Skip to main content
PMC home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1995 Aug;177(16):4772–4778. doi: 10.1128/jb.177.16.4772-4778.1995

Integration of heterologous DNA into the genome of Paracoccus denitrificans is mediated by a family of IS1248-related elements and a second type of integrative recombination event.

R J Van Spanning 1, W N Reijnders 1, A H Stouthamer 1
PMCID: PMC177244  PMID: 7642505

Abstract

All members of the IS1248 family residing in the genome of Paracoccus denitrificans have been isolated by using a set of insertion sequence entrapment vectors. The family consists of five closely related members that integrate the entrapment vectors at distinct sites. One of these, IS1248b, was sequenced and, except for a single base change, shown to be identical to the previously isolated IS1248a. Southern analysis of genomic DNA with labeled IS1248 revealed different hybridization patterns for different isolates of P. denitrificans and Thiosphaera pantotropha. No hybridization was observed with DNA from Thiobacillus versutus and more distantly related species. From a comparison of the fingerprints it was shown that one of the members of the IS1248 family found in P. denitrificans DSM413 is absent in strain NCIB8944, although they are catalogued in international strain catalogues as identical strains. Furthermore, strains Pd1222 and Pd1235, both derivatives of P. denitrificans DSM413, were shown to have different patterns of IS1248 hybridizing restriction fragments. In 14 of 18 strains, the entrapment vectors used in this study were incorporated into the genome via IS1248-mediated cointegrate formation. In the other four strains, the entrapment vectors were shown to be integrated through a different mechanism not involving IS1248.

Full Text

The Full Text of this article is available as a PDF (420.2 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Bott M., Ritz D., Hennecke H. The Bradyrhizobium japonicum cycM gene encodes a membrane-anchored homolog of mitochondrial cytochrome c. J Bacteriol. 1991 Nov;173(21):6766–6772. doi: 10.1128/jb.173.21.6766-6772.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Chen C. W., Yu T. W., Chung H. M., Chou C. F. Discovery and characterization of a new transposable element, Tn4811, in Streptomyces lividans 66. J Bacteriol. 1992 Dec;174(23):7762–7769. doi: 10.1128/jb.174.23.7762-7769.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chepuri V., Lemieux L., Au D. C., Gennis R. B. The sequence of the cyo operon indicates substantial structural similarities between the cytochrome o ubiquinol oxidase of Escherichia coli and the aa3-type family of cytochrome c oxidases. J Biol Chem. 1990 Jul 5;265(19):11185–11192. [PubMed] [Google Scholar]
  5. Coucheron D. H. A family of IS1031 elements in the genome of Acetobacter xylinum: nucleotide sequences and strain distribution. Mol Microbiol. 1993 Jul;9(1):211–218. doi: 10.1111/j.1365-2958.1993.tb01682.x. [DOI] [PubMed] [Google Scholar]
  6. De Meirsman C., Van Soom C., Verreth C., Van Gool A., Vanderleyden J. Nucleotide sequence analysis of IS427 and its target sites in Agrobacterium tumefaciens T37. Plasmid. 1990 Nov;24(3):227–234. doi: 10.1016/0147-619x(90)90006-x. [DOI] [PubMed] [Google Scholar]
  7. Ferrante A. A., Lessie T. G. Nucleotide sequence of IS402 from Pseudomonas cepacia. Gene. 1991 Jun 15;102(1):143–144. doi: 10.1016/0378-1119(91)90555-p. [DOI] [PubMed] [Google Scholar]
  8. Kitts P. A., Symington L. S., Dyson P., Sherratt D. J. Transposon-encoded site-specific recombination: nature of the Tn3 DNA sequences which constitute the recombination site res. EMBO J. 1983;2(7):1055–1060. doi: 10.1002/j.1460-2075.1983.tb01545.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Knight A. I., Ni H., Cartwright K. A., McFadden J. J. Identification and characterization of a novel insertion sequence, IS1106, downstream of the porA gene in B15 Neisseria meningitidis. Mol Microbiol. 1992 Jun;6(11):1565–1573. doi: 10.1111/j.1365-2958.1992.tb00878.x. [DOI] [PubMed] [Google Scholar]
  10. Ludwig W., Mittenhuber G., Friedrich C. G. Transfer of Thiosphaera pantotropha to Paracoccus denitrificans. Int J Syst Bacteriol. 1993 Apr;43(2):363–367. doi: 10.1099/00207713-43-2-363. [DOI] [PubMed] [Google Scholar]
  11. Mariani F., Piccolella E., Colizzi V., Rappuoli R., Gross R. Characterization of an IS-like element from Mycobacterium tuberculosis. J Gen Microbiol. 1993 Aug;139(8):1767–1772. doi: 10.1099/00221287-139-8-1767. [DOI] [PubMed] [Google Scholar]
  12. Paulus F., Canaday J., Vincent F., Bonnard G., Kares C., Otten L. Sequence of the iaa and ipt region of different Agrobacterium tumefaciens biotype III octopine strains: reconstruction of octopine Ti plasmid evolution. Plant Mol Biol. 1991 Apr;16(4):601–614. doi: 10.1007/BF00023425. [DOI] [PubMed] [Google Scholar]
  13. Samyn B., Berks B. C., Page M. D., Ferguson S. J., van Beeumen J. J. Characterisation and amino acid sequence of cytochrome c-550 from Thiosphaera pantotropha. Eur J Biochem. 1994 Jan 15;219(1-2):585–594. doi: 10.1111/j.1432-1033.1994.tb19974.x. [DOI] [PubMed] [Google Scholar]
  14. Soto M. J., Zorzano A., Olivares J., Toro N. Sequence of ISRm4 from Rhizobium meliloti strain GR4. Gene. 1992 Oct 12;120(1):125–126. doi: 10.1016/0378-1119(92)90020-p. [DOI] [PubMed] [Google Scholar]
  15. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  16. Stouthamer A. H. Metabolic pathways in Paracoccus denitrificans and closely related bacteria in relation to the phylogeny of prokaryotes. Antonie Van Leeuwenhoek. 1992 Jan;61(1):1–33. doi: 10.1007/BF00572119. [DOI] [PubMed] [Google Scholar]
  17. Van Spanning R. J., Wansell C., Harms N., Oltmann L. F., Stouthamer A. H. Mutagenesis of the gene encoding cytochrome c550 of Paracoccus denitrificans and analysis of the resultant physiological effects. J Bacteriol. 1990 Feb;172(2):986–996. doi: 10.1128/jb.172.2.986-996.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Woese C. R. Bacterial evolution. Microbiol Rev. 1987 Jun;51(2):221–271. doi: 10.1128/mr.51.2.221-271.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. van Embden J., Cohen S. N. Molecular and genetic studies of an R factor system consisting of independent transfer and drug resistance plasmids. J Bacteriol. 1973 Nov;116(2):699–709. doi: 10.1128/jb.116.2.699-709.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES