VP1853 system

traitmech:000492 · CLASS · PROPOSED

A phage defense system in which an organism possesses a VP1853-family locus represented by the DefenseFinder VP1853__VP1853 custom HMM profile and experimentally linked to reduced bacteriophage plaquing when the cloned Vibrio parahaemolyticus RIMD 2210633 vp1853 cassette is expressed from a VSV105 plasmid.

Trait evidence (8)

DOI:10.1038/s41564-025-01927-7
Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.

Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems.
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx
VP_RS09025 Vp1853 Y WP_005483178.1 TIGR02391 family protein

Supplementary Table 8 lists VP_RS09025/Vp1853 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483178.1.
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx
VSV105-vp1853 VSV105 carrying gene vp1853 behind the lac promoter, cloned into KpnI by In-Fusion This Study

Supplementary Table 12 records the VSV105-vp1853 lac-expression plasmid used to express vp1853 behind the lac promoter.
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx
VP1853 λ 0.001 Small

Supplementary Table 9 identifies the VP1853/lambda phage-plating readout as a Fold Change value of 0.001 with a Small Plaque Size comment.
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx
>WP_005483178.1 TIGR02391 family protein [Vibrio parahaemolyticus]

Supplementary Data 1's VP1853 worksheet labels WP_005483178.1 from Vibrio parahaemolyticus as the PSI-BLAST query protein.
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx
Scientific Name Query Cover E value Per. ident Accession Vibrio parahaemolyticus 1 0 100 WP_005483178.1 Vibrio parahaemolyticus 1 0 100 WP_049875404.1

Supplementary Data 1's VP1853 worksheet records full-length 100% PSI-BLAST rows for WP_005483178.1 and WP_049875404.1.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| VP1853 | 10\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus |

The pinned DefenseFinder article registry maps the VP1853 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| VP1853__VP1853 | | VP1853 | Custom | 150 |

The pinned DefenseFinder HMM inventory records VP1853__VP1853 as a custom VP1853 profile.

VP1853 loci reduce bacteriophage plaquing

Conservative system-level sketch linking VP1853-family locus possession to reduced bacteriophage plaquing without resolving VP1853 component function or molecular output.

NONMECHANISTIC · The graph captures VP1853 as a RIMD 2210633 integron cassette with cloned phage-plating readouts, a PSI-BLAST homolog lead, one pinned DefenseFinder custom HMM-profile row, and no pinned DefenseFinder rule row. It does not assert native host breadth, exact profile-to-protein correspondence, molecular activity, phage trigger, substrate, complete homolog boundary, endogenous activity, or rule-level DefenseFinder detection criteria.

Edge evidence

VP1853 locus contributes to reduced bacteriophage plaquing RO:0002326
The cloned V. parahaemolyticus vp1853 integron cassette contributes to reduced bacteriophage plaquing in VSV105 plasmid-expression assays, and DefenseFinder represents the VP1853 family with one custom HMM profile.
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx VP_RS09025 Vp1853 Y WP_005483178.1 TIGR02391 family protein Supplementary Table 8 lists VP_RS09025/Vp1853 as a cloned RIMD 2210633 integron cassette with protein accession WP_005483178.1.
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx VSV105-vp1853 VSV105 carrying gene vp1853 behind the lac promoter, cloned into KpnI by In-Fusion This Study Supplementary Table 12 records the VSV105-vp1853 lac-expression plasmid used to express vp1853 behind the lac promoter.
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx VP1853 λ 0.001 Small Supplementary Table 9 identifies the VP1853/lambda phage-plating readout as a Fold Change value of 0.001 with a Small Plaque Size comment.
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx >WP_005483178.1 TIGR02391 family protein [Vibrio parahaemolyticus] Supplementary Data 1's VP1853 worksheet labels WP_005483178.1 from Vibrio parahaemolyticus as the PSI-BLAST query protein.
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx Scientific Name Query Cover E value Per. ident Accession Vibrio parahaemolyticus 1 0 100 WP_005483178.1 Vibrio parahaemolyticus 1 0 100 WP_049875404.1 Supplementary Data 1's VP1853 worksheet records full-length 100% PSI-BLAST rows for WP_005483178.1 and WP_049875404.1.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | VP1853__VP1853 | | VP1853 | Custom | 150 | The pinned DefenseFinder HMM inventory records VP1853__VP1853 as a custom VP1853 profile.
reduced bacteriophage plaquing confers VP1853 system METPO:2007700
VP1853-mediated bacteriophage plaquing reduction realizes the VP1853 system trait.
- https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx VP1853 λ 0.001 Small Supplementary Table 9 identifies the VP1853/lambda phage-plating readout as a Fold Change value of 0.001 with a Small Plaque Size comment.
VP1853 system is a phage defense system rdfs:subClassOf
VP1853 system possession is a phage-defense-system trait.
- DOI:10.1038/s41564-025-01927-7 Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence. Getz et al. identify nine previously unrecognized Vibrio parahaemolyticus integron cassettes as anti-phage defense systems.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | VP1853 | 10\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus | The pinned DefenseFinder article registry maps the VP1853 model namespace to the Getz et al. Vibrio parahaemolyticus integron-defense paper.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1038/s41564-025-01927-7

