Prophage genomics

Microbiology and Molecular Biology Reviews

Volumn 67, Issue 2, 2003, Pages 238-276

  Canchaya, Carlos ^a   Proux, Caroline ^a   Fournous, Ghislain ^a   Bruttin, Anne ^a   Brüssow, Harald ^a  

^a NESTLÉ RESEARCH CENTER   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENOME; GENE DELETION; GENE REARRANGEMENT; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POINT MUTATION; PROPHAGE; REVIEW; STREPTOCOCCUS PYOGENES;

ACTINOBACTERIA; ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; GAMMAPROTEOBACTERIA; GENOME, BACTERIAL; GENOMICS; HUMANS; MOLECULAR SEQUENCE DATA; PLANTS; PROPHAGES;

ACTINOBACTERIA (CLASS); ANIMALIA; BACTERIA (MICROORGANISMS); FIRMICUTES; GAMMAPROTEOBACTERIA; NEGIBACTERIA; POSIBACTERIA; PROTEOBACTERIA; STREPTOCOCCUS PYOGENES;

EID: 0038724281     PISSN: 10922172     EISSN: None     Source Type: Journal    
DOI: 10.1128/MMBR.67.2.238-276.2003     Document Type: Review

References (235)

1. Ackermann, H. W. 1998. Tailed bacteriophages: the order caudovirales. Adv. Virus Res. 51:135-201.
2. Akman, L., A. Yamashita, H. Watanabe, K. Oshima, T. Shiba, M. Hattori, and S. Aksoy. 2002. Genome sequence of the endocellular obligate symbiont of tsetse flies, Wigglesworthia glossinidia. Nat. Genet. 32:402-407.
3. Allison, G. E., D. Angeles, N. Tran-Dinh, and N. K. Verma. 2002. Complete genomic sequence of SfV, a serotype-converting temperate bacteriophage of Shigella flexneri. J. Bacteriol. 184:1974-1987.
4. Auvray, F., M. Coddeville, R. C. Ordonez, and P. Ritzenthaler. 1999. Unusual structure of the auB site of the site-specific recombination system of Lactobacillus delbrueckii bacteriophage mv4. J. Bacteriol. 181:7385-7389.
5. Auvray, F., M. Coddeville, P. Ritzenthaler, and L. Dupont. 1997. Plasmid integration in a wide range of bacteria mediated by the integrase of Lactobacillus delbrueckii bacteriophage mv4. J. Bacteriol. 179:1837-1845.
6. Ayora, S., R. Missich, P. Mesa, R. Lurz, S. Yang, E. H. Egelman, and J. C. Alonso. 2002. Homologous-pairing activity of the Bacillus subtilis bacteriophage SPP1 replication protein G35P. J. Biol. Chem. 277:35969-35979.
7. Baba, T., F. Takeuchi, M. Kuroda, H. Yuzawa, K. Aoki, A. Oguchi, Y. Nagai, N. Iwama, K. Asano, T. Naimi, H. Kuroda, L. Cui, K. Yamamoto, and K. Hiramatsu. 2002. Genome and virulence determinants of high virulence community-acquired MRSA. Lancet 359:1819-1827.
8. 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.
9. Barondess, J. J., and J. Beckwith. 1990. A bacterial virulence determinant encoded by lysogenic coliphage lambda. Nature 346:871-874.
10. 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. 177:1247-1253.
11. Bensing, B. A., I. R. Siboo, and P. M. Sullam. 2001. Proteins Pb1A and Pb1B of Streptococcus mitis, which promote binding to human platelets, are encoded within a lysogenic bacteriophage. Infect. Immun. 69:6186-6192.
12. Bentley, S. D., K. F. Chater, A. M. Cerdeno-Tarraga, G. L. Challis, N. R. Thomson, K. D. James, D. E. Harris, M. A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C. W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, S. Howarth, C. H. Huang, T. Kieser, L. Larke, L. Murphy, K. Oliver, S. O'Neil, E. Rabbinowitsch, M. A. Rajandream, K. Rutherford, S. Rutter, K. Seeger, D. Saunders, S. Sharp, R. Squares, S. Squares, K. Taylor, T. Warren, A. Wietzorrek, J. Woodward, B. G. Barrell, J. Parkhill, and D. A. Hopwood. 2002. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141-147.
13. 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 99:10078-10083.
14. Betley, M. J., and J. J. Mekalanos. 1985. Staphylococcal enterotoxin A is encoded by phage. Science 229:185-187.
15. Bhattacharyya, A., S. Stilwagen, N. Ivanova, M. D'Souza, A. Bernal, A. Lykidis, V. Kapatral, I. Anderson, N. Larsen, T. Los, G. Reznik, Selkov E Jr, T. L. Walunas, H. Feil, W. S. Feil, A. Purcell, J. L. Lassez, T. L. Hawkins, R. Haselkorn, R. Overbeek, P. F. Predki, and N. C. Kyrpides. 2002. Whole-genome comparative analysis of three phytopathogenic Xylella fastidiosa strains. Proc. Natl. Acad. Sci. USA 99:12403-12408.
16. Bibb, L. A., and G. F. Hatfull. 2002. Integration and excision of the Mycobacterium tuberculosis prophage-like element, phiRv1. Mol. Microbiol. 45:1515-1526.
17. Bishai, W.R., and J. R. Murphy. 1988. Bacteriophage gene products that cause human disease, p. 683-724. In R. Calendar (ed.), The bacteriophages. Plenum Press, New York, N.Y.
18. 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.
19. Boizet, B., Y. Lahbib-Mansais, L. Dupont, P. Ritzenthaler, and M. Mata. 1990. Cloning, expression and sequence analysis of an endolysin-encoding gene of Lactobacillus bulgaricus bacteriophage mv1. Gene 94:61-67.
20. Botstein, D. 1980. A theory of modular evolution for bacteriophages. Ann. N.Y. Acad. Sci. 354:484-490.
21. Boyce, J. D., B. E. Davidson, and A. J. Hillier. 1995. Identification of prophage genes expressed in lysogens of the Lactococcus lactis bacteriophage BK5-T. Appl. Environ. Microbiol. 61:4099-4104.
22. Boyd, E. F., and H. Brüssow. 2002. Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved. Trends Microbiol. 10:521-529.
23. Breuner, A., L. Brondsted, and K. Hammer. 1999. Novel organization of genes involved in prophage excision identified in the temperate lactococcal bacteriophage TP901-1. J. Bacteriol. 181:7291-7297.
24. Brondsted, L., and K. Hammer. 1999. Use of the integration elements encoded by the temperate lactococcal bacteriophage TP901-1 to obtain chromosomal single-copy transcriptional fusions in Lactococcus lactis. Appl. Environ. Microbiol. 65:752-758.
25. Brondsted, L., S. Ostergaard, M. Pedersen, K. Hammer, and F. K. Vogensen. 2001. Analysis of the complete DNA sequence of the temperate bacteriophage TP901-1: evolution, structure, and genome organization of lactococcal bacteriophages. Virology 283:93-109.
26. Broudy, T. B., V. Pancholi, and V. A. Fischetti. 2001. Induction of lysogenic bacteriophage and phage-associated toxin from group a streptococci during coculture with human pharyngeal cells. Infect. Immun. 69:1440-1443.
27. Brown, K. L., G. J. Sarkis, C. Wadsworth, and G. F. Hatfull. 1997. Transcriptional silencing by the mycobacteriophage L5 repressor. EMBO J. 16:5914-5921.
28. Brüssow, H., and F. Desiere. 2001. Comparative phage genomics and the evolution of Siphoviridae: insights from dairy phages. Mol. Microbiol. 39:213-222.
