Fractionation profiling: A fast and versatile approach for mapping vesicle proteomes and protein-protein interactions

Molecular Biology of the Cell

Volumn 25, Issue 20, 2014, Pages 3178-3194

  Borner, Georg H H ^a   Hein, Marco Y ^a   Hirst, Jennifer ^b   Edgar, James R ^b   Mann, Matthias ^a   Robinson, Margaret S ^b  

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CLATHRIN COATED VESICLE PROTEIN; PROTEIN; PROTEOME; UNCLASSIFIED DRUG; MEMBRANE PROTEIN; VESICULAR TRANSPORT ADAPTOR PROTEIN;

ANIMAL CELL; ARTICLE; CELL COMPOSITION; CELL FRACTIONATION; CLUSTER ANALYSIS; COATED VESICLE; COMPLEX FORMATION; DROSOPHILA; FRACTIONATION; HELA CELL LINE; HUMAN; HUMAN CELL; MEASUREMENT ACCURACY; MEMBRANE VESICLE; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN TRANSPORT; PROTEOMICS; QUANTITATIVE ASSAY; STOICHIOMETRY; VALIDATION STUDY; ANIMAL; CHEMISTRY; CLATHRIN-COATED VESICLE; METABOLISM; PROCEDURES; PROTEIN ANALYSIS;

ADAPTOR PROTEINS, VESICULAR TRANSPORT; ANIMALS; CELL FRACTIONATION; CLATHRIN-COATED VESICLES; DROSOPHILA; HELA CELLS; HUMANS; MEMBRANE PROTEINS; PROTEIN INTERACTION MAPPING; PROTEOME;

EID: 84908147624     PISSN: 10591524     EISSN: 19394586     Source Type: Journal    
DOI: 10.1091/mbc.E14-07-1198     Document Type: Article

References (47)

