Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Response of Bacillus halodurans C-125 wild-type and OLE-OAP knockout cells to acute ethanol stress

ABSTRACT: OLE RNA (Ornate, Large, Extremophilic RNA) is a large, noncoding RNA from extremophilic and/or anaerobic Firmicutes that binds to an integral membrane protein (OAP, OLE-Associated Protein) and localizes to the cell membrane. It is highly abundant in cells, and knockouts show increased sensitivity to short-chain alcohols, especially ethanol. We treated Bacillus halodurans C-125 cells (both wild-type and OLE-OAP knockouts) with 5% (v/v) ethanol for 3 hours to determine differences in their response to this stress. There are almost no significant differences between cells before ethanol stress, while after ethanol stress a small number (~40) genes show differences in expression between the two strains. These genes show little connection between their function, however, leading us to conclude that the majority of differential adaptation in kncokouts may occur at an earlier time or at the post-trancriptional level. These data also serve as a reference for a Gram-positive alkaliphile's response to acute ethanol stress.

ORGANISM(S): Halalkalibacterium halodurans

PROVIDER: GSE33303 | GEO | 2012/06/15

SECONDARY ACCESSION(S): PRJNA149331

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Response of Bacillus halodurans C-125 wild-type and OLE-OAP knockout cells to acute ethanol stress

Project description:OLE RNA (Ornate, Large, Extremophilic RNA) is a large, noncoding RNA from extremophilic and/or anaerobic Firmicutes that binds to an integral membrane protein (OAP, OLE-Associated Protein) and localizes to the cell membrane. It is highly abundant in cells, and knockouts show increased sensitivity to short-chain alcohols, especially ethanol. We treated Bacillus halodurans C-125 cells (both wild-type and OLE-OAP knockouts) with 5% (v/v) ethanol for 3 hours to determine differences in their response to this stress. There are almost no significant differences between cells before ethanol stress, while after ethanol stress a small number (~40) genes show differences in expression between the two strains. These genes show little connection between their function, however, leading us to conclude that the majority of differential adaptation in kncokouts may occur at an earlier time or at the post-trancriptional level. These data also serve as a reference for a Gram-positive alkaliphile's response to acute ethanol stress. Examination of wild-type and OLE-OAP knockout cells before and after ethanol stress, in duplicate (8 samples total)

2012-06-15 | E-GEOD-33303 | biostudies-arrayexpress

Rpn4- and Proteasome- Mediated Yeast Response to Ethanol Stress: a View from a Proteome

Project description:Distilled spirits production using S. cerevisiae requires understanding the mechanisms of yeast cell response to the alcohol stress. Reportedly, specific mutations in genes of the ubiquitin-proteasome system, e.g. RPN4, may result in strains exhibiting either hyper-resistance or increased sensitivity to different alcohols. In this work, we studied Rpn4-dependent response of different yeast strains to short-term ethanol exposure. Three S. cerevisiae strains were used: wild-type (WT), mutant strain with RPN4 gene deletion (rpn4-delta), and mutant strain with decreased proteasome activity due to PRE1 deregulation (YPL). The resistance tests demonstrated an increased sensitivity of mutant strains to ethanol compared with WT. Comparative proteomics analysis revealed significant differences in molecular responses to ethanol between different strains. GO analysis of proteins upregulated in WT showed enrichments represented by oxidative and heat responses, protein folding/unfolding and protein degradation. Enrichment of at least one of these responses was not observed in mutant strains. At the same time, trehalose synthesis and accumulation of stress granules were enhanced in the mutant strains. We suggest that these pathways could partially compensate for the failure of ubiquitin-proteasome system to cope with the ethanol stress. Also, we suggest impaired compensatory activation of autophagic degradation system in rpn4-delta strain and propose that Rpn4 can be a regulator for autophagy upon ethanol stress. These findings can be a basis for creating genetically modified yeast strains resistant to high levels of alcohol, being further used for fermentation in ethanol production.

2020-04-22 | PXD014236 | Pride

Escherichia coli displays a conserved membrane proteomic response to a range of alcohols

Project description:We characterised the changes in the inner and outer membrane proteome of Escherichia coli in response to alcohols of different chain lengths. The study provides a fundamental understanding of the key changes in the membrane proteome of E. coli under alcohol stress and reveals a conserved membrane proteomic response of E. coli to a range of alcohols.

2023-10-09 | PXD043021 | Pride

Expression Differences in Ethanol Stress Response Between Saccharomyces cerevisiae Parent W303-1A Strain and its Two Ethanol Tolerant Mutants

Project description:Saccharomyces spp. are widely used for ethanol production however fermentation productivity is negatively affected by the impact of ethanol accumulation on yeast metabolic rate and viability. This study used microarray and statistical two-way ANOVA analysis to compare and evaluate gene expression profiles of two previously generated ethanol-tolerant mutants, CM1 and SM1, with their parent, S. cerevisiae W303-1A, in the presence and absence of ethanol stress. Although sharing the same parentage, the mutants were created differently; SM1 by adaptive evolution involving long-term exposure to ethanol stress, and CM1 using chemical mutagenesis followed by adaptive evolution-based screening. Compared to the parent, differences in the expression levels of genes associated with a number of GO categories in the mutants suggest that their improved ethanol stress response is a consequence of increased mitochondrial and NADH oxidation activities, stimulating glycolysis and energy production. This leads to increased activity of energy-demanding processes associated with the production of proteins and plasma membrane components, which are necessary for acclimation to ethanol stress. It is suggested that a key function of the ethanol stress response is restoration of the NAD+/NADH redox balance, which increases glyceraldehyde-3-phosphate dehydrogenase activity, and higher glycolytic flux in the ethanol-stressed cell. Both mutants achieved this by a constitutive increase in carbon flux in the glycerol pathway as a means of increasing NADH oxidation.

2010-07-01 | GSE21120 | GEO

Effects of Ethanol Stress on Gene Expression in Saccharomyces cerevisiae

Project description:To identify genes involved in acclimatization of yeast to non-lethal ethanol stress, S. cerevisiae strain W303-1A was grown separately at 0% and 6.5% (v/v) ethanol, and gene expression profiles were compared using microarray analysis. A t-test with a p-value of 0.05 was applied for differences in gene expression across unstressed and stressed replicates of W303-1A. There were 1049 genes with significant differences in expression. Among the genes that passed the t-test, 46 genes were up-regulated 5-fold and more in ethanol stress and 149 by more than 3-fold. There were 40 genes down-regulated by more than a factor of 5 and 161 by more than a factor of 3; the remaining genes that passed the t-test had expression level differences lower than 3-fold. GenowizTM bioanalysis results that identify GO categories comprising stress induced (more than 3-fold) genes show the two highest ethanol stress induced categories to be Retrotransposition Nucleocapsid (z-score of 15.69) and Transposition RNA Mediated (z-score of 15.54). These categories were not reported in previous gene expression studies on ethanol stress (Alexandre et al. 2001, Chandler et al. 2004, Fujita et al. 2004, Hirasawa et al. 2007). Our further investigaition identifies lack of annotation and omission of the genes from the retrotransposition-associated categories in slide printing as possible causes of this inconsistency.

2010-03-30 | GSE20590 | GEO

Expression Differences in Ethanol Stress Response Between Saccharomyces cerevisiae Parent W303-1A Strain and its Two Ethanol Tolerant Mutants

