Skip to main content
SpringerLink
Log in

Carbohydrate Microarray Technology Applied to High-Throughput Mapping of Plant Cell Wall Glycans Using Comprehensive Microarray Polymer Profiling (CoMPP)

  • Protocol
  • First Online:
High-Throughput Glycomics and Glycoproteomics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1503))

Abstract

Cell walls are an important feature of plant cells and a major component of the plant glycome. They have both structural and physiological functions and are critical for plant growth and development. The diversity and complexity of these structures demand advanced high-throughput techniques to answer questions about their structure, functions and roles in both fundamental and applied scientific fields. Microarray technology provides both the high-throughput and the feasibility aspects required to meet that demand. In this chapter, some of the most recent microarray-based techniques relating to plant cell walls are described together with an overview of related contemporary techniques applied to carbohydrate microarrays and their general potential in glycoscience. A detailed experimental procedure for high-throughput mapping of plant cell wall glycans using the comprehensive microarray polymer profiling (CoMPP) technique is included in the chapter and provides a good example of both the robust and high-throughput nature of microarrays as well as their applicability to plant glycomics.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 139.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Singh A, Kumar N (2013) A review on DNA microarray technology. Int J Cur Res Rev 5(22):01–05

    Google Scholar 

  2. Trevino V, Falciani F, Barrera-Saldana HA (2007) DNA microarrays: a powerful genomic tool for biomedical and clinical research. Mol Med 13(9–10):527–541. doi:10.2119/2006-00107.Trevino

    CAS  PubMed  PubMed Central  Google Scholar 

  3. Wang CC, Huang YL, Ren CT, Lin CW, Hung JT, Yu JC, Yu AL, Wu CY, Wong CH (2008) Glycan microarray of Globo H and related structures for quantitative analysis of breast cancer. Proc Natl Acad Sci U S A 105(33):11661–11666. doi:10.1073/pnas.0804923105

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Scheible MB, Pardatscher G, Kuzyk A, Simmel FC (2014) Single molecule characterization of DNA binding and strand displacement reactions on lithographic DNA origami microarrays. Nano Lett 14(3):1627–1633. doi:10.1021/nl500092j

    Article  CAS  PubMed  Google Scholar 

  5. Galan MC, Benito-Alifonso D, Watt GM (2011) Carbohydrate chemistry in drug discovery. Org Biomol Chem 9(10):3598–3610. doi:10.1039/c0ob01017k

    Article  CAS  PubMed  Google Scholar 

  6. Schmidt D, Schuhmacher F, Geissner A, Seeberger PH, Pfrengle F (2015) Automated synthesis of arabinoxylan-oligosaccharides enables characterization of antibodies that recognize plant cell wall glycans. Chemistry 21(15):5709–5713. doi:10.1002/chem.201500065

    Article  CAS  PubMed  Google Scholar 

  7. de Moura FA, Macagnan FT, da Silva LP (2015) Oligosaccharide production by hydrolysis of polysaccharides: a review. Int J Food Sci Tech 50(2):275–281. doi:10.1111/ijfs.12681

    Article  Google Scholar 

  8. Liu Y (2010) Neoglycolipid (NGL)-based oligosaccharide microarrays and highlights of their recent applications in studies of the molecular basis of pathogen-host interactions. Biochem Soc Trans 38:1361–1367. doi:10.1042/Bst0381361

    Article  CAS  PubMed  Google Scholar 

  9. Pachamuthu K, Schmidt RR (2006) Synthetic routes to thiooligosaccharides and thioglycopeptides. Chem Rev 106(1):160–187. doi:10.1021/Cr040660c

    Article  CAS  PubMed  Google Scholar 

  10. Blixt O, Head S, Mondala T, Scanlan C, Huflejt ME, Alvarez R, Bryan MC, Fazio F, Calarese D, Stevens J, Razi N, Stevens DJ, Skehel JJ, van Die I, Burton DR, Wilson IA, Cummings R, Bovin N, Wong CH, Paulson JC (2004) Printed covalent glycan array for ligand profiling of diverse glycan binding proteins. Proc Natl Acad Sci U S A 101(49):17033–17038, doi:0407902101 [pii] 10.1073/pnas.0407902101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Shilova N, Navakouski M, Khasbiullina N, Blixt O, Bovin N (2012) Printed glycan array: antibodies as probed in undiluted serum and effects of dilution. Glycoconj J 29(2–3):87–91. doi:10.1007/s10719-011-9368-8

