1887

Abstract

Abstract

In order to determine the genome variability within , 20 strains representing the seven described genomovars and strain JM300 were analyzed by using various resolution levels of rare cutting enzymes. I and I fingerprints revealed a high degree of heterogeneity of restriction patterns that did not correlate with the division into genomovars. However, a fragment pattern comparison led to the establishment of several groups of clonal variants within genomovars. One circular chromosome ranging in size from 3.75 to 4.64 Mb constitutes the genome of strains. The I-I, I, and I low-resolution map of type strain CCUG 11256 shows the locations of 12 genes, including operons and the origin of replication. II digests of the 20 strains studied plus the positions of six genes allowed a comparison of the backbone organization within genomovars; the four operons seemed to be at similar locations with respect to the origin of replication, as did the rest of the genes. However, a comparison of II cleavage maps of the genomovar reference strains revealed a diverse genome organization in the genomovars relative to operons and gene locations. In most genomovars, operons are not arranged around the origin of replication but are equally distributed on the chromosome. Strain JM300 does not belong to any described genomovar, as determined from the organization of its genome. Large chromosomal rearrangements seem to be responsible for the differences in superordinate genome structure and must have played an important role in diversification and niche colonization. An ancestral chromosome is suggested, and some plausible pathways for the generation of the various genome structures are proposed.

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1997-01-01
2024-10-04
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References

  1. Anagnostopoulos C. 1990; Genetic rearrangements in Bacillus subtilis. 361–371 Drlica K., Riley M. The bacterial chromosome American Society for Microbiology; Washington, D.C.:
    [Google Scholar]
  2. Baggi G., Barbieri P., Galli E., Tollari S. 1987; Isolation of a Pseudomonas stutzeri strain that degrades O-xylene. Appl. Environ. Microbiol. 53:2129–2132
    [Google Scholar]
  3. Baya A. M., Brayton P. R., Brown V. L., Grimes D. J., Russek-Cohen E., Colwell R. R. 1986; Coincident plasmids and antimicrobial resistance in marine bacteria isolated from polluted and unpolluted Atlantic Ocean samples. Appl. Environ. Microbiol. 51:1285–1292
    [Google Scholar]
  4. Bennasar A., Rosselló-Mora R., Lalucat J., Moore E. R. B. 1996; 16S rRNA sequence analysis relative to genomovars of Pseudomonas stutzeri and proposal of Pseudomonas balearica sp. nov.. Int. J. Syst. Bacteriol. 46:200–205
    [Google Scholar]
  5. Birkenbihl R. P., Vielmetter W. 1989; Cosmid-derived map of Escherichia coli strain BHB2600 in comparison to the map of strain W3110. Nucleic Acids Res. 17:5057–5069
    [Google Scholar]
  6. Brewer B. J. 1990; Replication and transcriptional organization of the Escherichia coli chromosome. 61–83 Drlica K., Riley M. The bacterial chromosome American Society for Microbiology; Washington, D.C.:
    [Google Scholar]
  7. Canard B., Saint-Joanis B., Cole S. T. 1992; Genomic diversity and organization of virulence genes in the pathogenic anaerobe Clostridium perfringens. Mol. Microbiol. 6:1421–1429
    [Google Scholar]
  8. Carlson C. A., Pierson L. S., Rosen J. J., Ingraham J. L. 1983; Pseudomonas stutzeri and related species undergo natural transformation. J. Bacteriol. 153:93–99
    [Google Scholar]
  9. Carlson C. R., Gronstad A., Kolsto A.-B. 1992; Physical maps of the genomes of three Bacillus cereus strains. J. Bacteriol. 174:3750–3756
    [Google Scholar]
