Advertisement

Comparative Study of Differential Gene Expression in Closely Related Bacterial Species by Comparative Hybridization

  • Ruisheng AnEmail author
  • Parwinder S. Grewal
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 815)

Abstract

The ability to profile bacterial gene expression has markedly advanced the capacity to understand the molecular mechanisms of pathogenesis, epidemiology, and therapeutics. This advance has been coupled with the development of techniques that enable investigators to identify bacterial specifically expressed genes and promise to open new avenues of functional genomics by allowing researchers to focus on the identified differentially expressed genes. During the past two decades, a number of approaches have been developed to investigate bacterial genes differentially expressed in response to the changing environment, particularly during interaction with their hosts. The most commonly used techniques include in vivo expression technology, signature-tagged mutagenesis, differential fluorescence induction, and cDNA microarrays, which fall into two broad classes: mutagenesis-based technologies and hybridization-based technologies. Selective capture of transcribed sequences, a recently emerging method, is a hybridization-based technique. This technique is powerful in analyzing differential gene expression of the bacteria, with the superb ability to investigate the bacterial species with unknown genomic information. Herein, we describe the application of this technique in a comparative study of the gene expression between two closely related bacteria induced or repressed under a variety of conditions.

Key words

Closely related bacteria Differential gene expression Genomic presence Competitive hybridization Comparative hybridization Selective capture of transcribed sequences 

Notes

Acknowledgments

This work was supported by a competitive grant from the Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH, USA.

