Molecular genetic studies of model plants in the past few decades have identified many key genes and pathways controlling development, metabolism and environmental responses. Recent technological and informatics advances have led to unprecedented volumes of data that may uncover underlying principles of plants as biological systems. The newly emerged discipline of synthetic biology and related molecular engineering approaches is built on this strong foundation. Today, plant regulatory pathways can be reconstituted in heterologous organisms to identify and manipulate parameters influencing signalling outputs. Moreover, regulatory circuits that include receptors, ligands, signal transduction components, epigenetic machinery and molecular motors can be engineered and introduced into plants to create novel traits in a predictive manner. Here, we provide a brief history of plant synthetic biology and significant recent examples of this approach, focusing on how knowledge generated by the reference plant Arabidopsis thaliana has contributed to the rapid rise of this new discipline, and discuss potential future directions.
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The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815 (2000).
Medford, J. I. & Prasad, A. Plant synthetic biology takes root. Science 346, 162–163 (2014).
Purnick, P. E. & Weiss, R. The second wave of synthetic biology: from modules to systems. Nature Rev. Mol. Cell Biol. 10, 410–422 (2009).
Huang, H. H., Camsund, D., Lindblad, P. & Heidorn, T. Design and characterization of molecular tools for a synthetic biology approach towards developing cyanobacterial biotechnology. Nucleic Acids Res. 38, 2577–2593 (2010).
Jensen, P. E. & Leister, D. Cyanobacteria as an experimental platform for modifying bacterial and plant photosynthesis. Front. Bioeng. Biotechnol. 2, 7 (2014).
Liu, W. & Stewart, C. N. Jr Plant synthetic biology. Trends Plant Sci. 20, 309–317 (2015).
Farre, G., Twyman, R. M., Christou, P., Capell, T. & Zhu, C. Knowledge-driven approaches for engineering complex metabolic pathways in plants. Curr. Opin. Biotechnol. 32, 54–60 (2015).
Thodey, K., Galanie, S. & Smolke, C. D. A microbial biomanufacturing platform for natural and semisynthetic opioids. Nature Chem. Biol. 10, 837–844 (2014).
Zirpel, B., Stehle, F. & Kayser, O. Production of Δ9-tetrahydrocannabinolic acid from cannabigerolic acid by whole cells of Pichia (Komagataella) pastoris expressing Δ9-tetrahydrocannabinolic acid synthase from Cannabis sativa L. Biotechnol. Lett. 37, 1869–1875 (2015).
Doty, S. L. et al. Enhanced metabolism of halogenated hydrocarbons in transgenic plants containing mammalian cytochrome P450 2E1. Proc. Natl Acad. Sci. USA 97, 6287–6291 (2000).
Doty, S. L. et al. Enhanced phytoremediation of volatile environmental pollutants with transgenic trees. Proc. Natl Acad. Sci. USA 104, 16816–16821 (2007).
Yuan, L., Kurek, I., English, J. & Keenan, R. Laboratory-directed protein evolution. Microbiol. Mol. Biol. Rev. 69, 373–392 (2005).
Lehmann, M. & Wyss, M. Engineering proteins for thermostability: the use of sequence alignments versus rational design and directed evolution. Curr. Opin. Biotechnol. 12, 371–375 (2001).
Bornscheuer, U. T. & Pohl, M. Improved biocatalysts by directed evolution and rational protein design. Curr. Opin. Chem. Biol. 5, 137–143 (2001).
Schindler, T. D., Chen, L., Lebel, P., Nakamura, M. & Bryant, Z. Engineering myosins for long-range transport on actin filaments. Nature Nanotechnol. 9, 33–38 (2014).
Voigt, C. A., Mayo, S. L., Arnold, F. H. & Wang, Z. G. Computational method to reduce the search space for directed protein evolution. Proc. Natl Acad. Sci. USA 98, 3778–3783 (2001).
Antunes, M. S. et al. Programmable ligand detection system in plants through a synthetic signal transduction pathway. PLOS ONE 6, e16292 (2011).
Stock, A. M., Robinson, V. L. & Goudreau, P. N. Two-component signal transduction. Annu. Rev. Biochem. 69, 183–215 (2000).
Antunes, M. S. et al. A synthetic de-greening gene circuit provides a reporting system that is remotely detectable and has a re-set capacity. Plant Biotechnol. J. 4, 605–622 (2006).