  10. Church G. M., Gilbert W. 1984; Genomic sequencing. Proc. Natl. Acad. Sci. USA 81:1991–1995
    [Google Scholar]
  11. Cole S. T., Saint Girons I. 1994; Bacterial genomics. FEMS Microbiol. Rev. 14:139–160
    [Google Scholar]
  12. Coyle C. L., Zumft W. G., Kroneck P. M. H., Körner H., Jakob W. 1985; Nitrous oxide reductase from denitrifying Pseudomonas perfectornarina: purification and properties of a novel multicopper enzyme. Eur. J. Biochem. 153:459–467
    [Google Scholar]
  13. Dempsey J. A. F., Wallace A. B., Cannon J. G. 1995; The physical map of the chromosome of a serogroup A strain of Neisseria meningitidis shows complex rearrangements relative to the chromosomes of two mapped strains of the closely related species N. gonorrhoeae. J. Bacteriol. 177:6390–6400
    [Google Scholar]
  14. Döhler K., Huss V. A. R., Zumft W. G. 1987; Transfer of Pseudomonas perfectornarina Baumann, Bowditch, Baumann, and Beaman 1983 to Pseudomonas stutzeri (Lehmann and Neumann 1896) Sijderius 1946. Int. J. Syst. Bacteriol. 37:1–3
    [Google Scholar]
  15. Donald L. J., Molgat G. F., Duckworth H. W. 1989; Cloning, sequencing, and expression of the gene for NADH-sensitive citrate synthase of Pseudomonas aeruginosa. J. Bacteriol. 171:5542–5550
    [Google Scholar]
  16. Eckhardt T. 1978; A rapid method for identification of plasmid deoxyribonucleic acid in bacteria. Plasmid 1:584–588
    [Google Scholar]
  17. Ferguson S. T. 1994; Denitrification and its control. Antonie Leeuwenhoek 66:89–110
    [Google Scholar]
  18. Fonstein M., Haselkorn R. 1995; Physical mapping of bacterial genomes. J. Bacteriol. 177:3361–3369
    [Google Scholar]
  19. Fonstein M., Nikolskaya T., Haselkorn R. 1995; High-resolution alignment of a 1-megabase-long genome region of three strains of Rhodobacter capsulatus. J. Bacteriol. 177:2368–2372
    [Google Scholar]
  20. Fonstein M., Nikolskaya T., Zaporojets D., Nikolsky Y., Kulakauskas S., Mironov A. 1994; Tn10-mediated inversions fuse uridine Phosphorylase (udp) and rRNA genes of Escherichia coli. J. Bacteriol. 176:2265–2271
    [Google Scholar]
  21. François V., Louarn J., Rebollo J.-E., Louarn J.-M. 1990; Replication termination, nondivisible zones, and structure of the Escherichia coli chromosome. 335–340 Drlica K., Riley M. The bacterial chromosome American Society for Microbiology; Washington, D.C.:
    [Google Scholar]
  22. Fujita M., Futai M., Amemura A. 1990; In vivo expression of the Pseudomonas stutzeri maltotetraose-forming amylase gene (amvP). J. Bacteriol. 172:1595–1599
    [Google Scholar]
  23. Gauthier A., Turmel M., Lemieux C. 1991; A group I intron in the chloroplast large subunit rRNA gene of Chlamydomonas eugametos encodes a double-strand endonuclease that cleaves the homing site of this intron. Curr. Genet. 19:43–47
    [Google Scholar]
  24. Genschel J. Unpublished data
    [Google Scholar]
  25. Gorton T. S., Goh M. S., Geary S. J. 1995; Physical mapping of the Mycoplasma gallisepticum S6 genome with localization of selected genes. J. Bactcriol. 177:259–263
    [Google Scholar]
  26. Grothues D., Tümmler B. 1991; New approaches in genome analysis by pulsed-ficld gel electrophoresis: application to the analysis of Pseudomonas species. Mol. Microbiol. 5:2763–2776
    [Google Scholar]
  27. Hall L. M. C. 1994; Are point mutations or DNA rearrangements responsible for the restriction fragment length polymorphisms that are used to type bacteria?. Microbiology 140:197–204
    [Google Scholar]
  28. Haselkorn R. 1992; Developmentally regulated gene rearrangements in prokaryotes. Annu. Rev. Genet. 26:111–128
    [Google Scholar]
  29. Hill C. W., Harvey S., Gray J. A. 1990; Recombination between rRNA genes in Escherichia coli and Salmonella typhimurium. 335–340 Drlica K., Riley M. The bacterial chromosome American Society for Microbiology; Washington. D.C.:
