Thompson, A. J. et al. Ectopic expression of a tomato 9-cis-epoxycarotenoid dioxygenase gene causes over-production of abscisic acid. Plant J. 23, 363–374 (2000).
Google Scholar
Iuchi, S. et al. Regulation of drought tolerance by gene manipulation of 9-cis-epoxycarotenoid dioxygenase, a key enzyme in abscisic acid biosynthesis in Arabidopsis. Plant J. 27, 325–333 (2001).
Google Scholar
Feeney, M., Frigerio, L., Cui, Y. & Menassa, R. Following vegetative to embryonic cellular changes in leaves of Arabidopsis overexpressing LEAFY COTYLEDON2. Plant Physiol. 162, 1881–1896 (2013).
Google Scholar
Vanhercke, T. et al. Step changes in leaf oil accumulation via iterative metabolic engineering. Metab. Eng. 39, 237–246 (2017).
Google Scholar
He, R. et al. Overexpression of 9-cis-epoxycarotenoid dioxygenase cisgene in grapevine increases drought tolerance and results in pleiotropic effects. Front. Plant Sci. 9, 970 (2018).
Google Scholar
Brophy, J. A. N. Toward synthetic plant development. Plant Physiol. 188, 738–748 (2021).
Brophy, J. A. N., Magallon, K. J., Kniazev, K. & Dinneny, J. R. Synthetic genetic circuits enable reprogramming of plant roots. Preprint at https://www.biorxiv.org/content/10.1101/2022.02.02.478917v1 (2022).
Pires, N. D. et al. Recruitment and remodeling of an ancient gene regulatory network during land plant evolution. Proc. Natl Acad. Sci. USA 110, 9571–9576 (2013).
Google Scholar
Madrid, E., Chandler, J. W. & Coupland, G. Gene regulatory networks controlled by FLOWERING LOCUS C that confer variation in seasonal flowering and life history. J. Exp. Bot. 72, 4–14 (2021).
Google Scholar
Setty, Y., Mayo, A. E., Surette, M. G. & Alon, U. Detailed map of a cis-regulatory input function. Proc. Natl Acad. Sci. USA 100, 7702–7707 (2003).
Google Scholar
Krakauer, D. C., Müller, L., Prohaska, S. J. & Stadler, P. F. Design specifications for cellular regulation. Theory Biosci. 135, 231–240 (2016).
Google Scholar
Gardner, T. S., Cantor, C. R. & Collins, J. J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339–342 (2000).
Google Scholar
Elowitz, M. B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335–338 (2000).
Google Scholar
Lohmueller, J. J., Armel, T. Z. & Silver, P. A. A tunable zinc finger-based framework for Boolean logic computation in mammalian cells. Nucleic Acids Res. 40, 5180–5187 (2012).
Google Scholar
Nevozhay, D., Zal, T. & Balázsi, G. Transferring a synthetic gene circuit from yeast to mammalian cells. Nat. Commun. 4, 1451 (2013).
Google Scholar
Siuti, P., Yazbek, J. & Lu, T. K. Synthetic circuits integrating logic and memory in living cells. Nat. Biotechnol. 31, 448–452 (2013).
Google Scholar
Gaber, R. et al. Designable DNA-binding domains enable construction of logic circuits in mammalian cells. Nat. Chem. Biol. 10, 203–208 (2014).
Google Scholar
Roquet, N., Soleimany, A. P., Ferris, A. C., Aaronson, S. & Lu, T. K. Synthetic recombinase-based state machines in living cells. Science 353, aad8559 (2016).
Google Scholar
Weinberg, B. H. et al. Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells. Nat. Biotechnol. 35, 453–462 (2017).
Google Scholar
Müller, M. et al. Designed cell consortia as fragrance-programmable analog-to-digital converters. Nat. Chem. Biol. 13, 309–316 (2017).
Google Scholar
Guiziou, S., Mayonove, P. & Bonnet, J. Hierarchical composition of reliable recombinase logic devices. Nat. Commun. 10, 456 (2019).