References

  1. 1.
    Deb, D.K., Dahiya, P., Srivastava, K.K., Srivastava, R. and Srivastava, B.S. (2002) Selective identification of new therapeutic targets of Mycobacterium tuberculosis by IVIAT approach. Tuberculosis 82, 175–182.PubMedCrossRefGoogle Scholar
  2. 2.
    Handfield, M., Brady, L.J., Progulske-Fox, A. and Hillman, J.D. (2000) IVIAT: a novel method to identify microbial genes expressed specifically during human infections. Trends Microbiol. 8, 336–339.PubMedCrossRefGoogle Scholar
  3. 3.
    Handfield, M., Seifert, T. and Hillman, J.D. (2002) In vivo expression of bacterial genes during human infections. Methods Mol. Med. 71, 225–242.Google Scholar
  4. 4.
    Hang, L.M., John, M., Asaduzzaman, E.A., Bridges, C., Vanderspurt, T.J., Kirn, R.K., Taylor, R.K., Hillman, J.D., Progulske-Fox, A., Handfield, M., Ryan, E.T. and Calderwood, S.B. (2003) Use of in vivo-induced antigen technology (IVIAT) to identify genes uniquely expressed during human infection with Vibrio cholerae. Proc. Natl. Acad. Sci. USA 100, 8508–8513.PubMedCrossRefGoogle Scholar
  5. 5.
    Rollins, S.M., Peppercorn, A., Hang, L., Hillman, J.D., Calderwood, S.B., Handfield, M. and Ryan, E.T. (2005) Technoreview: in vivo induced antigen technology (IVIAT). Cull. Microbiol. 7, 1–9.CrossRefGoogle Scholar
  6. 6.
    Mahan, M.J., Slauch, J.M. and Mekalanos, J.J. (1993) Selection of bacterial virulence genes that are specifically induced in host tissues. Science 259, 686–688.PubMedCrossRefGoogle Scholar
  7. 7.
    Veal-Carr, W.L. and Stibitz, S. (2005) Demonstration of differential virulence gene promoter activation in vivo in Bordetella pertussis using RIVET. Mol. Microbiol. 55, 788–798.PubMedCrossRefGoogle Scholar
  8. 8.
    Angelichio, M.J. and Camilli, A. (2002) In vivo expression technology. Infect. Immun. 70, 6518–6523.PubMedCrossRefGoogle Scholar
  9. 9.
    Valdivia, R.H. and Falkow, S. (1996) Bacterial genetics by flow cytometry: rapid isolation of Salmonella typhimurium acid-inducible promoters by differential fluorescence induction. Mol. Microbiol. 22, 367–378.PubMedCrossRefGoogle Scholar
  10. 10.
    Hensel, M., Shea, J.E., Gleeson, C., Jones, M.D., Dalton, E. and Holden, D.W. (1995) Simultaneous identification of bacterial virulence genes by negative selection. Science 269, 400–403.PubMedCrossRefGoogle Scholar
  11. 11.
    Shea, J.E., Santangelo, J.D. and Feldman, R.G. (2000) Signature-tagged mutagenesis in the identification of virulence genes in pathogens. Curr. Opin. Microbiol. 3, 451–458.PubMedCrossRefGoogle Scholar
  12. 12.
    Lehoux, D.E. and Levesque, R.C. (2000) Detection of genes essential in specific niches by signature-tagged mutagenesis. Curr. Opin. Biotech. 11, 434–439.PubMedCrossRefGoogle Scholar
  13. 13.
    Mecsas, J. (2002) Use of signature-tagged mutagenesis in pathogenesis studies. Curr. Opin. Microbiol. 5, 33–37.PubMedCrossRefGoogle Scholar
  14. 14.
    Judson, N. and Mekalanos, J.J. (2000) TnAraOut, a transposon-based approach to identify and characterize essential bacterial genes. Nat. Biotech. 18, 740–745.CrossRefGoogle Scholar
  15. 15.
    Akerley, B.J., Rubin, E.J., Lampe, D.J. and Mekalanos, J.J. (1998) PCR-mediated detection of growth-attenuated mutants in large pools generated by in vitro transposon mutagenesis. Am. Soc. Microbiol. Gen. Meet. 98th, Atlanta.Google Scholar
  16. 16.
    Shelburne, S.A. and Musser, J.M. (2004) Virulence gene expression in vivo. Curr. Opin. Microbiol. 7, 283–289.PubMedCrossRefGoogle Scholar
  17. 17.
    To, K.Y. (2000) Identification of differential gene expression by high throughput analysis. Comb Chem High Throughput Screen 3, 235–241.PubMedGoogle Scholar
  18. 18.
    Boyce, J.D., Cullen, P.A. and Adler, B. (2004) Genomic-scale analysis of bacterial gene and protein expression in the host. Emerg. Infect. Dis. 10, 1357–1362.PubMedGoogle Scholar
  19. 19.
    Hinton, J.C., Hautefort, I., Eriksson, S., Thompson, A. and Rhen, M. (2004) Benefits and pitfalls of using microarrays to monitor bacterial gene expression during infection. Curr. Opin. Microbiol. 7, 277–282.PubMedCrossRefGoogle Scholar
  20. 20.
    Jansen, A. and Yu, J. (2006) Differential gene expression of pathogens inside infected hosts. Curr. Opin. Microbiol. 9, 138–142.PubMedCrossRefGoogle Scholar
