The phage nucleus synergizes with an anti-defense protein to resist bacterial immunity
Chimallivirus bacteriophages enclose their replicating genomes in a protein-based compartment termed the phage nucleus. While the phage nucleus segregates phage DNA from host immune proteins, it is not known if additional factors are required to protect against DNA-targeting host defenses. Here, we identify a chimallivirus-encoded DarG2-like antitoxin that localizes to the phage nucleus and provides protection against phage-targeting DarTG2 toxin-antitoxin systems. This protein, which we term AdfM (anti-darT factor macro), contains a macrodomain and removes DarT2-mediated ADP-ribose modifications from DNA. In the absence of AdfM, DarT2 modifies phage DNA and restricts chimallivirus replication despite being largely excluded from the phage nucleus. Increasing the nuclear concentration of DarT2 while decreasing the nuclear concentration of AdfM reduces phage replication. These results show that the phage nucleus is insufficient to completely protect the chimallivirus genome from host defenses; rather, it is one component of a multilayered counter-defense strategy.
Authors
- Joe Pogliano (ORCID: https://orcid.org/0000-0001-8989-2655)
- Chase J. Morgan (ORCID: https://orcid.org/0000-0002-7498-8678)
- Phoolwanti Rani (ORCID: https://orcid.org/0000-0002-6731-9003)
- Lydia R. Chambers (ORCID: https://orcid.org/0000-0001-6473-3084)
- Kevin D. Corbett (ORCID: https://orcid.org/0000-0001-5854-2388)
- Erica A. Birkholz (ORCID: https://orcid.org/0000-0003-2757-8120)
- Dwaipayan Basu
- Yingxing Li (ORCID: https://orcid.org/0000-0002-8984-9136)
- Benjamin A. Adler (ORCID: https://orcid.org/0000-0002-7488-3040)
- Elizabeth Villa
- Rui Liu (ORCID: https://orcid.org/0009-0002-1359-2730)
- Jennifer A. Doudna
- Kendall Hsieh
- Amar Deep
- Makaela Levine
Institutions
- QB3 (US)
- Howard Hughes Medical Institute (US)
- Lawrence Berkeley National Laboratory (US)
- University of California San Diego (US)
- Innovative Genomics Institute (US)
- University of California, Berkeley (US)
Publication Details
- Journal
- Cell Reports
- Published
- 2026-04-01
- DOI
- https://doi.org/10.1016/j.celrep.2026.117219
- Primary Topic
- Bacteriophages and microbial interactions
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Howard Hughes Medical Institute
- U.S. Department of Energy
- National Institute of General Medical Sciences
- National Institute of Allergy and Infectious Diseases