Skip to main content
SpringerLink
Log in

Synthetic Gene Networks in Plant Systems

  • Protocol
  • First Online:
Synthetic Gene Networks

Part of the book series: Methods in Molecular Biology ((MIMB,volume 813))

Abstract

Synthetic biology methods are routinely applied in the plant field as in other eukaryotic model systems. Several synthetic components have been developed in plants and an increasing number of studies report on the assembly into functional synthetic genetic circuits. This chapter gives an overview of the existing plant genetic networks and describes in detail the application of two systems for inducible gene expression. The ethanol-inducible system relies on the ethanol-responsive interaction of the AlcA transcriptional activator and the AlcR receptor resulting in the transcription of the gene of interest (GOI). In comparison, the translational fusion of GOI and the glucocorticoid receptor (GR) domain leads to the dexamethasone-dependent nuclear translocation of the GOI::GR protein. This chapter contains detailed protocols for the application of both systems in the model plants potato and Arabidopsis, respectively.

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 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
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. Fiedler, U., and Conrad, U. (1995) High-level production and long-term storage of engineered antibodies in transgenic tobacco seeds. Bio-Technology 13, 1090–93.

    Google Scholar 

  2. Antunes, M. S., Ha, S. B., Tewari-Singh, N., Morey, K. J., Trofka, A. M., Kugrens, P., Deyholos, M., and Medford, J. I. (2006) A synthetic de-greening gene circuit provides a reporting system that is remotely detectable and has a re-set capacity. Plant Biotechnology Journal 4, 605–22.

    Google Scholar 

  3. Itaya, M., Fujita, K., Kuroki, A., and Tsuge, K. (2008) Bottom-up genome assembly using the Bacillus subtilis genome vector. Nature Methods 5, 41–43.

    Google Scholar 

  4. Venter, M. (2007) Synthetic promoters: Genetic control through cis engineering. Trends in Plant Science 12, 118–24.

    Google Scholar 

  5. Rushton, P. J., Reinstadler, A., Lipka, V., Lippok, B., and Somssich, I. E. (2002) Synthetic plant promoters containing defined regulatory elements provide novel insights into pathogen- and wound-induced signaling. Plant Cell 14, 749–62.

    Google Scholar 

  6. Boch, J., Scholze, H., Schornack, S., Landgraf, A., Hahn, S., Kay, S., Lahaye, T., Nickstadt, A., and Bonas, U. (2009) Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326, 1509–12.

    Google Scholar 

  7. Moore, I., Samalova, M., and Kurup, S. (2006) Transactivated and chemically inducible gene expression in plants. Plant Journal 45, 651–83.

    Google Scholar 

  8. Padidam, M. (2003) Chemically regulated gene expression in plants. Current Opinion in Plant Biology 6, 169–77.

    Google Scholar 

  9. Roslan, H. A., Salter, M. G., Wood, C. D., White, M. R. H., Croft, K. P., Robson, F., Coupland, G., Doonan, J., Laufs, P., Tomsett, A. B., and Caddick, M. X. (2001) Characterization of the ethanol-inducible alc gene-expression system in Arabidopsis thaliana. Plant Journal 28, 225–35.

    Google Scholar 

  10. Junker, B. H., Chu, C. C., Sonnewald, U., Willmitzer, L., and Fernie, A. R. (2003) In plants the alc gene expression system responds more rapidly following induction with acetaldehyde than with ethanol. Febs Letters 535, 136–40.

    Google Scholar 

  11. Curtis, M. D., and Grossniklaus, U. (2003) A Gateway cloning vector set for high-throughput functional analysis of genes in planta. Plant Physiology 133, 462–69.

    Google Scholar 

  12. Zuo, J. R., Niu, Q. W., and Chua, N. H. (2000) An estrogen receptor-based transactivator XVE mediates highly inducible gene expression in transgenic plants. Plant Journal 24, 265–73.

    Google Scholar 

  13. Böhmdorfer, G., Tramontan, A., Luxa, K., and Bachmair, A. (2010) A synthetic biology approach allows inducible retrotransposition in whole plants. Systems and Synthetic Biology 4, 133–38.

    Google Scholar 

  14. Aoyama, T., and Chua, N. H. (1997) A glucocorticoid-mediated transcriptional induction system in transgenic plants. Plant Journal 11, 605–12.

    Google Scholar 

  15. Craft, J., Samalova, M., Baroux, C., Townley, H., Martinez, A., Jepson, I., Tsiantis, M., and Moore, I. (2005) New pOp/Lhg4 vectors for stringent glucocorticoid-dependent transgene expression in Arabidopsis. Plant Journal 41, 899–918.

    Google Scholar 

  16. Moore, I., Galweiler, L., Grosskopf, D., Schell, J., and Palme, K. (1998) A transcription activation system for regulated gene expression in transgenic plants. Proceedings of the National Academy of Sciences of the United States of America 95, 376–81.

    Google Scholar 

  17. You, Y. S., Marella, H., Zentella, R., Zhou, Y. Y., Ulmasov, T., Ho, T. H. D., and Quatrano, R. S. (2006) Use of bacterial quorum-sensing components to regulate gene expression in plants. Plant Physiology 140, 1205–12.

    Google Scholar 

  18. Padidam, M., Gore, M., Lu, D. L., and Smirnova, O. (2003) Chemical-inducible, ecdysone receptor-based gene expression system for plants. Transgenic Research 12, 101–09.

    Google Scholar 

  19. Gardner, M. J., Baker, A. J., Assie, J. M., Poethig, R. S., Haseloff, J. P., and Webb, A. A. R. (2009) Gal4 GFP enhancer trap lines for analysis of stomatal guard cell development and gene expression. Journal of Experimental Botany 60, 213–26.

    Google Scholar 

  20. Johnson, A. A. T., Hibberd, J. M., Gay, C., Essah, P. A., Haseloff, J., Tester, M., and Guiderdoni, E. (2005) Spatial control of transgene expression in rice (Oryza sativa L.) using the Gal4 enhancer trapping system. Plant Journal 41, 779–89.

    Google Scholar 

  21. Laplaze, L., Parizot, B., Baker, A., Ricaud, L., Martiniere, A., Auguy, F., Franche, C., Nussaume, L., Bogusz, D., and Haseloff, J. (2005) Gal4-GFP enhancer trap lines for genetic manipulation of lateral root ­development in arabidopsis thaliana. Journal of Experimental Botany 56, 2433–42.

    Google Scholar 

  22. Schwab, R., Ossowski, S., Riester, M., Warthmann, N., and Weigel, D. (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18, 1121–33.

    Google Scholar 

  23. Verhounig, A., Karcher, D., and Bock, R. (2010) Inducible gene expression from the plastid genome by a synthetic riboswitch. Proceedings of the National Academy of Sciences of the United States of America 107, 6204–09.

    Google Scholar 

  24. Baudry, A., Heim, M. A., Dubreucq, B., Caboche, M., Weisshaar, B., and Lepiniec, L. (2004) TT2, TT8, and TTG1 synergistically specify the expression of banyuls and proanthocyanidin biosynthesis in Arabidopsis thaliana. Plant Journal 39, 366–80.

    Google Scholar 

  25. Gunl, M., Liew, E. F., David, K., and Putterill, J. (2009) Analysis of a post-translational steroid induction system for gigantea in Arabidopsis. BMC Plant Biology 9:141.

    Google Scholar 

  26. Antunes, M. S., Morey, K. J., Tewari-Singh, N., Bowen, T. A., Smith, J. J., Webb, C. T., Hellinga, H. W., and Medford, J. I. (2009) Engineering key components in a synthetic eukaryotic signal transduction pathway. Molecular Systems Biology 5:270.

    Google Scholar 

  27. Meyer, D. E., and Chilkoti, A. (1999) Purification of recombinant proteins by fusion with thermally-responsive polypeptides. Nature Biotechnology 17, 1112–15.

    Google Scholar 

  28. Floss, D. M., Sack, M., Arcalis, E., Stadlmann, J., Quendler, H., Rademacher, T., Stoger, E., Scheller, J., Fischer, R., and Conrad, U. (2009) Influence of elastin-like peptide fusions on the quantity and quality of a tobacco-derived human immunodeficiency virus-neutralizing antibody. Plant Biotechnology Journal 7, 899–913.

    Google Scholar 

  29. Floss, D. M., Schallau, K., Rose-John, S., Conrad, U., and Scheller, J. (2010) Elastin-like polypeptides revolutionize recombinant protein expression and their biomedical application. Trends in Biotechnology 28, 37–45.

    Google Scholar 

  30. Young, E., and Alper, H. (2010) Synthetic biology: Tools to design, build, and optimize cellular processes. Journal of Biomedicine and Biotechnology. 130781.

    Google Scholar 

  31. Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R., Algire, M. A., Benders, G. A., Montague, M. G., Ma, L., Moodie, M. M., Merryman, C., Vashee, S., Krishnakumar, R., Assad-Garcia, N., Andrews-Pfannkoch, C., Denisova, E. A., Young, L., Qi, Z., Segall-Shapiro, T. H., Calvey, C. H., Parmar, P. P., Hutchison III, C. A., Smith, H. O., and Venter, J. C. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52–56.

