Plant synthetic biology for molecular engineering of signalling and development

Abstract

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.

Figure 1. A schematic diagram of an idealized plant cell with synthetic engineered pathways to produce a plant with ideal traits and functionality

Each synthetic engineered component is coloured in red. Figure courtesy of Haruko Hirukawa (ITbM, Japan).

Figure 2. An engineered ABA receptor can perceive a fungicide and trigger an ABA response

a, Endogenous ABA signalling. Binding of ABA to the PYR1 receptor promotes PYR1–PP2C association, which in turn activates the downstream protein kinase SnRK2. Active SnRK2 triggers ABA responses, including stomatal closure and drought tolerance. b, Mandipropamid treatment does not elicit an ABA response in wild-type plants. c, In a plant expressing the engineered PYR1^MANDI receptor, mandipropamid treatment triggers ABA response and, consequently, drought tolerance. d,e, Potential and idealized translational application of a synthetic ligand–receptor system in a crop field. Here, a transgenic tomato crop plant expressing PYR1^MANDI is outcompeted by nearby weeds (d). During drought season, mandipropamid application triggers ABA response to the transgenic tomato plant, thereby boosting its drought tolerance. Surrounding non-transgenic weeds do not respond to the chemical spray. Mandipropamid has already been approved by the Environmental Protection Agency as a fungicide (reg. no. 100-1281) for field application.

Figure 3. Mode of action of YLG

a, Perception of SL (top, left) by the SL receptor results in hydrolysis of SL, releasing the D-ring (top, right). YLG (bottom, left) is also recognized by the SL receptor with high affinity. The receptor perception cleaves off the D-ring of YLG, releasing a fluorescein derivative, which emits green fluorescence. b, Visualization of YLG perception in germinating Striga seeds. Although both YLG and the synthetic SL analogue GR24 trigger germination, strong green fluorescence is visible in the roots of only YLG-treated seedlings. Scale bar, 0.5 mm; DMSO, dimethylsulfoxide. Figure courtesy of Shinya Hagihara, Kenichiro Itami and Masahiko Yoshimura (ITbM, Japan).

Figure 4. A synthetic epigenetic timer for gene expression

a, The endogenous timer. During flower development, KNU is covered with H3K27me2 repressive marks (red stars). The PcG complex maintains such marks (top). Binding of AG to the KNU promoter elements triggers eviction of PcG (middle). After two days, cell-division-dependent loss of repressive histone marks facilitates KNU gene expression in the flower meristem (bottom; right). b, A partially synthetic timer. On dexamethasone (Dex) treatment, LacI–GR, a synthetic DNA-binding protein consisting of the LacI DNA-binding domain fused to the glucocorticoid receptor (GR), can trigger the eviction of the PcG complex from the KNU promoter region that contains Lac operator (LacOp) sequences (middle). This leads to KNU gene expression after two days, thus mimicking the AG action (bottom, right). c, A completely synthetic timer. YFP driven by an unrelated promoter can be silenced with repressive histone marks (asterisks) if a Polycomb response element from KNU (KNU PRE) is inserted (top). A synthetic DNA-binding protein consisting of GR fused with TAL that is designed to bind near the AG-binding site, TAL–GR, can trigger the eviction of PcG (middle). This leads to YFP reporter gene expression in cultured cells (bottom; right).