Whole genome mRNA expression profiling during Candida albicans growth in complete human serum and butanol
Ontology highlight
ABSTRACT:
ORGANISM(S): Candida albicans
PROVIDER: GSE168874 | GEO | 2023/12/27
REPOSITORIES: GEO
Similar Datasets
Project description:In order to get an insight into the complex interplay of mRNAs during the growth in complete human serum, the mRNA polulation of Candida albiacns NCCPF 400034 taken at 0, 20, 45, and 120 minutes was extracted and sequenced by Next Generation sequencing techniques.
2023-12-27 | GSE168619 | GEO
Project description:The presence of anti-microbial phenolic compounds, such as the model compound ferulic acid, in biomass hydrolysates poses significant challenges to the widespread use of biomass in conjunction with whole cell biocatalysis or fermentation. Biofuel toxicity must also be overcome to allow for efficient production of next generation biofuels such as butanol, isopropanol, and others for widespread usage. Currently, these inhibitory compounds must be removed through additional downstream processing or sufficiently diluted to create environments suitable for most industrially important microbial strains. This study explores the high ferulic acid and n-butanol tolerance in Lactobacillus brevis (L. brevis), a lactic acid bacteria often found in fermentation processes, by global transcriptional response analysis. The transcriptional profile of L. brevis under ferulic acid and butanol stress reveals that the presence of ferulic acid primarily triggers the expression of membrane proteins to counteract ferulic acid induced changes in membrane fluidity and ion leakage. In contrast to the ferulic acid stress response, butanol addition to growing cultures uniquely induced the entire fatty acid synthesis pathway in the midst of a generalized stress response. Overexpression of the rate-limiting acetyl-CoA carboxylase subunits (AccABCD) in E. coli to increase lipid synthesis had no effect on butanol tolerance, suggesting that additional engineering is necessary to produce sufficient levels of appropriate fatty acids to confer butanol tolerance. Several promising routes for understanding both phenolic acid and butanol tolerance have been identified based upon these findings. These insights may be used to guide further engineering of model industrial organisms to better tolerate both classes of inhibitors in processed biomass used for biofuel production.
2011-12-31 | GSE24944 | GEO
Project description:The presence of anti-microbial phenolic compounds, such as the model compound ferulic acid, in biomass hydrolysates poses significant challenges to the widespread use of biomass in conjunction with whole cell biocatalysis or fermentation. Biofuel toxicity must also be overcome to allow for efficient production of next generation biofuels such as butanol, isopropanol, and others for widespread usage. Currently, these inhibitory compounds must be removed through additional downstream processing or sufficiently diluted to create environments suitable for most industrially important microbial strains. This study explores the high ferulic acid and n-butanol tolerance in Lactobacillus brevis (L. brevis), a lactic acid bacteria often found in fermentation processes, by global transcriptional response analysis. The transcriptional profile of L. brevis under ferulic acid and butanol stress reveals that the presence of ferulic acid primarily triggers the expression of membrane proteins to counteract ferulic acid induced changes in membrane fluidity and ion leakage. In contrast to the ferulic acid stress response, butanol addition to growing cultures uniquely induced the entire fatty acid synthesis pathway in the midst of a generalized stress response. Overexpression of the rate-limiting acetyl-CoA carboxylase subunits (AccABCD) in E. coli to increase lipid synthesis had no effect on butanol tolerance, suggesting that additional engineering is necessary to produce sufficient levels of appropriate fatty acids to confer butanol tolerance. Several promising routes for understanding both phenolic acid and butanol tolerance have been identified based upon these findings. These insights may be used to guide further engineering of model industrial organisms to better tolerate both classes of inhibitors in processed biomass used for biofuel production. Cultures were grown to OD ~ 0.2 in MRS media (baffled flasks), T = 30 C, 100 rpm. Butanol was then added to the cultures. Samples were harvested 15, 75, and 135 min after butanol addition. Each time point has 3 biological replicates, and dye swaps were incorporated into the microarray experiments.
2011-12-31 | E-GEOD-24944 | biostudies-arrayexpress
Project description:Combination of butanol-hyperproducing and hypertolerant phenotypes is essential for developing microbial strains suitable for industrial production of bio-butanol, i.e. one of most promising liquid biofuels. Clostridium cellulovorans is among the microbial strains with the highest potential for direct production of n-butanol from lignocellulosic wastes, a process that would significantly reduce the cost of bio-butanol. However, butanol exhibits higher toxicity compared to ethanol and C. cellulovorans tolerance to this solvent is low. In the present investigation, comparative proteomics was used to study the response of C. cellulovorans to butanol challenge and understand the tolerance mechanisms activated in this condition. The most important response concerned modulation of protein biosynthesis, folding and degradation. Coherent with previous studies on other bacteria, several heat shock proteins (involved in protein quality control) were upregulated. Globally, our data indicates that protein biosynthesis is reduced, likely not to overload heat shock proteins. Several additional metabolic adaptations were triggered by butanol exposure such as the upregulation of V- and F-type ATPases (involved in ATP synthesis/generation of proton motive force), enzymes involved in amino acid biosynthesis, proteins involved in cell envelope re-arrangement and a redistribution of carbon flux through fermentative pathways. These analyses eventually suggested several potential gene targets for metabolic engineering strategies aimed at improving butanol tolerance in C. cellulovorans.
2021-08-13 | PXD024183 | Pride
Project description:The goal of this study is to explore genes that are differentially expressed in E. coli C strains (wt and a butanol-tolerant mutant) after 1-butanol treatment. The butanol-tolerant mutant strain PKH5000 (denoted by 'E' for 'evolved') were derived from KCTC 2571 (wt) (denoted by 'A' for 'ancestral') by proton beam irradiation. 0 and 1 in sample title mean before and after butanol treatment, respectively.
2013-07-01 | GSE47589 | GEO
Project description:Clostridium acetobutylicum is well-known for its butanol production. Butanol toxicity is a major drawback for the generation of high-butanol producing strains. Here, the transcriptional response a steady state, acidogenic (pH 6), phosphate-limited Clostridium acetobutylicum chemostat culture to different levels of n-butanol (0.25-1%) was investigated. For the butanol challenge experiments butanol (1-butanol) was added (a) to the supplying medium and (b) to the culture vessel to guarantee an immediate change in the butanol concentration. Addition of butanol to the culture was timed to match the supply of the new medium through the feedlines. The butanol concentration was increased stepwise in intervals of 66.6 h (5 volume changes) to moderate butanol concentrations of 0.25%, 0.5%, 0.75% and 1% (v/v).
2012-01-30 | E-MEXP-3571 | biostudies-arrayexpress
Project description:n-Butanol has been proposed as an alternative biofuel to ethanol, and both Escherichia coli and Saccharomyces cerevisiae have been engineered to produce it. Unfortunately, n-butanol is more toxic than ethanol to these organisms. To understand the basis for its toxicity, cell wide studies were conducted at the transcript, protein and metabolite levels to obtain a global view of the n-butanol stress response. Analysis of the data indicate that n-butanol stress has components common to other stress responses and includes perturbation in respiratory functions (nuo, cyo operons), oxidative stress (sodC, katG, yqhD), heat shock and cell envelope stress (rpoE, clpB, htpG, degP, cpxPR), metabolite transport (malE, opp operon) and biosynthesis. Inducible expression of the yqhD gene was found to improve the host’s tolerance to exogenous n-butanol and confirms the role of this gene in coping with butanol stress. To survey for other potential candidates that may serve to improve host tolerance, mutant strains in several candidates which show changes at the transcript and protein levels were examined for sensitivity during butanol exposure. Chassis engineering based on these cues may be required in a high production titer, butanol-producing host.
2009-12-31 | GSE16973 | GEO
Project description:Clostridium acetobutylicum is a Gram positive, endospore forming firmicute that has been known as the model organims for ABE (acetone-butanol-ethanol) fermentation. With its ability to consume a wide variety of substrates, C. acetobutylicum carries out a biphasic ABE fermentation, which consists of the acidogenic growth phase with the formation of butyric acid and acetic acid, followed by the solventogenic stationary phase with the formation of acetone, butanol and ethanol, characterised by the reassimilation of acids. The production butanol is of renewed ineterest both as a potential biofuel and bulk chemical production. Both butanol and butyrate posses toxic characteristic and here, we focus on understanding and modeling the stress response of C. acetobutylicum to one of the two important toxic metabolites: butanol.
2013-08-20 | GSE48031 | GEO
Project description:We report the application of a high-throughput technique, RNA-seq, to study the transcriptomic response of P. putida BIRD1 in the presence of butanol with the aim to study in more detail the mechanisms involved in butanol response. Our work is the first global transcriptomic analysis done in P. putida BIRD1 in the presence of butanol.
2016-04-06 | GSE66235 | GEO
Project description:Butanol is a bulk chemical feedstock and a promising fuels. Microbial production of butanol is challenging primarily because of its toxicity and low titer of production. Transcript regulator factor Rob plays an important role in butanol-tolerant functional revealed by our previous study. In this study, the mutant strain DTrob (AT686-687 deletion in rob gene) could tolerate 1.25 %(v/v) butanol. And the per unit intracellular butanol concentration and transcriptome of wild-type and DTrob were further compared to understand the regulation mechanism of Rob for butanol tolerance. A total of 285 DEGs (differentially expression genes) were identified by bioinformatic analysis, and they may function in transport and localization according to the GO functional annotations and the functional annotation of gene product in NCBI database. Eighteen DEGs representing different functional categories were selected for real-time quantitative PCR (qPCR) for confirming the dependability of RNA-seq data. The deletion strains of glgS or yibT gene, which were down-regulated by Rob, had butanol-toleranct characteristic, indicating that the deletion or downregulated expression of the two genes down-regulated by Rob could improve the butanol tolerance. This study reveals the transcript regulator factor Rob could regulate and control the expression of the butanol tolerant genes, and its inactivation would result in an improved butanol tolerance.
2019-09-17 | GSE120032 | GEO