Structural basis of Gabija anti-phage defence and viral immune evasion
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Abstract
Bacteria encode hundreds of diverse defence systems that protect them from viral infection and inhibit phage propagation 1–5 . Gabija is one of the most prevalent anti-phage defence systems, occurring in more than 15% of all sequenced bacterial and archaeal genomes 1,6,7 , but the molecular basis of how Gabija defends cells from viral infection remains poorly understood. Here we use X-ray crystallography and cryo-electron microscopy (cryo-EM) to define how Gabija proteins assemble into a supramolecular complex of around 500 kDa that degrades phage DNA. Gabija protein A (GajA) is a DNA endonuclease that tetramerizes to form the core of the anti-phage defence complex. Two sets of Gabija protein B (GajB) dimers dock at opposite sides of the complex and create a 4:4 GajA–GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo. We show that a phage-encoded protein, Gabija anti-defence 1 (Gad1), directly binds to the Gabija GajAB complex and inactivates defence. A cryo-EM structure of the virally inhibited state shows that Gad1 forms an octameric web that encases the GajAB complex and inhibits DNA recognition and cleavage. Our results reveal the structural basis of assembly of the Gabija anti-phage defence complex and define a unique mechanism of viral immune evasion.
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- Authors
- Antine, S. P., Johnson, A. G., Mooney, S. E., Leavitt, A., Mayer, M. L., Yirmiya, E., Amitai, G., Sorek, R., & Kranzusch, P. J.
- Affiliations
- Harvard University (US)
- Weizmann Institute of Science (IL)
- Corresponding author
- Kranzusch, Philip J.
- ORCID
- Venue
- Nature
- Published
- 2023-11-22
- Volume
- 625
- Issue
- 7994
- Pages
- 360-365
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC10781630
- OpenAlex
- W4388913741
- Cited by
- 125
- References
- 57
- Citations by year
- 2026: 40 · 2025: 42 · 2024: 33 · 2023: 9 · 2022: 1
- FWCI
- 20.06
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- U.S. Department of Energy (DE‐ AC02‐06CH11357, AC02‐06CH11357, grid.436923.9, S10OD021527, P30 GM124165, S10RR029205, 06CH11357, 436923.9, DE-AC02-)
- Burroughs Wellcome Fund (P30 GM124165)
- Cancer Research Institute
- Oregon Health and Science University (grid.436923.9, 436923.9)
- Life Sciences Research Foundation
- G. Harold and Leila Y. Mathers Foundation (P30 GM124165)
- Parker Institute for Cancer Immunotherapy (P30 GM124165)
- Mark Foundation For Cancer Research (P30 GM124165)
- Open Philanthropy Project
- Deutsche Forschungsgemeinschaft (464312965, DE-AC02-06CH11357, SPP2330)
- Israel Science Foundation (MAPATS Grant 2720/22)
- Council for Higher Education
- National Institutes of Health (1dp2gm146250-01, 1s10od021527-01, DE-AC02–06CH11357, GM124165)
- Office of Science (AC02‐06CH11357, DE-AC02, 06CH11357, grid.436923.9, DE-AC02-06CH11357)
- National Institute of General Medical Sciences (DP2 GM146250, U24GM129547, P30GM124165)
- National Center for Research Resources (S10RR029205)
- Division of Chemistry
- Biological and Environmental Research (DEAC0206CH11357, S10OD021527, P30 GM124165, grid.436923.9)
- Argonne National Laboratory (DE- AC02-06-CH11357, DE-AC02, AC02–06CH11357, 06CH11357, P30 GM124165)
- Topics
- Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- phage resistance, viral immune evasion, protein complex formation, protein tetramerization, phage-host interactions
- MeSH terms
- Bacteria, Bacterial Proteins, Bacteriophages, Deoxyribonucleases, DNA, DNA, Viral, Humans, Virus Diseases, Crystallography, X-Ray, Cryoelectron Microscopy, Protein Multimerization, Immune Evasion
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