Quorum Sensing pp 173-187 | Cite as

Global Expression Analysis of Quorum-Sensing Controlled Genes

  • Martin SchusterEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 692)


Transcript profiling has improved our understanding of quorum-sensing gene regulation on a global scale. Here, we describe methods for high-quality sample preparation for use in DNA microarray and real-time PCR experiments.

Key words

Transcriptome Microarray RNA isolation cDNA synthesis Real-time PCR Quorum sensing Pseudomonas aeruginosa 



Parts of the cDNA synthesis procedure are based on a protocol by Matt Wolfgang, University of North Carolina. Thanks to Joon-Hee Lee, University of Pusan, South Korea, for his suggestions on real-time PCR.


  1. 1.
    Goodman, A. L., and Lory, S. (2004) Analysis of regulatory networks in Pseudomonas aeruginosa by genomewide transcriptional profiling, Curr. Opin. Microbiol. 7, 39–44.PubMedCrossRefGoogle Scholar
  2. 2.
    Schuster, M., and Greenberg, E. P. (2006) A network of networks: quorum-sensing gene regulation in Pseudomonas aeruginosa, Int. J. Med. Microbiol. 296, 73–81.PubMedCrossRefGoogle Scholar
  3. 3.
    Williams, P., Winzer, K., Chan, W. C., and Camara, M. (2007) Look who’s talking: communication and quorum sensing in the bacterial world, Philos. Trans. R. Soc. London. 362, 1119–1134.CrossRefGoogle Scholar
  4. 4.
    Waters, C. M., and Bassler, B. L. (2005) Quorum sensing: cell-to-cell communication in bacteria, Annu. Rev. Cell Dev. Biol. 21, 319–346.PubMedCrossRefGoogle Scholar
  5. 5.
    Hense, B. A., Kuttler, C., Muller, J., Rothballer, M., Hartmann, A., and Kreft, J. U. (2007) Does efficiency sensing unify diffusion and quorum sensing?, Nat. Rev. 5, 230–239.CrossRefGoogle Scholar
  6. 6.
    Stover, C. K., Pham, X. Q., Erwin, A. L., Mizoguchi, S. D., Warrener, P., Hickey, M. J., Brinkman, F. S., Hufnagle, W. O., Kowalik, D. J., Lagrou, M., Garber, R. L., Goltry, L., Tolentino, E., Westbrock-Wadman, S., Yuan, Y., Brody, L. L., Coulter, S. N., Folger, K. R., Kas, A., Larbig, K., Lim, R., Smith, K., Spencer, D., Wong, G. K., Wu, Z., and Paulsen, I. T. (2000) Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen, Nature. 406, 947–948.CrossRefGoogle Scholar
  7. 7.
    Hentzer, M., Wu, H., Andersen, J. B., Riedel, K., Rasmussen, T. B., Bagge, N., Kumar, N., Schembri, M. A., Song, Z., Kristoffersen, P., Manefield, M., Costerton, J. W., Molin, S., Eberl, L., Steinberg, P., Kjelleberg, S., Hoiby, N., and Givskov, M. (2003) Attenuation of Pseudomonas aeruginosa virulence by quorum sensing inhibitors, EMBO J. 22, 3803–3815.PubMedCrossRefGoogle Scholar
  8. 8.
    Schuster, M., Lohstroh, C. P., Ogi, T., and Greenberg, E. P. (2003) Identification, timing and signal specificity of Pseudomonas aeruginosa quorum-controlled genes: a transcriptome analysis, J. Bacteriol. 185, 2066–2079.PubMedCrossRefGoogle Scholar
  9. 9.
    Wagner, V. E., Bushnell, D., Passador, L., Brooks, A. I., and Iglewski, B. H. (2003) Microarray analysis of Pseudomonas aeruginosa quorum-sensing regulons: effects of growth phase and environment, J. Bacteriol. 185, 2080–2095.PubMedCrossRefGoogle Scholar
  10. 10.
    Schuster, M., Hawkins, A. C., Harwood, C. S., and Greenberg, E. P. (2004) The Pseudomonas aeruginosa RpoS regulon and its relationship to quorum sensing, Mol. Microbiol. 51, 973–985.PubMedCrossRefGoogle Scholar
  11. 11.
    Bagge, N., Schuster, M., Hentzer, M., Ciofu, O., Givskov, M., Greenberg, E. P., and Hoiby, N. (2004) Pseudomonas aeruginosa biofilms exposed to imipenem exhibit changes in global gene expression and beta-lactamase and alginate production, Antimicrob. Agents. Chemother. 48, 1175–1187.PubMedCrossRefGoogle Scholar
  12. 12.
    Sonnleitner, E., Schuster, M., Sorger-Domenigg, T., Greenberg, E. P., and Blasi, U. (2006) Hfq-dependent alterations of the transcriptome profile and effects on quorum sensing in Pseudomonas aeruginosa, Mol. Microbiol. 59, 1542–1558.PubMedCrossRefGoogle Scholar
  13. 13.
    Rampioni, G., Schuster, M., Greenberg, E. P., Bertani, I., Grasso, M., Venturi, V., Zennaro, E., and Leoni, L. (2007) RsaL provides quorum sensing homeostasis and functions as a global regulator of gene expression in Pseudomonas aeruginosa, Mol. Microbiol. 66, 1557–1565.PubMedCrossRefGoogle Scholar
  14. 14.
    Palmer, K. L., Mashburn, L. M., Singh, P. K., and Whiteley, M. (2005) Cystic fibrosis sputum supports growth and cues key aspects of Pseudomonas aeruginosa physiology, J. Bacteriol. 187, 5267–5277.PubMedCrossRefGoogle Scholar
  15. 15.
    Banin, E., Vasil, M. L., and Greenberg, E. P. (2005) Iron and Pseudomonas aeruginosa biofilm formation, Proc. Natl. Acad. Sci. U.S.A. 102, 11076–11081.PubMedCrossRefGoogle Scholar
  16. 16.
    Yarwood, J. M., Volper, E. M., and Greenberg, E. P. (2005) Delays in Pseudomonas aeruginosa quorum-controlled gene expression are conditional, Proc. Natl. Acad. Sci. U.S.A. 102, 9008–9013.PubMedCrossRefGoogle Scholar
  17. 17.
    Mardis, E. R. (2008) Next-generation DNA sequencing methods, Annu. Rev. Genomics Hum. Genet. 9, 387–402.PubMedCrossRefGoogle Scholar
  18. 18.
    Pettersson, E., Lundeberg, J., and Ahmadian, A. (2009) Generations of sequencing technologies, Genomics. 93, 105–111.PubMedCrossRefGoogle Scholar
  19. 19.
    Wolfinger, R. D., Gibson, G., Wolfinger, E. D., Bennett, L., Hamadeh, H., Bushel, P., Afshari, C., and Paules, R. S. (2001) Assessing gene significance from cDNA microarray expression data via mixed models, J. Comput. Biol. 8, 625–637.PubMedCrossRefGoogle Scholar
  20. 20.
    Kendziorski, C., Irizarry, R. A., Chen, K. S., Haag, J. D., and Gould, M. N. (2005) On the utility of pooling biological samples in microarray experiments, Proc. Natl. Acad. Sci. U.S.A. 102, 4252–4257.PubMedCrossRefGoogle Scholar
  21. 21.
    Peng, X., Wood, C. L., Blalock, E. M., Chen, K. C., Landfield, P. W., and Stromberg, A. J. (2003) Statistical implications of pooling RNA samples for microarray experiments, BMC Bioinformatics. 4, 26.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Department of MicrobiologyOregon State UniversityCorvallisUSA

Personalised recommendations