A Cytosolic Bypass and G6P Shunt in Plants Lacking Peroxisomal Hydroxypyruvate Reductase

Chloroplastic Aspartyl-tRNA Synthetase Is Required for Chloroplast Development, Photosynthesis and Photorespiratory Metabolism

Photorespiration is a complex metabolic process linked to primary plant metabolism and influenced by environmental factors, yet its regulation remains poorly understood. In this study, we identified the asprs3-1 mutant, which displays a photorespiratory phenotype with leaf chlorosis, stunted growth, and diminished photosynthesis under ambient CO2, but normal growth under elevated CO2 conditions. Map-based cloning and genetic complementation identified AspRS3 as the mutant gene, encoding an aspartyl-tRNA synthetase. AspRS3 is localised in both chloroplasts and mitochondria, with the chloroplast being the primary site of its physiological function. The AspRS3 mutation impacts the expression of plastid-encoded and photosynthesis-related genes, leading to decreased levels of chloroplast-encoded proteins such as ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (RBCL) and ferredoxin-dependent glutamate synthase (Fd-GOGAT). Furthermore, we observed an accumulation of photorespiratory intermediates, including glycine and glycerate, and reactive oxygen species (ROS) in asprs3-1. However, under high CO2, the expression of these proteins, the accumulation of photorespiratory intermediates, and ROS levels in asprs3-1 did not significantly differ from those in the wild type. We propose that elevated CO2 mitigates the asprs3-1 phenotype by inhibiting Rubisco oxygenation and photorespiratory metabolism. This study highlights the role of aminoacyl-tRNA synthetases in regulating photorespiration and provides new insights into its metabolic control.

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.

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.

Hydrogen peroxide sulfenylates and inhibits the photorespiratory enzyme PGLP1 to modulate plant thermotolerance

Climate change is resulting in more frequent and rapidly changing temperatures at both extremes that severely affect the growth and production of plants, particularly crops. Oxidative stress caused by high temperatures is one of the most damaging factors for plants. However, the role of hydrogen peroxide (H2O2) in modulating plant thermotolerance is largely unknown, and the regulation of photorespiration essential for C3 species remains to be fully clarified. Here, we report that heat stress promotes H2O2 accumulation in chloroplasts and that H2O2 stimulates sulfenylation of the chloroplast-localized photorespiratory enzyme 2-phosphoglycolate phosphatase 1 (PGLP1) at cysteine 86, inhibiting its activity and promoting the accumulation of the toxic metabolite 2-phosphoglycolate. We also demonstrate that PGLP1 has a positive function in plant thermotolerance, as PGLP1 antisense lines have greater heat sensitivity and PGLP1-overexpressing plants have higher heat-stress tolerance than the wild type. Together, our results demonstrate that heat-induced H2O2 in chloroplasts sulfenylates and inhibits PGLP1 to modulate plant thermotolerance. Furthermore, targeting CATALASE2 to chloroplasts can largely prevent the heat-induced overaccumulation of H2O2 and the sulfenylation of PGLP1, thus conferring thermotolerance without a plant growth penalty. These findings reveal that heat-induced H2O2 in chloroplasts is important for heat-caused plant damage.

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.

Equisetum praealtum and E. hyemale have abundant Rubisco with a high catalytic turnover rate and low CO2 affinity

The kinetic properties of Rubisco, a key enzyme for photosynthesis, have been examined in numerous plant species. However, this information on some plant groups, such as ferns, is scarce. This study examined Rubisco carboxylase activity and leaf Rubisco levels in seven ferns, including four Equisetum plants (E. arvense, E. hyemale, E. praealtum, and E. variegatum), considered living fossils. The turnover rates of Rubisco carboxylation (kcatc) in E. praealtum and E. hyemale were comparable to those in the C4 plants maize (Zea mays) and sorghum (Sorghum bicolor), whose kcatc values are high. Rubisco CO2 affinity, estimated from the percentage of Rubisco carboxylase activity under CO2 unsaturated conditions in kcatc in these Equisetum plants, was low and also comparable to that in maize and sorghum. In contrast, kcatc and CO2 affinities of Rubisco in other ferns, including E. arvense and E. variegatum were comparable with those in C3 plants. The N allocation to Rubisco in the ferns examined was comparable to that in the C3 plants. These results indicate that E. praealtum and E. hyemale have abundant Rubisco with high kcatc and low CO2 affinity, whereas the carboxylase activity and abundance of Rubisco in other ferns were similar to those in C3 plants. Herein, the Rubisco properties of E. praealtum and E. hyemale were discussed regarding their evolution and physiological implications.

