Abstract
Large-scale and high throughput approaches increasingly play an essential role in the study of biological systems, which are per se highly complex. Therefore, they need to be examined by these extensive methods to receive information about the large genomic and proteomic networks. In plant biology, this purpose has a strong support through the accessability of the complete genome sequence of the model plant Arabidopsis thaliana. This brief review intends to focus on the basics and the state-of-the-art of these high-throughput technologies and their application to plant proteomics. It describes protein microarrays, the use of antibodies, 2-DE and MS methods and the yeast two hybrid system, which are emerging as the major technologies for plant proteomics.
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References
Anderson, N.G., Matheson, A. and Anderson, N.L. 2001. Back to the future: the human protein index (HPI) and the agenda for post-proteomic biology. Proteomics 1: 3–12.
Arenkov, P., Kukhtin, A., Gemmell, A., Voloshchuk, S., Chupeeva, V. and Mirzabekov, A. 2000. Protein microchips: use for immunoassay and enzymatic reactions. Anal. Biochem. 278: 123–131.
Bahrman, N., de Vienne, D., Thiellement, H. and Hofmann, J.P. 1985. Two-dimensional gel electrophoresis of proteins for genetic studies in Douglas fir (Pseudotsuga menziesii). Biochem. Genet. 23: 247–255.
Battel, P.L., Roecklein, J.A., senGupta, D. and Fields, S. 1996. A protein linkage map of Escherichia coli bacteriophage T7. Nature Genet. 12: 72–77.
Blackstock, W.P. and Weir, M.P. 1999. Proteomics: quantitative and physical mapping of cellular proteins. Trends Biotechnol. 17: 121–127.
Büssow, K., Cahill, D., Nietfeld, W., Bancroft, D., Scherzinger, E., Lehrach, H. and Walter, G. 1998. A method for global protein expression and antibody screening of high-density filters of an arrayed cDNA library. Nucl. Acids Res. 26: 5007–5008.
Büssow, K., Nordhoff, E., Lübbert, C., Lehrach, H. and Walter, G. 2000. A human cDNA library for high-throughput protein expression screening. Genomics 65: 1–8.
Büssow, K., Konthur, Z., Lueking, A., Lehrach, H. and Walter, G. 2001. Protein array technology. Am. J.Pharmacogenomics 1: 37–43.
Cahill, D.J., Nordhoff, E., O’Brien, J., Klose, J., Eickhoff, H. and Lehrach, H. 2000. Bridging genomics and proteomics. In: S. Pennington and M. Dunn (Eds.) Proteomics, BIOS Scientific Publishers, pp. 1–17.
Cahill, D.J. 2000. Protein arrays: a high throughput solution for proteomics research? In: W. Blackstock and M. Mann (Eds) Proteomics: A Trends Guide, Elsevier Science, Amsterdam, pp. 49–53.
Chang, W.W., Huang, L., Shen, M., Webster, C., Burlingame, A.L. and Roberts, J.K. 2000. Patterns of protein synthesis and tolerance of anoxia in root tips of maize seedlings acclimated to a low-oxygen environment, and identification of proteins by mass spectrometry. Plant Physiol. 122: 295–318.
Clark, M.D., Panopoulou, G.D., Cahill, D.J., Bussow, K. and Lehrach, H. 1999. Construction and analysis of arrayed cDNA libraries. Meth. Enzymol. 303: 205–233.
Damerval, C., de Vienne, D., Zivy, M. and Thiellement, H. 1986. Technical improvements in two-dimensional electrophoresis increase the level of genetic variation detected in wheat-seedling proteins. Electrophoresis 7: 52–54.
Damerval, C. and Le Guilloux, M. 1998. Characterization of novel proteins affected by the 02 mutation and expressed during maize endosperm development. Mol. Gen. Genet. 257: 354–361.
de Wildt, R., Mundy, C.R., Gorick, B.D. and Tomlinson, I.M. 2000. Antibody arrays for high throughput screening of antibody-antigen interactions. Nature Biotechnol. 18: 989–994.
