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Chapter 3 : Bacteriophages and the Bacterial Genome

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Abstract:

This chapter focuses on the doublestranded DNA (dsDNA) phages, and especially on the temperate phages. While virulent phages certainly perform transduction and engage in evolutionary sparring with their hosts and so influence their evolution, the chapter focuses mainly on the complex interactions of temperate phages with their hosts. Bacteriophages may thus have contributed to the current compact nature of bacterial genomes. The approximately 100 currently published bacterial genome complete nucleotide sequences, and about 285 prophages are related to known bacteriophages. Of the more than 280 prophages in the currently sequenced bacterial genomes, only a few are known to be fully functional bacteriophages. There are two rather complex types of genetic entity in which this appears to have happened: the phage tail-like bacteriocins and the gene transfer agents. To date, protection from other phages and disease virulence factors are the lysogenic conversion genes that have been discovered and studied in the laboratory, but this likely reflects their ease of study and the lifestyles of the hosts studied. Our ideas about how bacteriophages have affected the nature of the bacterial chromosome are necessarily based on extrapolations from things we know about bacteriophage biology and from inferences based on the current structure of the bacterial genomes, and not on direct observation of those processes over evolutionary time.

Citation: Casjens S, Hendrix R. 2005. Bacteriophages and the Bacterial Genome, p 39-52. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch3
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References

/content/book/10.1128/9781555817640.chap3
1. Bagdian, G.,, O. Luderitz,, and A. M. Staub. 1966. Immunochemical studies on Salmonella. XI. Chemical modification correlated with conversion of group B Salmonella by bacteriophage 27. Ann. N. Y. Acad. Sci. 133:405424.
2. Banks, D. J.,, S. B. Beres,, and J. M. Musser. 2002. The fundamental contribution of phages to GAS evolution, genome diversification and strain emergence. Trends Microbiol. 10:515521.
3. Barondess, J. J.,, and J. Beckwith. 1995. bor gene of phage lambda, involved in serum resistance, encodes a widely conserved outer membrane lipoprotein. J. Bacteriol. 177:12471253.
4. Bejar, S.,, F. Bouche,, and J. P. Bouche. 1988. Cell division inhibition gene dicB is regulated by a locus similar to lambdoid bacteriophage immunity loci. Mol. Gen. Genet. 212:1119.
5. Benzer, S. 1959. On the topology of genetic fine structure. Proc. Natl. Acad. Sci. USA 45:16071620.
6. Beres, S. B.,, G. L. Sylva,, K. D. Barbian,, B. Lei,, J. S. Hoff,, N. D. Mammarella,, M. Y. Liu,, J. C. Smoot,, S. F. Porcella,, L. D. Parkins,, D. S. Campbell,, T. M. Smith,, J. K. McCormick,, D. Y. Leung,, P. M. Schlievert,, and J. M. Musser. 2002. Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence. Proc. Natl. Acad. Sci. USA 99: 1007810083.
7. Bergh, O.,, K. Y. Borsheim,, G. Bratbak,, and M. Heldal. 1989. High abundance of viruses found in aquatic environments. Nature 340:467468.
8. Bergthorsson, U.,, and H. Ochman. 1998. Distribution of chromosome length variation in natural isolates of Escherichia coli. Mol. Biol. Evol. 15:616.
9. Bertani, G. 1999. Transduction-like gene transfer in the methanogen Methanococcus voltae. J. Bacteriol. 181:29923002.
10. Betley, M. J.,, and J. J. Mekalanos. 1985. Staphylococcal enterotoxin A is encoded by phage. Science 229:185187.
11. Beutin, L.,, E. Strauch,, and I. Fischer. 1999. Isolation of Shigella sonnei lysogenic for a bacteriophage encoding gene for production of Shiga toxin. Lancet 353:1498.
12. Beutin, L.,, U. H. Stroeher,, and P. A. Manning. 1993. Isolation of enterohemolysin (Ehly2)-associated sequences encoded on temperate phages of Escherichia coli. Gene 132:9599.
13. Bishai, W.,, and J. Murphy,. 1988. Bacteriophage gene products that cause human disease, p. 683724. In R. Calendar (ed.), The Bacteriophages, vol. 2. Plenum Press, New York, N.Y.
14. Blasband, A. J.,, W. R. Marcotte, Jr., and C. A. Schnaitman. 1986. Structure of the lc and nmpC outer membrane porin protein genes of lambdoid bacteriophage. J. Biol. Chem. 261:1272312732.
15. Boyd, E. F.,, and H. Brussow. 2002. Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved. Trends Microbiol. 10: 521529.
16. Bray, D.,, and P. Robbins. 1967. Mechanism of e15 conversion studied with bacteriophage mutants. J. Mol. Biol. 30:457475.
17. Campbell, A. 1994. Comparative molecular biology of lambdoid phages. Annu. Rev. Microbiol. 48:193222.
18. Campbell, A. M. 2002. Preferential orientation of natural lambdoid prophages and bacterial chromosome organization. Theor. Popul. Biol. 61:503507.
19. Canchaya, C.,, C. Proux,, G. Fournous,, A. Bruttin,, and H. Brussow. 2003. Prophage genomics. Microbiol. Mol. Biol. Rev. 67:238276.
