Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Unravelling developmental dynamics: transient intervention and live imaging in plants

Nature Reviews Molecular Cell Biology volume 8, pages 491–501 (2007)Cite this article

Key Points

  • Pattern formation in plants involves spatial and temporal regulation of gene activities and the regulation of cell behaviour. Therefore, understanding the mechanisms of pattern formation can be addressed by using transient perturbation and live-imaging methods.

  • The challenge in plant-cell live imaging is to achieve the required spatial and temporal resolution without compromising the biological integrity. This can be achieved by using appropriate imaging systems and optics, and fluorophores as well as protein tags that target the fluorescent proteins to different intracellular compartments.

  • The main challenge in the post-genomic world is to convert genomic and proteomic maps into maps of functional molecular interactions within living cells. The simultaneous visualization of nucleic-acid and protein dynamics and their interactions is crucial and can be achieved through multi-modal imaging methods.

  • The local cell–cell communication machinery intersects with global hormonal signals to influence plant development. The simultaneous and dynamic visualization of hormonal responses along with cell-fate determinants and cell behaviours is required.

  • The process of cell-fate specification involves the conversion of transient temporal signals into stable genetic circuits that involve feedforward and feedback control of gene activation. Transient perturbations followed by real-time imaging of gene-expression patterns and cellular events have led to better mechanistic insights.

  • Quantitative and dynamic understanding of signalling molecules is crucial and requires the development of new fluorescent probes that reflect the true dynamics; these probes also have to be combined with kinetic imaging methods. Quantitative imaging also requires the development of computational methods to navigate, visualize and track image data over time.

Abstract

Plant development is dynamic in nature. This is exemplified in developmental patterning, in which roots and shoots rapidly elongate while simultaneously giving rise to precisely positioned new organs over a time course of minutes to hours. In this Review, we emphasize the insights gained from simultaneous use of live imaging and transient perturbation technologies to capture the dynamic properties of plant processes.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Spatial and temporal resolution in plant cells and tissues.
Figure 2: FRAP and FRET measurements in plant cells.
Figure 3: FLIM measurement of protein–protein interactions in the living plant cell.
Figure 4: Multi-channel confocal imaging of Arabidopsis thaliana SAM, labelled with three spectrally variant fluorescent proteins.
Figure 5: Cell ablations, transient intervention and live imaging.

Similar content being viewed by others

References

  1. Davidson, E. H. (ed.) Genomic Regulatory Systems: Development and Evolution (Academic, San Diego, 2001).

  2. Meyerowitz, E. M. Genetic control review of cell division patterns in developing plants. Cell 88, 299–308 (1997). A comprehensive review on genetic control of different modes of cell-division patterns in shoot and floral meristems of A. thaliana.

    Article  CAS  PubMed  Google Scholar 

  3. Hussey, P. J. (ed.) The Plant Cytoskeleton in Cell Differentiation and Development. Annual Plant Reviews Vol. 10 (Blackwell, Oxford, 2004).

  4. Ball, E. Cell division patterns in living shoot apices. Phytomorphology 10, 377–396 (1960).

    Google Scholar 

  5. Megason, S. G. & Fraser, S. E. Digitizing life at the level of the cell: high performance laser-scanning microscopy and image analysis for in toto imaging of development. Mech. Dev. 120, 1407–1420 (2003). A comprehensive review on live imaging and image-processing methods that can be applied to study cell–cell interactions during development.

    Article  CAS  PubMed  Google Scholar 

  6. Fricker, M., Runions, J. & Moore, I. Quantitative fluorescence microscopy: from art to science. Annu. Rev. Plant Biol. 2, 79–107 (2006).

    Article  CAS  Google Scholar 

  7. Knight, M. R., Campbell, A. K., Smith, S. M. & Trewavas, A. J. Transgenic plant aequorin reports the effects of touch and cold-shock and elicitors on cytoplasmic calcium. Nature 352, 524–526 (1991).

    Article  CAS  PubMed  Google Scholar 

  8. Knight, M. R., Read, N. D., Campbell, A. K. & Trewavas, A. J. Imaging calcium dynamics in living plants using semi-synthetic recombinant aequorins. J. Cell Biol. 121, 83–90 (1993).

