Duration: 10/01/2027 to 09/30/2032

Administrative Advisor(s):

NIFA Reps:

Non-Technical Summary

Statement of Issues and Justification

Necessity of Photosynthesis Research

Photosynthesis is one of the most important biological processes on Earth. Photosynthetic organisms use light as an energy source to reduce carbon dioxide to carbohydrates and release oxygen as a byproduct through water oxidation. Importantly, humankind and majority of animals depend on oxygen in the air. Equally, process of photosynthesis provides a means to supply food, feed, fiber, natural chemicals, and biofuel feedstocks. Directly, or indirectly, it is the source of all our food. Therefore, agricultural production is directly affected by limitations in the rate and yield of photosynthesis and the capacity to utilize fixed carbon (15, 17, 29). The efficiency of the process, even in the most productive crops, is well below the theoretical maximum, indicating opportunity for improvement. Other challenges are that feeding an exponentially growing global population, supplying sufficient energy to sustain this global population can or need to be addressed using photosynthetic organisms (8, 26). Therefore, the need for state-of the-art photosynthesis research to improve the efficiency and productivity of this process has never been more critical.

Collaborators participating in this regional project will place considerable focus on understanding and improving the response of photosynthesis to genetic, developmental and environmental factors that limit productivity. The research of the group spans all levels of organization, from the genetic, molecular and cellular levels through the leaf, whole plant, and canopy. Particular emphasis will be placed on abiotic stresses (i.e., heat, cold, drought and salinity), nitrogen- and water-use efficiency, carbon flux pathways, and the signal transduction mechanisms that initiate plant responses, because these are critical to developing a robust agriculture (2). Factors that enhance or limit agricultural productivity generally do so by impacting photosynthesis. The gains in yield of the major crops over the past half-century have come about primarily from breeding for greater harvest index and through management, particularly the application of fertilizer (8). Yield potential is determined by light availability, light capture, energy conversion, and plant architecture. For our major crops, energy conversion to biomass falls far below the maximum potential, primarily limited by photosynthetic efficiency (29). Therefore, photosynthetic capacity and efficiency are bottlenecks to further raising productivity. Future yield gains will depend on increasing total production with the use of biotechnology to improve the basic efficiency of the photosynthetic process (17). A detailed understanding of the conversion of energy captured to chemical form for the synthesis and utilization of organic molecules will inform engineering of improved photosynthesis. For maximum benefit, the efficiency of photosynthesis must also be resilient to changes in temperature, CO₂, and water availability.

 

Importance and Consequences

Extreme weather events diminish the yields of major crops used for the production of food, feed, fiber, and biofuels, posing threats to local and global sustainability (6). Sustaining the productivity of traditional crops will require improvements in the efficiency and resiliency of photosynthesis that go beyond traditional breeding and selection (17). Similarly, the development of novel feedstocks for biofuel/chemicals generation in a way that is sustainable, commercially-viable, not in competition with food production requires novel approaches and non-traditional crops, including algae and cyanobacteria (1, 20). Innovative thinking will be required beyond traditional agricultural systems and crops, to new systems dedicated to the production of biofuels and chemicals and into the origins of photosynthesis. Only a combined and vertically-integrated effort incorporating all aspects of photosynthetic biology will ensure that appropriate solutions can be found for some of these most pressing problems currently facing humanity. If we are to meet future agriculture challenges using sustainable methods, it is essential that holistic approaches based on a detailed understanding of photosynthesis processes be used to develop crops that can tolerate and adapt to dynamic environments. Failure to do so now will limit our future ability to produce sufficient food, feed, fiber, and fuel.

