How IGI researchers are using plants to capture and store carbon — and why CRISPR is the key
Recently, the IGI announced an ambitious new project to supercharge the ability of plants and soils to capture carbon from the atmosphere with the goal of using genomic tools to help fight climate change. A key part of this plan relies on improving photosynthesis in crop plants, so we wanted to take a deeper look at this topic. What does it mean to improve photosynthesis, and why do we think we have the ability to do so now?
How Does Photosynthesis Work?
Photosynthesis is an ancient process and an ingenious innovation. By taking up carbon dioxide and converting it into sugar, early single-celled organisms were able to turn very little – light energy and air – into life. Over time, photosynthesis filled our atmosphere with oxygen and evolved aquatic microorganisms into complex land plants: two crucial events that shaped the planet we live on today.
To dive deeper into how photosynthesis works, let’s shine a little light on a part of the cell called the chloroplast. Like mitochondria, chloroplasts are a “powerhouse” of the plant cell, responsible for making energy. They contain the pigment chlorophyll, which gives plants, algaes, and other photosynthetic organisms their characteristic green hue.
Chlorophyll captures light energy from the sun. This makes two things happen: 1) the release of oxygen from water molecules into the air we breathe, and 2) accumulating energy that can be used to power other cellular reactions. The main reaction this energy is used for is actually making and storing more energy through carbon fixation. In carbon fixation, plants take carbon dioxide out of the atmosphere and use it to make sugar. Plants use sugar as a way to store up energy – think about the energy rush you can get from eating candy! RuBisCO is the enzyme responsible for carbon fixation and has long been the focus of photosynthesis engineering research. You can see an overview of photosynthesis here or learn about it more in depth here.
Why Engineer Photosynthesis?
Two big changes are occurring at once, with big implications for our food system.
First, we live in a rapidly growing world: the global population passed eight billion people in November 2022, and an additional billion are expected to join us over the next 15 years. With an increased population count comes an increased demand for food, giving rise to a grand challenge.
Second, increasing levels of carbon dioxide and other greenhouse gasses in the atmosphere are increasing global temperatures, wreaking havoc on weather patterns, raising sea levels, and threatening global food supply.
Engineering photosynthesis can be part of the solution for both of these challenges: Enhancing photosynthesis could make plants grow bigger, with greater yield, increasing food supply, while also taking more carbon dioxide out of the atmosphere, helping slow or stop global warming. In fact, the Intergovernmental Panel on Climate Change estimates that carbon sequestration by agriculture could remove ~3.8 gigatons of carbon from the atmosphere in a single a year, a weight equivalent to over 30 million adult blue whales.
“I think climate change is an existential threat, and if I can make any difference in terms of combating it, I want to do that,” says Krishna Niyogi, a leading Investigator in IGI’s photosynthesis efforts and Professor of Plant and Microbial Biology at UC Berkeley.
What Have People Tried So Far?
Imagine pouring a drink from a bottle into a cup – what stands between you and a full glass? The flow of your drink, slowed by the neck of the bottle, is how researchers see limitations in photosynthesis. Enzymes are proteins that speed up chemical reactions. Enzymes that do their job slowly bottleneck the whole reaction, holding back the enzymes that do the next step and slowing everything down.
RuBisCO is the most notorious of these enzymes and its problems are twofold: first, it’s a slowpoke: it does its job of fixing carbon dioxide about 20 times slower than the average enzyme. Second, it can also make mistakes by grabbing the wrong kind of molecule, which generates a toxic byproduct that the cell has to spend energy cleaning up. So, scientists have tried to either speed up RuBisCO or make it less error-prone, but neither of these approaches have worked well so far. A different strategy done by the Ort lab at the University of Illinois – engineering to quicken clean-up of the aforementioned toxic byproduct – is promising, showing increases in plant biomass between 19-37% in plant field trials.
Another approach has been engineering ways of supplying more carbon dioxide to RuBisCO. This work has yet to produce the necessary increase in carbon fixation for plant improvement, but the avenue remains open.
Yet another approach for engineering photosynthesis is adding additional copies of enzymes to speed up carbon fixation. This has proven to be trickier than initially thought, and results in the lab are not always borne out in results in greenhouses and open field trials.
CRISPR & Photosynthesis Engineering
Previously, genetic engineering of photosynthesis involved moving genes from one plant species to another, making what we know as transgenics or “GMOs.”
“The way we did it before was transgenic, where we took the genes from the lab plant Arabidopsis and put them into the food plants that we were studying,” says Niyogi, “But all along we had in the back of our minds that we might be able to use CRISPR to edit the plant’s own genes and achieve the same thing.” Think of this approach as unlocking a plant’s own potential, by giving it a genetic nudge in the right direction.
This new, non-transgenic approach is especially helpful for getting regulatory approval to bring engineered plants to a broader audience, e.g. for food crops.
Niyogi’s CRISPR strategy is making a plant more thrifty with its resources: if a plant saves energy by cutting back on less essential processes, it has more energy to spend on taking carbon dioxide out of the atmosphere through photosynthesis. For example, much like us, plants can be disrupted by getting too much light. While we get sunburns from spending too much time outside, plants experience similar stresses from excess light, including damage to DNA and photosynthetic machinery.
Niyogi’s previous research focused on optimizing this way for plants to recover and prepare for photosynthesis faster. With the gene editing capabilities afforded by CRISPR, it is possible this could now be accomplished without relying on outside genetic help.
“That’s where the power of CRISPR tools really comes in,” explains Flora Wang, a graduate student working on this project. “You can create transgene-free plants that function so much better by making a relatively small change.”
Using conventional genomic techniques Niyogi’s approach to quickening light recovery had resulted in 15% larger plants – the same percent increase in supply projected to meet global food demand in future. With CRISPR, there might be even more room to grow.
Good Gene Hunting
To paraphrase an old adage, “To know where you are going, you must know where you came from.” This reflects the guiding principle behind the research of David Savage, IGI Investigator and Associate Professor in the Department of Molecular and Cell Biology. Savage is developing a toolkit for exploring plant genetics in preparation for CRISPR engineering. While Niyogi’s approach to photosynthetic engineering is diving deep into known mechanisms, Savage is taking a step back to help identify additional genes that could yield plant improvement.
A plant like wheat has over 120,000 genes – that’s more than five times as many genes as the human genome! Finding the genes that could result in improved photosynthesis is a task akin to finding the metaphorical needle in a haystack. David Ding, a systems biologist in the Savage lab, commented on this challenge: “The bottleneck is to understand what genetic changes will give you the right traits.”
To speed up this discovery process, Savage has innovated a sweeping approach, studying thousands of genes in parallel rather than one by one. Instead of using whole plants, which is costly, laborious, and slow, researchers in the Savage lab are using CRISPR to target genes in individual plant cells. Thousands of these individual cells – and individual genes – can be tested at the same time, accelerating searches through the genome.
“If we can look at the effect of changing genes before we go into full plants,” Ding says, “We can potentially examine many, many more genes than was previously possible.”
Cleaner, Faster CRISPR
Savage is also working to improve the editing power of CRISPR in plants. Historically, plant breeding required multiple generations to make sure that all of your plants had the trait – and corresponding version of a gene – of interest. Because of the large genomes of many plants, this can be tricky! For example, humans have two copies of every gene. But bread wheat has six copies of each gene! To get a new trait stably in wheat, each copy must be correct.
With conventional breeding, this takes years to decades to accomplish. Savage aims to not only deploy CRISPR to make specific edits to a plant genome, but also to improve its editing efficiency. The goal is to make edits across all copies of a gene simultaneously, drastically cutting back the time necessary to reach the successfully engineered plant.
“Whether it’s organic or not, our food is all engineered because plant breeders and thousands of years of human engineers have evolved these plants, and CRISPR is just the latest step in that,” says Savage. “If we understand enough about the deeper aspects of plant biology, we can achieve those important plant qualities through less invasive means with CRISPR.”
Out of the Lab and Into the Field
While CRISPR has allowed scientists to ask and answer questions at a faster speed than ever before, there remain some hurdles on the way to improved photosynthesis. One challenge is the translatability of research between plant species.
“The vast diversity of plants makes them hard to work with,” says Savage. “One of the challenges will be to figure out how to take one advance and quickly assess whether that advance will or won’t work in a related species.”
Many researchers anticipate slotting CRISPR-engineered plants into our current industrial agricultural practices – a minimally disruptive way of fixing more carbon.
As Ding puts it, “You could scale this technology up by producing many, many plants that are all 10% more efficient and put 10% more carbon back into the soil.” Combining improved photosynthesis with sustainable farming practices would not only maximize carbon removal, but also regenerate soil for future use.
There is a human element to this research beyond the technical details: CRISPR-edited plants will need to be adopted by farmers and growers in order to deliver their benefits at a scale that can have the impact that’s needed.
“If you communicate your science, it’s going to be of interest to farmers that this is so much better than traditional crops that we’re working with,” says Wang. And of course, these crops must move from farm to table, and consumers must also have a say. “There’s definitely a lot of work that needs to go into effective science communication and talking with the public.”
The goal is to provide a win-win-win: farmers will get increased crop yields, consumers preferred varieties of foods will be preserved, and, most importantly, all of humanity will benefit from reducing carbon in the atmosphere.