Project description:Citramalate is a chemical of potential industrial importance. Efficient fermentations have been developed using recombinant E. coli as the chassis. The experiments explore the transcriptional reprogramming that occurs upon induction of citramalate production.
Project description:Small molecules not only are convenient and useful for controlling cell fates, but also can provide better understanding of the molecular mechanisms of cell-fate transitions. Here, we identified that spleen tyrosine kinase (Syk) inhibitor R406 could significantly promote the early stage of mouse chemical reprogramming. Furthermore, R406 alleviated the Syk-calcineurin (Cn)-nuclear factor of activated T cells (NFAT) signaling cascade-mediated suppression of glycine, serine and threonine metabolic genes transcriptionally, which is previously unrecognized. In turn, R406 upregulated metabolites of glycine, serine and threonine metabolism and downstream transsulfuration cysteine biosynthesis pathway and cysteine metabolism. Subsequently, increased cellular hydrogen sulfide (H2S) after R406 treatment downregulated oxidative phosphorylation (OXPHOS) and reactive oxygen species (ROS), modulated redox homeostasis, and significantly enhanced chemical reprogramming. In sum, our studies have not only improved the chemical reprogramming technique, but also identified interesting molecular mechanisms of chemical-induced pluripotent reprogramming, which hold great potentials in regenerative medicine.
Project description:2,5-furan dicarboxylic acid (FDCA) is the top-12 value-added chemicals derived from biomass that may serve as a 'green' substitute for terephthalate acid (TPA) in polyesters. FDCA can be synthesized chemically from 5-(hydroxymethyl) furfural (HMF), which is produced from fructose or glucose. To investigate impact of the production chain of FDCA on terrestrial ecosystem and unravel molecular pathways invoked and the biological process affected in the animal, a microarray analysis was applied to measure the transcriptome-wide response in soil invertebrates Folsomia candida. Microarrays examined transcriptional changes at EC50 concentrations of FDCA, HMF and TPA spiked in sterilized LUFA 2.2 soils. The results indicated FDCA and TPA caused no significant change in gene expression, which may due to the low chemical water solubility leading to slow uptake by the animal from the pore water after. A substantial number of genes were significantly regulated in F. candida after exposure to HMF. Gene Ontology analysis showed many biological process were significantly affected, such as nucleic acid metabolism, transcriptional metabolic process, cell developmental process and oxidation-reduction process. Transcriptional profile also indicated HMF can be biotransformed by F. candida into SMF which is genotoxic and mutagenic. The current research shows that environmental risk of the FDCA production chain from biomass is not due to the final product but to the intermediate HMF. We used a one-color microarray design where each sample was hybridized to a single array
Project description:An ability to map the global interactions of a chemical entity with chromatin genome-wide could provide new insights into the mechanisms by which a small molecule perturbs cellular functions. we developed a method that uses chemical derivatives and massively parallel DNA sequencing (Chem-Seq) to identify the sites bound by small chemical molecules throughout the human genome. We developed in vivo and in vitro Chem-Seq protocols with a biotinylated derivative of small molecules. In the in vivo protocol, Cells were first treated with biotinylated ligand and cross-linked with formaldehyde at the same time. Cells were then lysed, sonicated to shear the DNA, and streptavidin beads were used to isolate biotinylated ligand and associated chromatin fragments. We then used massively parallel sequencing to identify the enriched DNA fragments, and mapped these sequences to the genome. In in vitrol protocol, MM1.S cells were fixed and the derived sonicated lysate incubated with biotinylated drug to enrich for bound chromatin regions in vitro. We then used massively parallel sequencing to identify the enriched DNA fragments, and mapped these sequences to the genome.
