Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli

Anders Ståhlberg¹^,2^,8 , Karin Elbing³ , José Manuel Andrade-Garda⁴ , Björn Sjögreen⁵ , Amin Forootan⁶ and Mikael Kubista¹^,7

¹TATAA Biocenter, Odinsgatan 28, 411 03 Göteborg, Sweden

²Stem Cell Center, Lund University, BMC B10, 221 84 Lund, Sweden

³Deparment of Cell and Molecular Biology, Göteborg University, BOX 462, 405 30 Göteborg, Sweden

⁴Department of Analytical Chemistry, University of A Coruna, A Zapateira s/n, E-15071 A Coruna, Spain

⁵Center for Applied Scientific Computing, Lawrence Livermore National Laboratory, Box 808, L-365, Livermore, CA 94551, USA

⁶MultiD Analyses AB, Odinsgatan 28, 411 03 Göteborg, Sweden

⁷Institute of Biotechnology, Academy of Sciences of the Czech Republic, Videnska 1083, Prague 4, 142 20, Czech Republic

⁸Department of Clinical Neuroscience and Rehabilitation, Institute of Neurosciences and Physiology, Sahlgrenska Academy at Göteborg University, Medicinaregatan 9A, 413 90 Göteborg, Sweden

author email corresponding author email

BMC Genomics 2008, 9:170doi:10.1186/1471-2164-9-170


Published:	16 April 2008

Abstract

Background

The large sensitivity, high reproducibility and essentially unlimited dynamic range of real-time PCR to measure gene expression in complex samples provides the opportunity for powerful multivariate and multiway studies of biological phenomena. In multiway studies samples are characterized by their expression profiles to monitor changes over time, effect of treatment, drug dosage etc. Here we perform a multiway study of the temporal response of four yeast Saccharomyces cerevisiae strains with different glucose uptake rates upon altered metabolic conditions.

Results

We measured the expression of 18 genes as function of time after addition of glucose to four strains of yeast grown in ethanol. The data are analyzed by matrix-augmented PCA, which is a generalization of PCA for 3-way data, and the results are confirmed by hierarchical clustering and clustering by Kohonen self-organizing map. Our approach identifies gene groups that respond similarly to the change of nutrient, and genes that behave differently in mutant strains. Of particular interest is our finding that ADH4 and ADH6 show a behavior typical of glucose-induced genes, while ADH3 and ADH5 are repressed after glucose addition.

Conclusion

Multiway real-time PCR gene expression profiling is a powerful technique which can be utilized to characterize functions of new genes by, for example, comparing their temporal response after perturbation in different genetic variants of the studied subject. The technique also identifies genes that show perturbed expression in specific strains.