Skip to main content
NCBI home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1992 Jun;174(12):4157–4165. doi: 10.1128/jb.174.12.4157-4165.1992

Characterization of a major polymorphic tandem repeat in Mycobacterium tuberculosis and its potential use in the epidemiology of Mycobacterium kansasii and Mycobacterium gordonae.

P W Hermans 1, D van Soolingen 1, J D van Embden 1
PMCID: PMC206128  PMID: 1350781

Abstract

In this study, the occurrence of repeated DNA sequences in the chromosome of Mycobacterium tuberculosis was investigated systematically. By screening a M. tuberculosis lambda gt-11 gene library with labeled total chromosomal DNA, five strongly hybridizing recombinants were selected, and these contained DNA sequences that were present in multiple copies in the chromosome of M. tuberculosis. These recombinants all contained repeated sequences belonging to a single family of repetitive DNA, which shares homology with a previously described repeated sequence present in recombinant pPH7301. Sequences analysis of pPH7301 showed the presence of a 10-bp sequence that was tandemly repeated and invariably separated by 5-bp unique spacer sequences. Southern blot analysis revealed that the majority of the repeated DNA in M. tuberculosis is composed of this family of repetitive DNA. Because the 10-bp repeats are slightly heterogeneous in sequence, we designated this DNA as a major polymorphic tandem repeat, MPTR. The presence of this repeated sequence in various other mycobacterial species was investigated. Among the MPTR-containing mycobacterial species the chromosomal location of the repetitive DNA is highly variable. The potential use of this polymorphism in the epidemiology of mycobacterioses is discussed.

Full text

PDF
4157

Images in this article

4159Image
on p.4159
4159Image
on p.4159
4161Image
on p.4161
4162Image
on p.4162
4162Image
on p.4162
4163Image
on p.4163
4163Image
on p.4163