  21. 21.
    Graham, J.E. and Clark-Curtiss, J.E. (1999) Identification of Mycobacterium tuberculosis RNAs synthesized in response to phagocytosis by human macrophages by selective capture of transcribed sequences (SCOTS). Proc. Natl. Acad. Sci. USA 96, 11554–11559.PubMedCrossRefGoogle Scholar
  22. 22.
    Liu, S., Graham, J.E., Bigelow, L., Morse, P.D., 2nd and Wilkinson, B.J. (2002) Identification of Listeria monocytogenes genes expressed in response to growth at low temperature. Appl. Environ. Microbiol. 68, 1697–1705.PubMedCrossRefGoogle Scholar
  23. 23.
    Hou, J.Y., Graham, J.E. and Clark-Curtiss, J.E. (2002) Mycobacterium avium genes expressed during growth in human macrophages detected by selective capture of transcribed sequences (SCOTS). Infect. Immun. 70, 3714–3726.PubMedCrossRefGoogle Scholar
  24. 24.
    Daigle, F., Graham, J.E. and Curtiss, R., 3 rd (2001) Identification of Salmonella typhi genes expressed within macrophages by selective capture of transcribed sequences (SCOTS). Mol. Microbiol. 41, 1211–1222.PubMedCrossRefGoogle Scholar
  25. 25.
    Dozois, C.M., Daigle, F. and Curtiss, R., 3 rd (2003) Identification of pathogen-specific and conserved genes expressed in vivo by an avian pathogenic Escherichia coli strain. Proc. Natl. Acad. Sci. USA 100, 247–252.PubMedCrossRefGoogle Scholar
  26. 26.
    Baltes, N., Buettner, F.F. and Gerlach, G.F. (2007) Selective capture of transcribed sequences (SCOTS) of Actinobacillus pleuropneumoniae in the chronic stage of disease reveals an HlyX-regulated autotransporter protein. Vet. Microbiol. 123, 110–121.PubMedCrossRefGoogle Scholar
  27. 27.
    Graham, J.E., Peek, R.M., Jr., Krishna, U. and Cover, T.L. (2002) Global analysis of Helicobacter pylori gene expression in human gastric mucosa. Gastroenterology 123, 1637–1648.PubMedCrossRefGoogle Scholar
  28. 28.
    An, R., Sreevatsan, S. and Grewal, P.S. (2008) Moraxella osloensis gene expression in the slug host Deroceras reticulatum. BMC Microbiol. 8, 19.PubMedCrossRefGoogle Scholar
  29. 29.
    An, R., Sreevatsan, S. and Grewal, P.S. (2009) Comparative in vivo gene expression of the closely related bacteria Photorhabdus temperata and Xenorhabdus koppenhoeferi upon infection of the same insect host, Rhizotrogus majalis. BMC Genomics 10, 433.PubMedCrossRefGoogle Scholar
  30. 30.
    Haydel, S.E. and Clark-Curtiss, J.E. (2004) Global expression analysis of two-component system regulator genes during Mycobacterium tuberculosis growth in human macrophages. FEMS Microbiol. Lett. 236, 341–347.PubMedCrossRefGoogle Scholar
  31. 31.
    Aljanabi, S.M. and Martinez, I. (1997) Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic Acids Res. 25, 4692–4693.PubMedCrossRefGoogle Scholar
  32. 32.
    Sambrook, J., Russell, D.W. and Russell, D. (2000) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, New York.Google Scholar
  33. 33.
    Heck, K.L., Jr., Belle, G.V. and Simberloff, D. (1975) Explicit calculation of the rarefaction diversity measurement and the determination of sufficient sample size. Ecology 56, 1459–1461.CrossRefGoogle Scholar
  34. 34.
    Wang, Y.L. and Morse, D. (2006) Rampant polyuridylylation of plastid gene transcripts in the dinoflagellate Lingulodinium. Nucleic Acids Res. 34, 613–619.PubMedCrossRefGoogle Scholar
  35. 35.
    Suga, K., Mark Welch, D., Tanaka, Y., Sakakura, Y. and Hagiwara, A. (2007) Analysis of expressed sequence tags of the cyclically parthenogenetic rotifer Brachionus plicatilis. PLoS ONE 2, e671.PubMedCrossRefGoogle Scholar
  36. 36.
    Zhu, X.C., Tu, Z.J., Coussens, P.M., Kapur, V., Janagama, H., Naser, S. and Sreevatsan, S. (2008) Transcriptional analysis of diverse strains Mycobacterium avium subspecies paratuberculosis in primary bovine monocyte derived macrophages. Microb. Infect. 10, 1274–1282.CrossRefGoogle Scholar
  37. 37.
    Frias-Lopez, J., Shi, Y., Tyson, G.W., Coleman, M.L., Schuster, S.C., Chisholm, S.W. and Delong, E.F. (2008) Microbial community gene expression in ocean surface waters. PNAS 105, 3805–3810.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of EntomologyThe Ohio State UniversityWoosterUSA

Personalised recommendations