    Article  CAS  PubMed  Google Scholar 

  9. Cheung, A. Y. & Wu, H. M. Overexpression of an Arabidopsis formin stimulates supernumerary actin cable formation from pollen tube cell membrane. Plant Cell 16, 257–269 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Fu, Y., Wu, G. & Yang, Z. Rop GTPase–dependent dynamics of tip-localized F-actin controls tip growth in pollen tubes. J. Cell Biol. 152, 1019–1032 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Shaner, N. C., Steinbach, P. A. & Tsien, R. Y. A guide to choosing fluorescent proteins. Nature Methods 2, 905–909 (2005). An excellent guide to choosing appropriate fluorescent proteins based on brightness and expression, photostability, oligomerization, toxicity, environmental sensitivity, and for multiple labelling.

    Article  CAS  PubMed  Google Scholar 

  12. Haseloff, J. & Siemering, K. R. The uses of green fluorescent protein in plants. Methods Biochem. Anal. 47, 259–284 (2006).

    PubMed  Google Scholar 

  13. Cheng, P. C. in Handbook of Biological Confocal Microscopy 3rd edn Ch. 21 (ed. Pawley, J. B.) 414–439 (Springer, New York, 2006).

    Book  Google Scholar 

  14. Moreno, N., Bougourd, S., Haseloff, J. & Feijo, J. A. in Handbook of Biological Confocal Microscopy 3rd edn Ch. 44 (ed. Pawley, J. B.) 769–787 (Springer, New York, 2006). This chapter provides information about appropriate imaging methods and imaging systems for fluorescent labelling of plant cells.

    Book  Google Scholar 

  15. Stephens, D.J. & Allan, V.J. Light microscopy techniques for live cell imaging. Science 300, 82–86 (2003).

    Article  CAS  PubMed  Google Scholar 

  16. Pawley, J. B. (ed.) Handbook of Biological Confocal Microscopy, 3rd edn (Springer, New York, 2006). An excellent guide to the principles and practices of confocal microscopy.

  17. Reddy, G. V. & Meyerowitz, E. M. Stem-cell homeostasis and growth dynamics can be uncoupled in the Arabidopsis shoot apex. Science 310, 663–667 (2005). Uses transient gene silencing and live imaging to gain mechanistic insights into the process of stem-cell maintenance in the A. thaliana shoot apex.

    Article  PubMed  Google Scholar 

  18. Heisler, M. G. et al. Auxin transport dynamics and gene expression patterns during primordium development in the Arabidopsis inflorescence meristem. Curr. Biol. 15, 1899–1911 (2005). Demonstrates the power of the multi-channel live-imaging method in revealing the developmental sequence of flower primordium formation in the A. thaliana shoot apex.

    Article  CAS  PubMed  Google Scholar 

  19. Paredez, A. R,. Somerville, C. R. & Ehrhardt, D. W. Visualization of cellulose synthase demonstrates functional association with microtubules. Science 312, 1491–1495 (2006). Uses spinning disk confocal microscopy to reveal cellulose synthase dynamics during cell deposition.

    Article  CAS  PubMed  Google Scholar 

  20. Feijo, J. A. & Moreno, N. Imaging plant cells by two-photon excitation. Protoplasma 223, 1–32 (2004). A comprehensive review that covers aspects related to the application of two-photon confocal microscopy, based on comparisons drawn with confocal microscopy.

    Article  PubMed  Google Scholar 

  21. Hettinger, J. W. et al. Optical coherence microscopy. A technology for rapid, in vivo, non-destructive visualization of plants and plant cells. Plant Physiol. 123, 3–16 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Reeves, A., Parsons, R. L., Hettinger, J. W. & Medford, J. I. In vivo three-dimensional imaging of plants with optical coherence microscopy. J. Microsc. 208, 177–189 (2002).

    Article  CAS  PubMed  Google Scholar 

  23. Swedlow, J. R., Hu, K., Andrews, P. D., Roos, D. S. & Murray, J. M. Measuring tubulin content in Toxoplasma gondii: a comparison of laser-scanning confocal and wide-field fluorescence microscopy. Proc. Natl Acad. Sci. USA 99, 2014–2019 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Cutler, S. R., Ehrhardt, D. W., Griffitts, J. S. & Somerville, C. R. Random GFP::cDNA fusions enable visualization of subcellular structures in cells of Arabidopsis at a high frequency. Proc. Natl Acad. Sci. USA. 97, 3718–3723 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Haseloff, J. GFP variants for multispectral imaging of living cells. Methods Cell Biol., 58, 139–151 (1999).