20. Casjens, S. 1998. The diverse and dynamic structure of bacterial genomes. Annu. Rev. Genet. 32:339377.
21. Casjens, S. 2003. Prophages and bacterial genomics: what have we learned so far? Mol. Microbiol. 49:277300.
22. Casjens, S.,, N. Palmer,, R. van Vugt,, W. M. Huang,, B. Stevenson,, P. Rosa,, R. Lathigra,, G. Sutton,, J. Peterson,, R. J. Dodson,, D. Haft,, E. Hickey,, M. Gwinn,, O. White,, and C. M. Fraser. 2000. A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochete Borrelia burgdorferi. Mol. Microbiol. 35:490516.
23. Cheetham, B. F.,, D. B. Tattersall,, G. A. Bloomfield,, J. I. Rood,, and M. E. Katz. 1995. Identification of a gene encoding a bacteriophage-related integrase in a vap region of the Dichelobacter nodosus genome. Gene 162:5358.
24. Cheetham, F.,, and M. Katz. 1995. A role for bacteriophages in the evolution and transfer of bacterial virulence determinants. Mol. Microbiol. 18:201208.
25. Clark, C. A.,, J. Beltrame,, and P. A. Manning. 1991. 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 107:4352.
26. Coleman, D. C.,, D. J. Sullivan,, R. J. Russell,, J. P. Arbuthnott,, B. F. Carey,, and H. M. Pomeroy. 1989. Staphylococcus aureus bacteriophages mediating the simultaneous lysogenic conversion of beta-lysin, staphylokinase and enterotoxin A: molecular mechanism of triple conversion. J. Gen. Microbiol. 135:16791697.
27. Ebel-Tsipis, J.,, and D. Botstein. 1971. Superinfection exclusion by P22 prophage in lysogens of Salmonella typhimurium. 1. Exclusion of generalized transducing particles. Virology 45:629637.
28. Eggers, C. H.,, S. Casjens,, S. F. Hayes,, C. F. Garon,, C. J. Damman,, D. B. Oliver,, and D. S. Samuels. 2000. Bacteriophages of spirochetes. J. Mol. Microbiol. Biotechnol. 2:365373.
29. Eggers, C. H.,, S. Casjens,, and D. S. Samuels,. 2001. Bacteriophages of Borrelia burgdorferi and other spirochetes, p. 3544. In M. Saier, and J. Garcia-Lara (ed.), The Spirochetes. Molecular and Cellular Biology. Horizon Scientific Press, Wymondham, United Kingdom.
30. Eklund, M. W.,, F. T. Poysky,, J. A. Meyers,, and G. A. Pelroy. 1974. Interspecies conversion of Clostridium botulinum type C to Clostridium novyi type A by bacteriophage. Science 186:456458.
31. Engelberg-Kulka, H.,, M. Reches,, S. Narasimhan,, R. Schoulaker- Schwarz,, Y. Klemes,, E. Aizenman,, and G. Glaser. 1998. rexB of bacteriophage lambda is an anti-cell death gene. Proc. Natl. Acad. Sci. USA 95:1548115486.
32. Ferretti, J. J.,, W. M. McShan,, D. Ajdic,, D. J. Savic,, G. Savic,, K. Lyon,, C. Primeaux,, S. Sezate,, A. N. Suvorov,, S. Kenton,, H. S. Lai,, S. P. Lin,, Y. Qian,, H. G. Jia,, F. Z. Najar,, Q. Ren,, H. Zhu,, L. Song,, J. White,, X. Yuan,, S. W. Clifton,, B. A. Roe,, and R. McLaughlin. 2001. Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc. Natl. Acad. Sci. USA 98:46584663.
33. Figueroa-Bossi, N.,, S. Uzzau,, D. Maloriol,, and L. Bossi. 2001. Variable assortment of prophages provides a transferable repertoire of pathogenic determinants in Salmonella. Mol. Microbiol. 39:260271.
34. Fitzgerald, J. R.,, S. R. Monday,, T. J. Foster,, G. A. Bohach,, P. J. Hartigan,, W. J. Meaney,, and C. J. Smyth. 2001. Characterization of a putative pathogenicity island from bovine Staphylococcus aureus encoding multiple superantigens. J. Bacteriol. 183:6370.
35. Freeman, V. 1951. Studies on the virulence of bacteriophage-infected strains of Corynebacterium diphtheriae. J. Bacteriol. 61:675688.
36. Glaser, P.,, L. Frangeul,, C. Buchrieser,, C. Rusniok,, A. Amend,, F. Baquero,, P. Berche,, H. Bloecker,, P. Brandt,, T. Chakraborty,, A. Charbit,, F. Chetouani,, E. Couve,, A. de Daruvar,, P. Dehoux,, E. Domann,, G. Dominguez-Bernal,, E. Duchaud,, L. Durant,, O. Dussurget,, K. D. Entian,, H. Fsihi,, F. G. Portillo,, P. Garrido,, L. Gautier,, W. Goebel,, N. Gomez-Lopez,, T. Hain,, J. Hauf,, D. Jackson,, L. M. Jones,, U. Kaerst,, J. Kreft,, M. Kuhn,, F. Kunst,, G. Kurapkat,, E. Madueno,, A. Maitournam,, J. M. Vicente,, E. Ng,, H. Nedjari,, G. Nordsiek,, S. Novella,, B. de Pablos,, J. C. Perez-Diaz,, R. Purcell,, B. Remmel,, M. Rose,, T. Schlueter,, N. Simoes,, A. Tierrez,, J. A. Vazquez-Boland,, H. Voss,, J. Wehland,, and P. Cossart. 2001. Comparative genomics of Listeria species. Science 294:849852.