29. Brüssow, H., M. Fremont, A. Bruttin, J. Sidoti, A. Constable, and V. Fryder. 1994. Detection and classification of Streptococcus thermophilus bacteriophages isolated from industrial milk fermentation. Appl. Environ. Microbiol. 60:4537-4543.
30. Brüssow, H., and R. W. Hendrix. 2002. Phage genomics: small is beautiful. Cell 108:13-16.
31. Bruttin, A., F. Desiere, N. d'Amico, J. P. Guerin, J. Sidoti, B. Huni, S. Lucchini, and H. Brüssow. 1997. Molecular ecology of Streptococcus thermophilus bacteriophage infections in a cheese factory. Appl. Environ. Microbiol. 63:3144-3150.
32. Bruttin, A., F. Desiere, S. Lucchini, S. Foley, and H. Brüssow. 1997. Characterization of the lysogeny DNA module from the temperate Streptococcus thermophilus bacteriophage phi Sfi21. Virology 233:136-148.
33. Bruttin, A., S. Foley, and H. Brüssow. 1997. The site-specific integration system of the temperate Streptococcus thermophilus bacteriophage phiSfi21. Virology 237:148-158.
34. Bruttin, A., S. Foley, and H. Brüssow. 2002. DNA-binding activity of the Streptococcus thermophilus phage Sfi21 repressor. Virology 303:100-109.
35. Bushman, F. 2002. Lateral DNA transfer: mechanisms and consequences. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
36. Campbell, A. M. 1996. Cryptic prophages, p. 2041-2046. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B, Magasarik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.) Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. ASM, press, Washington, D.C.
37. Canchaya, C., F. Desiere, W. M. McShan, J. J. Ferretti, J. Parkhill, and H. Briissow. 2002. Genome analysis of an inducible prophage and prophage remnants integrated in the Streptococcus pyogenes strain SF370. Virology 302:245-258.
38. Carroll, D., M. A. Kehoe, D. Cavanagh, and D. C. Coleman. 1995. Novel organization of the site-specific integration and excision recombination functions of the Staphylococcus aureus serotype F virulence-converting phages phi 13 and phi 42. Mol. Microbiol. 16:877-893.
39. Chan, K., S. Baker, C. C. Kim, C. S. Detweiler, G. Dougan,and S. Falkow. 2003, Genomic comparison of Salmonella enterica serovars and Salmonella bongori by use of an S. enterica serovar Typhimurium DNA microarray. J. Bacteriol. 185:553-563.
40. 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 162:53-58.
41. Chen, F., and J. Lu. 2002. Genomic sequence and evolution of marine cyanophage P60: a new insight on lytic and lysogenic phages. Appl. Environ. Microbiol. 68:2589-2594.
42. Chopin, A., A. Bolotin, A. Sorokin, S. D. Ehrlich, and M. Chopin. 2001. Analysis of six prophages in Lactococcus lactis IL 1403: different genetic structure of temperate and virulent phage populations. Nucleic Acids Res. 29:644-651.
43. Clark, A. J., W. Inwood, T. Cloutier, and T. S. Dhillon. 2001. Nucleotide sequence of coliphage HK620 and the evolution of lambdoid phages. J. Mol. Biol. 311:657-679.
44. Coffey, A. and R. P. Ross. 2002. Bacteriophage-resistance systems in dairy starter strains: molecular analysis to application. Antonie Leeuwenhoek 82:303-321.
45. Cole, S. T., K. Eiglmeier, J. Parkhill, K. D. James, N. R. Thomson, P. R. Wheeler, N. Honore, T. Garnier, C. Churcher, D. Harris, K. Mungall, D. Basham, D. Brown, T. Chillingworth, R. Connor, R. M. Davies, K. Devlin, S. Duthoy, T. Feltwell, A. Fraser, N. Hamlin, S. Holroyd, T. Hornsby, K. Jagels, C. Lacroix, J. Maclean, S. Moule, L. Murphy, K. Oliver, M. A. Quail, M. A. Rajandream, K. M. Rutherford, S. Rutter, K. Seeger, S. Simon, M. Simmonds, J. Skelton, R. Squares, S. Squares, K. Stevens, K. Taylor, S. Whitehead, J. R. Woodward, and B. G. Barrell. 2001. Massive gene decay in the leprosy bacillus. Nature 409:1007-1011.
46. 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. 135:1679-1697.
47. Crutz-Le Coq, A. M., B. Cesselin, J. Commissaire, and J. Anba. 2002. Sequence analysis of the lactococcal bacteriophage bIL170: insights into structural proteins and HNH endonucleases in dairy phages. Microbiology 148:985-1001.
48. 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, S. M. Trindade dos, 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.
49. Davis, B. M., and M. K. Waldor. 2000. CTXphi contains a hybrid genome derived from tandemly integrated elements. Proc. Natl. Acad. Sci. USA 97:8572-8577.
50. Deng, W., V. Burland, G. Plunkett, III, A. Boutin, G. F. Mayhew, P. Liss, N. T. Perna, D. J. Rose, B. Mau, S. Zhou, D. C. Schwartz, J. D. Fetherston, L. E. Lindler, R. R. Brubaker, G. V. Plano, S. C. Straley, K. A. McDonough, M. L. Nilles, J. S. Matson, F. R. Blattner, and R. D. Perry. 2002. Genome sequence of Yersinia pestis KIM. J. Bacteriol. 184:4601-4611.
51. Desiere, F., S. Lucchini, and H. Brüssow. 1999. Comparative sequence analysis of the DNA packaging, head, and tail morphogenesis modules in the temperate cos-site Streptococcus thermophilus bacteriophage Sfi21. Virology 260:244-253.
52. Desiere, F., C. Mahanivong, A. J. Hillier, P. S. Chandry, B. E. Davidson, and H. Brüssow. 2001. Comparative genomics of lactococcal phages: insight from the complete genome sequence of Lactococcus lactis phage BK5-T. Virology 283:240-252.
53. Desiere, F., W. M. McShan, D. van Sinderen, J. J. Ferretti, and H. Brüssow. 2001. Comparative genomics reveals close genetic relationships between phages from dairy bacteria and pathogenic Streptococci: evolutionary implications for prophage-host interactions. Virology 288:325-341.
54. Desiere, F., R. D. Pridmore, and H. Brüssow. 2000. Comparative genomics of the late gene cluster from Lactobacillus phages. Virology 275:294-305.
55. Diaz, E., R. Lopez, and J. L. Garcia. 1992. EJ-1, a temperate bacteriophage of Streptococcus pneumoniae with a Myoviridae morphotype. J. Bacteriol. 174:5516-5525.
56. Di Pierro, M., R. Lu, S. Uzzau, W. Wang, K. Margaretten, C. Pazzani, F. Maimone, and A. Fasano. 2001. Zonula occludens toxin structure-function analysis. Identification of the fragment biologically active on tight junctions and of the zonulin receptor binding domain. J. Biol. Chem. 276:19160-19165.
57. Dodd, I. B., and J. B. Egan. 1996. The Escherichia coli retrons Ec67 and Ec86 replace DNA between the cos site and a transcription terminator of a 186-related prophage. Virology 219:115-124.
58. Doolittle, W. F. 1999. Phylogenetic classification and the universal tree. Science 284:2124-2129.
59. Dopazo, J., A. Mendoza, J. Herrero, F. Caldara, Y. Humbert, L. Friedli, M. Guerrier, E. Grand-Schenk, C. Gandin, M. de Francesco, A. Polissi, G. Buell, G. Feger, E. Garcia, M. Peitsch, and J. F. Garcia-Bustos. 2001. Annotated draft genomic sequence from a Streptococcus pneumoniae type 19F clinical isolate. Microb. Drug Resist. 7:99-125.
