Table of Contents
Sequencing
Volume 2012 (2012), Article ID 953609, 5 pages
http://dx.doi.org/10.1155/2012/953609
Research Article

Identification of Prophages and Prophage Remnants within the Genome of Avibacterium paragallinarum Bacterium

Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein 9300, South Africa

Received 10 September 2012; Revised 21 November 2012; Accepted 28 November 2012

Academic Editor: Alexei Sorokin

Copyright © 2012 Y. Roodt et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. W. O. K. Grabow, “Bacteriophages: update on application as models for viruses in water,” Water SA, vol. 27, no. 2, pp. 251–268, 2001. View at Google Scholar · View at Scopus
  2. D. Nelson, “Phage taxonomy: we agree to disagree,” Journal of Bacteriology, vol. 186, no. 21, pp. 7029–7031, 2004. View at Publisher · View at Google Scholar · View at Scopus
  3. H. Brüssow, C. Canchaya, and W. D. Hardt, “Phages and the evolution of bacterial pathogens: from genomic rearrangements to lysogenic conversion,” Microbiology and Molecular Biology Reviews, vol. 68, no. 3, pp. 560–602, 2004. View at Publisher · View at Google Scholar · View at Scopus
  4. P. L. Wagner and M. K. Waldor, “Bacteriophage control of bacterial virulence,” Infection and Immunity, vol. 70, no. 8, pp. 3985–3993, 2002. View at Publisher · View at Google Scholar · View at Scopus
  5. G. Resch, E. M. Kulik, F. S. Dietrich, and J. Meyer, “Complete genomic nucleotide sequence of the temperate bacteriophage AaΦ23 of Actinobacillus actinomycetemcomitans,” Journal of Bacteriology, vol. 186, no. 16, pp. 5523–5528, 2004. View at Publisher · View at Google Scholar · View at Scopus
  6. H. Brüssow and R. W. Hendrix, “Phage genomics: small is beautiful,” Cell, vol. 108, no. 1, pp. 13–16, 2002. View at Publisher · View at Google Scholar · View at Scopus
  7. K. V. Srividhya, V. Alaguraj, G. Poornima et al., “Identification of prophages in bacterial genomes by dinucleotide relative abundance difference,” PLoS ONE, vol. 2, no. 11, Article ID e1193, 2007. View at Publisher · View at Google Scholar · View at Scopus
  8. Y. Tan, K. Zhang, X. Rao et al., “Whole genome sequencing of a novel temperate bacteriophage of P.aeruginosa: evidence of tRNA gene mediating integration of the phage genome into the host bacterial chromosome,” Cellular Microbiology, vol. 9, no. 2, pp. 479–491, 2007. View at Publisher · View at Google Scholar · View at Scopus
  9. C. Balding, S. A. Bromley, R. W. Pickup, and J. R. Saunders, “Diversity of phage integrases in Enterobacteriaceae: development of markers for environmental analysis of temperate phages,” Environmental Microbiology, vol. 7, no. 10, pp. 1558–1567, 2005. View at Publisher · View at Google Scholar · View at Scopus
  10. A. E. Scott, A. R. Timms, P. L. Connerton, C. Loc Carrillo, K. Adzfa Radzum, and I. F. Connerton, “Genome dynamics of Campylobacter jejuni in response to bacteriophage predation,” PLoS Pathogens, vol. 3, no. 8, p. e119, 2007. View at Publisher · View at Google Scholar · View at Scopus
  11. L. S. Frost, R. Leplae, A. O. Summers, and A. Toussaint, “Mobile genetic elements: the agents of open source evolution,” Nature Reviews Microbiology, vol. 3, no. 9, pp. 722–732, 2005. View at Publisher · View at Google Scholar · View at Scopus
  12. K. Kume, A. Sawata, and Y. Nakase, “Haemophilus infections in chickens. I. Characterization of Haemophilus paragallinarum isolated from chickens affected with coryza,” The Japanese Journal of Veterinary Science, vol. 40, no. 1, pp. 65–73, 1978. View at Google Scholar · View at Scopus
