Micronutrient deficiencies, also known as hidden hunger, affect over two billion people around the world. This happens not from lack of food, but from a lack of vitamins and micronutrients, even in diets that seem sufficient in calories. Surprisingly, seeds, the basis of much of our diet, are rich in energy but often poor in essential vitamins like provitamin A, folate, and vitamin E. Plants have the ability to synthesize provitamin A, folate, and vitamin E, but some of the key genes for the biosynthesis are not active in seeds. One of these plants includes the soybean. In this project, we aim to unlock the natural potential of seeds by engineering the promoters of key genes (as highlighted in red) for vitamin biosynthesis from soybean, including provitamin A, vitamin E and vitamin B9. Those genes are less active in seeds and therefore their promoters will be our target for engineering. These promoters have been cloned by our lab team.
In order to predict the gene expression pattern in seeds by their promoter sequence, we utilized machine learning. We trained a Convolutional Neuron Network model using a set of seed and non-seed specific gene promoters from genome data and transcriptomic data.
With this model, can input prospective mutations in native gene promoters as a simulation and predict that whether that mutation can increase the gene expression in seeds. We are actively utilizing this model to predict mutation patterns we can plug into the optimized construct we have created in the lab: a plasmid used for prospective agrobacterium transformation called pCNHP.
As a visible proof of concept, we introduced a RUBY reporter system. The wild type promoter will not have high activity in the seeds, therefore the RUBY reporter will not work in seeds. When a mutated promoter can successfully activate the target gene, it produces red pigment in the seed—so we can see activation in real time. We have successfully assembled a construct containing the promoter sequences (PSY promoter, HPT promoter, ACDS promoter, GTPCHI promoter, etc) and the RUBY reporter gene. The activity of those wild type and mutated promoters are testing in Arabidopsis transformations. (
Eventually, prime editing on those promoters will be performed to enhance crop nutritional value without introducing foreign genes, and, given the integration into the seed genome, sustainable and nutritionally-enhanced soybeans will be fortified.