60. Dozois, C. M., F. Daigle, and R. Curtiss, III. 2003. Identification of pathogen-specific and conserved genes expressed in vivo by an avian pathogenic Escherichia coli strain. Proc. Natl. Acad. Sci. USA. 100:247-252.
61. Duplessis, M., and S. Moineau. 2001. Identification of a genetic determinant responsible for host specificity in Streptococcus thermophilus bacteriophages. Mol. Microbiol. 41:325-336.
62. Durmaz, E., and T. R. Klaenhammer. 2000. Genetic analysis of chromosomal regions of Lactococcus lactis acquired by recombinant lytic phages. Appl. Environ. Microbiol. 66:895-903.
63. Dziejman, M., E. Balon, D. Boyd, C. M. Fraser, J. F. Heidelberg, and J. J. Mekalanos. 2002. Comparative genomic analysis of Vibrio cholerae: genes that correlate with cholera endemic and pandemic disease. Proc. Natl. Acad. Sci. USA 99:1556-1561.
64. Edwards, R. A., G. J. Olsen, and S. R. Maloy. 2002. Comparative genomics of closely related salmonellae. Trends Microbiol. 10:94-99.
65. Eggers, C. H., B. J. Kimmel, J. L. Bono, A. F. Elias, P. Rosa, and D. S. Samuels. 2001. Transduction by phiBB-1, a bacteriophage of Borrelia butgdorferi. J. Bacteriol. 183:4771-4778.
66. Eklund, M. W., F. T. Poysky, and S. M. Reed. 1972. Bacteriophage and the toxigenicity of Clostridium botulinum type D. Nat. New Biol. 235:16-17.
67. Eklund, M. W., F. T. Poysky, S. M. Reed, and C. A. Smith. 1971. Bacteriophage and the toxigenicity of Clostridium botulinum type C. Science 172:480-482.
68. 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 98:4658-4663.
69. Figueroa-Bossi, N., and L. Bossi. 1999. Inducible prophages contribute to Salmonella virulence in mice. Mol. Microbiol. 33:167-176.
70. 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.
71. Foley, S., A. Bruttin, and H. Brüssow. 2000. Widespread distribution of a group I intron and its three deletion derivatives in the lysin gene of Streptococcus thermophilus bacteriophages. J. Virol. 74:611-618.
72. Ford, M. E., G. J. Sarkis, A. E. Belanger, R. W. Hendrix, and G. F. Hatfull. 1998. Genome structure of mycobacteriophage D29: implications for phage evolution. J. Mol. Biol. 279:143-164.
73. Ford, M. E., Stenstrom, C., R. W. Hendrix, and G. F. Hatfull. 1998. Mycobacteriophage TM4: genome structure and gene expression. Tubercle Lung Dis. 79:63-73.
74. Garcia, E., J. L. Garcia, P. Garcia, A. Arraras, J. M. Sanchez-Puelles, and R. Lopez. 1988. Molecular evolution of lytic enzymes of Streptococcuspneumoniae and its bacteriophages. Proc. Natl. Acad. Sci. USA 85:914-918.
75. Garcia, P., J. C. Alonso, and J. E. Suarez. 1997. Molecular analysis of the cos region of the Lactobacillus casei bacteriophage A2. Gene product 3, gp3, specifically binds to its downstream cos region. Mol. Microbiol. 23:505-514.
76. Garcia, P., V. Ladero, J. C. Alonso, and J. E. Suarez. 1999. Cooperative interaction of Cl protein regulates lysogeny of Lactobacillus casei by bacteriophage A2. J. Virol. 73:3920-3929.
77. Gerdes, K. 2000. Toxin-antitoxin modules may regulate synthesis of macromolecules during nutritional stress. J. Bacteriol. 182:561-572.
78. Gindreau, E., R. Lopez, and P. Garcia. 2000. MM1, a temperate bacteriophage of the type 23F Spanish/USA multiresistant epidemic clone of Streptococcus pneumoniae: structural analysis of the site-specific integration system. J. Virol. 74:7803-7813.
79. 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 294:849-852.
80. Glaser, P., C. Rusniok, C. Buchrieser, F. Chevalier, L. Frangeul, T. Msadek, M. Zouine, E. Couve, L. Lalioui, C. Poyart, P. Trieu-Cuot, and F. Kunst. 2002. Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease. Mol. Microbiol. 45:1499-1513.
81. Haggard-Ljungquist, E., C. Halling, and R. Calendar. 1992. DNA sequences of the tail fiber genes of bacteriophage P2: evidence for horizontal transfer of tail fiber genes among unrelated bacteriophages. J. Bacteriol. 174:1462-1477.
82. Halperin, S. A., P. Ferrieri, E. D. Gray, E. L. Kaplan, and L. W. Wannamaker. 1987. Antibody response to bacteriophage hyaluronidase in acute glomerulonephritis after group A streptococcal infection. J. Infect. Dis. 155:253-261.
83. Hambly, E., F. Tetart, C. Desplats, W. H. Wilson, H. M. Krisch, and N. H. Mann. 2001. A conserved genetic module that encodes the major virion components in both the coliphage T4 and the marine cyanophage S-PM2. Proc. Natl. Acad. Sci. USA 98:11411-11416.
84. Hatfull, G. F., and G. J. Sarkis. 1993. DNA sequence, structure and gene expression of mycobacteriophage L5: a phage system for mycobacterial genetics. Mol. Microbiol. 7:395-405.
85. Heidelberg, J. F., J. A. Eisen, W. C. Nelson, R. A. Clayton, M. L. Gwinn, R. J. Dodson, D. H. Haft, E. K. Hickey, J. D. Peterson, L. Umayam, S. R. Gill, K. E. Nelson, T. D. Read, H. Tettelin, D. Richardson, M. D. Ermolaeva, J. Vamathevan, S. Bass, H. Qin, I. Dragoi, P. Sellers, L. McDonald, T. Utterback, R. D. Fleishmann, W. C. Nierman, and O. White. 2000. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 406:477-483.
86. Heidelberg, J. F., I. T. Paulsen, K. E. Nelson, E. J. Gaidos, W. C. Nelson, T. D. Read, J. A. Eisen, R. Seshadri, N. Ward, B. Methe, R. A. Clayton, T. Meyer, A. Tsapin, J. Scott, M. Beanan, L. Brinkac, S. Daugherty, R. T. DeBoy, R. J. Dodson, A. S. Durkin, D. H. Haft, J. F. Kolonay, R. Madupu, J. D. Peterson, L. A. Umayam, O. White, A. M. Wolf, J. Vamathevan, J. Weidman, M. Impraim, K. Lee, K. Berry, C. Lee, J. Mueller, H. Khouri, J. Gill, T. R. Utterback, L. A. McDonald, T. V. Feldblyum, H. O. Smith, J. C. Venter, K. H. Nealson, and C. M. Fraser. 2002. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat. Biotechnol. 20:1118-1123.
87. Heinrich, J., M. Velleman, and H. Schuster. 1995. The tripartite immunity system of phages P1 and P7. FEMS Microbiol. Rev. 17:121-126.
88. 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.
89. 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 96:2192-2197.
90. Hill, D. F., N. J. Short, R. N. Perham, and G. B. Petersen. 1991. DNA sequence of the filamentous bacteriophage Pfl. J. Mol. Biol. 218:349-364.
91. Ho, T. D., and J. M. Slauch. 2001. Characterization of grvA, an antivirulence gene on the gifsy-2 phage in Salmonella enterica serovar Typhimurium. J. Bacteriol. 183:611-620.
