DS-30 system

traitmech:000470 · CLASS · PROPOSED

A phage defense system in which an organism possesses the four-gene DefensePredictor-discovered system 30 locus cataloged as working transcriptional unit ABC3 and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

Trait evidence (13)

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
ABC3 NZ_QOYR01000032.1 GCF_003333645.1 + True False True True DefensePredictor hits 1906 4621 hypothetical protein, hypothetical protein, hypothetical protein, DUF2326 domain-containing protein WP_001553315.1, WP_000534626.1, WP_000628292.1, WP_087889773.1 8.95063706554687 6.906754778648663 True True Predicted novel defense gene DS-30

The final Science supplementary Table S6 maps working_id ABC3 to DS_name DS-30, marks the cloned transcriptional unit as defensive, and records four product accessions in NZ_QOYR01000032.1 positions 1906-4621.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
SECphi27 5.1 pLAND 24-05-31_EV_CRDO_BRNT_ABC3.png 100000000 ABC3 24-05-31 24-05-31_EV_CRDO_BRNT_ABC3.png 5 1 Y 100000 3 True M9 30

The final Science supplementary Table S7 Systems sheet reports an ABC3 assay row with a SECphi27 phage readout, a smaller-plaque-size call, and a -log(EOP) value of 3.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ABC3 DS-30 True

The final Science supplementary Table S8 maps ABC3 to replicated display name DS-30.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ABC3 2.0 182.0 WP_000534626.1 ABC-3C C-term PF20275.3 CTD10 ; C-terminal domain 10 of the ABC-three component (ABC-3C) systems hhpred_7102862.hhr 26.0 176.0 1.0 2024-07-30 00:00:00

The final Science supplementary Table S8 reports a high-probability CTD10 HHpred hit for ABC3 protein 2, WP_000534626.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ABC3 3.0 77.0 WP_000628292.1 ABC-3C Mid PF20293.3 MC6 ; ABC-three component (ABC-3C) system Middle Component 6 hhpred_3406401.hhr 1.0 75.0 1.0 2024-07-30 00:00:00

The final Science supplementary Table S8 reports a high-probability MC6 HHpred hit for ABC3 protein 3, WP_000628292.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ABC3 4.0 565.0 WP_087889773.1 ABC ATPase 5XEI_A Chromosome partition protein Smc; Condensin, Smc, head domain, ABC-ATPase, hhpred_6417130.hhr 1.0 540.0 1.0 2024-07-30 00:00:00

The final Science supplementary Table S8 reports a high-probability ABC ATPase HHpred hit for ABC3 protein 4, WP_087889773.1.
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ABC3 1.0 86.0 WP_001553315.1 FtsL 8HHF_L Cell division protein FtsL; Bacterial cell division, divisome, FtsB, FtsL, FtsQ, FtsBLQ, membrane protein complex, heterotrimer, MEMBRANE PROTEIN hhpred_2515914.hhr 2.0 53.0 0.942 2024-07-30 00:00:00

The final Science supplementary Table S8 reports an FtsL HHpred hit for ABC3 protein 1, WP_001553315.1.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Lamassu-Fam__Lmu_DS-30A | | Lamassu-Fam | Custom | 50 |

The pinned DefenseFinder HMM inventory records Lamassu-Fam__Lmu_DS-30A as a custom Lamassu-Fam profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Lamassu-Fam__LmuA_DS-30B | | Lamassu-Fam | Custom | 60 |

The pinned DefenseFinder HMM inventory records Lamassu-Fam__LmuA_DS-30B as a custom Lamassu-Fam profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Lamassu-Fam__LmuB_DS-30D | | Lamassu-Fam | Custom | 150 |

The pinned DefenseFinder HMM inventory records Lamassu-Fam__LmuB_DS-30D as a custom Lamassu-Fam profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Lamassu-Fam__LmuC_DS-30C | | Lamassu-Fam | Custom | 20 |

The pinned DefenseFinder HMM inventory records Lamassu-Fam__LmuC_DS-30C as a custom Lamassu-Fam profile.

DS-30 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the four-gene DS-30 locus to reduced bacteriophage plaquing without resolving DS-30 component functions or molecular output.

