identifier: traitmech:000332 label: Nhi system definition: A phage defense system in which an organism possesses an Nhi-family locus represented by the DefenseFinder Nhi__Nhi profile and exemplified by a single enzyme with nuclease and helicase activities that protects against diverse staphylococcal phages, prevents phage DNA accumulation, and is inferred to target and degrade phage-specific replication intermediates. definition_source: DOI:10.1016/j.chom.2022.03.001 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Nhi synonym_type: RELATED_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md evidence: - reference: DOI:10.1016/j.chom.2022.03.001 snippet: Here, we describe a unique mode of nucleic acid immunity mediated by a single enzyme with nuclease and helicase activities, herein referred to as Nhi (nuclease-helicase immunity) notes: Bari et al. define Nhi as nuclease-helicase immunity mediated by one enzyme with nuclease and helicase activities. - reference: DOI:10.1016/j.chom.2022.03.001 snippet: This enzyme provides robust protection against diverse staphylococcal phages and prevents phage DNA accumulation in cells stripped of all other known defenses notes: Bari et al. support Nhi as a system that protects against diverse staphylococcal phages and prevents phage DNA accumulation even without other known defenses. - reference: DOI:10.1016/j.chom.2022.03.001 snippet: Our observations support a model in which Nhi targets and degrades phage-specific replication intermediates notes: Bari et al. infer that Nhi targets and degrades phage-specific replication intermediates. - reference: DOI:10.1016/j.chom.2022.03.001 snippet: Nhi homologs are distributed in diverse bacteria and exhibit functional conservation notes: Bari et al. support functional conservation of Nhi homologs across diverse bacteria. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Nhi | 10\.1101/776245 | A unique mode of nucleic acid immunity performed by a single multifunctional enzyme notes: The DefenseFinder article registry maps the named Nhi model namespace to the Bari et al. nuclease-helicase immunity preprint. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Nhi\tNhi\t1\t1\tNhi__Nhi" notes: The DefenseFinder rules table models Nhi as a one-component system requiring the Nhi__Nhi profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Nhi__Nhi | Nhi__Nhi | Nhi | Custom | 100 |' notes: The DefenseFinder HMM inventory records Nhi__Nhi under the Nhi model namespace. canonical_examples: - taxon_id: NCBITaxon:1282 taxon_label: Staphylococcus epidermidis note: Bari et al. characterized Nhi from the Staphylococcus epidermidis RP62a locus and showed that this single nuclease-helicase enzyme protects against diverse staphylococcal phages. reference: DOI:10.1016/j.chom.2022.03.001 causal_graphs: - graph_id: nhi_locus_restricts_staphylococcal_phages title: Nhi loci provide nuclease-helicase phage defense description: Conservative system-level sketch linking an Nhi locus to nuclease-helicase immunity, phage-replication-intermediate degradation, prevention of phage DNA accumulation, and the Nhi system trait. scope_status: NONMECHANISTIC scope_notes: The graph captures Nhi as a named single-profile phage defense system without asserting the direct phage trigger, the exact nuclease-helicase substrate, an accession-level natural host protein, or the full taxonomic breadth of functional homologs. nodes: - node_id: nhi_locus label: Nhi locus node_type: GENETIC_ELEMENT description: An Nhi-family anti-phage defense locus represented by the DefenseFinder Nhi__Nhi profile. - node_id: nhi_nuclease_helicase_immunity label: Nhi nuclease-helicase immunity node_type: BIOLOGICAL_PROCESS description: Nucleic acid immunity mediated by one enzyme with nuclease and helicase activities. - node_id: phage_specific_replication_intermediate_degradation label: phage-specific replication intermediate degradation node_type: BIOLOGICAL_PROCESS description: Targeting and degradation of phage-specific replication intermediates by Nhi. - node_id: phage_dna_accumulation_prevention label: phage DNA accumulation prevention node_type: BIOLOGICAL_PROCESS description: Prevention of phage DNA accumulation during Nhi anti-phage activity. - node_id: nhi_system_trait label: Nhi system node_type: TRAIT grounding: traitmech:000332 description: Possession of a genome-encoded Nhi nuclease-helicase phage-defense system. - node_id: phage_defense_system label: phage defense system node_type: TRAIT grounding: traitmech:000209 description: Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection. edges: - subject: nhi_locus predicate: contributes to predicate_id: RO:0002326 object: nhi_nuclease_helicase_immunity description: The Nhi locus encodes a single-enzyme nuclease-helicase immunity system, and DefenseFinder models Nhi as a one-profile system. evidence: - reference: DOI:10.1016/j.chom.2022.03.001 snippet: Here, we describe a unique mode of nucleic acid immunity mediated by a single enzyme with nuclease and helicase activities, herein referred to as Nhi (nuclease-helicase immunity) notes: Bari et al. describe Nhi as immunity mediated by one enzyme with nuclease and helicase activities. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "Nhi\tNhi\t1\t1\tNhi__Nhi" notes: The DefenseFinder rules table models Nhi as a one-component system requiring the Nhi__Nhi profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| Nhi__Nhi | Nhi__Nhi | Nhi | Custom | 100 |' notes: The DefenseFinder HMM inventory records Nhi__Nhi under the Nhi model namespace. - subject: nhi_nuclease_helicase_immunity predicate: contributes to predicate_id: RO:0002326 object: phage_specific_replication_intermediate_degradation description: Nhi nuclease-helicase immunity is inferred to target and degrade phage-specific replication intermediates. evidence: - reference: DOI:10.1016/j.chom.2022.03.001 snippet: Our observations support a model in which Nhi targets and degrades phage-specific replication intermediates notes: Bari et al. support this as a model for Nhi rather than as a completely resolved direct-substrate assignment. - subject: phage_specific_replication_intermediate_degradation predicate: contributes to predicate_id: RO:0002326 object: phage_dna_accumulation_prevention description: Degradation of phage-specific replication intermediates explains Nhi-dependent prevention of phage DNA accumulation. evidence: - reference: DOI:10.1016/j.chom.2022.03.001 snippet: This enzyme provides robust protection against diverse staphylococcal phages and prevents phage DNA accumulation in cells stripped of all other known defenses notes: Bari et al. directly observed prevention of phage DNA accumulation in Nhi-containing cells; the replication-intermediate target is recorded as the authors' model. - reference: DOI:10.1016/j.chom.2022.03.001 snippet: Our observations support a model in which Nhi targets and degrades phage-specific replication intermediates notes: Bari et al. model Nhi as targeting and degrading phage-specific replication intermediates. - subject: phage_dna_accumulation_prevention predicate: confers predicate_id: METPO:2007700 object: nhi_system_trait description: Preventing phage DNA accumulation realizes the Nhi phage-defense trait. evidence: - reference: DOI:10.1016/j.chom.2022.03.001 snippet: This enzyme provides robust protection against diverse staphylococcal phages and prevents phage DNA accumulation in cells stripped of all other known defenses notes: Bari et al. connect Nhi to protection against staphylococcal phages and to prevention of phage DNA accumulation. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: Nhi | 10\.1101/776245 | A unique mode of nucleic acid immunity performed by a single multifunctional enzyme notes: The DefenseFinder article registry maps the named Nhi model namespace to the Bari et al. nuclease-helicase immunity preprint. - subject: nhi_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Nhi system possession is a bacterial phage-defense system. evidence: - reference: DOI:10.1016/j.chom.2022.03.001 snippet: highlighting the versatility of such compact weapons as major players in antiphage defense notes: Bari et al. place Nhi among compact anti-phage defense systems. discussions: - discussion_id: nhi-trigger-and-substrate-gap prompt: Resolve the Nhi phage trigger, exact replication-intermediate substrate, accession-level natural host protein, and homolog breadth before minting narrower mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Bari et al. support Nhi as a compact single-enzyme nuclease-helicase immunity system that prevents phage DNA accumulation and is inferred to target and degrade phage-specific replication intermediates. DefenseFinder models Nhi with a one-profile rule, but this first system-level record leaves the direct phage trigger, exact substrate, natural-host accession, and full taxonomic breadth of functional homologs unresolved. attaches_to: - causal_graphs#nhi_locus_restricts_staphylococcal_phages posed_by: codex posed_date: '2026-09-21' curation_history: - timestamp: '2026-09-21T16:05:11Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted Nhi system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v209. llm_assisted: true