SEARCH

SEARCH BY CITATION

References

  • Agron, P.G., Walker, R.L., Kinde, H., Sawyer, S.J., Hayes, D.C., Wollard, J., et al. (2001) Identification by subtractive hybridization of sequences specific for Salmonella enterica serovar Enteritidis. Appl Environ Microbiol 67: 49844991.
  • Allison, G.E., Angeles, D., Tran-Dinh, N., and Verma, N.K. (2002) Complete genomic sequence of SfV, a serotype-converting temperate bacteriophage of Shigella flexneri. J Bacteriol 184: 19741987.
  • Alonso, J.C., Luder, G., Stiege, A.C., Chai, S., Weise, F., and Trautner, T.A. (1997) The complete nucleotide sequence and functional organization of Bacillus subtilis bacteriophage SPP1. Gene 204: 201212.
  • Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 33893402.
  • Anilionis, A., Ostapchuk, P., and Riley, M. (1980) Identification of a second cryptic lambdoid prophage locus in the E. coli K12 chromosome. Mol Gen Genet 180: 479481.
  • Bail, O. (1925) Der kolistamm 88 von Gildmeister und Herzberg. Med Klin (Munich) 21: 12711273.
  • Banks, D.J., Beres, S.B., and Musser, J.M. (2002) The fundamental contribution of phages to GAS evolution, genome diversification and strain emergence. Trends Microbiol 10: 515521.
  • Bao, Q., Tian, Y., Li, W., Xu, Z., Xuan, Z., Hu, S., et al. (2002) A complete sequence of the T. tengcongensis genome. Genome Res 12: 689700.
  • Barreiro, V., and Haggard-Ljungquist, E. (1992) Attachment sites for bacteriophage P2 on the Escherichia coli chromosome: DNA sequences, localization on the physical map, and detection of a P2-like remnant in E. coli K-12 derivatives. J Bacteriol 174: 40864093.
  • Bejar, S., Bouche, F., and Bouche, J.P. (1988) Cell division inhibition gene dicB is regulated by a locus similar to lambdoid bacteriophage immunity loci. Mol Gen Genet 212: 1119.
  • Bentley, S., Chater, K., Cerdeno-Tarrage, A., Challis, G., Thomson, R., James, K., et al. (2002) Complete genome sequence of the model actinomycete Streptococcus coelicolor A3(2). Nature 417: 141147.
  • Beres, S.B., Sylva, G.L., Barbian, K.D., Lei, B., Hoff, J.S., Mammarella, N.D., et al. (2002) Genome sequence of a serotype M3 strain of group A Streptococcus: phage-encoded toxins, the high-virulence phenotype, and clone emergence. Proc Natl Acad Sci USA 99: 1007810083.
  • Bergh, O., Borsheim, K., Bratbak, G., and Heldal, M. (1989) High abundance of viruses found in aquatic environments. Nature 340: 467468.
  • Bertani, G. (1951) Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol 62: 293299.
  • Bertani, E., and Six, E. (1988) The P2-like phages and their parasite P4. In The Bacteriophages, Vol. 2. Calendar, R. (ed.). New York: Plenum Press, pp. 73143.
  • Bishai, W., and Murphy, J. (1988) Bacteriophage gene products that cause human disease. In The Bacteriophages, Vol. 2. Calendar, R. (ed.). New York: Plenum Press, pp. 683724.
  • Blaisdell, B.E., Campbell, A.M., and Karlin, S. (1996) Similarities and dissimilarities of phage genomes. Proc Natl Acad Sci USA 93: 58545859.
  • Blasband, A.J., Marcotte, W.R., Jr, and Schnaitman, C.A. (1986) Structure of the lc and nmpC outer membrane porin protein genes of lambdoid bacteriophage. J Biol Chem 261: 1272312732.
  • Blattner, F.R., Plunkett, G., III, Bloch, C.A., Perna, N.T., Burland, V., Riley, M., et al. (1997) The complete genome sequence of Escherichia coli K-12. Science 277: 14531474.
  • Bolotin, A., Wincker, P., Mauger, S., Jaillon, O., Malarme, K., Weissenbach, J., et al. (2001) The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403. Genome Res 11: 731753.
  • Bordet, J. (1925) Le probléme de l’autolyse microbienne transmissible ou du bactériophage. Ann Inst Pasteur 39: 711763.
  • Botstein, D. (1980) A theory of modular evolution in bacteriophages. Ann NY Acad Sci 354: 484491.
  • Bouchard, J.D., and Moineau, S. (2000) Homologous recombination between a lactococcal bacteriophage and the chromosome of its host strain. Virology 270: 6575.
  • Boyd, E.F., and Brussow, H. (2002) Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved. Trends Microbiol 10: 521529.
  • Boyd, E.F., Davis, B.M., and Hochhut, B. (2001) Bacteriophage–bacteriophage interactions in the evolution of pathogenic bacteria. Trends Microbiol 9: 137144.
  • Brandt, K., Tilsala-Timisjarvi, A., and Alatossava, T. (2001) Phage-related DNA polymorphism in dairy and probiotic Lactobacillus. Micron 32: 5965.
  • Brikun, I., Suziedelis, K., and Berg, D.E. (1994) DNA sequence divergence among derivatives of Escherichia coli K-12 detected by arbitrary primer PCR (random amplified polymorphic DNA) fingerprinting. J Bacteriol 176: 16731682.
  • Brody, H., Greener, A., and Hill, C.W. (1985) Excision and reintegration of the Escherichia coli K-12 chromosomal element e14. J Bacteriol 161: 11121117.
