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Genome-wide DNA sampling by Ago nuclease from the cyanobacterium Synechococcus elongatus

Olina, Anna and Kuzmenko, Anton and Ninova, Maria and Aravin, Alexei A. and Kulbachinskiy, Andrey and Esyunina, Daria (2020) Genome-wide DNA sampling by Ago nuclease from the cyanobacterium Synechococcus elongatus. RNA Biology, 17 (5). pp. 677-688. ISSN 1547-6286. https://resolver.caltech.edu/CaltechAUTHORS:20200212-142110986

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Abstract

Members of the conserved Argonaute (Ago) protein family provide defense against invading nucleic acids in eukaryotes in the process of RNA interference. Many prokaryotes also contain Ago proteins that are predicted to be active nucleases, however, their functional activities in host cells remain poorly understood. Here, we characterize the in vitro and in vivo properties of the SeAgo protein from the mesophilic cyanobacterium Synechococcus elongatus. We show that SeAgo is a DNA-guided nuclease preferentially acting on single-stranded DNA targets, with nonspecific guide-independent activity observed for double-stranded substrates. The SeAgo gene is steadily expressed in S. elongatus, however, its deletion or overexpression does not change the kinetics of cell growth. When purified from its host cells or from heterologous E. coli, SeAgo is loaded with small guide DNAs whose formation depends on the endonuclease activity of the argonaute protein. SeAgo co-purifies with SSB proteins suggesting that they may also be involved in DNA processing. The SeAgo-associated small DNAs are derived from diverse genomic locations, with certain enrichment for the proposed sites of chromosomal replication initiation and termination, but show no preference for an endogenous plasmid. Therefore, promiscuous genome sampling by SeAgo does not have great effects on cell physiology and plasmid maintenance.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1080/15476286.2020.1724716DOIArticle
ORCID:
AuthorORCID
Olina, Anna0000-0003-1844-2109
Kuzmenko, Anton0000-0001-7169-0561
Ninova, Maria0000-0001-5051-5502
Aravin, Alexei A.0000-0002-6956-8257
Kulbachinskiy, Andrey0000-0002-2292-6424
Esyunina, Daria0000-0002-3706-4425
Additional Information:© 2020 Informa UK Limited. Received 15 Aug 2019, Accepted 12 Jan 2020, Accepted author version posted online: 03 Feb 2020, Published online: 16 Feb 2020. We thank Denis Yudin for helpful discussions. This work was supported by grants of the Russian Foundation for Basic Research (18-29-07086) and Russian Science Foundation (16-14-10377). The authors declare no competing interests. This work was supported by the Russian Science Foundation [16-14-10377];Российский Фонд Фундаментальных Исследований (РФФИ) [18-29-07086].
Funders:
Funding AgencyGrant Number
Russian Foundation for Basic Research18-29-07086
Russian Science Foundation16-14-10377
Subject Keywords:Argonaute, programmable DNA nuclease, SeAgo, Synechococcus elongatus, ori and ter sites
Issue or Number:5
Record Number:CaltechAUTHORS:20200212-142110986
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200212-142110986
Official Citation:Anna Olina, Anton Kuzmenko, Maria Ninova, Alexei A. Aravin, Andrey Kulbachinskiy & Daria Esyunina (2020) Genome-wide DNA sampling by Ago nuclease from the cyanobacterium Synechococcus elongatus, RNA Biology, 17:5, 677-688, DOI: 10.1080/15476286.2020.1724716
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:101249
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:12 Feb 2020 22:31
Last Modified:16 Nov 2020 22:39

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