The Nuclear Proteome of a Vertebrate

Current Biology

Volumn 25, Issue 20, 2015, Pages 2663-2671

  Wühr, Martin ^a   Güttler, Thomas ^a   Peshkin, Leonid ^a   McAlister, Graeme C ^a   Sonnett, Matthew ^a   Ishihara, Keisuke ^a   Groen, Aaron C ^a   Presler, Marc ^a   Erickson, Brian K ^a   Mitchison, Timothy J ^a   Kirschner, Marc W ^a   Gygi, Steven P ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMPHIBIAN PROTEIN; NUCLEAR PROTEIN; PROTEOME;

ANIMAL; CELL NUCLEUS; CYTOPLASM; GENETICS; METABOLISM; OOCYTE; XENOPUS;

AMPHIBIAN PROTEINS; ANIMALS; CELL NUCLEUS; CYTOPLASM; NUCLEAR PROTEINS; OOCYTES; PROTEOME; XENOPUS;

EID: 84945568319     PISSN: 09609822     EISSN: 18790445     Source Type: Journal    
DOI: 10.1016/j.cub.2015.08.047     Document Type: Article

References (53)

1. T. Cavalier-Smith Cell evolution and Earth history: stasis and revolution Philos. Trans. R. Soc. Lond. B Biol. Sci. 361 2006 969 1006
2. I.K. Poon, and D.A. Jans Regulation of nuclear transport: central role in development and transformation? Traffic 6 2005 173 186
3. M.P. Rout, J.D. Aitchison, A. Suprapto, K. Hjertaas, Y. Zhao, and B.T. Chait The yeast nuclear pore complex: composition, architecture, and transport mechanism J. Cell Biol. 148 2000 635 651
4. D. Mohr, S. Frey, T. Fischer, T. Güttler, and D. Görlich Characterisation of the passive permeability barrier of nuclear pore complexes EMBO J. 28 2009 2541 2553
5. D. Görlich, P. Henklein, R.A. Laskey, and E. Hartmann A 41 amino acid motif in importin-alpha confers binding to importin-beta and hence transit into the nucleus EMBO J. 15 1996 1810 1817
6. S. Bagley, M.W. Goldberg, J.M. Cronshaw, S. Rutherford, and T.D. Allen The nuclear pore complex J. Cell Sci. 113 2000 3885 3886
7. E. Izaurralde, U. Kutay, C. von Kobbe, I.W. Mattaj, and D. Görlich The asymmetric distribution of the constituents of the Ran system is essential for transport into and out of the nucleus EMBO J. 16 1997 6535 6547
8. P.L. Paine, C.F. Austerberry, L.J. Desjarlais, and S.B. Horowitz Protein loss during nuclear isolation J. Cell Biol. 97 1983 1240 1242
9. J.W. Newport, K.L. Wilson, and W.G. Dunphy A lamin-independent pathway for nuclear envelope assembly J. Cell Biol. 111 1990 2247 2259
10. M.A. D'Angelo, D.J. Anderson, E. Richard, and M.W. Hetzer Nuclear pores form de novo from both sides of the nuclear envelope Science 312 2006 440 443
11. M.T. Bohnsack, K. Regener, B. Schwappach, R. Saffrich, E. Paraskeva, E. Hartmann, and D. Görlich Exp5 exports eEF1A via tRNA from nuclei and synergizes with other transport pathways to confine translation to the cytoplasm EMBO J. 21 2002 6205 6215
12. L. Einck, and M. Bustin Functional histone antibody fragments traverse the nuclear envelope J. Cell Biol. 98 1984 205 213
13. G.C. McAlister, D.P. Nusinow, M.P. Jedrychowski, M. Wühr, E.L. Huttlin, B.K. Erickson, R. Rad, W. Haas, and S.P. Gygi MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes Anal. Chem. 86 2014 7150 7158
14. M. Wühr, W. Haas, G.C. McAlister, L. Peshkin, R. Rad, M.W. Kirschner, and S.P. Gygi Accurate multiplexed proteomics at the MS2 level using the complement reporter ion cluster Anal. Chem. 84 2012 9214 9221
15. M. Wühr, R.M. Freeman Jr., M. Presler, M.E. Horb, L. Peshkin, S.P. Gygi, and M.W. Kirschner Deep proteomics of the Xenopus laevis egg using an mRNA-derived reference database Curr. Biol. 24 2014 1467 1475
16. D.J. Pagliarini, S.E. Calvo, B. Chang, S.A. Sheth, S.B. Vafai, S.E. Ong, G.A. Walford, C. Sugiana, A. Boneh, W.K. Chen, and et al. A mitochondrial protein compendium elucidates complex I disease biology Cell 134 2008 112 123
17. M. Uhlen, P. Oksvold, L. Fagerberg, E. Lundberg, K. Jonasson, M. Forsberg, M. Zwahlen, C. Kampf, K. Wester, S. Hober, and et al. Towards a knowledge-based Human Protein Atlas Nat. Biotechnol. 28 2010 1248 1250
18. UniProt Consortium Update on activities at the Universal Protein Resource (UniProt) in 2013 Nucleic Acids Res. 41 2013 D43 D47
19. S. Rastogi, and B. Rost LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana Nucleic Acids Res. 39 2011 D230 D234
20. M.A. Harris, J. Clark, A. Ireland, J. Lomax, M. Ashburner, R. Foulger, K. Eilbeck, S. Lewis, B. Marshall, C. Mungall, et al. Gene Ontology Consortium The Gene Ontology (GO) database and informatics resource Nucleic Acids Res. 32 2004 D258 D261
21. P.L. Paine, and C.M. Feldherr Nucleocytoplasmic exchange of macromolecules Exp. Cell Res. 74 1972 81 98
22. A. Ruepp, B. Waegele, M. Lechner, B. Brauner, I. Dunger-Kaltenbach, G. Fobo, G. Frishman, C. Montrone, and H.W. Mewes CORUM: the comprehensive resource of mammalian protein complexes - 2009 Nucleic Acids Res. 38 2010 D497 D501
23. K.E. Sawin, and T.J. Mitchison Mitotic spindle assembly by two different pathways in vitro J. Cell Biol. 112 1991 925 940
24. A.W. Murray, and M.W. Kirschner Cyclin synthesis drives the early embryonic cell cycle Nature 339 1989 275 280
25. P. Hartl, E. Olson, T. Dang, and D.J. Forbes Nuclear assembly with lambda DNA in fractionated Xenopus egg extracts: an unexpected role for glycogen in formation of a higher order chromatin intermediate J. Cell Biol. 124 1994 235 248
26. V.M. Merwade, D.R. Maidment, and B.R. Hodges Geospatial representation of river channels J. Hydrol. Eng. 10 2005 243 251
27. R. Wang, and M.G. Brattain The maximal size of protein to diffuse through the nuclear pore is larger than 60kDa FEBS Lett. 581 2007 3164 3170
28. P. Popken, A. Ghavami, P.R. Onck, B. Poolman, and L.M. Veenhoff Size-dependent leak of soluble and membrane proteins through the yeast nuclear pore complex Mol. Biol. Cell 26 2015 1386 1394
29. T. Güttler, and D. Görlich Ran-dependent nuclear export mediators: a structural perspective EMBO J. 30 2011 3457 3474
30. N. Kudo, N. Matsumori, H. Taoka, D. Fujiwara, E.P. Schreiner, B. Wolff, M. Yoshida, and S. Horinouchi Leptomycin B inactivates CRM1/exportin 1 by covalent modification at a cysteine residue in the central conserved region Proc. Natl. Acad. Sci. USA 96 1999 9112 9117
31. C.J. Walker, J.J. Oaks, R. Santhanam, P. Neviani, J.G. Harb, G. Ferenchak, J.J. Ellis, Y. Landesman, A.K. Eisfeld, N.Y. Gabrail, and et al. Preclinical and clinical efficacy of XPO1/CRM1 inhibition by the karyopherin inhibitor KPT-330 in Ph+ leukemias Blood 122 2013 3034 3044
32. W.T. Senapedis, E. Baloglu, and Y. Landesman Clinical translation of nuclear export inhibitors in cancer Semin. Cancer Biol. 27 2014 74 86
33. J.G. Turner, J. Dawson, M.F. Emmons, C.L. Cubitt, M. Kauffman, S. Shacham, L.A. Hazlehurst, and D.M. Sullivan CRM1 Inhibition Sensitizes Drug Resistant Human Myeloma Cells to Topoisomerase II and Proteasome Inhibitors both In Vitro and Ex Vivo J. Cancer 4 2013 614 625
34. G. Manning, D.B. Whyte, R. Martinez, T. Hunter, and S. Sudarsanam The protein kinase complement of the human genome Science 298 2002 1912 1934
35. M. Chartier, T. Chénard, J. Barker, and R. Najmanovich Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree PeerJ 1 2013 e126
36. C. Dingwall, S.V. Sharnick, and R.A. Laskey A polypeptide domain that specifies migration of nucleoplasmin into the nucleus Cell 30 1982 449 458
37. P.L. Paine, L.C. Moore, and S.B. Horowitz Nuclear envelope permeability Nature 254 1975 109 114
38. U. Aebi, J. Cohn, L. Buhle, and L. Gerace The nuclear lamina is a meshwork of intermediate-type filaments Nature 323 1986 560 564
39. P. Horton, K.J. Park, T. Obayashi, N. Fujita, H. Harada, C.J. Adams-Collier, and K. Nakai WoLF PSORT: protein localization predictor Nucleic Acids Res. 35 2007 W585 W587
40. A.L. Mosley, L. Florens, Z. Wen, and M.P. Washburn A label free quantitative proteomic analysis of the Saccharomyces cerevisiae nucleus J. Proteomics 72 2009 110 120
41. F.M. Boisvert, Y. Ahmad, M. Gierlinski, F. Charriere, D. Lamont, M. Scott, G. Barton, and A.I. Lamond A quantitative spatial proteomics analysis of proteome turnover in human cells Mol. Cell. Proteomics 11 2012 M111.011429
42. C.M. Feldherr, and J. Pomerantz Mechanism for the selection of nuclear polypeptides in Xenopus oocytes J. Cell Biol. 78 1978 168 175
43. M.W. Hetzer The role of the nuclear pore complex in aging of post-mitotic cells Aging (Albany, N.Y.) 2 2010 74 75
44. S. Jäkel, J.M. Mingot, P. Schwarzmaier, E. Hartmann, and D. Görlich Importins fulfil a dual function as nuclear import receptors and cytoplasmic chaperones for exposed basic domains EMBO J. 21 2002 377 386
45. B.K. Erickson, M.P. Jedrychowski, G.C. McAlister, R.A. Everley, R. Kunz, and S.P. Gygi Evaluating multiplexed quantitative phosphopeptide analysis on a hybrid quadrupole mass filter/linear ion trap/orbitrap mass spectrometer Anal. Chem. 87 2015 1241 1249
46. J.B. Gurdon, T.R. Elsdale, and M. Fischberg Sexually mature individuals of Xenopus laevis from the transplantation of single somatic nuclei Nature 182 1958 64 65
47. K. Katholnig, M. Poglitsch, M. Hengstschläger, and T. Weichhart Lysis gradient centrifugation: a flexible method for the isolation of nuclei from primary cells Methods Mol. Biol. 1228 2015 15 23
48. A. Mir, and J. Heasman How the mother can help: studying maternal Wnt signaling by anti-sense-mediated depletion of maternal mRNAs and the host transfer technique Methods Mol. Biol. 469 2008 417 429
49. J. Gerhart, M. Wu, and M. Kirschner Cell cycle dynamics of an M-phase-specific cytoplasmic factor in Xenopus laevis oocytes and eggs J. Cell Biol. 98 1984 1247 1255
50. G.D. Fasman Practical Handbook of Biochemistry and Molecular Biology 1989 Taylor and Francis
51. H.A. Sober CRC Handbook of Biochemistry: Selected Data for Molecular Biology 1970 CRC Press
52. P.G. Squire, and M.E. Himmel Hydrodynamics and protein hydration Arch. Biochem. Biophys. 196 1979 165 177
53. J.A. Vizcaino, E.W. Deutsch, R. Wang, A. Csordas, F. Reisinger, D. Rios, J.A. Dianes, Z. Sun, T. Farrah, N. Bandeira, and et al. ProteomeXchange provides globally coordinated proteomics data submission and dissemination Nature Biotechnology 32 2014 223 226