  • Bruggemann, H., Baumer, S., Fricke, W.F., Wiezer, A., Liesegang, H., Decker, I., et al. (2003) The genome sequence of Clostridium tetani, the causative agent of tetanus disease. Proc Natl Acad Sci USA 100: 13161321.
  • Brussow, H., and Hendrix, R.W. (2002) Phage genomics: small is beautiful. Cell 108: 1316.
  • Bunny, K., Liu, J., and Roth, J. (2002) Phenotypes of lexA mutations in Salmonella enterica: evidence for a lethal lexA null phenotype due to the Fels-2 prophage. J Bacteriol 184: 62356249.
  • Campbell, A. (1962) The episomes. Adv Genet 11: 101118.
  • Campbell, A. (1994) Comparative molecular biology of lambdoid phages. Annu Rev Microbiol 48: 193222.
  • Campbell, A. (1996) Cryptic prophages. In Escherichia coli and Salmonella: Cellular and Molecular Biology. Neidhardt, F. (ed.). Washington, DC: American Society for Microbiology Press, pp. 20412046.
  • Campbell, A., and Botstein, D. (1983) Evolution of the lambdoid phages. In Lambda II. Hendrix, R., Roberts, J.W., Stahl, F.W., and Weisberg, R. (eds). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 365380.
  • Campbell, A., Schneider, S.J., and Song, B. (1992) Lambdoid phages as elements of bacterial genomes (integrase/phage 21/Escherichia coli K-12/icd gene). Genetica 86: 259267.
  • Canchaya, C., Desiere, F., McShan, W., Ferretti, J., Parkhill, J., and Brussow, H. (2002) Genome analysis of an inducible prophage and prophage remnants integrated into Streptococcus pyogenes strain SF370. Virology 302: 245258.
  • Casjens, S. (1997) Principles of virion structure, function and assembly. In Structural Biology of Viruses. Chiu, W., Burnett, R., and Garcea, R. (eds). Oxford: Oxford University Press, pp. 337.
  • Casjens, S., and Hendrix, R. (1988) Control mechanisms in dsDNA bacteriophage assembly. In The Bacteriophages, Vol. 1. Calendar, R. (ed.). New York: Plenum Press, pp. 1591.
  • Casjens, S., and Hendrix, R. (2003) Bacteriophage roles in bacterial chromosome evolution. In The Bacterial Chromosome. Higgins, P. (ed.). Washington, DC: American Society for Microbiology Press, (in press).
  • Casjens, S., Hatfull, G., and Hendrix, R. (1992) Evolution of dsDNA tailed-bacteriophage genomes. Semin Virol 3: 383397.
  • Casjens, S., Van Vugt, R., Tilly, K., Rosa, P.A., and Stevenson, B. (1997) Homology throughout the multiple 32-kilobase circular plasmids present in Lyme disease spirochetes. J Bacteriol 179: 217227.
  • Casjens, S., Palmer, N., Van Vugt, R., Mun Huang, W., Stevenson, B., Rosa, P., et al. (2000) A bacterial genome in flux: the twelve linear and nine circular extrachromosomal DNAs in an infectious isolate of the Lyme disease spirochaete Borrelia burgdorferi. Mol Microbiol 35: 490516.
  • Chang, C.C., Gilsdorf, J.R., DiRita, V.J., and Marrs, C.F. (2000) Identification and genetic characterization of Haemophilus influenzae genetic island 1. Infect Immun 68: 26302637.
  • Chang, K.H., Wen, F.S., Tseng, T.T., Lin, N.T., Yang, M.T., and Tseng, Y.H. (1998) Sequence analysis and expression of the filamentous phage φLf gene I encoding a 48-kDa protein associated with host cell membrane. Biochem Biophys Res Commun 245: 313318.
  • Cheetham, B.F., and Katz, M.E. (1995) A role for bacteriophages in the evolution and transfer of bacterial virulence determinants. Mol Microbiol 18: 201208.
  • Chopin, M.C., Chopin, A., Rouault, A., and Galleron, N. (1989) Insertion and amplification of foreign genes in the Lactococcus lactis subsp. lactis chromosome. Appl Environ Microbiol 55: 17691774.
  • Chopin, A., Bolotin, A., Sorokin, A., Ehrlich, S.D., and Chopin, M. (2001) Analysis of six prophages in Lactococcus lactis IL1403: different genetic structure of temperate and virulent phage populations. Nucleic Acids Res 29: 644651.
  • Conter, A., Bouche, J.P., and Dassain, M. (1996) Identification of a new inhibitor of essential division gene ftsZ as the kil gene of defective prophage Rac. J Bacteriol 178: 51005104.
  • Damman, C.J., Eggers, C.H., Samuels, D.S., and Oliver, D.B. (2000) Characterization of Borrelia burgdorferi BlyA and BlyB proteins: a prophage-encoded holin-like system. J Bacteriol 182: 67916797.
  • Davis, B.M., Kimsey, H.H., Chang, W., and Waldor, M.K. (1999) The Vibrio cholerae O139 Calcutta bacteriophage CTXφ is infectious and encodes a novel repressor. J Bacteriol 181: 67796787.
  • Deng, W., Burland, V., Plunkett, G., III, Boutin, A., Mayhew, G.F., Liss, P., et al. (2002) Genome sequence of Yersinia pestis KIM. J Bacteriol 184: 46014611.
  • Dep, M.S., Mendz, G.L., Trend, M.A., Coloe, P.J., Fry, B.N., and Korolik, V. (2001) Differentiation between Campylobacter hyoilei and Campylobacter coli using genotypic and phenotypic analyses. Int J Syst Evol Microbiol 51: 819826.
  • Desiere, F., Mahanivong, C., Hillier, A.J., Chandry, P.S., Davidson, B.E., and Brussow, H. (2001) Comparative genomics of lactococcal phages: insight from the complete genome sequence of Lactococcus lactis phage BK5-T. Virology 283: 240252.
  • Dosch, D.C., Helmer, G.L., Sutton, S.H., Salvacion, F.F., and Epstein, W. (1991) Genetic analysis of potassium transport loci in Escherichia coli: evidence for three constitutive systems mediating uptake potassium. J Bacteriol 173: 687696.
  • Eggers, C.H., and Samuels, D.S. (1999) Molecular evidence for a new bacteriophage of Borrelia burgdorferi. J Bacteriol 181: 73087313.
  • Eggers, C.H., Casjens, S., Hayes, S.F., Garon, C.F., Damman, C.J., Oliver, D.B., et al. (2000) Bacteriophages of spirochetes. J Mol Microbiol Biotechnol 2: 365373.
  • Emmerth, M., Goebel, W., Miller, S.I., and Hueck, C.J. (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: 56525661.
  • Espion, D., Kaiser, K., and Dambly-Chaudiere, C. (1983) A third defective lambdoid prophage of Escherichia coli K12 defined by the lambda derivative, lambdaqin111. J Mol Biol 170: 611633.
  • Evans, R., Seeley, N.R., and Kuempel, P.L. (1979) Loss of rac locus DNA in merozygotes of Escherichia coli K12. Mol Gen Genet 175: 245250.
  • Faubladier, M., and Bouche, J.P. (1994) Division inhibition gene dicF of Escherichia coli reveals a widespread group of prophage sequences in bacterial genomes. J Bacteriol 176: 11501156.
  • Feinstein, S.I., and Low, K.B. (1982) Zygotic induction of the rac locus can cause cell death in E. coli. Mol Gen Genet 187: 231235.
  • Ferretti, J.J., McShan, W.M., Ajdic, D., Savic, D.J., Savic, G., Lyon, K., et al. (2001) Complete genome sequence of an M1 strain of Streptococcus pyogenes. Proc Natl Acad Sci USA 98: 46584663.
  • Figueroa-Bossi, N., and Bossi, L. (1999) Inducible prophages contribute to Salmonella virulence in mice. Mol Microbiol 33: 167176.
  • Fleischmann, R.D., Adams, M.D., White, O., Clayton, R.A., Kirkness, E.F., Kerlavage, A.R., et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269: 496512.
  • Fleischmann, R., Alland, D., Eisen, J., Carpenter, L., White, O., Peterson, J., et al. (2002) Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol 184: 54795490.
  • Fouts, K.E., Wasie-Gilbert, T., Willis, D.K., Clark, A.J., and Barbour, S.D. (1983) Genetic analysis of transposon-induced mutations of the Rac prophage in Escherichia coli K-12 which affect expression and function of recE. J Bacteriol 156: 718726.
  • Fraser, C.M., Casjens, S., Huang, W.M., Sutton, G.G., Clayton, R., Lathigra, R., et al. (1997) Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390: 580586.
  • Freifelder, D., and Meselson, M. (1970) Topological relationship of prophage lambda to the bacterial chromosome in lysogenic cells. Proc Natl Acad Sci USA 65: 200205.
  • Galibert, F., Finan, T.M., Long, S.R., Puhler, A., Abola, P., Ampe, F., et al. (2001) The composite genome of the legume symbiont Sinorhizobium meliloti. Science 293: 668672.
  • Garcia-Vallve, S., Palau, J., and Romeu, A. (1999) Horizontal gene transfer in glycosyl hydrolases inferred from codon usage in Escherichia coli and Bacillus subtilis. Mol Biol Evol 16: 11251134.
  • George, D.G., Yeh, L.S., and Barker, W.C. (1983) Unexpected relationships between bacteriophage lambda hypothetical proteins and bacteriophage T4 tail-fiber proteins. Biochem Biophys Res Commun 115: 10611068.
  • Gerstein, M. (1998) Measurement of the effectiveness of transitive sequence comparison, through a third ‘intermediate’ sequence. Bioinformatics 14: 707714.
  • Ghelardini, P., La Valle, R., and Paolozzi, L. (1994) The Mu gem operon: its role in gene expression, recombination and cell cycle. Genetica 94: 151156.
  • Gildmeister, E., and Herzberg, K. (1924) Zur theorie der bakteriophagen (d’Herelle Lysine). 6. Mitteilung über das d’Herellesche phanomen. Zentr Bakteriol Parasitenk I Abt Orig 93: 402420.
  • Girons, I.S., Bourhy, P., Ottone, C., Picardeau, M., Yelton, D., Hendrix, R.W., et al. (2000) The LE1 bacteriophage replicates as a plasmid within Leptospira biflexa: construction of an L. biflexa–Escherichia coli shuttle vector. J Bacteriol 182: 57005705.
  • Glaser, P., Frangeul, L., Buchrieser, C., Rusniok, C., Amend, A., Baquero, F., et al. (2001) Comparative genomics of Listeria species. Science 294: 849852.
  • Goodman, S.D., and Scocca, J.J. (1988) Identification and arrangement of the DNA sequence recognized in specific transformation of Neisseria gonorrhoeae. Proc Natl Acad Sci USA 85: 69826986.
  • Gratia, J.P. (1989) Products of defective lysogeny in Serratia marcescens SMG 38 and their activity against Escherichia coli and other Enterobacteria. J Gen Microbiol 135: 2535.
  • Greener, A., and Hill, C.W. (1980) Identification of a novel genetic element in Escherichia coli K-12. J Bacteriol 144: 312321.
  • Harshey, R. (1988) Phage Mu. In The Bacteriophages, Vol. 1. Calendar, R. (ed.). New York: Plenum Press, pp. 193234.
  • Hayashi, T., Makino, K., Ohnishi, M., Kurokawa, K., Ishii, K., Yokoyama, K., et al. (2001a) Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res 8: 1122.
  • Hayashi, T., Makino, K., Ohnishi, M., Kurokawa, K., Ishii, K., Yokoyama, K., et al. (2001b) Complete genome sequence of enterohemorrhagic Escherichia coli O157: H7 and genomic comparison with a laboratory strain K-12. DNA Res 8 (Suppl.): 4752.
  • Heidelberg, J.F., Paulsen, I.T., Nelson, K.E., Gaidos, E.J., Nelson, W.C., Read, T.D., et al. (2002) Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nature Biotechnol 20: 11181123.
  • Hendrix, R.W., and Duda, R.L. (1998) Bacteriophage HK97 head assembly: a protein ballet. Adv Virus Res 50: 235288.
  • Hendrix, R.W., Smith, M.C., Burns, R.N., Ford, M.E., and Hatfull, G.F. (1999) Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc Natl Acad Sci USA 96: 21922197.
  • Hendrix, R.W., Lawrence, J.G., Hatfull, G.F., and Casjens, S. (2000) The origins and ongoing evolution of viruses. Trends Microbiol 8: 504508.
  • Huggins, A.R., and Sandine, W.E. (1977) Incidence and properties of temperate bacteriophages induced from lactic streptococci. Appl Environ Microbiol 33: 184191.
  • Humphrey, S.B., Stanton, T.B., Jensen, N.S., and Zuerner, R.L. (1997) Purification and characterization of VSH-1, a generalized transducing bacteriophage of Serpulina hyodysenteriae. J Bacteriol 179: 323329.
  • Ikeda, H., and Tomizowa, J. (1968) Prophage P1, an extrachromosoal replication unit. Cold Spring Harb Symp Quant Biol 33: 791798.
  • Inal, J.M., and Karunakaran, K.V. (1996) φ20, a temperate bacteriophage isolated from Bacillus anthracis exists as a plasmidial prophage. Curr Microbiol 32: 171175.
  • Jian, W., Li, Z., Zhang, Z., Baker, M., Prevelige, P., and Chiu, W. (2003) Coat protein fold and maturation transition of bacteriophage P22 seen at sub-nanometer resolution. Nature Struct Biol 10: 131135.
  • Jin, Q., Yuan, Z., Xu, J., Wang, Y., Shen, Y., Lu, W., et al. (2002) Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res 30: 44324441.
  • Jin, S., Chen, Y., Christie, G.E., and Benedik, M.J. (1996) Regulation of the Serratia marcescens extracellular nuclease: positive control by a homolog of P2 Ogr encoded by a cryptic prophage. J Mol Biol 256: 264278.
  • Juhala, R.J., Ford, M.E., Duda, R.L., Youlton, A., Hatfull, G.F., and Hendrix, R.W. (2000) Genomic sequences of bacteriophages HK97 and HK022: pervasive genetic mosaicism in the lambdoid bacteriophages. J Mol Biol 299: 2751.
  • Kaiser, K. (1980) The origin of Q-independent derivatives of phage lambda. Mol Gen Genet 179: 547554.
  • Kaiser, K., and Murray, N.E. (1979) Physical characterisation of the ‘Rac prophage’ in E. coli K12. Mol Gen Genet 175: 159174.
  • King, G., and Murray, N.E. (1995) Restriction alleviation and modification enhancement by the Rac prophage of Escherichia coli K-12. Mol Microbiol 16: 769777.
  • Kirby, J., Trempy, J., and Gottesman, S. (1994) Excision of a P4-like cryptic prophage leads to Alp protease expression in Escherichia coli. J Bacteriol 176: 20682081.
  • Klee, S.R., Nassif, X., Kusecek, B., Merker, P., Beretti, J.L., Achtman, M., et al. (2000) Molecular and biological analysis of eight genetic islands that distinguish Neisseria meningitidis from the closely related pathogen Neisseria gonorrhoeae. Infect Immun 68: 20822095.
  • Klein, R., Baranyl, U., Rossler, N., Greineder, B., Scholz, H., and Witte, A. (2002) Natrialba magadii virus φCh1: first complete nucleotide sequence and functional organization of a virus infecting a haloalkaliphilic archaeon. Mol Microbiol 45: 851863.
  • Kofoid, E., Rappleye, C., Stojiljkovic, I., and Roth, J. (1999) The 17-gene ethanolamine (eut) operon of Salmonella typhimurium encodes five homologues of carboxysome shell proteins. J Bacteriol 181: 53175329.
  • Krogh, S., O'Reilly, M., Nolan, N., and Devine, K.M. (1996) The phage-like element PBSX and part of the skin element, which are resident at different locations on the Bacillus subtilis chromosome, are highly homologous. Microbiology 142: 20312040.
  • Kropinski, A.M. (2000) Sequence of the genome of the temperate, serotype-converting, Pseudomonas aeruginosa bacteriophage D3. J Bacteriol 182: 60666074.