    [Google Scholar]
  30. Holloway B. W., Dharmsthiti S., Krishnapillai V., Morgan A. F., Obeyesekere V., Ratnaningsih E., Sinclair M., Strom D., Zhang C. 1990; Patterns of gene linkages in Pseudomonas species. 97–105 Drlica K., Rilev M. The bacterial chromosome American Society for Microbiology; Washington. D.C.:
    [Google Scholar]
  31. Holloway B. W., Morgan A. F. 1986; Genome organization in Pseudomonas. Annu. Rev. Microbiol. 40:79–105
    [Google Scholar]
  32. Holloway B. W., Römliny U., Tümmler B. 1994; Genomic mapping of Pseudomonas aeruginosa PAO. Microbiology 140:2907–2929
    [Google Scholar]
  33. Holmes B. 1986; Identification and distribution of Pseudomonas stutzeri in clinical material. J. Appl. Bactcriol. 60:401–411
    [Google Scholar]
  34. Honeycutt R. J., McClelland M., Sobral B. W. S. 1993; Physical map of the genome of Rluzobium meliloti 1021. J. Bactcriol. 175:6945–6952
    [Google Scholar]
  35. Hungerer C., Troup B., Römling U., Jahn D. 1995; Cloning, mapping and characterization of the Pseudomonas aeruginosa hemL gene. Mol. Gen. Genet. 248:375–380
    [Google Scholar]
  36. Jahn D. Unpublished data
    [Google Scholar]
  37. Jiang Q., Hiratsuka K., Taylor D. E. 1996; Variability of gene order in different Helicobacter pylori strains contributes to genome diversity. Mol. Microbiol. 20:833–842
    [Google Scholar]
  38. Komoda Y., Enomoto M., Tominaga A. 1991; Large inversion in Escherichia coli K-12 1485IN between inversely oriented IS3 elements near lac and cdd. Genetics 129:639–645
    [Google Scholar]
  39. Kraviec S., Riley M. 1990; Organization of the bacterial chromosome. Microbiol. Rev. 54:502–539
    [Google Scholar]
  40. Kukor J. J., Olsen R. H., Ballon D. P. 1988; Cloning and expression of the catA and the catBC gene clusters from Pseudomonas aeruginosa PAO. J. Bactcriol. 170:4458–4465
    [Google Scholar]
  41. Ladefoged S. A., Christiansen G. 1992; Physical and genetic mapping of the genomes of five Mycoplasma hominis strains by pulsed-field gel electrophoresis. J. Bacteriol. 174:2199–2207
    [Google Scholar]
  42. Leblond P., Redenbach M., Cullum J. 1993; Physical map of the Sireptomyces lividans 66 chromosome and comparison with that of related strain Streptomyces coelicolor A3. J. Bacteriol. 175:3422–3429
    [Google Scholar]
  43. Le Bourgeois P., Lautier M., Van der Berghe L., Gasson M. J., Ritzenthaler P. 1995; Physical and genetic map of the Lactococcus lactis subsp. cremons MG1363 chromosome: comparison with that of Lactococcus lactis subsp. lactis IL 1403 reveals a large genome inversion. J. Bacteriol. 177:2840–2850
    [Google Scholar]
  44. Liu S.-H., Sanderson K. E. 1995; The chromosome of Salmonella paratyphi A is inverted by recombination between rrn H and rind. J. Bacteriol. 177:6585–6592
    [Google Scholar]
  45. Liu S.-L., Hessel A., Cheng H.-Y. M., Sanderson K. E. 1994; The XhaI-BlnI-CeuI genomic cleavage map of Salmonella paratyphi B. J. Bacteriol. 176:1014–1024
    [Google Scholar]
  46. Liu S.-L., Hessel A., Sanderson K. E. 1993; Genomic mapping with \-Ceu\. an intron encoded endonuclease specific for genes for ribosomal RNA. in Salmonella spp.. Escherichia coli, and other bacteria. Proc. Natl. Acad. Sci. USA 90:6874–6878
    [Google Scholar]
  47. Liu S.-L., Hessel A., Sanderson K. E. 1993; The XhaI-BlnI-CeuI genomic cleavage map of Salmonella entendis shows an inversion relative to Salmonella typhimurium LT2. Mol. Microbiol. 10:655–664
    [Google Scholar]
  48. Liu S.-L., Sanderson E. 1995; Rearrangements in the genome of the bacterium Salmonella typhi. Proc. Natl. Acad. Sci. USA 92:1018–1022
    [Google Scholar]
  49. Liu S.-L., Sanderson K. E. 1995; Genomic cleavage map of Salmonella typhi Ty2. J. Bacteriol. 177:5099–5107
