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Nature (2025)Cite this article
In microbial communities, viruses compete for host cells and have evolved diverse mechanisms to inhibit competitors. One strategy is superinfection exclusion, whereby an established viral infection prevents a secondary infection of the same cell¹. This phenomenon has been shown to have an important role in the spread of eukaryotic viruses. Here we determine that superinfection exclusion proteins in bacterial viruses (bacteriophages, hereafter phages) perform a similar role, promoting viral spread through the bacterial community. We characterize a phage protein that alters the dynamics of a common phage receptor, the type IV pilus. This protein, known as Zip, does not abrogate pilus activity, but fine-tunes it, providing a strong phage defence without a fitness cost. Notably, Zip also prevents internalization and destruction of newly released phage progeny, a phenomenon that we call the anti-Kronos effect after the Greek god who consumed his offspring. Zip activity promotes the accumulation of free phages in bacterial lysogen communities, thereby enhancing viral spread. We further demonstrate that the anti-Kronos effect is conserved across diverse prophage-encoded superinfection exclusion systems. Our results identify the mechanistic basis of a superinfection exclusion system that safeguards phage progeny and provide insights into the conservation of viral defence mechanisms among bacterial and eukaryotic systems.
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We thank the members of the Maxwell, Davidson and Gitai laboratories for discussions, and A. Aertsen and Y. Casters for their discussions on superinfection exclusion in Salmonella. This study was supported by grants from the Canadian Institutes of Health Research to K.L.M. (PJT-165936) and A.R.D. (FDN-15427), and a Natural Sciences and Engineering Research Council Arthur B. McDonald Fellowship to K.L.M. (SMFSU-581368-2023). K.L.M. is the Canada Research Chair in Bacteriophage Biology and Therapeutics (CRC-2023-00010) and A.R.D. is the Canada Research Chair in Bacteriophage-Based Technologies (CRC-2017-00011). V.L.T. is supported by a Career Transition Award granted by the Emerging Pandemic & Infections Consortium (EPIC) at the University of Toronto. M.D.K. is supported by the National Institutes of Health (R35GM155280).
Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
Véronique L. Taylor, Pramalkumar H. Patel, Megha Shah, Alan R. Davidson & Karen L. Maxwell
Department of Biology, Texas A&M University, College Station, TX, USA
Ahmed Yusuf & Matthias D. Koch
Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
Cayla M. Burk, Kristina M. Sztanko & Alan R. Davidson
Department of Molecular Biology, Princeton University, Princeton, NJ, USA
Zemer Gitai
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V.L.T. and K.L.M. conceptualized the project. Phage experiments, genome deletions, plasmid construction, protein purification, bacterial-two hybrid assays and motility assays were performed by V.L.T., with assistance from M.S. and P.H.P.; C.M.B. performed the fluorescence localization assays. A.Y. and M.D.K performed the in vivo pilus dynamics and quantification. K.M.S. generated a phage knockout used in the study. Z.G., A.R.D., V.L.T., M.D.K. and K.L.M. contributed to experimental design. The manuscript was written by V.L.T. and K.L.M., and all of the authors contributed to editing the manuscript and support the conclusions.
Correspondence to Karen L. Maxwell.
The authors declare no competing interests.
Nature thanks Julia van Kessel and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
a, Bacterial Two Hybrid assay querying potential Zip interaction with proteins involved in P. aeruginosa pilus assembly, three biological replicates are shown. b, Twitching motility assays for PAO1, JBD26 lysogen, JBD26^∆zip lysogen, and PAO1 expressing Zip-GFP from a plasmid. Three independent biological replicates are shown. One-way ANOVA performed for each graph where significant p-values are noted (***p < 0.05) **** (p < 0.0001).
Source Data
a, DNA sequences of the predicted promoter regions of the zip genes found in phages JBD26, JBD24, and PA8. b, Protein sequence alignment of Zip homologues found in complete phage genomes. A sequence identity cut-off of 95% was used to remove redundant sequences. c, The zip genes in phages JBD26 and JBD68 share a common genomic context downstream of the phage tail operon, while PA8 is encoded at the other end of the morphogenetic region, upstream of the small terminase gene. d, Expanded genomic context of the anti-Kronos factors characterized in Fig. 4. Head decoration (HD), head-tail-joining (HTJ), tail assembly chaperone (TAC) and tail terminator (TT) genes.
a, Genome alignment of the phages used in the main study and the adsorption assay. b, Adsorption assay in P. aeruginosa of designated phages against i. wild-type ii. lysogens. Three biological replicates were performed and analysed by a two-way ANOVA with Šidák’s multiple comparison was performed where significant p-values are noted ****(p < 0.0001).
Source Data
This file contains Supplementary Figs. 1 and 2.
Supplementary Table 1: Zip homologues and whether they co-localize with morphogenic genes. Supplementary Table 2: Gp50 homologues and whether they co-localize with morphogenic genes. Supplementary Table 3: Gp40-41 homologues and whether they co-localize with morphogenic genes. Supplementary Table 4: Wzy_β-Iap homologues and whether they co-localize with morphogenic genes. Supplementary Table 5: Gp15 homologues and whether they co-localize with morphogenic genes. Supplementary Table 6: Gtr homologues and whether they co-localize with morphogenic genes. Supplementary Table 7: Tarp homologues and whether they co-localize with morphogenic genes. Supplementary Table 8: Cor homologues and whether they co-localize with morphogenic genes.
List of strains and plasmids used in the study.
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Taylor, V.L., Patel, P.H., Shah, M. et al. Prophages block cell surface receptors to preserve their viral progeny. Nature (2025). https://doi.org/10.1038/s41586-025-09260-z
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Received: 18 March 2024
Accepted: 09 June 2025
Published: 16 July 2025
DOI: https://doi.org/10.1038/s41586-025-09260-z
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