Proteomic analysis of monkey embryonic stem cell During differentiation

Journal of Proteome Research

Volumn 8, Issue 3, 2009, Pages 1527-1539

  Nasrabadi, Davood ^a   Larijani, Mehran Rezaei ^a   Pirhaji, Leila ^a   Gourabi, Hamid ^a   Shahverdi, Abdolhossein ^a   Baharvand, Hossein ^a,b   Salekdeh, Ghasem Hosseini ^a,c,d  

^a ROYAN INSTITUTE FOR REPRODUCTIVE BIOMEDICINE   (Iran)

^b UNIVERSITY OF SCIENCE AND CULTURE   (Iran)

^c AGRICULTURAL BIOTECHNOLOGY RESEARCH INSTITUTE OF IRAN   (Iran)

^d AGRICULTURAL BIOTECHNOLOGY RESEARCH INSTITUTE OF IRAN ABRII   (Iran)

Author keywords

Differentiation, monkey; Embryonic; Interaction,.network; Proteomics; Stem cells

Indexed keywords

ADENINE PHOSPHORIBOSYLTRANSFERASE; ADENOSYLHOMOCYSTEINASE; ADIPOPHILIN; ALPHA 1 ANTITRYPSIN; ALPHA ACTIN; ALPHA CRYSTALLIN; ALPHA ENOLASE; APOLIPOPROTEIN A1; CELL PROTEIN; CLATHRIN; ELONGATION FACTOR 1BETA; ENOYL COENZYME A HYDRATASE; EZRIN; FETUIN A; GLUTATHIONE TRANSFERASE; GLUTATHIONE TRANSFERASE M1; GROWTH FACTOR RECEPTOR BOUND PROTEIN 2; HEAT SHOCK PROTEIN 70; INITIATION FACTOR 4E; KERATIN TYPE I; KERATIN TYPE II; LIPOCORTIN 5; LYSOZYME; NUCLEOPHOSMIN; PROTEIN 14 3 3; PROTEIN DISULFIDE ISOMERASE; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE; RAS PROTEIN; TRANSALDOLASE; VIMENTIN;

AMINO ACID SEQUENCE; ANIMAL CELL; ARTICLE; CELL CYCLE PROGRESSION; CELL DIFFERENTIATION; CELL ENERGY; CELL GROWTH; CELL METABOLISM; CELL PROLIFERATION; CELL RENEWAL; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; EMBRYONIC STEM CELL; GENE IDENTIFICATION; GENETIC TRANSCRIPTION; MASS SPECTROMETRY; MONKEY; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN SYNTHESIS; PROTEOMICS; RNA TRANSLATION; SIGNAL TRANSDUCTION;

ANIMALS; CELL DIFFERENTIATION; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; EMBRYONIC STEM CELLS; MACACA FASCICULARIS; MICE; PROTEIN INTERACTION MAPPING; PROTEOME; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION;

EID: 65249184400     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr800880v     Document Type: Article

References (54)

