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Chapter 29 : A Plethora of Putative Phages and Prophages

Author: Sherwood R. Casjens1
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Affiliations: 1: Pathology Department, University of Utah, Salt Lake City, UT 84112
Content Type: Monograph
Publication Year: 2011

Category: History of Science; Microbial Genetics and Molecular Biology

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Abstract:

Several facts enticed the author to look beyond for undocumented prophages in other bacterial genome sequences. At the beginning the author was very uncertain about whether there would be any interest in prophages or, on the other hand, whether the prophage abundance he was finding was considered to already be known and thus boring. In addition to fully intact prophages, many bacterial genomes harbor "defective" prophages that have suffered deletions of genes essential for full phage functionality. The prophages, whose genomic locations are shown in this chapter, are in fact very instructive cases. A curious observation regarding the prophages is that the genome-wide screen of Lawley and others for genes that are required for long-term systemic infection of the mouse was answered by mutations in (among many others) genes that encode virion assembly proteins in five of the above prophages. The remaining possibly phage-related genes in the LT2 chromosome consist of a few other fragmentary integrase-like sequences and phage lysis-like genes. These could be the remains of otherwise essentially completely deleted prophages, but the former could also be from other types of mobile elements. Another interesting feature that emerged from early prophage surveys was the fact that different isolates of the same bacterial species often have quite different prophage contents, indicating that prophages are coming and going rather quickly on the overall evolutionary scale.

Citation: Casjens S. 2011. A Plethora of Putative Phages and Prophages, p 291-306. In Maloy S, Hughes K, Casadesús J (ed), The Lure of Bacterial Genetics. ASM Press, Washington, DC. doi: 10.1128/9781555816810.ch29

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A Plethora of Putative Phages and Prophages
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Citation: Casjens S. 2011. A Plethora of Putative Phages and Prophages, p 291-306. In Maloy S, Hughes K, Casadesús J (ed), The Lure of Bacterial Genetics. ASM Press, Washington, DC. doi: 10.1128/9781555816810.ch29
/content/10.1128/9781555816810.ch29.ch29fig01
FIGURE 1
Prophages in the serovar Typhimurium LT2 chromosome. The LT2 chromosome is represented by the circle and the prophages are shown as expanded regions on the outside; Def1–4 are the four defective prophages. Gene locus tag names are given on the outside for the genes at each end of the prophage elements. A scale in mbp is shown by ticks that cross the circle. Ticks inside the circle denote the prophage end adjacent to the integrase gene (if this gene is present), and the native gene into which the prophage integrated is given inside the circle.
10.1128/9781555816810/f0295-01_thmb.gif
10.1128/9781555816810/f0295-01.gif
Image of FIGURE 1
FIGURE 1

Prophages in the serovar Typhimurium LT2 chromosome. The LT2 chromosome is represented by the circle and the prophages are shown as expanded regions on the outside; Def1–4 are the four defective prophages. Gene locus tag names are given on the outside for the genes at each end of the prophage elements. A scale in mbp is shown by ticks that cross the circle. Ticks inside the circle denote the prophage end adjacent to the integrase gene (if this gene is present), and the native gene into which the prophage integrated is given inside the circle.

Citation: Casjens S. 2011. A Plethora of Putative Phages and Prophages, p 291-306. In Maloy S, Hughes K, Casadesús J (ed), The Lure of Bacterial Genetics. ASM Press, Washington, DC. doi: 10.1128/9781555816810.ch29
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/content/10.1128/9781555816810.ch29.ch29fig02
FIGURE 2
Gifsy-1 prophage excision. The Gifsy-1 prophage is shown as an open rounded rectangle with the identical sequences at the two ends of the prophage aligned vertically at the bottom (only one strand, 5’ to 3’ left to right, is shown). Translation (of the strand not shown) is right to left of the gene below and the putative orphan N-terminal fragment above (the translated regions are shown in bold). Two regions of identity between the two prophage ends (14 bp on the left and 13 bp on the right) are indicated by thin horizontal lines between the two sequences. Excisive and integrative recombination has been reported to occur between the left 14-bp regions which is the site ( ); such a recombination event during integration or excision regenerates an intact gene that encodes a protein with unchanged amino acid sequence.
