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Cited by 26CRISPR and Genetic EngineeringBacterial Genetics and BiotechnologyBacteriophages and microbial interactions

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Bacterial Argonaute nucleases reveal different modes of DNA targeting in vitro and in vivo

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Lisitskaya, Lidiya, Kropocheva, Ekaterina, Agapov, Aleksei, Prostova, Maria, Panteleev, Vladimir, Yudin, Denis, Ryazansky, Sergei, Kuzmenko, Anton, Aravin, Alexei A, Esyunina, Daria, Kulbachinskiy, Andrey·2023·Nucleic Acids Research
DOI 10.1093/nar/gkad290PMC PMC10250240

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Abstract

Prokaryotic Argonaute proteins (pAgos) are homologs of eukaryotic Argonautes (eAgos) and are also thought to play a role in cell defense against invaders. However, pAgos are much more diverse than eAgos and little is known about their functional activities and target specificities in vivo. Here, we describe five pAgos from mesophilic bacteria that act as programmable DNA endonucleases and analyze their ability to target chromosomal and invader DNA. In vitro, the analyzed proteins use small guide DNAs for precise cleavage of single-stranded DNA at a wide range of temperatures. Upon their expression in Escherichia coli, all five pAgos are loaded with small DNAs preferentially produced from plasmids and chromosomal regions of replication termination. One of the tested pAgos, EmaAgo from Exiguobacterium marinum, can induce DNA interference between homologous sequences resulting in targeted processing of multicopy plasmid and genomic elements. EmaAgo also protects bacteria from bacteriophage infection, by loading phage-derived guide DNAs and decreasing phage DNA content and phage titers. Thus, the ability of pAgos to target multicopy elements may be crucial for their protective function. The wide spectrum of pAgo activities suggests that they may have diverse functions in vivo and paves the way for their use in biotechnology.

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Metadata

Authors
Lisitskaya, L., Kropocheva, E., Agapov, A., Prostova, M., Panteleev, V., Yudin, D., Ryazansky, S., Kuzmenko, A., Aravin, A. A., Esyunina, D., & Kulbachinskiy, A.
Affiliations
  • Russian Academy of Sciences (RU)
  • Kurchatov Institute (RU)
  • California Institute of Technology (US)
Corresponding author
Kulbachinskiy, Andrey
ORCID
Venue
Nucleic Acids Research
Publisher
Oxford University Press (OUP)
Published
2023-04-24
Volume
51
Issue
10
Pages
5106-5124
ISSN
  • 0305-1048 (ISSN-L)
  • 1362-4962
DOI
10.1093/nar/gkad290
PMC
PMC10250240
OpenAlex
W4366816650
Cited by
26
References
2
Citations by year
2026: 7 · 2025: 10 · 2024: 6 · 2023: 2
FWCI
2.23
Type
journal article
Language
en
Open access
Licence
Locations
  • Nucleic Acids Research (publishedVersion, cc-by-nc)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Funders
  • Ministry of Science and Higher Education (075-15-2021-1062)
  • Russian Science Foundation (20-74-10127, 19-14-00359)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
  • Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
Keywords
bacteriophage defense, phage resistance, replication termination, Escherichia coli, single-stranded DNA cleavage, mesophilic bacteria
MeSH terms
Bacteria, DNA, DNA, Bacterial, Endonucleases, Plasmids, Prokaryotic Cells, Eukaryota, Argonaute Proteins

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