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TitleNucleic-acid-triggered NADase activation of a short prokaryotic Argonaute.
Journal, issue, pagesNature, Vol. 625, Issue 7996, Page 822-831, Year 2024
Publish dateOct 2, 2023
AuthorsXiaopan Gao / Kun Shang / Kaixiang Zhu / Linyue Wang / Zhixia Mu / Xingke Fu / Xia Yu / Bo Qin / Hongtao Zhu / Wei Ding / Sheng Cui /
PubMed AbstractArgonaute (Ago) proteins mediate RNA- or DNA-guided inhibition of nucleic acids. Although the mechanisms used by eukaryotic Ago proteins and long prokaryotic Ago proteins (pAgos) are known, that used ...Argonaute (Ago) proteins mediate RNA- or DNA-guided inhibition of nucleic acids. Although the mechanisms used by eukaryotic Ago proteins and long prokaryotic Ago proteins (pAgos) are known, that used by short pAgos remains elusive. Here we determined the cryo-electron microscopy structures of a short pAgo and the associated TIR-APAZ proteins (SPARTA) from Crenotalea thermophila (Crt): a free-state Crt-SPARTA; a guide RNA-target DNA-loaded Crt-SPARTA; two Crt-SPARTA dimers with distinct TIR organization; and a Crt-SPARTA tetramer. These structures reveal that Crt-SPARTA is composed of a bilobal-fold Ago lobe that connects with a TIR lobe. Whereas the Crt-Ago contains a MID and a PIWI domain, Crt-TIR-APAZ has a TIR domain, an N-like domain, a linker domain and a trigger domain. The bound RNA-DNA duplex adopts a B-form conformation that is recognized by base-specific contacts. Nucleic acid binding causes conformational changes because the trigger domain acts as a 'roadblock' that prevents the guide RNA 5' ends and the target DNA 3' ends from reaching their canonical pockets; this disorders the MID domain and promotes Crt-SPARTA dimerization. Two RNA-DNA-loaded Crt-SPARTA dimers form a tetramer through their TIR domains. Four Crt-TIR domains assemble into two parallel head-to-tail-organized TIR dimers, indicating an NADase-active conformation, which is supported by our mutagenesis study. Our results reveal the structural basis of short-pAgo-mediated defence against invading nucleic acids, and provide insights for optimizing the detection of SPARTA-based programmable DNA sequences.
External linksNature / PubMed:37783228
MethodsEM (single particle)
Resolution3.27 - 3.5 Å
Structure data

35700

8isy

EMDB-35700, PDB-8isy:
Cryo-EM structure of free-state Crt-SPARTA
Method: EM (single particle) / Resolution: 3.27 Å

35701

8isz

EMDB-35701, PDB-8isz:
Cryo-EM structure of Crt-SPARTA-gRNA-tDNA monomer
Method: EM (single particle) / Resolution: 3.27 Å

35702

8it0

EMDB-35702, PDB-8it0:
Cryo-EM structure of Crt-SPARTA-gRNA-tDNA dimer (conformation-2)
Method: EM (single particle) / Resolution: 3.5 Å

35703

8it1

EMDB-35703, PDB-8it1:
Cryo-EM structure of Crt-SPARTA-gRNA-tDNA tetramer (NADase active form)
Method: EM (single particle) / Resolution: 3.41 Å

36986

8k9g

EMDB-36986, PDB-8k9g:
Cryo-EM structure of Crt-SPARTA-gRNA-tDNA dimer (conformation-1)
Method: EM (single particle) / Resolution: 3.49 Å

Source
  • thermoflavifilum thermophilum (bacteria)
  • synthetic construct (others)
KeywordsDNA BINDING PROTEIN / Ago / DNA/RNA / DNA BINDING PROTEIN/DNA/RNA / DNA BINDING PROTEIN-DNA-RNA complex / Dimer / Tetramer / DNA/RNA/CELL INVASION / CELL INVASION / DNA-RNA-CELL INVASION complex

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