While other studies have used CRISPR/Cas9 gene editing to disable or decrease gene expression, the new study published in Science Advances used gene editing for the first time without bias to increase gene expression and subsequent photosynthetic activity
A team from the Institute for Innovative Genomes at the University of California, Berkeley (UCB) was able to increase gene expression in agricultural crops by altering its upstream regulatory DNA. While other studies have used CRISPR/Cas9 gene editing to disable or decrease gene expression, the new study published in Science Advances used unbiased gene editing for the first time to increase gene expression and subsequent photosynthetic activity.
"Tools like CRISPR/Cas9 accelerate our ability to adjust gene expression in tumors, and not just neutralize genes or turn them off. Previous studies have shown that this tool can be used to downregulate the expression of genes involved in important trade-offs, such as those between plant structure and fruit size," said Drub Patel-Tepper, lead author of the study and a former postdoctoral researcher in Nyoggi's lab at UCB.
"This is the first study, to our knowledge, in which we asked whether we could use the same approach to increase gene expression and improve activity later in an unbiased way."
Unlike synthetic biology strategies that use genes from other organisms to improve photosynthesis, the genes involved in the photoprotection process are naturally found in all plants.
Inspired by a 2018 Nature Communications paper that improved the water-use efficiency of a model crop by overexpressing one of these genes, PsbS, in plants, Chris Newgy's lab wanted to figure out how to change the plants' natural gene expression without adding foreign DNA.
According to the Food and Agriculture Organization of the United Nations, rice provides at least 20% of the world's calories, and because it has only one copy of each of the three key photoprotection genes in plants, it was an ideal model system for this gene editing research.
The Nioggi lab performed this work as part of the Realizing Increased Photosynthetic Efficiency (RIPE) project, an international research project led by the University of Illinois, which aims to increase global food production by developing food crops that convert solar energy into food more efficiently and is supported by the Bill and Melinda Gates Foundation. Research for Food and Agriculture and the UK Foreign, Commonwealth and Development Office.
The lab's plan was to use CRISPR/Cas9 to modify the upstream DNA of the target gene, which controls the amount of the gene and when the gene will be expressed. They wondered if these changes would affect the activity later and to what extent. Even they were surprised by the results.
"The DNA changes that increased gene expression were much larger than we expected and larger than we've actually seen reported in other similar studies," said Patel-Tepper, now an AAAS fellow for science and technology policy at the United States Department of Agriculture.
"We were a little surprised, but I think it shows how plastic plants and crops are. They are used to major changes in their DNA from millions of years of evolution and thousands of years of domestication. As plant biologists, we can take advantage of this 'leeway' to make big changes in just a few years to help plants grow more efficiently or adapt to climate change."
In this study, the RIPE researchers learned that inversions, or 'flipping' of the regulatory DNA, resulted in increased PsbS gene expression. What was unique about this project was that after the largest DNA reversal was made, team members performed an RNA sequencing experiment to compare how the activity of all the genes in the rice genome changed with and without their changes.
What they found was a very small number of differentially expressed genes, far fewer than similar genome sequencing studies, indicating that their approach did not impair the activity of other essential processes.
Patel-Tepper added that although the team has shown that this method is possible, it is still not being used or the success rates are low. About 1% of the plants they created had the desired phenotype.
"We have shown a proof of concept here, that we can use CRISPR/Cas9 to create variants in key genes in crops and get the same jumps as we would get with the usual approaches of plant breeding, but on a very targeted trait that we want to engineer and in a much shorter period of time" said Patel- claw
"It's certainly more difficult than using a transgenic plant approach, but by changing something that already exists, we may be able to pre-empt regulatory issues that could slow down how we get tools like this into the hands of farmers."
CRISPR/Cas9, gene editing, photosynthesis, gene expression, rice, plant genome, regulatory genes, laboratory mutants, RIPE project, agriculture, food crops, photosynthetic efficiency, climate change, plant engineering, synthetic biology, plant science, crop improvement, research Genetics, University of California Berkeley, University of Illinois
