Nhi system

traitmech:000332 · CLASS · PROPOSED

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.

Trait evidence (7)

DOI:10.1016/j.chom.2022.03.001
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)

Bari et al. define Nhi as nuclease-helicase immunity mediated by one enzyme with nuclease and helicase activities.
DOI:10.1016/j.chom.2022.03.001
This enzyme provides robust protection against diverse staphylococcal phages and prevents phage DNA accumulation in cells stripped of all other known defenses

Bari et al. support Nhi as a system that protects against diverse staphylococcal phages and prevents phage DNA accumulation even without other known defenses.
DOI:10.1016/j.chom.2022.03.001
Our observations support a model in which Nhi targets and degrades phage-specific replication intermediates

Bari et al. infer that Nhi targets and degrades phage-specific replication intermediates.
DOI:10.1016/j.chom.2022.03.001
Nhi homologs are distributed in diverse bacteria and exhibit functional conservation

Bari et al. support functional conservation of Nhi homologs across diverse bacteria.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Nhi | 10\.1101/776245 | A unique mode of nucleic acid immunity performed by a single multifunctional enzyme

The DefenseFinder article registry maps the named Nhi model namespace to the Bari et al. nuclease-helicase immunity preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Nhi Nhi 1 1 Nhi__Nhi

The DefenseFinder rules table models Nhi as a one-component system requiring the Nhi__Nhi profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Nhi__Nhi | Nhi__Nhi | Nhi | Custom | 100 |

The DefenseFinder HMM inventory records Nhi__Nhi under the Nhi model namespace.

Nhi loci provide nuclease-helicase phage defense

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.

NONMECHANISTIC · 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.

Edge evidence

Nhi locus contributes to Nhi nuclease-helicase immunity RO:0002326
The Nhi locus encodes a single-enzyme nuclease-helicase immunity system, and DefenseFinder models Nhi as a one-profile system.
- DOI:10.1016/j.chom.2022.03.001 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) Bari et al. describe Nhi as immunity mediated by one enzyme with nuclease and helicase activities.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Nhi Nhi 1 1 Nhi__Nhi The DefenseFinder rules table models Nhi as a one-component system requiring the Nhi__Nhi profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | Nhi__Nhi | Nhi__Nhi | Nhi | Custom | 100 | The DefenseFinder HMM inventory records Nhi__Nhi under the Nhi model namespace.
Nhi nuclease-helicase immunity contributes to phage-specific replication intermediate degradation RO:0002326
Nhi nuclease-helicase immunity is inferred to target and degrade phage-specific replication intermediates.
- DOI:10.1016/j.chom.2022.03.001 Our observations support a model in which Nhi targets and degrades phage-specific replication intermediates Bari et al. support this as a model for Nhi rather than as a completely resolved direct-substrate assignment.
phage-specific replication intermediate degradation contributes to phage DNA accumulation prevention RO:0002326
Degradation of phage-specific replication intermediates explains Nhi-dependent prevention of phage DNA accumulation.
- DOI:10.1016/j.chom.2022.03.001 This enzyme provides robust protection against diverse staphylococcal phages and prevents phage DNA accumulation in cells stripped of all other known defenses Bari et al. directly observed prevention of phage DNA accumulation in Nhi-containing cells; the replication-intermediate target is recorded as the authors' model.
- DOI:10.1016/j.chom.2022.03.001 Our observations support a model in which Nhi targets and degrades phage-specific replication intermediates Bari et al. model Nhi as targeting and degrading phage-specific replication intermediates.
phage DNA accumulation prevention confers Nhi system METPO:2007700
Preventing phage DNA accumulation realizes the Nhi phage-defense trait.
- DOI:10.1016/j.chom.2022.03.001 This enzyme provides robust protection against diverse staphylococcal phages and prevents phage DNA accumulation in cells stripped of all other known defenses Bari et al. connect Nhi to protection against staphylococcal phages and to prevention of phage DNA accumulation.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Nhi | 10\.1101/776245 | A unique mode of nucleic acid immunity performed by a single multifunctional enzyme The DefenseFinder article registry maps the named Nhi model namespace to the Bari et al. nuclease-helicase immunity preprint.
Nhi system is a phage defense system rdfs:subClassOf
Nhi system possession is a bacterial phage-defense system.
- DOI:10.1016/j.chom.2022.03.001 highlighting the versatility of such compact weapons as major players in antiphage defense Bari et al. place Nhi among compact anti-phage defense systems.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1016/j.chom.2022.03.001

Parent traits (1)

phage defense system traitmech:000209

Synonyms (1)

Nhi RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

Staphylococcus epidermidis NCBITaxon:1282 DOI:10.1016/j.chom.2022.03.001 Bari et al. characterized Nhi from the Staphylococcus epidermidis RP62a locus and showed that this single nuclease-helicase enzyme protects against diverse staphylococcal phages.

Discussions and Knowledge Gaps (1)

Open questions attached to this trait. Seeded by just knowledge-gap-scan and curated; see the corpus-wide index.

Resolve the Nhi phage trigger, exact replication-intermediate substrate, accession-level natural host protein, and homolog breadth before minting narrower mechanism children.

KNOWLEDGE GAP OPEN nhi-trigger-and-substrate-gap · raised by codex · 2026-09-21

Attached to causal_graphs#nhi_locus_restricts_staphylococcal_phages

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.

Curation history

2026-09-21T16:05:11Z · MINTED_TRAITMECH_ID · codex
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.