HEC-04 system

traitmech:000465 · CLASS · PROPOSED

A phage defense system in which an organism possesses the single-gene HEC-04 Hma-embedded candidate locus, encoding an ABC ATPase fused to a TOPRIM-family nuclease domain, that can reduce bacteriophage plaquing.

Trait evidence (5)

DOI:10.1101/2024.01.29.577857
an ATPase fused to a TOPRIM domain (HEC-04)

Payne et al. identify HEC-04 as a Hma-embedded antiviral candidate encoding an ATPase fused to a TOPRIM domain.
DOI:10.1101/2024.01.29.577857
A quantitative assessment of the remaining systems showed that these were able to reduce the EOP of at least two phages by several orders of magnitude compared to the control

Payne et al. support reduced plaquing for the active Hma-embedded candidate systems after excluding inactive HEC-01 and HEC-09 candidates.
DOI:10.1101/2024.01.29.577857
For HEC-04, mutation of key active site residues in either the ABC ATPase or nuclease domains demonstrated their essential roles in defence

Payne et al. show that HEC-04 defense requires intact ABC ATPase and nuclease active-site residues.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| HEC-04 | 10\.1101/2024\.01\.29\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |

The pinned DefenseFinder article registry maps the HEC-04 source key to the Payne et al. Hma-embedded-candidate preprint.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| HEC-04__HEC-04 | | HEC-04 | Custom | 200 |

The pinned DefenseFinder HMM inventory records HEC-04__HEC-04 as a custom HEC-04 profile.

HEC-04 loci reduce bacteriophage plaquing

Conservative system-level sketch linking the single-gene HEC-04 locus to reduced bacteriophage plaquing and HEC-04 system possession.

NONMECHANISTIC · The graph captures HEC-04 at candidate locus and anti-phage-output level without asserting native host breadth, the direct viral trigger or substrate, exact molecular output, or a DefenseFinder detection rule absent from the pinned rules table.

Edge evidence

HEC-04 locus contributes to reduced bacteriophage plaquing RO:0002326
The HEC-04 locus contributes to reduced bacteriophage plaquing when ABC ATPase and nuclease active-site residues are intact.
- DOI:10.1101/2024.01.29.577857 an ATPase fused to a TOPRIM domain (HEC-04) Payne et al. identify HEC-04 as encoding an ATPase-TOPRIM fused protein.
- DOI:10.1101/2024.01.29.577857 For HEC-04, mutation of key active site residues in either the ABC ATPase or nuclease domains demonstrated their essential roles in defence Payne et al. show that HEC-04 requires intact ATPase and nuclease domains for defense.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | HEC-04__HEC-04 | | HEC-04 | Custom | 200 | The pinned DefenseFinder HMM inventory records HEC-04__HEC-04 as a custom HEC-04 profile.
reduced bacteriophage plaquing confers HEC-04 system METPO:2007700
HEC-04-mediated plaquing reduction realizes the HEC-04 system trait.
- DOI:10.1101/2024.01.29.577857 A quantitative assessment of the remaining systems showed that these were able to reduce the EOP of at least two phages by several orders of magnitude compared to the control Payne et al. support reduced efficiency of plaquing for the active HEC systems.
- DOI:10.1101/2024.01.29.577857 For HEC-04, mutation of key active site residues in either the ABC ATPase or nuclease domains demonstrated their essential roles in defence Payne et al. support ABC ATPase and nuclease active-site requirements for HEC-04-mediated defense.
HEC-04 system is a phage defense system rdfs:subClassOf
HEC-04 system possession is a phage-defense-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | HEC-04 | 10\.1101/2024\.01\.29\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems | The pinned DefenseFinder article registry maps the HEC-04 source key to the Payne et al. Hma-embedded-candidate preprint.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1101/2024.01.29.577857

Parent traits (1)

phage defense system traitmech:000209

Synonyms (2)

HEC-04 EXACT_SYNONYM · DOI:10.1101/2024.01.29.577857
HEC-04__HEC-04 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 HEC-04 native host breadth, sensitive-phage breadth, ATPase-TOPRIM molecular output, and rule-level detection criteria before minting narrower HEC-04 mechanism children.

KNOWLEDGE GAP OPEN hec-04-defensefinder-model-gap · raised by codex · 2026-09-29

Attached to causal_graphs#hec_04_locus_reduces_phage_plaquing

Payne et al. support HEC-04 as a single-gene Hma-embedded candidate anti-phage system whose ABC ATPase and nuclease domains are both required for defense, and the pinned DefenseFinder HMM inventory records one HEC-04 profile row. The pinned rules table has no HEC-04 row, and the first-pass record does not yet resolve natural host breadth, phage target breadth, or the direct molecular output.

Evidence

DOI:10.1101/2024.01.29.577857
an ATPase fused to a TOPRIM domain (HEC-04)
DOI:10.1101/2024.01.29.577857
For HEC-04, mutation of key active site residues in either the ABC ATPase or nuclease domains demonstrated their essential roles in defence
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| HEC-04 | 10\.1101/2024\.01\.29\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| HEC-04__HEC-04 | | HEC-04 | Custom | 200 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-29T14:17:47Z · MINTED_TRAITMECH_ID · codex
Minted HEC-04 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 single-gene candidate-locus level because the pinned DefenseFinder HEC-04 HMM row is not backed by a pinned rules row; the replacement placeholder is reserved in proposals/metpo_traitmech_v342.
2026-09-29T14:17:48Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed HEC-04 system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support heterologous efficiency-of-plaquing assays and a DefenseFinder HEC-04 HMM row, but not a direct named native microbial isolate exemplar with experimentally verified endogenous HEC-04 activity. No paid research was used.