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TgvAB system

traitmech:000412 · CLASS · PROPOSED

A restriction-modification system in which an organism possesses a two-gene TgvAB locus embedded in the Vibrio cholerae VPI-2 type I R-M cluster, encoding TgvA and TgvB modification-dependent restriction proteins related to GmrSD type IV restriction enzymes that restrict glucosylated hmC-containing T-even-like phage DNA.

Trait evidence (7)

TgvAB restricts glucosylated T-even-like phage DNA

Conservative system-level sketch linking a two-gene TgvAB locus to modification-dependent type IV restriction of glucosylated hmC-containing T-even-like phage DNA and TgvAB system possession.

NONMECHANISTIC · The graph captures TgvAB at VPI-2, T-even-like-phage, and type-IV-restriction level without asserting complete native host breadth, exact TgvA/TgvB subunit stoichiometry, or a DefenseFinder rule-level profile combination.

TgvAB restricts glucosylated T-even-like phage DNA Interactive directed graph showing evidence-backed causal relationships for TgvAB system.

Edge evidence

  • TgvAB locus enables TgvAB-dependent type IV restriction RO:0002327

    A TgvAB locus encodes both proteins required for modification-dependent restriction of T-even phage DNA.

  • TgvAB-dependent type IV restriction mitigates glucosylated hmC phage DNA METPO:2007407

    TgvAB-dependent type IV restriction targets T-even-like phage DNA bearing glucosylated 5-hydroxymethylcytosine.

    • DOI:10.1128/jb.00143-24 TgvAB targets phage DNA with glucosylated 5-hydroxymethylcytosine (5hmC) bases Gomez and Waters directly connect the TgvAB system to targeting glucosylated 5-hydroxymethylcytosine during phage defense.
  • TgvAB-dependent type IV restriction mitigates T-even-like phage propagation METPO:2007407

    Restriction of hypermodified T-even-like phage DNA inhibits productive phage propagation.

    • DOI:10.1128/jb.00145-24 potent anti-phage activity against diverse members of the Tevenvirinae Vizzarro et al. support TgvAB anti-phage activity against hypermodified phages.
    • DOI:10.1128/jb.00143-24 TgvAB targets phage DNA with glucosylated 5-hydroxymethylcytosine (5hmC) bases Gomez and Waters identify glucosylated 5-hydroxymethylcytosine as the phage-DNA modification targeted by TgvAB.
  • TgvAB-dependent type IV restriction confers TgvAB system METPO:2007700

    TgvAB-dependent type IV restriction realizes the TgvAB system trait.

    • DOI:10.1128/jb.00145-24 novel modification-dependent type IV restriction system that recognizes hypermodified cytosines Vizzarro et al. frame TgvAB as a type IV restriction system recognizing hypermodified cytosines.
    • DOI:10.1128/jb.00143-24 both TgvA and TgvB are required for defense against T2, T4, and T6 Gomez and Waters report that both encoded TgvAB components are required for anti-phage activity.
    • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | TgvAB | 10\.1128/jb\.00145-24 | Vibrio cholerae pathogenicity island 2 encodes two distinct types of restriction systems | The pinned DefenseFinder article registry maps the named TgvAB system to the Vizzarro et al. VPI-2 restriction-systems paper. The pinned rules table (https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv) does not list TgvAB, so the registry and HMM rows support a named system-possession trait rather than complete DefenseFinder detection criteria.
  • TgvAB system is a restriction-modification system rdfs:subClassOf

    TgvAB is a GmrSD-related type IV restriction system in the broader restriction-modification family.

    • DOI:10.1128/jb.00145-24 the two genes embedded within the T1RM system encode a novel two-protein modification-dependent restriction system related to the GmrSD family of type IV restriction enzymes Vizzarro et al. place TgvAB among GmrSD-family type IV restriction enzymes.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1128/jb.00145-24

Parent traits (1)

Synonyms (3)

  • TgvAB EXACT_SYNONYM · DOI:10.1128/jb.00145-24
  • TgvAB__TgvA RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  • TgvAB__TgvB 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 TgvAB native host breadth, TgvA/TgvB biochemical roles, phage substrate breadth, and DefenseFinder rule or model coverage before minting narrower TgvAB mechanism children.

KNOWLEDGE GAP OPEN tgvab-defensefinder-rule-gap · raised by codex · 2026-09-27

Attached to causal_graphs#tgvab_type_iv_restriction

Vizzarro et al. and Gomez and Waters support TgvAB as a two-component VPI-2 type IV restriction system that restricts glucosylated hmC-containing T-even phage DNA, and the pinned DefenseFinder HMM inventory carries TgvA and TgvB custom profiles. The pinned DefenseFinder rules table has no TgvAB row, and the evidence does not yet resolve native host breadth, the individual TgvA versus TgvB biochemical roles, full phage substrate breadth, or a rule-level profile combination.

Evidence

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted TgvAB system as a DOI-backed GENOMICS TraitRecord under restriction-modification system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at two-component TgvAB/type-IV-restriction level because the pinned DefenseFinder HMM rows are not backed by a pinned rules row; the replacement placeholder is reserved in proposals/metpo_traitmech_v289.