Sequence diversity of Pseudomonas aeruginosa: Impact on population structure and genome evolution

Journal of Bacteriology

Volumn 182, Issue 11, 2000, Pages 3125-3135

  Kiewitz, Claudia ^a   Tümmler, Burkhard ^a  

^a HANNOVER MEDICAL SCHOOL   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL COLONIZATION; BACTERIAL GROWTH; GENE SEQUENCE; GENOTYPE; NONHUMAN; PRIORITY JOURNAL; PSEUDOMONAS AERUGINOSA; SEQUENCE ANALYSIS;

DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; EVOLUTION; GENES, BACTERIAL; GENETIC CODE; GENOME, BACTERIAL; GENOTYPE; PSEUDOMONAS AERUGINOSA; RESTRICTION MAPPING; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; VARIATION (GENETICS);

BACTERIA (MICROORGANISMS); NEGIBACTERIA; PILA; PSEUDOMONAS; PSEUDOMONAS AERUGINOSA; SALMONELLA;

EID: 0034076694     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.182.11.3125-3135.2000     Document Type: Article

References (59)

1. Alonso, A., F. Rojo, and J. L. Martinez. 1999. Environmental and clinical isolates of Pseudomonas aeruginosa show pathogenic and biodegradative properties irrespective of their origin. Environ. Microbiol. 1:421-430.
2. Andersson, S. G. E., and C. G. Kurland. 1990. Codon preferences in free-living microorganisms. Microbiol. Rev. 54:198-210.
3. Bingen, E., E. Denamur, B. Picard, P. Goullet, N. Lambert-Zechovsky, P. Foucaud, J. Navarro, and J. Elion. 1992. Molecular epidemiological analysis of Pseudomonas aeruginosa strains causing failure of antibiotic therapy in cystic fibrosis. Eur. J. Clin. Microbiol. Infect. Dis. 11:432-437.
4. Boyd, E. F., K. Nelson, F. S. Wang, T. S. Whittam, and R. K. Selander. 1994. Molecular genetic basis of allelic polymorphism in malate dehydrogenase (mdh) in natural populations of Escherichia coli and Salmonella enterica. Proc. Natl. Acad. Sci. USA 91:1280-1284.
5. Bradbury, J. F. 1986. Guide to plant pathogenic bacteria. C.A.B. International Mycological Institute. Kew, Surrey, United Kingdom.
6. Campa, M., M. Bendinelli, and H. Friedman (ed.). 1993. Pseudomonas aeruginosa as an opportunistic pathogen. Plenum Press, New York, N.Y.
7. Charnock, C., and T. Bergan. 1992. Multilocus enzyme electrophoresis of major O-antigen reference strains of Pseudomonas aeruginosa. Eur. J. Clin. Microbiol. Infect. Dis. 11:810-816.
8. Chen, W. P., and T. T. Kuo. 1993. A simple and rapid method for the preparation of Gram-negative bacterial genomic DNA. Nucleic Acids Res. 21:2260.
9. Danchin, A., and A. Hénaut. 1997. The map of the cell is in the chromosome. Curr. Opin. Genet. Dev. 7:852-854.
10. Devereux, J., P. Haeberli, and O. Smithies. 1984. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 12:387-395.
11. Donald, L. J., G. F. Molgat, and H. W. Duckworth. 1989. Cloning, sequencing, and expression of the gene for NADH-sensitive citrate synthase of Pseudomonas aeruginosa. J. Bacteriol. 171:5542-5550.
12. Enright, M. C., and B. G. Spratt. 1999. Multilocus sequence typing. Trends Microbiol. 7:482-487.
13. Feil, E. J., M. C. Maiden, M. Achtman, and B. G. Spratt. 1999. The relative contributions of recombination and mutation to the divergence of clones of Neisseria meningitidis. Mol. Biol. Evol. 16:1496-1502.
14. Foght, J. M., D. W. S. Westlake, W. M. Johnson, and H. F. Ridgway. 1996. Environmental gasoline-utilizing isolates and clinical isolates of Pseudomonas aeruginosa are taxonomically indistinguishable by chemotaxonomic and molecular techniques. Microbiology 142:2333-2340.
15. Govan, J. R., and V. Deretic. 1996. Microbial pathogenesis in cystic fibrosis: mucoid Pseudomonas aeruginosa and Burkholderia cepacia. Microbiol. Rev. 60:539-574.
16. Griffith, S. J., C. Nathan, R. K. Selander, W. Chamberlin, S. Gordon, S. Kabins, and R. A. Weinstein. 1989. The epidemiology of Pseudomonas aeruginosa in oncology patients in a general hospital. J. Infect. Dis. 160: 1030-1036.
