Sims, A. et al. Superinfection exclusion creates spatially distinct influenza virus populations. PLoS Biol. 21, e3001941 (2023).
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).
McAllister, W. T. & Barrett, C. L. Superinfection exclusion by bacteriophage T7. J. Virol. 24, 709–711 (1977).
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).
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).
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).
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).
Lu, M. J. & Henning, U. Superinfection exclusion by T-even-type coliphages. Trends Microbiol. 2, 137–139 (1994).
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).
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).
Kuzio, J. & Kropinski, A. M. O-antigen conversion in Pseudomonas aeruginosa PAO1 by bacteriophage D3. J. Bacteriol. 155, 203–212 (1983).
Newton, G. J. et al. Three-component-mediated serotype conversion in Pseudomonas aeruginosa by bacteriophage D3. Mol. Microbiol. 39, 1237–1247 (2001).
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).
Shah, M. et al. A phage-encoded anti-activator inhibits quorum sensing in Pseudomonas aeruginosa. Mol. Cell 81, 571–583 (2021).
Burrows, L. L. Pseudomonas aeruginosa twitching motility: type IV pili in action. Annu. Rev. Microbiol. 66, 493–520 (2012).
O’Toole, G. A. & Kolter, R. Flagellar and twitching motility are necessary for Pseudomonas aeruginosa biofilm development. Mol. Microbiol. 30, 295–304 (1998).
Bondy-Denomy, J. et al. Prophages mediate defense against phage infection through diverse mechanisms. ISME J. 10, 2854–2866 (2016).
Tsao, Y.-F. et al. Phage morons play an important role in Pseudomonas aeruginosa phenotypes. J. Bacteriol. 200, e00189-18 (2018).
Battesti, A. & Bouveret, E. The bacterial two-hybrid system based on adenylate cyclase reconstitution in Escherichia coli. Methods 58, 325–334 (2012).
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).
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).
Llontop, E. E. et al. The PilB-PilZ-FimX regulatory complex of the type IV pilus from Xanthomonas citri. PLoS Pathog. 17, e1009808 (2021).
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).
Chang, Y.-W. et al. Architecture of the type IVa pilus machine. Science 351, aad2001 (2016).
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).
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).
Whiteley, M. & Greenberg, E. P. Promoter specificity elements in Pseudomonas aeruginosa quorum-sensing-controlled genes. J. Bacteriol. 183, 5529–5534 (2001).
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).
Sztanko, K. M. et al. Prophages express a type IV pilus component to provide anti-phage defence. Preprint at bioRxiv https://doi.org/10.1101/2024.03.29.587342 (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).
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).
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).
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).
Labrie, S. J., Samson, J. E. & Moineau, S. Bacteriophage resistance mechanisms. Nat. Rev. Microbiol. 8, 317–327 (2010).
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).
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).
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).
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).
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).
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).
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).
Silpe, J. E. & Bassler, B. L. A host-produced quorum-sensing autoinducer controls a phage lysis-lysogeny decision. Cell 176, 268–280 (2019).
Hunter, M. & Fusco, D. Superinfection exclusion: a viral strategy with short-term benefits and long-term drawbacks. PLoS Comput. Biol. 18, e1010125 (2022).
Weller, S. K. & Sawitzke, J. A. Recombination promoted by DNA viruses: phage λ to herpes simplex virus. Annu. Rev. Microbiol. 68, 237–258 (2014).
Read, A. F. The evolution of virulence. Trends Microbiol. 2, 73–76 (1994).
Guy, B. et al. HIV F/3′ orf encodes a phosphorylated GTP-binding protein resembling an oncogene product. Nature 330, 266–269 (1987).
Kwon, Y. et al. Structural basis of CD4 downregulation by HIV-1 Nef. Nat. Struct. Mol. Biol. 27, 822–828 (2020).
Doron, S. et al. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359, eaar4120 (2018).
Georjon, H. & Bernheim, A. The highly diverse antiphage defence systems of bacteria. Nat. Rev. Microbiol. 21, 686–700 (2023).
Hampton, H. G., Watson, B. N. J. & Fineran, P. C. The arms race between bacteria and their phage foes. Nature 577, 327–336 (2020).
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).
Csörgő, B. et al. A compact Cascade-Cas3 system for targeted genome engineering. Nat. Methods 17, 1183–1190 (2020).
Hmelo, L. R. et al. Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic exchange. Nat. Protoc. 10, 1820–1841 (2015).
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).
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).
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).
Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).
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).
Sayers, E. W. et al. Database resources of the national center for biotechnology information. Nucleic Acids Res. 50, D20–D26 (2022).
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).
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).
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).
Kulikov, E. E. et al. Equine intestinal O-Seroconverting temperate coliphage Hf4s: genomic and biological characterization. Appl. Environ. Microbiol. 87, e01124-21 (2021).
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).
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).
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).
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).
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).
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).
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).
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).
Coetzee, J. N. Lysogenic conversion in the genus proteus. Nature 189, 946–947 (1961).
Bielmann, R. et al. Receptor binding proteins of Listeria monocytogenes bacteriophages A118 and P35 recognize serovar-specific teichoic acids. Virology 477, 110–118 (2015).
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).
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).
Ingmer, H., Gerlach, D. & Wolz, C. Temperate phages of Staphylococcus aureus. Microbiol. Spectr. https://doi.org/10.1128/microbiolspec.gpp3-0058-2018 (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).
