Abstract
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.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Goodman, A. L., and Lory, S. (2004) Analysis of regulatory networks in Pseudomonas aeruginosa by genomewide transcriptional profiling, Curr. Opin. Microbiol. 7, 39–44.
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.
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.
Waters, C. M., and Bassler, B. L. (2005) Quorum sensing: cell-to-cell communication in bacteria, Annu. Rev. Cell Dev. Biol. 21, 319–346.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Mardis, E. R. (2008) Next-generation DNA sequencing methods, Annu. Rev. Genomics Hum. Genet. 9, 387–402.
Pettersson, E., Lundeberg, J., and Ahmadian, A. (2009) Generations of sequencing technologies, Genomics. 93, 105–111.
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.
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.
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.
Acknowledgements
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.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Schuster, M. (2011). Global Expression Analysis of Quorum-Sensing Controlled Genes. In: Rumbaugh, K. (eds) Quorum Sensing. Methods in Molecular Biology, vol 692. Humana Press. https://doi.org/10.1007/978-1-60761-971-0_13
Download citation
DOI: https://doi.org/10.1007/978-1-60761-971-0_13
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-60761-970-3
Online ISBN: 978-1-60761-971-0
eBook Packages: Springer Protocols