Selected Publications
Education
- Ph.D. University of Tuebingen, Tuebingen Germany 2003
- M.S. University of Tokyo, Tokyo Japan 2000
- B.S. University of Tokyo, Tokyo Japan 1998
Research Interests
Organisms have their own ways to sense external stimuli such as the availability of nutrients, changes in the environment, and invasion by pathogenic organisms and then adjust their physiology accordingly. I am especially interested in how nitrogen compounds are sensed and allocated in plants.
Nitrogen sensing and adjustment occur rapidly and reversibly, especially at the single-cell level. To understand how nitrogen metabolites are sensed, transported and metabolized, , we must be able to measure the net flux of nitrogen metabolites such as amino acids. This flux includes transport, metabolism and compartmentation at the single cell level as well as exchange between cells.
Genetically encoded nanosensors are powerful tools in measuring the dynamic metabolite concentration change in living cells. Many variants of sensors were developed for biologically significant molecules such as calcium, sugar, ATP and inositol tri-phosphate. We are currently developing FRET sensors for amino acids. I previously developed FRET nano-sensors for glutamate, which is the primary excitatory neurotransmitter in the mammalian brain, and also one of the dominant amino acids transported in the plant body. We are going to develop sensors for other important amino acids, such as glutamine and GABA to detect the flux of nitrogen in living plant cells. By combining sensors with different genetic backgrounds, we will be able to provide a comprehensive view of amino acid flux in plant cells.
We are also interested in the potential role of amino acids as signaling molecules. Plants have homologs of ionotropic glutamate receptors (iGluRs) that are involved in various cellular sensing mechanisms such as nitrogen-carbon balance, touch or cold. However, the ligands and roles of these receptors are largely unknown. We intend to identify ligands to iGluRs by using FRET to detect the conformational change of the protein. Together with the fine amino acid "map" obtained by FRET amino acid sensors, we would like to identify biological processes in which amino acids work as signaling molecules.
Movie: Neuronal cells in action: real-time extracellular glutamate concentration can be visualized by measuring the ratio between Yellow Fluorescent Protein (YFP) and Cyan fluorescent protein (CFP) Click here to view (QuickTime, 5MB) Also see Okumoto 2005 PNAS 102 8740-45
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Experience
- Assistant Professor, PPWS, Virginia Tech, 2007-
- Postdoctoral Fellow, Dr. Wolf Frommer, Carnegie Institution of Washingon, Stanford 2003-2007
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Selected Publications
- Gu, H*., Lalonde, S.*, Okumoto, S.*, Looger, L.L., Scharff-Poulsen, A.M., Grossman, A.R., Kossmann, J., Jakobsen, I., and Frommer, W.B. (2006). A novel analytical method for in vivo phosphate tracking. FEBS Lett. *Authors contributed equally
- Hirner, A., Ladwig, F., Stransky, H., Okumoto, S., Keinath, M., Harms, A., Frommer, W.B., and Koch, W. (2006). Arabidopsis LHT1 is a high-affinity transporter for cellular amino acid uptake in both root epidermis and leaf mesophyll. Plant Cell 18, 1931-1946.
- Deuschle, K., Chaudhuri, B., Okumoto, S., Lager, I., Lalonde, S., and Frommer, W.B. (2006). Rapid metabolism of glucose detected with FRET glucose nanosensors in epidermal cells and intact roots of Arabidopsis RNA-silencing mutants. Plant Cell 18, 2314-2325.
- Deuschle, K.*, Okumoto, S.*, Fehr, M.*, Looger, L.L., Kozhukh, L., and Frommer, W.B. (2005). Construction and optimization of a family of genetically encoded metabolite sensors by semirational protein engineering. Protein Sci 14, 2304-2314. *Authors contributed equally
- Deuschle, K., Fehr, M., Hilpert, M., Lager, I., Lalonde, S., Looger, L.L., Okumoto, S., Persson, J., Schmidt, A., and Frommer, W.B. (2005). Genetically encoded sensors for metabolites. Cytometry A 64A, 3-9.
- Okumoto, S., Looger, L.L., Micheva, K.D., Reimer, R.J., Smith, S.J., and Frommer, W.B. (2005). Detection of glutamate release from neurons by genetically encoded surface-displayed FRET nanosensors. Proc Natl Acad Sci U S A 102, 8740-8745.
- Fehr, M., Okumoto, S., Deuschle, K., Lager, I., Looger, L.L., Persson, J., Kozhukh, L., Lalonde, S., and Frommer, W.B. (2005). Development and use of fluorescent nanosensors for metabolite imaging in living cells. Biochem Soc Trans 33, 287-290.
- Okumoto, S., Deuschle, K., Fehr, M., Hilpert, M., Lager, I., Lalonde, S., Looger, L.L., Persson, J., Schmidt, A., and Frommer, W.B. (2004a). Genetically Encoded Sensors for Ions and Metabolites. Soil Science and Plant Nutrition 50, 947-953.
- Okumoto, S., Koch, W., Tegeder, M., Fischer, W.N., Biehl, A., Leister, D., Stierhof, Y.D., and Frommer, W.B. (2004b). Root phloem-specific expression of the plasma membrane amino acid proton co-transporter AAP3. J Exp Bot 55, 2155-2168.
- Burkle, L., Cedzich, A., Dopke, C., Stransky, H., Okumoto, S., Gillissen, B., Kuhn, C., and Frommer, W.B. (2003). Transport of cytokinins mediated by purine transporters of the PUP family expressed in phloem, hydathodes, and pollen of Arabidopsis. Plant J 34, 13-26.
- Okumoto, S.*, Schmidt, R.*, Tegeder, M., Fischer, W.N., Rentsch, D., Frommer, W.B., and Koch, W. (2002). High affinity amino acid transporters specifically expressed in xylem parenchyma and developing seeds of Arabidopsis. J Biol Chem 277, 45338-45346. *Authors contributed equally
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