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Clone-Based Functional Genomics

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Plant Systems Biology

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 553))

Abstract

Annotated genomes have provided a wealth of information about gene structure and gene catalogs in a wide range of species. Taking advantage of these developments, novel techniques have been implemented to investigate systematically diverse aspects of gene and protein functions underpinning biology processes. Here, we review functional genomics applications that require the mass production of cloned sequence repertoires, including ORFeomes and silencing tag collections. We discuss the techniques employed in large-scale cloning projects and we provide an up-to-date overview of the clone resources available for model plant species and of the current applications that may be scaled up for systematic plant gene studies.

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References

  1. Hieter, P. and Boguski, M. (1997) Functional genomics: it’s all how you read it. Science. 278, 601–602.

    PubMed  CAS  Google Scholar 

  2. Fleischmann, R.D., Adams, M.D., White, O., et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science. 269, 496–512.

    PubMed  CAS  Google Scholar 

  3. Goffeau, A., Barrell, B.G., Bussey, H., et al. (1996) Life with 6,000 genes. Science. 274, 546, 563–567.

    Google Scholar 

  4. C. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science. 282, 2012–2018.

    Google Scholar 

  5. Adams, M.D., Celniker, S.E., Holt, R.A., et al. (2000) The genome sequence of Drosophila melanogaster. Science. 287, 2185–2195.

    PubMed  Google Scholar 

  6. Venter, J.C., Adams, M.D., Myers, E.W., et al. (2001) The sequence of the human genome. Science. 291, 1304–1351.

    PubMed  CAS  Google Scholar 

  7. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature. 408, 796–815.

    Google Scholar 

  8. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature. 436, 793–800.

    Google Scholar 

  9. Tuskan, G.A., DiFazio, S., Jansson, S., et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science. 313, 1596–1604.

    PubMed  CAS  Google Scholar 

  10. Jaillon, O., Aury, J.M., Noel, B., et al. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature. 449, 463–467.

    PubMed  CAS  Google Scholar 

  11. Smith, V., Botstein, D., and Brown, P.O. (1995) Genetic footprinting: a genomic strategy for determining a gene’s function given its sequence. Proc. Natl. Acad. Sci. USA. 92, 6479–6483.

    PubMed  CAS  Google Scholar 

  12. Smith, V., Chou, K.N., Lashkari, D., Botstein, D., and Brown, P.O. (1996) Functional analysis of the genes of yeast chromosome V by genetic footprinting. Science. 274, 2069–2074.

    PubMed  CAS  Google Scholar 

  13. Giaever, G., Chu, A.M., Ni, L., et al. (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature. 418, 387–391.

    PubMed  CAS  Google Scholar 

  14. Yuan, D.S., Pan, X., Ooi, S.L., et al. (2005) Improved microarray methods for profiling the yeast knockout strain collection. Nucleic Acids Res. 33, e103.

    PubMed  Google Scholar 

  15. Tong, A.H., Evangelista, M., Parsons, A.B., et al. (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science. 294, 2364–2368.

    PubMed  CAS  Google Scholar 

  16. Tong, A.H., Lesage, G., Bader, G.D., et al. (2004) Global mapping of the yeast genetic interaction network. Science. 303, 808–813.

    PubMed  CAS  Google Scholar 

  17. Ossowski, S., Schwab, R., and Weigel, D. (2008) Gene silencing in plants using artificial microRNAs and other small RNAs. Plant J. 53, 674–690.

    PubMed  CAS  Google Scholar 

  18. Perrimon, N. and Mathey-Prevot, B. (2007) Applications of high-throughput RNA interference screens to problems in cell and developmental biology. Genetics. 175, 7–16.

    PubMed  CAS  Google Scholar 

  19. Scherr, M. and Eder, M. (2007) Gene silencing by small regulatory RNAs in mammalian cells. Cell Cycle. 6, 444–449.

    PubMed  CAS  Google Scholar 

  20. Boutros, M., Kiger, A.A., Armknecht, S., et al. (2004) Genome-wide RNAi analysis of growth and viability in Drosophila cells. Science. 303, 832–835.