Parent traits (1)

phage defense system traitmech:000209

Synonyms (3)

VP1853 EXACT_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
Vp1853 RELATED_SYNONYM · https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx
VP1853__VP1853 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 VP1853 native host breadth, exact single-component activity, profile-to-protein mapping, homolog boundary, full phage breadth, molecular output, and rule-level DefenseFinder criteria before minting narrower VP1853 mechanism children.

KNOWLEDGE GAP OPEN vp1853-defensefinder-model-gap · raised by codex · 2026-09-30

Attached to causal_graphs#vp1853_locus_reduces_bacteriophage_plaquing

Getz et al. support VP1853 as one of nine RIMD 2210633 integron-encoded cassettes whose cloned expression reduced phage plaquing, Supplementary Tables 8, 9, and 12 map VP1853 to VP_RS09025/Vp1853, WP_005483178.1, VSV105-vp1853, and a phage-plating fold change, and Supplementary Data 1 reports PSI-BLAST homologs. The pinned DefenseFinder HMM inventory records one VP1853 custom profile row. The pinned rules table has no VP1853 row, and the first-pass record does not resolve native host breadth, complete phage breadth, direct profile-to-protein correspondence, molecular output, or endogenous activity.

Evidence

DOI:10.1038/s41564-025-01927-7
Intrigued by this discovery, we cloned 57 integron gene cassettes and identified 9 previously unrecognized systems that mediate defence.
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx
VP_RS09025 Vp1853 Y WP_005483178.1 TIGR02391 family protein
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx
VSV105-vp1853 VSV105 carrying gene vp1853 behind the lac promoter, cloned into KpnI by In-Fusion This Study
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM2_ESM.xlsx
VP1853 λ 0.001 Small
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx
>WP_005483178.1 TIGR02391 family protein [Vibrio parahaemolyticus]
https://media.springernature.com/original/springer-static/esm/art%3A10.1038%2Fs41564-025-01927-7/MediaObjects/41564_2025_1927_MOESM3_ESM.xlsx
Scientific Name Query Cover E value Per. ident Accession Vibrio parahaemolyticus 1 0 100 WP_005483178.1 Vibrio parahaemolyticus 1 0 100 WP_049875404.1
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| VP1853 | 10\.1038/s41564-025-01927-7 | Integrons are anti-phage defence libraries in Vibrio parahaemolyticus |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| VP1853__VP1853 | | VP1853 | Custom | 150 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-30T12:56:22Z · MINTED_TRAITMECH_ID · codex
Minted VP1853 system as a DOI-backed GENOMICS TraitRecord under phage defense system after an ignored-and-hidden duplicate review found no exact same-scope live TraitMech, METPO, history, or prior proposal record; kept the graph at cloned integron-cassette level because molecular output, native activity, and rule rows remain unresolved; proposals/metpo_traitmech_v369 reserves the replacement placeholder.
2026-09-30T12:56:23Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed VP1853 system canonical_examples and left them empty because Getz et al. directly support cloned VP1853 VSV105-plasmid assays, PSI-BLAST homologs, and a DefenseFinder VP1853 model, but not a direct named native microbial isolate exemplar with experimentally verified endogenous VP1853 activity. No paid research was used.