    Article  CAS  PubMed  Google Scholar 

  26. Haseloff, J. in Imaging Living Cells (eds Rizzuto, R. & Fasolato, C.) 40–94 (Springer, Berlin, 1999).

    Google Scholar 

  27. Wagner, D. Chromatin regulation of plant development. Curr. Opin. Plant Biol. 6, 20–28 (2003).

    Article  CAS  PubMed  Google Scholar 

  28. Ringrose, L. & Paro, R. Epigenetic regulation of cellular memory by the Polycomb and Trithorax group proteins. Annu. Rev. Genet. 38, 413–443 (2004).

    Article  CAS  PubMed  Google Scholar 

  29. Shav-Tal, Y. & Singer, R. H. RNA localization. J. Cell Sci. 118, 4077–4081 (2005).

    Article  CAS  PubMed  Google Scholar 

  30. Dirks, R. W. & Tanke, H. J. Advances in fluorescent tracking of nucleic acids in living cells. Biotechniques 40, 489–496. A comprehensive review on fluorescent techniques to label nucleic acids to follow chromatin and RNA dynamics.

  31. Fang, Y. & Spector, D. L. Centromere positioning and dynamics in living Arabidopsis plants. Mol. Biol. Cell 16, 5710–5718 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Costa, S. & Shaw, P. Chromatin organization and cell fate switch respond to positional information in Arabidopsis. Nature 439, 493–496 (2006). 3D fluorescence in situ hybridization was used on intact A. thaliana root epidermal tissues to follow chromatin organization during cell-fate specification.

    Article  CAS  PubMed  Google Scholar 

  33. Robinett, C. A. et al. In vivo localization of DNA sequences and visualization of large-scale chromatin organization using lac operator/repressor recognition. J. Cell Biol. 135, 1685–1700 (1996).

    Article  CAS  PubMed  Google Scholar 

  34. Tsukamoto, T., et al. Visualization of gene activity in living cells. Nature Cell Biol. 2, 871–878 (2000).

    Article  CAS  PubMed  Google Scholar 

  35. Bertrand, E. P. et al. Localization of ASH1 mRNA particles in living yeast. Mol. Cell 2, 437–445 (1998).

    Article  CAS  PubMed  Google Scholar 

  36. Hamada S. et al. The transport of prolamine RNAs to prolamine protein bodies in living rice endosperm cells. Plant Cell 10, 2253–2264 (2003).

    Article  CAS  Google Scholar 

  37. Nagai, T. et al. A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications. Nature Biotech. 20, 87–90 (2002).

    Article  CAS  Google Scholar 

  38. Cotlet, M., Goodwin, P. M., Waldo, G. S. & Werner, J. H. A comparison of the fluorescence dynamics of single molecules of a green fluorescent protein: one- versus two-photon excitation. ChemPhysChem. 7, 250–260 (2006).

    Article  CAS  PubMed  Google Scholar 

  39. Griffin, B. A., Adams, S. R. & Tsien, R. Y. Specific covalent labeling of recombinant protein molecules inside live cells. Science 281, 269–272 (1998).

    Article  CAS  PubMed  Google Scholar 

  40. Lippincott-Schwartz, J. & Patterson, G. H. Development and use of fluorescent protein markers in living cells. Science 300, 87–91 (2003). An excellent review on the development of photosensitive fluorescent proteins and methods for live imaging.

    Article  CAS  PubMed  Google Scholar 

  41. Li, X. et al. Generation of destabilized green fluorescent protein as a transcription reporter. J. Biol. Chem. 273, 34970–34975 (1998).

    Article  CAS  PubMed  Google Scholar 

  42. Ward, T. H. & Brandizzi, F. Dynamics of proteins in Golgi membranes: comparisons between mammalian and plant cells highlighted by photobleaching techniques. Cell. Mol. Life Sci. 61, 172–185 (2004).

    Article  CAS  PubMed  Google Scholar 

  43. Fang, Y., Hearn, S., & Spector, D. L. Tissue-specific expression and dynamic organization of SR splicing factors in Arabidopsis. Mol. Biol. Cell 15, 2664–2673 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Chang, H. Y. et al. Dynamic interaction of NtMAP65-1a with microtubules in vivo. J. Cell Sci. 118, 3195–3201 (2005).

