DRT3 system

traitmech:000545 · CLASS · PROPOSED

A DRT system in which an organism possesses a genome-encoded DefenseFinder DRT_3 subtype locus represented by the mandatory DRT_3__drt3a and DRT_3__drt3b profiles.

Trait evidence (7)

DOI:10.1126/science.aba0372
We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems

Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems.
DOI:10.1126/science.aba0372
We named these genes defense-associated RTs (DRTs)

Gao et al. coined the defense-associated RT naming that underlies the DRT system family.
DOI:10.1126/science.aba0372
In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity

Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues.
DOI:10.1126/science.aba0372
the UG3 (drt3a) and UG8 (drt3b) RTs are components of the same defense system (DRT type 3), with both RTs required for defense activity

Gao et al. support the two reverse-transcriptase components of the DRT type 3 defense system.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DRT | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes |

The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DRT_3__drt3a | DRT_3__drt3a | DRT_3 | Custom | 150 | | DRT_3__drt3b | DRT_3__drt3b | DRT_3 | Custom | 250 | | DRT_3__SLATT | | DRT_3 | Custom | 20 |

The pinned DefenseFinder HMM inventory records DRT_3__drt3a, DRT_3__drt3b, and DRT_3__SLATT under the DRT_3 model namespace, with DRT_3__SLATT lacking an emitted HMM name.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
DRT DRT_3 2 2 DRT_3__drt3a, DRT_3__drt3b

The pinned DefenseFinder rules table models DRT_3 as a DRT subsystem requiring DRT_3__drt3a and DRT_3__drt3b.

DRT3 loci support DRT antiphage defense

Conservative system-level sketch linking a DRT3 locus to reverse-transcriptase-dependent DRT phage defense and DRT3 system possession.

NONMECHANISTIC · The graph captures DRT3 at DefenseFinder subtype-locus level without asserting the direct DRT3 reverse-transcriptase products, phage trigger, native host breadth, sensitive phage breadth, non-coding RNA or DRT_3__SLATT partner-feature role, profile-to-activity criteria, or whether every DefenseFinder DRT_3 prediction is a complete experimentally active DRT3 locus.

Edge evidence

DRT3 locus contributes to DRT reverse-transcriptase active-site activity RO:0002326
DRT3 loci are represented in DefenseFinder by custom defense-associated reverse transcriptase profiles.
- DOI:10.1126/science.aba0372 We named these genes defense-associated RTs (DRTs) Gao et al. coined the defense-associated RT naming that underlies the DRT system family.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DRT_3__drt3a | DRT_3__drt3a | DRT_3 | Custom | 150 | | DRT_3__drt3b | DRT_3__drt3b | DRT_3 | Custom | 250 | The pinned DefenseFinder HMM inventory records DRT_3__drt3a and DRT_3__drt3b under the DRT_3 model namespace.
DRT reverse-transcriptase active-site activity confers DRT3 system METPO:2007700
The first-pass DRT3 system trait is realized by a DefenseFinder DRT_3 subtype locus within the reverse-transcriptase-dependent DRT family.
- DOI:10.1126/science.aba0372 We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems Gao et al. experimentally support defense-associated reverse transcriptases as active antiphage systems.
- DOI:10.1126/science.aba0372 In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity Gao et al. connect DRT antiphage activity to conserved reverse-transcriptase active-site residues.
- DOI:10.1126/science.aba0372 the UG3 (drt3a) and UG8 (drt3b) RTs are components of the same defense system (DRT type 3), with both RTs required for defense activity Gao et al. support the two reverse-transcriptase components of the DRT type 3 defense system.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv DRT DRT_3 2 2 DRT_3__drt3a, DRT_3__drt3b The pinned DefenseFinder rules table models DRT_3 as a DRT subsystem requiring DRT_3__drt3a and DRT_3__drt3b.
DRT3 system is a DRT system rdfs:subClassOf
DRT3 system possession is a DRT-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | DRT | 10\.1126/science\.aba0372 | Diverse enzymatic activities mediate antiviral immunity in prokaryotes | The pinned DefenseFinder article registry maps the DRT source key to the Gao et al. prokaryotic antiviral-immunity paper.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv DRT DRT_3 2 2 DRT_3__drt3a, DRT_3__drt3b The pinned DefenseFinder rules table models DRT_3 as a DRT subsystem requiring DRT_3__drt3a and DRT_3__drt3b.

Provenance

Identifier source: TraitMech local identifier
Definition source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Parent traits (1)

DRT system traitmech:000279

Synonyms (3)

DRT_3 RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
DRT_3__drt3a RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
DRT_3__drt3b 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 the DRT3 reverse-transcriptase products, direct phage trigger, host breadth, non-coding RNA or DRT_3__SLATT partner-feature role, and DRT_3 profile-to-activity criteria before minting DRT3 mechanism or component children.

KNOWLEDGE GAP OPEN drt3-profile-activity-gap · raised by codex · 2026-10-02

Attached to causal_graphs#drt3_locus_reverse_transcriptase_defense

Gao et al. support defense-associated reverse transcriptases as a broad antiphage-system family and the two RT components of DRT type 3, while the pinned DefenseFinder HMM inventory and rules table support DRT_3 as a two-required-profile DRT subsystem. This first-pass record leaves the exact DRT3 RT products, phage trigger, host breadth, DRT_3__SLATT role, and profile-to-activity requirements unresolved.

Evidence

DOI:10.1126/science.aba0372
We discovered that a family of uncharacterized reverse transcriptases (RTs) are active defense systems
DOI:10.1126/science.aba0372
In all cases, mutations in the RT active site [(Y/F)xDD to (Y/F)xAA, where x is any amino acid] abolished activity
DOI:10.1126/science.aba0372
the UG3 (drt3a) and UG8 (drt3b) RTs are components of the same defense system (DRT type 3), with both RTs required for defense activity
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DRT_3__drt3a | DRT_3__drt3a | DRT_3 | Custom | 150 | | DRT_3__drt3b | DRT_3__drt3b | DRT_3 | Custom | 250 | | DRT_3__SLATT | | DRT_3 | Custom | 20 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
DRT DRT_3 2 2 DRT_3__drt3a, DRT_3__drt3b

Curation history

2026-10-02T12:40:28Z · MINTED_TRAITMECH_ID · codex
Minted DRT3 system as a DOI- and DefenseFinder-backed GENOMICS TraitRecord under the DRT system parent after an ignored-and-hidden duplicate review found no exact live DRT3 TraitMech, METPO, history, or prior proposal record; the replacement placeholder is reserved in proposals/metpo_traitmech_v422.
2026-10-02T12:40:29Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DRT3 system during initial curation and left canonical_examples empty because Gao et al. and the pinned DefenseFinder tables support DRT type 3 and the DRT_3 model namespace but not an accession-backed native microbial taxon exemplar tied to DRT_3__drt3a and DRT_3__drt3b and experimentally verified endogenous DRT3 activity. No paid research was used.