identifier: traitmech:000094
label: CRISPR-Cas system
definition: A genomics trait describing possession of a CRISPR-Cas adaptive immune
  system that records fragments of invading nucleic acids in CRISPR arrays and uses
  Cas proteins to recognize and cleave matching sequences.
definition_source: DOI:10.1038/s41579-019-0299-x
trait_category: GENOMICS
term_kind: CLASS
mapping_status: REVIEWED
parent_traits:
- METPO:1000188
synonyms:
- synonym_text: CRISPR array
  synonym_type: RELATED_SYNONYM
  source: DOI:10.1038/s41579-019-0299-x
evidence:
- reference: DOI:10.1038/s41579-019-0299-x
  notes: Makarova et al. present an evolutionary classification of CRISPR-Cas systems
    into two classes, six types, and many subtypes.
- reference: DOI:10.1016/j.molcel.2014.03.011
  notes: Barrangou & Marraffini review CRISPR-Cas as prokaryotic adaptive immunity
    against invading genetic elements.
canonical_examples:
- taxon_id: NCBITaxon:1308
  taxon_label: Streptococcus thermophilus
  note: "Organism in which CRISPR-Cas adaptive immunity was experimentally demonstrated (Barrangou et al. 2007); dairy model for CRISPR biology."
  reference: PMID:17379808
causal_graphs:
- graph_id: crispr_adaptive_immunity
  title: CRISPR-Cas adaptive immunity against invading nucleic acids
  description: Evidence-backed causal sketch linking Cas-protein-mediated CRISPR machinery
    to defense against invading mobile genetic elements.
  nodes:
  - node_id: crispr_trait
    label: CRISPR-Cas system
    node_type: TRAIT
    grounding: traitmech:000094
    description: Possession of CRISPR arrays and Cas proteins for adaptive immunity.
  - node_id: cas_proteins
    label: Cas proteins
    node_type: GENE_OR_PROTEIN
    description: CRISPR-associated nucleases and accessory proteins.
  - node_id: defense_response_to_virus
    label: defense response to virus
    node_type: BIOLOGICAL_PROCESS
    grounding: GO:0051607
    description: Cleavage of invading viral or plasmid nucleic acids.
  - node_id: cas1_cas2_complex
    label: Cas1-Cas2 complex
    node_type: GENE_OR_PROTEIN
    description: Cas1-Cas2 integrase complex that captures and integrates new spacers.
  - node_id: spacer_acquisition
    label: spacer acquisition (adaptation)
    node_type: BIOLOGICAL_PROCESS
    description: Integration of invader-derived fragments as new spacers into the
      CRISPR array.
  - node_id: crispr_array_transcription
    label: CRISPR array transcription and processing
    node_type: BIOLOGICAL_PROCESS
    description: Transcription of the CRISPR array and processing of the precursor
      into mature crRNAs.
  - node_id: crrna
    label: crRNA
    node_type: GENE_OR_PROTEIN
    description: Mature CRISPR RNA that guides Cas effectors to complementary targets.
  - node_id: crrna_effector_complex
    label: crRNA-Cas effector complex
    node_type: GENE_OR_PROTEIN
    description: Ribonucleoprotein complex of crRNA and Cas effector(s) performing
      interference.
  - node_id: invading_nucleic_acid
    label: invading nucleic acid target
    node_type: CHEMICAL
    description: Foreign DNA or RNA from phages, plasmids, or other mobile genetic
      elements.
  - node_id: phage_plasmid_pressure
    label: phage and plasmid pressure
    node_type: ENVIRONMENTAL_FACTOR
    description: Selective pressure from invading bacteriophages and plasmids.
  edges:
  - subject: cas_proteins
    predicate: enables
    object: crispr_trait
    description: Cas nucleases together with CRISPR arrays realize the adaptive immune
      system.
    evidence:
    - reference: DOI:10.1038/s41579-019-0299-x
      notes: Makarova et al. classify CRISPR-Cas systems by Cas-protein content.
    predicate_id: RO:0002327
  - subject: crispr_trait
    predicate: participates in
    object: defense_response_to_virus
    description: CRISPR-Cas mounts sequence-specific defense against invading genetic
      elements.
    evidence:
    - reference: DOI:10.1016/j.molcel.2014.03.011
      notes: Barrangou & Marraffini frame CRISPR-Cas as prokaryotic adaptive immunity.
    predicate_id: biolink:participates_in
  - subject: cas1_cas2_complex
    predicate: integrates spacers via
    object: spacer_acquisition
    description: Cas1-Cas2 complexes act as molecular recorders that integrate new
      spacers into the CRISPR array during adaptation.
    evidence:
    - reference: DOI:10.5483/bmbrep.2023-0050
      notes: Cas1-Cas2 complexes function as molecular recorders to integrate spacers;
        core adaptation edge, broad across canonical CRISPR-Cas systems.
  - subject: crispr_array_transcription
    predicate: produces
    object: crrna
    description: Transcription and processing of the CRISPR array yields mature crRNAs.
    evidence:
    - reference: DOI:10.1016/j.heliyon.2024.e39538
      notes: CRISPR arrays are transcribed and processed into crRNAs; general edge
        across systems.
    predicate_id: METPO:2000202
  - subject: crrna
    predicate: guides
    object: crrna_effector_complex
    description: crRNA assembles with Cas effector(s) to form the interference-competent
      effector complex.
    evidence:
    - reference: DOI:10.5483/bmbrep.2023-0050
      notes: Effector-crRNA complexes drive the RNA-guided interference pathways.
  - subject: crrna_effector_complex
    predicate: cleaves
    object: invading_nucleic_acid
    description: The crRNA-Cas effector complex recognizes and cleaves complementary
      invading nucleic acid targets.
    evidence:
    - reference: DOI:10.5483/bmbrep.2023-0050
      notes: Effector-crRNA complexes perform RNA-guided interference against invading
        targets; high-level interference edge.
  - subject: phage_plasmid_pressure
    predicate: selects for
    object: crispr_trait
    description: Selective pressure from invading phages and plasmids favors maintenance
      of CRISPR-Cas immunity.
    evidence:
    - reference: DOI:10.5483/bmbrep.2023-0050
      notes: CRISPR-Cas protects hosts from invasion by bacteriophages and plasmids;
        broad ecological selection edge.
    predicate_id: METPO:2007401
curation_history:
- timestamp: '2026-06-05T00:00:00Z'
  curator: claude
  action: PROPOSED_FROM_RESEARCH
  changes: Proposed candidate GENOMICS trait (CRISPR-Cas system) from literature research
    to fill the genome-defense-system gap.
  llm_assisted: true
- timestamp: '2026-06-08T14:00:00Z'
  curator: claude
  action: CURATED_CAUSAL_GRAPH
  changes: Added evidence-backed causal graph (CRISPR adaptive immunity) with GO node
    grounding and RO/biolink predicate groundings; promoted PROPOSED to REVIEWED.
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 5 evidence-backed generic edges (7 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:11Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (METPO:2000202×1, METPO:2007401×1).
  llm_assisted: true