Abstract
This review discusses the challenges facing research in ‘functional glycomics’ and the novel technologies that are being developed to advance the field. The structural complexity of glycans and glycoconjugates makes studies of both their structures and recognition difficult. However, these intricate structures can be captured from their natural sources, isolated and fluorescently-tagged for detailed structural analysis and for presentation on glycan microarrays for functional recognition by glycan-binding proteins. These advances in glycan preparation and manipulation enable the streamlining of functional glycomics studies and will help to propel the field forward in studying natural, biologically relevant glycans.
Similar content being viewed by others
References
Cummings, R.D., Pierce, J.M.: The challenge and promise of glycomics. Chem. Biol. (Oxford, U K) 21(1), 1–15 (2014)
Paulson, J.C., Blixt, O., Collins, B.E.: Sweet spots in functional glycomics. Nat. Chem. Biol. 2(5), 238–248 (2006)
Smith, D.F., Cummings, R.D.: Application of microarrays for deciphering the structure and function of the human glycome. Mol. Cell. Proteomics 12(4), 902–912 (2013)
Taniguchi, N., Hancock, W., Lubman, D.M., Rudd, P.M.: The second golden Age of glycomics: from functional glycomics to clinical applications. J. Proteome Res. 8(2), 425–426 (2009)
Cummings, R.D.: The repertoire of glycan determinants in the human glycome. Mol. Biosyst. 5(10), 1087–1104 (2009)
Gahoi, N., Ray, S., Srivastava, S.: Array-based proteomic approaches to study signal transduction pathways: prospects, merits and challenges. Proteomics 15(2–3), 218–231 (2015)
Marino, K., Bones, J., Kattla, J.J., Rudd, P.M.: A systematic approach to protein glycosylation analysis: a path through the maze. Nat. Chem. Biol. 6(10), 713–723 (2010)
Zaia, J.: Mass spectrometry and glycomics. OMICS 14(4), 401–418 (2010)
Jensen, P.H., Karlsson, N.G., Kolarich, D., Packer, N.H.: Structural analysis of N- and O-glycans released from glycoproteins. Nat. Protoc. 7(7), 1299–1310 (2012)
Lundborg, M., Widmalm, G.: Structural analysis of glycans by NMR chemical shift prediction. Anal. Chem. 83(5), 1514–1517 (2011)
North, S.J., Hitchen, P.G., Haslam, S.M., Dell, A.: Mass spectrometry in the analysis of N-linked and O-linked glycans. Curr. Opin. Struct. Biol. 19(5), 498–506 (2009)
Toukach, F.V., Ananikov, V.P.: Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations. Chem. Soc. Rev. 42(21), 8376–8415 (2013)
Wang, L.X., Davis, B.G.: Realizing the promise of chemical glycobiology. Chem. Sci. 4(9), 3381–3394 (2013)
Castagner, B., Seeberger, P.H.: Automated solid phase oligosaccharide synthesis. Top. Curr. Chem. 278, 289–309 (2007)
Hsu, C.-H., Hung, S.-C., Wu, C.-Y., Wong, C.-H.: Toward automated oligosaccharide synthesis. Angew. Chem. Int. Ed. 50(50), 11872–11923 (2011)
Marino, P.A., Muthana, S.M., Gildersleeve, J.C.: Glycan microarrays: powerful tools for biomarker discovery. Cancer. Biomark 14(1), 29–41 (2014)
Smith, D.F., Song, X., Cummings, R.D.: Use of glycan microarrays to explore specificity of glycan-binding proteins. Methods Enzymol. 480, 417–444 (2010)
Fukui, S., Feizi, T., Galustian, C., Lawson, A.M., Chai, W.: Oligosaccharide microarrays for high-throughput detection and specificity assignments of carbohydrate-protein interactions. Nat. Biotechnol. 20, 1011–1017 (2002)
Blixt, O., Head, S., Mondala, T., Scanlan, C., Huflejt, M.E., Alvarez, R., Bryan, M.C., Fazio, F., Calarese, D., Stevens, J., Razi, N., Stevens, D.J., Skehel, J.J., van Die, I., Burton, D.R., Wilson, I.A., Cummings, R., Bovin, N., Wong, C.H., Paulson, J.C.: Printed covalent glycan array for ligand profiling of diverse glycan binding proteins. Proc. Natl. Acad. Sci. U. S. A. 101(49), 17033–17038 (2004)
