The future of bacteriophage biology

Nature Reviews Genetics

Volumn 4, Issue 6, 2003, Pages 471-477

  Campbell, Allan ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOPHAGE; DNA DAMAGE; DNA SEQUENCE; ECOSYSTEM; FOOD INDUSTRY; GENE CONTROL; GENE MAPPING; GENETIC VARIABILITY; GENOME ANALYSIS; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; NONHUMAN; PATHOGENICITY; PHAGE DISPLAY; PHYLOGENY; PRIORITY JOURNAL; REVIEW; SEQUENCE ANALYSIS;

BACTERIA; BACTERIOPHAGES; ECOLOGY; EVOLUTION; FORECASTING; MOLECULAR BIOLOGY; PEPTIDE LIBRARY;

UNIDENTIFIED BACTERIOPHAGE;

EID: 0038102232     PISSN: 14710056     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrg1089     Document Type: Review

References (59)

1. Twort, F. W. An investigation on the nature of ultramicroscopic viruses. Lancet 189, 1241-1243 (1916).
2. Ellis, E. L. & Delbrück, M. The growth of bacteriophage. J. Gen. Physiol 22, 365-384 (1939).
3. Campbell, A. & Botstein, D. in Lambda II (eds Hendrix, R. W., Roberts, J. W., Stahl, F. W. & Weisberg, R. A.) 356-381 (Cold Spring Harbor Laboratory Press, New York, 1983).
4. Hendrix, R. W. Bacteriophages: evolution of the majority. Theoret. Pop. Biol. 61, 471-480 (2002).
5. Hendrix, R. W., Smith, M. C., Burns, R. N., Ford, M. E. & Hatfull, G. F. Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc. Natl Acad. Sci. USA 96, 2192-2197 (1999).
6. Rybchin, V. N. & Svarchevsky, A. N. The plasmid prophage N15: a linear DNA with covalently closed ends. Mol. Microbiol. 33, 895-903 (1999).
7. Gribaldo, S. & Philippe, H. Ancient phylogenetic relationships. Theoret. Pop. Biol. 61, 391-408 (2002).
8. Clark, A. J., Inwood, W., Cloutier, T. & Dhillon, T. S. Nucleotide sequence of coliphage HK620 and the evolution of lambdoid phages. J. Mol. Biol. 311, 657-679 (2001).
9. Bamford, D. H., Burnett, R. D. & Stuart, D. J. Evolution of viral structure. Theoret. Pop. Biol. 61, 461-470 (2002).
10. Wang, L., Junker, D. & Collisson, E. W. Evidence of natural recombination within the S1 gene of infectious bronchitis virus. Viriology 192, 710-716 (1993).
11. Lai, M. M. C. & Holmes, K. V. in Fundamental Virology (eds Knipe, D. M. & Howley, P. M.) 641-664 (Lippincott, Williams & Wilkins, Philadelphia, 2001).
12. Wommack, K. E. & Colwell, R. R. Viroplankton: viruses in aquatic ecosystems. Microbial Mol. Biol. Rev. 64, 69-114 (2000).
13. Wilhelm, S. W. & Suttle, C. A, Viruses and nutrient cycles in the sea. Bioscience 49, 781-787 (1999).
14. Suttle, C. A. & Chan, A. M. Dynamics and distribution of cyanophages and their effect on marine Synechococcus spp. Appl. Environ. Microbiol. 60, 3167-3174 (1994).
15. Suttle, C. A. The significance of viruses to mortality in aquatic microbial communities. Microb. Ecol. 28, 237-243 (1994).
16. Fuhrman, J. A. & Suttle, C. A. Viruses in marine planktonic systems. Oceanography 6, 50-62 (1993).
17. Molineaux, I. J. No syringes please, ejection of DNA from the virion is enzyme driven. Mol. Microbiol. 40, 1-8 (2001).
18. Zavdev, S. K. & Shemyakin, M. F. RNA polymerase-dependent mechanism for the stepwise T7 phage transport from the virion into E. coli. Nucleic Acids. Res. 10, 1635-1652 (1982).
19. Garcia, L. R. & Molineux, I. J. Rate of translocation of bacteriophage T7 DNA across the membranes of Escherichia coli. J. Bacteriol. 177, 4066-4076 (1995).
