Mining transcriptomic data to identify Saccharomyces cerevisiae signatures related to improved and repressed ethanol production under fermentation

Saccharomyces cerevisiae is known for its outstanding ability to produce ethanol in industry. Identifying the dynamic of gene expression in S. cerevisiae in response to fermentation is required for the establishment of any ethanol production improvement program. The goal of this study was to identify the discriminative genes between improved and repressed ethanol production as well as clarifying the molecular responses to this process through mining the transcriptomic data. Through 11 machine learning based algorithms from RapidMiner employed on available microarray datasets related to yeast fermentation performance under Mg 2+ and Cu 2+ supplementation, 172 probe sets were identified by at least 5 AWAs. Some have been identified as being involved in carbohydrate metabolism, oxidative phosphorylation, and ethanol fermentation. Principal component analysis (PCA) and heatmap clustering were also validated the top-ranked selective probe sets. According to decision tree models, 17 roots with 100% performance were identified. OLI1 and CYC3 were identified as the roots with the best performance, demonstrated by the most weighting algorithms and linked to top two significant enriched pathways including porphyrin biosynthesis and oxidative phosphorylation. ADH5 and PDA1 are also recognized as differential top-ranked genes that contribute to ethanol production. According to the regulatory clustering analysis, Tup1 has a significant effect on the top-ranked target genes CYC3 and ADH5 genes. This study provides a basic understanding of the S. cerevisiae cell molecular mechanism and responses to two different medium conditions (Mg 2+ and Cu 2+ ) during the fermentation process.

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Effects of Saccharomyces Cerevisiae Strains on Chemical Profiles of Cabernet Sauvignon Wines: Based on the Combined Results of 1H NMR, HS-SPME/GC-MS and HPLC-DAD-ESI-MS/MS

Current Topics in Nutraceutical Research ◽

10.37290/ctnr2641-452x.18:115-131 ◽

2018 ◽

Vol 18 (2) ◽

pp. 115-131

Author(s):

Liang Heng-Yu ◽

Su Ning ◽

Guo Kun ◽

Wang Yuan ◽

Yang De-Yu

Keyword(s):

Saccharomyces Cerevisiae ◽

Principal Component ◽

Grape Juice ◽

Pilot Scale ◽

Ethyl Esters ◽

Cabernet Sauvignon ◽

Esi Ms ◽

H Nmr ◽

Chemical Profiles ◽

Indigenous Yeasts

Five Saccharomyces cerevisiae strains (Chinese indigenous yeasts SC5, WC5, SC8, CC17 and commercial starter F15) were inoculated into Cabernet sauvignon grape must and fermented at pilot scale. For the first time, combination of 1H NMR, HS-SPME/GC-MS and HPLC-DAD-ESI-MS/MS metabonomic profiling techniques was performed to analyze the global chemical fingerprints of sampled wines at the end of alcoholic and malolactic fermentation respectively, then 13 non-volatile flavor compounds, 52 volatile organic aromas and 43 polyphenolic molecules were identified and determined correspondently. All principal component analysis (PCA) of two fermentation stages based on the analytical results of 1H NMR, HS-SPME/GC-MS and HPLC-DAD-ESI-MS/MS divided these strains into three clusters: (1) SC5 and SC8, (2) WC5 and F15 and (3) CC17. The wine fermented by indigenous yeast, CC17, showed a very unique chemical profile, such as low pH and high color intensity, reduced amino acids (including proline) and the lowest total higher alcohols levels, most of the fixed acids, glycerol, ethyl esters and anthocyanins concentrations. The statistical results indicate that CC17 strain possesses very special anabolism and catabolism abilities on such substances in grape juice and has potentiality to produce characteristic wines with high qualities.

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Enhancement of catabolite regulatory genes in Saccharomyces cerevisiae to increase ethanol production using hydrolysate from red seaweed Gloiopeltis furcata

Journal of Biotechnology ◽

10.1016/j.jbiotec.2021.04.004 ◽

2021 ◽

Vol 333 ◽

pp. 1-9

Author(s):

Yu Rim Park ◽

Ji Won Yang ◽

In Yung Sunwoo ◽

Byeong-Kwan Jang ◽

Soo Rin Kim ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Ethanol Production ◽

Regulatory Genes ◽

Red Seaweed

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Upregulation of COX4-2 via HIF-1α in Mitochondrial COX4-1 Deficiency

Cells ◽

10.3390/cells10020452 ◽

2021 ◽

Vol 10 (2) ◽

pp. 452

Author(s):

Liza Douiev ◽

Chaya Miller ◽

Shmuel Ruppo ◽

Hadar Benyamini ◽

Bassam Abu-Libdeh ◽

...