37. Groman, N. B. 1984. Conversion by corynephages and its role in the natural history of diphtheria. J. Hyg. 93:405417.
38. Hardt, W. D.,, L. M. Chen,, K. E. Schuebel,, X. R. Bustelo,, and J. E. Galan. 1998. S. typhimurium encodes an activator of Rho GTPases that induces membrane ruffling and nuclear responses in host cells. Cell 93:815826.
39. Hauser, D.,, M. W. Eklund,, P. Boquet,, and M. R. Popoff. 1994. Organization of the botulinum neurotoxin C1 gene and its associated non-toxic protein genes in Clostridium botulinum C 468. Mol. Gen. Genet. 243:631640.
40. Hayashi, T.,, K. Makino,, M. Ohnishi,, K. Kurokawa,, K. Ishii,, K. Yokoyama,, C. G. Han,, E. Ohtsubo,, K. Nakayama,, T. Murata,, M. Tanaka,, T. Tobe,, T. Iida,, H. Takami,, T. Honda,, C. Sasakawa,, N. Ogasawara,, T. Yasunaga,, S. Kuhara,, T. Shiba,, M. Hattori,, and H. Shinagawa. 2001. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8:1122.
41. Hayashi, T.,, K. Makino,, M. Ohnishi,, K. Kurokawa,, K. Ishii,, K. Yokoyama,, C. G. Han,, E. Ohtsubo,, K. Nakayama,, T. Murata,, M. Tanaka,, T. Tobe,, T. Iida,, H. Takami,, T. Honda,, C. Sasakawa,, N. Ogasawara,, T. Yasunaga,, S. Kuhara,, T. Shiba,, M. Hattori,, and H. Shinagawa. 2001. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12 (Supplement). DNA Res. 8(Suppl.):4752.
42. Hellwage, J.,, T. Meri,, T. Heikkila,, A. Alitalo,, J. Panelius,, P. Lahdenne,, I. J. Seppala,, and S. Meri. 2001. The complement regulator factor H binds to the surface protein OspE of Borrelia burgdorferi. J. Biol. Chem. 276:84278435.
43. Hemphill, H. E.,, I. Gage,, S. A. Zahler,, and R. Z. Korman. 1980. Prophage-mediated production of a bacteriocinlike substance by SP beta lysogens of Bacillus subtilis. Can. J. Microbiol. 26:13281333.
44. Hendrix, R. W.,, J. G. Lawrence,, G. F. Hatfull,, and S. Casjens. 2000. The origins and ongoing evolution of viruses. Trends Microbiol. 8:504508.
45. Hendrix, R. W.,, M. C. Smith,, R. N. Burns,, M. E. Ford,, and G. F. Hatfull. 1999. Evolutionary relationships among diverse bacteriophages and prophages: all the world’s a phage. Proc. Natl. Acad. Sci. USA 96:21922197.
46. Huan, P. T.,, R. Taylor,, A. A. Lindberg,, and N. K. Verma. 1995. Immunogenicity of the Shigella flexneri serotype Y (SFL 124) vaccine strain expressing cloned glucosyl transferase gene of converting bacteriophage SfX. Microbiol. Immunol. 39:467472.
47. Huan, P. T.,, B. L. Whittle,, D. A. Bastin,, A. A. Lindberg,, and N. K. Verma. 1997. Shigella flexneri type-specific antigen V: cloning, sequencing and characterization of the glucosyl transferase gene of temperate bacteriophage SfV. Gene 195:207216.
48. Humphrey, S. B.,, T. B. Stanton,, N. S. Jensen,, and R. L. Zuerner. 1997. Purification and characterization of VSH-1, a generalized transducing bacteriophage of Serpulina hyodysenteriae. J. Bacteriol. 179:323329.
49. Ikeda, H.,, and J. Tomizawa. 1965. Transducing particles in generalized transduction by phage P1. I. Molecular origins of the fragments. J. Mol. Biol. 14:85109.
50. Johnson, L. P.,, and P. M. Schlievert. 1984. Group A streptococcal phage T12 carries the structural gene for pyrogenic exotoxin type A. Mol. Gen. Genet. 194:5256.
51. Johnson, L. P.,, P. M. Schlievert,, and D. W. Watson. 1980. Transfer of group A streptococcal pyrogenic exotoxin production to nontoxigenic strains of lysogenic conversion. Infect. Immun. 28:254257.
52. Juhala, R. J.,, M. E. Ford,, R. L. Duda,, A. Youlton,, G. F. Hatfull,, and R. W. Hendrix. 2000. Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. J. Mol. Biol. 299:2751.
53. Kaiser, K. 1980. The origin of Q-independent derivatives of phage lambda. Mol. Gen. Genet. 179:547554.
54. Kaiser, K.,, and N. Murray. 1980. On the nature of SbcA mutations in E. coli K-12. Mol. Gen. Genet. 179:555563.
55. Kaiser, K.,, and N. E. Murray. 1979. Physical characterisation of the ‘‘Rac prophage’’ in E. coli K12. Mol. Gen. Genet. 175:159174.
