Transcriptome analysis of differential responses of diploid and haploid yeast to ethanol stress

Li, Bingzhi; Cheng, Jing-Sheng; Ding, Ming-Zhu; Yang, Yuan

doi:10.1016/j.jbiotec.2010.06.013

Cited by 46 publications

(33 citation statements)

References 34 publications

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“…Edges were weighted by the number of observations of each classification of interaction. Each node was assigned quantitative information computed using ASAPRatio as described above or from existing published SILAC (27) and microarray-based gene expression (28,29) data sets.…”

Section: Faims-mentioning

confidence: 99%

Nanospray FAIMS Fractionation Provides Significant Increases in Proteome Coverage of Unfractionated Complex Protein Digests

Swearingen

Hoopmann

Johnson

et al. 2012

Molecular & Cellular Proteomics

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High-field asymmetric waveform ion mobility spectrometry (FAIMS) is an atmospheric pressure ion mobility technique that can be used to reduce sample complexity and increase dynamic range in tandem mass spectrometry experiments. FAIMS fractionates ions in the gas-phase according to characteristic differences in mobilities in electric fields of different strengths. Undesired ion species such as solvated clusters and singly charged chemical background ions can be prevented from reaching the mass analyzer, thus decreasing chemical noise. To date, there has been limited success using the commercially available Thermo Fisher FAIMS device with both standard ESI and nanoLC-MS. We have modified a Thermo Fisher electrospray source to accommodate a fused silica pulled tip capillary column for nanospray ionization, which will enable standard laboratories access to FAIMS technology. Our modified source allows easily obtainable stable spray at flow rates of 300 nL/min when coupled with FAIMS. The modified electrospray source allows the use of sheath gas, which provides a fivefold increase in signal obtained when nanoLC is coupled to FAIMS. In this work, nanoLC-FAIMS-MS and nanoLC-MS were compared by analyzing a tryptic digest of a 1:1 mixture of SILAC-labeled haploid and diploid yeast to demonstrate the performance of nanoLC-FAIMS-MS, at different compensation voltages, for post-column fractionation of complex protein digests. The effective dynamic range more than doubled when FAIMS was used. In total, 10,377 unique stripped peptides and 1649 unique proteins with SILAC ratios were identified from the combined nanoLC-FAIMS-MS experiments, compared with 6908 unique stripped peptides and 1003 unique proteins with SILAC ratios identified from the combined nanoLC-MS ex-

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Section: Faims-mentioning

confidence: 99%

Nanospray FAIMS Fractionation Provides Significant Increases in Proteome Coverage of Unfractionated Complex Protein Digests

Swearingen

Hoopmann

Johnson

et al. 2012

Molecular & Cellular Proteomics

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“…Today, DNA microarray and quantitative real-time PCR (qPCR) can be used to determine the intracellular state and analyze the transcriptional responses of S. cerevisiae under high temperature fermentation. Such research will improve our understanding of the yeast cell's response to high temperature fermentation and provide some clues for breeding thermotolerant yeast strains (Gasch et al 2000;Li et al 2010;Varela et al 2005).…”

Section: Introductionmentioning

confidence: 99%

Transcriptional analysis of Saccharomyces cerevisiae during high-temperature fermentation

et al. 2013

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DNA microarrays were used to investigate the transcriptional response of Saccharomyces cerevisiae genes under high temperature fermentation. Up to 35.73 % of yeast genes were up-regulated or down-regulated at least two-fold in their expression level at the late stage of fermentation. Nine genes involved in the pathways of glycolysis, ethanol generation and stress response were selected for study of their transcription profiles during high temperature fermentation processes by using quantitative real-time PCR assay. Our data indicated that the genes involved in trehalose biosynthesis and encoding heat shock proteins (HSPs) were significantly induced, while the genes involved in ethanol production were down-regulated during the 40°C fermentation. Specially, HSP26 displayed the highest transcription level of 166.19±15.82-fold at 6 h, indicating that this gene may play important roles at the onset of 40°C fermentation. Moreover, transcription levels of the nine genes were reduced significantly and returned to normal levels compared with controls after the samples were treated at 30°C for another 2 h. The results of this study suggest that these genes and their related pathways are involved in the response to high temperature; these findings will be helpful in improving the characteristics and fermentation capacity of industrial yeast strains by metabolic engineering.

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“…Recently, comprehensive biological technologies such as metabolomics, transcriptomics, and proteomics have been used for systematically comparing metabolic features of diploid and haploid yeast to provide insights into difference of haploid and diploid yeast in pheromone pathway and ethanol tolerance mechanism (de Godoy et al 2008;Ding et al 2010;Li et al 2010). This study revealed that metabolite profiles originating from three strains (MN8140XX, MT8-1X405, and NBRC1440X) were distinctive and distinguished by PCA (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Haploid cells of the opposite mating type secrete mating pheromones which cause the cells to be propagated asexually as diploid (Elion 2000). As reported previously, compared to diploid strains, haploid strains produced in the laboratory are difficult to use for bioethanol production because they have a lower tolerance to acid, ethanol, and other fermentation inhibitors (Garay-Arroyo et al 2004;Li et al 2010;Martin and Jönsson 2003). However, hybridization is one of the simplest and most effective ways to improve and combine the traits of parent haploid strains (Yamada et al 2010a).…”

Section: Introductionmentioning

confidence: 99%

Improvements in ethanol production from xylose by mating recombinant xylose-fermenting Saccharomyces cerevisiae strains

Kato

Suyama

Yamada

et al. 2012

Appl Microbiol Biotechnol

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To improve the ability of recombinant Saccharomyces cerevisiae strains to utilize the hemicellulose components of lignocellulosic feedstocks, the efficiency of xylose conversion to ethanol needs to be increased. In the present study, xylose-fermenting, haploid, yeast cells of the opposite mating type were hybridized to produce a diploid strain harboring two sets of xylose-assimilating genes encoding xylose reductase, xylitol dehydrogenase, and xylulokinase. The hybrid strain MN8140XX showed a 1.3- and 1.9-fold improvement in ethanol production compared to its parent strains MT8-1X405 and NBRC1440X, respectively. The rate of xylose consumption and ethanol production was also improved by the hybridization. This study revealed that the resulting improvements in fermentation ability arose due to chromosome doubling as well as the increase in the copy number of xylose assimilation genes. Moreover, compared to the parent strain, the MN8140XX strain exhibited higher ethanol production under elevated temperatures (38 °C) and acidic conditions (pH 3.8). Thus, the simple hybridization technique facilitated an increase in the xylose fermentation activity.

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Transcriptome analysis of differential responses of diploid and haploid yeast to ethanol stress

Cited by 46 publications

References 34 publications

Nanospray FAIMS Fractionation Provides Significant Increases in Proteome Coverage of Unfractionated Complex Protein Digests

Nanospray FAIMS Fractionation Provides Significant Increases in Proteome Coverage of Unfractionated Complex Protein Digests

Transcriptional analysis of Saccharomyces cerevisiae during high-temperature fermentation

Improvements in ethanol production from xylose by mating recombinant xylose-fermenting Saccharomyces cerevisiae strains

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