Characterization and Analysis of the Composition and Dynamics of the Mammalian Riboproteome

Cell Reports

Volumn 4, Issue 6, 2013, Pages 1276-1287

  Reschke, Markus ^a   Clohessy, John G ^a   Seitzer, Nina ^a   Goldstein, Daniel P ^a   Breitkopf, Susanne B ^a   Schmolze, Daniel B ^a   Ala, Ugo ^a,b   Asara, John M ^a   Beck, Andrew H ^a   Pandolfi, PierPaolo ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

^b UNIVERSITY OF TURIN   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; RIBOPROTEOME; RNA BINDING PROTEIN; UNCLASSIFIED DRUG;

ARTICLE; BIOINFORMATICS; CANCER CELL CULTURE; CELL TYPE; CONTROLLED STUDY; GENE AMPLIFICATION; GENETICS; HUMAN; HUMAN CELL; ISOTOPE LABELING; MASS SPECTROMETRY; POLYSOME; PRIORITY JOURNAL; PROSTATE CANCER; PROTEIN ANALYSIS; RIBOSOME; STABLE ISOTOPE LABELING BY AMINO ACIDS IN CELL CULTURE; WESTERN BLOTTING;

ANIMALS; CELL LINE, TUMOR; CELLS, CULTURED; GENE AMPLIFICATION; HUMANS; MALE; MAMMALS; MASS SPECTROMETRY; PROSTATIC NEOPLASMS; PROTEOME; PROTEOMICS; RIBOSOMES; TRANSCRIPTOME;

EID: 84884549053     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2013.08.014     Document Type: Article

References (26)

1. Baltz A.G., Munschauer M., Schwanhäusser B., Vasile A., Murakawa Y., Schueler M., Youngs N., Penfold-Brown D., Drew K., Milek M., et al. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Mol. Cell 2012, 46:674-690.
2. Beroukhim R., Mermel C.H., Porter D., Wei G., Raychaudhuri S., Donovan J., Barretina J., Boehm J.S., Dobson J., Urashima M., et al. The landscape of somatic copy-number alteration across human cancers. Nature 2010, 463:899-905.
3. Blobel G., Sabatini D. Dissociation of mammalian polyribosomes into subunits by puromycin. Proc. Natl. Acad. Sci. USA 1971, 68:390-394.
4. Brown J.R., Hanna M., Tesar B., Werner L., Pochet N., Asara J.M., Wang Y.E., Dal Cin P., Fernandes S.M., Thompson C., et al. Integrative genomic analysis implicates gain of PIK3CA at 3q26 and MYC at 8q24 in chronic lymphocytic leukemia. Clin. Cancer Res. 2012, 18:3791-3802.
5. Burrows C., Abd Latip N., Lam S.-J., Carpenter L., Sawicka K., Tzolovsky G., Gabra H., Bushell M., Glover D.M., Willis A.E., Blagden S.P. The RNA binding protein Larp1 regulates cell division, apoptosis and cell migration. Nucleic Acids Res. 2010, 38:5542-5553.
6. Castello A., Fischer B., Eichelbaum K., Horos R., Beckmann B.M., Strein C., Davey N.E., Humphreys D.T., Preiss T., Steinmetz L.M., et al. Insights into RNA biology from an atlas of mammalian mRNA-binding proteins. Cell 2012, 149:1393-1406.
7. Cerami E., Gao J., Dogrusoz U., Gross B.E., Sumer S.O., Aksoy B.A., Jacobsen A., Byrne C.J., Heuer M.L., Larsson E., et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012, 2:401-404.
8. Cox J., Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol. 2008, 26:1367-1372.
9. Cox J., Neuhauser N., Michalski A., Scheltema R.A., Olsen J.V., Mann M. Andromeda: a peptide search engine integrated into the MaxQuant environment. J.Proteome Res. 2011, 10:1794-1805.
10. Darnell J.C., Van Driesche S.J., Zhang C., Hung K.Y.S., Mele A., Fraser C.E., Stone E.F., Chen C., Fak J.J., Chi S.W., et al. FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism. Cell 2011, 146:247-261.
11. Fabian M.R., Sonenberg N. The mechanics of miRNA-mediated gene silencing: a look under the hood of miRISC. Nat. Struct. Mol. Biol. 2012, 19:586-593.
12. Feldman M.E., Apsel B., Uotila A., Loewith R., Knight Z.A., Ruggero D., Shokat K.M. Active-site inhibitors of mTOR target rapamycin-resistant outputs of mTORC1 and mTORC2. PLoS Biol. 2009, 7:e38.
13. Fuchs G., Diges C., Kohlstaedt L.A., Wehner K.A., Sarnow P. Proteomic analysis of ribosomes: translational control of mRNA populations by glycogen synthase GYS1. J.Mol. Biol. 2011, 410:118-130.
14. Grisendi S., Bernardi R., Rossi M., Cheng K., Khandker L., Manova K., Pandolfi P.P. Role of nucleophosmin in embryonic development and tumorigenesis. Nature 2005, 437:147-153.
15. Grisendi S., Mecucci C., Falini B., Pandolfi P.P. Nucleophosmin and cancer. Nat. Rev. Cancer 2006, 6:493-505.
16. Hsu P.P., Kang S.A., Rameseder J., Zhang Y., Ottina K.A., Lim D., Peterson T.R., Choi Y., Gray N.S., Yaffe M.B., et al. The mTOR-regulated phosphoproteome reveals a mechanism of mTORC1-mediated inhibition of growth factor signaling. Science 2011, 332:1317-1322.
17. Huang W., Sherman B.T., Lempicki R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009, 4:44-57.
18. Jackson R.J., Hellen C.U.T., Pestova T.V. The mechanism of eukaryotic translation initiation and principles of its regulation. Nat. Rev. Mol. Cell Biol. 2010, 11:113-127.
19. Kharas M.G., Lengner C.J., Al-Shahrour F., Bullinger L., Ball B., Zaidi S., Morgan K., Tam W., Paktinat M., Okabe R., et al. Musashi-2 regulates normal hematopoiesis and promotes aggressive myeloid leukemia. Nat. Med. 2010, 16:903-908.
20. Kolasa I.K., Rembiszewska A., Felisiak A., Ziolkowska-Seta I., Murawska M., Moes J., Timorek A., Dansonka-Mieszkowska A., Kupryjanczyk J. PIK3CA amplification associates with resistance to chemotherapy in ovarian cancer patients. Cancer Biol. Ther. 2009, 8:21-26.
21. Narla A., Ebert B.L. Ribosomopathies: human disorders of ribosome dysfunction. Blood 2010, 115:3196-3205.
22. Ong S.-E., Blagoev B., Kratchmarova I., Kristensen D.B., Steen H., Pandey A., Mann M. 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.
23. Spellman D.S., Deinhardt K., Darie C.C., Chao M.V., Neubert T.A. Stable isotopic labeling by amino acids in cultured primary neurons: application to brain-derived neurotrophic factor-dependent phosphotyrosine-associated signaling. Mol. Cell. Proteomics 2008, 7:1067-1076.
24. Thoreen C.C., Sabatini D.M. Rapamycin inhibits mTORC1, but not completely. Autophagy 2009, 5:725-726.
25. Xue S., Barna M. Specialized ribosomes: a new frontier in gene regulation and organismal biology. Nat. Rev. Mol. Cell Biol. 2012, 13:355-369.
26. Yu Y., Yoon S.-O., Poulogiannis G., Yang Q., Ma X.M., Villén J., Kubica N., Hoffman G.R., Cantley L.C., Gygi S.P., Blenis J. Phosphoproteomic analysis identifies Grb10 as an mTORC1 substrate that negatively regulates insulin signaling. Science 2011, 332:1322-1326.