Synaptosome Proteomics

  • Fengju Bai
  • Frank A. Witzmann
Part of the Subcellular Biochemistry book series (SCBI, volume 43)


Synaptic Vesicle Postsynaptic Density Synaptic Protein Immobilize Metal Affinity Chromatography Peptide Mass Fingerprint 
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  1. Akimoto, Y., Comer, F.I., Cole, R.N., Kudo, A., Kawakami, H., Hirano, H. and Hart, G.W. (2003) Localization of the O-GlcNAc transferase and O-GlcNAc-modified proteins in rat cerebellar cortex. Brain Res. 966, 194–205.PubMedCrossRefGoogle Scholar
  2. Barry, M.F. and Ziff, E.B. (2002) Receptor trafficking and the plasticity of excitatory synapses. Curr. Opin. Neurobiol. 12, 279–286.PubMedCrossRefGoogle Scholar
  3. Beranova-Giorgianni, S., Pabst, M.J., Russell, T.M., Giorgianni, F., Goldowitz, D. and Desiderio, D.M. (2002) Preliminary analysis of the mouse cerebellum proteome. Brain Res. Mol. Brain Res. 98, 135–140.PubMedCrossRefGoogle Scholar
  4. Booth, R.F. and Clark, J.B. (1978) A rapid method for the preparation of relatively pure metabolically competent synaptosomes from rat brain. Biochem. J. 176, 365–370.PubMedGoogle Scholar
  5. Boyd-Kimball, D., Castegna, A., Sultana, R., Poon, H.F., Petroze, R., Lynn, B.C., Klein, J.B. and Butterfield, D.A. (2005) Proteomic identification of proteins oxidized by A[beta] (1–42) in synaptosomes: implications for Alzheimer’s disease. Brain Res. 1044, 206–215.PubMedCrossRefGoogle Scholar
  6. Cheng, D., Hoogenraad, C.C., Rush, J., Ramm, E., Schlager, M.A., Duong, D.M., Xu, P., Wijayawardana, S.R., Hanfelt, J., Nakagawa, T., Sheng, M. and Peng, J. (2006) Relative and absolute quantification of postsynaptic density proteome isolated from rat forebrain and cerebellum. Mol. Cell. Proteomics 5, 1158–1170.PubMedCrossRefGoogle Scholar
  7. Cole, R.N. and Hart, G.W. (2001) Cytosolic O-glycosylation is abundant in nerve terminals. J. Neurochem. 79, 1080–1089.PubMedCrossRefGoogle Scholar
  8. Collins, M.O. and Yu, L. et al. (2005a) Proteomic analysis of in vivo phosphorylated synaptic proteins. J. Biol. Chem. 280, 5972–5982.PubMedCrossRefGoogle Scholar
  9. Collins, M.O. and Yu, L. et al. (2005b) Robust enrichment of phosphorylated species in complex mixtures by sequential protein and peptide metal-affinity chromatography and analysis by tandem mass spectrometry. Sci. STKE 2005, 16.CrossRefGoogle Scholar
  10. Coughenour, H.D., Spaulding, R.S. and Thompson, C.M. (2004) The synaptic vesicle proteome: a comparative study in membrane protein identification. Proteomics 4, 3141–3155.PubMedCrossRefGoogle Scholar
  11. DeGiorgis, J.A., Jaffe, H., Moreira, J.E., Carlotti, C.G., Leite, J.P., Pant, H.C. and Dosemeci, A. (2005) Phosphoproteomic Analysis of Synaptosomes from Human Cerebral Cortex. J. Proteome Res. 4, 306–315.PubMedCrossRefGoogle Scholar
  12. Dosemeci, A., Tao-Cheng, J.H., Vinade, L. and Jaffe, H. (2006) Preparation of postsynaptic density fraction from hippocampal slices and proteomic analysis. Biochem. Biophys. Res. Commun. 339, 687–694.PubMedCrossRefGoogle Scholar
  13. Edgar, P.F., Douglas, J.E., Knight, C., Cooper, G.J., Faull, R.L. and Kydd, R. (1999) Proteome map of the human hippocampus. Hippocampus 9, 644–650.PubMedCrossRefGoogle Scholar
  14. Fountoulakis, M., Schuller, E., Hardmeier, R., Berndt, P. and Lubec, G. (1999) Rat brain proteins: two-dimensional protein database and variations in the expression level. Electrophoresis 20, 3572–3579.PubMedCrossRefGoogle Scholar
