HEC-03 system

traitmech:000418 · CLASS · PROPOSED

A phage defense system in which an organism possesses the two-gene HEC-03 Hma-embedded candidate locus, encoding an ABC ATPase and an associated PilT N-terminal domain protein, that can reduce bacteriophage plaquing.

Trait evidence (6)

DOI:10.1101/2024.01.29.577857
The candidate systems encoded diverse protein families, including three ATPases associated with either a topoisomerase-primase (TOPRIM) (HEC-01), nuclease-related (NERD) (HEC-02), or PilT N-terminal (PIN) (HEC-03) domain-containing protein

Payne et al. identify HEC-03 as a candidate two-gene Hma-embedded antiviral system pairing an ATPase with a PilT N-terminal-domain protein.
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 the two-gene systems HEC-02 and HEC-03, both genes were required for defence

Payne et al. show that both genes in the two-gene HEC-03 candidate system were required for defense.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| HEC-03 | 10\.1101/2024\.01\.29\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems |

The pinned DefenseFinder article registry maps the HEC-03 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-03__HEC-03A | | HEC-03 | Custom | 50 |

The pinned DefenseFinder HMM inventory records HEC-03__HEC-03A as a custom HEC-03 profile.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| HEC-03__HEC-03B | | HEC-03 | Custom | 150 |

The pinned DefenseFinder HMM inventory records HEC-03__HEC-03B as a custom HEC-03 profile.

HEC-03 loci reduce bacteriophage plaquing

Conservative system-level sketch linking the two-gene HEC-03 locus to reduced bacteriophage plaquing and HEC-03 system possession.

NONMECHANISTIC · The graph captures HEC-03 at candidate locus and anti-phage-output level without asserting native host breadth, exact profile-to-component mapping, the direct viral trigger or substrate, exact molecular output, or a DefenseFinder detection rule absent from the pinned rules table.

Edge evidence

HEC-03 locus contributes to reduced bacteriophage plaquing RO:0002326
The two-gene HEC-03 locus contributes to reduced bacteriophage plaquing when both HEC-03 genes are present.
- DOI:10.1101/2024.01.29.577857 The candidate systems encoded diverse protein families, including three ATPases associated with either a topoisomerase-primase (TOPRIM) (HEC-01), nuclease-related (NERD) (HEC-02), or PilT N-terminal (PIN) (HEC-03) domain-containing protein Payne et al. identify HEC-03 as pairing an ATPase with a PilT N-terminal-domain protein.
- DOI:10.1101/2024.01.29.577857 For the two-gene systems HEC-02 and HEC-03, both genes were required for defence Payne et al. show that HEC-03 requires both genes for defense.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | HEC-03__HEC-03A | | HEC-03 | Custom | 50 | The pinned DefenseFinder HMM inventory records HEC-03__HEC-03A as a custom HEC-03 profile.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md | HEC-03__HEC-03B | | HEC-03 | Custom | 150 | The pinned DefenseFinder HMM inventory records HEC-03__HEC-03B as a custom HEC-03 profile.
reduced bacteriophage plaquing confers HEC-03 system METPO:2007700
HEC-03-mediated plaquing reduction realizes the HEC-03 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 the two-gene systems HEC-02 and HEC-03, both genes were required for defence Payne et al. show that complete HEC-03 requires both genes for defense.
HEC-03 system is a phage defense system rdfs:subClassOf
HEC-03 system possession is a phage-defense-system trait.
- https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | HEC-03 | 10\.1101/2024\.01\.29\.577857 | New antiviral defences are genetically embedded within prokaryotic immune systems | The pinned DefenseFinder article registry maps the HEC-03 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 (1)

HEC-03 EXACT_SYNONYM · DOI:10.1101/2024.01.29.577857

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-03 native host breadth, exact HEC-03A/HEC-03B component functions, sensitive-phage breadth, molecular output, and rule-level detection criteria before minting narrower HEC-03 mechanism children.

KNOWLEDGE GAP OPEN hec-03-defensefinder-model-gap · raised by codex · 2026-09-27

Attached to causal_graphs#hec_03_locus_reduces_phage_plaquing

Payne et al. support HEC-03 as an Hma-embedded candidate anti-phage system whose two genes are both required for defense, and the pinned DefenseFinder HMM inventory records HEC-03A and HEC-03B profile rows. The pinned rules table has no HEC-03 row, and the first-pass record does not yet resolve natural host breadth, HEC-03 profile-to-component mapping, phage target breadth, or the direct molecular output.

Evidence

DOI:10.1101/2024.01.29.577857
The candidate systems encoded diverse protein families, including three ATPases associated with either a topoisomerase-primase (TOPRIM) (HEC-01), nuclease-related (NERD) (HEC-02), or PilT N-terminal (PIN) (HEC-03) domain-containing protein
DOI:10.1101/2024.01.29.577857
For the two-gene systems HEC-02 and HEC-03, both genes were required for defence
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
| HEC-03 | 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-03__HEC-03A | | HEC-03 | Custom | 50 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| HEC-03__HEC-03B | | HEC-03 | Custom | 150 |
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv

Curation history

2026-09-27T21:21:54Z · MINTED_TRAITMECH_ID · codex
Minted HEC-03 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 two-gene candidate-locus level because the pinned DefenseFinder HEC-03 HMM rows are not backed by pinned rules rows; the replacement placeholder is reserved in proposals/metpo_traitmech_v295.
2026-09-27T21:21:55Z · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex
Reviewed HEC-03 system during canonical-example issue 444 enforcement and left canonical_examples empty because the sources support heterologous efficiency-of-plaquing assays and DefenseFinder HEC-03 HMM rows, but not a direct named native microbial isolate exemplar with experimentally verified endogenous HEC-03 activity. No paid research was used.