Genome-wide identification and quantification of protein synthesis in cultured cells and whole tissues by puromycin-associated nascent chain proteomics (PUNCH-P)

Nature Protocols

Volumn 9, Issue 4, 2014, Pages 751-760

  Aviner, Ranen ^a   Geiger, Tamar ^a   Elroy Stein, Orna ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; BIOTIN; PUROMYCIN; RESIN; STREPTAVIDIN;

ANIMAL TISSUE; ARTICLE; BINDING AFFINITY; CELL CULTURE; CHEMICAL LABELING; CLINICAL PROTOCOL; COMPLEX FORMATION; CYTOLYSIS; ELUTION; EXPERIMENTAL DESIGN; GENE EXPRESSION; HELA CELL; INTERMETHOD COMPARISON; LIQUID CHROMATOGRAPHY; MOLECULAR DYNAMICS; MOUSE; NONHUMAN; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN ANALYSIS; PROTEIN PURIFICATION; PROTEIN SYNTHESIS; PROTEOMICS; PUROMYCIN ASSOCIATED NASCENT CHAIN PROTEOMICS; QUANTITATIVE ANALYSIS; RNA SEQUENCE; SEDIMENTATION; SENSITIVITY ANALYSIS; TANDEM MASS SPECTROMETRY; TISSUE CULTURE; ULTRACENTRIFUGATION; ANIMAL CELL; CATALYSIS; CONTROLLED STUDY; GENE IDENTIFICATION; GENOME ANALYSIS; HELA CELL LINE; RIBOSOME; CHEMISTRY; GENETICS; PROCEDURES;

BIOTIN; CELLS, CULTURED; CHROMATOGRAPHY, LIQUID; PROTEIN BIOSYNTHESIS; PROTEOMICS; PUROMYCIN; RIBOSOMES; TANDEM MASS SPECTROMETRY; ULTRACENTRIFUGATION;

EID: 84897133420     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2014.051     Document Type: Article

References (25)

1. Calkhoven, C.F., Muller, C. & Leutz, A. Translational control of gene expression and disease. Trends Mol. Med. 8, 577-583 (2002).
2. Holcik, M. & Sonenberg, N. Translational control in stress and apoptosis. Nat. Rev. Mol. Cell Biol. 6, 318-327 (2005).
3. Vogel, C. & Marcotte, E.M. Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nat. Rev. Genet. 13, 227-232 (2012).
4. Ingolia, N.T., Ghaemmaghami, S., Newman, J.R. & Weissman, J.S. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324, 218-223 (2009).
5. Schwanhausser, B., Gossen, M., Dittmar, G. & Selbach, M. Global analysis of cellular protein translation by pulsed SILAC. Proteomics 9, 205-209 (2009).
6. Dieterich, D.C., Link, A.J., Graumann, J., Tirrell, D.A. & Schuman, E.M. Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT). Proc. Natl. Acad. Sci. USA 103, 9482-9487 (2006).
7. Howden, A.J. et al. QuaNCAT: quantitating proteome dynamics in primary cells. Nat. Methods 10, 343-346 (2013).
8. Aviner, R., Geiger, T. & Elroy-Stein, O. Novel proteomic approach (PUNCH-P) reveals cell cycle-specific fluctuations in mRNA translation. Genes Dev. 27, 1834-1844 (2013).
9. Pestka, S. Inhibitors of ribosome functions. Annu. Rev. Microbiol. 25, 487-562 (1971).
10. Baliga, B.S., Cohen, S.A. & Munro, H.N. Effect of cycloheximide on the reaction of puromycin with polysome-bound peptidyl-tRNA. FEBS Lett. 8, 249-252 (1970).
11. David, A. et al. Nuclear translation visualized by ribosome-bound nascent chain puromycylation. J. Cell Biol. 197, 45-57 (2012).
12. Kramer, G. et al. Identification and quantitation of newly synthesized proteins in Escherichia coli by enrichment of azidohomoalanine-labeled peptides with diagonal chromatography. Mol. Cell Proteomics 8, 1599-1611 (2009).
13. Vaughan, M.H. Jr., Pawlowski, P.J. & Forchhammer, J. Regulation of protein synthesis initiation in HeLa cells deprived of single essential amino acids. Proc. Natl. Acad. Sci. USA 68, 2057-2061 (1971).
14. Schwanhausser, B. et al. Global quantification of mammalian gene expression control. Nature 473, 337-342 (2011).
15. Liu, J., Xu, Y., Stoleru, D. & Salic, A. Imaging protein synthesis in cells and tissues with an alkyne analog of puromycin. Proc. Natl. Acad. Sci. USA 109, 413-418 (2012).
16. Schmidt, E.K., Clavarino, G., Ceppi, M. & Pierre, P. SUnSET, a nonradioactive method to monitor protein synthesis. Nat. Methods 6, 275-277 (2009).
17. Starck, S.R., Green, H.M., Alberola-Ila, J. & Roberts, R.W. A general approach to detect protein expression in vivo using fluorescent puromycin conjugates. Chem. Biol. 11, 999-1008 (2004).
18. Croons, V., Martinet, W., Herman, A.G. & De Meyer, G.R. Differential effect of the protein synthesis inhibitors puromycin and cycloheximide on vascular smooth muscle cell viability. J. Pharmacol. Exp. Ther. 325, 824-832 (2008).
19. Wharton, S.A. & Hipkiss, A.R. Abnormal proteins of shortened length are preferentially degraded in the cytosol of cultured MRC5 fibroblasts. FEBS Lett. 168, 134-138 (1984).
20. Dissous, C., Caner, F. & Krembel, J. Isopycnic centrifugation of free and membrane-bound polysomes from rat liver. Eur. J. Biochem. 44, 161-170 (1974).
21. Tagwerker, C. et al. A tandem affinity tag for two-step purification under fully denaturing conditions: application in ubiquitin profiling and protein complex identification combined with in vivo cross-linking. Mol. Cell Proteomics 5, 737-748 (2006).
22. Holmberg, A. et al. The biotin-streptavidin interaction can be reversibly broken using water at elevated temperatures. Electrophoresis 26, 501-510 (2005).
23. Ong, S.E. & Mann, M. A practical recipe for stable isotope labeling by amino acids in cell culture (SILAC). Nat. Protoc. 1, 2650-2660 (2006).
24. Scopes, R.K. & Smith, J.A. Analysis of proteins. Curr. Protoc. Mol. Biol. 90, 10.0.1-10.0.23 (2010).
25. Rappsilber, J., Mann, M. & Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2, 1896-1906 (2007).