Integrated flux and pool size analysis in plant central metabolism reveals unique roles of glycine and serine during photorespiration

Guard cell-specific glycine decarboxylase manipulation affects Arabidopsis photosynthesis, growth and stomatal behavior

Photorespiration is a mandatory metabolic repair shunt of carbon fixation by the Calvin-Benson cycle in oxygenic phototrophs. Its extent depends mainly on the CO2 : O2 ratio in chloroplasts, which is regulated via stomatal movements. Despite a comprehensive understanding of the role of photorespiration in mesophyll cells, its role in guard cells (GC) is unknown. Therefore, a key enzyme of photorespiration, glycine decarboxylase (GDC), was specifically manipulated by varying glycine decarboxylase H-protein (GDC-H) expression in Arabidopsis GC. Multiple approaches were used to analyze the transgenic lines growth, their gas exchange and Chl fluorescence, alongside metabolomics and microscopic approaches. We observed a positive correlation of GC GDC-H expression with growth, photosynthesis and carbohydrate biosynthesis, suggesting photorespiration is involved in stomatal regulation. Gas exchange measurements support this view, as optimized GC photorespiration improved plant acclimation toward conditions requiring a high photorespiratory capacity. Microscopic analysis revealed that altered photorespiratory flux also affected GC starch accumulation patterns, eventually serving as an underlying mechanism for altered stomatal behavior. Collectively, our data suggest photorespiration is involved in the regulatory circuit that coordinates stomatal movements with CO2 availability. Thus, the manipulation of photorespiration in GC has the potential to engineer crops maintaining growth and photosynthesis under future climates.

A cytosolic glyoxylate shunt complements the canonical photorespiratory pathway in Arabidopsis

Photorespiration functions in part to support photosynthetic performance, especially under stress such as high light, yet the underlying mechanisms are poorly understood. To identify modulators of photorespiration under high light, we have isolated genetic suppressors of the photorespiratory mutant hpr1 (hydroxypyruvate reductase 1) from Arabidopsis. A suppressor that partially rescues hpr1 is mapped to GLYR1, which encodes the cytosolic glyoxylate reductase 1 that converts glyoxylate to glycolate. Independent glyr1 mutants also partially rescue hpr1 and another photorespiratory mutant, catalase 2. Our genetic, transcriptomic and metabolic profiling analyses together reveal a connection between cytosolic glyoxylate and a non-canonical photorespiratory route mediated by HPR2, which we name the photorespiratory glyoxylate shunt. This shunt complements the canonical photorespiratory pathway and is especially critical when high photorespiratory fluxes are required and when the major photorespiratory pathway is deficient. Our findings support the metabolic flexibility of photorespiration and may help to improve crop performance under stress.

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.

Non-canonical plant metabolism

Metabolism is essential for plant growth and has become a major target for crop improvement by enhancing nutrient use efficiency. Metabolic engineering is also the basis for producing high-value plant products such as pharmaceuticals, biofuels and industrial biochemicals. An inherent problem for such engineering endeavours is the tendency to view metabolism as a series of distinct metabolic pathways-glycolysis, the tricarboxylic acid cycle, the Calvin-Benson cycle and so on. While these canonical pathways may represent a dominant or frequently occurring flux mode, systematic analyses of metabolism via computational modelling have emphasized the inherent flexibility of the metabolic network to carry flux distributions that are distinct from the canonical pathways. Recent experimental estimates of metabolic network fluxes using 13C-labelling approaches have revealed numerous instances in which non-canonical pathways occur under different conditions and in different tissues. In this Review, we bring these non-canonical pathways to the fore, summarizing the evidence for their occurrence and the context in which they operate. We also emphasize the importance of non-canonical pathways for metabolic engineering. We argue that the introduction of a high-flux pathway to a desired metabolic product will, by necessity, require non-canonical supporting fluxes in central metabolism to provide the necessary carbon skeletons, energy and reducing power. We illustrate this using the overproduction of isoprenoids and fatty acids as case studies.

Design and implementation of aerobic and ambient CO2-reduction as an entry-point for enhanced carbon fixation

The direct reduction of CO2 into one-carbon molecules is key to highly efficient biological CO2-fixation. However, this strategy is currently restricted to anaerobic organisms and low redox potentials. In this study, we introduce the CORE cycle, a synthetic metabolic pathway that converts CO2 to formate at aerobic conditions and ambient CO2 levels, using only NADPH as a reductant. Combining theoretical pathway design and analysis, enzyme bioprospecting and high-throughput screening, modular assembly and adaptive laboratory evolution, we realize the CORE cycle in vivo and demonstrate that the cycle supports growth of E. coli by supplementing C1-metabolism and serine biosynthesis from CO2. We further analyze the theoretical potential of the CORE cycle as a new entry-point for carbon in photorespiration and autotrophy. Overall, our work expands the solution space for biological carbon reduction, offering a promising approach to enhance CO2 fixation processes such as photosynthesis, and opening avenues for synthetic autotrophy.

Alternatives to photorespiration: A system-level analysis reveals mechanisms of enhanced plant productivity

Photorespiration causes a substantial decrease in crop yield because of mitochondrial decarboxylation. Alternative pathways (APs) have been designed to relocate the decarboxylation step or even fix additional carbon. To improve the success of transferring those engineered APs from model species to crops, we must understand how they will interact with metabolism and how plant physiology affects their performance. Here, we used multiple mathematical modeling techniques to analyze and compare existing AP designs. We show that carbon-fixing APs are the most promising candidates to replace native photorespiration in major crop species. Our results demonstrate the different metabolic routes that APs use to increase yield and which plant physiology can profit the most from them. We anticipate our results to guide the design of new APs and to help improve existing ones.

The effects of photosynthetic rate on respiration in light, starch/sucrose partitioning, and other metabolic fluxes within photosynthesis

In the future, plants may encounter increased light and elevated CO2 levels. How consequent alterations in photosynthetic rates will impact fluxes in photosynthetic carbon metabolism remains uncertain. Respiration in light (RL) is pivotal in plant carbon balance and a key parameter in photosynthesis models. Understanding the dynamics of photosynthetic metabolism and RL under varying environmental conditions is essential for optimizing plant growth and agricultural productivity. However, measuring RL under high light and high CO2 (HLHC) conditions poses challenges using traditional gas exchange methods. In this study, we employed isotopically nonstationary metabolic flux analysis (INST-MFA) to estimate RL and investigate photosynthetic carbon flux, unveiling nuanced adjustments in Camelina sativa under HLHC. Despite numerous flux alterations in HLHC, RL remained stable. HLHC affects several factors influencing RL, such as starch and sucrose partitioning, vo/vc ratio, triose phosphate partitioning, and hexose kinase activity. Analysis of A/Ci curve operational points reveals that HLHC's major changes primarily stem from CO2 suppressing photorespiration. Integration of these fluxes into a simplified model predicts changes in CBC labeling under HLHC. This study extends our prior discovery that incomplete CBC labeling is due to unlabeled carbon reimported during RL, offering insights into manipulating labeling through adjustments in photosynthetic rates.

Enhanced cadmium tolerance in perennial ryegrass via exogenous application of Enterobacter hormaechei strain X20

Cadmium (Cd) contamination in soils poses a critical environmental challenge, jeopardizing both agricultural productivity and food safety. The utilization of plant growth-promoting rhizobacteria (PGPR) emerges as a promising strategy for mitigating the adverse effects of heavy metal stress on plant health and development. This study investigates the effectiveness of Enterobacter hormaechei X20 in enhancing Cd tolerance in perennial ryegrass, a species renowned for its phytoremediation potential. Strain X20 demonstrated multiple PGPR traits, including phosphate solubilization, indole-3-acetic acid (IAA) production, and siderophore secretion. Under Cd stress, X20 significantly stimulated plant growth, elevated canopy height, and preserved leaf water content. Additionally, X20 inoculation enhanced Cd uptake and reestablished ion homeostasis by augmenting Fe2+, Cu2+, Zn2+, and Mn2+ levels. It also improved photosynthetic efficiency, particularly by optimizing PSII activity, and strengthened antioxidant defense, alleviating oxidative stress. Metabolomic analysis revealed significant modulations in amino acid and sugar metabolism, marked by increased in serine and glycine levels under Cd stress. Furthermore, fructose and glucose levels rose, while sucrose levels declined, reflecting metabolic reprogramming that facilitates stress adaptation. These findings suggest that Enterobacter hormaechei X20 holds great promise as a bioinoculant for enhancing phytoremediation efficiency and plant resilience in Cd-contaminated soils, providing a sustainable strategy for managing heavy metal pollution in agriculture.

Improved photorespiration has a major impact on the root metabolome of Arabidopsis

Photorespiration is an essential metabolic repair process in oxygenic photosynthesis, as it detoxifies Rubisco's inhibitory oxygenase byproduct, 2-phosphoglycolate (2-PG). It has been demonstrated that improving endogenous photorespiration in C3 plants through enzyme overexpression can enhance photosynthesis and promote plant growth. However, the potential impact of improved photorespiration in leaves on heterotrophic roots remained unexplored. To address this, we conducted a metabolome analysis of Arabidopsis leaves and roots using transgenic lines with enhanced glycine decarboxylase (GDC) activity, achieved by overexpressing the mitochondrial lipoamide dehydrogenase (mtLPD1) subunit. In the leaves, mtLPD1 overexpression primarily resulted in reduced steady-state levels of intermediates associated with photorespiration, the tricarboxylic acid (TCA) cycle, and soluble sugars, while intermediates related to nitrogen metabolism were elevated. In roots, where mtLPD1 expression was unchanged, we observed contrasting accumulation patterns in the transgenic lines compared to the wildtype, including increased levels of photorespiratory and TCA-cycle intermediates. Notably, we also detected elevated amounts of soluble sugars, nitrate, and starch. Phloem exudate analysis revealed altered metabolite profiles in the overexpressors, particularly with respect to photorespiratory intermediates linked to the GDC reaction, as well as soluble sugars and metabolites involved in cellular redox homeostasis. This suggested an increased transport of these metabolites from shoots to roots, thereby altering sink organ metabolism. In summary, we hypothesize that optimizing photorespiration enhances photosynthesis, which leads to an increased export of carbon surplus to heterotrophic tissues. Thus, improving photorespiration may hold potential for increasing yields in beet- and tuber-forming plants.

Triacylglycerol stability limits futile cycles and inhibition of carbon capture in oil-accumulating leaves

Engineering plant vegetative tissue to accumulate triacylglycerols (TAG, e.g. oil) can increase the amount of oil harvested per acre to levels that exceed current oilseed crops. Engineered tobacco (Nicotiana tabacum) lines that accumulate 15% to 30% oil of leaf dry weight resulted in starkly different metabolic phenotypes. In-depth analysis of the leaf lipid accumulation and 14CO2 tracking describe metabolic adaptations to the leaf oil engineering. An oil-for-membrane lipid tradeoff in the 15% oil line (referred to as HO) was surprisingly not further exacerbated when lipid production was enhanced to 30% (LEAFY COTYLEDON 2 (LEC2) line). The HO line exhibited a futile cycle that limited TAG yield through exchange with starch, altered carbon flux into various metabolite pools and end products, and suggested interference of the glyoxylate cycle with photorespiration that limited CO2 assimilation by 50%. In contrast, inclusion of the LEC2 transcription factor in tobacco improved TAG stability, alleviated the TAG-to-starch futile cycle, and recovered CO2 assimilation and plant growth comparable to wild type but with much higher lipid levels in leaves. Thus, the unstable production of storage reserves and futile cycling limit vegetative oil engineering approaches. The capacity to overcome futile cycles and maintain enhanced stable TAG levels in LEC2 demonstrated the importance of considering unanticipated metabolic adaptations while engineering vegetative oil crops.

Metabolic flux analysis to increase oil in seeds

Ensuring an adequate food supply and enough energy to sustainably support future global populations will require enhanced productivity from plants. Oilseeds can help address these needs; but the fatty acid composition of seed oils is not always optimal, and higher yields are required to meet growing demands. Quantitative approaches including metabolic flux analysis can provide insights on unexpected metabolism (i.e. when metabolism is different than in a textbook) and can be used to guide engineering efforts; however, as metabolism is context specific, it changes with tissue type, local environment, and development. This review describes recent insights from metabolic flux analysis in oilseeds and indicates engineering opportunities based on emerging topics and developing technologies that will aid quantitative understanding of metabolism and enable efforts to produce more oil. We also suggest that investigating the key regulators of fatty acid biosynthesis, such as transcription factors, and exploring metabolic signals like phytohormones in greater depth through flux analysis could open new pathways for advancing genetic engineering and breeding strategies to enhance oil crop production.

Metabolic engineering of the serine/glycine network as a means to improve the nitrogen content of crops

In plants, L-serine (Ser) biosynthesis occurs through various pathways and is highly dependent on the atmospheric CO2 concentration, especially in C3 species, due to the association of the Glycolate Pathway of Ser Biosynthesis (GPSB) with photorespiration. Characterization of a second plant Ser pathway, the Phosphorylated Pathway of Ser Biosynthesis (PPSB), revealed that it is at the crossroads of carbon, nitrogen, and sulphur metabolism. The PPSB comprises three sequential reactions catalysed by 3-phosphoglycerate dehydrogenase (PGDH), 3-phosphoSer aminotransferase (PSAT) and 3-phosphoSer phosphatase (PSP). PPSB was overexpressed in plants exhibiting two different modes of photosynthesis: Arabidopsis (C3 metabolism), and maize (C4 metabolism), under ambient (aCO2) and elevated (eCO2) CO2 growth conditions. Overexpression in Arabidopsis of the PGDH1 gene alone or PGDH1, PSAT1 and PSP1 in combination increased the Ser levels but also the essential amino acids threonine (aCO2), isoleucine, leucine, lysine, phenylalanine, threonine and methionine (eCO2) compared to the wild-type. These increases translated into higher protein levels. Likewise, starch levels were also increased in the PPSB-overexpressing lines. In maize, PPSB-deficient lines were obtained by targeting PSP1 using Cas9 endonuclease. We concluded that the expression of PPSB in maize male gametophyte is required for viable pollen development. Maize lines overexpressing the AtPGDH1 gene only displayed higher protein levels but not starch at both aCO2 and eCO2 conditions, this translated into a significant rise in the nitrogen/carbon ratio. These results suggest that metabolic engineering of PPSB in crops could enhance nitrogen content, particularly under upcoming eCO2 conditions where the activity of GPSB is limited.