Park, S., Shin, I.: Fabrication of carbohydrate chips for studying protein-carbohydrate interactions. Angew. Chem. Int. Ed. Engl. 41(17), 3180–3182 (2002)
Song, X., Heimburg-Molinaro, J., Cummings, R.D., Smith, D.F.: Chemistry of natural glycan microarrays. Curr. Opin. Chem. Biol. 18, 70–77 (2014)
Alvarez, R.A., Blixt, O.: Identification of ligand specificities for glycan-binding proteins using glycan arrays. Methods Enzymol. 415, 292–310 (2006)
Rillahan, C.D., Paulson, J.C.: Glycan microarrays for decoding the glycome. Annu. Rev. Biochem. 80, 797–823 (2011)
Han, X., Zheng, Y., Munro, C.J., Ji, Y., Braunschweig, A.B...: Carbohydrate nanotechnology: hierarchical assembly using nature’s other information carrying biopolymers. Curr. Opin. Biotechnol. 34C, 41–47 (2014)
Song, X., Lasanajak, Y., Rivera-Marrero, C., Luyai, A., Willard, M., Smith, D.F., Cummings, R.D.: Generation of a natural glycan microarray using 9-fluorenylmethyl chloroformate (FmocCl) as a cleavable fluorescent tag. Anal. Biochem. 395(2), 151–160 (2009)
Song, X., Lasanajak, Y., Xia, B., Heimburg-Molinaro, J., Rhea, J.M., Ju, H., Zhao, C., Molinaro, R.J., Cummings, R.D., Smith, D.F.: Shotgun glycomics: a microarray strategy for functional glycomics. Nat. Methods 8(1), 85–90 (2011)
Palma, A.S., Feizi, T., Childs, R.A., Chai, W., Liu, Y.: The neoglycolipid (NGL)-based oligosaccharide microarray system poised to decipher the meta-glycome. Curr. Opin. Chem. Biol. 18, 87–94 (2014)
Muthana, S.M., Gildersleeve, J.C.: Glycan microarrays: powerful tools for biomarker discovery. Cancer. Biomark 14(1), 29–41 (2014)
Breitling, J., Aebi, M.: N-linked protein glycosylation in the endoplasmic reticulum. Cold Spring Harb. Perspect. Biol. 5(8), a013359 (2013)
Stanley, P., Schachter, H., Taniguchi, N.: N-Glycans (Chapter 8) In: Essentials of Glycobiology, Cold Spring Harbor Laboratories Press (2009)
Tarentino, A.L., Plummer Jr., T.H., Maley, F.: The release of intact oligosaccharides from specific glycoproteins by endo-beta-N-acetylglucosaminidase H. J Biol. Chem. 249(3), 818–824 (1974)
Elder, J.H., Alexander, S.: endo-beta-N-acetylglucosaminidase F: endoglycosidase from Flavobacterium meningosepticum that cleaves both high-mannose and complex glycoproteins. Proc. Natl. Acad. Sci. U. S. A. 79(15), 4540–4544 (1982)
Plummer Jr., T.H., Tarentino, A.L.: Purification of the oligosaccharide-cleaving enzymes of Flavobacterium meningosepticum. Glycobiology 1(3), 257–263 (1991)
Takahashi, N., Nishibe, H.: Some characteristics of a new glycopeptidase acting on aspartylglycosylamine linkages. J. Biochem. 84(6), 1467–1473 (1978)
Taga, E.M., Waheed, A., Van Etten, R.L.: Structural and chemical characterization of a homogeneous peptide N-glycosidase from almond. Biochemistry 23(5), 815–822 (1984)
Tretter, V., Altmann, F., Marz, L.: Peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase F cannot release glycans with fucose attached alpha 1–3 to the asparagine-linked N-acetylglucosamine residue. Eur J Biochem. FEBS 199(3), 647–652 (1991)
Yosizawa, Z., Sato, T., Schmid, K.: Hydrazinolysis of alpha-1-acid glycoprotein. Biochim. Biophys. Acta 121(2), 417–420 (1966)
Nakakita, S., Sumiyoshi, W., Miyanishi, N., Hirabayashi, J.: A practical approach to N-glycan production by hydrazinolysis using hydrazine monohydrate. Biochem. Biophys. Res. Commun. 362(3), 639–645 (2007)
Huang, Y., Mechref, Y., Novotny, M.V.: Microscale nonreductive release of O-linked glycans for subsequent analysis through MALDI mass spectrometry and capillary electrophoresis. Anal. Chem. 73(24), 6063–6069 (2001)