Chang, C., Kwok, S. F., Bleecker, A. B. & Meyerowitz, E. M. Arabidopsis ethylene-response gene ETR1: similarity of product to two-component regulators. Science 262, 539–544 (1993).
Kakimoto, T. CKI1, a histidine kinase homolog implicated in cytokinin signal transduction. Science 274, 982–985 (1996).
Imamura, A. et al. Response regulators implicated in His-to-Asp phosphotransfer signaling in Arabidopsis. Proc. Natl Acad. Sci. USA 95, 2691–2696 (1998).
Inoue, T. et al. Identification of CRE1 as a cytokinin receptor from Arabidopsis. Nature 409, 1060–1063 (2001).
To, J. P. et al. Cytokinin regulates type-A Arabidopsis response regulator activity and protein stability via two-component phosphorelay. Plant Cell 19, 3901–3914 (2007).
Tan, X. et al. Mechanism of auxin perception by the TIR1 ubiquitin ligase. Nature 446, 640–645 (2007).
Shimada, A. et al. Structural basis for gibberellin recognition by its receptor GID1. Nature 456, 520–523 (2008).
Nishimura, N. et al. Structural mechanism of abscisic acid binding and signaling by dimeric PYR1. Science 326, 1373–1379 (2009).
Santiago, J. et al. The abscisic acid receptor PYR1 in complex with abscisic acid. Nature 462, 665–668 (2009).
Miyazono, K. et al. Structural basis of abscisic acid signalling. Nature 462, 609–614 (2009).
Sheard, L. B. et al. Jasmonate perception by inositol-phosphate-potentiated COI1-JAZ co-receptor. Nature 468, 400–405 (2010).
Hothorn, M. et al. Structural basis of steroid hormone perception by the receptor kinase BRI1. Nature 474, 467–471 (2011).
She, J. et al. Structural insight into brassinosteroid perception by BRI1. Nature 474, 472–476 (2011).
Sun, Y. et al. Structural basis for flg22-induced activation of the Arabidopsis FLS2-BAK1 immune complex. Science 342, 624–628 (2013).
Brunoud, G. et al. A novel sensor to map auxin response and distribution at high spatio-temporal resolution. Nature 482, 103–106 (2012).
Liao, C. Y. et al. Reporters for sensitive and quantitative measurement of auxin response. Nature Methods 12, 207–210 (2015).
Larrieu, A. et al. A fluorescent hormone biosensor reveals the dynamics of jasmonate signalling in plants. Nature Commun. 6, 6043 (2015).
Jones, A. M. et al. Abscisic acid dynamics in roots detected with genetically encoded FRET sensors. Elife 3, e01741 (2014).
Waadt, R. et al. FRET-based reporters for the direct visualization of abscisic acid concentration changes and distribution in Arabidopsis. Elife 3, e01739 (2014).
Park, S. Y. et al. Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science 324, 1068–1071 (2009).
Peterson, F. C. et al. Structural basis for selective activation of ABA receptors. Nature Struct. Mol. Biol. 17, 1109–1113 (2010).
Park, S. Y. et al. Agrochemical control of plant water use using engineered abscisic acid receptors. Nature 23, 545–548 (2015).
Thornton, J. W. Resurrecting ancient genes: experimental analysis of extinct molecules. Nature Rev. Genet. 5, 366–375 (2004).
Harms, M. J. & Thornton, J. W. Analyzing protein structure and function using ancestral gene reconstruction. Curr. Opin. Struct. Biol. 20, 360–366 (2010).
Nelson, D. C. et al. F-box protein MAX2 has dual roles in karrikin and strigolactone signaling in Arabidopsis thaliana. Proc. Natl Acad. Sci. USA 108, 8897–8902 (2011).
Waters, M. T. et al. Specialisation within the DWARF14 protein family confers distinct responses to karrikins and strigolactones in Arabidopsis. Development 139, 1285–1295 (2012).
Delaux, P. M. et al. Origin of strigolactones in the green lineage. New Phytol. 195, 857–871 (2012).
Toth, R. & van der Hoorn, R. A. Emerging principles in plant chemical genetics. Trends Plant Sci. 15, 81–88 (2010).
Blackwell, H. E. & Zhao, Y. Chemical genetic approaches to plant biology. Plant Physiol. 133, 448–455 (2003).
Hayashi, K. et al. Small-molecule agonists and antagonists of F-box protein–substrate interactions in auxin perception and signaling. Proc. Natl Acad. Sci. USA 105, 5632–5637 (2008).
