DS-37 system

traitmech:000459 · CLASS · PROPOSED

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 37 locus cataloged as working transcriptional unit SC24 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
SC24 NZ_QOXM01000003.1 GCF_003334665.1 + True False False True DefensePredictor hits 26984 28375 hypothetical protein WP_000982358.1 6.427335289528256 -2.24248116892434 True False Predicted novel defense gene DS-37

The final Science supplementary Table S6 maps working_id SC24 to DS_name DS-37, marks the cloned transcriptional unit as defensive, and records NZ_QOXM01000003.1 positions 26984-28375 with product accession WP_000982358.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas1 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 3000000 SC24 24-07-24 24-07-24_TRNA_MF4L_SC24_EV.png 0 1 1 6.477121254719663 True LB 37

The final Science supplementary Table S7 reports an SC24 assay row with a Bas1 phage readout and a -log(EOP) value of 6.477.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas9 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 600000000 SC24 24-07-24 24-07-24_TRNA_MF4L_SC24_EV.png 3 10 10000 4.778151250383644 True LB 37

The final Science supplementary Table S7 reports an SC24 assay row with a Bas9 phage readout and a -log(EOP) value of 4.778.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
SC24 DS-37 True

The final Science supplementary Table S8 maps SC24 to replicated display name DS-37.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
SC24 1.0 463.0 WP_000982358.1 PDDEXK PF08378.16 NERD ; Nuclease-related domain hhpred_2278954.hhr 154.0 204.0 0.47 2024-07-29 00:00:00 210-212 199.0

The final Science supplementary Table S8 reports a low-probability PDDEXK HHpred lead for WP_000982358.1 in SC24; this first-pass record records it as source context without resolving DS-37 molecular activity.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-37 | 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-37 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-37__DS-37 | | DS-37 | Custom | 300 |

The pinned DefenseFinder HMM inventory records DS-37__DS-37 as a custom DS-37 profile.

DS-37 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the single-gene DS-37 locus to reduced bacteriophage plaquing without resolving DS-37 component function or molecular output.

NONMECHANISTIC · The graph captures DS-37 as the validated SC24 transcriptional unit with one product accession, one low-probability PDDEXK HHpred row for WP_000982358.1 in Table S8, and one DefenseFinder DS-37 profile row. It does not assert exact profile-to-protein correspondence, PDDEXK domain interpretation, nuclease chemistry, native host breadth, DS-37 molecular output, complete phage breadth, or DefenseFinder rule-level detection criteria.

Edge evidence

DS-37 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-37/SC24 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 SC24 NZ_QOXM01000003.1 GCF_003334665.1 + True False False True DefensePredictor hits 26984 28375 hypothetical protein WP_000982358.1 6.427335289528256 -2.24248116892434 True False Predicted novel defense gene DS-37 The final Science supplementary Table S6 maps working_id SC24 to DS_name DS-37, marks the cloned transcriptional unit as defensive, and records NZ_QOXM01000003.1 positions 26984-28375 with product accession WP_000982358.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas1 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 3000000 SC24 24-07-24 24-07-24_TRNA_MF4L_SC24_EV.png 0 1 1 6.477121254719663 True LB 37 The final Science supplementary Table S7 reports an SC24 assay row with a Bas1 phage readout and a -log(EOP) value of 6.477.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas9 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 600000000 SC24 24-07-24 24-07-24_TRNA_MF4L_SC24_EV.png 3 10 10000 4.778151250383644 True LB 37 The final Science supplementary Table S7 reports an SC24 assay row with a Bas9 phage readout and a -log(EOP) value of 4.778.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx SC24 DS-37 True The final Science supplementary Table S8 maps SC24 to replicated display name DS-37.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-37__DS-37 | | DS-37 | Custom | 300 | The pinned DefenseFinder HMM inventory records DS-37__DS-37 as a custom DS-37 profile.
reduced bacteriophage plaquing confers DS-37 system METPO:2007700
DS-37-mediated phage plaquing reduction realizes the DS-37 system trait.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx SC24 NZ_QOXM01000003.1 GCF_003334665.1 + True False False True DefensePredictor hits 26984 28375 hypothetical protein WP_000982358.1 6.427335289528256 -2.24248116892434 True False Predicted novel defense gene DS-37 The final Science supplementary Table S6 maps working_id SC24 to DS_name DS-37, marks the cloned transcriptional unit as defensive, and records NZ_QOXM01000003.1 positions 26984-28375 with product accession WP_000982358.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas1 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 3000000 SC24 24-07-24 24-07-24_TRNA_MF4L_SC24_EV.png 0 1 1 6.477121254719663 True LB 37 The final Science supplementary Table S7 reports an SC24 assay row with a Bas1 phage readout and a -log(EOP) value of 6.477.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas9 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 600000000 SC24 24-07-24 24-07-24_TRNA_MF4L_SC24_EV.png 3 10 10000 4.778151250383644 True LB 37 The final Science supplementary Table S7 reports an SC24 assay row with a Bas9 phage readout and a -log(EOP) value of 4.778.
- 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-37 system is a phage defense system rdfs:subClassOf
DS-37 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-37 | 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-37 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-37 EXACT_SYNONYM · DOI:10.1126/science.adv7924
SC24 RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
DS-37__DS-37 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-37 native host breadth, exact component activity, profile-to-protein mapping, low-probability PDDEXK HHpred-domain interpretation, nuclease chemistry, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-37 mechanism children.

KNOWLEDGE GAP OPEN ds-37-defensefinder-model-gap · raised by codex · 2026-09-29

Attached to causal_graphs#ds_37_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-37 as the defensive SC24 transcriptional unit and final Science Tables S6/S7/S8 map it to one product accession, Bas1 and Bas9 phage readouts, display name DS-37, and one low-probability PDDEXK HHpred row. The pinned DefenseFinder HMM inventory records one DS-37 custom profile row. The pinned rules table has no DS-37 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, PDDEXK domain interpretation, nuclease chemistry, molecular output, or endogenous DS-37 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
SC24 NZ_QOXM01000003.1 GCF_003334665.1 + True False False True DefensePredictor hits 26984 28375 hypothetical protein WP_000982358.1 6.427335289528256 -2.24248116892434 True False Predicted novel defense gene DS-37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas1 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 3000000 SC24 24-07-24 24-07-24_TRNA_MF4L_SC24_EV.png 0 1 1 6.477121254719663 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas9 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 600000000 SC24 24-07-24 24-07-24_TRNA_MF4L_SC24_EV.png 3 10 10000 4.778151250383644 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
SC24 DS-37 True
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
SC24 1.0 463.0 WP_000982358.1 PDDEXK PF08378.16 NERD ; Nuclease-related domain hhpred_2278954.hhr 154.0 204.0 0.47 2024-07-29 00:00:00 210-212 199.0
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-37 | 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-37__DS-37 | | DS-37 | Custom | 300 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-29T10:28:09Z · MINTED_TRAITMECH_ID · codex
Minted DS-37 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 SC24 transcriptional-unit level because the low-probability PDDEXK row and rule rows remain unresolved, and proposals/metpo_traitmech_v336 reserves the replacement placeholder.
2026-09-29T10:28:10Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-37 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned SC24 assays in E. coli MG1655 and a DefenseFinder DS-37 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-37 activity. No paid research was used.