Structural basis for auto-inhibition and activation of a short prokaryotic Argonaute associated TIR-APAZ defense system

Abstract

Short prokaryotic Ago accounts for most prokaryotic Argonaute (pAgo) and is involved in defending bacteria against invading nucleic acids. Short prokaryotic Ago associated with APAZ-TIR (SPARTA) has been shown to oligomerize and deplete NAD+ upon guide-mediated target DNA recognition. However, the molecular basis of SPARTA inhibition and activation remains unknown. Here we determine the cryo-EM structures of Crenotalea thermophila SPARTA in its inhibited, transient, as well as activated states. The SPARTA is auto-inhibited by its acidic tail, which occupies the guide-target binding channel. Guide mediated target binding expels this acidic tail and triggers substantial conformational changes to expose Ago-Ago dimerization interface. As a result, SPARTA assembles into an active TIR-APAZ4/short Ago4 octamer, where the four TIR domains are rearranged and packed to form NADase active sites. Together with biochemical evidence, our results provide a panoramic vision explaining SPARTA auto-inhibition and activation, and expand understanding of pAgo mediated bacterial defense systems.