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.

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.

The time course of acclimation to the stress of triose phosphate use limitation

Triose phosphate utilisation (TPU) limits the maximum rate at which plants can photosynthesise. However, TPU is almost never found to be limiting photosynthesis under ambient conditions for plants. This, along with previous results showing adaptability of TPU at low temperature, suggest that TPU capacity is regulated to be just above the photosynthetic rate achievable under the prevailing conditions. A set of experiments were performed to study the adaptability of TPU capacity when plants are acclimated to elevated CO₂ concentrations. Plants held at 1500 ppm CO₂ were initially TPU limited. After 30 h they no longer exhibited TPU limitations but they did not elevate their TPU capacity. Instead, the maximum rates of carboxylation and electron transport declined. A timecourse of regulatory responses was established. A step increase of CO₂ first caused PSI to be oxidised but after 40 s both PSI and PSII had excess electrons as a result of acceptor-side limitations. Electron flow to PSI slowed and the proton motive force increased. Eventually, non-photochemical quenching reduced electron flow sufficiently to balance the TPU limitation. Over several minutes rubisco deactivated contributing to regulation of metabolism to overcome the TPU limitation.

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.

Carbon-negative synthetic biology: challenges and emerging trends of cyanobacterial technology

Global warming and climate instability have spurred interest in using renewable carbon resources for the sustainable production of chemicals. Cyanobacteria are ideal cellular factories for carbon-negative production of chemicals owing to their great potentials for directly utilizing light and CO₂ as sole energy and carbon sources, respectively. However, several challenges in adapting cyanobacterial technology to industry, such as low productivity, poor tolerance, and product harvesting difficulty, remain. Synthetic biology may finally address these challenges. Here, we summarize recent advances in the production of value-added chemicals using cyanobacterial cell factories, particularly in carbon-negative synthetic biology and emerging trends in cyanobacterial applications. We also propose several perspectives on the future development of cyanobacterial technology for commercialization.

Overexpression of Chloroplast Triosephosphate Isomerase Marginally Improves Photosynthesis at Elevated CO2 Levels in Rice

We recently suggested that chloroplast triosephosphate isomerase (cpTPI) has moderate control over the rate of CO2 assimilation (A) at elevated CO2 levels via the capacity for triose phosphate utilization (TPU) in rice (Oryza sativa L.) from its antisense-suppression study. In the present study, the effects of cpTPI overexpression on photosynthesis were examined in transgenic rice plants overexpressing the gene encoding cpTPI. The amounts of cpTPI protein in the two lines of transgenic plants were 4.8- and 12.1-folds higher than in wild-type plants, respectively. The magnitude of the increase approximately corresponded to the increase in transcript levels of cpTPI. A at CO2 levels of 100 and 120 Pa increased by 6-9% in the transgenic plants, whereas those at ambient and low CO2 levels were scarcely affected. Similar increases were observed for TPU capacity estimated from the CO2 response curves of A. These results indicate that the overexpression of cpTPI marginally improved photosynthesis at elevated CO2 levels via improvement in TPU capacity in rice. However, biomass production at a CO2 level of 120 Pa did not increase in transgenic plants, suggesting that the improvement in photosynthesis by cpTPI overexpression was not sufficient to improve biomass production in rice.

Effects of different concentrations of CO2 on Scenedesmus obliquus to overcome sludge extract toxicity and accumulate biomass