Synthetic photorespiratory bypass improves rice productivity by enhancing photosynthesis and nitrogen uptake

Photorespiration, often considered as a wasteful process, is a key target for bioengineering to improve crop yields. Several photorespiratory bypasses have been designed to efficiently metabolize 2-phosphoglycolate and increase the CO2 concentration in chloroplasts, thereby reducing photorespiration. However, the suppression of primary nitrate assimilation remains an issue when photorespiration is inhibited. In this study, we designed a carbon and nitrogen metabolism-coupled photorespiratory bypass, termed the GCBG bypass, in rice (Oryza sativa) chloroplasts. Our results demonstrated efficient assembly and expression of the GCBG bypass in rice chloroplasts, which affected the levels of typical metabolites and their derivatives of natural photorespiration and enhanced the photosynthetic efficiency. Metabolomic analyses revealed that oxaloacetate, produced from glycolate in chloroplasts, positively impacted amino acid synthesis, energy metabolism, and sugar synthesis. The engineered GCBG plants showed an average yield increase of 19.0% (17.8% to 20.2%) compared with wild-type plants under natural growth conditions, alongside improved nitrogen uptake, which compensated for 44.1% of yield losses under nitrogen-limited conditions. In summary, the GCBG bypass substantially improved the photosynthetic efficiency, biomass, and yield in rice by integrating carbon and nitrogen metabolism. This study introduces a strategy for engineering high-yielding rice or other crops with improved photosynthetic efficiency and nitrogen uptake.

Photorespiratory Metabolism and Its Regulatory Links to Plant Defence Against Pathogens

When plants face biotic stress, the induction of defence responses imposes a massive demand for carbon and energy resources, which could decrease the reserves allocated towards growth. These growth-defence trade-offs have important implications for plant fitness and productivity and influence the outcome of plant-pathogen interactions. Biotic stress strongly affects plant cells' primary metabolism, including photosynthesis and respiration, the main source of energy and carbon skeletons for plant growth, development, and defence. Although the nature of photosynthetic limitations imposed by pathogens is variable, infection often increases photorespiratory pressure, generating conditions that promote ribulose-1,5-bisphosphate oxygenation, leading to a metabolic shift from assimilation to photorespiration. Photorespiration, the significant metabolic flux following photosynthesis, protects the photosynthetic apparatus from photoinhibition. However, recent studies reveal that its role is far beyond photoprotection. The intermediates of the photorespiratory cycle regulate photosynthesis, and photorespiration interacts with the metabolic pathways of nitrogen and sulphur, shaping the primary metabolism for stress responses. This work aims to present recent insights into the integration of photorespiration within the network of primary metabolism under biotic stress. It also explores the potential implications of regulating photosynthetic-photorespiratory metabolism for plant defence against bacterial and fungal pathogens.

The 'photosynthetic C1 pathway' links carbon assimilation and growth in California poplar

Although primarily studied in relation to photorespiration, serine metabolism in chloroplasts may play a key role in plant CO2 fertilization responses by linking CO2 assimilation with growth. Here, we show that the phosphorylated serine pathway is part of a 'photosynthetic C1 pathway' and demonstrate its high activity in foliage of a C3 tree where it rapidly integrates photosynthesis and C1 metabolism contributing to new biomass via methyl transfer reactions, imparting a large natural 13C-depleted signature. Using 13CO2-labelling, we show that leaf serine, the S-methyl group of leaf methionine, pectin methyl esters, and the associated methanol released during cell wall expansion during growth, are directly produced from photosynthetically-linked C1 metabolism, within minutes of light exposure. We speculate that the photosynthetic C1 pathway is highly conserved across the photosynthetic tree of life, is responsible for synthesis of the greenhouse gas methane, and may have evolved with oxygenic photosynthesis by providing a mechanism of directly linking carbon and ammonia assimilation with growth. Although the rise in atmospheric CO2 inhibits major metabolic pathways like photorespiration, our results suggest that the photosynthetic C1 pathway may accelerate and represents a missing link between enhanced photosynthesis and plant growth rates during CO2 fertilization under a changing climate.

Sink-source driven metabolic acclimation of winter oilseed rape leaves (Brassica napus L.) to drought

The crop cycle of winter oilseed rape (WOSR) incorporates source-to-sink remobilisation during the vegetative stage as a principal factor influencing the ultimate seed yield. These processes are supported by the coordinated activity of the plant's central metabolism. However, climate change-induced drought will affect the metabolic acclimation of WOSR sink/source relationships at this vegetative stage, with consequences that remain to be determined. In this study, we subjected WOSR to severe soil dehydration for 18 days and analysed the physiological and metabolic acclimation of sink and source leaves along the kinetics in combination with measurements of enzymatic activities and transcript levels. Overall, the acclimation of WOSR to drought led to subtle regulations of central metabolism in relation to leaf growth and Pro-induced osmotic adjustment. Notably, sink leaves drastically reduced their growth and transiently accumulated starch. Subsequent starch degradation correlated with the induction of beta-amylases, sucrose transporters, pyrroline-5-carboxylate synthases and proline accumulation. The functioning of the tricarboxylic acid cycle was also altered in sink leaves, as evidenced by variations in citrate, malate and associated enzymatic activities. The metabolic origin of Pro in sink leaves is discussed in relation to Pro accumulation in source leaves and the up-regulation of amino acid permease 1 and glutamine synthetase genes.

FERONIA regulates salt tolerance in Arabidopsis by controlling photorespiratory flux

Photorespiration is an energetically costly metabolic pathway in plants that responds to environmental stresses. The molecular basis of the regulation of the photorespiratory cycle under stress conditions remains unclear. Here, we discovered that FERONIA (FER) regulates photorespiratory flow under salt stress in Arabidopsis (Arabidopsis thaliana). FER mutation results in hypersensitivity to salt stress, but disruption of ferredoxin-dependent glutamate synthase 1 (GLU1), an enzyme that participates in the photorespiratory pathway by producing glutamate, greatly suppresses fer-4 hypersensitivity to salt stress primarily due to reduced glycine yield. In contrast, disrupting mitochondrial serine hydroxymethyltransferase1 (SHM1), which is supposed to increase glycine levels by hampering the conversion of glycine to serine in the photorespiratory cycle, aggravates fer-4 hypersensitivity to salt stress. Biochemical data show that FER interacts with and phosphorylates SHM1, and this phosphorylation modulates SHM1 stability. Additionally, the production of proline and its intermediate △1-pyrroline-5-carboxylate (P5C), which are both synthesized from glutamate, also contributes to fer-4 hypersensitivity to salt stress. In conclusion, this study elucidates the functional mechanism of FER in regulating salt tolerance by modulating photorespiratory flux, which greatly broadens our understanding of how plants adapt to high salinity.

