Sims, A. et al. Superinfection exclusion creates spatially distinct influenza virus populations. PLoS Biol. 21, e3001941 (2023).
Google Scholar
Puck, T. T. & Lee, H. H. Mechanism of cell wall penetration by viruses: II. Demonstration of cyclic permeability change accompanying virus infection of Escherichia coli B cells. J. Exp. Med. 101, 151–175 (1955).
Google Scholar
McAllister, W. T. & Barrett, C. L. Superinfection exclusion by bacteriophage T7. J. Virol. 24, 709–711 (1977).
Google Scholar
Zhang, X.-F. et al. A self-perpetuating repressive state of a viral replication protein blocks superinfection by the same virus. PLoS Pathog. 13, e1006253 (2017).
Google Scholar
Laliberte, J. P. & Moss, B. A novel mode of poxvirus superinfection exclusion that prevents fusion of the lipid bilayers of viral and cellular membranes. J. Virol. 88, 9751–9768 (2014).
Google Scholar
Doceul, V., Hollinshead, M., van der Linden, L. & Smith, G. L. Repulsion of superinfecting virions: a mechanism for rapid virus spread. Science 327, 873–876 (2010).
Google Scholar
Pedruzzi, I., Rosenbusch, J. P. & Locher, K. P. Inactivation in vitro of the Escherichia coli outer membrane protein FhuA by a phage T5-encoded lipoprotein. FEMS Microbiol. Lett. 168, 119–125 (1998).
Google Scholar
Lu, M. J. & Henning, U. Superinfection exclusion by T-even-type coliphages. Trends Microbiol. 2, 137–139 (1994).
Google Scholar
Cumby, N., Edwards, A. M., Davidson, A. R. & Maxwell, K. L. The bacteriophage HK97 gp15 moron element encodes a novel superinfection exclusion protein. J. Bacteriol. 194, 5012–5019 (2012).
Google Scholar
Cumby, N., Reimer, K., Mengin-Lecreulx, D., Davidson, A. R. & Maxwell, K. L. The phage tail tape measure protein, an inner membrane protein and a periplasmic chaperone play connected roles in the genome injection process of E. coli phage HK97. Mol. Microbiol. 96, 437–447 (2015).
Google Scholar
Kuzio, J. & Kropinski, A. M. O-antigen conversion in Pseudomonas aeruginosa PAO1 by bacteriophage D3. J. Bacteriol. 155, 203–212 (1983).
Google Scholar
Newton, G. J. et al. Three-component-mediated serotype conversion in Pseudomonas aeruginosa by bacteriophage D3. Mol. Microbiol. 39, 1237–1247 (2001).
Google Scholar
Chung, I.-Y., Jang, H.-J., Bae, H.-W. & Cho, Y.-H. A phage protein that inhibits the bacterial ATPase required for type IV pilus assembly. Proc. Natl Acad. Sci. USA 111, 11503–11508 (2014).
Google Scholar
Shah, M. et al. A phage-encoded anti-activator inhibits quorum sensing in Pseudomonas aeruginosa. Mol. Cell 81, 571–583 (2021).
Google Scholar
Burrows, L. L. Pseudomonas aeruginosa twitching motility: type IV pili in action. Annu. Rev. Microbiol. 66, 493–520 (2012).
Google Scholar
O’Toole, G. A. & Kolter, R. Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development. Mol. Microbiol. 30, 295–304 (1998).
Google Scholar
Bondy-Denomy, J. et al. Prophages mediate defense against phage infection through diverse mechanisms. ISME J. 10, 2854–2866 (2016).
Google Scholar
Tsao, Y.-F. et al. Phage morons play an important role in Pseudomonas aeruginosa phenotypes. J. Bacteriol. 200, e00189-18 (2018).
Google Scholar
Battesti, A. & Bouveret, E. The bacterial two-hybrid system based on adenylate cyclase reconstitution in Escherichia coli. Methods 58, 325–334 (2012).
Google Scholar
Alm, R. A., Bodero, A. J., Free, P. D. & Mattick, J. S. Identification of a novel gene, pilZ, essential for type 4 fimbrial biogenesis in Pseudomonas aeruginosa. J. Bacteriol. 178, 46–53 (1996).