Selected References

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

  1. Bradley S. G. Relationships among mycobacteria and nocardiae based upon deoxyribonucleic acid reassociation. J Bacteriol. 1973 Feb;113(2):645–651. doi: 10.1128/jb.113.2.645-651.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Cirillo J. D., Barletta R. G., Bloom B. R., Jacobs W. R., Jr A novel transposon trap for mycobacteria: isolation and characterization of IS1096. J Bacteriol. 1991 Dec;173(24):7772–7780. doi: 10.1128/jb.173.24.7772-7780.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Clark-Curtiss J. E., Docherty M. A. A species-specific repetitive sequence in Mycobacterium leprae DNA. J Infect Dis. 1989 Jan;159(1):7–15. doi: 10.1093/infdis/159.1.7. [DOI] [PubMed] [Google Scholar]
  4. Collins D. M., Gabric D. M., De Lisle G. W. Identification of a repetitive DNA sequence specific to Mycobacterium paratuberculosis. FEMS Microbiol Lett. 1989 Jul 15;51(1):175–178. doi: 10.1016/0378-1097(89)90503-x. [DOI] [PubMed] [Google Scholar]
  5. Deonier R. C., Otsubo E., Lee H. J., Davidson N. Electron microscope heteroduplex studies of sequence relations among plasmids of Escherichia coli. VII. Mapping the ribosomal RNA genes of plasmid F14. J Mol Biol. 1974 Nov 15;89(4):619–629. doi: 10.1016/0022-2836(74)90039-4. [DOI] [PubMed] [Google Scholar]
  6. Eisenach K. D., Crawford J. T., Bates J. H. Repetitive DNA sequences as probes for Mycobacterium tuberculosis. J Clin Microbiol. 1988 Nov;26(11):2240–2245. doi: 10.1128/jcm.26.11.2240-2245.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Engel H. W., Berwald L. G., Grange J. M., Kubin M. Phage typing of Mycobacterium kansasii. Tubercle. 1980 Mar;61(1):11–19. doi: 10.1016/0041-3879(80)90054-9. [DOI] [PubMed] [Google Scholar]
  8. Engel H. W., Berwald L. G., Havelaar A. H. The occurrence of Mycobacterium kansasii in tapwater. Tubercle. 1980 Mar;61(1):21–26. doi: 10.1016/0041-3879(80)90055-0. [DOI] [PubMed] [Google Scholar]
  9. Fasske E., Schröder K. H. Granulomatous pulmonary reactions after instillation of Mycobacterium gordonae. Light and electron microscopic investigations on the rat model. Med Microbiol Immunol. 1989;178(3):149–161. doi: 10.1007/BF00198014. [DOI] [PubMed] [Google Scholar]
  10. Gengoux P., Portaels F., Lachapelle J. M., Minnikin D. E., Tennstedt D., Tamigneau P. Skin granulomas due to Mycobacterium gordonae. Int J Dermatol. 1987 Apr;26(3):181–184. doi: 10.1111/j.1365-4362.1987.tb00888.x. [DOI] [PubMed] [Google Scholar]
  11. Geysen H. M., Meloen R. H., Barteling S. J. Use of peptide synthesis to probe viral antigens for epitopes to a resolution of a single amino acid. Proc Natl Acad Sci U S A. 1984 Jul;81(13):3998–4002. doi: 10.1073/pnas.81.13.3998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Green E. P., Tizard M. L., Moss M. T., Thompson J., Winterbourne D. J., McFadden J. J., Hermon-Taylor J. Sequence and characteristics of IS900, an insertion element identified in a human Crohn's disease isolate of Mycobacterium paratuberculosis. Nucleic Acids Res. 1989 Nov 25;17(22):9063–9073. doi: 10.1093/nar/17.22.9063. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Grosskinsky C. M., Jacobs W. R., Jr, Clark-Curtiss J. E., Bloom B. R. Genetic relationships among Mycobacterium leprae, Mycobacterium tuberculosis, and candidate leprosy vaccine strains determined by DNA hybridization: identification of an M. leprae-specific repetitive sequence. Infect Immun. 1989 May;57(5):1535–1541. doi: 10.1128/iai.57.5.1535-1541.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hermans P. W., Schuitema A. R., Van Soolingen D., Verstynen C. P., Bik E. M., Thole J. E., Kolk A. H., van Embden J. D. Specific detection of Mycobacterium tuberculosis complex strains by polymerase chain reaction. J Clin Microbiol. 1990 Jun;28(6):1204–1213. doi: 10.1128/jcm.28.6.1204-1213.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hermans P. W., van Soolingen D., Bik E. M., de Haas P. E., Dale J. W., van Embden J. D. Insertion element IS987 from Mycobacterium bovis BCG is located in a hot-spot integration region for insertion elements in Mycobacterium tuberculosis complex strains. Infect Immun. 1991 Aug;59(8):2695–2705. doi: 10.1128/iai.59.8.2695-2705.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hermans P. W., van Soolingen D., Dale J. W., Schuitema A. R., McAdam R. A., Catty D., van Embden J. D. Insertion element IS986 from Mycobacterium tuberculosis: a useful tool for diagnosis and epidemiology of tuberculosis. J Clin Microbiol. 1990 Sep;28(9):2051–2058. doi: 10.1128/jcm.28.9.2051-2058.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Jeffreys A. J., Wilson V., Thein S. L. Hypervariable 'minisatellite' regions in human DNA. Nature. 1985 Mar 7;314(6006):67–73. doi: 10.1038/314067a0. [DOI] [PubMed] [Google Scholar]
  18. Kiss A., Sain B., Venetianer P. The number of rRNA genes in Escherichia coli. FEBS Lett. 1977 Jul 1;79(1):77–79. doi: 10.1016/0014-5793(77)80354-2. [DOI] [PubMed] [Google Scholar]
  19. Kunze Z. M., Wall S., Appelberg R., Silva M. T., Portaels F., McFadden J. J. IS901, a new member of a widespread class of atypical insertion sequences, is associated with pathogenicity in Mycobacterium avium. Mol Microbiol. 1991 Sep;5(9):2265–2272. doi: 10.1111/j.1365-2958.1991.tb02157.x. [DOI] [PubMed] [Google Scholar]
  20. Lam S., Roth J. R. IS200: a Salmonella-specific insertion sequence. Cell. 1983 Oct;34(3):951–960. doi: 10.1016/0092-8674(83)90552-4. [DOI] [PubMed] [Google Scholar]
  21. Malone R. E., Chattoraj D. K., Faulds D. H., Stahl M. M., Stahl F. W. Hotspots for generalized recombination in the Escherichia coli chromosome. J Mol Biol. 1978 Jun 5;121(4):473–491. doi: 10.1016/0022-2836(78)90395-9. [DOI] [PubMed] [Google Scholar]