    PubMed  CAS  Google Scholar 

  21. Ramadan, N., Flockhart, I., Booker, M., Perrimon, N., and Mathey-Prevot, B. (2007) Design and implementation of high-throughput RNAi screens in cultured Drosophila cells. Nat. Protoc. 2, 2245–2264.

    PubMed  CAS  Google Scholar 

  22. Berns, K., Hijmans, E.M., Mullenders, J., et al. (2004) A large-scale RNAi screen in human cells identifies new components of the p53 pathway. Nature. 428, 431–437.

    PubMed  CAS  Google Scholar 

  23. Du, G., Yonekubo, J., Zeng, Y., Osisami, M., and Frohman, M.A. (2006) Design of expression vectors for RNA interference based on miRNAs and RNA splicing. FEBS J. 273, 5421–5427.

    PubMed  CAS  Google Scholar 

  24. Paddison, P.J., Silvam, J.M., Conklin, D.S., et al. (2004) A resource for large-scale RNA-interference-based screens in mammals. Nature. 428, 427–431.

    PubMed  CAS  Google Scholar 

  25. Fields, S. and Song, O. (1989) A novel genetic system to detect protein--protein interactions. Nature. 340, 245–246.

    PubMed  CAS  Google Scholar 

  26. Ito, T., Chiba, T., Ozawa, R., Yoshida, M., Hattori, M., and Sakaki, Y. (2001) A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA. 98, 4569–4574.

    PubMed  CAS  Google Scholar 

  27. Uetz, P., Giot, L., Cagney, G., et al. (2000) A comprehensive analysis of protein--protein interactions in Saccharomyces cerevisiae. Nature. 403, 623–627.

    PubMed  CAS  Google Scholar 

  28. Yu, H., Braun, P., Yildirim, M.A., et al. (2008) High-quality binary protein interaction map of the yeast interactome network. Science 322, 104–110.

    Google Scholar 

  29. Giot, L., Bader, J.S., Brouwer, C., et al. (2003) A protein interaction map of Drosophila melanogaster. Science. 302, 1727–1736.

    PubMed  CAS  Google Scholar 

  30. Li, S., Armstrong, C.M., Bertin, N., et al. (2004) A map of the interactome network of the metazoan C. elegans. Science. 303, 540–543.

    PubMed  CAS  Google Scholar 

  31. Gandhi, T.K., Zhong, J., Mathivanan, S., et al. (2006) Analysis of the human protein interactome and comparison with yeast, worm and fly interaction datasets. Nat. Genet. 38, 285–293.

    PubMed  CAS  Google Scholar 

  32. Rual, J.F., Venkatesan, K., Hao, T., et al. (2005) Towards a proteome-scale map of the human protein--protein interaction network. Nature. 437, 1173–1178.

    PubMed  CAS  Google Scholar 

  33. Stelzl, U., Worm, U., Lalowski, M., et al. (2005) A human protein--protein interaction network: a resource for annotating the proteome. Cell. 122, 957–968.

    PubMed  CAS  Google Scholar 

  34. Rossi, F., Charlton, C.A., and Blau, H.M. (1997) Monitoring protein--protein interactions in intact eukaryotic cells by β-galactosidase complementation. Proc. Natl. Acad. Sci. USA. 94, 8405–8410.

    PubMed  CAS  Google Scholar 

  35. Olson, K.R. and Eglen, R.M. (2007) β galactosidase complementation: a cell-based luminescent assay platform for drug discovery. Assay Drug Dev. Technol. 5, 137–144.

    PubMed  CAS  Google Scholar 

  36. Galarneau, A., Primeau, M., Trudeau, L.E., and Michnick, S.W. (2002) β-lactamase protein fragment complementation assays as in vivo and in vitro sensors of protein protein interactions. Nat. Biotechnol. 20, 619–622.

