Peroxisomal hydroxypyruvate reductase is not essential for photorespiration in Arabidopsis but its absence causes an increase in the stoichiometry of photorespiratory CO2 release

Regulation of Microalgal Photosynthetic Electron Transfer

The global ecosystem relies on the metabolism of photosynthetic organisms, featuring the ability to harness light as an energy source. The most successful type of photosynthesis utilizes a virtually inexhaustible electron pool from water, but the driver of this oxidation, sunlight, varies on time and intensity scales of several orders of magnitude. Such rapid and steep changes in energy availability are potentially devastating for biological systems. To enable a safe and efficient light-harnessing process, photosynthetic organisms tune their light capturing, the redox connections between core complexes and auxiliary electron mediators, ion passages across the membrane, and functional coupling of energy transducing organelles. Here, microalgal species are the most diverse group, featuring both unique environmental adjustment strategies and ubiquitous protective mechanisms. In this review, we explore a selection of regulatory processes of the microalgal photosynthetic apparatus supporting smooth electron flow in variable environments.

Thioredoxins o1 and h2 jointly adjust mitochondrial dihydrolipoamide dehydrogenase-dependent pathways towards changing environments

Thioredoxins (TRXs) are central to redox regulation, modulating enzyme activities to adapt metabolism to environmental changes. Previous research emphasized mitochondrial and microsomal TRX o1 and h2 influence on mitochondrial metabolism, including photorespiration and the tricarboxylic acid (TCA) cycle. Our study aimed to compare TRX-based regulation circuits towards environmental cues mainly affecting photorespiration. Metabolite snapshots, phenotypes and CO2 assimilation were compared among single and multiple TRX mutants in the wild-type and the glycine decarboxylase T-protein knockdown (gldt1) background. Our analyses provided evidence for additive negative effects of combined TRX o1 and h2 deficiency on growth and photosynthesis. Especially metabolite accumulation patterns suggest a shared regulation mechanism mainly on mitochondrial dihydrolipoamide dehydrogenase (mtLPD1)-dependent pathways. Quantification of pyridine nucleotides, in conjunction with 13C-labelling approaches, and biochemical analysis of recombinant mtLPD1 supported this. It also revealed mtLPD1 inhibition by NADH, pointing at an additional measure to fine-tune it's activity. Collectively, we propose that lack of TRX o1 and h2 perturbs the mitochondrial redox state, which impacts on other pathways through shifts in the NADH/NAD+ ratio via mtLPD1. This regulation module might represent a node for simultaneous adjustments of photorespiration, the TCA cycle and branched chain amino acid degradation under fluctuating environmental conditions.

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.

Measurement of Photorespiratory Oxygen Exchange by Membrane Inlet Mass Spectrometry

Photosynthesis and metabolism in plants involve oxygen as both a product and substrate. Oxygen is taken up during photorespiration and respiration and produced through water splitting during photosynthesis. To distinguish between processes that produce or consume O2 in leaves, isotope mass separation and detection by mass spectrometry allows measurement of evolution and uptake of O2 as well as CO2 uptake. This chapter describes how to calculate the rate of Rubisco oxygenation and carboxylation from in vivo gas exchange of stable isotopes of 16O2 and 18O2 with a closed cuvette system for leaf discs and membrane inlet mass spectrometry.

Measurement of O2 Uptake and Evolution in Leaves In Vivo Using Stable Isotopes and Membrane Inlet Mass Spectrometry

Oxygen is both product and substrate of photosynthesis and metabolism in plants, by oxygen evolution through water splitting and uptake by photorespiration and respiration. It is important to investigate these processes simultaneously in leaves, especially in response to environmental variables, such as light and temperature. To distinguish between processes that evolve or take up O2 in leaves in the light, in vivo gas exchange of stable isotopes of oxygen and membrane inlet mass spectrometry is used. A closed-cuvette system for gas exchange of leaf discs is described, using the stable isotopes 16O2 and 18O2, with a semi-permeable membrane gas inlet and isotope mass separation and detection by mass spectrometry. Measurement of evolution and uptake, as well as CO2 uptake, at a range of light levels allows composition of a light response curve, here described for French bean (Phaseolus vulgaris) and maize (Zea mays) leaf discs.

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.

Different photorespiratory mechanisms in conifer leaves, where peroxisomes have intrinsically low catalase activity

Photorespiration is an essential metabolic mechanism associated with photosynthesis; however, little is known about the photorespiratory pathway of conifer gymnosperms. Metabolite analyses of the leaves of 27 tree species showed that the mean glycerate content in conifer leaves was lower than that in angiosperm leaves. We performed experiments where [13 C]-serine was fed to detached shoots of a conifer (Cryptomeria japonica), via the transpiration stream, and compared the labeling patterns of photorespiratory metabolites with those of an angiosperm tree (Populus nigra), because glycerate is produced from serine via hydroxypyruvate in peroxisomes. In P. nigra, hydroxypyruvate, glycerate and glycine were labeled with 13 C, whereas in C. japonica, glycolate and a non-canonical photorespiratory metabolite, formate, were also labeled, suggesting that an H2 O2 -mediated non-enzymatic decarboxylation (NED) reaction occurs in C. japonica. We analyzed changes in the metabolite contents of leaves kept in the dark and leaves exposed to illuminated photorespiration-promoting conditions: a positive relationship between formate and serine levels in C. japonica implied that the active C1 -metabolism pathway synthesizes serine from formate. Leaf gas exchange analyses revealed that CO2 produced through NED was recaptured by chloroplasts. Database analysis of the peroxisomal targeting signal motifs of an H2 O2 -scavenging enzyme, catalase, derived from various species, including nine coniferous species, as well as analyses of peroxisomal fractions isolated from C. japonica and P. nigra leaves indicated that conifer peroxisomes had less catalase activity. These results suggest that NED and the subsequent C1 metabolism are involved in the photorespiratory pathway of conifer leaves, where peroxisomes have intrinsically low catalase activity.

