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FRET imaging and in silico simulation: analysis of the signaling network of nerve growth factor-induced neuritogenesis

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Brain Cell Biology

Abstract

Genetically encoded probes based on Förster resonance energy transfer (FRET) enable us to decipher spatiotemporal information encoded in complex tissues such as the brain. Firstly, this review focuses on FRET probes wherein both the donor and acceptor are fluorescence proteins and are incorporated into a single molecule, i.e. unimolecular probes. Advantages of these probes lie in their easy loading into cells, the simple acquisition of FRET images, and the clear evaluation of data. Next, we introduce our recent study which encompasses FRET imaging and in silico simulation. In nerve growth factor-induced neurite outgrowth in PC12 cells, we found positive and negative signaling feedback loops. We propose that these feedback loops determine neurite-budding sites. We would like to emphasize that it is now time to accelerate crossover research in neuroscience, optics, and computational biology.

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References

  • Aoki, K., Nakamura, T., and Matsuda, M. (2004). Spatio-temporal regulation of Rac1 and Cdc42 activity during nerve growth factor-induced neurite outgrowth in PC12 cells. J. Biol. Chem. 279, 713–719.

    Article  PubMed  CAS  Google Scholar 

  • Aoki, K., Nakamura, T., Fujikawa, K., and Matsuda, M. (2005). Local Phosphatidylinositol 3,4,5-Trisphosphate Accumulation Recruits Vav2 and Vav3 to Activate Rac1/Cdc42 and Initiate Neurite Outgrowth in Nerve Growth Factor-stimulated PC12 Cells. Mol. Biol. Cell 16, 2207–2217.

    Article  PubMed  CAS  Google Scholar 

  • Aoki, K., Nakamura, T., Inoue, T., Meyer, T., and Matsuda, M. (2007). An essential role for the SHIP2-dependent negative feedback loop in neuritogenesis of nerve growth factor-stimulated PC12 cells. J. Cell Biol. 177, 817–827.

    Article  PubMed  CAS  Google Scholar 

  • Braun, D.C., Garfield, S. H., and Blumberg, P. M. (2005). Analysis by fluorescence resonance energy transfer of the interaction between ligands and protein kinase Cdelta in the intact cell. J. Biol. Chem. 280, 8164–8171.

    Article  PubMed  CAS  Google Scholar 

  • Brumbaugh, J., Schleifenbaum, A., Gasch, A., Sattler, M., and Schultz, C. (2006). A dual parameter FRET probe for measuring PKC and PKA activity in living cells. J. Am. Chem. Soc. 128, 24–25.

    Article  PubMed  CAS  Google Scholar 

  • Cassman, M. (2003) Computational biology. Counting on the neuron. Science 300, 756–757.

    Article  PubMed  CAS  Google Scholar 

  • Craske, M.L., Fivaz, M., Batada, N.N., and Meyer, T. (2005) Spines and neurite branches function as geometric attractors that enhance protein kinase C action. J. Cell Biol. 170, 1147–1158.

    Article  PubMed  CAS  Google Scholar 

  • Dyson, J.M., O’Malley, C.J., Becanovic, J., Munday, A.D., Berndt, M.C., Coghill, I.D., Nandurkar, H.H., Ooms, L.M., and Mitchell, C.A. 2001. The SH2-containing inositol polyphosphate 5-phosphatase, SHIP-2, binds filamin and regulates submembraneous actin. J. Cell Biol. 155, 1065–1080.

    Article  PubMed  CAS  Google Scholar 

  • Fiala, A., Spall, T., Diegelmann, S., Eisermann, B., Sachse, S., Devaud, J. M., Buchner, E., and Galizia, C. G. (2002). Genetically expressed cameleon in Drosophila melanogaster is used to visualize olfactory information in projection neurons. Curr. Biol. 12, 1877–1884.

    Article  PubMed  CAS  Google Scholar 

  • Fink, C.C., Slepchenko, B., Moraru I.I., Schaff, J., Watras, J., and Loew, L.M. (1999) Morphological control of inositol-1,4,5-trisphosphate-dependent signals. J. Cell Biol. 147, 929–935.

    Article  PubMed  CAS  Google Scholar 

  • Fujioka, A., Terai, K., Itoh, R. E., Aoki, K., Nakamura, T., Kuroda, S., Nishida, E., and Matsuda, M. (2006). Dynamics of the Ras/ERK MAPK cascade as monitored by fluorescent probes. J. Biol. Chem. 281, 8917–8926.

    Article  PubMed  CAS  Google Scholar 

  • Hailey, D.W., Davis, T. N., and Muller, E. G. (2002). Fluorescence resonance energy transfer using color variants of green fluorescent protein. Methods Enzymol. 351, 34–49.

    Article  PubMed  CAS  Google Scholar 

  • Hell, S.W., Dyba, M., and Jakobs, S. (2004). Concepts for nanoscale resolution in fluorescence microscopy. Curr. Opin. Neurobiol. 14, 599–609.

    Article  PubMed  CAS  Google Scholar 

  • Higashijima, S., Masino, M. A., Mandel, G., and Fetcho, J. R. (2003). Imaging neuronal activity during zebrafish behavior with a genetically encoded calcium indicator. J. Neurophysiol. 90, 3986–3997.

    Article  PubMed  Google Scholar 

  • Inoue, T., Heo, W. D., Grimley, J. S., Wandless, T. J., and Meyer, T. (2005). An inducible translocation strategy to rapidly activate and inhibit small GTPase signaling pathways. Nat. Methods 2, 415–418.

    Article  PubMed  CAS  Google Scholar 

  • Itoh, R.E., Kurokawa, K., Ohba, Y., Yoshizaki, H., Mochizuki, N., and Matsuda, M. (2002). Activation of rac and cdc42 video imaged by fluorescent resonance energy transfer-based single-molecule probes in the membrane of living cells. Mol. Cell. Biol. 22, 6582–6591.

    Article  PubMed  CAS  Google Scholar 

  • Je, H.S., Yang, F., Zhou, J., and Lu, B. (2006). Neurotrophin 3 induces structural and functional modification of synapses through distinct molecular mechanisms. J. Cell Biol. 175, 1029–1042.

    Article  PubMed  CAS  Google Scholar 

  • Kiyokawa, E., Hara, S., Nakamura, T., and Matsuda, M. (2006). Fluorescence (Förster) resonance energy transfer imaging of oncogene activity in living cells. Cancer Sci. 97, 8–15.

    Article  PubMed  CAS  Google Scholar 

  • Kurokawa, K., Mochizuki, N., Ohba, Y., Mizuno, H., Miyawaki, A., and Matsuda, M. (2001). A pair of fluorescent resonance energy transfer-based probes for tyrosine phosphorylation of the CrkII adaptor protein in vivo. J. Biol. Chem. 276, 31305–31310.

    Article  PubMed  CAS  Google Scholar 

  • Kurokawa, K., Takaya, A., Fujioka, A., Terai, K., and Matsuda, M. (2004) Visualizing the signal transduction pathways in living cells with GFP-based FRET probes. Acta Histochem.Cytochem. 37, 347–355.

    Article  CAS  Google Scholar 

  • Lakowicz, K. R. (2006). Energy transfer. In Principles of Fluorescence Spectroscopy, 3rd edn. Springer, New York, pp. 443–475.

  • Meinhardt, H. (1999). Orientation of chemotactic cells and growth cones: models and mechanisms. J. Cell Sci. 112, 2867–2874.

    PubMed  CAS  Google Scholar 

  • Meinhardt, H., and Gierer, A. (2000). Pattern formation by local self-activation and lateral inhibition. Bioessays 22, 753–760.

    Article  PubMed  CAS  Google Scholar 

  • Miyawaki, A. (2003). Visualization of the spatial and temporal dynamics of intracellular signaling. Dev. Cell 4, 295–305.

    Article  PubMed  CAS  Google Scholar 

  • Miyawaki, A. (2005). Innovations in the imaging of brain functions using fluorescent proteins. Neuron 48, 189–199.

