ArticleNucleic acids research2025
Exploring the diversity of anti-defense systems across prokaryotes, phages and mobile genetic elements.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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54 citing papers in PubMed.
- Article
- Systematic mapping of bacteriophage gene essentiality with HIDEN-SEQ.Nature microbiology · 2026Article
- An expanded realm of anti-CRISPR-associated proteins and regulatory mechanisms.Nucleic acids research · 2026Article
- Acquisition and erosion of toxin-antitoxin systems in bacterial chromosomes.Molecular biology and evolution · 2026Article
- Rumen DNA virome plasticity and viral metabolic potential are associated with seasonal adaptation in grazing yak and cattle on the Qinghai-Tibet Plateau.Journal of animal science and biotechnology · 2026Article
- Phage-encoded NARP3 system rebuilds NADScience advances · 2026Article
- The leading region of many plasmids is adapted for translational efficiency.Nucleic acids research · 2026Article
- Panorama: A robust pangenome-based method for predicting and comparing biological systems across species.PLoS computational biology · 2026Article
- The pQBR mercury resistance plasmids: a model set of sympatric environmental mobile genetic elements.Microbial genomics · 2026Article
- The biology of jumbo phages.Nature communications · 2026Review
- Eco-evolutionary dynamics of defense systems in mobile genetic elements: Cui bono?Research square · 2026Article
- Evolutionary interplay: virulence, endolysin-like hydrolases, and defense correlations in the Erwinia amylovora pangenome.BMC microbiology · 2026Article
- Balancing of immune activation and suppression during phage infection.bioRxiv : the preprint server for biology · 2026Article
- A bacterial CARD-NLR-like immune system controls the release of gene transfer agents.Nature microbiology · 2026Article
- Eco-evolutionary dynamics of defense systems in mobile genetic elements: Cui bono?bioRxiv : the preprint server for biology · 2026Article
- Analysis of a Novel T1-like Phage KanT1 Reveals a Standalone SH3 Domain as a Widespread Component ofInternational journal of molecular sciences · 2026Article
- Phage homing endonuclease amplifies anti-defense genes to evade bacterial immunity.Nature communications · 2026Article
- A phage-encoded sponge protein suppresses bacterial TIR-Caspase immune signaling.Nature communications · 2026Article
- Rage against the mean: a perspective on measuring fitness of individual phage particles.Npj viruses · 2026Review
- Selection of porin and LPS mutants during infection by phage T4 facilitates the emergence of β-lactam resistance in Escherichia coli.npj antimicrobials and resistance · 2026Article
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10 authors.
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Abstract
The co-evolution of prokaryotes, phages and mobile genetic elements (MGEs) has driven the diversification of defense and anti-defense systems alike. Anti-defense proteins have diverse functional domains, sequences and are typically small, creating a challenge to detect anti-defense homologs across prokaryotic and phage genomes. To date, no tools comprehensively annotate anti-defense proteins within a desired sequence. Here, we developed 'AntiDefenseFinder'-a free open-source tool and web service that detects 156 anti-defense systems of one or more proteins in any genomic sequence. Using this dataset, we identified 47 981 anti-defense systems distributed across prokaryotes and their viruses. We found that some genes co-localize in 'anti-defense islands', including Escherichia coli T4 and Lambda phages, although many appear standalone. Eighty-nine per cent anti-defense systems localize only or preferentially in MGE. However, >80% of anti-Pycsar protein 1 (Apyc1) resides in nonmobile regions of bacterial genomes. Evolutionary analysis and biochemical experiments revealed that Apyc1 likely originated in bacteria to regulate cyclic nucleotide (cNMP) signaling, but phage co-opted Apyc1 to overcome cNMP-utilizing defenses. With the AntiDefenseFinder tool, we hope to facilitate the identification of the full repertoire of anti-defense systems in MGEs, the discovery of new protein functions and a deeper understanding of host-pathogen arms race.
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