RnlAB system

traitmech:000367 · CLASS · PROPOSED

A phage defense system in which an organism possesses a genome-encoded RnlAB toxin-antitoxin locus represented by DefenseFinder as a two-profile model requiring RnlAB__RnlA and RnlAB__RnlB.

Trait evidence (10)

PMID:20980243
RNase LS was originally identified as a potential antagonist of bacteriophage T4 infection. When T4 dmd is defective, RNase LS activity rapidly increases after T4 infection and cleaves T4 mRNAs to antagonize T4 reproduction.

Koga et al. frame RnlA-dependent RNase LS activity as a potential antagonist of bacteriophage T4 dmd mutants.
PMID:20980243
Here we show that rnlA, a structural gene of RNase LS, encodes a novel toxin, and that rnlB (formally yfjO), located immediately downstream of rnlA, encodes an antitoxin against RnlA.

Koga et al. identify rnlA as the RNase LS toxin gene and rnlB as the neighboring cognate antitoxin gene.
PMID:20980243
Pull-down analysis showed a specific interaction between RnlA and RnlB.

Koga et al. support direct RnlA/RnlB interaction by pull-down analysis.
PMID:20980243
All of these results suggested that rnlA-rnlB define a new toxin-antitoxin (TA) system.

Koga et al. define rnlA-rnlB as a new toxin-antitoxin system.
PMID:22403819
Predicted proteins encoded by these two ORFs were found to share a weak homology with RnlA and RnlB, respectively, a toxin–antitoxin system encoded on the E. coli K-12 chromosome.

Otsuka and Yonesaki describe RnlA/RnlB as a toxin-antitoxin system encoded on the Escherichia coli K-12 chromosome.
PMID:22403819
T4 phage Dmd suppressed the toxicities of both RnlA and LsoA by direct interaction, the first example of a phage with an antitoxin against multiple toxins.

Otsuka and Yonesaki support T4 Dmd as a phage antitoxin that suppresses RnlA toxicity by direct interaction.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
RnlAB | 10\.1534/genetics\.110\.121798 | Escherichia coli rnlA and rnlB compose a novel toxin-antitoxin system

The DefenseFinder article registry maps the named RnlAB system to Koga et al.'s rnlA-rnlB toxin-antitoxin paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
RnlAB RnlAB 2 2 RnlAB__RnlA, RnlAB__RnlB

The DefenseFinder rules table models RnlAB as a two-profile system requiring the RnlAB__RnlA and RnlAB__RnlB profiles.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| RnlAB__RnlA | RnlAB__RnlA | RnlAB | Custom | 20 |

The DefenseFinder HMM inventory records RnlAB__RnlA under RnlAB.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| RnlAB__RnlB | RnlAB__RnlB | RnlAB | Custom | 20 |

The DefenseFinder HMM inventory records RnlAB__RnlB under RnlAB.

RnlAB loci support RnlA-dependent RNase LS activity

Conservative system-level sketch linking possession of an RnlAB locus to RnlA-dependent RNase LS activity against bacteriophage T4 dmd mutants without asserting a wild-type-phage trigger, broad phage host range, or exact RnlAB profile-to-activity mapping.

NONMECHANISTIC · The graph captures RnlAB as a named DefenseFinder two-profile phage-defense system while leaving natural phage breadth, wild-type T4 evasion through Dmd, induction or activation routes in non-T4 contexts, and RnlAB profile-to-activity mapping unresolved.