  • Kuhn, J., and Campbell, A. (2001) The bacteriophage lambda attachment site in wild strains of Escherichia coli. J Mol Evol 53: 607614.
  • Kunst, F., Ogasawara, N., Moszer, I., Albertini, A.M., Alloni, G., Azevedo, V., et al. (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390: 249256.
  • Kuroda, M., Ohta, T., Uchiyama, I., Baba, T., Yuzawa, H., Kobayashi, I., et al. (2001) Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet 357: 12251240.
  • Lander, E.S., Linton, L.M., Birren, B., Nusbaum, C., Zody, M.C., Baldwin, J., et al. (2001) Initial sequencing and analysis of the human genome. Nature 409: 860921.
  • Lang, A.S., and Beatty, J.T. (2001) The gene transfer agent of Rhodobacter capsulatus and ‘constitutive transduction’ in prokaryotes. Arch Microbiol 175: 241249.
  • Lang, A.S., Beatty, J.T., LeBlanc, H., Towers, G., Harris, J., Lang, G., et al. (2000) Genetic analysis of a bacterial genetic exchange element: the gene transfer agent of Rhodobacter capsulatus. Proc Natl Acad Sci USA 97: 859864.
  • Lawrence, J.G., Hendrix, R.W., and Casjens, S. (2001) Where are the bacterial pseudogenes? Trends Microbiol 9: 535540.
  • Lawrence, J.G., Hatfull, G., and Hendrix, R. (2002) The imbroglios of viral taxonomy: genetic exchange and the failings of phenetic approaches. J Bacteriol 184: 48914905.
  • Lazarevic, V., Dusterhoft, A., Soldo, B., Hilbert, H., Mauel, C., and Karamata, D. (1999) Nucleotide sequence of the Bacillus subtilis temperate bacteriophage SPβc2. Microbiology 145: 10551067.
  • Lederberg, E. (1951) Lysogenicity in E. coli K-12. Genetics 36: 560.
  • Lewis, R.J., Brannigan, J.A., Offen, W.A., Smith, I., and Wilkinson, A.J. (1998) An evolutionary link between sporulation and prophage induction in the structure of a repressor: anti-repressor complex. J Mol Biol 283: 907912.
  • Lin, N.T., Chang, R.Y., Lee, S.J., and Tseng, Y.H. (2001) Plasmids carrying cloned fragments of RF DNA from the filamentous phage φLf can be integrated into the host chromosome via site-specific integration and homologous recombination. Mol Gen Genet 266: 425435.
  • Lindsey, D.F., Mullin, D.A., and Walker, J.R. (1989) Characterization of the cryptic lambdoid prophage DLP12 of Escherichia coli and overlap of the DLP12 integrase gene with the tRNA gene argU. J Bacteriol 171: 61976205.
  • Loessner, M.J., Inman, R.B., Lauer, P., and Calendar, R. (2000) Complete nucleotide sequence, molecular analysis and genome structure of bacteriophage A118 of Listeria monocytogenes: implications for phage evolution. Mol Microbiol 35: 324340.
  • Low, K.B. (1973) Restoration of the rac locus of recombinant forming ability in recB and recC merozygotes of Escherichia coli K12. Mol Gen Genet 122: 119130.
  • Lucchini, S., Desiere, F., and Brussow, H. (1999) Comparative genomics of Streptococcus thermophilus phage species supports a modular evolution theory. J Virol 73: 86478656.
  • Lwoff, A. (1953) Lysogeny. Bacteriol Rev 17: 269337.
  • Lwoff, A. (1966) The prophage and I. In Phage and the Origins of Molecular Biology. Cairns, J., Stent, G., and Watson, J. (eds). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 8899.
  • McClelland, M., Florea, L., Sanderson, K., Clifton, S.W., Parkhill, J., Churcher, C., et al. (2000) Comparison of the Escherichia coli K-12 genome with sampled genomes of a Klebsiella pneumoniae and three Salmonella enterica serovars, Typhimurium, Typhi and Paratyphi. Nucleic Acids Res 28: 49744986.
  • McClelland, M., Sanderson, K.E., Spieth, J., Clifton, S.W., Latreille, P., Courtney, L., et al. (2001) Complete genome sequence of Salmonella enterica serovar Typhimurium LT2. Nature 413: 852856.
  • McDonnell, G.E., Wood, H., Devine, K.M., and McConnell, D.J. (1994) Genetic control of bacterial suicide: regulation of the induction of PBSX in Bacillus subtilis. J Bacteriol 176: 58205830.
  • McDonough, M.A., and Butterton, J.R. (1999) Spontaneous tandem amplification and deletion of the shiga toxin operon in Shigella dysenteriae 1. Mol Microbiol 34: 10581069.
  • Mahajan, S.K., Chu, C.C., Willis, D.K., Templin, A., and Clark, A.J. (1990) Physical analysis of spontaneous and mutagen-induced mutants of Escherichia coli K-12 expressing DNA exonuclease VIII activity. Genetics 125: 261273.
  • Mahdi, A.A., Sharples, G.J., Mandal, T.N., and Lloyd, R.G. (1996) Holliday junction resolvases encoded by homologous rusA genes in Escherichia coli K-12 and phage 82. J Mol Biol 257: 561573.
  • Masui, S., Kamoda, S., Sasaki, T., and Ishikawa, H. (2000) Distribution and evolution of bacteriophage WO in Wolbachia, the endosymbiont causing sexual alterations in arthropods. J Mol Evol 51: 491497.
