Efficient extraction of nucleolar proteins for interactome analyses

Proteomics

Volumn 10, Issue 16, 2010, Pages 3045-3050

  Chamousset, Delphine ^a   Mamane, Sarah ^a   Boisvert, François Michel ^b   Trinkle Mulcahy, Laura ^a  

^a UNIVERSITY OF OTTAWA   (Canada)

^b UNIVERSITY OF DUNDEE   (United Kingdom)

Author keywords

Animal proteomics; Nucleolus; Protein phosphatase; Quantitative proteomics; Stable isotope labeling by amino acids in cell culture

Indexed keywords

NUCLEOLIN; PHOSPHOPROTEIN PHOSPHATASE; PROTEIN INTERACTING WITH PROTEIN KINASE C; PROTEOME;

ARTICLE; EXOSOME; HELA CELL; HUMAN; ISOTOPE LABELING; NONHUMAN; NUCLEOLUS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; QUANTITATIVE ANALYSIS;

CARBON ISOTOPES; CELL NUCLEOLUS; HELA CELLS; HUMANS; ISOTOPE LABELING; NUCLEAR PROTEINS; PEPTIDE FRAGMENTS; PHOSPHOPROTEIN PHOSPHATASES; PROTEOMICS; SIGNAL TRANSDUCTION; TRYPSIN;

ANIMALIA; MAMMALIA;

EID: 77955614928     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.201000162     Document Type: Article

References (24)

1. Trinkle-Mulcahy, L., Boulon, S., Lam, Y., Urcia, R. et al., Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes. J. Cell. Biol. 2008, 183, 223-239.
2. Trinkle-Mulcahy, L., Andersen, J., Lam, Y., Moorhead, G. et al., Repo-Man recruits PP1 gamma to chromatin and is essential for cell viability. J. Cell. Biol. 2006, 175, 679-692.
3. Ranish, J. A., Yi, E. C., Leslie, D. M., Purvine, S. O. et al., The study of macromolecular complexes by quantitative proteomics. Nat. Genet. 2003, 33, 349-355.
4. Tackett, A. J., DeGrasse, J. A., Sekedat, M. D., Oefflinger, M. et al., I-DIRT, a general method for distinguishing between specific and nonspecific protein interactions. J. Prot. Res. 2005, 4, 1752-1756.
5. Selbach, M., Mann, M., Protein interaction screening by quantitative immunoprecipitation combined with knockdown (QUICK). Nat. Met. 2006, 3, 981-983.
6. Boisvert, F. M., Lam, Y. W., Lamont, D., Lamond, A. I., A quantitative proteomics analysis of subcellular proteome localization and changes induced by DNA damage. Mol. Cell. Proteomics 2010, 9, 457-470.
7. Shaw, P. J., Jordan, E. G., The nucleolus. Annu. Rev. Cell Dev. Biol. 1995, 11, 93-121.
8. Andersen, J., Lyon, C.E., Fox, A. H., Leung, A. K. et al., Directed proteomics analysis of the human nucleolus. Curr. Biol. 2002, 12, 13-25.
9. Muramatsu, M., Onishi, T., in: Stein, G., Stein, J., Kleinsmith, L. J. (Eds.), Methods in Cell Biology Vol. XVII: Chromatin and Chromosomal Protein Research, Academic Press, New York 1978, pp. 141-161.
10. Pederson, T., The plurifunctional nucleolus. Nucleic Acids Res. 1998, 26, 3871-3876.
11. Boisvert, F. M., van Koningsbruggen, S., Navascues, J., Lamond, A. I., The multifunctional nucleolus. Nat. Rev. Mol. Cell Biol. 2007, 8, 574-585.
12. Scherl, A., Couté, Y., Déon, C., Callé, A. et al., Functional proteomic analysis of human nucleolus. Mol. Biol. Cell 2002, 13, 4100-4109.
13. Pendle, A. F., Clark, G. P., Boon, R., Lewandowska, D. et al., Proteomic analysis of the Arabidopsis nucleolus suggests novel nucleolar functions. Mol. Biol. Cell 2005, 16, 260-269.
14. Andersen, J., Lam, Y. W., Leung, A. K. L., Ong, S. E. et al., Nucleolar proteome dynamics. Nature 2005, 433, 77-83.
15. Dignam, J. D., Lebovitz, R. M., Roeder, R. G., Accurate transcription initiation by RNA Polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res. 1983, 11, 1475-1489.
16. Wang, C., Query, C. C., Meier, U. T., Ribonucleoprotein particles pseudouridylate rRNA independently of their association with phosphorylated Nopp140. Mol. Cell. Biol. 2002, 22, 8457-8466.
17. Corsetti, M. T., Levi, G., Lancia, F., Sanseverino, L. et al., Nucleolar localization of three Hox homeoproteins. J. Cell. Sci. 1995, 108, 187-193.
18. Trinkle-Mulcahy, L., Andrews, P. D., Wickramasinghe, S., Sleeman, J. et al., Time-lapse imaging reveals dynamic relocalization of PP1γ throughout the mammalian cell cycle. Mol. Biol. Cell 2003, 14, 107-117.
19. Rothbauer, U., Zolghadr, K., Muyldermans, S., Schepers, A. et al., A versatile nanotrap for biochemical and functional studies with fluorescent fusion proteins. Mol. Cell. Proteomics 2008, 7, 282-289.
20. Cox, J., Mann, M., MaxQuant enables high peptide identification rates, individual p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008, 26, 1367-1372.
21. Hendrickx, A., Beullens, M., Ceulemans, H., Den Abt, T. et al., Docking motif-guided mapping of the interactome of protein phosphatase-1. Chem. Biol. 2009, 16, 365-371.
22. Welting, T. J., van Venrooij, W. J., Pruijn, G. J., Mutual interactions between subunits of the human RNase MRP ribonucleoprotein complex. Nucleic Acids Res. 2004, 32, 2138-2146.
23. Meier, U. T., The many facets of H/ACA ribonucleoproteins. Chromosoma 2005, 1-14.
24. Shen, V., Kiledjian, M., A view to a kill: structure of the RNA exosome. Cell 2006, 127, 1093-1095.