    PubMed  CAS  Google Scholar 

  37. Cabantous, S., Terwilliger, T.C., and Waldo, G.S. (2005) Protein tagging and detection with engineered self-assembling fragments of green fluorescent protein. Nat. Biotechnol. 23, 102–107.

    PubMed  CAS  Google Scholar 

  38. Remy, I. and Michnick, S.W. (1999) Clonal selection and in vivo quantitation of protein interactions with protein-fragment complementation assays. Proc. Natl. Acad. Sci. USA. 96, 5394–5399.

    PubMed  CAS  Google Scholar 

  39. Remy, I., Campbell-Valois, F.X., and Michnick, S.W. (2007) Detection of protein–protein interactions using a simple survival protein-fragment complementation assay based on the enzyme dihydrofolate reductase. Nat. Protoc. 2, 2120–2125.

    PubMed  CAS  Google Scholar 

  40. Fetchko, M. and Stagljar, I. (2004) Application of the split-ubiquitin membrane yeast two-hybrid system to investigate membrane protein interactions. Methods. 32, 349–362.

    PubMed  CAS  Google Scholar 

  41. Thaminy, S., Miller, J., and Stagljar, I. (2004) The split-ubiquitin membrane-based yeast two-hybrid system. Methods Mol. Biol. 261, 297–312.

    PubMed  CAS  Google Scholar 

  42. Gavin, A.C., Bosche, M., and Krause, R., et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature. 415, 141–147.

    PubMed  CAS  Google Scholar 

  43. Gavin, A.C., Aloy, P., Grandi, P., et al. (2006) Proteome survey reveals modularity of the yeast cell machinery. Nature. 440, 631–636.

    PubMed  CAS  Google Scholar 

  44. Yashiroda, Y., Matsuyama, A., and Yoshida, M. (2008) New insights into chemical biology from ORFeome libraries. Curr. Opin. Chem. Biol. 12, 55–59.

    PubMed  CAS  Google Scholar 

  45. Aslanidis, C. and de Jong, P.J. (1990) Ligation-independent cloning of PCR products (LIC-PCR). Nucleic Acids Res. 18, 6069–6074.

    PubMed  CAS  Google Scholar 

  46. Dong, Y., Burch-Smith, T.M., Liu, Y., Mamillapalli, P., and Dinesh-Kumar, S.P. (2007) A ligation-independent cloning tobacco rattle virus vector for high-throughput virus-induced gene silencing identifies roles for NbMADS4-1 and -2 in floral development. Plant Physiol. 145, 1161–1170.

    PubMed  CAS  Google Scholar 

  47. Nour-Eldin, H.H., Hansen, B.G., Norholm, M.H., Jensen, J.K., and Halkier, B.A. (2006) Advancing uracil-excision based cloning towards an ideal technique for cloning PCR fragments. Nucleic Acids Res. 34, e122.

    PubMed  Google Scholar 

  48. Geu-Flores, F., Nour-Eldin, H.H., Nielsen, M.T., and Halkier, B.A. (2007) USER fusion: a rapid and efficient method for simultaneous fusion and cloning of multiple PCR products. Nucleic Acids Res. 35, e55.

    PubMed  Google Scholar 

  49. Bitinaite, J., Rubino, M., Varma, K.H., Schildkraut, I., Vaisvila, R., and Vaiskunaite, R. (2007) USER friendly DNA engineering and cloning method by uracil excision. Nucleic Acids Res. 35, 1992–2002.

    PubMed  CAS  Google Scholar 

  50. Hamann, T. and Møller, B.L. (2007) Improved cloning and expression of cytochrome P450s and cytochrome P450 reductase in yeast. Protein Expr. Purif. 56, 121–127.

    PubMed  CAS  Google Scholar 

  51. Nagano, Y., Takao, S., Kudo, T., Iizasa, E., and Anai, T. (2007) Yeast-based recombineering of DNA fragments into plant transformation vectors by one-step transformation. Plant Cell Rep. 26, 2111–2117.

