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    Inaugural J-WAFS Grand Challenge aims to develop enhanced crop variants and move them from lab to land

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    According to MIT’s charter, established in 1861, part of the Institute’s mission is to advance the “development and practical application of science in connection with arts, agriculture, manufactures, and commerce.” Today, the Abdul Latif Jameel Water and Food Systems Lab (J-WAFS) is one of the driving forces behind water and food-related research on campus, much of which relates to agriculture. In 2022, J-WAFS established the Water and Food Grand Challenge Grant to inspire 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 expertise, 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 down to a smaller set of invited concept papers, followed by the final 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 — how to make photosynthesis more efficient. The team will receive $1.5 million over three years to facilitate a multistage research project that combines cutting-edge innovations in synthetic and computational biology. If successful, this project could create major benefits for agriculture and food systems worldwide.

    “Food systems are a major source of global greenhouse gas emissions, and they are also increasingly vulnerable to the impacts of climate change. That’s why when we talk about climate change, we have to talk about food systems, and vice versa,” says Maria T. Zuber, MIT’s vice president for research. “J-WAFS is central to MIT’s efforts to address the interlocking challenges of climate, water, and food. This new grant program aims to catalyze innovative projects that will have real and meaningful impacts on water and food. I congratulate Professor Shoulders and the rest of the research team on being the inaugural recipients of this grant.”

    Shoulders will work with Bryan Bryson, associate professor of biological engineering, as well as Bin Zhang, associate professor of chemistry, and Mary Gehring, a professor in the Department of Biology and the Whitehead Institute for Biomedical Research. Robert Wilson from the Shoulders lab will 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 at the Scripps Research Institute. A milestone-based collaboration will also take place 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 true 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 new breakfast cereal; it just might be the key to an agricultural revolution

    A growing global population, the effects of climate change, and social and political conflicts like the war in Ukraine are all threatening food supplies, particularly grain crops. Current projections estimate that crop production must increase by at least 50 percent over the next 30 years to meet 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 draw carbon dioxide (CO2) from the atmosphere and transform it into sugars and cellulose for growth, a process known as carbon fixation. RuBisCO is essential for capturing the CO2 from the air to initiate conversion of CO2 into energy-rich molecules like glucose. This reaction occurs during the second stage of photosynthesis, also known as the Calvin cycle. Without RuBisCO, the chemical reactions that account for virtually all carbon acquisition in life could not 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 less than six carbon dioxide molecules per second, often limiting the rate of plant photosynthesis. Another problem is that oxygen (O2) molecules and carbon dioxide molecules are relatively similar in shape and chemical properties, and RuBisCO is unable to fully discriminate between the two. The inadvertent fixation of oxygen by RuBisCO leads to energy and carbon loss. What’s more, at higher temperatures RuBisCO reacts even more frequently with oxygen, which will contribute to decreased photosynthetic efficiency in many staple crops as our climate warms.

    The scientific consensus is that genetic engineering and synthetic biology approaches could revolutionize photosynthesis and offer protection against crop losses. To date, crop RuBisCO engineering has been impaired by technological obstacles that have limited any success in significantly enhancing crop production. Excitingly, genetic engineering and synthetic biology tools are now at a point where they can be applied and tested with the aim of creating crops with new 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 improve the biochemistry of photosynthesis, specifically focusing on RuBisCO. Shoulders and his team are planning to build what they call the Enhanced Photosynthesis in Crops (EPiC) platform. The project will evolve and design better crop RuBisCO in the laboratory, followed by validation of the improved enzymes in plants, ultimately resulting in the deployment of enhanced RuBisCO in field trials to evaluate the impact on crop yield. 

    Several recent developments make high-throughput engineering of crop RuBisCO possible. RuBisCO requires a complex chaperone network for proper assembly and function 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 ability to recombinantly produce plant RuBisCO outside of plant chloroplasts by reconstructing this chaperone network in Escherichia coli (E. coli). Whitney has now established that the RuBisCO enzymes from a range of agriculturally relevant crops, including potato, carrot, strawberry, and tobacco, can also be expressed using this technology. Whitney and Wilson have further developed a range of RuBisCO-dependent E. coli screens that can identify improved RuBisCO from complex gene libraries. Moreover, 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 can accelerate the steps of natural evolution simultaneously in an uninterrupted cycle in the lab, allowing for rapid testing of protein sequences. While Shoulders and Badran both have prior experience with cutting-edge directed evolution platforms, this will be the first time directed evolution is applied to RuBisCO from plants.

