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Transcriptome profiling of Issatchenkia orientalis under ethanol stress.

ABSTRACT: Issatchenkia orientalis, a non-Saccharomyces yeast that can resist a wide variety of environmental stresses, has potential use in winemaking and bioethanol production. Little is known about gene expression or the physiology of I. orientalis under ethanol stress. In this study, high-throughput RNA sequencing was used to investigate the transcriptome profile of I. orientalis in response to ethanol. 502 gene transcripts were differentially expressed, of which 451 were more abundant, and 51 less abundant, in cells subjected to 4 h of ethanol stress (10% v/v). Annotation and statistical analyses suggest that multiple genes involved in ergosterol biosynthesis, trehalose metabolism, and stress response are differentially expressed under these conditions. The up-regulation of molecular chaperones HSP90 and HSP70, and also genes associated with the ubiquitin-proteasome proteolytic pathway suggests that ethanol stress may cause aggregation of misfolded proteins. Finally, ethanol stress in I. orientalis appears to have a nitrogen starvation effect, and many genes involved in nutrient uptake were up-regulated.

SUBMITTER: Miao Y

PROVIDER: S-EPMC5849708 | biostudies-literature | 2018 Mar

REPOSITORIES: biostudies-literature

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Transcriptome profiling of Issatchenkia orientalis under ethanol stress.

Miao Yingjie Y Xiong Guotong G Li Ruoyun R Wu Zufang Z Zhang Xin X Weng Peifang P

AMB Express 20180313 1

Issatchenkia orientalis, a non-Saccharomyces yeast that can resist a wide variety of environmental stresses, has potential use in winemaking and bioethanol production. Little is known about gene expression or the physiology of I. orientalis under ethanol stress. In this study, high-throughput RNA sequencing was used to investigate the transcriptome profile of I. orientalis in response to ethanol. 502 gene transcripts were differentially expressed, of which 451 were more abundant, and 51 less abu ...[more]

PMID: 29536208

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Project description:UNLABELLED: BACKGROUND:High tolerance to ethanol is a desirable characteristics for ethanologenic strains used in industrial ethanol fermentation. A deeper understanding of the molecular mechanisms underlying ethanologenic strains tolerance of ethanol stress may guide the design of rational strategies to increase process performance in industrial alcoholic production. Many extensive studies have been performed in Saccharomyces cerevisiae and Escherichia coli. However, the physiological basis and genetic mechanisms involved in ethanol tolerance for Zymomonas mobilis are poorly understood on genomic level. To identify the genes required for tolerance to ethanol, microarray technology was used to investigate the transcriptome profiling of the ethanologenic Z. mobilis in response to ethanol stress. RESULTS:We successfully identified 127 genes which were differentially expressed in response to ethanol. Ethanol up- or down-regulated genes related to cell wall/membrane biogenesis, metabolism, and transcription. These genes were classified as being involved in a wide range of cellular processes including carbohydrate metabolism, cell wall/membrane biogenesis, respiratory chain, terpenoid biosynthesis, DNA replication, DNA recombination, DNA repair, transport, transcriptional regulation, some universal stress response, etc. CONCLUSION:In this study, genome-wide transcriptional responses to ethanol were investigated for the first time in Z. mobilis using microarray analysis.Our results revealed that ethanol had effects on multiple aspects of cellular metabolism at the transcriptional level and that membrane might play important roles in response to ethanol. Although the molecular mechanism involved in tolerance and adaptation of ethanologenic strains to ethanol is still unclear, this research has provided insights into molecular response to ethanol in Z. mobilis. These data will also be helpful to construct more ethanol resistant strains for cellulosic ethanol production in the future.

Project description:The use of yeasts tolerant to acid (low pH) and salt stress is of industrial importance for several bioproduction processes. To identify new candidate genes having potential roles in low-pH tolerance, we screened an expression genomic DNA library of a multiple-stress-tolerant yeast, Issatchenkia orientalis (Pichia kudriavzevii), for clones that allowed Saccharomyces cerevisiae cells to grow under highly acidic conditions (pH 2.0). A genomic DNA clone containing two putative open reading frames was obtained, of which the putative protein-coding gene comprising 1629 bp was retransformed into the host. This transformant grew significantly at pH 2.0, and at pH 2.5 in the presence of 7.5% Na2SO4. The predicted amino acid sequence of this new gene, named I. orientalis GAS1 (IoGAS1), was 60% identical to the S. cerevisiae Gas1 protein, a glycosylphosphatidylinositol-anchored protein essential for maintaining cell wall integrity, and 58-59% identical to Candida albicans Phr1 and Phr2, pH-responsive proteins implicated in cell wall assembly and virulence. Northern hybridization analyses indicated that, as for the C. albicans homologs, IoGAS1 expression was pH-dependent, with expression increasing with decreasing pH (from 4.0 to 2.0) of the medium. These results suggest that IoGAS1 represents a novel pH-regulated system required for the adaptation of I. orientalis to environments of diverse pH. Heterologous expression of IoGAS1 complemented the growth and morphological defects of a S. cerevisiae gas1Δ mutant, demonstrating that IoGAS1 and the corresponding S. cerevisiae gene play similar roles in cell wall biosynthesis. Site-directed mutagenesis experiments revealed that two conserved glutamate residues (E161 and E262) in the IoGas1 protein play a crucial role in yeast morphogenesis and tolerance to low pH and salt stress. Furthermore, overexpression of IoGAS1 in S. cerevisiae remarkably improved the ethanol fermentation ability at pH 2.5, and at pH 2.0 in the presence of salt (5% Na2SO4), compared to that of a reference strain. Our results strongly suggest that constitutive expression of the IoGAS1 gene in S. cerevisiae could be advantageous for several fermentation processes under these stress conditions.

Project description:Hexaploid wheat is the main cereal food crop for most people but it is highly influenced by climatic variations. The influence of these climatic variations was studies in wheat genotype WH -1184 in field conditions under two different environments (normal and late sown) and it was found that the genotype is less yielding under late sown conditions. To study the effects of heat stress at transcript level, it was grown under two different conditions (WH-1184 control and heat treated) in pots and transcriptome analysis based on Illumina Novoseq 6000 was carried out for the identification of the differentially expressed genes (DEGs) and metabolic processes or gene regulations influenced by heat stress which lead to a reduction in both quality and quantity of wheat production. These DEGs were utilized to set up a subsequent unigene assembly and GO analysis was performed using unigenes to analyze functions of DEGs which were classified into three main domains, i.e., biological process, cellular component, and molecular function. KEGG (Kyoto Encyclopedia of Genes and Genomes) ontology was used to visualize the physiological processes or to identify KEGG pathways that provide plants their ability to shield in adverse conditions of heat stress. From KEGG ontology, it was reported that genes which encoded protein detoxification and ABC1 domain-containing protein were upregulated while genes thatencoded glutathione transferase (GST), peroxidase, and chitinase enzymes were downregulated. Downregulation of these enzymes during heat stress causes oxidative damages in plants while upregulated proteins play a main role in detoxification to protect plants from heat stress. It was hypothesized that the yield of WH-1184 decreased 44% under heat stress due to the downregulation of genes that encoded GST, peroxidase, and chitinase enzymes which can protect plants from oxidative damage. Hence, upregulation of these genes might be helpful for the adaptation of this genotype under heat stress condition.

Dataset Information

Transcriptome profiling of Issatchenkia orientalis under ethanol stress.

Publications

Transcriptome profiling of Issatchenkia orientalis under ethanol stress.

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