Loss of peroxisomal NAD kinase 3 (NADK3) affects photorespiration metabolism in Arabidopsis

Nicotinamide adenine dinucleotides (NAD⁺ and NADP⁺) are electron mediators involved in various metabolic pathways. NADP(H) are produced by NAD kinase (NADK) through the phosphorylation of NAD(H). The Arabidopsis NADK3 (AtNADK3) is reported to preferentially phosphorylate NADH to NADPH and is localized in the peroxisome. To elucidate the biological function of AtNADK3 in Arabidopsis, we compared metabolites of nadk1, nadk2 and nadk3 Arabidopsis T-DNA inserted mutants. Metabolome analysis revealed that glycine and serine, which are intermediate metabolites of photorespiration, both increased in the nadk3 mutants. Plants grown for 6 weeks under short-day conditions showed increased NAD(H), indicating a decrease in the phosphorylation ratio in the NAD(P)(H) equilibrium. Furthermore, high CO₂ (0.15%) treatment induced a decrease in glycine and serine in nadk3 mutants. The nadk3 showed a significant decrease in post-illumination CO₂ burst, suggesting that the photorespiratory flux was disrupted in the nadk3 mutant. In addition, an increase in CO₂ compensation points and a decrease in CO₂ assimilation rate were observed in the nadk3 mutants. These results indicate that the lack of AtNADK3 causes a disruption in the intracellular metabolism, such as in amino acid synthesis and photorespiration.

Photorespiration - Rubisco's repair crew

The photorespiratory repair pathway (photorespiration in short) was set up from ancient metabolic modules about three billion years ago in cyanobacteria, the later ancestors of chloroplasts. These prokaryotes developed the capacity for oxygenic photosynthesis, i.e. the use of water as a source of electrons and protons (with O₂ as a by-product) for the sunlight-driven synthesis of ATP and NADPH for CO₂ fixation in the Calvin cycle. However, the CO₂-binding enzyme, ribulose 1,5-bisphosphate carboxylase (known under the acronym Rubisco), is not absolutely selective for CO₂ and can also use O₂ in a side reaction. It then produces 2-phosphoglycolate (2PG), the accumulation of which would inhibit and potentially stop the Calvin cycle and subsequently photosynthetic electron transport. Photorespiration removes the 2-PG and in this way prevents oxygenic photosynthesis from poisoning itself. In plants, the core of photorespiration consists of ten enzymes distributed over three different types of organelles, requiring interorganellar transport and interaction with several auxiliary enzymes. It goes together with the release and to some extent loss of freshly fixed CO₂. This disadvantageous feature can be suppressed by CO₂-concentrating mechanisms, such as those that evolved in C₄ plants thirty million years ago, which enhance CO₂ fixation and reduce 2PG synthesis. Photorespiration itself provided a pioneer variant of such mechanisms in the predecessors of C₄ plants, C₃-C₄ intermediate plants. This article is a review and update particularly on the enzyme components of plant photorespiration and their catalytic mechanisms, on the interaction of photorespiration with other metabolism and on its impact on the evolution of photosynthesis. This focus was chosen because a better knowledge of the enzymes involved and how they are embedded in overall plant metabolism can facilitate the targeted use of the now highly advanced methods of metabolic network modelling and flux analysis. Understanding photorespiration more than before as a process that enables, rather than reduces, plant photosynthesis, will help develop rational strategies for crop improvement.

Acclimation to elevated CO2 affects the C/N balance by reducing de novo N-assimilation

Plants exposed to elevated atmospheric CO₂ concentrations show an increased photosynthetic activity. However, after prolonged exposure, the activity declines. This acclimation to elevated CO₂ is accompanied by a rise in the carbon-to-nitrogen ratio of the biomass. Hence, increased sugar accumulation and sequential downregulation of photosynthetic genes, as well as nitrogen depletion and reduced protein content, have been hypothesized as the cause of low photosynthetic performance. However, the reason for reduced nitrogen content in plants at high CO₂ is unclear. Here, we show that reduced photorespiration at increased CO₂ -to-O₂ ratio leads to reduced de novo assimilation of nitrate, thus shifting the C/N balance. Metabolic modeling of acclimated and non-acclimated plants revealed the photorespiratory pathway to function as a sink for already assimilated nitrogen during the light period, providing carbon skeletons for de novo assimilation. At high CO₂ , low photorespiratory activity resulted in diminished nitrogen assimilation and eventually resulted in reduced carbon assimilation. For the hpr1-1 mutant, defective in reduction of hydroxy-pyruvate, metabolic simulations show that turnover of photorespiratory metabolites is expanded into the night. Comparison of simulations for hpr1-1 with those for the wild type allowed investigating the effect of a perturbed photorespiration on N-assimilation.