    Artificial intelligence is changing the 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 new chemical functionalities on the properties of RuBisCO. Bryson will employ artificial intelligence and machine learning to search the RuBisCO activity landscape for optimal sequences. The computational and biological arms of the EPiC platform will work together to both validate and inform each other’s approaches to accelerate the overall engineering effort.

    Shoulders and the group will deploy their designed enzymes in tobacco plants to evaluate 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 Nicotiana benthamianaI, where transient expression can be deployed. Transient expression is a speedy approach to test whether novel engineered RuBisCO variants can be correctly synthesized in leaf chloroplasts. Variants that pass this quality-control checkpoint at MIT will be passed to the Whitney Lab at the Australian National University for stable transformation into Nicotiana tabacum (tobacco), enabling robust measurements of photosynthetic improvement. In a final step, Professor Long at the University of Illinois at Urbana-Champaign will perform field trials of the most promising variants.

    Even small improvements could have a big impact

    A common criticism of efforts to improve RuBisCO is that natural evolution has not already identified a better enzyme, possibly implying that none will be found. Traditional views have speculated a catalytic trade-off between RuBisCO’s specificity factor for CO2 / O2 versus its CO2 fixation efficiency, leading to the belief that specificity factor improvements might be offset by even slower carbon fixation or vice versa. This trade-off has been suggested to explain why natural evolution has been slow to achieve a better 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 fact that Wilson and Whitney have previously used directed evolution to improve CO2 fixation efficiency by 50 percent in RuBisCO from cyanobacteria (the ancient progenitors of plant chloroplasts) while simultaneously 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 aspects 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 close to such an improvement and it translates to crops, the results could help transform agriculture,” Shoulders says. “If our accomplishments are more modest, it will still recruit massive new investments to this essential field.”

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

    “Our collaborative team of biochemists and synthetic biologists, computational biologists, and chemists is deeply integrated with plant biologists and field trial experts, yielding a robust feedback loop for enzyme engineering,” Shoulders adds. “Together, this team will be able to make a concerted effort using the most modern, state-of-the-art techniques to engineer crop RuBisCO with an eye to helping make meaningful gains in securing a stable crop supply, hopefully with accompanying improvements in both food and water security.” More

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      MIT Climate and Sustainability Consortium announces recipients of inaugural MCSC Seed Awards

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      The MIT Climate and Sustainability Consortium (MCSC) has awarded 20 projects a total of $5 million over two years in its first-ever 2022 MCSC Seed Awards program. The winning projects are led by principal investigators across all five of MIT’s schools.

      The goal of the MCSC Seed Awards is to engage MIT researchers and link the economy-wide work of the consortium to ongoing and emerging climate and sustainability efforts across campus. The program offers further opportunity to build networks among the awarded projects to deepen the impact of each and ensure the total is greater than the sum of its parts.

      For example, to drive progress under the awards category Circularity and Materials, the MCSC can facilitate connections between the technologists at MIT who are developing recovery approaches for metals, plastics, and fiber; the urban planners who are uncovering barriers to reuse; and the engineers, who will look for efficiency opportunities in reverse supply chains.

      “The MCSC Seed Awards are designed to complement actions previously outlined in Fast Forward: MIT’s Climate Action Plan for the Decade and, more specifically, the Climate Grand Challenges,” says Anantha P. Chandrakasan, dean of the MIT School of Engineering, Vannevar Bush Professor of Electrical Engineering and Computer Science, and chair of the MIT Climate and Sustainability Consortium. “In collaboration with seed award recipients and MCSC industry members, we are eager to engage in interdisciplinary exploration and propel urgent advancements in climate and sustainability.” 

      By supporting MIT researchers with expertise in economics, infrastructure, community risk assessment, mobility, and alternative fuels, the MCSC will accelerate implementation of cross-disciplinary solutions in the awards category Decarbonized and Resilient Value Chains. Enhancing Natural Carbon Sinks and building connections to local communities will require associations across experts in ecosystem change, biodiversity, improved agricultural practice and engagement with farmers, all of which the consortium can begin to foster through the seed awards.

