identifier: traitmech:000335 label: CmdTAC system definition: An abortive infection system in which an organism possesses a cmdTAC toxin-antitoxin-chaperone locus whose CmdC chaperone senses viral capsid proteins and whose CmdA antitoxin degradation liberates the CmdT ADP-ribosyltransferase to modify messenger RNA, arrest translation, and inhibit bacteriophage replication. definition_source: DOI:10.1038/s41586-024-08102-8 trait_category: GENOMICS term_kind: CLASS mapping_status: PROPOSED parent_traits: - traitmech:000214 synonyms: - synonym_text: CmdTAC synonym_type: EXACT_SYNONYM source: DOI:10.1038/s41586-024-08102-8 - synonym_text: cmdTAC synonym_type: EXACT_SYNONYM source: https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ - synonym_text: cmdTAC toxin-antitoxin-chaperone locus synonym_type: RELATED_SYNONYM source: DOI:10.1038/s41586-024-08102-8 - synonym_text: PD-T4-9 synonym_type: RELATED_SYNONYM source: DOI:10.1038/s41586-024-08102-8 evidence: - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ snippet: Here we characterize the widely distributed anti-phage defence system CmdTAC, which provides robust defence against infection by the T-even family of phages notes: Vassallo et al. name CmdTAC as a widely distributed anti-phage defense system that protects against T-even phages. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ snippet: was discovered in the genome of the wild E. coli isolate ECOR22 through a functional genetic screen for anti-phage defence systems notes: Vassallo et al. trace the CmdTAC system to a functional anti-phage defense screen of Escherichia coli ECOR22. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ snippet: CmdC detects infection by sensing viral capsid proteins, ultimately leading to the activation of a toxic ADP-ribosyltransferase effector protein, CmdT notes: CmdC senses phage infection through viral capsid proteins and activates the CmdT ADP-ribosyltransferase effector. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ snippet: newly synthesized capsid protein triggers dissociation of the chaperone CmdC from the CmdTAC complex, leading to destabilization and degradation of the antitoxin CmdA notes: Newly synthesized phage capsid protein can dissociate the CmdC chaperone from the complex and destabilize CmdA. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ snippet: CmdT modifies the N6 position of adenine in GA dinucleotides within single-stranded RNAs, leading to arrest of mRNA translation and inhibition of viral replication notes: Vassallo et al. support CmdT modification of single-stranded RNA as the translation-arresting antiphage effector output. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ snippet: These results are consistent with CmdTAC functioning via an Abi mechanism. notes: Vassallo et al. interpret the low-MOI protection and center-of-infection results as consistent with an abortive-infection mechanism. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md snippet: CmdTAC | 10\.1038/s41586-024-08102-8 | Anti-viral defence by an mRNA ADP-ribosyltransferase that blocks translation notes: The DefenseFinder article registry maps the named CmdTAC system to the Vassallo et al. CmdTAC mechanism paper. Its CmdTAC row is name-to-paper evidence; the pinned rule and HMM rows model the same DefenseFinder system under the PD-T4-9 namespace. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-9.md snippet: 'The PD-T4-9 is composed of 3 proteins: PD-T4-9_A, PD-T4-9_B and PD-T4-9_C.' notes: The DefenseFinder wiki names the three protein components in the PD-T4-9 model. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-9.md snippet: The PD-T4-9 system in *Vibrio parahaemolyticus* (GCF_001700835.1, NZ_CP010883) is composed of 3 proteins PD-T4-9_C (WP_065870458.1) PD-T4-9_B (WP_141106056.1) PD-T4-9_A (WP_065870460.1) notes: The DefenseFinder wiki illustrates a predicted PD-T4-9 locus in RefSeq assembly GCF_001700835.1 on NZ_CP010883. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "PD-T4-9\tPD-T4-9\t2\t2\tPD-T4-9__PD-T4-9_A, PD-T4-9__PD-T4-9_C\tPD-T4-9__PD-T4-9_B\t\ \t" notes: The pinned DefenseFinder rules table models PD-T4-9 with PD-T4-9__PD-T4-9_A and PD-T4-9__PD-T4-9_C as required profiles and PD-T4-9__PD-T4-9_B as an accessory profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| PD-T4-9__PD-T4-9_A | PD-T4-9__PD-T4-9_A | PD-T4-9 | Custom | 20 | | PD-T4-9__PD-T4-9_B | PD-T4-9__PD-T4-9_B | PD-T4-9 | Custom | 20 | | PD-T4-9__PD-T4-9_C | PD-T4-9__PD-T4-9_C | PD-T4-9 | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records PD-T4-9__PD-T4-9_A, PD-T4-9__PD-T4-9_B, and PD-T4-9__PD-T4-9_C under the PD-T4-9 system namespace. - reference: DOI:10.1038/s41586-024-08102-8 snippet: PD-T4-9 also contains a third component, a SecB-like chaperone, suggesting that it is related to an enigmatic class of TA systems called toxin-antitoxin-chaperone (TAC) systems, so we renamed this system CmdTAC notes: Vassallo et al. state that PD-T4-9 was renamed CmdTAC after they recognized its SecB-like chaperone component. canonical_examples: - taxon_id: NCBITaxon:562 taxon_label: Escherichia coli note: Vassallo et al. report that cmdTAC was discovered in wild Escherichia coli isolate ECOR22 through a functional anti-phage defense screen. reference: DOI:10.1038/s41586-024-08102-8 causal_graphs: - graph_id: cmdtac_mrna_adp_ribosylation_aborts_phage title: CmdTAC activation blocks phage translation description: Conservative system-level sketch linking a CmdTAC locus to CmdC capsid sensing, CmdA degradation, CmdT-mediated mRNA modification, translation arrest, and abortive phage defense. scope_status: NONMECHANISTIC scope_notes: The graph captures CmdTAC as a named toxin-antitoxin-chaperone abortive-infection system from Escherichia coli ECOR22 while leaving phage specificity beyond Tevenvirinae, escape routes, and natural family breadth unresolved. nodes: - node_id: cmdtac_locus label: cmdTAC locus node_type: GENETIC_ELEMENT description: A toxin-antitoxin-chaperone locus encoding CmdT, CmdA, and CmdC anti-phage defense components. - node_id: cmdc_capsid_sensing label: CmdC viral capsid sensing node_type: BIOLOGICAL_PROCESS description: Detection of newly synthesized viral capsid protein through CmdC. - node_id: cmda_degradation label: CmdA antitoxin degradation node_type: BIOLOGICAL_PROCESS description: Destabilization and degradation of the CmdA antitoxin after phage-triggered chaperone dissociation. - node_id: cmdt_mrna_adp_ribosylation label: CmdT mRNA ADP-ribosylation node_type: MOLECULAR_FUNCTION description: ADP-ribosyltransferase activity by liberated CmdT against single-stranded mRNA. - node_id: mrna_translation_arrest label: mRNA translation arrest node_type: BIOLOGICAL_PROCESS description: Arrest of mRNA translation after CmdT-mediated messenger-RNA modification. - node_id: cmdtac_system_trait label: CmdTAC system node_type: TRAIT grounding: traitmech:000335 description: Possession of a genome-encoded CmdTAC abortive-infection phage-defense system. - node_id: abortive_infection_system_trait label: abortive infection system node_type: TRAIT grounding: traitmech:000214 description: Possession of a genome-encoded abortive-infection phage-defense system. edges: - subject: cmdtac_locus predicate: contributes to predicate_id: RO:0002326 object: cmdc_capsid_sensing description: The cmdTAC locus encodes CmdC, which can sense viral capsid proteins. evidence: - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ snippet: CmdC detects infection by sensing viral capsid proteins notes: Vassallo et al. connect CmdC to viral capsid protein sensing. - subject: cmdc_capsid_sensing predicate: contributes to predicate_id: RO:0002326 object: cmda_degradation description: Newly synthesized capsid protein can trigger CmdC dissociation from CmdTAC and destabilize the CmdA antitoxin. evidence: - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ snippet: newly synthesized capsid protein triggers dissociation of the chaperone CmdC from the CmdTAC complex notes: Vassallo et al. place phage capsid-driven CmdC dissociation upstream of antitoxin destabilization. - subject: cmda_degradation predicate: contributes to predicate_id: RO:0002326 object: cmdt_mrna_adp_ribosylation description: CmdC dissociation and CmdA degradation liberate the CmdT ADP-ribosyltransferase. evidence: - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ snippet: destabilization and degradation of the antitoxin CmdA, with consequent liberation of the CmdT ADP-ribosyltransferase notes: Vassallo et al. place CmdA degradation upstream of CmdT liberation. - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ snippet: CmdT co-precipitated with both CmdA and CmdC notes: CmdT co-precipitated with both its antitoxin and chaperone partners. - subject: cmdt_mrna_adp_ribosylation predicate: contributes to predicate_id: RO:0002326 object: mrna_translation_arrest description: Liberated CmdT modifies mRNA and blocks translation. evidence: - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ snippet: CmdT selectively modifies mRNA to block translation and abort the phage infection notes: Vassallo et al. connect CmdT-mediated mRNA modification to translation arrest. - subject: mrna_translation_arrest