Catalase protects against nonenzymatic decarboxylations during photorespiration in Arabidopsis thaliana

Photorespiration recovers carbon that would be otherwise lost following the oxygenation reaction of rubisco and production of glycolate. Photorespiration is essential in plants and recycles glycolate into usable metabolic products through reactions spanning the chloroplast, mitochondrion, and peroxisome. Catalase in peroxisomes plays an important role in this process by disproportionating H2O2 resulting from glycolate oxidation into O2 and water. We hypothesize that catalase in the peroxisome also protects against nonenzymatic decarboxylations between hydrogen peroxide and photorespiratory intermediates (glyoxylate and/or hydroxypyruvate). We test this hypothesis by detailed gas exchange and biochemical analysis of Arabidopsis thaliana mutants lacking peroxisomal catalase. Our results strongly support this hypothesis, with catalase mutants showing gas exchange evidence for an increased stoichiometry of CO2 release from photorespiration, specifically an increase in the CO2 compensation point, a photorespiratory-dependent decrease in the quantum efficiency of CO2 assimilation, increase in the 12CO2 released in a 13CO2 background, and an increase in the postillumination CO2 burst. Further metabolic evidence suggests this excess CO2 release occurred via the nonenzymatic decarboxylation of hydroxypyruvate. Specifically, the catalase mutant showed an accumulation of photorespiratory intermediates during a transient increase in rubisco oxygenation consistent with this hypothesis. Additionally, end products of alternative hypotheses explaining this excess release were similar between wild type and catalase mutants. Furthermore, the calculated rate of hydroxypyruvate decarboxylation in catalase mutant is much higher than that of glyoxylate decarboxylation. This work provides evidence that these nonenzymatic decarboxylation reactions, predominately hydroxypyruvate decarboxylation, can occur in vivo when photorespiratory metabolism is genetically disrupted.

Thioredoxin-mediated regulation of (photo)respiration and central metabolism

Thioredoxins (TRXs) are ubiquitous proteins engaged in the redox regulation of plant metabolism. Whilst the light-dependent TRX-mediated activation of Calvin-Benson cycle enzymes is well documented, the role of extraplastidial TRXs in the control of the mitochondrial (photo)respiratory metabolism has been revealed relatively recently. Mitochondrially located TRX o1 has been identified as a regulator of alternative oxidase, enzymes of, or associated with, the tricarboxylic acid (TCA) cycle, and the mitochondrial dihydrolipoamide dehydrogenase (mtLPD) involved in photorespiration, the TCA cycle, and the degradation of branched chain amino acids. TRXs are seemingly a major point of metabolic regulation responsible for activating photosynthesis and adjusting mitochondrial photorespiratory metabolism according to the prevailing cellular redox status. Furthermore, TRX-mediated (de)activation of TCA cycle enzymes contributes to explain the non-cyclic flux mode of operation of this cycle in illuminated leaves. Here we provide an overview on the decisive role of TRXs in the coordination of mitochondrial metabolism in the light and provide in silico evidence for other redox-regulated photorespiratory enzymes. We further discuss the consequences of mtLPD regulation beyond photorespiration and provide outstanding questions that should be addressed in future studies to improve our understanding of the role of TRXs in the regulation of central metabolism.

Identification and Characterization of Genes Encoding the Hydroxypyruvate Reductases in Chlamydomonas Reveal Their Distinct Roles in Photorespiration

Photorespiration plays an important role in maintaining normal physiological metabolism in higher plants and other oxygenic organisms, such as algae. The unicellular eukaryotic organism Chlamydomonas is reported to have a photorespiration system different from that in higher plants, and only two out of nine genes encoding photorespiratory enzymes have been experimentally characterized. Hydroxypyruvate reductase (HPR), which is responsible for the conversion of hydroxypyruvate into glycerate, is poorly understood and not yet explored in Chlamydomonas. To identify the candidate genes encoding hydroxypyruvate reductases in Chlamydomonas (CrHPR) and uncover their elusive functions, we performed sequence comparison, enzyme activity measurement, subcellular localization, and analysis of knockout/knockdown strains. Together, we identify five proteins to be good candidates for CrHPRs, all of which are detected with the activity of hydroxypyruvate reductase. CrHPR1, a nicotinamide adenine dinucleotide (NADH)-dependent enzyme in mitochondria, may function as the major component of photorespiration. Its deletion causes severe photorespiratory defects. CrHPR2 takes part in the cytosolic bypass of photorespiration as the compensatory pathway of CrHPR1 for the reduction of hydroxypyruvate. CrHPR4, with NADH as the cofactor, may participate in photorespiration by acting as the chloroplastidial glyoxylate reductase in glycolate-quinone oxidoreductase system. Therefore, the results reveal that CrHPRs are far more complex than previously recognized and provide a greatly expanded knowledge base for studies to understand how CrHPRs perform their functions in photorespiration. These will facilitate both modification of photorespiration and genetic engineering for crop improvement by synthetic biology.

Pentose Phosphate Pathway Reactions in Photosynthesizing Cells

The pentose phosphate pathway (PPP) is divided into an oxidative branch that makes pentose phosphates and a non-oxidative branch that consumes pentose phosphates, though the non-oxidative branch is considered reversible. A modified version of the non-oxidative branch is a critical component of the Calvin–Benson cycle that converts CO₂ into sugar. The reaction sequence in the Calvin–Benson cycle is from triose phosphates to pentose phosphates, the opposite of the typical direction of the non-oxidative PPP. The photosynthetic direction is favored by replacing the transaldolase step of the normal non-oxidative PPP with a second aldolase reaction plus sedoheptulose-1,7-bisphosphatase. This can be considered an anabolic version of the non-oxidative PPP and is found in a few situations other than photosynthesis. In addition to the strong association of the non-oxidative PPP with photosynthesis metabolism, there is recent evidence that the oxidative PPP reactions are also important in photosynthesizing cells. These reactions can form a shunt around the non-oxidative PPP section of the Calvin–Benson cycle, consuming three ATP per glucose 6-phosphate consumed. A constitutive operation of this shunt occurs in the cytosol and gives rise to an unusual labeling pattern of photosynthetic metabolites while an inducible shunt in the stroma may occur in response to stress.