92. Hooper, L. V., and J. I. Gordon. 2001. Commensal host-bacterial relationships in the gut. Science 292:1115-1118.
93. Hoskins, J., W. E. Alborn, Jr., J. Arnold, L. C. Blaszczak, S. Burgett, B. S. DeHoff, S. T. Estrem, L. Fritz, D. J. Fu, W. Fuller, C. Geringer, R. Gilmour, J. S. Glass, H. Khoja, A. R. Kraft, R. E. Lagace, D. J. LeBlanc, L. N. Lee, E. J. Lefkowitz, J. Lu, P. Matsushima, S. M. McAhren, M. McHenney, K. McLeaster, C. W. Mundy, T. I. Nicas, F. H. Norris, M. O'Gara, R. B. Peery, G. T. Robertson, P. Rockey, P. M. Sun, M. E. Winkler, Y. Yang, M. Young-Bellido, G. Zhao, C. A. Zook, R. H. Baltz, S. R. Jaskunas, P. R. Rosteck, Jr., P. L. Skatrud, and J. I. Glass. 2001. Genome of the bacterium Streptococcus pneumoniae strain R6. J. Bacteriol. 183:5709-5717.
94. Huber, K. E., and M. K. Waldor. 2002. Filamentous phage integration requires the host recombinases XerC and XerD. Nature 417:656-659.
95. Iandolo, J. J., V. Worrell, K. H. Groicher, Y. Qian, R. Tian, S. Kenton, A. Dorman, H. Ji, S. Lin, P. Loh, S. Qi, H. Zhu, and B. A. Roe. 2002. Comparative analysis of the genomes of the temperate bacteriophages phi 11, phi 12 and phi 13 of Staphylococcus aureus 8325. Gene 289:109-118.
96. Ikebe, T., A. Wada, Y. Inagaki, K. Sugama, R. Suzuki, D. Tanaka, A. Tamaru, Y. Fujinaga, Y. Abe, Y. Shimizu, and H. Watanabe. 2002. Dissemination of the phage-associated novel superantigen gene speL in recent invasive and noninvasive Streptococcus pyogenes M3/T3 isolates in Japan. Infect. Immun. 70:3227-3233.
97. Inagaki, Y., F. Myouga, H. Kawabata, S. Yamai, and H. Watanabe. 2000. Genomic differences in Streptococcuspyogenes serotype M3 between recent isolates associated with toxic shock-like syndrome and past clinical isolates. J. Infect. Dis. 181:975-983.
98. Jimenez, J. I., B. Minambres, J. L. Garcia, and E. Diaz. 2002. Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ. Microbiol. 4:824-841.
99. Jin, Q., Z. Yuan, J. Xu, Y. Wang, Y. Shen, W. Lu, J. Wang, H. Liu, J. Yang, F. Yang, X. Zhang, J. Zhang, G. Yang, H. Wu, D. Qu, J. Dong, L. Sun, Y. Xue, A. Zhao, Y. Gao, J. Zhu, B. Kan, K. Ding, S. Chen, H. Cheng, Z. Yao, B. He, R. Chen, D. Ma, B. Qiang, Y. Wen, Y. Hou, and J. Yu. 2002. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and 0157. Nucleic Acids Res. 30:4432-4441.
100. Johnsen, M. G., H. Neve, F. K. Vogensen, and K. Hammer. 1995. Virion positions and relationships of lactococcal temperate bacteriophage TP901-1 proteins. Virology 212:595-606.
101. 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.
102. Kakikawa, M., S. Ohkubo, T. Sakate, M. Sayama, A. Taketo, and K. Kodaira. 2000. Purification and DNA-binding properties of the cro-type regulatory repressor protein cng encoded by the Lactobacillus plantarun phage phi g1e. Gene 249:161-169.
103. Kaneko, J., T. Kimura, S. Narita, T. Tomita, and Y. Kamio. 1998. Complete nucleotide sequence and molecular characterization of the temperate staphylococcal bacteriophage phiPVL carrying Panton-Valentine leukocidin genes. Gene 215:57-67.
104. 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 399:375-379.
105. Kazmi, S. U., R. Kansal, R. K. Aziz, M. Hooshdaran, A. Norrby-Teglund, D. E. Low, A. B. Halim, and M. Kotb. 2001. Reciprocal, temporal expression of SpeA and SpeB by invasive MITI group a streptococcal isolates in vivo. Infect. Immun. 69:4988-4995.
106. 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 plantaram WCFS1. Proc. Natl. Acad. Sci. USA 100:1990-1995.
107. Kropinski, A. M. 2000. Sequence of the genome of the temperate, serotype-converting, Pseudomonas aeruginosa bacteriophage D3. J. Bacteriol. 182:6066-6074.
108. Kunst, F., N. Ogasawara, I. Moszer, A. M. Albertini, G. Alloni, V. Azevedo, M. G. Bertero, P. Bessieres, A. Bolotin, S. Borchert, R. Borriss, L. Boursier, A. Brans, M. Braun, S. C. Brignell, S. Bron, S. Brouillet, C. V. Bruschi, B. Caldwell, V. Capuano, N. M. Carter, S. K. Choi, J. J. Codani, I. F. Connerton, A. Danchin, and 1997. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390:249-256.
109. 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 meticillin-resistant Staphylococcus aureus. Lancet 357:1225-1240.
110. Ladero, V., P. Garcia, J. C. Alonso, and J. E. Suarez. 1999. A2 cro, the lysogenic cycle repressor, specifically binds to the genetic switch region of Lactobacillus casei bacteriophage A2. Virology 262:220-229.
111. Ladero, V., P. Garcia, J. C. Alonso, and J. E. Suarez. 2002. Interaction of the Cro repressor with the lysis/lysogeny switch of the Lactobacillus casei temperate bacteriophage A2. J. Gen. Virol. 83:2891-2895.
112. Laird, W., and N. Groman. 1976. Orientation of the tox gene in the prophage of corynebacteriophage beta. J. Virol. 19:228-231.
113. 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 97:859-864.
114. Lawrence, J. G., G. F. Hatfull, and R. W. Hendrix. 2002. Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J. Bacteriol. 184:4891-4905.
115. Lawrence, J. G., R. W. Hendrix, and S. Casjens. 2001. Where are the pseudogenes in bacterial genomes? Trends Microbiol 9:535-540.
116. Lawrence, J. G. and H. Ochman. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Natl. Acad. Sci. USA 95:9413-9417.
117. Lawrence, J. G., and J. R. Roth. 1999. Genomic flux: genome evolution by gene loss and acquisition, p. 263-289. In R. L. Charlebois (ed.), Organization of the prokaryotic genome. ASM Press, Washington, D.C.
118. Lazarevic, V., A. Dusterhoft, B. Soldo, H. Hilbert, C. Mauel, and D. Karamata. 1999. Nucleotide sequence of the Bacillus subtilis temperate bacteriophage SPbetac2. Microbiology 145:1055-1067.
119. Lee, C. Y., and J. J. Iandolo. 1986. Lysogenic conversion of staphylococcal lipase is caused by insertion of the bacteriophage L54a genome into the lipase structural gene. J. Bacteriol. 166:385-391.
120. Lee, M. H., L. Pascopella, W. R. Jacobs, Jr., and G. F. Hatfull. 1991. Site-specific integration of mycobacteriophage L5: integration-proficient vectors for Mycobacterium smegmatis, Mycobacterium tuberculosis, and bacille Calmette-Guerin. Proc. Natl. Acad. Sci. USA 88:3111-3115.
121. Lee, Y., D. Choi, and H. Kende. 2001. Expansins: ever-expanding numbers and functions. Curr. Opin. Plant Biol. 4:527-532.
122. Le Marrec, C., D. van Sinderen, L. Walsh, E. Stanley, E. Vlegels, S. Moineau, P. Heinze, G. Fitzgerald, and B. Fayard. 1997. Two groups of bacteriophages infecting Streptococcus thermophilus can be distinguished on the basis of mode of packaging and genetic determinants for major structural proteins. Appl. Environ. Microbiol. 63:3246-3253.