    Article  CAS  PubMed  Google Scholar 

  12. Park S, Gildersleeve JC, Blixt O, Shin I (2013) Carbohydrate microarrays. Chem Soc Rev 42(10):4310–4326. doi:10.1039/C2cs35401b

    Article  CAS  PubMed  Google Scholar 

  13. Feizi T, Chai WG (2004) Oligosaccharide microarrays to decipher the glyco code. Nat Rev Mol Cell Biol 5(7):582–588. doi:10.1038/Nrm1428

    Article  CAS  PubMed  Google Scholar 

  14. Pedersen HL, Fangel JU, McCleary B, Ruzanski C, Rydahl MG, Ralet MC, Farkas V, von Schantz L, Marcus SE, Andersen MCF, Field R, Ohlin M, Knox JP, Clausen MH, Willats WGT (2012) Versatile high resolution oligosaccharide microarrays for plant glycobiology and cell wall research. J Biol Chem 287(47):39429–39438. doi:10.1074/jbc.M112.396598

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Maolanon NN, Blaise M, Sorensen KK, Thygesen MB, Clo E, Sullivan JT, Ronson CW, Stougaard J, Blixt O, Jensen KJ (2014) Lipochitin oligosaccharides immobilized through oximes in glycan microarrays bind LysM proteins. Chembiochem 15(3):425–434. doi:10.1002/cbic.201300520

    Article  CAS  PubMed  Google Scholar 

  16. Bohorov O, Andersson-Sand H, Hoffmann J, Blixt O (2006) Arraying glycomics: a novel bi-functional spacer for one-step microscale derivatization of free reducing glycans. Glycobiology 16(12):21c–27c. doi:10.1093/glycob/cwl044

    Article  CAS  PubMed  Google Scholar 

  17. Clo E, Blixt O, Jensen KJ (2010) Chemoselective reagents for covalent capture and display of glycans in microarrays. Eur J Org Chem 3:540–554. doi:10.1002/ejoc.200901234

    Article  Google Scholar 

  18. Park S, Lee MR, Shin I (2007) Fabrication of carbohydrate chips and their use to probe protein-carbohydrate interactions. Nat Protoc 2(11):2747–2758. doi:10.1038/nprot.2007.373

    Article  CAS  PubMed  Google Scholar 

  19. Rillahan CD, Paulson JC (2011) Glycan microarrays for decoding the glycome. Annu Rev Biochem 80(80):797–823. doi:10.1146/annurev-biochem-061809-152236

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Raman R, Venkataraman M, Ramakrishnan S, Lang W, Raguram S, Sasisekharan R (2006) Advancing glycomics: implementation strategies at the consortium for functional glycomics. Glycobiology 16(5):82r–90r. doi:10.1093/glycob/cwj080

    Article  CAS  PubMed  Google Scholar 

  21. Venkataraman M, Sasisekharan R, Raman R (2015) Glycan array data management at Consortium for Functional Glycomics. Methods Mol Biol 1273:181–190. doi:10.1007/978-1-4939-2343-4_13

    Article  CAS  PubMed  Google Scholar 

  22. Jeffree CE (1993) Immobilization of pectin, xyloglucan and other soluble plant polysaccharides on blotting membranes. New Phytologist 125 (4), 695–706, doi: 10.1111/j.1469-8137.1993.tb03918.x

  23. Wang D, Liu S, Trummer BJ, Deng C, Wang A (2002) Carbohydrate microarrays for the recognition of cross-reactive molecular markers of microbes and host cells. Nat Biotechnol 20(3):275–281. doi:10.1038/nbt0302-275

    Article  CAS  PubMed  Google Scholar 

  24. Willats WG, Rasmussen SE, Kristensen T, Mikkelsen JD, Knox JP (2002) Sugar-coated microarrays: a novel slide surface for the high-throughput analysis of glycans. Proteomics 2(12):1666–1671. doi:10.1002/1615-9861(200212)2:12<1666::AID-PROT1666>3.0.CO;2-E

    Article  CAS  PubMed  Google Scholar 

  25. Barbulovic-Nad I, Lucente M, Sun Y, Zhang MJ, Wheeler AR, Bussmann M (2006) Bio-microarray fabrication techniques—a review. Crit Rev Biotechnol 26(4):237–259. doi:10.1080/07388550600978358