Rubisco carboxylase/oxygenase: From the enzyme to the globe: A gas exchange perspective

Rubisco is the primary carboxylase of the photosynthetic process, the most abundant enzyme in the biosphere, and also one of the best-characterized enzymes. Rubisco also functions as an oxygenase, a discovery made 50 years ago by Bill Ogren. Carboxylation of ribulose bisphosphate (RuBP) is the first step of the photosynthetic carbon reduction cycle and leads to the assimilation of CO₂, whereas the oxygenase activity necessitates the recycling of phosphoglycolate through the photorespiratory carbon oxidation cycle with concomitant loss of CO₂. Since the discovery of Rubisco's dual function, the biochemical properties of Rubisco have underpinned the mechanistic mathematical models of photosynthetic CO₂ fixation which link Rubisco kinetic properties to gas exchange of leaves. This has allowed assessments of global CO₂ exchange and predictions of how Rubisco has and will shape the environmental responses of crop and global photosynthesis in future climates. Rubisco's biochemical properties, including its slow catalytic turnover and poor affinity for CO₂, constrain crop growth and therefore improving its activity and regulation and minimising photorespiration are key targets for crop improvement.

Wasteful, essential, evolutionary stepping stone? The multiple personalities of the photorespiratory pathway

The photorespiratory pathway, in short photorespiration, is a metabolic repair system that enables the CO₂ fixation enzyme Rubisco to sustainably operate in the presence of oxygen, that is, during oxygenic photosynthesis of plants and cyanobacteria. Photorespiration is necessary because an auto-inhibitory metabolite, 2-phosphoglycolate (2PG), is produced when Rubisco binds oxygen instead of CO₂ as a substrate and must be removed, to avoid collapse of metabolism, and recycled as efficiently as possible. The basic principle of recycling 2PG very likely evolved several billion years ago in connection with the evolution of oxyphotobacteria. It comprises the multi-step combination of two molecules of 2PG to form 3-phosphoglycerate. The biochemistry of this process dictates that one out of four 2PG carbons is lost as CO₂ , which is a long-standing plant breeders' concern because it represents by far the largest fraction of respiratory processes that reduce gross-photosynthesis of major crops down to about 50% and less, lowering potential yields. In addition to the ATP needed for recycling of the 2PG carbon, extra energy is needed for the refixation of liberated equal amounts of ammonia. It is thought that the energy costs of photorespiration have an additional negative impact on crop yields in at least some environments. This paper discusses recent advances concerning the origin and evolution of photorespiration, and gives an overview of contemporary and envisioned strategies to engineer the biochemistry of, or even avoid, photorespiration.

Flexibility in the Energy Balancing Network of Photosynthesis Enables Safe Operation under Changing Environmental Conditions

Given their ability to harness chemical energy from the sun and generate the organic compounds necessary for life, photosynthetic organisms have the unique capacity to act simultaneously as their own power and manufacturing plant. This dual capacity presents many unique challenges, chiefly that energy supply must be perfectly balanced with energy demand to prevent photodamage and allow for optimal growth. From this perspective, we discuss the energy balancing network using recent studies and a quantitative framework for calculating metabolic ATP and NAD(P)H demand using measured leaf gas exchange and assumptions of metabolic demand. We focus on exploring how the energy balancing network itself is structured to allow safe and flexible energy supply. We discuss when the energy balancing network appears to operate optimally and when it favors high capacity instead. We also present the hypothesis that the energy balancing network itself can adapt over longer time scales to a given metabolic demand and how metabolism itself may participate in this energy balancing.

Photorespiration in the context of Rubisco biochemistry, CO2 diffusion and metabolism

Photorespiratory metabolism is essential for plants to maintain functional photosynthesis in an oxygen-containing environment. Because the oxygenation reaction of Rubisco is followed by the loss of previously fixed carbon, photorespiration is often considered a wasteful process and considerable efforts are aimed at minimizing the negative impact of photorespiration on the plant's carbon uptake. However, the photorespiratory pathway has also many positive aspects, as it is well integrated within other metabolic processes, such as nitrogen assimilation and C₁ metabolism, and it is important for maintaining the redox balance of the plant. The overall effect of photorespiratory carbon loss on the net CO₂ fixation of the plant is also strongly influenced by the physiology of the leaf related to CO₂ diffusion. This review outlines the distinction between Rubisco oxygenation and photorespiratory CO₂ release as a basis to evaluate the costs and benefits of photorespiration.

Thioredoxin h2 contributes to the redox regulation of mitochondrial photorespiratory metabolism

Thioredoxins (TRXs) are important proteins involved in redox regulation of metabolism. In plants, it has been shown that the mitochondrial metabolism is regulated by the mitochondrial TRX system. However, the functional significance of TRX h2, which is found at both cytosol and mitochondria, remains unclear. Arabidopsis plants lacking TRX h2 showed delayed seed germination and reduced respiration alongside impaired stomatal and mesophyll conductance, without impacting photosynthesis under ambient O₂ conditions. However, an increase in the stoichiometry of photorespiratory CO₂ release was found during O₂ -dependent gas exchange measurements in trxh2 mutants. Metabolite profiling of trxh2 leaves revealed alterations in key metabolites of photorespiration and in several metabolites involved in respiration and amino acid metabolism. Decreased abundance of serine hydroxymethyltransferase and glycine decarboxylase (GDC) H and L subunits as well as reduced NADH/NAD⁺ ratios were also observed in trxh2 mutants. We further demonstrated that the redox status of GDC-L is altered in trxh2 mutants in vivo and that recombinant TRX h2 can deactivate GDC-L in vitro, indicating that this protein is redox regulated by the TRX system. Collectively, our results demonstrate that TRX h2 plays an important role in the redox regulation of mitochondrial photorespiratory metabolism.

