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

Brianna Duncan-Lowey; Nitzan Tal; Alex G Johnson; Shaun Rawson; Megan L Mayer; Shany Doron; Adi Millman; Sarah Melamed; Taya Fedorenko; Assaf Kacen; Alexander Brandis; Tevie Mehlman; Gil Amitai; Rotem Sorek; Philip J Kranzusch

doi:10.1016/j.cell.2023.01.012

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

Cell. 2023 Mar 2;186(5):987-998.e15. doi: 10.1016/j.cell.2023.01.012. Epub 2023 Feb 9.

Authors

Affiliations

¹ Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA.
² Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
³ Harvard Center for Cryo-Electron Microscopy, Harvard Medical School, Boston, MA 02115, USA.
⁴ Department of Immunology, Weizmann Institute of Science, Rehovot 7610001, Israel.
⁵ Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel.
⁶ Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel. Electronic address: rotem.sorek@weizmann.ac.il.
⁷ Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, MA 02115, USA. Electronic address: philip_kranzusch@dfci.harvard.edu.

Abstract

RADAR is a two-protein bacterial defense system that was reported to defend against phage by "editing" messenger RNA. Here, we determine cryo-EM structures of the RADAR defense complex, revealing RdrA as a heptameric, two-layered AAA+ ATPase and RdrB as a dodecameric, hollow complex with twelve surface-exposed deaminase active sites. RdrA and RdrB join to form a giant assembly up to 10 MDa, with RdrA docked as a funnel over the RdrB active site. Surprisingly, our structures reveal an RdrB active site that targets mononucleotides. We show that RdrB catalyzes ATP-to-ITP conversion in vitro and induces the massive accumulation of inosine mononucleotides during phage infection in vivo, limiting phage replication. Our results define ATP mononucleotide deamination as a determinant of RADAR immunity and reveal supramolecular assembly of a nucleotide-modifying machine as a mechanism of anti-phage defense.

Keywords: adenosine deaminase; anti-phage immunity; phage.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

ATPases Associated with Diverse Cellular Activities
Adenosine Deaminase / metabolism
Adenosine Triphosphate
Bacteriophages* / metabolism
Cryoelectron Microscopy / methods

Substances

ATPases Associated with Diverse Cellular Activities
Adenosine Triphosphate
Adenosine Deaminase