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

Ståhlberg A, Elbing K, Andrade-Garda JM, Sjögreen B, Forootan A, Kubista M - BMC Genomics (2008)

Bottom Line: In multiway studies samples are characterized by their expression profiles to monitor changes over time, effect of treatment, drug dosage etc.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.The technique also identifies genes that show perturbed expression in specific strains.

View Article: PubMed Central - HTML - PubMed

Affiliation: TATAA Biocenter, Odinsgatan 28, 411 03 Göteborg, Sweden. anders.stahlberg@neuro.gu.se

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.

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Related in: MedlinePlus

Summary of gene classification. Genes are arranged into five groups after PCA: group I (genes induced upon glucose addition), group II (genes repressed upon glucose addition), group III (genes with expression profiles that passes through a maximum), group IV (genes with expression profiles that passes through a minimum) and group V (no regulation). PCA classification was confirmed by hierarchical clustering and Kohonen SOM.
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Figure 8: Summary of gene classification. Genes are arranged into five groups after PCA: group I (genes induced upon glucose addition), group II (genes repressed upon glucose addition), group III (genes with expression profiles that passes through a maximum), group IV (genes with expression profiles that passes through a minimum) and group V (no regulation). PCA classification was confirmed by hierarchical clustering and Kohonen SOM.

Mentions: The yeast multiway expression profiles, based on the expression of 15 genes of interest measured at eight time points in fours strains, analyzed catenated by the three analytical methods Principal component analysis, hierarchical clustering and self-organized maps yield highly consistent results. The genes can be divided into four groups (Figure 8) characterized by different combinations of the two main loading vectors of the PCA, they form four hierarchical clusters, and they separate in a SOM with small number of neurons. PGK1 in HXT-TM6* strain falls outside these groups in all analyses, indicating it has a distinct expression profile. A further noteworthy observation is that the responses of MIG1, PGK1 and SUC2, in agreement with our previous study [3], depend on the glycolytic rate. The previously rather unknown ADH3-6 genes and also HSP12, respond to glucose stimuli. HSP12 is strongly repressed also in a strain depleted of all glucose transporters, which suggests that Hsp12 senses extracellular glucose. ADH4 and ADH6 are transiently stimulated by glucose, although neither has been reported to participate in ethanol production [12,35]. ADH3 and ADH5 are repressed in a seemingly glycolytic rate dependent manor (Figure 8). The detailed temporal expression profiles are quite different in the different strains but our results suggest that there is a fine-tuning regulatory mechanism for the ADH3-6 genes that involves glucose. Finally, as the regulation of the ADH1, ADH2 and PDC1 genes remain the same in all strains capable of glucose metabolism our study confirms that the differences in ethanol production between the strains is not regulated at the ethanol production branch.


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

Ståhlberg A, Elbing K, Andrade-Garda JM, Sjögreen B, Forootan A, Kubista M - BMC Genomics (2008)

Summary of gene classification. Genes are arranged into five groups after PCA: group I (genes induced upon glucose addition), group II (genes repressed upon glucose addition), group III (genes with expression profiles that passes through a maximum), group IV (genes with expression profiles that passes through a minimum) and group V (no regulation). PCA classification was confirmed by hierarchical clustering and Kohonen SOM.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2335116&req=5

Figure 8: Summary of gene classification. Genes are arranged into five groups after PCA: group I (genes induced upon glucose addition), group II (genes repressed upon glucose addition), group III (genes with expression profiles that passes through a maximum), group IV (genes with expression profiles that passes through a minimum) and group V (no regulation). PCA classification was confirmed by hierarchical clustering and Kohonen SOM.
Mentions: The yeast multiway expression profiles, based on the expression of 15 genes of interest measured at eight time points in fours strains, analyzed catenated by the three analytical methods Principal component analysis, hierarchical clustering and self-organized maps yield highly consistent results. The genes can be divided into four groups (Figure 8) characterized by different combinations of the two main loading vectors of the PCA, they form four hierarchical clusters, and they separate in a SOM with small number of neurons. PGK1 in HXT-TM6* strain falls outside these groups in all analyses, indicating it has a distinct expression profile. A further noteworthy observation is that the responses of MIG1, PGK1 and SUC2, in agreement with our previous study [3], depend on the glycolytic rate. The previously rather unknown ADH3-6 genes and also HSP12, respond to glucose stimuli. HSP12 is strongly repressed also in a strain depleted of all glucose transporters, which suggests that Hsp12 senses extracellular glucose. ADH4 and ADH6 are transiently stimulated by glucose, although neither has been reported to participate in ethanol production [12,35]. ADH3 and ADH5 are repressed in a seemingly glycolytic rate dependent manor (Figure 8). The detailed temporal expression profiles are quite different in the different strains but our results suggest that there is a fine-tuning regulatory mechanism for the ADH3-6 genes that involves glucose. Finally, as the regulation of the ADH1, ADH2 and PDC1 genes remain the same in all strains capable of glucose metabolism our study confirms that the differences in ethanol production between the strains is not regulated at the ethanol production branch.

Bottom Line: In multiway studies samples are characterized by their expression profiles to monitor changes over time, effect of treatment, drug dosage etc.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.The technique also identifies genes that show perturbed expression in specific strains.

View Article: PubMed Central - HTML - PubMed

Affiliation: TATAA Biocenter, Odinsgatan 28, 411 03 Göteborg, Sweden. anders.stahlberg@neuro.gu.se

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.

Show MeSH
Related in: MedlinePlus