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. 

Enhancing carbon fixation in plants - Creating control systems for L-sugar biosynthesis in plants

We are developing genetic circuits to flip the plants metabolism from turning the carbon that it fixes via photosynthesis from D-sugars that microbes can easily break down, to L-sugars that they cannot. This resistance to breakdown is because L-sugars, which are the mirror image of D-sugars in terms of shape, are very rarely produced in nature and so are not recognized by active site of microbial enzymes, as these microbes have not evolved to eat them. This will allow carbon, once fixed as an L-sugar, to stay fixed and not be released back into the air via microbial decomposition once the plant dies. Control systems are needed to make sure the plant can initialy pursue its natural metabolism to grow enough leaves, roots, and stems to ensure efficient carbon fixation by keep the L-sugar biosynthesis genes tightly off. These control systems are designed to, upon activation via spraying with an agro chemical, strongly activate the expression of the L-sugar biosynthesis genes and repress the genes that channel carbon into D-sugars. 

Synthetic lichen - Exploring the morphological basis of symbiosis

Symbiosis between microbes plays a major role in maintaining the consortia that colonize the world’s biomes. Lichens are a product of microbial symbiosis that incorporates aspects of both metabolism and morphology, making them a great model to study these processes. The metabolic aspect of this relationship is thought to occur via a mutualistic exchange of carbon and sometimes nitrogen that is fixed by the photobiont (photosynthesizing partner), often cyanobacteria or algae, for minerals and/or micronutrients from the mycobiont (the filamentous fungal partner). In addition to metabolism, there is also a significant morphological aspect to the lichen symbiosis where in the mycobiont creates a compartment within its mycelial structure for the photobiont to grow. This morphology has been thought to contribute to the resilience lichen by enabling a level of desiccation and UV tolerance the free-living photobiont might not possess. The balance between the metabolic contributions of the photobiont and the morphological contributions of the mycobiont might explain the ecological stability and success of lichen symbiosis. However, the morphological contribution of the mycobiont to lichen symbiosis remains largely unexplored. This is in part because it is very challenging to study these relationships in natural lichens due their slow growth, heterogeneity in non-primary members, and the lack of tools to engineer the members of natural lichenaceous consortia. We are using synthetic biology to create a synthetic lichen from free-living filamentous fungi and cyanobacteria. To do this we are building a cell-cell signaling system based on the plant growth hormone auxin that lets cyanobacteria signal to fungi, and installing genetic circuits in Aspergillus fungi to drive the formation of a lichen-like thallus in response to this signal.  

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. 

A talk that outlines how our lab thinks about engineering multicellular organisms.