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Time series expression data during phosphate limitation for E. coli K12 JP6015/pMU91

ABSTRACT: A fermentation strategies with phosphate feeding was applied to elongate transition inti phosphate limitation for an tryptophan overproducing E. coli strain High frequency sampling together with the applied fermentation strategy should provide high resolution insights into regulatory regimes involved in phosphate response The first sampling timepoint was set as a reference time point after 2,5 h fermentation time to cover phosphate excess conditions. Additional 9 sampling time points were selected based on process dynamics as soon as the phosphate concentrations became sensitive

ORGANISM(S): Escherichia coli

SUBMITTER: Tom Schuhmacher

PROVIDER: E-GEOD-56447 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Time series expression data during phosphate limitation for E. coli K12 JP6015/pMU91

Project description:A fermentation strategies with phosphate feeding was applied to elongate transition inti phosphate limitation for an tryptophan overproducing E. coli strain High frequency sampling together with the applied fermentation strategy should provide high resolution insights into regulatory regimes involved in phosphate response

2014-04-03 | GSE56447 | GEO

The sulfur metabolism during Acetogenesis and Solventogenesis of Clostridium acetobutylicum

Project description:The batch fermentation of Clostridium acetobutylicum is characterized by an acetogenic growth phase during exponential growth when mainly acetate and butyrate are fermentation products. Then, at the end of exponential growth and during stationary phase, the organism switches to solventogenic growth and large amounts of acetone, ethanol and butanol are produced. These growth phases can be studied independent from each other in a phosphate-limited continuous culture. In transcription analysis of continuous cultures using DNA microarrays it became evident that, among others, operons involved in sulfur assimilation are strongly up-regulated during solventogenesis. Using the ClosTron technique we constructed two knock-out mutants in the genes CAC0105 and CAC0930 annotated as involved in sulfate reduction and cysteine biosynthesis. Complementation experiments were carried out with sulfite and cysteine to prove the predicted function. The fermentation experiments of wild type and mutants using phosphate-limited and sulfur-limited continuous culture demonstrated that less sulfur source was consumed in solventogenic phase and the efficiency of cysteine uptake became lower. DNA microarrays were performed to study the difference of transcriptional expression when the wild type was challenged with insufficient sulfur source and the mccB (CAC0930) mutant was inactivated in the continuous culture. The result provided insights into understanding the sulfur metabolism regulatory.

2015-04-15 | E-MTAB-2745 | biostudies-arrayexpress

Physiological and genomic analysis of Saccharomyces cerevisiae artificial hybrids with improved fermentation performance and mannoprotein release capacity

Project description:Yeast mannoproteins contribute to several aspects of wine quality by protecting wine against protein haze, reducing astringency, retaining aroma compounds and stimulating growth of lactic-acid bacteria. The selection of a yeast strain simultaneously overproducing mannoproteins and showing good fermentative characteristics is a difficult task. In this work, a Saccharomyces cerevisiae x Saccharomyces cerevisiae hybrid bearing the two oenologically relevant features was constructed and a reduction in the amount of bentonite necessary for wine stabilization was observed for wines fermented with the generated strain. Additionally, different copy numbers of some genes probably related with these physiological features were detected in this hybrid. Hybrid share with parental Sc1 similar copy number of genes SPR1, SWP1, MNN10 and YPS7 related to cell wall integrity and with parental Sc2 similar copy number of some glycolytic genes as GPM1 and HXK1 as well as genes involved in hexose transport as HXT9, HXT11 and HXT12. This work demonstrates that artificial hybridization and stabilization in winemaking conditions constitute an effective approach to obtain yeast strains with desirable physiological features as mannoprotein overproducing capacity and improved fermentation performance, characteristics genetically depending on the coordinated expression of a multitude of different genes. In this work, genetically stable mannoprotein overproducing Saccharomyces cerevisiae strains simultaneously showing excellent fermentation capacities were obtained by hybridization methods giving rise to non-GMO strains. The potential relationship between the copy number of specific genes and the improved features was also evaluated by means of aCGH analysis of parental and hybrid strains.

2015-03-30 | GSE48117 | GEO

Expression data from yeast strain VIN13 in small and large scale alcoholic fermentations.