  15. Gao, Y., Wells, L., Comer, F.I., Parker, G.J. and Hart, G.W. (2001) Dynamic O-glycosylation of nuclear and cytosolic proteins: cloning and characterization of a neutral, cytosolic beta-N-acetylglucosaminidase from human brain. J. Biol. Chem. 276, 9838–9845.PubMedCrossRefGoogle Scholar
  16. Gauss, C., Kalkum, M., Lowe, M., Lehrach, H. and Klose, J. (1999) Analysis of the mouse proteome. (I) Brain proteins: separation by two-dimensional electrophoresis and identification by mass spectrometry and genetic variation. Electrophoresis 20, 575–600.PubMedCrossRefGoogle Scholar
  17. Grant, S.G. (2003) Systems biology in neuroscience: bridging genes to cognition. Curr. Opin. Neurobiol. 13, 577–582.PubMedCrossRefGoogle Scholar
  18. Grant, S.G. (2006) The synapse proteome and phosphoproteome: a new paradigm for synapse biology. Biochem. Soc. Trans. 34, 59–63.PubMedCrossRefGoogle Scholar
  19. Gray, E.G. (1959) Axo-somatic and axo-dendritic synapses of the cerebral cortex: an electron microscope study. J. Anat. 93, 420–433.PubMedGoogle Scholar
  20. Gray, E.G. and Whittaker, V.P. (1962) The isolation of nerve endings from brain: an electron-microscopic study of cell fragments derived by homogenization and centrifugation. J. Anat. 96, 79–88.PubMedGoogle Scholar
  21. Gygi, S.P., Rist, B., Gerber, S.A., Turecek, F., Gelb, M.H. and Aebersold, R. (1999) Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat. Biotechnol. 17, 994–999.PubMedCrossRefGoogle Scholar
  22. Han, W., Rhee, J.S., Maximov, A., Lao, Y., Mashimo, T., Rosenmund, C. and Sudhof, T.C. (2004) N-glycosylation is essential for vesicular targeting of synaptotagmin 1. Neuron 41, 85–99.PubMedCrossRefGoogle Scholar
  23. Hansen, K.C., Schmitt-Ulms, G., Chalkley, R.J., Hirsch, J., Baldwin, M.A. and Burlingame, A.L. (2003) Mass spectrometric analysis of protein mixtures at low levels using cleavable 13C-isotope-coded affinity tag and multidimensional chromatography. Mol. Cell Proteomics 2, 299–314.PubMedGoogle Scholar
  24. Hansson, E. and Ronnback, L. (2003) Glial neuronal signaling in the central nervous system. FASEB J. 17, 341–348.PubMedCrossRefGoogle Scholar
  25. Husi, H., Ward, M.A., Choudhary, J.S., Blackstock, W.P. and Grant, S.G. (2000) Proteomic analysis of NMDA receptor-adhesion protein signaling complexes. Nat. Neurosci. 3, 661–669.PubMedCrossRefGoogle Scholar
  26. Ideker, T., Galitski, T. and Hood, L. (2001) A new approach to decoding life: systems biology. Annu. Rev. Genomics Hum. Genet. 2, 343–372.PubMedCrossRefGoogle Scholar
  27. Iyer, S.P. and Hart, G.W. (2003) Dynamic nuclear and cytoplasmic glycosylation: enzymes of O-GlcNAc cycling. Biochemistry 42, 2493–2499.PubMedCrossRefGoogle Scholar
  28. Jiang, C. and Schuman, E.M. (2002) Regulation and function of local protein synthesis in neuronal dendrites. Trends in Biochem. Sci. 27, 506–513.CrossRefGoogle Scholar
  29. Johnson, S.A. and Hunter, T. (2005) Kinomics: methods for deciphering the kinome. Nat. Methods 2, 17–25.PubMedCrossRefGoogle Scholar
  30. Jordan, B. and Ziff, E. (2006) Getting to synaptic complexes through systems biology. Genome Biol. 7, 214.PubMedCrossRefGoogle Scholar
  31. Jordan, B.A., Fernholz, B.D., Boussac, M., Xu, C., Grigorean, G., Ziff, E.B. and Neubert, T.A. (2004) Identification and Verification of Novel Rodent Postsynaptic Density Proteins. Mol. Cell Proteomics 3, 857–871.PubMedCrossRefGoogle Scholar
  32. Jordan, B.A., Fernholz, B.D., Neubert, T.A. and Ziff, E.B. (2006) New tricks for an old dog: proteomics of the PSD. In: The Dynamic Synapse: Molecular Methods in Ionotropic Receptor Biology. J.T. Kittler and S.J. Moss, eds. (Boca Raton: CRC/Taylor & Francis) pp. 37–55.Google Scholar