56. Kaneko, J.,, T. Kimura,, S. Narita,, T. Tomita,, and Y. Kamio. 1998. Complete nucleotide sequence and molecular characterization of the temperate staphylococcal bacteriophage fPVL carrying Panton-Valentine leukocidin genes. Gene 215:5767.
57. Karaolis, D. K.,, S. Somara,, D. R. Maneval, Jr., J. A. Johnson, and J. B. Kaper. 1999. A bacteriophage encoding a pathogenicity island, a type-IV pilus and a phage receptor in cholera bacteria. Nature 399:375379.
58. Kleerebezem, M.,, J. Boekhorst,, R. van Kranenburg,, D. Molenaar,, O. P. Kuipers,, R. Leer,, R. Tarchini,, S. A. Peters,, H. M. Sandbrink,, M. W. Fiers,, W. Stiekema,, R. M. Lankhorst,, P. A. Bron,, S. M. Hoffer,, M. N. Groot,, R. Kerkhoven,, M. de Vries,, B. Ursing,, W. M. de Vos,, and R. J. Siezen. 2003. Complete genome sequence of Lactobacillus plantarum WCFS1. Proc. Natl. Acad. Sci. USA 100:19901995.
59. Krogh, S.,, M. O’Reilly,, N. Nolan,, and K. M. Devine. 1996. The phage-like element PBSX and part of the skin element, which are resident at different locations on the Bacillus subtilis chromosome, are highly homologous. Microbiology 142:20312040.
60. Kropinski, A. M. 2000. Sequence of the genome of the temperate, serotype-converting, Pseudomonas aeruginosa bacteriophage D3. J. Bacteriol. 182:60666074.
61. Kuroda, M.,, T. Ohta,, I. Uchiyama,, T. Baba,, H. Yuzawa,, I. Kobayashi,, L. Cui,, A. Oguchi,, K. Aoki,, Y. Nagai,, J. Lian,, T. Ito,, M. Kanamori,, H. Matsumaru,, A. Maruyama,, H. Murakami,, A. Hosoyama,, Y. Mizutani-Ui,, N. K. Takahashi,, T. Sawano,, R. Inoue,, C. Kaito,, K. Sekimizu,, H. Hirakawa,, S. Kuhara,, S. Goto,, J. Yabuzaki,, M. Kanehisa,, A. Yamashita,, K. Oshima,, K. Furuya,, C. Yoshino,, T. Shiba,, M. Hattori,, N. Ogasawara,, H. Hayashi,, and K. Hiramatsu. 2001. Whole genome sequencing of methicillin-resistant Staphylococcus aureus. Lancet 357:12251240.
62. Lang, A. S.,, and J. T. Beatty. 2000. Genetic analysis of a bacterial genetic exchange element: the gene transfer agent of Rhodobacter capsulatus. Proc. Natl. Acad. Sci. USA 97:859864.
63. Lang, A. S.,, and J. T. Beatty. 2001. The gene transfer agent of Rhodobacter capsulatus and ‘‘constitutive transduction’’ in prokaryotes. Arch. Microbiol. 175:241249.
64. Lawrence, J. G.,, R. W. Hendrix,, and S. Casjens. 2001. Where are the bacterial pseudogenes? Trends Microbiol. 9:535540.
65. Lawrence, J. G.,, and J. R. Roth. 1996. Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143:18431860.
66. Lindsay, J. A.,, A. Ruzin,, H. F. Ross,, N. Kurepina,, and R. P. Novick. 1998. The gene for toxic shock toxin is carried by a family of mobile pathogenicity islands in Staphylococcus aureus. Mol. Microbiol. 29:527543.
67. Lindsey, D. F.,, D. A. Mullin,, and J. R. Walker. 1989. Characterization of the cryptic lambdoid prophage DLP12 of Escherichia coli and overlap of the DLP12 integrase gene with the tRNA gene argU. J. Bacteriol. 171:61976205.
68. Mahdi, A. A.,, G. J. Sharples,, T. N. Mandal,, and R. G. Lloyd. 1996. Holliday junction resolvases encoded by homologous rusA genes in Escherichia coli K-12 and phage 82. J. Mol. Biol. 257:561573.
69. Masignani, V.,, M. M. Giuliani,, H. Tettelin,, M. Comanducci,, R. Rappuoli,, and V. Scarlato. 2001. Mu-like prophage in serogroup B Neisseria meningitidis coding for surface-exposed antigens. Infect. Immun. 69:25802588.
70. Masters, M., 1996. Generalized transduction, p. 24212441. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., vol. 2. ASM Press, Washington, D.C.
71. Mavris, M.,, P. A. Manning,, and R. Morona. 1997. Mechanism of bacteriophage SfII-mediated serotype conversion in Shigella flexneri. Mol. Microbiol. 26:939950.
72. McDonough, M. A.,, and J. R. Butterton. 1999. Spontaneous tandem amplification and deletion of the shiga toxin operon in Shigella dysenteriae 1. Mol. Microbiol. 34:10581069.
73. Miao, E. A.,, and S. I. Miller. 1999. Bacteriophages in the evolution of pathogen-host interactions. Proc. Natl. Acad. Sci. USA 96:94529454.
74. Milkman, R.,, E. A. Raleigh,, M. McKane,, D. Cryderman,, P. Bilodeau,, and K. McWeeny. 1999. Molecular evolution of the Escherichia coli chromosome. V. Recombination patterns among strains of diverse origin. Genetics 153:539554.