Google Scholar
Kus, J. V., Tullis, E., Cvitkovitch, D. G. & Burrows, L. L. Significant differences in type IV pilin allele distribution among Pseudomonas aeruginosa isolates from cystic fibrosis (CF) versus non-CF patients. Microbiology 150, 1315–1326 (2004).
Google Scholar
Llontop, E. E. et al. The PilB-PilZ-FimX regulatory complex of the type IV pilus from Xanthomonas citri. PLoS Pathog. 17, e1009808 (2021).
Google Scholar
Koch, M. D., Black, M. E., Han, E., Shaevitz, J. W. & Gitai, Z. Pseudomonas aeruginosa distinguishes surfaces by stiffness using retraction of type IV pili. Proc. Natl Acad. Sci. USA 119, e2119434119 (2022).
Google Scholar
Chang, Y.-W. et al. Architecture of the type IVa pilus machine. Science 351, aad2001 (2016).
Google Scholar
Koch, M. D., Fei, C., Wingreen, N. S., Shaevitz, J. W. & Gitai, Z. Competitive binding of independent extension and retraction motors explains the quantitative dynamics of type IV pili. Proc. Natl Acad. Sci. USA 118, e2014926118 (2021).
Google Scholar
González-Valdez, A., Servín-González, L., Juárez, K., Hernandez-Aligio, A. & Soberón-Chávez, G. The effect of specific rhlA-las-box mutations on DNA binding and gene activation by Pseudomonas aeruginosa quorum-sensing transcriptional regulators RhlR and LasR. FEMS Microbiol. Lett. 356, 217–225 (2014).
Google Scholar
Whiteley, M. & Greenberg, E. P. Promoter specificity elements in Pseudomonas aeruginosa quorum-sensing-controlled genes. J. Bacteriol. 183, 5529–5534 (2001).
Google Scholar
Siehnel, R. et al. A unique regulator controls the activation threshold of quorum-regulated genes in Pseudomonas aeruginosa. Proc. Natl Acad. Sci. USA 107, 7916–7921 (2010).
Google Scholar
Sztanko, K. M. et al. Prophages express a type IV pilus component to provide anti-phage defence. Preprint at bioRxiv (2024).
Hao, Y., Murphy, K., Lo, R. Y., Khursigara, C. M. & Lam, J. S. Single-nucleotide polymorphisms found in the migA and wbpX glycosyltransferase genes account for the intrinsic lipopolysaccharide defects exhibited by Pseudomonas aeruginosa PA14. J. Bacteriol. 197, 2780–2791 (2015).
Google Scholar
Robbins, P. W. & Uchida, T. Studies on the chemical basis of the phage conversion of O-antigens in the E-group Salmonellae. Biochemistry 1, 323–335 (1962).
Google Scholar
Kupczok, A., Bailey, Z. M., Refardt, D. & Wendling, C. C. Co-transfer of functionally interdependent genes contributes to genome mosaicism in lambdoid phages. Microb. Genom. 8, mgen000915 (2022).
Google Scholar
Egido, J. E., Costa, A. R., Aparicio-Maldonado, C., Haas, P.-J. & Brouns, S. J. J. Mechanisms and clinical importance of bacteriophage resistance. FEMS Microbiol. Rev. 46, fuab048 (2022).
Google Scholar
Labrie, S. J., Samson, J. E. & Moineau, S. Bacteriophage resistance mechanisms. Nat. Rev. Microbiol. 8, 317–327 (2010).
Google Scholar
Taylor, V. L., Fitzpatrick, A. D., Islam, Z. & Maxwell, K. L. The diverse impacts of phage morons on bacterial fitness and virulence. Adv. Virus Res. 103, 1–31 (2019).
Google Scholar
Berryhill, B. A. et al. The book of Lambda does not tell us that naturally occurring lysogens of Escherichia coli are likely to be resistant as well as immune. Proc. Natl Acad. Sci. USA 120, e2212121120 (2023).
Google Scholar
Hancock, R. E., Hantke, K. & Braun, V. Iron transport of Escherichia coli K-12: involvement of the colicin B receptor and of a citrate-inducible protein. J. Bacteriol. 127, 1370–1375 (1976).