20. Garcia, L. R. & Molineux, I. J. Translocation and specific cleavage of bacteriophage T7 DNA in vivo by Eco KI. Proc. Natl Acad. Sci. USA 96, 12430-12435 (1999).
21. Simpson, A. A. et al. Structure of the bacteriophage φ29 DNA packaging motor. Nature 408, 745-750 (2000).
22. Smith, D. E. et al. The bacteriophage straight φ29 portal motor can package DNA against a large internal force. Nature 413, 748-752 (2001).
23. Nunes-Duby, S. E., Azaro, M. A. & Landy, A. Swapping DNA strands and sensing homology without branch migration in λ-site-specific recombination. Curr. Biol. 5, 139-148 (1996).
24. Nunes-Duby, S. E., Matsumoto, L. & Landy, A. Site-specific recombination intermediates trapped with suicide substrates. Cell 50, 779-788 (1987).
25. Segall, A. M. & Nash, H. A. Architectural flexibility in λ-site-specific recombination: three alternate conformations channel the attL site into three distinct pathways. Genes Cells 1, 453-463 (1986).
26. Segall, A. M. Analysis of higher order intermediates and synapsis in the bent-L pathway of bacteriophage λ-site-specific recombination J. Biol. Chem. 273, 24256-24265 (1998).
27. Kovach, M. J., Tirumalai, R. & Landy, A. Site-specific photo-cross-linking between λ-integrase and its DNA recombination target. J. Biol. Chem. 277, 14520-14538 (2002).
28. Wojciak, J. M., Sankar, D., Landy, A. & Chubb, R. T. Arm-site binding for λ-integrase: solution structure and functional characterization of its amino-terminal domain. Proc. Natl Acad. Sci. USA 99, 3434-3439 (2002).
29. Ptashne, M. A Genetic Switch: Phage and Higher Organisms. 2nd Edn (Blackwell Science, Malden, Massachusetts, and Cell Press, Cambridge, Massachusetts, 1992).
30. Révet, B., von Wilchen-Bergmann, B., Bessent, H., Barker, A. & Müller-Hill, B. Four dimers of λ-repressor bound to two suitably spaced pairs of λ-operators form octamers and DNA loops over long distances. Curr. Biol. 9, 151-154 (1999).
31. Dodd, I. B., Perkins, A. J., Tsenitsides, D. & Egan, J. B. Octamerization of λ-cl repressor is needed for effective repression of P(RM) and switching from lysogeny. Genes Dev. 15, 3013-3022 (2001).
32. Ptashne, M. & Gann, A. Genes and Signals (Cold Spring Harbor Laboratory Press, New York, 2002).
33. Senear, D. F. et al. The primary self-assembly reaction of bacteriophage cl repressor dimers is to octamer. Biochemistry 32, 6179-6189 (1993).
34. Darnell, J., Lodish, H. & Baltimore, D. Molecular Cell Biology (Scientific American Books, New York, 1996).
35. Reichardt, L. & Kaiser, A. D. Control of λ-repressor synthesis. Proc. Natl Acad. Sci. USA 68, 2185-2189 (1971).
36. Arkin, A., Ross, J. & McAdams, H. H. Stochastic kinetics analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells. Genetics 149, 1633-1648 (1998).
37. Kourilsky P. Lysogenization by bacteriophage-λ. I. Multiple infection and the lysogenic response. Mol. Gen. Genet. 122, 183-195 (1993).
38. Merril, C. R. et al. Long-circulating bacteriophage as antibacterial agents. Proc. Natl Acad. Sci. USA 93, 3188-3192 (1996).
39. Sulalvelidze, A., Alavidze, Z. & Morris, J. G. Bacteriophage therapy. Antimicrob. Agents Chemother. 45, 649-659 (2001).
