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 Our research is focused on construction of metabolic engineering platform by using comparative genomics and metabolic flux analysis techniques, and application of this platform to important bioprocesses including butanol fermentation, biohydrogen production, and bioremediation
Principal Investigator: Dr. Chen Yang, Professor. Email: cyang@cibt.ac.cn
Staff: Li-Xia Liu, Research Intern
Postdoctoral Fellow: Dr. Yong-Zhen Tao
Graduate Students: Qing-Xiang Zheng; Yi Ding; Deng Liu
Glycerate 2-Kinase of Thermotoga maritima and Genomic Reconstruction of Related Metabolic Pathways
Members of a novel Glycerate-2-kinase family (GK-II) were tentatively identified in a broad range of species, including eukaryotes, archaea, and many bacteria. The main objective of this study was to apply comparative genomics for the reconstruction of metabolic pathways associated with GK-II in all bacteria, and in particular in T. maritima. Comparative analysis of ~400 bacterial genomes revealed a remarkable variety of pathways that lead to GK-II-driven utilization of glycerate via a glycolysis/gluconeogenesis route. In the case of T. maritima, a three-step serine degradation pathway was inferred based on tentative identification of two additional enzymes, serine-pyruvate aminotransferase and hydroxypyruvate reductase (TM1400 and TM1401, respectively) that convert serine to glycerate via hydroxypyruvate. Both enzymatic activities were experimentally verified, and the entire pathway was validated by its in vitro reconstitution
Profiling of Central Metabolism in Human Cancer Cells by Two-dimensional NMR, GC-MS Analysis, and Isotopomer Modeling
Tracking metabolic profiles has the potential to reveal crucial enzymatic steps that could be targeted in the drug discovery process. It is of special importance for various types of cancer known to be associated with substantial rewiring of metabolic networks. We developed an integrated approach for the analysis of metabolome that allows us to simultaneously assess pathway activities (fluxes) and concentrations of a large number of the key components involved in central metabolism of human cells. This is accomplished by in vivo labeling with [U-13C]glucose followed by two-dimensional NMR spectroscopy and GC-MS analysis. A comprehensive isotopomer model was developed, which enabled us to compare fluxes through the key central metabolic pathways including glycolysis, pentose phosphate pathway, tricarboxylic acid cycle, anaplerotic reactions, and biosynthetic pathways of fatty acids and amino acids. The validity and strength of this approach is illustrated by its application to a number of perturbations to breast cancer cells, including exposure to hypoxia, drug treatment, and tumor progression. We observed significant differences in the activities of specific metabolic pathways resulting from these perturbations and providing new mechanistic insights.
Publications:
Yang C, Rodionov DA, Rodionova IA, Li XQ, Osterman A. (2008) Glycerate 2-kinase family and genomic reconstruction of related metabolic pathways. Case study in Thermotoga maritima. Journal of Bacteriology 190: 1773-1782. Knowles LM, Yang C, Osterman A, Smith JW. (2008) Inhibition of fatty-acid synthase induces caspase-8-mediated tumor cell apoptosis by up-regulating DDIT4. Journal of Biological Chemistry 283: 31378-31384. Richardson AD, Yang C, Osterman A, Smith JW. (2008) Central carbon metabolism in the progression of mammary carcinoma. Breast Cancer Research and Treatment 110: 297-307. Yang C, Richardson AD, Osterman A, Smith JW. (2008) Profiling of Central Metabolism in Human Cancer Cells by Two-dimensional NMR, GC-MS Analysis, and Isotopomer Modeling. Metabolomics 4: 13-29.
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