Net photosynthetic CO2 assimilation: more than just CO2 and O2 reduction cycles

Net photosynthetic assimilation in C₃ plants is mostly viewed as a simple balance between CO₂ fixation by Rubisco-catalyzed carboxylation and CO₂ production by photorespiration (and to a lower extent, by day respiration) that can be easily manipulated during gas exchange experiments using the CO₂  : O₂ ratio of the environment. However, it now becomes clear that it is not so simple, because the photosynthetic response to gaseous conditions involves 'ancillary' metabolisms, even in the short-term. That is, carbon and nitrogen utilization by pathways other than the Calvin cycle and the photorespiratory cycle, as well as rapid signaling events, can influence the observed rate of net photosynthesis. The potential impact of such ancillary metabolisms is assessed as well as how it must be taken into account to avoid misinterpretation of photosynthetic CO₂ response curves or low O₂ effects in C₃ leaves.

Knockdown of glycine decarboxylase complex alters photorespiratory carbon isotope fractionation in Oryza sativa leaves

The influence of reduced glycine decarboxylase complex (GDC) activity on leaf atmosphere CO2 and 13CO2 exchange was tested in transgenic Oryza sativa with the GDC H-subunit knocked down in leaf mesophyll cells. Leaf measurements on transgenic gdch knockdown and wild-type plants were carried out in the light under photorespiratory and low photorespiratory conditions (i.e. 18.4 kPa and 1.84 kPa atmospheric O2 partial pressure, respectively), and in the dark. Under approximately current ambient O2 partial pressure (18.4 kPa pO2), the gdch knockdown plants showed an expected photorespiratory-deficient phenotype, with lower leaf net CO2 assimilation rates (A) than the wild-type. Additionally, under these conditions, the gdch knockdown plants had greater leaf net discrimination against 13CO2 (Δo) than the wild-type. This difference in Δo was in part due to lower 13C photorespiratory fractionation (f) ascribed to alternative decarboxylation of photorespiratory intermediates. Furthermore, the leaf dark respiration rate (Rd) was enhanced and the 13CO2 composition of respired CO2 (δ13CRd) showed a tendency to be more depleted in the gdch knockdown plants. These changes in Rd and δ13CRd were due to the amount and carbon isotopic composition of substrates available for dark respiration. These results demonstrate that impairment of the photorespiratory pathway affects leaf 13CO2 exchange, particularly the 13C decarboxylation fractionation associated with photorespiration.

Photometric screens identified Arabidopsis peroxisome proteins that impact photosynthesis under dynamic light conditions

Plant peroxisomes function collaboratively with other subcellular organelles, such as chloroplasts and mitochondria, in several metabolic processes. To comprehensively investigate the impact of peroxisomal function on photosynthesis, especially under conditions that are more relevant to natural environments, a systematic screen of over 150 Arabidopsis mutants of genes encoding peroxisomal proteins was conducted using the automated Dynamic Environment Photosynthesis Imager (DEPI). Dynamic and high-light (HL) conditions triggered significant photosynthetic defects in a subset of the mutants, including those of photorespiration (PR) and other peroxisomal processes, some of which may also be related to PR. Further analysis of the PR mutants revealed activation of cyclic electron flow (CEF) around photosystem I and higher accumulation of hydrogen peroxide (H₂ O₂ ) under HL conditions. We hypothesize that impaired PR disturbs the balance of ATP and NADPH, leading to the accumulation of H₂ O₂ that activates CEF to produce ATP to compensate for the imbalance of reducing equivalents. The identification of peroxisomal mutants involved in PR and other peroxisomal functions in the photometric screen will enable further investigation of regulatory links between photosynthesis and PR and interorganellar interaction at the mechanistic level.

Photorespiration differs among Arabidopsis thaliana ecotypes and is correlated with photosynthesis

A greater understanding of natural variation in photosynthesis will inform strategies for crop improvement by revealing overlooked opportunities. We use Arabidopsis thaliana ecotypes as a model system to assess (i) how photosynthesis and photorespiration covary and (ii) how mesophyll conductance influences water use efficiency (WUE). Phenotypic variation in photorespiratory CO2 efflux was correlated with assimilation rates and two metrics of photosynthetic capacity (i.e. VCmax and Jmax); however, genetic correlations were not detected between photosynthesis and photorespiration. We found standing genetic variation-as broad-sense heritability-for most photosynthetic traits, including photorespiration. Genetic correlation between photosynthetic electron transport and carboxylation capacities indicates that these traits are genetically constrained. Winter ecotypes had greater mesophyll conductance, maximum carboxylation capacity, maximum electron transport capacity, and leaf structural robustness when compared with spring ecotypes. Stomatal conductance varied little in winter ecotypes, leading to a positive correlation between integrated WUE and mesophyll conductance. Thus, variation in mesophyll conductance can modulate WUE among A. thaliana ecotypes without a significant loss in assimilation. Genetic correlations between traits supplying energy and carbon to the Calvin-Benson cycle are consistent with biochemical models, suggesting that selection on either of these traits would improve all of them. Similarly, the lack of a genetic correlation between photosynthesis and photorespiration suggests that the positive scaling of these two traits can be broken.