NONMECHANISTIC · The graph captures DS-30 as the validated ABC3 transcriptional unit with four product accessions, ABC-3C, SMC-family, and FtsL HHpred-domain rows, and four Lamassu-Fam custom HMM-profile rows. It does not assert native host breadth, exact profile-to-protein correspondence, DS-30/Lamassu-Fam component activity, Lamassu subtype chemistry, LmuC requirement, complete phage breadth, or DS-30-specific DefenseFinder rule-level detection criteria.

Edge evidence

DS-30 locus contributes to reduced bacteriophage plaquing RO:0002326
The DS-30/ABC3 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 ABC3 NZ_QOYR01000032.1 GCF_003333645.1 + True False True True DefensePredictor hits 1906 4621 hypothetical protein, hypothetical protein, hypothetical protein, DUF2326 domain-containing protein WP_001553315.1, WP_000534626.1, WP_000628292.1, WP_087889773.1 8.95063706554687 6.906754778648663 True True Predicted novel defense gene DS-30 The final Science supplementary Table S6 maps working_id ABC3 to DS_name DS-30, marks the cloned transcriptional unit as defensive, and records four product accessions in NZ_QOYR01000032.1 positions 1906-4621.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx SECphi27 5.1 pLAND 24-05-31_EV_CRDO_BRNT_ABC3.png 100000000 ABC3 24-05-31 24-05-31_EV_CRDO_BRNT_ABC3.png 5 1 Y 100000 3 True M9 30 The final Science supplementary Table S7 Systems sheet reports an ABC3 assay row with a SECphi27 phage readout, a smaller-plaque-size call, and a -log(EOP) value of 3.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx ABC3 DS-30 True The final Science supplementary Table S8 maps ABC3 to replicated display name DS-30.
reduced bacteriophage plaquing confers DS-30 system METPO:2007700
DS-30-mediated phage plaquing reduction realizes the DS-30 system trait.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx ABC3 NZ_QOYR01000032.1 GCF_003333645.1 + True False True True DefensePredictor hits 1906 4621 hypothetical protein, hypothetical protein, hypothetical protein, DUF2326 domain-containing protein WP_001553315.1, WP_000534626.1, WP_000628292.1, WP_087889773.1 8.95063706554687 6.906754778648663 True True Predicted novel defense gene DS-30 The final Science supplementary Table S6 maps working_id ABC3 to DS_name DS-30, marks the cloned transcriptional unit as defensive, and records four product accessions in NZ_QOYR01000032.1 positions 1906-4621.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx SECphi27 5.1 pLAND 24-05-31_EV_CRDO_BRNT_ABC3.png 100000000 ABC3 24-05-31 24-05-31_EV_CRDO_BRNT_ABC3.png 5 1 Y 100000 3 True M9 30 The final Science supplementary Table S7 Systems sheet reports an ABC3 assay row with a SECphi27 phage readout, a smaller-plaque-size call, and a -log(EOP) value of 3.
- https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx ABC3 DS-30 True The final Science supplementary Table S8 maps ABC3 to replicated display name DS-30.
- 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-30 system is a Lamassu system rdfs:subClassOf
DS-30 system possession is represented in DefenseFinder by DS-30 custom profiles under Lamassu-Fam.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | Lamassu-Fam__Lmu_DS-30A | | Lamassu-Fam | Custom | 50 | The pinned DefenseFinder HMM inventory records Lamassu-Fam__Lmu_DS-30A as a custom Lamassu-Fam profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | Lamassu-Fam__LmuA_DS-30B | | Lamassu-Fam | Custom | 60 | The pinned DefenseFinder HMM inventory records Lamassu-Fam__LmuA_DS-30B as a custom Lamassu-Fam profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | Lamassu-Fam__LmuB_DS-30D | | Lamassu-Fam | Custom | 150 | The pinned DefenseFinder HMM inventory records Lamassu-Fam__LmuB_DS-30D as a custom Lamassu-Fam profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | Lamassu-Fam__LmuC_DS-30C | | Lamassu-Fam | Custom | 20 | The pinned DefenseFinder HMM inventory records Lamassu-Fam__LmuC_DS-30C as a custom Lamassu-Fam profile.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1126/science.adv7924

Parent traits (1)

Lamassu system traitmech:000232

Synonyms (6)

DS-30 EXACT_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ABC3 RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
Lamassu-Fam__Lmu_DS-30A RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Lamassu-Fam__LmuA_DS-30B RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Lamassu-Fam__LmuB_DS-30D RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
Lamassu-Fam__LmuC_DS-30C 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-30 native host breadth, exact profile-to-protein correspondence, DS-30/Lamassu-Fam component activities, Lamassu subtype and effector chemistry, LmuC requirement, complete phage breadth, and DS-30-specific DefenseFinder rule-level criteria before minting narrower DS-30 mechanism children.

