Ontology highlight
ABSTRACT:
PROVIDER: PRJEB39663 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Exogenous isopentenol was added to a culture of E. coli and the RNA expression response was measured using Nimblegen arrays. Genes highly upregulated were then subsequently overexpressed to improve the tolerance to isopentenol toxicity. In addition a subset of genes that improved the tolerance were also overexpressed in a producing strain, leading to improved production over the empty vector control. This work is described in Foo et al, Improving microbial bio-gasoline production in E. coli using tolerance engineering (in preparation) Six independent biological replicates were grown in M9 medium. 0.2% v/v isopentenol was added to 3 cultures while 3 cultures received no treatment, and 2.5 hr later total RNA was extracted. One sample from each culture was hybridized.
2013-12-10 | E-GEOD-53138 | biostudies-arrayexpress
Project description:Mining of fungal genomes uncovered their great potential for the production of novel secondary metabolites (SMs). However most of them stay silent under standard laboratory cultivation conditions. Co-cultivation of fungi with organism that occur in their natural habitat has shown to be trigger for the activation of such silent SM gene clusters. Recently, we showed that the cultivation of Aspergillus nidulans with the bacterium Streptomyces rapamycinicus leads to the activation of the orsellinic acid gene cluster. Hence we decided to study this interaction further to gain insight into the regulation of SM gene clusters and more specifically to study the chromatin remodelling network actuve upon co-cultivation of the two organisms. This study gives novel insight into the regulation of the orsellinic acid gene cluster and the interaction of the two organisms. To the best of our knowledge this is the first report of mapping the chromatin landscape of microbial interactions, making this study a role model for the analysis of similar systems.
2018-10-12 | E-MTAB-5819 | biostudies-arrayexpress
Project description:Chassis strain suitable for producing multiple compounds is a central concept in synthetic biology. Design of a chassis using computational, first-principle, models is particularly attractive due to the predictability and control it offers, including against phenotype reversal due to adaptive mutations. Yet, the theory of model-based chassis design has not been put to experimental test. Here, we report two Saccharomyces cerevisiae chassis strains for dicarboxylic acid production based on genome-scale metabolic modelling. The chassis strain, harboring gene knockouts in serine biosynthesis and in pentose-phosphate pathway, is geared for higher flux towards three target products - succinate, fumarate and malate - but does not appreciably secrete any. Introducing modular product-specific mutations resulted in improved secretion of the corresponding acid as predicted by the model. Adaptive laboratory evolution of the chassis-derived producer cells further improved production for succinate and fumarate attesting to the evolutionary robustness of the underlying growth-product coupling. In the case of malate, which exhibited decreased production during evolution, the multi-omics analysis revealed flux bypass at peroxisomal malate dehydrogenase not accounted in the model. Transcriptomics, proteomics and metabolomics analysis showed overall concordance with the flux re-routing predicted by the model. Together, our results provide experimental evidence for model-based design of microbial chassis and have implications for computer-aided design of microbial cell factories.
2021-07-20 | PXD020611 | Pride
Project description:D-glucose, D-xylose and L-arabinose are three major monosaccharides in the plant cell wall. Complete utilization of all three sugars is still a bottleneck for second-generation cellulolytic bioethanol production, especially for L-arabinose. However, little is known about the gene expression profiles during L-arabinose utilization in fungi at genome-wide level and a comparison of the genome-wide fungal response to these three major monosaccharides has not yet been reported. To better understand the microbial response and utilization of L-arabinose for subsequent microbial engineering for co-fermentation all three sugars, we performed transcriptome analysis of N. crassa grown on L-arabinose, compared with that on D-xylose and D-glucose. RNA was extracted from cultures of N. carassa in early growth stage growing with D-glucose, L-arabinose or D-xylose as carbon source; duplicate cultures were sampled in some conditions.
