In-depth quantitative proteomic analysis of de novo protein synthesis induced by brain-derived neurotrophic factor

Journal of Proteome Research

Volumn 13, Issue 12, 2014, Pages 5707-5714

  Zhang, Guoan ^a   Bowling, Heather ^a   Hom, Nancy ^b   Kirshenbaum, Kent ^b   Klann, Eric ^b   Chao, Moses V ^a   Neubert, Thomas A ^a  

^a NEW YORK UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NEW YORK UNIVERSITY   (United States)

Author keywords

BDNF; BONCAT; mass spectrometry; proteomics; pulsed SILAC; translation

Indexed keywords

ALANINE; ALKYNE; AZIDOHOMOALANINE; BRAIN DERIVED NEUROTROPHIC FACTOR; METHIONINE; PROTEOME; STABLE ISOTOPE; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

ARTICLE; BIOORTHOGONAL NONCANONICAL AMINO ACID TAGGING; CONTROLLED STUDY; CYCLOADDITION; HUMAN; HUMAN CELL; ISOTOPE LABELING; PROTEIN ANALYSIS; PROTEIN ISOLATION; PROTEIN SYNTHESIS; PROTEOMICS; QUANTITATIVE ANALYSIS; STABLE ISOTOPE LABELING BY AMINO ACID IN CELL CULTURE; STEADY STATE; ANALOGS AND DERIVATIVES; CHEMISTRY; DRUG EFFECTS; HEK293 CELL LINE; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; METABOLISM; PROCEDURES; REPRODUCIBILITY;

ALANINE; BRAIN-DERIVED NEUROTROPHIC FACTOR; CHROMATOGRAPHY, LIQUID; HEK293 CELLS; HUMANS; MASS SPECTROMETRY; PROTEIN BIOSYNTHESIS; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS;

EID: 84915758543     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/pr5006982     Document Type: Article

References (31)

1. 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, 376-86
2. Doherty, M. K.; Whitehead, C.; McCormack, H.; Gaskell, S. J.; Beynon, R. J. Proteome dynamics in complex organisms: using stable isotopes to monitor individual protein turnover rates Proteomics 2005, 5, 522-33
3. Selbach, M.; Schwanhausser, B.; Thierfelder, N.; Fang, Z.; Khanin, R.; Rajewsky, N. Widespread changes in protein synthesis induced by microRNAs Nature 2008, 455, 58-63
4. 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. U.S.A. 2006, 103, 9482-7
5. Hatzenpichler, R.; Scheller, S.; Tavormina, P. L.; Babin, B. M.; Tirrell, D. A.; Orphan, V. J. In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry Environ. Microbiol. 2014, 16, 2568-90
6. Shen, W.; Liu, H. H.; Schiapparelli, L.; McClatchy, D.; He, H. Y.; Yates, J. R., III; Cline, H. T. Acute synthesis of CPEB is required for plasticity of visual avoidance behavior in Xenopus Cell Rep. 2014, 6, 737-47
7. Lu, Y. Y.; Sweredoski, M. J.; Huss, D.; Lansford, R.; Hess, S.; Tirrell, D. A. Prometastatic GPCR CD97 is a direct target of tumor suppressor microRNA-126 ACS Chem. Biol. 2014, 9, 334-8
8. Eichelbaum, K.; Winter, M.; Berriel Diaz, M.; Herzig, S.; Krijgsveld, J. Selective enrichment of newly synthesized proteins for quantitative secretome analysis Nat. Biotechnol. 2012, 30, 984-90
9. Howden, A. J.; Geoghegan, V.; Katsch, K.; Efstathiou, G.; Bhushan, B.; Boutureira, O.; Thomas, B.; Trudgian, D. C.; Kessler, B. M.; Dieterich, D. C.; Davis, B. G.; Acuto, O. QuaNCAT: quantitating proteome dynamics in primary cells Nat. Methods 2013, 10, 343-6
10. Somasekharan, S. P.; Stoynov, N.; Rotblat, B.; Leprivier, G.; Galpin, J. D.; Ahern, C. A.; Foster, L. J.; Sorensen, P. H. Identification and quantification of newly synthesized proteins translationally regulated by YB-1 using a novel Click-SILAC approach J. Proteomics 2012, 77, e1-10
11. Bagert, J. D.; Xie, Y. J.; Sweredoski, M. J.; Qi, Y.; Hess, S.; Schuman, E. M.; Tirrell, D. A. Quantitative, time-resolved proteomic analysis by combining bioorthogonal noncanonical amino acid tagging and pulsed stable isotope labeling by amino acids in cell culture Mol. Cell Proteomics 2014, 13, 1352-8
12. Reichardt, L. F. Neurotrophin-regulated signalling pathways Philos. Trans. R. Soc., B 2006, 361, 1545-64
13. Huang, E. J.; Reichardt, L. F. Neurotrophins: roles in neuronal development and function Annu. Rev. Neurosci. 2001, 24, 677-736
14. Huang, E. J.; Reichardt, L. F. Trk receptors: roles in neuronal signal transduction Annu. Rev. Biochem. 2003, 72, 609-42
15. Link, A. J.; Vink, M. K.; Tirrell, D. A. Preparation of the functionalizable methionine surrogate azidohomoalanine via copper-catalyzed diazo transfer Nat. Protoc. 2007, 2, 1879-83
16. Rappsilber, J.; Mann, M.; Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips Nat. Protoc. 2007, 2, 1896-906
17. Villen, J.; Gygi, S. P. The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry Nat. Protoc. 2008, 3, 1630-8
18. McNulty, D. E.; Annan, R. S. Hydrophilic interaction chromatography reduces the complexity of the phosphoproteome and improves global phosphopeptide isolation and detection Mol. Cell Proteomics 2008, 7, 971-80
19. Michalski, A.; Damoc, E.; Hauschild, J. P.; Lange, O.; Wieghaus, A.; Makarov, A.; Nagaraj, N.; Cox, J.; Mann, M.; Horning, S. Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer Mol. Cell Proteomics 2011, 10, M111.011015
20. 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, 1367-72
21. Dennis, G., Jr.; Sherman, B. T.; Hosack, D. A.; Yang, J.; Gao, W.; Lane, H. C.; Lempicki, R. A. DAVID: database for annotation, visualization, and integrated discovery Genome Biol. 2003, 4, P3
22. Jensen, L. J.; Kuhn, M.; Stark, M.; Chaffron, S.; Creevey, C.; Muller, J.; Doerks, T.; Julien, P.; Roth, A.; Simonovic, M.; Bork, P.; von Mering, C. STRING 8-a global view on proteins and their functional interactions in 630 organisms Nucleic Acids Res. 2009, 37, D412-6
23. Choi, K. Y.; Lippert, D. N.; Ezzatti, P.; Mookherjee, N. Defining TNF-alpha and IL-1beta induced nascent proteins: combining bio-orthogonal non-canonical amino acid tagging and proteomics J. Immunol. Methods 2012, 382, 189-95
24. Hodas, J. J.; Nehring, A.; Hoche, N.; Sweredoski, M. J.; Pielot, R.; Hess, S.; Tirrell, D. A.; Dieterich, D. C.; Schuman, E. M. Dopaminergic modulation of the hippocampal neuropil proteome identified by bioorthogonal noncanonical amino acid tagging (BONCAT) Proteomics 2012, 12, 2464-76
25. Vaquerizas, J. M.; Kummerfeld, S. K.; Teichmann, S. A.; Luscombe, N. M. A census of human transcription factors: function, expression and evolution Nat. Rev. Genet. 2009, 10, 252-63
26. Gaiddon, C.; Loeffler, J. P.; Larmet, Y. Brain-derived neurotrophic factor stimulates AP-1 and cyclic AMP-responsive element dependent transcriptional activity in central nervous system neurons J. Neurochem 1996, 66, 2279-86
27. Lin, X.; Cui, H.; Bulleit, R. F. BDNF accelerates gene expression in cultured cerebellar granule neurons Dev. Brain Res. 1998, 105, 277-86
28. Yin, Y.; Edelman, G. M.; Vanderklish, P. W. The brain-derived neurotrophic factor enhances synthesis of Arc in synaptoneurosomes Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 2368-73
29. Calella, A. M.; Nerlov, C.; Lopez, R. G.; Sciarretta, C.; von Bohlen und Halbach, O.; Bereshchenko, O.; Minichiello, L. Neurotrophin/Trk receptor signaling mediates C/EBPalpha, -beta and NeuroD recruitment to immediate-early gene promoters in neuronal cells and requires C/EBPs to induce immediate-early gene transcription Neural Dev. 2007, 2, 4
30. Jeanneteau, F.; Deinhardt, K.; Miyoshi, G.; Bennett, A. M.; Chao, M. V. The MAP kinase phosphatase MKP-1 regulates BDNF-induced axon branching Nat. Neurosci. 2010, 13, 1373-9
31. Yang, E.; van Nimwegen, E.; Zavolan, M.; Rajewsky, N.; Schroeder, M.; Magnasco, M.; Darnell, J. E., Jr. Decay rates of human mRNAs: correlation with functional characteristics and sequence attributes Genome Res. 2003, 13, 1863-72