DS-32 system

traitmech:000455 · CLASS · PROPOSED

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 32 locus cataloged as working transcriptional unit NADR 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
NADR NZ_QOXQ01000027.1 GCF_003333945.1 + True False False True DefensePredictor hits 48629 50261 hypothetical protein, NADAR family protein WP_000097610.1, WP_032260665.1 9.822610074734904 6.906754778648663 True True Predicted novel defense gene DS-32

The final Science supplementary Table S6 maps working_id NADR to DS_name DS-32, marks the cloned transcriptional unit as defensive, and records NZ_QOXQ01000027.1 positions 48629-50261 with product accessions WP_000097610.1 and WP_032260665.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas26 1.2 pLAND 24-03-08_EV_HHHD_PIN2_CRDO.png 500000000 NADR 24-03-12 24-03-12_SVIR_PIN8_NTTI_NADR.png 4 10 Y 100000 3.6989700043360187 True LB 37

The final Science supplementary Table S7 reports a NADR assay row with a Bas26 phage readout and a -log(EOP) value of 3.699.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
NADR DS-32 True

The final Science supplementary Table S8 maps NADR to replicated display name DS-32.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
NADR 1.0 343.0 WP_000097610.1 RecR 8K3F_A Recombination protein RecR; Recombination mediator protein hhpred_1157231.hhr 1.0 65.0 0.6827 2024-04-16 00:00:00

The final Science supplementary Table S8 reports a lower-probability RecR HHpred hit for WP_000097610.1 in NADR.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
NADR 1.0 343.0 WP_000097610.1 PRTase 3DMP_D Uracil phosphoribosyltransferase hhpred_1157231.hhr 129.0 196.0 0.942 2024-04-16 00:00:00

The final Science supplementary Table S8 reports a high-probability PRTase HHpred hit for WP_000097610.1 in NADR.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
NADR 2.0 203.0 WP_032260665.1 NADAR PF08719.15 NADAR ; NADAR domain hhpred_3126143.hhr 13.0 159.0 0.9992 2024-04-16 00:00:00

The final Science supplementary Table S8 reports a high-probability NADAR HHpred hit for WP_032260665.1 in NADR.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-32 | 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-32 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-32__DS-32A | | DS-32 | Custom | 150 |

The pinned DefenseFinder HMM inventory records DS-32__DS-32A as a custom DS-32 profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-32__DS-32B | | DS-32 | Custom | 210 |

The pinned DefenseFinder HMM inventory records DS-32__DS-32B as a custom DS-32 profile.

DS-32 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the two-gene DS-32 locus to reduced bacteriophage plaquing without resolving DS-32 component function or molecular output.

NONMECHANISTIC · The graph captures DS-32 as the validated NADR transcriptional unit with two product accessions, lower-probability RecR and high-probability PRTase HHpred rows for WP_000097610.1, a high-probability NADAR HHpred row for WP_032260665.1, and two DefenseFinder DS-32 profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, DS-32 molecular activity, trigger, substrate, complete phage breadth, RecR, PRTase, or NADAR HHpred-domain interpretation, or DefenseFinder rule-level detection criteria.