Keyword(s):

Oxygen Consumption ◽

Oxidative Phosphorylation ◽

Nuclear Localization ◽

Target Genes ◽

Compensatory Mechanism ◽

Terminal Electron Acceptor ◽

Human Foreskin Fibroblasts ◽

Mitochondrial Respiratory Complex ◽

Mrna Transcripts ◽

Oxphos System

Cytochrome-c-oxidase (COX) subunit 4 (COX4) plays important roles in the function, assembly and regulation of COX (mitochondrial respiratory complex 4), the terminal electron acceptor of the oxidative phosphorylation (OXPHOS) system. The principal COX4 isoform, COX4-1, is expressed in all tissues, whereas COX4-2 is mainly expressed in the lungs, or under hypoxia and other stress conditions. We have previously described a patient with a COX4-1 defect with a relatively mild presentation compared to other primary COX deficiencies, and hypothesized that this could be the result of a compensatory upregulation of COX4-2. To this end, COX4-1 was downregulated by shRNAs in human foreskin fibroblasts (HFF) and compared to the patient’s cells. COX4-1, COX4-2 and HIF-1α were detected by immunocytochemistry. The mRNA transcripts of both COX4 isoforms and HIF-1 target genes were quantified by RT-qPCR. COX activity and OXPHOS function were measured by enzymatic and oxygen consumption assays, respectively. Pathways were analyzed by CEL-Seq2 and by RT-qPCR. We demonstrated elevated COX4-2 levels in the COX4-1-deficient cells, with a concomitant HIF-1α stabilization, nuclear localization and upregulation of the hypoxia and glycolysis pathways. We suggest that COX4-2 and HIF-1α are upregulated also in normoxia as a compensatory mechanism in COX4-1 deficiency.

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Transcriptome Analysis Reveals a Promotion of Carotenoid Production by Copper Ions in Recombinant Saccharomyces cerevisiae

Microorganisms ◽

10.3390/microorganisms9020233 ◽

2021 ◽

Vol 9 (2) ◽

pp. 233

Author(s):

Buli Su ◽

Anzhang Li ◽

Ming-Rong Deng ◽

Honghui Zhu

Keyword(s):

Saccharomyces Cerevisiae ◽

Transcriptome Analysis ◽

Gene Expression Analysis ◽

Target Genes ◽

Copper Ions ◽

Carotenoid Production ◽

Carotenoid Accumulation ◽

Nutritional Components ◽

Differential Gene ◽

First Time

We previously constructed a Saccharomyces cerevisiae carotenoid producer BL03-D-4 which produced much more carotenoid in YPM (modified YPD) media than YPD media. In this study, the impacts of nutritional components on carotenoid accumulation of BL03-D-4 were investigated. When using YPM media, the carotenoid yield was increased 10-fold compared to using the YPD media. To elucidate the hidden mechanism, a transcriptome analysis was performed and showed that 464 genes changed significantly in YPM media. Furthermore, inspired by the differential gene expression analysis which indicated that ADY2, HES1, and CUP1 showed the most remarkable changes, we found that the improvement of carotenoid accumulation in YPM media was mainly due to the copper ions, since supplementation of 0.08 mM CuSO4 in YPD media could increase carotenoid yield 9.2-fold. Reverse engineering of target genes was performed and carotenoid yield could be increased 6.4-fold in YPD media through overexpression of ACE1. The present study revealed for the first time the prominent promotion of carotenoid yield by copper ions in engineered S. cerevisiae and provided a new target ACE1 for genetic engineering of S. cerevisiae for the bioproduction of carotenoids.

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A Genome-Wide Screen in Saccharomyces cerevisiae Reveals a Critical Role for Oxidative Phosphorylation in Cellular Tolerance to Lithium Hexafluorophosphate

Cells ◽

10.3390/cells10040888 ◽

2021 ◽

Vol 10 (4) ◽

pp. 888

Author(s):

Xuejiao Jin ◽

Jie Zhang ◽

Tingting An ◽

Huihui Zhao ◽

Wenhao Fu ◽

...

Keyword(s):

Saccharomyces Cerevisiae ◽

Oxidative Phosphorylation ◽

Cellular Response ◽

Critical Role ◽

Lithium Ion ◽

Deletion Mutants ◽

High Concentration ◽

Genome Wide ◽

A Genome ◽

Lithium Hexafluorophosphate

Lithium hexafluorophosphate (LiPF6) is one of the leading electrolytes in lithium-ion batteries, and its usage has increased tremendously in the past few years. Little is known, however, about its potential environmental and biological impacts. In order to improve our understanding of the cytotoxicity of LiPF6 and the specific cellular response mechanisms to it, we performed a genome-wide screen using a yeast (Saccharomyces cerevisiae) deletion mutant collection and identified 75 gene deletion mutants that showed LiPF6 sensitivity. Among these, genes associated with mitochondria showed the most enrichment. We also found that LiPF6 is more toxic to yeast than lithium chloride (LiCl) or sodium hexafluorophosphate (NaPF6). Physiological analysis showed that a high concentration of LiPF6 caused mitochondrial damage, reactive oxygen species (ROS) accumulation, and ATP content changes. Compared with the results of previous genome-wide screening for LiCl-sensitive mutants, we found that oxidative phosphorylation-related mutants were specifically hypersensitive to LiPF6. In these deletion mutants, LiPF6 treatment resulted in higher ROS production and reduced ATP levels, suggesting that oxidative phosphorylation-related genes were important for counteracting LiPF6-induced toxicity. Taken together, our results identified genes specifically involved in LiPF6-modulated toxicity, and demonstrated that oxidative stress and ATP imbalance maybe the driving factors in governing LiPF6-induced toxicity.

