Biotin tagging coupled with amino acid-coded mass tagging for efficient and precise screening of interaction proteome in mammalian cells

Proteomics

Volumn 9, Issue 24, 2009, Pages 5414-5424

  He, Yu Fei ^a   Bao, Hui Min ^a   Xiao, Xiao Feng ^a   Zuo, Shuai ^a   Du, Ru Yun ^a   Tang, Si Wei ^a   Yang, Peng Yuan ^a   Chen, Xian ^a,b  

^a FUDAN UNIVERSITY   (China)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

Author keywords

14 3 3 ; Affinity purification; Amino acid coded mass tagging; Biotin tagging; Protein protein interaction; Technology

Indexed keywords

AMINO ACID; BIOTIN; PROTEOME; STRATIFIN; STREPTAVIDIN;

AFFINITY LABELING; ARTICLE; BIOINFORMATICS; HUMAN; HUMAN CELL; LIQUID CHROMATOGRAPHY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN PURIFICATION; QUANTITATIVE ANALYSIS; TANDEM MASS SPECTROMETRY;

14-3-3 PROTEINS; AMINO ACID SEQUENCE; ANIMALS; BIOTIN; BIOTINYLATION; CELL LINE; GENETIC VECTORS; HUMANS; MAGNETICS; MOLECULAR SEQUENCE DATA; PROTEIN INTERACTION MAPPING; PROTEOME; PROTEOMICS; STREPTAVIDIN; TRANSFECTION;

MAMMALIA;

EID: 73149098468     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200800864     Document Type: Article

References (36)