    Article  CAS  PubMed  Google Scholar 

  45. Shaw, S. L., Kamyar, R., & Ehrhardt, D. W. Sustained microtubule treadmilling in Arabidopsis cortical arrays. Science 300, 1715–1718 (2003). Uses live imaging and FRAP methods to reveal microtubule dynamics in A. thaliana.

    Article  CAS  PubMed  Google Scholar 

  46. Kohler, R. H., Schwille, P., Webb, W. W. & Hanson, M. R. Active protein transport through plastid tubules: velocity quantified by fluorescence correlation spectroscopy. J. Cell Sci. 113, 3921–3930 (2000).

    CAS  PubMed  Google Scholar 

  47. Chow, B. & McCourt, P. Hormone signalling from a developmental context. J. Exp. Bot. 55, 247–251 (2004).

    Article  CAS  PubMed  Google Scholar 

  48. Ulmasov, T., Murfett, J., Hagen, G. & Guilfoyle, T. Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements. Plant Cell 9, 1963–1971 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Leyser, O. Dynamic integration of auxin transport and signalling. Curr. Biol. 16, 424–433 (2006).

    Article  CAS  Google Scholar 

  50. Galweiler, L. et al. Regulation of polar auxin transport by AtPIN1 in Arabidopsis vascular tissue. Science 282, 2226–2230 (1998).

    Article  CAS  PubMed  Google Scholar 

  51. Reinhardt, D. et al. Regulation of phyllotaxis by polar auxin transport. Nature 426, 255–260 (2003).

    Article  CAS  PubMed  Google Scholar 

  52. Paciorek, T. et al. Auxin inhibits endocytosis and promotes its own efflux from cells. Nature 435, 1251–1256 (2005).

    Article  CAS  PubMed  Google Scholar 

  53. Ferreira, F. J. & Kieber, J. J. Cytokinin signaling. Curr. Opin. Plant Biol. 8, 518–525 (2005).

    Article  CAS  PubMed  Google Scholar 

  54. Giulini, A., Wang, J. & Jackson, D. Control of phyllotaxy by the cytokinin inducible response regulator homologue ABPHYL1. Nature 430, 1031–1034 (2004).

    Article  CAS  PubMed  Google Scholar 

  55. Leibfried, A. et al. WUSCHEL controls meristem function by direct regulation of cytokinin-inducible response regulators. Nature 438, 1172–1175 (2005).

    Article  CAS  PubMed  Google Scholar 

  56. Yanai, O. et al. Arabidopsis KNOXI proteins activate cytokinin biosynthesis. Curr. Biol. 15, 1566–1571 (2005).

    Article  CAS  PubMed  Google Scholar 

  57. Christmann, A., Hoffmann, T., Teplova, I., Grill, E. & Muller, A. Generation of active pools of abscisic acid revealed by in vivo imaging of water-stressed Arabidopsis. Plant Physiol. 137, 209–219 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Jares-Erijman, E. A. & Jovin, T. M. FRET imaging. Nature Biotech. 21, 1387–1395 (2003).

    Article  CAS  Google Scholar 

  59. Van Roessel, P. & Brand, A. H. Imaging into the future: visualizing gene expression and protein interactions with fluorescent proteins. Nature Cell Biol. 4, e15–e20 (2002).

    Article  CAS  PubMed  Google Scholar 

  60. Kato, N., Pontier, D. & Lam, E. Spectral profiling for the simultaneous observation of four distinct fluorescent proteins and detection of protein–protein interaction via fluorescence resonance energy transfer in tobacco leaf nuclei. Plant Physiol. 129, 931–942 (2002). Uses four spectral variants of fluorescent proteins for simultaneous visualization and protein–protein interactions.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Russinova, E. et al. Heterodimerization and endocytosis of Arabidopsis brassinosteroid receptors BRI1 and AtSERK3 (BAK1). Plant Cell 16, 3216–3229 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Shah, K. et al. Subcellular localization and oligomerization of the Arabidopsis thaliana somatic embryogenesis receptor kinase 1 protein. J. Mol. Biol. 309, 641–655 (2001).

    Article  CAS  PubMed  Google Scholar 

  63. Immink, R. G. et al. Analysis of MADS box protein–protein interactions in living plant cells. Proc. Natl Acad. Sci. USA 99, 2416–2421 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Fu, Y., Gu, Y., Zheng, Z., Wasteneys, G. & Yang, Z. Arabidopsis interdigitating cell growth requires two antagonistic pathways with opposing action on cell morphogenesis. Cell 120, 687–700 (2005).

