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TitleNucleic acid mediated activation of a short prokaryotic Argonaute immune system.
Journal, issue, pagesNat Commun, Vol. 15, Issue 1, Page 4852, Year 2024
Publish dateJun 6, 2024
AuthorsJithesh Kottur / Radhika Malik / Aneel K Aggarwal /
PubMed AbstractA short prokaryotic Argonaute (pAgo) TIR-APAZ (SPARTA) defense system, activated by invading DNA to unleash its TIR domain for NAD(P) hydrolysis, was recently identified in bacteria. We report the ...A short prokaryotic Argonaute (pAgo) TIR-APAZ (SPARTA) defense system, activated by invading DNA to unleash its TIR domain for NAD(P) hydrolysis, was recently identified in bacteria. We report the crystal structure of SPARTA heterodimer in the absence of guide-RNA/target-ssDNA (2.66 Å) and a cryo-EM structure of the SPARTA oligomer (tetramer of heterodimers) bound to guide-RNA/target-ssDNA at nominal 3.15-3.35 Å resolution. The crystal structure provides a high-resolution view of SPARTA, revealing the APAZ domain as equivalent to the N, L1, and L2 regions of long pAgos and the MID domain containing a unique insertion (insert57). Cryo-EM structure reveals regions of the PIWI (loop10-9) and APAZ (helix αN) domains that reconfigure for nucleic-acid binding and decrypts regions/residues that reorganize to expose a positively charged pocket for higher-order assembly. The TIR domains amass in a parallel-strands arrangement for catalysis. We visualize SPARTA before and after RNA/ssDNA binding and uncover the basis of its active assembly leading to abortive infection.
External linksNat Commun / PubMed:38844755 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.66 - 3.37 Å
Structure data

EMDB-41945: Locally refined (symmetry based) cryo-EM map of the dimer of the SPARTA oligomer with guide RNA and target DNA
Method: EM (single particle) / Resolution: 3.15 Å

EMDB-41947: Locally refined (symmetry based) cryo-EM map of the second dimer of the SPARTA oligomer with guide RNA and target DNA
Method: EM (single particle) / Resolution: 3.17 Å

EMDB-41948: Focused refined cryo-EM map of the TIR domains of the SPARTA oligomer
Method: EM (single particle) / Resolution: 3.37 Å

EMDB-41959: Original Cryo-EM map of the SPARTA oligomer with guide RNA and target DNA
Method: EM (single particle) / Resolution: 3.35 Å

41966

8u72

EMDB-41966, PDB-8u72:
Cryo-EM structure of the SPARTA oligomer with guide RNA and target DNA
Method: EM (single particle) / Resolution: 3.15 Å

PDB-8u7b:
Crystal structure of Apo form of Short Prokaryotic Argonaute TIR-APAZ (SPARTA) heterodimer
Method: X-RAY DIFFRACTION / Resolution: 2.66 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

ChemComp-PRO:
PROLINE

ChemComp-MN:
Unknown entry

Source
  • thermoflavifilum thermophilum (bacteria)
  • synthetic construct (others)
KeywordsRNA BINDING PROTEIN/RNA/DNA / RNA / DNA / Argonaute / TIR / immune system / RNA BINDING PROTEIN-RNA-DNA complex / RNA BINDING PROTEIN / SPARTA / Short Prokaryotic Argonaute / APAZ

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