  33. Kennedy, M.B. (1993) The postsynaptic density. Curr. Opin. Neurobiol. 3, 732–737.PubMedCrossRefGoogle Scholar
  34. Khidekel, N., Ficarro, S.B., Peters, E.C. and Hsieh-Wilson, L.C. (2004) Exploring the O-GlcNAc proteome: direct identification of O-GlcNAc-modified proteins from the brain. Proc. Natl Acad. Sci. U.S.A. 101, 13132–13137.PubMedCrossRefGoogle Scholar
  35. Kim, S.I., Voshol, H., van Oostrum, J., Hastings, T.G., Cascio, M. and Glucksman, M.J. (2004) Neuroproteomics: expression profiling of the brain’s proteomes in health and disease. Neurochem. Res. 29, 1317–1331.PubMedCrossRefGoogle Scholar
  36. Korolchuk, V. and Banting, G. (2003) Kinases in clathrin-mediated endocytosis. Biochem. Soc. Trans. 31, 857–860.PubMedCrossRefGoogle Scholar
  37. Kramer, M.L. (2006) A new multiphasic buffer system for benzyldimethyl-n-hexadecylammonium chloride polyacrylamide gel electrophoresis of proteins providing efficient stacking. Electrophoresis 27, 347–356.PubMedCrossRefGoogle Scholar
  38. Krapfenbauer, K., Fountoulakis, M. and Lubec, G. (2003) A rat brain protein expression map including cytosolic and enriched mitochondrial and microsomal fractions. Electrophoresis 24, 1847–1870.PubMedCrossRefGoogle Scholar
  39. Langen, H., Berndt, P., Roder, D., Cairns, N., Lubec, G. and Fountoulakis, M. (1999) Two-dimensional map of human brain proteins. Electrophoresis 20, 907–916.PubMedCrossRefGoogle Scholar
  40. Leng, A., Feldon, J. and Ferger, B. (2004) Long-term social isolation and medial prefrontal cortex: dopaminergic and cholinergic neurotransmission. Pharmacol. Biochem. Behav. 77, 371–379.PubMedCrossRefGoogle Scholar
  41. Leski, M.L. and Steward, O. (1996) Protein synthesis within dendrites: ionic and neurotransmitter modulation of synthesis of particular polypeptides characterized by gel electrophoresis. Neurochem. Res. 21, 681–690.PubMedCrossRefGoogle Scholar
  42. Li, K.W., Hornshaw, M.P., Van Der Schors, R.C., Watson, R., Tate, S., Casetta, B., Jimenez, C.R., Gouwenberg, Y., Gundelfinger, E.D., Smalla, K.H. and Smit, A.B. (2004) Proteomics analysis of rat brain postsynaptic density. Implications of the diverse protein functional groups for the integration of synaptic physiology. J. Biol. Chem. 279, 987–1002.PubMedCrossRefGoogle Scholar
  43. Lisman, J., Schulman, H. and Cline, H. (2002) The molecular basis of CaMKII function in synaptic and behavioural memory. Nat. Rev. Neurosci. 3, 175–190.PubMedCrossRefGoogle Scholar
  44. Morciano, M., Burre, J., Corvey, C., Karas, M., Zimmermann, H. and Volknandt, W. (2005) Immunoisolation of two synaptic vesicle pools from synaptosomes: a proteomics analysis. J. Neurochem. 95, 1732–1745.PubMedCrossRefGoogle Scholar
  45. Mouledous, L., Hunt, S., Harcourt, R., Harry, J.L., Williams, K.L. and Gutstein, H.B. (2003) Proteomic analysis of immunostained, laser-capture microdissected brain samples. Electrophoresis 24, 296–302.PubMedCrossRefGoogle Scholar
  46. Nagy, A. and Delgado-Escueta, A.V. (1984) Rapid preparation of synaptosomes from mammalian brain using nontoxic isoosmotic gradient material (Percoll). J. Neurochem. 43, 1114–1123.PubMedCrossRefGoogle Scholar
  47. Nazarian, J., Bouri, K. and Hoffman, E.P. (2005) Intracellular expression profiling by laser capture micro dissection: three novel components of the neuromuscular junction. Physiol. Genomics 21, 70–80.PubMedCrossRefGoogle Scholar
  48. Palay, S.L. (1958) The morphology of synapses in the central nervous system. Exp. Cell Res. 14, 275–293.PubMedGoogle Scholar
