DS-33 system

traitmech:000456 · CLASS · PROPOSED

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 33 locus cataloged as working transcriptional unit GNAT 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
GNAT NZ_QOWT01000046.1 GCF_003334765.1 + True False False True DefensePredictor hits 6922 8901 hypothetical protein, hypothetical protein WP_014639476.1, WP_000354965.1 9.45173070144912 3.204412762840645 True True Predicted novel defense gene DS-33

The final Science supplementary Table S6 maps working_id GNAT to DS_name DS-33, marks the cloned transcriptional unit as defensive, and records NZ_QOWT01000046.1 positions 6922-8901 with product accessions WP_014639476.1 and WP_000354965.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas26 1.2 pLAND 24-03-08_EV_HHHD_PIN2_CRDO.png 500000000 GNAT 24-03-09 24-03-09_GNAT_NADR_D390_DRAT.png 2 100 Y 10000 4.698970004336019 True LB 37

The final Science supplementary Table S7 reports a GNAT assay row with a Bas26 phage readout and a -log(EOP) value of 4.699.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
GNAT DS-33 True

The final Science supplementary Table S8 maps GNAT to replicated display name DS-33.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
GNAT 2.0 333.0 WP_000354965.1 Csa3 6W11_B CRISPR locus-related putative DNA-binding protein Csa3; CARF, CRISPR-Cas, cyclic oligoadenylate, cA4 hhpred_9793887.hhr 25.0 110.0 0.5601 2024-04-16 00:00:00

The final Science supplementary Table S8 reports a lower-probability Csa3 HHpred hit for WP_000354965.1 in GNAT.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
GNAT 1.0 320.0 WP_014639476.1 HEPN PF18737.5 HEPN_MAE_28990 ; MAE_28990/MAE_18760-like HEPN hhpred_9884029.hhr 144.0 306.0 0.9842 2024-04-15 00:00:00

The final Science supplementary Table S8 reports a high-probability HEPN HHpred hit for WP_014639476.1 in GNAT.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-33 | 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-33 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-33__DS-33 | | DS-33 | Custom | 220 |

The pinned DefenseFinder HMM inventory records DS-33__DS-33 as a custom DS-33 profile.

DS-33 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the two-gene DS-33 locus to reduced bacteriophage plaquing without resolving DS-33 component function or molecular output.

NONMECHANISTIC · The graph captures DS-33 as the validated GNAT transcriptional unit with two product accessions, a lower-probability Csa3 HHpred row for WP_000354965.1, a high-probability HEPN HHpred row for WP_014639476.1, and one DefenseFinder DS-33 profile row. It does not assert native host breadth, exact profile-to-protein correspondence, DS-33 molecular activity, trigger, substrate, complete phage breadth, Csa3 or HEPN HHpred-domain interpretation, or DefenseFinder rule-level detection criteria.