Google Scholar
Samsonov, V. V., Samsonov, V. V. & Sineoky, S. P. DcrA and dcrB Escherichia coli genes can control DNA injection by phages specific for BtuB and FhuA receptors. Res. Microbiol. 153, 639–646 (2002).
Google Scholar
Scandella, D. & Arber, W. Phage λ DNA injection into Escherichia coli pel− mutants is restored by mutations in phage genes V or H. Virology 69, 206–215 (1976).
Google Scholar
De Smet, J. et al. High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection. ISME J. 10, 1823–1835 (2016).
Google Scholar
Høyland-Kroghsbo, N. M. et al. Quorum sensing controls the Pseudomonas aeruginosa CRISPR-Cas adaptive immune system. Proc. Natl Acad. Sci. USA 114, 131–135 (2017).
Google Scholar
Silpe, J. E. & Bassler, B. L. A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Cell 176, 268–280 (2019).
Google Scholar
Hunter, M. & Fusco, D. Superinfection exclusion: a viral strategy with short-term benefits and long-term drawbacks. PLoS Comput. Biol. 18, e1010125 (2022).
Google Scholar
Weller, S. K. & Sawitzke, J. A. Recombination promoted by DNA viruses: phage λ to herpes simplex virus. Annu. Rev. Microbiol. 68, 237–258 (2014).
Google Scholar
Read, A. F. The evolution of virulence. Trends Microbiol. 2, 73–76 (1994).
Google Scholar
Guy, B. et al. HIV F/3′ orf encodes a phosphorylated GTP-binding protein resembling an oncogene product. Nature 330, 266–269 (1987).
Google Scholar
Kwon, Y. et al. Structural basis of CD4 downregulation by HIV-1 Nef. Nat. Struct. Mol. Biol. 27, 822–828 (2020).
Google Scholar
Doron, S. et al. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359, eaar4120 (2018).
Google Scholar
Georjon, H. & Bernheim, A. The highly diverse antiphage defence systems of bacteria. Nat. Rev. Microbiol. 21, 686–700 (2023).
Google Scholar
Hampton, H. G., Watson, B. N. J. & Fineran, P. C. The arms race between bacteria and their phage foes. Nature 577, 327–336 (2020).
Google Scholar
Aziz, R. K. et al. The RAST server: rapid annotations using subsystems technology. BMC Genom. 9, 75 (2008).
Qiu, D., Damron, F. H., Mima, T., Schweizer, H. P. & Yu, H. D. PBAD-based shuttle vectors for functional analysis of toxic and highly regulated genes in Pseudomonas and Burkholderia spp. and other bacteria. Appl. Environ. Microbiol. 74, 7422–7426 (2008).
Google Scholar
Csörgő, B. et al. A compact Cascade-Cas3 system for targeted genome engineering. Nat. Methods 17, 1183–1190 (2020).
Google Scholar
Hmelo, L. R. et al. Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic exchange. Nat. Protoc. 10, 1820–1841 (2015).
Google Scholar
Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L. A. RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat. Biotechnol. 31, 233–239 (2013).
Google Scholar
Farinha, M. A. & Kropinski, A. M. Construction of broad-host-range plasmid vectors for easy visible selection and analysis of promoters. J. Bacteriol. 172, 3496–3499 (1990).
Google Scholar
Liberati, N. T. et al. An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants. Proc. Natl Acad. Sci. USA 103, 2833–2838 (2006).
Google Scholar
Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).
Google Scholar
McCallum, M. et al. PilN binding modulates the structure and binding partners of the Pseudomonas aeruginosa type IVa pilus protein PilM. J. Biol. Chem. 291, 11003–11015 (2016).
Google Scholar
Sayers, E. W. et al. Database resources of the national center for biotechnology information. Nucleic Acids Res. 50, D20–D26 (2022).
Google Scholar
Xuan, G., Lin, H. & Wang, J. Expression of a phage-encoded Gp21 protein protects Pseudomonas aeruginosa against phage infection. J. Virol. 96, e01769-21 (2022).
Google Scholar
Kozyrev, D., Svarchevskiĭ, A., Zaĭtsev, E. & Rybchin, V. Lysogenic conversion induced by phages phi 80. I. A description of the phenomenon and the cloning of the conversion gene. Genetika 18, 555–560 (1982).
