Photorespiration

Effects of Vibrio parahaemolyticus on physiology and metabolism of Thalassiosira weissflogii in the co-culture system

Diatoms are crucial primary producers in the marine environment, and their interactions with bacteria exert an important role in the ecosystem. There has been scarce research exploring how diatoms adapt to algal-bacterial environments. In this study, we investigated the physiological and transcriptional distinctions of Thalassiosira weissflogii when grown alone (axenic) and with the bacteria Vibrio parahaemolyticus (co-culture). Although the bacteria did not significantly impact the growth of T. weissflogii, they did affect its photosynthetic efficiency and pigment biosynthesis. The balance of carbon and nitrogen metabolism, as well as energy pathways, including the tricarboxylic acid cycle and glycolysis, was also disrupted. T. weissflogii might be capable of maintaining normal growth by upregulating cell cycle-related proteins and utilizing certain bacterial metabolites, such as indole-3-acetic acid. Moreover, T. weissflogii reinforced its cell wall in response to V. parahaemolyticus infection by increasing chitin biosynthesis and inhibiting chitinase activity. This study explored the effects of Vibrio on diatoms from a molecular and metabolic perspective and provided a comprehensive overview of metabolism variations. The results indicate the significant impacts of algal-bacterial interactions on primary producers and offer new insights into the environmental adaptations of diatoms.

IMPORTANCE

The significance of this study lies in its contribution to filling the knowledge gap regarding the interactions between diatoms and pathogenic Vibrio. Although extensive research has been conducted on either diatoms or bacteria separately, the mechanisms by which bacteria influence diatom physiological functions and ecosystem processes remain underexplored. Our study reveals that Vibrio can significantly alter diatom photosynthesis efficiency and gene expression patterns, providing new insights into how microbial interactions affect element cycling and primary production in marine ecosystems. These findings may have important implications for marine aquaculture, environmental monitoring, and related fields.

Engineering of photorespiration-dependent glycine betaine biosynthesis improves photosynthetic carbon fixation and panicle architecture in rice

In C3 plants, photorespiration is an energy expensive pathway that competes with photosynthetic CO2 assimilation and releases CO2 into the atmosphere, potentially reducing C3 plant productivity by 20%-50%. Consequently, reducing the flux through photorespiration has been recognized as a major way to improve C3 crop photosynthetic carbon fixation and productivity. While current research efforts in engineering photorespiration are mainly based on the modification of chloroplast glycolate metabolic steps, only limited studies have explored optimizations in other photorespiratory metabolic steps. Here, we engineered an imGS bypass within the rice mitochondria to bypass the photorespiratory glycine toward glycine betaine, thereby, improving the photosynthetic carbon fixation in rice. The imGS transgenic rice plants exhibited significant accumulation of glycine betaine, reduced photorespiration, and elevated photosynthesis and photosynthate levels. Additionally, the introduction of imGS bypass into rice leads to an increase in the number of branches and grains per panicle which may be related to cytokinin and gibberellin signaling pathways. Taken together, these results suggest diverting mitochondrial glycine from photorespiration toward glycine betaine synthesis can effectively enhance carbon fixation and panicle architecture in rice, offering a promising strategy for developing functional mitochondrial photorespiratory bypasses with the potential to enhance plant productivity.

Nitrogen source type modulates heat stress response in coral symbiont (Cladocopium goreaui)

Ocean warming due to climate change endangers coral reefs, and regional nitrogen overloading exacerbates the vulnerability of reef-building corals as the dual stress disrupts coral-Symbiodiniaceae mutualism. Different forms of nitrogen may create different interactive effects with thermal stress, but the underlying mechanisms remain elusive. To address the gap, we measured and compared the physiological and transcriptional responses of the Symbiodiniaceae Cladocopium goreaui to heat stress (31°C) when supplied with different types of nitrogen (nitrate, ammonium, or urea). Under heat stress (HS), cell proliferation and photosynthesis of C. goreaui declined, while cell size, lipid storage, and total antioxidant capacity increased, both to varied extents depending on the nitrogen type. Nitrate-cultured cells exhibited the most robust acclimation to HS, as evidenced by the fewest differentially expressed genes (DEGs) and less ROS accumulation, possibly due to activated nitrate reduction and enhanced ascorbate biogenesis. Ammonium-grown cultures exhibited higher algal proliferation and ROS scavenging capacity due to enhanced carotenoid and ascorbate quenching, but potentially reduced host recognizability due to the downregulation of N-glycan biosynthesis genes. Urea utilization led to the greatest ROS accumulation as genes involved in photorespiration, plant respiratory burst oxidase (RBOH), and protein refolding were markedly upregulated, but the greatest cutdown in photosynthate potentially available to corals as evidenced by photoinhibition and selfish lipid storage, indicating detrimental effects of urea overloading. The differential warming nitrogen-type interactive effects documented here has significant implication in coral-Symbiodiniaceae mutualism, which requires further research.IMPORTANCERegional nitrogen pollution exacerbates coral vulnerability to globally rising sea-surface temperature, with different nitrogen types exerting different interactive effects. How this occurs is poorly understood and understudied. This study explored the underlying mechanism by comparing physiological and transcriptional responses of a coral symbiont to heat stress under different nitrogen supplies (nitrate, ammonium, and urea). The results showed some common, significant responses to heat stress as well as some unique, N-source dependent responses. These findings underscore that nitrogen eutrophication is not all the same, the form of nitrogen pollution should be considered in coral conservation, and special attention should be given to urea pollution.

Strategies for adaptation to high light in plants

Plants absorb light energy for photosynthesis via photosystem complexes in their chloroplasts. However, excess light can damage the photosystems and decrease photosynthetic output, thereby inhibiting plant growth and development. Plants have developed a series of light acclimation strategies that allow them to withstand high light. In the first line of defense against excess light, leaves and chloroplasts move away from the light and the plant accumulates compounds that filter and reflect the light. In the second line of defense, known as photoprotection, plants dissipate excess light energy through non-photochemical quenching, cyclic electron transport, photorespiration, and scavenging of excess reactive oxygen species. In the third line of defense, which occurs after photodamage, plants initiate a cycle of photosystem (mainly photosystem II) repair. In addition to being the site of photosynthesis, chloroplasts sense stress, especially light stress, and transduce the stress signal to the nucleus, where it modulates the expression of genes involved in the stress response. In this review, we discuss current progress in our understanding of the strategies and mechanisms employed by plants to withstand high light at the whole-plant, cellular, physiological, and molecular levels across the three lines of defense.

Photosynthesis: Genetic Strategies Adopted to Gain Higher Efficiency

The global challenge of feeding an ever-increasing population to maintain food security requires novel approaches to increase crop yields. Photosynthesis, the fundamental energy and material basis for plant life on Earth, is highly responsive to environmental conditions. Evaluating the operational status of the photosynthetic mechanism provides insights into plants' capacity to adapt to their surroundings. Despite immense effort, photosynthesis still falls short of its theoretical maximum efficiency, indicating significant potential for improvement. In this review, we provide background information on the various genetic aspects of photosynthesis, explain its complexity, and survey relevant genetic engineering approaches employed to improve the efficiency of photosynthesis. We discuss the latest success stories of gene-editing tools like CRISPR-Cas9 and synthetic biology in achieving precise refinements in targeted photosynthesis pathways, such as the Calvin-Benson cycle, electron transport chain, and photorespiration. We also discuss the genetic markers crucial for mitigating the impact of rapidly changing environmental conditions, such as extreme temperatures or drought, on photosynthesis and growth. This review aims to pinpoint optimization opportunities for photosynthesis, discuss recent advancements, and address the challenges in improving this critical process, fostering a globally food-secure future through sustainable food crop production.

Enhancing Photosynthesis and Plant Productivity through Genetic Modification

Enhancing crop photosynthesis through genetic engineering technologies offers numerous opportunities to increase plant productivity. Key approaches include optimizing light utilization, increasing cytochrome b6f complex levels, and improving carbon fixation. Modifications to Rubisco and the photosynthetic electron transport chain are central to these strategies. Introducing alternative photorespiratory pathways and enhancing carbonic anhydrase activity can further increase the internal CO2 concentration, thereby improving photosynthetic efficiency. The efficient translocation of photosynthetically produced sugars, which are managed by sucrose transporters, is also critical for plant growth. Additionally, incorporating genes from C4 plants, such as phosphoenolpyruvate carboxylase and NADP-malic enzymes, enhances the CO2 concentration around Rubisco, reducing photorespiration. Targeting microRNAs and transcription factors is vital for increasing photosynthesis and plant productivity, especially under stress conditions. This review highlights potential biological targets, the genetic modifications of which are aimed at improving photosynthesis and increasing plant productivity, thereby determining key areas for future research and development.