  • Masui, S., Kuroiwa, H., Sasaki, T., Inui, M., Kuroiwa, T., and Ishikawa, H. (2001) Bacteriophage WO and virus-like particles in Wolbachia, an endosymbiont of arthropods. Biochem Biophys Res Commun 283: 10991104.
  • Mediavilla, J., Jain, S., Kriakov, J., Ford, M.E., Duda, R.L., Jacobs, W.R., Jr, Et Al. (2000) Genome organization and characterization of mycobacteriophage Bxb1. Mol Microbiol 38: 955970.
  • Meselson, M. (1967) Reciprocal recombination in prophage lambda. J Cell Physiol 70 (Suppl. 1): 113118.
  • Miao, E.A., and Miller, S.I. (1999) Bacteriophages in the evolution of pathogen–host interactions. Proc Natl Acad Sci USA 96: 94529454.
  • Milkman, R., and Bridges, M.M. (1990) Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics 126: 505517.
  • Mizuno, M., Masuda, S., Takemaru, K., Hosono, S., Sato, T., Takeuchi, M., et al. (1996) Systematic sequencing of the 283 kb 210 degrees-232 degrees region of the Bacillus subtilis genome containing the skin element and many sporulation genes. Microbiology 142: 31033111.
  • Montag, D., and Henning, U. (1987) An open reading frame in the Escherichia coli bacteriophage lambda genome encodes a protein that functions in assembly of the long tail fibers of bacteriophage T4. J Bacteriol 169: 58845886.
  • Moreira, D. (2000) Multiple independent horizontal transfers of informational genes from bacteria to plasmids and phages: implications for the origin of bacterial replication machinery. Mol Microbiol 35: 15.
  • Morgan, G., Hatfull, G., Casjens, S., and Hendrix, R. (2002) Bacteriophage Mu genome sequence: analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus. J Mol Biol 317: 337359.
  • Morimyo, M., Hongo, E., Hama-Inaba, H., and Machida, I. (1992) Cloning and characterization of the mvrC gene of Escherichia coli K-12 which confers resistance against methyl viologen toxicity. Nucleic Acids Res 20: 31593165.
  • Nakayama, K., Kanaya, S., Ohnishi, M., Terawaki, Y., and Hayashi, T. (1999) The complete nucleotide sequence of φCTX, a cytotoxin-converting phage of Pseudomonas aeruginosa: implications for phage evolution and horizontal gene transfer via bacteriophages. Mol Microbiol 31: 399419.
  • Nakayama, K., Takashima, K., Ishihara, H., Shinomiya, T., Kageyama, M., Kanaya, S., et al. (2000) The R-type pyocin of Pseudomonas aeruginosa is related to P2 phage, and the F-type is related to lambda phage. Mol Microbiol 38: 213231.
  • Nelson, K.E., Weinel, C., Paulsen, I.T., Dodson, R.J., Hilbert, H., Martins dos Santos, V.A., et al. (2002) Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4: 799808.
  • Nguyen, A.H., Tomita, T., Hirota, M., Sato, T., and Kamio, Y. (1999) A simple purification method and morphology and component analyses for carotovoricin Er, a phage-tail-like bacteriocin from the plant pathogen Erwinia carotovora Er. Biosci Biotechnol Biochem 63: 13601369.
  • Nolling, J., Breton, G., Omelchenko, M.V., Makarova, K.S., Zeng, Q., Gibson, R., et al. (2001) Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bacteriol 183: 48234838.
  • Ochman, H., and Wilson, A.C. (1987) Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J Mol Evol 26: 7486.
  • Ohnishi, M., Kurokawa, K., and Hayashi, T. (2001) Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol 9: 481485.
  • Ojaimi, C., Brooks, C., Casjens, S., Rosa, P., Elias, A., Barbour, A., et al. (2003) Profiling temperature-induced changes in Borrelia burgdorferi gene expression using whole genome arrays. Infect Immun 71: 16891705.
  • Okamato, K., Mudd, J., Mangon, J., Huang, W.M., and Marmur, J. (1968) Properties of the defective phage of Bacillus subtilis. J Mol Biol 34: 413428.
  • Osawa, R., Iyoda, S., Nakayama, S.I., Wada, A., Yamai, S., and Watanabe, H. (2000) Genotypic variations of Shiga toxin-converting phages from enterohaemorrhagic Escherichia coli O157:H7 isolates. J Med Microbiol 49: 565574.
  • Pappenheimer, A.M., Jr, and Murphy, J.R. (1983) Studies on the molecular epidemiology of diphtheria. Lancet 2: 923926.
  • Parkhill, J., Achtman, M., James, K.D., Bentley, S.D., Churcher, C., Klee, S.R., et al. (2000) Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491. Nature 404: 502506.
  • Parkhill, J., Dougan, G., James, K.D., Thomson, N.R., Pickard, D., Wain, J., et al. (2001a) Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 413: 848852.
  • Parkhill, J., Wren, B.W., Thomson, N.R., Titball, R.W., Holden, M.T., Prentice, M.B., et al. (2001b) Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413: 523527.
  • Pedulla, M.L., Ford, M.E., Karthikeyan, T., Houtz, J.M., Hendrix, R.W., Hatfull, G.F., et al. (2003) Corrected sequence of the bacteriophage P22 genome. J Bacteriol 185: 14751477.
  • Perna, N.T., Plunkett, G., III, Burland, V., Mau, B., Glasner, J.D., Rose, D.J., et al. (2001) Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409: 529533.
  • Perna, N., Glasner, J., Burland, V., and Plunkett, G. III (2002) The Genomes of Escherichia coli K-12 and Pathogenic E. coli. In Escherichia coli: Virulence Mechanisms of a Versatile Pathogen. Donnenberg, M. (ed.). San Diego, CA: Academic Press, pp. 353.
