identifier: traitmech:000501 label: Kongming system definition: 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. definition_source: DOI:10.1126/science.ads6055 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000209 synonyms: - synonym_text: Kongming synonym_type: EXACT_SYNONYM source: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md - synonym_text: Kongming system synonym_type: EXACT_SYNONYM source: DOI:10.1038/s41467-026-74710-9 - synonym_text: Kongming immune system synonym_type: EXACT_SYNONYM source: DOI:10.1038/s41467-026-74710-9 evidence: - reference: DOI:10.1126/science.ads6055 snippet: In this study, we reveal a bacterial antiphage system that mediates immune signaling through nucleobase modification. notes: Zeng et al. describe the Science Kongming paper's antiphage system as a nucleobase-modification immune-signaling pathway. - reference: DOI:10.1126/science.ads6055 snippet: Immunity is triggered by phage nucleotide kinases, which, combined with the system-encoded adenosine deaminase, produce deoxyinosine triphosphates (dITPs) as immune messengers. notes: Zeng et al. connect phage-triggered Kongming immunity to system-dependent production of dITP immune messengers. - reference: DOI:10.1126/science.ads6055 snippet: 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. notes: Zeng et al. place dITP upstream of an effector that depletes NAD and drives infected-cell death. - reference: DOI:10.1038/s41467-026-74710-9 snippet: 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). notes: Li et al. name the Kongming effector complex and its KomB and KomC components. - reference: DOI:10.1038/s41467-026-74710-9 snippet: The Kongming system is activated by an atypical signaling nucleotide, dITP, generated upon phage infection. notes: Li et al. describe dITP as a phage-infection-generated Kongming activation signal. - reference: DOI:10.1038/s41467-026-74710-9 snippet: 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. notes: Li et al. connect dITP-bound KomB to activation of KomC NADase activity within the Kongming KomBC effector complex. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| Kongming | 10\.1126/science\.ads6055 | Base-modified nucleotides mediate immune signaling in bacteria | ' notes: The pinned DefenseFinder article registry maps the named Kongming system to the Zeng et al. Science paper. causal_graphs: - graph_id: kongming_ditp_nadase_defense title: Kongming loci activate dITP-linked NADase defense description: Conservative system-level sketch linking a Kongming locus to phage-triggered dITP signaling, KomBC activation, NAD depletion, infected-cell death, and Kongming system possession. scope_status: NONMECHANISTIC scope_notes: 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. nodes: - node_id: kongming_locus label: Kongming locus node_type: GENETIC_ELEMENT description: A Kongming anti-phage locus encoding dITP immune-signaling and KomBC effector functions. - node_id: ditp_immune_signaling label: dITP immune signaling node_type: BIOLOGICAL_PROCESS description: Production of deoxyinosine triphosphate immune messengers after phage infection. - node_id: komc_nadase_activation label: KomC NADase activation node_type: BIOLOGICAL_PROCESS description: Activation of KomC NADase activity in the KomBC effector complex after dITP binding to KomB. - node_id: nad_depletion_cell_death label: NAD depletion-linked infected-cell death node_type: BIOLOGICAL_PROCESS description: Depletion of cellular NAD followed by death of infected cells during population-level defense. - node_id: kongming_system_trait label: Kongming system node_type: TRAIT grounding: traitmech:000501 description: Possession of a genome-encoded Kongming phage-defense system. - node_id: phage_defense_system label: phage defense system node_type: TRAIT grounding: traitmech:000209 description: Possession of one or more genome-encoded immune systems that inhibit bacteriophage infection. edges: - subject: kongming_locus predicate: contributes to predicate_id: RO:0002326 object: ditp_immune_signaling description: Kongming loci mediate phage-triggered production of dITP immune messengers. evidence: - reference: DOI:10.1126/science.ads6055 snippet: In this study, we reveal a bacterial antiphage system that mediates immune signaling through nucleobase modification. notes: Zeng et al. describe the Science Kongming paper's antiphage system as a nucleobase-modification immune-signaling pathway. - reference: DOI:10.1126/science.ads6055 snippet: Immunity is triggered by phage nucleotide kinases, which, combined with the system-encoded adenosine deaminase, produce deoxyinosine triphosphates (dITPs) as immune messengers. notes: Zeng et al. connect phage-triggered Kongming immunity to system-dependent production of dITP immune messengers. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| Kongming | 10\.1126/science\.ads6055 | Base-modified nucleotides mediate immune signaling in bacteria | ' notes: The pinned DefenseFinder article registry maps the named Kongming system to the Zeng et al. Science paper. - subject: ditp_immune_signaling predicate: activates predicate_id: RO:0002213 object: komc_nadase_activation description: dITP binding activates KomC NADase activity in the Kongming KomBC effector complex. evidence: - reference: DOI:10.1038/s41467-026-74710-9 snippet: The Kongming system is activated by an atypical signaling nucleotide, dITP, generated upon phage infection. notes: Li et al. describe dITP as a phage-infection-generated Kongming activation signal. - reference: DOI:10.1038/s41467-026-74710-9 snippet: 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. notes: Li et al. connect dITP-bound KomB to activation of KomC NADase activity within the Kongming KomBC effector complex. - subject: komc_nadase_activation predicate: contributes to predicate_id: RO:0002326 object: nad_depletion_cell_death description: KomBC effector activation mediates NAD depletion that can kill phage-infected cells. evidence: - reference: DOI:10.1126/science.ads6055 snippet: 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. notes: Zeng et al. place dITP upstream of an effector that depletes NAD and drives infected-cell death. - reference: DOI:10.1038/s41467-026-74710-9 snippet: 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). notes: Li et al. name the Kongming effector complex and its KomB and KomC components. - reference: DOI:10.1038/s41467-026-74710-9 snippet: 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. notes: Li et al. connect dITP-bound KomB to activation of KomC NADase activity within the Kongming KomBC effector complex. - subject: nad_depletion_cell_death predicate: confers predicate_id: METPO:2007700 object: kongming_system_trait description: dITP-triggered NAD depletion and infected-cell death realize the Kongming system trait. evidence: - reference: DOI:10.1126/science.ads6055 snippet: 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. notes: Zeng et al. place dITP upstream of an effector that depletes NAD and drives infected-cell death. - subject: kongming_system_trait predicate: is a predicate_id: rdfs:subClassOf object: phage_defense_system description: Kongming system possession is a phage-defense-system trait. evidence: - reference: DOI:10.1126/science.ads6055 snippet: In this study, we reveal a bacterial antiphage system that mediates immune signaling through nucleobase modification. notes: Zeng et al. describe the Science Kongming paper's antiphage system as a nucleobase-modification immune-signaling pathway. - reference: DOI:10.1038/s41467-026-74710-9 snippet: The Kongming system is activated by an atypical signaling nucleotide, dITP, generated upon phage infection. notes: Li et al. describe dITP as a phage-infection-generated Kongming activation signal. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| Kongming | 10\.1126/science\.ads6055 | Base-modified nucleotides mediate immune signaling in bacteria | ' notes: The pinned DefenseFinder article registry maps the named Kongming system to the Zeng et al. Science paper. discussions: - discussion_id: kongming-profile-host-and-component-gap prompt: 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. kind: KNOWLEDGE_GAP status: OPEN rationale: 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: - reference: DOI:10.1126/science.ads6055 snippet: Immunity is triggered by phage nucleotide kinases, which, combined with the system-encoded adenosine deaminase, produce deoxyinosine triphosphates (dITPs) as immune messengers. notes: Zeng et al. connect phage-triggered Kongming immunity to system-dependent production of dITP immune messengers. - reference: DOI:10.1038/s41467-026-74710-9 snippet: 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). notes: Li et al. name the Kongming effector complex and its KomB and KomC components. - reference: DOI:10.1038/s41467-026-74710-9 snippet: 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. notes: Li et al. connect dITP-bound KomB to activation of KomC NADase activity within the Kongming KomBC effector complex. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: '| Kongming | 10\.1126/science\.ads6055 | Base-modified nucleotides mediate immune signaling in bacteria | ' notes: The pinned DefenseFinder article registry maps the named Kongming system to the Zeng et al. Science paper. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md notes: A structured first-pass search of the pinned DefenseFinder HMM inventory found no exact Kongming row. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv notes: A structured first-pass search of the pinned DefenseFinder rules table found no exact Kongming system row. attaches_to: - causal_graphs#kongming_ditp_nadase_defense posed_by: codex posed_date: '2026-09-30' curation_history: - timestamp: '2026-09-30T22:04:45Z' curator: codex action: MINTED_TRAITMECH_ID changes: 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. llm_assisted: true - timestamp: '2026-09-30T22:04:46Z' curator: codex action: REVIEW_CANONICAL_EXAMPLE_EVIDENCE_GAP changes: 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. llm_assisted: true