1887

Abstract

The genome rearrangements in sequential clone K isolates from the airways of a patient with cystic fibrosis were determined by an integrated approach of mapping, sequencing and bioinformatics. Restriction mapping uncovered an 89 kb deletion of PAO sequence between and in clone K, and two 106 kb insertions either adjacent to this deletion or several hundred kilobases away, close to the locus. These 106 kb blocks of extra DNA also co-existed as the circular plasmid pKLK106 in several clone K isolates and were found to be closely related to plasmid pKLC102 in clone C isolates. The breakpoints of the deletion in clone K and the sequences for the reversible integration of the plasmid in clones C and K were located within the 3’ end of the lysine tRNA structural genes ( site). pKLK106 sequentially recombined with either of the two tRNA genes in clone K isolates. The site of the hypervariable region has been utilized by clone C to target its plasmid pKLC102 into the chromosome; the site of the region has been employed by strain PAO to incorporate a DNA block encoding pyocin, transposases and IS elements. The use of typical phage attachment sites by conjugative genetic elements could be one of the major mechanisms used by to generate the mosaic genome structure of blocks of species-, clone- and strain-specific DNA. The example described here demonstrates the potential impact of systematic genome analysis of sequential isolates from the same habitat on our understanding of the evolution of microbial genomes.

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2000-10-01
2024-03-28
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References

  1. Auvray F., Coddeville M., Ritzenthaler P., Dupont L. 1997; Plasmid integration in a wide range of bacteria mediated by the integrase of Lactobacillus delbrueckii bacteriophage mv4. J Bacteriol 179:1837–1845
    [Google Scholar]
  2. Auvray F., Coddeville M., Ordonez R. C., Ritzenthaler P. 1999; Unusual structure of the attB site of the site-specific recombination system of Lactobacillus delbrueckii bacteriophage mv4. J Bacteriol 181:7385–7389
    [Google Scholar]
  3. Besemer J., Borodovsky M. 1999; Heuristic approach to deriving models for gene finding. Nucleic Acids Res 27:3911–3920 [CrossRef]
    [Google Scholar]
  4. Blanc-Potard A. B., Groisman E. A. 1997; The Salmonella selC locus contains a pathogenicity island mediating intramacrophage survival. EMBO J 16:5376–5385 [CrossRef]
    [Google Scholar]
  5. Brown D. P., Idler K. B., Backer D. M., Donadio S., Katz L. 1994; Characterization of the genes and attachment sites for site-specific integration of plasmid pSE101 in Saccharopolyspora erythraea and Streptomyces lividans. Mol Gen Genet 242:185–193 [CrossRef]
    [Google Scholar]
  6. de Bruijn F. J., Lupski J. R., Weinstock G. M. 1998 Bacterial Genomes: Physical Structure and Analysis New York: Chapman & Hall;
    [Google Scholar]
  7. Bruttin A., Foley S., Brussow H. 1997; The site-specific integration system of the temperate Streptococcus thermophilus bacteriophage ϕSfi21. Virology 237:148–158 [CrossRef]
    [Google Scholar]
  8. Burrows L. L., Charter D. F., Lam J. S. 1996; Molecular characterization of the Pseudomonas aeruginosa serotype O5 (PAO1) B-band lipopolysaccharide gene cluster. Mol Microbiol 22:481–495 [CrossRef]
    [Google Scholar]
  9. Campbell A. M. 1996; Bacteriophages. In Escherichia coli and Salmonella: Cellular and Molecular Biology, 2nd edn. pp. 2325–2338Edited by Neidhardt F. C.others Washington, DC: American Society for Microbiology;
    [Google Scholar]
  10. Casjens S. 1998; The diverse and dynamic structure of bacterial genomes. Annu Rev Genet 32:339–377 [CrossRef]
    [Google Scholar]
  11. Chen W. P., Kuo T. T. 1993; A simple and rapid method for the preparation of gram-negative bacterial genomic DNA. Nucleic Acids Res 21:2260 [CrossRef]
    [Google Scholar]
  12. Grothues D., Tümmler B. 1991; New approaches in genome analysis by pulsed-field gel electrophoresis: application to the analysis of Pseudomonas species. Mol Microbiol 5:2763–2776 [CrossRef]
    [Google Scholar]
  13. Hacker J., Blum-Oehler G., Mühldorfer I., Tschäpe H. 1997; Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol Microbiol 23:1089–1097 [CrossRef]
    [Google Scholar]
  14. Hayashi T., Matsumoto H., Ohnishi M., Terawaki Y. 1993; Molecular analysis of a cytotoxin-converting phage, ϕCTX, of Pseudomonas aeruginosa: structure of the attP-cos-ctx region and integration into the serine tRNA gene. Mol Microbiol 7:657–667 [CrossRef]
    [Google Scholar]
  15. Heuer T., Bürger C., Tümmler B. 1998a; Smith/Birnstiel mapping of genome rearrangements in Pseudomonas aeruginosa. Electrophoresis 19:495–499 [CrossRef]
    [Google Scholar]
  16. Heuer T., Bürger C., Maaß G., Tümmler B. 1998b; Cloning of prokaryotic genomes in yeast artificial chromosomes: application to the population genetics of Pseudomonas aeruginosa. Electrophoresis 19:486–494 [CrossRef]
    [Google Scholar]
  17. Hou Y. M. 1999; Transfer RNAs and pathogenicity islands. Trends Biochem Sci 24:295–298 [CrossRef]
    [Google Scholar]
  18. Kiewitz C., Tümmler B. 2000; Sequence diversity of Pseudomonas aeruginosa: impact on population structure and genome evolution. J Bacteriol 182:3125–3135 [CrossRef]
    [Google Scholar]
  19. Kropinski A. M., Farinha M. A., Jansons I. 1994; Nucleotide sequence of the Pseudomonas aeruginosa insertion sequence IS222: another member of the IS3 family. Plasmid 31:222–228 [CrossRef]
    [Google Scholar]
  20. Liu S. L., Hessel A., Sanderson K. E. 1993; Genomic mapping with I-CeuI, an intron-encoded endonuclease specific for genes for ribosomal RNA, in Salmonella spp., Escherichia coli, and other bacteria. Proc Natl Acad Sci U S A 90:6874–6878 [CrossRef]
    [Google Scholar]
  21. Lowe T. M., Eddy S. R. 1997; tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964 [CrossRef]
    [Google Scholar]
  22. Nakayama K., Kanaya S., Ohnishi M., Terawaki Y., 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 31:399–419 [CrossRef]
    [Google Scholar]
  23. Papadopoulos D., Schneider D., Meier-Eiss J., Arber W., Lenski R. E., Blot M. 1999; Genomic evolution during a 10,000-generation experiment with bacteria. Proc Natl Acad Sci U S A 96:3807–3812 [CrossRef]
    [Google Scholar]
  24. Raynal A., Tuphile K., Gerbaud C., Luther T., Guerineau M., Pernodet J. L. 1998; Structure of the chromosomal insertion site for pSAM2: functional analysis in Escherichia coli. Mol Microbiol 28:333–342 [CrossRef]
    [Google Scholar]
  25. Römling U., Tümmler B. 1993; Comparative mapping of the Pseudomonas aeruginosa PAO genome with rare-cutter linking clones or two-dimensional pulsed-field gel electrophoresis protocols. Electrophoresis 14:283–289 [CrossRef]
    [Google Scholar]
  26. Römling U., Fiedler B., Boßhammer J., Grothues D., Greipel J., von der Hardt H., Tümmler B. 1994; Epidemiology of chronic Pseudomonas aeruginosa infections in cystic fibrosis. J Infect Dis 170:1616–1621 [CrossRef]
    [Google Scholar]
  27. Römling U., Greipel J., Tümmler B. 1995; Gradient of genomic diversity in the Pseudomonas aeruginosa chromosome. Mol Microbiol 17:323–332 [CrossRef]
    [Google Scholar]
  28. Römling U., Schmidt K. D., Tümmler B. 1997; Large genome rearrangements discovered by the detailed analysis of 21 Pseudomonas aeruginosa clone C isolates found in environment and disease habitats. J Mol Biol 271:386–404 [CrossRef]
    [Google Scholar]
  29. Schmidt K. D., Tümmler B., Römling U. 1996; Comparative genome mapping of Pseudomonas aeruginosa PAO with P. aeruginosa C, which belongs to a major clone in cystic fibrosis patients and aquatic habitats. J Bacteriol 178:85–93
    [Google Scholar]
  30. Spangenberg C., Fislage R., Sierralta W., Tümmler B., Römling U. 1995; Comparison of type IV-pilin genes of Pseudomonas aeruginosa of various habitats has uncovered a novel unusual sequence. FEMS Microbiol Lett 125:265–273 [CrossRef]
    [Google Scholar]
  31. Staskawicz B., Dahlbeck D., Keen N., Napoli C. 1987; Molecular characterization of cloned avirulence genes from race 0 and race 1 of Pseudomonas syringae pv. glycinea. J Bacteriol 169:5789–5794
    [Google Scholar]
  32. Thompson J. D., Higgins D. G., Gibson T. J. 1994; clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680 [CrossRef]
    [Google Scholar]
  33. Tümmler B., Kiewitz C. 1999; Cystic fibrosis: an inherited susceptibility to bacterial respiratory infections. Mol Med Today 5:351–358 [CrossRef]
    [Google Scholar]
  34. Van Mellaert L., Mei L., Lammertyn E., Schacht S., Anné J. 1998; Site-specific integration of bacteriophage VWB genome into Streptomyces venezuelae and construction of a VWB-based integrative vector. Microbiology 144:3351–3358 [CrossRef]
    [Google Scholar]
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