TraitMech

TraitMech › GENOMICS

PARIS system

traitmech:000237 · CLASS · PROPOSED

An abortive infection system in which an organism possesses a phage anti-restriction-induced system locus encoding an AriA ABC ATPase sensor and an AriB TOPRIM-family nuclease whose activation by phage anti-restriction or other foreign proteins releases AriB to inhibit translation through lysine tRNA cleavage and block bacteriophage propagation.

Trait evidence (8)

  • DOI:10.1016/j.chom.2022.02.018
    We validate the activity of diverse systems and describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein

    Rousset et al. support PARIS as a named abortive infection system activated by a phage anti-restriction protein.

  • DOI:10.1016/j.chom.2022.02.018
    phage anti-restriction-induced system (PARIS), an abortive infection system that triggers growth arrest upon sensing an anti-restriction protein

    Rousset et al. support the PARIS long-form name and the growth-arrest output of the system.

  • DOI:10.1038/s41586-024-07772-8
    operates as a toxin-antitoxin system, in which the antitoxin AriA sequesters and inactivates the toxin AriB until triggered by the T7 phage counterdefence protein Ocr

    Deep et al. support defining the Ocr-triggered PARIS mechanism around the AriA antitoxin and AriB toxin.

  • DOI:10.1038/s41586-024-07772-8
    AriB is a toprim/OLD-family nuclease, the activation of which arrests cell growth and inhibits phage propagation by globally inhibiting protein translation through specific cleavage of a lysine tRNA

    Deep et al. support the AriB nuclease, lysine-tRNA cleavage, translational-inhibition, growth-arrest, and phage-propagation outputs.

  • DOI:10.1038/s41586-024-07874-3
    The phage antirestriction induced system (PARIS) is a defence system, often encoded in viral genomes, that is composed of a 55 kDa ABC ATPase (AriA) and a 35 kDa TOPRIM nuclease (AriB)

    Burman et al. independently support the AriA ABC ATPase and AriB TOPRIM nuclease components.

  • DOI:10.1038/s41586-024-07874-3
    ATP-dependent detection of foreign proteins triggers the release of AriB, which assembles into a homodimeric nuclease that blocks infection by cleaving host lysine transfer RNA

    Burman et al. support an activation model in which foreign-protein detection releases AriB to cleave host lysine tRNA.

  • DOI:10.1038/s41586-024-07874-3
    Phage T5 subverts PARIS immunity through expression of a lysine transfer RNA variant that is not cleaved by PARIS, thereby restoring viral infection

    Burman et al. support recording T5 lysine tRNA anti-defense as a reviewed counter-defense gap before minting narrower PARIS subtype children.

  • DOI:10.1016/j.chom.2022.02.018
    While the system from E. coli B185 provided robust defense when expressed from its natural promoter

    Rousset et al. support E. coli as a canonical organism by cloning the E. coli B185 PARIS system with its native promoter and observing robust antiphage defense.

PARIS loci couple phage anti-restriction sensing to AriB tRNA cleavage

Evidence-backed process sketch linking a complete PARIS locus to AriA/AriB immune-complex assembly, foreign-protein sensing, AriB activation, host lysine tRNA cleavage, translational inhibition, and inhibition of phage propagation.

NONMECHANISTIC · The graph stays at the PARIS-family level and uses characterized E. coli B185 AriA/AriB examples without asserting one universal phage trigger, Ocr response, Ptr1/Ptr2 response, T5 lysine tRNA suppressor, exact AriA/AriB stoichiometry, or anti-anti-restriction context across all PARIS loci.

PARIS loci couple phage anti-restriction sensing to AriB tRNA cleavage Interactive directed graph showing evidence-backed causal relationships for PARIS system.

Edge evidence

  • PARIS locus contributes to AriA/AriB immune complex assembly RO:0002326

    PARIS loci encode AriA and AriB components that assemble into an immune complex.

    • DOI:10.1038/s41586-024-07874-3 Here we show that AriA and AriB assemble into a 425 kDa supramolecular immune complex Burman et al. support AriA/AriB complex assembly as a direct PARIS system activity.
  • AriA/AriB immune complex assembly enables foreign protein sensing RO:0002327

    The AriA/AriB immune complex detects foreign proteins in an ATP-dependent way.

