Structural basis of ssDNA-guided NADase activation of prokaryotic SPARTA system

Abstract Short prokaryotic Argonaute and the associated TIR-APAZ (SPARTA) proteins constitute a prokaryotic immune system, mediating RNA- or DNA-guided target single-stranded DNA (ssDNA) to activate NADase activity and induce cell death by degrading NAD+ in response to invading plasmids. Although the guide RNA-mediated targeting mechanism of SPARTA has been established, the functional role and mechanisms of guide DNA-mediated SPARTA remain poorly understood. Here, we report two crystal structures of Crenotalea thermophila SPARTA complexes with 5′-phosphorylated 21-nt guide DNA and complementary target ssDNA lengths of 15 or 20 nt. The structures demonstrate specific recognition of the 5′-OH or 3′-OH groups in target DNA by SPARTA, while not recognizing the 5′-P group in guide DNA. This suggests distinct recognition models for guide DNA and guide RNA, indicating different activation mechanisms. Furthermore, these two structures reveal disparate models for recognizing guide DNA and target DNA, providing insights into the length requirement for SPARTA activation.