Edge evidence

RnlAB locus contributes to RnlA-dependent RNase LS activity RO:0002326
Koga et al. show that rnlA encodes the RNase LS toxin and rnlB encodes the cognate antitoxin; DefenseFinder models RnlAB as a two-profile system.
- PMID:20980243 Here we show that rnlA, a structural gene of RNase LS, encodes a novel toxin, and that rnlB (formally yfjO), located immediately downstream of rnlA, encodes an antitoxin against RnlA. Koga et al. identify rnlA as the RNase LS toxin gene and rnlB as the antitoxin gene.
- PMID:20980243 Pull-down analysis showed a specific interaction between RnlA and RnlB. Koga et al. show that RnlA and RnlB specifically interact.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md RnlAB | 10\.1534/genetics\.110\.121798 | Escherichia coli rnlA and rnlB compose a novel toxin-antitoxin system The DefenseFinder article registry maps the named RnlAB system to Koga et al.'s rnlA-rnlB toxin-antitoxin paper.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv RnlAB RnlAB 2 2 RnlAB__RnlA, RnlAB__RnlB The DefenseFinder rules table models RnlAB as a two-profile system requiring the RnlAB__RnlA and RnlAB__RnlB profiles.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | RnlAB__RnlA | RnlAB__RnlA | RnlAB | Custom | 20 | The DefenseFinder HMM inventory records RnlAB__RnlA under RnlAB.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | RnlAB__RnlB | RnlAB__RnlB | RnlAB | Custom | 20 | The DefenseFinder HMM inventory records RnlAB__RnlB under RnlAB.
RnlA-dependent RNase LS activity confers RnlAB system METPO:2007700
RnlA-dependent RNase LS activity against T4 dmd-mutant mRNAs realizes the RnlAB system trait.
- PMID:20980243 RNase LS was originally identified as a potential antagonist of bacteriophage T4 infection. When T4 dmd is defective, RNase LS activity rapidly increases after T4 infection and cleaves T4 mRNAs to antagonize T4 reproduction. Koga et al. support RNase LS antagonism of T4 dmd-mutant reproduction.
- PMID:22403819 T4 phage Dmd suppressed the toxicities of both RnlA and LsoA by direct interaction, the first example of a phage with an antitoxin against multiple toxins. Otsuka and Yonesaki show phage Dmd can suppress RnlA toxicity by direct interaction.
RnlAB system is a phage defense system rdfs:subClassOf
RnlAB system possession is a phage-defense-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md RnlAB | 10\.1534/genetics\.110\.121798 | Escherichia coli rnlA and rnlB compose a novel toxin-antitoxin system The DefenseFinder article registry maps the named RnlAB system to Koga et al.'s rnlA-rnlB toxin-antitoxin paper.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv RnlAB RnlAB 2 2 RnlAB__RnlA, RnlAB__RnlB The DefenseFinder rules table models RnlAB as a two-profile system requiring the RnlAB__RnlA and RnlAB__RnlB profiles.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1534/genetics.110.121798

Parent traits (1)

phage defense system traitmech:000209

Synonyms (3)

RnlAB RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
RnlAB__RnlA RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
RnlAB__RnlB RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.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.

Escherichia coli K-12 NCBITaxon:83333 DOI:10.1111/j.1365-2958.2012.07975.x Otsuka and Yonesaki describe the RnlA/RnlB toxin-antitoxin system as encoded on the Escherichia coli K-12 chromosome.

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 natural RnlAB phage breadth, wild-type T4 evasion through Dmd, induction or activation routes in non-T4 contexts, and RnlAB profile-to-activity mapping before minting narrower RnlAB mechanism children.

KNOWLEDGE GAP OPEN rnlab-phage-breadth-evasion-gap · raised by codex · 2026-09-22

Attached to causal_graphs#rnlab_locus_antagonizes_t4_dmd_mutants

Koga et al. support RnlA/RnlB as an Escherichia coli K-12 toxin-antitoxin system whose RNase LS activity can antagonize T4 dmd mutants, Otsuka and Yonesaki show that T4 phage Dmd suppresses RnlA toxicity, and DefenseFinder models RnlAB as a two-profile system with RnlAB__RnlA and RnlAB__RnlB markers. Natural phage breadth, wild-type T4 evasion, non-T4 activation contexts, and profile-to-activity mapping remain unresolved.

Evidence

PMID:22403819
T4 phage Dmd suppressed the toxicities of both RnlA and LsoA by direct interaction, the first example of a phage with an antitoxin against multiple toxins.

Curation history

2026-09-22T13:54:00Z · MINTED_TRAITMECH_ID · codex
Minted RnlAB 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_v244.