Label-free mass spectrometry proteome quantification of human embryonic kidney cells following 24 hours of sialic acid overproduction

Proteome Science

Volumn 11, Issue 1, 2013, Pages

  Parviainen, Ville I ^a   Joenväärä, Sakari ^a   Tohmola, Niina ^a   Renkonen, Risto ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

Author keywords

Label free quantification; Mass spectrometry; Proteomics; Sialic acid

Indexed keywords

MANNOSAMINE; N ACETYLMANNOSAMINE; PROTEOME; SIALIC ACID; UNCLASSIFIED DRUG;

ARTICLE; CELL JUNCTION; CONTROLLED STUDY; EMBRYO; EPITHELIUM CELL; HUMAN; HUMAN CELL; KIDNEY CELL; MASS SPECTROMETRY; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN METABOLISM; PROTEIN TRANSPORT; QUANTITATIVE ANALYSIS; SIGNAL TRANSDUCTION;

EUKARYOTA;

EID: 84880875215     PISSN: None     EISSN: 14775956     Source Type: Journal    
DOI: 10.1186/1477-5956-11-38     Document Type: Article

References (45)

1. Varki A. Sialic Acids. Essentials of glycobiology 2009, 199-217. New York: CSHL Press, Varki A, Schauer R, 2.
2. Mendla K, Baumkötter J, Rosenau C, Ulrich-Bott B, Cantz M. Defective lysosomal release of glycoprotein-derived sialic acid in fibroblasts from patients with sialic acid storage disease. Biochem J 1988, 250(1):261. 1148842, 2451509.
3. Tanner ME. The enzymes of sialic acid biosynthesis. Bioorg Chem 2005, 33(3):216. 10.1016/j.bioorg.2005.01.005, 15888312.
4. Murayama T, Zuber C, Seelentag WK, Li W, Kemmner W, Heitz PU, Roth J. Colon carcinoma glycoproteins carrying α 2, 6-linked sialic acid reactive with Sambucus Nigra agglutinin are not constitutively expressed in normal human colon mucosa and are distinct from sialyl-tn antigen. Int J Cancer 1997, 70(5):575-581. 10.1002/(SICI)1097-0215(19970304)70:5<575::AID-IJC14>3.0.CO;2-C, 9052758.
5. Tian Y, Esteva FJ, Song J, Zhang H. Altered expression of sialylated glycoproteins in breast cancer using hydrazide chemistry and mass spectrometry. Mol Cell Proteomics 2012, 11(6). M111.011403.
6. Kaneko Y, Yamamoto H, Kersey DS, Colley KJ, Leestma JE, Moskal JR. The expression of Galβ1, 4GlcNAc α2, 6 sialyltransferase and α2, 6-linked sialoglycoconjugates in human brain tumors. Acta Neuropathol 1996, 91(3):284-292. 10.1007/s004010050427, 8834541.
7. Dall'Olio F, Chiricolo M. Sialyltransferases in cancer. Glycoconj J 2001, 18(11-12):841-850.
8. Lau KS, Partridge EA, Grigorian A, Silvescu CI, Reinhold VN, Demetriou M, Dennis JW. Complex N-glycan number and degree of branching cooperate to regulate cell proliferation and differentiation. Cell 2007, 129(1):123-134. 10.1016/j.cell.2007.01.049, 17418791.
9. Almaraz RT, Tian Y, Bhattarcharya R, Tan E, Chen SH, Dallas MR, Chen L, Zhang Z, Zhang H, Konstantopoulos K. Metabolic flux increases glycoprotein sialylation: implications for cell adhesion and cancer metastasis. Mol Cell Proteomics 2012, 11(7). M112.017558.
10. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 1999, 17(10):994-999. 10.1038/13690, 10504701.
11. Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S. Multiplexed Protein Quantitation in Saccharomyces cerevisiae Using Amine-reactive Isobaric Tagging Reagents* S. Mol Cell Proteomics 2004, 3(12):1154-1169. 10.1074/mcp.M400129-MCP200, 15385600.
12. Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, 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(5):376-386. 10.1074/mcp.M200025-MCP200, 12118079.
13. Shevchenko A, Chernushevich I, Ens W, Standing KG, Thomson B, Wilm M, Mann M. Rapid'de novo'peptide sequencing by a combination of nanoelectrospray, isotopic labeling and a quadrupole/time-of-flight mass spectrometer. Rapid Commun Mass Spectrom 1997, 11(9):1015-1024. 10.1002/(SICI)1097-0231(19970615)11:9<1015::AID-RCM958>3.0.CO;2-H, 9204576.
14. Ishihama Y, Oda Y, Tabata T, Sato T, Nagasu T, Rappsilber J, Mann M. Exponentially modified protein abundance index (emPAI) for estimation of absolute protein amount in proteomics by the number of sequenced peptides per protein. Mol Cell Proteomics 2005, 4(9):1265-1272. 10.1074/mcp.M500061-MCP200, 15958392.
15. Silva JC, Gorenstein MV, Li GZ, Vissers JP, Geromanos SJ. Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Mol Cell Proteomics 2006, 5(1):144-156.
16. Wang Z, Sun Z, Li AV, Yarema KJ. Roles for UDP-GlcNAc 2-epimerase/ManNAc 6-kinase outside of sialic acid biosynthesis: modulation of sialyltransferase and BiP expression, GM3 and GD3 biosynthesis, proliferation, and apoptosis, and ERK1/2 phosphorylation. J Biol Chem 2006, 281(37):27016-27028. 10.1074/jbc.M604903200, 16847058.
17. Shen Z, Li P, Ni RJ, Ritchie M, Yang CP, Liu GF, Ma W, Liu GJ, Ma L, Li SJ, Wei ZG, Wang HX, Wang BC. Label-free quantitative proteomics analysis of etiolated maize seedling leaves during greening. Mol Cell Proteomics 2009, 8(11):2443-2460. 10.1074/mcp.M900187-MCP200, 2773713, 19666873.
18. Silva JC, Denny R, Dorschel C, Gorenstein MV, Li GZ, Richardson K, Wall D, Geromanos SJ. Simultaneous qualitative and quantitative analysis of the escherichia coli proteome a sweet tale. Mol Cell Proteomics 2006, 5(4):589-607.
19. Vissers JP, Langridge JI, Aerts JM. Analysis and quantification of diagnostic serum markers and protein signatures for Gaucher disease. Mol Cell Proteomics 2007, 6(5):755-766. 10.1074/mcp.M600303-MCP200, 17293593.
20. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-2504. 10.1101/gr.1239303, 403769, 14597658.
21. Maere S, Heymans K, Kuiper M. BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 2005, 21(16):3448-3449. 10.1093/bioinformatics/bti551, 15972284.
22. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25(1):25-29. 10.1038/75556, 3037419, 10802651.
23. Da Wei H, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2008, 4(1):44-57.
24. Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 2009, 37(1):1-13. 10.1093/nar/gkn923, 2615629, 19033363.
25. Cowley MJ, Pinese M, Kassahn KS, Waddell N, Pearson JV, Grimmond SM, Biankin AV, Hautaniemi S, Wu J. PINA v2. 0: mining interactome modules. Nucleic Acids Res 2012, 40(D1):D862-D865. 10.1093/nar/gkr967, 3244997, 22067443.
26. Wu J, Vallenius T, Ovaska K, Westermarck J, Mäkelä TP, Hautaniemi S. Integrated network analysis platform for protein-protein interactions. Nat Methods 2008, 6(1):75-77.
27. Behnia R, Munro S. Organelle identity and the signposts for membrane traffic. Nature 2005, 438(7068):597-604. 10.1038/nature04397, 16319879.
28. Zerial M, McBride H. Rab proteins as membrane organizers. Nat Rev Mol Cell Biol 2001, 2(2):107-117. 10.1038/35052055, 11252952.