    Article  PubMed  CAS  Google Scholar 

  • Miyawaki, A., Llopis, J., Heim, R., McCaffery, J. M., Adams, J. A., Ikura, M., and Tsien, R. Y. (1997). Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin. Nature 388, 882–887.

    Article  PubMed  CAS  Google Scholar 

  • Mochizuki, N., Yamashita, S., Kurokawa, K., Ohba, Y., Nagai, T., Miyawaki, A., and Matsuda, M. (2001). Spatio-temporal images of growth-factor-induced activation of Ras and Rap1. Nature 411, 1065–1068.

    Article  PubMed  CAS  Google Scholar 

  • Nagai, Y., Miyazaki, M., Aoki, R., Zama, T., Inouye, S., Hirose, K., Iino, M., and Hagiwara, M. (2000). A fluorescent indicator for visualizing cAMP-induced phosphorylation in vivo. Nat. Biotechnol. 18, 313–316.

    Article  PubMed  CAS  Google Scholar 

  • Nakamura, T., Aoki, K., and Matsuda, M. (2005). FRET imaging in nerve growth cones reveals a high level of RhoA activity within the peripheral domain. Brain Res. Mol. Brain Res. 139, 277–287.

    Article  PubMed  CAS  Google Scholar 

  • Nakamura, T., Kurokawa, K., Kiyokawa, E., and Matsuda, M. (2006). Analysis of the spatiotemporal activation of rho GTPases using Raichu probes. Methods Enzymol. 406, 315–332.

    Article  PubMed  CAS  Google Scholar 

  • Nikolenko, V., Nemet, B., and Yuste, R. (2003). A two-photon and second-harmonic microscope. Methods 30, 3–15.

    Article  PubMed  CAS  Google Scholar 

  • Nye, S.H., Squinto, S.P., Glass, D.J., Stitt, T.N., Hantzopoulos, P., Macchi, M.J., Lindsay, N.S., Ip, N.Y., and Yancopoulos, G.D. (1992) K-252a and staurosporine selectively block of neurotrophin receptors and neurotrophin-mediated responses. Mol. Biol. Cell 3, 677–686.

    PubMed  CAS  Google Scholar 

  • Paternotte, N., Zhang, J., Vandenbroere, I., Backers, K., Blero, D., Kioka, N., Vanderwinden, J.M., Pirson, I., and Erneux, C. 2005. SHIP2 interaction with the cytoskeletal protein Vinexin. FEBS J. 272, 6052–6066.

    Article  PubMed  CAS  Google Scholar 

  • Prasad, N., Topping, R.S., and Decker, S.J. 2001. SH2-Containing Inositol 5’-Phosphatase SHIP2 Associates with the p130Cas Adapter Protein and Regulates Cellular Adhesion and Spreading. Mol. Cell. Biol. 21, 1416–1428.

    Article  PubMed  CAS  Google Scholar 

  • Sasagawa, S., Ozaki, Y., Fujita, K., and Kuroda, S. (2005). Prediction and validation of the distinct dynamics of transient and sustained ERK activation. Nat. Cell Biol. 7, 365–373.

    Article  PubMed  CAS  Google Scholar 

  • Sato, M., Hida, N., Ozawa, T., and Umezawa, Y. (2000). Fluorescent indicators for cyclic GMP based on cyclic GMP-dependent protein kinase Iα and green fluorescent proteins. Anal. Chem. 72, 5918–5924.

    Article  PubMed  CAS  Google Scholar 

  • Sato, M., Ueda, Y., Takagi, T., and Umezawa, Y. (2003). Production of PtdInsP3 at endomembranes is triggered by receptor endocytosis. Nat. Cell Biol. 5, 1016–1022.

    Article  PubMed  CAS  Google Scholar 

  • Sekar, R.B. and Periasamy, A. (2003). Fluorescence resonance energy transfer (FRET) microscopy imaging of live cell protein localizations. J. Cell Biol. 160, 629–633.

    Article  PubMed  CAS  Google Scholar 

  • Sorkin, A., McClure, M., Huang, F., and carter, R. (2000) Interaction of EGF receptor and grb2 in living cells visualized by fluorescence resonance energy transfer (FRET) microscopy. Curr. Biol. 10, 1395–1398.

