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Development of Bacterial Species-Specific DNA Probes Based on Ribosomal RNA Genes Using PCR

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Book cover Diagnostic Bacteriology Protocols

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 46))

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Abstract

DNA probes are being used increasingly to detect and identify microorganisms, particularly pathogenic bacteria in a variety of areas. These include medicine, the food industry, and the environment. Various strategies have been used to develop DNA probes for specific bacteria that include the use of genes for antigenic determinants and virulence factors, randomly cloned DNA fragments, high copy number sequences including insertion elements, and ribosomal RNA (rRNA) genes (1–7). The sequences used for DNA probes ought to be both highly abundant as well as specific for the organism of interest. Therefore, rRNA is a potential target for the development of DNA probes.

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References

  1. Matsuo, K., Yamaguchi, R., Yamazaki, A., Tasaka, H., and Yamada, T. (1988) Cloning and expression of the Mycobacterium bovis BCG gene for extracellular alpha antigen. J. Bacteriol. 170, 3847–3854.

    PubMed  CAS  Google Scholar 

  2. Yamaguchi, R., Matsuo, K., Yamazaki, A., Abe, C., Nagai, S., Terasaka, K., and Yamada, T. (1989) Cloning and characterisation of the gene for immunogenic pro tein MPB64 of Mycobacterium bovis BCG. Infect. Immunol. 57, 283–288.

    CAS  Google Scholar 

  3. Leimeister-Wachter, M., Haffner, C., Domann, E., Goebel, W., and Chakraborty, T. (1990) Identification of a gene that positively regulates expression of listeriolysin, the major virulence factor of Listerta monocytogenes. Proc. Natl. Acad. Sci. USA 87, 8336–8340.

    Article  PubMed  CAS  Google Scholar 

  4. Hiney, M. P., Dawson, M. T., Smith, P. R., Gannon, F., and Powell, R. (1992) DNA probe for Aeromonas salmonicida. Appl. Environ. Microbiol. 58, 1035–1042.

    Google Scholar 

  5. Eisenach, K. D., Crawford, J. T., and Bates, J. H. (1988) Repetitive DNA sequences as probes for Mycobacterium tuberculosis. J. Clin. Microbiol. 26, 2240–2245.

    PubMed  CAS  Google Scholar 

  6. Barry, T., Powell, R., and Gannon, F. (1990) A general method to generate DNA probes for microorganisms. Biotechnology 8, 233–236.

    Article  PubMed  CAS  Google Scholar 

  7. Barry, T., Colleran, G., Glennon, M., Dunican, L. K., and Gannon, F. (1991) The 16S/23S ribosomal spacre region as a target for DNA probes to identify Eubacteria. PCR Meth. Appl. 1, 51–56.

    CAS  Google Scholar 

  8. King, T. C., Sirdeskmukh, R., and Schlessinger, D. (1986) Nucleolytic processing of ribonucleic acid transcripts in procaryotes. Microbiol. Rev. 50, 428–451.

    PubMed  CAS  Google Scholar 

  9. Kenerley, M. E., Morgan, E. A., Post, L., Lindahl, L., and Nomura, M. (1977) Characterisation of hybrid plasmids carrying individual ribosomal ribonucleic acid transcription units of Escherichia coli. J. Bacteriol. 132, 931–949.

    PubMed  CAS  Google Scholar 

  10. Kiss, A., Sain, B., and Venetianer, P. (1977) The number of rRNA genes in Escherichia coli. Febs Lett. 79, 77–79.

    Article  PubMed  CAS  Google Scholar 

  11. Canard, B. and Cole, S. T. (1989) Genome organization of the anaerobic pathogen Clostridium perfringens Proc. Natl. Acad. Sci. USA 86, 6676–6680.

    Article  PubMed  CAS  Google Scholar 

  12. Gray, M. W., Sankoff, D., and Cedergren, R. J. (1984) On the evolutionary descent of organisms and organelles: a global phylogeny based on a highly conserved structural core in small subunit ribosomal RNA. Nucleic Acids Res. 12, 5837–5852.

    Article  PubMed  CAS  Google Scholar 

  13. Neefs, J. M., Vander Peer, Y., Hendnks, L., and de Wachter, R. (1990) Compilation of small ribosomal subunit RNA sequences. Nuclerc Acids Res. 18(Suppl.), 2237–2317.

    CAS  Google Scholar 

  14. Gutell, R. R., Weiser, B., Woese, C. R., and Noller, H. F. (1985) Comparative anatomy of 16S-like ribosomal RNA. Prog. Nucleic Acid Res. Mol. Blol. 32, 155–216.

    Article  CAS  Google Scholar 

  15. Brosius, J., Dull, T. J., Sleeter, D., and Noller, H. F. (1981) Gene organisation and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol. 148, 107–127.

    Article  PubMed  CAS  Google Scholar 

  16. Dams, E., Hendriks, L., Vander Peer, Y., Neefs, J. M., Smits, G., Vandenbempt, I., and de Wachter, R. (1988) Compilation of small ribosomal subunit RNA sequences. Nucleic Acids Res. 16(Suppl.), 87–173.

    Google Scholar 

  17. Olsen, G. J., Lane, D. J., Giovannoni, S. J., Pace, N., and Stahl, D. A. (1986) Microbial ecology and evolution: a ribosomal RNA approach. Annu. Rev. Microbiol. 40, 337–365.

    Article  PubMed  CAS  Google Scholar 

  18. Fox, G. E. and Stackebrandt, E. (1987) The application of 16S rRNA cataloguing and 5S rRNA sequencing in bacterial systematics. Meth. Microbiol. 19, 405–458.

    Article  CAS  Google Scholar 

  19. Casanova, J.-L., Pannetier, C., Jaulin, C., and Kourilsky, P. (1990) Optimal conditions for directly sequencing double-stranded PCR products with Sequenase. Nucleic Acids Res. 18, 4028.

    Article  PubMed  CAS  Google Scholar 

  20. Higgins, D. G. and Sharp, P. M. (1988) A package for performing multiple sequence alignment on a microcomputer. Gene 73, 237–244.

    Article  PubMed  CAS  Google Scholar 

  21. Higgins, D. G., Bleasby, A. J., and Fuchs, R. (1992) Improved software for multiple sequence alignment. CABZOS 8, 189–191.

    CAS  Google Scholar 

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Author information

Authors and Affiliations

  1. BioResearch Ireland, National Diagnostics Centre, University College, Galway, Ireland

    Terry J. Smith, Majella Maher, Frank Gannon & Michael T. Dawson

Authors
  1. Terry J. Smith
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  2. Majella Maher
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  3. Frank Gannon
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  4. Michael T. Dawson
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Editor information

Editors and Affiliations

  1. Dalgety plc, Cambridge, UK

    Jenny Howard

  2. Department of Medicine, University of Cambridge, UK

    David M. Whitcombe

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© 1995 Humana Press Inc.

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Smith, T.J., Maher, M., Gannon, F., Dawson, M.T. (1995). Development of Bacterial Species-Specific DNA Probes Based on Ribosomal RNA Genes Using PCR. In: Howard, J., Whitcombe, D.M. (eds) Diagnostic Bacteriology Protocols. Methods in Molecular Biology™, vol 46. Humana Press. https://doi.org/10.1385/0-89603-297-3:247

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  • DOI: https://doi.org/10.1385/0-89603-297-3:247

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-297-2

  • Online ISBN: 978-1-59259-533-4

  • eBook Packages: Springer Protocols

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