1. Wolf, D. P.; Kuo, H. C.; Pau, K. Y. F.; Lester, L. Progress with nonhuman primate embryonic stem cells. Biol. Reprod. 2004, 71, 1766-1771.
2. Byrne, J. A.; Mitalipov, S. M.; Clepper, L.; Wolf, D. P. Transcriptional profiling of rhesus monkey embryonic stem cells. Biol. Reprod. 2006, 75 (6), 908.
3. Gygi, S. P.; Rochon, Y.; Franza, B. R.; Aebersold, R. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 1999, 19 (3), 1720.
4. Baharvand, H.; Fathi, A.; van Hoof, D.; Salekdeh, G. H. Concise review: trends in stem cell proteomics. Stem Cells 2007, 25 (8), 1888.
5. Kurisaki, A.; Hamazaki, T. S.; Okabayashi, K.; Iida, T.; Nishine, T.; Chonan, R.; Kido, H.; Tsunasawa, S.; Nishimura, O.; Asashima, M.; Sugino, H. Chromatin-related proteins in pluripotent mouse embryonic stem cells are downregulated after removal ofleukemia inhibitory factor. Biochem. Biophys. Res. Commun. 2005, 335 (3), 667-675.
6. Baharvand, H.; Fathi, A.; Gourabi, H.; Mollamohammadi, S.; Salekdeh, G. H. Identification of mouse embryonic stem cell- associated proteins. J. Proteome Res. 2008, 7 (1), 412-423.
7. Guo, X.; Ying, W.; Wan, J.; Hu, Z.; Qian, X.; Zhang, H.; He, F. Proteomic characterization of early-stage differentiation of mouse embryonic stem cells into neural cells induced by all-trans retinoic acid in vitro. Electrophoresis 2001, 22 (14), 3067-3075.
8. Van Hoof, D.; Passier, R.; Ward-Van Oostwaard, D.; Pinkse, M. W.; Heck, A. J.; Mummery, C. L.; Krijgsveld, J. A quest for human and mouse embryonic stem cell-specific proteins. Mol. Cell. Proteomics 2006, 5 (7), 1261-1273.
9. Suemori, H.; Nakatsuji, N. Growth and differentiation of cyno molgus monkey ES cells. Methods Enzymol. 2003, 365, 419-429.
10. Blum, H.; Beier, H.; Gross, H. J. Improved silver staining of plant proteins, RNA and DNA in polyacrylamide gels. Electrophoresis 1987, 8, 93-99.
11. Neuhoff, V.; Arold, N; Taube, D; Ehrhardt, W. Improved staining of proteins in polyacrylamide gels including isoelectric focusing gels with clear background at nanogram sensitivity using Coo-massie Brilliant Blue G-250 and R-250. Electrophoresis 1988, 9 (6), 255-262.
12. Ray, S.; Turi, R. H. Determination of number of clusters in k-means clustering and application in colour image segmentation. Proceed-
13. ings of the 4th International Conference on Advances in Pattern Recognition and Digital Techniques (ICAPRDT'99), Calcutta, India 1999, pp 137-143.
14. Kaufman, L.; Rousseeuw, P. J. Finding Groups in Data. An Introduction to Cluster Analysis. Wiley Series in Probability and Mathematical Statistics. Applied Probability and Statistics; Wiley: New York, 1990.
15. von Mering, C.; Jensen, L. J.; Kuhn, M.; Chaffron, S.; Doerks, T.; Kruger, B.; Snel, B.; Bork, P. STRING 7-recent developments in the integration and prediction of protein interactions. Nucleic Acids Res. 2007, 35 (Database issue), D358.
16. Han, J. D. J.; Bertin, N.; Hao, T.; Goldberg, D. S.; Berriz, G. F.; Zhang, L. V.; Dupuy, D.; Walhout, A. J. M.; Cusick, M. E.; Roth, F. P. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 2004, 430 (6995), 8893.
17. Jorgensen, P.; Tyers, M. How Cells Coordinate Growth and Division. Curr. Biol. 2004, 14 (23), 1014-1027.
18. Ruggero, D.; Pandolfi, P. P. Does the ribosome translate cancer. Nat. Rev. Cancer 2003, 3 (3), 179-192.
19. Desrivieres, S.; Kuhn, K.; Muller, J.; Glaser, M.; Laria, N. C. P.; Korder, J.; Sonnentag, M.; Neumann, T.; Schwarz, J.; Schafer, J. Comparison of the nuclear proteomes of mammary epithelial cells at different stages of functional differentiation. Proteomics 2007, 2007, 2019-2037.
