Genomic and Genetic Analysis of Bordetella Bacteriophages Encoding Reverse Transcriptase-Mediated Tropism-Switching Cassettes

Journal of Bacteriology

Volumn 186, Issue 5, 2004, Pages 1503-1517

  Liu, Minghsun ^a   Gingery, Mari ^a   Doulatov, Sergei R ^a   Liu, Yichin ^b,f   Hodes, Asher ^a   Baker, Stephen ^c   Davis, Paul ^c   Simmonds, Mark ^c   Churcher, Carol ^c   Mungall, Karen ^c   Quail, Michael A ^c   Preston, Andrew ^d   Harvill, Eric T ^a,g   Maskell, Duncan J ^d   Eiserling, Frederick A ^a   Parkhill, Julian ^c   Miller, Jeff F ^a,e  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b YALE UNIVERSITY   (United States)

^c WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^d UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f BRIGHAM AND WOMEN S HOSPITAL   (United States)

^g PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA ADENINE METHYLTRANSFERASE; DOUBLE STRANDED DNA; NUCLEOTIDE; RNA DIRECTED DNA POLYMERASE; SPACER DNA;

ANIMAL EXPERIMENT; ARTICLE; BACTERIAL GENOME; BACTERIOPHAGE; BORDETELLA; CONTROLLED STUDY; FRAMESHIFT MUTATION; GENE CASSETTE; GENE SWITCHING; GENETIC ANALYSIS; GENOMICS; HYBRID GENE; MOUSE; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DOMAIN; RAT; RESPIRATORY TRACT INFECTION; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION;

ANIMALS; BACTERIOPHAGES; BASE SEQUENCE; BORDETELLA; GENOME, VIRAL; LYSOGENY; MICE; MICE, INBRED C57BL; MOLECULAR SEQUENCE DATA; MUTATION; RATS; RATS, WISTAR; RNA-DIRECTED DNA POLYMERASE; SEQUENCE ANALYSIS, DNA; TEMPLATES, GENETIC; TRANSDUCTION, GENETIC; VIRAL PROTEINS;

ANIMALIA; BACTERIA (MICROORGANISMS); BORDETELLA; NEGIBACTERIA; PROKARYOTA; UNIDENTIFIED BACTERIOPHAGE;

EID: 10744224321     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.186.5.1503-1517.2004     Document Type: Article

References (48)