    [Google Scholar]
  50. Liu S.-L., Sanderson K. E. 1995; I-CeuI reveals conservation of the genome of independent strains of Salmonella typhimurium. J. Bacteriol. 177:3355–3357
    [Google Scholar]
  51. López-García P., St. Jean A., Amils R., Charlebois R. L. 1995; Genomic stability in the archaeae Haloferax volcanii and Haloferax mediteiranei. J. Bacteriol. 177:1405–1408
    [Google Scholar]
  52. Lorenz M. G., Wackernagel W. 1994; Bacterial gene transfer by natural genetic transformation in the environment. Microbiol. Rev. 58:563–602
    [Google Scholar]
  53. Ludwig W., Kirchhof G., Klugbauer N., Weizenegger M., Betzl D., Ehrmann M., Hertel C., Jilg S., Tatzel R., Zitzelsberger H., Liebl S., Hochberger M., Shah J., Lane D., Wallnöfer P. R., Scheifer K. H. 1992; Complete 23S ribosomal RNA sequences of Gram-positive bacteria with a low DNA G + C content. Syst. Appl. Microbiol. 15:487–501
    [Google Scholar]
  54. Mahan M. J., Segall A. M., Roth J. R. 1990; Recombination events that rearrange the chromosome: barriers to inversion. 341–349 Drlica K., Riley M. The bacterial chromosome American Society for Microbiology; Washington. D.C.:
    [Google Scholar]
  55. Marshall P., Lemieux C. 1992; I-CeuI endonuclease recognizes a sequence of 19 base pairs and preferentially cleaves the coding strand of the Chlamydomonas moewusii chloroplast large subunit rRNA gene. Nucleic Acids Res. 20:6401–6407
    [Google Scholar]
  56. Morgan A. F., Dean H. F. 1985; Chromosome map of Pseudomonas putida PPN. and a comparison of gene order with the Pseudomonas aeruginosa PAO chromosome map. J. Gen. Microbiol. 131:885–896
    [Google Scholar]
  57. Obradors N., Aguilar J. 1991; Efficient biodegradation of high-molecular-weight polyethylene glycols by pure cultures of Pseudomonas stutzeri. Appl. Environ. Microbiol. 57:2383–2388
    [Google Scholar]
  58. Ojaimi C., Davidson B. E., Saint Girons I., Old I. G. 1994; Conservation of gene arrangement and an unusual organization of rRNA genes in the linear chromosomes of the Lyme disease spirochaetes Borrelia burgdorferi, B. garinii and B. afzelii. Microbiology 140:2931–2940
    [Google Scholar]
  59. Palleroni N. J. 1993; Structure of the bacterial genome. 57–98 Goodfellow M., O’Donnell A. G. Handbook of new bacterial systematics Academic Press, Ltd.; London, United Kingdom:
    [Google Scholar]
  60. Perkins J. D., Heath J. D., Sharma B. R., Weinstock G. M. 1993; XbaI and BlnI genomic cleavage maps of Escherichia coli K-12 strain MG1655 and comparative analysis of other strains. J. Mol. Biol. 232:419–445
    [Google Scholar]
  61. Pyle L. E., Taylor T., Finch L. R. 1990; Genomic maps of some strains within the Mycoplasma mycoides cluster. J. Bactcriol. 172:7265–7268
    [Google Scholar]
  62. Rainey P. B., Bailey M. J. 1996; Physical and genetic map of the Pseudomonas fluoresceins SBW25 chromosome. Mol. Microbiol. 19:521–533
    [Google Scholar]
  63. Rainey P. B., Thompson I. P., Palleroni N. J. 1994; Genome and fatty acid analysis of Pseudomonas stutzeri. Int. J. Syst. Bacteriol. 44:54–61
    [Google Scholar]
  64. Riley M., Sanderson K. E. 1990; Comparative genetics of Escherichia coli and Salmonella typhimurium. 85–95 Drlica K., Riley M. The bacterial chromosome American Society for Microbiology; Washington. D.C.:
    [Google Scholar]
  65. Rodley P. D., Römling U., Tümmler B. 1995; A physical genome map of the Burkholderia cepacia type strain. Mol. Microbiol. 17:57–67
    [Google Scholar]
  66. Römling U., Greipel J., Tümmler B. 1995; Gradient of genomic diversity in the Pseudomonas aeruginosa chromosome. Mol. Microbiol. 17:323–332
    [Google Scholar]
  67. Römling L., Grothues D., Bautsch W., Tümmler B. 1989; A physical genome map of Pseudomonas aeruginosa PAO. EMBO J. 8:4081–4089