    Google Scholar 

  32. Jia, H., Van Loock, B., Liao, M., Verbelen, J. P., and Vissenberg, K. (2007) Combination of the alcr/alca ethanol switch and Gal4/VP16-UAS enhancer trap system enables spatial and temporal control of transgene expression in arabidopsis. Plant Biotechnology Journal 5, 477–82.

    Google Scholar 

  33. Sakvarelidze, L., Tao, Z., Bush, M., Roberts, G. R., Leader, D. J., Doonan, J. H., and Rawsthorne, S. (2007) Coupling the Gal4 UAS system with alcR for versatile cell type-specific chemically inducible gene expression in Arabidopsis. Plant Biotechnology Journal 5, 465–76.

    Google Scholar 

  34. Scheller, J., Leps, M., and Conrad, U. (2006) Forcing single-chain variable fragment production in tobacco seeds by fusion to elastin-like polypeptides. Plant Biotechnology Journal 4, 243–49.

    Google Scholar 

  35. Czauderna, T., Klukas, C., and Schreiber, F. (2010) Editing, validating and translating of SBGN maps. Bioinformatics 26, 2340–41.

    Google Scholar 

  36. Junker, B. H., Klukas, C., and Schreiber, F. (2006) Vanted: A system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics 7, 109.

    Google Scholar 

  37. Le Novère, N., Hucka, M., Mi, H. Y., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., Bergman, F. T., Gauges, R., Ghazal, P., Kawaji, H., Li, L., Matsuoka, Y., Villeger, A., Boyd, S. E., Calzone, L., Courtot, M., Dogrusoz, U., Freeman, T. C., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G. M., Goryanin, I., Kell, D. B., Sander, C., Sauro, H., Snoep, J. L., Kohn, K., and Kitano, H. (2009) The systems biology graphical notation. Nature Biotechnology 27, 735–41.

    Google Scholar 

  38. Junker, A., Hartmann, A., Schreiber, F., and Bäumlein, H. (2010) An engineer’s view on regulation of seed development. Trends in Plant Science 15, 303–07.

    Google Scholar 

  39. Sambrook, J., Fritsch, E. F., and Maniatis, T. (2001) Molecular cloning: A laboratory manual, Cold Spring Harbour Laboratory Press, New York.

    Google Scholar 

  40. Deblaere, R., Bytebier, B., Degreve, H., Deboeck, F., Schell, J., Vanmontagu, M., and Leemans, J. (1985) Efficient octopine Ti plasmid-derived vectors for Agrobacterium-mediated gene-transfer to plants. Nucleic Acids Research 13, 4777–88.

    Google Scholar 

  41. Sweetman, J. P., Chu, C. C., Qu, N., Greenland, A. J., Sonnewald, U., and Jepson, I. (2002) Ethanol vapor is an efficient inducer of the alc gene expression system in model and crop plant species. Plant Physiology 129, 943–48.

    Google Scholar 

  42. Höfgen, R., and Willmitzer, L. (1988) Storage of competent cells for Agrobacterium transformation. Nucleic Acids Research 16, 9877.

    Google Scholar 

  43. Clough, S. J., and Bent, A. F. (1998) Floral dip: A simplified method for agrobacterium-mediated transformation of Arabidopsis thaliana. Plant Journal 16, 735–43.

    Google Scholar 

  44. Rocha-Sosa, M., Sonnewald, U., Frommer, W., Stratmann, M., Schell, J., and Willmitzer, L. (1989) Both developmental and metabolic signals activate the promoter of a class-I patatin gene. Embo Journal 8, 23–29.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany

    Astrid Junker & Björn H. Junker

Authors
  1. Astrid Junker
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Björn H. Junker
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Björn H. Junker .

Editor information

Editors and Affiliations

  1. Inst. Biologie II, Zentrum für Biologische Signalstudien, Universität Freiburg, Stübeweg 51, Freiburg, 79108, Germany

    Wilfried Weber

  2. Dept. Ingenieurwissenschaften, Biosysteme (BSSE), ETH Zürich, Mattenstr. 26, Basel, 4058, Switzerland

    Martin Fussenegger

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Junker, A., Junker, B.H. (2012). Synthetic Gene Networks in Plant Systems. In: Weber, W., Fussenegger, M. (eds) Synthetic Gene Networks. Methods in Molecular Biology, vol 813. Humana Press. https://doi.org/10.1007/978-1-61779-412-4_21

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-412-4_21

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-411-7

  • Online ISBN: 978-1-61779-412-4

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation