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TitleStructural and mechanistic insights into the activation of a short prokaryotic argonaute system from archaeon Sulfolobus islandicus.
Journal, issue, pagesNucleic Acids Res, Vol. 53, Issue 3, Year 2025
Publish dateJan 24, 2025
AuthorsZhikang Dai / Yu Chen / Zeyuan Guan / Xueting Chen / Keyi Tan / Kaiyue Yang / Xuhui Yan / Yidong Liu / Zhou Gong / Wenyuan Han / Tingting Zou /
PubMed AbstractProkaryotic Argonaute proteins (pAgos) defend the host against invading nucleic acids, including plasmids and viruses. Short pAgo systems confer immunity by inducing cell death upon detecting ...Prokaryotic Argonaute proteins (pAgos) defend the host against invading nucleic acids, including plasmids and viruses. Short pAgo systems confer immunity by inducing cell death upon detecting invading nucleic acids. However, the activation mechanism of the SiAgo system, comprising a short pAgo from the archaeon Sulfolobus islandicus and its associated proteins SiAga1 and SiAga2, remains largely unknown. Here, we determined the cryo-electron microscopy structures of the SiAgo-Aga1 apo complex and the RNA-DNA-bound SiAgo-Aga1 complex at resolutions of 2.7 and 3.0 Å, respectively. Our results revealed that a positively charged pocket is generated from the interaction between SiAgo and SiAga1, exhibiting an architecture similar to APAZ-pAgo of short pAgo systems and accommodating the nucleic acids. Further investigation elucidated the conserved mechanism of nucleic acid recognition by SiAgo-Aga1. Both the SiAgo-Aga1 interaction and nucleic acid recognition by the complex are essential for antiviral defense. Biochemical and structural analyses demonstrated that SiAgo-Aga1 undergoes extensive conformational changes upon binding to the RNA-DNA duplex, thereby licensing its interaction with the effector SiAga2 to trigger the immune response. Overall, our findings highlight the evolutionary conservation of Agos across phylogenetic clades and provide structural insights into the activation mechanism of the SiAgo system.
External linksNucleic Acids Res / PubMed:39898546 / PubMed Central
MethodsEM (single particle)
Resolution2.7 - 3.0 Å
Structure data

60273

8znj

EMDB-60273, PDB-8znj:
Cryo-EM structure of a short prokaryotic Argonaute system from archaeon Suldolobus islandicus
Method: EM (single particle) / Resolution: 3.0 Å

63074

9lgw

EMDB-63074, PDB-9lgw:
Cryo-EM structure of SiAgo-Aga1 complex
Method: EM (single particle) / Resolution: 2.7 Å

Chemicals

ChemComp-MG:
Unknown entry

Source
  • Sulfolobus islandicus (strain M.16.4 / Kamchatka #3) (archaea)
  • saccharolobus islandicus m.16.4 (archaea)
KeywordsRNA BINDING PROTEIN/RNA/DNA / Argonaute / RNA BINDING PROTEIN-RNA-DNA complex / DNA BINDING PROTEIN

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