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TitleFilament assembly induced by the recognition of target DNA activates the prokaryotic Argonaute SPARDA system.
Journal, issue, pagesNat Commun, Vol. 17, Issue 1, Page 115, Year 2026
Publish dateJan 6, 2026
AuthorsWanyue Zhang / Yuchen Jiang / Yu Li / Xiangkai Zhen / Shuying Xu / Ning-Shao Xia / Shaowei Li / Xurong Wang / Qingbing Zheng / Songying Ouyang /
PubMed AbstractThe short prokaryotic Argonaute (pAgo) proteins, in conjunction with their associated effector molecules, constitute a defence mechanism in prokaryotes that protects against phage infections. The ...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.
External linksNat Commun / PubMed:41495039 / PubMed Central
MethodsEM (single particle) / EM (helical sym.)
Resolution2.64 - 2.77 Å
Structure data

65405

9vx1

EMDB-65405, PDB-9vx1:
The cryo-EM structure of gRNA-bound SPARDA complex
Method: EM (single particle) / Resolution: 2.77 Å

65406

9vx6

EMDB-65406, PDB-9vx6:
Helical structure of gRNA-tDNA SPARDA complex
Method: EM (helical sym.) / Resolution: 2.64 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • novosphingopyxis baekryungensis (bacteria)
  • bacteriophage sp. (virus)
KeywordsCELL INVASION / Cryo-EM / pAgo / DREN-APAZ / SPARDA

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