Takeuchi, J. et al. Designed abscisic acid analogs as antagonists of PYL-PP2C receptor interactions. Nature Chem. Biol. 10, 477–482 (2014).
Shani, E. et al. Gibberellins accumulate in the elongating endodermal cells of Arabidopsis root. Proc. Natl Acad. Sci. USA 110, 4834–4839 (2013).
Irani, N. G. et al. Fluorescent castasterone reveals BRI1 signaling from the plasma membrane. Nature Chem. Biol. 8, 583–589 (2012).
Tsuda, E. et al. Alkoxy-auxins are selective inhibitors of auxin transport mediated by PIN, ABCB, and AUX1 transporters. J. Biol. Chem. 286, 2354–2364 (2011).
Hayashi, K. et al. Auxin transport sites are visualized in planta using fluorescent auxin analogs. Proc. Natl Acad. Sci. USA 111, 11557–11562 (2014).
Rasmussen, A. et al. A fluorescent alternative to the synthetic strigolactone GR24. Mol. Plant 6, 100–112 (2013).
Tsuchiya, Y. et al. strigolactone receptors in Striga hermonthica with fluorescence. Science 349, 846–848 (2015).
Schaumberg, K. A. et al. Quantitative characterization of genetic parts and circuits for plant synthetic biology. Nature Methods 13, 94–100 (2016).
Ishizaki, K., Nishihama, R., Yamato, K. T. & Kohchi, T. Molecular genetic tools and techniques for Marchantia polymorpha research. Plant Cell Physiol. http://dx.doi.org/10.1093/pcp/pcv097 (2015).
Vernoux, T. et al. The auxin signalling network translates dynamic input into robust patterning at the shoot apex. Mol. Syst. Biol. 7, 508 (2011).
Prigge, M. J. & Bezanilla, M. Evolutionary crossroads in developmental biology: Physcomitrella patens. Development 137, 3535–3543 (2010).
Sun, B., Xu, Y., Ng, K. H. & Ito, T. A timing mechanism for stem cell maintenance and differentiation in the Arabidopsis floral meristem. Genes Dev. 23, 1791–1804 (2009).
Sun, B. et al. Timing mechanism dependent on cell division is invoked by Polycomb eviction in plant stem cells. Science 343, 1248559 (2014).
Wu, M.-F. et al. Auxin-regulated chromatin switch directs acquisition of flower primordium founder fate. eLife 4, e09269 (2015).
Hashimoto, T. Microtubules in plants. Arabidopsis Book 13, e0179 (2015).
Meagher, R. B. & Fechheimer, M. The Arabidopsis cytoskeletal genome. Arabidopsis Book 2, e0096 (2003).
Smith, L. G. & Oppenheimer, D. G. Spatial control of cell expansion by the plant cytoskeleton. Annu. Rev. Cell Dev. Biol. 21, 271–295 (2005).
Gutierrez, R., Lindeboom, J. J., Paredez, A. R., Emons, A. M. & Ehrhardt, D. W. Arabidopsis cortical microtubules position cellulose synthase delivery to the plasma membrane and interact with cellulose synthase trafficking compartments. Nature Cell Biol. 11, 797–806 (2009).
Li, S., Bashline, L., Lei, L. & Gu, Y. Cellulose synthesis and its regulation. Arabidopsis Book 12, e0169 (2014).
Morimatsu, M. et al. The molecular structure of the fastest myosin from green algae, Chara. Biochem. Biophys. Res. Commun. 270, 147–152 (2000).
Tominaga, M. et al. Cytoplasmic streaming velocity as a plant size determinant. Dev. Cell 27, 345–352 (2013).
Shcherbakova, D. M., Shemetov, A. A., Kaberniuk, A. A. & Verkhusha, V. V. Natural photoreceptors as a source of fluorescent proteins, biosensors, and optogenetic tools. Annu. Rev. Biochem. 84, 519–550 (2015).
Sorokina, O. et al. A switchable light-input, light-output system modelled and constructed in yeast. J. Biol. Eng. 3, 15 (2009).
Kennedy, M. J. et al. Rapid blue-light-mediated induction of protein interactions in living cells. Nature Methods 7, 973–975 (2010).
Shimizu-Sato, S., Huq, E., Tepperman, J. M. & Quail, P. H. A light-switchable gene promoter system. Nature Biotechnol. 20, 1041–1044 (2002).
Tyszkiewicz, A. B. & Muir, T. W. Activation of protein splicing with light in yeast. Nature Methods 5, 303–305 (2008).
Wong, S., Mosabbir, A. A. & Truong, K. An engineered split intein for photoactivated protein trans-splicing. PLoS ONE 10, e0135965 (2015).
Beyer, H. M. et al. Red light-regulated reversible nuclear localization of proteins in mammalian cells and zebrafish. ACS Synth. Biol. 4, 951–958 (2015).
Nishimura, K., Fukagawa, T., Takisawa, H., Kakimoto, T. & Kanemaki, M. An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nature Methods 6, 917–922 (2009).
Havens, K. A. et al. A synthetic approach reveals extensive tunability of auxin signaling. Plant Physiol. 160, 135–142 (2012).
Zhang, L., Ward, J. D., Cheng, Z. & Dernburg, A. F. The auxin-inducible degradation (AID) system enables versatile conditional protein depletion in C. elegans. Development 142, 4374–4384 (2015).
Liang, F. S., Ho, W. Q. & Crabtree, G. R. Engineering the ABA plant stress pathway for regulation of induced proximity. Sci. Signal. 4, rs2 (2011).
Khakhar, A., Bolten, N. J., Nemhauser, J. & Klavins, E. Cell–cell communication in yeast using auxin biosynthesis and auxin responsive CRISPR transcription factors. ACS Synth. Biol. http://dx.doi.org/10.1021/acssynbio.5b00064 (2015).
Pierre-Jerome, E., Jang, S. S., Havens, K. A., Nemhauser, J. L. & Klavins, E. Recapitulation of the forward nuclear auxin response pathway in yeast. Proc. Natl Acad. Sci. USA 111, 9407–9412 (2014).
Guseman, J. M. et al. Auxin-induced degradation dynamics set the pace for lateral root development. Development 142, 905–909 (2015).
Ort, D. R. et al. Redesigning photosynthesis to sustainably meet global food and bioenergy demand. Proc. Natl Acad. Sci. USA 112, 8529–8536 (2015).
Jiang, W. et al. Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice. Nucleic Acids Res. 41, e188 (2013).
Baltes, N. J., Gil-Humanes, J., Cermak, T., Atkins, P. A. & Voytas, D. F. DNA replicons for plant genome engineering. Plant Cell 26, 151–163 (2014).
Wu, H. Y. et al. AGROBEST: an efficient Agrobacterium-mediated transient expression method for versatile gene function analyses in Arabidopsis seedlings. Plant Methods 10, 19 (2014).
Fahlgren, N., Gehan, M. A. & Baxter, I. Lights, camera, action: high-throughput plant phenotyping is ready for a close-up. Curr. Opin. Plant Biol. 24C, 93–99 (2015).
Yordanov, B. et al. A computational method for automated characterization of genetic components. ACS Synth. Biol. 3, 578–588 (2014).
Jang, S. S., Oishi, K. T., Egbert, R. G. & Klavins, E. Specification and simulation of synthetic multicelled behaviors. ACS Synth. Biol. 1, 365–374 (2012).
Fernandez-Castane, A., Feher, T., Carbonell, P., Pauthenier, C. & Faulon, J. L. Computer-aided design for metabolic engineering. J. Biotechnol. 192, 302–313 (2014).
Oberortner, E. & Densmore, D. Web-based software tool for constraint-based design specification of synthetic biological systems. ACS Synth. Biol. 4, 757–760 (2015).
Stevens, J. T. & Myers, C. J. Dynamic modeling of cellular populations within iBioSim. ACS Synth. Biol. 2, 223–229 (2013).
We thank D. Wagner (Univ. Pennsylvania, USA) for sharing unpublished materials; S. Hagihara, M. Yoshimura and K. Itami (Institute of Transformative Biomolecules (ITbM), Nagoya Univ., Japan) for providing diagrams and unpublished Striga seedling images for Fig. 3; H. Hirukawa and S. Hagihara (ITbM) for the illustrations for Figs 1 and 3; and M. Maes (Univ. Washington, USA) for proofreading. Funding for synthetic biology research in J.L.N.'s laboratory is provided by the National Institute of Health (R01 GM107084) and the National Science Foundation (MCB-1411949). K.U.T. is an investigator of Howard Hughes Medical Institute and Gordon and Betty Moore Foundation (HHMI-GBMF), and her group is supported by a grant (GBMF3035).
The authors declare no competing financial interests.
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Nemhauser, J., Torii, K. Plant synthetic biology for molecular engineering of signalling and development. Nature Plants 2, 16010 (2016). https://doi.org/10.1038/nplants.2016.10
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