Project description:Transcriptomic analyses of fermenting yeast are increasingly being carried out under small scale simulated winemaking conditions. It is not known to what degree data generated from such experiments are a reflection of transcriptional processes in large-scale commercial fermentation tanks. In this experiment we set out to determine the effect of scale, or fermentation volume, on the transcriptional respone of wine yeast strains. Parallel fermentations were carried out in laboratory fermentation vials and commercial fermentation tanks using the same wine media and inoculated yeast strain. Comparative transcriptomic analyses were carried out at three time points during alcoholic fermentation. Fermentations were carried out in Chardonnay wine must in triplicate for both the lab-scale (80ml) and commercial scale (300L) fermentations. Sampling of yeast for RNA extractions were performed at day 2 of fermentation (during the exponential growth phase of the yeast cells), and again at day 5 (early stationary growth phase) and day 10 (late stationary growth phase) of fermentation.

2011-03-02 | E-GEOD-27086 | biostudies-arrayexpress

Custom home-build DNA-microarray to compare transcriptomes of wild-type and a small regulatory intergenic RNA (sRNA132) deletion mutant of Haloferax volcanii 30 minutes after the onset of phosphate starvation

Project description:The operon for a phosphate-specific ABC transporter (HVO_A0477-80) was identified as a putative target of sRNA132. Both the sRNA132 and the operon transcript accumulated under low phosphate concentrations, indicating a positive regulatory mechanism of sRNA132. A kinetic analysis revealed that sRNA132 is essential shortly after the onset of phosphate starvation, while other regulatory processes take over after several hours.The importance of the sRNA132 for the expression of the operon was highest about 30 minutes after the onset of phosphate starvation, therefore, the transcriptomes of the wild-type and the sRNA deletion mutant were compared at this time point using this home-build DNA microarray.

2019-03-26 | E-MTAB-7834 | biostudies-arrayexpress

Ribosome profiling experiment characterising early response of Lactococcus Lactis infected in sk1 bacteriophage

Project description:Time-series ribosome profiling experiment. It consists of mock and sk1 bacteriophage infected samples of Lactococcus Lactis at three different timepoints; 2,5 and 15 minutes post infection

2024-02-26 | GSE231968 | GEO

Physiological and genomic analysis of Saccharomyces cerevisiae artificial hybrids with improved fermentation performance and mannoprotein release capacity

2015-03-30 | E-GEOD-48117 | biostudies-arrayexpress

Effects of polychlorinated biphenyls (PCBs) and their hydroxylated metabolites (OH-PCBs) on Arabidopsis thaliana.

Project description:The transcriptomic response of A. thaliana to 2,5-dichlorobiphenyl (2,5-DCB) and its OH-metabolite, 4'-OH-2,5-DCB, was then examined using whole-genome expression microarrays (Affymetrix).

2017-06-15 | GSE99345 | GEO

Comparative transcriptome analysis between an original and a recombinant wine yeast strain defective for KNR4/SMI1

Project description:EKD-13 is among the recently developed mannoprotein overproducing strains. It is a recombinant derivative of the well known EC1118 commercial strain, in which the ORF of all the alleles of KNR4/SMI1 was replaced by different integration cassettes. Lack of Knr4p resulted in a negligible impairment in fermentation kinetics and a net reduction in bentonite requirements to attain complete protein stabilization of white wines made out of natural grape must. In order to improve the technological characterization of this strain, and to better understand the mechanisms underlying mannoprotein oversecretion, we have analyzed kinetics of mannoprotein release and autolysis during fermentation and aging, and we have performed a genome wide expression analysis in two different steps of the fermentation process. The results give some additional clues on KNR4 function in S. cerevisiae as well as on the best application conditions for this recombinant strain.

2011-02-28 | GSE26965 | GEO

Transcription profiling of Clostridium acetobutylicum during acidogenesis and solventogenesis

Project description:Clostridium acetobutylicum is characterized by its acetone-butanol (AB) fermentation which can be reproducibly established under continuous grow conditions in a chemostat. At pH 5.7 cells show typical acidogenic metabolism and mainly produce the acids acetate and butyrate. After lowering and further control the external pH at 4.5 the exponentially growing cells switch towards stable solvent production with the dominating fermentation products acetone and butanol. Here we present a comprehensive comparison of proteome and transcriptome data of continuously growing cells of C. acetobutylicum in a chemostat culture under phosphate limitation at pH 5.7 (acidogenesis) and pH 4.5 (solventogenesis).

2010-11-10 | E-MEXP-2503 | biostudies-arrayexpress

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