20. Wei, C. L.; Miura, T.; Robson, P.; Lim, S. K.; Xu, X. Q.; Lee, M. Y. C.; Gupta, S.; Stanton, L.; Luo, Y.; Schmitt, J. Transcriptome profiling of human and murine ESCs identifies divergent paths required to maintain the stem cell state. Stem Cells 2005, 23, 166-185.
21. Bommer, U. A.; Thiele, B. J. The translationally controlled tumour protein (TCTP). Int. J. Biochem. Cell Biol. 2004, 36 (3), 379-385.
22. Gachet, Y.; Tournier, S.; Millar, J. B. A.; Hyams, J. S. A MAP kinase-dependent actin checkpoint ensures proper spindle orientation in fission yeast. Nature 2001, 412, 352-354.
23. Wang, D.; Gao, L. Proteomic analysis of neural differentiation of mouse embryonic stem cells. Proteomics 2005, 5 (17), 4414-4426.
24. Wang, D.; Gao, L. Proteomic analysis of neural differentiation of mouse embryonic stem cells. Proteomics 2005, 5 (17), 4414-4426.
25. Yan, L.; Fei, K.; Bridge, D.; Sarras Jr, M. P. A cnidarian homologue of translationally controlled tumor protein (P23/TCTP). Dev. Genes Evol. 2000, 210 (10), 507-511.
26. Kang, Y. J.; Olson, M. O. J.; Busch, H. Phosphorylation of acid-soluble proteins in isolated nucleoli of novikoff hepatoma ascites cells-effects of divalent cations. J. Biol. Chem. 1974, 249 (17), 55805585.
27. Chan, W. Y.; Liu, Q. R.; Borjigin, J.; Busch, H.; Rennert, O. M.; Tease, L. A.; Chan, P. K. Characterization of the cDNA encoding human nucleophosmin and studies of its role in normal and abnormal growth. Biochemistry 1989, 28 (3), 1033-1039.
28. Baharvand, H.; Hajheidari, M.; Ashtiani, S. K.; Salekdeh, G. H. Proteomic signature of human embryonic stem cells. Proteomics 2006, 6 (12), 3544-3549.
29. Wang, B. B.; Lu, R.; Wang, W. C.; Jin, Y. Inducible and reversible suppression of Npm1 gene expression using stably integrated small interfering RNA vector in mouse embryonic stem cells. Biochem. Biophys. Res. Commun. 2006, 347 (4), 1129-1137.
30. 2+-binding domains in reticulocalbin, an endoplasmic reticulum resident Ca2+-binding protein with multiple EF-hand motifs. J. Biochemistry 1997, 121 (1), 145.
31. Kent, J.; Lee, M.; Schedl, A.; Boyle, S.; Fantes, J.; Powell, M.; Rushmere, N.; Abbott, C.; van Heyningen, V.; Bickmore, W. A. The reticulocalbin gene maps to the WAGR region in human and to the small eye harwell deletion in mouse. Genomics 1997, 42 (2), 260-267.
32. Yu, L. R.; Zeng, R.; Shao, X. X.; Wang, N.; Xu, Y. H.; Xia, Q. C. Identification of differentially expressed proteins between human hepatoma and normal liver cell lines by two-dimensional electrophoresis and liquidchromatography-ion trap mass spectrometry. Electrophoresis 2000, 21 (14), 3058-3068.
33. Tong, A.; Zhang, H.; Li, Z.; Gou, L.; Wang, Z.; Wei, H.; Tang, M.; Liang, S.; Chen, L.; Huang, C. Proteomic analysis of liver cancer
34. cells treated with suberonylanilide hydroxamic acid. Cancer Chemother. Pharmacol. 2008, 61 (5), 791-802.
35. Rechsteiner, M.; Rogers, S. W. PEST sequences and regulation by proteolysis. Trends Biochem. Sci. 1996, 21 (7), 267-271.
36. Mori, T.; Li, Y.; Hata, H.; Kochi, H. NIRF is a ubiquitin ligase that is capable of ubiquitinating PCNP, a PEST-containing nuclear protein. FEBS Lett. 2004, 557 (1-3), 209-214.
37. Nakamura, H.; Izumoto, Y.; Kambe, H.; Kuroda, T.; Mori, T.; Kawamura, K.; Yamamoto, H.; Kishimoto, T. Molecular cloning of complementary DNA for a novel human hepatoma-derived growth factor. Its homology with high mobility group-1 protein. J. Biol. Chem. 1994, 269 (40), 25143-25149.