Lighting the way: Compelling open questions in photosynthesis research

Photosynthesis-the conversion of energy from sunlight into chemical energy-is essential for life on Earth. Yet there is much we do not understand about photosynthetic energy conversion on a fundamental level: how it evolved and the extent of its diversity, its dynamics, and all the components and connections involved in its regulation. In this commentary, researchers working on fundamental aspects of photosynthesis including the light-dependent reactions, photorespiration, and C4 photosynthetic metabolism pose and discuss what they view as the most compelling open questions in their areas of research.

Rubisco supplies pyruvate for the 2-C-methyl-D-erythritol-4-phosphate pathway

RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE (Rubisco) produces pyruvate in the chloroplast through β-elimination of the aci-carbanion intermediate1. Here we show that this side reaction supplies pyruvate for isoprenoid, fatty acid and branched-chain amino acid biosynthesis in photosynthetically active tissue. 13C labelling studies of intact Arabidopsis plants demonstrate that the total carbon commitment to pyruvate is too large for phosphoenolpyruvate to serve as a precursor. Low oxygen stimulates Rubisco carboxylase activity and increases pyruvate production and flux through the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway, which supplies the precursors for plastidic isoprenoid biosynthesis2,3. Metabolome analysis of mutants defective in phosphoenolpyruvate or pyruvate import and biochemical characterization of isolated chloroplasts further support Rubisco as the main source of pyruvate in chloroplasts. Seedlings incorporated exogenous,13C-labelled pyruvate into MEP pathway intermediates, while adult plants did not, underscoring the developmental transition in pyruvate sourcing. Rubisco β-elimination leading to pyruvate constituted 0.7% of the product profile in in vitro assays, which translates to 2% of the total carbon leaving the Calvin-Benson-Bassham cycle. These insights solve the "pyruvate paradox"4, improve the fit of metabolic models for central metabolism and connect the MEP pathway directly to carbon assimilation.

Zn-Al and Mg-Al layered double hydroxide nanoparticles improved primary and secondary metabolism of geranium plants

Layer double hydroxide (LDH) nanoparticles (NPs) have been applied to enhance plant growth and productivity. However, their effects on carbon and nitrogen metabolism of aromatic plants, are not well understood. Therefore, we investigated the impact of foliar application of Zn-Al LDH and Mg-Al LDH NPs (10 ppm) on the growth and metabolism of geranium plants. Zn-Al LDH and Mg-Al LDH NPs significantly increased the dry biomass, photosynthetic pigment, and Zn and Mg uptake by treated plants. These increases were consistent with increased primary metabolism such as soluble sugars and their metabolic enzymes (invertase and amylase). The supply of high sugar levels induced TCA organic accumulation, providing a pathway for amino acid biosynthesis. Among amino acids, proline level and its biosynthetic enzymes such as pyrroline-5-carboxylate reductase (P5CR), ornithine aminotransferase (OAT), and pyrroline-5-carboxylate synthetase (P5CS), glutamine synthetase (GS), and arginase were increased. Increased primary metabolites can then be channeled into secondary metabolic pathways, leading to higher levels of secondary metabolites including tocopherols, phenolics, and flavonoids. These observed increases in primary and secondary metabolites also improve the biological value of geranium plants. Overall, our research highlights the potential of Zn-Al LDH and Mg-Al LDH NPs as elicitors to enhance metabolism in geranium plants, thereby improving their growth bioactivity.

Evaluating the contribution of plant metabolic pathways in the light to the ATP:NADPH demand using a meta-analysis of isotopically non-stationary metabolic flux analyses

Balancing the ATP: NADPH demand from plant metabolism with supply from photosynthesis is essential for preventing photodamage and operating efficiently, so understanding its drivers is important for integrating metabolism with the light reactions of photosynthesis and for bioengineering efforts that may radically change this demand. It is often assumed that the C3 cycle and photorespiration consume the largest amount of ATP and reductant in illuminated leaves and as a result mostly determine the ATP: NADPH demand. However, the quantitative extent to which other energy consuming metabolic processes contribute in large ways to overall ATP: NADPH demand remains unknown. Here, we used the metabolic flux networks of numerous recently published isotopically non-stationary metabolic flux analyses (INST-MFA) to evaluate flux through the C3 cycle, photorespiration, the oxidative pentose phosphate pathway, the tricarboxylic acid cycle, and starch/sucrose synthesis and characterize broad trends in the demand of energy across different pathways and compartments as well as in the overall ATP:NADPH demand. These data sets include a variety of species including Arabidopsis thaliana, Nicotiana tabacum, and Camelina sativa as well as varying environmental factors including high/low light, day length, and photorespiratory levels. Examining these datasets in aggregate reveals that ultimately the bulk of the energy flux occurred in the C3 cycle and photorespiration, however, the energy demand from these pathways did not determine the ATP: NADPH demand alone. Instead, a notable contribution was revealed from starch and sucrose synthesis which might counterbalance photorespiratory demand and result in fewer adjustments in mechanisms which balance the ATP deficit.

Formate-tetrahydrofolate ligase: supplying the cytosolic one-carbon network in roots with one-carbon units originating from glycolate

The metabolism of tetrahydrofolate (H4PteGlun)-bound one-carbon (C1) units (C1 metabolism) is multifaceted and required for plant growth, but it is unclear what of many possible synthesis pathways provide C1 units in specific organelles and tissues. One possible source of C1 units is via formate-tetrahydrofolate ligase, which catalyzes the reversible ATP-driven production of 10-formyltetrahydrofolate (10-formyl-H4PteGlun) from formate and tetrahydrofolate (H4PteGlun). Here, we report biochemical and functional characterization of the enzyme from Arabidopsis thaliana (AtFTHFL). We show that the recombinant AtFTHFL has lower Km and kcat values with pentaglutamyl tetrahydrofolate (H4PteGlu5) as compared to monoglutamyl tetrahydrofolate (H4PteGlu1), resulting in virtually identical catalytic efficiencies for the two substrates. Stable transformation of Arabidopsis plants with the EGFP-tagged AtFTHFL, followed with fluorescence microscopy, demonstrated cytosolic signal. Two independent T-DNA insertion lines with impaired AtFTHFL function had shorter roots compared to the wild type plants, demonstrating the importance of this enzyme for root growth. Overexpressing AtFTHFL led to the accumulation of H4PteGlun + 5,10-methylene-H4PteGlun and serine, accompanied with the depletion of formate and glycolate, in roots of the transgenic Arabidopsis plants. This metabolic adjustment supports the hypothesis that AtFTHFL feeds the cytosolic C1 network in roots with C1 units originating from glycolate, and that these units are then used mainly for biosynthesis of serine, and not as much for the biosynthesis of 5-methyl-H4PteGlun, methionine, and S-adenosylmethionine. This finding has implications for any future attempts to engineer one-carbon unit-requiring products through manipulation of the one-carbon metabolic network in non-photosynthetic organs.

