Bacterial Argonaute proteins aid cell division in the presence of topoisomerase inhibitors in Escherichia coli

Prokaryotic Argonaute (pAgo) proteins are guide-dependent nucleases that likely function in host defense against invaders. Recently, it was shown that TtAgo from Thermus thermophilus also participates in the completion of DNA replication by decatenating chromosomal DNA. Here, we demonstrate that two cyanobacterial DNA-guided DNA nucleases, SeAgo from Synechococcus elongatus and LrAgo from Limnothrix roseae, aid cell division in Escherichia coli in the presence of the type II topoisomerase inhibitor ciprofloxacin. In E. coli, both pAgos are preferentially loaded with small DNAs (smDNAs) corresponding to the sites of replication termination. The amount of pAgo-associated smDNAs from the termination sites is significantly increased in the presence ciprofloxacin, suggesting that smDNA biogenesis depends on DNA replication. Ciprofloxacin also enhances asymmetry in the distribution of smDNAs around Chi-sites, indicating that it induces double-strand breaks that serve as a source of smDNA during their processing by RecBCD. While active in E. coli, SeAgo does not protect its native host S. elongatus from the ciprofloxacin action. The results suggest that pAgo nucleases may help to complete replication of chromosomal DNA in various bacteria by targeting the sites of termination, and may change their functional activities depending on the host species.