TraitMech

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BREX system

traitmech:000210 · CLASS · PROPOSED

A genomics trait describing possession of a bacteriophage exclusion defense system that uses host DNA methylation to discriminate self from non-self and inhibit phage DNA replication.

Trait evidence (5)

  • DOI:10.15252/embj.201489455
    We denote this novel defense system BREX (Bacteriophage Exclusion) and show that it allows phage adsorption but blocks phage DNA replication

    Goldfarb et al. define BREX as a bacteriophage-exclusion defense system and distinguish its post-adsorption block from receptor-loss and phage-adsorption phenotypes.

  • DOI:10.15252/embj.201489455
    methylation on non-palindromic TAGGAG motifs in the bacterial genome guides self/non-self discrimination and is essential for the defensive function of the BREX system

    Goldfarb et al. support the methylation-based self/non-self discrimination clause in the local definition.

  • DOI:10.15252/embj.201489455
    confers resistance to a broad range of phages, including both virulent and temperate ones

    A Bacillus cereus six-gene BREX cassette conferred broad phage resistance when integrated into Bacillus subtilis, supporting BREX as a locus-encoded system trait.

  • DOI:10.1128/AEM.01001-19
    The bacteriophage exclusion (BREX) system is a novel prokaryotic defense system against bacteriophages

    Hui et al. independently define bacteriophage exclusion as a prokaryotic defense system against bacteriophages.

  • DOI:10.1128/AEM.01001-19
    identified a complete cassette of a classic type I BREX system

    Hui et al. identified a complete type I BREX cassette in the Lactobacillus casei Zhang genome.

BREX methylation guides antiphage discrimination

Evidence-backed causal sketch linking a BREX locus to host-DNA methylation, self/non-self discrimination, and blocked phage-DNA replication.

MECHANISTIC · The graph captures Goldfarb et al.'s experimentally supported host-methylation and post-adsorption phage-replication block without asserting that the molecular coupling between marked host DNA and blocked phage DNA is fully resolved.

BREX methylation guides antiphage discrimination Interactive directed graph showing evidence-backed causal relationships for BREX system.

Edge evidence

  • BREX locus encodes PglX adenine methyltransferase

    Type I BREX loci encode PglX adenine methyltransferases.

    • DOI:10.1128/AEM.01001-19 identified a complete cassette of a classic type I BREX system The complete L. casei Zhang type I BREX cassette contains the pglX locus encoding PglX.
  • PglX adenine methyltransferase contributes to BREX host DNA methylation RO:0002326

    PglX methyltransferase activity methylates BREX recognition motifs in host DNA.

    • DOI:10.1128/AEM.01001-19 this work confirmed that the L. casei Zhang pglX gene product is a functional adenine MTase Hui et al. showed that pglX disruption removed m6A methylation at the recognition motif in L. casei Zhang.
  • BREX host DNA methylation contributes to BREX self/non-self discrimination RO:0002326

    Host DNA methylation guides BREX self/non-self discrimination.

    • DOI:10.15252/embj.201489455 methylation on non-palindromic TAGGAG motifs in the bacterial genome guides self/non-self discrimination Goldfarb et al. established methylation as the self/non-self mark for the characterized BREX system.
  • BREX self/non-self discrimination confers BREX system METPO:2007700

    Methylation-guided self/non-self discrimination realizes the BREX defense trait.

    • DOI:10.15252/embj.201489455 is essential for the defensive function of the BREX system Goldfarb et al. established methylation-based self/non-self discrimination as essential to BREX defense.
  • BREX self/non-self discrimination mitigates phage DNA replication METPO:2007407

    BREX methylation-guided discrimination blocks replication of unmethylated phage DNA.

    • DOI:10.15252/embj.201489455 allows phage adsorption but blocks phage DNA replication The edge records the observed post-adsorption replication block; the exact biochemical coupling remains a molecular knowledge gap.
  • BREX system is a phage defense system rdfs:subClassOf

    BREX possession is a methylation-based phage-defense system.

    • DOI:10.15252/embj.201489455 We denote this novel defense system BREX (Bacteriophage Exclusion) Goldfarb et al. place BREX in the phage defense system family.

Protein and taxon examples

Graph nodeProteinTaxonUniProt statusRole and evidence
PglX adenine methyltransferase UniProtKB:P0DQP1
Adenine-specific methyltransferase PglX (pglX) 		Lacticaseibacillus casei str. Zhang
NCBITaxon:498216 		REVIEWED
retrieved 2026-09-15 · entry v19 · sequence v1

L. casei Zhang PglX methylates BREX recognition motifs as the type I BREX adenine methyltransferase.

  • DOI:10.1128/AEM.01001-19 this work confirmed that the L. casei Zhang pglX gene product is a functional adenine MTase that is an essential component of a type I BREX system Hui et al. experimentally disrupted L. casei Zhang pglX; UniProt verifies the reviewed PglX accession.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.15252/embj.201489455

Parent traits (1)

Synonyms (2)

  • bacteriophage exclusion EXACT_SYNONYM · DOI:10.15252/embj.201489455
  • bacteriophage exclusion system EXACT_SYNONYM · DOI:10.1128/AEM.01001-19

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.

  • Lacticaseibacillus casei str. Zhang NCBITaxon:498216 DOI:10.1128/AEM.01001-19 The strain historically named Lactobacillus casei Zhang carries a complete type I BREX cassette whose pglX component is required for BREX-linked methylation and plasmid restriction phenotypes.

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 molecular coupling between BREX-guided host methylation and phage-DNA replication arrest before adding more specific BREX mechanism edges.

KNOWLEDGE GAP OPEN brex-molecular-coupling-gap · raised by codex · 2026-09-15

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.

Goldfarb et al. showed that methylation is essential and that BREX blocks phage DNA replication after adsorption, but the exact biochemical coupling between the methylation mark and blocked phage replication remains insufficient for a more specific causal edge.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted BREX system as a DOI-backed GENOMICS TraitRecord under the phage defense 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_v87.