identifier: traitmech:000080
label: dormancy
definition: A reversible physiological state of greatly reduced metabolic activity
  that allows a cell to survive unfavorable conditions and later resuscitate, generating
  a microbial seed bank.
definition_source: DOI:10.1038/nrmicro2504
trait_category: PHYSIOLOGY
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000059
synonyms:
- synonym_text: dormant state
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1038/nrmicro2504
evidence:
- reference: DOI:10.1038/nrmicro2504
  notes: Lennon & Jones review microbial seed banks and the mechanisms by which microorganisms
    enter and exit dormancy; parent of VBNC and persister sub-variants.
- reference: DOI:10.1038/nrmicro1557
  notes: Lewis links dormancy to persister-cell survival and infectious disease.
canonical_examples:
- taxon_id: NCBITaxon:1773
  taxon_label: Mycobacterium tuberculosis
  note: "Paradigm of bacterial dormancy/non-replicating persistence (latent infection; DosR regulon)."
  reference: PMID:8675308
causal_graphs:
- graph_id: dormancy_seed_bank
  title: Reversible dormancy and resuscitation
  description: Evidence-backed causal sketch linking unfavorable conditions to a reversible
    dormant state forming a microbial seed bank.
  nodes:
  - node_id: dormancy_trait
    label: dormancy
    node_type: TRAIT
    grounding: traitmech:000080
    description: Capacity to enter a reversible low-activity state.
  - node_id: unfavorable_conditions
    label: unfavorable conditions
    node_type: ENVIRONMENTAL_FACTOR
    description: Stress or resource limitation triggering dormancy.
  - node_id: dormancy_process
    label: dormancy process
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0022611
    description: Entry into a reversible quiescent state.
  - node_id: nutrient_heat_stress
    label: nutrient limitation or heat stress
    node_type: ENVIRONMENTAL_FACTOR
    description: Nutrient starvation or heat stress that triggers the stringent response.
  - node_id: ppgpp_stringent_response
    label: (p)ppGpp stringent response
    node_type: BIOLOGICAL_PROCESS
    description: Guanosine tetra/pentaphosphate-mediated stringent response reprogramming
      cell activity.
  - node_id: toxin_antitoxin_modules
    label: toxin-antitoxin modules
    node_type: GENE_OR_PROTEIN
    description: Chromosomal toxin-antitoxin systems (e.g. hipAB, mazEF, relBE) inducing
      growth arrest.
  - node_id: ribosome_hibernation_factors
    label: ribosome hibernation factors (RMF/HPF/RaiA)
    node_type: GENE_OR_PROTEIN
    description: Factors that bind ribosomes to silence translation during dormancy.
  - node_id: protein_synthesis
    label: protein synthesis
    node_type: BIOLOGICAL_PROCESS
    description: Translation of mRNA into protein.
    grounding: GO:0006412
  - node_id: ribosome
    label: ribosome
    node_type: ORGANELLE
    description: Ribonucleoprotein machine for protein synthesis, protected during
      dormancy.
    grounding: GO:0005840
  - node_id: rpf_proteins
    label: resuscitation-promoting factors (Rpf)
    node_type: GENE_OR_PROTEIN
    description: Peptidoglycan-hydrolase Rpf proteins that reactivate dormant/VBNC
      cells.
  edges:
  - subject: unfavorable_conditions
    predicate: causes
    object: dormancy_process
    description: Adverse conditions induce entry into dormancy.
    evidence:
    - reference: DOI:10.1038/nrmicro2504
      notes: Lennon & Jones review entry/exit from dormancy (seed banks).
    predicate_id: biolink:causes
  - subject: dormancy_process
    predicate: enables
    object: dormancy_trait
    description: The dormancy process realizes the dormancy trait.
    evidence:
    - reference: DOI:10.1038/nrmicro1557
      notes: Lewis links dormancy to long-term survival.
    predicate_id: RO:0002327
  - subject: nutrient_heat_stress
    predicate: activates
    object: ppgpp_stringent_response
    description: Nutrient limitation and heat stress activate the (p)ppGpp stringent
      response.
    evidence:
    - reference: DOI:10.1186/s12866-024-03628-3
      notes: The stringent response mediated by (p)ppGpp is activated by nutrient/heat
        stresses.
    predicate_id: RO:0002213
  - subject: ppgpp_stringent_response
    predicate: causes
    object: dormancy_process
    description: (p)ppGpp reprograms cellular activity, resulting in slow growth or
      dormancy.
    evidence:
    - reference: DOI:10.1186/s12866-024-03628-3
      notes: (p)ppGpp can reprogram cellular life activities resulting in slow cell
        growth or dormancy.
    predicate_id: biolink:causes
  - subject: ppgpp_stringent_response
    predicate: upregulates
    object: toxin_antitoxin_modules
    description: (p)ppGpp upregulates multiple toxin-antitoxin modules.
    evidence:
    - reference: DOI:10.1186/s12866-024-03628-3
      notes: (p)ppGpp upregulates multiple TA modules (hipAB, dinJ/yafQ, mazEF, mqsRA,
        relBE, yafNO and hokB).
  - subject: ribosome_hibernation_factors
    predicate: turns off
    object: protein_synthesis
    description: Ribosome hibernation factors turn off protein synthesis during dormancy.
    evidence:
    - reference: DOI:10.3389/fmicb.2024.1386179
      notes: Classical ribosome hibernation factors (RMF, HPF, YfiA) turn off protein
        synthesis.
  - subject: ribosome_hibernation_factors
    predicate: protects
    object: ribosome
    description: Hibernation factor binding protects ribosomes from ribonuclease degradation.
    evidence:
    - reference: DOI:10.3389/fmicb.2024.1386179
      notes: Hibernation factors directly block ribonucleases from entering the ribosome
        in response to starvation.
  - subject: rpf_proteins
    predicate: promotes
    object: dormancy_process
    description: Rpf proteins promote resuscitation (exit) of dormant/VBNC bacteria.
    evidence:
    - reference: DOI:10.3390/microorganisms12081528
      notes: Rpfs reactivate dormant bacteria at very low concentrations.
    predicate_id: RO:0002213
curation_history:
- timestamp: '2026-06-04T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate PHYSIOLOGY axis class (dormancy) to parent the VBNC
    and persister-cell sub-variants.
  llm_assisted: true
- timestamp: '2026-06-08T13:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (reversible dormancy) with GO node grounding
    and biolink/RO predicate groundings; promoted PROPOSED to REVIEWED.
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 6 evidence-backed generic edges (7 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:14Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002213×2, biolink:causes×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:34Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 2 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0006412×1, GO:0005840×1).
  llm_assisted: true