29. Grosshans BL, Ortiz D, Novick P. Rabs and their effectors: achieving specificity in membrane traffic. Proc Natl Acad Sci 2006, 103(32):11821-11827. 10.1073/pnas.0601617103, 1567661, 16882731.
30. Short B, Haas A, Barr FA. Golgins and GTPases, giving identity and structure to the Golgi apparatus. Biochimica et Biophysica Acta (BBA)-Mol Cell Res 2005, 1744(3):383-395.
31. Liwosz A, Lei T, Kukuruzinska MA. N-glycosylation affects the molecular organization and stability of E-cadherin junctions. J Biol Chem 2006, 281(32):23138-23149. 10.1074/jbc.M512621200, 16682414.
32. Vagin O, Tokhtaeva E, Yakubov I, Shevchenko E, Sachs G. Inverse correlation between the extent of N-glycan branching and intercellular adhesion in epithelia. J Biol Chem 2008, 283(4):2192-2202. 2423813, 18025087.
33. Takeichi M. Cadherin cell adhesion receptors as a morphogenetic regulator. Science 1991, 251(5000):1451-1455. 10.1126/science.2006419, 2006419.
34. Lampugnani MG, Corada M, Andriopoulou P, Esser S, Risau W, Dejana E. Cell confluence regulates tyrosine phosphorylation of adherens junction components in endothelial cells. J Cell Sci 1997, 110(17):2065-2077.
35. Kamei T, Matozaki T, Sakisaka T, Kodama A, Yokoyama S, Peng Y, Nakano K, Takaishi K, Takai Y. Coendocytosis of cadherin and c-Met coupled to disruption of cell-cell adhesion in MDCK cells-regulation by Rho, Rac and Rab small G proteins. Oncogene 1999, 18(48):6776. 10.1038/sj.onc.1203114, 10597286.
36. Palacios F, Schweitzer JK, Boshans RL, D'Souza-Schorey C. ARF6-GTP recruits Nm23-H1 to facilitate dynamin-mediated endocytosis during adherens junctions disassembly. Nat Cell Biol 2002, 4(12):929-936. 10.1038/ncb881, 12447393.
37. Cavallaro U, Dejana E. Adhesion molecule signalling: not always a sticky business. Nat Rev Mol Cell Biol 2011, 12(3):189-197. 10.1038/nrm3068, 21346732.
38. Iwahana H, Oka J, Mizusawa N, Kudo E, Ii S, Yoshimoto K, Holmes E, Itakura M. Molecular cloning of human amidophosphoribosyltransferase. Biochem Biophys Res Commun 1993, 190(1):192-200. 10.1006/bbrc.1993.1030, 8380692.
39. Powell SM, Zalkin H, Dixon JE. Cloning and characterization of the cDNA encoding human adenylosuccinate synthetase. FEBS Lett 1992, 303(1):4-10. 10.1016/0014-5793(92)80465-S, 1592113.
40. Halim A, LeGros L, Geller A, Kotb M. Expression and functional interaction of the catalytic and regulatory subunits of human methionine adenosyltransferase in mammalian cells. J Biol Chem 1999, 274(42):29720-29725. 10.1074/jbc.274.42.29720, 10514445.
41. Nordgren KK, Peng Y, Pelleymounter LL, Moon I, Abo R, Feng Q, Eckloff B, Yee VC, Wieben E, Weinshilboum RM. Methionine adenosyltransferase 2A/2B and methylation: gene sequence variation and functional genomics. Drug Metab Disposition 2011, 39(11):2135-2147.
42. Bereman MS, Egertson JD, MacCoss MJ. Comparison between procedures using SDS for shotgun proteomic analyses of complex samples. Proteomics 2011, 11(14):2931-2935. 10.1002/pmic.201100045, 3517139, 21656683.
43. Dennis G, Sherman BT, Hosack DA, Yang J, Gao W, Lane HC, Lempicki RA. DAVID: database for annotation, visualization, and integrated discovery. Genome Biol 2003, 4(5):P3. 10.1186/gb-2003-4-5-p3, 3720094, 12734009.
44. The Database for Annotation, Visualization and Integrated Discovery (DAVID) [http://david.abcc.ncifcrf.gov/].
45. Ingenuity Systems [http://www.ingenuity.com].