Measurement of O2 Uptake and Evolution in Leaves In Vivo Using Stable Isotopes and Membrane Inlet Mass Spectrometry

Oxygen is both product and substrate of photosynthesis and metabolism in plants, by oxygen evolution through water splitting and uptake by photorespiration and respiration. It is important to investigate these processes simultaneously in leaves, especially in response to environmental variables, such as light and temperature. To distinguish between processes that evolve or take up O₂ in leaves in the light, in vivo gas exchange of stable isotopes of oxygen and membrane inlet mass spectrometry is used. A closed-cuvette system for gas exchange of leaf disks is described, using the stable isotopes ¹⁶O₂ and ¹⁸O₂, with a semipermeable membrane gas inlet and isotope mass separation and detection by mass spectrometry. Measurement of evolution and uptake, as well as CO₂ uptake, at a range of light levels allows composition of a light-response curve, here described for French bean and maize leaf disks.

Aldehyde dehydrogenases and the hypothesis of a glycolaldehyde shunt pathway of photorespiration

Aldehyde dehydrogenase enzymes (ALDHs) catalyse the oxidation of a broad range of aliphatic and aromatic aldehydes to their corresponding carboxylic acids using NAD⁺ or NADP⁺ as cofactors. In our article published in Scientific Reports, we demonstrated that mutations in Arabidopsis ALDH3I1 and ALDH7B4 genes altered the cellular contents of NAD(P)H, the total as well as the reduction state of glutathione; and decreased the efficiency of photosynthesis, thus placing ALDH activity as an important source of reducing power for cellular redox homeostasis. Our results also revealed that the ALDHs contribute to the reducing power required for the nitrate assimilation. Here, we discussed and elucidated the innovative hypothesis of the glycolaldehyde shunt pathway of photorespiration that would involve ALDHs generating in contrast to the known core photorespiration reactions, a net gain of two moles of NAD(P)H to support nitrate assimilation, glutathione homeostasis and ROS detoxification.

Estimation of Photorespiratory Fluxes by Gas Exchange

Photorespiratory fluxes can be easily estimated by photosynthetic gas exchange using an infrared gas analyzer and applying the Farquhar, von Caemmerer, and Berry (Farquhar et al. Planta 149:78-90, 1980) photosynthesis model. For a more direct measurement of photorespiratory CO₂ release from glycine decarboxylation, infrared gas analysis can be coupled to membrane-inlet mass spectrometry, capable of separating the total CO₂ concentration into its ¹²CO₂ and ¹³CO₂ components in a continuous online fashion. This chapter discusses how to calculate rates of photorespiration from Rubisco kinetics and describes in detail a method for measuring the CO₂ release from glycine decarboxylation using ¹³CO₂.

Inside out: efflux of carbon dioxide from leaves represents more than leaf metabolism

High concentrations of inorganic carbon in the xylem, produced from root, stem, and branch respiration, travel via the transpiration stream and eventually exit the plant through distant tissues as CO2. Unlike previous studies that focused on the efflux of CO2 from roots and woody tissues, we focus on efflux from leaves and the potential effect on leaf respiration measurements. We labeled transported inorganic carbon, spanning reported xylem concentrations, with 13C and then manipulated transpiration rates in the dark in order to vary the rates of inorganic carbon supply to cut leaves from Brassica napus and Populus deltoides. We used tunable diode laser absorbance spectroscopy to directly measure the rate of gross 13CO2 efflux, derived from inorganic carbon supplied from outside of the leaf, relative to gross 12CO2 efflux generated from leaf cells. These experiemnts showed that 13CO2 efflux was dependent upon the rate of inorganic carbon supply to the leaf and the rate of transpiration. Our data show that the gross leaf efflux of xylem-transported CO2 is likely small in the dark when rates of transpiration are low. However, gross leaf efflux of xylem-transported CO2 could approach half the rate of leaf respiration in the light when transpiration rates and branch inorganic carbon concentrations are high, irrespective of the grossly different petiole morphologies in our experiment.

The redox control of photorespiration: from biochemical and physiological aspects to biotechnological considerations

Photorespiration is a complex and tightly regulated process occurring in photosynthetic organisms. This process can alter the cellular redox balance, notably via the production and consumption of both reducing and oxidizing equivalents. Under certain circumstances, these equivalents, as well as reactive oxygen or nitrogen species, can become prominent in subcellular compartments involved in the photorespiratory process, eventually promoting oxidative post-translational modifications of proteins. Keeping these changes under tight control should therefore be of primary importance. In order to review the current state of knowledge about the redox control of photorespiration, we primarily performed a careful description of the known and potential redox-regulated or oxidation sensitive photorespiratory proteins, and examined in more details two interesting cases: the glycerate kinase and the glycine cleavage system. When possible, the potential impact and subsequent physiological regulations associated with these changes have been discussed. In the second part, we reviewed the extent to which photorespiration contributes to cellular redox homeostasis considering, in particular, the set of peripheral enzymes associated with the canonical photorespiratory pathway. Finally, some recent biotechnological strategies to circumvent photorespiration for future growth improvements are discussed in the light of these redox regulations.

