Z'
  curator: claude
  action: RENAME_PREDICATE_LABELS
  changes: 'Renamed 2 causal-edge predicate label(s) to align with existing groundings:
    maintains → regulates ×1; supports → enables ×1.'
  llm_assisted: true
- timestamp: '2026-05-24T04:13:21Z'
  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: '2026-05-24T04:38:00Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (CHEBI:65015×1).
  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:
    triggers → causes ×1.'
  llm_assisted: true
- timestamp: '2026-05-26T05:00:49Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:causes×1).
  llm_assisted: true
- timestamp: '2026-06-15T07:19:08Z'
  curator: claude
  action: FIX_NODE_GROUNDING_CURIE
  changes: Overwrote 1 causal-node grounding(s) to corrected CURIEs (phase-2 id-label
    fix; verified vs OAK).
  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 5 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002211×2, RO:0002213×1, RO:0002327×1, biolink:associated_with×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:0006970×1, METPO:1007720×1).
  llm_assisted: true