    • DOI:10.1038/s41586-024-07874-3 ATP-dependent detection of foreign proteins triggers the release of AriB Burman et al. support AriA-dependent foreign protein detection as the triggering event for PARIS activation.
  • foreign protein sensing activates AriB nuclease activation RO:0002213

    T7 Ocr or other foreign-protein detection releases AriB from AriA and activates the AriB nuclease.

    • DOI:10.1038/s41586-024-07772-8 After Ocr binding, the AriA hexamer undergoes a structural rearrangement, releasing AriB and allowing it to dimerize and activate Deep et al. support Ocr-triggered AriB release and dimerization in the E. coli B185 PARIS system.
  • AriB nuclease activation contributes to lysine tRNA cleavage RO:0002326

    Activated AriB cleaves host lysine transfer RNA.

    • DOI:10.1038/s41586-024-07874-3 AriB, which assembles into a homodimeric nuclease that blocks infection by cleaving host lysine transfer RNA Burman et al. support host lysine-tRNA cleavage by activated AriB.
  • lysine tRNA cleavage contributes to translation inhibition RO:0002326

    AriB-mediated lysine tRNA cleavage inhibits host-cell translation.

    • DOI:10.1038/s41586-024-07772-8 globally inhibiting protein translation through specific cleavage of a lysine tRNA Deep et al. connect AriB lysine-tRNA cleavage to global inhibition of protein translation.
  • translation inhibition mitigates phage propagation METPO:2007407

    PARIS-associated translational arrest blocks phage infection.

    • DOI:10.1038/s41586-024-07772-8 arrests cell growth and inhibits phage propagation by globally inhibiting protein translation Deep et al. support the growth-arrest and phage-inhibition output of AriB activation.
  • translation inhibition confers PARIS system METPO:2007700

    AriB-dependent translational inhibition realizes the PARIS abortive-infection phenotype.

    • DOI:10.1016/j.chom.2022.02.018 Therefore, ariAB seem to halt growth in infected cells, preventing the completion of the phage cycle, a typical feature of abortive infection systems Rousset et al. connect AriA/AriB to growth arrest, phage-cycle inhibition, and abortive infection.
  • PARIS system is a abortive infection system rdfs:subClassOf

    PARIS system possession is an abortive-infection system trait.

    • DOI:10.1016/j.chom.2022.02.018 describe PARIS, an abortive infection system triggered by a phage-encoded anti-restriction protein Rousset et al. explicitly describe PARIS as an abortive infection system.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1016/j.chom.2022.02.018

Parent traits (1)

Synonyms (2)

  • phage anti-restriction-induced system EXACT_SYNONYM · DOI:10.1016/j.chom.2022.02.018
  • phage antirestriction induced system EXACT_SYNONYM · DOI:10.1038/s41586-024-07874-3

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.

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 PARIS trigger specificity, AriA/AriB stoichiometry, phage T5 lysine-tRNA suppression, and non-Ocr phage triggers before minting narrower PARIS subtype children.

KNOWLEDGE GAP OPEN paris-trigger-and-counterdefense-gap · raised by codex · 2026-09-18

Not yet attached to a section of this record — a curator sets attaches_to (e.g. causal_graphs#some_edge) so the gap shows beside the mechanism it concerns.

Rousset et al. discovered PARIS as an abortive infection system triggered by T7 Ocr; Deep et al. resolved Ocr-dependent AriA release of AriB for the E. coli B185 system; and Burman et al. showed that T5 Ptr1 and Ptr2 can activate PARIS while a phage T5 lysine tRNA variant can evade AriB cleavage. The first TraitRecord therefore stays at the broad PARIS-system level until separate subtype review resolves which foreign-protein triggers, AriB activities, and anti-defense suppressors apply across each PARIS family.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted PARIS system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v114.

  2. · ADVERSARIAL_REVIEW_REPAIR · codex

    Resolved PR #976 review issue #977 by scoping the PARIS canonical example note to the Rousset et al. E. coli B185 evidence cited by that example.