75. Mirold, S.,, W. Rabsch,, M. Rohde,, S. Stender,, H. Tschape,, H. Russmann,, E. Igwe,, and W. D. Hardt. 1999. Isolation of a temperate bacteriophage encoding the type III effector protein SopE from an epidemic Salmonella typhimurium strain. Proc. Natl. Acad. Sci. USA 96:98459850.
76. Miyamoto, H.,, W. Nakai,, N. Yajima,, A. Fujibayashi,, T. Higuchi,, K. Sato,, and A. Matsushiro. 1999. Sequence analysis of Stx2-converting phage VT2-Sa shows a great divergence in early regulation and replication regions. DNA Res. 6:235240.
77. Mizuno, M.,, S. Masuda,, K. Takemaru,, S. Hosono,, T. Sato,, M. Takeuchi,, and Y. Kobayashi. 1996. Systematic sequencing of the 283 kb 210 degrees-232 degrees region of the Bacillus subtilis genome containing the SKIN element and many sporulation genes. Microbiology 142:31033111.
78. Moreira, D. 2000. Multiple independent horizontal transfers of informational genes from bacteria to plasmids and phages: implications for the origin of bacteial replication machinery. Mol. Microbiol. 35:15.
79. Morgan, G.,, G. Hatfull,, S. Casjens,, and R. Hendrix. 2002. Bacteriophage Mu genome sequence: analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus. J. Mol. Biol. 317:337359.
80. Morimyo, M.,, E. Hongo,, H. Hama-Inaba,, and I. Machida. 1992. Cloning and characterization of the mvrC gene of Escherichia coli K-12 which confers resistance against methyl viologen toxicity. Nucleic Acids Res. 20:31593165.
81. Muniesa, M.,, J. Recktenwald,, M. Bielaszewska,, H. Karch,, and H. Schmidt. 2000. Characterization of a shiga toxin 2e-converting bacteriophage from an Escherichia coli strain of human origin. Infect. Immun. 68:48504855.
82. Nakagawa, I.,, K. Kurokawa,, A. Yamashita,, M. Nakata,, Y. Tomiyasu,, N. Okahashi,, S. Kawabata,, K. Yamazaki,, T. Shiba,, T. Yasunaga,, H. Hayashi,, M. Hattori,, and S. Hamada. 2003. Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution. Genome Res. 13:10421055.
83. Nakayama, K.,, S. Kanaya,, M. Ohnishi,, Y. Terawaki,, and T. Hayashi. 1999. The complete nucleotide sequence of fCTX, a cytotoxin-converting phage of Pseudomonas aeruginosa: implications for phage evolution and horizontal gene transfer via bacteriophages. Mol. Microbiol. 31:399419.
84. Nakayama, K.,, K. Takashima,, H. Ishihara,, T. Shinomiya,, M. Kageyama,, S. Kanaya,, M. Ohnishi,, T. Murata,, H. Mori,, and T. Hayashi. 2000. The R-type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F-type is related to lambda phage. Mol. Microbiol. 38:213231.
85. Neely, M. N.,, and D. I. Friedman. 1998. Arrangement and functional identification of genes in the regulatory region of lambdoid phage H-19B, a carrier of a Shiga-like toxin. Gene 223:105113.
86. Nelson, K. E.,, R. A. Clayton,, S. R. Gill,, M. L. Gwinn,, R. J. Dodson,, D. H. Haft,, E. K. Hickey,, J. D. Peterson,, W. C. Nelson,, K. A. Ketchum,, L. McDonald,, T. R. Utterback,, J. A. Malek,, K. D. Linher,, M. M. Garrett,, A. M. Stewart,, M. D. Cotton,, M. S. Pratt,, C. A. Phillips,, D. Richardson,, J. Heidelberg,, G. G. Sutton,, R. D. Fleischmann,, J. A. Eisen,, and C. M. Fraser. 1999. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399:323329.
87. Nguyen, A. H.,, T. Tomita,, M. Hirota,, T. Sato,, and Y. Kamio. 1999. A simple purification method and morphology and component analyses for carotovoricin Er, a phage-taillike bacteriocin from the plant pathogen Erwinia carotovora Er. Biosci. Biotechnol. Biochem. 63:13601369.
88. Ohnishi, M.,, K. Kurokawa,, and T. Hayashi. 2001. Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol. 9:481485.
89. Osawa, R.,, S. Iyoda,, S. I. Nakayama,, A. Wada,, S. Yamai,, and H. Watanabe. 2000. Genotypic variations of Shiga toxin-converting phages from enterohaemorrhagic Escherichia coli O157:H7 isolates. J. Med. Microbiol. 49:565574.
90. Paul, J. H. 1999. Microbial gene transfer: an ecological perspective. J. Mol. Microbiol. Biotechnol. 1:4550.
91. Pedulla, M. L.,, M. E. Ford,, J. M. Houtz,, T. Karthikeyan,, C. Wadsworth,, J. A. Lewis,, D. Jacobs-Sera,, J. Falbo,, J. Gross,, N. R. Pannunzio,, W. Brucker,, V. Kumar,, J. Kandasamy,, L. Keenan,, S. Bardarov,, J. Kriakov,, J. G. Lawrence,, W. R. Jacobs, Jr., R. W. Hendrix, and G. F. Hatfull. 2003. Origins of highly mosaic mycobacteriophage genomes. Cell 113:171182.
