Future proofing photosynthesis

“Do you like to eat and breathe?” Of all the questions Amanda Cavanagh envisioned her PhD mentor asking her at their initial meeting, that one wasn’t anywhere on her list. Caught off guard, she could only stammer that yes, yes, she did. Quite a lot. “Then you might want to think about photosynthesis,” said David Kubien, a biochemist at the University of New Brunswick. When Cavanagh did, the phenomenon immediately captivated her and hasn’t let go since. Now at the University of Essex, Cavanagh has focused her curiosity on an enzyme called RuBisCO, which lassos abiotic carbon dioxide and embeds it in the biosphere in the form of organic carbon molecules, such as sugar. It’s the entry point for the organic carbon on the planet.

“All the carbon in our bodies, all the carbon that we eat—all of this is just passing through this one enzyme. Which is a little mind boggling,” Cavanagh says.

Even more baffling to a then 20-something Cavanagh was the reality that, from an efficiency standpoint, RuBisCO was terrible. As much as 25% of the time, the enzyme grabs a molecule of oxygen instead of CO₂. Rather than an ultraprecise biomolecule, RuBisCO acts like an arcade claw machine, snatching whatever is closest when its active site opens. From her home in Canada, Cavanagh could see winters dwindling, and wanted to know how the RuBisCO claw machine would change as the planet warms. The answer? Nothing good. Any benefit of rising CO₂ levels would be more than offset by heat and water stress.

Although biochemists have known for decades about RuBisCO and its lack of molecular precision, a trait known as enzyme promiscuity, Cavanagh and a small cadre of other scientists don’t want to just dissect this characteristic They want to fix it. Their Gates Foundation–funded group, known as the RIPE (Realizing Increased Photosynthetic Efficiency) Project, is trying to re-engineer photosynthesis and bolster the world’s food supply in the face of climate change.

Beyond tweaking RuBisCO function, researchers are also looking into everything from leaf color and shape to boosting plants’ ability to cope with excess light. Even small increases in photosynthetic efficiency could lead to dramatic improvements in the world’s food supply.

RIPE’s leader, Stephen Long of the University of Illinois Urbana-Champaign, admits that success is a long shot, but one upon which the future of the planet depends, especially in the face of continually rising CO₂ levels. “We don’t just need to increase photosynthesis, we need to future proof it,” Long says.

Ripe for improvement

The germ of the idea for the RIPE Project came in the early 2000s. Conventional plant breeders had already optimized factors like plant size and were working on disease resistance. Based smack in the center of North America’s corn and soybean belts, plant biologist Long knew that the dovetailing issues of climate change and population growth posed a threat for the new century. Down the hall from Long’s laboratory, fellow plant biologist and biochemist Donald Ort had begun to ask whether improving photosynthesis efficiency would improve crop yields.

“For plants like soybean, wheat, and rice, the theoretical maximum efficiency of photosynthesis is 4.6%. What we see, even in our best crops, is more like 1%,” Long says. “So that really tells you there’s a lot of room for improvement.”

Answering the question of how to improve photosynthesis would require the researchers to build a digital twin of the whole process, modeling all of its 120-plus steps in near-atomic detail. Thankfully for Long and Ort, Illinois not only had a lot of farmland, it was then home to one of the world’s largest supercomputing complexes. Precious server time enabled the pair to identify six potential pathways to improving photosynthesis. Combining all six, they calculated, could improve crop yields by up to 50% (Plant Cell Env. 2006, DOI: 10.1111/j.1365-3040.2005.01493.x). These gains would be even higher when compared with declines in agricultural output due to climate change (Science 2006, DOI: 10.1126/science.1114722).

The technocentric possibilities Ort and Long proposed soon attracted the attention of the Bill and Melinda Gates Foundation. In 2012, the organization provided an initial $25 million investment in the RIPE Project. The project has since received an additional $92 million in from a range of sources. Over the past 8 years, the group has grown to 104 team members across seven institutions, all of whom are trying to tackle aspects of photosynthesis.

“Plant photosynthesis didn’t evolve for efficiency; it evolved for reproductive success. It also evolved at a time that is very different from now, so it’s not very well suited to current conditions. As conditions continue to change, that provides further challenges,” says Robert Blankenship, professor emeritus of botany and chemistry at Washington University in St. Louis who is not a part of RIPE. “I don’t see any reason why people won’t be able to improve it.”

Hacking a process that operates at a maximum efficiency of 2–3% sounds like a breeze, but the sheer number of moving parts involved in photosynthesis means that researchers must balance the impacts of thousands of chemical reactions. With the help of advanced computer modeling, the UIUC scientists whittled down their options to a few of the reactions that are the most in need of improvement and the most amenable to biochemical tinkering.

RuBisCO and its wasteful knack for grabbing oxygen instead of CO₂, a process known as photorespiration, seemed like an obvious place to start.