  • Pfister, P., Wasserfallen, A., Stettler, R., and Leisinger, T. (1998) Molecular genomics of methanobacterium phage ΨM2. Mol Microbiol 30: 233244.
  • Popp, A., Hertwig, S., Lurz, R., and Appel, B. (2000) Comparative study of temperate bacteriophages isolated from Yersinia. Syst Appl Microbiol 23: 469478.
  • Ramirez, M., Severina, E., and Tomasz, A. (1999) A high incidence of prophage carriage among natural isolates of Streptococcus pneumoniae. J Bacteriol 181: 36183625.
  • Rapp, B., and Wall, J. (1987) Genetic transfer in Desulfovibrio desulfuricans. Proc Natl Acad Sci USA 84: 91289130.
  • Ravin, V.K. (1968) The functioning of the genes of temperate bacteriophage in lysogenic cells. Genetika 4: 119124 (in Russian).
  • Ravin, V., and Shulga, M.G. (1970) The evidence of extrachromosomal location phage prophage N15. Virology 40: 800805.
  • Ravin, V., Ravin, N., Casjens, S., Ford, M.E., Hatfull, G.F., and Hendrix, R.W. (2000) Genomic sequence and analysis of the atypical temperate bacteriophage N15. J Mol Biol 299: 5373.
  • Read, T.D., Brunham, R.C., Shen, C., Gill, S.R., Heidelberg, J.F., White, O., et al. (2000) Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39. Nucleic Acids Res 28: 13971406.
  • Recktenwald, J., and Schmidt, H. (2002) The nucleotide sequence of Shiga toxin (Stx) 2e-encoding phage φP27 is not related to other Stx phage genomes, but the modular genetic structure is conserved. Infect Immun 70: 18961908.
  • Redfield, R.J., and Campbell, A. (1987) Structure of cryptic λ prophages. J Mol Biol 198: 393404.
  • Reid, S.D., Herbelin, C.J., Bumbaugh, A.C., Selander, R.K., and Whittam, T.S. (2000) Parallel evolution of virulence in pathogenic Escherichia coli. Nature 406: 6467.
  • Retallack, D.M., Johnson, L.L., and Friedman, D.I. (1994) Role for 10Sa RNA in the growth of lambda-P22 hybrid phage. J Bacteriol 176: 20822089.
  • Rudd, K.E. (1999) Novel intergenic repeats of Escherichia coli K-12. Res Microbiol 150: 653664.
  • Ruzin, A., Lindsay, J., and Novick, R.P. (2001) Molecular genetics of SaPI1 – a mobile pathogenicity island in Staphylococcus aureus. Mol Microbiol 41: 365377.
  • Sandt, C.H., and Hill, C.W. (2000) Four different genes responsible for nonimmune immunoglobulin-binding activities within a single strain of Escherichia coli. Infect Immun 68: 22052214.
  • Schicklmaier, P., Moser, E., Wieland, T., Rabsch, W., and Schmieger, H. (1998) A comparative study on the frequency of prophages among natural isolates of Salmonella and Escherichia coli with emphasis on generalized transducers. Antonie Van Leeuwenhoek 73: 4954.
  • Schlosser, A., Kluttig, S., Hamann, A., and Bakker, E.P. (1991) Subcloning, nucleotide sequence, and expression of trkG, a gene that encodes an integral membrane protein involved in potassium uptake via the Trk system of Escherichia coli. J Bacteriol 173: 31703176.
  • Schmieger, H., and Schicklmaier, P. (1999) Transduction of multiple drug resistance of Salmonella enterica serovar typhimurium DT104. FEMS Microbiol Lett 170: 251256.
  • Shimizu, T., Ohtani, K., Hirakawa, H., Ohshima, K., Yamashita, A., Shiba, T., et al. (2002) Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc Natl Acad Sci USA 99: 9961001.
  • Da Silva, A.C., Ferro, J.A., Reinach, F.C., Farah, C.S., Furlan, L.R., Quaggio, R.B., et al. (2002) Comparison of the genomes of two Xanthomonas pathogens with differing host specificities. Nature 417: 459463.
  • Simpson, A.J., Reinach, F.C., Arruda, P., Abreu, F.A., Acencio, M., Alvarenga, R., et al. (2000) The genome sequence of the plant pathogen Xylella fastidiosa. Nature 406: 151157.
  • Six, E. (1963) A defective phage depending on phage P2. Bacteriol Proc 80: 138.
  • Smith, M.C., Burns, N., Sayers, J.R., Sorrell, J.A., Casjens, S.R., and Hendrix, R.W. (1998) Bacteriophage collagen. Science 279: 1834.
  • Smith, M.C., Burns, R.N., Wilson, S.E., and Gregory, M.A. (1999) The complete sequence of the Streptomyces temperate phage φC31: evolutionary relationships to other viruses. Nucleic Acids Res 27: 21452155.
  • Smith, T.J., Blackman, S.A., and Foster, S.J. (2000) Autolysins of Bacillus subtilis: multiple enzymes with multiple functions. Microbiology 146: 249262.
  • Smoot, J.C., Barbian, K.D., Van Gompel, J.J., Smoot, L.M., Chaussee, M.S., Sylva, G.L., et al. (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: 46684673.
  • Stanley, E., Fitzgerald, G.F., Le Marrec, C., Fayard, B., and Van Sinderen, D. (1997) Sequence analysis and characterization of φO1205, a temperate bacteriophage infecting Streptococcus thermophilus CNRZ1205. Microbiology 143: 34173429.