92. Penner, M.,, I. Morad,, L. Snyder,, and G. Kaufmann. 1995. Phage T4-coded Stp: double-edged effector of coupled DNA and tRNA-restriction systems. J. Mol. Biol. 249:857868.
93. Perlak, F. J.,, C. L. Mendelsohn,, and C. B. Thorne. 1979. Converting bacteriophage for sporulation and crystal formation in Bacillus thuringiensis. J. Bacteriol. 140:699706.
94. Perna, N.,, J. Glasner,, V. Burland,, and G. Plunkett III,. 2002. The genomes of Escherichia coli K-12 and pathogenic E. coli, p. 353. In M. Donnenberg (ed.), Escherichia coli. Virulence Mechanisms of a Versatile Pathogen. Academic Press, New York, N.Y.
95. Perna, N. T.,, G. Plunkett III,, V. Burland,, B. Mau,, J. D. Glasner,, D. J. Rose,, G. F. Mayhew,, P. S. Evans,, J. Gregor,, H. A. Kirkpatrick,, G. Posfai,, J. Hackett,, S. Klink,, A. Boutin,, Y. Shao,, L. Miller,, E. J. Grotbeck,, N. W. Davis,, A. Lim,, E. T. Dimalanta,, K. D. Potamousis,, J. Apodaca,, T. S. Anantharaman,, J. Lin,, G. Yen,, D. C. Schwartz,, R. A. Welch,, and F. R. Blattner. 2001. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409:529533.
96. Plasterk, R. H.,, and P. van de Putte. 1985. The invertible PDNA segment in the chromosome of Escherichia coli. EMBO J. 4:237242.
97. Plunkett, G., III,, D. J. Rose,, T. J. Durfee,, and F. R. Blattner. 1999. Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product. J. Bacteriol. 181:17671778.
98. Rapp, B.,, and J. Wall. 1987. Genetic transfer in Desulfovibrio desulfuricans. Proc. Natl. Acad. Sci. USA 84: 91289130.
99. Reidl, J.,, and J. J. Mekalanos. 1995. Characterization of Vibrio cholerae bacteriophage K139 and use of a novel minitransposon to identify a phage-encoded virulence factor. Mol. Microbiol. 18:685701.
100. Roth, J. R.,, N. Benson,, T. Galitski,, K. Haack,, J. G. Lawrence,, and L. Miesel,. 1996. Rearrangements of the bacterial chromosome: formation and applications, p. 22562276. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., vol. 2. ASM Press, Washington, D.C.
101. Sandt, C. H.,, and C. W. Hill. 2000. Four different genes responsible for nonimmune immunoglobulin-binding activities within a single strain of Escherichia coli. Infect. Immun. 68:22052214.
102. Schicklmaier, P.,, E. Moser,, T. Wieland,, W. Rabsch,, and H. Schmieger. 1998. A comparative study on the frequency of prophages among natural isolates of Salmonella and Escherichia coli with emphasis on generalized transducers. Antonie Leeuwenhoek 73:4954.
103. Schmieger, H. 1999. Molecular survey of the Salmonella phage typing system of Anderson. J. Bacteriol. 181:16301635.
104. Seldin, L.,, and E. G. Penido. 1990. Production of a bacteriophage, a phage tail-like bacteriocin and an antibiotic by Bacillus azotofixans. An. Acad. Bras. Cienc. 62:8594.
105. Shinedling, S.,, D. Parma,, and L. Gold. 1987. Wild-type bacteriophage T4 is restricted by the lambda rex genes. J. Virol. 61:37903794.
106. Silver-Mysliwiec, T. H.,, and M. G. Bramucci. 1990. Bacteriophage-enhanced sporulation: comparison of spore-converting bacteriophages PMB12 and SP10. J. Bacteriol. 172:19481953.
107. Simpson, A. A.,, Y. Tao,, P. G. Leiman,, M. O. Badasso,, Y. He,, P. J. Jardine,, N. H. Olson,, M. C. Morais,, S. Grimes,, D. L. Anderson,, T. S. Baker,, and M. G. Rossmann. 2000. Structure of the bacteriophage f29 DNA packaging motor. Nature 408:745750.