17. Grothues, D., and B. Tümmler. 1991. New approaches in genome analysis by pulsed-field gel electrophoresis: application to the analysis of Pseudomonas species. Mol. Microbiol. 5:2763-2776.
18. Hacker, J., G. Blum-Oehler, I. Mühldorfer, and H. Tschape. 1997. Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol. Microbiol. 23:1089-1097.
19. Heuer, T., C. Bürger, G. Maaß, and B. Tümmler. 1998 Cloning of prokaryotic genomes in yeast artificial chromosomes: application to the population genetics of Pseudomonas aeruginosa. Electrophoresis 19:486-494.
20. Holloway, B. W., U. Römling, and B. Tümmler. 1994. Genomic mapping of Pseudomonas aeruginosa PAO. Microbiology 140:2907-2929.
21. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules, p. 21-132. In H. N. Munro (ed.), Mammalian protein metabolism. Academic Press, New York, N.Y.
22. Karlin, S., J. Mrázek, and A. M. Campbell. 1998. Codon usages in different gene classes of the Escherichia coli genome. Mol. Microbiol. 29:1341-1355.
23. Kumar, S., K. Tamura, and M. Nei. 1994. MEGA: molecular evolutionary genetics analysis software for microcomputers. Comput. Appl. Biosci. 10: 189-191.
24. Lodge, J. M., S. D. Minchin, L. J. V. Piddock, and S. J. W. Busby. 1990. Cloning, sequencing and analysis of the structural gene and regulatory region of the Pseudomonas aeruginosa chromosomal ampC β-lactamase. Biochem. J. 272:627-631.
25. Maiden, M. C. J., J. A. Bygraves, E. Feil, G. Morelli, J. E. Russell, R. Urwin, Q. Zhang, J. Zhou, K. Zurth, D. A. Caugant, I. M. Feavers, M. Achtman, and B. G. Spratt. 1998. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc. Natl. Acad. Sci. USA 95:3140-3145.
26. Martin, C., E. F. Boyd, R. Quentin, P. Massicot, and R. K. Selander. 1999. Enzyme polymorphism in Pseudomonas aeruginosa strains recovered from cystic fibrosis patients in France. Microbiology 145:2587-2594.
27. Maynard Smith, J., N. H. Smith, M. O'Rourke, and B. G. Spratt. 1993. How clonal are bacteria? Proc. Natl. Acad. Sci. USA 90:4384-4388.
28. Médigue, C., T. Rouxel, P. Vigier, A. Hénaut, and A. Danchin. 1991. Evidence for horizontal gene transfer in Escherichia coli speciation. J. Mol. Biol. 222:851-856.
29. Milkman, R. 1996. Recombinational exchange among clonal populations, p. 2663-2684. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. American Society for Microbiology, Washington, D.C.
30. Musser, J. M. 1996. Molecular population genetic analysis of emerged bacterial pathogens: selected insights. Emerg. Infect. Dis. 2:1-17.
31. Nelson, K., and R. K. Selander. 1992. Evolutionary genetics of the proline permease gene (putP) and the control region of the proline utilization operon in populations of Salmonella and Escherichia coli. J. Bacteriol. 174: 6886-6895.
32. Nelson, K., and R. K. Selander. 1994. Intergeneric transfer and recombination of the 6-phosphogluconate dehydrogenase gene (gnd) in enteric bacteria. Proc. Natl. Acad. Sci. USA 91:10227-10231.
33. Nelson, K., T. S. Whittam, and R. K. Selander. 1991. Nucleotide polymorphism and evolution in the glyceraldehyde-3-phosphate dehydrogenase gene (gapA) in natural populations of Salmonella and Escherichia coli. Proc. Natl. Acad. Sci. USA 88:6667-6671.
34. Nelson, K., F. S. Wang, E. F. Boyd, and R. K. Selander. 1997. Size and sequence polymorphism in the isocitrate dehydrogenase kinase/phosphatase gene (aceK) and flanking regions in Salmonella enterica and Escherichia coli. Genetics 147:1509-1520.
35. OECD. 1997. Consensus document on information used in the assessment of environmental applications involving Pseudomonas. Series on Harmonization of Regulatory Oversight in Biotechnology, no. 6. OECD, Paris, France.
36. Rhame, L. G., E. J. Stevens, S. F. Wolfort, J. Shao, R. G. Tompkins, and F. M. Ausubel. 1995. Common virulence factors for bacterial pathogenicity in plants and animals. Science 268:1899-1902.
