Project description:Fusarium graminearum is an efficient plant pathogen found in crops worldwide. Major causal agent of Fusarium head blight on wheat in Europe, this filamentous fungus can also produce toxic mycotoxins and a variety of secondary metabolites in developing kernels. These secondary metabolites are produced as the result of a cascade of coordinated regulations of an arsenal of genes dispersed accross the genome. Previous study highlighted the roles of the histone marks H3K27me3 and H3K4me3 in regulating the metabolism of F. graminearum. Here, we applied HiC in combination to transcriptomics to explore the functional components of 3D organization of the four chromosomes in the nucleus. We show that the orchestration of genome regulation is mediated by histone-dependant highly topologically structured chromatin that organizes chromosomes in territories to potentiate coordinated genome regulation.
Project description:This study aimed to investigate the microRNA expression profile of mechnically strained human periodontal ligament-derived stem cells, and SurePrint G3 Human v16 miRNA Array (Agilent) was employed as a screening platform. We discovered 39 differentially expressed microRNAs between the stretched and the static control group.
Project description:The present study aims to evaluate the response of the three Mediterranean local grapevines ‘Garnacha Blanca’, ‘Garnacha Tinta’, and ‘Macabeo’ to treatments with biocontrol products (BPs), a botanical extract (Akivi, Dittrichia viscosa extract) and a beneficial microorganism (Bacillus UdG, Bacillus velezensis). A combination of transcriptomics and metabolomics approaches were chosen in order to study grapevine gene expression and to identify gene marker candidates, as well as, to determine grapevine metabolites differentially concentrated in response to BPs treatments. Grapevine plants were cultivated in greenhouse controlled conditions and submitted to the treatments, and thereafter, leaves were sampled 24h after treatment to conduct gene expression study by RNA-sequencing for ‘Garnacha Blanca’ leaves extract and by RT-qPCR for the three cultivars. Differentially expressed genes (DEGs) were investigated for both treatments and highly influenced DEGs were selected to be tested in the three cultivars as treatment gene markers. In addition, extraction of leaf components was performed to quantify metabolites such as phytohormones, organic acids, and phenols. Considering all the upregulated and downregulated genes and enhanced metabolites concentrations, the treatments had an effect on jasmonic acid, ethylene, and phenylpropanoids defense pathways. In addition, several DEG markers were identified presenting a stable overexpression after the treatments in the three grapevine cultivars. These gene markers could be used to monitor the activity of the products in field treatments in future research. Further research will be necessary to confirm these first results under field conditions.
Project description:To avoid the complex switches and to reduce the limitations of different metabolic stages on the synthesis of metabolites, we designed a Streptomyces self-sustained system (StSS) that contains two functional modules, the primary metabolism module (PM) and the secondary metabolism module (SM). Here, the transcriptomic of hrdB regulatory strain in the secondary metabolism was analyzed.
Project description:Purpose of study was to investigate whole genome expression changes of a strain with deletion of the two-component system TctD-TctE and determine genes dysregulate relative to the parental wildtype to gain insight into possible regulatory targets of TctD-TctE. TctD-TctE is a two-component system in Pseudomonas aeruginosa that responds to and regulates uptake of tricarboxylic acids such as citric acid. It accomplishes this through derepression of the porin encoding the gene opdH, thereby regulating influx of citrate metabolites from the surrounding environment. Deletion of the tctED operon (ΔtctED) resulted in a reduced growth phenotype when citric acid is present in media. In the ΔtctED strain the presence of citric acid was found to have an inhibitory effect on growth. When the alternative carbon source arginine was present, wildtype levels of growth could not be restored. Static cultures of ΔtctED had low cell density in the presence of citric acid but maintained the same levels of biofilm formation compared to conditions when no citric acid was present. This suggests a dysregulation of biofilm formation in the presence of citric acid. In the ΔtctED strain there was also greater accumulation of tobramycin within the biofilm compared to the PA14 wildtype strain. Additionally, analysis of whole-genome expression found that multiple metabolic genes were dysregulated in ΔtctED. Here it is concluded that TctD-TctE is involved in biofilm tolerance to tobramycin in the presence of citrate metabolites.