 

Technical Feasibility

Plant genomic research is being pushed to new boundaries, with long-read DNA sequencing technologies and genome resequencing enabling the capture of genetic variation in plant populations with the depth never seen before (23). Complementarily, progress has been achieved in the improvement of high-throughput phenotyping and its data processing with the use of AI (18, 21, 25, 27). Merging both of these technical advancements will accelerate unlocking information coded in plant genomes on complex photosynthetic processes. One of the recent examples is the use of the machine learning-enabled phenotyping of stomatal density to identify genes associated with water use efficiency (WUE) in sorghum (7). Moreover, with the wealth of genetic sequence and recent advances in protein structure prediction with the AI-driven AlphaFold platform, the gap in structural variability in non-model systems can be addressed (14). Our knowledge and analysis of primary metabolism of photosynthesis in plants and associated metabolic networks have advanced to levels that can enable the rational design of novel crops, for example, establishing crassulacean acid metabolism (CAM) in plants with C₃ or C₄ photosynthesis (28). The recent substantial advances in CRISPR/Cas like systems, such as prime and base editing, and discoveries of novel CRISPR-associated proteins will play a crucial role in precise genetic modifications for enhancing photosynthetic efficiency (5). However, matters like off-target effects and the lack of efficient delivery methods still need to be addressed. Moreover, photosynthesis is one of the most complex processes found in nature, requiring hundreds of genes and proteins, and multiple and overlapping levels of regulation. Thus, to enable rapid progress in basic discovery and to devise strategies for the improvement of photosynthesis in crops, facile model organisms such as Arabidopsis (24) or model microalgae and cyanobacteria such as Chlamydomonas (11) and Synechocystis (10) will have to be employed to quickly identify the most promising directions for photosynthetic pathway and crop productivity improvement. One of the recent examples is the use of a directed evolution study in cyanobacteria to identify beneficial substitutions in the codon region of a crucial protein for the photosystem II repair system (10). While tested in plants, this genetic modification led to better growth both under control and stress conditions. Following this guidance, collaboration with geneticists and breeders, associating traits with genomic regions of mapping populations can support marker-assisted selection (4, 9, 19). Such an integrated approach requires multifaceted expertise and, thus, will benefit from synergy derived from a multi-state investigator effort.

 

Multi State Effort

Providing a conceptual framework through the current project, this group of scientists, bringing together a complementary set of expertise, and others located throughout the US have already successfully made progress on understanding diverse aspects of photosynthesis. While global issues as laid out above will be addressed, practical solutions to these problems often have local solutions (e.g., by taking into account plant hardiness zones to which specific crop species are adapted). Continued effort by the current group will contribute towards these main goals while also enabling local solutions of particular value to the participating states. Partners in this undertaking are listed for each focus area below.

 

Likely Impacts

Efforts by the group are organized into four themes (Objectives). While the details and outcomes will be discussed below in the main body of the proposal, likely impacts falling under these themes can be briefly summarized as follows:

1. Strategies to optimize the assembly and function of the photosynthetic membrane. Chloroplasts are the organelles that perform photosynthesis in both plants and algae. Chloroplasts also contain a large number of enzymes, highlighting the role of this organelle as a primary biochemical production factory. As semi-autonomous organelles, chloroplasts do not function by themselves but rely on extensive communication with other organelles and compartments within the cell, and with the whole plant. The import of nuclear-encoded proteins or membrane lipids assembled at the endoplasmic reticulum provide two examples of such interactions (16, 22). Within the chloroplast, the capture and conversion of light energy by photosynthesis occurs at a specialized structure called the thylakoid membrane, which is itself dynamically remodeled in response to developmental and stress cues. The architectural dynamics of the stacked grana thylakoids are involved in regulating and maintaining photosynthetic efficiency. Studies will focus on how thylakoid membranes change their shape, the functional consequences of structural alterations, and effects of whole-plant stresses and developmental cues on the thylakoid membrane and chloroplast lipid changes. Likely impacts include detailed mechanistic understanding of how thylakoid membrane structural dynamics across multiple length scales, from protein landscape reorganization to grana architecture, regulate photosynthetic energy conversion and photoprotection in response to environmental cues; the identification of proteins and critical for lipid transport, thylakoid biogenesis and repair; the development of tools to assess chloroplast membrane connectivity and protein complex organization in intact plant tissue; and foundational knowledge informing strategies to engineer stress-resilient crops and bioinspired artificial photosynthetic systems (MI-ABR, WA-AES).