Google Scholar
Zúñiga, A. et al. Rational programming of history-dependent logic in cellular populations. Nat. Commun. 11, 4758 (2020).
Google Scholar
Bowyer, J. E., Ding, C., Weinberg, B. H., Wong, W. W. & Bates, D. G. A mechanistic model of the BLADE platform predicts performance characteristics of 256 different synthetic DNA recombination circuits. PLoS Comput. Biol. 16, e1007849 (2020).
Google Scholar
Schreiber, T., Prange, A. & Tissier, A. F. Split-TALE—a TALE-based two-component system for synthetic biology applications in planta. Plant Physiol. 179, 1001–1012 (2019).
Bernabé-Orts, J. M. et al. A memory switch for plant synthetic biology based on the phage ϕC31 integration system. Nucleic Acids Res. 48, 3379–3394 (2020).
Google Scholar
Lloyd, J. P. B. & Lister, R. Epigenome plasticity in plants. Nat. Rev. Genet. 23, 55–68 (2022).
Jones, J. M. & Gellert, M. The taming of a transposon: V(D)J recombination and the immune system. Immunol. Rev. 200, 233–248 (2004).
Google Scholar
Takahashi, K. & Yamanaka, S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126, 663–676 (2006).
Google Scholar
Engler, C. et al. A golden gate modular cloning toolbox for plants. ACS Synth. Biol. 3, 839–843 (2014).
Google Scholar
Diamos, A. G. & Mason, H. S. Chimeric 3′ flanking regions strongly enhance gene expression in plants. Plant Biotechnol. J. 16, 1971–1982 (2018).
Google Scholar
Andreou, A. I., Nirkko, J., Ochoa-Villarreal, M. & Nakayama, N. Mobius Assembly for Plant Systems highlights promoter–terminator interaction in gene regulation. Preprint at https://www.biorxiv.org/content/10.1101/2021.03.31.437819v1 (2021).
Efroni, I. et al. Root regeneration triggers an embryo-like sequence guided by hormonal interactions. Cell 165, 1721–1733 (2016).
Google Scholar
Wu, F.-H. et al. Tape-Arabidopsis Sandwich—a simpler Arabidopsis protoplast isolation method. Plant Methods 5, 16 (2009).
Google Scholar
Schaumberg, K. A. et al. Quantitative characterization of genetic parts and circuits for plant synthetic biology. Nat. Methods 13, 94–100 (2016).
Google Scholar
Padidam, M. & Cao, Y. Elimination of transcriptional interference between tandem genes in plant cells. Biotechniques 31, 328–330, 332–334 (2001).
Nagaya, S., Kawamura, K., Shinmyo, A. & Kato, K. The HSP terminator of Arabidopsis thaliana increases gene expression in plant cells. Plant Cell Physiol. 51, 328–332 (2010).
Google Scholar
Rayson, S. et al. A role for nonsense-mediated mRNA decay in plants: pathogen responses are induced in Arabidopsis thaliana NMD mutants. PLoS ONE 7, e31917 (2012).
Google Scholar
Lloyd, J. P. B. & Davies, B. SMG1 is an ancient nonsense-mediated mRNA decay effector. Plant J. 76, 800–810 (2013).
Google Scholar
Causier, B., Hopes, T., McKay, M., Paling, Z. & Davies, B. Plants utilise ancient conserved peptide upstream open reading frames in stress-responsive translational regulation. Plant Cell Environ. 45, 1229–1241 (2022).
Sanfaçon, H. & Hohn, T. Proximity to the promoter inhibits recognition of cauliflower mosaic virus polyadenylation signal. Nature 346, 81–84 (1990).
Google Scholar
Han, Y.-J., Kim, Y.-M., Hwang, O.-J. & Kim, J.-I. Characterization of a small constitutive promoter from Arabidopsis translationally controlled tumor protein (AtTCTP) gene for plant transformation. Plant Cell Rep. 34, 265–275 (2015).