38. Jonsson, Z. O.; Jha, S.; Wohlschlegel, J. A.; Dutta, A. Rvb1p/Rvb2p recruit Arp5p and assemble a functional Ino80 chromatin remodeling complex. Mol. Cell 2004, 16 (3), 465-477.
39. Wood, M. A.; McMahon, S. B.; Cole, M. D. An ATPase/Helicase complex is an essential cofactor for oncogenic transformation by c-Myc. Mol. Cell 2000, 5 (2), 321-330.
40. Boguski, M. S.; McCormick, F. Proteins regulating Ras and its relatives. Nature 1993, 366 (6456), 643-654.
41. Quilliam, L. A.; Khosravi-Far, R.; Huff, S. Y.; Der, C. J. Guanine nucleotide exchange factors: activators of the Ras superfamily of proteins. BioEssays 1995, 17 (5), 395-404.
42. Blatch, G. L.; Laessle, M. The tetratricopeptide repeat: a structural motif mediating protein-protein interactions. BioEssays 1999, 21 (11), 932-939.
43. Marty, C.; Browning, D. D.; Ye, R. D. Identification of tetratri-copeptide repeat 1 as an adaptor protein that interacts with heterotrimeric G proteins and the small GTPase Ras. Mol. Cell. Biol. 2003, 23 (11), 3847-3858.
44. Parker, F.; Maurier, F.; Delumeau, I.; Duchesne, M.; Faucher, D.; Debussche, L.; Dugue, A.; Schweighoffer, F.; Tocque, B. A Ras-GTPase-activating protein SH3-domain-binding protein. Mol. Cell. Biol. 1996, 16 (6), 2561-2569.
45. Gallouzi, I.; Parker, F.; Chebli, K.; Maurier, F.; Labourier, E.; Barlat, I.; Capony, J. P.; Tocque, B.; Tazi, J. A novel phosphorylation-dependent RNase activity of GAP-SH3 binding protein: a potential link between signal transduction and RNAstability. Mol. Cell. Biol. 1998, 18 (7), 3956-3965.
46. Kociok, N.; Esser, P.; Unfried, K.; Parker, F.; Schraermeyer, U.; Grisanti, S.; Toque, B.; Heimann, K. Upregulation of the RAS-GTPase activating protein (GAP)-binding protein (G3BP) in proliferating RPE cells. J. Cell. Biochem. 1999, 74, 194-201.
47. Dang, C. V. c-Myc target genes involved in cell growth, apoptosis, and metabolism. Mol. Cell. Biol. 1999, 19, 1-11.
48. Chen, C. S.; Mrksich, M.; Huang, S.; Whitesides, G. M.; Ingber, D. E.Geometric control of cell life and death. Science 1997, 276 (5317), 1425.
49. Watt, F. M.; Jordan, P. W.; O'Neill, C. H. Cell shape controls terminal differentiation of human epidermal keratinocytes. Proc. Natl. Acad. Sci. U.S.A. 1988, 85 (15), 5576-5580.
50. Roskelley, C. D.; Desprez, P. Y.; Bissell, M. J. Extracellular matrix- dependent tissue-specific gene expression in mammary epithelial cells requires both physical and biochemical signal transduction. Proc. Natl. Acad. Sci. U.S.A. 1994, 91 (26), 12378-12382.
51. Pittenger, M. F.; Mackay, A. M.; Beck, S. C.; Jaiswal, R. K.; Douglas, R.; Mosca, J. D.; Moorman, M. A.; Simonetti, D. W.; Craig, S.; Marshak, D. R. Multilineage potential of adult human mesenchy-mal stem cells. Science 1999, 284 (5411), 143.
52. McBeath, R.; Pirone, D. M.; Nelson, C. M.; Bhadriraju, K.; Chen, C. S. Cell shape, cytoskeletal tension, and RhoA regulate stem cell lineage commitment. Dev. Cell 2004, 6 (4), 483-495.
53. Hynes, R. O.; Huang, S.; Chen, C. S.; Ingber, D. E. Control of Cyclin D1, p27Kip1, and cell cycle progression in human capillary endothelial cells by cell shape and cytoskeletal tension. Mol. Biol. Cell 1998, 9 (11), 3179-3193.
54. Bruneel, A.; Labas, V.; Mailloux, A.; Sharma, S.; Royer, N.; Vinh, J.; Pernet, P.; Vaubourdolle, M.; Baudin, B. Proteomics of human umbilical vein endothelial cells applied to etoposide-induced apoptosis. Proteomics 2005, 5 (15), 3876-3884. PR800880V