      “Funding opportunities across campus has been a top priority since launching the MCSC,” says Jeremy Gregory, MCSC executive director. “It is our honor to support innovative teams of MIT researchers through the inaugural 2022 MCSC Seed Awards program.”

      The winning projects are tightly aligned with the MCSC’s areas of focus, which were derived from a year of highly engaged collaborations with MCSC member companies. The projects apply across the member’s climate and sustainability goals.

      The MCSC’s 16 member companies span many industries, and since early 2021, have met with members of the MIT community to define focused problem statements for industry-specific challenges, identify meaningful partnerships and collaborations, and develop clear and scalable priorities. Outcomes from these collaborations laid the foundation for the focus areas, which have shaped the work of the MCSC. Specifically, the MCSC Industry Advisory Board engaged with MIT on key strategic directions, and played a critical role in the MCSC’s series of interactive events. These included virtual workshops hosted last summer, each on a specific topic that allowed companies to work with MIT and each other to align key assumptions, identify blind spots in corporate goal-setting, and leverage synergies between members, across industries. The work continued in follow-up sessions and an annual symposium.

      “We are excited to see how the seed award efforts will help our member companies reach or even exceed their ambitious climate targets, find new cross-sector links among each other, seek opportunities to lead, and ripple key lessons within their industry, while also deepening the Institute’s strong foundation in climate and sustainability research,” says Elsa Olivetti, the Esther and Harold E. Edgerton Associate Professor in Materials Science and Engineering and MCSC co-director.

      As the seed projects take shape, the MCSC will provide ongoing opportunities for awardees to engage with the Industry Advisory Board and technical teams from the MCSC member companies to learn more about the potential for linking efforts to support and accelerate their climate and sustainability goals. Awardees will also have the chance to engage with other members of the MCSC community, including its interdisciplinary Faculty Steering Committee.

      “One of our mantras in the MCSC is to ‘amplify and extend’ existing efforts across campus; we’re always looking for ways to connect the collaborative industry relationships we’re building and the work we’re doing with other efforts on campus,” notes Jeffrey Grossman, the Morton and Claire Goulder and Family Professor in Environmental Systems, head of the Department of Materials Science and Engineering, and MCSC co-director. “We feel the urgency as well as the potential, and we don’t want to miss opportunities to do more and go faster.”

      The MCSC Seed Awards complement the Climate Grand Challenges, a new initiative to mobilize the entire MIT research community around developing the bold, interdisciplinary solutions needed to address difficult, unsolved climate problems. The 27 finalist teams addressed four broad research themes, which align with the MCSC’s focus areas. From these finalist teams, five flagship projects were announced in April 2022.

      The parallels between MCSC’s focus areas and the Climate Grand Challenges themes underscore an important connection between the shared long-term research interests of industry and academia. The challenges that some of the world’s largest and most influential companies have identified are complementary to MIT’s ongoing research and innovation — highlighting the tremendous opportunity to develop breakthroughs and scalable solutions quickly and effectively. Special Presidential Envoy for Climate John Kerry underscored the importance of developing these scalable solutions, including critical new technology, during a conversation with MIT President L. Rafael Reif at MIT’s first Climate Grand Challenges showcase event last month.

      Both the MCSC Seed Awards and the Climate Grand Challenges are part of MIT’s larger commitment and initiative to combat climate change; this was underscored in “Fast Forward: MIT’s Climate Action Plan for the Decade,” which the Institute published in May 2021.

      The project titles and research leads for each of the 20 awardees listed below are categorized by MCSC focus area.

