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DNA targeting and interference by a bacterial Argonaute nuclease

Kuzmenko, Anton and Oguienko, Anastasiya and Esyunina, Daria and Yudin, Denis and Petrova, Mayya and Kudinova, Alina and Maslova, Olga and Ninova, Maria and Ryazansky, Sergei and Leach, David and Aravin, Alexei A. and Kulbachinskiy, Andrey (2020) DNA targeting and interference by a bacterial Argonaute nuclease. Nature, 587 (7835). pp. 632-637. ISSN 0028-0836. https://resolver.caltech.edu/CaltechAUTHORS:20200304-081912707

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[img] Image (JPEG) (Extended Data Fig. 5: Whole-genome analysis of DNA content in the wild-type and tus− E. coli strains depending on the expression of CbAgo) - Supplemental Material
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[img] Image (JPEG) (Extended Data Fig. 7: Targeting of plasmid and phage DNA by CbAgo) - Supplemental Material
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[img] Image (JPEG) (Extended Data Fig. 8: Loss of plasmids after various number of passages in E. coli strains with or without CbAgo) - Supplemental Material
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[img] Image (JPEG) (Extended Data Fig. 10: Co-occurrence of pAgo proteins, DSB repair systems and CRISPR–Cas in prokaryotic genomes) - Supplemental Material
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Abstract

Members of the conserved Argonaute protein family use small RNA guides to locate their mRNA targets and regulate gene expression and suppress mobile genetic elements in eukaryotes. Argonautes are also present in many bacterial and archaeal species. Unlike eukaryotic proteins, several prokaryotic Argonaute proteins use small DNA guides to cleave DNA, a process known as DNA interference. However, the natural functions and targets of DNA interference are poorly understood, and the mechanisms of DNA guide generation and target discrimination remain unknown. Here we analyse the activity of a bacterial Argonaute nuclease from Clostridium butyricum (CbAgo) in vivo. We show that CbAgo targets multicopy genetic elements and suppresses the propagation of plasmids and infection by phages. CbAgo induces DNA interference between homologous sequences and triggers DNA degradation at double-strand breaks in the target DNA. The loading of CbAgo with locus-specific small DNA guides depends on both its intrinsic endonuclease activity and the cellular double-strand break repair machinery. A similar interaction was reported for the acquisition of new spacers during CRISPR adaptation, and prokaryotic genomes that encode Ago nucleases are enriched in CRISPR–Cas systems. These results identify molecular mechanisms that generate guides for DNA interference and suggest that the recognition of foreign nucleic acids by prokaryotic defence systems involves common principles.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1038/s41586-020-2605-1DOIArticle
https://rdcu.be/b50QiPublisherFree ReadCube access
https://doi.org/10.1101/2020.03.01.971358DOIDiscussion Paper
https://github.com/AntKuzmenko/CbAgo_DNAi.gitRelated ItemCode
ORCID:
AuthorORCID
Kuzmenko, Anton0000-0001-7169-0561
Oguienko, Anastasiya0000-0002-8473-6378
Esyunina, Daria0000-0002-3706-4425
Yudin, Denis0000-0002-4103-0543
Petrova, Mayya0000-0001-5411-0457
Ninova, Maria0000-0001-5051-5502
Ryazansky, Sergei0000-0002-3171-2997
Leach, David0000-0003-4964-6913
Aravin, Alexei A.0000-0002-6956-8257
Kulbachinskiy, Andrey0000-0002-2292-6424
Alternate Title:pAgo-induced DNA interference protects bacteria from invader DNA
Additional Information:© 2020 Nature Publishing Group. Received 05 March 2020; Accepted 24 July 2020; Published 30 July 2020. We thank M. A. White for strains with engineered I-SceI sites, G. Smith for RecBCD antibodies, S. Lysenkov for the help with statistical analysis and A. Olina for the help with the phage experiments. D.Y. would like to thank M. Kolesnik for discussions. The project was in part supported by the Ministry of Science and Higher Education of the Russian Federation (14.W03.31.0007), Russian Science Foundation (19-14-00359, analysis of DSB formation), Russian Foundation for Basic Research (18-29-07086). A.A.A. is supported by an HHMI Faculty Scholar Award. D.L. is supported by grant MR/M019160/1 from the MRC (UK). Data availability: All data generated during this study are included in the published Article and the Extended Data and are available from the Gene Expression Omnibus (GEO) database with the accession number GSE148596. Code availability: The code used for data analysis is available at the GitHub repository at https://github.com/AntKuzmenko/CbAgo_DNAi.git. Author Contributions: A. Kuzmenko, A.A.A. and A. Kulbachinskiy conceptualized the study. A. Kuzmenko, D.Y. and D.E. constructed strains. A. Kuzmenko, A.O., D.Y. and D.E. prepared smDNA libraries. A. Kuzmenko, A.O. and D.E. prepared genomic DNA libraries. A. Kuzmenko, A.O. and D.Y. analysed sequencing data, M.N. and S.R. helped with data analysis. S.R. performed phylogenetic analysis. D.L. conceptualized experiments with engineered DSBs. A. Kuzmenko, A. Kudinova, O.M., M.P., A.O. and D.E. performed experiments on plasmid elimination and phage infection. All authors interpreted the results. A. Kuzmenko and A.O. prepared the figures. A. Kulbachinskiy and A.A.A. wrote the manuscript with contribution from other authors. The authors declare no competing interests.
Funders:
Funding AgencyGrant Number
Ministry of Education and Science of the Russian Federation14.W03.31.0007
Russian Science Foundation19-14-00359
Russian Foundation for Basic Research18-29-07086
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Medical Research Council (UK)MR/M019160/1
Subject Keywords:Bacterial host response; Phage biology; RNAi
Issue or Number:7835
Record Number:CaltechAUTHORS:20200304-081912707
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200304-081912707
Official Citation:Kuzmenko, A., Oguienko, A., Esyunina, D. et al. DNA targeting and interference by a bacterial Argonaute nuclease. Nature 587, 632–637 (2020). https://doi.org/10.1038/s41586-020-2605-1
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:101694
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:04 Mar 2020 18:49
Last Modified:02 Dec 2020 18:04

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