Project description:The microbiota plays a major role in cancer. How the microbiota interacts with nutrients to produce regulatory metabolites is of significance for cancer therapy. Using a host-microbe-drug-nutrient 4-way screening approach, we evaluated the role of nutrition at the molecular level in the context of 5-fluorouracil toxicity. Notably, we identified the metabolite 2-methylisocitrate to be produced and enriched in human tumor-associated microbiomes. 2-methylisocitrate exhibits anti-proliferative properties across genetically- and tissue-diverse cancer cell lines, 3D spheroids, and an in vivo Drosophila gut tumor model, where it reduced tumor dissemination and increased survival. Drug-metabolite screening traced the chemotherapeutic signatures indicating synergy between 5-fluorouracil and 2-methylisocitrate, and multi-omic analyses revealed that 2-methylisocitrate acts via multiple cellular pathways linking metabolism and DNA damage to regulate chemotherapy. Finally, building on nature’s template, we altered the chemical structure of 2-methylisocitrate, enhancing its potency. This work highlights the great impact of microbiome-derived metabolites on tumor proliferation, and their potential as promising co-adjuvants for cancer treatment.
Project description:More than 90% of cancer cases in head and neck region are oral squamous cell carcinoma. Recent studies identified several tumor-specific metabolites for the screening or diagnosis of OSCC patients. However, the metabolic reprogramming of OSCC is not well understood. Here, we compared the metabolites between cancerous and paracancerous tissues of OSCC patients and investigated the metabolism of γ-aminobutyrate in OSCC derived cells. Our data revealed that the increase of γ-aminobutyrate was promoted by the synthesis of glutamate beyond the mitochondria, which was regulated by glutamine synthetase. This study is not only benefit for understanding the pathological mechanisms of OSCC, but also has application prospects for the diagnosis and therapy of OSCC.
Project description:Bacterial antimicrobial compounds and global regulatory networks are typically studied as separate systems, limiting our understanding of how these functions might be integrated. Here we reveal a dual-function system in the biocontrol strain Pseudomonas sp. MUP55, where the pvf cluster simultaneously functions as a global regulator of specialized metabolism and produces direct antimicrobial compounds. Metabolomic and transcriptomic analysis of a ∆pvfC mutant showed extensive global change of the regulation of metabolites and gene expression, with effects on specialized metabolites. Remarkably, pvfC differentially regulates dual siderophore systems and uncouples typically co-regulated small regulatory RNAs in the Gac/Rsm cascade. Heterologous expression confirmed the pvf cluster produces compounds with direct antimicrobial activity independent of its regulatory functions. Comparative genomic analysis revealed the MUP55 pvf cluster contains a rare additional pvfE gene found in only 3.4% of identified pvf clusters. This evolutionary integration of regulatory and defensive functions within a single genetic system provides an efficient strategy for bacterial competitive fitness and resource allocation, expanding our understanding of how beneficial microbes coordinate cellular processes while maintaining environmental competitiveness
Project description:The collection of metabolites circulating in the human blood, termed the serum metabolome, contains a plethora of biomarkers and causative agents. Although the origin of specific compounds is known, we have a poor understanding of the key determinants of most metabolites. Here, we measured the levels of 1251 circulating metabolites in serum samples from a healthy human cohort of 491 individuals, and devised machine learning algorithms to predict their levels in held-out subjects based on a comprehensive profile consisting of host genetics, gut microbiome, clinical parameters, diet, lifestyle, anthropometric measurements and medication data. Notably, we obtained statistically significant predictions for over 76% of the profiled metabolites. Despite using the strict out-of-sample prediction metric, which is a lower bound for the explained variance, diet and microbiome each explained hundreds of metabolites, with over 50% of the variance explained in some metabolites. We further validated the robustness of the microbiome related associations by showing a high replication rate in two geographically independent cohorts that were not available to us when developing the algorithms. We also demonstrate that some of these interactions are causal, as some metabolites we predicted to be positively associated with bread increased in level following a randomized clinical trial of bread intervention. Microbiome-explained metabolites were enriched with unnamed metabolites, and we devised an algorithm that accurately predicts their biological pathway, finding that they mainly include food components, aromatic amino acids and secondary bile acid derivatives. Overall, our results unravel potential determinants of over 800 metabolites, paving the way towards mechanistic understanding of alterations in metabolites under different conditions and to designing interventions for manipulating circulating metabolite levels.
Project description:We developed a mass spectrometry-based screening method for higher throughput in vitro enzyme assays and quantified the effects of 79 metabolites on the activity of 20 central Escherichia coli enzymes.