・Achilleos, A., Wehman, A. M., Nance, J. PAR-3 mediates the initial clustering and apical localization of junction and polarity proteins during C. elegans intestinal epithelial cell polarization. Development 1842, 1833–1842 (2010).
・Aizawa, H., Wakatsuki, S., Ishii, A., Moriyama, K., Sasaki, Y., Ohashi, K., Sekine- Aizawa, Y., Sehara-Fujisawa, A., Mizuno,K., Goshima, Y., Phosphorylation of cofilin by LIM-kinase is necessary for semaphorin 3A-induced growth cone collapse. Nat. Neurosci. 4, 367–373 (2001).
・Augustine, G. J,. How does calcium trigger neurotransmitter release? Curr. Opin. Neurobiol. 11, 320–326 (2001).
・Aurandt, J., Vikis, H. G., Gutkind, J. S., Ahn, N., Guan, K. L., The semaphorin receptor plexin-B1 signals through a direct interaction with the Rho-specific nucleotide exchange factor, LARG. Proc. Natl Acad. Sci. USA 99, 12085–12090 (2002).
・Arber, S., Barbayannis, F. A., Hanser, H., Schneider, C., Stanyon, C. A., Bernard, O. and Caroni, P. Regulation of actin dynamics through phosphorylation of cofilin by LIM-kinase. Nature 393, 805–809 (1998).
・Bagnard, D., Lohrum, M., Uziel, D., Püschel, A. W., Bolz, J., Semaphorins act as attractive and repulsive guidance signals during the development of cortical projections. Development 125, 5043–5053 (1998).
・Barlow, A. L., Macleod, A., Noppen, S., Sanderson, J., Guérin, C. J., Microscopy M icroanalysis Colocalization Analysis in Fluorescence Micrographs : Verification of a More Accurate Calculation of Pearson ’ s Correlation Coefficient. Microsc Microanal. 6. 710–724 (2010).
・Behar, O., Golden, J. A, Mashimo, H., Schoen, F. J., Fishman, M. C,. Semaphorin III is needed for normal patterning and growth of nerves, bones and heart. Nature 383, 525–528 (1996).
・Brenner, S., The genetics of Caenorhabditis elegans. Genetics. 77, 71–94 (1974).
・Brodin, L., Löw, P., Shupliakov, O., Sequential steps in clathrin-mediated synaptic vesicle endocytosis. Curr. Opin. Neurobiol. 10, 312–320 (2000).
・Brose, N., Petrenko, A. G., Südhof, T. C., Jahn, R., Synaptotagmin: a calcium sensor on the synaptic vesicle surface. Science 256, 1021–1025 (1992).
・Bucci, C, Parton, R. G., Mather, I. H., Stunnenberg, H., Simons, K., Hoflack, B, Zerial, M., The Small GTPase rab5 Functions as a Regulatory Factor in the Early Endocytic Pathway. Cell. 70, 715–728 (1992).
・Bucci, C., Thomsen, P., Nicoziani, P., McCarthy, J., van Deurs B. Rab7 : A Key to Lysosome Biogenesi. Mol Biol Cell. 11, 467–480 (2000).
・Campbell, D. S., Holt, C. E., Chemotropic responses of retinal growth cones mediated by rapid local protein synthesis and degradation. Neuron 32, 1013–1026 (2001).
・Carcea, I., Ma'ayan, A., Mesias, R., Sepulveda, B., Salton, S. R., Benson, D. L., Flotillin-Mediated Endocytic Events Dictate Cell Type-Specific Responses to Semaphorin 3A. J Neurosci. 30(45):15317-29 (2010).
・Castellani, V., Chedotal, A., Schachner, M., Faivre-Sarrailh, C., Rougon, G., Analysis of the L1-deficient mouse phenotype reveals cross-talk between Sema3A and L1 signaling pathways in axonal guidance, Neuron. 27. 237–249. (2000).
・Castellani V., De Angelis, D., Kenwrick, S., Rougon, G., Cis and trans interactions of L1 with neuropilin-1 control axonal responses to semaphorin 3A. EMBO J., 21. 6348– 6357. (2002).
・Castellani, V., Falk, J., Rougon, G., Semaphorin3A-induced receptor endocytosis during axon guidance responses is mediated by L1 CAM. Mol Cell Neurosci. 26. 89-100. (2004).
・Chapman, E. R., Jahn, R., Calcium-dependent interaction of the cytoplasmic region of synaptotagmin with membranes. Autonomous function of a single C2-homologous domain. J. Biol. Chem. 269, 5735–41 (1994).
・Chapman, E. R., Desai, R. C., Davis, A. F., Tornehl, C. K., Delineation of the oligomerization, AP-2 binding, and synprint binding region of the C2B domain of synaptotagmin. J. Biol. Chem. 273, 32966–32972 (1998).
・Chapman, E. R. SYNAPTOTAGMIN : Synaptotagmin: A Ca(2+) sensor that triggers exocytosis?. Nat Rev Mol Cell Biol. (7):498-508.3, 1–11 (2002).
・Chapman, E. R., How Does Synaptotagmin Trigger Neurotransmitter Release ? Annurev. Biochem. 77:615-41 (2008).
・Chen C. C., Schweinsberg, P. J, Vashist, S., Mareiniss, D. P., Lambie, E. J., Grant, B. D., RAB-10 Is Required for Endocytic Recycling in the Caenorhabditis elegans Intestine. Mol Biol Cell. 3. 1286–1297 (2006).
・Chen, Y. A., Scheller, R. H., SNARE-mediated membrane fusion. Nat. Rev. Mol. Cell Biol. 2, 98–106 (2001).