10.1128/9781555816810/f0296-01_thmb.gif
10.1128/9781555816810/f0296-01.gif
Image of FIGURE 2
FIGURE 2

Gifsy-1 prophage excision. The Gifsy-1 prophage is shown as an open rounded rectangle with the identical sequences at the two ends of the prophage aligned vertically at the bottom (only one strand, 5’ to 3’ left to right, is shown). Translation (of the strand not shown) is right to left of the gene below and the putative orphan N-terminal fragment above (the translated regions are shown in bold). Two regions of identity between the two prophage ends (14 bp on the left and 13 bp on the right) are indicated by thin horizontal lines between the two sequences. Excisive and integrative recombination has been reported to occur between the left 14-bp regions which is the site ( ); such a recombination event during integration or excision regenerates an intact gene that encodes a protein with unchanged amino acid sequence.

Citation: Casjens S. 2011. A Plethora of Putative Phages and Prophages, p 291-306. In Maloy S, Hughes K, Casadesús J (ed), The Lure of Bacterial Genetics. ASM Press, Washington, DC. doi: 10.1128/9781555816810.ch29
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FIGURE 3
Comparison of serovar Typhimurium LT2 and serovar Choleraesuis SC-67 Gifsy-2 prophages. The matrix comparison was performed with DNA Strider ( ) using a scanning window of 17 identities per 23 bp. Above, the phage lambda-like transcription pattern of Gifsy-2 is shown along with the locations of some of the gene clusters.
10.1128/9781555816810/f0300-01_thmb.gif
10.1128/9781555816810/f0300-01.gif
Image of FIGURE 3
FIGURE 3

Comparison of serovar Typhimurium LT2 and serovar Choleraesuis SC-67 Gifsy-2 prophages. The matrix comparison was performed with DNA Strider ( ) using a scanning window of 17 identities per 23 bp. Above, the phage lambda-like transcription pattern of Gifsy-2 is shown along with the locations of some of the gene clusters.

Citation: Casjens S. 2011. A Plethora of Putative Phages and Prophages, p 291-306. In Maloy S, Hughes K, Casadesús J (ed), The Lure of Bacterial Genetics. ASM Press, Washington, DC. doi: 10.1128/9781555816810.ch29
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References

/content/book/10.1128/9781555816810.ch29
1. Ammendola, S.,, P. Pasquali,, F. Pacello,, G. Rotilio,, M. Castor,, S. J. Libby,, N. Figueroa-Bossi,, L. Bossi,, F. C. Fang, and, A. Battistoni. 2008. Regulatory and structural differences in the Cu, Zn-superoxide dismutases of Salmonella enterica and their significance for virulence.J. Biol. Chem. 283: 13688– 13699.
2. Andrews-Polymenis, H. L.,, W. Rabsch,, S. Porwollik,, M. McClelland,, C. Rosetti,, L. G. Adams, and, A. J. Baumler. 2004. Host restriction of Salmonella enterica serotype Typhimurium pigeon isolates does not correlate with loss of discrete genes.J. Bacteriol. 186: 2619– 2628.
3. Bacciu, D.,, G. Falchi,, A. Spazziani,, L. Bossi,, G. Marogna,, G. S. Leori,, S. Rubino, and, S. Uzzau. 2004. Transposition of the heat-stable toxin astA gene into a gifsy-2-related prophage of Salmonella enterica serovar Abortusovis. J. Bacteriol. 186: 4568– 4574.
4. 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: 515– 521.
5. Bezdek, M., and, P. Amati. 1967. Properties of P22 and A related Salmonella typhimurium phage. I. General features and host specificity. Virology 31: 272– 278.
6. Blattner, F. R.,, G. Plunkett III,, C. A. Bloch,, N. T. Perna,, V. Burland,, M. Riley,, J. Collado-Vides,, J. D. Glasner,, C. K. Rode,, G. F. Mayhew,, J. Gregor,, N. W. Davis,, H. A. Kirkpatrick,, M. A. Goeden,, D. J. Rose,, B. Mau, and, Y. Shao. 1997. The complete genome sequence of Escherichia coli K-12. Science 277: 1453– 1474.
7. Bogomolnaya, L. M.,, C. A. Santiviago,, H. J. Yang,, A. J. Baumler, and, H. L. Andrews-Polymenis. 2008. ‘Form variation’ of the O12 antigen is critical for persistence of Salmonella typhimurium in the murine intestine. Mol. Microbiol. 70: 1105– 1119.
