Cell-specific labeling enzymes for analysis of cell-cell communication in continuous co-culture

Molecular and Cellular Proteomics

Volumn 13, Issue 7, 2014, Pages 1866-1876

  Tape, Christopher J ^a,b   Norrie, Ida C ^a   Worboys, Jonathan D ^a   Lim, Lindsay ^a   Lauffenburger, Douglas A ^b   Jørgensen, Claus ^a,c  

^a INSTITUTE OF CANCER RESEARCH   (United Kingdom)

^b Massachusetts Institute of Technology Cambridge   (United States)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CARBOXYLYASE; DIAMINOPIMELIC ACID; LYSINE; LYSINE RACEMASE; MESO 2,6 DIAMINOPIMELATE; RACEMASE; UNCLASSIFIED DRUG; AMINO ACID; BACTERIAL PROTEIN; DIAMINOPIMELIC ACID DECARBOXYLASE; ISOMERASE; LYSA PROTEIN, MYCOBACTERIUM TUBERCULOSIS;

ARTICLE; CELL COMMUNICATION; CELL LABELING; CELL LYSATE; CELL PROLIFERATION; CELL SPECIFICITY; COCULTURE; ENDOPLASMIC RETICULUM; ENZYME PHOSPHORYLATION; EPITHELIUM TUMOR; EUKARYOTIC CELL; FIBROBLAST; GENE SYNTHESIS; ISOTOPE LABELING; METHANOCALDOCOCCUS JANNASCHII; MYCOBACTERIUM AVIUM; MYCOBACTERIUM LEPRAE; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; TUMOR CELL; AMINO ACID SEQUENCE; ANIMAL; ARABIDOPSIS; C3H MOUSE; ENZYMOLOGY; GENETICS; HELICOBACTER PYLORI; METABOLISM; METHANOCALDOCOCCUS; MOUSE; PHOSPHORYLATION; PROCEDURES; PROTEUS MIRABILIS; SIGNAL TRANSDUCTION; STAINING; TUMOR CELL LINE;

AMINO ACID ISOMERASES; AMINO ACID SEQUENCE; AMINO ACIDS; ANIMALS; ARABIDOPSIS; BACTERIAL PROTEINS; CARBOXY-LYASES; CELL COMMUNICATION; CELL LINE, TUMOR; CELL PROLIFERATION; COCULTURE TECHNIQUES; DIAMINOPIMELIC ACID; ENDOPLASMIC RETICULUM; HELICOBACTER PYLORI; METHANOCALDOCOCCUS; MICE; MICE, INBRED C3H; MYCOBACTERIUM TUBERCULOSIS; PHOSPHORYLATION; PROTEOMICS; PROTEUS MIRABILIS; SIGNAL TRANSDUCTION; STAINING AND LABELING;

EID: 84904106705     PISSN: 15359476     EISSN: 15359484     Source Type: Journal    
DOI: 10.1074/mcp.O113.037119     Document Type: Article

References (29)