Edge evidence

DS-33 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-33/GNAT 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 GNAT NZ_QOWT01000046.1 GCF_003334765.1 + True False False True DefensePredictor hits 6922 8901 hypothetical protein, hypothetical protein WP_014639476.1, WP_000354965.1 9.45173070144912 3.204412762840645 True True Predicted novel defense gene DS-33 The final Science supplementary Table S6 maps working_id GNAT to DS_name DS-33, marks the cloned transcriptional unit as defensive, and records NZ_QOWT01000046.1 positions 6922-8901 with product accessions WP_014639476.1 and WP_000354965.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas26 1.2 pLAND 24-03-08_EV_HHHD_PIN2_CRDO.png 500000000 GNAT 24-03-09 24-03-09_GNAT_NADR_D390_DRAT.png 2 100 Y 10000 4.698970004336019 True LB 37 The final Science supplementary Table S7 reports a GNAT assay row with a Bas26 phage readout and a -log(EOP) value of 4.699.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx GNAT DS-33 True The final Science supplementary Table S8 maps GNAT to replicated display name DS-33.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx GNAT 2.0 333.0 WP_000354965.1 Csa3 6W11_B CRISPR locus-related putative DNA-binding protein Csa3; CARF, CRISPR-Cas, cyclic oligoadenylate, cA4 hhpred_9793887.hhr 25.0 110.0 0.5601 2024-04-16 00:00:00 The final Science supplementary Table S8 reports a lower-probability Csa3 HHpred hit for WP_000354965.1 in GNAT.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx GNAT 1.0 320.0 WP_014639476.1 HEPN PF18737.5 HEPN_MAE_28990 ; MAE_28990/MAE_18760-like HEPN hhpred_9884029.hhr 144.0 306.0 0.9842 2024-04-15 00:00:00 The final Science supplementary Table S8 reports a high-probability HEPN HHpred hit for WP_014639476.1 in GNAT.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | DS-33__DS-33 | | DS-33 | Custom | 220 | The pinned DefenseFinder HMM inventory records DS-33__DS-33 as a custom DS-33 profile.
reduced bacteriophage plaquing confers DS-33 system METPO:2007700
DS-33-mediated phage plaquing reduction realizes the DS-33 system trait.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx GNAT NZ_QOWT01000046.1 GCF_003334765.1 + True False False True DefensePredictor hits 6922 8901 hypothetical protein, hypothetical protein WP_014639476.1, WP_000354965.1 9.45173070144912 3.204412762840645 True True Predicted novel defense gene DS-33 The final Science supplementary Table S6 maps working_id GNAT to DS_name DS-33, marks the cloned transcriptional unit as defensive, and records NZ_QOWT01000046.1 positions 6922-8901 with product accessions WP_014639476.1 and WP_000354965.1.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas26 1.2 pLAND 24-03-08_EV_HHHD_PIN2_CRDO.png 500000000 GNAT 24-03-09 24-03-09_GNAT_NADR_D390_DRAT.png 2 100 Y 10000 4.698970004336019 True LB 37 The final Science supplementary Table S7 reports a GNAT assay row with a Bas26 phage readout and a -log(EOP) value of 4.699.
- 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-33 system is a phage defense system rdfs:subClassOf
DS-33 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-33 | 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-33 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-33 EXACT_SYNONYM · DOI:10.1126/science.adv7924
GNAT RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
DS-33__DS-33 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-33 native host breadth, exact component activities, profile-to-protein mapping, Csa3 and HEPN HHpred-domain interpretation, complete phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower DS-33 mechanism children.

KNOWLEDGE GAP OPEN ds-33-defensefinder-model-gap · raised by codex · 2026-09-29

Attached to causal_graphs#ds_33_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-33 as the defensive GNAT transcriptional unit and final Science Tables S6/S7/S8 map it to two product accessions, a Bas26 phage readout, display name DS-33, and two HHpred rows. The pinned DefenseFinder HMM inventory records one DS-33 custom profile row. The pinned rules table has no DS-33 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, component activities, molecular output, or endogenous DS-33 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
GNAT NZ_QOWT01000046.1 GCF_003334765.1 + True False False True DefensePredictor hits 6922 8901 hypothetical protein, hypothetical protein WP_014639476.1, WP_000354965.1 9.45173070144912 3.204412762840645 True True Predicted novel defense gene DS-33
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
Bas26 1.2 pLAND 24-03-08_EV_HHHD_PIN2_CRDO.png 500000000 GNAT 24-03-09 24-03-09_GNAT_NADR_D390_DRAT.png 2 100 Y 10000 4.698970004336019 True LB 37
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
GNAT DS-33 True
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
GNAT 2.0 333.0 WP_000354965.1 Csa3 6W11_B CRISPR locus-related putative DNA-binding protein Csa3; CARF, CRISPR-Cas, cyclic oligoadenylate, cA4 hhpred_9793887.hhr 25.0 110.0 0.5601 2024-04-16 00:00:00
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
GNAT 1.0 320.0 WP_014639476.1 HEPN PF18737.5 HEPN_MAE_28990 ; MAE_28990/MAE_18760-like HEPN hhpred_9884029.hhr 144.0 306.0 0.9842 2024-04-15 00:00:00
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| DS-33 | 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-33__DS-33 | | DS-33 | Custom | 220 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-29T08:03:43Z · MINTED_TRAITMECH_ID · codex
Minted DS-33 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 GNAT transcriptional-unit level because Csa3 and HEPN activity and rule rows remain unresolved, and proposals/metpo_traitmech_v333 reserves the replacement placeholder.
2026-09-29T08:03:44Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-33 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned GNAT assays in E. coli MG1655 and a DefenseFinder DS-33 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-33 activity. No paid research was used.