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

Abstract

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. 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. Multiway real-time PCR gene expression profiling is a powerful technique which can be utilized to characterize functions of new genes by, formore » 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.« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [6]
+ Show Author Affiliations
  1. TATAA Biocenter, Göteborg (Sweden); Lund Univ. (Sweden); Sahlgrenska Academy at Göteborg Univ. (Sweden)
  2. Göteborg Univ. (Sweden)
  3. Univ. of A Coruna (Spain)
  4. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  5. MultiD Analyses AB, Göteborg (Sweden)
  6. TATAA Biocenter, Göteborg (Sweden); Academy of Sciences of the Czech Republic, Prague (Czech Republic)
Publication Date:
Research Org.:
Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI Identifier:
1626463
Resource Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 9; Journal Issue: 1; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biotechnology & Applied Microbiology; Genetics & Heredity; Principal Component Analysis; Hierarchical Cluster; Ethanol Production; Glucose Addition; Score Vector

Citation Formats

Ståhlberg, Anders, Elbing, Karin, Andrade-Garda, José Manuel, Sjögreen, Björn, Forootan, Amin, and Kubista, Mikael. Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli. United States: N. p., 2008. Web. doi:10.1186/1471-2164-9-170.
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Ståhlberg, Anders, Elbing, Karin, Andrade-Garda, José Manuel, Sjögreen, Björn, Forootan, Amin, & Kubista, Mikael. Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli. United States. https://doi.org/10.1186/1471-2164-9-170
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Ståhlberg, Anders, Elbing, Karin, Andrade-Garda, José Manuel, Sjögreen, Björn, Forootan, Amin, and Kubista, Mikael. Wed . "Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli". United States. https://doi.org/10.1186/1471-2164-9-170. https://www.osti.gov/servlets/purl/1626463.
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@article{osti_1626463,
title = {Multiway real-time PCR gene expression profiling in yeast Saccharomyces cerevisiae reveals altered transcriptional response of ADH-genes to glucose stimuli},
author = {Ståhlberg, Anders and Elbing, Karin and Andrade-Garda, José Manuel and Sjögreen, Björn and Forootan, Amin and Kubista, Mikael},
abstractNote = {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. 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. 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.},
doi = {10.1186/1471-2164-9-170},
journal = {BMC Genomics},
number = 1,
volume = 9,
place = {United States},
year = {Wed Apr 16 00:00:00 EDT 2008},
month = {Wed Apr 16 00:00:00 EDT 2008}
}
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https://doi.org/10.1186/1471-2164-9-170
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