Impacts of Drought on Photosynthesis in Major Food Crops and the Related Mechanisms of Plant Responses to Drought

Drought stress is one of the most critical threats to crop productivity and global food security. This review addresses the multiple effects of drought on the process of photosynthesis in major food crops. Affecting both light-dependent and light-independent reactions, drought leads to severe damage to photosystems and blocks the electron transport chain. Plants face a CO2 shortage provoked by stomatal closure, which triggers photorespiration; not only does it reduce carbon fixation efficiency, but it also causes lower overall photosynthetic output. Drought-induced oxidative stress generates reactive oxygen species (ROS) that damage cellular structures, including chloroplasts, further impairing photosynthetic productivity. Plants have evolved a variety of adaptive strategies to alleviate these effects. Non-photochemical quenching (NPQ) mechanisms help dissipate excess light energy as heat, protecting the photosynthetic apparatus under drought conditions. Alternative electron pathways, such as cyclical electron transmission and chloroplast respiration, maintain energy balance and prevent over-reduction of the electron transport chain. Hormones, especially abscisic acid (ABA), ethylene, and cytokinin, modulate stomatal conductance, chlorophyll content, and osmotic adjustment, further increasing the tolerance to drought. Structural adjustments, such as leaf reordering and altered root architecture, also strengthen tolerance. Understanding these complex interactions and adaptive strategies is essential for developing drought-resistant crop varieties and ensuring agricultural sustainability.

Evaluating bio-physicochemical properties of raw powder prepared from whole larvae containing liquid silk of the domestic silkworm

The domestic silkworm, Bombyx mori, has been widely used in silk production for centuries. It is also used as a bioreactor by the textile and pharmaceutical industries to mass produce recombinant bioactive proteins containing silk-based materials. Furthermore, silkworms are well-known as a source of food and have also been orally administered to prevent and treat several human disorders. In this study, we aimed to investigate the inherent bio-physicochemical properties of edible silkworms to accurately evaluate their clinical and nutritional potential. We prepared raw powder from whole larvae of silkworm. The yield rate of the powder derived from dried larvae was almost 100% (98.1-99.1% in replicates). As "percentage yield" translates to "Budomari" in Japanese, this raw powder was named "B100rw." We further prepared B100dn that was denatured through autoclaving. Thereafter, we examined whether B100rw sustained the original bio-physicochemical properties by comparing it with B100dn. There was no significant difference in nutritional content between B100rw and B100dn. B100rw contained proteins derived from silkworm larvae and mulberry leaves, whereas the proteins of B100dn were mostly degraded. On measuring the enzymatic activity of both powders using trehalase as an indicator enzyme, B100rw was found to maintain trehalase activity. B100rw also maintained a random coil conformation, similar to that of liquid silk. This suggested that B100rw sustained the unique bio-physicochemical properties of living larvae. These findings may facilitate the development of novel food products or orally administered vaccines.

The serine-glycine-one-carbon metabolic network orchestrates changes in nitrogen and sulfur metabolism and shapes plant development

L-serine (Ser) and L-glycine (Gly) are critically important for the overall functioning of primary metabolism. We investigated the interaction of the phosphorylated pathway of Ser biosynthesis (PPSB) with the photorespiration-associated glycolate pathway of Ser biosynthesis (GPSB) using Arabidopsis thaliana PPSB-deficient lines, GPSB-deficient mutants, and crosses of PPSB with GPSB mutants. PPSB-deficient lines mainly showed retarded primary root growth. Mutation of the photorespiratory enzyme Ser-hydroxymethyltransferase 1 (SHMT1) in a PPSB-deficient background resumed primary root growth and induced a change in the plant metabolic pattern between roots and shoots. Grafting experiments demonstrated that metabolic changes in shoots were responsible for the changes in double mutant development. PPSB disruption led to a reduction in nitrogen (N) and sulfur (S) contents in shoots and a general transcriptional response to nutrient deficiency. Disruption of SHMT1 boosted the Gly flux out of the photorespiratory cycle, which increased the levels of the one-carbon (1C) metabolite 5,10-methylene-tetrahydrofolate and S-adenosylmethionine. Furthermore, disrupting SHMT1 reverted the transcriptional response to N and S deprivation and increased N and S contents in shoots of PPSB-deficient lines. Our work provides genetic evidence of the biological relevance of the Ser-Gly-1C metabolic network in N and S metabolism and in interorgan metabolic homeostasis.

Identification and Functional Characterization of cis-Regulatory Elements of Key Photorespiratory Genes in Response to Short-Term Abiotic Stress Conditions

The cis-regulatory elements (CREs) are the short stretches of noncoding DNA upstream of a gene, which play a critical role in fine-tuning gene expression. Photorespiration is a multi-organellar, energy-expensive biochemical process that remains intricately linked to photosynthesis and is conserved in plants. Recently, much focus has been devoted in generating plants with engineered alternative photorespiratory bypasses to enhance photosynthetic efficiency without compromising the beneficial aspect of photorespiration. Varied constitutive or inducible promoters for generating transgenic plants harboring multiple transgenes have been introduced over years; however, most of them suffer from unintended effects. Consequently, a demand for synthetic tunable promoters based on canonical CRE signatures derived from native genes is on the rise. Here, in this chapter, we have provided a detailed method for in silico identification and characterization of CREs associated with photorespiration. In addition to the detailed protocol, we have presented an example of a typical result and explained the significance of the result. Specifically, the method covers how to identify and generate tunable synthetic promoters based on native CREs using three key photorespiratory genes from Arabidopsis and two web-based tools, namely, PlantPAN3.0 and AthaMap. Finally, we have also furnished a protocol on how to test the efficacies of the synthetic promoters harboring predicted CREs using transient tobacco expression coupled with luciferase-based promoter assay in response to ambient conditions and under short-term abiotic stress conditions.

Glycolate oxidase gene family identification and functional analyses in cotton resistance to Verticillium wilt

Glycolate oxidase (GOX) plays an important role in the regulation of photorespiration and photosynthesis in plants. However, as one of the main enzymes to produce the second messenger hydrogen peroxide (H2O2), its functions in response to pathogens are still poorly understood. In this study, we carried out genome-wide identification, and 14 GOX genes were identified in Gossypium hirsutum. These GOX genes are located on 10 chromosomes and divided into hydroxyacid-oxidases (HAOX) and GOX groups. After infection with Verticillium dahliae Kleb., six GOX gene expression levels were changed. Moreover, H2O2, salicylic acid (SA), and the content and activity of GOX increased in cotton. GhHAOX2-D-silenced plants showed more wilting than control plants after infection with V. dahliae. Additionally, H2O2 accumulation and SA content were reduced in GhHAOX2-D-silenced plants. The expression levels of GhPAL, GhPAD4, and GhPR1 and the lignin content of the silenced plants were significantly lower than those of the control plants. These results indicate that GhHAOX2-D is a positive regulator of Verticillium wilt tolerance in cotton and may promote H2O2 accumulation via the synergistic effects of GOX genes and SA. Collectively, GOX genes play an important role in cotton resistance to Verticillium wilt.

A synthetic light-inducible photorespiratory bypass enhances photosynthesis to improve rice growth and grain yield

Bioengineering of photorespiratory bypasses is an effective strategy for improving plant productivity by modulating photosynthesis. In previous work, two photorespiratory bypasses, the GOC and GCGT bypasses, increased photosynthetic rates but decreased seed-setting rate in rice (Oryza sativa), probably owing to excess photosynthate accumulation in the stem. To solve this bottleneck, we successfully developed a new synthetic photorespiratory bypass (called the GMA bypass) in rice chloroplasts by introducing Oryza sativa glycolate oxidase 1 (OsGLO1), Cucurbita maxima malate synthase (CmMS), and Oryza sativa ascorbate peroxidase7 (OsAPX7) into the rice genome using a high-efficiency transgene stacking system. Unlike the GOC and GCGT bypass genes driven by constitutive promoters, OsGLO1 in GMA plants was driven by a light-inducible Rubisco small subunit promoter (pRbcS); its expression dynamically changed in response to light, producing a more moderate increase in photosynthate. Photosynthetic rates were significantly increased in GMA plants, and grain yields were significantly improved under greenhouse and field conditions. Transgenic GMA rice showed no reduction in seed-setting rate under either test condition, unlike previous photorespiratory-bypass rice, probably reflecting proper modulation of the photorespiratory bypass. Together, these results imply that appropriate engineering of the GMA bypass can enhance rice growth and grain yield without affecting seed-setting rate.

