Dpd system

traitmech:000278 · CLASS · PROPOSED

A phage defense system in which an organism possesses a Dpd genomic island whose dpdA-K genes install 7-deazaguanine derivatives into DNA and are modeled by DefenseFinder as a multi-profile Dpd system.

Trait evidence (7)

DOI:10.1073/pnas.1518570113
2'-deoxy-preQ0 and 2'-deoxy-7-amido-7-deazaguanosine in enzymatic hydrolysates of DNA extracted from the pathogenic, Gram-negative bacteria Salmonella enterica serovar Montevideo

Thiaville et al. experimentally detected 7-deazaguanine-derived DNA modifications in a bacterium carrying the Dpd island.
DOI:10.1073/pnas.1518570113
rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA

Thiaville et al. name the S. Montevideo 7-deazapurine DNA-modification cluster as dpdA-K.
DOI:10.1073/pnas.1518570113
the modifications were detected in DNA from other organisms containing these clusters, including Kineococcus radiotolerans, Comamonas testosteroni, and Sphingopyxis alaskensis

Thiaville et al. support treating Dpd as a recurrent bacterial system rather than a one-off S. Montevideo sequence feature.
DOI:10.1073/pnas.1518570113
strongly suggests a restriction-modification role for the cluster in Enterobacteriaceae

Thiaville et al. connect the Dpd cluster to a likely restriction-modification role based on transformation efficiencies of modified and unmodified plasmids.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Dpd | 10\.1073/pnas\.1518570113 | Novel genomic island modifies DNA with 7-deazaguanine derivatives

The DefenseFinder article registry maps the named Dpd system to the Thiaville et al. DNA-modification paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
Dpd Dpd 4 4 Dpd__DpdA, Dpd__DpdB, Dpd__DpdC, Dpd__DpdD, Dpd__DpdE, Dpd__DpdF, Dpd__DpdG, Dpd__DpdH, Dpd__DpdI, Dpd__DpdJ, Dpd__DpdK

The DefenseFinder rules table models Dpd as a multi-profile defense system requiring a subset of DpdA-K profiles.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Dpd__DpdA | Dpd__DpdA | Dpd

The DefenseFinder HMM inventory records DpdA in the Dpd model namespace.

Dpd islands install 7-deazaguanine DNA modifications

Conservative system-level sketch linking a Dpd genomic island to 7-deazaguanine DNA modification, a likely restriction-modification output, and the Dpd system trait.

NONMECHANISTIC · The graph captures Dpd as a DNA-modification system with a DefenseFinder model while leaving its exact restriction target, modified motif, phage substrate range, DpdA-K component functions, and optional FolE/QueC/QueD/QueE profile requirements unresolved.

Edge evidence

Dpd genomic island contributes to 7-deazaguanine DNA modification RO:0002326
The Dpd cluster installs 7-deazaguanine derivatives in DNA.
- DOI:10.1073/pnas.1518570113 rename the genes of the S. Montevideo cluster as dpdA-K for 7-deazapurine in DNA Thiaville et al. name the genes of the 7-deazapurine DNA-modification cluster as dpdA-K.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md Dpd__DpdA | Dpd__DpdA | Dpd DefenseFinder includes DpdA in the custom Dpd model profile inventory.
7-deazaguanine DNA modification contributes to restriction-modification behavior RO:0002326
Modified Dpd DNA is associated with restriction-modification behavior in Enterobacteriaceae.
- DOI:10.1073/pnas.1518570113 strongly suggests a restriction-modification role for the cluster in Enterobacteriaceae Thiaville et al. connect Dpd modification to a likely restriction-modification role without resolving the exact restriction component or substrate.
restriction-modification behavior confers Dpd system METPO:2007700
DefenseFinder models Dpd as a multi-profile defense system rooted in DpdA-K DNA modification.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv Dpd Dpd 4 4 Dpd__DpdA, Dpd__DpdB, Dpd__DpdC, Dpd__DpdD, Dpd__DpdE, Dpd__DpdF, Dpd__DpdG, Dpd__DpdH, Dpd__DpdI, Dpd__DpdJ, Dpd__DpdK The DefenseFinder rules table supports Dpd as a named defense-system model with DpdA-K profiles.
Dpd system is a phage defense system rdfs:subClassOf
Dpd system possession is a phage-defense-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md Dpd | 10\.1073/pnas\.1518570113 | Novel genomic island modifies DNA with 7-deazaguanine derivatives DefenseFinder associates Dpd with the Thiaville et al. DNA-modification paper.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1073/pnas.1518570113

Parent traits (1)

phage defense system traitmech:000209

Synonyms (2)

Dpd EXACT_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
dpdA-K RELATED_SYNONYM · DOI:10.1073/pnas.1518570113

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 Dpd restriction targets, phage specificity, and DpdA-K component functions before minting narrower Dpd mechanism children.

KNOWLEDGE GAP OPEN dpd-restriction-mechanism-gap · raised by codex · 2026-09-19

Attached to causal_graphs#dpd_dna_modification_defense

Thiaville et al. support dpdA-K-dependent installation of 7-deazaguanine derivatives into DNA and a likely restriction-modification role, and DefenseFinder supports Dpd as a named multi-profile defense model. This first record does not yet resolve the universal restriction target, modified motif, antiphage substrate breadth, or the necessity of each profiled component across natural Dpd loci.

Curation history

2026-09-19T18:31:00Z · MINTED_TRAITMECH_ID · codex
Minted Dpd system as a DOI-backed GENOMICS TraitRecord under phage defense system 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_v155.