    Article  PubMed  CAS  Google Scholar 

  • Suzuki, H., Kerr, R., Bianchi, L., Frokjaer-Jensen, C., Slone, D., Xue, J., Gerstbrein, B., Driscoll, M., and Schafer, W. R. (2003). In vivo imaging of C. elegans mechanosensory neurons demonstrates a specific role for the MEC-4 channel in the process of gentle touch sensation. Neuron 39, 1005–1017.

    Article  PubMed  CAS  Google Scholar 

  • Takao, K., Okamoto, K. I., Nakagawa, T., Neve, R. L., Nagai, T., Miyawaki, A., Hashikawa, S.Kobayashi, T., and Hayashi, Y. (2005). Visualization of Synaptic Ca2+ /Calmodulin-Dependent Protein Kinase II Activity in Living Neurons. J. Neurosci. 25, 3107–3112.

    Article  PubMed  CAS  Google Scholar 

  • Terai, K. and Matsuda, M. (2005). Ras binding opens c-Raf to expose the docking site for mitogen-activated protein kinase kinase. EMBO Rep. 6, 251–255.

    Article  PubMed  CAS  Google Scholar 

  • Ting, A.Y., Kain, K.H., Klemke, R.L., and Tsien, R. Y. (2001). Genetically encoded fluorescent reporters of protein tyrosine kinase activities in living cells. Proc. Natl. Acad. Sci. U.S.A . 98, 15003–15008.

    Article  PubMed  CAS  Google Scholar 

  • Turing, A. (1952). The chemical basis of morphogenesis. Phil. Trans. B. 237, 37–72.

    Article  Google Scholar 

  • Violin, J.D., Zhang, J., Tsien, R. Y., and Newton, A. C. (2003). A genetically encoded fluorescent reporter reveals oscillatory phosphorylation by protein kinase C. J. Cell Biol. 161, 899–909.

    Article  PubMed  CAS  Google Scholar 

  • Yamada, A., Hirose, K., Hashimoto, A., and Iino, M. (2005). Real-time imaging of myosin II regulatory light-chain phosphorylation using a new protein biosensor. Biochem. J. 385, 589–594.

    Article  PubMed  CAS  Google Scholar 

  • Yoshizaki, H., Ohba, Y., Kurokawa, K., Itoh, R.E., Nakamura, T., Mochizuki, N., Nagashima, K., and Matsuda, M. (2003). Activity of Rho-family G proteins during cell divison as visualized with FRET-based probes. J. Cell Biol. 162, 223–232.

    Article  PubMed  CAS  Google Scholar 

  • Zhang, J., Ma, Y., Taylor, S.S., and Tsien, R.Y. (2001). Genetically encoded reporters of protein kinase A activity reveal impact of substrate tethering. Proc. Natl. Acad. Sci. U.S.A. 98, 14997–15002.

    Article  PubMed  CAS  Google Scholar 

  • Zhang, H., Webb, D.J., Asmussen, H., Niu, S., and Horwitz, A.F. (2005). A GIT1/PIX/Rac/PAK signaling module regulates spine morphogenesis and synapse formation through MLC. J. Neurosci. 25, 3379–3388.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

Work in the laboratory was supported by grants from the Ministry of Education, Culture, Sports, Science, and Technology of Japan.

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  1. Laboratory of Bioimaging and Cell Signaling, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan

    Takeshi Nakamura, Kazuhiro Aoki & Michiyuki Matsuda

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  1. Takeshi Nakamura
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  2. Kazuhiro Aoki
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  3. Michiyuki Matsuda
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Correspondence to Takeshi Nakamura.

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Nakamura, T., Aoki, K. & Matsuda, M. FRET imaging and in silico simulation: analysis of the signaling network of nerve growth factor-induced neuritogenesis. Brain Cell Bio 36, 19–30 (2008). https://doi.org/10.1007/s11068-008-9028-5

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  • DOI: https://doi.org/10.1007/s11068-008-9028-5

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