DS-16 system

traitmech:000439 · CLASS · PROPOSED

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 16 locus cataloged as working transcriptional unit PLIK and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

Trait evidence (11)

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
PLIK NZ_QOYD01000001.1 GCF_003333765.1 - True False True True DefensePredictor hits 281241 284220 hypothetical protein, DUF3696 domain-containing protein WP_001676492.1, WP_001676491.1 10.6830001978657 5.517452896464706 True True Structural defense homolog DS-16

The final Science supplementary Table S6 maps working_id PLIK to DS_name DS-16, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000001.1 positions 281241-284220 with product accessions WP_001676492.1 and WP_001676491.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas26 2.2 pLAND 24-03-12_EV.png 2400000000 PLIK 24-03-21 24-03-21_PLIK_REPB_2.png 7 31 Y 310000000 0.8888495478773333 True LB 37

The final Science supplementary Table S7 reports a PLIK assay row with a Bas26 phage readout and smaller plaques.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
T4 2.1 pLAND 24-03-12_EV.png 200000000 PLIK 24-03-21 24-03-21_PLIK_REPB.png 3 100 100000 3.3010299956639813 True LB 37

The final Science supplementary Table S7 reports a PLIK assay row with a T4 phage readout and a -log(EOP) value of 3.301.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
PLIK DS-16 True

The final Science supplementary Table S8 maps PLIK to replicated display name DS-16.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
PLIK 2.0 341.0 WP_001676492.1 RelE 4NRN_A metal-bound toxin; Toxin; hhpred_4269994.hhr 239.0 335.0 0.8002 2024-04-15 00:00:00

The final Science supplementary Table S8 reports a RelE HHpred hit for WP_001676492.1 in PLIK.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
PLIK 1.0 656.0 WP_001676491.1 ABC ATPase 6QJ0_A Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein; condensin SMC complex ATPase hhpred_2524462.hhr 1.0 572.0 0.997 2024-04-15 00:00:00

The final Science supplementary Table S8 reports an ABC ATPase HHpred hit for WP_001676491.1 in PLIK.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-16 | 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-16 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-16__DS-16A | | DS-16 | Custom | 500 |

The pinned DefenseFinder HMM inventory records DS-16__DS-16A as a custom DS-16 profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-16__DS-16B | | DS-16 | Custom | 50 |

The pinned DefenseFinder HMM inventory records DS-16__DS-16B as a custom DS-16 profile.

DS-16 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the two-gene DS-16 locus to reduced bacteriophage plaquing without resolving DS-16 component function or molecular output.

NONMECHANISTIC · The graph captures DS-16 as the validated PLIK transcriptional unit with two product accessions, RelE and ABC ATPase HHpred-domain rows, and two DefenseFinder DS-16 profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, DS-16A or DS-16B molecular activity, trigger, substrate, phage breadth, or DefenseFinder rule-level detection criteria.