Photorespiration: regulation and new insights on the potential role of persulfidation

Photorespiration has been considered a 'futile' cycle in C3 plants, necessary to detoxify and recycle the metabolites generated by the oxygenating activity of Rubisco. However, several reports indicate that this metabolic route plays a fundamental role in plant metabolism and constitutes a very interesting research topic. Many open questions still remain with regard to photorespiration. One of these questions is how the photorespiratory process is regulated in plants and what factors contribute to this regulation. In this review, we summarize recent advances in the regulation of the photorespiratory pathway with a special focus on the transcriptional and post-translational regulation of photorespiration and the interconnections of this process with nitrogen and sulfur metabolism. Recent findings on sulfide signaling and protein persulfidation are also described.

3-Alkyl-2-Methoxypyrazines: Overview of Their Occurrence, Biosynthesis and Distribution in Edible Plants

Pyrazines are ubiquitous in nature - biosynthesized by microorganisms, insects, and plants. Due to their great structural diversity, they own manifold biological functions. Alkyl- and alkoxypyrazines for instance play a key role as semiochemicals, but also as important aroma compounds in foods. Especially 3-alkyl-2-methoxypyrazines (MPs) have been of great research interest. MPs are associated with green and earthy attributes. They are responsible for the distinctive aroma properties of numerous vegetables. Moreover, they have a strong influence on the aroma of wines, in which they are primarily grape-derived. Over the years various methods have been developed and implemented to analyse the distribution of MPs in plants. In addition, the biosynthetic pathway of MPs has always been of particular interest. Different pathways and precursors have been proposed and controversially discussed in the literature. While the identification of genes encoding O-methyltransferases gave important insights into the last step of MP-biosynthesis, earlier biosynthetic steps and precursors remained unknown. It was not until 2022 that in vivo feeding experiments with stable isotope labeled compounds revealed l-leucine and l-serine as important precursors for IBMP. This discovery gave evidence for a metabolic interface between the MP-biosynthesis and photorespiration.

Growth and fatty acid distribution over lipid classes in Nannochloropsis oceanica acclimated to different temperatures

After light, temperature is the most relevant environmental parameter in outdoors cultivation of microalgae. Suboptimal and supraoptimal temperatures negatively impact growth and photosynthetic performance with a subsequent effect on lipid accumulation. It is generally recognised that lower temperatures trigger an increase in fatty acid desaturation while higher temperatures trigger the opposite reaction. The effect of temperature on lipid classes has been less studied in microalgae and in certain cases, the effect of light cannot be completely excluded. In this research, the effect of temperature on growth, photosynthesis, and lipid class accumulation in Nannochloropsis oceanica was studied at a fixed light gradient with a constant incident light intensity (670 μmol m^-2 s^-1). A turbidostat approach was used to achieve temperature acclimated cultures of Nannochloropsis oceanica. Optimal growth was found at 25-29°C, while growth was completely arrested at temperatures higher than 31°C and lower than 9°C. Acclimation to low temperatures triggered a decrease in absorption cross section and photosynthesis rates with a tipping point at 17°C. Reduced light absorption was correlated with a decrease in content of the plastid lipids monogalactosyldiacylglycerol and sulfoquinovosyldiacylglycerol. The increase of diacylglyceryltrimethylhomo-serine content at lower temperatures indicated a relevant role of this lipid class in temperature tolerance. Triacylglycerol content increased at 17°C and decreased at 9°C emphasising a metabolic switch in stress response. Total and polar eicosapentaenoic acid content remained constant at 3.5 and 2.4% w/w, despite the fluctuating lipid contents. Results show an extensive mobilisation of eicosapentaenoic acid between polar lipids classes at 9°C to ensure cell survival under critical conditions.

Energetic considerations for engineering novel biochemistries in photosynthetic organisms

Humans have been harnessing biology to make valuable compounds for generations. From beer and biofuels to pharmaceuticals, biology provides an efficient alternative to industrial processes. With the continuing advancement of molecular tools to genetically modify organisms, biotechnology is poised to solve urgent global problems related to environment, increasing population, and public health. However, the light dependent reactions of photosynthesis are constrained to produce a fixed stoichiometry of ATP and reducing equivalents that may not match the newly introduced synthetic metabolism, leading to inefficiency or damage. While photosynthetic organisms have evolved several ways to modify the ATP/NADPH output from their thylakoid electron transport chain, it is unknown if the native energy balancing mechanisms grant enough flexibility to match the demands of the synthetic metabolism. In this review we discuss the role of photosynthesis in the biotech industry, and the energetic considerations of using photosynthesis to power synthetic biology.

Enhancing crop yields through improvements in the efficiency of photosynthesis and respiration

The rate with which crop yields per hectare increase each year is plateauing at the same time that human population growth and other factors increase food demand. Increasing yield potential (Y p ) of crops is vital to address these challenges. In this review, we explore a component ofY p that has yet to be optimised - that being improvements in the efficiency with which light energy is converted into biomass (ε c ) via modifications to CO2 fixed per unit quantum of light (α), efficiency of respiratory ATP production (ε prod ) and efficiency of ATP use (ε use ). For α, targets include changes in photoprotective machinery, ribulose bisphosphate carboxylase/oxygenase kinetics and photorespiratory pathways. There is also potential forε prod to be increased via targeted changes to the expression of the alternative oxidase and mitochondrial uncoupling pathways. Similarly, there are possibilities to improveε use via changes to the ATP costs of phloem loading, nutrient uptake, futile cycles and/or protein/membrane turnover. Recently developed high-throughput measurements of respiration can serve as a proxy for the cumulative energy cost of these processes. There are thus exciting opportunities to use our growing knowledge of factors influencing the efficiency of photosynthesis and respiration to create a step-change in yield potential of globally important crops.

Role of C4 photosynthetic enzyme isoforms in C3 plants and their potential applications in improving agronomic traits in crops

As compared to C3, C4 plants have higher photosynthetic rates and better tolerance to high temperature and drought. These traits are highly beneficial in the current scenario of global warming. Interestingly, all the genes of the C4 photosynthetic pathway are present in C3 plants, although they are involved in diverse non-photosynthetic functions. Non-photosynthetic isoforms of carbonic anhydrase (CA), phosphoenolpyruvate carboxylase (PEPC), malate dehydrogenase (MDH), the decarboxylating enzymes NAD/NADP-malic enzyme (NAD/NADP-ME), and phosphoenolpyruvate carboxykinase (PEPCK), and finally pyruvate orthophosphate dikinase (PPDK) catalyze reactions that are essential for major plant metabolism pathways, such as the tricarboxylic acid (TCA) cycle, maintenance of cellular pH, uptake of nutrients and their assimilation. Consistent with this view differential expression pattern of these non-photosynthetic C3 isoforms has been observed in different tissues across the plant developmental stages, such as germination, grain filling, and leaf senescence. Also abundance of these C3 isoforms is increased considerably in response to environmental fluctuations particularly during abiotic stress. Here we review the vital roles played by C3 isoforms of C4 enzymes and the probable mechanisms by which they help plants in acclimation to adverse growth conditions. Further, their potential applications to increase the agronomic trait value of C3 crops is discussed.

Progress and prospects of C4 trait engineering in plants

Incorporating C₄ photosynthetic traits into C₃ crops is a rational approach for sustaining future demands for crop productivity. Using classical plant breeding, engineering this complex trait is unlikely to achieve its target. Therefore, it is critical and timely to implement novel biotechnological crop improvement strategies to accomplish this goal. However, a fundamental understanding of C₃ , C₄ , and C₃ -C₄ intermediate metabolism is crucial for the targeted use of biotechnological tools. This review assesses recent progress towards engineering C₄ photosynthetic traits in C₃ crops. We also discuss lessons learned from successes and failures of recent genetic engineering attempts in C₃ crops, highlighting the pros and cons of using rice as a model plant for short-, medium- and long-term goals of genetic engineering. This review provides an integrated approach towards engineering improved photosynthetic efficiency in C₃ crops for sustaining food, fibre and fuel production around the globe.

