Genome‐wide transcriptional response of a Saccharomyces cerevisiae strain with an altered redox metabolism

Abstract

The genome-wide transcriptional response of a Saccharomyces cerevisiae strain deleted in GDH1 that encodes a NADP(+)-dependent glutamate dehydrogenase was compared to a wild-type strain under anaerobic steady-state conditions. The GDH1-deleted strain has a significantly reduced NADPH requirement, and therefore, an altered redox metabolism. Identification of genes with significantly changed expression using a t-test and a Bonferroni correction yielded only 16 transcripts when accepting two false-positives, and 7 of these were Open Reading Frames (ORFs) with unknown function. Among the 16 transcripts the only one with a direct link to redox metabolism was GND1, encoding phosphogluconate dehydrogenase. To extract additional information we analyzed the transcription data for a gene subset consisting of all known genes encoding metabolic enzymes that use NAD(+) or NADP(+). The subset was analyzed for genes with significantly changed expression again with a t-test and correction for multiple testing. This approach was found to enrich the analysis since GND1, ZWF1 and ALD6, encoding the most important enzymes for regeneration of NADPH under anaerobic conditions, were down-regulated together with eight other genes encoding NADP(H)-dependent enzymes. This indicates a possible common redox-dependent regulation of these genes. Furthermore, we showed that it might be necessary to analyze the expression of a subset of genes to extract all available information from global transcription analysis.

Uncovering transcriptional regulation of metabolism by using metabolic network topology

“…We first analyzed transcription data from a wild-type strain of S. cerevisiae and a mutant with deletion of the gene GDH1, which encodes for NADPH-dependent glutamate dehydrogenase, an enzyme that plays an important role in ammonia assimilation. Physiological analysis of this strain demonstrated an effect on redox metabolism, as observed through increased ethanol yield and decreased glycerol yield (15). However, conventional transcriptome analysis of this mutant, in which differentially expressed genes are identified by using a statistical test (e.g., t test analysis with Bonferroni correction), did not enable identification of the overall effect of this genetic perturbation on the metabolism.…”

Sampling the Solution Space in Genome-Scale Metabolic Networks Reveals Transcriptional Regulation in Key Enzymes

“…Data from growth on four different carbon sources (glucose, maltose, ethanol and acetate) in chemostat cultures and five deletion mutants (grr1Δ, hxk2Δ, mig1Δ, mig1Δmig2Δ and gdh1Δ) grown in batch cultures were used. The exchange fluxes and gene expression data for the mentioned conditions have been published earlier [15]–[17].…”

“…The experiments for the gdh1Δ mutant were performed in chemostat cultures [17] with the same dilution rate. The only observed change in exchange fluxes was a small decrease in glycerol production and only a few significant changes were identified in the metabolic fluxes.…”

Yeast as a Prototype for Systems Biology

“…Despite the importance of redox in metabolism, little knowledge exists about the transcriptional changes that emulate following a redox perturbation. As a fundamental study to identify redox-sensitive genes, a S. cerevisiae strain with cofactor modifications in the glutamate generation pathway was compared with the reference strain [16]. Gdh1 (encoding glutamate dehydrogenase) is one of the principal NADPH-consuming pathways in biomass synthesis, consuming more than half of NADPH generated.…”

“…16 Different stages of the cell cycle and the checkpoints for DNA damage, replication, and mitosis. The proteins that are believed to detect the faults at each checkpoint are indicated below the cell cycle stage.…”