Response of the thermoacidophilic Archaeon Sulfolobus acidocaldarius to solvent stress
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Sulfolobus Acidocaldarius
SUBMITTER: 
Trong Khoa Pham
LAB HEAD: Khoa Pham
PROVIDER: PXD023858 | Pride | 2021-03-15
REPOSITORIES: Pride
Similar Datasets
Project description:To study the cellular global response of the thermoacidophilic Archaeon Sulfolobus acidocaldarius upon solvent exposure we performed transcriptome comparing the response of planktonic and biofilm cells in absence and presence 1-butanol. S. acidocaldarius was grown in Petri dishes (static incubation) in the absence and presence of 0.5% and 1% (v/v) 1-butanol at 76°C for four days. Planktonic and biofilm cells were harvested and the transcriptional response towards 1-butanol was analysed via RNA-seq. In detail:Biofilm and planktonic cell samples (supernatant after static incubation) were generated in Petri dishes (92 x 16 mm, Polystyrene, without cams, Sarstedt) as described before. Cells grown under six different conditions, including Biofilm-Control (BF0), Biofilm-0.5% (v/v) 1-Butanol (BF05), Biofilm-1% (v/v) 1-Butanol (BF1), Planktonic-Control (PL0), Planktonic-0.5% (v/v) 1-Butanol (PL05), Planktonic-1% (v/v) 1-Butanol (PL1), were seperated, harvested by centrifugation (10 min, 5,000 x g, 4 °C) and immediately frozen at -70 °C. Isolation of cells was performed in triplicates with ten technical replicas each. Samples were pooled to obtain sufficient cell mass for further processing. RNA was isolated using Trizol (Thermo Fisher Scientific). In accordance, sequencing libraries were prepared via Illumina TruSeq stranded mRNA using Ribozero for RNA depletion. Sequencing was performed on a MiSeq instrument (Illumina, San Diego, California, USA) using v3 chemistry with a read length of 2x76 nt.
2021-02-20 | E-MTAB-10093 | biostudies-arrayexpress
Project description:Transcriptional Response of the thermoacidophilic Archaeon Sulfolobus acidocaldarius to solvent stress exemplified by 1-butanol exposure
| PRJEB43039 | ENA
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: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. All microarray experiments were carried out in triplicate (rep1-3). Probes were spotted in duplicate on separate area of each microarray slide, which produces two GPR files (a and b suffixes).
2013-07-01 | E-GEOD-47589 | biostudies-arrayexpress
Project description:Halorubrum lacusprofundi is an important member of Deep Lake in Antarctica, representing ~10% of the lake population (DeMaere et al., 2013). Deep Lake is in the Vestfold Hills, East Antarctica (68°33’36.8S, 78°11’48.7E) and is 36 m deep, monomictic, and perennially cold (down to -20°C) (DeMaere et al., 2013; Williams et al., 2014; Tschitschko et al., 2015; Tschitschko et al., 2016). In this project, using quantitative proteomics (8-plex iTRAQ labeling), proteins, pathways and cellular processes important for biofilm formation were determined for Hrr. lacusprofundi. The data provided a new level of understanding about molecular mechanisms and regulatory networks involved in adaptation of Hrr. lacusprofundi to biofilm formation. DeMaere, M. Z., Williams, T. J., Allen, M. A., Brown, M. V., Gibson, J. A., Rich, J., et al. (2013) High level of intergenera gene exchange shapes the evolution of haloarchaea in an isolated Antarctic lake. Proc Natl Acad Sci USA 110: 16939-16944. Tschitschko, B., Williams, T. J., Allen, M. A., Páez-Espino, D., Kyrpides, N., Zhong, L., et al. (2015) Antarctic archaea–virus interactions: metaproteome-led analysis of invasion, evasion and adaptation. ISME J 9: 2094-2107. Tschitschko, B., Williams, T. J., Allen, M. A., Zhong, L., Raftery, M. J., and Cavicchioli, R. (2016) Ecophysiological distinctions of haloarchaea from a hypersaline Antarctic lake determined using metaproteomics. Appl Environ Microbiol 82: 3165 – 3173. Williams, T. J., Allen, M. A., DeMaere, M. Z., Kyrpides, N. C., Tringe, S. G., Woyke, T., and Cavicchioli, R. (2014) Microbial ecology of an Antarctic hypersaline lake: genomic assessment of ecophysiology among dominant haloarchaea. ISME J 8: 1645-1658.
2016-12-13 | PXD004202 | Pride
Project description: Not available
| S-EPMC8208165 | biostudies-literature
Project description:Transcriptome analysis of isolated mutants using the method Visualizing Evolution in Real-Time (VERT) for the study of n-butanol tolerance. The samples were isolated from an evolution experiment picking samples at different times based in the evolution dynamics obtained with VERT. Mutants were grown in chemostats at 0.8% (v/v) of n-butanol and compared with the expression of wild-type to the same concentration of solvent. Three biological replicas. Each sample represents an isolated mutant. The reference for each mutant corresponds to wild-type, both exposed to the same concentration of n-butanol (0.8% (v/v)).
2012-03-30 | E-GEOD-30005 | biostudies-arrayexpress
Project description:Genomic Library Enrichment to determine the n-Butanol Tolerant related genes in E. coli. The samples involves a series of batch transfers to increasing concentrations of n-butanol and controls (always grew in absence of the solvent) Two technical replicas. Samples 1, 3, 5, and 7 are the serial transfers (samples 15, 13, 11, and 9 are their respective replicas). Samples 2, 4, 6 and 8 are the controls grown in absence of n-butanol (samples 16, 14, 12 and 10 are their respective replicas)
2012-09-19 | E-GEOD-26223 | biostudies-arrayexpress