Cholera disease is caused by the bacterium Vibrio cholerae. The seventh pandemic V. cholerae strains possess two molecular immune systems to eliminate invasive mobile genetic elements, which are thought to be crucial for its evolutionary success. While for one of these systems the mechanism of action was known, the mechanism of the DdmDE system, consisting of the DdmD and DdmE proteins, was unkown. The Jinek and Blokesch labs could now determine the mechanism of this system showing that DdmE is a prokaryotic Argonaute, which is guided by DNA to its plasmid targets, and then recruits DdmD. DdmD then degrades the target plasmids through its helicase and nuclease activities. The elucidation of the mechanism will aid the usage of the system for biotechnological applications. The findings have been published in Science in the article "Molecular mechanism of plasmid elimination by the DdmDE defense system".
Abstract from corresponding Preprint:
Seventh pandemic Vibrio cholerae strains contain two hallmark pathogenicity islands that encode the DNA defense modules DdmABC and DdmDE. Here we use cryo-EM to reveal the mechanistic basis for plasmid defense by DdmDE. A cryo-EM structure of the DdmD helicase-nuclease reveals that it adopts an auto-inhibited dimeric architecture. The prokaryotic Argonaute protein DdmE uses a DNA guide to target plasmid DNA. A 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 non-target DNA strand. Finally, in vitro studies reveal that DdmD translocates in the 5’ to 3’ direction, while partially degrading the plasmid DNA. These findings provide critical insights into the architecture and mechanism of DdmDE systems in plasmid elimination.
Read the Publication in Science
Read the Corresponding Preprint on bioRxiv (Open Access)
Publication: L. Loeff, D.W. Adams, C. Chanez, S. Stutzmann, L. Righi, M. Blokesch and M. Jinek (2024) Molecular mechanism of plasmid elimination by the DdmDE defense system Science, 385(6705), 188-194
Preprint: L. Loeff, D.W. Adams, C. Chanez, S. Stutzmann, L. Righi, M. Blokesch and M. Jinek (2024) Molecular mechanism of plasmid elimination by the DdmDE defense system bioRxiv doi.org/10.1101/2024.05.10.593530
Abstract, figure and title from Loeff et al (2024) bioRxiv published under a CC-BY-NC-ND 4.0 license.