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Published on: December 14, 2019
Molecular mechanism of plasmid elimination by the DdmDE defense system
Luuk Loeff1, David W Adams2, Christelle Chanez1
1Department of Biochemistry, University of Zurich, Zurich, Switzerland.
Abstract:
Seventh-pandemic Vibrio cholerae strains contain two pathogenicity islands that encode the DNA defense modules DdmABC and DdmDE. In this study, we used cryogenic electron microscopy to determine the mechanistic basis for plasmid defense by DdmDE. The helicase-nuclease DdmD adopts an autoinhibited dimeric architecture. The prokaryotic Argonaute protein DdmE uses a DNA guide to target plasmid DNA. The structure of the DdmDE complex, validated by in vivo mutational studies, shows that DNA binding by DdmE triggers disassembly of the DdmD dimer and loading of monomeric DdmD onto the nontarget DNA strand. In vitro studies indicate that DdmD translocates in the 5'-to-3' direction, while partially degrading the plasmid DNA. These findings provide critical insights into the mechanism of DdmDE systems in plasmid elimination.
Insights
The DdmDE DNA defense system in Vibrio cholerae eliminates plasmids by targeting specific DNA sequences. This study reveals how DdmDE disassembles and degrades foreign DNA, providing insights into bacterial defense mechanisms.
Area of Science:
- Molecular Biology
- Microbiology
- Structural Biology
Background:
- Seventh-pandemic *Vibrio cholerae* strains possess pathogenicity islands encoding DNA defense modules.
- The DdmABC and DdmDE modules are crucial for bacterial defense against foreign DNA, particularly plasmids.
Purpose of the Study:
- To elucidate the mechanistic basis of plasmid DNA defense mediated by the DdmDE system.
- To determine the structural and functional roles of DdmD and DdmE in DNA targeting and degradation.
Main Methods:
- Cryogenic electron microscopy (cryo-EM) was employed to determine the structure of the DdmDE complex.
- In vivo mutational studies and in vitro biochemical assays were utilized to validate the structural findings and assess DNA degradation activity.
Main Results:
- The helicase-nuclease DdmD forms an autoinhibited dimer, while the Argonaute protein DdmE uses guide DNA to target specific sequences.
- DdmE binding to target DNA induces DdmD dimer disassembly and loading of monomeric DdmD onto the non-target DNA strand.
- DdmD exhibits 5'-to-3' translocation activity and degrades the targeted plasmid DNA.
Conclusions:
- The DdmDE system provides a novel mechanism for plasmid elimination in *Vibrio cholerae*.
- Structural and functional insights into DdmDE advance our understanding of prokaryotic adaptive immunity and DNA defense strategies.
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