8. Bose, M., and, R. D. Barber. 2006. Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences. In Silico Biol. 6: 223– 227.
9. Boyd, E. F., and, H. Brussow. 2002. Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved. Trends Microbiol. 10: 521– 529.
10. Brandt, K.,, A. Tilsala-Timisjarvi, and, T. Alatossava. 2001. Phage-related DNA polymorphism in dairy and probiotic Lactobacillus. Micron 32: 59– 65.
11. Brussow, H.,, C. Canchaya, and, W. D. Hardt. 2004. Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion. Microbiol. Mol. Biol. Rev. 68: 560– 602.
12. Bunny, K.,, J. Liu, and, J. Roth. 2002. Phenotypes of lexA mutations in Salmonella enterica: evidence for a lethal lexA null phenotype due to the Fels-2 prophage. J. Bacteriol. 184: 6235– 6249.
13. Campbell, A. 1962. The episomes. Advan. Genet. 11: 101– 118.
14. Canchaya, C.,, C. Proux,, G. Fournous,, A. Bruttin, and, H. Brussow. 2003. Prophage genomics. Microbiol. Mol. Biol. Rev. 67: 238– 276.
15. Casjens, S. 2000. Borrelia genomes in the year 2000. J. Mol. Microbiol. Biotechnol. 2: 401– 410.
16. Casjens, S. 2003. Prophages in bacterial genomics: what have we learned so far? Molec. Microbiol. 249: 277– 300.
17. Casjens, S.,, C. H. Eggers, and, I. Schwartz. 2010. Borrelia genomics: chromosome, plasmids, bacteriophages and genetic variation. In D. S. Samuels and, J. Radolf (ed.), Borrelia: Molecular and Cellular Biology. Caister Academic Press, Norfolk, United Kingdom.
18. Casjens, S.,, G. Hatfull, and, R. Hendrix. 1992. Evolution of dsDNA tailed-bacteriophage genomes. Semin. Virol. 3: 383– 397.
19. Casjens, S., and, R. Hendrix. 2005. Bacteriophage roles in bacterial chromosome evolution, p. 39– 52. In P. Higgins (ed.), The Bacterial Chromosome. ASM Press, Washington, DC.
20. 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: 490– 516.
21. Casjens, S.,, R. van Vugt,, K. Tilly,, P. A. Rosa, and, B. Stevenson. 1997. Homology throughout the multiple 32-kilobase circular plasmids present in Lyme disease spirochetes. J. Bacteriol. 179: 217– 227.
22. Casjens, S. R. 2005. Comparative genomics and evolution of the tailed-bacteriophages. Curr. Opin. Microbiol. 8: 451– 458.
23. Casjens, S. R. 2008. Diversity among the tailed-bacteriophages that infect the Enterobacteriaceae. Res. Microbiol. 159: 340– 348.
24. Casjens, S. R.,, E. B. Gilcrease,, D. A. Winn-Stapley,, P. Schicklmaier,, H. Schmieger,, M. L. Pedulla,, M. E. Ford,, J. M. Houtz,, G. F. Hatfull, and, R. W. Hendrix. 2005. The generalized transducing Salmonella bacteriophage ES18: complete genome sequence and DNA packaging strategy. J. Bacteriol. 187: 1091– 1104.
25. Cheetham, B. F., and, M. E. Katz. 1995. A role for bacteriophages in the evolution and transfer of bacterial virulence determinants. Mol. Microbiol. 18: 201– 208.
26. Cooke, F. J.,, J. Wain,, M. Fookes,, A. Ivens,, N. Thomson,, D. J. Brown,, E. J. Threlfall,, G. Gunn,, G. Foster, and, G. Dougan. 2007. Prophage sequences defining hot spots of genome variation in Salmonella enterica serovar Typhimurium can be used to discriminate between field isolates.J. Clin. Microbiol. 45: 2590– 2598.
27. Coombes, B. K.,, M. E. Wickham,, N. F. Brown,, S. Lemire, L. Bossi,, W. W. Hsiao,, F. S. Brinkman, and, B. B. Finlay. 2005. Genetic and molecular analysis of GogB, a phage-encoded type III-secreted substrate in Salmonella enterica serovar Typhimurium with autonomous expression from its associated phage.J. Mol. Biol. 348: 817– 830.