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  67. Bracha-Drori, K. et al. Detection of protein–protein interactions in plants using bimolecular fluorescence complementation. Plant J. 40, 419–427 (2004).

    Article  CAS  PubMed  Google Scholar 

  68. Kost, B., Spielhofer, P., & Chua, N. H. A GFP–mouse talin fusion protein labels plant actin filaments in vivo and visualizes the actin cytoskeleton in growing pollen tubes. Plant J. 16, 393–401 (1998).

    Article  CAS  PubMed  Google Scholar 

  69. Fu, Y., Li, H. & Yang, Z. The ROP2 GTPase controls the formation of cortical fine F-actin and the early phase of directional cell expansion during Arabidopsis organogenesis. Plant Cell 14, 777–794 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Sheahan, M. B., Staiger, C. J., Rose, R. J. & McCurdy, D. W. A green fluorescent protein fusion to actin-binding domain 2 of Arabidopsis fimbrin highlights new features of a dynamic actin cytoskeleton in live plant cells. Plant Physiol. 136, 3968–3978 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Yuan, M., Shaw, P. J., Warn, R. M. & Lloyd, C. W. Dynamic reorientation of cortical microtubules, from transverse to longitudinal, in living plant cells. Proc. Natl Acad. Sci. USA 91, 6050–6053 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Hush, J. M., Wadsworth, P., Callaham, D. A. & Hepler, P. K. Quantification of microtubule dynamics in living plant cells using fluorescence redistribution after photobleaching. J. Cell Sci. 107, 775–784 (1994).

    PubMed  Google Scholar 

  73. Marc, J. et al. A GFP–MAP4 reporter gene for visualizing cortical microtubule rearrangements in living epidermal cells. Plant Cell. 10, 1927–1940 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  74. Boisnard-Lorig, C. et al. Dynamic analyses of the expression of the HISTONE::YFP fusion protein in Arabidopsis show that syncytial endosperm is divided in mitotic domains. Plant Cell 13, 495–509 (2001). Investigates the dynamics of cell-division patterns during A. thaliana endosperm development by using chromatin-localized HISTONE:YFP and live imaging.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Reddy, G. V., Heisler, M. G., Ehrhardt, D. W. & Meyerowitz, E. M. Real-time lineage analysis reveals oriented cell divisions associated with morphogenesis at the shoot apex of Arabidopsis thaliana. Development 131, 4225–4237 (2004). Uses a novel live-imaging method to visualize the dynamics of growth patterns in actively growing shoot apical meristems of A. thaliana.

    Article  CAS  PubMed  Google Scholar 

  76. Cutler, S. R. & Somerville, C. R. Imaging plant cell death: GFP-Nit1 aggregation marks an early step of wound and herbicide induced cell death. BMC Plant Biol. 5, 4 (2005). Describes a novel fluorescent marker to follow early events of cell death in A. thaliana.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Kohler, R. H., Zipfel, W. R., Webb, W. W. & Hanson, M. R. The green fluorescent protein as a marker to visualize plant mitochondria in vivo. Plant J. 11, 613–621 (1997).

    Article  CAS  PubMed  Google Scholar 

  78. Stathopoulos, A. & Levine, M. Genomic regulatory networks and animal development. Dev. Cell 4, 449–462 (2005).

    Article  CAS  Google Scholar 

  79. Grandjean, O. et al. In vivo analysis of cell division, cell growth, and differentiation at the shoot apical meristem in Arabidopsis. Plant Cell 16, 74–87 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Moore, I., Samalova, M. & Kurup, S. Transactivated and chemically inducible gene expression in plants. Plant J. 45, 651–683 (2006). An excellent review on available transactivation systems to achieve spatio-temporal manipulation of gene expression.

    Article  CAS  PubMed  Google Scholar 

  81. Laplaze, L. et al. GAL4-GFP enhancer trap lines for genetic manipulation of lateral root development in Arabidopsis thaliana. J. Exp. Bot. 56, 2433–2442 (2005).

    Article  CAS  PubMed  Google Scholar 

  82. Moore, I., Galweiler, L., Grosskopf, D., Schell, J. & Palme, K. A transcription activation system for regulated gene expression in transgenic plants. Proc. Natl Acad. Sci. USA 95, 376–381 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Craft, J. et al. New pOp/LhG4 vectors for stringent glucocorticoid-dependent transgene expression in Arabidopsis. Plant J. 41, 899–918 (2005).

    Article  CAS  PubMed  Google Scholar 

  84. Schoof, H. et al. The stem cell population of Arabidopsis shoot meristems in maintained by a regulatory loop between the CLAVATA and WUSCHEL genes. Cell 100, 635–644 (2000).

    Article  CAS  PubMed  Google Scholar 

  85. Eshed, Y., Baum, S. F., Perea. J. V. & Bowman, J. L. Establishment of polarity in lateral organs of plants. Curr. Biol. 11, 1251–1260 (2001).

    Article  CAS  PubMed  Google Scholar 

  86. Sabatini, S, Heidstra, R, Wildwater, M & Scheres, B. SCARECROW is involved in positioning the stem cell niche in the Arabidopsis root meristem. Genes Dev. 17, 354–358 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Aida, M. et al. The PLETHORA genes mediate patterning of the Arabidopsis root stem cell niche. Cell 119, 109–120 (2004).

    Article  CAS  PubMed  Google Scholar 

  88. Aoyama, T. & Chua, N. H. A glucocorticoid-mediated transcriptional induction system in transgenic plants. Plant J. 11, 605–612 (1997).

    Article  CAS  PubMed  Google Scholar 

  89. Helliwell, C. & Waterhouse, P. Constructs and methods for high throughput gene silencing in plants. Methods 30, 289–295 (2003). A good guide describing the constructs and methods for generating fold-back RNAs that can mediate gene silencing.

    Article  CAS  PubMed  Google Scholar 

  90. Wielopolska, A., Townley, H., Moore, I., Waterhouse, P. & Helliwell, C. A high throughput inducible RNAi vector for plants. Plant Biotechnol. J. 3, 583–590 (2005). Describes the development of constructs that are required for inducible gene silencing.

    Article  CAS  PubMed  Google Scholar 

  91. Schwab, R., Ossowski, S., Riester, M., Warthmann, N. & Weigel, D. Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18, 1121–1133 (2006). Reports the use of artificial microRNAs to achieve targeted gene silencing.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Deveaux, Y. et al. The ethanol switch: a tool for tissue-specific gene induction during plant development. Plant J. 36, 918–923 (2003).

    Article  CAS  PubMed  Google Scholar 

  93. Zuo, J., Niu, Q. W. & Chua, N. H. Technical advance: an estrogen receptor-based transactivator XVE mediates highly inducible gene expression in transgenic plants. Plant J. 24, 265–273 (2000).

    Article  CAS  PubMed  Google Scholar 

  94. Sieburth, L. E., Drews, G. N. & Meyerowitz, E. M. Non-autonomy of AGAMOUS function in flower development: use of a Cre/loxP method for mosaic analysis in Arabidopsis. Development 125, 4303–4312 (1998).

    CAS  PubMed  Google Scholar 

  95. Kurup, S. et al. Marking cell lineages in living tissues. Plant J. 42, 444–453 (2005). Describes a novel, heat-shock inducible, transposon-based system to positively mark lineages in A. thaliana.

    Article  CAS  PubMed  Google Scholar 

  96. Markel, H., Chandler, J. & Werr, W. Translational fusions with the engrailed repressor domain efficiently convert plant transcription factors into dominant-negative functions. Nucleic Acids Res. 30, 4709–4719 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Hiratsu, K., Matsui, K., Koyama, T. & Ohme-Takagi, M. Dominant repression of target genes by chimeric repressors that include the EAR motif, a repression domain, in Arabidopsis. Plant J. 34, 733–739 (2003).

    Article  CAS  PubMed  Google Scholar 

  98. Jay, D. G. Selective destruction of protein function by chromophore-assisted laser inactivation. Proc. Natl Acad. Sci. USA 85, 5454–5458 (1988).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Tour, O., Meijer, R. M., Zacharias, D. A., Adams, S. R. & Tsien, R. Y. Genetically targeted chromophore-assisted light inactivation. Nature Biotech. 21, 1505–1508 (2003).

