Reprogramming Plants Using Synthetic Transcription Factors and Systemically Maintained RNA Scaffolds

Transcriptional programs sculpt plant morphology and metabolism to meet environmental challenges like droughts or pests. These same programs have been manipulated through selective breeding over generations to increase agricultural productivity and robustness. Studying the genetic basis of these improved traits has elucidated the specific alterations in the expression levels of key master regulator genes that lead to phenotypic improvement. However, breeding these traits into elite crop lines can be challenging for several reasons, including long timescales, linkage drag and hybrid incompatibility. Additionally, the reliance on natural variation for traits has not fully leveraged our understanding of plant biology for forward engineering of crops.

We aim to overcome these challenges by designing a flexible system of synthetic transcription factors to rapidly reprogram development and metabolism in an agriculturally relevant manner. Our system, called VipariNama (Sanskrit: to change), uses RNA scaffolds to assemble transcription factors at loci of interest to modulate gene expression. We are designing these RNA scaffolds to be systemically transported and maintained in the plant through the use of parts from RNA viruses that have been optimized using a combination of next generation sequencing based screens and machine learning aided in-silico evolution. We plan to utilize this system to reprogram the metabolism of maize and create lines with enhanced production of beta-carotene and the natural insecticide DIMBOA. We are also using this system to create semi-dwarfed varieties of tomato by reprogramming gibberellin-driven developmental pathways in a tissue specific manner.