28. da Silva, A. C.,, J. A. Ferro,, F. C. Reinach,, C. S. Farah,, L. R. Furlan,, R. B. Quaggio,, C. B. Monteiro-Vitorello,, M. A. Van Sluys,, N. F. Almeida,, L. M. Alves,, A. M. do Amaral,, M. C. Bertolini,, L. E. Camargo,, G. Camarotte,, F. Cannavan,, J. Cardozo,, F. Chambergo,, L. P. Ciapina,, R. M. Cicarelli,, L. L. Coutinho,, J. R. Cursino-Santos,, H. El-Dorry,, J. B. Faria,, A. J. Ferreira,, R. C. Ferreira,, M. I. Ferro,, E. F. Formighieri,, M. C. Franco,, C. C. Greggio,, A. Gruber,, A. M. Katsuyama,, L. T. Kishi,, R. P. Leite,, E. G. Lemos,, M. V. Lemos,, E. C. Locali,, M. A. Machado,, A. M. Madeira,, N. M. Martinez-Rossi,, E. C. Martins,, J. Meidanis,, C. F. Menck,, C. Y. Miyaki,, D. H. Moon,, L. M. Moreira,, M. T. Novo,, V. K. Okura,, M. C. Oliveira,, V. R. Oliveira,, H. A. Pereira,, A. Rossi,, J. A. Sena,, C. Silva,, R. F. de Souza,, L. A. Spinola,, M. A. Takita,, R. E. Tamura,, E. C. Teixeira,, R. I. Tezza,, M. Trindade dos Santos,, D. Truffi,, S. M. Tsai,, F. F. White,, J. C. Setubal, and, J. P. Kitajima. 2002. Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417: 459– 463.
29. Deleu, S.,, K. Choi,, J. M. Reece, and, S. B. Shears. 2006. Pathogenicity of Salmonella: SopE-mediated membrane ruffling is independent of inositol phosphate signals. FEBS Lett. 580: 1709– 1715.
30. Dep, M. S.,, G. L. Mendz,, M. A. Trend,, P. J. Coloe,, B. N. Fry, and, V. Korolik. 2001. Differentiation between Campylobacter hyoilei and Campylocbater coli using genotypic and phenotypic analyses. Int.J. Syst. Evol. Microbiol. 51: 819– 826.
31. Douglas, S. E. 1994. DNA Strider. A Macintosh program for handling protein and nucleic acid sequences. Methods Mol. Biol. 25: 181– 194.
32. Drahovska, H.,, E. Mikasova,, T. Szemes,, A. Ficek,, M. Sasik,, V. Majtan, and, J. Turna. 2007. Variability in occurrence of multiple prophage genes in Salmonella typhimurium strains isolated in Slovak Republic. FEMS Microbiol. Lett. 270: 237– 244.
33. Eggers, C. H.,, S. Casjens, and, D. S. Samuels. 2001. Bacteriophages of Borrelia burgdorferi and other spirochetes, p. 35– 44. In M. Saier and, J. Gar-cia-Lara (ed.), The Spirochetes. Molecular and Cellular Biology. Horizon Scientific Press, Wiltshire, United Kingdom.
34. Eggers, C. H.,, B. J. Kimmel,, J. L. Bono,, A. F. Elias,, P. Rosa, and, D. S. Samuels. 2001. Transduction by ϕBB–1, a bacteriophage of Borrelia burgdorferi. J. Bacteriol. 183: 4771– 4778.
35. Eggers, C. H., and, D. S. Samuels. 1999. Molecular evidence for a new bacteriophage of Borrelia burgdorferi. J. Bacteriol. 181: 7308– 7313.
36. Ehrbar, K., and, W. D. Hardt. 2005. Bacterio-phage-encoded type III effectors in Salmonella enterica subspecies 1 serovar Typhimurium. Infect. Genet. Evol. 5: 1– 9.
37. Emmerth, M.,, W. Goebel,, S. I. Miller, and, C. J. Hueck. 1999. Genomic subtraction identifies Salmonella typhimurium prophages, F-related plasmid sequences, and a novel fimbrial operon, stf which are absent in Salmonella typhi. J. Bacteriol. 181: 5652– 5661.
38. Figueroa-Bossi, N., and, L. Bossi. 1999. Inducible prophages contribute to Salmonella virulence in mice. Mol. Microbiol. 33: 167– 176.
