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Shigeki Watanabe, Ph.D.

Shigeki Watanabe, Ph.D.

Academic Titles: 
Assistant Professor
Position Title: 
Principal Investigator

BCMB Graduate Program

Department of Cell Biology 
Johns Hopkins University School of Medicine  
725 N. Wolfe Street, 100 Biophysics
Baltimore, MD 21205 

Research topic: Cellular and molecular characterizations of rapid changes during synaptic plasticity

For information processing and integration, neurons undergo rapid cellular and molecular reorganization. At the level of a synapse, the entire structure of the postsynaptic compartment, dendritic spines, can alter rapidly to mediate synaptic plasticity. At the molecular level, the addition of receptors to the surface of spines is associated with strengthening of synapses while their removal is associated with weakening and neurodegeneration. Many of these changes take place on a millisecond time scale. Despite the importance of these changes to the organism, remarkably little is known about either how the morphology of spines is regulated or how the surface occupancy of receptors is regulated. What are the morphological changes that trigger synaptic plasticity? How are receptors redistributed during this process? What are the molecular pathways that mediate the redistribution? We aim to answer these questions using cutting-edge electron microscopy techniques in combination with molecular and biochemical approaches.

Membrane dynamics. We pioneered the “flash-and-freeze” approach that adds temporal information to electron micrographs.  Electron microscopy traditionally only captures a static image of cells. To visualize membrane dynamics, we combined optogenetic stimulation of neurons with high-pressure freezing. By varying the intervals between stimulation and freezing, we can essentially make a “flip-book” of cellular dynamics at a millisecond temporal resolution. Using this approach, we are studying the cellular and molecular mechanisms underlying rapid membrane trafficking at synapses.

Molecular topology and dynamics. We developed a correlative super-resolution fluorescence microscopy and electron microscopy approach that visualizes proteins in electron micrographs. We found a method that preserves fluorescence through harsh fixation and plastic embedding. We perform super-resolution and electron microscopy imaging on the same ultrathin sections of tissues and map the molecular topology onto the subcellular structures. This technique can be used to pinpoint the locations of proteins within their subcellular context. In combination with the “flash-and-freeze” approach, we are studying the molecular dynamics at synapses.


Research Interest: 
High-resolution, ultrafast kinetics of synaptic membrane trafficking events
Lab Members:
Namesort descending Classification Email Phone
Sumana Raychaudhuri, Ph.D. Postdoctoral Fellow sraycha1@jhmi.edu 410-955-7291
Selected Publications:
Watanabe, S. (2015). Slow or fast? A tale of synaptic vesicle recycling. Science, 350, 46-7.
Watanabe, S., T. Trimbuch, M. Camacho-Pérez, B.R. Rost, B. Brokowski, B. Söhl-Kielczynski, A. Felies, M.W. Davis, C. Rosenmund, and E.M. Jorgensen. 2014. Clathrin regenerates synaptic vesicles from edosomes. Nature 515, p228-33,  DOI 10.1038/nature13846. PMCID: PMC4291189.
Watanabe, S., Q. Liu, M.W. Davis , N. Thomas, J. Richards, G. Hollopeter, M. Gu, N.B. Jorgensen and E.M. Jorgensen. 2013. Ultrafast endocytosis at the C. elegans neuromuscular junction.  eLife  2:e00723.  PMCID: PMC3762212.
Gu, M., Q. Liu, S. Watanabe, L. Sun, B. Grant, and E.M. Jorgensen. 2013. AP2 hemicomplexes contribute independently to synaptic vesicle endocytosis. eLife 2, p00190.  PMCID: PMC3591783.
Shao, Z., Watanabe, S., Christensen, R., Jorgensen, E.M., and Colón-Ramos, D.A., (2013). Synapse location during growth depends on glia location, Cell 154, 337-350. PMCID: PMC3808971.
Watanabe, S., B. Rost., M. Camacho, M. W. Davis, B. Söhl-Kielczynski, A. Felies, C. Rosenmund and E.M. Jorgensen. 2013. Ultrafast endocytosis at mouse hippocampal synapses.  Nature. 504, 242-7.  doi: 10.1038/12809. PMCID: PMC3957339.
Watanabe, S., Richards, J., Hollopeter, G., Hobson, R.J., Davis, M.W., and Jorgensen, E.M. 2012. Nano-fEM: protein localization using correlative photo-activated localization microscopy and electron microscopy. Journal of Visual Experiments 3, e3995. doi: 10.3791/3995. PMCID: PMC3566706
Hobson, R.J., Q. Liu, S. Watanabe and E.M. Jorgensen. 2011. Complexin maintains vesicles in the primed state in C. elegans. Current Biology 21, p106-113. PMCID: PMC348763.
Watanabe, S., A. Punge , G. Hollopeter , K.I. Willig, R.J. Hobson  , M.W. Davis , S.W. Hell , and E.M. Jorgensen. 2011. Protein localization in electron micrographs using fluorescence nanoscopy.  Nature Methods 8, p80-84. PMCID: PMC3059187.
Oikonomou, G., Perens, E. A., Lu, Y., Watanabe, S., Jorgensen, E. M., and Shaham, S. (2011). Opposing activities of LIT-1/NLK and DAF-6/patched-related direct sensory compartment morphogenesis in C. elegans. PLoS Biol. 9, e1001121. PMCID: PMC3153439.
Ou, C.-Y., Poon, V. Y., Maeder, C. I., Watanabe, S., Lehrman, E. K., Fu, A. K. Y., Park, M., Fu, W.-Y., Jorgensen, E. M., Ip, N. Y., et al. (2010). Two cyclin-dependent kinase pathways are essential for polarized trafficking of presynaptic components. Cell 141, 846–858. PMCID: PMC3168554.
Pellettieri, J., Fitzgerald, P., Watanabe, S., Mancuso, J., Green, D. R., and Sánchez Alvarado, A. (2010). Cell death and tissue remodeling in planarian regeneration. Dev. Biol. 338, 76–85. PMCID: PMC2835816.
Hammarlund, M., Palfreyman, M. T., Watanabe, S., Olsen, S., and Jorgensen, E. M. (2007). Open syntaxin docks synaptic vesicles. PLoS Biol. 5, e198. PMCID: PMC3048763.