Yu, G., Zhang, Y., Zhang, Z., Song, L., Wang, P., Chai, W.: Effect and limitation of excess ammonium on the release of O-glycans in reducing forms from glycoproteins under mild alkaline conditions for glycomic and functional analysis. Anal. Chem. 82(22), 9534–9542 (2010)
Song, X., Ju, H., Zhao, C., Lasanajak, Y.: Novel strategy to release and tag N-glycans for functional glycomics. Bioconjug. Chem. 25(10), 1881–1887 (2014)
Endo, Y., Kobata, A.: Partial purification and characterization of an endo-alpha-N-acetylgalactosaminidase from the culture of medium of Diplococcus pneumoniae. J. Biochem. 80(1), 1–8 (1976)
Carlson, D.M.: Oligosaccharides isolated from pig submaxillary mucin. J. Biol. Chem. 241(12), 2984–2986 (1966)
Carlson, D.M.: Structures and immunochemical properties of oligosaccharides isolated from pig submaxillary mucins. J. Biol. Chem. 243(3), 616–626 (1968)
Wang, C., Fan, W., Zhang, P., Wang, Z., Huang, L.: One-pot nonreductive O-glycan release and labeling with 1-phenyl-3-methyl-5-pyrazolone followed by ESI-MS analysis. Proteomics 11(21), 4229–4242 (2011)
Zauner, G., Koeleman, C.A., Deelder, A.M., Wuhrer, M.: Mass spectrometric O-glycan analysis after combined O-glycan release by beta-elimination and 1-phenyl-3-methyl-5-pyrazolone labeling. Biochim. Biophys. Acta 1820(9), 1420–1428 (2012)
Merry, A.H., Neville, D.C.A., Royle, L., Matthews, B., Harvey, D.J., Dwek, R.A., Rudd, P.M.: Recovery of intact 2-aminobenzamide-labeled o-glycans released from glycoproteins by hydrazinolysis. Anal. Biochem. 304(1), 91–99 (2002)
Patel, T., Bruce, J., Merry, A., Bigge, C., Wormald, M., Parekh, R., Jaques, A.: Use of hydrazine to release in intact and unreduced form both N- and O-linked oligosaccharides from glycoproteins. Biochemistry 32(2), 679–693 (1993)
Chai, W., Feizi, T., Yuen, C.T., Lawson, A.M.: Nonreductive release of O-linked oligosaccharides from mucin glycoproteins for structure/function assignments as neoglycolipids: application in the detection of novel ligands for E-selectin. Glycobiology 7(6), 861–872 (1997)
Miura, Y., Kato, K., Takegawa, Y., Kurogochi, M., Furukawa, J., Shinohara, Y., Nagahori, N., Amano, M., Hinou, H., Nishimura, S.: Glycoblotting-assisted O-glycomics: ammonium carbamate allows for highly efficient o-glycan release from glycoproteins. Anal. Chem. 82(24), 10021–10029 (2010)
Prasanphanich, N.S., Song, X., Heimburg-Molinaro, J., Luyai, A., Lasanajak, Y., Cutler, C., Smith, D.F., Cummings, R.D.: An intact reducing glycan promotes the specific immune response to lacto-N-neotetraose-BSA neoglycoconjugates. Bioconjug. Chem. 26(3), 559–571 (2015)
Ito, M., Yamagata, T.: A novel glycosphingolipid-degrading enzyme cleaves the linkage between the oligosaccharide and ceramide of neutral and acidic glycosphingolipids. J. Biol. Chem. 261(30), 14278–14282 (1986)
Ito, M., Yamagata, T.: Purification and characterization of glycosphingolipid-specific endoglycosidases (endoglycoceramidases) from a mutant strain of Rhodococcus sp. Evidence for three molecular species of endoglycoceramidase with different specificities. J. Biol. Chem. 264(16), 9510–9519 (1989)
Ashida, H., Yamamoto, K., Kumagai, H., Tochikura, T.: Purification and characterization of membrane-bound endoglycoceramidase from Corynebacterium sp. Eur J Biochem. FEBS 205(2), 729–735 (1992)
Ishibashi, Y., Nakasone, T., Kiyohara, M., Horibata, Y., Sakaguchi, K., Hijikata, A., Ichinose, S., Omori, A., Yasui, Y., Imamura, A., Ishida, H., Kiso, M., Okino, N., Ito, M.: A novel endoglycoceramidase hydrolyzes oligogalactosylceramides to produce galactooligosaccharides and ceramides. J. Biol. Chem. 282(15), 11386–11396 (2007)