    PubMed  CAS  Google Scholar 

  52. Liu, Q.H., Li, M.Z., Leibham, D., Cortez, D., and Elledge, S.J. (1998) The univector plasmid-fusion system, a method for rapid construction of recombinant DNA without restriction enzymes. Curr. Biol. 8, 1300–1309.

    PubMed  CAS  Google Scholar 

  53. Benoit, R.M., Wilhelm, R.N., Scherer-Becker, D., and Ostermeier, C. (2006) An improved method for fast, robust, and seamless integration of DNA fragments into multiple plasmids. Protein Expr. Purif. 45, 66–71.

    PubMed  CAS  Google Scholar 

  54. Hartley, J.L., Temple, G.F., and Brasch, M.A. (2000) DNA cloning using in vitro site-specific recombination. Genome Res. 10, 1788–1795.

    PubMed  CAS  Google Scholar 

  55. Cheo, D.L., Titus, S.A., Byrd, D.R., Hartley, J.L., Temple, G.F., and Brasch, M.A. (2004) Concerted assembly and cloning of multiple DNA segments using in vitro site-specific recombination: functional analysis of multi-segment expression clones. Genome Res. 14, 2111–2120.

    PubMed  CAS  Google Scholar 

  56. Sasaki, Y., Sone, T., Yoshida, S., et al. (2004) Evidence for high specificity and efficiency of multiple recombination signals in mixed DNA cloning by the Multisite Gateway system. J. Biotechnol. 107, 233–243.

    PubMed  CAS  Google Scholar 

  57. Curtis, M.D. and Grossniklaus, U. (2003) A Gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiol. 133, 462–469.

    PubMed  CAS  Google Scholar 

  58. Karimi, M., Inzé, D., and Depicker, A. (2002) GATEWAYTM vectors for Agrobacterium-mediated plant transformation. Trends Plant Sci. 7, 193–195.

    PubMed  CAS  Google Scholar 

  59. Wesley, S.V., Helliwell, C.A., Smith, N.A., et al. (2001) Construct design for efficient, effective and high-throughput gene silencing in plants. Plant J. 27, 581–590.

    PubMed  CAS  Google Scholar 

  60. Earley, K.W., Haag, J.R., Pontes, O., et al. (2006) Gateway-compatible vectors for plant functional genomics and proteomics. Plant J. 45, 616–629.

    PubMed  CAS  Google Scholar 

  61. Hilson, P. (2006) Cloned sequence repertoires for small- and large-scale biology. Trends Plant Sci. 11, 133–141.

    PubMed  CAS  Google Scholar 

  62. Karimi, M., Bleys, A., Vanderhaeghen, R., and Hilson, P. (2007) Building blocks for plant gene assembly. Plant Physiol. 145, 1183–1191.

    PubMed  CAS  Google Scholar 

  63. Karimi, M., De Meyer, B., and Hilson, P. (2005) Modular cloning in plant cells. Trends Plant Sci. 10, 103–105.

    PubMed  CAS  Google Scholar 

  64. Wakasa, Y., Yasuda, H., and Takaiwa, F. (2006) High accumulation of bioactive peptide in transgenic rice seeds by expression of introduced multiple genes. Plant Biotechnol. J. 4, 499–510.

    PubMed  CAS  Google Scholar 

  65. Van Leene, J., Stals, H., Eeckhout, D., et al. (2007) A tandem affinity purification-based technology platform to study the cell cycle interactome in Arabidopsis thaliana. Mol. Cell Proteomics. 6, 1226–1138.

    PubMed  Google Scholar 

  66. Seki, M., Narusaka, M., Kamiya, A., et al. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science. 296, 141–145.

    PubMed  Google Scholar 

  67. Kikuchi, S., Satoh, K., Nagata, T., et al. (2003) Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science. 301, 376–379.

    PubMed  Google Scholar 

  68. Yamada, K., Lim, J., Dale, J.M., et al. (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science. 302, 842–846.

    PubMed  CAS  Google Scholar 

  69. Nanjo, T., Futamura, N., Nishiguchi, M., Igasaki, T., Shinozaki, K., and Shinohara, K. (2004) Characterization of full-length enriched expressed sequence tags of stress-treated poplar leaves. Plant Cell Physiol. 45, 1738–1748.

