Towards a Holistic Understanding of Cellular Metabolism
Our lab aims to achieve a quantitative, comprehensive understanding of cellular metabolism. Our motivation for studying metabolism is two-fold. From a basic science perspective, the molecular connections involved in metabolism are the best understood of any major biochemical network. Accordingly, metabolism provides a unique opportunity for quantitative analysis. From a practical perspective, derangements of metabolism are a major cause of disease, and small molecules that inhibit metabolism are the basis of many important pharmaceuticals. Accordingly, systems-level analysis of metabolism is likely to yield discoveries of medical significance.
A major barrier to understanding metabolism has been lack of appropriate tools. Our lab has developed methods for measuring a wide range of cellular metabolites using state-of-the-art mass spectrometry technology. We have used these tools to discover a novel metabolite involved in the pathogenesis of cancer (Dang et al., 2009). We have innovated approaches to quantitating metabolic fluxes by interpreting isotope-labeling data within a rigorous chemical-kinetic framework.
These analytical tools enable us to effectively re-examine long-standing and fundamental questions regarding regulation of metabolism: How are metabolite concentrations and fluxes controlled? How do microbes adapt to changing nutrient availability? How do cancer cells survive in the hypoxic environment of a tumor? In this vein, we have developed predictive, dynamic models of E. coli nitrogen metabolism (Yuan et al., 2009). Through such efforts, we are identifying key features of cellular metabolic regulation, such as competition among metabolites for enzyme active sites (Bennett et al., 2009). A future objective is to understand coordination across different nutrient systems, leading to quantitative models of the entirety of core metabolism. Such models will incorporate not just metabolite data, but also data on enzyme transcription, covalent modification, and localization. In addition to basic science utility, they will enable optimization of biofuel production.
Metabolomic tools are also opening new avenues of investigation, such as investigation into the metabolism of parasite-infected human cells. We have studied malaria and viral infections. In the latter case, we identified a dramatic up-regulation of fatty acid biosynthesis in response to viral infection. Inhibition of this pathway blocks viral replication, thereby suggesting a new strategy for antiviral therapy (Munger et al., 2008). We now aim to understand how and why viruses hijack metabolism. We also aim to identify new therapeutics based on these discoveries.
Ongoing research efforts of our fall into the following general categories:
- Technology development
- Metabolic regulation in model microorganisms (Escherichia coli, Saccharomyces cerevisiae)
- Biofuel production (Clostridium acetobutylicum)
- Metabolic impact of viral and malaria infection
- Cancer cell metabolism
All projects involve a mix of biological experiments, metabolomics, and computation.
Selected Recent Publications
- Lu, W., Clasquin, M. F., Melamud, E., Amador-Noguez, D., Caudy, A. A., Rabinowitz, J. D. (2010) Metabolomic analysis via reversed-phase ion-pairing liquid chromatography coupled to a stand alone orbitrap mass spectrometer. Anal. Chem., 82: 3212-3221.
- Ward, P. S., Patel, J., Wise, D. R., Abdel-Wahab, O., Bennett, B. D., Coller, H. A., Cross, J. R., Fantin, V. R., Hedvat, C. V., Perl, A. E., Rabinowitz, J. D., Carroll, M., Su, S. M., Sharp, K. A., Levine, T. L., Thompson, C. B. (2010). The common feature of leukemia-associated IDH1 and IDH2 mutations is a neomorphic enzyme activity converting alpha-ketoglutarate to 2-hydroxyglutarate. Cancer Cell, 17: 215-6.
- Boer, V. M., Crutchfield, C. A., Bradley, P. H., Botstein, D., Rabinowitz, J. D. (2010). Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations. Mol. Biol. Cell, 21: 198-211.
- Dang, L., White, D.W., Gross, S., Bennett, B.D., Bittinger, M.A., Driggers, E.M., Fantin, V.R., Jang, H.G., Jin, S., Keenan, M.C., Marks, M., Prins, R.M., Ward, P.S., Yen, K.E., Liau, L.M., Rabinowitz, J.D., Cantley, L.C., Thompson, C.B., Vander Heiden, M.G., Su, S.M. (2009).
Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature, 462: 739-44.
- Yuan, J., Doucette, C., Fowler, W. U., Feng, X. J., Piazza, M., Rabitz, H. A., Wingreen, N. S., Rabinowitz, J. D. (2009). Metabolomics-driven quantitative analysis of ammonia assimilation in E. coli. Mol. Syst. Biol., 5:302.
- Bennett, B. D., Kimball, E. H., Gao, M., Osterhout, R., Van Dien, S. J., Rabinowitz, J. D. (2009). Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli. Nat. Chem. Biol., 5: 593-9.
- Olszewski, K. L., Morrisey, J. M., Wilinski, D., Burns, J. M., Vaidya, A. B., Rabinowitz, J. D., Llinás, M. (2009). Host parasite interactions revealed by Plasmodium falciparum metabolomics. Cell Host Microbe, 5:191-9.
- Bradley, P. H., Brauer, M. J., Rabinowitz, J. D., Troyanskaya, O. (2009). Coordinated concentration changes of transcript and metabolites in Saccharomyces cerevisiae. PLoS Comp. Biol., 5: e1000270.
- Munger, J., Bennett, B. D., Parikh, A., Feng, X. J., McArdle, J., Rabitz, H. A., Shenk, T., Rabinowitz, J. D. (2008). Systems-level metabolic flux profiling identifies fatty acid synthesis as a target for anti-viral therapy. Nat. Biotechnol., 26: 1179-1186.
- Kwon, Y. K., Lu, W., Melamud, E., Khanam, N., Bognar, A., Rabinowitz, J. D. (2008). A domino effect in antifolate drug action in Escherichia coli. Nat. Chem. Biol., 4: 602-608.