1. Allen CL, Goulding D, Field MC (2003). Clathrin-mediated endocytosis is essential in Trypanosoma brucei. EMBO J 22, 4991-5002.
2. Antrobus R, Borner GH (2011). Improved elution conditions for native co-immunoprecipitation. PLoS One 6, e18218.
3. Bassik MC, Kampmann M, Lebbink RJ, Wang S, Hein MY, Poser I, Weibezahn J, Horlbeck MA, Chen S, Mann M, et al. (2013). A systematic mammalian genetic interaction map reveals pathways underlying ricin susceptibility. Cell 152, 909-922.
4. Blondeau F, Ritter B, Allaire PD, Wasiak S, Girard M, Hussain NK, Angers A, Legendre-Guillemin V, Roy L, Boismenu D, et al. (2004). Tandem MS analysis of brain clathrin-coated vesicles reveals their critical involvement in synaptic vesicle recycling. Proc Natl Acad Sci USA 101, 3833-3838.
5. Bonaldi T, Straub T, Cox J, Kumar C, Becker PB, Mann M (2008). Combined use of RNAi and quantitative proteomics to study gene function in Drosophila. Mol Cell 31, 762-772.
6. Bonnemaison ML, Eipper BA, Mains RE (2013). Role of adaptor proteins in secretory granule biogenesis and maturation. Front Endocrinol 4, 101.
7. Borner GH, Antrobus R, Hirst J, Bhumbra GS, Kozik P, Jackson LP, Sahlender DA, Robinson MS (2012). Multivariate proteomic profiling identifies novel accessory proteins of coated vesicles. J Cell Biol 197, 141-160.
8. Borner GH, Harbour M, Hester S, Lilley KS, Robinson MS (2006). Comparative proteomics of clathrin-coated vesicles. J Cell Biol 175, 571-578.
9. Borner GH, Rana AA, Forster R, Harbour M, Smith JC, Robinson MS (2007). CVAK104 is a novel regulator of clathrin-mediated SNARE sorting. Traffic 8, 893-903.
10. Cox J, Mann M (2008). MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat Biotechnol 26, 1367-1372.
11. Cox J, Neuhauser N, Michalski A, Scheltema RA, Olsen JV, Mann M (2011). Andromeda: a peptide search engine integrated into the MaxQuant environment. J Proteome Res 10, 1794-1805.
12. Dunkley TP, Watson R, Griffin JL, Dupree P, Lilley KS (2004). Localization of organelle proteins by isotope tagging (LOPIT). Mol Cell Proteomics 3, 1128-1134.
13. Ewing RM, Chu P, Elisma F, Li H, Taylor P, Climie S, McBroom-Cerajewski L, Robinson MD, O'Connor L, Li M, et al. (2007). Large-scale mapping of human protein-protein interactions by mass spectrometry. Mol Syst Biol 3, 89.
14. Eyster CA, Higginson JD, Huebner R, Porat-Shliom N, Weigert R, Wu WW, Shen RF, Donaldson JG (2009). Discovery of new cargo proteins that enter cells through clathrin-independent endocytosis. Traffic 10, 590-599.
15. Faini M, Beck R, Wieland FT, Briggs JA (2013). Vesicle coats: structure, function, and general principles of assembly. Trends Cell Biol 23, 279-288.
16. Foster LJ, de Hoog CL, Zhang Y, Zhang Y, Xie X, Mootha VK, Mann M (2006). A mammalian organelle map by protein correlation profiling. Cell 125, 187-199.
17. Girard M, Allaire PD, McPherson PS, Blondeau F (2005). Non-stoichiometric relationship between clathrin heavy and light chains revealed by quantitative comparative proteomics of clathrin-coated vesicles from brain and liver. Mol Cell Proteomics 4, 1145-1154.
18. Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, et al. (2012). A census of human soluble protein complexes. Cell 150, 1068-1081.
19. Heerssen H, Fetter RD, Davis GW (2008). Clathrin dependence of synaptic-vesicle formation at the Drosophila neuromuscular junction. Curr Biol 18, 401-409.
20. Heisler FF, Loebrich S, Pechmann Y, Maier N, Zivkovic AR, Tokito M, Hausrat TJ, Schweizer M, Bahring R, Holzbaur EL, et al. (2011). Muskelin regulates actin filament-and microtubule-based GABA(A) receptor transport in neurons. Neuron 70, 66-81.
21. Hirst J, Borner GH, Antrobus R, Peden AA, Hodson NA, Sahlender DA, Robinson MS (2012). Distinct and overlapping roles for AP-1 and GGAs revealed by the knocksideways system. Curr Biol 22, 1711-1716.
22. Hirst J, Sahlender DA, Choma M, Sinka R, Harbour ME, Parkinson M, Robinson MS (2009). Spatial and functional relationship of GGAs and AP-1 in Drosophila and HeLa cells. Traffic 10, 1696-1710.
23. Huh WK, Falvo JV, Gerke LC, Carroll AS, Howson RW, Weissman JS, O'Shea EK (2003). Global analysis of protein localization in budding yeast. Nature 425, 686-691.
