DS-15 system

traitmech:000438 · CLASS · PROPOSED

A phage defense system in which an organism possesses the three-gene DefensePredictor-discovered system 15 locus cataloged as working transcriptional unit AAA1 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

Trait evidence (11)

DOI:10.1126/science.adv7924
To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain

DeWeirdt et al. experimentally validated 42 predicted transcriptional units as phage-defense systems in E. coli.
DOI:10.1126/science.adv7924
We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.

DeWeirdt et al. name validated transcriptional units as DefensePredictor discovered systems.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
AAA1 NZ_QOXE01000046.1 GCF_003334165.1 - True False True True DefensePredictor hits 29629 31530 hypothetical protein, hypothetical protein, AAA family ATPase WP_000957441.1, WP_060581740.1, WP_001619161.1 11.46862191778244 2.030866871531279 True True Predicted novel defense gene DS-15

The final Science supplementary Table S6 maps working_id AAA1 to DS_name DS-15, marks the cloned transcriptional unit as defensive, and records NZ_QOXE01000046.1 positions 29629-31530 with product accessions WP_000957441.1, WP_060581740.1, and WP_001619161.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas1 4.2 pLAND 24-05-17_EV_HHNH.png 5000000 AAA1 24-05-17 24-05-17_VAME_AAA1_PD3A_PDP7.png 2 100 10000 2.6989700043360187 True LB 37

The final Science supplementary Table S7 reports an AAA1 assay row with a Bas1 phage readout and a -log(EOP) value of 2.699.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
AAA1 DS-15 True

The final Science supplementary Table S8 maps AAA1 to replicated display name DS-15.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
AAA1 1.0 281.0 WP_001619161.1 MinD ATPase SCOP_d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeoglobus fulgidus [TaxId: 2234]} | CLASS: Alpha and beta proteins (a/b), FOLD: P-loop containing nucleoside triphosphate hydrolases, SUPFAM: P-loop containing nucleoside triphosphate hydrolases, FAM: Nitrogenase iron protein-like hhpred_6736485.hhr 3.0 268.0 1.0 2024-07-29 00:00:00

The final Science supplementary Table S8 reports a MinD ATPase HHpred hit for WP_001619161.1 in AAA1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
AAA1 3.0 221.0 WP_000957441.1 DUF6988 PF22491.1 DUF6988 ; Family of unknown function (DUF6988) hhpred_7907160.hhr 68.0 144.0 0.94 2024-07-29 00:00:00

The final Science supplementary Table S8 reports a DUF6988 HHpred hit for WP_000957441.1 in AAA1.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-15 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems |

The pinned DefenseFinder article registry maps the DS-15 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-15__DS-15A | | DS-15 | Custom | 300 |

The pinned DefenseFinder HMM inventory records DS-15__DS-15A as a custom DS-15 profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-15__DS-15B | | DS-15 | Custom | 20 |

The pinned DefenseFinder HMM inventory records DS-15__DS-15B as a custom DS-15 profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-15__DS-15C | | DS-15 | Custom | 20 |

The pinned DefenseFinder HMM inventory records DS-15__DS-15C as a custom DS-15 profile.

DS-15 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the three-gene DS-15 locus to reduced bacteriophage plaquing without resolving DS-15 component function or effector activity.

NONMECHANISTIC · The graph captures DS-15 as the validated AAA1 transcriptional unit with three product accessions, final Table S8 MinD ATPase and DUF6988 HHpred-domain rows, and three DefenseFinder DS-15 profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, exact AAA family ATPase or DUF6988 chemistry, phage target breadth, or DefenseFinder rule-level detection criteria.

Edge evidence

DS-15 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-15/AAA1 locus contributes to reduced bacteriophage plaquing when plasmid expressed.
- DOI:10.1126/science.adv7924 To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain DeWeirdt et al. experimentally validate DefensePredictor-discovered systems by assaying cloned transcriptional units against E. coli phages.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx AAA1 NZ_QOXE01000046.1 GCF_003334165.1 - True False True True DefensePredictor hits 29629 31530 hypothetical protein, hypothetical protein, AAA family ATPase WP_000957441.1, WP_060581740.1, WP_001619161.1 11.46862191778244 2.030866871531279 True True Predicted novel defense gene DS-15 The final Science supplementary Table S6 maps working_id AAA1 to DS_name DS-15, marks the cloned transcriptional unit as defensive, and records NZ_QOXE01000046.1 positions 29629-31530 with product accessions WP_000957441.1, WP_060581740.1, and WP_001619161.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas1 4.2 pLAND 24-05-17_EV_HHNH.png 5000000 AAA1 24-05-17 24-05-17_VAME_AAA1_PD3A_PDP7.png 2 100 10000 2.6989700043360187 True LB 37 The final Science supplementary Table S7 reports an AAA1 assay row with a Bas1 phage readout and a -log(EOP) value of 2.699.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-15__DS-15A | | DS-15 | Custom | 300 | The pinned DefenseFinder HMM inventory records DS-15__DS-15A as a custom DS-15 profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-15__DS-15B | | DS-15 | Custom | 20 | The pinned DefenseFinder HMM inventory records DS-15__DS-15B as a custom DS-15 profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-15__DS-15C | | DS-15 | Custom | 20 | The pinned DefenseFinder HMM inventory records DS-15__DS-15C as a custom DS-15 profile.
reduced bacteriophage plaquing confers DS-15 system METPO:2007700
DS-15-mediated phage plaquing reduction realizes the DS-15 system trait.
- DOI:10.1126/science.adv7924 We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8. DeWeirdt et al. name each validated transcriptional unit as a DefensePredictor discovered system.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx AAA1 NZ_QOXE01000046.1 GCF_003334165.1 - True False True True DefensePredictor hits 29629 31530 hypothetical protein, hypothetical protein, AAA family ATPase WP_000957441.1, WP_060581740.1, WP_001619161.1 11.46862191778244 2.030866871531279 True True Predicted novel defense gene DS-15 The final Science supplementary Table S6 maps working_id AAA1 to DS_name DS-15, marks the cloned transcriptional unit as defensive, and records NZ_QOXE01000046.1 positions 29629-31530 with product accessions WP_000957441.1, WP_060581740.1, and WP_001619161.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas1 4.2 pLAND 24-05-17_EV_HHNH.png 5000000 AAA1 24-05-17 24-05-17_VAME_AAA1_PD3A_PDP7.png 2 100 10000 2.6989700043360187 True LB 37 The final Science supplementary Table S7 reports an AAA1 assay row with a Bas1 phage readout and a -log(EOP) value of 2.699.
DS-15 system is a phage defense system rdfs:subClassOf
DS-15 system possession is a phage-defense-system trait.
- DOI:10.1126/science.adv7924 To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain DeWeirdt et al. validate DSs as anti-phage systems.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | DS-15 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems | The pinned DefenseFinder article registry maps the DS-15 source key to the preprint DOI for the DeWeirdt et al. DefensePredictor study, which has since been published in Science.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1126/science.adv7924

Parent traits (1)

phage defense system traitmech:000209

Synonyms (5)

DS-15 EXACT_SYNONYM · DOI:10.1126/science.adv7924
AAA1 RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
DS-15__DS-15A RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
DS-15__DS-15B RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
DS-15__DS-15C 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 DS-15 native host breadth, exact profile-to-protein mapping, DS-15A/DS-15B/DS-15C component activities, sensitive-phage breadth, exact AAA family ATPase and DUF6988 chemistry, and rule-level DefenseFinder criteria before minting narrower DS-15 mechanism children.

KNOWLEDGE GAP OPEN ds-15-defensefinder-model-gap · raised by codex · 2026-09-28

Attached to causal_graphs#ds_15_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-15 as the defensive AAA1 transcriptional unit that reduced Bas1 plaquing when cloned in E. coli MG1655, the final Table S8 HHpred sheet reports MinD ATPase and DUF6988 hits across two AAA1 products, and the pinned DefenseFinder HMM inventory records DS-15A, DS-15B, and DS-15C custom profile rows. The pinned rules table has no DS-15 row, and the first-pass record does not resolve native host breadth, exact profile-to-protein correspondence, direct ATPase or DUF6988 activity, phage target breadth, or endogenous DS-15 activity.

Evidence

DOI:10.1126/science.adv7924
To test for anti-phage defense, we placed each TU with its predicted native promoter region on a low-copy number plasmid in E. coli MG1655 and challenged these strains with a panel of 24 diverse E. coli phages (Fig. 3; fig. S2). In total, 42 (45% of 94) of the cloned TUs produced smaller plaque sizes or reduced the efficiency of plating (EOP) at least ten-fold relative to an empty vector control strain
DOI:10.1126/science.adv7924
We refer to these validated TUs as DefensePredictor discovered systems (DSs), with genes in multi-gene TUs denoted by an alphabetical suffix, e.g., DS-8A is the first gene of DS-8.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
AAA1 NZ_QOXE01000046.1 GCF_003334165.1 - True False True True DefensePredictor hits 29629 31530 hypothetical protein, hypothetical protein, AAA family ATPase WP_000957441.1, WP_060581740.1, WP_001619161.1 11.46862191778244 2.030866871531279 True True Predicted novel defense gene DS-15
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas1 4.2 pLAND 24-05-17_EV_HHNH.png 5000000 AAA1 24-05-17 24-05-17_VAME_AAA1_PD3A_PDP7.png 2 100 10000 2.6989700043360187 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
AAA1 DS-15 True
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
AAA1 1.0 281.0 WP_001619161.1 MinD ATPase SCOP_d1hyqa_ c.37.1.10 (A:) Cell division regulator MinD {Archaeoglobus fulgidus [TaxId: 2234]} | CLASS: Alpha and beta proteins (a/b), FOLD: P-loop containing nucleoside triphosphate hydrolases, SUPFAM: P-loop containing nucleoside triphosphate hydrolases, FAM: Nitrogenase iron protein-like hhpred_6736485.hhr 3.0 268.0 1.0 2024-07-29 00:00:00
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
AAA1 3.0 221.0 WP_000957441.1 DUF6988 PF22491.1 DUF6988 ; Family of unknown function (DUF6988) hhpred_7907160.hhr 68.0 144.0 0.94 2024-07-29 00:00:00
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-15 | 10\.1101/2025\.01\.08\.631726 | DefensePredictor: A machine learning model to discover novel prokaryotic immune systems |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-15__DS-15A | | DS-15 | Custom | 300 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-15__DS-15B | | DS-15 | Custom | 20 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-15__DS-15C | | DS-15 | Custom | 20 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-28T16:50:13Z · MINTED_TRAITMECH_ID · codex
Minted DS-15 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned AAA1 transcriptional-unit level because the pinned DefenseFinder DS-15 HMM rows are not backed by a rules row; proposals/metpo_traitmech_v315 reserves the replacement placeholder.
2026-09-28T16:50:14Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-15 system canonical_examples and left them empty because DeWeirdt et al. support cloned AAA1 plaquing assays in E. coli MG1655 plus DefenseFinder DS-15 models, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-15 activity. No paid research was used.