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Structure paper

TitleRetron-Eco1 assembles NAD-hydrolyzing filaments that provide immunity against bacteriophages.
Journal, issue, pagesMol Cell, Vol. 84, Issue 11, Page 2185-2202.e12, Year 2024
Publish dateJun 6, 2024
AuthorsArturo Carabias / Sarah Camara-Wilpert / Mario Rodríguez Mestre / Blanca Lopéz-Méndez / Ivo A Hendriks / Ruiliang Zhao / Tillmann Pape / Anders Fuglsang / Sean Hoi-Ching Luk / Michael L Nielsen / Rafael Pinilla-Redondo / Guillermo Montoya /
PubMed AbstractRetrons are toxin-antitoxin systems protecting bacteria against bacteriophages via abortive infection. The Retron-Eco1 antitoxin is formed by a reverse transcriptase (RT) and a non-coding RNA (ncRNA) ...Retrons are toxin-antitoxin systems protecting bacteria against bacteriophages via abortive infection. The Retron-Eco1 antitoxin is formed by a reverse transcriptase (RT) and a non-coding RNA (ncRNA)/multi-copy single-stranded DNA (msDNA) hybrid that neutralizes an uncharacterized toxic effector. Yet, the molecular mechanisms underlying phage defense remain unknown. Here, we show that the N-glycosidase effector, which belongs to the STIR superfamily, hydrolyzes NAD during infection. Cryoelectron microscopy (cryo-EM) analysis shows that the msDNA stabilizes a filament that cages the effector in a low-activity state in which ADPr, a NAD hydrolysis product, is covalently linked to the catalytic E106 residue. Mutations shortening the msDNA induce filament disassembly and the effector's toxicity, underscoring the msDNA role in immunity. Furthermore, we discovered a phage-encoded Retron-Eco1 inhibitor (U56) that binds ADPr, highlighting the intricate interplay between retron systems and phage evolution. Our work outlines the structural basis of Retron-Eco1 defense, uncovering ADPr's pivotal role in immunity.
External linksMol Cell / PubMed:38788717
MethodsEM (single particle)
Resolution2.43 - 4.41 Å
Structure data

18313

8qbk

EMDB-18313, PDB-8qbk:
Retron-Eco1 filament with ADP-ribosylated Effector (local map with 1 segment)
Method: EM (single particle) / Resolution: 2.99 Å

18314

8qbl

EMDB-18314, PDB-8qbl:
Retron-Eco1 filament with inactive effector (E106A, 2 segments)
Method: EM (single particle) / Resolution: 2.66 Å

18315

8qbm

EMDB-18315, PDB-8qbm:
Retron-Eco1 filament with ADP-ribosylated Effector (full map with 2 segments)
Method: EM (single particle) / Resolution: 3.09 Å

EMDB-18317: Retron-Eco1 filament (2 segments)
Method: EM (single particle) / Resolution: 4.41 Å

EMDB-19792: Retron-Eco1 -1 turn mutant filament with ADP-ribosylated Effector (Consensus refinement)
Method: EM (single particle) / Resolution: 2.43 Å

EMDB-19793: Retron-Eco1 filament with ADP-ribosylated Effector (Consensus refinement)
Method: EM (single particle) / Resolution: 3.13 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-AR6:
[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM

Source
  • escherichia coli bl21(de3) (bacteria)
KeywordsIMMUNE SYSTEM / retron / N-glycosidase / DNA-RNA-Protein complex

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