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Cryo-EM structure of the RADAR supramolecular anti-phage defense complex.

Brianna Duncan-Lowey1, Nitzan Tal2, Alex G Johnson1

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The RADAR bacterial defense system uses RdrA and RdrB proteins to convert ATP to ITP, limiting phage replication. This nucleotide modification is key to RADAR

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Area of Science:

  • Bacterial immunity and defense mechanisms
  • Structural biology and cryo-electron microscopy
  • Molecular mechanisms of nucleotide metabolism

Background:

  • RADAR (Recognition of DNA-associated activity) is a bacterial defense system.
  • It was previously understood to defend against bacteriophages by modifying messenger RNA.
  • The detailed molecular structure and mechanism remained largely unknown.

Purpose of the Study:

  • To determine the cryo-electron microscopy (cryo-EM) structures of the RADAR defense complex.
  • To elucidate the molecular mechanism by which RADAR confers anti-phage immunity.
  • To identify the specific nucleotide modification involved in defense.

Main Methods:

  • Cryo-electron microscopy (cryo-EM) to resolve high-resolution structures of the RADAR complex.
  • Biochemical assays to test enzymatic activity in vitro.
  • In vivo experiments to observe nucleotide accumulation during phage infection.

Main Results:

  • Cryo-EM structures revealed RdrA as a heptameric AAA+ ATPase and RdrB as a dodecameric complex with deaminase active sites.
  • RdrA and RdrB form a large assembly (up to 10 MDa) with RdrA positioned over RdrB's active site.
  • RdrB catalyzes ATP to inosine triphosphate (ITP) conversion in vitro and leads to ITP accumulation during phage infection, inhibiting phage replication.

Conclusions:

  • RADAR immunity is determined by ATP mononucleotide deamination, not RNA editing.
  • The study reveals a novel mechanism of anti-phage defense through supramolecular assembly of a nucleotide-modifying machine.
  • This work redefines the function of the RADAR system in bacterial defense.