      Decarbonized and resilient value chains

      “Collaborative community mapping toolkit for resilience planning,” led by Miho Mazereeuw, associate professor of architecture and urbanism in the Department of Architecture and director of the Urban Risk Lab (a research lead on Climate Grand Challenges flagship project) and Nicholas de Monchaux, professor and department head in the Department of Architecture
      “CP4All: Fast and local climate projections with scientific machine learning — towards accessibility for all of humanity,” led by Chris Hill, principal research scientist in the Department of Earth, Atmospheric and Planetary Sciences and Dava Newman, director of the MIT Media Lab and the Apollo Program Professor in the Department of Aeronautics and Astronautics
      “Emissions reductions and productivity in U.S. manufacturing,” led by Mert Demirer, assistant professor of applied economics at the MIT Sloan School of Management and Jing Li, assistant professor and William Barton Rogers Career Development Chair of Energy Economics in the MIT Sloan School of Management
      “Logistics electrification through scalable and inter-operable charging infrastructure: operations, planning, and policy,” led by Alex Jacquillat, the 1942 Career Development Professor and assistant professor of operations research and statistics in the MIT Sloan School of Management
      “Powertrain and system design for LOHC-powered long-haul trucking,” led by William Green, the Hoyt Hottel Professor in Chemical Engineering in the Department of Chemical Engineering and postdoctoral officer, and Wai K. Cheng, professor in the Department of Mechanical Engineering and director of the Sloan Automotive Laboratory
      “Sustainable Separation and Purification of Biochemicals and Biofuels using Membranes,” led by John Lienhard, the Abdul Latif Jameel Professor of Water in the Department of Mechanical Engineering, director of the Abdul Latif Jameel Water and Food Systems Lab, and director of the Rohsenow Kendall Heat Transfer Laboratory; and Nicolas Hadjiconstantinou, professor in the Department of Mechanical Engineering, co-director of the Center for Computational Science and Engineering, associate director of the Center for Exascale Simulation of Materials in Extreme Environments, and graduate officer
      “Toolkit for assessing the vulnerability of industry infrastructure siting to climate change,” led by Michael Howland, assistant professor in the Department of Civil and Environmental Engineering

      Circularity and Materials

      “Colorimetric Sulfidation for Aluminum Recycling,” led by Antoine Allanore, associate professor of metallurgy in the Department of Materials Science and Engineering
      “Double Loop Circularity in Materials Design Demonstrated on Polyurethanes,” led by Brad Olsen, the Alexander and I. Michael Kasser (1960) Professor and graduate admissions co-chair in the Department of Chemical Engineering, and Kristala Prather, the Arthur Dehon Little Professor and department executive officer in the Department of Chemical Engineering
      “Engineering of a microbial consortium to degrade and valorize plastic waste,” led by Otto Cordero, associate professor in the Department of Civil and Environmental Engineering, and Desiree Plata, the Gilbert W. Winslow (1937) Career Development Professor in Civil Engineering and associate professor in the Department of Civil and Environmental Engineering
      “Fruit-peel-inspired, biodegradable packaging platform with multifunctional barrier properties,” led by Kripa Varanasi, professor in the Department of Mechanical Engineering
      “High Throughput Screening of Sustainable Polyesters for Fibers,” led by Gregory Rutledge, the Lammot du Pont Professor in the Department of Chemical Engineering, and Brad Olsen, Alexander and I. Michael Kasser (1960) Professor and graduate admissions co-chair in the Department of Chemical Engineering
      “Short-term and long-term efficiency gains in reverse supply chains,” led by Yossi Sheffi, the Elisha Gray II Professor of Engineering Systems, professor in the Department of Civil and Environmental Engineering, and director of the Center for Transportation and Logistics
      The costs and benefits of circularity in building construction, led by Siqi Zheng, the STL Champion Professor of Urban and Real Estate Sustainability at the MIT Center for Real Estate and Department of Urban Studies and Planning, faculty director of the MIT Center for Real Estate, and faculty director for the MIT Sustainable Urbanization Lab; and Randolph Kirchain, principal research scientist and co-director of MIT Concrete Sustainability Hub

      Natural carbon sinks

      “Carbon sequestration through sustainable practices by smallholder farmers,” led by Joann de Zegher, the Maurice F. Strong Career Development Professor and assistant professor of operations management in the MIT Sloan School of Management, and Karen Zheng the George M. Bunker Professor and associate professor of operations management in the MIT Sloan School of Management
      “Coatings to protect and enhance diverse microbes for improved soil health and crop yields,” led by Ariel Furst, the Raymond A. (1921) And Helen E. St. Laurent Career Development Professor of Chemical Engineering in the Department of Chemical Engineering, and Mary Gehring, associate professor of biology in the Department of Biology, core member of the Whitehead Institute for Biomedical Research, and graduate officer
      “ECO-LENS: Mainstreaming biodiversity data through AI,” led by John Fernández, professor of building technology in the Department of Architecture and director of MIT Environmental Solutions Initiative
      “Growing season length, productivity, and carbon balance of global ecosystems under climate change,” led by Charles Harvey, professor in the Department of Civil and Environmental Engineering, and César Terrer, assistant professor in the Department of Civil and Environmental Engineering