    Article  CAS  Google Scholar 

  100. Tanabe, T. et al. Multiphoton excitation-evoked chromophore-assisted laser inactivation using green fluorescent protein. Nature Methods 2, 503–505 (2005). Uses GFP as a photosensitizer to achieve CALI.

    Article  CAS  PubMed  Google Scholar 

  101. Bulina, M. E. et al. A genetically encoded photosensitizer. Nature Biotech. 24, 95–99 (2006).

    Article  CAS  Google Scholar 

  102. van den Berg, C., Willemsen, V., Hage, W., Weisbeek, P. & Scheres, B. Cell fate in the Arabidopsis root meristem determined by directional signaling. Nature 378, 62–65 (1995).

    Article  CAS  PubMed  Google Scholar 

  103. van den Berg, C., Willemsen, V., Hendriks. G., Weisbeek, P. & Scheres, B. Short-range control of cell differentiation in the Arabidopsis root meristem. Nature 390, 287–289 (1997).

    Article  CAS  PubMed  Google Scholar 

  104. Xu, J. et al. A molecular framework for plant regeneration. Science 311, 385–388 (2006). Combines fluorescent cell-type-specific markers, cell ablations and live imaging to follow the wound-induced regeneration process in A. thaliana roots.

    Article  CAS  PubMed  Google Scholar 

  105. Wildwater, M. et al. The RETINOBLASTOMA-RELATED gene regulates stem cell maintenance in Arabidopsis roots. Cell 123, 1337–1349 (2005). Combines spatially controlled gene manipulation, cell ablations and live imaging to gain mechanistic insights into the function of RETINOBLASTOMA in stem-cell specification and cell division.

    Article  CAS  PubMed  Google Scholar 

  106. Levesque, M. P. et al. Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis. PLoS Biol. 4, e143 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  107. Wellmer, F., Alves-Ferreira, M., Dubois, A., Riechmann, J. L. & Meyerowitz, E. M. Genome-wide analysis of gene expression during early Arabidopsis flower development. PLoS Genet. 2, e117 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Schmid, et al. Dissection of floral induction pathways using global expression analysis. Development 130, 6001–6012 (2003).

    Article  CAS  PubMed  Google Scholar 

  109. Phizicky, E. et al. Protein analysis on a proteomic scale. Nature 422, 208–215 (2003).

    Article  CAS  PubMed  Google Scholar 

  110. de Reuille, P. B., Bohn-Courseau, I., Godin, C. & Traas, J. A protocol to analyse cellular dynamics during plant development. Plant J. 44, 1045–1053 (2005).

    Article  CAS  PubMed  Google Scholar 

  111. Rudge, T. & Haseloff, J. in Lecture Notes in Computer Science: Advances in Artificial Life 3630, 78–87 (2005).

    Google Scholar 

  112. de Reuille, P. B. et al. Computer simulations reveal properties of the cell–cell signaling network at the shoot apex in Arabidopsis. Proc. Natl Acad. Sci. USA 103, 1627–1632 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Smith, R. S. et al. A plausible model of phyllotaxis. Proc. Natl Acad. Sci. USA 103, 1301–1306 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  114. Jonsson, H. et al. Modeling the organization of the WUSCHEL expression domain in the shoot apical meristem. Bioinformatics (Suppl. 1), i232–i240 (2005).

  115. Jonsson, H., Heisler, M. G., Shapiro, B. E., Meyerowitz, E. M. & Mjolsness, E. An auxin-driven polarized transport model for phyllotaxis. Proc. Natl Acad. Sci. USA 103, 1633–1638 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Birnbaum, K. et al. A gene expression map of the Arabidopsis root. Science 302, 1956–1960 (2003). This study combines fluorescence-activated cell sorting, expression profiling and computational approaches to deduce a cell-type-specific gene expression map of the A. thaliana root meristem.

    Article  CAS  PubMed  Google Scholar 

  117. Sonnichsen, B. et al. Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans. Nature 434, 462–469 (2005). Combines high-throughput gene silencing and time-lapse imaging for phenotypic profiling of events in early nematode development.

    Article  CAS  PubMed  Google Scholar 

  118. Gunsalus, K. C. et al. Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature 436, 861–865 (2005). Data derived from high-throughput phenotyping are integrated with genomics and proteomics data to deduce modules that are involved in cytokinesis during early cell divisions in nematode development.