Edge evidence

DS-32 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-32/NADR locus contributes to reduced bacteriophage plaquing in heterologous E. coli MG1655 plasmid-expression assays.
- 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. describe the plasmid-based phage challenge used to validate predicted transcriptional units.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx NADR NZ_QOXQ01000027.1 GCF_003333945.1 + True False False True DefensePredictor hits 48629 50261 hypothetical protein, NADAR family protein WP_000097610.1, WP_032260665.1 9.822610074734904 6.906754778648663 True True Predicted novel defense gene DS-32 The final Science supplementary Table S6 maps working_id NADR to DS_name DS-32, marks the cloned transcriptional unit as defensive, and records NZ_QOXQ01000027.1 positions 48629-50261 with product accessions WP_000097610.1 and WP_032260665.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas26 1.2 pLAND 24-03-08_EV_HHHD_PIN2_CRDO.png 500000000 NADR 24-03-12 24-03-12_SVIR_PIN8_NTTI_NADR.png 4 10 Y 100000 3.6989700043360187 True LB 37 The final Science supplementary Table S7 reports a NADR assay row with a Bas26 phage readout and a -log(EOP) value of 3.699.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx NADR DS-32 True The final Science supplementary Table S8 maps NADR to replicated display name DS-32.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx NADR 1.0 343.0 WP_000097610.1 RecR 8K3F_A Recombination protein RecR; Recombination mediator protein hhpred_1157231.hhr 1.0 65.0 0.6827 2024-04-16 00:00:00 The final Science supplementary Table S8 reports a lower-probability RecR HHpred hit for WP_000097610.1 in NADR.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx NADR 1.0 343.0 WP_000097610.1 PRTase 3DMP_D Uracil phosphoribosyltransferase hhpred_1157231.hhr 129.0 196.0 0.942 2024-04-16 00:00:00 The final Science supplementary Table S8 reports a high-probability PRTase HHpred hit for WP_000097610.1 in NADR.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx NADR 2.0 203.0 WP_032260665.1 NADAR PF08719.15 NADAR ; NADAR domain hhpred_3126143.hhr 13.0 159.0 0.9992 2024-04-16 00:00:00 The final Science supplementary Table S8 reports a high-probability NADAR HHpred hit for WP_032260665.1 in NADR.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-32__DS-32A | | DS-32 | Custom | 150 | The pinned DefenseFinder HMM inventory records DS-32__DS-32A as a custom DS-32 profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-32__DS-32B | | DS-32 | Custom | 210 | The pinned DefenseFinder HMM inventory records DS-32__DS-32B as a custom DS-32 profile.
reduced bacteriophage plaquing confers DS-32 system METPO:2007700
DS-32-mediated phage plaquing reduction realizes the DS-32 system trait.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx NADR NZ_QOXQ01000027.1 GCF_003333945.1 + True False False True DefensePredictor hits 48629 50261 hypothetical protein, NADAR family protein WP_000097610.1, WP_032260665.1 9.822610074734904 6.906754778648663 True True Predicted novel defense gene DS-32 The final Science supplementary Table S6 maps working_id NADR to DS_name DS-32, marks the cloned transcriptional unit as defensive, and records NZ_QOXQ01000027.1 positions 48629-50261 with product accessions WP_000097610.1 and WP_032260665.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas26 1.2 pLAND 24-03-08_EV_HHHD_PIN2_CRDO.png 500000000 NADR 24-03-12 24-03-12_SVIR_PIN8_NTTI_NADR.png 4 10 Y 100000 3.6989700043360187 True LB 37 The final Science supplementary Table S7 reports a NADR assay row with a Bas26 phage readout and a -log(EOP) value of 3.699.
- 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. The DS nomenclature is used for DefensePredictor discovered systems.
DS-32 system is a phage defense system rdfs:subClassOf
DS-32 system possession is a phage-defense-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 validated TUs as DefensePredictor discovered systems.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | DS-32 | 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-32 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-32 EXACT_SYNONYM · DOI:10.1126/science.adv7924
NADR RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
DS-32__DS-32A RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
DS-32__DS-32B 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-32 native host breadth, exact component activities, profile-to-protein mapping, RecR, PRTase, and NADAR HHpred-domain interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-32 mechanism children.

KNOWLEDGE GAP OPEN ds-32-defensefinder-model-gap · raised by codex · 2026-09-29

Attached to causal_graphs#ds_32_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-32 as the defensive NADR transcriptional unit and final Science Tables S6/S7/S8 map it to two product accessions, a Bas26 phage readout, display name DS-32, and three HHpred rows. The pinned DefenseFinder HMM inventory records two DS-32 custom profile rows. The pinned rules table has no DS-32 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, component activities, molecular output, or endogenous DS-32 activity.

Evidence

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
NADR NZ_QOXQ01000027.1 GCF_003333945.1 + True False False True DefensePredictor hits 48629 50261 hypothetical protein, NADAR family protein WP_000097610.1, WP_032260665.1 9.822610074734904 6.906754778648663 True True Predicted novel defense gene DS-32
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas26 1.2 pLAND 24-03-08_EV_HHHD_PIN2_CRDO.png 500000000 NADR 24-03-12 24-03-12_SVIR_PIN8_NTTI_NADR.png 4 10 Y 100000 3.6989700043360187 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
NADR DS-32 True
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
NADR 1.0 343.0 WP_000097610.1 RecR 8K3F_A Recombination protein RecR; Recombination mediator protein hhpred_1157231.hhr 1.0 65.0 0.6827 2024-04-16 00:00:00
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
NADR 1.0 343.0 WP_000097610.1 PRTase 3DMP_D Uracil phosphoribosyltransferase hhpred_1157231.hhr 129.0 196.0 0.942 2024-04-16 00:00:00
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
NADR 2.0 203.0 WP_032260665.1 NADAR PF08719.15 NADAR ; NADAR domain hhpred_3126143.hhr 13.0 159.0 0.9992 2024-04-16 00:00:00
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-32 | 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-32__DS-32A | | DS-32 | Custom | 150 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-32__DS-32B | | DS-32 | Custom | 210 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-29T07:25:23Z · MINTED_TRAITMECH_ID · codex
Minted DS-32 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 NADR transcriptional-unit level because RecR, PRTase, NADAR activity and rule rows remain unresolved, and proposals/metpo_traitmech_v332 reserves the replacement placeholder.
2026-09-29T07:25:24Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-32 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned NADR assays in E. coli MG1655 and a DefenseFinder DS-32 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-32 activity. No paid research was used.