2010-07-01 | E-GEOD-21120 | biostudies-arrayexpress

Ethanol cellular defense induce unfolded protein response in yeast

Project description:Ethanol is a valuable industrial product and a common metabolite used by many cell types. However, this molecule produces high levels of cytotoxicity affecting cellular performance at several levels. In the presence of ethanol, cells must adjust some of their components, such as the membrane lipids to maintain homeostasis. In the case of microorganism as Saccharomyces cerevisiae, ethanol is one of the principal products of their metabolism and is the main stress factor during fermentation. Although many efforts have been made, mechanisms of ethanol tolerance are not fully understood and very little evidence is available to date for specific signaling by ethanol in the cell. This work studied two Saccharomyces cerevisiae strains, CECT10094 and Temohaya-26, isolated from flor wine and traditional fermentations respectively, which differ in ethanol tolerance, in order to understand the molecular mechanisms underlying the ethanol stress response and the reasons for different ethanol tolerance. The transcriptome was analyzed after ethanol stress and, among others, an increased activation of genes related with the unfolded protein response (UPR) and its transcription factor, Hac1p, was observed in the tolerant strain CECT10094. We observed that this strain also resist more UPR agents than Temohaya-26 and the UPR-ethanol stress correlation was corroborated observing growth of 15 more strains and discarding UPR correlation with other stresses as thermal or oxidative stress. Furthermore, higher activation of UPR pathway in the tolerant strain CECT10094 was observed using a UPR mCherry reporter. Finally, we observed UPR activation in response to ethanol stress in other S. cerevisiae ethanol tolerant strains as the wine strains T73 and EC1118.

2016-02-03 | GSE44863 | GEO

Systems Biology Analysis of Zymomonas mobilis ZM4 Ethanol Stress Responses

Project description:Background Zymomonas mobilis ZM4 is a capable ethanologenic bacterium with high ethanol productivity and ethanol tolerance. Previous studies indicated that several stress-related proteins and changes in the ZM4 membrane lipid composition may contribute to ethanol tolerance. However, the molecular mechanisms of its ethanol stress response have not been elucidated fully. Methodology/Principal Findings In this study, ethanol stress responses were investigated using systems biology approaches. Medium supplementation with an initial 47 g/L (6% v/v) ethanol reduced Z. mobilis ZM4 glucose consumption, growth rate and ethanol productivity compared to that of untreated controls. A proteomic analysis of early exponential growth identified about one thousand proteins, or approximately 55% of the predicted ZM4 proteome. Proteins related to metabolism and stress response such as chaperones and key regulators were more abundant in the early ethanol stress condition. Transcriptomic studies indicated that the response of ZM4 to ethanol is dynamic, complex and involves many genes from all the different functional categories. Most down-regulated genes were related to translation and ribosome biogenesis, while the ethanol-upregulated genes were mostly related to cellular processes and metabolism. Transcriptomic data were used to update Z. mobilis ZM4 operon models. Furthermore, correlations among the transcriptomic, proteomic and metabolic data were examined. Among significantly expressed genes or proteins, we observe higher correlation coefficients when fold-change values are higher. Conclusions Our study has provided insights into the responses of Z. mobilis to ethanol stress through an integrated “omics” approach for the first time. This systems biology study elucidated key Z. mobilis ZM4 metabolites, genes and proteins that form the foundation of its distinctive physiology and its multifaceted response to ethanol stress.

2013-09-04 | GSE21165 | GEO

eQTL Mapping of the Yeast Ethanol Response

Project description:In a previous study, we identified extensive natural variation in the response to acute ethanol treatment in three yeast strains: a lab strain derived from the commonly used S288c (DBY8268), vineyard isolate M22, and oak soil strain YPS163. Many expression differences persisted across several modules of co-regulated genes, implicating trans-acting systemic differences in ethanol sensing and/or response. To understand the genetic basis for these expression differences, we performed eQTL mapping analysis of the response to acute ethanol stress in ~100 F2 strains from two crosses: DBY8268x M22 and DBY8268 x YPS163.

2014-10-02 | GSE54196 | GEO

Transcriptional responses to chronic oxidative stress in skeletal muscle

Project description:We measured gene expression differences in the extensor digitorum longus (edl) skeletal muscle between wild-type and mice lacking Cu, Zn-superoxide dismutase to determine the effect of chronic oxidative stress on skeletal muscle. We analyzed 4 edl samples from WT mice and 4 samples from the SOD1 knockouts.

2011-04-26 | E-GEOD-28837 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data