Differential centrifugation-based biochemical fractionation of the Drosophila adult CNS

Nature Protocols

Volumn 9, Issue 12, 2014, Pages 2796-2808

  Depner, Harald ^a   Lützkendorf, Janine ^a   Babkir, Husam A ^a   Sigrist, Stephan J ^a,b   Holt, Matthew G ^c  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^c UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

BRUCHPILOT; CYSTEINE STRING PROTEIN; LIPRIN ALPHA; MEMBRANE PROTEIN; PROTEIN SYD 1; RIM BINDING PROTEIN; SYNAPTOTAGMIN I; UNCLASSIFIED DRUG; DROSOPHILA PROTEIN;

ADULT; ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CELL FRACTIONATION; CENTRAL NERVOUS SYSTEM; CENTRIFUGATION; CONTROLLED STUDY; DROSOPHILA; NONHUMAN; POSTSYNAPTIC POTENTIAL; PRESYNAPTIC POTENTIAL; PROTEIN ANALYSIS; REPRODUCIBILITY; SYNAPTOSOME; ANIMAL; CHEMISTRY; FRACTIONATION; HEAD; ISOLATION AND PURIFICATION; PROCEDURES; SYNAPSE; SYNAPTIC TRANSMISSION; WORKFLOW;

ANIMALS; CENTRAL NERVOUS SYSTEM; CENTRIFUGATION; CHEMICAL FRACTIONATION; DROSOPHILA; DROSOPHILA PROTEINS; HEAD; REPRODUCIBILITY OF RESULTS; SYNAPSES; SYNAPTIC TRANSMISSION; SYNAPTOSOMES; WORKFLOW;

EID: 84911489137     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2014.192     Document Type: Article

References (75)