39. Figueroa-Bossi, N.,, E. Coissac,, P. Netter, and, L. Bossi. 1997. Unsuspected prophage-like elements in Salmonella typhimurium. Molec. Microbiol. 25: 161– 173.
40. 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: 260– 271.
41. Flanigan, A., and, J. F. Gardner. 2007. Interaction of the Gifsy-1 Xis protein with the Gifsy-1 attP sequence. J. Bacteriol. 189: 6303– 6311.
42. Fouts, D. E. 2006. Phage Finder: automated identification and classification of prophage regions in complete bacterial genome sequences. Nucleic Acids Res. 34: 5839– 5851.
43. Fraser, C. M.,, S. Casjens,, W. M. Huang,, G. G. Sutton,, R. Clayton,, R. Lathigra,, O. White,, K. A. Ketchum,, R. Dodson,, E. K. Hickey,, M. Gwinn,, B. Dougherty,, J. F. Tomb,, R. D. Fleischmann,, D. Richardson,, J. Peterson,, A. R. Kerlavage,, J. Quackenbush,, S. Salzberg,, M. Hanson,, R. van Vugt,, N. Palmer,, M. D. Adams,, J. Gocayne, and, J. C. Venter. 1997. Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390: 580– 586.
44. Freeman, V. 1951. Studies on the virulence of bacteriophage-infected strains of Corynebacterium diphtheriae. J. Bacteriol. 61: 675– 688.
45. Fukazawa, Y., and, P. Hartman. 1964. A P22 bacteriophage mutant defective in antigenic conversion. Virology 23: 279– 283.
46. Gunn, J. S.,, C. M. Alpuche-Aranda,, W. P. Loomis,, W. J. Belden, and, S. I. Miller. 1995. Characterization of the Salmonella typhimurium pagC/pagD chromosomal region. J. Bacteriol. 177: 5040– 5047.
47. Hardt, W. D.,, H. Urlaub, and, J. E. Galan. 1998. A substrate of the centisome 63 type III protein secretion system of Salmonella typhimurium is encoded by a cryptic bacteriophage. Proc. Natl. Acad. Sci. USA 95: 2574– 2579.
48. Hayashi, T.,, K. Makino,, M. Ohnishi,, K. Kuro-kawa,, 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: 11– 22.
49. Hendrix, R., and, S. Casjens. 2006. Bacteriophage λ and its genetic neighborhood, p. 409– 447. In R. Calendar (ed.), The Bacteriophages, 2nd ed. Oxford Press, New York City, NY.
50. Hendrix, R., and, S. Casjens. 2008. Role of bacteriophages in the generation and spread of bacterial pathogens, p. 79– 112. In M. Hensel and, H. Schmidt (ed.), Advances in Molecular and Cellular Microbiology, vol. 16. Horizontal Gene Transfer in the Evolution of Pathogenesis. Cambridge University Press, Cambridge, United Kingdom.
51. Hendrix, R. W. 2002. Bacteriophages: evolution of the majority. Theor. Popul. Biol. 61: 471– 480.
52. Hendrix, R. W.,, J. G. Lawrence,, G. F. Hatfull, and, S. Casjens. 2000. The origins and ongoing evolution of viruses. Trends Microbiol. 8: 504– 508.
53. Hensel, M. 2004. Evolution of pathogenicity islands of Salmonella enterica. Int. J. Med. Microbiol. 294: 95– 102.
54. Hermans, A. P.,, T. Abee,, M. H. Zwietering, and, H J. Aarts. 2005. Identification of novel Salmonella enterica serovar Typhimurium DT104-specific prophage and nonprophage chromosomal sequences among serovar Typhimurium isolates by genomic subtractive hybridization. Appl. Environ. Microbiol. 71: 4979– 4985.
55. Hermans, A. P.,, A. M. Beuling,, A. H. van Hoek,, H. J. Aarts,, T. Abee, and, M. H. Zwietering. 2006. Distribution of prophages and SGI-1 antibiotic-resistance genes among different Salmonella enterica serovar Typhimurium isolates. Microbiology 152: 2137– 2147.
56. Ho, T. D.,, N. Figueroa-Bossi,, M. Wang,, S. Uzzau,, L. Bossi, and, J. M. Slauch. 2002. Identification of GtgE, a novel virulence factor encoded on the Gifsy-2 bacteriophage of Salmonella enterica serovar Typhimurium. J. Bacteriol. 184: 5234– 5239.