Large amounts of toxic excess sludge as well as high concentrations of carbon dioxide can be produced in coal-gasification industry. Microalgae has huge potential in the use of nutrients, the removal of toxic organic matter in excess sludge and CO₂ fixation. At the same time, the cultivation of the microalgae and the accumulation of high-quality biomass are also the key problems of concern. In this study, the growth and biomass synthesis of Scenedesmus obliquus cultured in sludge extract under 0%-15% (v/v) CO₂ were investigated. Results indicated that the highest microalgae biomass yield of 1.609 ± 0.012 g/L can be achieved under 15% CO₂ on the 30th day. The maximal photochemical efficiency of PSⅡ (Fv/Fm) decreased in the first 12 h and then increased with the culture time, and the decline amplitude decreased with the increase of the CO₂ concentration, indicating that CO₂ slowed down the toxic inhibition of sludge extract to Scenedesmus obliquus, which was expressed as the down-regulation of p53 signaling pathway and protein A0A383WFI7. Proteomic analysis showed that under high-concentration CO₂, the protein interaction network with the protein of photosystem II assembly (A0A383VSL5) as the core protein regulated the growth of Scenedesmus obliquus in terms of energy metabolism and material transportation. On the 4th day, Methyltransf_11 domain-containing protein (A0A383VH03) was up-regulated and promoted lipid synthesis, leading to the accumulation of lipids in Scenedesmus obliquus in the early stage and the increase of polysaccharides in the later stage. Collectively, this study revealed the regulation mechanism of CO₂ on toxicity removal and carbon distribution of Scenedesmus obliquus.

Effects of suppression of chloroplast phosphoglycerate kinase on photosynthesis in rice

As chloroplast phosphoglycerate kinase (cpPGK) is one of the enzymes which has the highest capacity among the Calvin-Benson cycle enzymes, it has not been regarded as a determinant for photosynthetic capacity. However, it was reported that the rate of CO₂ assimilation decreased under high irradiance and normal [CO₂] levels in the Arabidopsis cpPGK-knockdown mutant, implying that cpPGK has a control over photosynthetic capacity at a normal [CO₂] level. In the present study, the contribution of cpPGK to photosynthetic capacity was evaluated in transgenic rice plants with decreased amounts of cpPGK protein under high irradiance and various [CO₂] levels. The gene encoding cpPGK was suppressed using RNA interference techniques. Two lines of transgenic plants, Pi3 and Pi5, in which the amount of cpPGK protein decreased to 21% and 76% of that in wild-type plants, respectively, were obtained. However, there was no substantial difference in the rates of CO₂ assimilation between wild-type and transgenic plants. The rates of CO₂ assimilation decreased only slightly at elevated [CO₂] levels in the transgenic line Pi3 and did not differ between wild-type plants and the transgenic line Pi5, irrespective of [CO₂] level. These results clearly indicate that cpPGK does not have a strong control over photosynthetic capacity at various [CO₂] levels in rice.

Interaction of Nitrate Assimilation and Photorespiration at Elevated CO2

It has been shown repeatedly that exposure to elevated atmospheric CO₂ causes an increased C/N ratio of plant biomass that could result from either increased carbon or - in relation to C acquisition - reduced nitrogen assimilation. Possible reasons for diminished nitrogen assimilation are controversial, but an impact of reduced photorespiration at elevated CO₂ has frequently been implied. Using a mutant defective in peroxisomal hydroxy-pyruvate reductase (hpr1-1) that is hampered in photorespiratory turnover, we show that indeed, photorespiration stimulates the glutamine-synthetase 2 (GS) / glutamine-oxoglutarate-aminotransferase (GOGAT) cycle, which channels ammonia into amino acid synthesis. However, mathematical flux simulations demonstrated that nitrate assimilation was not reduced at elevated CO₂, pointing to a dilution of nitrogen containing compounds by assimilated carbon at elevated CO₂. The massive growth reduction in the hpr1-1 mutant does not appear to result from nitrogen starvation. Model simulations yield evidence for a loss of cellular energy that is consumed in supporting high flux through the GS/GOGAT cycle that results from inefficient removal of photorespiratory intermediates. This causes a futile cycling of glycolate and hydroxy-pyruvate. In addition to that, accumulation of serine and glycine as well as carboxylates in the mutant creates a metabolic imbalance that could contribute to growth reduction.

Intramolecular carbon isotope signals reflect metabolite allocation in plants

Stable isotopes at natural abundance are key tools to study physiological processes occurring outside the temporal scope of manipulation and monitoring experiments. Whole-molecule carbon isotope ratios (13C/12C) enable assessments of plant carbon uptake yet conceal information about carbon allocation. Here, we identify an intramolecular 13C/12C signal at tree-ring glucose C-5 and C-6 and develop experimentally testable theories on its origin. More specifically, we assess the potential of processes within C3 metabolism for signal introduction based (inter alia) on constraints on signal propagation posed by metabolic networks. We propose that the intramolecular signal reports carbon allocation into major metabolic pathways in actively photosynthesizing leaf cells including the anaplerotic, shikimate, and non-mevalonate pathway. We support our theoretical framework by linking it to previously reported whole-molecule 13C/12C increases in cellulose of ozone-treated Betula pendula and a highly significant relationship between the intramolecular signal and tropospheric ozone concentration. Our theory postulates a pronounced preference for leaf cytosolic triose-phosphate isomerase to catalyse the forward reaction in vivo (dihydroxyacetone phosphate to glyceraldehyde 3-phosphate). In conclusion, intramolecular 13C/12C analysis resolves information about carbon uptake and allocation enabling more comprehensive assessments of carbon metabolism than whole-molecule 13C/12C analysis.

