DS-28 system

traitmech:000452 · CLASS · PROPOSED

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 28 locus cataloged as working transcriptional unit ANEX and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

Trait evidence (10)

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
ANEX NZ_RRWS01000106.1 GCF_003892555.1 + True False False True DefensePredictor hits 2434 3695 hypothetical protein, HEPN family nuclease WP_000494510.1, WP_000528930.1 7.693635438050782 1.093286044385436 True True Predicted novel defense gene DS-28

The final Science supplementary Table S6 maps working_id ANEX to DS_name DS-28, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000106.1 positions 2434-3695 with product accessions WP_000494510.1 and WP_000528930.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas60 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 400000 ANEX 24-07-24 24-07-24_ANEX_NADH_APE1_NLRH.png 1 1 10 4.6020599913279625 True LB 37

The final Science supplementary Table S7 reports an ANEX assay row with a Bas60 phage readout and a -log(EOP) value of 4.602.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ANEX DS-28 True

The final Science supplementary Table S8 maps ANEX to replicated display name DS-28.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ANEX 1.0 163.0 WP_000528930.1 HEPN PF18736.6 pEK499_p136 ; HEPN pEK499 p136 hhpred_5242066.hhr 1.0 153.0 1.0 2024-07-30 00:00:00

The final Science supplementary Table S8 reports a high-probability HEPN HHpred hit for WP_000528930.1 in ANEX.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ANEX 2.0 252.0 WP_000494510.1 TF 6J9E_J RNA polymerase, transcription termination, anti-termination, RNAP clamp, phage, transcription initiation, P7, NusA, Xanthomonos oryzae, Xp10, transcription hhpred_1617000.hhr 143.0 178.0 0.326 2024-07-30 00:00:00

The final Science supplementary Table S8 reports a lower-probability TF HHpred hit for WP_000494510.1 in ANEX.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-28 | 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-28 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-28__DS-28A | | DS-28 | Custom | 100 |

The pinned DefenseFinder HMM inventory records DS-28__DS-28A as a custom DS-28 profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-28__DS-28B | | DS-28 | Custom | 100 |

The pinned DefenseFinder HMM inventory records DS-28__DS-28B as a custom DS-28 profile.

DS-28 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the two-gene DS-28 locus to reduced bacteriophage plaquing without resolving DS-28 component function or molecular output.

NONMECHANISTIC · The graph captures DS-28 as the validated ANEX transcriptional unit with two product accessions, one high-probability HEPN HHpred-domain row, one lower-probability TF HHpred-domain row, and two DefenseFinder DS-28 profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, DS-28 molecular activity, trigger, substrate, complete phage breadth, HEPN or transcription-factor HHpred-domain interpretation, or DefenseFinder rule-level detection criteria.

