Genome manipulation by guide-directed Argonaute cleavage.

Argonaute Proteins / genetics DNA Escherichia coli / genetics Plasmids Prokaryotic Cells / metabolism Sequence Homology Genome, Bacterial

Journal

Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011

Informations de publication

Date de publication:
08 05 2023
Historique:
accepted: 12 03 2023
revised: 24 02 2023
received: 12 08 2022
medline: 9 5 2023
pubmed: 18 3 2023
entrez: 17 3 2023
Statut: ppublish

Résumé

Many prokaryotic argonautes (pAgos) mediate DNA interference by using small DNA guides to cleave target DNA. A recent study shows that CbAgo, a pAgo from Clostridium butyricum, induces DNA interference between homologous sequences and generates double-stranded breaks (DSBs) in target DNAs. This mechanism enables the host to defend against invading DNAs such as plasmids and viruses. However, whether such a CbAgo-mediated DNA cleavage is mutagenic remains unexplored. Here we demonstrate that CbAgo, directed by plasmid-encoded guide sequences, can cleave genome target sites and induce chromosome recombination between downstream homologous sequences in Escherichia coli. The recombination rate correlates well with pAgo DNA cleavage activity and the mechanistic study suggests the recombination involves DSBs and RecBCD processing. In RecA-deficient E. coli strain, guide-directed CbAgo cleavage on chromosomes severely impairs cell growth, which can be utilized as counter-selection to assist Lambda-Red recombineering. These findings demonstrate the guide-directed cleavage of pAgo on the host genome is mutagenic and can lead to different outcomes according to the function of the host DNA repair machinery. We anticipate this novel DNA-guided interference to be useful in broader genetic manipulation. Our study also provides an in vivo assay to characterize or engineer pAgo DNA cleavage activity.

Identifiants

DOI: 10.1093/nar/gkad188 PMID: 36928676 PMC: PMC10164581
pubmed: 36928676
pii: 7079637
doi: 10.1093/nar/gkad188
pmc: PMC10164581
doi:

Substances chimiques

Argonaute Proteins 0
DNA 9007-49-2

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

4078-4085

Informations de copyright

© The Author(s) 2023. Published by Oxford University Press on behalf of Nucleic Acids Research.

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Auteurs

Shan Huang (S)

Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 114-96, 1200 East California Boulevard, Pasadena, CA 91125, USA.
ORCID: 0000-0002-4436-3327

Kaihang Wang (K)

Division of Biology and Biological Engineering, California Institute of Technology, MC 114-96, 1200 East California Boulevard, Pasadena, CA 91125, USA.

Stephen L Mayo (SL)

Division of Chemistry and Chemical Engineering, California Institute of Technology, MC 114-96, 1200 East California Boulevard, Pasadena, CA 91125, USA.
Division of Biology and Biological Engineering, California Institute of Technology, MC 114-96, 1200 East California Boulevard, Pasadena, CA 91125, USA.
ORCID: 0000-0002-9785-5018

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Classifications MeSH

questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Nucléoprotéines › Protéines de liaison à l'ARN › Ribonucléoprotéines › Complexe réprimant l'expression de l'ARN › Protéines Argonaute › Genome manipulation by guide-directed...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › Genome manipulation by guide-directed...
questionsmedicales.fr › Bactéries › Proteobacteria › Gammaproteobacteria › Enterobacteriaceae › Escherichia › Escherichia coli › Genome manipulation by guide-directed...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Plasmides › Genome manipulation by guide-directed...
questionsmedicales.fr › Cellules › Cellules procaryotes › Genome manipulation by guide-directed...
questionsmedicales.fr › Phénomènes génétiques › Similitude de séquences › Genome manipulation by guide-directed...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Génome microbien › Génome bactérien › Genome manipulation by guide-directed...