    PubMed  Google Scholar 

  70. Thao, S., Zhao, Q., Kimball, T., et al. (2004) Results from high-throughput DNA cloning of Arabidopsis thaliana target genes using site-specific recombination. J. Struct. Funct. Genomics. 5, 267–276.

    PubMed  Google Scholar 

  71. Underwood, B.A. Vanderhaeghen, R., Whitford, R., Town, C.D., and Hilson, P. (2006) Simultaneous high-throughput recombinational cloning of open reading frames in closed and open configurations. Plant Biotechnol. J. 4, 317–324.

    PubMed  CAS  Google Scholar 

  72. Benhamed, M., Martin-Magniette, M.L., Taconnat, L., et al. Genome scale Arabidopsis promoter array identifies targets of the histone acetyltransferase GCN5. Submitted.

    Google Scholar 

  73. Deplancke, B., Mukhopadhyay, A., Ao, W., et al. (2006) A gene-centered C. elegans protein-DNA interaction network. Cell. 125, 1193–1205.

    PubMed  CAS  Google Scholar 

  74. De Sutter, V., Vanderhaeghen, R., Tilleman, S., et al. (2005) Exploration of jasmonate signalling via automated and standardized transient expression assays in tobacco cells. Plant J. 44, 1065–1076.

    PubMed  Google Scholar 

  75. Berger, B., Stracke, R., Yatusevich, R., Weisshaar, B., Flugge, U.I., and Gigolashvili, T. (2007) A simplified method for the analysis of transcription factor-promoter interactions that allows high-throughput data generation. Plant J. 50, 911–916.

    PubMed  CAS  Google Scholar 

  76. Paz-Ares, J. and the REGIA Consortium (2002) REGIA, an EU project on functional genomics of transcription factors from Arabidopsis thaliana. Comp. Funct. Genom. 3, 102–108.

    Google Scholar 

  77. Gong, W., Shen, Y.P., Ma, L.G., et al. (2004) Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes. Plant Physiol. 135, 773–782.

    PubMed  CAS  Google Scholar 

  78. Smith, N.A. Singh, S.P., Wang, M.B., Stoutjesdijk, P.A., Green, A.G., and Waterhouse, P.M. (2000) Total silencing by intron-spliced hairpin RNAs. Nature. 407, 319–320.

    PubMed  CAS  Google Scholar 

  79. Helliwell, C. and Waterhouse, P. (2003) Constructs and methods for high-throughput gene silencing in plants. Methods. 30, 289–295.

    PubMed  CAS  Google Scholar 

  80. Hilson, P., Allemeersch, J., Altmann, T., et al. (2004) Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res. 14, 2176–2189.

    PubMed  CAS  Google Scholar 

  81. Alvarez, J.P., Pekker, I., Goldshmidt, A., Blum, E., Amsellem, Z., and Eshed, Y. (2006) Endogenous and synthetic microRNAs stimulate simultaneous, efficient, and localized regulation of multiple targets in diverse species. Plant Cell. 18, 1134–1151.

    PubMed  CAS  Google Scholar 

  82. Schwab, R., Ossowski, S., Riester, M., Warthmann, N., and Weigel, D. (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell. 18, 1121–1133.

    PubMed  CAS  Google Scholar 

  83. Robertson, D. (2004) VIGS vectors for gene silencing: many targets, many tools. Annu. Rev. Plant Biol. 55, 495–519.

    PubMed  CAS  Google Scholar 

  84. Wielopolska, A., Townley, H., Moore, I., Waterhouse, P., and Helliwell, C. (2005) A high-throughput inducible RNAi vector for plants. Plant Biotechnol. J. 3, 583–590.

    PubMed  CAS  Google Scholar 

  85. Ichikawa, T., Nakazawa, M., Kawashima, M., et al. (2006) The FOX hunting system: an alternative gain-of-function gene hunting technique. Plant J. 48, 974–985.