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Differential activation mechanisms of two isoforms of Gcr1 transcription factor generated from spliced and un-spliced transcripts in Saccharomyces cerevisiae

Nucleic Acids Research ◽

10.1093/nar/gkaa1221 ◽

2020 ◽

Author(s):

Seungwoo Cha ◽

Chang Pyo Hong ◽

Hyun Ah Kang ◽

Ji-Sook Hahn

Keyword(s):

Saccharomyces Cerevisiae ◽

Transcription Factor ◽

Target Genes ◽

Gene Encoding ◽

Metabolic Switch ◽

Differential Activation ◽

N Terminus ◽

Activation Mechanisms ◽

In Trans ◽

Separate Activation

Abstract Gcr1, an important transcription factor for glycolytic genes in Saccharomyces cerevisiae, was recently revealed to have two isoforms, Gcr1U and Gcr1S, produced from un-spliced and spliced transcripts, respectively. In this study, by generating strains expressing only Gcr1U or Gcr1S using the CRISPR/Cas9 system, we elucidate differential activation mechanisms of these two isoforms. The Gcr1U monomer forms an active complex with its coactivator Gcr2 homodimer, whereas Gcr1S acts as a homodimer without Gcr2. The USS domain, 55 residues at the N-terminus existing only in Gcr1U, inhibits dimerization of Gcr1U and even acts in trans to inhibit Gcr1S dimerization. The Gcr1S monomer inhibits the metabolic switch from fermentation to respiration by directly binding to the ALD4 promoter, which can be restored by overexpression of the ALD4 gene, encoding a mitochondrial aldehyde dehydrogenase required for ethanol utilization. Gcr1U and Gcr1S regulate almost the same target genes, but show unique activities depending on growth phase, suggesting that these isoforms play differential roles through separate activation mechanisms depending on environmental conditions.

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Ethanol Production from Concentrated Food Waste Hydrolyzates Using Free and Immobilized Yeast Saccharomyces cerevisiae H058

Advance Journal of Food Science and Technology ◽

10.19026/ajfst.12.2830 ◽

2016 ◽

Vol 12 (1) ◽

pp. 15-26

Author(s):

Shoubao Yan ◽

Cuie Shi ◽

Shunchang Wang ◽

Kegui Zhang ◽

Qianqian Tong

Keyword(s):

Saccharomyces Cerevisiae ◽

Ethanol Production ◽

Food Waste ◽

Immobilized Yeast

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Effects of Ultrasound on Fermentation of Glucose to Ethanol by Saccharomyces cerevisiae

Fermentation ◽

10.3390/fermentation5010016 ◽

2019 ◽

Vol 5 (1) ◽

pp. 16 ◽

Cited By ~ 5

Author(s):

Luis Huezo ◽

Ajay Shah ◽

Frederick Michel

Keyword(s):

Saccharomyces Cerevisiae ◽

Mass Transfer ◽

Glucose Uptake ◽

Ethanol Production ◽

Ethanol Yield ◽

Biofuel Production ◽

Inhibitory Effects ◽

Negative Effects ◽

Intraparticle Mass Transfer ◽

Improve Mass Transfer

Previous studies have shown that pretreatment of corn slurries using ultrasound improves starch release and ethanol yield during biofuel production. However, studies on its effects on the mass transfer of substrates and products during fermentation have shown that it can have both beneficial and inhibitory effects. In this study, the effects of ultrasound on mass transfer limitations during fermentation were examined. Calculation of the external and intraparticle observable moduli under a range of conditions indicate that no external or intraparticle mass transfer limitations should exist for the mass transfer of glucose, ethanol, or carbon dioxide. Fermentations of glucose to ethanol using Saccharomyces cerevisiae were conducted at different ultrasound intensities to examine its effects on glucose uptake, ethanol production, and yeast population and viability. Four treatments were compared: direct ultrasound at intensities of 23 and 32 W/L, indirect ultrasound (1.4 W/L), and no-ultrasound. Direct and indirect ultrasound had negative effects on yeast performance and viability, and reduced the rates of glucose uptake and ethanol production. These results indicate that ultrasound during fermentation, at the levels applied, is inhibitory and not expected to improve mass transfer limitations.

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