1. Lüscher, C. & Isaac, J.T. The synapse: center stage for many brain diseases. J. Physiol. 587, 727-729 (2009).
2. Brenner, S. The genetics of Caenorhabditis elegans. Genetics 77, 71-94 (1974).
3. Suzuki, D.T., Grigliatti, T. & Williamson, R. Temperature-sensitive mutations in Drosophila melanogaster. VII. A mutation (parats) causing reversible adult paralysis. Proc. Natl.Acad. Sci. USA 68, 890-893 (1971).
4. Bellen, H.J., Tong, C. & Tsuda, H. 100 years of Drosophila research and its impact on vertebrate neuroscience: a history lesson for the future. Nat. Rev. Neurosci. 11, 514-522 (2010).
5. Richmond, J.E. & Broadie, K.S. The synaptic vesicle cycle: exocytosis and endocytosis in Drosophila and C. elegans. Curr. Opin. Neurobiol. 12, 499-507 (2002).
6. Chia, P.H., Li, P. & Shen, K. Cell biology in neuroscience: cellular and molecular mechanisms underlying presynapse formation. J. Cell Biol. 203, 11-22 (2013).
7. Schoch, S. et al. Redundant functions of RIM1? and RIM2? in Ca2+-triggered neurotransmitter release. EMBO J. 25, 5852-5863 (2006).
8. Südhof, T.C. The presynaptic active zone. Neuron 75, 11-25 (2012).
9. Bronk, P. et al. Drosophila Hsc70-4 is critical for neurotransmitter exocytosis in vivo. Neuron 30, 475-488 (2001).
10. Hiesinger, P.R. et al. The v-ATPase V0 subunit a1 is required for a late step in synaptic vesicle exocytosis in Drosophila. Cell 121, 607-620 (2005).
11. Lu, H., Leung, H.T., Wang, N., Pak, W.L. & Shieh, B.H. Role of Ca2+/calmodulin-dependent protein kinase II in Drosophila photoreceptors. J. Biol. Chem. 284, 11100-11109 (2009).
12. Bachmann, A. et al. A perisynaptic ménage a trois between Dlg, DLin-7, and Metro controls proper organization of Drosophila synaptic junctions. J. Neurosci. 30, 5811-5824 (2010).
13. Owald, D. et al. A Syd-1 homologue regulates pre-And postsynaptic maturation in Drosophila. J. Cell Biol. 188, 565-579 (2010).
14. Nuwal, T., Heo, S., Lubec, G. & Buchner, E. Mass spectrometric analysis of synapsins in Drosophila melanogaster and identification of novel phosphorylation sites. J. Proteome Res. 10, 541-550 (2011).
15. Popescu, D.C., Ham, A.J. & Shieh, B.H. Scaffolding protein INAD regulates deactivation of vision by promoting phosphor ylation of transient receptor potential by eye protein kinase C in Drosophila. J. Neurosci. 26, 8570-8577 (2006).
16. Wagh, D.A. et al. Bruchpilot, a protein with homology to ELKS/CAST, is required for s tructural integrity and function of synaptic active zones in Drosophila. Neuron 49, 833-844 (2006).
17. Kittel, R.J. et al. Bruchpilot promotes active zone assembly, Ca2+ channel clustering, and vesicle release. Science 312, 1051-1054 (2006).
18. Fouquet, W. et al. Maturation of active zone assembly by Drosophila Bruchpilot. J. Cell Biol. 186, 129-145 (2009).
19. Bodzon-Kulakowska A.,et al Methods for samples preparation in proteomic research. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 849 1-31, 2007).
20. Huttner, W.B., Schiebler, W., Greengar d, P. & De Camilli, P. Synapsin I (protein I), a nerve terminal-specific phosphoprotein. III. Its association with synaptic vesicles studied in a highly purified synaptic vesicle preparation. J. Cell Biol. 96, 1374-1388 (1983) .
21. Ahmed, S., Holt, M., Riedel, D. & Jahn, R. Small-scale isolation of synaptic vesicles from mammalian brain. Nat. Protoc. 8, 998-1009 (2013).
22. Takamori, S. et al. Molecular anatomy of a trafficking organelle. Cell 127, 831-846 (2006).
23. Nagy, A., Baker, R.R., Morris, S.J. & Whittaker, V.P. The preparation and characterization of synaptic vesicles of high purity. Brain Res. 109, 285-309 (1976).
24. van de Goor, J., Ramaswami, M. & Kelly, R. Redistribution of synaptic vesicles and their proteins in temperat ure-sensitive shibirets1 mutant Drosophila. Proc. Natl. Acad. Sci. USA 92, 5739-5743 (1995).
25. Kelly, L.E. The regulation of phosphorylation of a specific protein in synaptosomal fractions from Drosophila heads : The effects of light and two visual mutants. Cell Mol. Neurobiol. 3, 127-141 (1983).