    PubMed  CAS  Google Scholar 

  86. Weiste, C., Iven, T., Fischer, U., Onate-Sanchez, L., and Droge-Laser, W. (2007) In planta ORFeome analysis by large-scale over-expression of GATEWAY®-compatible cDNA clones: screening of ERF transcription factors involved in abiotic stress defense. Plant J. 52, 382–390.

    PubMed  CAS  Google Scholar 

  87. Ogawa, Y., Dansako, T., Yano, K., et al. (2008) Efficient and high-throughput vector construction and Agrobacterium-mediated transformation of Arabidopsis thaliana suspension-cultured cells for functional genomics. Plant Cell Physiol. 49, 242–250.

    PubMed  CAS  Google Scholar 

  88. Seki, M., Carninci, P., Nishiyama, Y., Hayashizaki, Y., and Shinozaki, K. (1998) High-efficiency cloning of Arabidopsis full-length cDNA by biotinylated CAP trapper. Plant J. 15, 707–720.

    PubMed  CAS  Google Scholar 

  89. Koroleva, O.A., Tomlinson, M.L., Leader, D., Shaw, P., and Doonan, J.H. (2005) High-throughput protein localization in Arabidopsis using Agrobacterium-mediated transient expression of GFP-ORF fusions. Plant J. 41, 162–174.

    PubMed  CAS  Google Scholar 

  90. Nelson, B.K., Cai, X., and Nebenfuhr, A. (2007) A multicolored set of in vivo organelle markers for co-localization studies in Arabidopsis and other plants. Plant J. 51, 1126–1136.

    PubMed  CAS  Google Scholar 

  91. Lalonde, S., Ehrhardt, D.W., Loque, D., Chen, J., Rhee, S.Y., and Frommer, W.B. (2008) Molecular and cellular approaches for the detection of protein--protein interactions: latest techniques and current limitations. Plant J. 53, 610–635.

    PubMed  CAS  Google Scholar 

  92. Miernyk, J.A. and Thelen, J.J. (2008) Biochemical approaches for discovering protein--protein interactions. Plant J. 53, 597–609.

    PubMed  CAS  Google Scholar 

  93. de Folter, S., Immink, R.G., Kieffer, M., et al. (2005) Comprehensive interaction map of the Arabidopsis MADS box transcription factors. Plant Cell. 17, 1424–1433.

    PubMed  Google Scholar 

  94. Obrdlik, P., El-Bakkoury, M., Hamacher, T., et al. (2004) K+ channel interactions detected by a genetic system optimized for systematic studies of membrane protein interactions. Proc. Natl. Acad. Sci. USA. 101, 12242–12247.

    PubMed  CAS  Google Scholar 

  95. Chen, H., Zou, Y., Shang, Y., et al. (2008) Firefly luciferase complementation imaging assay for protein--protein interactions in plants. Plant Physiol. 146, 368–376.

    PubMed  CAS  Google Scholar 

  96. Hink, M.A., Bisselin, T., and Visser, A.J. (2002) Imaging protein--protein interactions in living cells. Plant Mol. Biol. 50, 871–883.

    PubMed  CAS  Google Scholar 

  97. Subramanian, C., Xu, Y., Johnson, C.H., and von Arnim, A.G. (2004) In vivo detection of protein--protein interaction in plant cells using BRET. Methods Mol. Biol. 284, 271–286.

    PubMed  CAS  Google Scholar 

  98. Subramanian, C., Woo, J., Cai, X., et al. (2006) A suite of tools and application notes for in vivo protein interaction assays using bioluminescence resonance energy transfer (BRET). Plant J. 48, 138–152.

    PubMed  CAS  Google Scholar 

  99. Hu, C.D., Chinenov, Y., and Kerppola, T.K. (2002) Visualization of interactions among bZIP and Rel family proteins in living cells using bimolecular fluorescence complementation. Mol. Cell. 9, 789–798.