Google Scholar
Weber, E., Engler, C., Gruetzner, R., Werner, S. & Marillonnet, S. A modular cloning system for standardized assembly of multigene constructs. PLoS ONE 6, e16765 (2011).
Google Scholar
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).
Google Scholar
Heidstra, R., Welch, D. & Scheres, B. Mosaic analyses using marked activation and deletion clones dissect Arabidopsis SCARECROW action in asymmetric cell division. Genes Dev. 18, 1964–1969 (2004).
Google Scholar
Vergunst, A. C., Jansen, L. E. & Hooykaas, P. J. Site-specific integration of Agrobacterium T-DNA in Arabidopsis thaliana mediated by Cre recombinase. Nucleic Acids Res. 26, 2729–2734 (1998).
Google Scholar
Vergunst, A. C. & Hooykaas, P. J. Cre/lox-mediated site-specific integration of Agrobacterium T-DNA in Arabidopsis thaliana by transient expression of cre. Plant Mol. Biol. 38, 393–406 (1998).
Google Scholar
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).
Google Scholar
Marquès-Bueno, M. D. M. et al. A versatile Multisite Gateway-compatible promoter and transgenic line collection for cell type-specific functional genomics in Arabidopsis. Plant J. 85, 320–333 (2016).
Google Scholar
Craft, J. et al. New pOp/LhG4 vectors for stringent glucocorticoid-dependent transgene expression in Arabidopsis. Plant J. 41, 899–918 (2005).
Google Scholar
Weinberg, B. H. et al. High-performance chemical- and light-inducible recombinases in mammalian cells and mice. Nat. Commun. 10, 4845 (2019).
Google Scholar
Odell, J., Caimi, P., Sauer, B. & Russell, S. Site-directed recombination in the genome of transgenic tobacco. Mol. Gen. Genet. 223, 369–378 (1990).
Google Scholar
Russell, S. H., Hoopes, J. L. & Odell, J. T. Directed excision of a transgene from the plant genome. Mol. Gen. Genet. 234, 49–59 (1992).
Google Scholar
Schürholz, A.-K. et al. A comprehensive toolkit for inducible, cell type-specific gene expression in Arabidopsis. Plant Physiol. 178, 40–53 (2018).
Google Scholar
Clough, S. J. & Bent, A. F. Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 16, 735–743 (1998).
Google Scholar
Logemann, E., Birkenbihl, R. P., Ülker, B. & Somssich, I. E. An improved method for preparing Agrobacterium cells that simplifies the Arabidopsis transformation protocol. Plant Methods 2, 16 (2006).
Google Scholar
Shimada, T. L., Shimada, T. & Hara-Nishimura, I. A rapid and non-destructive screenable marker, FAST, for identifying transformed seeds of Arabidopsis thaliana. Plant J. 61, 519–528 (2010).
Google Scholar
Engler, C., Gruetzner, R., Kandzia, R. & Marillonnet, S. Golden Gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. PLoS ONE 4, e5553 (2009).
Google Scholar
Patron, N. J. et al. Standards for plant synthetic biology: a common syntax for exchange of DNA parts. New Phytol. 208, 13–19 (2015).
Google Scholar
Libiakova, G., Jørgensen, B., Palmgren, G., Ulvskov, P. & Johansen, E. Efficacy of an intron-containing kanamycin resistance gene as a selectable marker in plant transformation. Plant Cell Rep. 20, 610–615 (2001).
Google Scholar
Wick, R. R., Judd, L. M., Gorrie, C. L. & Holt, K. E. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 13, e1005595 (2017).
Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Google Scholar
Naseer, S. et al. Casparian strip diffusion barrier in Arabidopsis is made of a lignin polymer without suberin. Proc. Natl Acad. Sci. USA 109, 10101–10106 (2012).
Google Scholar
Wickham, H. ggplot2: Elegant Graphics for Data Analysis (Springer, 2016).
Lloyd, J. P. B. et al. Synthetic memory circuits for programmable cell reconfiguration in plants. https://doi.org/10.5281/zenodo.6381286 (2022).