24. Kobayashi N, Yang J, Ueda A, Suzuki T, Tomaru K, Takeno M, Okuda K, Ishigatsubo Y (2007). RanBPM, Muskelin, p48EMLP, p44CTLH, and the armadillo-repeat proteins ARMC8alpha and ARMC8beta are components of the CTLH complex. Gene 396, 236-247.
25. Kristensen AR, Gsponer J, Foster LJ (2012). A high-throughput approach for measuring temporal changes in the interactome. Nat Methods 9, 907-909.
26. Leto D, Saltiel AR (2012). Regulation of glucose transport by insulin: traffic control of GLUT4. Nature reviews. Mol Cell Biol 13, 383-396.
27. Menssen R, Schweiggert J, Schreiner J, Kusevic D, Reuther J, Braun B, Wolf DH (2012). Exploring the topology of the Gid complex, the E3 ubiquitin ligase involved in catabolite-induced degradation of gluconeogenic enzymes. J Biol Chem 287, 25602-25614.
28. Montpetit A, Cote S, Brustein E, Drouin CA, Lapointe L, Boudreau M, Meloche C, Drouin R, Hudson TJ, Cossette P (2008). Disruption of AP1S1, causing a novel neurocutaneous syndrome, perturbs development of the skin and spinal cord. PLoS Genet 4, e1000296.
29. Nagaraj N, Kulak NA, Cox J, Neuhauser N, Mayr K, Hoerning O, Vorm O, Mann M (2012). System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap. Mol Cell Proteomics 11, M111.013722.
30. Nagaraj N, Wisniewski JR, Geiger T, Cox J, Kircher M, Kelso J, Paabo S, Mann M (2011). Deep proteome and transcriptome mapping of a human cancer cell line. Mol Syst Biol 7, 548.
31. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M (2002). Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol Cell Proteomics 1, 376-386.
32. Pierce BL, Kibriya MG, Tong L, Jasmine F, Argos M, Roy S, Paul-Brutus R, Rahaman R, Rakibuz-Zaman M, Parvez F, et al. (2012). Genome-wide association study identifies chromosome 10q24.32 variants associated with arsenic metabolism and toxicity phenotypes in Bangladesh. PLoS Genet 8, e1002522.
33. Pinheiro C, Longatto-Filho A, Azevedo-Silva J, Casal M, Schmitt FC, Baltazar F (2012). Role of monocarboxylate transporters in human cancers: state of the art. J Bioenerg Biomembr 44, 127-139.
34. Rappsilber J, Mann M, Ishihama Y (2007). Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc 2, 1896-1906.
35. Robinson MS (2004). Adaptable adaptors for coated vesicles. Trends Cell Biol 14, 167-174.
36. Romani B, Cohen EA (2012). Lentivirus Vpr and Vpx accessory proteins usurp the cullin4-DDB1 (DCAF1) E3 ubiquitin ligase. Curr Opin Virol 2, 755-763.
37. Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Mewes HW (2010). CORUM: the comprehensive resource of mammalian protein complexes-2009. Nucleic Acids Res 38, D497-501.
38. Sandvig K, Pust S, Skotland T, van Deurs B (2011). Clathrin-independent endocytosis: mechanisms and function. Curr Opin Cell Biol 23, 413-420.
39. Schwanhausser B, Busse D, Li N, Dittmar G, Schuchhardt J, Wolf J, Chen W, Selbach M (2011). Global quantification of mammalian gene expression control. Nature 473, 337-342.
40. Shevchenko A, Tomas H, Havlis J, Olsen JV, Mann M (2006). In-gel digestion for mass spectrometric characterization of proteins and proteomes. Nat Protoc 1, 2856-2860.
41. Tarpey PS, Stevens C, Teague J, Edkins S, O'Meara S, Avis T, Barthorpe S, Buck G, Butler A, Cole J, et al. (2006). Mutations in the gene encoding the Sigma 2 subunit of the adaptor protein 1 complex, AP1S2, cause X-linked mental retardation. Am J Hum Genet 79, 1119-1124.
42. Tomko RJ Jr, Hochstrasser M (2013). Molecular architecture and assembly of the eukaryotic proteasome. Annu Rev Biochem 82, 415-445.
43. Umasankar PK, Sanker S, Thieman JR, Chakraborty S, Wendland B, Tsang M, Traub LM (2012). Distinct and separable activities of the endocytic clathrin-coat components Fcho1/2 and AP-2 in developmental patterning. Nat Cell Biol 14, 488-501.
44. Valiyaveettil M, Bentley AA, Gursahaney P, Hussien R, Chakravarti R, Kureishy N, Prag S, Adams JC (2008). Novel role of the muskelin-RanBP9 complex as a nucleocytoplasmic mediator of cell morphology regulation. J Cell Biol 182, 727-739.
45. van Weering JR, Verkade P, Cullen PJ (2010). SNX-BAR proteins in phosphoinositide-mediated, tubular-based endosomal sorting. Semin Cell Dev Biol 21, 371-380.
46. Yebenes H, Mesa P, Munoz IG, Montoya G, Valpuesta JM (2011). Chaperonins: two rings for folding. Biochem Sci 36, 424-432.
47. Yu S, Liang Y (2012). A trapper keeper for TRAPP, its structures and functions. Cell Mol Life Sci 69, 3933-3944.