108. Simpson, A. J.,, F. C. Reinach,, P. Arruda,, F. A. Abreu,, M. Acencio,, R. Alvarenga,, L. M. Alves,, J. E. Araya,, G. S. Baia,, C. S. Baptista,, M. H. Barros,, E. D. Bonaccorsi,, S. Bordin,, J. M. Bove,, M. R. Briones,, M. R. Bueno,, A. A. Camargo,, L. E. Camargo,, D. M. Carraro,, H. Carrer,, N. B. Colauto,, C. Colombo,, F. F. Costa,, M. C. Costa,, C. M. Costa-Neto,, L. L. Coutinho,, M. Cristofani,, E. Dias-Neto,, C. Docena,, H. El-Dorry,, A. P. Facincani,, A. J. Ferreira,, V. C. Ferreira,, J. A. Ferro,, J. S. Fraga,, S. C. Franca,, M. C. Franco,, M. Frohme,, L. R. Furlan,, M. Garnier,, G. H. Goldman,, M. H. Goldman,, S. L. Gomes,, A. Gruber,, P. L. Ho,, J. D. Hoheisel,, M. L. Junqueira,, E. L. Kemper,, J. P. Kitajima,, J. E. Krieger,, E. E. Kuramae,, F. Laigret,, M. R. Lambais,, L. C. Leite,, E. G. Lemos,, M. V. Lemos,, S. A. Lopes,, C. R. Lopes,, J. A. Machado,, M. A. Machado,, A. M. Madeira,, H. M. Madeira,, C. L. Marino,, M. V. Marques,, E. A. Martins,, E. M. Martins,, A. Y. Matsukuma,, C. F. Menck,, E. C. Miracca,, C. Y. Miyaki,, C. B. Monteriro- Vitorello,, D. H. Moon,, M. A. Nagai,, A. L. Nascimento,, L. E. Netto,, A. Nhani, Jr.,, F. G. Nobrega,, L. R. Nunes,, M. A. Oliveira,, M. C. de Oliveira,, R. C. de Oliveira,, D. A. Palmieri,, A. Paris,, B. R. Peixoto,, G. A. Pereira,, H. A. Pereira, Jr.,, J. B. Pesquero,, R. B. Quaggio,, P. G. Roberto,, V. Rodrigues,, M. R. A. J. de,, V. E. de Rosa, Jr.,, R. G. de Sa,, R. V. Santelli,, H. E. Sawasaki,, A. C. da Silva,, A. M. da Silva,, F. R. da Silva,, W. A. da Silva, Jr.,, J. F. da Silveira, et al. 2000. The genome sequence of the plant pathogen Xylella fastidiosa. Nature 406:151157.
109. Snyder, L.,, and G. Kaufmann,. 1994. T4 phage exclusion mechansims, p. 391396. In J. Karam (ed.), Molecular Biology of Bacteriophage T4. ASM Press, Washington, D.C.
110. Steensma, H. Y. 1981. Effect of defective phages on the cell membrane of Bacillus subtilis and partial characterization of the phage protein involved in killing. J. Gen. Virol. 56:275286.
111. Stevenson, B.,, N. El-Hage,, M. E. Hines,, J. H. Miller,, and K. Babb. 2002. Differential binding of host complement inhibitor factor H by Borrelia burgdoferi Erp surface proteins: a possible mechanism behind the expansive host range of Lyme disease spirochetes. Infect. Immun. 70:491497.
112. Stewart, A. W.,, and M. G. Johnson. 1977. Increased numbers of heat-resistant spores produced by two strains of Clostridium perfringens bearing temperate phage s9. J. Gen. Microbiol. 103:4550.
113. Susskind, M. M.,, D. Botstein,, and A. Wright. 1974. Superinfection exclusion by P22 prophage in lysogens of Salmonella typhimurium. III. Failure of superinfecting phage DNA to enter sieA+lysogens. Virology 62:350366.
114. Susskind, M. M.,, A. Wright,, and D. Botstein. 1974. Superinfection exclusion by P22 prophage in lysogens of Salmonella typhimurium. IV. Genetics and physiology of sieB exclusion. Virology 62:367384.
115. Takeda, Y.,, and J. R. Murphy. 1978. Bacteriophage conversion of heat-labile enterotoxin in Escherichia coli. J. Bacteriol. 133:172177.
116. Thaler, J. O.,, S. Baghdiguian,, and N. Boemare. 1995. Purification and characterization of xenorhabdicin, a phage tail-like bacteriocin, from the lysogenic strain F1 of Xenorhabdus nematophilus. Appl. Environ. Microbiol. 61:20492052.
117. Unkmeir, A.,, and H. Schmidt. 2000. Structural analysis of phage-borne stx genes and their flanking sequences in shiga toxin-producing Escherichia coli and Shigella dysenteriae type 1 strains. Infect. Immun. 68:48564864.
118. Vaca Pacheco, S.,, O. Garcia Gonzalez,, and G. L. Paniagua Contreras. 1997. The lom gene of bacteriophage lambda is involved in Escherichia coli K12 adhesion to human buccal epithelial cells. FEMS Microbiol. Lett. 156:129132.
119. Vaca-Pacheco, S.,, G. L. Paniagua-Contreras,, O. Garcia- Gonzalez,, and M. de la Garza. 1999. The clinically isolated FIZ15 bacteriophage causes lysogenic conversion in Pseudomonas aeruginosa PAO1. Curr. Microbiol. 38:239243.
120.. Van Sluys, M. A.,, M. C. de Oliveira,, C. B. Monteiro-Vitorello,, C. Y. Miyaki,, L. R. Furlan,, L. E. A. Camargo,, A. C. R. da Silva,, D. H. Moon,, M. A. Takita,, E. G. M. Lemos,, M. A. Machado,, M. I. T. Ferro,, F. R. da Silva,, M. H. S. Goldman,, G. H. Goldman,, M. V. F. Lemos,, H. El-Dorry,, S. M. Tsai,, H. Carrer,, D. M. Carraro,, R. C. de Oliveira,, L. R. Nunes,, W. J. Siqueira,, L. L. Coutinho,, E. T. Kimura,, E. S. Ferro,, R. Harakava,, E. E. Kuramae,, C. L. Marino,, E. Giglioti,, I. L. Abreu,, L. M. C. Alves,, A. M. do Amaral,, G. S. Baia,, S. R. Blanco,, M. S. Brito,, F. S. Cannavan,, A. V. Celestino,, A. F. da Cunha,, R. C. Fenille,, J. A. Ferro,, E. F. Formighieri,, L. T. Kishi,, S. G. Leoni,, A. R. Oliveira,, V. E. Rosa, Jr.,, F. T. Sassaki,, J. A. D. Sena,, A. A. de Souza,, D. Truffi,, F. Tsukumo,, G. M. Yanai,, L. G. Zaros,, E. L. Civerolo,, A. J. G. Simpson,, N. F. Almeida, Jr.,, J. C. Setubal,, and J. P. Kitajima. 2003. Comparative analyses of the complete genome sequences of Pierce’s disease and citrus variegated chlorosis strains of Xylella fastidiosa. J. Bacteriol. 185:10181026.
121. Voelker, L. L.,, and K. Dybvig. 1999. Sequence analysis of the Mycoplasma arthritidis bacteriophage MAV1 genome identifies the putative virulence factor. Gene 233:101107.
122. Wagner, P. L.,, M. N. Neely,, X. Zhang,, D. W. Acheson,, M. K. Waldor,, and D. I. Friedman. 2001. Role for a phage promoter in Shiga toxin 2 expression from a pathogenic Escherichia coli strain. J. Bacteriol. 183:20812085.
123. Wagner, P. L.,, and M. K. Waldor. 2002. Bacteriophage control of bacterial virulence. Infect. Immun. 70:39853993.
124. Waldor, M. K.,, and J. J. Mekalanos. 1996. Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272:19101914.
125. Wang, F. S.,, T. S. Whittam,, and R. K. Selander. 1997. Evolutionary genetics of the isocitrate dehydrogenase gene (icd) in Escherichia coli and Salmonella enterica. J. Bacteriol. 179:65516559.
126. Weisberg, R. A., 1996. Specialized transduction, p. 24422448. In F. C. Neidhardt,, R. Curtiss III,, J. L. Ingraham,, E. C. C. Lin,, K. B. Low,, B. Magasanik,, W. S. Reznikoff,, M. Riley,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd ed., vol. 2. ASM Press, Washington, D.C.
127. Whitman, W. B.,, D. C. Coleman,, and W. J. Wiebe. 1998. Prokaryotes: the unseen majority. Proc. Natl. Acad. Sci. USA 95:65786583.
128. Whittle, G.,, G. A. Bloomfield,, M. E. Katz,, and B. F. Cheetham. 1999. The site-specific integration of genetic elements may modulate thermostable protease production, a virulence factor in Dichelobacter nodosus, the causative agent of ovine footrot. Microbiology 145:28452855.
129. Wommack, K. E.,, and R. R. Colwell. 2000. Virioplankton: viruses in aquatic ecosystems. Microbiol. Mol. Biol. Rev. 64:69114.
130. Wright, A. 1971. Mechanism of conversion of Salmonella O antigen by bacteriophage epsilon 34. J. Bacteriol. 105:927936.
131. Yamaguchi, T.,, T. Hayashi,, H. Takami,, K. Nakasone,, M. Ohnishi,, K. Nakayama,, S. Yamada,, H. Komatsuzawa,, and M. Sugai. 2000. Phage conversion of exfoliative toxin A production in Staphylococcus aureus. Mol. Microbiol. 38: 694705.
132. Yamamoto, K. 1967. The origin of bacteriophage P221. Virology 33:545547.
133. Yarmolinsky, M. B.,, and N. Sternberg,. 1988. Bacteriophage P1, p. 291438. In R. Calendar (ed.), The Bacteriophages, vol. 2. Plenum Press, New York, N.Y.
134. Yen, H. C.,, N. T. Hu,, and B. L. Marrs. 1979. Characterization of the gene transfer agent made by an overproducer mutant of Rhodopseudomonas capsulata. J. Mol. Biol. 131:157168.
135. Yokoyama, K.,, K. Makino,, Y. Kubota,, C. H. Yutsudo,, S. Kimura,, K. Kurokawa,, K. Ishii,, M. Hattori,, I. Tatsuno,, H. Abe,, T. Iida,, K. Yamamoto,, M. Onishi,, T. Hayashi,, T. Yasunaga,, T. Honda,, C. Sasakawa,, and H. Shinagawa. 1999. Complete nucleotide sequence of the prophage VT2- Sakai carrying the verotoxin 2 genes of the enterohemorrhagic Escherichia coli O157:H7 derived from the Sakai outbreak. Genes Genet. Syst. 74:227239.
136. Young, B.,, Y. Fukazawa,, and P. Hartman. 1964. A P22 bacteriophage mutant defective in antigen conversion. Virology 23:279283.
137. Zink, R.,, M. J. Loessner,, and S. Scherer. 1995. Characterization of cryptic prophages (monocins) in Listeria and sequence analysis of a holin/endolysin gene. Microbiology 141:25772584.

Tables

Generic image for table
Table 1.

Prophages in some completely sequenced bacterial genomes

Citation: Casjens S, Hendrix R. 2005. Bacteriophages and the Bacterial Genome, p 39-52. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch3
Generic image for table
Table 2.

Some bacteriophages with genes that affect the interaction of pathogenic bacteria with their eukaryote hosts

Citation: Casjens S, Hendrix R. 2005. Bacteriophages and the Bacterial Genome, p 39-52. In Higgins N (ed), The Bacterial Chromosome. ASM Press, Washington, DC. doi: 10.1128/9781555817640.ch3

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