In keeping with MIT’s charter, established in 1861, a part of the Institute’s mission is to advance the “development and practical application of science in reference to arts, agriculture, manufactures, and commerce.” Today, the Abdul Latif Jameel Water and Food Systems Lab (J-WAFS) is certainly one of the driving forces behind water and food-related research on campus, much of which pertains to agriculture. In 2022, J-WAFS established the Water and Food Grand Challenge Grant to encourage MIT researchers to work toward a water-secure and food-secure future for our changing planet. Not unlike MIT’s Climate Grand Challenges, the J-WAFS Grand Challenge seeks to leverage multiple areas of experience, programs, and Institute resources. The initial call for statements of interests returned 23 letters from MIT researchers spanning 18 departments, labs, and centers. J-WAFS hosted workshops for the proposers to present and discuss their initial ideas. These were winnowed right down to a smaller set of invited concept papers, followed by the ultimate proposal stage. 

Today, J-WAFS is delighted to report that the inaugural J-WAFS Grand Challenge Grant has been awarded to a team of researchers led by Professor Matt Shoulders and research scientist Robert Wilson of the Department of Chemistry. A panel of expert, external reviewers highly endorsed their proposal, which tackles a longstanding problem in crop biology — learn how to make photosynthesis more efficient. The team will receive $1.5 million over three years to facilitate a multistage research project that mixes cutting-edge innovations in synthetic and computational biology. If successful, this project could create major advantages for agriculture and food systems worldwide.

“Food systems are a significant source of world greenhouse gas emissions, they usually are also increasingly vulnerable to the impacts of climate change. That’s why after we discuss climate change, now we have to discuss food systems, and vice versa,” says Maria T. Zuber, MIT’s vice chairman for research. “J-WAFS is central to MIT’s efforts to handle the interlocking challenges of climate, water, and food. This recent grant program goals to catalyze revolutionary projects that can have real and meaningful impacts on water and food. I congratulate Professor Shoulders and the remainder of the research team on being the inaugural recipients of this grant.”

Shoulders will work with Bryan Bryson, associate professor of biological engineering, in addition to Bin Zhang, associate professor of chemistry, and Mary Gehring, a professor within the Department of Biology and the Whitehead Institute for Biomedical Research. Robert Wilson from the Shoulders lab might be coordinating the research effort. The team at MIT will work with outside collaborators Spencer Whitney, a professor from the Australian National University, and Ahmed Badran, an assistant professor on the Scripps Research Institute. A milestone-based collaboration may even happen with Stephen Long, a professor from the University of Illinois at Urbana-Champaign. The group consists of experts in continuous directed evolution, machine learning, molecular dynamics simulations, translational plant biochemistry, and field trials.

“This project seeks to fundamentally improve the RuBisCO enzyme that plants use to convert carbon dioxide into the energy-rich molecules that constitute our food,” says J-WAFS Director John H. Lienhard V. “This difficult problem is a real grand challenge, calling for extensive resources. With J-WAFS’ support, this long-sought goal may finally be achieved through MIT’s leading-edge research,” he adds.

RuBisCO: No, it’s not a recent breakfast cereal; it just is likely to be the important thing to an agricultural revolution

A growing global population, the consequences of climate change, and social and political conflicts just like the war in Ukraine are all threatening food supplies, particularly grain crops. Current projections estimate that crop production must increase by not less than 50 percent over the following 30 years to fulfill food demands. One key barrier to increased crop yields is a photosynthetic enzyme called Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (RuBisCO). During photosynthesis, crops use energy gathered from light to attract carbon dioxide (CO₂) from the atmosphere and transform it into sugars and cellulose for growth, a process often called carbon fixation. RuBisCO is important for capturing the CO₂ from the air to initiate conversion of CO₂ into energy-rich molecules like glucose. This response occurs throughout the second stage of photosynthesis, also often called the Calvin cycle. Without RuBisCO, the chemical reactions that account for virtually all carbon acquisition in life couldn’t occur.

Unfortunately, RuBisCO has biochemical shortcomings. Notably, the enzyme acts slowly. Many other enzymes can process a thousand molecules per second, but RuBisCO in chloroplasts fixes lower than six carbon dioxide molecules per second, often limiting the speed of plant photosynthesis. One other problem is that oxygen (O₂) molecules and carbon dioxide molecules are relatively similar in shape and chemical properties, and RuBisCO is unable to completely discriminate between the 2. The inadvertent fixation of oxygen by RuBisCO results in energy and carbon loss. What’s more, at higher temperatures RuBisCO reacts much more steadily with oxygen, which is able to contribute to decreased photosynthetic efficiency in lots of staple crops as our climate warms.

The scientific consensus is that genetic engineering and artificial biology approaches could revolutionize photosynthesis and offer protection against crop losses. Up to now, crop RuBisCO engineering has been impaired by technological obstacles which have limited any success in significantly enhancing crop production. Excitingly, genetic engineering and artificial biology tools are actually at a degree where they could be applied and tested with the aim of making crops with recent or improved biological pathways for producing more food for the growing population.