Suppression of chloroplast triose phosphate isomerase evokes inorganic phosphate-limited photosynthesis in rice

The availability of inorganic phosphate (Pi) for ATP synthesis is thought to limit photosynthesis at elevated [CO2] when Pi regeneration via sucrose or starch synthesis is limited. We report here another mechanism for the occurrence of Pi-limited photosynthesis caused by insufficient capacity of chloroplast triose phosphate isomerase (cpTPI). In cpTPI-antisense transgenic rice (Oryza sativa) plants with 55%-86% reductions in cpTPI content, CO2 sensitivity of the rate of CO2 assimilation (A) decreased and even reversed at elevated [CO2]. The pool sizes of the Calvin-Benson cycle metabolites from pentose phosphates to 3-phosphoglycerate increased at elevated [CO2], whereas those of ATP decreased. These phenomena are similar to the typical symptoms of Pi-limited photosynthesis, suggesting sufficient capacity of cpTPI is necessary to prevent the occurrence of Pi-limited photosynthesis and that cpTPI content moderately affects photosynthetic capacity at elevated [CO2]. As there tended to be slight variations in the amounts of total leaf-N depending on the genotypes, relationships between A and the amounts of cpTPI were examined after these parameters were expressed per unit amount of total leaf-N (A/N and cpTPI/N, respectively). A/N at elevated [CO2] decreased linearly as cpTPI/N decreased before A/N sharply decreased, owing to further decreases in cpTPI/N. Within this linear range, decreases in cpTPI/N by 80% led to decreases up to 27% in A/N at elevated [CO2]. Thus, cpTPI function is crucial for photosynthesis at elevated [CO2].

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.

The induction of pyrenoid synthesis by hyperoxia and its implications for the natural diversity of photosynthetic responses in Chlamydomonas

In algae, it is well established that the pyrenoid, a component of the carbon-concentrating mechanism (CCM), is essential for efficient photosynthesis at low CO₂. However, the signal that triggers the formation of the pyrenoid has remained elusive. Here, we show that, in Chlamydomonas reinhardtii, the pyrenoid is strongly induced by hyperoxia, even at high CO₂ or bicarbonate levels. These results suggest that the pyrenoid can be induced by a common product of photosynthesis specific to low CO₂ or hyperoxia. Consistent with this view, the photorespiratory by-product, H₂O₂, induced the pyrenoid, suggesting that it acts as a signal. Finally, we show evidence for linkages between genetic variations in hyperoxia tolerance, H₂O₂ signaling, and pyrenoid morphologies.

The impact of photorespiration on plant primary metabolism through metabolic and redox regulation

Photorespiration is an inevitable trait of all oxygenic phototrophs, being the only known metabolic route that converts the inhibitory side-product of Rubisco's oxygenase activity 2-phosphoglycolate (2PG) back into the Calvin-Benson (CB) cycle's intermediate 3-phosphoglycerate (3PGA). Through this function of metabolite repair, photorespiration is able to protect photosynthetic carbon assimilation from the metabolite intoxication that would occur in the present-day oxygen-rich atmosphere. In recent years, much plant research has provided compelling evidence that photorespiration safeguards photosynthesis and engages in cross-talk with a number of subcellular processes. Moreover, the potential of manipulating photorespiration to increase the photosynthetic yield potential has been demonstrated in several plant species. Considering this multifaceted role, it is tempting to presume photorespiration itself is subject to a suite of regulation mechanisms to eventually exert a regulatory impact on other processes, and vice versa. The identification of potential pathway interactions and underlying regulatory aspects has been facilitated via analysis of the photorespiratory mutant phenotype, accompanied by the emergence of advanced omics' techniques and biochemical approaches. In this mini-review, I focus on the identification of enzymatic steps which control the photorespiratory flux, as well as levels of transcriptional, posttranslational, and metabolic regulation. Most importantly, glycine decarboxylase (GDC) and 2PG are identified as being key photorespiratory determinants capable of controlling photorespiratory flux and communicating with other branches of plant primary 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.

