Oligomerization-mediated activation of a short prokaryotic Argonaute – Nature

While eukaryotic Argonautes and long prokaryotic Argonautes (pAgos) cleave nucleic acids, some short pAgos lack nuclease activity and hydrolyze NAD(P)⁺ to induce bacterial cell death¹. We present a hierarchical activation pathway for SPARTA, a short pAgo consisting of an Ago protein and an associated protein TIR-APAZ². SPARTA progresses through distinct oligomeric forms, including a monomeric apo state, a monomeric RNA/DNA-bound state, two dimeric RNA/DNA-bound states, and a tetrameric RNA/DNA-bound active state. These snapshots together identify oligomerization as a mechanistic principle of SPARTA activation. Apo SPARTA is inactive, its RNA/DNA-binding channel occupied an auto-inhibitory motif in TIR-APAZ. Upon RNA/DNA binding, SPARTA transitions from a monomer to a symmetric and then an asymmetric dimer, in which two TIR domains interact via charge and shape complementarity. Next, two dimers assemble into a tetramer with a central TIR cluster responsible for hydrolyzing NAD(P)⁺. Additionally, we observed unique features of SPARTA-RNA/DNA interactions, including competition between the DNA 3’ end and the auto-inhibitory motif, interactions between the RNA G2 nucleotide and Ago, and splaying of the RNA-DNA duplex by two loops exclusive to short pAgos. Together, our findings contribute a mechanistic basis for the activation of short pAgos, a large section of the Ago superfamily.