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| Title | Oligomerization-mediated activation of a short prokaryotic Argonaute. |
|---|---|
| Journal, issue, pages | Nature, Vol. 621, Issue 7977, Page 154-161, Year 2023 |
| Publish date | Jul 26, 2023 |
 Authors | Zhangfei Shen / Xiao-Yuan Yang / Shiyu Xia / Wei Huang / Derek J Taylor / Kotaro Nakanishi / Tian-Min Fu /  |
| PubMed Abstract | Although eukaryotic and long prokaryotic Argonaute proteins (pAgos) cleave nucleic acids, some short pAgos lack nuclease activity and hydrolyse NAD(P) to induce bacterial cell death. Here we present ...Although eukaryotic and long prokaryotic Argonaute proteins (pAgos) cleave nucleic acids, some short pAgos lack nuclease activity and hydrolyse NAD(P) to induce bacterial cell death. Here we present a hierarchical activation pathway for SPARTA, a short pAgo consisting of an Argonaute (Ago) protein and TIR-APAZ, an associated protein. SPARTA progresses through distinct oligomeric forms, including a monomeric apo state, a monomeric RNA-DNA-bound state, two dimeric RNA-DNA-bound states and a tetrameric RNA-DNA-bound active state. These snapshots together identify oligomerization as a mechanistic principle of SPARTA activation. The RNA-DNA-binding channel of apo inactive SPARTA is occupied by an auto-inhibitory motif in TIR-APAZ. After the binding of RNA-DNA, SPARTA transitions from a monomer to a symmetric dimer and then an asymmetric dimer, in which two TIR domains interact through charge and shape complementarity. Next, two dimers assemble into a tetramer with a central TIR cluster responsible for hydrolysing NAD(P). In addition, we observe unique features of interactions between SPARTA and RNA-DNA, including competition between the DNA 3' end and the auto-inhibitory motif, interactions between the RNA G2 nucleotide and Ago, and splaying of the RNA-DNA duplex by two loops exclusive to short pAgos. Together, our findings provide a mechanistic basis for the activation of short pAgos, a large section of the Ago superfamily. |
 External links | Nature / PubMed:37494956 / PubMed Central |
| Methods | EM (single particle) |
| Resolution | 2.48 - 3.52 Å |
| Structure data | EMDB-29033, PDB-8fex: EMDB-29043, PDB-8ffi:  EMDB-29219: Raw map for structure of tetramerized short MapSPARTA (short prokaryotic Agronuate) system upon guide RNA-mediated target ssDNA binding  EMDB-29222: Focused refined map of TIR domain for MapSPARTA  EMDB-29223: Focused map for corner area4 of MapSPARTA  EMDB-29224: Local refined map of corner area 3 for the MapSPARTA  EMDB-29225: Focused refinement of corner area2 for MapSPARTA  EMDB-29226: Focused refinement for corner area1 of MapSPARTA EMDB-40672, PDB-8sp0: EMDB-40673, PDB-8sp3:  EMDB-40679: Incomplete map of Maribacter polysiphoniae Argonaute (MapSPARTA) bound with guide RNA and target DNA duplex. EMDB-40680, PDB-8spo: EMDB-40713, PDB-8squ: |
| Chemicals |  ChemComp-MG:  ChemComp-NAD: |
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 Keywords | IMMUNE SYSTEM / Argonuate / TIR domain / Oligomerization / NAD+ / pAgo / SPARTA / Argonuare / NAD / Argonaute / TIR / bacterial Immume system / Short prokaryotic argonaute / NADase activity / Bacterial immune system / MapSPARTA / Short pAgo / Prokaryotic Argonaute / gRNA mediated DNA binding / Microbiology / microbic immune system |
maribacter polysiphoniae (bacteria)