123. Lin, N. T., R. Y. Chang, S. J. Lee, and Y. H. Tseng. 2001. Plasmids carrying cloned fragments of RF DNA from the filamentous phage (phi)Lf can be integrated into the host chromosome via site-specific integration and homologous recombination. Mol. Genet. Genomics 266:425-435.
124. Lin, W., K. J. Fullner, R. Clayton, J. A. Sexton, M. B. Rogers, K. E. Calia, S. B. Calderwood, C. Fraser, and J. J. Mekalanos. 1999. Identification of a Vibrio cholerae RTX toxin gene cluster that is tightly linked to the cholera toxin prophage. Proc. Natl. Acad. Sci. USA 96:1071-1076.
125. Loessner, M. J., R. B. Inman, P. Lauer, and R. Calendar. 2000. Complete nucleotide sequence, molecular analysis and genome structure of bacteriophage A118 of Listeria monocytogenes: implications for phage evolution. Mol. Microbiol. 35:324-340.
126. Lofdahl, S., J. Zabielski, and L. Philipson. 1981. Structure and restriction enzyme maps of the circularly permuted DNA of staphylococcal bacteriophage phi 11. J. Virol. 37:784-794.
127. Lucchini, S., F. Desiere, and H. Brüssow. 1999. Comparative genomics of Streptococcus thermophilus phage species supports a modular evolution theory. J. Virol. 73:8647-8656.
128. Lucchini, S., F. Desiere, and H. Brüssow. 1999. Similarly organized lysogeny modules in temperate Siphoviridae from low GC content gram-positive bacteria. Virology 263:427-435.
129. Lucchini, S., F. Desiere, and H. Brüssow. 1999. The genetic relationship between virulent and temperate Streptococcus thermophilus bacteriophages: whole genome comparison of cos-site phages Sfi19 and Sfi21. Virology 260:232-243.
130. Lurz, R., E. V. Orlova, D. Gunther, P. Dube, A. Droge, F. Weise, M. van Heel, and P. Tavares. 2001. Structural organisation of the head-to-tail interface of a bacterial virus. J. Mol. Biol. 310:1027-1037.
131. Madsen, P. L., and K. Hammer. 1998. Temporal transcription of the lactococcal temperate phage TP901-1 and DNA sequence of the early promoter region. Microbiology 144:2203-2215.
132. Madsen, P. L., A. H. Johansen, K. Hammer, and L. Brondsted. 1999. The genetic switch regulating activity of early promoters of the temperate lactococcal bacteriophage TP901-1. J. Bacteriol. 181:7430-7438.
133. Madsen, S. M., D. Mills, G. Djordjevic, H. Israelsen, and T. R. Klaenhammer. 2001. Analysis of the genetic switch and replication region of a P335-type bacteriophage with an obligate lytic lifestyle on Lactococcus lactis. Appl. Environ. Microbiol. 67:1128-1139.
134. Mahanivong, C., J. D. Boyce, B. E. Davidson, and A. J. Hillier. 2001. Sequence analysis and molecular characterization of the Lactococcus lactis temperate bacteriophage BK5-T. Appl. Environ. Microbiol. 67:3564-3576.
135. Makino, K., K. Yokoyama, 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 cnterohemorrhagic Eschelichia coli O157;H7 derived from the Sakai outbreak. Genes Genet. Syst. 74:227-239.
136. Maniloff, J., and H. W. Ackermann. 1998. Taxonomy of bacterial viruses: establishment of tailed virus genera and the order Caudovirales. Arch. Virol. 143:2051-2063.
137. Maniloff, J., G. J. Kampo, and C. C. Dascher. 1994. Sequence analysis of a unique temperature phage: mycoplasma virus L2. Gene 141:1-8.
138. Mavris, M., P. A. Manning, and R. Morona. 1997. Mechanism of bacteriophage SfII-mediated serotype conversion in Shigella flexneri. Mol. Microbiol. 26:939-950.
139. 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.
140. McGrath, S., G. F. Fitzgerald, and D. van Sinderen. 2002. Identification and characterization of phage-resistance genes in temperate lactococcal bacteriophages. Mol. Microbiol. 43:509-520.
141. Mediavilla, J., S. Jain, J. Kriakov, M. E. Ford, R. L. Duda, W. R. Jacobs, Jr., R. W. Hendrix, and G. F. Hatfull. 2000. Genome organization and characterization of mycobacteriophage Bxb1. Mol. Microbiol. 38:955-970.
142. Mikkonen, M., L. Dupont, T. Alatossava, and P. Ritzenthaler. 1996. Defective site-specific integration elements are present in the genome of virulent bacteriophage LL-H of Lactobacillus delbrueckii. Appl. Environ. Microbiol. 62:1847-1851.
143. 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.
144. Mirold, S., W. Rabsch, H. Tschape, and W. D. Hardt. 2001. Transfer of the Salmonella type III effector sopE between unrelated phage families. J. Mol. Biol. 312:7-16.
145. Moineau, S., S. Pandian, and T. Klaenhammer. 2002. Evolution of a lytic bacteriophage via DNA acquisition from the Lactococcus lactis chromosome. Appl. Environ. Microbiol. 60:1832-1841.
146. Molineux I. J. 1999. T7-like phages (Podoviridae), p. 1722-1729. In A. Granoff and R. Webster (ed.), Encyclopedia of virology. Academic Press, Ltd., London, United Kingdom.
147. Morgan, G. J., G. F. Hatfull, S. Casjens, and R. W. Hendrix. 2002. Bacteriophage Mu genome sequence: analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus. J. Mol. Biol. 317:337-359.
148. Moszer, I., E. P. Rocha, and A. Danchin. 1999. Codon usage and lateral gene transfer in Bacillus subtilis. Curr. Opin. Microbiol. 2:524-528.
149. 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. 68:4850-4855.
150. Murray, A. E., D. Lies, G. Li, K. Nealson, J. Zhou, and J. M. Tiedje. 2001. DNA/DNA hybridization to microarrays reveals gene-specific differences between closely related microbial genomes. Proc. Natl. Acad. Sci. USA 98:9853-9858.
151. Nakayama, K., S. Kanaya, M. Ohnishi, Y. Terawaki, and T. Hayashi. 1999. The complete nucleotide sequence of phi CTX, a cytotoxin-converting phage of Pseudomonas aeruginosa: implications for phage evolution and horizontal gene transfer via bacteriophages. Mol. Microbiol. 31:399-419.
152. 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. 38:213-231.
153. Narita, S., J. Kaneko, J. Chiba, Y. Piemont, S. Jarraud, J. Etienne, and Y. Kamio. 2001. Phage conversion of Panton-Valentine leukocidin in Staphylococcus aureus: molecular analysis of a PVL-converting phage, phiSLT. Gene 268:195-206.
154. Nauta, A., B. B. van den, H. Karsens, G. Venema, and J. Kok. 1997. Design of thermolabile bacteriophage repressor mutants by comparative molecular modeling. Nat. Biotechnol. 15:980-983.
155. Nauta, A., D. van Sinderen, H. Karsens, E. Smit, G. Venema, and J. Kok. 1996. Inducible gene expression mediated by a repressor-operator system isolated from Lactococcus lactis bacteriophage r1t. Mol. Microbiol. 19:1331-1341.
156. Neely, M. N., and D. I. Friedman. 1998. Functional and genetic analysis of regulatory regions of coliphage H-19B: location of shiga-like toxin and lysis genes suggest a role for phage functions in toxin release. Mol. Microbiol. 28:1255-1267.
157. Nesbit, C. E., M. E. Levin, M. K. Donnelly-Wu, and G. F. Hatfull. 1995. Transcriptional regulation of repressor synthesis in mycobacteriophage L5. Mol. Microbiol. 17:1045-1056.
