Research

VipariNama - Designing viruses to engineer plants

Plant synthetic biology generally involves the addition of one or more foreign elements to the plants genome to re-program some aspect of its biology. Modifying the genome of a plant is a very time consuming and costly process, taking several years for some crop plants. To overcome this challenge we are designing gene delivery tools based on plant viruses that can deliver genetic cargos systemically, thereby sidestepping transformation and turning years long experiments into a matter of weeks. We plan to build on our early success with ViN vectors by using next-generation sequencing-enabled screens coupled with machine-learning aided design to re-engineer RNA viruses away from their natural behavior and towards optimal gene delivery platforms. We are also using similar techniques to create ribozyme-based tools for controlling gene expression, viral containment, and novel herbicides.

Molecular Bonsai - Understanding and engineering dwarfing phenotypes

The capacity to predictably engineer plant organ size could dramatically improve crop productivity and resilience to climate change. A historical example of this is the semi-dwarfed plant varieties that drove the Green-revolution, which arose from mutations in the signaling pathway of the plant hormone gibberellin. We are using transcriptomic analysis of plants dwarfed through environmental conditioning to both identify and mathematically model the pathways that regulate dwarfing across a range of plants, and to explore how conserved these mechanisms are. These models will let us predict what genetic changes would be needed to create plants with a desired organ size. As part of this work we are using high throughput yeast-based screens to identify mutations that change the sensitivity of these signaling proteins to Gibberellin, and so could be used reprogram organ size in plants. We are also using synthetic transcription factors to make the expression changes that our models predict would lead to dwarfing to test if this approach can be used to engineer dwarfing phenotypes.

Plants that smell and taste themselves - Engineering the flavor and fragrance of tomato

The flavors and fragrances of crops like tomato can bring us joy, alter our moods, and are a critical part of our cultural identities. Improving this trait is an important way to encourage people to adopt plant-based diets and thereby reduce the impact of food production on climate change. Flavor and fragrance of tomato plants are a product of primary and secondary metabolites synthesized by a complex knot of biosynthetic pathways. These molecules are bound by receptors, called GPCRs, in the mouth and nose, whose combinatorial activation is thought to lead to the perception of specific tastes and smells. We are using high throughput screens to identify which of these GPCRs are activated by tomato compounds. We are then developing yeast based biosensors expressing these GPCRs as part of a synthetic signaling cascade to study what sorts of genome edits will lead to improved flavor. We are also working to create tomato lines that express these synthetic signaling cascades linked to pigment biosynthesis, to create plants able to perceive how much of a flavor or fragrance they are producing and report it by changing color, as a tool for engineering flavor and fragrance. In the future we hope to expand the use of this strategy to engineer both the flavor of other crops and other aspects of plant secondary metabolism.

Picking pollinators - Engineering flowers to enhance pollinator recruitment

The colors, patterns, and fragrances of flowers have evolved to attract animals, from humans who have built a multibillion-dollar industry on their aesthetic beauty, to pollinators, whose interactions with plants are critical for the global food system. As plant-pollinator interactions are disrupted by climate change and the populations of traditional pollinators are crashing, there is an urgent need to understand how these features can be engineered to both enhance recruitment of native pollinators and create new plant-pollinator interactions. To meet these challenges we are developing a toolkit to build biosynthetic pathways capable of altering the color of petunia petals across a broad range of colors and characterizing how this impacts the fragrances they emit. We are also developing reaction-diffusion pattern formation circuits based on synthetic transcription factors, which mimic natural pathways, to engineer these colors into patterns of spots and stripes, as these high contrast patterns have been shown to enhance pollinator recruitment. Finally we also plan to optimize expression of a recently discovered fungal auto-luminescence pathway in petunia flowers as a way to recruit novel night-time pollinators.