Metabolite Profiling in Arabidopsisthaliana with Moderately Impaired Photorespiration Reveals Novel Metabolic Links and Compensatory Mechanisms of Photorespiration

Photorespiration is an integral component of plant primary metabolism. Accordingly, it has been often observed that impairing the photorespiratory flux negatively impacts other cellular processes. In this study, the metabolic acclimation of the Arabidopsisthaliana wild type was compared with the hydroxypyruvate reductase 1 (HPR1; hpr1) mutant, displaying only a moderately reduced photorespiratory flux. Plants were analyzed during development and under varying photoperiods with a combination of non-targeted and targeted metabolome analysis, as well as ¹³C- and ¹⁴C-labeling approaches. The results showed that HPR1 deficiency is more critical for photorespiration during the vegetative compared to the regenerative growth phase. A shorter photoperiod seems to slowdown the photorespiratory metabolite conversion mostly at the glycerate kinase and glycine decarboxylase steps compared to long days. It is demonstrated that even a moderate impairment of photorespiration severely reduces the leaf-carbohydrate status and impacts on sulfur metabolism. Isotope labeling approaches revealed an increased CO₂ release from hpr1 leaves, most likely occurring from enhanced non-enzymatic 3-hydroxypyruvate decarboxylation and a higher flux from serine towards ethanolamine through serine decarboxylase. Collectively, the study provides evidence that the moderate hpr1 mutant is an excellent tool to unravel the underlying mechanisms governing the regulation of metabolic linkages of photorespiration with plant primary metabolism.

Potassium modulates central carbon metabolism to participate in regulating CO2 transport and assimilation in Brassica napus leaves

Potassium (K) regulates plant metabolism and enhances plant's ability to adapt to adversity. However, under different K deficiency stress, the net photosynthetic rate (A_n) was reduced, influenced by CO₂ conductance or biochemical capacities. The interplay between metabolome and photosynthetic characteristics under K deficiency stress was analyzed to explore the mechanisms by which K regulates photosynthetic capacity. With increasing K deficiency stress, dominations limiting A_n varied from CO₂ conductance to biochemical limitations. Multivariate analyses indicated that organic acids, amino acids and sedoheptulose-7-bisphosphate were significantly related to A_n, CO₂ conductance and carboxylation rate. Under moderate K deficiency, organic acids were up-regulated. Acidification of subcellular compartments reduced sedoheptulose-1,7-bisphosphatase activity, inducing downregulation of sedoheptulose-7-bisphosphate and hindrance of ribulose bisphosphate regeneration. Moreover, increased CO₂ shortage with increasing K deficiency induced a shift of increased citric acid to amino acid synthesis, causing excessive accumulation of amino acids. In addition, the reduced serine level indicated impaired photorespiration. These two changes triggered more serious reduction in photosynthetic capacity. The intimate, changes in photosynthetic capacities were tightly coupled with shifts in central C metabolism, which provides insights into the methods used to enhance A_n and plant's adaptability to abiotic stresses, through the regulation of C metabolites using molecular technology.

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

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

Source of 12C in Calvin-Benson cycle intermediates and isoprene emitted from plant leaves fed with 13CO2

Feeding 14CO2 was crucial to uncovering the path of carbon in photosynthesis. Feeding 13CO2 to photosynthesizing leaves emitting isoprene has been used to develop hypotheses about the sources of carbon for the methylerythritol 4-phosphate pathway, which makes the precursors for terpene synthesis in chloroplasts and bacteria. Both photosynthesis and isoprene studies found that products label very quickly (<10 min) up to 80-90% but the last 10-20% of labeling requires hours indicating a source of 12C during photosynthesis and isoprene emission. Furthermore, studies with isoprene showed that the proportion of slow label could vary significantly. This was interpreted as a variable contribution of carbon from sources other than the Calvin-Benson cycle (CBC) feeding the methylerythritol 4-phosphate pathway. Here, we measured the degree of label in isoprene and photosynthetic metabolites 20 min after beginning to feed 13CO2. Isoprene labeling was the same as labeling of photosynthesis intermediates. High temperature reduced the label in isoprene and photosynthesis intermediates by the same amount indicating no role for alternative carbon sources for isoprene. A model assuming glucose, fructose, and/or sucrose reenters the CBC as ribulose 5-phosphate through a cytosolic shunt involving glucose 6-phosphate dehydrogenase was consistent with the observations.

