DS-31 system

traitmech:000454 · CLASS · PROPOSED

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 31 locus cataloged as working transcriptional unit RED7 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
RED7 NZ_QOWW01000064.1 GCF_003334245.1 - True False False True DefensePredictor hits 6615 7667 hypothetical protein WP_001703029.1 8.059866321466373 1.02528101558256 True True Predicted novel defense gene DS-31

The final Science supplementary Table S6 maps working_id RED7 to DS_name DS-31, marks the cloned transcriptional unit as defensive, and records NZ_QOWW01000064.1 positions 6615-7667 with product accession WP_001703029.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas19 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 2200000 RED7 24-07-25 24-07-25_PDP1_RED1_PDP4_RED7.png 0 1 1 6.342422680822207 True LB 37

The final Science supplementary Table S7 reports a RED7 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
RED7 DS-31 True

The final Science supplementary Table S8 maps RED7 to replicated display name DS-31.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
RED7 1.0 350.0 WP_001703029.1 PDDEXK PF03838.19 RecU ; Recombination protein U hhpred_7098417.hhr 56.0 182.0 0.99 2024-07-28 00:00:00 201-203 187.0

The final Science supplementary Table S8 reports a high-probability PDDEXK HHpred hit for WP_001703029.1 in RED7.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-31 | 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-31 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-31__DS-31 | | DS-31 | Custom | 170 |

The pinned DefenseFinder HMM inventory records DS-31__DS-31 as a custom DS-31 profile.

DS-31 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the single-gene DS-31 locus to reduced bacteriophage plaquing without resolving DS-31 component function or molecular output.

NONMECHANISTIC · The graph captures DS-31 as the validated RED7 transcriptional unit with one product accession, one high-probability PDDEXK HHpred-domain row, and one DefenseFinder DS-31 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-31 molecular activity, trigger, substrate, complete phage breadth, PDDEXK HHpred-domain interpretation, or DefenseFinder rule-level detection criteria.

Edge evidence

DS-31 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-31/RED7 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 RED7 NZ_QOWW01000064.1 GCF_003334245.1 - True False False True DefensePredictor hits 6615 7667 hypothetical protein WP_001703029.1 8.059866321466373 1.02528101558256 True True Predicted novel defense gene DS-31 The final Science supplementary Table S6 maps working_id RED7 to DS_name DS-31, marks the cloned transcriptional unit as defensive, and records NZ_QOWW01000064.1 positions 6615-7667 with product accession WP_001703029.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas19 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 2200000 RED7 24-07-25 24-07-25_PDP1_RED1_PDP4_RED7.png 0 1 1 6.342422680822207 True LB 37 The final Science supplementary Table S7 reports a RED7 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx RED7 DS-31 True The final Science supplementary Table S8 maps RED7 to replicated display name DS-31.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx RED7 1.0 350.0 WP_001703029.1 PDDEXK PF03838.19 RecU ; Recombination protein U hhpred_7098417.hhr 56.0 182.0 0.99 2024-07-28 00:00:00 201-203 187.0 The final Science supplementary Table S8 reports a high-probability PDDEXK HHpred hit for WP_001703029.1 in RED7.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-31__DS-31 | | DS-31 | Custom | 170 | The pinned DefenseFinder HMM inventory records DS-31__DS-31 as a custom DS-31 profile.
reduced bacteriophage plaquing confers DS-31 system METPO:2007700
DS-31-mediated phage plaquing reduction realizes the DS-31 system trait.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx RED7 NZ_QOWW01000064.1 GCF_003334245.1 - True False False True DefensePredictor hits 6615 7667 hypothetical protein WP_001703029.1 8.059866321466373 1.02528101558256 True True Predicted novel defense gene DS-31 The final Science supplementary Table S6 maps working_id RED7 to DS_name DS-31, marks the cloned transcriptional unit as defensive, and records NZ_QOWW01000064.1 positions 6615-7667 with product accession WP_001703029.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas19 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 2200000 RED7 24-07-25 24-07-25_PDP1_RED1_PDP4_RED7.png 0 1 1 6.342422680822207 True LB 37 The final Science supplementary Table S7 reports a RED7 assay row with a Bas19 phage readout and a -log(EOP) value of 6.342.
- 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-31 system is a phage defense system rdfs:subClassOf
DS-31 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-31 | 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-31 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-31 EXACT_SYNONYM · DOI:10.1126/science.adv7924
RED7 RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
DS-31__DS-31 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-31 native host breadth, exact single-component activity, profile-to-protein mapping, PDDEXK HHpred-domain interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-31 mechanism children.

KNOWLEDGE GAP OPEN ds-31-defensefinder-model-gap · raised by codex · 2026-09-29

Attached to causal_graphs#ds_31_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-31 as the defensive RED7 transcriptional unit and final Science Tables S6/S7/S8 map it to product accession WP_001703029.1, a Bas19 phage readout, display name DS-31, and a PDDEXK HHpred row. The pinned DefenseFinder HMM inventory records one DS-31 custom profile row. The pinned rules table has no DS-31 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, PDDEXK activity, molecular output, or endogenous DS-31 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
RED7 NZ_QOWW01000064.1 GCF_003334245.1 - True False False True DefensePredictor hits 6615 7667 hypothetical protein WP_001703029.1 8.059866321466373 1.02528101558256 True True Predicted novel defense gene DS-31
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas19 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 2200000 RED7 24-07-25 24-07-25_PDP1_RED1_PDP4_RED7.png 0 1 1 6.342422680822207 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
RED7 DS-31 True
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
RED7 1.0 350.0 WP_001703029.1 PDDEXK PF03838.19 RecU ; Recombination protein U hhpred_7098417.hhr 56.0 182.0 0.99 2024-07-28 00:00:00 201-203 187.0
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-31 | 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-31__DS-31 | | DS-31 | Custom | 170 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-29T06:35:29Z · MINTED_TRAITMECH_ID · codex
Minted DS-31 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 RED7 transcriptional-unit level because PDDEXK activity and rule rows remain unresolved, and proposals/metpo_traitmech_v331 reserves the replacement placeholder.
2026-09-29T06:35:30Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-31 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned RED7 assays in E. coli MG1655 and a DefenseFinder DS-31 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-31 activity. No paid research was used.