Why RuBisCO?

At its core, photosynthesis converts the sun’s energy to usable sugars. This biochemical transformation relies not on a magic wand and sleight of hand but on a series of chemical reactions during which a plant cell must coordinate ping-ponging photons, highly reactive free radicals, and toxic by-products. It is a convoluted, energy-intensive series of chemical reactions reminiscent of what might happen if Rube Goldberg and MacGyver were to put their heads together. Photosynthesis isn’t just a single process. It connects two interrelated biological pathways, and both must proceed in synchronization for a plant to have success.

When sunlight hits a plant leaf, the photons of light are absorbed by chlorophyll and its associated carotenoid proteins. There, the energy of the light oxidizes two water molecules, forming molecular oxygen and releasing four protons and four electrons. Those electrons then reduce a molecule called a plastoquinone to plastoquinol, starting a run of reduction reactions that continues along the electron transport chain until the final step, where the enzyme cofactor nicotinamide adenine dinucleotide phosphate (NADP⁺) reduces to NADPH. Meanwhile, the hydrogen ions from the two split water molecules create a molecule of adenosine triphosphate (ATP) for energy (Essays Biochem. 2016, DOI: 10.1042/EBC20160016).

But leaves also absorb CO₂, and the enzyme RuBisCO (a portmanteau of ribulose-1,5-bisphosphate-carboxylase/oxygenase) is how that gas becomes fixed in more-complex carbon-containing molecules in plants.

When the system works, RuBisCO catalyzes the reaction of that CO₂ with a five-carbon sugar called ribulose-1,5-bisphosphate (RuBP) as one part of a catalytic cycle called the Calvin-Benson cycle. In that cycle, RuBP plus CO₂ produces two molecules of a compound called 3-phosphoglyceric acid (PGA). The ATP produced in the previous pathway phosphorylates PGA, which is then reduced by NADPH to glyceraldehyde 3-phosphate (GAP). For every six molecules of GAP produced, five are used to replenish the plant’s supply of RuBP, and the remaining GAP molecule can be converted to sugar.

But RuBisCO can also grab hold of O₂ instead of CO₂ because when the enzyme first evolved billions of years ago, atmospheric O₂ didn’t exist. And if RuBisCO grabs O₂, instead of making two PGA molecules, the cycle starts with one molecule of PGA and one molecule of 2-phosphoglycolate.

This causes two problems, explains Christine Raines, a plant biologist at the University of Essex. Not only does the plant get merely half of the molecules it wants, but 2-phosphogycolate is toxic to the plant. To detoxify, the plant uses valuable NADPH and ATP to produce ammonia (also toxic, though less so) and CO₂.

Some of the earliest biochemical investigations of the Calvin-Benson cycle showed that as much as one-quarter of the energy produced by photosynthesis is wasted by RuBisCO’s proclivity to oxygen (Plant Cell 2005, DOI: 10.1105/tpc.105.035873). Add in other losses, such as a plant’s inability to absorb all visible light, delays in adjusting to shifts between shade and sun, and the energy invested in building the parts of the plant humans don’t eat, and scientists estimate that photosynthesis has an efficiency of 1%. As CO₂ levels in the atmosphere continue shooting skyward from the burning of fossil fuels, the situation is getting worse. Increasing heat and water stress more than offset any improvements from increased CO₂ levels (Nat. Plants 2016, DOI: 10.1038/nplants.2016.132). Throw in a global human population estimated to reach 10 billion by 2058 and stalling improvements in crop yields from traditional breeding methods and it’s a perfect storm for a hunger crisis.

How do you solve a problem like RuBisCO?

Improving RuBisCO efficiency is complicated because the protein itself is complicated. It is by far the most abundant protein on the planet, making up half of the soluble protein in every leaf, not to mention its presence in photosynthetic bacteria and marine life (Proc. Natl. Acad. Sci. U.S.A. 2018, DOI: 10.1073/pnas.1816654116). Weighing in at 560 kDa—8.7 times as large as hemoglobin—RuBisCO is large and complex (CBE Life Sci. Educ. 2009, DOI: 10.1187/cbe.09-01-0003). Cells use an assembly line with a series of molecular chaperones to ensure that RuBisCO folds correctly. These chaperones also help supervise the five-step catalytic process at the heart of RuBisCO. This complexity brings plenty of opportunities to innovate, says Elizabete Carmo-Silva, a crop physiologist at Lancaster University, but even more ways to make RuBisCO perform worse.

“Plants invest a lot of resources into making sufficient RuBisCO to carry out photosynthesis at adequate rates. It represents a massive investment of nitrogen and other nutrients,” Carmo-Silva says. “The activity of RuBisCO is finely regulated.” So instead of modifying RuBisCO directly, many researchers are looking to tweak RuBisCO regulation, or the molecular machinery that creates the RuBisCO substrates.