Re-evaluating the energy balance of the many routes of carbon flow through and from photorespiration

Photorespiration is an essential process related to photosynthesis that is initiated following the oxygenation reaction catalyzed by rubisco, the initial enzyme of the Calvin-Benson-Bassham cycle. This reaction produces an inhibitory intermediate that is recycled back into the Calvin-Benson-Bassham cycle by photorespiration which requires the use of energy and the release of a portion of the carbon as CO2. The energy use and CO2 release of canonical photorespiration form a foundation for biochemical models used to describe and predict leaf carbon exchange and energy use (ATP and NAPDH). The ATP and NADPH demand of canonical photorespiration is thought to be different than that of the Calvin-Benson-Bassham cycle, requiring increased flexibility in the ratio of ATP and NADPH from the light reactions. Photorespiration requires many reactions across the chloroplasts, mitochondria and peroxisomes and involves many intermediates. Growing evidence indicates that these intermediates do not all stay in photorespiration as typically assumed and instead feed into other aspects of metabolism and leave as glycine, serine, and methylene-THF. Here we discuss how alternative flux through and from canonical photorespiration alters the ATP and NADPH requirements of metabolism following rubisco oxygenation using additional derivations of biochemical models of leaf photosynthesis and energetics. Using these new derivations, we determine that the ATP and NADPH demands of photorespiration are highly sensitive to alternative flux in ways that fundamentally changes how photorespiration contributes to the ratio of total ATP and NADPH demand. Specifically, alternative flows of carbon through photorespiration could reduce ATP and NADPH demand ratio to values below what is produced from linear electron transport.

The long and tortuous path towards improving photosynthesis by engineering elevated mesophyll conductance

The growing demand for global food production is likely to be a defining issue facing humanity over the next 50 years. To tackle this challenge, there is a desire to bioengineer crops with higher photosynthetic efficiencies, to increase yields. Recently, there has been a growing interest in engineering leaves with higher mesophyll conductance (gm), which would allow CO2 to move more efficiently from the substomatal cavities to the chloroplast stroma. However, if crop yield gains are to be realised through this approach, it is essential that the methodological limitations associated with estimating gm are fully appreciated. In this review, we summarise these limitations, and outline the uncertainties and assumptions that can affect the final estimation of gm. Furthermore, we critically assess the predicted quantitative effect that elevating gm will have on assimilation rates in crop species. We highlight the need for more theoretical modelling to determine whether altering gm is truly a viable route to improve crop performance. Finally, we offer suggestions to guide future research on gm, which will help mitigate the uncertainty inherently associated with estimating this parameter.

Photorespiratory glycine contributes to photosynthetic induction during low to high light transition

Leaves experience near-constant light fluctuations daily. Past studies have identified many limiting factors of slow photosynthetic induction when leaves transition from low light to high light. However, the contribution of photorespiration in influencing photosynthesis during transient light conditions is largely unknown. This study employs dynamic measurements of gas exchange and metabolic responses to examine the contribution of photorespiration in constraining net rates of carbon assimilation during light induction. This work indicates that photorespiratory glycine accumulation during the early light induction contributes 5-7% to the additional carbon fixed relative to the low light conditions. Mutants with large glycine pools under photorespiratory conditions (5-formyl THF cycloligase and hydroxypyruvate reductase 1) showed a transient spike in net CO2 assimilation during light induction, with glycine buildup accounting for 22-36% of the extra carbon assimilated. Interestingly, levels of many C3 cycle intermediates remained relatively constant in both mutants and wild-type throughout the light induction period where glycine accumulated, indicating that recycling of carbon into the C3 cycle via photorespiration is not needed to maintain C3 cycle activity under transient conditions. Furthermore, our data show that oxygen transient experiments can be used as a proxy to identify the photorespiratory component of light-induced photosynthetic changes.

Flux Calculation for Primary Metabolism Reveals Changes in Allocation of Nitrogen to Different Amino Acid Families When Photorespiratory Activity Changes

Photorespiration, caused by oxygenation of the enzyme Rubisco, is considered a wasteful process, because it reduces photosynthetic carbon gain, but it also supplies amino acids and is involved in amelioration of stress. Here, we show that a sudden increase in photorespiratory activity not only reduced carbon acquisition and production of sugars and starch, but also affected diurnal dynamics of amino acids not obviously involved in the process. Flux calculations based on diurnal metabolite profiles suggest that export of proline from leaves increases, while aspartate family members accumulate. An immense increase is observed for turnover in the cyclic reaction of glutamine synthetase/glutamine-oxoglutarate aminotransferase (GS/GOGAT), probably because of increased production of ammonium in photorespiration. The hpr1-1 mutant, defective in peroxisomal hydroxypyruvate reductase, shows substantial alterations in flux, leading to a shift from the oxoglutarate to the aspartate family of amino acids. This is coupled to a massive export of asparagine, which may serve in exchange for serine between shoot and root.

Spliceosomal complex components are critical for adjusting the C:N balance during high-light acclimation

Plant acclimation to an ever-changing environment is decisive for growth, reproduction, and survival. Light availability limits biomass production on both ends of the intensity spectrum. Therefore, the adjustment of plant metabolism is central to high-light (HL) acclimation, and the accumulation of photoprotective anthocyanins is commonly observed. However, mechanisms and factors regulating the HL acclimation response are less clear. Two Arabidopsis mutants of spliceosome components exhibiting a pronounced anthocyanin overaccumulation in HL were isolated from a forward genetic screen for new factors crucial for plant acclimation. Time-resolved physiological, transcriptome, and metabolome analysis revealed a vital function of the spliceosome components for rapidly adjusting gene expression and metabolism. Deficiency of INCREASED LEVEL OF POLYPLOIDY1 (ILP1), NTC-RELATED PROTEIN1 (NTR1), and PLEIOTROPIC REGULATORY LOCUS1 (PRL1) resulted in a marked overaccumulation of carbohydrates and strongly diminished amino acid biosynthesis in HL. While not generally limited in N-assimilation, ilp1, ntr1, and prl1 showed higher glutamate levels and reduced amino acid biosynthesis in HL. The comprehensive analysis reveals a function of the spliceosome components in the conditional regulation of the carbon:nitrogen balance and the accumulation of anthocyanins during HL acclimation. The importance of gene expression, metabolic regulation, and re-direction of carbon towards anthocyanin biosynthesis for HL acclimation are discussed.

Isotopically nonstationary metabolic flux analysis of plants: recent progress and future opportunities

Metabolic flux analysis (MFA) is a valuable tool for quantifying cellular phenotypes and to guide plant metabolic engineering. By introducing stable isotopic tracers and employing mathematical models, MFA can quantify the rates of metabolic reactions through biochemical pathways. Recent applications of isotopically nonstationary MFA (INST-MFA) to plants have elucidated nonintuitive metabolism in leaves under optimal and stress conditions, described coupled fluxes for fast-growing algae, and produced a synergistic multi-organ flux map that is a first in MFA for any biological system. These insights could not be elucidated through other approaches and show the potential of INST-MFA to correct an oversimplified understanding of plant metabolism.