Fenn, J.B., Mann, M., Meng, C.K., Wong, S.F. and Whitehouse, C.M. 1989. Electrospray ionization for mass spectrometry of large biomolecules. Science 246: 64–71.
Fields, S. and Song, O. 1989. A novel genetic system to detect protein-protein interactions. Nature 340: 245–246.
Finley, R.L. and Brent, R. 1994. Interaction mating reveals binary and ternary connections between Drosophila cell cycle regulators. Proc. Natl. Acad. Sci. USA 91: 12980–12984.
Fromont-Racine, M., Rain, J.C. and Legrain, P. 1997. Toward a functional analysis of the yeast genome through exhaustive two hybrid screens. Nature Genet. 16: 277–282.
Galaud, J.P., Carriere, M., Pauly, N., Canut, H., Chalon, P., Caput, D. and Pont-Lezica, R.F. 1999. Construction of two ordered cDNA libraries enriched in genes encoding plasmalemma and tonoplast proteins from a high-efficiency expression library. Plant J. 17: 111–118.
Gallardo, K., Job, C., Groot, S.P.C., Puype, M., Demol, H., Vandek-erckhove, J. and Job, D. 2001. Proteomic analysis of Arabidopsis seed germination and priming. Plant Physiol. 126: 835–848.
Ge, H. 2000. UPA, a universal protein array system for quantitative detection of protein-protein, protein-DNA, protein-RNA and protein-ligand interactions. Nucl. Acids Res. 28: e3.
Giege, P., Konthur, Z., Walter, G. and Brennicke, A. 1998. An ordered Arabidopsis thaliana mitochondrial cDNA library on high-density filters allows rapid systematic analysis of plant gene expression: a pilot study. Plant J. 15: 721–726.
Griffiths, A.D., Williams, S.C., Hartley, O., Tomlinson, I.M., Wa-terhouse, P., Crosby, W.L., Kontermann, R.E., Jones, P.T., Low, N.M., Allison, T.J. et al. 1994. Isolation of high affinity human antibodies directly from large synthetic repertoires. EMBO J. 13: 3245–3260.
Gygi, S.P., Rochon, Y., Franza, B.R. and Aebershold, R. 1999. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19: 1720–1730.
Haab, B.B., Dunham, M.J. and Brown, P.O. 2001. Protein microar-rays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol. 1: 1–22.
Hefta, L.J., Wu, A.M., Neumaier, M. and Shively, J.E. 1996. Measuring antibody affinity using biosensors. In: J. McCafferty, H.R. Hoogenboom and D.J. Chiswell (Eds.) Antibody Engineering: A Practical Approach, IRL Press, Oxford, pp. 119–145.
Henzel, W.J., Billed, T.M., Stults, J.T., Wong, S.C., Grimley, C. and Watanabe, C. 1993. Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc. Natl. Acad. Sci. USA 90: 5011–5015.
Heyman, J.A., Cornthwaite, J., Foncerrada, L., Gilmore, J.R., Gontang, E., Hartman, K.J., Hernandez, C.L., Hood, R., Hull, H.M., Lee, W.Y., Marcil, R., Marsh, E.J., Mudd, K.M., Patino, M.J., Purcell, T.J., Rowland, J.J., Sindici, M.L. and Hoeffler, J.P. 1999. Genome-scale cloning and expression of individual open reading frames using topoisomerase I-mediated ligation. Genome Res. 9: 383–392.
Hyodo, H., Takemura, M., Yokota, A., Ohyama, K. and Kohchi, T. 2000. Systematic isolation of highly transcribed genes in inflorescence apices in Arabidopsis thaliana from an equalized cDNA library. Biosci. Biotechnol. Biochem. 64: 1538–1541.
Jahn, T., Dietrich, J., Andersen, B., Leidvik, B., Otter, C., Briving, C., Kuhlbrandt, W. and Palmgren, M.G. 2001. Large scale expression, purification and 2D-crystallization of recombinant plant plasma membrane H+-ATPase. J. Mol. Biol. 309: 465–476.
Jarillo, J.A., Capel, J., Tang, R.H., Yang, H.Q., Alonso, J.M., Ecker, J.R. and Cashmore, A.R. 2001. An Arabidopsis circadian clock component interacts with both CRY1 and phyB. Nature 410: 487–490.
Kamo, M., Kawakami, T., Miyatake, N. and Tsugita, A. 1995. Separation and characterization of Arabidopsis thaliana proteins by two-dimensional gel electrophoresis. Electrophoresis 16: 423–300.
Karas, M., Bahr, U., Ingendoh, A. and Hillenkamp, F. 1989. Laser desorption-ionization mass spectrometrie of proteins with masses 100,000 to 250,000 dalton. Angew. Chem. Int. Ed. Engl. 28:760–761.
Klose, J. 1975. Protein mapping by combined isoelectric focusing and electrophoresis of mouse tissues. A novel approach to testing for induced point mutations in mammals. Humangenetik 26: 231–243.
Klose, J. and Kobalz, U. 1995. Two-dimensional electrophoresis of proteins: an updated protocol and implications for a functional analysis of the genome. Electrophoresis 16: 1034–1059.
Klose, J. 1999. Large-gel 2-D electrophoresis. In: A.J. Link (Ed.) 2-D Proteome Analysis Protocols, Humana Press, Totowa, NJ, pp. 147–172.
Komatsu, S., Muhammad, A and Rakwal, R. 1999. Separation and characterization of proteins from green and etiolated shoots of rice (Oryza sativa L.): towards a rice proteome. Electrophoresis 20: 630–636.
Kristoffersen, P., Teichmann, T., Stracke, R. and Palme, K. 1996. Signal sequence trap to clone cDNAs encoding secreted or membrane-associated plant proteins. Anal. Biochem. 243: 127–132.
Legrain, P., Wojcik, J. and Gauthier, J.M. 2001. Protein-protein interaction maps: a lead towards cellular functions. Trends Genet. 117: 346–352.
Leymarie, J., Damerval, C., Marcotte, L., Combes, V. and Vartanian, N. 1996. Two-dimensional protein patterns of Arabidopsis wild-type and auxin-insensitive mutants, axrl, axr2, reveal interactions between drought and hormonal responses. Plant Cell Physiol. 37: 966–975.
Lueking, A., Horn, M., Eickhoff, H., Büssow, K., Lehrach, H. and Walter, G. 1999. Protein microarrays for gene expression and antibody screening. Anal. Biochem. 270: 103–111.
Lueking, A., Konthur, Z., Eickhoff, H., Büssow, K., Lehrach, H. and Cahill, D.J. 2001. Protein microarrays — a tool for the post-genomic era. Curr. Genomics 2: 151–159.
MacBeath, G. and Schreiber, S.L. 2000. Printing proteins as microarrays for high-throughput function determination. Science 289: 1760–1763.
Malmqvist, M. 1993. Surface plasmon resonance for detection and measurement of antibody-antigen affinity and kinetics. Curr. Opin. Immunol. 5: 282–286.
Munder, T. and Hinnen, A. 1999. Yeast cells as tools for target-oriented screening. Appl. Microbiol. Biotechnol. 52: 311–320.
Nissim, A., Hoogenboom, H.R., Tomlinson, I.M., Flynn, G., Midg-ley, C., Lane, D. and Winter, G. 1994. Antibody fragments from a’ single pot’ phage display library as immunochemical reagents. EMBO J. 13:692–698.
O’Farrell, PH. 1975. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250: 4007–4021.
Ouellet, F., Overvoorde, P.J. and Theologis, A. 2001. IAA17/AXR3. Biochemical insight into an auxin mutant phenotype. Plant Cell 13: 829–842.