1. Garden, G. A., and La Spada, A. R. (2012) Intercellular (mis)communication in neurodegenerative disease. Neuron 73, 886-901
2. Ong, S. E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., and Mann, M. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 1, 376-386
3. Jorgensen, C., Sherman, A., Chen, G. I., Pasculescu, A., Poliakov, A., Hsiung, M., Larsen, B., Wilkinson, D. G., Linding, R., and Pawson, T. (2009) Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells. Science 326, 1502-1509
4. Gauthier, N. P., Soufi, B., Walkowicz, W. E., Pedicord, V. A., Mavrakis, K. J., Macek, B., Gin, D. Y., Sander, C., and Miller, M. L. (2013) Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments. Nat. Methods 10(8), 768-73
5. Dewey, D. L., and Work, E. (1952) Diaminopimelic acid decarboxylase. Nature 169, 533-534
6. Huang, H. T., Kita, D. A., and Davisson, J. W. (1952) Racemization of lysine by Proteus vulgaris. J. Am. Chem. Soc. 80, 1006-1007
7. Maclean, B., Tomazela, D. M., Abbatiello, S. E., Zhang, S., Whiteaker, J. R., Paulovich, A. G., Carr, S. A., and Maccoss, M. J. (2010) Effect of collision energy optimization on the measurement of peptides by selected reaction monitoring (SRM) mass spectrometry. Anal. Chem. 82, 10116-10124
8. MacLean, B., Tomazela, D. M., Shulman, N., Chambers, M., Finney, G. L., Frewen, B., Kern, R., Tabb, D. L., Liebler, D. C., and MacCoss, M. J. (2010) Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26, 966-968
9. Wisniewski, J. R., Zougman, A., Nagaraj, N., and Mann, M. (2009) Universal sample preparation method for proteome analysis. Nat. Methods 6, 359-362
10. Kall, L., Canterbury, J. D., Weston, J., Noble, W. S., and MacCoss, M. J. (2007) Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat. Methods 4, 923-925 (Pubitemid 350042380)
11. Taus, T., Kocher, T., Pichler, P., Paschke, C., Schmidt, A., Henrich, C., and Mechtler, K. (2011) Universal and confident phosphorylation site localization using phosphoRS. J. Proteome Res. 10, 5354-5362
12. Vizcaino, J. A., Cote, R. G., Csordas, A., Dianes, J. A., Fabregat, A., Foster, J. M., Griss, J., Alpi, E., Birim, M., Contell, J., O'Kelly, G., Schoenegger, A., Ovelleiro, D., Perez-Riverol, Y., Reisinger, F., Rios, D., Wang, R., and Hermjakob, H. (2013) The PRoteomics IDEntifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 41, D1063-D1069
13. Hu, T., Wu, D., Chen, J., Ding, J., Jiang, H., and Shen, X. (2008) The catalytic intermediate stabilized by a "down" active site loop for diaminopimelate decarboxylase from Helicobacter pylori. Enzymatic characterization with crystal structure analysis. J. Biol. Chem. 283, 21284-21293
14. Petersen, T. N., Brunak, S., von Heijne, G., and Nielsen, H. (2011) SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat. Methods 8, 785-786
15. Munro, S., and Pelham, H. R. (1987) A C-terminal signal prevents secretion of luminal ER proteins. Cell 48, 899-907
16. Samuel, C. E. (1993) The eIF-2 alpha protein kinases, regulators of translation in eukaryotes from yeasts to humans. J. Biol. Chem. 268, 7603-7606
17. Gokulan, K., Rupp, B., Pavelka, M. S., Jr., Jacobs, W. R., Jr., and Sacchettini, J. C. (2003) Crystal structure of Mycobacterium tuberculosis diaminopimelate decarboxylase, an essential enzyme in bacterial lysine biosynthesis. J. Biol. Chem. 278, 18588-18596 (Pubitemid 36799486)
18. Wu, H. M., Kuan, Y. C., Chu, C. H., Hsu, W. H., and Wang, W. C. (2012) Crystal structures of lysine-preferred racemases, the non-antibiotic selectable markers for transgenic plants. PLoS One 7, e48301
19. Saqib, K. M., Hay, S. M., and Rees, W. D. (1994) The expression of Escherichia coli diaminopimelate decarboxylase in mouse 3T3 cells. Biochim. Biophys. Acta 1219, 398-404 (Pubitemid 24319699)
20. Hundal, H. S., and Taylor, P. M. (2009) Amino acid transceptors: gate keepers of nutrient exchange and regulators of nutrient signaling. Am. J. Physiol. Endocrinol. Metab. 296, E603-E613
21. Rechavi, O., Kalman, M., Fang, Y., Vernitsky, H., Jacob-Hirsch, J., Foster, L. J., Kloog, Y., and Goldstein, I. (2010) Trans-SILAC: sorting out the non-cell-autonomous proteome. Nat. Methods 7, 923-927
22. Herve, J. C., and Derangeon, M. (2013) Gap-junction-mediated cell-to-cell communication. Cell Tissue Res. 352, 21-31
23. Bandi, H. R., Ferrari, S., Krieg, J., Meyer, H. E., and Thomas, G. (1993) Identification of 40 S ribosomal protein S6 phosphorylation sites in Swiss mouse 3T3 fibroblasts stimulated with serum. J. Biol. Chem. 268, 4530-4533 (Pubitemid 23073004)
24. Roux, P. P., Shahbazian, D., Vu, H., Holz, M. K., Cohen, M. S., Taunton, J., Sonenberg, N., and Blenis, J. (2007) RAS/ERK signaling promotes sitespecific ribosomal protein S6 phosphorylation via RSK and stimulates cap-dependent translation. J. Biol. Chem. 282, 14056-14064 (Pubitemid 47100467)
25. Shahbazian, D., Roux, P. P., Mieulet, V., Cohen, M. S., Raught, B., Taunton, J., Hershey, J. W., Blenis, J., Pende, M., and Sonenberg, N. (2006) The mTOR/PI3K and MAPK pathways converge on eIF4B to control its phosphorylation and activity. EMBO J. 25, 2781-2791 (Pubitemid 43980385)
26. Lee, S. J., Pfluger, P. T., Kim, J. Y., Nogueiras, R., Duran, A., Pages, G., Pouyssegur, J., Tschop, M. H., Diaz-Meco, M. T., and Moscat, J. (2010) A functional role for the p62-ERK1 axis in the control of energy homeostasis and adipogenesis. EMBO Rep. 11, 226-232
27. Linares, J. F., Amanchy, R., Greis, K., Diaz-Meco, M. T., and Moscat, J. (2011) Phosphorylation of p62 by cdk1 controls the timely transit of cells through mitosis and tumor cell proliferation. Mol. Cell. Biol. 31, 105-117
28. Jenzora, A., Behrendt, B., Small, J. V., Wehland, J., and Stradal, T. E. (2005) PREL1 provides a link from Ras signalling to the actin cytoskeleton via Ena/VASP proteins. FEBS Lett. 579, 455-463 (Pubitemid 40092426)
29. Yoshimura, T., Kawano, Y., Arimura, N., Kawabata, S., Kikuchi, A., and Kaibuchi, K. (2005) GSK-3beta regulates phosphorylation of CRMP-2 and neuronal polarity. Cell 120, 137-149