High serine:glyoxylate aminotransferase activity lowers leaf daytime serine levels, inducing the phosphoserine pathway in Arabidopsis

Serine:glyoxylate aminotransferase (SGAT) converts glyoxylate and serine to glycine and hydroxypyruvate during photorespiration. Besides this, SGAT operates with several other substrates including asparagine. The impact of this enzymatic promiscuity on plant metabolism, particularly photorespiration and serine biosynthesis, is poorly understood. We found that elevated SGAT activity causes surprisingly clear changes in metabolism and interferes with photosynthetic CO2 uptake and biomass accumulation of Arabidopsis. The faster serine turnover during photorespiration progressively lowers day-time leaf serine contents and in turn induces the phosphoserine pathway. Transcriptional upregulation of this additional route of serine biosynthesis occurs already during the day but particularly at night, efficiently counteracting night-time serine depletion. Additionally, higher SGAT activity results in an increased use of asparagine as the external donor of amino groups to the photorespiratory pathway but does not alter leaf asparagine content at night. These results suggest leaf SGAT activity needs to be dynamically adjusted to ensure (i) variable flux through the photorespiratory pathway at a minimal consumption of asparagine and (ii) adequate serine levels for other cellular metabolism.

Physiological evidence for plasticity in glycolate/glycerate transport during photorespiration

Photorespiration recycles fixed carbon following the oxygenation reaction of Ribulose, 1-5, carboxylase oxygenase (Rubisco). The recycling of photorespiratory C2 to C3 intermediates is not perfectly efficient and reduces photosynthesis in C3 plants. Recently, a plastidic glycolate/glycerate transporter (PLGG1) in photorespiration was identified in Arabidopsis thaliana, but it is not known how critical this transporter is for maintaining photorespiratory efficiency. We examined a mutant deficient in PLGG1 (plgg1-1) using modeling, gas exchange, and Rubisco biochemistry. Under low light (under 65 μmol m(-2) s(-1) PAR), there was no difference in the quantum efficiency of CO2 assimilation or in the photorespiratory CO2 compensation point of plgg1-1, indicating that photorespiration proceeded with wild-type efficiency under sub-saturating light irradiances. Under saturating light irradiance (1200 μmol m(-2) s(-1) PAR), plgg1-1 showed decreased CO2 assimilation that was explained by decreases in the maximum rate of Rubisco carboxylation and photosynthetic linear electron transport. Decreased rates of Rubisco carboxylation resulted from probable decreases in the Rubisco activation state. These results suggest that glycolate/glycerate transport during photorespiration can proceed in moderate rates through an alternative transport process with wild-type efficiencies. These findings also suggest that decreases in net CO2 assimilation that occur due to disruption to photorespiration can occur by decreases in Rubisco activity and not necessarily decreases in the recycling efficiency of photorespiration.

The regulatory interplay between photorespiration and photosynthesis

The Calvin-Benson cycle and the photorespiratory pathway form the photosynthetic-photorespiratory supercycle that is responsible for nearly all biological CO2 fixation on Earth. In essence, supplementation with the photorespiratory pathway is necessary because the CO2-fixing enzyme of the Calvin-Benson cycle, ribulose 1,5-bisphosphate carboxylase (Rubisco), catalyses several side reactions including the oxygenation of ribulose 1,5-bisphosphate, which produces the noxious metabolite phosphoglycolate. The photorespiratory pathway recycles the phosphoglycolate to 3-phosphoglycerate and in this way allows the Calvin-Benson cycle to operate in the presence of molecular oxygen generated by oxygenic photosynthesis. While the carbon flow through the individual and combined subprocesses is well known, information on their regulatory interaction is very limited. Regulatory feedback from the photorespiratory pathway to the Calvin-Benson cycle can be presumed from numerous inhibitor experiments and was demonstrated in recent studies with transgenic plants. This complexity illustrates that we are not yet ready to rationally engineer photosynthesis by altering photorespiration since despite massive understanding of the core photorespiratory pathway our understanding of its interaction with other pathways and processes remains fragmentary.

Perspectives for a better understanding of the metabolic integration of photorespiration within a complex plant primary metabolism network

Photorespiration is an essential high flux metabolic pathway that is found in all oxygen-producing photosynthetic organisms. It is often viewed as a closed metabolic repair pathway that serves to detoxify 2-phosphoglycolic acid and to recycle carbon to fuel the Calvin-Benson cycle. However, this view is too simplistic since the photorespiratory cycle is known to interact with several primary metabolic pathways, including photosynthesis, nitrate assimilation, amino acid metabolism, C1 metabolism and the Krebs (TCA) cycle. Here we will review recent advances in photorespiration research and discuss future priorities to better understand (i) the metabolic integration of the photorespiratory cycle within the complex network of plant primary metabolism and (ii) the importance of photorespiration in response to abiotic and biotic stresses.

Why small fluxes matter: the case and approaches for improving measurements of photosynthesis and (photo)respiration

Since its inception, the Farquhar et al. (1980) model of photosynthesis has been a mainstay for relating biochemistry to environmental conditions from chloroplast to global levels in terrestrial plants. Many variables could be assigned from basic enzyme kinetics, but the model also required measurements of maximum rates of photosynthetic electron transport (J max ), carbon assimilation (Vcmax ), conductance of CO2 into (g s ) and through (g m ) the leaf, and the rate of respiration during the day (R d ). This review focuses on improving the accuracy of these measurements, especially fluxes from photorespiratory CO2, CO2 in the transpiration stream, and through the leaf epidermis and cuticle. These fluxes, though small, affect the accuracy of all methods of estimating mesophyll conductance and several other photosynthetic parameters because they all require knowledge of CO2 concentrations in the intercellular spaces. This review highlights modified methods that may help to reduce some of the uncertainties. The approaches are increasingly important when leaves are stressed or when fluxes are inferred at scales larger than the leaf.

Improved method for measuring the apparent CO2 photocompensation point resolves the impact of multiple internal conductances to CO2 to net gas exchange

There is a growing interest in accurate and comparable measurements of the CO2 photocompensation point (Γ*), a vital parameter to model leaf photosynthesis. The Γ* is measured as the common intersection of several CO2 response curves, but this method may incorrectly estimate Γ* by using linear fits to extrapolate curvilinear responses and single conductances to convert intercellular photocompensation points (Ci *) to chloroplastic Γ*. To determine the magnitude and minimize the impact of these artefacts on Γ* determinations, we used a combination of meta-analysis, modelling and original measurements to develop a framework to accurately determine Ci *. Our modelling indicated that the impact of using linear fits could be minimized based on the measurement CO2 range. We also propose a novel method of analysing common intersection measurements using slope-intercept regression. Our modelling indicated that slope-intercept regression is a robust analytical tool that can help determine if a measurement is biased because of multiple internal conductances to CO2 . Application of slope-intercept regression to Nicotiana tabacum and Glycine max revealed that multiple conductances likely have little impact to Ci * measurements in these species. These findings present a robust and easy to apply protocol to help resolve key questions concerning CO2 conductance through leaves.

Temperature response of in vivo Rubisco kinetics and mesophyll conductance in Arabidopsis thaliana: comparisons to Nicotiana tabacum

Biochemical models are used to predict and understand the response of photosynthesis to rising temperatures and CO2 partial pressures. These models require the temperature dependency of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) kinetics and mesophyll conductance to CO2 (g(m)). However, it is not known how the temperature response of Rubisco kinetics differs between species, and comprehensive in vivo Rubisco kinetics that include gm have only been determined in the warm-adapted Nicotiana tabacum. Here, we measured the temperature response of Rubisco kinetics and gm in N. tabacum and the cold-adapted Arabidopsis thaliana using gas exchange and (13)CO2 isotopic discrimination on plants with genetically reduced levels of Rubisco. While the individual Rubisco kinetic parameters in N. tabacum and A. thaliana were similar across temperatures, they collectively resulted in significantly different modelled rates of photosynthesis. Additionally, gm increased with temperature in N. tabacum but not in A. thaliana. These findings highlight the importance of considering species-dependent differences in Rubisco kinetics and gm when modelling the temperature response of photosynthesis.

Steady-state models of photosynthesis

In the challenge to increase photosynthetic rate per leaf area mathematical models of photosynthesis can be used to help interpret gas exchange measurements made under different environmental conditions and predict underlying photosynthetic biochemistry. To do this successfully it is important to improve the modelling of temperature dependencies of CO₂ assimilation and gain better understanding of internal CO₂ diffusion limitations. Despite these shortcomings steady-state models of photosynthesis provide simple easy to use tools for thought experiments to explore photosynthetic pathway changes such as redirecting photorespiratory CO₂, inserting bicarbonate pumps into C₃ chloroplasts or inserting C₄ photosynthesis into rice. Here a number of models derived from the C₃ model by Farquhar, von Caemmerer and Berry are discussed and compared.

Current methods for estimating the rate of photorespiration in leaves

Photorespiration is a process that competes with photosynthesis, in which Rubisco oxygenates, instead of carboxylates, its substrate ribulose 1,5-bisphosphate. The photorespiratory metabolism associated with the recovery of 3-phosphoglycerate is energetically costly and results in the release of previously fixed CO2. The ability to quantify photorespiration is gaining importance as a tool to help improve plant productivity in order to meet the increasing global food demand. In recent years, substantial progress has been made in the methods used to measure photorespiration. Current techniques are able to measure multiple aspects of photorespiration at different points along the photorespiratory C2 cycle. Six different methods used to estimate photorespiration are reviewed, and their advantages and disadvantages discussed.

Influence of temperature on measurements of the CO2 compensation point: differences between the Laisk and O2-exchange methods

The CO2 compensation point in the absence of day respiration (Γ*) is a key parameter for modelling leaf CO2 exchange. Γ* links the kinetics of ribulose-1,5-bisphosphate carboxylase-oxygenase (Rubisco) with the stoichiometry of CO2 released per Rubisco oxygenation from photorespiration (α), two essential components of biochemical models of photosynthesis. There are two main gas-exchange methods for measuring Γ*: (i) the Laisk method, which requires estimates of mesophyll conductance to CO2 (g m) and (ii) measurements of O2 isotope exchange, which assume constant values of α and a fixed stoichiometry between O2 uptake and Rubisco oxygenation. In this study, the temperature response of Γ* measured using the Laisk and O2-exchange methods was compared under ambient (25 °C) and elevated (35 °C) temperatures to determine whether both methods yielded similar results. Previously published temperature responses of Γ* estimated with the Laisk and O2-exchange methods in Nicotiana tabacum demonstrated that the Laisk-derived model of Γ* was more sensitive to temperature compared with the O2-exchange model. Measurements in Arabidopsis thaliana indicated that the Laisk and O2-exchange methods produced similar Γ* at 25 °C; however, Γ* values from O2 exchange were lower at 35 °C compared with the Laisk method. Compared with a photorespiratory mutant (pmdh1pmdh2hpr) with increased α, wild-type (WT) plants had lower Laisk values of Γ* at 25 °C but were not significantly different at 35 °C. These differences between Laisk and O2 exchange values of Γ* at 35 °C could be explained by temperature sensitivity of α in WT and/or errors in the assumptions of O2 exchange. The differences between Γ* measured using the Laisk and O2-exchange method with temperature demonstrate that assumptions used to measure Γ*, and possibly the species-specific validity of these assumptions, need to be considered when modelling the temperature response of photosynthesis.