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Plant Proteomics pp 365–378Cite as

Generation of Plant Protein Microarrays and Investigation of Antigen-Antibody Interactions

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 355))

Abstract

The application of proteomics methods, such as the protein microarray technology, in plant science has been strongly supported by the completion of genome sequencing projects of Arabidopsis thaliana and rice. In this chapter we describe a method to generate plant protein microarrays and to use them for characterizing monoclonal antibodies or polyclonal sera with regard to their specificity and cross-reactivity. The method starts with characterized E. coli cDNA expression clones encoding His-tagged plant proteins. After expression and purification of these recombinant proteins in high throughput, protein microarrays are generated utilizing a contact printer. For the detection of the recombinant proteins on the microarrays, an anti-RGS-His6 antibody is used. To characterize specific antibodies, the microarrays are incubated with the respective antibody solutions followed by fluorescently labeled secondary antibodies. Signal detection is performed by means of an arrayscanner system. Protein microarrays containing the whole proteome of a plant will represent the ideal format to test antibody specificity and cross-reactivity in the future.

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References

  1. LaBaer, J. and Ramachandran, N. (2005) Protein microarrays as tools for functional proteomics. Curr. Opin. Chem. Biol. 9, 14–19.

    Article  CAS  PubMed  Google Scholar 

  2. Feilner, T., Kreutzberger, J., Niemann, B., et al. (2004) Proteomic studies using microarrays. Curr. Proteomics 1, 283–295.

    CAS  Google Scholar 

  3. Templin, M. F., Stoll, D., Schwenk, J. M., Potz, O., Kramer, S., and Joos, T. O. (2003) Protein microarrays: promising tools for proteomic research. Proteomics 3, 2155–2166.

    Article  CAS  PubMed  Google Scholar 

  4. Zhu, H. and Snyder, M. (2003) Protein chip technology. Curr. Opin. Chem. Biol. 7, 55–63.

    Article  CAS  PubMed  Google Scholar 

  5. Miller, J. C., Zhou, H., Kwekel, J., et al. (2003) Antibody microarray profiling of human prostate cancer sera: antibody screening and identification of potential biomarkers. Proteomics 3, 56–63.

    Article  CAS  PubMed  Google Scholar 

  6. Nielsen, U. B. and Geierstanger, B. H. (2004) Multiplexed sandwich assays in microarray format. J. Immunol. Methods 290, 107–120.

    Article  CAS  PubMed  Google Scholar 

  7. Shao, W., Zhou, Z., Laroche, I., et al. (2003) Optimization of Rolling-Circle Amplified Protein Microarrays for Multiplexed Protein Profiling. J. Biomed. Biotechnol. 2003, 299–307.

    Article  PubMed  Google Scholar 

  8. Kramer, A., Feilner, T., Possling, A., et al. (2004) Identification of barley CK2alpha targets by using the protein microarray technology. Phytochem. 65, 1777–1784.

    Article  CAS  Google Scholar 

  9. Zhu, H., Klemic, J. F., Chang, S., et al. (2000) Analysis of yeast protein kinases using protein chips. Nat. Genet. 26, 283–289.

    Article  CAS  PubMed  Google Scholar 

  10. Boutell, J. M., Hart, D. J., Godber, B. L., Kozlowski, R. Z., and Blackburn, J. M. (2004) Functional protein microarrays for parallel characterisation of p53 mutants. Proteomics 4, 1950–1958.

    Article  CAS  PubMed  Google Scholar 

  11. Chan, S. M., Ermann, J., Su, L., Fathman, C. G., and Utz, P. J. (2004) Protein microarrays for multiplex analysis of signal transduction pathways. Nat. Med. 10, 1390–1396.

    Article  CAS  PubMed  Google Scholar 

  12. Haab, B. B., Dunham, M. J., and Brown, P. O. (2001) Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol. 2, RESEARCH0004.

    Google Scholar 

  13. Michaud, G. A., Salcius, M., Zhou, F., et al. (2003) Analyzing antibody specificity with whole proteome microarrays. Nat. Biotechnol. 21, 1509–1512.

    Article  CAS  PubMed  Google Scholar 

  14. Kersten, B., Feilner, T., Kramer, A., et al. (2003) Generation of Arabidopsis protein chips for antibody and serum screening. Plant Mol. Biol. 52, 999–1010.

    Article  CAS  PubMed  Google Scholar 

  15. Lueking, A., Possling, A., Huber, O., et al. (2003) A nonredundant human protein chip for antibody screening and serum profiling. Mol. Cell. Proteomics 2, 1342–1349.

