The ongoing cycle of co-evolution between bacteria and bacteriophages has led to the development of complex defense mechanisms in bacteria. For example, restriction-modification and the adaptive CRISPR-Cas systems target bacteriophage nucleic acids, helping to combat infection in its early stages. Additionally, small molecule defenses, such as prokaryotic viperins, produce modified nucleotides that inhibit viral transcription. Finally, abortive infection systems, like CBASS, act in later stages of infection by halting phage replication, slowing cell metabolism, or triggering programmed cell death. These are just a few examples of anti-phage systems with elucidated mechanisms of action. A recent discovery that genes encoding defense systems in prokaryotes tend to cluster in genomic regions called defense islands has led to the identification of numerous novel, previously unknown antiviral systems [1]. QatABCD is one of these newly discovered defense systems that can restrict P1, λ, and T3 dsDNA bacteriophages in E. coli [2]. Additionally, our data has shown that it can protect against Bas18 and Bas24 phages. However, the precise molecular mechanism of its action remains elusive.
Bioinformatic analysis of the proteins in this system revealed active sites typical of ATPases (QatA), 7-cyano-7-deazaguanine (PreQ\(_{0}\)) synthase (QatC), and TatD nuclease (QatD). It is hypothesized that a small molecule, 7-cyano-7-deazaguanine (PreQ\(_{0}\)), may be required for the system’s activity and could act as a signaling molecule. In this study, we tested the influence of separate gene deletions and mutations in the putative active sites for the QatABCD defence against different bacteriophages.