    Article  CAS  PubMed  Google Scholar 

  26. Clo E, Kracun SK, Nudelman AS, Jensen KJ, Liljeqvist JA, Olofsson S, Bergstrom T, Blixt O (2012) Characterization of the viral O-glycopeptidome: a novel tool of relevance for vaccine design and serodiagnosis. J Virol 86(11):6268–6278. doi:10.1128/Jvi.00392-12

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Moller I, Sorensen I, Bernal AJ, Blaukopf C, Lee K, Obro J, Pettolino F, Roberts A, Mikkelsen JD, Knox JP, Bacic A, Willats WGT (2007) High-throughput mapping of cell-wall polymers within and between plants using novel microarrays. Plant J 50(6):1118–1128. doi:10.1111/j.1365-313X.2007.03114.x

    Article  CAS  PubMed  Google Scholar 

  28. Yu HY, Nguyen K, Royce T, Qian J, Nelson K, Snyder M, Gerstein M (2007) Positional artifacts in microarrays: experimental verification and construction of COP, an automated detection tool. Nucleic Acids Res 35(2):8, doi:ARTN E8, 10.1093/nar/gkl871

    Article  Google Scholar 

  29. Pappaert K, Ottevaere H, Thienpont H, Van Hummelen P, Desmet G (2006) Diffusion limitation: a possible source for the occurrence of doughnut patterns on DNA microarrays. Biotechniques 41(5):609–616. doi:10.2144/000112293

    Article  CAS  PubMed  Google Scholar 

  30. Allison DB, Cui XQ, Page CP, Sabripour M (2006) Microarray data analysis: from disarray to consolidation and consensus (vol 7, pg 55, 2006). Nat Rev Genet 7(5):406. doi:10.1038/nrg1869

    Article  CAS  Google Scholar 

  31. Glaab E, Garibaldi JM, Krasnogor N (2009) ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization. BMC Bioinformatics 10:358, doi: Artn 358, 10.1186/1471-2105-10-358

    Article  PubMed  PubMed Central  Google Scholar 

  32. Uttamchandani M, Huang X, Chen GYJ, Yao SQ (2005) Nanodroplet profiling of enzymatic activities in a microarray. Bioorg Med Chem Lett 15(8):2135–2139. doi:10.1016/j.bmcl.2005.02.019

    Article  CAS  PubMed  Google Scholar 

  33. Shah MM, Fujiyama K, Flynn CR, Joshi L (2003) Sialylated endogenous glycoconjugates in plant cells. Nat Biotechnol 21(12):1470–1471. doi:10.1038/nbt912

    Article  CAS  PubMed  Google Scholar 

  34. Strasser R (2014) Biological significance of complex N-glycans in plants and their impact on plant physiology. Front Plant Sci 5:363. doi:10.3389/fpls.2014.00363.ARTN363

    Article  PubMed  PubMed Central  Google Scholar 

  35. Strasser R (2012) Challenges in O-glycan engineering of plants. Front Plant Sci 3:218. doi:10.3389/fpls.2012.00218.ARTN218

    Article  PubMed  PubMed Central  Google Scholar 

  36. Bellincampi D, Cervone F, Lionetti V (2014) Plant cell wall dynamics and wall-related susceptibility in plant-pathogen interactions. Front Plant Sci 5:228. doi:10.3389/fpls.2014.00228

    Article  PubMed  PubMed Central  Google Scholar 

  37. Perrot-Rechenmann C (2010) Cellular responses to auxin: division versus expansion. Csh Perspect Biol 2(5):a001446. doi:10.1101/cshperspect.a001446

    Google Scholar 

  38. Carpita NC, Gibeaut DM (1993) Structural models of primary-cell walls in flowering plants—consistency of molecular-structure with the physical-properties of the walls during growth. Plant J 3(1):1–30. doi:10.1111/j.1365-313X.1993.tb00007.x

    Article  CAS  PubMed  Google Scholar 

  39. Boerjan W, Ralph J, Baucher M (2003) Lignin biosynthesis. Annu Rev Plant Biol 54:519–546. doi:10.1146/annurev.arplant.54.031902.134938

    Article  CAS  PubMed  Google Scholar 

  40. Rytioja J, Hilden K, Yuzon J, Hatakka A, de Vries RP, Makela MR (2014) Plant-polysaccharide-degrading enzymes from basidiomycetes. Microbiol Mol Biol Rev 78(4):614–649. doi:10.1128/MMBR.00035-14

    Article  PubMed  PubMed Central  Google Scholar 

  41. Burton RA, Gidley MJ, Fincher GB (2010) Heterogeneity in the chemistry, structure and function of plant cell walls. Nat Chem Biol 6(10):724–732. doi:10.1038/nchembio.439

    Article  CAS  PubMed  Google Scholar 

  42. Coutinho PM, Starn M, Blanc E, Henrissat B (2003) Why are there so many carbohydrate-active enzyme-related genes in plants? Trends Plant Sci 8(12):563–565. doi:10.1016/j.tplants.2003.10.002

    Article  CAS  PubMed  Google Scholar 

  43. Popper ZA, Fry SC (2004) Primary cell wall composition of pteridophytes and spermatophytes. New Phytol 164(1):165–174. doi:10.1111/j.1469-8137.2004.01146.x

    Article  CAS  Google Scholar 

  44. Pauly M, Keegstra K (2010) Plant cell wall polymers as precursors for biofuels. Curr Opin Plant Biol 13(3):305–312. doi:10.1016/j.pbi.2009.12.009

    Article  CAS  PubMed  Google Scholar 

  45. Petersen BL, Egelund J, Damager I, Faber K, Jensen JK, Yang Z, Bennett EP, Scheller HV, Ulvskov P (2009) Assay and heterologous expression in Pichia pastoris of plant cell wall type-II membrane anchored glycosyltransferases. Glycoconj J 26(9):1235–1246. doi:10.1007/s10719-009-9242-0

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Vidal-Melgosa S, Pedersen HL, Schuckel J, Arnal G, Dumon C, Amby DB, Monrad RN, Westereng B, Willats WGT (2015) A new versatile microarray-based method for high throughput screening of carbohydrate-active enzymes. J Biol Chem 290(14):9020–9036. doi:10.1074/jbc.M114.630673

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Moller IE, Pettolino FA, Hart C, Lampugnani ER, Willats WG, Bacic A (2012) Glycan profiling of plant cell wall polymers using microarrays. J Vis Exp 70, e4238. doi:10.3791/4238

    PubMed  Google Scholar 

  48. Sorensen I, Pettolino FA, Bacic A, Ralph J, Lu FC, O’Neill MA, Fei ZZ, Rose JKC, Domozych DS, Willats WGT (2011) The charophycean green algae provide insights into the early origins of plant cell walls. Plant J 68(2):201–211. doi:10.1111/j.1365-313X.2011.04686.x

    Article  PubMed  Google Scholar 

  49. Zhang H, Fangel JU, Willats WGT, Selig MJ, Lindedam J, Jorgensen H, Felby C (2014) Assessment of leaf/stem ratio in wheat straw feedstock and impact on enzymatic conversion. GCB Bioenergy 6(1):90–96. doi:10.1111/gcbb.12060

    Article  CAS  Google Scholar 

  50. Moore JP, Nguema-Ona E, Fangel JU, Willats WGT, Hugo A, Vivier MA (2014) Profiling the main cell wall polysaccharides of grapevine leaves using high-throughput and fractionation methods. Carbohydr Polym 99:190–198. doi:10.1016/j.carbpol.2013.08.013

    Article  CAS  PubMed  Google Scholar 

  51. Fangel JU, Ulvskov P, Knox JP, Mikkelsen MD, Harholt J, Popper ZA, Willats WGT (2012) Cell wall evolution and diversity. Front Plant Sci 3:152. doi:10.3389/fpls.2012.00152

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Moller IE, De Fine Licht HH, Harholt J, Willats WG, Boomsma JJ (2011) The dynamics of plant cell-wall polysaccharide decomposition in leaf-cutting ant fungus gardens. PLoS One 6(3), e17506. doi:10.1371/journal.pone.0017506

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Sorensen I, Pettolino FA, Wilson SM, Doblin MS, Johansen B, Bacic A, Willats WGT (2008) Mixed-linkage (1 -> 3), (1 -> 4)-beta-D-glucan is not unique to the poales and is an abundant component of Equisetum arvense cell walls. Plant J 54(3):510–521. doi:10.1111/j.1365-313X.2008.03453.x

    Article  PubMed  Google Scholar 

  54. Umu OC, Frank JA, Fangel JU, Oostindjer M, da Silva CS, Bolhuis EJ, Bosch G, Willats WG, Pope PB, Diep DB (2015) Resistant starch diet induces change in the swine microbiome and a predominance of beneficial bacterial populations. Microbiome 3:16. doi:10.1186/s40168-015-0078-5

    Article  PubMed  PubMed Central  Google Scholar 

  55. Johnsen HR, Striberny B, Olsen S, Vidal-Melgosa S, Fangel JU, Willats WG, Rose JK, Krause K (2015) Cell wall composition profiling of parasitic giant dodder (Cuscuta reflexa) and its hosts: a priori differences and induced changes. New Phytol 207(3):805–816. doi:10.1111/nph.13378

    Article  CAS  PubMed  Google Scholar 

  56. Gao Y, Fangel JU, Willats WGT, Vivier MA, Moore JP (2015) Dissecting the polysaccharide-rich grape cell wall changes during winemaking using combined high-throughput and fractionation methods. Carbohydr Polym 133:567–577

    Article  CAS  PubMed  Google Scholar 

  57. Wang D, Collins N (2013) The 10 anniversary of carbohydrate microarrays (2002–2012). J Proteomics Bioinform 6(2), e22

    Article  PubMed  PubMed Central  Google Scholar 

  58. Mravec J, Kracun SK, Rydahl MG, Westereng B, Miart F, Clausen MH, Fangel JU, Daugaard M, Van Cutsem P, Licht HHD, Hofte H, Malinovsky FG, Domozych DS, Willats WGT (2014) Tracking developmentally regulated post-synthetic processing of homogalacturonan and chitin using reciprocal oligosaccharide probes. Development 141(24):4841–4850. doi:10.1242/Dev.113365

    Article  CAS  PubMed  Google Scholar 

  59. Lombard V, Ramulu HG, Drula E, Coutinho PM, Henrissat B (2014) The carbohydrate-active enzymes database (CAZy) in 2013. Nucleic Acids Res 42(D1):D490–D495. doi:10.1093/Nar/Gkt1178

    Article  CAS  PubMed  Google Scholar 

  60. Kracun SK, Schuckel J, Westereng B, Thygesen LG, Monrad RN, Eijsink VG, Willats WG (2015) A new generation of versatile chromogenic substrates for high-throughput analysis of biomass-degrading enzymes. Biotechnol Biofuels 8:70. doi:10.1186/s13068-015-0250-y

    Article  PubMed  PubMed Central  Google Scholar 

  61. Agger JW, Isaksen T, Varnai A, Vidal-Melgosa S, Willats WGT, Ludwig R, Horn SJ, Eijsink VGH, Westereng B (2014) Discovery of LPMO activity on hemicelluloses shows the importance of oxidative processes in plant cell wall degradation. Proc Natl Acad Sci U S A 111(17):6287–6292. doi:10.1073/pnas.1323629111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Section for Plant Glycobiology, Department for Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871, Frederiksberg C, Denmark

    Stjepan Krešimir Kračun, Jonatan Ulrik Fangel, Maja Gro Rydahl, Henriette Lodberg Pedersen, Silvia Vidal-Melgosa & William George Tycho Willats

Authors
  1. Stjepan Krešimir Kračun
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jonatan Ulrik Fangel
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Maja Gro Rydahl
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Henriette Lodberg Pedersen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Silvia Vidal-Melgosa
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. William George Tycho Willats
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Stjepan Krešimir Kračun .

Editor information

Editors and Affiliations

  1. Faculty of Pharmacy and Biochemistry, University of Zagreb, Zagreb, Croatia

    Gordan Lauc

  2. Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands

    Manfred Wuhrer

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media New York

About this protocol

Cite this protocol

Kračun, S.K., Fangel, J.U., Rydahl, M.G., Pedersen, H.L., Vidal-Melgosa, S., Willats, W.G.T. (2017). Carbohydrate Microarray Technology Applied to High-Throughput Mapping of Plant Cell Wall Glycans Using Comprehensive Microarray Polymer Profiling (CoMPP). In: Lauc, G., Wuhrer, M. (eds) High-Throughput Glycomics and Glycoproteomics. Methods in Molecular Biology, vol 1503. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6493-2_12

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6493-2_12

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6491-8

  • Online ISBN: 978-1-4939-6493-2

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation