DS-41 system

traitmech:000463 · CLASS · PROPOSED

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 41 locus cataloged as working transcriptional unit AAA2 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

Trait evidence (9)

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
AAA2 NZ_QOYD01000024.1 GCF_003333765.1 - True False False True DefensePredictor hits 5322 6830 hypothetical protein WP_033812887.1 7.980074950371131 4.119037174812478 True True Remote defense homolog DS-41

The final Science supplementary Table S6 maps working_id AAA2 to DS_name DS-41, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000024.1 positions 5322-6830 with product accession WP_033812887.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas1 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 3000000 AAA2 24-07-17 24-07-17_AAA2_RMOR_NERD_NUCS.png 1 3 30 5 True LB 37

The final Science supplementary Table S7 Systems sheet reports an AAA2 assay row with a Bas1 phage readout and a -log(EOP) value of 5.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
T4 6.2 pLAND 24-07-17_AAA2_VPUS_VAME_EV.png 20000000 AAA2 24-07-17 24-07-17_AAA2_VPUS_VAME_EV.png 1 10 100 5.301029995663981 True LB 37

The final Science supplementary Table S7 Systems sheet reports an AAA2 assay row with a T4 phage readout and a -log(EOP) value of 5.301.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
AAA2 DS-41 True

The final Science supplementary Table S8 maps AAA2 to replicated display name DS-41.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
AAA2 1.0 502.0 WP_033812887.1 AAA+ ATPase 2QBY_A Cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain hhpred_7261390.hhr 8.0 488.0 0.996 2024-07-29 00:00:00

The final Science supplementary Table S8 reports a high-probability AAA+ ATPase HHpred hit for WP_033812887.1 in AAA2.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-41 | 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-41 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-41__DS-41 | | DS-41 | Custom | 200 |

The pinned DefenseFinder HMM inventory records DS-41__DS-41 as a custom DS-41 profile.

DS-41 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the single-gene DS-41 locus to reduced bacteriophage plaquing without resolving DS-41 component function or molecular output.

NONMECHANISTIC · The graph captures DS-41 as the validated AAA2 transcriptional unit with one product accession, one high-probability AAA+ ATPase HHpred row for WP_033812887.1, and one DefenseFinder DS-41 profile row. It does not assert exact profile-to-protein correspondence, AAA+ ATPase activity, native host breadth, DS-41 molecular output, complete phage breadth, or DefenseFinder rule-level detection criteria.

Edge evidence

DS-41 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-41/AAA2 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 AAA2 NZ_QOYD01000024.1 GCF_003333765.1 - True False False True DefensePredictor hits 5322 6830 hypothetical protein WP_033812887.1 7.980074950371131 4.119037174812478 True True Remote defense homolog DS-41 The final Science supplementary Table S6 maps working_id AAA2 to DS_name DS-41, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000024.1 positions 5322-6830 with product accession WP_033812887.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas1 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 3000000 AAA2 24-07-17 24-07-17_AAA2_RMOR_NERD_NUCS.png 1 3 30 5 True LB 37 The final Science supplementary Table S7 Systems sheet reports an AAA2 assay row with a Bas1 phage readout and a -log(EOP) value of 5.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx T4 6.2 pLAND 24-07-17_AAA2_VPUS_VAME_EV.png 20000000 AAA2 24-07-17 24-07-17_AAA2_VPUS_VAME_EV.png 1 10 100 5.301029995663981 True LB 37 The final Science supplementary Table S7 Systems sheet reports an AAA2 assay row with a T4 phage readout and a -log(EOP) value of 5.301.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx AAA2 DS-41 True The final Science supplementary Table S8 maps AAA2 to replicated display name DS-41.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx AAA2 1.0 502.0 WP_033812887.1 AAA+ ATPase 2QBY_A Cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain hhpred_7261390.hhr 8.0 488.0 0.996 2024-07-29 00:00:00 The final Science supplementary Table S8 reports a high-probability AAA+ ATPase HHpred hit for WP_033812887.1 in AAA2.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-41__DS-41 | | DS-41 | Custom | 200 | The pinned DefenseFinder HMM inventory records DS-41__DS-41 as a custom DS-41 profile.
reduced bacteriophage plaquing confers DS-41 system METPO:2007700
DS-41-mediated phage plaquing reduction realizes the DS-41 system trait.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx AAA2 NZ_QOYD01000024.1 GCF_003333765.1 - True False False True DefensePredictor hits 5322 6830 hypothetical protein WP_033812887.1 7.980074950371131 4.119037174812478 True True Remote defense homolog DS-41 The final Science supplementary Table S6 maps working_id AAA2 to DS_name DS-41, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000024.1 positions 5322-6830 with product accession WP_033812887.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas1 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 3000000 AAA2 24-07-17 24-07-17_AAA2_RMOR_NERD_NUCS.png 1 3 30 5 True LB 37 The final Science supplementary Table S7 Systems sheet reports an AAA2 assay row with a Bas1 phage readout and a -log(EOP) value of 5.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx T4 6.2 pLAND 24-07-17_AAA2_VPUS_VAME_EV.png 20000000 AAA2 24-07-17 24-07-17_AAA2_VPUS_VAME_EV.png 1 10 100 5.301029995663981 True LB 37 The final Science supplementary Table S7 Systems sheet reports an AAA2 assay row with a T4 phage readout and a -log(EOP) value of 5.301.
- 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-41 system is a phage defense system rdfs:subClassOf
DS-41 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-41 | 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-41 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 (3)

DS-41 EXACT_SYNONYM · DOI:10.1126/science.adv7924
AAA2 RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
DS-41__DS-41 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-41 native host breadth, exact component activity, profile-to-protein mapping, AAA+ ATPase interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-41 mechanism children.

KNOWLEDGE GAP OPEN ds-41-defensefinder-model-gap · raised by codex · 2026-09-29

Attached to causal_graphs#ds_41_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-41 as the defensive AAA2 transcriptional unit and final Science Tables S6/S7/S8 map it to one product accession, Bas1 and T4 phage readouts, display name DS-41, and a high-probability AAA+ ATPase HHpred row. The pinned DefenseFinder HMM inventory records one DS-41 custom profile row. The pinned rules table has no DS-41 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, AAA+ ATPase activity, molecular output, or endogenous DS-41 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
AAA2 NZ_QOYD01000024.1 GCF_003333765.1 - True False False True DefensePredictor hits 5322 6830 hypothetical protein WP_033812887.1 7.980074950371131 4.119037174812478 True True Remote defense homolog DS-41
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas1 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 3000000 AAA2 24-07-17 24-07-17_AAA2_RMOR_NERD_NUCS.png 1 3 30 5 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
T4 6.2 pLAND 24-07-17_AAA2_VPUS_VAME_EV.png 20000000 AAA2 24-07-17 24-07-17_AAA2_VPUS_VAME_EV.png 1 10 100 5.301029995663981 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
AAA2 DS-41 True
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
AAA2 1.0 502.0 WP_033812887.1 AAA+ ATPase 2QBY_A Cell division control protein 6 homolog 1; winged-helix domain, helix-turn-helix, AAA+ ATPase domain hhpred_7261390.hhr 8.0 488.0 0.996 2024-07-29 00:00:00
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-41 | 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-41__DS-41 | | DS-41 | Custom | 200 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-29T12:49:10Z · MINTED_TRAITMECH_ID · codex
Minted DS-41 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 AAA2 transcriptional-unit level because AAA+ ATPase activity and rule rows remain unresolved, and proposals/metpo_traitmech_v340 reserves the replacement placeholder.
2026-09-29T12:49:11Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-41 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned AAA2 assays in E. coli MG1655 and a DefenseFinder DS-41 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-41 activity. No paid research was used.