1. Adams, M. H. 1959. Bacteriophages. Interscience Publishers, Inc., New York, N.Y.
2. Akerley, B. J., P. A. Cotter, and J. F. Miller. 1995. Ectopic expression of the flagellar regulon alters development of the Bordetella-host interaction. Cell 80:611-620.
3. Akerley, B. J., D. M. Monack, S. Falkow, and J. F. Miller. 1992. The bvgAS locus negatively controls motility and synthesis of flagella in Bordetella bronchiseptica. J. Bacteriol. 174:980-990.
4. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped Blast and PSI-Blast: a new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
5. Ausubel, F. M., R. Brent, R. E. Kingston, and D. D. Moore. 1995. Short protocols in molecular biology. John Wiley & Sons, Inc., New York, N.Y.
6. Belkum, A., S. Scherer, L. Alphen, and H. Verbrugh. 1998. Short-sequence DNA repeats in prokaryotic genomes. Microbiol. Mol. Biol. Rev. 62:275-293.
7. Bernhardt, T. G., I. N. Wang, D. K. Struck, and R. Young. 2001. A protein antibiotic in the phage Qbeta virion: diversity in lysis targets. Science 292:2326-2329.
8. Cotter, P. A., and V. J. DiRita. 2000. Bacterial virulence gene regulation: an evolutionary perspective. Annu. Rev. Microbiol. 54:519-565.
9. Cotter, P. A., and J. F. Miller. 2000. Bordetella, p. 619-674. In E. Groisman (ed.), Principles of bacterial pathogenesis. Academic Press, San Diego, Calif.
10. Ermolaeva, M. D., H. G. Khalak, O. White, H. O. Smith, and S. L. Salzberg. 2000. Prediction of transcription terminators in bacterial genomes. J. Mol. Biol. 301:27-33.
11. Figurski, D. H., and D. R. Helinski. 1979. Replication of an origin-containing derivative of plasmid RK2 dependent on a plasmid function provided in trans. Proc. Natl. Acad. Sci. USA 76:1648-1652.
12. Harvill, E. T., P. A. Cotter, M. H. Yuk, and J. F. Miller. 1999. Probing the function of Bordetella bronchiseptica adenylate cyclase toxin by manipulating host immunity. Infect Immun. 67:1493-1500.
13. Hausmann, R., and M. Messerschmid. 1988. Inhibition of gene expression of T7-related phages by prophage P1. Mol. Gen. Genet. 212:543-547.
14. Henderson, I. R., P. Owen, and J. P. Nataro. 1999. Molecular switches - the ON and OFF of bacterial phase variation. Mol. Microbiol. 33:919-932.
15. Kaszubska, W., C. Aiken, C. D. O'Connor, and R. I. Gumport. 1989. Purification, cloning and sequence analysis of RsrI DNA methyltransferase: lack of homology between two enzymes, RsrI and EcoRI, that methylate the same nucleotide in identical recognition sequences. Nucleic Acids Res. 17:10403-10425.
16. Kwiatkowski, B., B. Boschek, H. Thiele, and S. Stirm. 1982. Endo-N-acetyl-neuraminidase associated with bacteriophage particles. J. Virol. 43:697-704.
17. Landt, O., H. P. Grunert, and U. Hahn. 1990. A general method for rapid site-directed mutagenesis with the polymerase chain reaction. Gene 96:125-128.
18. Legoux, R., P. Lelong, C. Jourde, C. Feuillerat, J. Capdevielle, V. Sure, et al. 1996. N-Acetyl-heparosan lyase of Escherichia coli K5: gene cloning and expression. J. Bacteriol. 178:7260-7264.
19. Lehnherr, H., A. M. Hansen, and T. Ilyina. 1998. Penetration of the bacterial cell wall: a family of lytic transglycosylases in bacteriophages and conjugative plasmids. Mol. Microbiol. 30:454-457.
20. Levinson, G., and G. A. Gutman. 1987. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 4:203-221.
21. Liu, M., R. Deora, S. R. Doulatov, M. Gingery, F. A. Eiserling, A. Preston, J. Duncan, R. W. Simons, P. A. Cotter, J. Parkhill, and J. F. Miller. 2002. Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage. Science 295:2091-2094.
22. Loeffler, J. M., D. Nelson, and V. A. Fischetti. 2001. Rapid killing of Streptococcus pneumoniae with a bacteriophage cell wall hydrolase. Science 294:2170-2172.
23. Luneberg, E., B. Mayer, N. Daryab, O. Kooistra, U. Zahringer, M. Rohde, et al. 2001. Chromosomal insertion and excision of a 30 kb unstable genetic element is responsible for phase variation of lipopolysaccharide and other virulence determinants in Legionella pneumophila. Mol. Microbiol. 39:1259-1271.
24. Magrini, V., D. Salmi, D. Thomas, S. K. Herbert, P. L. Hartzell, and P. Youderian. 1997. Temperate Myxococcus xanthus phage Mx8 encodes a DNA adenine methylase, Mox. J. Bacteriol. 179:4254-4263.
