Plasmid targeting and destruction by the DdmDE bacterial defence system
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 1 . Here we reveal the activation pathway of the DNA de...
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description | 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
1
. 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)
2
. 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.
Using cryo-electron microscopy, insights into the structural and mechanistic function of the DdmDE system that is responsible for plasmid elimination in
Vibrio cholerae
seventh pandemic strains are explored. |
doi_str_mv | 10.1038/s41586-024-07515-9 |
format | Article |
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1
. 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)
2
. 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.
Using cryo-electron microscopy, insights into the structural and mechanistic function of the DdmDE system that is responsible for plasmid elimination in
Vibrio cholerae
seventh pandemic strains are explored.</description><identifier>ISSN: 0028-0836</identifier><identifier>ISSN: 1476-4687</identifier><identifier>EISSN: 1476-4687</identifier><identifier>DOI: 10.1038/s41586-024-07515-9</identifier><identifier>PMID: 38740055</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>101/28 ; 631/326/88 ; 631/45/500 ; 631/535/1258/1259 ; Antibiotics ; Argonaute Proteins - chemistry ; Argonaute Proteins - metabolism ; Argonaute Proteins - ultrastructure ; Bacteria ; Bacterial Proteins - chemistry ; Bacterial Proteins - metabolism ; Bacterial Proteins - ultrastructure ; Biochemistry ; Clearances ; Cryoelectron Microscopy ; Defense ; Deoxyribonucleases - chemistry ; Deoxyribonucleases - metabolism ; Deoxyribonucleases - ultrastructure ; Deoxyribonucleic acid ; DNA ; DNA helicase ; DNA Helicases - chemistry ; DNA Helicases - metabolism ; DNA Helicases - ultrastructure ; DNA structure ; DNA, Single-Stranded - genetics ; DNA, Single-Stranded - metabolism ; Electron microscopy ; Gene regulation ; Genomes ; Humanities and Social Sciences ; Microscopy ; Models, Molecular ; multidisciplinary ; Mutation ; Nuclease ; Nucleic acids ; Plasmids ; Plasmids - genetics ; Plasmids - immunology ; Plasmids - metabolism ; Post-transcription ; Protein Domains ; Protein Multimerization ; Proteins ; Science ; Science (multidisciplinary) ; Sensors ; Single-stranded DNA ; Transcription factors ; Vibrio cholerae - genetics ; Vibrio cholerae - immunology ; Vibrio cholerae - pathogenicity</subject><ispartof>Nature (London), 2024-06, Vol.630 (8018), p.961-967</ispartof><rights>The Author(s), under exclusive licence to Springer Nature Limited 2024. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><rights>2024. The Author(s), under exclusive licence to Springer Nature Limited.</rights><rights>Copyright Nature Publishing Group Jun 27, 2024</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c305t-a243412b615a2788ed321cb141c9c1ef198d15a947d48128515a59983408afa3</citedby><cites>FETCH-LOGICAL-c305t-a243412b615a2788ed321cb141c9c1ef198d15a947d48128515a59983408afa3</cites><orcidid>0000-0002-6198-1194 ; 0000-0003-0456-0753 ; 0009-0001-4294-0258</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1038/s41586-024-07515-9$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1038/s41586-024-07515-9$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38740055$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Bravo, Jack P. K.</creatorcontrib><creatorcontrib>Ramos, Delisa A.</creatorcontrib><creatorcontrib>Fregoso Ocampo, Rodrigo</creatorcontrib><creatorcontrib>Ingram, Caiden</creatorcontrib><creatorcontrib>Taylor, David W.</creatorcontrib><title>Plasmid targeting and destruction by the DdmDE bacterial defence system</title><title>Nature (London)</title><addtitle>Nature</addtitle><addtitle>Nature</addtitle><description>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
1
. 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)
2
. 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.
Using cryo-electron microscopy, insights into the structural and mechanistic function of the DdmDE system that is responsible for plasmid elimination in
Vibrio cholerae
seventh pandemic strains are explored.</description><subject>101/28</subject><subject>631/326/88</subject><subject>631/45/500</subject><subject>631/535/1258/1259</subject><subject>Antibiotics</subject><subject>Argonaute Proteins - chemistry</subject><subject>Argonaute Proteins - metabolism</subject><subject>Argonaute Proteins - ultrastructure</subject><subject>Bacteria</subject><subject>Bacterial Proteins - chemistry</subject><subject>Bacterial Proteins - metabolism</subject><subject>Bacterial Proteins - ultrastructure</subject><subject>Biochemistry</subject><subject>Clearances</subject><subject>Cryoelectron Microscopy</subject><subject>Defense</subject><subject>Deoxyribonucleases - chemistry</subject><subject>Deoxyribonucleases - metabolism</subject><subject>Deoxyribonucleases - ultrastructure</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA helicase</subject><subject>DNA Helicases - chemistry</subject><subject>DNA Helicases - metabolism</subject><subject>DNA Helicases - ultrastructure</subject><subject>DNA structure</subject><subject>DNA, Single-Stranded - genetics</subject><subject>DNA, Single-Stranded - metabolism</subject><subject>Electron microscopy</subject><subject>Gene regulation</subject><subject>Genomes</subject><subject>Humanities and Social Sciences</subject><subject>Microscopy</subject><subject>Models, Molecular</subject><subject>multidisciplinary</subject><subject>Mutation</subject><subject>Nuclease</subject><subject>Nucleic acids</subject><subject>Plasmids</subject><subject>Plasmids - genetics</subject><subject>Plasmids - immunology</subject><subject>Plasmids - metabolism</subject><subject>Post-transcription</subject><subject>Protein Domains</subject><subject>Protein Multimerization</subject><subject>Proteins</subject><subject>Science</subject><subject>Science (multidisciplinary)</subject><subject>Sensors</subject><subject>Single-stranded DNA</subject><subject>Transcription factors</subject><subject>Vibrio cholerae - genetics</subject><subject>Vibrio cholerae - immunology</subject><subject>Vibrio cholerae - pathogenicity</subject><issn>0028-0836</issn><issn>1476-4687</issn><issn>1476-4687</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kD1PwzAQhi0EoqXwBxiQJRaWgD9je0S0FKRKMHS3HNspqfJR7GTov8eQAhIDk2Xdc-_dPQBcYnSLEZV3kWEu8wwRliHBMc_UEZhiJvKM5VIcgylCRGZI0nwCzmLcIoQ4FuwUTKgULH34FCxfaxObysHehI3vq3YDTeug87EPg-2rroXFHvZvHs5dM1_Awtjeh8rUCSl9az2M-9j75hyclKaO_uLwzsD6cbF-eMpWL8vnh_tVZinifWYIowyTIsfcECGld5RgW2CGrbLYl1hJl0qKCcckJjJdZbhSkjIkTWnoDNyMsbvQvQ9pSd1U0fq6Nq3vhqjTECapEgwn9PoPuu2G0KblEiVSOs9znigyUjZ0MQZf6l2oGhP2GiP9aVmPlnWyrL8sa5Warg7RQ9F499PyrTUBdARiKrUbH35n_xP7AXcchWQ</recordid><startdate>20240627</startdate><enddate>20240627</enddate><creator>Bravo, Jack P. 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K.</au><au>Ramos, Delisa A.</au><au>Fregoso Ocampo, Rodrigo</au><au>Ingram, Caiden</au><au>Taylor, David W.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Plasmid targeting and destruction by the DdmDE bacterial defence system</atitle><jtitle>Nature (London)</jtitle><stitle>Nature</stitle><addtitle>Nature</addtitle><date>2024-06-27</date><risdate>2024</risdate><volume>630</volume><issue>8018</issue><spage>961</spage><epage>967</epage><pages>961-967</pages><issn>0028-0836</issn><issn>1476-4687</issn><eissn>1476-4687</eissn><abstract>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
1
. 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)
2
. 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.
Using cryo-electron microscopy, insights into the structural and mechanistic function of the DdmDE system that is responsible for plasmid elimination in
Vibrio cholerae
seventh pandemic strains are explored.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>38740055</pmid><doi>10.1038/s41586-024-07515-9</doi><tpages>7</tpages><orcidid>https://orcid.org/0000-0002-6198-1194</orcidid><orcidid>https://orcid.org/0000-0003-0456-0753</orcidid><orcidid>https://orcid.org/0009-0001-4294-0258</orcidid></addata></record> |
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subjects | 101/28 631/326/88 631/45/500 631/535/1258/1259 Antibiotics Argonaute Proteins - chemistry Argonaute Proteins - metabolism Argonaute Proteins - ultrastructure Bacteria Bacterial Proteins - chemistry Bacterial Proteins - metabolism Bacterial Proteins - ultrastructure Biochemistry Clearances Cryoelectron Microscopy Defense Deoxyribonucleases - chemistry Deoxyribonucleases - metabolism Deoxyribonucleases - ultrastructure Deoxyribonucleic acid DNA DNA helicase DNA Helicases - chemistry DNA Helicases - metabolism DNA Helicases - ultrastructure DNA structure DNA, Single-Stranded - genetics DNA, Single-Stranded - metabolism Electron microscopy Gene regulation Genomes Humanities and Social Sciences Microscopy Models, Molecular multidisciplinary Mutation Nuclease Nucleic acids Plasmids Plasmids - genetics Plasmids - immunology Plasmids - metabolism Post-transcription Protein Domains Protein Multimerization Proteins Science Science (multidisciplinary) Sensors Single-stranded DNA Transcription factors Vibrio cholerae - genetics Vibrio cholerae - immunology Vibrio cholerae - pathogenicity |
title | Plasmid targeting and destruction by the DdmDE bacterial defence system |
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