Wiegandt, H., Baschang, G.: The isolation of the sugar portion of glycosphingolipids by ozonolysis and fragmentation. Z Naturforsch B 20, 164–166 (1965)
Hakomori, S.I.: Release of carbohydrates from sphingoglycolipid by osmium-catalyzed periodate oxidation followed by treatment with mild alkali. J. Lipid Res. 7(6), 789–792 (1966)
Song, X., Smith, D.F., Cummings, R.D.: Nonenzymatic release of free reducing glycans from glycosphingolipids. Anal. Biochem. 429, 82–87 (2012). Copyright (C) 2013 American Chemical Society (ACS). All Rights Reserved
Noti, C., de Paz, J.L., Polito, L., Seeberger, P.H.: Preparation and use of microarrays containing synthetic heparin oligosaccharides for the rapid analysis of heparin-protein interactions. Chemistry 12(34), 8664–8686 (2006)
Park, T.J., Lee, M.Y., Dordick, J.S., Linhardt, R.J.: Signal amplification of target protein on heparin glycan microarray. Anal. Biochem. 383(1), 116–121 (2008)
Hase, S., Ikenaka, T., Matsushima, Y.: Structure analyses of oligosaccharides by tagging of the reducing end sugars with a fluorescent compound. Biochem. Biophys. Res. Commun. 85(1), 257–263 (1978)
Bigge, J.C., Patel, T.P., Bruce, J.A., Goulding, P.N., Charles, S.M., Parekh, R.B.: Nonselective and efficient fluorescent labeling of glycans using 2-amino benzamide and anthranilic acid. Anal. Biochem. 230(2), 229–238 (1995)
Anumula, K.R.: Single tag for total carbohydrate analysis. Anal. Biochem. 457, 31–37 (2014)
Xia, B., Kawar, Z.S., Ju, T., Alvarez, R.A., Sachdev, G.P., Cummings, R.D.: Versatile fluorescent derivatization of glycans for glycomic analysis. Nat. Methods 2(11), 845–850 (2005)
Song, X., Xia, B., Lasanajak, Y., Smith, D.F., Cummings, R.D.: Quantifiable fluorescent glycan microarrays. Glycoconj. J. 25(1), 15–25 (2008)
de Boer, A.R., Hokke, C.H., Deelder, A.M., Wuhrer, M.: General microarray technique for immobilization and screening of natural glycans. Anal. Chem. 79(21), 8107–8113 (2007)
Song, X., Xia, B., Stowell, S.R., Lasanajak, Y., Smith, D.F., Cummings, R.D.: Novel fluorescent glycan microarray strategy reveals ligands for galectins. Chem. Biol. 16(1), 36–47 (2009)
Luyai, A., Lasanajak, Y., Smith, D.F., Cummings, R.D., Song, X.: Facile preparation of fluorescent neoglycoproteins using p-nitrophenyl anthranilate as a heterobifunctional linker. Bioconjug. Chem. 20(8), 1618–1624 (2009)
Song, X., Johns, B.A., Ju, H., Lasanajak, Y., Zhao, C., Smith, D.F., Cummings, R.D.: Novel cleavage of reductively aminated glycan-tags by N-bromosuccinimide to regenerate free, reducing glycans. ACS Chem. Biol. 8(11), 2478–2483 (2013)
Yamada, K., Hirabayashi, J., Kakehi, K.: Analysis of O-glycans as 9-fluorenylmethyl derivatives and its application to the studies on glycan array. Anal Chem (Washington, DC, U S) 85, 3325–3333 (2013)
de Boer, A.R., Hokke, C.H., Deelder, A.M., Wuhrer, M.: Serum antibody screening by surface plasmon resonance using a natural glycan microarray. Glycoconj. J 25(1), 75–84 (2008)
Song, X., Lasanajak, Y., Xia, B., Smith, D.F., Cummings, R.D.: Fluorescent glycosylamides produced by microscale derivatization of free glycans for natural glycan microarrays. ACS Chem. Biol. 4(9), 741–750 (2009)
Yu, Y., Lasanajak, Y., Song, X., Hu, L., Ramani, S., Mickum, M.L., Ashline, D.J., Prasad, B.V., Estes, M.K., Reinhold, V.N., Cummings, R.D., Smith, D.F.: Human milk contains novel glycans that are potential decoy receptors for neonatal rotaviruses. Mol. Cell. Proteomics: MCP 13(11), 2944–2960 (2014)