KNOWLEDGE GAP OPEN ds-30-lamassu-family-model-gap · raised by codex · 2026-09-29

Attached to causal_graphs#ds_30_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-30 as the defensive ABC3 transcriptional unit and final Science Tables S6/S7/S8 map it to four product accessions, a SECphi27 phage readout, four HHpred-domain rows, and display name DS-30. The pinned DefenseFinder HMM inventory records four Lamassu-Fam DS-30 custom profile rows. The pinned DefenseFinder rules table only lists generic Lamassu-Fam effector-subtype rows, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, LmuC requirement, molecular output, subtype-specific Lamassu chemistry, or endogenous DS-30 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
ABC3 NZ_QOYR01000032.1 GCF_003333645.1 + True False True True DefensePredictor hits 1906 4621 hypothetical protein, hypothetical protein, hypothetical protein, DUF2326 domain-containing protein WP_001553315.1, WP_000534626.1, WP_000628292.1, WP_087889773.1 8.95063706554687 6.906754778648663 True True Predicted novel defense gene DS-30
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx
SECphi27 5.1 pLAND 24-05-31_EV_CRDO_BRNT_ABC3.png 100000000 ABC3 24-05-31 24-05-31_EV_CRDO_BRNT_ABC3.png 5 1 Y 100000 3 True M9 30
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ABC3 DS-30 True
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ABC3 2.0 182.0 WP_000534626.1 ABC-3C C-term PF20275.3 CTD10 ; C-terminal domain 10 of the ABC-three component (ABC-3C) systems hhpred_7102862.hhr 26.0 176.0 1.0 2024-07-30 00:00:00
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ABC3 3.0 77.0 WP_000628292.1 ABC-3C Mid PF20293.3 MC6 ; ABC-three component (ABC-3C) system Middle Component 6 hhpred_3406401.hhr 1.0 75.0 1.0 2024-07-30 00:00:00
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ABC3 4.0 565.0 WP_087889773.1 ABC ATPase 5XEI_A Chromosome partition protein Smc; Condensin, Smc, head domain, ABC-ATPase, hhpred_6417130.hhr 1.0 540.0 1.0 2024-07-30 00:00:00
https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S8.xlsx
ABC3 1.0 86.0 WP_001553315.1 FtsL 8HHF_L Cell division protein FtsL; Bacterial cell division, divisome, FtsB, FtsL, FtsQ, FtsBLQ, membrane protein complex, heterotrimer, MEMBRANE PROTEIN hhpred_2515914.hhr 2.0 53.0 0.942 2024-07-30 00:00:00
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Lamassu-Fam__Lmu_DS-30A | | Lamassu-Fam | Custom | 50 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Lamassu-Fam__LmuA_DS-30B | | Lamassu-Fam | Custom | 60 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Lamassu-Fam__LmuB_DS-30D | | Lamassu-Fam | Custom | 150 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| Lamassu-Fam__LmuC_DS-30C | | Lamassu-Fam | Custom | 20 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-29T17:57:26Z · MINTED_TRAITMECH_ID · codex
Minted DS-30 system as a DOI-backed GENOMICS TraitRecord under Lamassu system after an ignored-and-hidden duplicate review found no exact live TraitMech, METPO, history, or prior proposal record; kept the graph at ABC3 transcriptional-unit level because native host breadth, exact DS-30 profile-to-component mapping, Lamassu subtype chemistry, LmuC requirement, complete phage breadth, and DefenseFinder rule-level criteria remain unresolved, and proposals/metpo_traitmech_v347 reserves the replacement placeholder.
2026-09-29T17:57:27Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed DS-30 system canonical_examples and left them empty because DeWeirdt et al. directly support cloned ABC3 assays in E. coli MG1655 and Lamassu-Fam DS-30 profile rows, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-30 activity. No paid research was used.