The impact of prophages on bacterial chromosomes

Molecular Microbiology

Volumn 53, Issue 1, 2004, Pages 9-18

  Canchaya, Carlos ^a   Fournous, Ghislain ^a   Brüssow, Harald ^a  

^a NESTLÉ RESEARCH CENTER   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; TRANSFER RNA;

AMINO ACID SEQUENCE; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIAL VIRULENCE; BACTERIUM IDENTIFICATION; CHROMOSOME REARRANGEMENT; DNA DETERMINATION; DNA MICROARRAY; GENE DISRUPTION; GENE EXPRESSION; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; HOST; METHODOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROPHAGE; SALMONELLA; SHORT SURVEY; SPECIES;

BACTERIA; DNA, VIRAL; GENOME, BACTERIAL; PROPHAGES;

ANIMALIA; BACTERIA (MICROORGANISMS); NEGIBACTERIA; POSIBACTERIA; SALMONELLA; UNIDENTIFIED BACTERIOPHAGE;

EID: 3142514466     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1365-2958.2004.04113.x     Document Type: Short Survey

References (52)

1. Baba, T., Takeuchi, F., Kuroda, M., Yuzawa, H., Aoki, K., Oguchi, A., et al. (2002) Genome and virulence determinants of high virulence community-acquired MRSA. Lancet 359: 1819-1827.
2. Barondess, J.J., and Beckwith, J. (1990) A bacterial virulence determinant encoded by lysogenic coliphage lambda. Nature 346: 871-874.
3. 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: 10078-10083.
4. Boyd, E.F., and Brüssow, H. (2002) Common themes among bacteriophage-encoded virulence factors and diversity among the bacteriophages involved. Trends Microbiol 10: 521-529.
5. Broudy, T.B., and Fischetti, V.A. (2003) In vivo lysogenic conversion of Tox(-) Streptococcus pyogenes to Tox(+) with lysogenic streptococci or free phage. Infect Immun 71: 3782-3786.
6. Broudy, T.B., Pancholi, V., and Fischetti, V.A. (2001) Induction of lysogenic bacteriophage and phage-associated toxin from group A streptococci during coculture with human pharyngeal cells. Infect Immun 69: 1440-1443.
7. Broudy, T.B., Pancholi, V., and Fischetti, V.A. (2002) The in vitro interaction of Streptococcus pyogenes with human pharyngeal cells induces a phage-encoded extracellular DNase. Infect Immun 70: 2805-2811.
8. Brüssow, H., and Hendrix, R.W. (2002) Phage genomics: small is beautiful. Cell 108: 13-16.
9. Bruttin, A., Foley, S., and Brüssow, H. (1997) The site-specific integration system of the temperate Streptococcus thermophilus bacteriophage phiSfi21. Virology 237: 148-158.
10. Campbell, A.M. (1992) Chromosomal insertion sites for phages and plasmids. J Bacteriol 174: 7495-7499.
11. Campbell, A.M. (2002) Preferential orientation of natural lambdoid prophages and bacterial chromosome organization. Theor Popul Biol 61: 503-507.
12. Campbell, A., Schneider, S.J., and Song, B. (1992) Lambdoid phages as elements of bacterial genomes (integrase/ phage21/Escherichia coli K-12/icd gene). Genetica 86: 259-267.
13. Canchaya, C., Desiere, F., McShan, W.M., Ferretti, J.J., Parkhill, J., and Brüssow, H. (2002) Genome analysis of an inducible prophage and prophage remnants integrated in the Streptococcus pyogenes strain SF370. Virology 302: 245-258.
14. Canchaya, C., Proux, C., Fournous, G., Bruttin, A., and Brüssow, H. (2003) Prophage genomics. Microbiol Mol Biol Rev 67: 238-276.
15. Casjens, S. (2003) Prophages and bacterial genomics: what have we learned so far? Mol Microbiol 49: 277-300.
16. Cerdeno-Tarraga, A.M., Efstratiou, A., Dover, L.G., Holden, M.T., Pallen, M., Bentley, S.D., et al. (2003) The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129. Nucleic Acids Res 31: 6516-6523.
17. Chan, K., Baker, S., Kim, C.C., Detweiler, C.S., Dougan, G., and Falkow, S. (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.
18. 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: 4601-4611.
19. Doolittle, W.F. (1999) Phylogenetic classification and the universal tree. Science 284: 2124-2129.
20. Dozois, C.M., Daigle, F., and Curtiss, R. (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.
21. Dziejman, M., Balon, E., Boyd, D., Fraser, C.M., Heidelberg, J.F., and Mekalanos, J.J. (2002) Comparative genomic analysis of Vibrio cholerae: genes that correlate with cholera endemic and pandemic disease. Proc Natl Acad Sci USA 99: 1556-1561.
22. Fitzgerald, J.R., Sturdevant, D.E., Mackie, S.M., Gill, S.R., and Musser, J.M. (2001) Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic. Proc Natl Acad Sci USA 98: 8821-8826.
23. Fournous, G. (2003) Automatisation de la recherche et de l'analyse de prophages dans les génomes bactériens. Travail de DEA, Université Henri Poincaré, Nancy, France.
24. Gamage, S.D., Strasser, J.E., Chalk, C.L., and Weiss, A.A. (2003) Nonpathogenic Escherichia coli can contribute to the production of Shiga toxin. Infect Immun 71: 3107-3115.
25. Glaser, P., Frangeul, L., Buchrieser, C., Rusniok, C., Amend, A., Baquero, F., et al. (2001) Comparative genomics of Listeria species. Science 294: 849-852.
26. Glaser, P., Rusniok, C., Buchrieser, C., Chevalier, F., Frangeul, L., Msadek, T., et al. (2002) Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease. Mol Microbiol 45: 1499-1513.
