Research team uses CRISPR/Cas9 to change photosynthesis for the first time

A team from the Innovative Genomics Institute at the University of California, Berkeley (UCB) has induced an increase in gene expression in a food crop by altering its upstream regulatory DNA. While other studies have used CRISPR/Cas9 gene editing to knock out or reduce the expression of genes, new research published in Scientific progress is the first unbiased approach to gene editing to increase gene expression and downstream photosynthetic activity.

“Tools like CRISPR/Cas9 accelerate our ability to fine-tune gene expression in crops, rather than just turning off or ‘switching off’ genes. Previous research has shown that this tool can be used to reduce the expression of genes involved in important trade-offs, such as those between plant architecture and fruit size,” said Dhruv Patel-Tupper, lead author of the study and former postdoctoral researcher in the study. Niyogi lab at UCB.

“To our knowledge, this is the first study in which we have asked whether we can use the same approach to increase the expression of a gene and improve its downstream activity in an unbiased manner.”

Unlike synthetic biology strategies that use genes from other organisms to enhance photosynthesis, the genes involved in the photoprotection process are found naturally in all plants.

Inspired by a 2018 Nature communication In a paper that improved the water use efficiency of a model crop by overexpressing one of these genes, PsbS, in plants, the Niyogi lab and its leader Kris Niyogi set out to figure out how to increase the expression of a plant’s native genes. can be changed without adding foreign DNA.

According to the Food and Agriculture Organization, rice provides at least 20% of the world’s calories, and because rice contains only one copy of each of the three major photoprotection genes in plants, it was an ideal model system for this gene editing research.

The Niyogi lab continued this work as part of Realizing Increased Photosynthetic Efficiency (RIPE), an international research project led by the University of Illinois that aims to increase global food production by developing food crops that use the sun’s energy more efficiently transform food, with support from the Bill & Melinda Gates Foundation, the Foundation for Food & Agriculture Research and the UK Foreign, Commonwealth & Development Office.

The lab’s plan was to use CRISPR/Cas9 to alter the DNA upstream of the target gene, which controls how much of the gene is expressed and when. They wondered whether implementing these changes would impact downstream operations, and to what extent. Even they were surprised by the results.

“The changes in DNA that increased gene expression were much larger than we expected and larger than we’ve seen in other similar stories,” said Patel-Tupper, now an AAAS Science and Technology Policy Fellow at the USDA.

“We were a little surprised, but I think this shows how much plasticity plants and crops have. They are used to these big changes in their DNA as a result of millions of years of evolution and thousands of years of domestication. As plant biologists, we can give that ‘wiggle room ‘ to make major changes in just a handful of years, so that plants can grow more efficiently or adapt to climate change.”

In this study, RIPE researchers found that inversions, or ‘flipping’ of the regulatory DNA, resulted in increased gene expression of PsbS. Unique to this project: After the major inversion in the DNA was performed, the team members performed an RNA sequencing experiment to compare how the activity of all genes in the rice genome changed with and without their modifications.

What they found was a very small number of differentially expressed genes, much smaller than comparable transcriptome studies, suggesting that their approach did not compromise the activity of other essential processes.

Patel-Tupper added that while the team has shown that this method is possible, it is still relatively rare. About 1% of the plants they produced had the desired phenotype.

“We have shown proof-of-concept here that we can use CRISPR/Cas9 to generate variants in key crop genes and make the same leaps as traditional plant breeding approaches, but on a very targeted trait that we want to develop and target. a much faster time frame,” said Patel-Tupper.

“It’s certainly more difficult than using a transgenic plant approach, but by changing something that’s already there, we can potentially avoid regulatory issues that could slow how quickly we get these types of tools into the hands of farmers.”