Cytokinin Deficiency Alters Leaf Proteome and Metabolome during Effector-Triggered Immunity in Arabidopsis thaliana Plants

The involvement of cytokinins (CK) in biotic stresses has been recognized, while knowledge regarding the effects of CK deficiency on plant response against pathogens is less abundant. Thus, the purpose of this study was to reveal the effects of CK deficiency on proteomics and metabolomic responses of flg22-triggered immunity. We conducted a series of histochemical assays to investigate the activity of the downstream pathways caused by flg22, such as accumulation of ROS, induction of defence genes, and callose deposition, that occurred in Arabidopsis thaliana transgenic lines overexpressing the Hordeum vulgare CKX2 gene (HvCKX2), which are therefore CK-deficient. We also used GC and LC-MS-based technology to quantify variations in stress hormone levels and metabolomic and proteomic responses in flg22-treated HvCKX2 and wild-type Arabidopsis plants. We found that CK deficiency alters the flg22-triggered plant defence response, especially through induction of callose deposition, upregulation of defence response-related proteins, increased amino acid biosynthesis, and regulation of plant photosynthesis. We also indicated that JA might be an important contributor to immune response in plants deficient in CKs. The present study offers new evidence on the fundamental role of endogenous CK in the response to pathogens, as well as the possibility of altering plant biotic tolerance by manipulating CK pools.

Biosynthetic approaches to efficient assimilation of CO2via photorespiration modification in plant chassis

Plant chassis has emerged as the platform with great potential for bioproduction of high value-added products such as recombinant protein, vaccine and natural product. However, as the primary metabolic pathway, photorespiration results in the loss of photosynthetically fixed carbon compounds and limits the exploration of plant chassis. People are endeavored to reduce the photorespiration energy or carbon loss based on variation screening or genetic engineering. Insomuch as protein engineering of Rubisco has not resulted in the significant improvement of Rubisco specificity which is linked to the direct CO2 fixation, the biosynthetic approaches of photorespiration bypass are gaining much more attention and manifested great potentiality in conferring efficient assimilation of CO2 in plant chassis. In this review, we summarize the recent studies on the metabolic pathway design and implementation of photorespiration alternative pathway aiming to provide clues to efficiently enhance carbon fixation via the modification of photorespiration in plant chassis for bioproduction. These will benefit the development of plant synthetic metabolism for biorefineries via improvement of artificial carbon sequestration cycle, particularly for the mitigation of serious challenges such as extreme climate change, food and energy shortages in the future.

Mitochondrial and peroxisomal NAD+ uptake are important for improved photosynthesis and seed yield under elevated CO2 concentrations

As sessile organisms, plants must adapt their physiology and developmental processes to cope with challenging environmental circumstances, such as the ongoing elevation in atmospheric carbon dioxide (CO₂ ) levels. Nicotinamide adenine dinucleotide (NAD⁺ ) is a cornerstone of plant metabolism and plays an essential role in redox homeostasis. Given that plants impaired in NAD metabolism and transport often display growth defects, low seed production and disturbed stomatal development/movement, we hypothesized that subcellular NAD distribution could be a candidate for plants to exploit the effects of CO₂ fertilization. We report that an efficient subcellular NAD⁺ distribution is required for the fecundity-promoting effects of elevated CO₂ levels. Plants with reduced expression of either mitochondrial (NDT1 or NDT2) or peroxisomal (PXN) NAD⁺ transporter genes grown under elevated CO₂ exhibited reduced total leaf area compared with the wild-type while PXN mutants also displayed reduced leaf number. NDT2 and PXN lines grown under elevated CO₂ conditions displayed reduced rosette dry weight and lower photosynthetic rates coupled with reduced stomatal conductance. Interestingly, high CO₂ doubled seed production and seed weight in the wild-type, whereas the mutants were less responsive to increases in CO₂ levels during reproduction, producing far fewer seeds than the wild-type under both CO₂ conditions. These data highlight the importance of mitochondrial and peroxisomal NAD⁺ uptake mediated by distinct NAD transporter proteins to modulate photosynthesis and seed production under high CO₂ levels.

From Soil Amendments to Controlling Autophagy: Supporting Plant Metabolism under Conditions of Water Shortage and Salinity

Crop resistance to environmental stress is a major issue. The globally increasing land degradation and desertification enhance the demand on management practices to balance both food and environmental objectives, including strategies that tighten nutrient cycles and maintain yields. Agriculture needs to provide, among other things, future additional ecosystem services, such as water quantity and quality, runoff control, soil fertility maintenance, carbon storage, climate regulation, and biodiversity. Numerous research projects have focused on the food–soil–climate nexus, and results were summarized in several reviews during the last decades. Based on this impressive piece of information, we have selected only a few aspects with the intention of studying plant–soil interactions and methods for optimization. In the short term, the use of soil amendments is currently attracting great interest to cover the current demand in agriculture. We will discuss the impact of biochar at water shortage, and plant growth promoting bacteria (PGPB) at improving nutrient supply to plants. In this review, our focus is on the interplay of both soil amendments on primary reactions of photosynthesis, plant growth conditions, and signaling during adaptation to environmental stress. Moreover, we aim at providing a general overview of how dehydration and salinity affect signaling in cells. With the use of the example of abscisic acid (ABA) and ethylene, we discuss the effects that can be observed when biochar and PGPB are used in the presence of stress. The stress response of plants is a multifactorial trait. Nevertheless, we will show that plants follow a general concept to adapt to unfavorable environmental conditions in the short and long term. However, plant species differ in the upper and lower regulatory limits of gene expression. Therefore, the presented data may help in the identification of traits for future breeding of stress-resistant crops. One target for breeding could be the removal and efficient recycling of damaged as well as needless compounds and structures. Furthermore, in this context, we will show that autophagy can be a useful goal of breeding measures, since the recycling of building blocks helps the cells to overcome a period of imbalanced substrate supply during stress adjustment.

ATTED-II v11: A Plant Gene Coexpression Database Using a Sample Balancing Technique by Subagging of Principal Components

ATTED-II (https://atted.jp) is a gene coexpression database for nine plant species based on publicly available RNAseq and microarray data. One of the challenges in constructing condition-independent coexpression data based on publicly available gene expression data is managing the inherent sampling bias. Here, we report ATTED-II version 11, wherein we adopted a coexpression calculation methodology to balance the samples using principal component analysis and ensemble calculation. This approach has two advantages. First, omitting principal components with low contribution rates reduces the main contributors of noise. Second, balancing large differences in contribution rates enables considering various sample conditions entirely. In addition, based on RNAseq- and microarray-based coexpression data, we provide species-representative, integrated coexpression information to enhance the efficiency of interspecies comparison of the coexpression data. These coexpression data are provided as a standardized z-score to facilitate integrated analysis with different data sources. We believe that with these improvements, ATTED-II is more valuable and powerful for supporting interspecies comparative studies and integrated analyses using heterogeneous data.

Gene co-expression reveals the modularity and integration of C4 and CAM in Portulaca

C4 photosynthesis and Crassulacean acid metabolism (CAM) have been considered as largely independent adaptations despite sharing key biochemical modules. Portulaca is a geographically widespread clade of over 100 annual and perennial angiosperm species that primarily use C4 but facultatively exhibit CAM when drought stressed, a photosynthetic system known as C4 + CAM. It has been hypothesized that C4 + CAM is rare because of pleiotropic constraints, but these have not been deeply explored. We generated a chromosome-level genome assembly of Portulaca amilis and sampled mRNA from P. amilis and Portulaca oleracea during CAM induction. Gene co-expression network analyses identified C4 and CAM gene modules shared and unique to both Portulaca species. A conserved CAM module linked phosphoenolpyruvate carboxylase to starch turnover during the day-night transition and was enriched in circadian clock regulatory motifs in the P. amilis genome. Preservation of this co-expression module regardless of water status suggests that Portulaca constitutively operate a weak CAM cycle that is transcriptionally and posttranscriptionally upregulated during drought. C4 and CAM mostly used mutually exclusive genes for primary carbon fixation, and it is likely that nocturnal CAM malate stores are shuttled into diurnal C4 decarboxylation pathways, but we found evidence that metabolite cycling may occur at low levels. C4 likely evolved in Portulaca through co-option of redundant genes and integration of the diurnal portion of CAM. Thus, the ancestral CAM system did not strongly constrain C4 evolution because photosynthetic gene networks are not co-regulated for both daytime and nighttime functions.