158. Neve, H., K. I. Zenz, F. Desiere, A. Koch, K. J. Heller, and H. Brussow. 1998. Comparison of the lysogeny modules from the temperate Streptococcus thermophilus bacteriophages TP-J34 and Sfi21: implications for the modular theory of phage evolution. Virology 241:61-72.
159. Nolling, J., G. Breton, M. V. Omelchenko, K. S. Makarova, Q. Zeng, R. Gibson, H. M. Lee, J. Dubois, D. Qiu, J. Hitti, Y. I. Wolf, R. L. Tatusov, F. Sabathe, L. Doucette-Stamm, P. Soucaille, M. J. Daly, G. N. Bennett, E. V. Koonin, and D. R. Smith. 2001. Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J. Bacteriol. 183:4823-4838.
160. Ohnishi, M., K. Kurokawa, and T. Hayashi. 2001. Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol. 9:481-485.
161. Ohnishi, M., J. Terajima, K. Kurokawa, K. Nakayama, T. Murata, K. Tamura, Y. Ogura, H. Watanabe, and T. Hayashi. 2002. Genomic diversity of enterohemorrhagic Escherichia coli 0157 revealed by whole genome PCR scanning. Proc. Natl. Acad. Sci. USA 99:17043-17048.
162. Oki, M., M. Kakikawa, S. Nakamura, E. T. Yamamura, K. Watanabe, M. Sasamoto, A. Taketo, and K. Kodaira. 1997. Functional and structural features of the holin HOL protein of the Lactobacillus plantarum phage phi gle: analysis in Escherichia coli system. Gene 197:137-145.
163. Pajunen, M. I., S. J. Kiljunen, M. E. Soderholm, and M. Skurnik. 2001. Complete genomic sequence of the lytic bacteriophage phiYeO3-12 of Yersinia enterocolitica serotype O:3. J. Bacteriol. 183:1928-1937.
164. Parkhill, J., G. Dougan, K. D. James, N. R. Thomson, D. Pickard, J. Wain, C. Churcher, K. L. Mungall, S. D. Bentley, M. T. Holden, M. Sebaihia, S. Baker, D. Basham, K. Brooks, T. Chillingworth, P. Connerton, A. Cronin, P. Davis, R. M. Davies, L. Dowd, N. White, J. Farrar, T. Feltwell, N. Hamlin, A. Haque, T. T. Hien, S. Holroyd, K. Jagels, A. Krogh, T. S. Larsen, S. Leather, S. Moule, P. O'Gaora, C. Parry, M. Quail, K. Rutherford, M. Simmonds, J. Skelton, K. Stevens, S. Whitehead, and B. G. Barrell. 2001. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413:848-852.
165. Pedersen, M., S. Ostergaard, J. Bresciani, and F. K. Vogensen. 2000. Mutational analysis of two structural genes of the temperate lactococcal bacteriophage TP901-1 involved in tail length determination and baseplate assembly. Virology 276:315-328.
166. 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 409:529-533.
167. Pfister, P., A. Wasserfallen, R. Stettler, and T. Leisinger. 1998. Molecular analysis of Methanobacterium phage psiM2. Mol. Microbiol. 30:233-244.
168. 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. 181:1767-1778.
169. Porwollik, S., R. M. Wong, and M. McClelland. 2002. Evolutionary genomics of Salmonella: gene acquisitions revealed by microarray analysis. Proc. Natl. Acad. Sci. USA 99:8956-8961.
170. Proft, T., S. L. Moffatt, C. J. Berkahn, and J. D. Fraser. 1999. Identification and characterization of novel superantigens from Streptococcus pyogenes. J. Exp. Med. 189:89-102.
171. Proux, C., D. van Sinderen, J. Suarez, P. Garcia, V. Ladero, G. F. Fitzgerald, F. Desiere, and H. Brüssow. 2002. The dilemma of phage taxonomy illustrated by comparative genomics of Sfi21-like Siphoviridae in lactic acid bacteria. J. Bacteriol. 184:6026-6036.
172. Pulkkinen, W. S., and S. I. Miller. 1991. A Salmonella typhimurium virulence protein is similar to a Yersinia enterocolitica invasion protein and a bacteriophage lambda outer membrane protein. J. Bacteriol. 173:86-93.
173. Ramirez, M., E. Severina, and A. Tomasz. 1999. A high incidence of prophage carriage among natural isolates of Streptococcus pneumoniae. J. Bacteriol. 181:3618-3625.
174. Ravin, V., N. Ravin, S. Casjens, M. E. Ford, G. F. Hatfull, and R. W. Hendrix. 2000. Genomic sequence and analysis of the atypical temperate bacteriophage N15. J. Mol. Biol. 299:53-73.
175. Recktenwald, J., and H. Schmidt. 2002. The nucleotide sequence of Shiga toxin (Stx) 2e-encoding phage phiP27 is not related to other Stx phage genomes, but the modular genetic structure is conserved. Infect. Immun. 70:1896-1908.
176. Rohwer, F. and R. Edwards. 2002. The phage proteomic tree: a genome-based taxonomy for phage. J. Bacteriol. 184:4529-4535.
177. Romero, A., R. Lopez, R. Lurz, and P. Garcia. 1990. Temperate bacteriophages of Streptococcus pneumoniae that contain protein covalently linked to the 5′ ends of their DNA. J. Virol. 64:5149-5155.
178. Ruzin, A., J. Lindsay, and R. P. Novick. 2001. Molecular genetics of SaPI1 - a mobile pathogenicity island in Staphylococcus aureus. Mol. Microbiol. 41:365-377.
179. Sasaki, Y., J. Ishikawa, A. Yamashita, K. Oshima, T. Kenri, K. Furuya, C. Yoshino, A. Horino, T. Shiba, T. Sasaki, and M. Hattori. 2002. The complete genomic sequence of Mycoplasma penetrans, an intracellular bacterial pathogen in humans. Nucleic Acids Res. 30:5293-5300.
180. Schell, M. A., M. Karmirantzou, B. Snel, D. Vilanova, B. Berger, G. Pessi, M. C. Zwahlen, F. Desiere, P. Bork, M. Delley, R. D. Pridmore, and F. Arigoni. 2002. The genome sequence of Bifidobacterium longum reflects its adaptation to the human gastrointestinal tract. Proc. Natl. Acad. Sci. USA 99:14422-14427.
181. Severina, E., M. Ramirez, and A. Tomasz. 1999. Prophage carriage as a molecular epidemiological marker in Streptococcus pneumoniae. J. Clin. Microbiol. 37:3308-3315.
182. Sharpies, G. J., E. L. Bolt, and R. G. Lloyd. 2002. RusA proteins from the extreme thcrmophile Aquifex aeolicus and lactococcal phage r1t resolve Holliday junctions. Mol. Microbiol. 44:549-559.
183. Sheehan, M. M., J. L. Garcia, R. Lopez, and P. Garcia. 1997. The lytic enzyme of the pneumococcal phage Dp-1: a chimeric lysin of intergeneric origin. Mol. Microbiol. 25:717-725.
184. Sheehan, M. M., E. Stanley, G. F. Fitzgerald, and D. van Sinderen. 1999. Identification and characterization of a lysis module present in a large proportion of bacteriophages infecting Streptococcus thermophilus. Appl. Environ. Microbiol. 65:569-577.
185. Shimizu, T., K. Ohtani, H. Hirakawa, K. Ohshima, A. Yamashita, T. Shiba, N. Ogasawara, M. Hattori, S. Kuhara, and H. Hayashi. 2002. Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc. Natl. Acad. Sci. USA 99:996-1001.
