DS-27 system

traitmech:000451 · CLASS · PROPOSED

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 27 locus cataloged as working transcriptional unit SMEK and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

Trait evidence (7)

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
SMEK NZ_QOXX01000051.1 GCF_003334605.1 + True False False True DefensePredictor hits 1216 2115 SMEK domain-containing protein WP_087896215.1 7.030671187100836 -2.208385407473748 True False Predicted novel defense gene DS-27

The final Science supplementary Table S6 maps working_id SMEK to DS_name DS-27, marks the cloned transcriptional unit as defensive, and records NZ_QOXX01000051.1 positions 1216-2115 with product accession WP_087896215.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
RB69 6.2 pLAND 24-07-17_AAA2_VPUS_VAME_EV.png 7000000 SMEK 24-07-25 24-07-25_SLIP_TMO1_PDX1_SMEK.png 3 10 10000 2.845098040014257 True LB 37

The final Science supplementary Table S7 reports a SMEK assay row with an RB69 phage readout and a -log(EOP) value of 2.845.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
SMEK DS-27 True

The final Science supplementary Table S8 maps SMEK to replicated display name DS-27.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-27 | 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-27 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-27__DS-27 | | DS-27 | Custom | 220 |

The pinned DefenseFinder HMM inventory records DS-27__DS-27 as a custom DS-27 profile.

DS-27 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the single-gene DS-27 locus to reduced bacteriophage plaquing without resolving DS-27 component function or molecular output.

NONMECHANISTIC · The graph captures DS-27 as the validated SMEK transcriptional unit with one product accession and one DefenseFinder DS-27 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-27 molecular activity, trigger, substrate, complete phage breadth, HHpred-domain interpretation, or DefenseFinder rule-level detection criteria.

Edge evidence

DS-27 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-27/SMEK 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 SMEK NZ_QOXX01000051.1 GCF_003334605.1 + True False False True DefensePredictor hits 1216 2115 SMEK domain-containing protein WP_087896215.1 7.030671187100836 -2.208385407473748 True False Predicted novel defense gene DS-27 The final Science supplementary Table S6 maps working_id SMEK to DS_name DS-27, marks the cloned transcriptional unit as defensive, and records NZ_QOXX01000051.1 positions 1216-2115 with product accession WP_087896215.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx RB69 6.2 pLAND 24-07-17_AAA2_VPUS_VAME_EV.png 7000000 SMEK 24-07-25 24-07-25_SLIP_TMO1_PDX1_SMEK.png 3 10 10000 2.845098040014257 True LB 37 The final Science supplementary Table S7 reports a SMEK assay row with an RB69 phage readout and a -log(EOP) value of 2.845.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx SMEK DS-27 True The final Science supplementary Table S8 maps SMEK to replicated display name DS-27.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-27__DS-27 | | DS-27 | Custom | 220 | The pinned DefenseFinder HMM inventory records DS-27__DS-27 as a custom DS-27 profile.
reduced bacteriophage plaquing confers DS-27 system METPO:2007700
DS-27-mediated phage plaquing reduction realizes the DS-27 system trait.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx SMEK NZ_QOXX01000051.1 GCF_003334605.1 + True False False True DefensePredictor hits 1216 2115 SMEK domain-containing protein WP_087896215.1 7.030671187100836 -2.208385407473748 True False Predicted novel defense gene DS-27 The final Science supplementary Table S6 maps working_id SMEK to DS_name DS-27, marks the cloned transcriptional unit as defensive, and records NZ_QOXX01000051.1 positions 1216-2115 with product accession WP_087896215.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx RB69 6.2 pLAND 24-07-17_AAA2_VPUS_VAME_EV.png 7000000 SMEK 24-07-25 24-07-25_SLIP_TMO1_PDX1_SMEK.png 3 10 10000 2.845098040014257 True LB 37 The final Science supplementary Table S7 reports a SMEK assay row with an RB69 phage readout and a -log(EOP) value of 2.845.
- 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-27 system is a phage defense system rdfs:subClassOf
DS-27 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-27 | 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-27 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-27 EXACT_SYNONYM · DOI:10.1126/science.adv7924
SMEK RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
DS-27__DS-27 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-27 native host breadth, exact single-component activity, profile-to-protein mapping, HHpred-domain interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-27 mechanism children.

KNOWLEDGE GAP OPEN ds-27-defensefinder-model-gap · raised by codex · 2026-09-29

Attached to causal_graphs#ds_27_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-27 as the defensive SMEK transcriptional unit and final Science Tables S6/S7/S8 map it to product accession WP_087896215.1, an RB69 phage readout, and display name DS-27. The pinned DefenseFinder HMM inventory records one DS-27 custom profile row. The pinned rules table has no DS-27 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, HHpred-domain interpretation, molecular output, or endogenous DS-27 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
SMEK NZ_QOXX01000051.1 GCF_003334605.1 + True False False True DefensePredictor hits 1216 2115 SMEK domain-containing protein WP_087896215.1 7.030671187100836 -2.208385407473748 True False Predicted novel defense gene DS-27
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
RB69 6.2 pLAND 24-07-17_AAA2_VPUS_VAME_EV.png 7000000 SMEK 24-07-25 24-07-25_SLIP_TMO1_PDX1_SMEK.png 3 10 10000 2.845098040014257 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
SMEK DS-27 True
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-27 | 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-27__DS-27 | | DS-27 | Custom | 220 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-29T04:13:10Z · MINTED_TRAITMECH_ID · codex
Minted DS-27 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 SMEK transcriptional-unit level because HHpred domain interpretation and rule rows remain unresolved, and proposals/metpo_traitmech_v328 reserves the replacement placeholder.
2026-09-29T04:13:11Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-27 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned SMEK assays in E. coli MG1655 and a DefenseFinder DS-27 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-27 activity. No paid research was used.