Panter, S., Thomson, R., de Bruxelles, G., Laver, D., Trevaskis, B. and Udvardi, M. 2000. Identification with proteomics of novel proteins associated with the peribacteroid membrane of soybean root nodules. Mol. Plant.-Microbe Interact. 13: 325–333.
Patton, W.F. 2000. A thousand points of light: the application of fluorescence detection technologies to two-dimensional gel electrophoresis and proteomics. Electrophoresis 21: 1123–1144.
Peltier, JB., Friso, G., Kalume, D.E., Roepstorff, P., Nilsson, F., Adamska, I. and van Wijk, K.J. 2000. Proteomics of the chloroplast: systematic identification and targeting analysis of lumenal and peripheral thylakoid proteins. Plant Cell 12: 319–341.
Porubleva, L., Vander Velden, K., Kothari, S., Livier, D.J. and Chitnis, P.R. 2001. The proteome of maize: use of gene sequence and expressed sequence tag data for identification of proteins with mass fingerprints. Electrophoresis 22: 1724–1738.
Quadroni, M. and James, P. 1999. Proteomics and automation. Electrophoresis 20: 664–677.
Quail, P.H. 2000. Phytochrome-interacting factors. Semin. Cell Dev. Biol. 11: 457–466.
Rain, J.C., Selig, L., De Reuse, H., Battaglia, V., Reverdy, C., Simon, S., Lenzen, G., Petel, F., Wojcik, J., Schächter, V., Chemama, Y., Labigne, A. and Legrain, P. 2001. The protein-protein interaction map of Helicobacter pylori. Nature 409: 211–215.
Rakwal, R. and Komatsu, S. 2000. Role of jasmonate in the rice (Oryza sativa L.) self-defense mechanism using proteome analysis. Electrophoresis 21: 2492–2500.
Rouquie, D., Peltier, J.B., MarquisMansion, M., Tournaire, C., Doumas, P. and Rossignol, M. 1997. Construction of a directory of tobacco plasma membrane proteins by combined two-dimensional gel electrophoresis and protein sequencing. Electrophoresis 20: 705–711.
Santoni, V., Bellini, C. and Caboche, M. 1994. Use of two-dimensional protein-pattern analysis for the characterization of Arabidopsis thaliana mutants. Planta 192: 557–566.
Santoni, V., Delarue, M., Caboche, M. and Bellini, C. 1997. A comparison of two-dimensional electrophoresis data with pheno-typical traits in Arabidopsis leads to the identification of a mutant (cril) that accumulates cytokinins. Planta 202: 62–69.
Schmidt, F., Lueking, A., Nordhoff, E., Gobom, J., Klose, J., Seitz, H., Egelhofer, V., Eickhoff, H., Lehrach, H. and Cahill, D.J. 2001. Generation of minimal protein identifiers of proteins from 2D gels and recombinant proteins. Electrophoresis (accepted for publication).
Schwikowski, B., Uetz, P. and Fields, S. 2000. A network of protein-protein interactions in yeast. Nature Biotechnol. 18: 1257–1261.
Shi, J.R., Dixon, R.A., Gonzales, R.A., Kjellbom, P. and Bhat-tacharyya, M.K. 1995. Identification of cDNA clones encoding valosin-containing protein and other plant plasma membrane-associated proteins by a general immunoscreening strategy. Proc. Natl. Acad. Sci. USA 92: 4457 461.
Thiellement, H., Bahrman, N., Damerval, C., Plomion, C., Rossignol, M., Santoni, V., de Vienne, D. and Zivy, M. 1999. Proteomics for genetic and physiological studies in plants. Electrophoresis 20: 2013–2026.
Touzet, P., de Vienne, D., Huet, J.C., Ouali, C., Bouet, F. and Zivy, M. 1996. Amino acid analysis of proteins separated by two-dimensional electrophoresis in maize: isoform detection and function identification. Electrophoresis 17: 1393–1401.
Tsugita, A., Kawakami, T., Uchiyama, Y., Kamo, M., Miyatake, N. and Nozu, Y. 1994. Separation and characterization of rice proteins. Electrophoresis 15: 708–720.
