NLR-like bNACHT system

traitmech:000408 · CLASS · PROPOSED

A phage defense system in which an organism possesses an NLR-related bacterial NACHT locus represented by DefenseFinder as an NLR_like_bNACHT01 or NLR_like_bNACHT09 single-profile model, encoding a NACHT-module STAND-family protein that can restrict bacteriophage production.

Trait evidence (12)

https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/
Here we show that proteins containing a NACHT module, the central feature of the animal nucleotide-binding domain and leucine-rich repeat-containing gene family (NLRs), are found in bacteria and defend against phages.

Kibby et al. support NACHT-module proteins as bacterial NLR-related proteins that defend against phages.
https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/
Genome context of bNACHT01, which is located near a CBASS system in Klebsiella pneumoniae MGH 35.

Kibby et al. identified a NACHT-module gene in Klebsiella pneumoniae MGH 35 before naming it bNACHT01.
https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/
We named this gene bacterial NACHT module-containing protein 1 (bNACHT01), and it did not appear to be in an operon with any other genes.

Kibby et al. named the selected NACHT-module gene bNACHT01.
https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/
bNACHT01 conferred over a 100-fold increase in protection against phage T4 and over a 1000-fold increase in protection against phages T5 and T6

bNACHT01 protected against phages T4, T5, and T6 in the E. coli heterologous assay.
https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/
bacteria expressing bNACHT01 restricted phage virion production and continued growing

Kibby et al. observed restricted phage virion production in bacteria expressing bNACHT01.
https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/
Mutation of R214 to alanine maintained expression of the protein but abrogated phage defense

An R214A mutation preserved bNACHT01 expression but abrogated defense, supporting a NACHT-dependent output.
https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/
Diverse bacterial NACHT proteins from different clades exhibited robust antiphage activity across a wide range of phages

Kibby et al. observed antiphage activity across diverse bacterial NACHT proteins.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
NLR | 10\.1101/2022\.07\.19\.500537 | Bacterial NLR-related proteins protect against phage

The DefenseFinder article registry maps the NLR family key to the Kibby et al. bNACHT preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
NLR NLR_like_bNACHT01 1 1 NLR_like_bNACHT01__NLR_like_bNACHT01

The DefenseFinder rules table models NLR_like_bNACHT01 as a one-profile NLR-family subsystem.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
NLR NLR_like_bNACHT09 1 1 NLR_like_bNACHT09__NLR_like_bNACHT09

The DefenseFinder rules table models NLR_like_bNACHT09 as a one-profile NLR-family subsystem.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| NLR_like_bNACHT01__NLR_like_bNACHT01 | NLR_like_bNACHT01__NLR_like_bNACHT01 | NLR_like_bNACHT01 | Custom | 250 |

The DefenseFinder HMM inventory records the NLR_like_bNACHT01 profile under the same-named model namespace.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| NLR_like_bNACHT09__NLR_like_bNACHT09 | NLR_like_bNACHT09__NLR_like_bNACHT09 | NLR_like_bNACHT09 | Custom | 400 |

The DefenseFinder HMM inventory records the NLR_like_bNACHT09 profile under the same-named model namespace.

NLR-like bNACHT loci restrict phage production

Conservative system-level sketch linking NLR-like bNACHT loci to bacteriophage restriction while leaving subtype triggers and effector outputs unresolved.

NONMECHANISTIC · The graph captures DefenseFinder NLR_like_bNACHT01 and NLR_like_bNACHT09 as named bNACHT phage-defense models supported by Kibby et al. bacterial NLR-related protein experiments while leaving natural host breadth, phage triggers, the exact profile-to-bNACHT01 or profile-to-bNACHT09 correspondences, and subtype-specific effector mechanisms unresolved.

