TraitMech

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DS-9 system

traitmech:000433 · CLASS · PROPOSED

A phage defense system in which an organism possesses the two-gene DefensePredictor-discovered system 9 locus cataloged with working_id MHAD and whose plasmid expression in E. coli MG1655 reduced bacteriophage plaquing.

Trait evidence (14)

DS-9 locus reduces bacteriophage plaquing

Conservative system-level sketch linking the two-gene DS-9 locus to reduced bacteriophage plaquing without resolving DS-9 component functions or effector activity.

NONMECHANISTIC · The graph captures DS-9 as the validated MHAD transcriptional unit with two product accessions and with DefenseFinder DS-9A and DS-9B profile rows. It does not assert native host breadth, exact DS-9A/DS-9B profile-to-protein correspondence, the direct viral trigger or metallophosphoesterase substrate, the HAD phosphatase target, phage target breadth, or DefenseFinder rule-level detection criteria.

DS-9 locus reduces bacteriophage plaquing Interactive directed graph showing evidence-backed causal relationships for DS-9 system.

Edge evidence

  • DS-9 locus contributes to reduced bacteriophage plaquing RO:0002326

    The DS-9/MHAD locus contributes to reduced bacteriophage plaquing when plasmid expressed.

    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx MHAD NZ_QOWZ01000056.1 GCF_003334705.1 - True False False True DefensePredictor hits 6224 8706 HAD-IA family hydrolase, metallophosphoesterase WP_000770925.1, WP_000665639.1 4.506698206217075 6.906754778648663 True True Predicted novel defense gene DS-9 The final Science supplementary Table S6 maps working_id MHAD to DS_name DS-9, marks the cloned transcriptional unit as defensive, and records NZ_QOWZ01000056.1 positions 6224-8706 with product accessions WP_000770925.1 and WP_000665639.1.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas1 1.2 pLAND 24-03-08_EV_HHHD_PIN2_CRDO.png 40000000 MHAD 24-03-08 24-03-08_NYND_GHOS_MHAD_UDNG.png 3 3 3000 4.1249387366083 True LB 37 The final Science supplementary Table S7 reports an MHAD assay row with a Bas1 phage readout and a -log(EOP) value of 4.125.
  • reduced bacteriophage plaquing confers DS-9 system METPO:2007700

    DS-9-mediated phage plaquing reduction realizes the DS-9 system trait.

    • DOI:10.1126/science.adv7924 The system DS-9 has two genes, the first harboring a metallophosphatase domain homologous to that of DS-8, and the second a predicted haloacid dehalogenase-like (HAD) phosphatase DeWeirdt et al. identify DS-9 as a two-gene metallophosphatase/HAD-phosphatase system.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx MHAD NZ_QOWZ01000056.1 GCF_003334705.1 - True False False True DefensePredictor hits 6224 8706 HAD-IA family hydrolase, metallophosphoesterase WP_000770925.1, WP_000665639.1 4.506698206217075 6.906754778648663 True True Predicted novel defense gene DS-9 The final Science supplementary Table S6 maps working_id MHAD to DS_name DS-9, marks the cloned transcriptional unit as defensive, and records NZ_QOWZ01000056.1 positions 6224-8706 with product accessions WP_000770925.1 and WP_000665639.1.
    • https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S7.xlsx Bas1 1.2 pLAND 24-03-08_EV_HHHD_PIN2_CRDO.png 40000000 MHAD 24-03-08 24-03-08_NYND_GHOS_MHAD_UDNG.png 3 3 3000 4.1249387366083 True LB 37 The final Science supplementary Table S7 reports an MHAD assay row with a Bas1 phage readout and a -log(EOP) value of 4.125.
  • DS-9 system is a phage defense system rdfs:subClassOf

    DS-9 system possession is a phage-defense-system trait.

    • 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. validate DSs as anti-phage systems.
    • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | DS-9 | 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-9 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)

Synonyms (4)

  • DS-9 EXACT_SYNONYM · DOI:10.1126/science.adv7924
  • MHAD RELATED_SYNONYM · https://pmc-oa-opendata.s3.amazonaws.com/PMC13092281.1/NIHMS2163519-supplement-Table_S6.xlsx
  • DS-9__DS-9A RELATED_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
  • DS-9__DS-9B 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-9 native host breadth, DS-9A/DS-9B profile-to-protein mapping, sensitive-phage breadth, direct metallophosphoesterase substrate, HAD phosphatase target, and rule-level detection criteria before minting narrower DS-9 mechanism children.

KNOWLEDGE GAP OPEN ds-9-defensefinder-model-gap · raised by codex · 2026-09-28

Attached to causal_graphs#ds_9_locus_reduces_phage_plaquing

DeWeirdt et al. support DS-9 as the defensive MHAD transcriptional unit that reduced Bas1 plaquing when cloned in E. coli MG1655, identify DS-9 as a two-gene system with metallophosphatase and HAD phosphatase domains, and report that DS-9A predicted catalytic-residue mutations caused a loss of defense. Final Science Table S7 mutant rows show D207A and N292A Bas1 protection loss relative to wild-type MHAD in a matched panel. The pinned DefenseFinder HMM inventory records two DS-9 profile rows. The pinned rules table has no DS-9 row, and the first-pass record does not resolve native host breadth, exact DS-9A/DS-9B profile-to-protein correspondence, direct metallophosphoesterase substrate, HAD phosphatase target, phage target breadth, endogenous DS-9 activity, or DefenseFinder rule-level detection criteria.

Evidence

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted DS-9 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 MHAD transcriptional-unit level because the DS-9A/DS-9B profile-to-protein mapping and rule-level DefenseFinder model remain unresolved; proposals/metpo_traitmech_v310 reserves the replacement placeholder.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    Reviewed DS-9 system canonical_examples and left them empty because DeWeirdt et al. support cloned MHAD plaquing assays in E. coli MG1655 plus DefenseFinder DS-9 model rows, but not a direct named native microbial isolate exemplar with experimentally verified endogenous DS-9 activity. No paid research was used.