      Social dimensions and adaptation

      “Anthro-engineering decarbonization at the million-person scale,” led by Manduhai Buyandelger, professor in the Anthropology Section, and Michael Short, the Class of ’42 Associate Professor of Nuclear Science and Engineering in the Department of Nuclear Science and Engineering
      “Sustainable solutions for climate change adaptation: weaving traditional ecological knowledge and STEAM,” led by Janelle Knox-Hayes, the Lister Brothers Associate Professor of Economic Geography and Planning and head of the Environmental Policy and Planning Group in the Department of Urban Studies and Planning, and Miho Mazereeuw, associate professor of architecture and urbanism in the Department of Architecture and director of the Urban Risk Lab (a research lead on a Climate Grand Challenges flagship project) More

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      in Environment

      Using plant biology to address climate change

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      On April 11, MIT announced five multiyear flagship projects in the first-ever Climate Grand Challenges, a new initiative to tackle complex climate problems and deliver breakthrough solutions to the world as quickly as possible. This article is the fourth in a five-part series highlighting the most promising concepts to emerge from the competition and the interdisciplinary research teams behind them.

      The impact of our changing climate on agriculture and food security — and how contemporary agriculture contributes to climate change — is at the forefront of MIT’s multidisciplinary project “Revolutionizing agriculture with low-emissions, resilient crops.” The project The project is one of five flagship winners in the Climate Grand Challenges competition, and brings together researchers from the departments of Biology, Biological Engineering, Chemical Engineering, and Civil and Environmental Engineering.

      “Our team’s research seeks to address two connected challenges: first, the need to reduce the greenhouse gas emissions produced by agricultural fertilizer; second, the fact that the yields of many current agricultural crops will decrease, due to the effects of climate change on plant metabolism,” says the project’s faculty lead, Christopher Voigt, the Daniel I.C. Wang Professor in MIT’s Department of Biological Engineering. “We are pursuing six interdisciplinary projects that are each key to our overall goal of developing low-emissions methods for fertilizing plants that are bioengineered to be more resilient and productive in a changing climate.”

      Whitehead Institute members Mary Gehring and Jing-Ke Weng, plant biologists who are also associate professors in MIT’s Department of Biology, will lead two of those projects.

      Promoting crop resilience

      For most of human history, climate change occurred gradually, over hundreds or thousands of years. That pace allowed plants to adapt to variations in temperature, precipitation, and atmospheric composition. However, human-driven climate change has occurred much more quickly, and crop plants have suffered: Crop yields are down in many regions, as is seed protein content in cereal crops.

      “If we want to ensure an abundant supply of nutritious food for the world, we need to develop fundamental mechanisms for bioengineering a wide variety of crop plants that will be both hearty and nutritious in the face of our changing climate,” says Gehring. In her previous work, she has shown that many aspects of plant reproduction and seed development are controlled by epigenetics — that is, by information outside of the DNA sequence. She has been using that knowledge and the research methods she has developed to identify ways to create varieties of seed-producing plants that are more productive and resilient than current food crops.

      But plant biology is complex, and while it is possible to develop plants that integrate robustness-enhancing traits by combining dissimilar parental strains, scientists are still learning how to ensure that the new traits are carried forward from one generation to the next. “Plants that carry the robustness-enhancing traits have ‘hybrid vigor,’ and we believe that the perpetuation of those traits is controlled by epigenetics,” Gehring explains. “Right now, some food crops, like corn, can be engineered to benefit from hybrid vigor, but those traits are not inherited. That’s why farmers growing many of today’s most productive varieties of corn must purchase and plant new batches of seeds each year. Moreover, many important food crops have not yet realized the benefits of hybrid vigor.”