    Article  CAS  PubMed  Google Scholar 

  119. Terskikh, A. et al. “Fluorescent timer”: protein that changes color with time. Science 290, 1585–1588 (2000).

    Article  CAS  PubMed  Google Scholar 

  120. Mirabella, R. et al. Use of the fluorescent timer DsRED-E5 as reporter to monitor dynamics of gene activity in plants. Plant Physiol. 135, 1879–1887 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Ando, R., Hama, H., Yamamoto-Hino, M., Mizuno, H. & Miyawaki, A. An optical marker based on the UV-induced green-to-red photoconversion of a fluorescent protein. Proc. Natl Acad. Sci. USA 99, 12651–12656 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Chudakov, D. M. et al. Kindling fluorescent proteins for precise in vivo photolabeling. Nature Biotech. 21, 191–194 (2003).

    Article  CAS  Google Scholar 

  123. Runions, J. Brach, T., Kuhner, S. & Hawes, C. Photoactivation of GFP reveals protein dynamics within the endoplasmic reticulum membrane. J. Exp. Bot. 50, 43–50 (2005).

    Google Scholar 

  124. Ando, R., Mizuno, H. & Miyawaki, A. Regulated fast nucleocytoplasmic shuttling observed by reversible protein highlighting. Science 306, 1370–1373 (2004). Describes the identification of a novel photosensitive fluorescent protein.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank D. Ehrhardt, Z. Yang and B. Scheres for providing the original photographs for the figures. We thank M. Heisler for providing transgenic seeds carrying fluorescent reporter constructs. We thank members of the Meyerowitz laboratory for useful discussions and comments on the manuscript. The live-imaging work in the Meyerowitz laboratory is supported by the US National Science Foundation, Department of Energy and Human Frontiers Science Program; work in the Reddy laboratory is supported by start-up funds from the University of California, Riverside.

Author information

Authors and Affiliations

  1. Department of Botany and Plant Sciences, 2150 Batchelor Hall, University of California, Riverside, 92521, California, USA

    G. Venugopala Reddy

  2. Division of Biology, California Institute of Technology, MC 156-29, 1200 East California Boulevard, Pasadena, 91125, California, USA

    Sean P. Gordon & Elliot M. Meyerowitz

Authors
  1. G. Venugopala Reddy
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Sean P. Gordon
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Elliot M. Meyerowitz
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to G. Venugopala Reddy.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Related links

Related links

FURTHER INFORMATION

Elliot M. Meyerowitz's homepage

Carnegie Institution plant-cell imaging

Haseloff laboratory

The Computable Plant

Glossary

Shoot apical meristem

A collection of undifferentiated cells that are located at the growing tip of a plant shoot.

Enhancer trap

A genetic method that allows detection of expression patterns of genes.

Fluorescence recovery after photobleaching

Microscopic imaging technique that destroys fluorescent protein chimaeras from a well-defined region within living cells. This method is used to deduce the diffusion speed of molecules in living cells.

Fluorescence correlation spectroscopy

A correlation function derived from fluorescence intensity fluctuations. This method is applied to deduce the concentration fluctuations of fluorescent molecules in solution.

Root gravitropism

A phenomenon that describes the tendency of the plant root system to grow towards the pull of gravity.

Root apical meristem

A collection of undifferentiated cells that are located near the growing tip of roots.

Fluorescence (Förster) resonance energy transfer

The excited donor fluorescent molecule transfers non-radiative energy to a second fluorescent molecule, the acceptor. The energy transfer depends on the distance between the fluorescent molecules.

Fluorescence lifetime-imaging microscopy

An imaging technique for obtaining an image that is based on the differences in the exponential decay rate of the fluorescence from a sample. It is used to deduce molecular interactions.

Ethanol-inducible (Alc) system; 17-β-oestradiol-inducible system

Genetically encoded transactivation systems, which can be activated by exposing the plant tissues to ethanol or oestrogen, respectively.

CRE/loxP and FLP/FRT-mediated recombination systems

Commonly used genetically encoded systems for sequence-specific recombination that induce recombination either between two different chromosomes or between different segments of a chromosome. The systems are used to mark cells by inducing or deleting genes.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Reddy, G., Gordon, S. & Meyerowitz, E. Unravelling developmental dynamics: transient intervention and live imaging in plants. Nat Rev Mol Cell Biol 8, 491–501 (2007). https://doi.org/10.1038/nrm2188

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrm2188

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing