TraitMech

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Druantia type II system

traitmech:000579 · CLASS · PROPOSED

A Druantia system in which an organism possesses a locus encoding DruE together with DruM, DruF and DruG.

Trait evidence (4)

  • DOI:10.1093/nar/gkab883
    the Druantia-like system lacks the type II requisite DruM and DruG proteins

    Payne et al., Results: Identification of new defence system variants, and Figure 2C: type II contains DruE/F/M/G; the proposed type IV shares DruE/F but replaces the type-II M/G architecture with DruL. This supports locus composition, not experimental dependence of each component in every host. The type-II distribution observed in RefSeq v201 is not a universal taxonomic limit.

  • DOI:10.65215/LTSpreprints.2026.06.18.000273
    DruE alone confers limited protection against a subset of coliphages in heterologous expression

    Hou et al., version 2 posted 2026-07-08, not peer reviewed; PDF https://langtaosha.org.cn/lts/en/preprint/download/273/1236, pages 5-6 and 18, Figure 1 and supplementary Figure S2. The Pf-5 druMFGE locus is the source. Purified DruE is an ATP-dependent 3-prime-to-5-prime helicase preferring 3-prime overhangs and forks, with an asymmetric homodimer. Standalone DruE in E. coli BL21 gave limited T7/T1 protection; R1241A reduced protection. Insoluble DruF/G prevented full-system reconstitution. Native-host phage defense and the link from unwinding to restriction remain untested or unresolved. Pf-5 deletion assays under mitomycin C suggest accessory control of toxicity, not a demonstrated defense trigger.

  • https://raw.githubusercontent.com/padlocbio/padloc-db/9e380165633a8d6aef93b5a164cea0f3359bd33f/sys/druantia_type_II.yaml
    core_genes: - DruE2 - DruF2 - DruG2 - DruM2

    Pinned executable PADLOC rule, retrieved 2026-10-03: minimum_core and minimum_total are both 4, maximum_separation is 3, and force_strand is FALSE. DruK is secondary, not a required fifth component; neutral and prohibited lists contain only NA. These are detection constraints, not evidence of active defense.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/definitions/DefenseFinder/Druantia/Druantia_II.xml
    <model inter_gene_max_space="5" min_mandatory_genes_required="1" min_genes_required="3" vers="2.0">

    Pinned executable DefenseFinder model, retrieved 2026-10-03: Druantia_II__DruM/F/G are accessory slots. DruF permits Druantia_IV__DruF4. Mandatory Druantia__DruE_1 permits Druantia__DruE_2, Druantia__DruE_3 or Druantia_IV__DruE4. One mandatory and three total matches are required; no forbidden slots are declared. A call alone need not establish the complete DruM/F/G/E architecture. Exchangeable matches and missing profiles do not establish biological equivalence or component absence.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1093/nar/gkab883

Parent traits (1)

Synonyms (1)

  • Type II Druantia system EXACT_SYNONYM · DOI:10.65215/LTSpreprints.2026.06.18.000273

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.

  • Pseudomonas protegens Pf-5 NCBITaxon:220664 DOI:10.65215/LTSpreprints.2026.06.18.000273 Natural locus possession in Pf-5, assembly GCF_000012265.1 identified by Hou et al. version 2, Figure 1a and Methods. Not a native-host phage-resistance example: infection assays used standalone DruE in engineered E. coli. NCBI resolves taxon 220664 to Pseudomonas protegens Pf-5.

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 full-system defense and accessory functions beyond isolated DruE assays.

KNOWLEDGE GAP OPEN druantia-type-ii-full-system-defense-gap · raised by codex · 2026-10-03

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.

DruM/F/G/E possession is an architecture class, not an assay result or a universal helicase mechanism. Hou et al. version 2 provides real DruE biochemistry; the remaining gap is not absence of protein evidence. RCSB entry 9WAE entity 1 maps Pf-5 PFL_3016 to UniProtKB:Q4KCB1, a live unreviewed entry checked 2026-10-03. No full-system causal graph is asserted because native-host phage restriction, accessory regulation and the unwinding-to-restriction transition are unresolved. The measured isolated-protein results remain in the evidence notes. Do not transfer type-III nuclease chemistry to type II or turn mitomycin-C growth effects into an infection trigger. A missing profile or incomplete assembly cannot establish component absence; inspect complete locus context. Organism-level subtype possession classes are not disjoint because a genome may encode several loci.

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Added literature-defined Druantia II possession with two DOI sources, four exact snippets, pinned executable detector rules and NCBI-resolved Pf-5 possession. Kept the version-2 preprint's isolated DruE assays distinct from full-system and native-host defense. Ignored-and-hidden novelty and allocation searches found no exact record or METPO term; reserved METPO:1053300 in v456. No protein-resolved full-system causal mechanism is asserted.

  2. · CORRECT_EVIDENCE_LOCATOR · codex

    Corrected the Payne evidence subsection locator to Results: Identification of new defence system variants after checking primary PMC8565338 XML; the snippet, architecture claim and Figure 2C locator are unchanged. Addresses issue #1639.