 

2. Photosynthetic Capture and Photorespiratory Release of CO₂. Photosynthetic carbon fixation and photorespiratory release of CO₂ have long been recognized as limitations to crop productivity. Carbon metabolism in photosynthesizing leaves involves the Calvin-Benson cycle but also other carbon fluxes. A more complete understanding of these carbon reactions will identify mechanisms leading to improved photosynthetic efficiency. The carboxylating and oxygenating enzyme, Rubisco, is central to these efforts. As temperature increases, photorespiratory pressure in C₃ plants increases due to decreased Rubisco specificity for CO₂ relative to O₂. However, the carboxylating activity of Rubisco is greater in C₄ and CAM photosynthetic pathways, relative to that in C₃ photosynthesis, despite the warmer ecozones these plants occupy. Understanding the gene expression regulation and regulatory network of C₄ and CAM metabolic activities is key to fully elucidate their evolutionary history for improved crop productivity. Additionally, the rates of photosynthesis in C₃, C₄, and CAM plants can be limited by the availability of CO₂ at the initial site of carboxylation. Understanding how leaf biochemical and anatomical traits influence the concentration of CO₂ at the site of carboxylation may guide strategies to increase photosynthetic rates. Studies will utilize genomic analysis, loss of function mutants, CO₂ isotope studies and metabolite analysis to understand carbon fluxes involved in C₄. Likely impacts include understanding factors regulating carbon fluxes in light-independent processes including effective CO₂ concentrations at carboxylation sites, the costs and benefits of ancillary carbon paths in photosynthesizing cells, and circadian regulation in C₃, C₄ and CAM photosynthesis, with application to crop improvement (NV-AES, WA-AES).

 

3. Mechanisms Regulating Photosynthate Partitioning. Plant productivity and crop yields are regulated by source-sink relationships, i.e., the capacity of plants to photosynthesize and convert the fixed carbon into harvestable sink organs (12).  Therefore, understanding of carbon partitioning regulation and its manipulation are essential not only to increase yield but also to “install” heterologous product formation in photosynthetic organisms.  This effort will contribute to breeding and engineering for commodity chemicals and specialty production that possess enhanced carbon flux to innate or new sinks, e.g., starch, oil and antioxidant products. Several related efforts are expected to have positive impacts on plant growth rates and yield. Starch is a central metabolite in both source and sink tissues (19). The “starch partitioning” project comprising genetic study to validate newly discovered FT1 allele that considerable explains variation in the leaf starch at grain fill, heading date, yield and biomass in wheat (19). FT1 allele, as well as additional key loci associated with leaf starch, will be converted to markers to assist selection in breeding programs to accelerate development of high-yielding cereals. Another approach seeks to evaluate how plastid-localized phosphorylase, Pho1, integrates starch metabolism (sink) with photosynthesis (source) via photosystem I redox properties (13). This will lead to information on mechanisms regulating photosynthate partitioning toward starch biosynthesis / accumulation.  Different variants of PHO1 will be synthesized to be expressed in rice for validation of their role in enhancing plant growth rates and grain yields. In addition, the contribution of non-foliar photosynthetic roles in producing seed biomass will be tested with the use of isotopic labeling and metabolic flux analysis. This work will define the role of non-leaf tissues in plant carbon partitioning and seed-filling processes. The “antioxidants enhancement project” investigates a strategy for enhancing crop productivity using an archaeal antioxidant molecule, coenzyme M (CoM). We have shown previously that foliar CoM application positively affects biomass yield in greenhouses (3). A variety of approaches will be tested to utilize CoM in agriculture, including development of a seed CoM coating technique and defining the strategies for expression of CoM in plants. The effect of CoM will be examined with the use of physiological and molecular tools. There is a strong potential to generate intellectual property that could contribute to the growing biotech industry. All of the above projects would benefit from the “fusion constructs” project, which will deliver a platform for overexpression of complete enzymatic pathways in heterologous systems. Output includes the ability to substantially enhance carbon partitioning toward a target pathway in biological systems and alleviate rate- and yield-limiting catalytic steps in the generation of renewable specialty and commodity products, including agricultural bioproducts, via the process of photosynthesis. Likely impacts include the definition of the mechanisms that regulate photosynthate partitioning into the biosynthetic pathways for sucrose, starch, lipids, and antioxidants. The effect of innate or heterologous sink strength on rates and capacity of photosynthesis will be assessed in each case. The above comprises an integrated approach to understanding carbon partitioning and its effect on product synthesis and accumulation (CA-AES, MO-ARS, MT-AES, NE-ARD, WA-AES).

 

4. Strategies to overcome limitations to photosynthetic, plant management, developmental, and environmental factors. Environmental stresses place major limitations on photosynthesis. These stresses, ranging from high light and excess salinity to phosphorus deficiency, drought, and heat, greatly affect photosynthesis and plant productivity. Moreover, leaf stomata, which dictate photosynthetic productivity by acting as the "gateway" for CO₂ influx, are subject to complex regulation and impose considerable limitations on photosynthesis under stress. Studies in this area will focus on understanding and developing solutions to these key environmental stress limitations. In terms of heat stress, work will investigate how photosynthetic cells respond to high temperatures across a spectrum of organisms from algae to crops, including species with unique adaptations such as CAM that enables photosynthesis in extremely water-limited environments. This research will explore the genetic mechanisms of heat stress tolerance across photosynthetic organisms (including algae and CAM plants) and examine how heat stress on pollen limits seed crop productivity and survival during heat waves. Drought stress is a major contributor to declines in photosynthesis and frequently occurs in combination with heat stress. Using soybean as a model system, we will focus on identifying genetic loci that underpin light reactions and gas exchange responses to combined drought and heat stress. The regulation of stomata is one of the most critical factors influencing plant tolerance to both drought and heat, as well as the photosynthetic response to a wide range of other environmental stressors. Consequently, we will place considerable focus on understanding stomatal regulation by the environment. This includes investigating the evolution of stomatal control, analyzing how stomatal response speed and dynamics influence yield at a population level, and modifying stomatal regulation to minimize limitations on photosynthesis under well-watered conditions. Activities in Objective 4 will be integrated with those of Objective 3 to provide a more holistic perspective on photosynthate partitioning as defined by genetic and environmental stress conditions. Likely impacts include a deeper understanding of the effects of abiotic stress on carbon fluxes, the development of genomic tools for crop improvement, and the creation of novel genetic resources for xeric conditions (IN-AES, IL-AES, FL-AES, NV-AES, MT-AES, MO-AES, NE-ARD).

 

Project alignment with the new USDA Science Priorities  

Throughout four objectives, our project will utilize integrated and holistic approaches to identify strategies to improve photosynthesis as a means of enhancing the machinery of food, fiber and bioenergy production. Crops with improved photosynthesis will increase Farmers' and Ranchers' Profitability (USDA Science Priority #1) through higher yields and better use of resources, including water and fertilizers. Specifically, work on stomatal regulation, CAM physiology and CO₂ fluxes will inform strategies to increase water-use efficiency to Promote Soil Health to Regenerate Long-Term Productivity of Land (USDA science Priority #4). Identifying strategies to manipulate photosynthate partitioning in Objective #3 will allow development of nutrient-rich crops for Improving Human Health through Precision Nutrition and Food Quality (USDA Science Priority #5) and installation of heterologous product formation in plants and algae for Expanding Markets and Creating New Uses of U.S. Agricultural Products (USDA Science Priority #2).

 

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3. Brown, J. H., Vijayan, J., Rodrigues de Queiroz, A. et al. 2025. Coenzyme M: an archaeal antioxidant as an agricultural biostimulant. Antioxidants. 14(2), 140.
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Related, Current and Previous Work

Objectives

1. Identify strategies to optimize the assembly and function of the photosynthetic membrane.
   
2. Identify strategies to modify biochemical and regulatory factors that impact the photosynthetic capture and photorespiratory release of CO2.
   
3. Identify strategies to manipulate photosynthate partitioning.
   
4. Develop strategies to overcome limitations to photosynthetic, plant management, developmental, and environmental factors.
   

Methods

Measurement of Progress and Results

Outputs

Outcomes or Projected Impacts

Milestones

Projected Participation

View Participation Form/Appendix E: Participation

Outreach Plan

Organization/Governance

Literature Cited

Attachments

Land Grant Participating States/Institutions

CA, DE, FL, HI, IL, IN, KS, MI, MO, MT, NE, NV, NY, WA, WI

Non Land Grant Participating States/Institutions

Danforth Plant Science Center