News

Synthetic memory circuits for stable cell reprogramming in plants

Synthetic memory circuits for stable cell reprogramming in plants
  • 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).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Vanhercke, T. et al. Step changes in leaf oil accumulation via iterative metabolic engineering. Metab. Eng. 39, 237–246 (2017).

    CAS 
    PubMed 

    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).

    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Krakauer, D. C., Müller, L., Prohaska, S. J. & Stadler, P. F. Design specifications for cellular regulation. Theory Biosci. 135, 231–240 (2016).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 

    Google Scholar 

  • Elowitz, M. B. & Leibler, S. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335–338 (2000).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Nevozhay, D., Zal, T. & Balázsi, G. Transferring a synthetic gene circuit from yeast to mammalian cells. Nat. Commun. 4, 1451 (2013).

    PubMed 

    Google Scholar 

  • Siuti, P., Yazbek, J. & Lu, T. K. Synthetic circuits integrating logic and memory in living cells. Nat. Biotechnol. 31, 448–452 (2013).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 

    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).

    PubMed 

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Müller, M. et al. Designed cell consortia as fragrance-programmable analog-to-digital converters. Nat. Chem. Biol. 13, 309–316 (2017).

    PubMed 

    Google Scholar 

  • Guiziou, S., Mayonove, P. & Bonnet, J. Hierarchical composition of reliable recombinase logic devices. Nat. Commun. 10, 456 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Zúñiga, A. et al. Rational programming of history-dependent logic in cellular populations. Nat. Commun. 11, 4758 (2020).

    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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).

    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 

    Google Scholar 

  • Engler, C. et al. A golden gate modular cloning toolbox for plants. ACS Synth. Biol. 3, 839–843 (2014).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Wu, F.-H. et al. Tape-Arabidopsis Sandwich—a simpler Arabidopsis protoplast isolation method. Plant Methods 5, 16 (2009).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Schaumberg, K. A. et al. Quantitative characterization of genetic parts and circuits for plant synthetic biology. Nat. Methods 13, 94–100 (2016).

    CAS 
    PubMed 

    Google Scholar 

  • Padidam, M. & Cao, Y. Elimination of transcriptional interference between tandem genes in plant cells. Biotechniques 31, 328–330, 332–334 (2001).

    Google Scholar 

  • 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).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 

  • Lloyd, J. P. B. & Davies, B. SMG1 is an ancient nonsense-mediated mRNA decay effector. Plant J. 76, 800–810 (2013).

    CAS 
    PubMed 

    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).

    PubMed 

    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).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 

    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).

    PubMed 
    PubMed Central 

    Google Scholar 

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

    CAS 
    PubMed 

    Google Scholar 

  • Weinberg, B. H. et al. High-performance chemical- and light-inducible recombinases in mammalian cells and mice. Nat. Commun. 10, 4845 (2019).

    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 

    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).

    CAS 
    PubMed 

    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).

    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 

    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).

    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 

    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).

    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 

    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).

    CAS 

    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).

    PubMed 
    PubMed Central 

    Google Scholar 

  • Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    CAS 
    PubMed 
    PubMed Central 

    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).

    CAS 
    PubMed 
    PubMed Central 

    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).

  • Share this post

    Similar Posts