Identification of Genes Associated with Stress Tolerance of High Ethanol–Producing Saccharomyces cerevisiae Strain, NCIM3186, by Differential Gene Expression Analysis

• Published in: Bioenergy research Vol. 15; no. 3; pp. 1459 - 1471
• Main Authors: Goud, Burragoni Sravanthi, Kim, Jae Hong, Ulaganathan, Kandasamy
• Format: Journal Article
• Language: English
• Published: New York Springer US 01.09.2022; Springer; Springer Nature B.V
• Subjects: Acetaldehyde; Alcohol; Alcohol, Denatured; Biofuels; Biomedical and Life Sciences; Cellular stress response; Chemoreception; Dextrose; Drug tolerance; Ethanol; Fermentation; Furfural; Gene expression; Genes; Glucose; Heat shock proteins; Life Sciences; Lignocellulose; Metabolism; Oxidative stress; Pattern analysis; Plant Breeding/Biotechnology; Plant Ecology; Plant Genetics and Genomics; Plant Sciences; Proteins; Ribonucleic acid; RNA; Saccharomyces cerevisiae; Superoxide dismutase; Thiamine; Trehalose; Wood Science & Technology; Yeast; Yeasts; United Kingdom > UK; Fermentome; Genome engineering; Bioethanol; Furfural; Ethanol; Lignocellulosic biomass
• ISSN: 1939-1234; 1939-1242
• DOI: 10.1007/s12155-021-10389-8

Lignocellulosic bioethanol production by Saccharomyces cerevisiae is constrained by different stresses. The main aim of this work was to study the complexities and identify the genes associated with the yeast stress response by using NGS-based high throughput RNA-seq analysis. In this study, a bioethanol-producing S. cerevisiae strain, NCIM3186, treated with 4% glucose for 4 h, 8% (v/v) ethanol for 2 h, and 1 g L −1 furfural for 4 h was employed for Illumina-based RNA-seq analysis. Comparative RNA-seq analysis and differential gene expression profiling using de novo assembled transcripts have unveiled 573 differentially expressed genes (DEGs), wherein thiamine metabolism genes, SOD2 , GRE2 , GLR1 , HSP12 , and GLC7 under furfural stress; TDH1 , HSP26 , glucose-sensing SNF1 , SSA3 , HXK1 , SNF1 , STR3 , ATG1 , and HXT7 under ethanol stress; and MSN2 , TPS2 , SNF2 , MEP3 , PHO4 , and STE20 under glucose stress treatments were highly up-regulated (> twofold). Moreover, seven ( TPS1 , TPS2 , SIN3 , PTK2 , SSQ1 , ZAP1 , DOA4 ) out of nine stuck fermentome genes which are essential for the timely completion of fermentation process have shown significant expression under stress. The expression of highly up-regulated genes, TDH1 , HXT6 , THI13 , and HSP12 , and two other unknown genes (UK-1, UK-2) were experimentally validated using qRT-PCR analysis. The expression pattern of DEGs in NCIM3186 signified the key role of oxidative stress response, trehalose accumulation, heat shock proteins, and thiamine metabolism under stress. This study serves as a significant value addition to RNA-seq-based research for the identification of stress associated genes in host yeast strains to be used in bioethanol production.