Edge evidence

NLR-like bNACHT locus contributes to bNACHT phage restriction RO:0002326
Kibby et al. showed that bacterial NACHT proteins can restrict bacteriophages, and DefenseFinder models two NLR_like_bNACHT subtypes.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ Here we show that proteins containing a NACHT module, the central feature of the animal nucleotide-binding domain and leucine-rich repeat-containing gene family (NLRs), are found in bacteria and defend against phages. Kibby et al. support NACHT-module proteins as bacterial NLR-related proteins that defend against phages.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ bNACHT01 conferred over a 100-fold increase in protection against phage T4 and over a 1000-fold increase in protection against phages T5 and T6 bNACHT01 protected against phages T4, T5, and T6 in the E. coli heterologous assay.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ bacteria expressing bNACHT01 restricted phage virion production and continued growing Kibby et al. observed restricted phage virion production in bacteria expressing bNACHT01.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv NLR NLR_like_bNACHT01 1 1 NLR_like_bNACHT01__NLR_like_bNACHT01 The DefenseFinder rules table models NLR_like_bNACHT01 as a one-profile NLR-family subsystem.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv NLR NLR_like_bNACHT09 1 1 NLR_like_bNACHT09__NLR_like_bNACHT09 The DefenseFinder rules table models NLR_like_bNACHT09 as a one-profile NLR-family subsystem.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | NLR_like_bNACHT01__NLR_like_bNACHT01 | NLR_like_bNACHT01__NLR_like_bNACHT01 | NLR_like_bNACHT01 | Custom | 250 | The DefenseFinder HMM inventory records the NLR_like_bNACHT01 profile under the same-named model namespace.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | NLR_like_bNACHT09__NLR_like_bNACHT09 | NLR_like_bNACHT09__NLR_like_bNACHT09 | NLR_like_bNACHT09 | Custom | 400 | The DefenseFinder HMM inventory records the NLR_like_bNACHT09 profile under the same-named model namespace.
bNACHT phage restriction confers NLR-like bNACHT system METPO:2007700
NACHT-module-dependent phage restriction realizes the NLR-like bNACHT system trait.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ bacteria expressing bNACHT01 restricted phage virion production and continued growing Kibby et al. observed restricted phage virion production in bacteria expressing bNACHT01.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ Mutation of R214 to alanine maintained expression of the protein but abrogated phage defense An R214A mutation preserved bNACHT01 expression but abrogated defense, supporting a NACHT-dependent output.
NLR-like bNACHT system is a phage defense system rdfs:subClassOf
NLR-like bNACHT system possession is a phage-defense-system trait.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ Here we show that proteins containing a NACHT module, the central feature of the animal nucleotide-binding domain and leucine-rich repeat-containing gene family (NLRs), are found in bacteria and defend against phages. Kibby et al. support NACHT-module proteins as bacterial NLR-related proteins that defend against phages.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/ Diverse bacterial NACHT proteins from different clades exhibited robust antiphage activity across a wide range of phages Kibby et al. observed antiphage activity across diverse bacterial NACHT proteins.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md NLR | 10\.1101/2022\.07\.19\.500537 | Bacterial NLR-related proteins protect against phage The DefenseFinder article registry maps the NLR family key to the Kibby et al. bNACHT preprint.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1016/j.cell.2023.04.015

Parent traits (1)

phage defense system traitmech:000209

Synonyms (4)

NLR RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
bNACHT RELATED_SYNONYM · DOI:10.1016/j.cell.2023.04.015
NLR_like_bNACHT01 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
NLR_like_bNACHT09 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

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.

Klebsiella pneumoniae NCBITaxon:573 DOI:10.1016/j.cell.2023.04.015 Kibby et al. identified the bNACHT01 locus in Klebsiella pneumoniae MGH 35 and found that bNACHT01 expressed from its endogenous promoter in Escherichia coli protected against phages T4, T5, and T6.

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 exact mapping between DefenseFinder NLR_like_bNACHT01 and NLR_like_bNACHT09 profiles and the experimentally tested bNACHT proteins, natural host breadth, phage triggers, and bNACHT effector mechanisms before minting narrower bNACHT subtype traits.

KNOWLEDGE GAP OPEN nlr-like-bnacht-mechanism-gap · raised by codex · 2026-09-27

Attached to causal_graphs#nlr_like_bnacht_loci_restrict_phage

Kibby et al. support bacterial NACHT proteins as NLR-related phage-defense proteins and DefenseFinder models NLR_like_bNACHT01 and NLR_like_bNACHT09 as single-profile NLR-family subsystems. This first system-level record leaves profile-to-assayed-protein correspondence and subtype-specific trigger and effector mechanisms unresolved.

Evidence

https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/
Here we show that proteins containing a NACHT module, the central feature of the animal nucleotide-binding domain and leucine-rich repeat-containing gene family (NLRs), are found in bacteria and defend against phages.
https://pmc.ncbi.nlm.nih.gov/articles/PMC10294775/
bNACHT01 conferred over a 100-fold increase in protection against phage T4 and over a 1000-fold increase in protection against phages T5 and T6
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
NLR NLR_like_bNACHT01 1 1 NLR_like_bNACHT01__NLR_like_bNACHT01
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
NLR NLR_like_bNACHT09 1 1 NLR_like_bNACHT09__NLR_like_bNACHT09
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| NLR_like_bNACHT01__NLR_like_bNACHT01 | NLR_like_bNACHT01__NLR_like_bNACHT01 | NLR_like_bNACHT01 | Custom | 250 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| NLR_like_bNACHT09__NLR_like_bNACHT09 | NLR_like_bNACHT09__NLR_like_bNACHT09 | NLR_like_bNACHT09 | Custom | 400 |

Curation history

2026-09-27T12:41:08Z · MINTED_TRAITMECH_ID · codex
Minted NLR-like bNACHT system as a DOI-, PMID-, and stable-URL-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_v285.
2026-09-27T12:41:09Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed NLR-like bNACHT system canonical-example evidence and kept the example at the Klebsiella pneumoniae species level because Kibby et al. identified the tested bNACHT01 locus from K. pneumoniae MGH 35 but assayed the endogenous-promoter construct heterologously in Escherichia coli. No paid research was used.
2026-09-27T13:11:20Z · ADDRESS_REVIEW_FINDINGS · codex
Corrected the Cell paper attribution from Ofir et al. to Kibby et al. and narrowed the R214A evidence note so it no longer places the residue inside the NACHT module beyond the curated snippet.
2026-09-27T13:27:10Z · ADD_BNACHT01_SOURCE_STRAIN_SNIPPET · codex
Added verbatim Kibby et al. evidence that the NACHT-module gene later named bNACHT01 was identified in Klebsiella pneumoniae MGH 35, directly supporting the canonical example taxon.