CmdTAC system

traitmech:000335 · CLASS · PROPOSED

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.

Trait evidence (12)

https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/
Here we characterize the widely distributed anti-phage defence system CmdTAC, which provides robust defence against infection by the T-even family of phages

Vassallo et al. name CmdTAC as a widely distributed anti-phage defense system that protects against T-even phages.
https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/
was discovered in the genome of the wild E. coli isolate ECOR22 through a functional genetic screen for anti-phage defence systems

Vassallo et al. trace the CmdTAC system to a functional anti-phage defense screen of Escherichia coli ECOR22.
https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/
CmdC detects infection by sensing viral capsid proteins, ultimately leading to the activation of a toxic ADP-ribosyltransferase effector protein, CmdT

CmdC senses phage infection through viral capsid proteins and activates the CmdT ADP-ribosyltransferase effector.
https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/
newly synthesized capsid protein triggers dissociation of the chaperone CmdC from the CmdTAC complex, leading to destabilization and degradation of the antitoxin CmdA

Newly synthesized phage capsid protein can dissociate the CmdC chaperone from the complex and destabilize CmdA.
https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/
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

Vassallo et al. support CmdT modification of single-stranded RNA as the translation-arresting antiphage effector output.
https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/
These results are consistent with CmdTAC functioning via an Abi mechanism.

Vassallo et al. interpret the low-MOI protection and center-of-infection results as consistent with an abortive-infection mechanism.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/List_system_article.md
CmdTAC | 10\.1038/s41586-024-08102-8 | Anti-viral defence by an mRNA ADP-ribosyltransferase that blocks translation

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.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-9.md
The PD-T4-9 is composed of 3 proteins: PD-T4-9_A, PD-T4-9_B and PD-T4-9_C.

The DefenseFinder wiki names the three protein components in the PD-T4-9 model.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-9.md
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)

The DefenseFinder wiki illustrates a predicted PD-T4-9 locus in RefSeq assembly GCF_001700835.1 on NZ_CP010883.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
PD-T4-9 PD-T4-9 2 2 PD-T4-9__PD-T4-9_A, PD-T4-9__PD-T4-9_C PD-T4-9__PD-T4-9_B

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.
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| 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 |

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.
DOI:10.1038/s41586-024-08102-8
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

Vassallo et al. state that PD-T4-9 was renamed CmdTAC after they recognized its SecB-like chaperone component.

CmdTAC activation blocks phage translation

Conservative system-level sketch linking a CmdTAC locus to CmdC capsid sensing, CmdA degradation, CmdT-mediated mRNA modification, translation arrest, and abortive phage defense.

NONMECHANISTIC · 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.

Edge evidence

cmdTAC locus contributes to CmdC viral capsid sensing RO:0002326
The cmdTAC locus encodes CmdC, which can sense viral capsid proteins.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ CmdC detects infection by sensing viral capsid proteins Vassallo et al. connect CmdC to viral capsid protein sensing.
CmdC viral capsid sensing contributes to CmdA antitoxin degradation RO:0002326
Newly synthesized capsid protein can trigger CmdC dissociation from CmdTAC and destabilize the CmdA antitoxin.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ newly synthesized capsid protein triggers dissociation of the chaperone CmdC from the CmdTAC complex Vassallo et al. place phage capsid-driven CmdC dissociation upstream of antitoxin destabilization.
CmdA antitoxin degradation contributes to CmdT mRNA ADP-ribosylation RO:0002326
CmdC dissociation and CmdA degradation liberate the CmdT ADP-ribosyltransferase.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ destabilization and degradation of the antitoxin CmdA, with consequent liberation of the CmdT ADP-ribosyltransferase Vassallo et al. place CmdA degradation upstream of CmdT liberation.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ CmdT co-precipitated with both CmdA and CmdC CmdT co-precipitated with both its antitoxin and chaperone partners.
CmdT mRNA ADP-ribosylation contributes to mRNA translation arrest RO:0002326
Liberated CmdT modifies mRNA and blocks translation.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ CmdT selectively modifies mRNA to block translation and abort the phage infection Vassallo et al. connect CmdT-mediated mRNA modification to translation arrest.
mRNA translation arrest confers CmdTAC system METPO:2007700
Translation arrest and viral-replication inhibition realize the CmdTAC system trait.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ arrest of mRNA translation and inhibition of viral replication Vassallo et al. connect CmdT-mediated mRNA modification to inhibited viral replication.
CmdTAC system is a abortive infection system rdfs:subClassOf
CmdTAC system possession is an abortive-infection phage-defense-system trait.
- https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/ These results are consistent with CmdTAC functioning via an Abi mechanism. Vassallo et al. interpret CmdTAC as consistent with an abortive-infection mechanism.

Provenance

Identifier source: TraitMech local identifier
Definition source: DOI:10.1038/s41586-024-08102-8

Parent traits (1)

abortive infection system traitmech:000214

Synonyms (4)

CmdTAC EXACT_SYNONYM · DOI:10.1038/s41586-024-08102-8
cmdTAC EXACT_SYNONYM · https://pmc.ncbi.nlm.nih.gov/articles/PMC11618068/
cmdTAC toxin-antitoxin-chaperone locus RELATED_SYNONYM · DOI:10.1038/s41586-024-08102-8
PD-T4-9 RELATED_SYNONYM · DOI:10.1038/s41586-024-08102-8

kg-microbe context

No kg-microbe node embedding matched this record in the 2026-04-25 deepwalk.

Canonical examples (1)

Organisms cited as exemplars of this trait. Taxon ids are NCBITaxon and link out to the NCBI record.

Escherichia coli NCBITaxon:562 DOI:10.1038/s41586-024-08102-8 Vassallo et al. report that cmdTAC was discovered in wild Escherichia coli isolate ECOR22 through a functional anti-phage defense screen.

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 CmdTAC family breadth and phage escape routes before minting narrower CmdTAC mechanism children.

KNOWLEDGE GAP OPEN cmdtac-family-and-model-coverage-gap · raised by codex · 2026-09-21

Attached to causal_graphs#cmdtac_mrna_adp_ribosylation_aborts_phage

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.

Evidence

DOI:10.1038/s41586-024-08102-8
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
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-9.md
The PD-T4-9 is composed of 3 proteins: PD-T4-9_A, PD-T4-9_B and PD-T4-9_C.
https://gitlab.pasteur.fr/mdm-lab/wiki/-/raw/ee7647d8/content/3.defense-systems/pd-t4-9.md
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)
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/DefenseFinder_rules.tsv
PD-T4-9 PD-T4-9 2 2 PD-T4-9__PD-T4-9_A, PD-T4-9__PD-T4-9_C PD-T4-9__PD-T4-9_B
https://raw.githubusercontent.com/mdmparis/defense-finder-models/afb0e5a8b466be53586b13266f5d38d98c3ac268/Liste_hmm_system.md
| 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 |

Curation history

2026-09-21T12:03:24Z · MINTED_TRAITMECH_ID · codex
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.
2026-09-21T12:26:31Z · ADDRESS_PR_REVIEW · codex
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.
2026-09-26T21:51:06Z · RESOLVE_DISCUSSION_SCOPE · codex
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.