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

RNA Biol. 2020 May;17(5):677-688. doi: 10.1080/15476286.2020.1724716. Epub 2020 Feb 16.


Members of the conserved Argonaute (Ago) protein family provide defence 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 non-specific 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.

Keywords: Argonaute; SeAgo; Synechococcus elongatus; ori and ter sites; programmable DNA nuclease.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Argonaute Proteins / chemistry
  • Argonaute Proteins / genetics*
  • Argonaute Proteins / metabolism*
  • Base Sequence
  • Binding Sites
  • DNA / chemistry
  • DNA / genetics
  • DNA / metabolism
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Enzyme Activation
  • Genome, Bacterial*
  • Genomics* / methods
  • Models, Biological
  • Models, Molecular
  • Molecular Conformation
  • Recombinant Proteins
  • Structure-Activity Relationship
  • Synechococcus / genetics*
  • Synechococcus / metabolism*


  • Argonaute Proteins
  • DNA-Binding Proteins
  • Recombinant Proteins
  • DNA

Supplementary concepts

  • Synechococcus elongatus

Grants and funding

This work was supported by the Russian Science Foundation [16-14-10377];Russian Foundation for Basic Research [18-29-07086].