DS-22 system

traitmech:000447 · CLASS · PROPOSED

A phage defense system in which an organism possesses the single-gene DefensePredictor-discovered system 22 locus cataloged as working transcriptional unit MVB1 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
MVB1 NZ_QOWO01000045.1 GCF_003334815.1 - True False False True DefensePredictor hits 10119 11351 hypothetical protein WP_000162952.1 9.664065793183475 -2.806015014798907 True False Predicted novel defense gene DS-22

The final Science supplementary Table S6 maps working_id MVB1 to DS_name DS-22, marks the cloned transcriptional unit as defensive, and records NZ_QOWO01000045.1 positions 10119-11351 with product accession WP_000162952.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas11 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 100000000 MVB1 24-07-17 24-07-17_MVB1_VPUS_VAME_EV.png 2 10 1000 5 True LB 37

The final Science supplementary Table S7 reports an MVB1 assay row with a Bas11 phage readout and a -log(EOP) value of 5.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
MVB1 DS-22 True

The final Science supplementary Table S8 maps MVB1 to replicated display name DS-22.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
MVB1 1.0 410.0 WP_000162952.1 Mvb12 PF09452.15 Mvb12 ; ESCRT-I subunit Mvb12 hhpred_4626820.hhr 33.0 64.0 0.72 2024-07-27 00:00:00

The final Science supplementary Table S8 reports a low-probability Mvb12 HHpred hit for WP_000162952.1 in MVB1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
MVB1 1.0 410.0 WP_000162952.1 JAB PF04002.20 RadC-like JAB domain hhpred_4626820.hhr 258.0 324.0 0.37 2024-07-27 00:00:00

The final Science supplementary Table S8 reports a low-probability JAB HHpred hit for WP_000162952.1 in MVB1.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-22 | 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-22 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-22__DS-22 | | DS-22 | Custom | 60 |

The pinned DefenseFinder HMM inventory records DS-22__DS-22 as a custom DS-22 profile.

DS-22 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the single-gene DS-22 locus to reduced bacteriophage plaquing without resolving DS-22 component function or molecular output.

NONMECHANISTIC · The graph captures DS-22 as the validated MVB1 transcriptional unit with one product accession and one DefenseFinder DS-22 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-22 molecular activity, trigger, substrate, low-confidence HHpred-domain interpretations, complete phage breadth, or DefenseFinder rule-level detection criteria.

Edge evidence

DS-22 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-22/MVB1 locus contributes to reduced bacteriophage plaquing when plasmid expressed.
- 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 validate DefensePredictor-discovered systems by assaying cloned transcriptional units against E. coli phages.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx MVB1 NZ_QOWO01000045.1 GCF_003334815.1 - True False False True DefensePredictor hits 10119 11351 hypothetical protein WP_000162952.1 9.664065793183475 -2.806015014798907 True False Predicted novel defense gene DS-22 The final Science supplementary Table S6 maps working_id MVB1 to DS_name DS-22, marks the cloned transcriptional unit as defensive, and records NZ_QOWO01000045.1 positions 10119-11351 with product accession WP_000162952.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas11 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 100000000 MVB1 24-07-17 24-07-17_MVB1_VPUS_VAME_EV.png 2 10 1000 5 True LB 37 The final Science supplementary Table S7 reports an MVB1 assay row with a Bas11 phage readout and a -log(EOP) value of 5.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx MVB1 DS-22 True The final Science supplementary Table S8 maps MVB1 to replicated display name DS-22.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-22__DS-22 | | DS-22 | Custom | 60 | The pinned DefenseFinder HMM inventory records DS-22__DS-22 as a custom DS-22 profile.
reduced bacteriophage plaquing confers DS-22 system METPO:2007700
DS-22-mediated phage plaquing reduction realizes the DS-22 system trait.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx MVB1 NZ_QOWO01000045.1 GCF_003334815.1 - True False False True DefensePredictor hits 10119 11351 hypothetical protein WP_000162952.1 9.664065793183475 -2.806015014798907 True False Predicted novel defense gene DS-22 The final Science supplementary Table S6 maps working_id MVB1 to DS_name DS-22, marks the cloned transcriptional unit as defensive, and records NZ_QOWO01000045.1 positions 10119-11351 with product accession WP_000162952.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas11 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 100000000 MVB1 24-07-17 24-07-17_MVB1_VPUS_VAME_EV.png 2 10 1000 5 True LB 37 The final Science supplementary Table S7 reports an MVB1 assay row with a Bas11 phage readout and a -log(EOP) value of 5.
- 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-22 system is a phage defense system rdfs:subClassOf
DS-22 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-22 | 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-22 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-22 EXACT_SYNONYM · DOI:10.1126/science.adv7924
MVB1 RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
DS-22__DS-22 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-22 native host breadth, exact single-component activity, profile-to-protein mapping, sensitive-phage breadth, low-confidence HHpred-domain interpretation, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-22 mechanism children.

KNOWLEDGE GAP OPEN ds-22-defensefinder-model-gap · raised by codex · 2026-09-28

Attached to causal_graphs#ds_22_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-22 as the defensive MVB1 transcriptional unit that reduced Bas11 plaquing when cloned in E. coli MG1655, and the pinned DefenseFinder HMM inventory records one DS-22 profile row. The pinned rules table has no DS-22 row, and the first-pass record does not resolve native host breadth, exact component activity, direct profile-to-protein correspondence, the Mvb12 and JAB HHpred-domain rows, phage target breadth, molecular output, or endogenous DS-22 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
MVB1 NZ_QOWO01000045.1 GCF_003334815.1 - True False False True DefensePredictor hits 10119 11351 hypothetical protein WP_000162952.1 9.664065793183475 -2.806015014798907 True False Predicted novel defense gene DS-22
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas11 6.1 pLAND 24-07-17_MVB1_VPUS_VAME_EV.png 100000000 MVB1 24-07-17 24-07-17_MVB1_VPUS_VAME_EV.png 2 10 1000 5 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
MVB1 DS-22 True
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
MVB1 1.0 410.0 WP_000162952.1 Mvb12 PF09452.15 Mvb12 ; ESCRT-I subunit Mvb12 hhpred_4626820.hhr 33.0 64.0 0.72 2024-07-27 00:00:00
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
MVB1 1.0 410.0 WP_000162952.1 JAB PF04002.20 RadC-like JAB domain hhpred_4626820.hhr 258.0 324.0 0.37 2024-07-27 00:00:00
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-22 | 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-22__DS-22 | | DS-22 | Custom | 60 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-28T23:30:13Z · MINTED_TRAITMECH_ID · codex
Minted DS-22 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 cloned MVB1 transcriptional-unit level because the pinned DefenseFinder DS-22 HMM row is not backed by a rules row, and proposals/metpo_traitmech_v324 reserves the replacement placeholder.
2026-09-28T23:30:14Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-22 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned MVB1 assays in E. coli MG1655 and a DefenseFinder DS-22 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-22 activity. No paid research was used.
2026-09-29T00:00:35Z · UPDATED_EVIDENCE · codex
Added exact final Table S8 MVB1 HHpred-domain rows for the low-probability Mvb12 and JAB hits so the DS-22 mechanism gap quotes the evidence it defers.
2026-09-29T00:11:21Z · UPDATED_SYNONYM_SOURCE · codex
Aligned the DS-22 exact-synonym source with adjacent DS system records by citing the DOI that defines the DS display-name convention.
2026-09-29T00:23:32Z · UPDATED_EVIDENCE · codex
Split the MVB1 Mvb12 and JAB Table S8 HHpred rows into separate evidence items so each snippet quotes one contiguous source row.