26. Higashi-Kovtun, M.E., Mosca, T.J., Dickman, D.K., Meinertzhagen, I.A. & Schwarz, T.L. Importin-?11 re gulates synaptic phosphorylated mothers against decapentaplegic, and thereby influences synaptic development and function at the Drosophila neuromuscular junction. J. Neurosci. 30, 5253-5268 (2010).
27. Ow ald, D. et al. Cooperation of Syd-1 with Neurexin synchronizes pre-with postsynaptic assembly. Nat. Neurosci. 15, 1219-1226 (2012).
28. Whittaker, V.P., Michaelson, I.A. & Kirkland, R.J. The separation of synaptic vesicles from nerve-ending particles (?synaptosomes?). Biochem. J. 90, 293-303 (1964).
29. Berninghausen, O. et al. Neurexin I? and neuroligin are localized on opposite membranes in mature central synapses. J. Neurochem. 103, 1855-1863 (2007).
30. Gama Sosa, M.A., De Gasperi, R. & Elder, G.A. Modeling human neurodegenerative diseases in transgenic systems. Hum. Genet. 131, 535-563 (2012).
31. Okray, Z. & Hassan, B.A. Genetic approaches in Drosophila for the study neurodevelopmental disorders. Neuropharmacology 68, 150-156 (2013).
32. Karpinar, D.P. et al. Pre-fibrillar ?-synuclein variants with impaired ?-structure increase neurotoxicity in Parkinson?s disease models. EMBO J. 28, 3256-3268 (2009).
33. Burré, J., Sharma, M. & Südhof, T.C. Systematic mutagenesis of ?-synuclein reveals distinct sequence requirements for physiological and pathological activities. J. Neurosci. 32, 15227-15242 (2012).
34. Neumüller, R.A. et al. Stringent analysis of gene function and protein-protein interactions using fluorescently tagged genes. Genetics 190, 931-940 (2012).
35. Nadal, M.S. et al. The CD26-related dipeptidyl aminopeptidase-like protein DPPX is a critical component of neuronal A-type K+ channels. Neuron 37, 449-461 (2003).
36. Jerng, H.H., Kunjilwar, K. & Pfaffinger, P.J. Multiprotein assembly of Kv4.2, KChIP3 and DPP10 produces ternary channel complexes with ISA-like properties. J. Physiol. 568, 767-788 (2005).
37. Boyken, J. et al. M olecular profiling of synaptic vesicle docking sites reveals novel proteins but few differences between glutamatergic and GABAergic synapses. Neuron 78, 285-297 (2013).
38. Dietzl, G. et al. A gen ome-wide transgenic RNAi library for conditional gene inactivation in Drosophila. Nature 448, 151-156 (2007).
39. Ni, J.Q. et al. A Drosophila resource of transgenic RNAi lines for neurogenetics. Genetics 182, 1089-1100 (2009).
40. Bellen, H.J. et al. The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes. Genetics 167, 761-781 (2004).
41. Rong, Y.S. et al. Targeted mutagenesis by homologous recombination in D. melanogaster. Genes Dev. 16, 1568-1581 (2002).
42. Venken, K.J. & Bellen, H.J. Emerging technologies for gene manipulation in Drosophila melanogaster. Nat. Rev. Genet. 6, 167-178 (2005).
43. Beumer, K., Bhattacharyya, G., Bibikova, M., Trautman, J.K. & Carroll, D. Efficient gene t argeting in Drosophila with zinc-finger nucleases. Genetics 172, 2391-2403 (2006).
44. Carroll, D. Genome engineering with zinc-finger nucleases. Genetics 188, 773-782 (2011).
45. Liu, J., Chen, Y. & Jiao, R. TALEN-mediated Drosophila genome editing: protocols and applications. Methods 69, 22-31 (2014).
46. Li, T. et al. Modularly as sembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes. Nucleic Acids Res. 39, 6315-6325 (2011).
47. Bassett, A.R. & Liu, J.L. CRISPR/Cas9 and genome editing in Drosophila. J. Genet. Genomics 41, 7-19 (2014).
48. Brand, A.H. & Perrimon, N. Targeted gene expression as a means of altering cell fates and generating dominant phenotypes. Development 118, 401-415 (1993).
49. Frank, C.A. et al. New approaches for studying synaptic development, function, and plasticity using Drosophila as a model system. J. Neurosci. 33, 17560-17568 (2013).
50. Dunkley, P.R., Jarvie, P.E. & Robinson, P.J. A rapid Percoll gradient procedure for preparation of synaptosomes. Nat. Protoc. 3, 1718-1728 (2008).
51. Peterson, G.L. A simplification of the protein assay method of Lowry et al. which is more generally applicable. Anal. Biochem. 83, 346-356 (1977).
52. Folin, O. & Ciocalteu, V. On tyrosine and tryptophane determinations in proteins. J. Biol. Chem. 73, 627-650 (1927).