  13. P. J. Zhang, M. Miao, H. Sun, Y. Gong, and P. J. Blackall, “Infectious coryza due to Haemophilus paragallinarum serovar B in China,” Australian Veterinary Journal, vol. 81, no. 1-2, pp. 96–97, 2003. View at Publisher · View at Google Scholar · View at Scopus
  14. P. J. Blackall, H. Christensen, T. Beckenham, L. L. Blackall, and M. Bisgaard, “Reclassification of Pasteurella gallinarum, [Haemophilus] paragallinarum, Pasteurella avium and Pasteurella volantium as Avibacterium gallinarum gen. nov., comb. nov., Avibacterium paragallinarum comb. nov., Avibacterium avium comb. nov. and Avibacterium volantium comb. nov,” International Journal of Systematic and Evolutionary Microbiology, vol. 55, no. 1, pp. 353–362, 2005. View at Publisher · View at Google Scholar · View at Scopus
  15. S. K. Highlander, S. Weissenberger, L. E. Alvarez, G. M. Weinstock, and P. B. Berget, “Complete nucleotide sequence of a P2 family lysogenic bacteriophage, φ{symbol}MhaA1-PHL101, from Mannheimia haemolytica serotype A1,” Virology, vol. 350, no. 1, pp. 79–89, 2006. View at Publisher · View at Google Scholar · View at Scopus
  16. P. J. Blackall and R. Yamamoto, “Infectious coryza,” in A Laboratory Manual for the Isolation and Identification of Avian Pathogens, H. G. Parchase, L. H. Arp, C. H. Domermuth, and J. E. Pearson, Eds., pp. 27–31, American Association of Avian Pathologists, Ames, Iowa, USA, 3rd edition, 1990. View at Google Scholar
  17. X. Chen, J. K. Miflin, P. Zhang, and P. J. Blackall, “Development and application of DNA probes and PCR tests for Haemophilus paragallinarum,” Avian Diseases, vol. 40, no. 2, pp. 398–407, 1996. View at Google Scholar · View at Scopus
  18. A. Mendoza-Espinoza, Y. Koga, and A. I. Zavaleta, “Amplified 16S ribosomal DNA restriction analysis for identification of Avibacterium paragallinarum,” Avian Diseases, vol. 52, no. 1, pp. 54–58, 2008. View at Publisher · View at Google Scholar · View at Scopus
  19. S. L. Salzberg, A. L. Deicher, S. Kasif, and O. White, “Microbial gene identification using interpolated Markov models,” Nucleic Acids Research, vol. 26, no. 2, pp. 544–548, 1998. View at Publisher · View at Google Scholar · View at Scopus
  20. A. L. Delcher, D. Harmon, S. Kasif, O. White, and S. L. Salzberg, “Improved microbial gene identification with GLIMMER,” Nucleic Acids Research, vol. 27, no. 23, pp. 4636–4641, 1999. View at Google Scholar · View at Scopus
  21. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990. View at Publisher · View at Google Scholar · View at Scopus
  22. T. F. Smith and M. S. Waterman, “Identification of common molecular subsequences,” Journal of Molecular Biology, vol. 147, no. 1, pp. 195–197, 1981. View at Google Scholar · View at Scopus
  23. S. R. Eddy, “Profile hidden Markov models,” Bioinformatics, vol. 14, no. 9, pp. 755–763, 1998. View at Google Scholar · View at Scopus
  24. A. Krogh, B. Larsson, G. Von Heijne, and E. L. L. Sonnhammer, “Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes,” Journal of Molecular Biology, vol. 305, no. 3, pp. 567–580, 2001. View at Publisher · View at Google Scholar · View at Scopus
  25. J. D. Bendtsen, H. Nielsen, G. Von Heijne, and S. Brunak, “Improved prediction of signal peptides: signalP 3.0,” Journal of Molecular Biology, vol. 340, no. 4, pp. 783–795, 2004. View at Publisher · View at Google Scholar · View at Scopus
  26. G. J. Morgan, G. F. Hatfull, S. Casjens, and R. W. Hendrix, “Bacteriophage Mu genome sequence: analysis and comparison with Mu-like prophages in Haemophilus, Neisseria and Deinococcus,” Journal of Molecular Biology, vol. 317, no. 3, pp. 337–359, 2002. View at Google Scholar