  • Starich, T., Cordes, P., and Zissler, J. (1985) Transposon tagging to detect a latent virus in Myxococcus xanthus. Science 230: 541543.
  • Stover, C.K., Pham, X.Q., Erwin, A.L., Mizoguchi, S.D., Warrener, P., Hickey, M.J., et al. (2000) Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406: 959964.
  • Susskind, M.M., and Botstein, D. (1978) Molecular genetics of bacteriophage P22. Microbiol Rev 42: 385413.
  • Susskind, M.M., and Botstein, D. (1980) Superinfection exclusion by lambda prophage in lysogens of Salmonella typhimurium. Virology 100: 212216.
  • Susskind, M.M., Botstein, D., and Wright, A. (1974) Superinfection exclusion by P22 prophage in lysogens of Salmonella typhimurium. III. Failure of superinfecting phage DNA to enter sieA+ lysogens. Virology 62: 350366.
  • Takemaru, K., Mizuno, M., Sato, T., Takeuchi, M., and Kobayashi, Y. (1995) Complete nucleotide sequence of a skin element excised by DNA rearrangement during sporulation in Bacillus subtilis. Microbiology 141: 323327.
  • Tang, S., Nutthall, S., Ngui, K., Fisher, C., Lopez, P., and Dyall-Smith, M. (2002) HF2: a double-stranded DNA tailed haloarcheal virus with a mosaic genome. Mol Microbiol 44: 283296.
  • Tettelin, H., Saunders, N.J., Heidelberg, J., Jeffries, A.C., Nelson, K.E., Eisen, J.A., et al. (2000) Complete genome sequence of Neisseria meningitidis serogroup B strain MC58. Science 287: 18091815.
  • Thaler, J.O., Baghdiguian, S., and Boemare, N. (1995) Purification and characterization of xenorhabdicin, a phage tail-like bacteriocin, from the lysogenic strain F1 of Xenorhabdus nematophilus. Appl Environ Microbiol 61: 20492052.
  • Van Sluys, M.A., De Oliveira, M.C., Monteiro-Vitorello, C.B., Miyaki, C.Y., Furlan, L.R., Camargo, L.E., et al. (2003) Comparative analyses of the complete genome sequences of Pierce's disease and citrus variegated chlorosis strains of Xylella fastidiosa. J Bacteriol 185: 10181026.
  • Van Vliet, F., Boyen, A., and Glansdorff, N. (1988) On interspecies gene transfer: the case of the argF gene of Escherichia coli. Ann Inst Pasteur Microbiol 139: 493496.
  • Wagner, P.L., and Waldor, M.K. (2002) Bacteriophage control of bacterial virulence. Infect Immun 70: 39853993.
  • Waldor, M.K. (1998) Bacteriophage biology and bacterial virulence. Trends Microbiol 6: 295297.
  • Waldor, M.K., and Mekalanos, J.J. (1996) Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272: 19101914.
  • Wall, J.D., Weaver, P.F., and Gest, H. (1975) Gene transfer agents, bacteriophages, and bacteriocins of Rhodopseudomonas capsulata. Arch Microbiol 105: 217224.
  • Wang, F.S., Whittam, T.S., and Selander, R.K. (1997) Evolutionary genetics of the isocitrate dehydrogenase gene (icd) in Escherichia coli and Salmonella enterica. J Bacteriol 179: 65516559.
  • Welch, R.A., Burland, V., Plunkett, G., III, Redford, P., Roesch, P., Rasko, D., et al. (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA 99: 1702017024.
  • Whatmore, A.M., and Dowson, C.G. (1999) The autolysin-encoding gene (lytA) of Streptococcus pneumoniae displays restricted allelic variation despite localized recombination events with genes of pneumococcal bacteriophage encoding cell wall lytic enzymes. Infect Immun 67: 45514556.
  • Wickner, S. (1984a) Oligonucleotide synthesis by Escherichia coli dnaG primase in conjunction with phage P22 gene 12 protein. J Biol Chem 259: 1404414047.
  • Wickner, S. (1984b) DNA-dependent ATPase activity associated with phage P22 gene 12 protein. J Biol Chem 259: 1403814043.
  • Willis, D.K., Satin, L.H., and Clark, A.J. (1985) Mutation-dependent suppression of recB21 recC22 by a region cloned from the Rac prophage of Escherichia coli K-12. J Bacteriol 162: 11661172.
  • Yamamoto, K. (1967) The origin of bacteriophage P221. Virology 33: 545547.
  • Yamamoto, N. (1969) Genetic evolution of bacteriophage. I. Hybrids between unrelated bacteriophages P22 and Fels2. Proc Natl Acad Sci USA 62: 6369.
  • Yen, H.C., Hu, N.T., and Marrs, B.L. (1979) Characterization of the gene transfer agent made by an overproducer mutant of Rhodopseudomonas capsulata. J Mol Biol 131: 157168.
  • Zinder, N., and Lederberg, J. (1952) Genetic exchange in Salmonella. J Bacteriol 64: 679699.
  • Zink, R., Loessner, M.J., and Scherer, S. (1995) Characterization of cryptic prophages (monocins) in Listeria and sequence analysis of a holin/endolysin gene. Microbiology 141: 25772584.
  • Zissler, J., Signer, E., and Sachaefer, F. (1971) The role of recombination in growth of bacteriophage lambda. In Bacteriophage Lambda. Hershey, A.D. (ed.). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, pp. 455475.