57. Hoyer, L. L.,, A. C. Hamilton,, S. M. Steen-bergen, and, E. R. Vimr. 1992. Cloning, sequencing and distribution of the Salmonella typhimurium LT2 sialidase gene, nanH, provides evidence for interspecies gene transfer. Mol. Microbiol. 6: 873– 884.
58. Jones, B. D., and, S. Falkow. 1994. Identification and characterization of a Salmonella typhimurium oxygen-regulated gene required for bacterial internalization. Infect. Immun. 62: 3745– 3752.
59. 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: 27– 51.
60. Kang, M. S.,, T. E. Besser,, D. D. Hancock,, S. Porwollik,, M. McClelland, and, D. R. Call. 2006. Identification of specific gene sequences conserved in contemporary epidemic strains of Salmonella enterica. Appl. Environ. Microbiol. 72: 6938– 6947.
61. Klee, S. R.,, X. Nassif,, B. Kusecek,, P. Merker,, J. L. Beretti,, M. Achtman, and, C R. Tinsley. 2000. Molecular and biological analysis of eight genetic islands that distinguish Neisseria meningitidis from the closely related pathogen Neisseria gonorrhoeae. Infect. Immun. 68: 2082– 2095.
62. Kropinski, A. M.,, I. V. Kovalyova,, S. J. Billington,, A. N. Patrick,, B. D. Butts,, J. A. Guichard,, T. J. Pitcher,, C. C. Guthrie,, A. D. Sydlaske,, L. M. Barnhill,, K. A. Havens,, K. R. Day,, D. R. Falk, and, M. R. McConnell. 2007. The genome of epsilon15, a serotype-converting, Group E1 Salmonella enterica-specific bacteriophage. Virology 369: 234– 244.
63. Kutsukake, K.,, H. Nakashima,, A. Tominaga, and, T. Abo. 2006. Two DNA invertases contribute to flagellar phase variation in Salmonella enterica serovar Typhimurium strain LT2. J. Bacteriol. 188: 950– 957.
64. Lawley, T. D.,, K. Chan,, L. J. Thompson,, C. C. Kim,, G. R. Govoni, and, D. M. Monack. 2006. Genome-wide screen for Salmonella genes required for long-term systemic infection of the mouse. PLoS Pathog. 2: e11.
65. Lima-Mendez, G.,, J. Van Helden,, A. Toussaint, and, R. Leplae. 2008. Prophinder: a computational tool for prophage prediction in prokaryotic genomes. Bioinformatics 24: 863– 865.
66. Lwoff, A. 1953. Lysogeny. Bacteriol. Rev. 17: 269– 337.
67. Lwoff, A. 1966. The prophage and I, p. 88– 99. In J. Cairns,, G. Stent, and, J. Watson (ed.), Phage and the Origins of Molecular Biology. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
68. McClelland, M.,, K. E. Sanderson,, J. Spieth,, S. W. Clifton,, P. Latreille,, L. Courtney,, S. Porwollik,, J. Ali,, M. Dante,, F. Du,, S. Hou,, D. Layman,, S. Leonard,, C. Nguyen,, K. Scott,, A. Holmes,, N. Grewal,, E. Mulvaney,, E. Ryan,, H. Sun,, L. Florea,, W. Miller,, T. Stoneking,, M. Nhan,, R. Waterston, and, R. K. Wilson. 2001. Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413: 852– 856.
69. Miao, E. A.,, M. Brittnacher,, A. Haraga,, R. L. Jeng,, M. D. Welch, and, S. I. Miller. 2003. Salmonella effectors translocated across the vacuolar membrane interact with the actin cytoskeleton. Mol. Microbiol. 48: 401– 415.
70. 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: 9845– 9850.
71. Mmolawa, P. T.,, H. Schmieger, and, M. W. Heuzenroeder. 2003. Bacteriophage ST64B, a genetic mosaic of genes from diverse sources isolated from Salmonella enterica serovar Typhimurium DT 64. J. Bacteriol. 185: 6481– 6485.
72. Mmolawa, P. T.,, H. Schmieger,, C. P. Tucker, and, M. W. Heuzenroeder. 2003. Genomic structure of the Salmonella enterica serovar Typhimurium DT 64 bacteriophage ST64T: evidence for modular genetic architecture. J. Bacteriol. 185: 3473– 3475.