25. Mattoo, S., A. K. Foreman-Wykert, P. A. Cotter, and J. F. Miller. 2001. Mechanisms of Bordetella pathogenesis. Front. Biosci. 6:E168-E186.
26. Mattoo, S., J. F. Miller, and P. A. Cotter. 2000. Role of Bordetella bronchiseptica fimbriae in tracheal colonization and development of a humoral immune response. Infect. Immun. 68:2024-2033.
27. Moak, M., and I. J. Molineux. 2000. Role of the Gp16 lytic transglycosylase motif in bacteriophage T7 virions at the initiation of infection. Mol. Microbiol. 37:345-355.
28. Nelson, D., L. Loomis, and V. A. Fischetti. 2001. Prevention and elimination of upper respiratory colonization of mice by group A streptococci by with a bacteriophage lytic enzyme. Proc. Natl. Acad. Sci. USA 98:4107-4112.
29. Nielsen, H., J. Engelbrecht, S. Brunak, and G. von Heijne. 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10:1-6.
30. Pedulla, M. L., M. E. Ford, J. M. Houtz, T. Karthikeyan, C. Wadsworth, J. A. Lewis, D. Jacobs-Sera, J. Falbo, J. Gross, N. R. Pannunzio, W. Brucker, V. Kumer, J. Kandasamy, L. Keenan, S. Bardarov, J. Kriakov, J. G. Lawrence, W. R. J. Jacobs, R. W. Hendrix, and G. F. Hatfull. 2003. Origins of highly mosaic mycobacteriophage genomes. Cell 113:171-182.
31. Rohwer, F., and R. Edwards. 2002. The Phage Proteomic Tree: a genome-based taxonomy for phage. J. Bacteriol. 184:4529-4535.
32. Rudolph, C., E. Freund-Molbert, and S. Stirm. 1975. Fragments of Klebsiella bacteriophage no. 11. Virology 64:236-246.
33. Rutherford, K., J. Parkhill, J. Crook, T. Horsnell, P. Rice, M. A. Rajandream, and B. Barrell. 2000. Artemis: sequence visualization and annotation. Bioinformatics 16:944-945.
34. Rydman, P. S., and D. H. Bamford. 2000. Bacteriophage PRD1 DNA entry uses a viral membrane-associated transglycosylase activity. Mol. Microbiol. 37:356-363.
35. Sambrook, J., T. Maniatis, and E. F. Fritsch. 1989. Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
36. Schmid, D., D. Pridmore, G. Capitani, R. Battistutta, J. R. Neeser, and A. Jann. 1997. Molecular organisation of the ice nucleation protein Ina V from Pseudomonas syringae. FEBS Lett. 414:590-594.
37. Simpson, A. J., F. C. Reinach, P. Arruda, F. A. Abreu, M. Acencio, R. Alvarenga, et al. 2000. The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis. Nature 406:151-157.
38. Summers, W. C. 2001. Bacteriophage therapy. Annu. Rev. Microbiol. 55:437-451.
39. Tautz, D., M. Trick, and G. A. Dover. 1986. Cryptic simplicity in DNA is a major source of genetic variation. Nature 322:652-656.
40. Trautner, T. A., B. Pawiek, U. Gunthert, U. Canosi, S. Jentsch, and M. Freund. 1980. Restriction and modification in Bacillus subtilis: identification of a gene in the temperate phage SP beta coding for a BsuR specific modification methyltransferase. Mol. Gen. Genet. 180:361-367.
41. Uhl, M. A., and J. F. Miller. 1996a. Central role of the BvgS receiver as a phosphorylated intermediate in a complex two-component phosphorelay. J. Biol. Chem. 271:33176-33180.
42. Uhl, M. A., and J. F. Miller. 1996b. Integration of multiple domains in a two-component sensor protein: the Bordetella pertussis BvgAS phosphorelay. EMBO J. 15:1028-1036.
43. Van der Plas, J., R. Oosterhoff-Teertstra, M. Borrias, and P. Weisbeek. 1992. Identification of replication and stability functions in the complete nucleotide sequence of plasmid pUH24 from the cyanobacterium Synechococcus sp. PCC 7942. Mol. Microbiol. 6:653-664.
44. 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 endosymbiont of Acyrthosiphon pisum. Virology 262:104-113.
45. Waldor, M. K., and J. J. Mekalanos. 19%. Lysogenic conversion by a filamentous phage encoding cholera toxin. Science 272:1910-1914.
46. Warren, G., and L. Corotto. 1989. The consensus sequence of ice nucleation proteins from Erwinia herbicola, Pseudomonas fluorescens and Pseudomonas syringae. Gene 85:239-242.
47. Wright, R., C. Stephens, and L. Shapiro. 1997. The CcrM DNA methyltransferase is widespread in the alpha subdivision of proteobacteria, and its essential functions are conserved in Rhizobium meliloti and Caulobacter crescentus. J. Bacteriol. 179:5869-5877.
48. Zhao, J. L., and C. S. Orser. 1990. Conserved repetition in the ice nucleation gene inaX from Xanthomonas campestris pv. translucens. Mol. Gen. Genet. 223:163-166.