Image-Based Analysis Revealing the Molecular Mechanism of Peroxisome Dynamics in Plants

Peroxisomes are present in eukaryotic cells and have essential roles in various biological processes. Plant peroxisomes proliferate by de novo biosynthesis or division of pre-existing peroxisomes, degrade, or replace metabolic enzymes, in response to developmental stages, environmental changes, or external stimuli. Defects of peroxisome functions and biogenesis alter a variety of biological processes and cause aberrant plant growth. Traditionally, peroxisomal function-based screening has been employed to isolate Arabidopsis thaliana mutants that are defective in peroxisomal metabolism, such as lipid degradation and photorespiration. These analyses have revealed that the number, subcellular localization, and activity of peroxisomes are closely related to their efficient function, and the molecular mechanisms underlying peroxisome dynamics including organelle biogenesis, protein transport, and organelle interactions must be understood. Various approaches have been adopted to identify factors involved in peroxisome dynamics. With the development of imaging techniques and fluorescent proteins, peroxisome research has been accelerated. Image-based analyses provide intriguing results concerning the movement, morphology, and number of peroxisomes that were hard to obtain by other approaches. This review addresses image-based analysis of peroxisome dynamics in plants, especially A. thaliana and Marchantia polymorpha.

HPR1 Is Required for High Light Intensity Induced Photorespiration in Arabidopsis thaliana

High light intensity as one of the stresses could lead to generation of large amounts of reactive oxygen species (ROS) in plants, resulting in severe plant growth retardation. The photorespiration metabolism plays an important role in producing and removing a variety of ROS, maintaining the dynamic balance of the redox reaction, and preventing photoinhibition. Arabidopsis hydroxypyruvate reductase 1 (HPR1) is a primary metabolic enzyme in the photorespiration cycle. However, the role of HPR1 in plants response to high light is not clear. Here, we found that the expression of HPR1 could be induced by high light intensity. The growth and photosynthetic capacity of hpr1 mutants are seriously affected under high light intensity. The absence of HPR1 suppresses the rates of photorepair of Photosystem II (PSII), aggravates the production of ROS, and accelerates photorespiration rates. Moreover, the activity of ROS scavenging enzymes in the hpr1 mutants is significantly higher. These results indicate that HPR1 is involved in plant response to high light intensity and is essential for maintaining the dynamic balance of ROS and photorespiration.

Elucidation of Triacylglycerol Overproduction in the C4 Bioenergy Crop Sorghum bicolor by Constraint-Based Analysis

Upregulation of triacylglycerols (TAGs) in vegetative plant tissues such as leaves has the potential to drastically increase the energy density and biomass yield of bioenergy crops. In this context, constraint-based analysis has the promise to improve metabolic engineering strategies. Here we present a core metabolism model for the C4 biomass crop Sorghum bicolor (iTJC1414) along with a minimal model for photosynthetic CO2 assimilation, sucrose and TAG biosynthesis in C3 plants. Extending iTJC1414 to a four-cell diel model we simulate C4 photosynthesis in mature leaves with the principal photo-assimilatory product being replaced by TAG produced at different levels. Independent of specific pathways and per unit carbon assimilated, energy content and biosynthetic demands in reducing equivalents are about 1.3 to 1.4 times higher for TAG than for sucrose. For plant generic pathways, ATP- and NADPH-demands per CO2 assimilated are higher by 1.3- and 1.5-fold, respectively. If the photosynthetic supply in ATP and NADPH in iTJC1414 is adjusted to be balanced for sucrose as the sole photo-assimilatory product, overproduction of TAG is predicted to cause a substantial surplus in photosynthetic ATP. This means that if TAG synthesis was the sole photo-assimilatory process, there could be an energy imbalance that might impede the process. Adjusting iTJC1414 to a photo-assimilatory rate that approximates field conditions, we predict possible daily rates of TAG accumulation, dependent on varying ratios of carbon partitioning between exported assimilates and accumulated oil droplets (TAG, oleosin) and in dependence of activation of futile cycles of TAG synthesis and degradation. We find that, based on the capacity of leaves for photosynthetic synthesis of exported assimilates, mature leaves should be able to reach a 20% level of TAG per dry weight within one month if only 5% of the photosynthetic net assimilation can be allocated into oil droplets. From this we conclude that high TAG levels should be achievable if TAG synthesis is induced only during a final phase of the plant life cycle.

Protein lipoylation in mitochondria requires Fe-S cluster assembly factors NFU4 and NFU5

Plants have evolutionarily conserved NifU (NFU)-domain proteins that are targeted to plastids or mitochondria. "Plastid-type" NFU1, NFU2, and NFU3 in Arabidopsis (Arabidopsis thaliana) play a role in iron-sulfur (Fe-S) cluster assembly in this organelle, whereas the type-II NFU4 and NFU5 proteins have not been subjected to mutant studies in any plant species to determine their biological role. Here, we confirmed that NFU4 and NFU5 are targeted to the mitochondria. The proteins were constitutively produced in all parts of the plant, suggesting a housekeeping function. Double nfu4 nfu5 knockout mutants were embryonic lethal, and depletion of NFU4 and NFU5 proteins led to growth arrest of young seedlings. Biochemical analyses revealed that NFU4 and NFU5 are required for lipoylation of the H proteins of the glycine decarboxylase complex and the E2 subunits of other mitochondrial dehydrogenases, with little impact on Fe-S cluster-containing respiratory complexes or aconitase. Consequently, the Gly-to-Ser ratio was increased in mutant seedlings and early growth improved with elevated CO2 treatment. In addition, pyruvate, 2-oxoglutarate, and branched-chain amino acids accumulated in nfu4 nfu5 mutants, further supporting defects in the other three mitochondrial lipoate-dependent enzyme complexes. NFU4 and NFU5 interacted with mitochondrial lipoyl synthase (LIP1) in yeast 2-hybrid and bimolecular fluorescence complementation assays. These data indicate that NFU4 and NFU5 have a more specific function than previously thought, most likely providing Fe-S clusters to lipoyl synthase.

A chloroplast Glycolate catabolic pathway bypassing the endogenous photorespiratory cycle enhances photosynthesis, biomass and yield in rice (Oryza sativa L.)

Photorespiration accounts for 20-50 % reduction in grain yield in C₃ crops. The process is essential to remove 2-phosphoglycolate produced due to the oxygenation activity of the ribulose-1,5-bisphosphate carboxylase oxygenase (RuBisCO) enzyme. Attempts were made to improve photosynthesis through enriched CO₂ concentration by installing numerous photorespiratory bypass modules in the chloroplast of several crops. In this study, we have introduced Escherichia coli glycolate catabolic pathway (ECGC) into rice chloroplast to bypass photorespiration partially (PB) or completely (FB). Five genes encoding glyoxylate carboligase (GCL), tartronic semialdehyde reductase (TSR), and three subunits of glycolate dehydrogenase (GDH) were introduced to get FB plants, whereas only the three subunits of GDH were introduced to get PB plants. Southern analysis confirmed stable integration of the transgenes and their expression was confirmed by RT-qPCR analysis in the T3 progenies. Both FB and PB transformed lines exhibited increased photosynthetic efficiency, biomass, and grain yield than wild type (WT) with empty vector control. The introduction of ECGC pathway favoured the carboxylase activity of RuBisCO while decreasing its oxygenase activity fostering the functioning of Calvin-Benson cycle and resulting in an increased carbon-assimilation that was manifested in their superior architecture and harvest index. These findings will support rice and related cereal crop breeding programs to increase yield under elevated temperature and arid conditions.

Oxygen overload

A structure that helps algae photosynthesize when carbon dioxide levels are low may also play a role during hyperoxia conditions.

Improving photosynthesis through the enhancement of Rubisco carboxylation capacity

Rising human population, along with the reduction in arable land and the impacts of global change, sets out the need for continuously improving agricultural resource use efficiency and crop yield (CY). Bioengineering approaches for photosynthesis optimization have largely demonstrated the potential for enhancing CY. This review is focused on the improvement of Rubisco functioning, which catalyzes the rate-limiting step of CO2 fixation required for plant growth, but also catalyzes the ribulose-bisphosphate oxygenation initiating the carbon and energy wasteful photorespiration pathway. Rubisco carboxylation capacity can be enhanced by engineering the Rubisco large and/or small subunit genes to improve its catalytic traits, or by engineering the mechanisms that provide enhanced Rubisco expression, activation and/or elevated [CO2] around the active sites to favor carboxylation over oxygenation. Recent advances have been made in the expression, assembly and activation of foreign (either natural or mutant) faster and/or more CO2-specific Rubisco versions. Some components of CO2 concentrating mechanisms (CCMs) from bacteria, algae and C4 plants has been successfully expressed in tobacco and rice. Still, none of the transformed plant lines expressing foreign Rubisco versions and/or simplified CCM components were able to grow faster than wild type plants under present atmospheric [CO2] and optimum conditions. However, the results obtained up to date suggest that it might be achievable in the near future. In addition, photosynthetic and yield improvements have already been observed when manipulating Rubisco quantity and activation degree in crops. Therefore, engineering Rubisco carboxylation capacity continues being a promising target for the improvement in photosynthesis and yield.

Rubisco Adaptation Is More Limited by Phylogenetic Constraint Than by Catalytic Trade-off

Rubisco assimilates CO2 to form the sugars that fuel life on earth. Correlations between rubisco kinetic traits across species have led to the proposition that rubisco adaptation is highly constrained by catalytic trade-offs. However, these analyses did not consider the phylogenetic context of the enzymes that were analyzed. Thus, it is possible that the correlations observed were an artefact of the presence of phylogenetic signal in rubisco kinetics and the phylogenetic relationship between the species that were sampled. Here, we conducted a phylogenetically resolved analysis of rubisco kinetics and show that there is a significant phylogenetic signal in rubisco kinetic traits. We re-evaluated the extent of catalytic trade-offs accounting for this phylogenetic signal and found that all were attenuated. Following phylogenetic correction, the largest catalytic trade-offs were observed between the Michaelis constant for CO2 and carboxylase turnover (∼21-37%), and between the Michaelis constants for CO2 and O2 (∼9-19%), respectively. All other catalytic trade-offs were substantially attenuated such that they were marginal (<9%) or non-significant. This phylogenetically resolved analysis of rubisco kinetic evolution also identified kinetic changes that occur concomitant with the evolution of C4 photosynthesis. Finally, we show that phylogenetic constraints have played a larger role than catalytic trade-offs in limiting the evolution of rubisco kinetics. Thus, although there is strong evidence for some catalytic trade-offs, rubisco adaptation has been more limited by phylogenetic constraint than by the combined action of all catalytic trade-offs.

Identification of Key Metabolic Pathways and Biomarkers Underlying Flowering Time of Guar (Cyamopsis tetragonoloba (L.) Taub.) via Integrated Transcriptome-Metabolome Analysis

Guar (Cyamopsis tetragonoloba (L.) Taub.) is an annual legume crop native to India and Pakistan. Seeds of the plant serve as a source of galactomannan polysaccharide (guar gum) used in the food industry as a stabilizer (E412) and as a gelling agent in oil and gas fracturing fluids. There were several attempts to introduce this crop to countries of more northern latitudes. However, guar is a plant of a short photoperiod, therefore, its introduction, for example, to Russia is complicated by a long day length during the growing season. Breeding of new guar varieties insensitive to photoperiod slowed down due to the lack of information on functional molecular markers, which, in turn, requires information on guar genome. Modern breeding strategies, e.g., genomic predictions, benefit from integration of multi-omics approaches such as transcriptome, proteome and metabolome assays. Here we present an attempt to use transcriptome-metabolome integration to understand the genetic determination of flowering time variation among guar plants that differ in their photoperiod sensitivity. This study was performed on nine early- and six delayed-flowering guar varieties with the goal to find a connection between 63 metabolites and 1,067 differentially expressed transcripts using Shiny GAM approach. For the key biomarker of flowering in guar myo-inositol we also evaluated the KEGG biochemical pathway maps available for Arabidopsis thaliana. We found that the phosphatidylinositol signaling pathway is initiated in guar plants that are ready for flowering through the activation of the phospholipase C (PLC) gene, resulting in an exponential increase in the amount of myo-inositol in its free form observed on GC-MS chromatograms. The signaling pathway is performed by suppression of myo-inositol phosphate kinases (phosphorylation) and alternative overexpression of phosphatases (dephosphorylation). Our study suggests that metabolome and transcriptome information taken together, provide valuable information about biomarkers that can be used as a tool for marker-assisted breeding, metabolomics and functional genomics of this important legume crop.

Two plastidic glycolate/glycerate translocator 1 isoforms function together to transport photorespiratory glycolate and glycerate in rice chloroplasts

The photorespiratory pathway is highly compartmentalized. As such, metabolite shuttles between organelles are critical to ensure efficient photorespiratory carbon flux. Arabidopsis plastidic glycolate/glycerate translocator 1 (PLGG1) has been reported as a key chloroplastic glycolate/glycerate transporter. Two homologous genes, OsPLGG1a and OsPLGG1b, have been identified in the rice genome, although their distinct functions and relationships remain unknown. Herein, our analysis of exogenous expression in oocytes and yeast shows that both OsPLGG1a and OsPLGG1b have the ability to transport glycolate and glycerate. Furthermore, we demonstrate in planta that the perturbation of OsPLGG1a or OsPLGG1b expression leads to extensive accumulation of photorespiratory metabolites, especially glycolate and glycerate. Under ambient CO2 conditions, loss-of-function osplgg1a or osplgg1b mutant plants exhibited significant decreases in photosynthesis efficiency, starch accumulation, plant height, and crop productivity. These morphological defects were almost entirely recovered when the mutant plants were grown under elevated CO2 conditions. In contrast to osplgg1a, osplgg1b mutant alleles produced a mild photorespiratory phenotype and had reduced accumulation of photorespiratory metabolites. Subcellular localization analysis showed that OsPLGG1a and OsPLGG1b are located in the inner and outer membranes of the chloroplast envelope, respectively. In vitro and in vivo experiments revealed that OsPLGG1a and OsPLGG1b have a direct interaction. Our results indicate that both OsPLGG1a and OsPLGG1b are chloroplastic glycolate/glycerate transporters required for photorespiratory metabolism and plant growth, and that they may function as a singular complex.

Mitochondrial movement during its association with chloroplasts in Arabidopsis thaliana

Plant mitochondria move dynamically inside cells and this movement is classified into two types: directional movement, in which mitochondria travel long distances, and wiggling, in which mitochondria travel short distances. However, the underlying mechanisms and roles of both types of mitochondrial movement, especially wiggling, remain to be determined. Here, we used confocal laser-scanning microscopy to quantitatively characterize mitochondrial movement (rate and trajectory) in Arabidopsis thaliana mesophyll cells. Directional movement leading to long-distance migration occurred at high speed with a low angle-change rate, whereas wiggling leading to short-distance migration occurred at low speed with a high angle-change rate. The mean square displacement (MSD) analysis could separate these two movements. Directional movement was dependent on filamentous actin (F-actin), whereas mitochondrial wiggling was not, but slightly influenced by F-actin. In mesophyll cells, mitochondria could migrate by wiggling, and most of these mitochondria associated with chloroplasts. Thus, mitochondria migrate via F-actin-independent wiggling under the influence of F-actin during their association with chloroplasts in Arabidopsis.

Oikawa et al. investigate the rate and trajectory of mitochondria in Arabidopsis thaliana mesophyll cells, using confocal laser-scanning microscopy. They find that mitochondria migrate via wiggling during their association with chloroplasts, providing insights into how mitochondria-chloroplast interaction affects the movement of mitochondria.

Small Molecule-Based Enzyme Inhibitors in the Treatment of Primary Hyperoxalurias

Primary hyperoxalurias (PHs) are a group of inherited alterations of the hepatic glyoxylate metabolism. PHs classification based on gene mutations parallel a variety of enzymatic defects, and all involve the harmful accumulation of calcium oxalate crystals that produce systemic damage. These geographically widespread rare diseases have a deep impact in the life quality of the patients. Until recently, treatments were limited to palliative measures and kidney/liver transplants in the most severe forms. Efforts made to develop pharmacological treatments succeeded with the biotechnological agent lumasiran, a siRNA product against glycolate oxidase, which has become the first effective therapy to treat PH1. However, small molecule drugs have classically been preferred since they benefit from experience and have better pharmacological properties. The development of small molecule inhibitors designed against key enzymes of glyoxylate metabolism is on the focus of research. Enzyme inhibitors are successful and widely used in several diseases and their pharmacokinetic advantages are well known. In PHs, effective enzymatic targets have been determined and characterized for drug design and interesting inhibitory activities have been achieved both in vitro and in vivo. This review describes the most recent advances towards the development of small molecule enzyme inhibitors in the treatment of PHs, introducing the multi-target approach as a more effective and safe therapeutic option.

Optimizing Sensor-Based Irrigation Management in a Soilless Vertical Farm for Growing Microgreens

With water resources constantly becoming scarcer, and 70% of freshwater used for the agriculture sector, there is a growing need for innovative methods to increase water use efficiency (WUE) of food production systems and provide nutrient-dense food to an increasing population. Sensor technology has recently been introduced to the horticulture industry to increase resource use efficiency and minimize the environmental impacts of excessive water use. Identifying the effects of irrigation levels on crop performance is crucial for the success of sensor-based water management. This research aimed to optimize WUE in a soilless microgreen production system through identification of an optimal irrigation level using a sensor that could facilitate the development of a more efficient, low-cost automated irrigation system. A dielectric moisture sensor was implemented to monitor water levels at five irrigation setpoints: 7.5, 17.5, 25, 30, and 35 percent of the effective volume of the container (EVC) during a 14-day growth cycle. To validate the sensor performance, the same irrigation levels were applied to a parallel trial, without sensor, and water levels were monitored gravimetrically. Plant water status and stress reaction were evaluated using infrared thermal imaging, and the accumulation of osmolytes (proline) was determined. Results showed that, proline concentration, canopy temperature (Tc), canopy temperature depression (CTD), and crop water stress index (CWSI) increased at 7.5% EVC in both sensor-based and gravimetric treatments, and infrared index (Ig) and fresh yield decreased. The dielectric moisture sensor was effective in increasing WUE. The irrigation level of 17.5% EVC was found to be optimal. It resulted in a WUE of 88 g/L, an improvement of 30% over the gravimetric method at the same irrigation level. Furthermore, fresh yield increased by 11.5%. The outcome of this study could contribute to the automation of precision irrigation in hydroponically grown microgreens.

A Synthetic Photorespiratory Shortcut Enhances Photosynthesis to Boost Biomass and Grain Yield in Rice

Several photorespiratory bypasses have been introduced into plants and shown to improve photosynthesis by increasing chloroplastic CO₂ concentrations or optimizing energy balance. We recently reported that an engineered GOC bypass could increase photosynthesis and productivity in rice. However, the grain yield of GOC plants was unstable, fluctuating in different cultivation seasons because of varying seed setting rates. In this study, we designed a synthetic photorespiratory shortcut (the GCGT bypass) consisting of genes encoding Oryza sativa glycolate oxidase and Escherichia coli catalase, glyoxylate carboligase, and tartronic semialdehyde reductase. The GCGT bypass was guided by an optimized chloroplast transit peptide that targeted rice chloroplasts and redirected 75% of carbon from glycolate metabolism to the Calvin cycle, identical to the native photorespiration pathway. GCGT transgenic plants exhibited significantly increased biomass production and grain yield, which were mainly attributed to enhanced photosynthesis due to increased chloroplastic CO₂ concentrations. Despite the increases in biomass production and grain yield, GCGT transgenic plants showed a reduced seed setting rate, a phenotype previously reported for the GOC plants. Integrative transcriptomic, physiological, and biochemical assays revealed that photosynthetic carbohydrates were not transported to grains in an efficient manner, thereby reducing the seed setting rate. Taken together, our results demonstrate that the GCGT photorespiratory shortcut confers higher yield by promoting photosynthesis in rice, mainly through increasing chloroplastic CO₂ concentrations.

A cyanobacterial photorespiratory bypass model to enhance photosynthesis by rerouting photorespiratory pathway in C3 plants

Plants employ photosynthesis to produce sugars for supporting their growth. During photosynthesis, an enzyme Ribulose 1,5 bisphosphate carboxylase/oxygenase (Rubisco) combines its substrate Ribulose 1,5 bisphosphate (RuBP) with CO2 to produce phosphoglycerate (PGA). Alongside, Rubisco also takes up O2 and produce 2-phosphoglycolate (2-PG), a toxic compound broken down into PGA through photorespiration. Photorespiration is not only a resource-demanding process but also results in CO2 loss which affects photosynthetic efficiency in C3 plants. Here, we propose to circumvent photorespiration by adopting the cyanobacterial glycolate decarboxylation pathway into C3 plants. For that, we have integrated the cyanobacterial glycolate decarboxylation pathway into a kinetic model of C3 photosynthetic pathway to evaluate its impact on photosynthesis and photorespiration. Our results show that the cyanobacterial glycolate decarboxylation bypass model exhibits a 10% increase in net photosynthetic rate (A) in comparison with C3 model. Moreover, an increased supply of intercellular CO2 (Ci) from the bypass resulted in a 54.8% increase in PGA while reducing photorespiratory intermediates including glycolate (- 49%) and serine (- 32%). The bypass model, at default conditions, also elucidated a decline in phosphate-based metabolites including RuBP (- 61.3%). The C3 model at elevated level of inorganic phosphate (Pi), exhibited a significant change in RuBP (+ 355%) and PGA (- 98%) which is attributable to the low availability of Ci. Whereas, at elevated Pi, the bypass model exhibited an increase of 73.1% and 33.9% in PGA and RuBP, respectively. Therefore, we deduce a synergistic effect of elevation in CO2 and Pi pool on photosynthesis. We also evaluated the integrative action of CO2, Pi, and Rubisco carboxylation activity (Vcmax) on A and observed that their simultaneous increase raised A by 26%, in the bypass model. Taken together, the study potentiates engineering of cyanobacterial decarboxylation pathway in C3 plants to bypass photorespiration thereby increasing the overall efficiency of photosynthesis.

Nitrogen assimilation and photosynthetic capacity of wheat genotypes under optimal and deficient nitrogen supply

The performance of two contrasting Bulgarian wheat varieties (Slomer, an old tall cultivar, and Enola, a modern semi-dwarf one) to nitrogen deficiency was compared by measuring biochemical parameters characterizing N uptake and assimilation as well as growth and photosynthetic activity of young seedlings. The old genotype displayed better photosynthetic capacity, higher N assimilation expressed by elevated amino acid synthesis and better overall performance under N limitation. This could be explained by the fact that selection of old varieties was performed mostly in environments with low nutrient availability and consequently these genotypes proved to be more suitable for growing on low-input conditions. Upon limiting N supply modern variety preferentially accumulated sugars while the old one retained higher amino acids levels. It was demonstrated that processes involved in N metabolism were tightly interrelated with photochemical reactions and carbon assimilation even at early developmental stage.

Methodology: an optimized, high-yield tomato leaf chloroplast isolation and stroma extraction protocol for proteomics analyses and identification of chloroplast co-localizing proteins

BACKGROUND

Chloroplasts are critical organelles that perceive and convey metabolic and stress signals to different cellular components, while remaining the seat of photosynthesis and a metabolic factory. The proteomes of intact leaves, chloroplasts, and suborganellar fractions of plastids have been evaluated in the model plant Arabidopsis, however fewer studies have characterized the proteomes of plastids in crops. Tomato (Solanum lycopersicum) is an important world-wide crop and a model system for the study of wounding, herbivory and fruit ripening. While significant advances have been made in understanding proteome and metabolome changes in fruit ripening, far less is known about the tomato chloroplast proteome or its subcompartments.

RESULTS

With the long-term goal of understanding chloroplast proteome dynamics in response to stress, we describe a high-yielding method to isolate intact tomato chloroplasts and stromal proteins for proteomic studies. The parameters that limit tomato chloroplast yields were identified and revised to increase yields. Compared to published data, our optimized method increased chloroplast yields by 6.7- and 4.3-fold relative to published spinach and Arabidopsis leaf protocols, respectively; furthermore, tomato stromal protein yields were up to 79-fold higher than Arabidopsis stromal proteins yields. We provide immunoblot evidence for the purity of the stromal proteome isolated using our enhanced methods. In addition, we leverage our nanoliquid chromatography tandem mass spectrometry (nanoLC-MS/MS) data to assess the quality of our stromal proteome. Using strict criteria, proteins detected by 1 peptide spectral match, by one peptide, or were sporadically detected were designated as low-level contaminating proteins. A set of 254 proteins that reproducibly co-isolated with the tomato chloroplast stroma were identified. The subcellular localization, frequency of detection, normalized spectral abundance, and functions of the co-isolating proteins are discussed.

CONCLUSIONS

Our optimized method for chloroplast isolation increased the yields of tomato chloroplasts eightfold enabling the proteomics analysis of the chloroplast stromal proteome. The set of 254 proteins that co-isolate with the chloroplast stroma provides opportunities for developing a better understanding of the extensive and dynamic interactions of chloroplasts with other organelles. These co-isolating proteins also have the potential for expanding our knowledge of proteins that are co-localized in multiple subcellular organelles.

Larix decidua and additional light affect the methane balance of forest soil and the abundance of methanogenic and methanotrophic microorganisms

Due to the activity of methane-oxidizing bacteria, forest soils are usually net sinks for the greenhouse gas methane (CH4). Despite several hints that CH4 balances might be influenced by vegetation, there are only few investigations dealing with this connection. Therefore, we studied this soil-plant-microbe interaction by using mesocosm experiments with forest soil and Larix decidua, a common coniferous tree species within the Alps. Gas measurements showed that the presence of L. decidua significantly reduced CH4 oxidation of the forest soil by ∼10% (-0.95 µmol m-2 h-1 for soil vs -0.85 µmol m-2 h-1 for soil plus L. decidua) leading to an increased net CH4 balance. Increased light intensity was used to intensify the influence of the plant on the soil's CH4 balance. The increase in light intensity strengthened the effect of the plant and led to a greater reduction of CH4 oxidation. Besides, we examined the impact of L. decidua and light on the abundance of methanogens and methanotrophs in the rhizosphere as compared with bulk soil. The abundance of both methane-oxidizing bacteria and methanogenic archaea was significantly increased in the rhizosphere compared with bulk soil but no significant response of methanogens and methanotrophs upon light exposure was established.

Involvement of abscisic acid, ABI5, and PPC2 in plant acclimation to low CO2

Phosphoenolpyruvate carboxylase (PEPC) plays a pivotal role in the photosynthetic CO2 fixation of C4 plants. However, the functions of PEPCs in C3 plants are less well characterized, particularly in relation to low atmospheric CO2 levels. Of the four genes encoding PEPC in Arabidopsis, PPC2 is considered as the major leaf PEPC gene. Here we show that the ppc2 mutants suffered a growth arrest when transferred to low atmospheric CO2 conditions, together with decreases in the maximum efficiency of PSII (Fv/Fm) and lower levels of leaf abscisic acid (ABA) and carbohydrates. The application of sucrose, malate, or ABA greatly rescued the growth of ppc2 lines under low CO2 conditions. Metabolite profiling analysis revealed that the levels of glycine and serine were increased in ppc2 leaves, while the abundance of photosynthetic metabolites was decreased under these conditions. The transcript levels of encoding enzymes involved in glycine or serine metabolism was decreased in ppc2 in an ABI5-dependent manner. Like the ppc2 mutants, abi5-1 mutants had lower photosynthetic rates and Fv/Fm compared with the wild type under photorespiratory conditions (i.e. low CO2 availability). However, the growth of these mutants was similar to that of the wild type under non-photorespiratory (low O2) conditions. The constitutive expression of ABI5 prevented the growth arrest of ppc2 lines under low CO2 conditions. These findings demonstrate that PPC2 plays an important role in the acclimation of Arabidopsis plants to low CO2 availability by linking photorespiratory metabolism to primary metabolism, and that this is mediated, at least in part, through ABA- and ABI5-dependent processes.

Rice yield formation under high day and night temperatures-A prerequisite to ensure future food security

Increasing temperatures resulting from climate change dramatically impact rice crop production in Asia. Depending on the specific stage of rice development, heat stress reduces tiller/panicle number, decreases grain number per plant and lower grain weight, thus negatively impacting yield formation. Hence improving rice crop tolerance to heat stress in terms of sustaining yield stability under high day temperature (HDT), high night temperature (HNT), or combined high day and night temperature (HDNT) will bolster future food security. In this review article, we highlight the phenological alterations caused by heat and the underlying molecular-physiological and genetic mechanisms operating under different types of heat conditions (HDT, HNT, and HDNT) to understand heat tolerance. Based on our synthesis of HDT, HNT, and HDNT effects on rice yield components, we outline future breeding strategies to contribute to sustained food security under climate change.

High Photosynthetic Rates in a Solanum pennellii Chromosome 2 QTL Is Explained by Biochemical and Photochemical Changes

Enhanced photosynthesis is strictly associated with to productivity and it can be accomplished by genetic approaches through identification of genetic variation. By using a Solanum pennellii introgression lines (ILs) population, it was previously verified that, under normal (CO2), IL 2-5 and 2-6 display increased photosynthetic rates by up to 20% in comparison with their parental background (M82). However, the physiological mechanisms involved in the enhanced CO2 assimilation exhibited by these lines remained unknown, precluding their use for further biotechnological applications. Thereby, here we attempted to uncover the physiological factors involved in the upregulation of photosynthesis in ILs 2-5 and 2-6 under normal (CO2) as well as under elevated (CO2). The results provide evidence for increased biochemical capacity (higher maximum carboxylation velocity and maximum electron transport rate) in plants from IL 2-5 and 2-6, whereas the diffusive components (stomatal and mesophyll conductances) were unaltered in these ILs in comparison to M82. Our analyses revealed that the higher photosynthetic rate observed in these ILs was associated with higher levels of starch as well as total protein levels, specially increased RuBisCO content. Further analyses performed in plants under high (CO2) confirmed that biochemical properties are involved in genetic variation on chromosome 2 related to enhanced photosynthesis.

Engineering Synthetic Signaling in Plants

Synthetic signaling is a branch of synthetic biology that aims to understand native genetic regulatory mechanisms and to use these insights to engineer interventions and devices that achieve specified design parameters. Applying synthetic signaling approaches to plants offers the promise of mitigating the worst effects of climate change and providing a means to engineer crops for entirely novel environments, such as those in space travel. The ability to engineer new traits using synthetic signaling methods will require standardized libraries of biological parts and methods to assemble them; the decoupling of complex processes into simpler subsystems; and mathematical models that can accelerate the design-build-test-learn cycle. The field of plant synthetic signaling is relatively new, but it is poised for rapid advancement. Translation from the laboratory to the field is likely to be slowed, however, by the lack of constructive dialogue between researchers and other stakeholders.

Prospects for Engineering Biophysical CO2 Concentrating Mechanisms into Land Plants to Enhance Yields

Although cyanobacteria and algae represent a small fraction of the biomass of all primary producers, their photosynthetic activity accounts for roughly half of the daily CO₂ fixation that occurs on Earth. These microorganisms are able to accomplish this feat by enhancing the activity of the CO₂-fixing enzyme Rubisco using biophysical CO₂ concentrating mechanisms (CCMs). Biophysical CCMs operate by concentrating bicarbonate and converting it into CO₂ in a compartment that houses Rubisco (in contrast with other CCMs that concentrate CO₂ via an organic intermediate, such as malate in the case of C₄ CCMs). This activity provides Rubisco with a high concentration of its substrate, thereby increasing its reaction rate. The genetic engineering of a biophysical CCM into land plants is being pursued as a strategy to increase crop yields. This review focuses on the progress toward understanding the molecular components of cyanobacterial and algal CCMs, as well as recent advances toward engineering these components into land plants.

The physical basis and practical consequences of biological promiscuity

Proteins interact with metabolites, nucleic acids, and other proteins to orchestrate the myriad catalytic, structural and regulatory functions that support life from the simplest microbes to the most complex multicellular organisms. These molecular interactions are often exquisitely specific, but never perfectly so. Adventitious "promiscuous" interactions are ubiquitous due to the thousands of macromolecules and small molecules crowded together in cells. Such interactions may perturb protein function at the molecular level, but as long as they do not compromise organismal fitness, they will not be removed by natural selection. Although promiscuous interactions are physiologically irrelevant, they are important because they can provide a vast reservoir of potential functions that can provide the starting point for evolution of new functions, both in nature and in the laboratory.

How do vascular plants perform photosynthesis in extreme environments? An integrative ecophysiological and biochemical story

In this work, we review the physiological and molecular mechanisms that allow vascular plants to perform photosynthesis in extreme environments, such as deserts, polar and alpine ecosystems. Specifically, we discuss the morpho/anatomical, photochemical and metabolic adaptive processes that enable a positive carbon balance in photosynthetic tissues under extreme temperatures and/or severe water-limiting conditions in C₃ species. Nevertheless, only a few studies have described the in situ functioning of photoprotection in plants from extreme environments, given the intrinsic difficulties of fieldwork in remote places. However, they cover a substantial geographical and functional range, which allowed us to describe some general trends. In general, photoprotection relies on the same mechanisms as those operating in the remaining plant species, ranging from enhanced morphological photoprotection to increased scavenging of oxidative products such as reactive oxygen species. Much less information is available about the main physiological and biochemical drivers of photosynthesis: stomatal conductance (g_s ), mesophyll conductance (g_m ) and carbon fixation, mostly driven by RuBisCO carboxylation. Extreme environments shape adaptations in structures, such as cell wall and membrane composition, the concentration and activation state of Calvin-Benson cycle enzymes, and RuBisCO evolution, optimizing kinetic traits to ensure functionality. Altogether, these species display a combination of rearrangements, from the whole-plant level to the molecular scale, to sustain a positive carbon balance in some of the most hostile environments on Earth.