73. Mukherjee, K.,, S. Parashuraman,, M. Raje, and, A. Mukhopadhyay. 2001. SopE acts as an Rab5-specific nucleotide exchange factor and recruits non-prenylated Rab5 on Salmonella-containing phagosomes to promote fusion with early endosomes.J. Biol. Chem. 276: 23607– 23615.
74. Nelson, K. E.,, C. Weinel,, I. T. Paulsen,, R. J. Dodson,, H. Hilbert,, V. A. Martins dos Santos,, D. E. Fouts,, S. R. Gill,, M. Pop,, M. Holmes,, L. Brinkac,, M. Beanan,, R. T. DeBoy,, S. Daugherty,, J. Kolonay,, R. Madupu,, W. Nelson,, O. White,, J. Peterson,, H. Khouri,, I. Hance,, P. Chris Lee,, E. Holtzapple,, D. Scanlan,, K. Tran,, A. Moazzez,, T. Utter-back,, M. Rizzo,, K. Lee,, D. Kosack,, D. Moestl,, H. Wedler,, J. Lauber,, D. Stjepandic,, J. Hoheisel,, M. Straetz,, S. Heim,, C. Kiewitz,, J. Eisen,, K. N. Timmis,, A. Dusterhoft,, B. Tummler, and, C. M. Fraser. 2002. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ. Microbiol. 4: 799– 808.
75. O’Brien, A. D.,, J. W. Newland,, S. F. Miller,, R. K. Holmes,, H. W. Smith, and, S. B. Formal. 1984. Shiga-like toxin-converting phages from Escherichia coli strains that cause hemorrhagic colitis or infantile diarrhea. Science 226: 694– 696.
76. Patel, J. C., and, J. E. Galan. 2006. Differential activation and function of Rho GTPases during Salmonella-host cell interactions. J. Cell Biol. 175: 453– 463.
77. Pedulla, M. L.,, M. E. Ford,, T. Karthikeyan,, J. M. Houtz,, R. W. Hendrix,, G. F. Hatfull,, A. R. Poteete,, E. B. Gilcrease,, D. A. Winn-Stapley, and, S. R. Casjens. 2003. Corrected sequence of the bacteriophage P22 genome. J. Bacteriol. 185: 1475– 1477.
78. Pelludat, C.,, S. Mirold, and, W. D. Hardt. 2003. The SopEϕ phage integrates into the ssrA gene of Salmonella enterica serovar Typhimurium A36 and is closely related to the Fels-2 prophage. J. Bacteriol. 185: 5182– 5191.
79. Perna, N.,, J. Glasner,, V. Burland, and, G. Plunkett III. 2002. The genomes of Esche-richia coli K-12 and pathogenic E. coli, p. 3– 53. In M. Donnenberg (ed.), Escherichia coli: Virulence Mechanisms of a Versatile Pathogen. Academic Press, San Diego, CA.
80. 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 entero-haemorrhagic Escherichia coli O157:H7. Nature 409: 529– 533.
81. Porwollik, S.,, R. M. Wong,, R. A. Helm,, K. K. Edwards,, M. Calcutt,, A. Eisenstark, and, M. McClelland. 2004. DNA amplification and rearrangements in archival Salmonella enterica serovar Typhimurium LT2 cultures. J. Bacteriol. 186: 1678– 1682.
82. Reen, F. J.,, E. F. Boyd,, S. Porwollik,, B. P. Murphy,, D. Gilroy,, S. Fanning, and, M. McClelland. 2005. Genomic comparisons of Salmonella enterica serovar Dublin, Agona, and Typhimurium strains recently isolated from milk filters and bovine samples from Ireland, using a Salmonella microarray. Appl. Environ. Microbiol. 71: 1616– 1625.
83. Rychlik, I.,, H. Hradecka, and, M. Malcova. 2008. Salmonella enterica serovar Typhimurium typing by prophage-specific PCR. Microbiology 154: 1384– 1389.
84. 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: 49– 54.
85. 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,, A. J. de M. Rosa,, 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,, M. L. Z. Silvestri,, W. J. Siqueira,, A. A. de Souza,, A. P. de Souza,, M. F. Terenzi,, D. Truffi,, S. M. Tsai,, M. H. Tsuhako,, H. Vallada,, M. A. Van Sluys,, S. Verjovski-Almeida,, A. L. Vettore,, M. A. Zago,, M. Zatz,, J. Meidanis and, J. C. Setubal. 2000. The genome sequence of the plant pathogen Xylella fastidiosa. Nature 406: 151– 157.
