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Effects of Ethanol Stress on Gene Expression in Saccharomyces cerevisiae

ABSTRACT: To identify genes involved in acclimatization of yeast to non-lethal ethanol stress, S. cerevisiae strain W303-1A was grown separately at 0% and 6.5% (v/v) ethanol, and gene expression profiles were compared using microarray analysis. A t-test with a p-value of 0.05 was applied for differences in gene expression across unstressed and stressed replicates of W303-1A. There were 1049 genes with significant differences in expression. Among the genes that passed the t-test, 46 genes were up-regulated 5-fold and more in ethanol stress and 149 by more than 3-fold. There were 40 genes down-regulated by more than a factor of 5 and 161 by more than a factor of 3; the remaining genes that passed the t-test had expression level differences lower than 3-fold. GenowizTM bioanalysis results that identify GO categories comprising stress induced (more than 3-fold) genes show the two highest ethanol stress induced categories to be Retrotransposition Nucleocapsid (z-score of 15.69) and Transposition RNA Mediated (z-score of 15.54). These categories were not reported in previous gene expression studies on ethanol stress (Alexandre et al. 2001, Chandler et al. 2004, Fujita et al. 2004, Hirasawa et al. 2007). Our further investigaition identifies lack of annotation and omission of the genes from the retrotransposition-associated categories in slide printing as possible causes of this inconsistency.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE20590 | GEO | 2010/03/30

SECONDARY ACCESSION(S): PRJNA124823

REPOSITORIES: GEO

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Project description:Zymomonas mobilis ZM4 produces near theoretical yields of ethanol with high specific productivity and recombinant strains are able to ferment both C-5 and C-6 sugars. However, the genetic and physiological basis of the ZM4 response to various industrially-relevant stresses is poorly understood. In this study, the dynamics of ZM4 oxygen stress responses were elucidated by characterizing the transcriptomic and metabolomic profiles of aerobic and anaerobic fermentations using whole-genome microarray analysis and gas chromatography-mass spectrometry. In the absence of oxygen, ZM4 consumed glucose more rapidly, had a higher growth rate, and ethanol was the major end-product. Under aerobic conditions, much less ethanol was observed with other end-products produced, including acetate, lactate, and acetoin. In the early exponential phase, no genes were detected as being significantly differentially expressed between aerobic and anaerobic conditions via microarray analysis. However, microarray analysis of the stationary phase cultures revealed that 166 genes were significantly differentially expressed by more than two-fold. Quantitative-PCR validated the expression values for seventeen genes from different categories of stationary phase microarray data. Transcripts for Entner-Doudoroff pathway genes and gene pdc, encoding a key enzyme leading to the ethanol production, were at least 30-fold more abundant under anaerobic conditions at stationary phase based on quantitative-PCR results. Expression of stress response genes was found to be greater under oxygen stress conditions. GC-MS analysis of stationary phase intracellular metabolites indicated that ZM4 under anaerobic conditions contained lower levels of amino acids, glucose and ED pathway intermediates, whereas metabolites such as ribitol, trehalose, myristic acid, glyceric acid, glucose 6-phosphate, mannose 6-phosphate, and 4-hydroxybutanoic acid were more abundant than under aerobic conditions. Transcriptomic and metabolomic data were consistent with faster glucose consumption and greater ethanol production under anaerobic conditions and suggested gene targets for deletion and improved fermentation. Keywords: Time course/ Stress Response

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Effects of Ethanol Stress on Gene Expression in Saccharomyces cerevisiae

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