    [Google Scholar]
  68. Römling U., Grothues D., Heuer T., Tümmler B. 1992; Physical genome analysis of bacteria. Electrophoresis 13:626–631
    [Google Scholar]
  69. Römling U., Heuer T., Tümmler B. 1994; Bacterial genome analysis by pulsed field gel electrophoresis techniques. 355–406 Chrambach A., Dunn M. J., Rafola B. J. Advances in electrophoresis VCH; Weinheim, Germany:
    [Google Scholar]
  70. Rossellö R., García-Valdés E., Lalucat J., Ursing J. 1991; Genotypic and phenotvpic diversity of Pseudomonas stutzeri. Syst. Appl. Microbiol. 14:150–157
    [Google Scholar]
  71. Rossellö R., García-Valdés E., Macario A. J. L., Lalucat J., Macario E. Conway de. 1992; Antigenic diversity of Pseudomonas stutzeri. Syst. Appl. Microbiol. 15:617–623
    [Google Scholar]
  72. Rossellö-Mora R. A., Lalucat J., Moore E. R. B. Syst. Appl. Microbiol. in press
    [Google Scholar]
  73. Rossellö-Mora R. A., Garcîa-Valdés E., Lalucat J. 1993; Taxonomic relationship between Pseudomonas perfectomarina and Pseudomonas stutzeri. Int. J. Syst. Bacteriol. 43:852–854
    [Google Scholar]
  74. Rossellö-Mora R. A., Lalucat J., Dott W., Kämpfer P. 1994; Biochemical and chemotaxonomic characterization of Pseudomonas stutzeri genomovars. J. Appl. Bactcriol. 76:226–233
    [Google Scholar]
  75. Rossellö-Mora R. A., Lalucat J., Garcia-Valdés E. 1994; Comparative biochemical and genetic analysis of naphthalene degradation among Pseudomonas stutzeri strains. Appl. Environ. Microbiol. 60:966–972
    [Google Scholar]
  76. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular cloning: a laboratory manual, 2nd ed.. Cold Spring Harbor Laboratory Press; Cold Spring Harbor, N.Y.:
    [Google Scholar]
  77. 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]
  78. Sinclair M. I., Holloway B. W. 1991; Chromosomal insertion of TOL transposons in Pseudomonas aeruginosa PAO. J. Gen. Microbiol. 137:1111–1120
    [Google Scholar]
  79. Southern E. M., Anand R., Brown W. R. A., Fletcher D. S. 1987; A model of separation of large DNA molecules by crossed field gel electrophoresis. Nucleic Acids Res. 15:5925–5943
    [Google Scholar]
  80. Stanier R. Y., Palleroni N. J., Doudoroff M. 1966; The aerobic pseudo-monads: a taxonomic study. J. Gen. Microbiol. 43:159–271
    [Google Scholar]
  81. Taylor D. E., Eaton M., Yan W., Chang N. 1992; Genome maps of Campylobacter jejuni and Campylobacter coli. J. Bacteriol. 174:2332–2337
    [Google Scholar]
  82. Thuring R. W., Sanders J. B., Borst P. A. 1975; Freeze-squeeze method for recovering long DNA from agarose gels. Anal. Biochem. 66:213–220
    [Google Scholar]
  83. Toda T., Itaya M. 1995; I-CeuI recognition sites in the rrn operons of the Bacillus subtilis 168 chromosome: inherent landmarks for genome analysis. Microbiology 141:1937–1945
    [Google Scholar]
  84. Ursing J. B., Rosselló-Mora R. A., García-Valdés E., Lalucat J. 1995; Taxonomic note: a pragmatic approach to the nomenclature of phenotypically similar genomic groups. Int. J. Syst. Bacteriol. 45:604
    [Google Scholar]
  85. Yee T. W., Smith D. W. 1990; Pseudomonas chromosomal replication origins: a bacterial class distinct from Escherichia coli-type origins. Proc. Natl. Acad. Sci. USA 87:1278–1282
    [Google Scholar]
  86. Zuerner R. L., Hermann J. L., Saint Girons I. 1993; Comparison of genetic maps for two Leptospira interrogans serovars provides evidence for two chromosomes and intraspecies heterogeneity. J. Bacteriol. 175:5445–5451
    [Google Scholar]
  87. Zumft W. G. 1992; The denitrifying prokaryotes. 554–582 Balows A., Trüper H. G., Dworkin M., Harder W., Schleifer K.-H. The prokaryotes Springer-Verlag; Berlin, Germany:
    [Google Scholar]
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