How I Used CRISPR to Edit Climate-Saving Plants
By Bianca Gibbs
CRISPR-Cas9, although a relatively new technology, has had multiple breakthroughs in numerous fields. This new gene editing technology has allowed scientists to easily and accurately edit genes like never before.
Meanwhile, we have been living with the effects of global warming and climate change. Forests have been destroyed by wildfires and temperatures are slowly, but surely, increasing due to human activity, and while there have been many different attempts to stop and reverse climate change, one has stood out from the rest: Carbon Capture.
Well…more specifically, carbon capture via gene editing plants.
History of CRISPR
CRISPR made its debut in 1987 when Yoshizumi Ishino and his team discovered repeating sequences in E. coli bacteria. In the 1990s, Francisco Mojica continued studying these sequences, and they were given the acronym CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) in 2002.
By 2005, Rodolphe Barrangou and Philippe Horvath demonstrated CRISPR’s antiviral function (to combat viruses) and in 2012, Jennifer Doudna and Emmanuelle Charpentier proved that CRISPR-Cas9 can be used for gene editing. Today, many researchers are working to use CRISPR-Cas9 to improve many aspects of our daily lives.
Constraints
The ocean holds about 25% of all carbon emissions. If we could allow seagrasses to hold the carbon that the ocean absorbs, then there would be more room for the ocean to hold even more carbon dioxide. This sets seagrass gene editing apart from other methods of carbon capture because of its high carbon storage not only in the seagrasses themselves but also in the ocean water.
Scenario
What would happen if we removed all seagrasses from the Earth? Seagrasses store around 10% of annually sequestered carbon, meaning that they store 10% of the carbon that is stored in various ways yearly. If we did not have seagrasses, then this carbon would most likely go into the atmosphere, and this would cause an additional heat increase to the planet. Our planet is currently around 1 degree Celsius above pre-industrial temperatures, and the removal of seagrasses would greatly impact the Earth’s temperature.
Is This Possible?
Many startups, such as Living Carbon, use gene editing in plants as a way to solve climate change. For example, Living Carbon restores land using gene-edited plants. This shows that it is possible to fight climate change using plants, and in my case, I would be using seagrasses to mitigate climate change instead of forest plants.
What is Carbon Capture?
Carbon capture is any process of removing CO2 from the atmosphere, which is already done naturally in plants through photosynthesis. There are many different ways to edit a plant for enhanced carbon capture, but one I want to focus on is RuBisCO, which I will get to in a second, but first, how does this technology work?
First off, you need to select what you want to edit and a method of editing (CRISPR-Cas9 is the simplest to use). Subsequently, you find a gene that you want to edit. In this case, we are editing the RuBisCO gene. CRISPR is made of a Cas9 protein and guide RNA (gRNA). The gRNA will then lead the Cas9 protein to where the DNA needs to be cut. Once it cuts the DNA, a couple of things can happen:
- The DNA naturally repairs itself, most likely disabling the gene.
- A complementary RNA is placed where the cut DNA is to input a desired trait (this would be an extra step in a gene editing procedure).
In this case, I am editing RuBisCO, whose main function is to take in CO2 and turn that into fuel for the plant.
By enhancing RuBisCO in plants, we can edit plants so they can intake more carbon and store more CO2 in the ground. With RuBisCO, we can enhance carbon capture in plants without making any major changes in other parts of the plant. With this technology, the main thing that would change in a gene-edited plant is its size due to the extra CO2 intake since plants use CO2 to make food and grow.
The changes in our planet have destroyed many ecosystems throughout the world, such as the wildfires in California and Canada. We need to take action to save our planet before it is too late and the damages become irreversible. Remember, there is no Planet B, and if we care for our planet it will take care of us!
For this project, I decided to use Benchling to simulate a CRISPR knockout. A CRISPR knockout is when CRISPR only cuts the DNA and does not make any further changes (shown in #1 and #2 above in the How CRISPR Works photo).
Since Benchling does not have any seagrasses to work with, I decided to use corn (otherwise known as Zea Mays) for this project.
As you can see here, we have a list of both on-target (how well the gene works in performing its function, in this case, it is how well Rubisco can photosynthesize), and off-target scores. Note that in Benchling, it is best for both scores to be balanced, and for the scores to be as high as possible.
Subsequently, you need to find which chromosome your gene is on. In corn (Zea mays), RuBisCO is located on chromosomes 1, 2, 4 and 10. Note that which chromosome each gene lies on depends on the plant.
I selected chromosome 1 since it was the only one that was available. Once you click on Set Genome Region, the on-target and off-target scores should balance out (or the lower scores should increase).
Voila! You have just completed a CRISPR knockout using Benchling.
By doing this, I was able to learn the basics of how gene editing works and how to complete the specific steps to finish a CRISPR knockout. I was also able to learn that genes lie on chromosomes and which gene lies on which chromosome depends on the plant.
Benchling
As I said before, I decided to use Benchling for this project, but what exactly is Benchling? Well, according to Benchling, Benchling is a cloud-based platform for biotechnology research and development. Using this platform, you can edit the genes of almost any organism, such as humans, animals, or plants.
When I first started at TKS, I heard about Benchling from several students, alumni, and directors and so I decided to use Benchling for this project. Benchling is used by many gene editing startups and companies today, such as the Innovative Genomics Institute, which was started by the co-discoverer of CRISPR-Cas9 as a gene editing tool, Jennifer Doudna.
With any great invention come some limitations. Since Benchling is a computer program rather than the genes inside of an actual plant, there is no saying that what happens in Benchling will happen in the plant as well. However, Benchling is simple and free to use, so it’s easier for those who don’t know much about gene editing or are new to it to use the platform.
Corn vs. Seagrasses
Of course, there are some major differences in the overall structure of corn and seagrasses. Other than the differences that make up their appearance, RuBisCO lies on different chromosomes for both of them.
Also, remember that seagrasses and seaweed are not the same thing! Seagrasses have root systems (similar to land plants) and seaweed only contains holdfasts (which hold them to rocks or other parts of the seafloor), there are also many other differences between seagrasses and seaweed, which you can read about here.
Other than not finding a seagrass in Benchling’s DNA system, I did not have any other challenges while doing this project.
Be Cautious!
Just remember, if you do decide to practice gene editing, you must be careful as to what you are editing. With gene editing, you are changing a very delicate system which could have terrible effects if done wrong. Be sure to check out any laws preventing you from doing experiments and be cautious when performing experiments.
Next Steps
Since I started TKS, I’ve wanted to start my own startup, but I wasn’t sure what I wanted to do. After a couple of months, I realized that gene editing is something I love! My next steps are to gain hands-on experience with gene editing in plants so I can better understand gene editing. I want to work with real plants so I can gain data on how to edit a real plant and how to measure results with different trials. I’ll be able to do this if I can find a plant to edit (I will most likely use a small plant) and a CRISPR kit to conduct my experiment.
TDLR
Gene editing with CRISPR-Cas9, although a new technology, has opened new doors for scientists looking for a simple way to edit genes. It’s made multiple breakthroughs in different fields and has helped scientists work to solve many different problems, such as climate change. By using the online simulator Benchling, I was able to do a CRISPR knockout and genetically edit the plant in the simulator. From this project, I learned the basics of gene editing in plants and how to use Benchling. For my next steps, I would like to use a real plant for my experiment and start my own startup.
Also, be sure to read my previous article on CRISPR and gene editing here!