186. Shinomiya, T. 1984. Phenotypic mixing of pyocin R2 and bacteriophage PS17 in Pseudomonas aeruginosa PAO. J. Virol. 49:310-314.
187. Simpson, A. J., F. C. Reinach, P. Arruda, F. A. Abreu, M. Acencio, R. Alvarenga, L. M. Alves, J. E. Araya, G. S. Bala, C. S. Baptista, M. H. Barros, E. D. Bonaccorsi, S. Bordin, J. M. Bove, M. R. Brones, 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. Cristofan, E. Das-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. Naga, 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 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. Silva, J. F. da Silveira, M. L. Silvestri, W. J. Siqueira, A. A. de Souza, A. P. de Souza, M. F. Terenzi, D. Truffi, S. M. Tsa, 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.
188. Smith, M. C., R. N. Burns, S. E. Wilson, and M. A. Gregory. 1999. The complete genome sequence of the Streptomyces temperate phage straight phiC31: evolutionary relationships to other viruses. Nucleic Acids Res. 27:2145-2155.
189. Smoot, J. C., K. D. Barbian, J. J. Van Gompel, L. M. Smoot, M. S. Chaussee, G. L. Sylva, D. E. Sturdevant, S. M. Ricklefs, S. F. Porcella, L. D. Parkins, S. B. Beres, D. S. Campbell, T. M. Smith, Q. Zhang, V. Kapur, J. A. Daly, L. G. Veasy, and J. M. Musser. 2002. Genome sequence and comparative microarray analysis of serotype M18 group A Streptococcus strains associated with acute rheumatic fever outbreaks. Proc. Natl. Acad. Sci. USA 99:4668-4673.
190. Smoot, L. M., J. C. Smoot, M. R. Graham, G. A. Somerville, D. E. Sturdevant, C. A. Migliaccio, G. L. Sylva, and J. M. Musser. 2001. Global differential gene expression in response to growth temperature alteration in group A Streptococcus. Proc. Natl. Acad. Sci. USA 98:10416-10421.
191. Sriskandan, S., M. Unnikrishnan, T. Krausz, and J. Cohen. 2000. Mitogenic factor (MF) is the major DNase of serotype M89 Streptococcus pyogenes. Microbiology 146:2785-2792.
192. Stanley, E., G. F. Fitzgerald, C. Le Marrec, B. Fayard, and D. van Sinderen. 1997. Sequence analysis and characterization of phi 01205, a temperate bacteriophage infecting Streptococcus thermophilus CNRZ1205. Microbiology 143:3417-3429.
193. Stanley, T. L., C. D. Ellermeier, and J. M. Slauch. 2000. Tissue-specific gene expression identifies a gene in the lysogenic phage Gifsy-I that affects Salmonella enterica serovar Typhimurium survival in Peyer's patches. J. Bacteriol. 182:4406-4413.
194. Stover, C. K., X. Q. Pham, A. L. Erwin, S. D. Mizoguchi, P. Warrener, M. J. Hickey, F. S. Brinkman, W. O. Hufnagle, D. J. Kowalik, M. Lagrou, R. L. Garber, L. Goltry, E. Tolentino, S. Westbrock-Wadman, Y. Yuan, L. L. Brody, S. N. Coulter, K. R. Folger, A. Kas, K. Larbig, R. Lim, K. Smith, D. Spencer, G. K. Wong, Z. Wu, I. T. Paulsen, J. Reizer, M. H. Saier, R. E. Hancock, S. Lory, and M. V. Olson. 2000. Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406:959-964.
195. Tacket, C. O., G. Losonsky, J. P. Nataro, S. J. Cryz, R. Edelman, A. Fasano, J. Michalski, J. B. Kaper, and M. M. Levine. 1993. Safety and immunogenicity of live oral cholera vaccine candidate CVD 110, a delta ctxA delta zot delta ace derivative of El Tor Ogawa Vibrio cholerae. J. Infect. Dis. 168:1536-1540.
196. Takami, H., K. Nakasone, Y. Takaki, G. Maeno, R. Sasaki, N. Masui, F. Fuji, C. Hirama, Y. Nakamura, N. Ogasawara, S. Kuhara, and K. Horikoshi. 2000. Complete genome sequence of the alkaliphilic bacterium Bacillus halodurans and genomic sequence comparison with Bacillus subtilis. Nucleic Acids Res. 28:4317-4331.
197. Takemaru, K., M. Mizuno, T. Sato, M. Takeuchi, and Y. Kobayashi. 1995. Complete nucleotide sequence of a skin element excised by DNA rearrangement during sporulation in Bacillus subtilis. Microbiology 141:323-327.
198. Tettelin, H., V. Masignani, M. J. Cieslewicz, J. A. Eisen, S. Peterson, M. R. Wessels, I. T. Paulsen, K. E. Nelson, I. Margarit, T. D. Read, L. C. Madoff, A. M. Wolf, M. J. Beanan, L. M. Brinkac, S. C. Daugherty, R. T. DeBoy, A. S. Durkin, J. F. Kolonay, R. Madupu, M. R. Lewis, D. Radune, N. B. Fedorova, D. Scanlan, H. Khouri, S. Mulligan, H. A. Carty, R. T. Cline, S. E. Van Aken, J. Gill, M. Scarselli, M. Mora, E. T. Iacobini, C. Brettoni, G. Galli, M. Mariani, F. Vegni, D. Maione, D. Rinaudo, R. Rappuoli, J. L. Telford, D. L. Kasper, G. Grandi, and C. M. Fraser. 2002. Complete genome sequence and comparative genomic analysis of an emerging human pathogen, serotype V Streptococcus agalactiae. Proc. Natl. Acad. Sci. USA 99:12391-12396.
199. Tettelin, H., K. E. Nelson, I. T. Paulsen, J. A. Eisen, T. D. Read, S. Peterson, J. Heidelberg, R. T. DeBoy, D. H. Haft, R. J. Dodson, A. S. Durkin, M. Gwinn, J. F. Kolonay, W. C. Nelson, J. D. Peterson, L. A. Umayam, O. White, S. L. Salzberg, M. R. Lewis, D. Radune, E. Holtzapple, H. Khouri, A. M. Wolf, T. R. Utterback, C. L. Hansen, L A. McDonald, T. V. Feldblyum, S. Angiuoli, T. Dickinson, E. K. Hickey, I. E. Holt, B. J. Loftus, F. Yang, H. O. Smith, J. C. Venter, B. A. Dougherty, D. A. Morrison, S. K. Hollingshead, and C. M. Fraser. 2001. Complete genome sequence of a virulent isolate of Streptococcus pneumoniae. Science 293:498-506.
200. Tremblay, D. M., and S. Moineau. 1999. Complete genomic sequence of the lytic bacteriophage DT1 of Streptococcus thermophilus. Virology 255:63-76.
201. 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. 68:4856-4864.
202. Vander Byl, C., and A. M. Kropinski. 2000. Sequence of the genome of Salmonella bacteriophage P22. J. Bacteriol. 182:6472-6481.
203. van der Wilk, F., A. M. Dullemans, M. Verbeek, and J. F. van den Heuvel. 1999. Isolation and characterization of APSE-1, a bacteriophage infecting the secondary ndosymbiont of Acyrthosiphon pisum. Virology 262:104-113.
204. van Ham, R. C., J. Kamerbeek, C. Palacos, C. Rausell, F. Abascal, U. Bastolla, J. M. Fernandez, L. Jimenez, M. Postigo, F. J. Silva, J. Tamames, E. Viguera, A. Latorre, A. Valencia, F. Moran, and A. Moya. 2003. Reductive genome evolution in Buchnera aphidicola. Proc. Natl. Acad. Sci. USA 100:581-586.