27. 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: 27-51.
28. Kazmi, S.U., Kansal, R., Aziz, R.K., Hooshdaran, M., Norrby-Teglund, A., Low, D.E., et al. (2001) Reciprocal, temporal expression of SpeA and SpeB by invasive M1T1 group a streptococcal isolates in vivo. Infect Immun 69: 4988-4995.
29. Kurland, C.G., Canback, B., and Berg, O.G. (2003) Horizontal gene transfer: a critical view. Proc Natl Acad Sci USA 100: 9658-9662.
30. Kuroda, M., Ohta, T., Uchiyama, I., Baba, T., Yuzawa, H., Kobayashi, I., et al. (2001) Whole genome sequencing of methicillin-resistant Staphylococcus aureus. Lancet 357: 1225-1240.
31. Lawrence, J.G., and Roth, J.R. (1999) Genomic flux; genomic evolution by gene loss and acquisition. In Organization of the Prokaryotic Genome. Charlebois, R.L. (ed.). Washington, DC: American Society for Microbiology Press, pp. 263-289.
32. Lawrence, J.G., Hendrix, R.W., and Casjens, S. (2003) Where are the pseudogenes in bacterial genomes. Trends Microbiol 9: 535-540.
33. Lee, C.Y., and Iandolo, J.J. (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.
34. 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: 1058-1069.
35. Magrini, V., Storms, M.L., and Youderian, P. (1999) Site-specific recombination of temperate Myxococcus xanthus phage Mx8: regulation of integrase activity by reversible, covalent modification. J Bacteriol 181: 4062-4070.
36. Makino, K., Yokoyama, K., Kubota, Y., Yutsudo, C.H., Kimura, S., Kurokawa, K., et al. (1999) Complete nucleotide sequence of the prophage VT2-Sakai carrying the verotoxin 2 genes of the enterohemorrhagic Escherichia coli O157:H7 derived from the Sakai outbreak. Genes Genet Syst 74: 227-239.
37. Nakagawa, I., Kurokawa, K., Yamashita, A., Nakata, M., Tomiyasu, Y., Okahashi, N., et al. (2003) Genome sequence of an M3 strain of Streptococcus pyogenes reveals a large-scale genomic rearrangement in invasive strains and new insights into phage evolution. Genome Res 13: 1042-1055.
38. Ohnishi, M., Kurokawa, K., and Hayashi, T. (2001) Diversification of Escherichia coli genomes: are bacteriophages the major contributors? Trends Microbiol 9: 481-485.
39. Porwollik, S., Wong, R.M., and McClelland, M. (2002) Evolutionary genomics of Salmonella: gene acquisitions revealed by microarray analysis. Proc Natl Acad Sci USA 99: 8956-8961.
40. Pridmore, D., Berger, B., Desiere, F., Vilanova, D., Barretto, C., Pittet, A.C., et al. (2004) The genome sequence of the probiotic intestinal bacterium Lactobacillus johnsonii NCC 533. Proc Natl Acad Sci USA 101: 2512-2517.
41. Smoot, L.M., Smoot, J.C., Graham, M.R., Somerville, G.A., Sturdevant, D.E., Migliaccio, C.A., et al. (2001) Global differential gene expression in response to growth temperature alteration in group A Streptococcus. Proc Natl Acad Sci USA 98: 10416-10421.
42. Smoot, J.C., Barbian, K.D., Van Gompel, J.J., Smoot, L.M., Chaussee, M.S., Sylva, G.L., et al. (2002a) 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.
43. Smoot, L.M., McCormick, J.K., Smoot, J.C., Hoe, N.P., Strickland, I., Cole, R.L., et al. (2002b) Characterization of two novel pyrogenic toxin superantigens made by an acute rheumatic fever clone of Streptococcus pyogenes associated with multiple disease outbreaks. Infect Immun 70: 7095-7104.
44. Sumby, P., and Waldor, M.K. (2003) Transcription of the toxin genes present within the Staphylococcal phage phiSa3ms is intimately linked with the phage's life cycle. J Bacteriol 185: 6841-6851.
45. Tettelin, H., Masignani, V., Cieslewicz, M.J., Eisen, J.A., Peterson, S., Wessels, M.R., et al. (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.
46. 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: 1018-1026.
47. Ventura, M., Canchaya, C., Pridmore, D., Berger, B., and Brüssow, H. (2003a) Integration and distribution of Lactobacillus johnsonii prophages. J Bacteriol 185: 4603-4608.
48. Ventura, M., Canchaya, C., Kleerebezem, M., de Vos, W.M., Siezen, R.J., and Brüssow, H. (2003b) The prophage sequences of Lactobacillus plantarum strain WCFS1. Virology 316: 245-255.
49. Ventura, M., Canchaya, C., Pridmore, R.D., and Brüssow, H. (2004) The Prophages of Lactobacillus johnsonii NCC 533: comparative genomics and transcription analysis. Virology 320: 229-242.
50. Voyich, J.M., Sturdevant, D.E., Braughton, K.R., Kobayashi, S.D., Lei, B., Virtaneva, K., et al. (2003) Genome-wide protective response used by group A Streptococcus to evade destruction by human polymorphonuclear leukocytes. Proc Natl Acad Sci USA 100: 1996-2001.
51. Wagner, P.L., Livny, J., Neely, M.N., Acheson, D.W., Friedman, D.I., and Waldor, M.K. (2002) Bacteriophage control of Shiga toxin 1 production and release by Escherichia coli. Mol Microbiol 44: 957-970.
52. Whiteley, M., Bangera, M.G., Bumgarner, R.E., Parsek, M.R., Teitzel, G.M., Lory, S., and Greenberg, E.P. (2001) Gene expression in Pseudomonas aeruginosa biofilms. Nature 413: 860-864.