DS-45 system

traitmech:000469 · CLASS · PROPOSED

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 45 locus cataloged as working transcriptional unit 2971 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
2971 NZ_QOYQ01000002.1 GCF_003334555.1 - True False True True DefensePredictor hits 13159 13704 hypothetical protein WP_223151192.1 1.37181361625243 -1.373840900048604 True False Structural defense homolog DS-45

The final Science supplementary Table S6 maps working_id 2971 to DS_name DS-45, marks the cloned transcriptional unit as defensive, and records NZ_QOYQ01000002.1 positions 13159-13704 with product accession WP_223151192.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas50 2.2 pLAND 24-03-12_EV.png 10000000000 2971 24-03-13 24-03-13_2971_HEP3_TMP4.png 7 14 Y 140000000 1.853871964321762 True LB 37

The final Science supplementary Table S7 Systems sheet reports a 2971 assay row with a Bas50 phage readout, a smaller-plaque-size call, and a -log(EOP) value of 1.854.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
2971 DS-45 True

The final Science supplementary Table S8 maps 2971 to replicated display name DS-45.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
2971 1.0 181.0 WP_223151192.1 DUF2971 PF11185.12 DUF2971 ; Protein of unknown function (DUF2971) hhpred_2594846.hhr 58.0 129.0 0.9694 2024-04-15 00:00:00

The final Science supplementary Table S8 reports a high-probability DUF2971 HHpred hit for WP_223151192.1 in working_id 2971.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-45 | 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-45 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-45__DS-45 | | DS-45 | Custom | 200 |

The pinned DefenseFinder HMM inventory records DS-45__DS-45 as a custom DS-45 profile.

DS-45 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the single-gene DS-45 locus to reduced bacteriophage plaquing without resolving DS-45 component function or molecular output.

NONMECHANISTIC · The graph captures DS-45 as the validated 2971 transcriptional unit with one product accession, one high-probability DUF2971 HHpred-domain row, and one DefenseFinder DS-45 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-45 molecular activity, complete phage breadth, DUF2971-domain interpretation, or DefenseFinder rule-level detection criteria.

Edge evidence

DS-45 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-45/2971 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 2971 NZ_QOYQ01000002.1 GCF_003334555.1 - True False True True DefensePredictor hits 13159 13704 hypothetical protein WP_223151192.1 1.37181361625243 -1.373840900048604 True False Structural defense homolog DS-45 The final Science supplementary Table S6 maps working_id 2971 to DS_name DS-45, marks the cloned transcriptional unit as defensive, and records NZ_QOYQ01000002.1 positions 13159-13704 with product accession WP_223151192.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas50 2.2 pLAND 24-03-12_EV.png 10000000000 2971 24-03-13 24-03-13_2971_HEP3_TMP4.png 7 14 Y 140000000 1.853871964321762 True LB 37 The final Science supplementary Table S7 Systems sheet reports a 2971 assay row with a Bas50 phage readout, a smaller-plaque-size call, and a -log(EOP) value of 1.854.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx 2971 DS-45 True The final Science supplementary Table S8 maps 2971 to replicated display name DS-45.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx 2971 1.0 181.0 WP_223151192.1 DUF2971 PF11185.12 DUF2971 ; Protein of unknown function (DUF2971) hhpred_2594846.hhr 58.0 129.0 0.9694 2024-04-15 00:00:00 The final Science supplementary Table S8 reports a high-probability DUF2971 HHpred hit for WP_223151192.1 in working_id 2971.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-45__DS-45 | | DS-45 | Custom | 200 | The pinned DefenseFinder HMM inventory records DS-45__DS-45 as a custom DS-45 profile.
reduced bacteriophage plaquing confers DS-45 system METPO:2007700
DS-45-mediated phage plaquing reduction realizes the DS-45 system trait.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx 2971 NZ_QOYQ01000002.1 GCF_003334555.1 - True False True True DefensePredictor hits 13159 13704 hypothetical protein WP_223151192.1 1.37181361625243 -1.373840900048604 True False Structural defense homolog DS-45 The final Science supplementary Table S6 maps working_id 2971 to DS_name DS-45, marks the cloned transcriptional unit as defensive, and records NZ_QOYQ01000002.1 positions 13159-13704 with product accession WP_223151192.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas50 2.2 pLAND 24-03-12_EV.png 10000000000 2971 24-03-13 24-03-13_2971_HEP3_TMP4.png 7 14 Y 140000000 1.853871964321762 True LB 37 The final Science supplementary Table S7 Systems sheet reports a 2971 assay row with a Bas50 phage readout, a smaller-plaque-size call, and a -log(EOP) value of 1.854.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx 2971 DS-45 True The final Science supplementary Table S8 maps 2971 to replicated display name DS-45.
- 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-45 system is a phage defense system rdfs:subClassOf
DS-45 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-45 | 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-45 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-45 EXACT_SYNONYM · DOI:10.1126/science.adv7924
2971 RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
DS-45__DS-45 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-45 native host breadth, DUF2971-domain activity, profile-to-protein mapping, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-45 mechanism children.

KNOWLEDGE GAP OPEN ds-45-defensefinder-model-gap · raised by codex · 2026-09-29

Attached to causal_graphs#ds_45_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-45 as the defensive 2971 transcriptional unit and final Science Tables S6/S7/S8 map it to one product accession, a Bas50 phage readout, one DUF2971 HHpred-domain row, and display name DS-45. The pinned DefenseFinder HMM inventory records one DS-45 custom profile row. The pinned rules table has no DS-45 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, molecular output, or endogenous DS-45 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
2971 NZ_QOYQ01000002.1 GCF_003334555.1 - True False True True DefensePredictor hits 13159 13704 hypothetical protein WP_223151192.1 1.37181361625243 -1.373840900048604 True False Structural defense homolog DS-45
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas50 2.2 pLAND 24-03-12_EV.png 10000000000 2971 24-03-13 24-03-13_2971_HEP3_TMP4.png 7 14 Y 140000000 1.853871964321762 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
2971 DS-45 True
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
2971 1.0 181.0 WP_223151192.1 DUF2971 PF11185.12 DUF2971 ; Protein of unknown function (DUF2971) hhpred_2594846.hhr 58.0 129.0 0.9694 2024-04-15 00:00:00
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-45 | 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-45__DS-45 | | DS-45 | Custom | 200 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-29T17:02:36Z · MINTED_TRAITMECH_ID · codex
Minted DS-45 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 2971 transcriptional-unit level because DUF2971 activity and rule rows remain unresolved, and proposals/metpo_traitmech_v346 reserves the replacement placeholder.
2026-09-29T17:02:37Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-45 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned 2971 assays in E. coli MG1655 and a DefenseFinder DS-45 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-45 activity. No paid research was used.