TraitMech

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Kongming system

traitmech:000501 · CLASS · PROPOSED

A phage defense system in which an organism possesses a Kongming locus that uses phage-triggered deoxyinosine triphosphate signaling to activate a KomBC effector complex and mediate NAD depletion-linked death of infected cells.

Trait evidence (7)

  • DOI:10.1126/science.ads6055
    In this study, we reveal a bacterial antiphage system that mediates immune signaling through nucleobase modification.

    Zeng et al. describe the Science Kongming paper's antiphage system as a nucleobase-modification immune-signaling pathway.

  • DOI:10.1126/science.ads6055
    Immunity is triggered by phage nucleotide kinases, which, combined with the system-encoded adenosine deaminase, produce deoxyinosine triphosphates (dITPs) as immune messengers.

    Zeng et al. connect phage-triggered Kongming immunity to system-dependent production of dITP immune messengers.

  • DOI:10.1126/science.ads6055
    The dITP signal activates a downstream effector to mediate depletion of cellular nicotinamide adenine dinucleotide (oxidized form), resulting in population-level defense through the death of infected cells.

    Zeng et al. place dITP upstream of an effector that depletes NAD and drives infected-cell death.

  • DOI:10.1038/s41467-026-74710-9
    One of them is the Kongming system, which includes an effector complex (KomBC), composed of a non-canonical purine NTP pyrophosphatase (KomB) and a SIR2 domain-containing protein (KomC).

    Li et al. name the Kongming effector complex and its KomB and KomC components.

  • DOI:10.1038/s41467-026-74710-9
    The Kongming system is activated by an atypical signaling nucleotide, dITP, generated upon phage infection.

    Li et al. describe dITP as a phage-infection-generated Kongming activation signal.

  • DOI:10.1038/s41467-026-74710-9
    Binding of dITP to KomB initiates progressive conformational rearrangements within the filament, ultimately remodeling the filament into a distinct architecture in which KomC adopts an active conformation with NADase activity.

    Li et al. connect dITP-bound KomB to activation of KomC NADase activity within the Kongming KomBC effector complex.

  • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
    | Kongming | 10\.1126/science\.ads6055 | Base-modified nucleotides mediate immune signaling in bacteria |

    The pinned DefenseFinder article registry maps the named Kongming system to the Zeng et al. Science paper.

Kongming loci activate dITP-linked NADase defense

Conservative system-level sketch linking a Kongming locus to phage-triggered dITP signaling, KomBC activation, NAD depletion, infected-cell death, and Kongming system possession.

NONMECHANISTIC · The graph captures Kongming as a named dITP-signaling phage-defense system while leaving exact locus breadth, natural host breadth, phage nucleotide-kinase inputs, profile-to-component mapping, and DefenseFinder HMM/rules detection criteria unresolved.

Kongming loci activate dITP-linked NADase defense Interactive directed graph showing evidence-backed causal relationships for Kongming system.

Edge evidence

  • Kongming locus contributes to dITP immune signaling RO:0002326

    Kongming loci mediate phage-triggered production of dITP immune messengers.

    • DOI:10.1126/science.ads6055 In this study, we reveal a bacterial antiphage system that mediates immune signaling through nucleobase modification. Zeng et al. describe the Science Kongming paper's antiphage system as a nucleobase-modification immune-signaling pathway.
    • DOI:10.1126/science.ads6055 Immunity is triggered by phage nucleotide kinases, which, combined with the system-encoded adenosine deaminase, produce deoxyinosine triphosphates (dITPs) as immune messengers. Zeng et al. connect phage-triggered Kongming immunity to system-dependent production of dITP immune messengers.
    • https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md | Kongming | 10\.1126/science\.ads6055 | Base-modified nucleotides mediate immune signaling in bacteria | The pinned DefenseFinder article registry maps the named Kongming system to the Zeng et al. Science paper.
  • dITP immune signaling activates KomC NADase activation RO:0002213

    dITP binding activates KomC NADase activity in the Kongming KomBC effector complex.

    • DOI:10.1038/s41467-026-74710-9 The Kongming system is activated by an atypical signaling nucleotide, dITP, generated upon phage infection. Li et al. describe dITP as a phage-infection-generated Kongming activation signal.
    • DOI:10.1038/s41467-026-74710-9 Binding of dITP to KomB initiates progressive conformational rearrangements within the filament, ultimately remodeling the filament into a distinct architecture in which KomC adopts an active conformation with NADase activity. Li et al. connect dITP-bound KomB to activation of KomC NADase activity within the Kongming KomBC effector complex.
  • KomC NADase activation contributes to NAD depletion-linked infected-cell death RO:0002326

    KomBC effector activation mediates NAD depletion that can kill phage-infected cells.

    • DOI:10.1126/science.ads6055 The dITP signal activates a downstream effector to mediate depletion of cellular nicotinamide adenine dinucleotide (oxidized form), resulting in population-level defense through the death of infected cells. Zeng et al. place dITP upstream of an effector that depletes NAD and drives infected-cell death.
    • DOI:10.1038/s41467-026-74710-9 One of them is the Kongming system, which includes an effector complex (KomBC), composed of a non-canonical purine NTP pyrophosphatase (KomB) and a SIR2 domain-containing protein (KomC). Li et al. name the Kongming effector complex and its KomB and KomC components.
    • DOI:10.1038/s41467-026-74710-9 Binding of dITP to KomB initiates progressive conformational rearrangements within the filament, ultimately remodeling the filament into a distinct architecture in which KomC adopts an active conformation with NADase activity. Li et al. connect dITP-bound KomB to activation of KomC NADase activity within the Kongming KomBC effector complex.
  • NAD depletion-linked infected-cell death confers Kongming system METPO:2007700

    dITP-triggered NAD depletion and infected-cell death realize the Kongming system trait.

    • DOI:10.1126/science.ads6055 The dITP signal activates a downstream effector to mediate depletion of cellular nicotinamide adenine dinucleotide (oxidized form), resulting in population-level defense through the death of infected cells. Zeng et al. place dITP upstream of an effector that depletes NAD and drives infected-cell death.
  • Kongming system is a phage defense system rdfs:subClassOf

    Kongming system possession is a phage-defense-system trait.

Provenance

Identifier source
TraitMech local identifier
Definition source
DOI:10.1126/science.ads6055

Parent traits (1)

Synonyms (3)

  • Kongming EXACT_SYNONYM · https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
  • Kongming system EXACT_SYNONYM · DOI:10.1038/s41467-026-74710-9
  • Kongming immune system EXACT_SYNONYM · DOI:10.1038/s41467-026-74710-9

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 Kongming natural host breadth, exact locus composition, phage nucleotide-kinase inputs, KomA/KomB/KomC profile boundaries, and DefenseFinder HMM/rule coverage before minting narrower Kongming mechanism or component traits.

KNOWLEDGE GAP OPEN kongming-profile-host-and-component-gap · raised by codex · 2026-09-30

Attached to causal_graphs#kongming_ditp_nadase_defense

Zeng et al. support a bacterial antiphage system that uses system-encoded adenosine deaminase and phage nucleotide kinases to produce dITP messengers, and Li et al. connect the named Kongming system to dITP-driven activation of the KomBC NADase effector. The pinned DefenseFinder article registry maps the Kongming source key to the Zeng et al. Science paper, but the pinned HMM inventory and rules table have no exact Kongming rows. This first-pass record therefore does not resolve the complete locus model, direct HMM/profile mapping, or native host breadth.

Evidence

Curation history

  1. · MINTED_TRAITMECH_ID · codex

    Minted Kongming system as a Science-, Nature-, and DefenseFinder-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; the replacement placeholder is reserved in proposals/metpo_traitmech_v378.

  2. · REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP · codex

    Reviewed Kongming system canonical_examples and left them empty because public Science, Nature, and DefenseFinder evidence supports the named phage-defense system but not a direct named native microbial isolate exemplar with experimentally verified endogenous Kongming activity. No paid research was used.