The end game(s) of photosynthetic carbon metabolism

The year 2024 marks 70 years since the general outline of the carbon pathway in photosynthesis was published. Although several alternative pathways are now known, it is remarkable how many organisms use the reaction sequence described 70 yrs ago, which is now known as the Calvin-Benson cycle or variants such as the Calvin-Benson-Bassham cycle or Benson-Calvin cycle. However, once the carbon has entered the Calvin-Benson cycle and is converted to a 3-carbon sugar, it has many potential fates. This review will examine the last stages of photosynthetic metabolism in leaves. In land plants, this process mostly involves the production of sucrose provided by an endosymbiont (the chloroplast) to its host for use and transport to the rest of the plant. Photosynthetic metabolism also usually involves the synthesis of starch, which helps maintain respiration in the dark and enables the symbiont to supply sugars during both the day and night. Other end products made in the chloroplast are closely tied to photosynthetic CO2 assimilation. These include serine from photorespiration and various amino acids, fatty acids, isoprenoids, and shikimate pathway products. I also describe 2 pathways that can short circuit parts of the Calvin-Benson cycle. These final processes of photosynthetic metabolism play many important roles in plants.

The role of metabolomics in informing strategies for improving photosynthesis

Photosynthesis plays a vital role in acclimating to and mitigating climate change, providing food and energy security for a population that is constantly growing, and achieving an economy with zero carbon emissions. A thorough comprehension of the dynamics of photosynthesis, including its molecular regulatory network and limitations, is essential for utilizing it as a tool to boost plant growth, enhance crop yields, and support the production of plant biomass for carbon storage. Photorespiration constrains photosynthetic efficiency and contributes significantly to carbon loss. Therefore, modulating or circumventing photorespiration presents opportunities to enhance photosynthetic efficiency. Over the past eight decades, substantial progress has been made in elucidating the molecular basis of photosynthesis, photorespiration, and the key regulatory mechanisms involved, beginning with the discovery of the canonical Calvin-Benson-Bassham cycle. Advanced chromatographic and mass spectrometric technologies have allowed a comprehensive analysis of the metabolite patterns associated with photosynthesis, contributing to a deeper understanding of its regulation. In this review, we summarize the results of metabolomics studies that shed light on the molecular intricacies of photosynthetic metabolism. We also discuss the methodological requirements essential for effective analysis of photosynthetic metabolism, highlighting the value of this technology in supporting strategies aimed at enhancing photosynthesis.

SIMPEL: using stable isotopes to elucidate dynamics of context specific metabolism

The capacity to leverage high resolution mass spectrometry (HRMS) with transient isotope labeling experiments is an untapped opportunity to derive insights on context-specific metabolism, that is difficult to assess quantitatively. Tools are needed to comprehensively mine isotopologue information in an automated, high-throughput way without errors. We describe a tool, Stable Isotope-assisted Metabolomics for Pathway Elucidation (SIMPEL), to simplify analysis and interpretation of isotope-enriched HRMS datasets. The efficacy of SIMPEL is demonstrated through examples of central carbon and lipid metabolism. In the first description, a dual-isotope labeling experiment is paired with SIMPEL and isotopically nonstationary metabolic flux analysis (INST-MFA) to resolve fluxes in central metabolism that would be otherwise challenging to quantify. In the second example, SIMPEL was paired with HRMS-based lipidomics data to describe lipid metabolism based on a single labeling experiment. Available as an R package, SIMPEL extends metabolomics analyses to include isotopologue signatures necessary to quantify metabolic flux.

The role of photorespiration in preventing feedback regulation via ATP synthase in Nicotiana tabacum

Photorespiration consumes substantial amounts of energy in the forms of adenosine triphosphate (ATP) and reductant making the pathway an important component in leaf energetics. Because of this high reductant demand, photorespiration is proposed to act as a photoprotective electron sink. However, photorespiration consumes more ATP relative to reductant than the C3 cycle meaning increased flux disproportionally increases ATP demand relative to reductant. Here we explore how energetic consumption from photorespiration impacts the flexibility of the light reactions in nicotiana tabacum. Specifically, we demonstrate that decreased photosynthetic efficiency (ϕII ) at low photorespiratory flux was related to feedback regulation at the chloroplast ATP synthase. Additionally, decreased ϕII at high photorespiratory flux resulted in the accumulation of photoinhibition at photosystem II centers. These results are contrary to the proposed role of photorespiration as a photoprotective electron sink. Instead, our results suggest a novel role of ATP consumption from photorespiration in maintaining ATP synthase activity, with implications for maintaining energy balance and preventing photodamage that will be critical for plant engineering strategies.

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.

Using Dynamic Gas Exchange Measurements During Oxygen Transients to Study Nonsteady-State Photorespiration

Leaf-level gas exchange is widely used to investigate the largest carbon fluxes in illuminated leaves, offering a nondestructive way to investigate the impact of photorespiration on plant carbon balance. Modern commercial gas exchange systems allow high temporal resolution measurements under changing environments, aiding the development of nonsteady-state approaches for measuring dynamic photosynthetic responses. Here, we describe a nonsteady-state technique for acquiring the dynamic response of net CO2 assimilation to changes in photorespiratory fluxes manipulated by O2 mole fractions. This technique allows for the screening of plant genotypes with variations in their efficiencies of photorespiration under nonsteady-state conditions.

Combining Gas Exchange and Rapid Quenching of Leaf Tissue for Mass Spectrometry Analysis Directly in Gas Exchange Cuvette

Isotopically nonstationary metabolic flux analysis (INST-MFA) is a powerful technique for studying plant central metabolism, which involves introducing a 13CO2 tracer to plant leaves and sampling the labeled metabolic intermediates during the transient period before reaching an isotopic steady state. The metabolic intermediates involved in the C3 cycle have exceptionally fast turnover rates, with some intermediates turning over many times a second. As a result, it is necessary to rapidly introduce the label and then rapidly quench the plant tissue to determine concentrations in the light or capture the labeling kinetics of these intermediates at early labeling time points. Here, we describe a rapid quenching (0.1-0.5 s) system for 13CO2 labeling experiments in plant leaves to minimize metabolic changes during labeling and quenching experiments. This system is integrated into a commercially available gas exchange analyzer to measure initial rates of gas exchange, precisely control ambient conditions, and monitor the conversion from 12CO2 to 13CO2.

Daylength variation affects growth, photosynthesis, leaf metabolism, partitioning, and metabolic fluxes

Daylength, a seasonal and latitudinal variable, exerts a substantial impact on plant growth. However, the relationship between daylength and growth is nonproportional, suggesting the existence of adaptive mechanisms. Thus, our study aimed to comprehensively investigate the adaptive strategies employed by plants in response to daylength variation. We grew false flax (Camelina sativa) plants, a model oilseed crop, under long-day (LD) and short-day (SD) conditions and used growth measurements, gas exchange measurements, and isotopic labeling techniques, including 13C, 14C, and 2H2O, to determine responses to different daylengths. Our findings revealed that daylength influences various growth parameters, photosynthetic physiology, carbon partitioning, metabolic fluxes, and metabolite levels. SD plants employed diverse mechanisms to compensate for reduced CO2 fixation in the shorter photoperiod. These mechanisms included enhanced photosynthetic rates and reduced respiration in the light (RL), leading to increased shoot investment. Additionally, SD plants exhibited reduced rates of the glucose 6-phosphate (G6P) shunt and greater partitioning of sugars into starch, thereby sustaining carbon availability during the longer night. Isotopic labeling results further demonstrated substantial alterations in the partitioning of amino acids and TCA cycle intermediates between rapidly and slowly turning over pools. Overall, the results point to multiple developmental, physiological, and metabolic ways in which plants adapt to different daylengths to maintain growth.