An epic plan for fighting food insecurity

The 2023 J-WAFS Grand Challenge project will use state-of-the-art, transformative protein engineering techniques drawn from biomedicine to enhance the biochemistry of photosynthesis, specifically specializing in RuBisCO. Shoulders and his team are planning to construct what they call the Enhanced Photosynthesis in Crops (EPiC) platform. The project will evolve and design higher crop RuBisCO within the laboratory, followed by validation of the improved enzymes in plants, ultimately leading to the deployment of enhanced RuBisCO in field trials to guage the impact on crop yield. 

Several recent developments make high-throughput engineering of crop RuBisCO possible. RuBisCO requires a posh chaperone network for correct assembly and performance in plants. Chaperones are like helpers that guide proteins during their maturation process, shielding them from aggregation while coordinating their correct assembly. Wilson and his collaborators previously unlocked the flexibility to recombinantly produce plant RuBisCO outside of plant chloroplasts by reconstructing this chaperone network in Whitney has now established that the RuBisCO enzymes from a variety of agriculturally relevant crops, including potato, carrot, strawberry, and tobacco, may also be expressed using this technology. Whitney and Wilson have further developed a variety of RuBisCO-dependent screens that may discover improved RuBisCO from complex gene libraries. Furthermore, Shoulders and his lab have developed sophisticated in vivo mutagenesis technologies that enable efficient continuous directed evolution campaigns. Continuous directed evolution refers to a protein engineering process that may speed up the steps of natural evolution concurrently in an uninterrupted cycle within the lab, allowing for rapid testing of protein sequences. While Shoulders and Badran each have prior experience with cutting-edge directed evolution platforms, this might be the primary time directed evolution is applied to RuBisCO from plants.

Artificial intelligence is changing the best way enzyme engineering is undertaken by researchers. Principal investigators Zhang and Bryson will leverage modern computational methods to simulate the dynamics of RuBisCO structure and explore its evolutionary landscape. Specifically, Zhang will use molecular dynamics simulations to simulate and monitor the conformational dynamics of the atoms in a protein and its programmed environment over time. This approach will help the team evaluate the effect of mutations and recent chemical functionalities on the properties of RuBisCO. Bryson will employ artificial intelligence and machine learning to look the RuBisCO activity landscape for optimal sequences. The computational and biological arms of the EPiC platform will work together to each validate and inform one another’s approaches to speed up the general engineering effort.

Shoulders and the group will deploy their designed enzymes in tobacco plants to guage their effects on growth and yield relative to natural RuBisCO. Gehring, a plant biologist, will assist with screening improved RuBisCO variants using the tobacco variety , where transient expression could be deployed. Transient expression is a speedy approach to check whether novel engineered RuBisCO variants could be accurately synthesized in leaf chloroplasts. Variants that pass this quality-control checkpoint at MIT might be passed to the Whitney Lab on the Australian National University for stable transformation into (tobacco), enabling robust measurements of photosynthetic improvement. In a final step, Professor Long on the University of Illinois at Urbana-Champaign will perform field trials of probably the most promising variants.

Even small improvements could have a huge impact

A standard criticism of efforts to enhance RuBisCO is that natural evolution has not already identified a greater enzyme, possibly implying that none might be found. Traditional views have speculated a catalytic trade-off between RuBisCO’s specificity factor for CO₂ / O₂ versus its CO₂ fixation efficiency, resulting in the idea that specificity factor improvements is likely to be offset by even slower carbon fixation or vice versa. This trade-off has been suggested to elucidate why natural evolution has been slow to realize a greater RuBisCO. But Shoulders and the team are convinced that the EPiC platform can unlock significant overall improvements to plant RuBisCO. This view is supported by the incontrovertible fact that Wilson and Whitney have previously used directed evolution to enhance CO₂ fixation efficiency by 50 percent in RuBisCO from cyanobacteria (the traditional progenitors of plant chloroplasts) while concurrently increasing the specificity factor. 

The EPiC researchers anticipate that their initial variants could yield 20 percent increases in RuBisCO’s specificity factor without impairing other features of catalysis. More sophisticated variants could lift RuBisCO out of its evolutionary trap and display attributes not currently observed in nature. “If we achieve anywhere near such an improvement and it translates to crops, the outcomes could help transform agriculture,” Shoulders says. “If our accomplishments are more modest, it would still recruit massive recent investments to this essential field.”

Successful engineering of RuBisCO could be a scientific feat of its own and ignite renewed enthusiasm for improving plant CO₂ fixation. Combined with other advances in photosynthetic engineering, resembling improved light usage, a recent green revolution in agriculture might be achieved. Long-term impacts of the technology’s success might be measured in improvements to crop yield and grain availability, in addition to resilience against yield losses under higher field temperatures. Furthermore, improved land productivity along with policy initiatives would assist in reducing the environmental footprint of agriculture. With more “crop per drop,” reductions in water consumption from agriculture could be a significant boost to sustainable farming practices.

“Our collaborative team of biochemists and artificial biologists, computational biologists, and chemists is deeply integrated with plant biologists and field trial experts, yielding a sturdy feedback loop for enzyme engineering,” Shoulders adds. “Together, this team will give you the chance to make a concerted effort using the most up-to-date, state-of-the-art techniques to engineer crop RuBisCO with an eye fixed to helping make meaningful gains in securing a stable crop supply, hopefully with accompanying improvements in each food and water security.”