Edge evidence

DS-28 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-28/ANEX 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 ANEX NZ_RRWS01000106.1 GCF_003892555.1 + True False False True DefensePredictor hits 2434 3695 hypothetical protein, HEPN family nuclease WP_000494510.1, WP_000528930.1 7.693635438050782 1.093286044385436 True True Predicted novel defense gene DS-28 The final Science supplementary Table S6 maps working_id ANEX to DS_name DS-28, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000106.1 positions 2434-3695 with product accessions WP_000494510.1 and WP_000528930.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas60 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 400000 ANEX 24-07-24 24-07-24_ANEX_NADH_APE1_NLRH.png 1 1 10 4.6020599913279625 True LB 37 The final Science supplementary Table S7 reports an ANEX assay row with a Bas60 phage readout and a -log(EOP) value of 4.602.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx ANEX DS-28 True The final Science supplementary Table S8 maps ANEX to replicated display name DS-28.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx ANEX 1.0 163.0 WP_000528930.1 HEPN PF18736.6 pEK499_p136 ; HEPN pEK499 p136 hhpred_5242066.hhr 1.0 153.0 1.0 2024-07-30 00:00:00 The final Science supplementary Table S8 reports a high-probability HEPN HHpred hit for WP_000528930.1 in ANEX.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx ANEX 2.0 252.0 WP_000494510.1 TF 6J9E_J RNA polymerase, transcription termination, anti-termination, RNAP clamp, phage, transcription initiation, P7, NusA, Xanthomonos oryzae, Xp10, transcription hhpred_1617000.hhr 143.0 178.0 0.326 2024-07-30 00:00:00 The final Science supplementary Table S8 reports a lower-probability TF HHpred hit for WP_000494510.1 in ANEX.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-28__DS-28A | | DS-28 | Custom | 100 | The pinned DefenseFinder HMM inventory records DS-28__DS-28A as a custom DS-28 profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-28__DS-28B | | DS-28 | Custom | 100 | The pinned DefenseFinder HMM inventory records DS-28__DS-28B as a custom DS-28 profile.
reduced bacteriophage plaquing confers DS-28 system METPO:2007700
DS-28-mediated phage plaquing reduction realizes the DS-28 system trait.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx ANEX NZ_RRWS01000106.1 GCF_003892555.1 + True False False True DefensePredictor hits 2434 3695 hypothetical protein, HEPN family nuclease WP_000494510.1, WP_000528930.1 7.693635438050782 1.093286044385436 True True Predicted novel defense gene DS-28 The final Science supplementary Table S6 maps working_id ANEX to DS_name DS-28, marks the cloned transcriptional unit as defensive, and records NZ_RRWS01000106.1 positions 2434-3695 with product accessions WP_000494510.1 and WP_000528930.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas60 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 400000 ANEX 24-07-24 24-07-24_ANEX_NADH_APE1_NLRH.png 1 1 10 4.6020599913279625 True LB 37 The final Science supplementary Table S7 reports an ANEX assay row with a Bas60 phage readout and a -log(EOP) value of 4.602.
- 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-28 system is a phage defense system rdfs:subClassOf
DS-28 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-28 | 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-28 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-28 EXACT_SYNONYM · DOI:10.1126/science.adv7924
ANEX RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
DS-28__DS-28A RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
DS-28__DS-28B 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-28 native host breadth, exact component activities, profile-to-protein mappings, HEPN and transcription-factor HHpred-domain interpretations, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-28 mechanism children.

KNOWLEDGE GAP OPEN ds-28-defensefinder-model-gap · raised by codex · 2026-09-29

Attached to causal_graphs#ds_28_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-28 as the defensive ANEX transcriptional unit and final Science Tables S6/S7/S8 map it to product accessions WP_000494510.1 and WP_000528930.1, a Bas60 phage readout, display name DS-28, a high-probability HEPN HHpred row, and a lower-probability TF HHpred row. The pinned DefenseFinder HMM inventory records two DS-28 custom profile rows. The pinned rules table has no DS-28 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, HEPN or transcription-factor activity, molecular output, or endogenous DS-28 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
ANEX NZ_RRWS01000106.1 GCF_003892555.1 + True False False True DefensePredictor hits 2434 3695 hypothetical protein, HEPN family nuclease WP_000494510.1, WP_000528930.1 7.693635438050782 1.093286044385436 True True Predicted novel defense gene DS-28
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas60 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 400000 ANEX 24-07-24 24-07-24_ANEX_NADH_APE1_NLRH.png 1 1 10 4.6020599913279625 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ANEX DS-28 True
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ANEX 1.0 163.0 WP_000528930.1 HEPN PF18736.6 pEK499_p136 ; HEPN pEK499 p136 hhpred_5242066.hhr 1.0 153.0 1.0 2024-07-30 00:00:00
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ANEX 2.0 252.0 WP_000494510.1 TF 6J9E_J RNA polymerase, transcription termination, anti-termination, RNAP clamp, phage, transcription initiation, P7, NusA, Xanthomonos oryzae, Xp10, transcription hhpred_1617000.hhr 143.0 178.0 0.326 2024-07-30 00:00:00
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-28 | 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-28__DS-28A | | DS-28 | Custom | 100 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-28__DS-28B | | DS-28 | Custom | 100 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-29T04:57:13Z · MINTED_TRAITMECH_ID · codex
Minted DS-28 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 ANEX transcriptional-unit level because HEPN and transcription-factor HHpred-domain interpretation and rule rows remain unresolved, and proposals/metpo_traitmech_v329 reserves the replacement placeholder.
2026-09-29T04:57:14Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-28 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned ANEX assays in E. coli MG1655 and a DefenseFinder DS-28 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-28 activity. No paid research was used.