1. Robinson, C. V., Sali, A., Baumeister, W., The molecular sociology of the cell. Nature 2007, 450, 973-982.
2. Papin, J. A., Hunter, T., Palsson, B. O., Subramaniam, S., Reconstruction of cellular signalling networks and analysis of their properties. Nat. Rev. Mol. Cell Biol. 2005, 6, 99-111.
3. Kocher, T., Superti-Furga, G., Mass spectrometry-based functional proteomics: from molecular machines to protein networks. Nat. Methods 2007, 4, 807-815.
4. Cravatt, B. F., Simon, G. M., Yates 3rd, J. R., The biological impact of mass-spectrometry-based proteomics. Nature 2007, 450, 991-1000.
5. Berggard, T., Linse, S., James, P., Methods for the detection and analysis of protein-protein interactions. Proteomics 2007, 7, 2833-2842.
6. Cusick, M. E., Klitgord, N., Vidal, M., Hill, D. E., Interactome: gateway into systems biology. Hum. Mol. Genet. 2005, 14, R171-181.
7. Gingras, A.-C., Gstaiger, M., Raught, B., Aebersold, R., Analysis of protein complexes using mass spectrometry. Nat. Rev. Mol. Cell Biol. 2007, 8, 645-654.
8. Rigaut, G., Shevchenko, A., Rutz, B., Wilm, M. et al., A generic protein purification method for protein complex characterization and proteome exploration. Nat. Biotechnol. 1999, 17, 1030-1032.
9. Chen, X., Sun, L., Yu, Y., Xue, Y., Yang, P., Amino acid-coded tagging approaches in quantitative proteomics. Expert Rev. Proteomics 2007, 4, 25-37.
10. Zhu, H., Pan, S., Gu, S., Bradbury, E. M., Chen, X., Amino acid residue specific stable isotope labeling for quantitative proteomics. Rapid Commun. Mass Spectrom. 2002, 16, 2115-2123.
11. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B. et al., Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1, 376-386.
12. Cox, J., Mann, M., Is proteomics the new genomics? Cell 2007, 130, 395-398.
13. Wang, T., Gu, S., Ronni, T., Du, Y. C., Chen, X., In vivo dual-tagging proteomic approach in studying signaling pathways in immune response. J. Proteome Res. 2005, 4, 941-949.
14. Wang, T., Chuang, T. H., Ronni, T., Gu, S. et al., Flightless I homolog negatively modulates the TLR pathway. J. Immunol. 2006, 176, 1355-1362.
15. Du, Y. C., Gu, S., Zhou, J., Wang, T. et al., The dynamic alterations of H2AX complex during DNA repair detected by a proteomic approach reveal the critical roles of Ca(2+)/calmodulin in the ionizing radiation-induced cell cycle arrest. Mol. Cell. Proteomics 2006, 5, 1033-1044.
16. Guerrero, C., Tagwerker, C., Kaiser, P., Huang, L., An integrated mass spectrometry-based proteomic approach: quantitative analysis of tandem affinity-purified in vivo cross-linked protein complexes (QTAX) to decipher the 26 S proteasome-interacting network. Mol. Cell. Proteomics 2006, 5, 366-378.
17. de Boer, E., Rodriguez, P., Bonte, E., Krijgsveld, J. et al., Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc. Natl. Acad. Sci. USA 2003, 100, 7480-7485
18. Howarth, M., Takao, K., Hayashi, Y., Ting, A. Y., Targeting quantum dots to surface proteins in living cells with biotin ligase. Proc. Natl. Acad. Sci. USA 2005, 102, 7583-7588.
19. Beckett, D., Kovaleva, E., Schatz, P. J., A minimal peptide substrate in biotin holoenzyme synthetase-catalyzed biotinylation. Protein Sci. 1999, 8, 921-929.
20. Aitken, A., 14-3-3 proteins: a historic overview. Semin. Cancer Biol. 2006, 16, 162-172.
21. Tzivion, G., Gupta, V. S., Kaplun, L., Balan, V., 14-3-3 proteins as potential oncogenes. Semin. Cancer Biol. 2006, 16, 203-213.
22. Coblitz, B., Wu, M., Shikano, S., Li, M., C-terminal binding: an expanded repertoire and function of 14-3-3 proteins. FEBS Lett. 2006, 580, 1531-1535.
23. Porter, G. W., Khuri, F. R., Fu, H., Dynamic 14-3-3/client protein interactions integrate survival and apoptotic pathways. Semin. Cancer Biol. 2006, 16, 193-202.
24. Chapman-Smith, A., Cronan J. E., Jr, In vivo enzymatic protein biotinylation. Biomol. Eng. 1999, 16, 119-125.
25. Sanchez, C., Sanchez, I., Demmers, J. A., Rodriguez, P. et al., Proteomics analysis of Ring1B/Rnf2 interactors identifies a novel complex with the Fbxl10/Jhdm1B histone demethylase and the Bcl6 interacting corepressor. Mol. Cell. Proteomics 2007, 6, 820-834.
26. Bramwell, M. E., Characterization of biotinylated proteins in mammalian cells using 125I-streptavidin. J. Biochem. Biophys. Methods 1987, 15, 125-132.
27. Burckstummer, T., Bennett, K. L., Preradovic, A., Schutze, G. et al., An efficient tandem affinity purification procedure for interaction proteomics in mammalian cells. Nat. Methods 2006, 3, 1013-1019.
28. Lee, M. H., Lozano, G., Regulation of the p53-MDM2 pathway by 14-3-3 sigma and other proteins. Semin. Cancer Biol. 2006, 16, 225-234.
29. Yang, H., Wen, Y. Y., Zhao, R., Lin, Y. L. et al., DNA damage-induced protein 14-3-3 sigma inhibits protein kinase B/Akt activation and suppresses Akt-activated cancer. Cancer Res. 2006, 66, 3096-3105.
30. Szul, T., Grabski, R., Lyons, S., Morohashi, Y. et al., Dissecting the role of the ARF guanine nucleotide exchange factor GBF1 in Golgi biogenesis and protein trafficking. J. Cell Sci. 2007, 120, 3929-3940.
31. Richter, S., Geldner, N., Schrader, J., Wolters, H. et al., Functional diversification of closely related ARF-GEFs in protein secretion and recycling. Nature 2007, 448, 488-492.
32. Manolea, F., Claude, A., Chun, J., Rosas, J., Melancon, P., Distinct functions for Arf guanine nucleotide exchange factors at the Golgi complex: GBF1 and BIGs are required for assembly and maintenance of the Golgi stack and trans-Golgi network, respectively. Mol. Biol. Cell 2008, 19, 523-535.
33. Citterio, C., Vichi, A., Pacheco-Rodriguez, G., Aponte, A. M. et al., Unfolded protein response and cell death after depletion of brefeldin A-inhibited guanine nucleotide-exchange protein GBF1. Proc. Natl. Acad. Sci. USA 2008, 105, 2877-2882.
34. Pandey, A., Blagoev, B., Kratchmarova, I., Fernandez, M. et al., Cloning of a novel phosphotyrosine binding domain containing molecule, Odin, involved in signaling by receptor tyrosine kinases. Oncogene 2002, 21, 8029-8036.
35. Morris, E. J., Michaud, W. A., Ji, J. Y., Moon, N. S. et al., Functional identification of Api5 as a suppressor of E2F-dependent apoptosis in vivo. PLoS Genet. 2006, 2, e196.
36. Wiese, S., Reidegeld, K. A., Meyer, H. E., Warscheid, B., Protein labeling by iTRAQ: a new tool for quantitative mass spectrometry in proteome research. Proteomics 2007, 7, 340-350.