・Christensen, C. R., Klingelhöfer, J., Tarabykina, S., Hulgaard, E. F., Kramerov, D., Lukanidin, E., Transcription of a novel mouse semaphorin gene, M-semaH, correlates with the metastatic ability of mouse tumor cell lines. Cancer Res. 58, 1238–1244 (1998).
・Colvin, R. A., Means, T. K., Diefenbach, T. J., Moita, L. F., Friday, R.P., Sever, S,, Campanella, G. S., Abrazinski, T., Manice, L. A., Moita, C., Andrews, N. W., Wu, D., Hacohen, N., Luster, A. D., Synaptotagmin-mediated vesicle fusion regulates cell migration. Nat Immunol. 6. 495-502. (2010).
・Costa, M., Raich, W., Agbunag, C., Leung, B, Hardin, J., Priess, J. R., A putative catenin-cadherin system mediates morphogenesis of the Caenorhabditis elegans embryo. J Cell Biol. 141, 297–308 (1998).
・Davletov, B. A., Sudhof, T. C., A Single C2 Domain From Synaptotagmin-I Is Sufficient for High-Affinity Ca2+/Phospholipid Binding. J. Biol. Chem. 268, 26386– 26390. (1993).
・Dell'Angelica, E. C., Payne, G. S., Intracellular cycling of lysosomal enzyme receptors: cytoplasmic tails' tales. Cell. 106. 395-8. (2001).
・Desai, R. C., Vyas, B., Earles, C. A., Littleton, J. T., Kowalchyck, J. A., Martin, T. F., Chapman, E. R., The C2B domain of synaptotagmin is a Ca2+-sensing module essential for exocytosis. J. Cell Biol. 150, 1125–1135 (2000).
・Desclozeaux, M., Venturato, J., Wylie, F. G., Kay J. G., Joseph, S. R., Le, H. T., Stow J. L., Active Rab11 and functional recycling endosome are required for E- cadherintrafficking and lumen formation during epithelial morphogenesis. Am J Physiol Cell Physiol. 295, C545-56. (2008).
・Diril, M. K., Wienisch, M., Jung, N., Stonin 2 Is an AP-2-Dependent Endocytic Sorting Adaptor for Synaptotagmin Internalization and Recycling. Dev. Cell, 1, 233– 244 (2006).
・Edwards, D. C., Sanders, L. C., Bokoch, G. M., Gill, G. N., Activation of LIM-kinase by Pak1 couples Rac/Cdc42 GTPase signalling to actin cytoskeletal dynamics. Nat. Cell Biol. 1, 253–259 (1999).
・Fan, J., Mansfield, S. G., Redmond, T., Gordon-Weeks, P. R., Raper, J. A., The organization of F-actin and microtubules in growth cones exposed to a brain-derived collapsing factor. J. Cell Biol. 121, 867–878 (1993).
・Fan, J., Raper, J. A., Localized collapsing cues can steer growth cones without inducing their full collapse. Neuron 14, 263–274 (1995).
・Fergestad, T., Broadie, K., Interaction of stoned and synaptotagmin in synaptic vesicle endocytosis. J. Neurosci. 21, 1218–27 (2001).
・Fire, A. White-Harrison, S., Dixon D., Vectors for ectopic expression in C. elegans Worm Breeder's Gazette 12, 17 (1992).
・Fisher, C. L., Pei, G. K., Modification of a PCR-based site-directed mutagenesis method. Biotechniques 23, 570-574. (1997).
・Fujii, T., Nakao, F., Shibata, Y., Shioi, G., Kodama, E., Fujisawa, H., Takagi, S., Caenorhabditis elegans PlexinA , PLX-1 , interacts with transmembrane semaphorins and regulates epidermal morphogenesis. Development. 129(9):2053-63. (2002).
・Gallegos, M. E., Balakrishnan, S., Chandramouli, P., Arora, S., Azameera, A., Babushekar, A., Bargoma, E., Bokhari, A., Chava, S. K., Das, P., Desai. M., Decena, D., Saramma, S. D., Dey, B., Doss, A. L., Gor, N., Gudiputi, L., Guo, C., Hande, S., Jensen M, Jones S, Jones N, Jorgens D, Karamchedu P, Kamrani K, Kolora LD, Kristensen, L., Kwan, K., Lau, H., Maharaj, P., Mander, N., Mangipudi, K., Menakuru, H., Mody, V., Mohanty, S., Mukkamala, S., Mundra, S. A., Nagaraju, S., Narayanaswamy, R., Ndungu-Case, C., Noorbakhsh, M., Patel, J., Patel, P., Pendem, S. V., Ponakala, A., Rath, M., Robles, M. C., Rokkam, D., Roth, C., Sasidharan, P., Shah, S., Tandon, S., Suprai, J., Truong, T. Q., Uthayaruban, R., Varma, A., Ved, U., Wang, Z., Yu, Z., The C. elegans Rab Family : Identification, Classification and Toolkit Construction. PLoS One. 7, 11, (2012).
・Gebauer, F., Hentze, M. W., Molecular Mechanisms of translational control. Nat Rev Mol Cell Biol. 10. 827-35. (2004).
・Gengyo-Ando, K., Kuroyanagi, H., Kobayashi, T., Murate, M., Fujimoto, K., Okabe, S., Mitani, S., The SM protein VPS-45 is required for RAB-5-dependent endocytic transport in Caenorhabditis elegans. EMBO Rep. 2. 152-7. (2007).
・Ghosh, P., Dahms, N. M., Kornfeld, S., Mannose 6-phosphate receptors: new twists in the tale. Nat Rev Mol Cell Biol. 4. 202-12. (2004).
・Goshima, Y., Hori, H., Sasaki, Y., Yang, T., Kagoshima-Maezono, M., Li, C., Takenaka, T., Nakamura, F., Takahashi, T., Strittmatter, S. M., Misu, Y., Kawakami, T., Growth Cone Neuropilin-1 Mediates Collapsin-1 / Sema III Facilitation of Antero- and Retrograde Axoplasmic Transport. J Neurobiol. 39(4). 579-89. (1999).
・Grant, B., Hirsh, D., Receptor-mediated Endocytosis in the Caenorhabditis elegans Oocyte. Mol Biol Cell. 10. 4311-26. (1999).
・Grant, B. D., Donaldson, J. G., Pathways and mechanisms of endocytic recycling. Nat Rev Mol Cell Biol. 9, 597-608. (2009).
・Grass, I., Thiel, S., Höning, S., Haucke, V., Recognition of a basic AP-2 binding motif within the C2B domain of synaptotagmin is dependent on multimerization. J. Biol. Chem. 279, 54872–80 (2004).
・Grant, B., Zhang, Y., Paupard, M. C., Lin, S. X., Hall, D. H., Hirsh, D., Evidence that RME-1 , a conserved C . elegans EH-domain protein , functions in endocytic recycling. Nat Cell Biol. 3. 573-9. (2001).
・Green, R. A., Kao, H. L., Audhya, A., Arur, S., Mayers, J. R., Fridolfsson, H. N., Schulman, M., Schloissnig, S., Niessen, S., Laband, K., Wang, S., Starr, D. A., Hyman, A. A., Schedl, T., Desai, A., Piano, F., Gunsalus, K. C., Oegema, K.. Resource, A., High-Resolution C. elegans Essential Gene Network Based on Phenotypic Profiling of a Complex Tissue. Cell 145, 470–482 (2010).
・Hall, K. T., Boumsell, L., Schultze, J. L., Boussiotis, V. A., Dorfman, D. M., Cardoso, A. A., Bensussan, A., Nadler, L. M,, Freeman, G. J., Human CD100, a novel leukocyte semaphorin that promotes B-cell aggregation and differentiation. Proc. Natl. Acad. Sci. U. S. A. 93, 11780–11785 (1996).
・Hara, K., Maruki, Y., Long, X., Yoshino, K., Oshiro, N., Hidayat, S., Tokunaga, C., Avruch, J., Yonezawa, K., Raptor, a binding partner of target of rapamycin (TOR), mediates TOR action. Cell 110, 177–189 (2002).
・Harris, T. W., Hartwieg, E., Horvitz, H. R., Jorgensen, E. M., Mutations in Synaptojanin Disrupt Synaptic Vesicle Recycling. J Cell Biol. 3. 589–599 (2000).
・Haucke, V., Neher, E., Sigrist, S. J., Protein scaffolds in the coupling of synaptic exocytosis and endocytosis. Nat Rev Neurosci. 3127-38. (2011).
・He, Z., Tessier-Lavigne, M., Neuropilin is a receptor for the axonal chemorepellent semaphorin III. Cell 90, 739–751 (1997).
・Hennig, K. M., Colombani, J., Neufeld, T. P., TOR coordinates bulk and targeted endocytosis in the Drosophila melanogaster fat body to regulate cell growth. 173, 963–974 (2006).
・Hennig, K. M., Colombani, J., Neufeld, T. P., Asymmetric endocytosis and remodeling of b1 -integrin adhesions during growth cone chemorepulsion by MAG. Nat. Publ. Gr. 13, 829–837 (2010).
・Hoopmann, P., Punge, A., Barysch, S. V., Westphal, V., Buckers, J., Opazo, F., Rizzoli, S. O. Endosomal sorting of readily releasable synaptic vesicles. Proceedings of the National Academy of Sciences of the United States of America, 107(44), 19055– 19060 (2010).
・Hu, H., Marton, T. F., Goodman, C. S., Plexin B mediates axon guidance in Drosophila by simultaneously inhibiting active Rac and enhancing RhoA signaling. Neuron 32, 39–51 (2001).
・Jacinto, E., Loewith, R., Schmidt, A., Lin, S., Rüegg, M. A., Hall, A., Hall, M. N., Mammalian TOR complex 2 controls the actin cytoskeleton and is rapamycin insensitive. Nat. Cell Biol. 6, 1122–1128 (2004).
・Jahn, R., Lang, T., Südhof, T. C., Membrane fusion. Cell 112, 519–533 (2003).
・Jeon C. Y., Kim H. J., Lee J. Y., Kim J. B., Kim S. C., Park J. B., p190RhoGAP and Rap-dependent RhoGAP (ARAP3) inactivate RhoA in response to nerve growth factor leading to neurite outgrowth from PC12 cells. Exp Mol Med., 42:335–344. (2010.)
・Jin, Z., Strittmatter, S. M., Rac1 mediates collapsin-1-induced growth cone collapse. J. Neurosci. 17, 6256–6263 (1997).
・Jung, N., Wienisch, M., Gu, M., Rand, J. B., Müller, S. L., Krause, G., Jorgensen, E. M., Klingauf, J., Haucke, V. Molecular basis of synaptic vesicle cargo recognition by the endocytic sorting adaptor stonin 2. J Cell Biol. 179.1497-510. (2007).
・Jurney, W. M., Gallo, G., Letourneau, P. C., McLoon, S. C., Rac1-mediated endocytosis during ephrin-A2- and semaphorin 3A-induced growth cone collapse. J. Neurosci. 22, 6019–6028 (2002).
・Kabayama, H., Takeuchi, M., Taniguchi, M., Tokushige, N., Kozaki, S., Mizutani, A., Nakamura, T., Mikoshiba, K., Syntaxin 1B Suppresses Macropinocytosis and Semaphorin 3A-Induced Growth Cone Collapse. J Neurosci. 31, 7357–7364 (2011).
・Kamath, R. S., Ahringer, J., Genome-wide RNAi screening in Caenorhabditis elegans. Methods. 30, 313–321 (2003).
・Kamiguchi, H., Hlavin, M. L., Yamasaki, M., Lemmon, V., Adhesion molecules and inherited diseases of the human nervous system. Annu Rev Neurosci. 21. 97-125. (1998)
・Kasai, K., Akagawa, K., Roles of the cytoplasmic and transmembrane domains of syntaxins in intracellular localization and trafficking. J Cell Sci. 114. 3115-24. (2001).
・Kawauchi, T., Sekine, K., Shikanai, M., Chihama, K., Tomita, K., Kubo, K., Nakajima, K., Nabeshima, Y., Hoshino, M., Article Rab GTPases-Dependent Endocytic Pathways Regulate Neuronal Migration and Maturation through N- Cadherin Trafficking. Neuron 67, 588–602 (2010).
・Keely, P. J., Rusyn, E. V, Cox, A. D. Parise, L. V., R-Ras signals through specific integrin alpha cytoplasmic domains to promote migration and invasion of breast epithelial cells. J. Cell Biol. 145, 1077–88 (1999).
・Kim D. H., Sarbasso,v D. D., Ali, S. M., King, J. E., Latek, R. R., Erdjument- Bromage, H., Tempst, P., Sabatini, D. M., mTOR Interacts with Raptor to Form a Nutrient-Sensitive Complex that Signals to the Cell Growth Machinery. Cell 110, 163–175 (2002).
・Kjaerulff, O., Brodin, L., Jung, A., The Structure and Function of Endophilin Proteins. Cell Biochem Biophys. 60. 137–154 (2011).
・Knust, E. Bossinger, O., Composition and Formation of Intercellular Junctions in Epithelial Cells. Science. 298. 1955-9.
・Koh, T. W., Bellen, H. J. Synaptotagmin I., a Ca2+ sensor for neurotransmitter release. Trends Neurosci. 26, 413–422 (2003).
・Kolodkin, A. L., Matthes, D. J., O'Connor, T. P., Patel, N. H., Admon, A., Bentley, D., Goodman, C. S., Fasciclin IVsequence, expression, and function during growth cone guidance in the grasshopper embryo. Neuron. 9, 831–845 (1992).
・Kolodkin, A. L., Matthes, D. J., Goodman, C. S., The semaphorin genes encode a family of transmembrane and secreted growth cone guidance molecules. Cell 75, 1389–1399 (1993).
・Kolodkin, A. L., Levengood, D. V., Rowe, E. G., Tai, Y. T., Giger, R. J., Ginty, D. D., Neuropilin is a semaphorin III receptor. Cell 90, 753-762. (1997)
・Köppen, M., Simske, J. S., Sims, P. A., Firestein, B. L., Hall, D. H., Radice, A. D., Rongo, C., Hardin, J. D., Cooperative regulation of AJM-1 controls junctional integrity in Caenorhabditis elegans epithelia. Nat Cell Biol. 3, 983–991 (2001).
・Kostich, M., Fire, A., Fambrough, D. M., Identification and molecular-genetic characterization of a LAMP / CD68-like protein from Caenorhabditis elegans. J Cell Sci. 2606, 2595–2606 (2000).
・Kruger, R. P., Aurandt, J., Guan, K. L. W., Semaphorins command cells to move. Nat Rev Mol Cell Biol. 6, 789–800 (2005).
・Kubota, Y, Sano, M., Goda, S,, Suzuki, N., Nishiwaki, K., The conserved oligomeric Golgi complex acts in organ morphogenesis via glycosylation of an ADAM protease in C . elegans. Development. 263–273 (2004).
・Kuhn, T. B., Brown, M. D., Wilcox, C. L., Raper, J. A., Bamburg, J., Myelin and collapsin-1 induce motor neuron growth cone collapse through different pathways: inhibition of collapse by opposing mutants of rac1. J. Neurosci. 19, 1965–1975 (1999).
・Lemmon, M. A. Membrane recognition by phospholipid-binding domains. Nat Rev Mol Cell Biol. 9. 99-111. (2008).
・Li, C., Sasaki, Y., Takei, K., Yamamoto H, Shouji M, Sugiyama Y, Kawakami T, Nakamura F, Yagi T, Ohshima T, Goshima Y. Correlation between Semaphorin3A- Induced Facilitation of Axonal Transport and Local Activation of a Translation Initiation Factor Eukaryotic Translation Initiation Factor 4E. J Neurosci. 24, 6161– 6170 (2004).
・Li Q, Lau A, Morris TJ, Guo L, Fordyce CB, Stanley EF. A syntaxin 1, Galpha(o), and N-type calcium channel complex at a presynaptic nerve terminal: analysis by quantitative immunocolocalization. J Neurosci. 24, 4070–4081 (2004).
・Liu Z, Fujii T, Nukazuka A, Kurokawa R, Suzuki M, Fujisawa H, Takagi S. C . elegans PlexinA PLX-1 mediates a cell contact-dependent stop signal in vulval precursor cells. Dev Biol. 282, 138–151 (2005).
・Luo, Y., Raible, D. Raper, JA. Collapsin: a protein in brain that induces the collapse and paralysis of neuronal growth cones. Cell 75, 217–227 (1993).
・Luzio JP, Poupon V, Lindsay MR, Mullock BM, Piper RC, Pryor PR. Membrane dynamics and the biogenesis of lysosomes. Mol Membr Biol. 20. 141-54. (2003).
・Maekawa, M. Signaling from Rho to the Actin Cytoskeleton Through Protein Kinases ROCK and LIM-kinase. Science. 285, 895–898 (1999).
・Mann F, Rougon G. Mechanisms of axon guidance : membrane dynamics and axonal transport in semaphorin signalling. J Neurochem. 102, 316–323 (2007).
・Maritzen, T. & Podufall, J. Stonins – Specialized Adaptors for Synaptic Vesicle Recycling and Beyond ? 8–15 (2010). doi:10.1111/j.1600-0854.2009.00971.x
・Martina JA, Bonangelino CJ, Aguilar RC, Bonifacino JS.: An Adaptor-like Protein that Interacts with Components of the Endocytic Machinery. J Cell Biol. 153, 1111– 1120 (2001).
・Maruyama, I. N., Brenner, S., A phorbol ester/diacylglycerol-binding protein encoded by the unc-13 gene of Caenorhabditis elegans. Proc Natl Acad Sci U S A. 88, 5729–5733 (1991).
・Matthes, D. J., Sink, H., Kolodkin, A. L., Goodman, C. S., Semaphorin II can function as a selective inhibitor of specific synaptic arborizations. Cell 81, 631–9 (1995).
・Matthew, W. D., Tsavaler, L., Reichardt, L. F., Identification of a synaptic vesicle- specific membrane protein with a wide distribution in neuronal and neurosecretory tissue. J. Cell Biol. 91, 257–269 (1981).
・Meléndez, A., Levine, B. T., Autophagy in C. elegans. WormBook. 24 1-26. (2009).
・Meléndez, A., Tallóczy, Z., Seaman, M., Eskelinen, E. L., Hall, D. H., Levine, B.. Autophagy genes are essential for dauer development and life-span extension in C. elegans. Science. 301. 1387-91. (2003).
・Meijer, A. J., Codogno, P., Regulation and role of autophagy in mammalian cells. Int J Biochem Cell Biol. 36, 2445-62. (2004).
・Mello, C., Fire, A., DNA transformation. Methods Cell Biol. 48, 451-82. (1995).
・Miao, H., Han, K., Gu, F., Stereologic estimates of glomerular volume in unilaterally nephrectomized rats. Anal Quant Cytol Histol. 21, 89-92. (1999).
・Mukhopadhyay, A., Funato, K., Stahl, P. D., Rab7 Regulates Transport from Early to Late Endocytic Compartments in Xenopus Oocytes. J Biol Chem. 272, 13055-9. (1997).
・Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Barrell, D., Bateman, A., Binns, D., Biswas, M., Bradley, P., Bork, P., Bucher, P., Copley, R. R., Courcelle, E., Das, U., Durbin, R., Falquet, L., Fleischmann, W., Griffiths-Jones, S., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lopez, R., Letunic, I., Lonsdale, D., Silventoinen, V., Orchard, S. E., Pagni, M., Peyruc, D., Ponting, C. P., Selengut, J. D., Servant, F., Sigrist, C. J., Vaughan, R., Zdobnov, E. M., The InterPro Database , 2003 brings increased coverage and new features. 31, 315–318 (2003).
・Moriyama, K., Iida, K., Yahara, I., Phosphorylation of Ser-3 of cofilin regulates its essential function on actin. Genes Cells 1, 73–86 (1996).
・Murthy, V. N., De Camilli, P.. Cell biology of the presynaptic terminal. Annu. Rev. Neurosci. 26, 701–728 (2003).
・Nakamura, F., Kawamoto, S., Goshima, Y., Kalb, R. G., Strittmatter, S. M., Semaphorin3A enhances endocytosis at sites of receptor-F-actin colocalization during growth cone collapse. J. Cell Biol. 149, 411–421 (2000).
・Negishi, M., Oinuma, I., Katoh, H., Plexins: axon guidance and signal transduction. Cell. Mol. Life Sci. 62, 1363–1371 (2005).
・Neher, E., Zucker, R. S., Multiple calcium-dependent processes related to secretion in bovine chromaffin cells. Neuron 10, 21–30 (1993).
・Nukazuka, A., Fujisawa, H., Inada, T., Oda, Y., Takagi, S., Semaphorin controls epidermal morphogenesis by stimulating mRNA translation via eIF2alpha in Caenorhabditis elegans. Genes Dev. 22, 1025-36. (2008).
・Nukazuka, A., Tamaki, S., Matsumoto, K., Oda, Y., A Shift of the TOR Adaptor from Rictor toward Raptor by Semaphorin in C . elegans. Nat Commun. 484. (2011).
・Oinuma, I., Ishikawa, Y., Katoh, H. Negishi, M. The Semaphorin 4D receptor Plexin-B1 is a GTPase activating protein for R-Ras. Science 305, 862–865 (2004).
・Ohashi, K., Nagata, K., Maekawa, M., Ishizaki, T., Narumiya, S., Mizuno, K., Rho- associated kinase ROCK activates LIM-kinase 1 by phosphorylation at threonine 508 within the activation loop. J. Biol. Chem. 275, 3577–82 (2000).
・Pang, Z. P., Südhof, T. C., Cell biology of Ca2+-triggered exocytosis. Curr Opin Cell Biol. 4. 496-505. (2010).
・Loll, P. J., Swain, E., Chen, Y., Turner, B. T., Zhang, J. F., Structure of the SH3 domain of rat endophilin A2. Acta Crystallogr Sect F Struct Biol Cryst Commun. 64, 243-6. (2008).
・Perin, M. S., Fried, V. A, Mignery, G. a, Jahn, R. Südhof, T. C., Phospholipid binding by a synaptic vesicle protein homologous to the regulatory region of protein kinase C. Nature 345, 260–263 (1990).
・Perin, M. S., Brose, N., Jahn, R., Sudhof, T. C., Domain structure of synaptotagmin (p65). J. Biol. Chem. 266, 623–629 (1991).
・Perrot, V., Vazquez-Prado, J., Gutkind, J. S., Plexin B regulates Rho through the guanine nucleotide exchange factors leukemia-associated Rho GEF (LARG) and PDZ-RhoGEF. J. Biol. Chem. 277, 43115–43120 (2002).
・Pfeffer, S. R., Multiple routes of protein transport from endosomes to the trans Golgi network. FEBS Lett. 583. 3811-6. (2009).
・Phillips, A. M., Smith, M., Ramaswami, M., Kelly, L. E., The Products of the Drosophila stoned Locus Interact with Synaptic Vesicles via Synaptotagmin. J Neurosci. 20, 8254–8261 (2000).
・Poteryaev, D., Datta, S., Ackema, K., Zerial, M. & Spang, A. Identification of the Switch in Early-to-Late Endosome Transition. Cell 141, 497–508 (2010).
・Posor, Y., Eichhorn-Gruenig, M., Puchkov, D., Schöneberg, J., Ullrich, A., Lampe, A., Müller, R., Zarbakhsh, S., Gulluni, F., Hirsch, E., Krauss, M., Schultz, C., Schmoranzer, J., Noé, F., Haucke, V., Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate. Nature. 499, 233-7 (2013).
・Reddy, A., Caler, E. V., Andrews, N. W., Plasma membrane repair is mediated by Ca(2+)-regulated exocytosis of lysosomes. Cell. 106. 157-69. (2001).
・Ringstad, N., Nemoto, Y., De Camilli, P., The SH3p4/Sh3p8/SH3p13 protein family: binding partners for synaptojanin and dynamin via a Grb2-like Src homology 3 domain. Proc Natl Acad Sci U S A. 94, 8569-74. (1997).
・Rink, J., Ghigo, E., Kalaidzidis, Y., Zerial, M. Médecine, F. De., Rab Conversion as a Mechanism of Progression from Early to Late Endosomes. Cell. 122, 735–749 (2005).
・Richter M, Murai K. K., Bourgin C, Pak D. T., Pasquale E. B., The EphA4 receptor regulates neuronal morphology through SPAR-mediated inactivation of Rap GTPases. J Neurosci. 27:14205– 14215. (2007).
・Roberts, R. L., Barbieri, M. A., Pryse, K. M., Chua, M., Morisaki, J. H., Stahl, P. D., Endosome fusion in living cells overexpressing GFP-rab5. J Cell Sci. 112, 3667-75. (1999).
・Rolls, M. M., Hall, D. H., Victor, M., Stelzer, E. H. K., Rapoport, T. A., Targeting of Rough Endoplasmic Reticulum Membrane Proteins and Ribosomes in Invertebrate Neurons. 13, 1778–1791 (2002).
・Rothman, J. E., Mechanism of Intracellular Protein-Transport. Nature 372, 55–63 (1994).
・Roy, P. J., Zheng, H., Warren, C. E. Culotti, J. G., mab-20 encodes Semaphorin-2a and is required to prevent ectopic cell contacts during epidermal morphogenesis in Caenorhabditis elegans. Development 127, 755–767 (2000).
・Sandoval, I.,V., Bakke O., Targeting of membrane proteins to endosomes and lysosomes. Trends Cell Biol. 4. 292-7. (1994).
・Sandri, C., Caccavari, F., Valdembri, D., Camillo, C., Veltel, S., The R-Ras / RIN2 / Rab5 complex controls endothelial cell adhesion and morphogenesis via active integrin endocytosis and Rac signaling. Cell Res. 22, 1479–1501 (2012).
・Sanford, S. D., Gatlin, J. C., Hökfelt, T., Pfenninger, K. H., Growth cone responses to growth and chemotropic factors. Eur J Neurosci. 28. 268-78. (2008).
・Sarbassov, D. D., Ali, S. M., Kim, D. H., Guertin, D. A., Latek, R. R., Erdjument- Bromage, H., Tempst, P., Sabatini, D. M., Rictor, a novel binding partner of mTOR, defines a rapamycin-insensitive and raptor-independent pathway that regulates the cytoskeleton. Curr Biol 14, 1296-302. (2004).
・Sato, M., Grant B. D., Harada, A., Sato, K., Rab11 is required for synchronous secretion of chondroitin proteoglycans after fertilization in Caenorhabditis elegans. J Cell Sci. 121, 3177-86. (2008)
・Sato, M., Saegusa, K., Sato, K., Hara, T., Harada, A., Sato, K., Caenorhabditis elegans SNAP-29 is required for organellar integrity of the endomembrane system and general exocytosis in intestinal epithelial cells. Mol Biol Cell. 22, 2579-87. (2011).
・Sato, T., Mushiake, S., Kato, Y., Sato, K., Sato, M., Takeda, N., Ozono, K., Miki, K., Kubo, Y., Tsuji, A., Harada, R., Harada, A., The Rab8 GTPase regulates apical protein localization in intestinal cells. Nature. 448, 366-9. (2007).
・Sawa, H, Lobel, L, Horvitz, H. R., The Caenorhabditis elegans gene lin-17, which is required for certain asymmetric cell divisions, encodes a putative seven- transmembrane protein similar to the Drosophila frizzled protein. Genes Dev. 10, 2189-97. (1996).
・Sbalzarini, I. F., Koumoutsakos, P., Feature point tracking and trajectory analysis for video imaging in cell biology. J Struct Biol. 151, 2-95. (2005)
・Schultz, M. L., Tecedor, L., Chang, M., Davidson, B. L., Clarifying lysosomal storage diseases. Trends Neurosci. 34, 401–410 (2011).