  22. McAdam R. A., Hermans P. W., van Soolingen D., Zainuddin Z. F., Catty D., van Embden J. D., Dale J. W. Characterization of a Mycobacterium tuberculosis insertion sequence belonging to the IS3 family. Mol Microbiol. 1990 Sep;4(9):1607–1613. doi: 10.1111/j.1365-2958.1990.tb02073.x. [DOI] [PubMed] [Google Scholar]
  23. Newbury S. F., Smith N. H., Robinson E. C., Hiles I. D., Higgins C. F. Stabilization of translationally active mRNA by prokaryotic REP sequences. Cell. 1987 Jan 30;48(2):297–310. doi: 10.1016/0092-8674(87)90433-8. [DOI] [PubMed] [Google Scholar]
  24. Noordhoek G. T., Hermans P. W., Paul A. N., Schouls L. M., van der Sluis J. J., van Embden J. D. Treponema pallidum subspecies pallidum (Nichols) and Treponema pallidum subspecies pertenue (CDC 2575) differ in at least one nucleotide: comparison of two homologous antigens. Microb Pathog. 1989 Jan;6(1):29–42. doi: 10.1016/0882-4010(89)90005-3. [DOI] [PubMed] [Google Scholar]
  25. Nyman K., Nakamura K., Ohtsubo H., Ohtsubo E. Distribution of the insertion sequence IS1 in gram-negative bacteria. Nature. 1981 Feb 12;289(5798):609–612. doi: 10.1038/289609a0. [DOI] [PubMed] [Google Scholar]
  26. Pearson W. R., Lipman D. J. Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444–2448. doi: 10.1073/pnas.85.8.2444. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Reddi P. P., Talwar G. P., Khandekar P. S. Repetitive DNA sequence of Mycobacterium tuberculosis: analysis of differential hybridization pattern with other mycobacteria. Int J Lepr Other Mycobact Dis. 1988 Dec;56(4):592–598. [PubMed] [Google Scholar]
  28. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T., Mullis K. B., Erlich H. A. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science. 1988 Jan 29;239(4839):487–491. doi: 10.1126/science.2448875. [DOI] [PubMed] [Google Scholar]
  29. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Schraufnagel D. E., Leech J. A., Pollak B. Mycobacterium kansasii: colonization and disease. Br J Dis Chest. 1986 Apr;80(2):131–137. doi: 10.1016/0007-0971(86)90033-1. [DOI] [PubMed] [Google Scholar]
  31. Shinnick T. M. The 65-kilodalton antigen of Mycobacterium tuberculosis. J Bacteriol. 1987 Mar;169(3):1080–1088. doi: 10.1128/jb.169.3.1080-1088.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Smith G. R., Kunes S. M., Schultz D. W., Taylor A., Triman K. L. Structure of chi hotspots of generalized recombination. Cell. 1981 May;24(2):429–436. doi: 10.1016/0092-8674(81)90333-0. [DOI] [PubMed] [Google Scholar]
  33. 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]
  34. Stahl D. A., Urbance J. W. The division between fast- and slow-growing species corresponds to natural relationships among the mycobacteria. J Bacteriol. 1990 Jan;172(1):116–124. doi: 10.1128/jb.172.1.116-124.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Stern M. J., Ames G. F., Smith N. H., Robinson E. C., Higgins C. F. Repetitive extragenic palindromic sequences: a major component of the bacterial genome. Cell. 1984 Jul;37(3):1015–1026. doi: 10.1016/0092-8674(84)90436-7. [DOI] [PubMed] [Google Scholar]
  36. Stewart G. C., Wilson F. E., Bott K. F. Detailed physical mapping of the ribosomal RNA genes of Bacillus subtilis. Gene. 1982 Sep;19(2):153–162. doi: 10.1016/0378-1119(82)90001-4. [DOI] [PubMed] [Google Scholar]
  37. Thierry D., Cave M. D., Eisenach K. D., Crawford J. T., Bates J. H., Gicquel B., Guesdon J. L. IS6110, an IS-like element of Mycobacterium tuberculosis complex. Nucleic Acids Res. 1990 Jan 11;18(1):188–188. doi: 10.1093/nar/18.1.188. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Thole J. E., Keulen W. J., De Bruyn J., Kolk A. H., Groothuis D. G., Berwald L. G., Tiesjema R. H., van Embden J. D. Characterization, sequence determination, and immunogenicity of a 64-kilodalton protein of Mycobacterium bovis BCG expressed in escherichia coli K-12. Infect Immun. 1987 Jun;55(6):1466–1475. doi: 10.1128/iai.55.6.1466-1475.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Thole J. E., Stabel L. F., Suykerbuyk M. E., De Wit M. Y., Klatser P. R., Kolk A. H., Hartskeerl R. A. A major immunogenic 36,000-molecular-weight antigen from Mycobacterium leprae contains an immunoreactive region of proline-rich repeats. Infect Immun. 1990 Jan;58(1):80–87. doi: 10.1128/iai.58.1.80-87.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Verbon A., Kuijper S., Jansen H. M., Speelman P., Kolk A. H. Antigens in culture supernatant of Mycobacterium tuberculosis: epitopes defined by monoclonal and human antibodies. J Gen Microbiol. 1990 May;136(5):955–964. doi: 10.1099/00221287-136-5-955. [DOI] [PubMed] [Google Scholar]
  41. Wolinsky E. Nontuberculous mycobacteria and associated diseases. Am Rev Respir Dis. 1979 Jan;119(1):107–159. doi: 10.1164/arrd.1979.119.1.107. [DOI] [PubMed] [Google Scholar]
  42. Woods S. A., Cole S. T. A family of dispersed repeats in Mycobacterium leprae. Mol Microbiol. 1990 Oct;4(10):1745–1751. doi: 10.1111/j.1365-2958.1990.tb00552.x. [DOI] [PubMed] [Google Scholar]
  43. Young R. A., Bloom B. R., Grosskinsky C. M., Ivanyi J., Thomas D., Davis R. W. Dissection of Mycobacterium tuberculosis antigens using recombinant DNA. Proc Natl Acad Sci U S A. 1985 May;82(9):2583–2587. doi: 10.1073/pnas.82.9.2583. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. van Soolingen D., Hermans P. W., de Haas P. E., Soll D. R., van Embden J. D. Occurrence and stability of insertion sequences in Mycobacterium tuberculosis complex strains: evaluation of an insertion sequence-dependent DNA polymorphism as a tool in the epidemiology of tuberculosis. J Clin Microbiol. 1991 Nov;29(11):2578–2586. doi: 10.1128/jcm.29.11.2578-2586.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES