DS-34 system

traitmech:000457 · CLASS · PROPOSED

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 34 locus cataloged as working transcriptional unit CITO 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
CITO NZ_QOXN01000005.1 GCF_003334015.1 + True False True True DefensePredictor hits 236284 238194 phage repressor protein CI, hypothetical protein WP_001589054.1, WP_000377448.1 8.290091443457554 3.623314765621056 True True Predicted novel defense gene DS-34

The final Science supplementary Table S6 maps working_id CITO to DS_name DS-34, marks the cloned transcriptional unit as defensive, and records NZ_QOXN01000005.1 positions 236284-238194 with product accessions WP_001589054.1 and WP_000377448.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas19 3.1 pLAND 24-04-10_CITO_AAA3_FDRT_EV.png 4000 CITO 24-04-10 24-04-10_CITO_AAA3_FDRT_EV.png 0 1 1 3.6020599913279625 True LB 37

The final Science supplementary Table S7 reports a CITO assay row with a Bas19 phage readout and a -log(EOP) value of 3.602.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
CITO DS-34 True

The final Science supplementary Table S8 maps CITO to replicated display name DS-34.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
CITO 1.0 308.0 WP_001589054.1 Phage repressor 2FJR_A Repressor protein CI; genetic switch, regulation, repressor hhpred_1741337.hhr 125.0 307.0 0.9987 2024-04-17 00:00:00

The final Science supplementary Table S8 reports a high-probability phage-repressor HHpred hit for WP_001589054.1 in CITO.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
CITO 1.0 308.0 WP_001589054.1 HTH PF08667.14 BetR ; BetR domain hhpred_1741337.hhr 20.0 88.0 0.9431 2024-04-17 00:00:00

The final Science supplementary Table S8 reports a high-probability HTH HHpred hit for WP_001589054.1 in CITO.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-34 | 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-34 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-34__DS-34A | | DS-34 | Custom | 120 |

The pinned DefenseFinder HMM inventory records DS-34__DS-34A as a custom DS-34 profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-34__DS-34B | | DS-34 | Custom | 50 |

The pinned DefenseFinder HMM inventory records DS-34__DS-34B as a custom DS-34 profile.

DS-34 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the two-gene DS-34 locus to reduced bacteriophage plaquing without resolving DS-34 component function or molecular output.

NONMECHANISTIC · The graph captures DS-34 as the validated CITO transcriptional unit with two product accessions, high-probability phage-repressor and HTH HHpred rows for WP_001589054.1, and two DefenseFinder DS-34 profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, DS-34 molecular activity, trigger, substrate, complete phage breadth, phage-repressor or HTH HHpred-domain interpretation, or DefenseFinder rule-level detection criteria.

Edge evidence

DS-34 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-34/CITO 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 CITO NZ_QOXN01000005.1 GCF_003334015.1 + True False True True DefensePredictor hits 236284 238194 phage repressor protein CI, hypothetical protein WP_001589054.1, WP_000377448.1 8.290091443457554 3.623314765621056 True True Predicted novel defense gene DS-34 The final Science supplementary Table S6 maps working_id CITO to DS_name DS-34, marks the cloned transcriptional unit as defensive, and records NZ_QOXN01000005.1 positions 236284-238194 with product accessions WP_001589054.1 and WP_000377448.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas19 3.1 pLAND 24-04-10_CITO_AAA3_FDRT_EV.png 4000 CITO 24-04-10 24-04-10_CITO_AAA3_FDRT_EV.png 0 1 1 3.6020599913279625 True LB 37 The final Science supplementary Table S7 reports a CITO assay row with a Bas19 phage readout and a -log(EOP) value of 3.602.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx CITO DS-34 True The final Science supplementary Table S8 maps CITO to replicated display name DS-34.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx CITO 1.0 308.0 WP_001589054.1 Phage repressor 2FJR_A Repressor protein CI; genetic switch, regulation, repressor hhpred_1741337.hhr 125.0 307.0 0.9987 2024-04-17 00:00:00 The final Science supplementary Table S8 reports a high-probability phage-repressor HHpred hit for WP_001589054.1 in CITO.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx CITO 1.0 308.0 WP_001589054.1 HTH PF08667.14 BetR ; BetR domain hhpred_1741337.hhr 20.0 88.0 0.9431 2024-04-17 00:00:00 The final Science supplementary Table S8 reports a high-probability HTH HHpred hit for WP_001589054.1 in CITO.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-34__DS-34A | | DS-34 | Custom | 120 | The pinned DefenseFinder HMM inventory records DS-34__DS-34A as a custom DS-34 profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-34__DS-34B | | DS-34 | Custom | 50 | The pinned DefenseFinder HMM inventory records DS-34__DS-34B as a custom DS-34 profile.
reduced bacteriophage plaquing confers DS-34 system METPO:2007700
DS-34-mediated phage plaquing reduction realizes the DS-34 system trait.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx CITO NZ_QOXN01000005.1 GCF_003334015.1 + True False True True DefensePredictor hits 236284 238194 phage repressor protein CI, hypothetical protein WP_001589054.1, WP_000377448.1 8.290091443457554 3.623314765621056 True True Predicted novel defense gene DS-34 The final Science supplementary Table S6 maps working_id CITO to DS_name DS-34, marks the cloned transcriptional unit as defensive, and records NZ_QOXN01000005.1 positions 236284-238194 with product accessions WP_001589054.1 and WP_000377448.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas19 3.1 pLAND 24-04-10_CITO_AAA3_FDRT_EV.png 4000 CITO 24-04-10 24-04-10_CITO_AAA3_FDRT_EV.png 0 1 1 3.6020599913279625 True LB 37 The final Science supplementary Table S7 reports a CITO assay row with a Bas19 phage readout and a -log(EOP) value of 3.602.
- 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-34 system is a phage defense system rdfs:subClassOf
DS-34 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-34 | 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-34 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-34 EXACT_SYNONYM · DOI:10.1126/science.adv7924
CITO RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
DS-34__DS-34A RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
DS-34__DS-34B 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-34 native host breadth, exact component activities, profile-to-protein mapping, phage-repressor and HTH HHpred-domain interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-34 mechanism children.

KNOWLEDGE GAP OPEN ds-34-defensefinder-model-gap · raised by codex · 2026-09-29

Attached to causal_graphs#ds_34_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-34 as the defensive CITO transcriptional unit and final Science Tables S6/S7/S8 map it to two product accessions, a Bas19 phage readout, display name DS-34, and two HHpred rows. The pinned DefenseFinder HMM inventory records two DS-34 custom profile rows. The pinned rules table has no DS-34 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, component activities, molecular output, or endogenous DS-34 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
CITO NZ_QOXN01000005.1 GCF_003334015.1 + True False True True DefensePredictor hits 236284 238194 phage repressor protein CI, hypothetical protein WP_001589054.1, WP_000377448.1 8.290091443457554 3.623314765621056 True True Predicted novel defense gene DS-34
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas19 3.1 pLAND 24-04-10_CITO_AAA3_FDRT_EV.png 4000 CITO 24-04-10 24-04-10_CITO_AAA3_FDRT_EV.png 0 1 1 3.6020599913279625 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
CITO DS-34 True
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
CITO 1.0 308.0 WP_001589054.1 Phage repressor 2FJR_A Repressor protein CI; genetic switch, regulation, repressor hhpred_1741337.hhr 125.0 307.0 0.9987 2024-04-17 00:00:00
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
CITO 1.0 308.0 WP_001589054.1 HTH PF08667.14 BetR ; BetR domain hhpred_1741337.hhr 20.0 88.0 0.9431 2024-04-17 00:00:00
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-34 | 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-34__DS-34A | | DS-34 | Custom | 120 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-34__DS-34B | | DS-34 | Custom | 50 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-29T08:40:09Z · MINTED_TRAITMECH_ID · codex
Minted DS-34 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 CITO transcriptional-unit level because phage-repressor and HTH activity and rule rows remain unresolved, and proposals/metpo_traitmech_v334 reserves the replacement placeholder.
2026-09-29T08:40:10Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-34 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned CITO assays in E. coli MG1655 and a DefenseFinder DS-34 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-34 activity. No paid research was used.