40. Smith, H. W. & Huggins, M. B. Successful treatment of experimental E. coli infections in mice using phage is generally superior over antibiotics. J. Gen. Microbiol. 128, 307-318 (1982).
41. Biswas, B. et al. Bacteriophage therapy rescues mice bacteremic from a vancomycin-resistant Enterococcus faecium. Infect. Immun. 70, 204-210 (2002).
42. Levin, B. R. & Bull, J. J. Phage therapy revisited: the population biology of a bacterial infection and its treatment with bacteriophages and antibiotics. Am. Nat. 147, 881-898 (1996).
43. Desiere, F., McShaun, W. M., van Sinderen, D., Ferretti, J. J. & Brussow, H. Comparative genomics reveals close genetic relationships between phages from dairy bacteria and pathogenic Streptococci: evolutionary implications for prophage-host interactions. Virology 288, 325-341 (2001).
44. Brussow, H. Phages of dairy bacteria. Ann. Rev. Microbiol. 55, 283-303 (2001).
45. Barrangow, R., Yoon, S. S., Breidt, F. & Klaenhammer, T. R. Characterization of six Leuconostoc fallax bacteriophages isolated from an industrial sauerkraut fermentation. Appl. Environ. Microbiol. 60, 5452-5458 (2002).
46. Djordjevic, G. M. & Klaenhammer, T. R. Bacteriophage-triggered defense systems: phage adaptation and design improvements. Appl. Environ. Microbiol. 63, 4370-4376 (1997).
47. Lucchini, S., Sidotic, J. & Brussow, H. Broad-range bacteriophage resistance in Staphylococcus thermophilus by insertional mutagenesis. Virology 275, 267-277 (2000).
48. Jiang, J., Abu-Shilbaych, L. & Rao, V. B. Display of a PorA peptide from Neisseria meningitidis on the bacteriophage T4 capsid surface. Infect. Immun. 65, 4770 (1997).
49. Malys, N., Chang, D. Y., Baumann, R, G., Xie, D. & Black, L. W. A bipartite bacteriophage T4 SOC and HOC randomized peptide display library: detection and analysis of phage T4 terminase (gp17) and late δ-factor (gp55) interaction. J. Mol. Biol. 319, 289-309 (2002).
50. Freeman, V. J. Studies of the virulence of bacteriophage-infected strains of Corynebacterium diphtheriae. J. Bacteriol. 61, 675-688 (1951).
51. Inoue, K. & Iida, H. Conversion of toxigenicity in Clostridium botulinum type C. Jpn. J. Microbiol. 14, 87-89 (1970).
52. Davis, B. M., Kimsey, H. H., Kane, A. V. & Waldor, M. K. A satellite phage-encoded antirepressor induces repressor aggregation and cholera toxin gene transfer. EMBO J. 21, 4240-4249 (2002).
53. Wagner, P. L. & Waldor, M. K. Bacteriophage control of bacterial virulence. Infection Immun. 70, 3985-3993 (2002).
54. Campbell, A. Transduction and segregation in Escherichia coll K-12. Virology 4, 366-384 (1957).
55. Plunkett, G., Rose, D.J., Durfee, T. S. & Blattner, F. D. Sequence of Shiga toxin 2 phage 933W from Escherichia coli O157:H7: Shiga toxin as a phage late-gene product. J. Bacteriol. 181, 1761-1778 (1998).
56. Mrázek, J. & Karlin, S. Detecting alien genes in bacterial genomes. Ann. NY Acad. Sci. 870, 314-329 (1999).
57. Campbell, A. in Mobile DNA II. (eds Craig, N. L., Craigie, R., Gellert, M. & Lambowitz, M.) 1024-1039 (ASM, Washington, 2002).
58. Hacker, J., Blum-Ohler, G., Muhldorfer, L. & Tschape, H. Pathogenicity islands of virulent bacteria: structure, function and impact on bacterial evolution. Mol. Microbiol. 236, 1088-1097 (1997).
59. Karlin, S., Campbell, A. M. & Mrázek, J. Comparative DNA analysis across diverse genomes. Ann. Rev. Genet. 32, 185-225 (1998).