    PubMed  CAS  Google Scholar 

  100. Bhat, R.A., Lahaye, T., and Panstruga, R. (2006) The visible touch: in planta visualization of protein--protein interactions by fluorophore-based methods. Plant Methods. 2, 12.

    PubMed  Google Scholar 

  101. Hu, C.D., Grinberg, A.V., and Kerppola, T.K. (2006) Visualization of protein interactions in living cells using bimolecular fluorescence complementation (BiFC) analysis. Curr. Protoc. Cell Biol. Chapter 21: Unit 21.3.

    Google Scholar 

  102. Walter, M., Chaban, C., Schutze, K., et al. (2004) Visualization of protein interactions in living plant cells using bimolecular fluorescence complementation. Plant J. 40, 428–438.

    PubMed  CAS  Google Scholar 

  103. Citovsky, V., Lee, L.Y., Vyas, S., et al. (2006) Subcellular localization of interacting proteins by bimolecular fluorescence complementation in planta. J. Mol. Biol. 362, 1120–1131.

    PubMed  CAS  Google Scholar 

  104. Beauchemin, C., Boutet, N., and Laliberte, J.F. (2007) Visualization of the interaction between the precursors of VPg, the viral protein linked to the genome of Turnip Mosaic Virus, and the translation eukaryotic initiation factor iso 4E in planta. J. Virol. 81, 775–782.

    PubMed  CAS  Google Scholar 

  105. Guo, H.-S., Fei, J.-F., Xie, Q., and Chua, N.-H. (2003) A chemical-regulated inducible RNAi system in plants. Plant J. 34, 383–392.

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  109. Feilner, T., Hultschig, C., Lee, J., et al. (2005) High-throughput identification of potential Arabidopsis MAP kinases substrates. Mol. Cell Proteomics. 4, 1558–1168.

    PubMed  CAS  Google Scholar 

  110. Feilner, T. and Kersten, B. (2007) Phosphorylation studies using plant protein microarrays. Methods Mol. Biol. 355, 379–390.

    PubMed  CAS  Google Scholar 

  111. Kersten, B. and Feilner, T. (2007) Generation of plant protein microarrays and investigation of antigen--antibody interactions. Methods Mol. Biol. 355, 365–378.

    PubMed  CAS  Google Scholar 

  112. Popescu, S.C., Popescu, G.V., Bachan, S., et al. (2007) Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays. Proc. Natl. Acad. Sci. USA. 104, 4730–4755.

    PubMed  CAS  Google Scholar 

  113. Himmelbach, A., Zierold, U., Hensel, G., et al. (2007) A set of modular binary vectors for transformation of cereals. Plant Physiol. 145, 1192–1200.

    PubMed  CAS  Google Scholar 

  114. Joubès, J., De Schutter, K., Verkest, A, Inzé, D., and De Veylder, L. (2004) Conditional, recombinase-mediated expression of genes in plant cell cultures. Plant J. 37, 889–896.

    PubMed  Google Scholar 

  115. Brand, L., Horler, M., Nuesch, E., et al. (2006) A versatile and reliable two-component system for tissue-specific gene induction in Arabidopsis. Plant Physiol. 141, 1194–1204.

    PubMed  CAS  Google Scholar 

  116. Brown, A.P., Affleck, V., Fawcett, T., and Slabas, A.R. (2006) Tandem affinity purification tagging of fatty acid biosynthetic enzymes in Synechocystis sp PCC6803 and Arabidopsis thaliana. J. Exp. Bot. 57, 1563–1571.

    PubMed  CAS  Google Scholar 

  117. Rohila, J.S., Chen, M., Chen, S., et al. (2006) Protein--protein interactions of tandem affinity purification-tagged protein kinases in rice. Plant J. 46, 1–13.

