TraitMech

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RloC system

traitmech:000366 · CLASS · PROPOSED

A phage defense system in which an organism possesses a genome-encoded RloC locus represented by DefenseFinder as a one-profile model requiring RloC__RloC.

Trait evidence (8)

  • PMID:18681940
    The conserved bacterial protein RloC, a distant homologue of the tRNA(Lys) anticodon nuclease (ACNase) PrrC, is shown here to act as a wobble nucleotide-excising and Zn(++)-responsive tRNase.

    Davidov and Kaufmann identify RloC as a conserved bacterial wobble nucleotide-excising, zinc-responsive tRNase related to PrrC.

  • PMID:18681940
    Geobacillus kaustophilus RloC expressed in Escherichia coli exhibited ACNase activity that differed from PrrC's in substrate preference and ability to excise the wobble nucleotide.

    Davidov and Kaufmann support wobble nucleotide excision by Geobacillus kaustophilus RloC expressed in Escherichia coli.

  • PMID:26031711
    In contrast, RloC is rarely linked to an RM protein, and its ACNase is regulated by an internal switch responsive to double-stranded DNA breaks.

    Bitton et al. describe RloC ACNase regulation by an internal switch that responds to double-stranded DNA breaks.

  • PMID:26031711
    Consistent with these predictions we show that Acinetobacter baylyi RloC expressed in Escherichia coli is activated by wild-type phage T4 but not by a mutant impaired in host DNA degradation.

    Bitton et al. show that Acinetobacter baylyi RloC expressed in Escherichia coli is activated by wild-type phage T4, but not by a host-DNA-degradation mutant.

  • PMID:26031711
    Nonetheless, T4's plating efficiency was inefficiently impaired by AbaRloC, presumably due to a decoy function of the phage encoded tRNA target, the absence of which exacerbated the restriction.

    Bitton et al. report that Acinetobacter baylyi RloC inefficiently impairs wild-type T4 plating and more strongly restricts a phage mutant lacking the decoy tRNA target.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    RloC | 10\.1111/j\.1365-2958\.2008\.06387\.x | RloC: a wobble nucleotide-excising and zinc-responsive bacterial tRNase

    The DefenseFinder article registry maps the named RloC system to Davidov and Kaufmann's wobble nucleotide-excising tRNase paper.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
    RloC RloC 1 1 RloC__RloC

    The DefenseFinder rules table models RloC as a one-profile system requiring the RloC__RloC profile.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
    | RloC__RloC | RloC__RloC | RloC | Custom | 120 |

    The DefenseFinder HMM inventory records RloC__RloC under RloC.

RloC loci encode DNA-break-responsive activation

Conservative system-level sketch linking possession of a DefenseFinder RloC locus to DNA-break-responsive RloC anticodon nuclease activation without asserting natural host breadth, the endogenous phage trigger, or exact RloC profile-to-activity mapping.

NONMECHANISTIC · The graph captures RloC as a named DefenseFinder one-profile phage-defense system while leaving natural host breadth, the endogenous DNA-break trigger, phage restriction strength, and RloC profile-to-activity mapping unresolved.

RloC loci encode DNA-break-responsive activation Interactive directed graph showing evidence-backed causal relationships for RloC system.

Edge evidence

  • RloC locus contributes to DNA-break-responsive RloC activation RO:0002326

    RloC encodes a wobble nucleotide-excising anticodon nuclease, Acinetobacter baylyi RloC responds to T4 host DNA degradation when expressed in Escherichia coli, and DefenseFinder models RloC as a one-profile system.

  • DNA-break-responsive RloC activation confers RloC system METPO:2007700

    DNA-break-responsive RloC anticodon nuclease activation realizes the RloC system trait.

    • PMID:26031711 Consistent with these predictions we show that Acinetobacter baylyi RloC expressed in Escherichia coli is activated by wild-type phage T4 but not by a mutant impaired in host DNA degradation. Bitton et al. show that wild-type phage T4 activates Acinetobacter baylyi RloC expressed in Escherichia coli.
    • PMID:26031711 Nonetheless, T4's plating efficiency was inefficiently impaired by AbaRloC, presumably due to a decoy function of the phage encoded tRNA target, the absence of which exacerbated the restriction. Bitton et al. report that Acinetobacter baylyi RloC inefficiently impairs wild-type T4 plating and more strongly restricts a phage mutant lacking the decoy tRNA target.
  • RloC system is a phage defense system rdfs:subClassOf

    RloC system possession is a phage-defense-system trait.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1111/j.1365-2958.2008.06387.x

Parent traits (1)

Synonyms (2)

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

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 RloC host breadth, endogenous RloC activation triggers, phage restriction strength, and RloC profile-to-activity mapping before minting narrower RloC mechanism children.

KNOWLEDGE GAP OPEN rloc-mechanism-gap · raised by codex · 2026-09-22

Attached to causal_graphs#rloc_locus_triggers_dna_break_responsive_activation

Davidov and Kaufmann support RloC as a bacterial wobble nucleotide-excising tRNase, Bitton et al. show that Acinetobacter baylyi RloC responds to phage T4 host DNA degradation in an Escherichia coli expression context, and DefenseFinder models RloC as a one-profile system with an RloC__RloC marker. Natural host breadth, native phage triggers, restriction strength, and profile-to-activity mapping remain unresolved.

Evidence

  • PMID:26031711
    The natural role of the conserved bacterial anticodon nuclease (ACNase) RloC is not known, but traits that set it apart from the homologous phage T4-excluding ACNase PrrC could provide relevant clues.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted RloC 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_v243.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    Reviewed the RloC canonical_examples gap and left canonical_examples empty: the current evidence supports RloC as a wobble nucleotide-excising tRNase, T4 activation of Acinetobacter baylyi RloC expressed in Escherichia coli, and the pinned DefenseFinder RloC profile, but does not cite a directly observed natural microbial taxon with a source-backed RloC locus broad enough for a canonical example. No paid research was used.