Carmo-Silva has begun to work on a chaperone called RuBisCO activase, which ensures that RuBisCO stays in its active conformation. Carmo-Silva calls it RuBisCO’s coffee, because it springs to action once it senses enough light to start photosynthesis.

But when temperatures soar above 35–40 °C, RuBisCO activase functions like decaf. Instead of beginning photosynthesis with pep and vigor as soon as the sun hits a leaf, RuBisCO staggers in belatedly, the protein equivalent of hitting the snooze button (J. Exp. Bot. 2008, DOI: 10.1093/jxb/ern053). So Carmo-Silva has been searching for thermotolerant variants of RuBisCO activase that can act like molecular espresso even during heat waves.

Meanwhile, 240 miles southeast in Essex, Cavanagh is now working alongside Raines on improving the synthesis of RuBP. An enzyme called SBPase (a popular abbreviation since the full name, sedoheptulose-bisphosphatase, “doesn’t exactly roll off the tongue,” Raines says) catalyzes one of the major steps in RuBP synthesis.

In 1997, Raines began lowering SBPase levels in Nicotiana tabacum (tobacco), which, along with Arabidopsis, are the lab rats of plant biology. Less SBPase meant less photosynthesis, and even small decreases in SBPase had dramatic impacts on plant growth (Planta 1997, DOI: 10.1007/s004250050226). Importantly, a subsequent study also showed that increasing SBPase levels increased carbon fixation by 6–12% in tobacco (Plant Physiol. 2005, DOI: 10.1104/pp.104.055046). The approach also showed benefits in wheat, tomato, and cucumber, but not in rice.

To Cavanagh, the most exciting part of this approach is that the regeneration of RuBP limits photosynthesis in environments with higher CO₂ levels. Speeding up a plant’s ability to replenish RuBP will allow its photosynthetic engines to rev even higher in these environments. “Yes, it helps in current conditions, but it’s also one of the targets that is even more helpful for future conditions,” she says.

The route that RuBisCO takes when it grabs oxygen instead of carbon dioxide, called photorespiration, could also be tweaked to improve yields. All photosynthetic plants contain RuBisCO that will mistakenly bind oxygen, but only land plants have evolved the complex mechanism of photorespiration. Photosynthetic bacteria have a much simpler pathway to rid themselves of toxic 2-phosphoglycolate. As part of her postdoctoral work, Cavanagh and RIPE colleagues introduced a synthetic version of this pathway into tobacco plants and switched off normal photorespiration. Field studies showed that these engineered plants had 25% more growth than controls, according to a 2019 study in Science (DOI: 10.1126/science.aat9077).

But RuBisCO is only one component of photosynthesis, and scientists have found plenty of additional targets.

Beyond RuBisCO

For photosynthetic plants, light can be too much of a good thing. More solar energy bombards the Earth each hour than the sum total of all energy used by humans throughout an entire year. But even the most efficient plant can’t use all that light energy. Much of it is the wrong wavelength—chlorophyll only absorbs red and blue wavelengths, reflecting green. Even with that filter, chlorophyll can still take on far more light energy than it can use, and that energy has to go somewhere. Plants’ solution is a process called non-photochemical quenching, or NPQ.

After absorbing solar energy, chlorophyll enters a singlet excited state. If singlet chlorophyll doesn’t transfer its excitation energy, it can decay to a triplet state, which can interact with the ground state of O₂ (itself a triplet) and create singlet oxygen, one of the most damaging and reactive oxygen species. To avoid that, singlet chlorophyll transfers the excess energy to nearby carotenoid proteins, which eventually release the energy as heat (Proc. Natl. Acad. Sci. U.S.A. 2003, DOI: 10.1073/pnas.0736959100).

Plants activate NPQ quickly in times of peak sunlight—a protective response to prevent what Krishna Niyogi, a molecular biologist at the University of California, Berkeley, describes as the botanical equivalent of a sunburn. But if clouds pass overhead and dim the light, NPQ processes remain active long after sunlight has reduced. As a result, plants miss out on valuable photosynthesis opportunities. The speed at which plants can switch off NPQ varies by species, and Niyogi is on the hunt for those organisms that can adapt to rapidly changing sunlight levels with the least loss of photosynthetic capacity.

Plants that have a faster off switch for NPQ—species like marine diatoms and flowering mustard plants— do in fact have improved efficiency in photosynthesis, according to work by Niyogi and others, but even species that are faster aren’t nearly fast enough to match how quickly light can change in nature. For that, synthetic biologists are working to engineer their own NPQ tweaks, including overexpressing key NPQ genes. Field trials of soybeans with tweaked NPQ processes increased seed production by 33% (Science 2022, DOI: 10.1126/science.adc9831).

“If this can scale, farmers would be very interested in it,” Niyogi says. “It’s much more than you would get from conventional plant breeding.”