53. Lowry, O.H., Rosebrough, N.J., Farr, A.L. & Randall, R.J. Protein measurement with the Folin phenol reagent. J. Biol. Chem. 193, 265-275 (1951).
54. Nichols, R.A., Wu, W.C., Haycock, J.W. & Greengard, P. Introduction of impermeant molecules into synaptosomes using freeze/thaw permeabilization. J. Neurochem. 52, 521-529 (1989).
55. Begley, J.G. et al. Cryopreservation of rat cortical synaptosomes and analysis of glucose and glutamate transporter activities, and mitochondrial function. Brain Res. Br ain Res. Protoc. 3, 76-82 (1998).
56. Daniel, J.A., Malladi, C.S., Kettle, E., McCluskey, A. & Robinson, P.J. Analysis of synaptic vesicle endocytosis in synaptosomes by high-content screening. Nat. Protoc. 7, 1439-1455 (2012).
57. VanBogelen, R.A. & Olson, E.R. Application of two-dimensional protein gels in biotechnology. Biotechnol. Annu Rev. 1, 69-103 (1995).
58. Matkovic, T. et al. The Bruchpilot cytomatrix determines the size of the readily releasable pool of synaptic vesicles. J. Cell Biol. 202, 667-683 (2013).
59. Kaufmann, N., D eProto, J., Ranjan, R., Wan, H. & Van Vactor, D. Drosophila Liprin-? and the receptor phosphatase Dlar control synapse morphogenesis. Neuron 34, 27-38 (2002).
60. Liu, K.S. et al. RI M-binding protein, a central part of the active zone, is essential for neurotransmitter release. Science 334, 1565-1569 (2011).
61. Littleton, J.T., Bellen, H.J. & Perin, M.S. Expression o f synaptotagmin in Drosophila reveals transport and localization of synaptic vesicles to the synapse. Development 118, 1077-1088 (1993).
62. Mackler J.M.,Drummond J.A.,Loewen C.A.,Robinson I.M.,Reist, N.E The C2B Ca2+-binding motif of synaptotagmin is required for synaptic transmission in vivo Nature 418, 340-344, 2002).
63. Zinsmaier, K.E., Eberle, K.K., Buchner, E., Walter, N. & Benzer, S. Paralysis and early death in cysteine string protein mutants of Drosophila. Science 263, 977-980 (1994).
64. Rubin, D.M. et al. Genomic structure and sequence analysis of Drosophila melanogaster HSC70 genes. Gene 128, 155-163 (1993).
65. Kirkpatrick, R.B. et al. Heavy chain dimers as well as complete antibodies are efficiently formed and secreted from Drosophila v ia a BiP-mediated pathway. J. Biol. Chem. 270, 19800-19805 (1995).
66. Khanna, M.R., Stanley, B.A. & Thomas, G.H. Towards a membrane proteome in Drosophila: a method for the isolation of plasma membrane. BMC Genomics 11, 302 (2010).
67. Sun, B. & Salvaterra, P.M. Characterization of Nervana, a Drosophila melanogaster neuron-specific glycoprotein antigen recognized by anti-horseradish peroxidase antibodies. J. Neurochem. 65, 434-443 (1995).
68. Jacobs, H., Stratmann, R. & Lehner, C. A screen for lethal mutations in the chromosomal region 59AB suggests that bellwether encodes the ? subuni t of the mitochondrial ATP synthase in Drosophila melanogaster. Mol. Gen. Genet. 259, 383-387 (1998).
69. Ziviani, E., Tao, R.N. & Whitworth, A.J. Drosophila Parkin requires PINK1 for mitochondrial translocation and ubiquitinates Mitofusin. Proc. Natl. Acad. Sci. USA 107, 5018-5023 (2010).
70. Celotto, A.M., Chiu, W.K., Van Voorhies, W. & Palladino, M.J. Modes of metabolic compensation during mitochondrial disease using the Drosophila model of ATP6 dysfunction. PLoS ONE 6, e25823 (2011).
71. Kabani, M. & Martineau, C.N. Multiple Hsp70 isoforms in the eukaryotic cytosol: mere redundancy or functional specificity? Curr. Genomics 9, 338-348 (2008).
72. Marchler, G. & Wu, C. Modulation of Drosophila heat shock transcription factor activity by the molecular chaperone DROJ1. EMBO J. 20, 499-509 (2001).
73. Georgatos, S.D., Meier, J. & Simos, G. Lamins and lamin-Associated proteins. Curr. Opin. Cell Biol. 6, 347-353 (1994).
74. Riemer, D. et al. Expression of Drosophila lamin C is developmentally regulated: analogies with vertebrate A-type lamins. J. Cell Sci. 108 (Part 10): 3189-3198 (1995).
75. Sisson, J.C., Field, C., Ventura, R ., Royou, A. & Sullivan, W. Lava lamp, a novel peripheral Golgi protein, is required for Drosophila melanogaster cellularization. J. Cell Biol. 151, 905-918 (2000).