Google Scholar
Vostrov, A. A., Vostrukhina, O. A., Svarchevsky, A. N. & Rybchin, V. N. Proteins responsible for lysogenic conversion caused by coliphages N15 and phi80 are highly homologous. J. Bacteriol. 178, 1484–1486 (1996).
Google Scholar
Kulikov, E. E. et al. Equine intestinal O-Seroconverting temperate coliphage Hf4s: genomic and biological characterization. Appl. Environ. Microbiol. 87, e01124-21 (2021).
Google Scholar
Perry, L. L. et al. Sequence analysis of Escherichia coli O157:H7 bacteriophage ΦV10 and identification of a phage-encoded immunity protein that modifies the O157 antigen. FEMS Microbiol. Lett. 292, 182–186 (2009).
Google Scholar
Wollin, R., Stocker, B. A. & Lindberg, A. A. Lysogenic conversion of Salmonella typhimurium bacteriophages A3 and A4 consists of O-acetylation of rhamnose of the repeating unit of the O-antigenic polysaccharide chain. J. Bacteriol. 169, 1003–1009 (1987).
Google Scholar
Villafane, R., Zayas, M., Gilcrease, E. B., Kropinski, A. M. & Casjens, S. R. Genomic analysis of bacteriophage ε34 of Salmonella enterica serovar Anatum (15+). BMC Microbiol. 8, 227 (2008).
Google Scholar
Kim, M. & Ryu, S. Spontaneous and transient defence against bacteriophage by phase-variable glucosylation of O-antigen in Salmonella enterica serovar Typhimurium. Mol. Microbiol. 86, 411–425 (2012).
Google Scholar
Kintz, E. et al. A BTP1 prophage gene present in invasive non-typhoidal Salmonella determines composition and length of the O-antigen of the lipopolysaccharide. Mol. Microbiol. 96, 263–275 (2015).
Google Scholar
Woods, D. E., Jeddeloh, J. A. & Fritz, D. L. & DeShazer, D. Burkholderia thailandensisE125 harbors a temperate bacteriophage specific for Burkholderia mallei. J. Bacteriol. 184, 4003–4017 (2002).
Allison, G. E. & Verma, N. K. Serotype-converting bacteriophages and O-antigen modification in Shigella flexneri. Trends Microbiol. 8, 17–23 (2000).
Google Scholar
Clark, C. A., Beltrame, J. & Manning, P. A. The oac gene encoding a lipopolysaccharide O-antigen acetylase maps adjacent to the integrase-encoding gene on the genome of Shigella flexneri bacteriophage Sf6. Gene 107, 43–52 (1991).
Google Scholar
Steiger, H., Müller, U. & Bauer, G. Non-receptivity for ϰ phage of ϰ-lysogenic Serratia and reactions to superinfection of receptive cells with a mutant prophage. Mol. Gen. Genet. 114, 358–367 (1972).
Google Scholar
Coetzee, J. N. Lysogenic conversion in the genus proteus. Nature 189, 946–947 (1961).
Google Scholar
Bielmann, R. et al. Receptor binding proteins of Listeria monocytogenes bacteriophages A118 and P35 recognize serovar-specific teichoic acids. Virology 477, 110–118 (2015).
Google Scholar
Williamson, S. J., McLaughlin, M. R. & Paul, J. H. Interaction of the ΦHSIC virus with its host: lysogeny or pseudolysogeny? Appl. Environ. Microbiol. 67, 1682–1688 (2001).
Google Scholar
Bisen, P. S., Bagchi, S. N. & Audholia, S. Nitrate reductase activity of a cyanobacterium Phormidium uncinatum after cyanophage LPP-1 infection. FEMS Microbiol. Lett. 33, 69–72 (1986).
Google Scholar
Ingmer, H., Gerlach, D. & Wolz, C. Temperate phages of Staphylococcus aureus. Microbiol. Spectr. (2019).
Sun, X., Göhler, A., Heller, K. J. & Neve, H. The ltp gene of temperate Streptococcus thermophilus phage TP-J34 confers superinfection exclusion to Streptococcus thermophilus and Lactococcus lactis. Virology 350, 146–157 (2006).
Google Scholar