DS-29 system

traitmech:000453 · CLASS · PROPOSED

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 29 locus cataloged as working transcriptional unit HEP3 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
HEP3 NZ_RRWI01000012.1 GCF_003892435.1 + True False True True DefensePredictor hits 2077 2862 hypothetical protein WP_061089765.1 9.79101703966607 -3.842009204807087 True False Predicted novel defense gene DS-29

The final Science supplementary Table S6 maps working_id HEP3 to DS_name DS-29, marks the cloned transcriptional unit as defensive, and records NZ_RRWI01000012.1 positions 2077-2862 with product accession WP_061089765.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas60 2.2 pLAND 24-03-12_EV.png 2200000000 HEP3 24-03-13 24-03-13_2971_HEP3_TMP4.png 1 100 1000 6.342422680822207 True LB 37

The final Science supplementary Table S7 reports an HEP3 assay row with a Bas60 phage readout and a -log(EOP) value of 6.342.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
HEP3 DS-29 True

The final Science supplementary Table S8 maps HEP3 to replicated display name DS-29.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
HEP3 1.0 261.0 WP_061089765.1 HEPN PF18867.6 HEPN-like_int ; HEPN-like integron domain hhpred_8060866.hhr 157.0 252.0 0.5936 2024-04-15 00:00:00

The final Science supplementary Table S8 reports a lower-probability HEPN-like HHpred hit for WP_061089765.1 in HEP3.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-29 | 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-29 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-29__DS-29 | | DS-29 | Custom | 100 |

The pinned DefenseFinder HMM inventory records DS-29__DS-29 as a custom DS-29 profile.

DS-29 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the single-gene DS-29 locus to reduced bacteriophage plaquing without resolving DS-29 component function or molecular output.

NONMECHANISTIC · The graph captures DS-29 as the validated HEP3 transcriptional unit with one product accession, one lower-probability HEPN-like HHpred-domain row, and one DefenseFinder DS-29 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-29 molecular activity, trigger, substrate, complete phage breadth, HEPN-like HHpred-domain interpretation, or DefenseFinder rule-level detection criteria.

Edge evidence

DS-29 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-29/HEP3 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 HEP3 NZ_RRWI01000012.1 GCF_003892435.1 + True False True True DefensePredictor hits 2077 2862 hypothetical protein WP_061089765.1 9.79101703966607 -3.842009204807087 True False Predicted novel defense gene DS-29 The final Science supplementary Table S6 maps working_id HEP3 to DS_name DS-29, marks the cloned transcriptional unit as defensive, and records NZ_RRWI01000012.1 positions 2077-2862 with product accession WP_061089765.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas60 2.2 pLAND 24-03-12_EV.png 2200000000 HEP3 24-03-13 24-03-13_2971_HEP3_TMP4.png 1 100 1000 6.342422680822207 True LB 37 The final Science supplementary Table S7 reports an HEP3 assay row with a Bas60 phage readout and a -log(EOP) value of 6.342.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx HEP3 DS-29 True The final Science supplementary Table S8 maps HEP3 to replicated display name DS-29.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx HEP3 1.0 261.0 WP_061089765.1 HEPN PF18867.6 HEPN-like_int ; HEPN-like integron domain hhpred_8060866.hhr 157.0 252.0 0.5936 2024-04-15 00:00:00 The final Science supplementary Table S8 reports a lower-probability HEPN-like HHpred hit for WP_061089765.1 in HEP3.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-29__DS-29 | | DS-29 | Custom | 100 | The pinned DefenseFinder HMM inventory records DS-29__DS-29 as a custom DS-29 profile.
reduced bacteriophage plaquing confers DS-29 system METPO:2007700
DS-29-mediated phage plaquing reduction realizes the DS-29 system trait.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx HEP3 NZ_RRWI01000012.1 GCF_003892435.1 + True False True True DefensePredictor hits 2077 2862 hypothetical protein WP_061089765.1 9.79101703966607 -3.842009204807087 True False Predicted novel defense gene DS-29 The final Science supplementary Table S6 maps working_id HEP3 to DS_name DS-29, marks the cloned transcriptional unit as defensive, and records NZ_RRWI01000012.1 positions 2077-2862 with product accession WP_061089765.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas60 2.2 pLAND 24-03-12_EV.png 2200000000 HEP3 24-03-13 24-03-13_2971_HEP3_TMP4.png 1 100 1000 6.342422680822207 True LB 37 The final Science supplementary Table S7 reports an HEP3 assay row with a Bas60 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-29 system is a phage defense system rdfs:subClassOf
DS-29 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-29 | 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-29 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-29 EXACT_SYNONYM · DOI:10.1126/science.adv7924
HEP3 RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
DS-29__DS-29 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-29 native host breadth, exact single-component activity, profile-to-protein mapping, HEPN-like HHpred-domain interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-29 mechanism children.

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

Attached to causal_graphs#ds_29_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-29 as the defensive HEP3 transcriptional unit and final Science Tables S6/S7/S8 map it to product accession WP_061089765.1, a Bas60 phage readout, display name DS-29, and a HEPN-like HHpred row. The pinned DefenseFinder HMM inventory records one DS-29 custom profile row. The pinned rules table has no DS-29 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, HEPN-like activity, molecular output, or endogenous DS-29 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
HEP3 NZ_RRWI01000012.1 GCF_003892435.1 + True False True True DefensePredictor hits 2077 2862 hypothetical protein WP_061089765.1 9.79101703966607 -3.842009204807087 True False Predicted novel defense gene DS-29
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas60 2.2 pLAND 24-03-12_EV.png 2200000000 HEP3 24-03-13 24-03-13_2971_HEP3_TMP4.png 1 100 1000 6.342422680822207 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
HEP3 DS-29 True
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
HEP3 1.0 261.0 WP_061089765.1 HEPN PF18867.6 HEPN-like_int ; HEPN-like integron domain hhpred_8060866.hhr 157.0 252.0 0.5936 2024-04-15 00:00:00
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-29 | 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-29__DS-29 | | DS-29 | Custom | 100 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-29T05:48:19Z · MINTED_TRAITMECH_ID · codex
Minted DS-29 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 HEP3 transcriptional-unit level because HEPN-like activity and rule rows remain unresolved, and proposals/metpo_traitmech_v330 reserves the replacement placeholder.
2026-09-29T05:48:20Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-29 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned HEP3 assays in E. coli MG1655 and a DefenseFinder DS-29 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-29 activity. No paid research was used.