predicate: confers predicate_id: METPO:2007700 object: cmdtac_system_trait description: Translation arrest and viral-replication inhibition realize the CmdTAC system trait. evidence: - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ snippet: arrest of mRNA translation and inhibition of viral replication notes: Vassallo et al. connect CmdT-mediated mRNA modification to inhibited viral replication. - subject: cmdtac_system_trait predicate: is a predicate_id: rdfs:subClassOf object: abortive_infection_system_trait description: CmdTAC system possession is an abortive-infection phage-defense-system trait. evidence: - reference: https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ snippet: These results are consistent with CmdTAC functioning via an Abi mechanism. notes: Vassallo et al. interpret CmdTAC as consistent with an abortive-infection mechanism. discussions: - discussion_id: cmdtac-family-and-model-coverage-gap prompt: Resolve CmdTAC family breadth and phage escape routes before minting narrower CmdTAC mechanism children. kind: KNOWLEDGE_GAP status: OPEN rationale: Vassallo et al. support CmdTAC as a toxin-antitoxin-chaperone abortive-infection system in which CmdC senses viral capsid proteins and liberates the CmdT mRNA ADP-ribosyltransferase. Vassallo et al. also state that PD-T4-9 was renamed CmdTAC, and the pinned DefenseFinder HMM inventory and rules table record PD-T4-9 with required PD-T4-9__PD-T4-9_A and PD-T4-9__PD-T4-9_C profiles plus accessory PD-T4-9__PD-T4-9_B. Phage specificity beyond Tevenvirinae, escape routes, and natural family breadth remain unresolved. attaches_to: - causal_graphs#cmdtac_mrna_adp_ribosylation_aborts_phage posed_by: codex posed_date: '2026-09-21' evidence: - reference: DOI:10.1038/s41586-024-08102-8 snippet: PD-T4-9 also contains a third component, a SecB-like chaperone, suggesting that it is related to an enigmatic class of TA systems called toxin-antitoxin-chaperone (TAC) systems, so we renamed this system CmdTAC notes: Vassallo et al. state that PD-T4-9 was renamed CmdTAC after they recognized its SecB-like chaperone component. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-9.md snippet: 'The PD-T4-9 is composed of 3 proteins: PD-T4-9_A, PD-T4-9_B and PD-T4-9_C.' notes: The DefenseFinder wiki names the three protein components in the PD-T4-9 model. - reference: https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-9.md snippet: The PD-T4-9 system in *Vibrio parahaemolyticus* (GCF_001700835.1, NZ_CP010883) is composed of 3 proteins PD-T4-9_C (WP_065870458.1) PD-T4-9_B (WP_141106056.1) PD-T4-9_A (WP_065870460.1) notes: The DefenseFinder wiki illustrates a predicted PD-T4-9 locus in RefSeq assembly GCF_001700835.1 on NZ_CP010883. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv snippet: "PD-T4-9\tPD-T4-9\t2\t2\tPD-T4-9__PD-T4-9_A, PD-T4-9__PD-T4-9_C\tPD-T4-9__PD-T4-9_B\t\ \t" notes: The pinned DefenseFinder rules table models PD-T4-9 with PD-T4-9__PD-T4-9_A and PD-T4-9__PD-T4-9_C as required profiles and PD-T4-9__PD-T4-9_B as an accessory profile. - reference: https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md snippet: '| PD-T4-9__PD-T4-9_A | PD-T4-9__PD-T4-9_A | PD-T4-9 | Custom | 20 | | PD-T4-9__PD-T4-9_B | PD-T4-9__PD-T4-9_B | PD-T4-9 | Custom | 20 | | PD-T4-9__PD-T4-9_C | PD-T4-9__PD-T4-9_C | PD-T4-9 | Custom | 20 |' notes: The pinned DefenseFinder HMM inventory records PD-T4-9__PD-T4-9_A, PD-T4-9__PD-T4-9_B, and PD-T4-9__PD-T4-9_C under the PD-T4-9 system namespace. curation_history: - timestamp: '2026-09-21T12:03:24Z' curator: codex action: MINTED_TRAITMECH_ID changes: Minted CmdTAC system as a DOI-backed GENOMICS TraitRecord under the abortive infection system parent 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_v212. llm_assisted: true - timestamp: '2026-09-21T12:26:31Z' curator: codex action: ADDRESS_PR_REVIEW changes: Corrected Vassallo et al. author attribution, tightened the CmdTAC system definition to attach mRNA modification to CmdT, carried the proposal-only locus label into the record as a RELATED_SYNONYM, and left the DefenseFinder article-registry row at record-level evidence instead of on the CmdC sensing edge. llm_assisted: true - timestamp: '2026-09-26T21:51:06Z' curator: codex action: RESOLVE_DISCUSSION_SCOPE changes: Recorded PD-T4-9 as a DefenseFinder related label for CmdTAC after an ignored-and-hidden duplicate review found that PD-T4-9 denotes the existing CmdTAC system; added the pinned PD-T4-9 DefenseFinder rule and HMM rows and resolved the DefenseFinder model-coverage half of the open CmdTAC knowledge gap. llm_assisted: true