・Serini, G., Valdembri, D., Zanivan, S., Morterra, G., Burkhardt, C., Caccavari, F., Zammataro, L., Primo, L., Tamagnone, L., Logan, M., Tessier-Lavigne, M., Taniguchi, M., Püschel, A. W., Bussolino, F., Class 3 semaphorins control vascular morphogenesis by inhibiting integrin function. Nature 424, 391–7 (2003).
・Shioi, G., Shoji, M., Nakamura, M., Ishihara, T., Katsura, I., Fujisawa, H., Takagi, S., Mutations Affecting Nerve Attachment of Caenorhabditis elegans. Genetics. 157, 11-22. (2001).
・Shoji, W., Yee, C. S., Kuwada, J. Y., Zebrafish semaphorin Z1a collapses specific growth cones and alters their pathway in vivo. Development. 25, 1275–83 (1998).
・Siebert, M., Sidransky, E., Westbroek, W., Glucocerebrosidase is shaking up the synucleinopathies. Brain. 137. 1304-22. (2014).
・Simonsen. A., Lippé, R., Christoforidis, S, Gaullier, J. M., Brech, A., Callaghan, J., Toh, B. H., Murphy, C., Zerial, M., Stenmark, H., EEA1 links PI(3)K function to Rab5 regulation of endosome fusion. Nature. 394, 4-8. (1998).
・Stimson, D. T., Estes, P. S., Rao, S., Krishnan, K. S., Kelly, L. E., Ramaswami, M. ,Drosophila stoned proteins regulate the rate and fidelity of synaptic vesicle internalization. J. Neurosci. 21, 3034–44 (2001).
・Song, S., Eckerle, S., Onichtchouk, D., Marrs, J. A., Nitschke, R., Driever, W., Pou5f1-dependent EGF expression controls E-cadherin endocytosis, cell adhesion, and zebrafish epiboly movements. Dev Cell. 4. 486-501. (2013).
・Stenmark, H., Parton, R. G., Steele-mortimer, O., Lutcke, A., Inhibition of rab5 GTPase activity stimulates membrane fusion. EMBO J. 13. 1287-96. (1994).
・Stenmark, H., Rab GTPases as coordinators of vesicle traffic. Nat Rev Mol Cell Biol. 8, 513-25. (2009).
・Strome, S., Powers, J., Dunn, M., Reese, K., Malone, C. J., White, J., Seydoux, G., Saxton, W., Spindle dynamics and the role of gamma-tubulin in early Caenorhabditis elegans embryos. Mol Biol Cell. 12, 1751–1764 (2001).
・Südhof, T. C., Synaptotagmins: why so many? J Biol Chem. 10. 7629-32. (2002)
・Swiercz, J. M., Kuner, R., Behrens, J.,Offermanns, S., Plexin-B1 directly interacts with PDZ-RhoGEF/LARG to regulate RhoA and growth cone morphology. Neuron 35, 51–63 (2002).
・Takahashi, T., Strittmatter, S. M., PlexinA1 Autoinhibition by the Plexin Sema Domain. Neuron 29, 429–439 (2001).
・Tamagnone, L., Artigiani, S., Chen, H., He, Z., Ming, G. I., Song, H., Chedotal, A., Winberg, M. L., Goodman, C. S., Poo, M., Tessier-Lavigne, M., Comoglio, P. M., Plexins are a large family of receptors for transmembrane, secreted, and GPI- anchored semaphorins in vertebrates. Cell 99, 71–80 (1999).
・Tamagnone, L., Comoglio, P. M., Signalling by semaphorin receptors: Cell guidance and beyond. Trends Cell Biol. 10, 377–383 (2000).
・Taniguchi, M., Yuasa, S., Fujisawa, H., Naruse, I., Saga, S., Mishina, M., Yagi, T., Disruption of Semaphorin III/D Gene Causes Severe Abnormality in Peripheral Nerve Projection. Neuron. 19, 519–530 (1997).
・Tessier-Lavigne, M., Goodman, ,C. S., The molecular biology of axon guidance. Science. 274, 1123-33. (1996).
・Toda, H., Mochizuki, H., Flores, R. Josowitz, R., Krasieva, T. B., Lamorte, V. J., Suzuki, E., Gindhart, J. G., Furukubo-Tokunaga, K., Tomoda, T., UNC-51/ATG1 kinase regulates axonal transport by mediating motor-cargo assembly. Genes Dev. 22, 3292-307. (2008).
・Togashi, K., von Schimmelmann, M. J., Nishiyama, M., Lim, C. S., Yoshida, N., Yun, B., Molday, R. S., Goshima, Y., Hong, K., Cyclic GMP-Gated CNG Channels Function in Sema3A-Induced Growth Cone Repulsion. Neuron. 58, 694-707. (2008).
・Tojima, T., Akiyama, H., Itofusa, R., Li, Y., Katayama, H., Miyawaki, A., Kamiguchi, H., Attractive axon guidance involves asymmetric membrane transport and exocytosis in the growth cone. Nat Neurosci. 10, 58-66. (2007).
・Tojima, T., Itofusa, R., Kamiguchi, H., Report Asymmetric Clathrin-Mediated Endocytosis Drives Repulsive Growth Cone Guidance. Neuron 66, 370–377 (2010).
・Tojima, T., Hines, J. H., Henley, J. R., Kamiguchi, H., Second messengers and membrane trafficking direct and organize growth cone steering. Nat Rev Neurosci. 12, 191-203. (2011).
・Tojima, T., Itofusa, R., Kamiguchi, H., Steering Neuronal Growth Cones by Shifting the Imbalance between Exocytosis and Endocytosis. J Neurosci. 34, 7165–7178 (2014).
・Tomoda. T,, Kim, J. H., Zhan, C., Hatten, M. E., Role of Unc51.1 and its binding partners in CNS axon outgrowth Role of Unc51.1 and its binding partners in CNS axon outgrowth. Genes Dev. 541–558 (2004).
・Tran, T. S., Rubio, M. E., Clem, R. L., Johnson, D., Case, L., Tessier-Lavigne, M., Huganir, R. L., Ginty, D. D., Kolodkin, A. L., Secreted semaphorins control spine distribution and morphogenesis in the postnatal CNS. Nature 462, 1065–1069 (2009).
・Uesugi, K., Oinuma, I., Katoh, H., Negishi, M., Different requi- rement for Rnd GTPases of R-Ras GAP activity of Plexin-C1 and Plexin-D1. J Biol Chem 284, 6743- 6751. (2009).
・Vitriol, E. A., Zheng, J. Q., Growth cone travel in space and time: the cellular ensemble of cytoskeleton, adhesion, and membrane. Neuron. 73. 1068-81. (2012).
・Walther, K., Krauss, M., Diril, M. K., Lemke, S., Ricotta, D., Honing, S., Kaiser, S., Haucke, V., Human stoned B interacts with AP-2 and synaptotagmin and facilitates clathrin-coated vesicle uncoating. EMBO Rep. 2, 634–640 (2001).
・Wicks, SR., de Vries, C. J., van Luenen, H. G., Plasterk, R. H., CHE-3, a cytosolic dynein heavy chain, is required for sensory cilia structure and function in Caenorhabditis elegans. Dev Biol. 307, 295–307 (2000).
・Winberg, M. L., Noordermeer, J. N., Tamagnone, L., Comoglio, P. M., Spriggs, M. K., Tessier-Lavigne, M., Goodman, C. S., Plexin A is a neuronal semaphorin receptor that controls axon guidance. Cell 95, 903–16 (1998).
・Wong, J. T., Yu, W. T., O'Connor, T. P., Transmembrane grasshopper Semaphorin I promotes axon outgrowth in vivo. Development 124, 3597–607 (1997).
・Wu, K. Y., He, M., Hou, Q. Q., Sheng, A. L., Yuan, L., Liu, F., Liu, W. W., Li, G., Jiang, X. Y., Luo, Z. G., Semaphorin 3A activates the guanosine triphosphatase Rab5 to promote growth cone collapse and organize callosal axon projections. Sci Signal. 7, 340. (2014).
・Yamada, T., Sakisaka, T., Hisata, S., Baba, T., Takai, Y., RA-RhoGAP, Rap-activated Rho GTPaseactivating protein implicated in neurite outgrowth through Rho. The Journal of biological chemistry. 280:33026–33034. (2005).
・Yamane, M., Yamashita, N., Yamamoto, H., Iizuka, A., Shouji, M., Usui, H., Goshima, Y., Biochemical and Biophysical Research Communications Semaphorin3A facilitates axonal transport through a local calcium signaling and tetrodotoxin- sensitive voltage-gated sodium channels. Biochem. Biophys. Res. Commun. 422, 333–338 (2012).
・Yamashita, N., Usui, H., Nakamura, F., Chen, S., Sasaki, Y., Hida, T., Suto, F., Taniguchi, M., Takei, K., Goshima, Y., Plexin-A4-dependent retrograde semaphorin 3A signalling regulates the dendritic localization of GluA2-containing AMPA receptors. Nat Commun. 5, 3424. (2014).
・Yao, J., Kwon, S. E., Gaffaney, J. D., Dunning, F. M. and Chapman, E. R. Uncoupling the roles of synaptotagmin I during endo- and exocytosis of synaptic vesicles. Nat. Neurosci. 15, 243–249 (2011).
・Yu, H. H., Araj, H. H., Ralls, S. A., Kolodkin, A. L., The transmembrane Semaphorin Sema I is required in Drosophila for embryonic motor and CNS axon guidance. Neuron 20, 207–220 (1998).
・Yu, X., Odera, S., Chuang, C. H., Lu, N., Zhou, Z., C. elegans Dynamin Mediates the Signaling of Phagocytic Receptor CED-1 for the Engulfment and Degradation of Apoptotic Cells. Dev Cell. 743–757 (2006).
・Yuan, T., Liu, L., Zhang, Y., Wei, L., Zhao, S., Zheng, X., Huang, X., Boulanger, J., Gueudry, C., Lu, J., Xie, L., Du, W., Zong, W., Yang, L., Salamero, J., Liu, Y., Chen, L.,.Diacylglycerol Guides the Hopping of Clathrin-Coated Pits along Microtubules for Exo-Endocytosis Article Diacylglycerol Guides the Hopping of Clathrin-Coated Pits along Microtubules for Exo-Endocytosis Coupling. Dev. Cell 35, 120–130 (2015).
・Zhang, J. Z., Davletov, B. A., Südhof, T. C., Anderson, R. G., Synaptotagmin I is a high affinity receptor for clathrin AP-2: Implications for membrane recycling. Cell 78, 751–760 (1994).
・Ziel, J. W., Hagedorn, E. J., Audhya, A., Sherwood, D. R., UNC - 6 (netrin) orients the invasive membrane of the anchor cell in C. elegans. Nat Cell Biol. 11, (2009).
・Zylbersztejn, K., Petkovic, M., Burgo, A., Deck, M., Garel, S., Marcos, S., Bloch- Gallego, E., Nothias, F., Serini, G., Bagnard, D., Binz, T., Galli, T., The vesicular SNARE Synaptobrevin is required for Semaphorin 3A axonal repulsion. J Cell Biol. 4, 37–46 (2012).