Tsugita, A., Kamo, M., Kawakami, T. and Ohki, Y. 1996. Two-dimensional electrophoresis of plant proteins and standardization of gel patterns. Electrophoresis 17: 855–865.
Tsugita, A. and Kamo, M. 1999. 2-D electrophoresis of plant proteins. Meth. Mol. Biol. 112: 95–97.
Tucker, C.L., Gera, J.F. and Uetz, P. 2001. Towards an understanding of complex networks. Trends Cell Biol. 11: 102–106.
Uetz, P. and Hughes R.E. 2000. Systematic and large-scale two-hybrid screens. Curr. Opin. Microbiol. 3: 303–308.
van Wijk, K.J. 2000. Proteomics of the chloroplast: experimentation and prediction. Trends Plant Sci. 5: 420–425.
van Wijk, K.J. 2001. Challenges and prospects of plant proteomics. Plant Physiol. 126: 501–508.
Vidal, M. and Legrain, P. 1999. Yeast forward and reverse ‘n’-hybrid-systems. Nucl. Acids Res. 27: 919–929.
Walhout, A.J. and Vidal, M. 2001. High throughput yeast two-hybrid assays for large-scale protein interaction mapping. Methods 24: 297–306.
Walhout, A.J.M., Temple, G.F., Brasch, M.A., Hartley, J.L., Lorson, M.A., van den Heuvel, S. and Vidal, M. 2000a. GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes. Meth. Enzymol. 328: 575–592.
Walhout, A.J., Sordella, R., Lu, X., Hartley, J.L., Temple, G.F., Brasch, M.A., Thierry-Mieg, N. and Vidal, M. 2000b. Protein interaction mapping in C. elegans using proteins involved in vulva development. Science 287: 116–122.
Walter, G., Büssow, K., Cahill, D., Lueking, A. and Lehrach, H. 2000. Protein arrays for gene expression and molecular interaction screening. Curr. Opin. Microbiol. 3: 298–302.
Walter, G., Konthur, Z. and Lehrach, H. 2001. High-throughput screening of surface displayed gene products. Comb. Chem. High Throughput Screen. 4: 193–205.
Wasinger, V.C., Cordwell, S.J., Cerpa-Poljak, A., Yan, J.X., Gooley, A.A., Wilkins, M.R., Duncan, M.W., Harris, R., Williams, K.L. and Humphery-Smith, I. 1995. Progress with gene-product mapping of the Mollicutes: Mycoplasma genitalium. Electrophoresis 16: 1090–1094.
Winter, G., Griffiths, A.D., Hawkins, R.E. and Hoogenboom, H.R. 1994. Making antibodies by phage display technology. Annu. Rev. Immunol. 12: 433–455.
Xenarios, I. and Eisenberg, D. 2001. Protein interaction databases. Curr. Opin. Biotechnol. 12: 334–339.
Yamaguchi, K. and Subramanian, A.R. 2000. The plastid ribosomal proteins. Identification of all the proteins in the 50S subunit of an organelle ribosome (chloroplast). J. Biol. Chem. 275: 28466–28482.
Yamaguchi, K., von Knoblauch, K. and Subramanian, A.R. 2000. The plastid ribosomal proteins. Identification of all the proteins in the 30S subunit of an organelle ribosome (chloroplast). J. Biol. Chem. 275: 28455–28465.
Zivy, M. and de Vienne, D. 2000. Proteomics: a link between genomics, genetics and physiology. Plant Mol. Biol. 44: 575–580.
Zivy, M., Thiellement, H., de Vienne, D. and Hofmann, J.-P. 1984. Study on nuclear and cytoplasmic genome expression in wheat by two-dimensional gel electrophoresis. Theor. Appl. Genetics 68: 335–345.
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Kersten, B. et al. (2002). Large-scale plant proteomics. In: Town, C. (eds) Functional Genomics. Springer, Dordrecht. https://doi.org/10.1007/978-94-010-0448-0_9
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