86. Slauch, J. M.,, A. A. Lee,, M. J. Mahan, and, J. J. Mekalanos. 1996. Molecular characterization of the oafA locus responsible for acetylation of Salmonella typhimurium O-antigen: oafA is a member of a family of integral membrane trans-acylases. J. Bacteriol. 178: 5904– 5909.
87. Smith, H. W.,, P. Green, and, Z. Parsell. 1983. Vero cell toxins in Escherichia coli and related bacteria: transfer by phage and conjugation and toxic action in laboratory animals, chickens and pigs. J. Gen. Microbiol. 129: 3121– 3137.
88. Srividhya, K. V.,, V. Alaguraj,, G. Poornima,, D. Kumar,, G. P. Singh,, L. Raghavenderan,, A. V. Katta,, P. Mehta, and, S. Krishnaswamy. 2007. Identification of prophages in bacterial genomes by dinucleotide relative abundance difference. PLoS One 2: e1193.
89. Stanley, E.,, G. F. Fitzgerald,, C. Le Marrec,, B. Fayard, and, D. van Sinderen. 1997. Sequence analysis and characterization of ϕO1205, a temperate bacteriophage infecting Streptococcus thermophilus CNRZ1205. Microbiology 143: 3417– 3429.
90. Stanley, T. L.,, C. D. Ellermeier, and, J. M. Slauch. 2000. Tissue-specific gene expression identifies a gene in the lysogenic phage Gifsy-1 that affects Salmonella enterica serovar Typhimurium survival in Peyer’s patches. J. Bacteriol. 182: 4406– 4413.
91. Tanaka, K.,, K. Nishimori,, S. Makino,, T. Nishimori,, T. Kanno,, R. Ishihara,, T. Sameshima,, M. Akiba,, M. Nakazawa,, Y. Yokomizo, and, I. Uchida. 2004. Molecular characterization of a prophage of Salmonella enterica serotype Typhimurium DT104. J. Clin. Microbiol. 42: 1807– 1812.
92. Thomson, N.,, S. Baker,, D. Pickard,, M. Fookes,, M. Anjum,, N. Hamlin,, J. Wain,, D. House,, Z. Bhutta,, K. Chan,, S. Falkow,, J. Parkhill,, M. Woodward,, A. Ivens, and, G. Dougan. 2004. The role of prophage-like elements in the diversity of Salmonella enterica serovars. J. Mol. Biol. 339: 279– 300.
93. Vander Byl, C., and, A. M. Kropinski. 2000. Sequence of the genome of Salmonella bacterio-phage P22. J. Bacteriol. 182: 6472– 6481.
94. Vernikos, G. S., and, J. Parkhill. 2006. Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics 22: 2196– 2203.
95. Villafane, R.,, M. Zayas,, E. B. Gilcrease,, A. M. Kropinski, and, S. R. Casjens. 2008. Genomic analysis of bacteriophage ∈ 34 of Salmonella enterica serovar Anatum (15+). BMC Microbiol. 8: 227.
96. Weintraub, A.,, B. N. Johnson,, B. A. Stocker, and, A. A. Lindberg. 1992. Structural and immunochemical studies of the lipopolysaccha-rides of Salmonella strains with both antigen O4 and antigen 09.J. Bacteriol. 174: 1916– 1922.
97. Worley, M. J.,, K. H. Ching, and, F. Heffron. 2000. Salmonella SsrB activates a global regulon of horizontally acquired genes. Mol. Microbiol. 36: 749– 761.
98. Yamamoto, N. 1969. Genetic evolution of bacteriophage. I. Hybrids between unrelated bacteriophages P22 and Fels 2. Proc. Natl. Acad. Sci. USA 62: 63– 69.
99. Yamamoto, N. 1978. Somatic 0-1 antigen conversion of Salmonella typhimurium by a type B phage P221dis, hybrid between P22 and Fels 1 phages.J. Gen. Virol. 41: 367– 376.
100. Zhang, H., and, R. T. Marconi. 2005. Demonstration of cotranscription and 1-methyl-3-nitroso-nitroguanidine induction of a 30-gene operon of Borrelia burgdorferi: evidence that the 32-kilobase circular plasmids are prophages. J. Bacteriol. 187: 7985– 7995.

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