    PubMed  CAS  Google Scholar 

  118. Liu, Y.L., Schiff, M., and Dinesh-Kumar, S.P. (2002) Virus-induced gene silencing in tomato. Plant J. 31, 777–786.

    PubMed  CAS  Google Scholar 

  119. Marjanac, G., De Paepe, A., Peck, I., Jacobs, A., De Buck, S., and Depicker, A. (2008) Evaluation of CRE-mediated excision approaches in Arabidopsis thaliana. Transgenic Res. 17, 239–250.

    PubMed  CAS  Google Scholar 

  120. Tzfira, T., Tian, G.W., Lacroix, B., et al. (2005) pSAT vectors: a modular series of plasmids for autofluorescent protein tagging and expression of multiple genes in plants. Plant Mol. Biol. 57, 503–516.

    PubMed  CAS  Google Scholar 

  121. Ehlert, A., Weltmeier, F., Wang, X., et al. (2006) Two-hybrid protein--protein interaction analysis in Arabidopsis protoplasts: establishment of a heterodimerization map of group C and group S bZIP transcription factors. Plant J. 46, 890–900.

    PubMed  CAS  Google Scholar 

  122. Xiao, Y.L., Malik, M., Whitelaw, C.A., and Town, C.D. (2002) Cloning and sequencing of cDNAs for hypothetical genes from chromosome 2 of Arabidopsis. Plant Physiol. 130, 2118–2128.

    PubMed  CAS  Google Scholar 

  123. Xiao, Y.L., Smith, S.R., Ishmael, N., et al. (2005) Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants. Plant Physiol. 139, 1323–1337.

    PubMed  CAS  Google Scholar 

  124. Stone, S.L., Hauksdottir, H., Troy, A., Herschleb, J., Kraft, E., and Callis, J. (2005) Functional analysis of the RING-type ubiquitin ligase family of Arabidopsis. Plant Physiol. 137, 13–30.

    PubMed  CAS  Google Scholar 

  125. Castelli, V., Aury, J.-M., Jaillon, O., et al. (2004) Whole genome sequence comparisons and “full-length” cDNA sequences: a combined approach to evaluate and improve Arabidopsis genome annotation. Genome Res. 14, 406–413.

    PubMed  Google Scholar 

  126. Thareau, V., Déhais, P., Serizet, C., Hilson, P., Rouzé, P., and Aubourg, S. (2003) Automatic design of gene-specific sequence tags for genome-wide functional studies. Bioinformatics. 19, 2191–2198.

    PubMed  CAS  Google Scholar 

  127. Sclep, G., Allemeersch, J., Liechti, R., et al. (2007) CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes. BMC Bioinformatics. 8, 400.

    PubMed  Google Scholar 

  128. Kerschen, A., Napoli, C.A., Jorgensen, R.A., and Muller, A.E. (2004) Effectiveness of RNA interference in transgenic plants. FEBS Lett. 566, 223–228.

    PubMed  CAS  Google Scholar 

  129. McGinnis, K., Chandler, V., Cone, K., et al. (2005) Transgene-induced RNA interference as a tool for plant functional genomics. Methods Enzymol. 392, 1–24.

    PubMed  CAS  Google Scholar 

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Acknowledgments

This work was supported by the 6th European Integrated Projects AGRON-OMICS (grant no. LSHG-CT-2006-037704). We thank Martine De Cock for help in preparing the manuscript.

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Authors and Affiliations

  1. Department of Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Gent, Belgium

    Annick Bleys, Mansour Karimi & Pierre Hilson

  2. Department of Molecular Genetics, Ghent University, Gent, Belgium

    Annick Bleys, Mansour Karimi & Pierre Hilson

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  1. Annick Bleys
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  2. Mansour Karimi
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  3. Pierre Hilson
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    © 2009 Humana Press, a part of Springer Science+Business Media, LLC

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    Bleys, A., Karimi, M., Hilson, P. (2009). Clone-Based Functional Genomics. In: Belostotsky, D. (eds) Plant Systems Biology. Methods in Molecular Biology™, vol 553. Humana Press. https://doi.org/10.1007/978-1-60327-563-7_8

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    • DOI: https://doi.org/10.1007/978-1-60327-563-7_8

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