DS-23 system

traitmech:000448 · CLASS · PROPOSED

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 23 locus cataloged as working transcriptional unit E2DP 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
E2DP NZ_RRVV01000032.1 GCF_003886345.1 + True False False True DefensePredictor hits 38754 40913 SEC-C metal-binding domain-containing protein WP_020231147.1 11.17818080568115 3.842009204807092 True True Predicted novel defense gene DS-23

The final Science supplementary Table S6 maps working_id E2DP to DS_name DS-23, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000032.1 positions 38754-40913 with product accession WP_020231147.1.
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 E2DP 24-07-24 24-07-24_ABIL_E2DP_COAT_DDML.png 0 1 1 6.342422680822207 True LB 37

The final Science supplementary Table S7 reports an E2DP 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
E2DP DS-23 True

The final Science supplementary Table S8 maps E2DP to replicated display name DS-23.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
E2DP 1.0 719.0 WP_020231147.1 ZF 2I9W_A Hypothetical protein; Cystatin-like fold, sec-c motif fold, structural genomics hhpred_7846250.hhr 693.0 716.0 0.98 2024-07-30 00:00:00

The final Science supplementary Table S8 reports a ZF HHpred hit for WP_020231147.1 in E2DP.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
E2DP 1.0 719.0 WP_020231147.1 PDDEXK cd22364 VC1899-like; putative nuclease domain found in Vibrio cholerae VC1899 and similar proteins. A putative nuclease domain found in Vibrio cholerae VC1899 and similar proteins belongs to a superfamily of PDDEXK nucleases hhpred_7846250.hhr 295.0 457.0 0.96 2024-07-30 00:00:00 110-112 96.0

The final Science supplementary Table S8 reports a PDDEXK HHpred hit for WP_020231147.1 in E2DP.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-23 | 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-23 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-23__DS-23 | | DS-23 | Custom | 200 |

The pinned DefenseFinder HMM inventory records DS-23__DS-23 as a custom DS-23 profile.

DS-23 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the single-gene DS-23 locus to reduced bacteriophage plaquing without resolving DS-23 component function or molecular output.

NONMECHANISTIC · The graph captures DS-23 as the validated E2DP transcriptional unit with one product accession, ZF and PDDEXK HHpred-domain rows, and one DefenseFinder DS-23 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-23 molecular activity, trigger, substrate, complete phage breadth, or DefenseFinder rule-level detection criteria.

Edge evidence

DS-23 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-23/E2DP 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 E2DP NZ_RRVV01000032.1 GCF_003886345.1 + True False False True DefensePredictor hits 38754 40913 SEC-C metal-binding domain-containing protein WP_020231147.1 11.17818080568115 3.842009204807092 True True Predicted novel defense gene DS-23 The final Science supplementary Table S6 maps working_id E2DP to DS_name DS-23, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000032.1 positions 38754-40913 with product accession WP_020231147.1.
- 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 E2DP 24-07-24 24-07-24_ABIL_E2DP_COAT_DDML.png 0 1 1 6.342422680822207 True LB 37 The final Science supplementary Table S7 reports an E2DP 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 E2DP DS-23 True The final Science supplementary Table S8 maps E2DP to replicated display name DS-23.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-23__DS-23 | | DS-23 | Custom | 200 | The pinned DefenseFinder HMM inventory records DS-23__DS-23 as a custom DS-23 profile.
reduced bacteriophage plaquing confers DS-23 system METPO:2007700
DS-23-mediated phage plaquing reduction realizes the DS-23 system trait.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx E2DP NZ_RRVV01000032.1 GCF_003886345.1 + True False False True DefensePredictor hits 38754 40913 SEC-C metal-binding domain-containing protein WP_020231147.1 11.17818080568115 3.842009204807092 True True Predicted novel defense gene DS-23 The final Science supplementary Table S6 maps working_id E2DP to DS_name DS-23, marks the cloned transcriptional unit as defensive, and records NZ_RRVV01000032.1 positions 38754-40913 with product accession WP_020231147.1.
- 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 E2DP 24-07-24 24-07-24_ABIL_E2DP_COAT_DDML.png 0 1 1 6.342422680822207 True LB 37 The final Science supplementary Table S7 reports an E2DP 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-23 system is a phage defense system rdfs:subClassOf
DS-23 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-23 | 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-23 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-23 EXACT_SYNONYM · DOI:10.1126/science.adv7924
E2DP RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
DS-23__DS-23 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-23 native host breadth, exact single-component activity, profile-to-protein mapping, ZF and PDDEXK HHpred-domain interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-23 mechanism children.

KNOWLEDGE GAP OPEN ds-23-defensefinder-model-gap · raised by codex · 2026-09-29

Attached to causal_graphs#ds_23_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-23 as the defensive E2DP transcriptional unit and final Science Tables S6/S7/S8 map it to product accession WP_020231147.1, a Bas19 phage readout, display name DS-23, and ZF and PDDEXK HHpred rows. The pinned DefenseFinder HMM inventory records one DS-23 custom profile row. The pinned rules table has no DS-23 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, ZF or PDDEXK activity, molecular output, or endogenous DS-23 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
E2DP NZ_RRVV01000032.1 GCF_003886345.1 + True False False True DefensePredictor hits 38754 40913 SEC-C metal-binding domain-containing protein WP_020231147.1 11.17818080568115 3.842009204807092 True True Predicted novel defense gene DS-23
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 E2DP 24-07-24 24-07-24_ABIL_E2DP_COAT_DDML.png 0 1 1 6.342422680822207 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
E2DP DS-23 True
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
E2DP 1.0 719.0 WP_020231147.1 ZF 2I9W_A Hypothetical protein; Cystatin-like fold, sec-c motif fold, structural genomics hhpred_7846250.hhr 693.0 716.0 0.98 2024-07-30 00:00:00
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
E2DP 1.0 719.0 WP_020231147.1 PDDEXK cd22364 VC1899-like; putative nuclease domain found in Vibrio cholerae VC1899 and similar proteins. A putative nuclease domain found in Vibrio cholerae VC1899 and similar proteins belongs to a superfamily of PDDEXK nucleases hhpred_7846250.hhr 295.0 457.0 0.96 2024-07-30 00:00:00 110-112 96.0
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-23 | 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-23__DS-23 | | DS-23 | Custom | 200 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-29T00:59:43Z · MINTED_TRAITMECH_ID · codex
Minted DS-23 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 E2DP transcriptional-unit level because ZF and PDDEXK chemistry and rule rows remain unresolved, and proposals/metpo_traitmech_v325 reserves the replacement placeholder.
2026-09-29T00:59:44Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-23 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned E2DP assays in E. coli MG1655 and a DefenseFinder DS-23 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-23 activity. No paid research was used.