Another approach is that being taken at the US Department of Agriculture, where plant physiologist Lisa Ainsworth has begun trying to alter photosynthesis rates by changing leaf shape. Leaf shape helps to control the percentage of ground area covered by leaves, and how much light penetrates the top layer of canopy.

Like many other plants, soybeans have a range of leaf shapes, from long and thin to nearly round, which are controlled by a single transcription factor. Ainsworth’s experiments showed that soybean plants with long, thin leaves were able to do more photosynthesis, since more light reached lower layers of leaves. This, in turn, resulted in a significant improvement in soybean yields (Ann. Bot. 2023, DOI: 10.1093/aob/mcac118).

“Modeling studies suggested that soybeans are already overinvesting in their leaves,” Ainsworth says. “We should be able to improve their yields in today’s atmosphere but also in future atmospheres.”

But none of the successes identified to date have resulted in the kind of agronomic slam dunk needed to clear potential regulatory hurdles in bringing a new, genetically modified seed to market, not to mention stave off the potential for global hunger. To get those kinds of results, scientists will need to start stacking the deck.

Cumulative gains

From the beginning of the RIPE Project, both Ort and Long knew that the kind of improvements they needed to observe in crop yields wouldn’t be gained by altering one enzyme or even one pathway. They would need to gather the cumulative effects of altering RuBisCO and photorespiration and leaf shape and any number of other changes as well as how plants with those alterations perform in various environments.

“We’ve demonstrated some of these changes on our farm, but that’s one location. To take this further, we need to test it in the crops that are suited for Africa and Southeast Asia,” Long says.

But any one of these molecular alterations could have unforeseen consequences. A change might increase photosynthesis but also make a plant require too much water or lead to a new vulnerability to disease. While running experiments in model plant species are faster than planting an entire field of wheat, they still require a lot of time and energy from RIPE scientists—time that the world may not necessarily have to spare. The Food and Agriculture Organization of the United Nations estimates that food production in 2060 will need to be double 2005 levels.

“That’s two breeding cycles away,” Ort says. “The window on making these changes is probably in 5 to 10 years if we’re going to address this issue.”

That’s why researchers are turning to computer modeling to understand the intricacies not only of making the initial gene edits but also of combining them. It’s part of Megan Matthews’s job to build these models. An engineer at the UIUC, Matthews wants to understand not only how combinations of genetic changes will affect photosynthesis but also whether these benefits will persist in different environmental conditions.

“It’s not like we want to increase photosynthesis just for the sake of increasing photosynthesis. There’s a goal, whether it’s increasing yields in food crops or increasing biomass for carbon capture or for bioenergy purposes,” Matthews says.

These goals are ambitious and well intentioned, says Thomas Sinclair, a retired crop scientist from North Carolina State University, but he’s not convinced that RIPE’s efforts will have the intended benefits. For one, an increase in photosynthesis rate might also require concomitant increases in fertilizer and water use. Think of it, he says, like baking cupcakes. If you want to bake more cupcakes, you’ll need more flour. But unless you also bring extra eggs and oil, having more flour doesn’t do you much good. Instead of investing millions in designing better plants, the world would be better served by improving the quality of farming practices in low-resource settings, Sinclair says.

“It’s a technology-driven thing to study photosynthesis now because we have the tools to do it. But I’m not convinced the payoff is there,” Sinclair says.

Perhaps an even bigger challenge for RIPE will be convincing farmers to plant the seeds and consumers to buy the resulting products. Sociologist Jennifer Kuzma, who has spent years studying consumer attitudes toward genetically modified foods, says for around 20% of the population, any sort of genetically modified organism (GMO) is a straightforward no-go. An equal proportion is drawn to technology and novelty, so probably wouldn’t need any convincing to try an engineered food. But the middle 60% aren’t completely against GMOs but they aren’t totally sold on the idea either. It’s these people on whom RIPE should focus its efforts to convince, Kuzma says.

“People make their decisions based on benefits and risks, sure, but they also base them on their worldviews and trust. Instead of saying, How we can get the public’s trust?, the industry should be saying, How can we become trustworthy?” Kuzma says.

RIPE should build trust by communicating their efforts to the public clearly and being transparent about what they’re doing and why. Going above and beyond the minimal US regulatory requirements will also help persuade consumers, she says.

A RIPE-engineered plant, though, is far in the future, and it isn’t yet clear which crop will make the final selection and what modifications it might contain. Plant biologists like Blankenship remain bullish on the idea that RIPE will be able to make significant improvements in photosynthesis efficiency, even if they don’t necessarily reach their goal of a 50% boost.

“I don’t see it as a pie-in-the-sky thing. I see this project as addressing a particular inefficiency in a directed way,” Blankenship says. “There’s no inherent barrier.”

Carrie Arnold is a freelance writer based in Virginia.