    Article  CAS  PubMed  Google Scholar 

  16. Ramachandran, N., Hainsworth, E., Bhullar, B., et al. (2004) Self-assembling protein microarrays. Science 305, 86–90.

    Article  CAS  PubMed  Google Scholar 

  17. Zhu, H., Bilgin, M., Bangham, R., et al. (2001) Global analysis of protein activities using proteome chips. Science 293, 2101–2105.

    Article  CAS  PubMed  Google Scholar 

  18. Kersten, B., Possling, A., Blaesing, F., Mirgorodskaya, E., Gobom, J., and Seitz, H. (2004) Protein microarray technology and ultraviolet crosslinking combined with mass spectrometry for the analysis of protein-DNA interactions. Anal. Biochem. 331, 303–313.

    Article  CAS  PubMed  Google Scholar 

  19. Snapyan, M., Lecocq, M., Guevel, L., Arnaud, M. C., Ghochikyan, A., and Sakanyan, V. (2003) Dissecting DNA-protein and protein-protein interactions involved in bacterial transcriptional regulation by a sensitive protein array method combining a near-infrared fluorescence detection. Proteomics 3, 647–657.

    Article  CAS  PubMed  Google Scholar 

  20. MacBeath, G. and Schreiber, S. L. (2000) Printing proteins as microarrays for high-throughput function determination. Science 289, 1760–1763.

    CAS  PubMed  Google Scholar 

  21. Kim, S. H., Tamrazi, A., Carlson, K. E., and Katzenellenbogen, J. A. (2005) A proteomic microarray approach for exploring ligand-initiated nuclear hormone receptor pharmacology, receptor-selectivity, and heterodimer functionality. Mol. Cell. Proteomics 4, 267–277.

    Article  CAS  PubMed  Google Scholar 

  22. Kim, T. E., Park, S. W., Cho, N. Y., et al. (2002) Quantitative measurement of serum allergen-specific IgE on protein chip. Exp. Mol. Med. 34, 152–158.

    CAS  PubMed  Google Scholar 

  23. Robinson, W. H., DiGennaro, C., Hueber, W., et al. (2002) Autoantigen microarrays for multiplex characterization of autoantibody responses. Nat. Med. 8, 295–301.

    Article  CAS  PubMed  Google Scholar 

  24. Angenendt, P., Glokler, J., Konthur, Z., Lehrach, H., and Cahill, D. J. (2003) 3D protein microarrays: performing multiplex immunoassays on a single chip. Anal. Chem. 75, 4368–4372.

    Article  CAS  PubMed  Google Scholar 

  25. Kersten, B., Wanker, E. E., Hoheisel, J. D., and Angenendt, P. (2005) Multiplexing approaches in protein microarray technology. Expert Rev. Proteomics 2, 499–510.

    Article  CAS  PubMed  Google Scholar 

  26. Kersten, B., Bürkle, L., Kuhn, E. J., et al. (2002) Large-scale plant proteomics. Plant Mol. Biol. 48, 133–141.

    Article  CAS  PubMed  Google Scholar 

  27. Kersten, B., Feilner, T., Angenendt, P., Giavalisco, P., Brenner, W., and Bürkle, L. (2004) Proteomic approaches in plant biology. Curr. Proteomics 1, 131–144.

    Article  CAS  Google Scholar 

  28. Agrawal, G. K., Yonekura, M., Iwahashi, Y., Iwahashi, H., and Rakwal, R. (2005) System, trends and perspectives of proteomics in dicot plants. Part III: Unraveling the proteomes influenced by the environment, and at the levels of function and genetic relationships. J. Chromatogr. B Anal. Technol. Biomed. Life. Sci. 815, 137–145.

    Article  CAS  Google Scholar 

  29. Agrawal, G. K., Yonekura, M., Iwahashi, Y., Iwahashi, H., and Rakwal, R. (2005) System, trends and perspectives of proteomics in dicot plants Part II: Proteomes of the complex developmental stages. J. Chromatogr. B Anal. Technol. Biomed. Life. Sci. 815, 125–136.

    Article  CAS  Google Scholar 

  30. Agrawal, G. K., Yonekura, M., Iwahashi, Y., Iwahashi, H., and Rakwal, R. (2005) System, trends and perspectives of proteomics in dicot plants Part I: Technologies in proteome establishment. J. Chromatogr. B Anal. Technol. Biomed. Life. Sci. 815, 109–123.

    Article  CAS  Google Scholar 

  31. Thiellement, H., Zivy, M., and Plomion, C. (2002) Combining proteomic and genetic studies in plants. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 782, 137–149.

    Article  CAS  PubMed  Google Scholar 

  32. Canovas, F. M., Dumas-Gaudot, E., Recorbet, G., Jorrin, J., Mock, H. P., and Rossignol, M. (2004) Plant proteome analysis. Proteomics 4, 285–298.

    Article  CAS  PubMed  Google Scholar 

  33. Feilner, T., Hultschig, C., Lee, J., et al. (2005) High-throughput identification of potential Arabidopsis MAP kinases substrates. Mol. Cell. Proteomics 4, 1558–1568.

    Article  CAS  PubMed  Google Scholar 

  34. Weiner, H., Faupel, T., and Bussow, K. (2004) Protein arrays from cDNA expression libraries, in Methods in Molecular Biology (Fung, E., ed.), Humana, Totowa, NJ, pp. 11–13.

    Google Scholar 

  35. Bussow, K., Cahill, D., Nietfeld, W., et al. (1998) A method for global protein expression and antibody screening on high-density filters of an arrayed cDNA library. Nucleic Acids Res. 26, 5007–5008.

    Article  CAS  PubMed  Google Scholar 

  36. Clark, M. D., Panopoulou, G. D., Cahill, D. J., Bussow, K., and Lehrach, H. (1999) Construction and analysis of arrayed cDNA libraries [Review]. Methods Enzymol. 303, 205–233.

    Article  CAS  PubMed  Google Scholar 

  37. Heyman, J. A., Cornthwaite, J., Foncerrada, L., et al. (1999) Genome-scale cloning and expression of individual open reading frames using topoisomerase I-mediated ligation. Genome Res. 9, 383–392.

    CAS  PubMed  Google Scholar 

  38. Walhout, A. J., Temple, G. F., Brasch, M. A., et al. (2000) GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Methods Enzymol. 328, 575–592.

    Article  CAS  PubMed  Google Scholar 

  39. Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248–254.

    Article  CAS  PubMed  Google Scholar 

  40. Soldatov, A. V., Nabirochkina, E. N., Georgieva, S. G., and Eickhoff, H. (2001) Adjustment of transfer tools for the production of micro-and macroarrays. Biotechniques 31, 848–854.

    CAS  PubMed  Google Scholar 

  41. Angenendt, P., Glokler, J., Murphy, D., Lehrach, H., and Cahill, D. J. (2002) Toward optimized antibody microarrays: a comparison of current microarray support materials. Anal. Biochem. 309, 253–260.

    Article  CAS  PubMed  Google Scholar 

  42. Angenendt, P., Glokler, J., Sobek, J., Lehrach, H., and Cahill, D. J. (2003) Next generation of protein microarray support materials: evaluation for protein and antibody microarray applications. J. Chromatogr. A 1009, 97–104.

    Article  CAS  PubMed  Google Scholar 

  43. Cordonnier, M. M., Greppin, H., and Pratt, L. H. (1986) Identification of a highly conserved domain on phytochrome from angiosperms to algae. Plant Physiol. 80, 982–987.

    Article  CAS  PubMed  Google Scholar 

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Author information

Authors and Affiliations

  1. RZPD German Resource Center for Genome Research GmbH, Berlin, Germany

    Birgit Kersten

  2. Department of Biochemistry, University College Cork, Cork, Ireland

    Tanja Feilner

Authors
  1. Birgit Kersten
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  2. Tanja Feilner
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Editor information

Editors and Affiliations

  1. UMR de Génétique Végétale, La Ferme du Moulon, Gif-sur-Yvette, France

    Hervé Thiellement , Michel Zivy  & Catherine Damerval ,  & 

  2. UMR de Chimie Biologique, Thiverval Grignon, France

    Valérie Méchin

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© 2007 Humana Press Inc., Totowa, NJ

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Kersten, B., Feilner, T. (2007). Generation of Plant Protein Microarrays and Investigation of Antigen-Antibody Interactions. In: Thiellement, H., Zivy, M., Damerval, C., Méchin, V. (eds) Plant Proteomics. Methods in Molecular Biology, vol 355. Humana Press. https://doi.org/10.1385/1-59745-227-0:365

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  • DOI: https://doi.org/10.1385/1-59745-227-0:365

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-635-1

  • Online ISBN: 978-1-59745-227-4

  • eBook Packages: Springer Protocols

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