DS-1 system

traitmech:000424 · CLASS · PROPOSED

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 1 locus cataloged as working transcriptional unit D390 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

Trait evidence (8)

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
D390 NZ_RRVY01000002.1 GCF_003886375.1 + True False True True DefensePredictor hits 220602 222994 hypothetical protein, nucleoid-associated protein WP_000150292.1, WP_000355468.1 12.74067081596784 -2.197224577336219 True False Predicted novel defense gene DS-1

The final Science supplementary Table S6 maps working_id D390 to DS_name DS-1, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000002.1 positions 220602-222994 with product accessions WP_000355468.1 and WP_000150292.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas1 1.2 pLAND 24-03-08_EV_HHHD_PIN2_CRDO.png 40000000 D390 24-03-12 24-03-12_PIN8_D390_NADR_PN12.png 0 1 1 7.6020599913279625 True True LB 37

The final Science supplementary Table S7 reports a D390 assay row with a 1-PFU Bas1 readout and a -log(EOP) value of 7.602.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
D390 DS-1 True

The final Science supplementary Table S8 maps D390 to replicated display name DS-1.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-1 | 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-1 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-1__DS-1A | | DS-1 | Custom | 30 |

The pinned DefenseFinder HMM inventory records DS-1__DS-1A as a custom DS-1 profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-1__DS-1B | | DS-1 | Custom | 50 |

The pinned DefenseFinder HMM inventory records DS-1__DS-1B as a custom DS-1 profile.

DS-1 loci reduce bacteriophage plaquing

Conservative system-level sketch linking the two-gene DS-1 locus to reduced bacteriophage plaquing without resolving DS-1 component functions or effector activity.

NONMECHANISTIC · The graph captures DS-1 as the validated D390 transcriptional unit with two product accessions and with DefenseFinder DS-1A and DS-1B profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, the direct viral trigger or substrate, exact molecular output, phage target breadth, or DefenseFinder rule-level detection criteria.

Edge evidence

DS-1 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-1/D390 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 D390 NZ_RRVY01000002.1 GCF_003886375.1 + True False True True DefensePredictor hits 220602 222994 hypothetical protein, nucleoid-associated protein WP_000150292.1, WP_000355468.1 12.74067081596784 -2.197224577336219 True False Predicted novel defense gene DS-1 The final Science supplementary Table S6 maps working_id D390 to DS_name DS-1, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000002.1 positions 220602-222994 with product accessions WP_000355468.1 and WP_000150292.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas1 1.2 pLAND 24-03-08_EV_HHHD_PIN2_CRDO.png 40000000 D390 24-03-12 24-03-12_PIN8_D390_NADR_PN12.png 0 1 1 7.6020599913279625 True True LB 37 The final Science supplementary Table S7 reports a D390 assay row with a 1-PFU Bas1 readout and a -log(EOP) value of 7.602.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-1__DS-1A | | DS-1 | Custom | 30 | The pinned DefenseFinder HMM inventory records DS-1__DS-1A as a custom DS-1 profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-1__DS-1B | | DS-1 | Custom | 50 | The pinned DefenseFinder HMM inventory records DS-1__DS-1B as a custom DS-1 profile.
reduced bacteriophage plaquing confers DS-1 system METPO:2007700
DS-1-mediated phage plaquing reduction realizes the DS-1 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 D390 NZ_RRVY01000002.1 GCF_003886375.1 + True False True True DefensePredictor hits 220602 222994 hypothetical protein, nucleoid-associated protein WP_000150292.1, WP_000355468.1 12.74067081596784 -2.197224577336219 True False Predicted novel defense gene DS-1 The final Science supplementary Table S6 maps working_id D390 to DS_name DS-1, marks the cloned transcriptional unit as defensive, and records NZ_RRVY01000002.1 positions 220602-222994 with product accessions WP_000355468.1 and WP_000150292.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas1 1.2 pLAND 24-03-08_EV_HHHD_PIN2_CRDO.png 40000000 D390 24-03-12 24-03-12_PIN8_D390_NADR_PN12.png 0 1 1 7.6020599913279625 True True LB 37 The final Science supplementary Table S7 reports a D390 assay row with a 1-PFU Bas1 readout and a -log(EOP) value of 7.602.
DS-1 system is a phage defense system rdfs:subClassOf
DS-1 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-1 | 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-1 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 (4)

DS-1 EXACT_SYNONYM · DOI:10.1126/science.adv7924
D390 RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
DS-1__DS-1A RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
DS-1__DS-1B 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-1 native host breadth, exact DS-1A/DS-1B component functions, profile-to-component mapping, sensitive-phage breadth, molecular output, and rule-level detection criteria before minting narrower DS-1 mechanism children.

KNOWLEDGE GAP OPEN ds-1-defensefinder-model-gap · raised by codex · 2026-09-28

Attached to causal_graphs#ds_1_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-1 as the defensive D390 transcriptional unit that reduced plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records DS-1A and DS-1B profile rows. The pinned rules table has no DS-1 row, and the first-pass record does not resolve native host breadth, exact component activities, profile-to-component mapping, phage target breadth, the direct molecular output, or endogenous DS-1 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
D390 NZ_RRVY01000002.1 GCF_003886375.1 + True False True True DefensePredictor hits 220602 222994 hypothetical protein, nucleoid-associated protein WP_000150292.1, WP_000355468.1 12.74067081596784 -2.197224577336219 True False Predicted novel defense gene DS-1
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas1 1.2 pLAND 24-03-08_EV_HHHD_PIN2_CRDO.png 40000000 D390 24-03-12 24-03-12_PIN8_D390_NADR_PN12.png 0 1 1 7.6020599913279625 True True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
D390 DS-1 True
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-1 | 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-1__DS-1A | | DS-1 | Custom | 30 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-1__DS-1B | | DS-1 | Custom | 50 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-28T02:18:00Z · MINTED_TRAITMECH_ID · codex
Minted DS-1 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 D390 transcriptional unit level because the pinned DefenseFinder DS-1 HMM rows are not backed by a rules row; proposals/metpo_traitmech_v301 reserves the replacement placeholder.
2026-09-28T02:18:01Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-1 system canonical_examples and left them empty because DeWeirdt et al. support cloned D390 plaquing assays in E. coli MG1655 plus a DefenseFinder DS-1 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-1 activity. No paid research was used.
2026-09-28T03:20:08Z · ADDRESSED_PR_REVIEW · codex
Addressed issue 1380 by rewriting the DS-1 definition so D390 is a DeWeirdt et al. working transcriptional-unit identifier rather than an implied E. coli transcriptional unit, expanding the DOI evidence snippets to explicitly state E. coli MG1655 low-copy plasmid expression, and syncing the METPO proposal definition.