Filament assembly induced by the recognition of target DNA activates the prokaryotic Argonaute SPARDA system

The short prokaryotic Argonaute (pAgo) proteins, in conjunction with their associated effector molecules, constitute a defence mechanism in prokaryotes that protects against phage infections. The SPARDA is characterized by its collateral nuclease activity, which, upon activation through target DNA recognition, non-specifically cleaves a wide range of nucleic acid substrates. Nevertheless, the structural underpinnings of its collateral activity have remained elusive. In this study, we investigate the NbaSPARDA system from Novosphingopyxis baekryungensis and reveal that RNA-guided DNA recognition triggers the assembly of a higher-order filamentous structure. This filamentation is essential for the tetramerization of the DREN nuclease domain, which in turn facilitates the accumulation and cleavage of substrate nucleic acids. Through the determination of the gRNA-bound and RNA-DNA duplex-bound cryo-EM structures, we delineate a sequential monomer-dimer-monomer-filament transition during SPARDA activation. These insights collectively elucidate a filament-dependent activation mechanism underpinning the short pAgo-mediated immune response, which is crucial for antiviral defence. The short Argonaute-based bacterial defence system SPARDA exhibits collateral nuclease activity during phage infection. Here, the authors show that target DNA-induced filament assembly of SPARDA leads to tetramerization and activation of the DREN nuclease domain.