37. Römling, U., J. Wingender, W. Müller, and B. Tümmler. 1994. A major Pseudomonas aeruginosa clone common to patients and aquatic habitats. Appl. Environ. Microbiol. 60:1734-1738.
38. Römling, U., J. Greipel, and B. Tümmler. 1995. Gradient of genomic diversity in the Pseudomonas aeruginosa chromosome. Mol. Microbiol. 17:323-332.
39. Römling, U., K. D. Schmidt, and B. Tümmler. 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.
40. Saint-Onge, A., F. Romeyer, P. Lebel, L. Masson, and R. Brousseau. 1992. Specificity of the Pseudomonas aeruginosa PAO1 lipoprotein I gene as a DNA probe and PCR target region within the Pseudomonadaceae. J. Gen. Microbiol. 138:733-741.
41. Saitou, N., and M. Nei. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4:406-425.
42. Sastry, P. A., B. B. Finlay, B. L. Pasloske, W. Paranchych, J. R. Pearlstone, and L. B. Smillie. 1985. Comparative studies of the amino acid and nucleotide sequences of pilin derived from Pseudomonas aeruginosa PAK and PAO. J. Bacteriol. 164:571-577.
43. Schmidt, K. D., B. Tümmler, and U. Römling. 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.
44. Selander, R. K., and J. M. Musser. 1990. Population genetics of bacterial pathogenesis, p. 11-36. In B. H. Iglewski and V. L. Clark (ed.), Molecular basis of bacterial pathogenesis, vol. X. The bacteria. Academic Press, San Diego, Calif.
45. Selander, R. K., D. A. Caugant, H. Ochman, J. M. Musser, M. N. Gilmour, and T. S. Whittam. 1986. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Appl. Environ, Microbiol. 51: 873-884.
46. Selander, R. K., J. Li, and K. Nelson. 1996. Evolutionary genetics of Salmonella enterica, p. 2691-2707. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. American Society for Microbiology, Washington, D.C.
47. Sharp, P. M., and W.-H. Li. 1987. The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15:1281-1295.
48. Sharp, P. M., and G. Matassi. 1994. Codon usage and genome evolution. Curr. Opin. Genet. Dev. 4:851-860.
49. Spangenberg, C., R. Fislage, W. Sierralta, B. Tümmler, and U. Römling. 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.
50. Spangenberg, C., T. Heuer, C. Bürger, and B. Tümmler. 1996. Genetic diversity of flagellins of Pseudomonas aeruginosa. FEBS Lett. 396:213-217.
51. Spangenberg, C., R. Fislage, U. Römling, and B. Tümmler. 1997. Disrespectful type IV pilins. Mol. Microbiol. 25:201-204.
52. Spangenberg, C., T. C. Montie, and B. Tümmler. 1998. Structural and functional implications of sequence diversity of Pseudomonas aeruginosa genes oriC, ampC and fliC. Electrophoresis 19:545-550.
53. Stephens, J. C. 1985. Statistical methods of DNA sequence analysis: detection of intragenic recombination or gene conversion. Mol. Biol. Evol. 2: 539-556.
54. Suerbaum, S., J. M. Smith, K. Bapumia, G. Morelli, N. H. Smith, E. Kunstmann, I. Dyrek, and M. Achtman. 1998. Free recombination within Helicobacter pylori. Proc. Natl. Acad. Sci. USA 13:12619-12624.
55. Totten, P. A., and S. Lory. 1990. Characterization of the type a flagellin gene from Pseudomonas aeruginosa PAK. J. Bacteriol. 172:7188-7199.
56. VanBogelen, R. A., K. Z. Abshire, A. Pertsemlidis, R. L. Clark, and F. C. Neidhardt. 1996. Gene-protein database of Escherichia coli K-12, 6th ed., p. 2067-2117. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. American Society for Microbiology, Washington, D.C.
57. Wang, F. S., T. S. Whittam, and R. K. Selander. 1997. Evolutionary genetics of the isocitrate dehydrogenase gene (icd) in Escherichia coli and Salmonella enterica. J. Bacteriol. 179:6551-6559.
58. Whittam, T. S. 1996. Genetic variation and evolutionary processes in natural populations of Escherichia coli, p. 2708-2720. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. American Society for Microbiology, Washington, D.C.
59. Yee, T. W., and D. W. Smith. 1990. Pseudomonas chromosomal replication origins: a bacterial class distinct from Escherichia coli-type origins. Proc. Natl. Acad. Sci. USA 87:1278-1282.