2014-03-17 | E-GEOD-51091 | biostudies-arrayexpress
Project description:The secretion of metabolites by plant roots is a key determinant of microbial growth and colonisation. We have used Pisum sativum and its natural symbiont Rhizobium leguminosarum (it can form N2 fixing nodules on pea roots) to study the natural metabolites secreted by roots. To do this root secretion was harvested from pea plants grown under sterile conditions. This root exudate was then concentrated and used as a sole carbon and nitrogen source for growth of the bacteria in the laboratory. These bacteria were harvested in mid-exponential growth and RNA extracted for microarray analysis. As control cultures the bacteria were grown on 30 mM pyruvate as a carbon source and 10 mM ammonium chloride as a nitrogen source and RNA extracted. Two colour microarrays were performed using root exudate cultures versus pyruvate ammonia grown cultures. This was done in biological triplicate.
2016-05-25 | E-MTAB-4790 | biostudies-arrayexpress
Project description:This project aimed to explore the microbial chemical ecology of a consortium derived from a water kefir fermentation through the integration of directed culturomics, compositional metagenomics and the identification of key metabolites with biological potential, through untargeted metabolomics.
2023-05-15 | MSV000091955 | MassIVE
Project description:A healthy rumen is crucial for normal growth and improved production performance of ruminant animals. Rumen microbes participate in and regulate rumen epithelial function, and the diverse metabolites produced by rumen microbes are important participants in rumen microbe-host interactions. SCFAs, as metabolites of rumen microbes, have been widely studied, and propionate and butyrate have been proven to promote rumen epithelial cell proliferation. Succinate, as an intermediate metabolite in the citric acid cycle, is a final product in the metabolism of certain rumen microbes, and is also an intermediate product in the microbial synthesis pathway of propionate. However, its effect on rumen microbes and rumen epithelial function has not been studied. It is unclear whether succinate can stimulate rumen epithelial development. Therefore, in this experiment, Chinese Tan sheep were used as experimental animals to conduct a comprehensive analysis of the rumen microbiota community structure and rumen epithelial transcriptome, to explore the role of adding succinate to the diet in the interaction between the rumen microbiota and host.
2023-06-12 | GSE233696 | GEO
Project description:A. niger and A. oryzae are two filamentous fungi widely used in industry to produce various enzymes (e.g. pectinases, amylases) and metabolites (e.g. citric acid). Using proteomics, the co-cultivation of these two fungi in wheat bran showed an equal distribution of the two strains forming mixed colonies with a broad range of carbohydrate active enzymes produced. This stable mixed microbial system seems suitable for subsequent commercial processes such as enzyme production. XlnR knock-out strains for both aspergilli were used to study the influence of plant cell wall degrading enzyme production on the fitness of the mixed culture.
2017-02-27 | PXD005532 | Pride
Project description:Phytoplankton and bacteria form the base of marine ecosystems and their interactions drive global biogeochemical cycles. The effect of bacteria and bacteria-produced compounds on diatoms range from synergistic to pathogenic and can affect the physiology and transcriptional patterns of the interacting diatom. Here, we investigate physiological and transcriptional changes in the marine diatom Thalassiosira pseudonana induced by extracellular metabolites of a known antagonistic bacterium Croceibacter atlanticus. Mono-cultures of C. atlanticus released compounds that inhibited diatom cell division and elicited a distinctive phenotype of enlarged cells with multiple plastids and nuclei, similar to what was observed when the diatom was co-cultured with the live bacteria. The extracellular C. atlanticus metabolites induced transcriptional changes in diatom pathways that include recognition and signaling pathways, cell cycle regulation, carbohydrate and amino acid production, as well as cell wall stability. Phenotypic analysis showed a disruption in the diatom cell cycle progression and an increase in both intra- and extracellular carbohydrates in diatom cultures after bacterial exudate treatment. The transcriptional changes and corresponding phenotypes suggest that extracellular bacterial metabolites, produced independently of direct bacterial-diatom interaction, may modulate diatom metabolism in ways that support bacterial growth.
2022-06-24 | GSE197934 | GEO