Ashline, D.J., Yu, Y., Lasanajak, Y., Song, X., Hu, L., Ramani, S., Prasad, V., Estes, M.K., Cummings, R.D., Smith, D.F., Reinhold, V.N.: Structural characterization by multistage mass spectrometry (MSn) of human milk glycans recognized by human rotaviruses. Mol. Cell. Proteomics: MCP 13(11), 2961–2974 (2014)
Yu, Y., Mishra, S., Song, X., Lasanajak, Y., Bradley, K.C., Tappert, M.M., Air, G.M., Steinhauer, D.A., Halder, S., Cotmore, S., Tattersall, P., Agbandje-McKenna, M., Cummings, R.D., Smith, D.F.: Functional glycomic analysis of human milk glycans reveals the presence of virus receptors and embryonic stem cell biomarkers. J. Biol. Chem. 287(53), 44784–44799 (2012)
Byrd-Leotis, L., Liu, R., Bradley, K.C., Lasanajak, Y., Cummings, S.F., Song, X., Heimburg-Molinaro, J., Galloway, S.E., Culhane, M.R., Smith, D.F., Steinhauer, D.A., Cummings, R.D.: Shotgun glycomics of pig lung identifies natural endogenous receptors for influenza viruses. Proc. Natl. Acad. Sci. U. S. A. 111(22), E2241–E2250 (2014)
van Diepen, A., Smit, C.H., van Egmond, L., Kabatereine, N.B., de Moira, A.P., Dunne, D.W., Hokke, C.H.: Differential anti-glycan antibody responses in Schistosoma mansoni-infected children and adults studied by shotgun glycan microarray. PLoS Neglected Trop Dis 6(11), e1922 (2012)
Song, X., Lasanajak, Y., Olson, L.J., Boonen, M., Dahms, N.M., Kornfeld, S., Cummings, R.D., Smith, D.F.: Glycan microarray analysis of P-type lectins reveals distinct phosphomannose glycan recognition. J. Biol. Chem. 284(50), 35201–35214 (2009)
Bohnsack, R.N., Song, X., Olson, L.J., Kudo, M., Gotschall, R.R., Canfield, W.M., Cummings, R.D., Smith, D.F., Dahms, N.M.: Cation-independent mannose 6-phosphate receptor: a composite of distinct phosphomannosyl binding sites. J. Biol. Chem. 284(50), 35215–35226 (2009)
Olson, L.J., Castonguay, A.C., Lasanajak, Y., Peterson, F.C., Cummings, R.D., Smith, D.F., Dahms, N.M.: Identification of a fourth mannose 6-phosphate binding site in the cation-independent mannose 6-phosphate receptor. Glycobiology (2015).
Padler-Karavani, V., Song, X., Yu, H., Hurtado-Ziola, N., Huang, S., Muthana, S., Chokhawala, H.A., Cheng, J., Verhagen, A., Langereis, M.A., Kleene, R., Schachner, M., de Groot, R.J., Lasanajak, Y., Matsuda, H., Schwab, R., Chen, X., Smith, D.F., Cummings, R.D., Varki, A.: Cross-comparison of protein recognition of sialic acid diversity on two novel sialoglycan microarrays. J. Biol. Chem. 287(27), 22593–22608 (2012)
Song, X., Yu, H., Chen, X., Lasanajak, Y., Tappert, M.M., Air, G.M., Tiwari, V.K., Cao, H., Chokhawala, H.A., Zheng, H., Cummings, R.D., Smith, D.F.: A sialylated glycan microarray reveals novel interactions of modified sialic acids with proteins and viruses. J. Biol. Chem. 286(36), 31610–31622 (2011)
Campbell, M.P., Ranzinger, R., Lutteke, T., Mariethoz, J., Hayes, C.A., Zhang, J., Akune, Y., Aoki-Kinoshita, K.F., Damerell, D., Carta, G., York, W.S., Haslam, S.M., Narimatsu, H., Rudd, P.M., Karlsson, N.G., Packer, N.H., Lisacek, F.: Toolboxes for a standardised and systematic study of glycans. BMC Bioinform 15 Suppl 1, S9 (2014)
Tharmalingam, T., Adamczyk, B., Doherty, M.A., Royle, L., Rudd, P.M.: Strategies for the profiling, characterisation and detailed structural analysis of N-linked oligosaccharides. Glycoconj. J. 30(2), 137–146 (2013)
Acknowledgments
The work of the authors in this area is supported by NIH Grant P41GM103694 to RDC.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Song, X., Heimburg-Molinaro, J., Smith, D.F. et al. Glycan microarrays of fluorescently-tagged natural glycans. Glycoconj J 32, 465–473 (2015). https://doi.org/10.1007/s10719-015-9584-8
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10719-015-9584-8