Edge evidence

DS-16 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-16/PLIK 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 PLIK NZ_QOYD01000001.1 GCF_003333765.1 - True False True True DefensePredictor hits 281241 284220 hypothetical protein, DUF3696 domain-containing protein WP_001676492.1, WP_001676491.1 10.6830001978657 5.517452896464706 True True Structural defense homolog DS-16 The final Science supplementary Table S6 maps working_id PLIK to DS_name DS-16, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000001.1 positions 281241-284220 with product accessions WP_001676492.1 and WP_001676491.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas26 2.2 pLAND 24-03-12_EV.png 2400000000 PLIK 24-03-21 24-03-21_PLIK_REPB_2.png 7 31 Y 310000000 0.8888495478773333 True LB 37 The final Science supplementary Table S7 reports a PLIK assay row with a Bas26 phage readout and smaller plaques.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx T4 2.1 pLAND 24-03-12_EV.png 200000000 PLIK 24-03-21 24-03-21_PLIK_REPB.png 3 100 100000 3.3010299956639813 True LB 37 The final Science supplementary Table S7 reports a PLIK assay row with a T4 phage readout and a -log(EOP) value of 3.301.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx PLIK DS-16 True The final Science supplementary Table S8 maps PLIK to replicated display name DS-16.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-16__DS-16A | | DS-16 | Custom | 500 | The pinned DefenseFinder HMM inventory records DS-16__DS-16A as a custom DS-16 profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-16__DS-16B | | DS-16 | Custom | 50 | The pinned DefenseFinder HMM inventory records DS-16__DS-16B as a custom DS-16 profile.
reduced bacteriophage plaquing confers DS-16 system METPO:2007700
DS-16-mediated phage plaquing reduction realizes the DS-16 system trait.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx PLIK NZ_QOYD01000001.1 GCF_003333765.1 - True False True True DefensePredictor hits 281241 284220 hypothetical protein, DUF3696 domain-containing protein WP_001676492.1, WP_001676491.1 10.6830001978657 5.517452896464706 True True Structural defense homolog DS-16 The final Science supplementary Table S6 maps working_id PLIK to DS_name DS-16, marks the cloned transcriptional unit as defensive, and records NZ_QOYD01000001.1 positions 281241-284220 with product accessions WP_001676492.1 and WP_001676491.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas26 2.2 pLAND 24-03-12_EV.png 2400000000 PLIK 24-03-21 24-03-21_PLIK_REPB_2.png 7 31 Y 310000000 0.8888495478773333 True LB 37 The final Science supplementary Table S7 reports a PLIK assay row with a Bas26 phage readout and smaller plaques.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx T4 2.1 pLAND 24-03-12_EV.png 200000000 PLIK 24-03-21 24-03-21_PLIK_REPB.png 3 100 100000 3.3010299956639813 True LB 37 The final Science supplementary Table S7 reports a PLIK assay row with a T4 phage readout and a -log(EOP) value of 3.301.
- 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-16 system is a phage defense system rdfs:subClassOf
DS-16 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-16 | 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-16 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-16 EXACT_SYNONYM · DOI:10.1126/science.adv7924
PLIK RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
DS-16__DS-16A RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
DS-16__DS-16B 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-16 native host breadth, exact profile-to-protein mapping, DS-16A/DS-16B component activities, RelE and ABC ATPase chemistry, sensitive-phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-16 mechanism children.

KNOWLEDGE GAP OPEN ds-16-defensefinder-model-gap · raised by codex · 2026-09-28

Attached to causal_graphs#ds_16_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-16 as the defensive PLIK transcriptional unit and final Science Tables S6/S7/S8 map it to product accessions WP_001676492.1 and WP_001676491.1, Bas26 and T4 phage readouts, display name DS-16, and RelE/ABC ATPase HHpred rows. The pinned DefenseFinder HMM inventory records DS-16A and DS-16B custom profile rows. The pinned rules table has no DS-16 row, and the first-pass record does not resolve native host breadth, phage breadth, direct profile-to-protein correspondence, RelE nuclease or ABC ATPase activity, molecular output, or endogenous DS-16 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
PLIK NZ_QOYD01000001.1 GCF_003333765.1 - True False True True DefensePredictor hits 281241 284220 hypothetical protein, DUF3696 domain-containing protein WP_001676492.1, WP_001676491.1 10.6830001978657 5.517452896464706 True True Structural defense homolog DS-16
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas26 2.2 pLAND 24-03-12_EV.png 2400000000 PLIK 24-03-21 24-03-21_PLIK_REPB_2.png 7 31 Y 310000000 0.8888495478773333 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
T4 2.1 pLAND 24-03-12_EV.png 200000000 PLIK 24-03-21 24-03-21_PLIK_REPB.png 3 100 100000 3.3010299956639813 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
PLIK DS-16 True
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
PLIK 2.0 341.0 WP_001676492.1 RelE 4NRN_A metal-bound toxin; Toxin; hhpred_4269994.hhr 239.0 335.0 0.8002 2024-04-15 00:00:00
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
PLIK 1.0 656.0 WP_001676491.1 ABC ATPase 6QJ0_A Structural maintenance of chromosomes protein,Structural maintenance of chromosomes protein; condensin SMC complex ATPase hhpred_2524462.hhr 1.0 572.0 0.997 2024-04-15 00:00:00
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-16 | 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-16__DS-16A | | DS-16 | Custom | 500 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| DS-16__DS-16B | | DS-16 | Custom | 50 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-28T17:24:00Z · MINTED_TRAITMECH_ID · codex
Minted DS-16 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 PLIK transcriptional-unit level because RelE/ABC ATPase chemistry and rule rows remain unresolved, and proposals/metpo_traitmech_v316 reserves the replacement placeholder.
2026-09-28T17:24:01Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-16 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned PLIK assays in E. coli MG1655 and DefenseFinder DS-16 models, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-16 activity. No paid research was used.