      The project Gehring leads, “Developing Clonal Seed Production to Fix Hybrid Vigor,” aims to enable food crop plants to create seeds that are both more robust and genetically identical to the parent — and thereby able to pass beneficial traits from generation to generation.

      The process of clonal (or asexual) production of seeds that are genetically identical to the maternal parent is called apomixis. Gehring says, “Because apomixis is present in 400 flowering plant species — about 1 percent of flowering plant species — it is probable that genes and signaling pathways necessary for apomixis are already present within crop plants. Our challenge is to tweak those genes and pathways so that the plant switches reproduction from sexual to asexual.”

      The project will leverage the fact that genes and pathways related to autonomous asexual development of the endosperm — a seed’s nutritive tissue — exist in the model plant Arabidopsis thaliana. In previous work on Arabidopsis, Gehring’s lab researched a specific gene that, when misregulated, drives development of an asexual endosperm-like material. “Normally, that seed would not be viable,” she notes. “But we believe that by epigenetic tuning of the expression of additional relevant genes, we will enable the plant to retain that material — and help achieve apomixis.”

      If Gehring and her colleagues succeed in creating a gene-expression “formula” for introducing endosperm apomixis into a wide range of crop plants, they will have made a fundamental and important achievement. Such a method could be applied throughout agriculture to create and perpetuate new crop breeds able to withstand their changing environments while requiring less fertilizer and fewer pesticides.

      Creating “self-fertilizing” crops

      Roughly a quarter of greenhouse gas (GHG) emissions in the United States are a product of agriculture. Fertilizer production and use accounts for one third of those emissions and includes nitrous oxide, which has heat-trapping capacity 298-fold stronger than carbon dioxide, according to a 2018 Frontiers in Plant Science study. Most artificial fertilizer production also consumes huge quantities of natural gas and uses minerals mined from nonrenewable resources. After all that, much of the nitrogen fertilizer becomes runoff that pollutes local waterways. For those reasons, this Climate Grand Challenges flagship project aims to greatly reduce use of human-made fertilizers.

      One tantalizing approach is to cultivate cereal crop plants — which account for about 75 percent of global food production — capable of drawing nitrogen from metabolic interactions with bacteria in the soil. Whitehead Institute’s Weng leads an effort to do just that: genetically bioengineer crops such as corn, rice, and wheat to, essentially, create their own fertilizer through a symbiotic relationship with nitrogen-fixing microbes.

      “Legumes such as bean and pea plants can form root nodules through which they receive nitrogen from rhizobia bacteria in exchange for carbon,” Weng explains. “This metabolic exchange means that legumes release far less greenhouse gas — and require far less investment of fossil energy — than do cereal crops, which use a huge portion of the artificially produced nitrogen fertilizers employed today.

      “Our goal is to develop methods for transferring legumes’ ‘self-fertilizing’ capacity to cereal crops,” Weng says. “If we can, we will revolutionize the sustainability of food production.”

      The project — formally entitled “Mimicking legume-rhizobia symbiosis for fertilizer production in cereals” — will be a multistage, five-year effort. It draws on Weng’s extensive studies of metabolic evolution in plants and his identification of molecules involved in formation of the root nodules that permit exchanges between legumes and nitrogen-fixing bacteria. It also leverages his expertise in reconstituting specific signaling and metabolic pathways in plants.

      Weng and his colleagues will begin by deciphering the full spectrum of small-molecule signaling processes that occur between legumes and rhizobium bacteria. Then they will genetically engineer an analogous system in nonlegume crop plants. Next, using state-of-the-art metabolomic methods, they will identify which small molecules excreted from legume roots prompt a nitrogen/carbon exchange from rhizobium bacteria. Finally, the researchers will genetically engineer the biosynthesis of those molecules in the roots of nonlegume plants and observe their effect on the rhizobium bacteria surrounding the roots.

      While the project is complex and technically challenging, its potential is staggering. “Focusing on corn alone, this could reduce the production and use of nitrogen fertilizer by 160,000 tons,” Weng notes. “And it could halve the related emissions of nitrous oxide gas.” More

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      in Environment

      How molecular biology could reduce global food insecurity

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      Staple crops like rice, maize, and wheat feed over half of the global population, but they are increasingly vulnerable to severe environmental risks. The effects of climate change, including changing temperatures, rainfall variability, shifting patterns of agricultural pests and diseases, and saltwater intrusion from sea-level rise, all contribute to decreased crop yields. As these effects continue to worsen, there will be less food available for a rapidly growing population. 

      Mary Gehring, associate professor of biology and a member of the Whitehead Institute for Biomedical Research, is growing increasingly concerned about the potentially catastrophic impacts of climate change and has resolved to do something about it.

      The Gehring Lab’s primary research focus is plant epigenetics, which refers to the heritable information that influences plant cellular function but is not encoded in the DNA sequence itself. This research is adding to our fundamental understanding of plant biology and could have agricultural applications in the future. “I’ve been working with seeds for many years,” says Gehring. “Understanding how seeds work is going to be critical to agriculture and food security,” she explains.

      Laying the foundation

      Gehring is using her expertise to help crops develop climate resilience through a 2021 seed grant from MIT’s Abdul Latif Jameel Water and Food Systems Lab (J-WAFS). Her research is aimed at discovering how we can accelerate the production of genetic diversity to generate plant populations that are better suited to challenging environmental conditions.

      Genetic variation gives rise to phenotypic variations that can help plants adapt to a wider range of climates. Traits such as flood resistance and salt tolerance will become more important as the effects of climate change are realized. However, many important plant species do not appear to have much standing genetic variation, which could become an issue if farmers need to breed their crops quickly to adapt to a changing climate. 

      In researching a nutritious crop that has little genetic variation, Gehring came across the pigeon pea, a species she had never worked with before. Pigeon peas are a legume eaten in Asia, Africa, and Latin America. They have some of the highest levels of protein in a seed, so eating more pigeon peas could decrease our dependence on meat, which has numerous negative environmental impacts. Pigeon peas also have a positive impact on the environment; as perennial plants, they live for three to five years and sequester carbon for longer periods of time. They can also help with soil restoration. “Legumes are very interesting because they’re nitrogen-fixers, so they create symbioses with microbes in the soil and fix nitrogen, which can renew soils,” says Gehring. Furthermore, pigeon peas are known to be drought-resistant, so they will likely become more attractive as many farmers transition away from water-intensive crops.

      Developing a strategy

      Using the pigeon pea plant, Gehring began to explore a universal technology that would increase the amount of genetic diversity in plants. One method her research group chose is to enhance transposable element proliferation. Genomes are made up of genes that make proteins, but large fractions are also made up of transposable elements. In fact, about 45 percent of the human genome is made up of transposable elements, Gehring notes. The primary function of transposable elements is to make more copies of themselves. Since our bodies do not need an infinite number of these copies, there are systems in place to “silence” them from copying. 

      Gehring is trying to reverse that silencing so that the transposable elements can move freely throughout the genome, which could create genetic variation by creating mutations or altering the promoter of a gene — that is, what controls a certain gene’s expression. Scientists have traditionally initiated mutagenesis by using a chemical that changes single base pairs in DNA, or by using X-rays, which can cause very large chromosome breaks. Gehring’s research team is attempting to induce transposable element proliferation by treatment with a suite of chemicals that inhibit transposable element silencing. The goal is to impact multiple sites in the genome simultaneously. “This is unexplored territory where you’re changing 50 genes at a time, or 100, rather than just one,” she explains. “It’s a fairly risky project, but sometimes you have to be ambitious and take risks.”

      Looking forward

      Less than one year after receiving the J-WAFS seed grant, the research project is still in its early stages. Despite various restrictions due to the ongoing pandemic, the Gehring Lab is now generating data on the Arabidopsis plant that will be applied to pigeon pea plants. However, Gehring expects it will take a good amount of time to complete this research phase, considering the pigeon pea plants can take upward of 100 days just to flower. While it might take time, this technology could help crops withstand the effects of climate change, ultimately contributing to J-WAFS’ goal of finding solutions to food system challenges.

      “Climate change is not something any of us can ignore. … If one of us has the ability to address it, even in a very small way, that’s important to try to pursue,” Gehring remarks. “It’s part of our responsibility as scientists to take what knowledge we have and try to apply it to these sorts of problems.” More