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TitleHigher-order assembly of a type IX retron enables exploitation for designer antimicrobials.
Journal, issue, pagesbioRxiv, Year 2026
Publish dateJul 13, 2026
AuthorsGrace N Hibshman / Linhan Wang / Nicole MacRae / Karen Zhang / Alfredo Florez / Seth L Shipman / Eva Nogales /
PubMed AbstractBacterial defense systems provide a rich reservoir for biotechnological innovation. Retrons are tripartite abortive infection systems that detect phage invasion using reverse-transcribed DNA (msDNA), ...Bacterial defense systems provide a rich reservoir for biotechnological innovation. Retrons are tripartite abortive infection systems that detect phage invasion using reverse-transcribed DNA (msDNA), but how they structurally couple threat detection to effector activation remains poorly understood. Here, we determine the cryo-EM structure and activation mechanism of retron-Kva2, a type IX retron from the human pathogen . We reveal that retron-Kva2 assembles into an asymmetric, higher-order ribonucleoprotein complex that sequesters a toxic dimeric HEPN RNase at its core. We identify a natural phage trigger as the phage T5 protein D5, which activates the retron through structural mimicry. Mirroring the retron-Kva2 winged-helix protein, the helix-turn-helix fold of D5 binds the msDNA sensor, driving conformational remodeling that unleashes HEPN-mediated tRNA cleavage and growth arrest. Because retron-Kva2 surveils a structural fold via msDNA binding, rather than a primary sequence, this recognition mechanism provides a broadly exploitable pathway for programmable activation. Harnessing this structure-based logic, we computationally designed synthetic triggers that activate retron-Kva2-mediated bacterial growth arrest . Our findings reveal the architectural basis of type IX retron immunity and establish a structure-guided paradigm for repurposing bacterial defense systems into precision-honed antimicrobial therapeutics.
External linksbioRxiv / PubMed:42523435 / PubMed Central
MethodsEM (single particle)
Resolution3.54 - 3.87 Å
Structure data

EMDB-77573: Retron-Kva2 Bottom Lobe
Method: EM (single particle) / Resolution: 3.87 Å

EMDB-77574: Peripheral Bottom Lobe RT
Method: EM (single particle) / Resolution: 3.67 Å

EMDB-77575: Retron-Kva2 Top Lobe
Method: EM (single particle) / Resolution: 3.71 Å

EMDB-77583: Retron-Kva2 Complex Consensus
Method: EM (single particle) / Resolution: 3.54 Å

77585

36ht

EMDB-77585, PDB-36ht:
Retron-Kva2 Complex Composite
Method: EM (single particle) / Resolution: 3.7 Å

Source
  • klebsiella variicola (bacteria)
KeywordsIMMUNE SYSTEM / Retron / Reverse transcriptase / Bacterial immune system / Abi / Ribonuclease

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