The role of Mig1, Mig2, Tup1 and Hap4 transcription factors in regulation of xylose and glucose fermentation in the thermotolerant yeast<i>Ogataea polymorpha</i>

Kurylenko, Olena; Ruchała, Justyna; Kruk, Barbara; Vasylyshyn, Roksolana; Szczepaniak, Justyna; Dmytruk, Kostyantyn V.; Sibirny, Andriy А.

doi:10.1093/femsyr/foab029

Cited by 9 publications

(8 citation statements)

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“…According to the regulatory clustering analysis, Tup1 has a significant effect on the top-ranked target genes. Tup1 is a transcriptional repressor in S. cerevisiae has the ability to repress target genes via various molecular mechanisms, and it contributes to carbon catabolite repression of transcription by glucose [53,54]. Regarding the results of this study on regulatory clustering analysis, the Tup1 mutant caused decreased expression in some of the target genes and up regulation in others.…”

Section: Discussionmentioning

confidence: 76%

“…Hap4 is a transcription factor involved in the regulation of the respiratory genes' expression and ethanol tolerance. The role of TUP1 and HAP4 in glucose fermentation have been studied and recently confirmed in thermotolerant yeast, Ogataea polymorpha [54]. Moreover, the overexpression of HAP4 gene caused enhanced glucose consumption and ethanol production in S. cerevisiae [55,56].…”

Section: Discussionmentioning

confidence: 99%

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Mining transcriptomic data to identifySaccharomyces cerevisiaesignatures related to improved and repressed ethanol production under fermentation

Sazegari

Niazi‎

Zinati

et al. 2021

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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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Section: Discussionmentioning

confidence: 76%

Section: Discussionmentioning

confidence: 99%

Mining transcriptomic data to identifySaccharomyces cerevisiaesignatures related to improved and repressed ethanol production under fermentation

Sazegari

Niazi‎

Zinati

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Tup1 is a transcriptional repressor in S . cerevisiae has the ability to repress target genes via various molecular mechanisms, and it contributes to carbon catabolite repression of transcription by glucose [ 56 , 57 ]. Regarding the results of this study on regulatory clustering analysis, the Tup1 mutant caused decreased expression in some of the target genes and up regulation in others.…”

Section: Discussionmentioning

confidence: 99%

“…HAP4 is a transcription factor involved in the regulation of the respiratory genes’ expression and ethanol tolerance. The role of TUP1 and HAP4 in glucose fermentation have been studied and recently confirmed in thermos-tolerant yeast, Ogataea polymorpha [ 57 ]. Moreover, the overexpression of HAP4 gene caused enhanced glucose consumption and ethanol production in S .…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2022

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Saccharomyces cerevisiae is known for its outstanding ability to produce ethanol in industry. Underlying the dynamics of gene expression in S. cerevisiae in response to fermentation could provide informative results, required for the establishment of any ethanol production improvement program. Thus, representing a new approach, this study was conducted 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. The significant differential expression probe sets were extracted from available microarray datasets related to yeast fermentation performance. To identify the most effective probe sets contributing to discriminate ethanol content, 11 machine learning algorithms from RapidMiner were employed. Further analysis including pathway enrichment and regulatory analysis were performed on discriminative probe sets. Besides, the decision tree models were constructed, the performance of each model was evaluated and the roots were identified. Based on the results, 171 probe sets were identified by at least 5 attribute weighting algorithms (AWAs) and 17 roots were recognized with 100% performance Some of the top ranked presets were found to be involved in carbohydrate metabolism, oxidative phosphorylation, and ethanol fermentation. Principal component analysis (PCA) and heatmap clustering validated the top-ranked selective probe sets. In addition, the top-ranked genes were validated based on GSE78759 and GSE5185 dataset. From all discriminative probe sets, 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 were 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 (Mg2+ and Cu2+) during the fermentation process.

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“…The important role of certain transcription factors in xylose and glucose alcoholic fermentation in O. polymorpha was found by us earlier. Thus, we have found significant and specific activation of xylose alcoholic fermentation due to knock out of the CAT8 and HAP4A genes encoding for transcription activators whereas overexpression of the mentioned genes suppressed this process [ 10 , 13 ]. At the same time, knock out of transcription activator genes MIG1 and MIG2 as well as knock out of transcription repressor gene TUP1 strongly inhibited xylose alcoholic fermentation [ 10 ].…”

Section: Discussionmentioning

confidence: 99%

The role of hexose transporter-like sensor hxs1 and transcription activator involved in carbohydrate sensing azf1 in xylose and glucose fermentation in the thermotolerant yeast Ogataea polymorpha

et al. 2022

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Background Fuel ethanol from lignocellulose could be important source of renewable energy. However, to make the process feasible, more efficient microbial fermentation of pentose sugars, mainly xylose, should be achieved. The native xylose-fermenting thermotolerant yeast Ogataea polymorpha is a promising organism for further development. Efficacy of xylose alcoholic fermentation by O. polymorpha was significantly improved by metabolic engineering. Still, genes involved in regulation of xylose fermentation are insufficiently studied. Results We isolated an insertional mutant of O.polymorpha with impaired ethanol production from xylose. The insertion occurred in the gene HXS1 that encodes hexose transporter-like sensor, a close homolog of Saccharomyces cerevisiae sensors Snf3 and Rgt2. The role of this gene in xylose utilization and fermentation was not previously elucidated. We additionally analyzed O.polymorpha strains with the deletion and overexpression of the corresponding gene. Strains with deletion of the HXS1 gene had slower rate of glucose and xylose consumption and produced 4 times less ethanol than the wild-type strain, whereas overexpression of HXS1 led to 10% increase of ethanol production from glucose and more than 2 times increase of ethanol production from xylose. We also constructed strains of O.polymorpha with overexpression of the gene AZF1 homologous to S. cerevisiae AZF1 gene which encodes transcription activator involved in carbohydrate sensing. Such transformants produced 10% more ethanol in glucose medium and 2.4 times more ethanol in xylose medium. Besides, we deleted the AZF1 gene in O. polymorpha. Ethanol accumulation in xylose and glucose media in such deletion strains dropped 1.5 and 1.8 times respectively. Overexpression of the HXS1 and AZF1 genes was also obtained in the advanced ethanol producer from xylose. The corresponding strains were characterized by 20–40% elevated ethanol accumulation in xylose medium. To understand underlying mechanisms of the observed phenotypes, specific enzymatic activities were evaluated in the isolated recombinant strains. Conclusions This paper shows the important role of hexose sensor Hxs1 and transcription factor Azf1 in xylose and glucose alcoholic fermentation in the native xylose-fermenting yeast O. polymorpha and suggests potential importance of the corresponding genes for construction of the advanced ethanol producers from the major sugars of lignocellulose.

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The role of Mig1, Mig2, Tup1 and Hap4 transcription factors in regulation of xylose and glucose fermentation in the thermotolerant yeastOgataea polymorpha

Cited by 9 publications

References 50 publications

Mining transcriptomic data to identifySaccharomyces cerevisiaesignatures related to improved and repressed ethanol production under fermentation

Mining transcriptomic data to identifySaccharomyces cerevisiaesignatures related to improved and repressed ethanol production under fermentation

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

The role of hexose transporter-like sensor hxs1 and transcription activator involved in carbohydrate sensing azf1 in xylose and glucose fermentation in the thermotolerant yeast Ogataea polymorpha

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