Activation of SPARDA defense system by filament assembly reveals beta-relay signaling mechanism widespread in prokaryotic Argonautes

2025 · doi:10.1101/2025.04.08.647717
preprint OA: closed
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The study investigates the SPARDA system, a short prokaryotic Argonaute (pAgo) DNase-associated defense mechanism, and shows it acts in anti-plasmid defense by degrading invading plasmid DNA and host DNA, leading to cell death and limiting invader spread. Using detection of invading DNA, the authors identify a “beta-relay” signaling mechanism in which recognition of the guide/target duplex is relayed through a structural region to other SPARDA sites, producing dramatic conformational changes and filament formation. The filament organizes DREN nuclease domains into tetrameric units poised to cleave dsDNA, and the authors report beta-relay presence across all pAgo clades. The paper does not explicitly discuss any limitation in the provided text, and it is focused on prokaryotic defense rather than human disease mechanisms. The paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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SUMMARY Present in all three domains of life, Argonaute (Ago) proteins use short oligonucleotides as guides to recognize complementary nucleic acid targets and are involved in RNA silencing (eukaryotes) or host defense against invading DNA (prokaryotes). Here, we show that the SPARDA (short prokaryotic Argonaute, DNase associated) system functions in anti-plasmid defense. Upon detection of invading plasmid DNA, it degrades both the invader and host DNA, inducing cell death and preventing further spread of the invader. Upon activation, the recognition signal of the bound guide/target duplex is relayed to other functional SPARDA sites through a structural region, which we termed ‘beta-relay’. The associated dramatic conformational changes trigger the formation of a filament, in which the DREN nuclease domains form tetramers poised to cleave dsDNA. Furthermore, we identified the presence of beta-relay in all pAgo clades, providing new insights into the structural mechanisms of pAgo proteins. Competing Interest Statement The authors have declared no competing interest. Footnotes ↵4 Lead contact

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