Quantitative transcription dynamic analysis reveals candidate genes and key regulators for ethanol tolerance in Saccharomyces cerevisiae

Abstract

BackgroundDerived from our lignocellulosic conversion inhibitor-tolerant yeast, we generated an ethanol-tolerant strain Saccharomyces cerevisiae NRRL Y-50316 by enforced evolutionary adaptation. Using a newly developed robust mRNA reference and a master equation unifying gene expression data analyses, we investigated comparative quantitative transcription dynamics of 175 genes selected from previous studies for an ethanol-tolerant yeast and its closely related parental strain.ResultsA highly fitted master equation was established and applied for quantitative gene expression analyses using pathway-based qRT-PCR array assays. The ethanol-tolerant Y-50316 displayed significantly enriched background of mRNA abundance for at least 35 genes without ethanol challenge compared with its parental strain Y-50049. Under the ethanol challenge, the tolerant Y-50316 responded in consistent expressions over time for numerous genes belonging to groups of heat shock proteins, trehalose metabolism, glycolysis, pentose phosphate pathway, fatty acid metabolism, amino acid biosynthesis, pleiotropic drug resistance gene family and transcription factors. The parental strain showed repressed expressions for many genes and was unable to withstand the ethanol stress and establish a viable culture and fermentation. The distinct expression dynamics between the two strains and their close association with cell growth, viability and ethanol fermentation profiles distinguished the tolerance-response from the stress-response in yeast under the ethanol challenge. At least 82 genes were identified as candidate and key genes for ethanol-tolerance and subsequent fermentation under the stress. Among which, 36 genes were newly recognized by the present study. Most of the ethanol-tolerance candidate genes were found to share protein binding motifs of transcription factors Msn4p/Msn2p, Yap1p, Hsf1p and Pdr1p/Pdr3p.ConclusionEnriched background of transcription abundance and enhanced expressions of ethanol-tolerance genes associated with heat shock proteins, trehalose-glycolysis-pentose phosphate pathways and PDR gene family are accountable for the tolerant yeast to withstand the ethanol stress, maintain active metabolisms, and complete ethanol fermentation under the ethanol stress. Transcription factor Msn4p appeared to be a key regulator of gene interactions for ethanol-tolerance in the tolerant yeast Y-50316.

Transcriptome analysis of Saccharomyces cerevisiae at the late stage of very high gravity (VHG) fermentation

“…Similar results have been observed for high hydrostatic pressure and ethanol stress, but the function of this gene is largely unknown (Fernandes et al, 2004;Ma and Liu, 2010). The up-regulation of PGM1 and GAL10 were the first observed during VHG fermentation.…”

Saccharomyces cerevisiae KNU5377 Stress Response during High-Temperature Ethanol Fermentation

“…Approximately 200 genes (e.g. PGK1, TDH, ADH, ZWF1, HSP104, HSP82, HSP42, HSP30, HSP26) are upregulated under ethanol stress (van Voorst et al, 2006), of which 58 are co-regulated by these transcription factors (Ma and Liu, 2010b). For example, inhibition of acid trehalase (ATH1) gene (Jung and Park, 2005) or overexprression of transcription factor MSN2 (Sasano et al, 2012) and Ras-cAMP pathway inhibitor 1 (RPI1) (Puria et al, 2009) promotes ethanol fermentation and tolerance in S. cerevisiae.…”

Evidence for a Role for the Plasma Membrane in the Nanomechanical Properties of the Cell Wall as Revealed by an Atomic Force Microscopy Study of the Response of Saccharomyces cerevisiae to Ethanol Stress

“…In addition, we investigated the role of the transcription factor Msn2/Msn4 in this AFM analysis of ethanol stress. The reason for this was that a large part of the transcriptomic response to ethanol stress is mediated through the general stress-responsive factor encoded by MSN2 and its orthologue MSN4 (7,29,30). This response is explained by the ethanolinduced translocation of Msn2 from the cytosol to the nucleus and the consecutive transcriptional activation of the binding of Msn2 to the stress response elements (STRE) present in the promoters of stress-related genes (31).…”

“…This response is explained by the ethanolinduced translocation of Msn2 from the cytosol to the nucleus and the consecutive transcriptional activation of the binding of Msn2 to the stress response elements (STRE) present in the promoters of stress-related genes (31). The potential function of YAP1 in this ethanol effect was also evaluated because this gene was inferred to be implicated in ethanol resistance, as indicated by its upregulation in an ethanol-tolerant S. cerevisiae strain obtained by enforced evolutionary adaptation (30).…”