Time-resolved systems analysis of the induction of high photosynthetic capacity in Arabidopsis during acclimation to high light

Induction of high photosynthetic capacity is a key acclimation response to high light (HL) for many herbaceous dicot plants; however, the signaling pathways that control this response remain largely unknown. Here, a systems biology approach was utilized to characterize the induction of high photosynthetic capacity in strongly and weakly acclimating Arabidopsis thaliana accessions. Plants were grown for 5 wk in a low light (LL) regime, and time-resolved photosynthetic physiological, metabolomic, and transcriptomic responses were measured during subsequent exposure to HL. The induction of high nitrogen (N) assimilation rates early in the HL shift was strongly predictive of the induction of photosynthetic capacity later in the HL shift. Accelerated N assimilation rates depended on the mobilization of existing organic acid (OA) reserves and increased de novo OA synthesis during the induction of high photosynthetic capacity. Enhanced sucrose biosynthesis capacity increased in tandem with the induction of high photosynthetic capacity, and increased starch biosynthetic capacity was balanced by increased starch catabolism. This systems analysis supports a model in which the efficient induction of N assimilation early in the HL shift begins the cascade of events necessary for the induction of high photosynthetic capacity acclimation in HL.

Increased activity of core photorespiratory enzymes and CO2 transfer conductances are associated with higher and more optimal photosynthetic rates under elevated temperatures in the extremophile Rhazya stricta

Increase photorespiration and optimising intrinsic water use efficiency are unique challenges to photosynthetic carbon fixation at elevated temperatures. To determine how plants can adapt to facilitate high rates of photorespiration at elevated temperatures while also maintaining water-use efficiency, we performed in-depth gas exchange and biochemical assays of the C3 extremophile, Rhazya stricta. These results demonstrate that R. stricta supports higher rates of photorespiration under elevated temperatures and that these higher rates of photorespiration correlate with increased activity of key photorespiratory enzymes; phosphoglycolate phosphatase and catalase. The increased photorespiratory enzyme activities may increase the overall capacity of photorespiration by reducing enzymatic bottlenecks and allowing minimal inhibitor accumulation under high photorespiratory rates. Additionally, we found the CO2 transfer conductances (stomatal and mesophyll) are re-allocated to increase the water-use efficiency in R. stricta but not necessarily the photosynthetic response to temperature. These results suggest important adaptive strategies in R. stricta that maintain photosynthetic rates under elevated temperatures with optimal water loss. The strategies found in R. stricta may inform breeding and engineering efforts in other C3 species to improve photosynthetic efficiency at high temperatures.

Four plus one: vacuoles serve in photorespiration

Photorespiration is inevitable for oxygenic photosynthesis. It has fascinated researchers over decades because of its multicompartmental organization. Recently, Lin and Tsay identified a vacuole glycerate transporter contributing to photorespiratory metabolism under short-term nitrogen depletion. This key finding adds a fifth interacting subcellular compartment and extends the photorespiratory metabolic repair module.

Triose phosphate utilization in leaves is modulated by whole-plant sink-source ratios and nitrogen budgets in rice

Triose phosphate utilization (TPU) is a biochemical process indicating carbon sink-source (im)balance within leaves. When TPU limits leaf photosynthesis, photorespiration-associated amino acid exports probably provide an additional carbon outlet and increase leaf CO2 uptake. However, whether TPU is modulated by whole-plant sink-source relations and nitrogen (N) budgets remains unclear. We address this question by model analyses of gas-exchange data measured on leaves at three growth stages of rice plants grown at two N levels. Sink-source ratio was manipulated by panicle pruning, by using yellower-leaf variant genotypes, and by measuring photosynthesis on adaxial and abaxial leaf sides. Across all these treatments, higher leaf N content resulted in the occurrence of TPU limitation at lower intercellular CO2 concentrations. Photorespiration-associated amino acid export was greater in high-N leaves, but was smaller in yellower-leaf genotypes, panicle-pruned plants, and for abaxial measurement. The feedback inhibition of panicle pruning on rates of TPU was not always observed, presumably because panicle pruning blocked N remobilization from leaves to grains and the increased leaf N content masked feedback inhibition. The leaf-level TPU limitation was thus modulated by whole-plant sink-source relations and N budgets during rice grain filling, suggesting a close link between within-leaf and whole-plant sink limitations.

Bringing home the carbon: photorespiratory CO2 recovery shows diverse efficiency in Brassicaceae

This article comments on:

Schlüter U, Bouvier JW, Guerreiro R, Malisic M, Kontny C, Westhoff P, Stich B, Weber APM. 2023. Brassicaceae display variation in efficiency of photorespiratory carbon-recapturing mechanisms. Journal of Experimental Botany 74, 6631–6649.

Isotopic clumping in wood as a proxy for photorespiration in trees

Photorespiration can limit gross primary productivity in terrestrial plants. The rate of photorespiration relative to carbon fixation increases with temperature and decreases with atmospheric [CO2]. However, the extent to which this rate varies in the environment is unclear. Here, we introduce a proxy for relative photorespiration rate based on the clumped isotopic composition of methoxyl groups (R-O-CH3) in wood. Most methoxyl C-H bonds are formed either during photorespiration or the Calvin cycle and thus their isotopic composition may be sensitive to the mixing ratio of these pathways. In water-replete growing conditions, we find that the abundance of the clumped isotopologue 13CH2D correlates with temperature (18-28 °C) and atmospheric [CO2] (280-1000 ppm), consistent with a common dependence on relative photorespiration rate. When applied to a global dataset of wood, we observe global trends of isotopic clumping with climate and water availability. Clumped isotopic compositions are similar across environments with temperatures below ~18 °C. Above ~18 °C, clumped isotopic compositions in water-limited and water-replete trees increasingly diverge. We propose that trees from hotter climates photorespire substantially more than trees from cooler climates. How increased photorespiration is managed depends on water availability: water-replete trees export more photorespiratory metabolites to lignin whereas water-limited trees either export fewer overall or direct more to other sinks that mitigate water stress. These disparate trends indicate contrasting responses of photorespiration rate (and thus gross primary productivity) to a future high-[CO2] world. This work enables reconstructing photorespiration rates in the geologic past using fossil wood.

Growth in fluctuating light buffers plants against photorespiratory perturbations

Photorespiration (PR) is the pathway that detoxifies the product of the oxygenation reaction of Rubisco. It has been hypothesized that in dynamic light environments, PR provides a photoprotective function. To test this hypothesis, we characterized plants with varying PR enzyme activities under fluctuating and non-fluctuating light conditions. Contrasting our expectations, growth of mutants with decreased PR enzyme levels was least affected in fluctuating light compared with wild type. Results for growth, photosynthesis and metabolites combined with thermodynamics-based flux analysis revealed two main causal factors for this unanticipated finding: reduced rates of photosynthesis in fluctuating light and complex re-routing of metabolic fluxes. Only in non-fluctuating light, mutants lacking the glutamate:glyoxylate aminotransferase 1 re-routed glycolate processing to the chloroplast, resulting in photooxidative damage through H2O2 production. Our results reveal that dynamic light environments buffer plant growth and metabolism against photorespiratory perturbations.