  49. Peng, J., Kim, M.J., Cheng, D., Duong, D.M., Gygi, S.P. and Sheng, M. (2004) Semiquantitative proteomic analysis of rat forebrain postsynaptic density fractions by mass spectrometry. J. Biol. Chem. 279, 21003–21011.PubMedCrossRefGoogle Scholar
  50. Phillips, G.R., Florens, L., Tanaka, H., Khaing, Z.Z., Fidler, L., Yates, Jr. 3rd and Colman, D.R. (2005) Proteomic comparison of two fractions derived from the transsynaptic scaffold. J. Neurosci. Res. 81, 762–775.PubMedCrossRefGoogle Scholar
  51. Phizicky, E.M. and Fields, S. (1995) Protein-protein interactions: methods for detection and analysis. Microbiol. Rev. 59, 94–123.PubMedGoogle Scholar
  52. Pocklington, A.J., Armstrong, J.D. and Grant, S.G. (2006) Organization of brain complexity—synapse proteome form and function. Brief. Funct. Genomic. Proteomic. 5, 66–73.PubMedCrossRefGoogle Scholar
  53. Prokai, L., Zharikova, A.D. and Stevens, S.M. Jr. (2005) Effect of chronic morphine exposure on the synaptic plasma-membrane subproteome of rats: a quantitative protein profiling study based on isotope-coded affinity tags and liquid chromatography/mass spectrometry. J. Mass Spectrom. 40, 169–175.PubMedCrossRefGoogle Scholar
  54. Purcell, A.L. and Carew, T.J. (2003) Tyrosine kinases, synaptic plasticity and memory: insights from vertebrates and invertebrates. Trends Neurosci. 26, 625–630.PubMedCrossRefGoogle Scholar
  55. Purves, D. (2004) Neuroscience. Sunderland, Massachusetts: Sinauer Associates.Google Scholar
  56. Raggiaschi, R., Lorenzetto, C., Diodato, E., Caricasole, A., Gotta, S. and Terstappen, G.C. (2006) Detection of phosphorylation patterns in rat cortical neurons by combining phosphatase treatment and DIGE technology. Proteomics 6, 748–756.PubMedCrossRefGoogle Scholar
  57. Rao, A. and Steward, O. (1993) Evaluation of RNAs present in synaptodendrosomes: dendritic, glial, and neuronal cell body contribution. J. Neurochem. 61, 835–844.PubMedCrossRefGoogle Scholar
  58. Routtenberg, A. and Rekart, J.L. (2005) Post-translational protein modification as the substrate for long-lasting memory. Trends Neurosci. 28, 12–19.PubMedCrossRefGoogle Scholar
  59. Satoh, K., Takeuchi, M., Oda, Y., Deguchi-Tawarada, M., Sakamoto, Y., Matsubara, K., Nagasu, T. and Takai, Y. (2002) Identification of activity-regulated proteins in the postsynaptic density fraction. Genes Cells 7, 187–197.PubMedCrossRefGoogle Scholar
  60. Schrimpf, S., Meskenaite, V., Brunner, E., Rutishauser, D., Walther, P., Eng, J., Aebersold, R. and Sonderegger, P. (2005) Proteomic analysis of synaptosomes using isotope-coded affinity tags and mass spectrometry. Proteomics 5, 2531–2541.PubMedCrossRefGoogle Scholar
  61. Slawson, C., Housley, M.P. and Hart, G.W. (2006) O-GlcNAc cycling: how a single sugar post-translational modification is changing the way we think about signaling networks. J. Cell Biochem. 97, 71–83.PubMedCrossRefGoogle Scholar
  62. Stevens, S.M. Jr., Zharikova, A.D. and Prokai, L. (2003) Proteomic analysis of the synaptic plasma membrane fraction isolated from rat forebrain. Brain Res. Mol. Brain Res. 117, 116–128.PubMedCrossRefGoogle Scholar
  63. Steward, O. and Schuman, E.M. (2003) Compartmentalized synthesis and degradation of proteins in neurons. Neuron 40, 347–359.PubMedCrossRefGoogle Scholar
  64. Trinidad, J.C., Specht, C.G., Thalhammer, A., Schoepfer, R. and Burlingame, A.L. (2006) Comprehensive Identification of Phosphorylation Sites in Postsynaptic Density Preparations. Mol. Cell Proteomics 5, 914–922.PubMedCrossRefGoogle Scholar
  65. Unlu, M., Morgan, M.E. and Minden, J.S. (1997) Difference gel electrophoresis: a single gel method for detecting changes in protein extracts. Electrophoresis 18, 2071–2077.PubMedCrossRefGoogle Scholar
  66. van Montfort, B.A., Canas, B., Duurkens, R., Godovac-Zimmermann, J. and Robillard, G.T. (2002) Improved in-gel approaches to generate peptide maps of integral membrane proteins with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. J. Mass Spectrom. 37, 322–330.PubMedCrossRefGoogle Scholar
  67. Villanueva, S. and Steward, O. (2001) Protein synthesis at the synapse: developmental changes, subcellular localization and regional distribution of polypeptides synthesized in isolated dendritic fragments. Brain Res. Mol. Brain Res. 91, 148–153.PubMedCrossRefGoogle Scholar
  68. Vosseller, K., Trinidad, J.C., Chalkley, R.J., Specht, C.G., Thalhammer, A., Lynn, A.J., Snedecor, J.O., Guan, S., Medzihradszky, K.F., Maltby, D.A., Schoepfer, R. and Burlingame, A.L. (2006) O-Linked N-Acetylglucosamine proteomics of postsynaptic density preparations using lectin weak affinity chromatography and mass spectrometry. Mol. Cell Proteomics 5, 923–934.PubMedCrossRefGoogle Scholar
  69. Walikonis, R.S., Jensen, O.N., Mann, M., Provance, D.W. Jr., Mercer, J.A. and Kennedy, M.B. (2000) Identification of proteins in the postsynaptic density fraction by mass spectrometry. J. Neurosci. 20, 4069–4080.PubMedGoogle Scholar
  70. Waltereit, R. and Weller, M. (2003) Signaling from cAMP/PKA to MAPK and synaptic plasticity. Mol. Neurobiol. 27, 99–106.PubMedCrossRefGoogle Scholar
  71. Whittaker, V.P. and Michaelson, I.A. et al. (1964) The separation of synaptic vesicles from nerve-ending particles (“synaptosomes”). Biochem. J. 90, 293–303.PubMedGoogle Scholar
  72. Williams, R.W. and Herrup, K. (1988) The control of neuron number. Annu. Rev. Neurosci. 11, 423–453.PubMedCrossRefGoogle Scholar
  73. Witzmann, F.A., Arnold, R.J., Bai, F., Hrncirova, P., Kimpel, M.W., Mechref, Y.S., McBride, W.J., Novotny, M.V., Pedrick, N.M., Ringham, H.N. and Simon, J.R. (2005) A proteomic survey of rat cerebral cortical synaptosomes. Proteomics 5, 2177–2201.PubMedCrossRefGoogle Scholar
  74. Witzmann, F.A., Li, J., Strother, W.N., McBride, W.J., Hunter, L., Crabb, D.W., Lumeng, L. and Li, T.K. (2003) Innate differences in protein expression in the nucleus accumbens and hippocampus of inbred alcohol-preferring and -nonpreferring rats. Proteomics 3, 1335–1344.PubMedCrossRefGoogle Scholar
  75. Wu, W.W., Wang, G., Baek, S.J. and Shen, R.F. (2006) Comparative study of three proteomic quantitative methods, DIGE, cICAT, and iTRAQ, using 2D gel- or LC-MALDI TOF/TOF. J. Proteome Res. 5, 651–658.PubMedCrossRefGoogle Scholar
  76. Yoshimura, Y., Yamauchi, Y., Shinkawa, T., Taoka, M., Donai, H., Takahashi, N., Isobe, T. and Yamauchi, T. (2004) Molecular constituents of the postsynaptic density fraction revealed by proteomic analysis using multidimensional liquid chromatography-tandem mass spectrometry. J. Neurochem. 88, 759–768.PubMedCrossRefGoogle Scholar
  77. Zoidl, G. and Dermietzel, R. (2002) On the search for the electrical synapse: a glimpse at the future. Cell Tissue Res. 310, 137–142.PubMedCrossRefGoogle Scholar

Copyright information

© Springer 2007

Authors and Affiliations

  • Fengju Bai
    • 1
  • Frank A. Witzmann
    • 2
  1. 1.Safety Sciences, Charles River Laboratories Preclinical ServicesUSA
  2. 2.Indiana University School of Medicine Biotechnology Research & Training CenterUSA

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