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TitlePlasmid targeting and destruction by the DdmDE bacterial defence system.
Journal, issue, pagesNature, Vol. 630, Issue 8018, Page 961-967, Year 2024
Publish dateMay 13, 2024
AuthorsJack P K Bravo / Delisa A Ramos / Rodrigo Fregoso Ocampo / Caiden Ingram / David W Taylor /
PubMed AbstractAlthough eukaryotic Argonautes have a pivotal role in post-transcriptional gene regulation through nucleic acid cleavage, some short prokaryotic Argonaute variants (pAgos) rely on auxiliary nuclease ...Although eukaryotic Argonautes have a pivotal role in post-transcriptional gene regulation through nucleic acid cleavage, some short prokaryotic Argonaute variants (pAgos) rely on auxiliary nuclease factors for efficient foreign DNA degradation. Here we reveal the activation pathway of the DNA defence module DdmDE system, which rapidly eliminates small, multicopy plasmids from the Vibrio cholerae seventh pandemic strain (7PET). Through a combination of cryo-electron microscopy, biochemistry and in vivo plasmid clearance assays, we demonstrate that DdmE is a catalytically inactive, DNA-guided, DNA-targeting pAgo with a distinctive insertion domain. We observe that the helicase-nuclease DdmD transitions from an autoinhibited, dimeric complex to a monomeric state upon loading of single-stranded DNA targets. Furthermore, the complete structure of the DdmDE-guide-target handover complex provides a comprehensive view into how DNA recognition triggers processive plasmid destruction. Our work establishes a mechanistic foundation for how pAgos utilize ancillary factors to achieve plasmid clearance, and provides insights into anti-plasmid immunity in bacteria.
External linksNature / PubMed:38740055
MethodsEM (single particle)
Resolution2.5 - 3.2 Å
Structure data

41781

8u0j

EMDB-41781, PDB-8u0j:
DdmE in complex with guide and target DNA
Method: EM (single particle) / Resolution: 3.1 Å

41785
EMDB entry, No image

8u0u

EMDB-41785, PDB-8u0u:
DdmD dimer in complex with ssDNA
Method: EM (single particle) / Resolution: 3.04 Å

41790
EMDB entry, No image

8u0w

EMDB-41790, PDB-8u0w:
DdmD monomer in complex with ssDNA
Method: EM (single particle) / Resolution: 2.99 Å

41865
EMDB entry, No image

8u3k

EMDB-41865, PDB-8u3k:
DdmDE handover complex
Method: EM (single particle) / Resolution: 2.5 Å

44825

9bqv

EMDB-44825: DdmD dimer apoprotein (CASP target)
PDB-9bqv: DdmD dimer apoprotein
Method: EM (single particle) / Resolution: 3.2 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • Streptococcus pyogenes (bacteria)
  • vibrio cholerae (bacteria)
  • synthetic construct (others)
KeywordsIMMUNE SYSTEM/DNA / DdmE / Argonaute / pAgo / IMMUNE SYSTEM / IMMUNE SYSTEM-DNA complex / DdmD / helicase / nuclease

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