Transgenic strategies to improve the thermotolerance of photosynthesis

Warming driven by the accumulation of greenhouse gases in the atmosphere is irreversible over at least the next century, unless practical technologies are rapidly developed and deployed at scale to remove and sequester carbon dioxide from the atmosphere. Accepting this reality highlights the central importance for crop agriculture to develop adaptation strategies for a warmer future. While nearly all processes in plants are impacted by above optimum temperatures, the impact of heat stress on photosynthetic processes stand out for their centrality. Here, we review transgenic strategies that show promise in improving the high-temperature tolerance of specific subprocesses of photosynthesis and in some cases have already been shown in proof of concept in field experiments to protect yield from high temperature-induced losses. We also highlight other manipulations to photosynthetic processes for which full proof of concept is still lacking but we contend warrant further attention. Warming that has already occurred over the past several decades has had detrimental impacts on crop production in many parts of the world. Declining productivity presages a rapidly developing global crisis in food security particularly in low income countries. Transgenic manipulation of photosynthesis to engineer greater high-temperature resilience holds encouraging promise to help meet this challenge.

Mechanisms of metabolic adaptation in the duckweed Lemna gibba: an integrated metabolic, transcriptomic and flux analysis

BACKGROUND

Duckweeds are small, rapidly growing aquatic flowering plants. Due to their ability for biomass production at high rates they represent promising candidates for biofuel feedstocks. Duckweeds are also excellent model organisms because they can be maintained in well-defined liquid media, usually reproduce asexually, and because genomic resources are becoming increasingly available. To demonstrate the utility of duckweed for integrated metabolic studies, we examined the metabolic adaptation of growing Lemna gibba cultures to different nutritional conditions.

RESULTS

To establish a framework for quantitative metabolic research in duckweeds we derived a central carbon metabolism network model of Lemna gibba based on its draft genome. Lemna gibba fronds were grown with nitrate or glutamine as nitrogen source. The two conditions were compared by quantification of growth kinetics, metabolite levels, transcript abundance, as well as by 13C-metabolic flux analysis. While growing with glutamine, the fronds grew 1.4 times faster and accumulated more protein and less cell wall components compared to plants grown on nitrate. Characterization of photomixotrophic growth by 13C-metabolic flux analysis showed that, under both metabolic growth conditions, the Calvin-Benson-Bassham cycle and the oxidative pentose-phosphate pathway are highly active, creating a futile cycle with net ATP consumption. Depending on the nitrogen source, substantial reorganization of fluxes around the tricarboxylic acid cycle took place, leading to differential formation of the biosynthetic precursors of the Asp and Gln families of proteinogenic amino acids. Despite the substantial reorganization of fluxes around the tricarboxylic acid cycle, flux changes could largely not be associated with changes in transcripts.

CONCLUSIONS

Through integrated analysis of growth rate, biomass composition, metabolite levels, and metabolic flux, we show that Lemna gibba is an excellent system for quantitative metabolic studies in plants. Our study showed that Lemna gibba adjusts to different nitrogen sources by reorganizing central metabolism. The observed disconnect between gene expression regulation and metabolism underscores the importance of metabolic flux analysis as a tool in such studies.

Improving photosynthetic efficiency toward food security: Strategies, advances, and perspectives

Photosynthesis in crops and natural vegetation allows light energy to be converted into chemical energy and thus forms the foundation for almost all terrestrial trophic networks on Earth. The efficiency of photosynthetic energy conversion plays a crucial role in determining the portion of incident solar radiation that can be used to generate plant biomass throughout a growth season. Consequently, alongside the factors such as resource availability, crop management, crop selection, maintenance costs, and intrinsic yield potential, photosynthetic energy use efficiency significantly influences crop yield. Photosynthetic efficiency is relevant to sustainability and food security because it affects water use efficiency, nutrient use efficiency, and land use efficiency. This review focuses specifically on the potential for improvements in photosynthetic efficiency to drive a sustainable increase in crop yields. We discuss bypassing photorespiration, enhancing light use efficiency, harnessing natural variation in photosynthetic parameters for breeding purposes, and adopting new-to-nature approaches that show promise for achieving unprecedented gains in photosynthetic efficiency.

Predicting plasticity of rosette growth and metabolic fluxes in Arabidopsis thaliana

Plants can rapidly mitigate the effects of suboptimal growth environments by phenotypic plasticity of fitness-traits. While genetic variation for phenotypic plasticity offers the means for breeding climate-resilient crop lines, accurate genomic prediction models for plasticity of fitness-related traits are still lacking. Here, we employed condition- and accession-specific metabolic models for 67 Arabidopsis thaliana accessions to dissect and predict plasticity of rosette growth to changes in nitrogen availability. We showed that specific reactions in photorespiration, linking carbon and nitrogen metabolism, as well as key pathways of central carbon metabolism exhibited substantial genetic variation for flux plasticity. We also demonstrated that, in comparison with a genomic prediction model for fresh weight (FW), genomic prediction of growth plasticity improves the predictability of FW under low nitrogen by 58.9% and by additional 15.4% when further integrating data on plasticity of metabolic fluxes. Therefore, the combination of metabolic and statistical modeling provides a stepping stone in understanding the molecular mechanisms and improving the predictability of plasticity for fitness-related traits.

Beyond photorespiration: the significance of glycine and serine in leaf metabolism

The elucidation and removal of photorespiratory metabolic constraints will be necessary to improve crop yield in the next agricultural revolution. Fu et al. studied metabolic fluxes in the photorespiratory pathway and report that serine is the major export, whereas dynamic alterations in glycine pools orchestrate CO2 assimilation during the induction and relaxation of photorespiration.

Laisk measurements in the nonsteady state: Tests in plants exposed to warming and variable CO2 concentrations

Light respiration (RL) is an important component of plant carbon balance and a key parameter in photosynthesis models. RL is often measured using the Laisk method, a gas exchange technique that is traditionally employed under steady-state conditions. However, a nonsteady-state dynamic assimilation technique (DAT) may allow for more rapid Laisk measurements. In 2 studies, we examined the efficacy of DAT for estimating RL and the parameter Ci* (the intercellular CO2 concentration where Rubisco's oxygenation velocity is twice its carboxylation velocity), which is also derived from the Laisk technique. In the first study, we compared DAT and steady-state RL and Ci* estimates in paper birch (Betula papyrifera) growing under control and elevated temperature and CO2 concentrations. In the second, we compared DAT-estimated RL and Ci* in hybrid poplar (Populus nigra L. × P. maximowiczii A. Henry "NM6") exposed to high or low CO2 concentration pre-treatments. The DAT and steady-state methods provided similar RL estimates in B. papyrifera, and we found little acclimation of RL to temperature or CO2; however, Ci* was higher when measured with DAT compared to steady-state methods. These Ci* differences were amplified by the high or low CO2 pre-treatments. We propose that changes in the export of glycine from photorespiration may explain these apparent differences in Ci*.