205. Van Kaer, L., Y. Gansemans, M. Van Montagu, and P. Dhaese, 1988. Interaction of the Bacillus subtilis phage phi 105 repressor DNA: a genetic analysis. EMBO J. 7:859-866.
206. van Sinderen, D., H. Karsens, J. Kok, P. Terpstra, M. H. Ruiters, G. Venema, and A. Nauta. 1996. Sequence analysis and molecular characterization of the temperate lactococcal bacteriophage r1t. Mol. Microbiol. 19:1343-1355.
207. Van Sluys, M. A., M. C. de Oliveira, C. B. Monteiro-Vitorello, C. Y. Miyaki, L. R. Furlan, L. E. Camargo, A. C. da Silva, D. H. Moon, M. A. Takita, E. G. Lemos, M. A. Machado, M. I. Ferro, F. R. da Silva, M. H. Goldman, G. H. Goldman, M. V. 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. 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. Sena, A. A. de Souza, D. Truffi, F. Tsukumo, G. M. Yanai, L. G. Zaros, E. L. Civerolo, A. J. 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. 185:1018-1026.
208. Vasala, A., L. Dupont, M. Baumann, P. Ritzenthaler, and T. Alatossava. 1993. Molecular comparison of the structural proteins encoding gene clusters of two related Lactobacillus delbrueckii bacteriophages. J. Virol. 67:3061-3068.
209. Ventura, M., A. Bruttin, C. Canchaya, and H. Brüssow. 2002. Transcription analysis of Streptococcus thermophilus phages in the lysogenic state. Virology 302:21-32.
210. Ventura, M., S. Foley, A. Bruttin, S. C. Chennoufi, C. Canchaya, and H. Brüssow. 2002. Transcription mapping as a tool in phage genomics: the case of the temperate Streptococcus thermophilus phage Sfi21. Virology 296:62-76.
211. Wagner, P. L., D. W. Acheson, and M. K. Waldor. 1999. Isogenic lysogens of diverse shiga toxin 2-encoding bacteriophages produce markedly different amounts of shiga toxin. Infect. Immun. 67:6710-6714.
212. Wagner, P. L., D. W. Acheson, and M. K. Waldor. 2001. Human neutrophils and their products induce Shiga toxin production by enterohemorrhagic Escherichia coli. Infect. Immun. 69:1934-1937.
213. Wagner, P. L., J. Livny, M. N. Neely, D. W. Acheson, D. I. Friedman, and M. K. Waldor. 2002. Bacteriophage control of Shiga toxin 1 production and release by Escherichia coli. Mol. Microbiol. 44:957-970.
214. 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. 183:2081-2085.
215. Wagner, P. L., and M. K. Waldor. 2002. Bacteriophage control of bacterial virulence. Infect. Immun. 70:3985-3993.
216. Waldor, M. K. 1998. Bacteriophage biology and bacterial virulence. Trends Microbiol. 6:295-297.
217. Waldor, M. K., and J. J. Mekalanos. 1996. Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272:1910-1914.
218. Weisberg, R. A., M. E. Gottesmann, R. W. Hendrix, and J. W. Little. 1999. Family values in the age of genomics: comparative analyses of temperate bacteriophage HK022. Annu. Rev. Genet. 33:565-602.
219. Welch, R. A., V. Burland, G. Plunkett, III, P. Redford, P. Roesch, D. Rasko, E. L. Buckles, S. R. Liou, A. Boutin, J. Hackett, D. Stroud, G. F. Mayhew, D. J. Rose, S. Zhou, D. C. Schwartz, N. T. Perna, H. L. Mobley, M. S. Donnenberg, and F. R. Blattner. 2002. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 99:17020-17024.
220. Whiteley, M., M. G. Bangera, R. E. Bumgarner, M. R. Parsek, G. M. Teitzel, S. Lory, and E. P. Greenberg. 2001. Gene expression in Pseudomonas aeruginosa biofilms. Nature 413:860-864.
221. Wilson, S. E., C. J. Ingham, I. S. Hunter, and M. C. Smith. 1995. Control of lytic development in the Streptomyces temperate phage phi C31. Mol. Microbiol. 16:131-143.
222. Winkler, K. C., J. de Waart, and C. Grootsen. 1965. Lysogenic conversion of staphylococci to loss of beta-toxin. J. Gen. Microbiol. 39:321-333.
223. Wood, H. E., M. T. Dawson, K. M. Devine, and D. J. McConnell. 1990. Characterization of PBSX, a defective prophage of Bacillus subtilis. J. Bacteriol. 172:2667-2674.
224. Woods, D. E., J. A. Jeddeloh, D. L. Fritz, and D. DeShazer. 2002. Burkholderia thailandensis E125 harbors a temperate bacteriophage specific for Burkholderia mallei. J. Bacteriol. 184:4003-4017.
225. 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. 38:694-705.
226. Yarwood, J. M., J. K. McCormick, M. L. Paustian, P. M. Orwin, V. Kapur, and P. M. Schlievert. 2002. Characterization and expression analysis of Staphylococcus aureus pathogenicity island 3. Implications for the evolution of staphylococcal pathogenicity islands. J. Biol. Chem. 277:13138-13147.
227. Ye, Z. H., S. L. Buranen, and C. Y. Lee. 1990. Sequence analysis and comparison of int and xis genes from staphylococcal bacteriophages L54a and phi 11. J. Bacteriol. 172:2568-2575.
228. Ye, Z. H., and C. Y. Lee. 1989. Nucleotide sequence and genetic characterization of staphylococcal bacteriophage L54a int and xis genes. J. Bacteriol. 171:4146-4153.
229. Yokoyama, K., K. Makino, Y. Kubota, M. Watanabe, S. Kimura, C. H. Yutsudo, K. Kurokawa, K. Ishii, M. Hattori, I. Tatsuno, H. Abe, M. Yoh, T. Iida, M. Ohnishi, T. Hayashi, T. Yasunaga, T. Honda, C. Sasakawa, and H. Shinagawa. 2000. Complete nucleotide sequence of the prophage VT1-Sakai carrying the Shiga toxin 1 genes of the enterohemorrhagic Escherichia coli O157:H7 strain derived from the Sakai outbreak. Gene 258:127-139.
230. Yu, C. E., and J. J. Ferretti. 1991. Molecular characterization of new group A streptococcal bacteriophages containing the gene for streptococcal erythrogenic toxin A (speA). Mol. Gen. Genet. 231:161-168.
231. Zahler S. A. 1993. Temperate bacteriophages, p. 831-842. In A. L. Sonenshein, J. A. Hoch, and R. Losick (ed.), Bacillus subtilis and other gram-positive bacteria. American Society for Microbiology, Washington, D.C.
232. Zillig, W., D. Prangishvilli, C. Schleper, M. Elferink, I. Holz, S. Albers, D. Janekovic, and D. Gotz. 1996. Viruses, plasmids and other genetic elements of thermophilic and hyperthermophilic Archaea. FEMS Microbiol. Rev. 18:225-236.
233. Zimmer, M., S. Scherer, and M. J. Loessner. 2002. Genomic analysis of Clostridium perfringens bacteriophage phi3626, which integrates into guaA and possibly affects sporulation. J. Bacteriol. 184:4359-4368.
234. Zou, D., J. Kaneko, S. Narita, and Y. Kamio. 2000. Prophage, phiPV83-pro, carrying panton-valentine leukocidin genes, on the Staphylococcus aureus P83 chromosome: comparative analysis of the genome structures of phiPV83-pro, phiPVL, phi11, and other phages. Biosci. Biotechnol. Biochem. 64:2631-2643.
235. Zuniga, M., B. Franke-Fayard, G. Venema, J. Kok, and A. Nauta. 2002. Characterization of the putative replisome organizer of the lactococcal bacteriophage r1t. J. Virol. 76:10234-10244.