Emerging research in plant photosynthesis

Photosynthesis involves capturing light energy and, most often, converting it to chemical energy stored as reduced carbon. It is the source of food, fuel, and fiber and there is a resurgent interest in basic research on photosynthesis. Plants make excellent use of visible light energy; leaves are ideally suited to optimize light use by having a large area per amount of material invested and also having leaf angles to optimize light utilization. It is thought that plants do not use green light but in fact they use green light better than blue light under some conditions. Leaves also have mechanisms to protect against excess light and how these work in a stochastic light environment is currently a very active area of current research. The speed at which photosynthesis can begin when leaves are first exposed to light and the speed of induction of protective mechanisms, as well as the speed at which protective mechanisms dissipate when light levels decline, have recently been explored. Research is also focused on reducing wasteful processes such as photorespiration, when oxygen instead of carbon dioxide is used. Some success has been reported in altering the path of carbon in photorespiration but on closer inspection there appears to be unforeseen effects contributing to the good news. The stoichiometry of interaction of light reactions with carbon metabolism is rigid and the time constants vary tremendously presenting large challenges to regulatory mechanisms. Regulatory mechanisms will be the topic of photosynthesis research for some time to come.

Modulation of photorespiration and nitrogen recycling in Fe-deficient cucumber leaves

Low Fe availability affects plant production mainly by impairing the photosynthetic pathway, since Fe plays an essential role in chlorophyll synthesis as well as in the photosynthetic electron transport chain. Under these conditions, plant cells require the activation of protective mechanisms to prevent photo-inhibition. Among these mechanisms, photorespiration (PR) has been relatively little investigated in Fe-deficient plants. The aim of this work was to investigate the effect of Fe deficiency on photorespiration by performing in vivo analysis in leaves as well as biochemical characterization of some PR-related enzyme activities in a peroxisome-purified fraction from cucumber leaves. Modelling of light response curves at both 21 and 2% pO₂ revealed a slowing down of PR under Fe deficiency. The activity of some PR-involving enzymes as well as the contents of glycine and serine were affected under Fe deficiency. Furthermore, nitrate reductase, the glutamine synthetase-glutamate synthase (GS-GOGAT) cycle and hydroxypyruvate dehydrogenase isoform activities were differentially altered under Fe deficiency. The dataset indicates that, in Fe-deficient cucumber leaves, the modulation of PR involves the induction of some PR-related pathways, such as the photorespiratory N recycling and cytosolic photorespiratory bypass processes.

Photorespiration-how is it regulated and how does it regulate overall plant metabolism?

Under the current atmospheric conditions, oxygenic photosynthesis requires photorespiration to operate. In the presence of low CO2/O2 ratios, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) performs an oxygenase side reaction, leading to the formation of high amounts of 2-phosphoglycolate during illumination. Given that 2-phosphoglycolate is a potent inhibitor of photosynthetic carbon fixation, it must be immediately removed through photorespiration. The core photorespiratory cycle is orchestrated across three interacting subcellular compartments, namely chloroplasts, peroxisomes, and mitochondria, and thus cross-talks with a multitude of other cellular processes. Over the past years, the metabolic interaction of photorespiration and photosynthetic CO2 fixation has attracted major interest because research has demonstrated the enhancement of C3 photosynthesis and growth through the genetic manipulation of photorespiration. However, to optimize future engineering approaches, it is also essential to improve our current understanding of the regulatory mechanisms of photorespiration. Here, we summarize recent progress regarding the steps that control carbon flux in photorespiration, eventually involving regulatory proteins and metabolites. In this regard, both genetic engineering and the identification of various layers of regulation point to glycine decarboxylase as the key enzyme to regulate and adjust the photorespiratory carbon flow. Potential implications of the regulation of photorespiration for acclimation to environmental changes along with open questions are also discussed.

Functional and Structural Leaf Plasticity Determine Photosynthetic Performances during Drought Stress and Recovery in Two Platanus orientalis Populations from Contrasting Habitats

In the context of climatic change, more severe and long-lasting droughts will modify the fitness of plants, with potentially worse consequences on the relict trees. We have investigated the leaf phenotypic (anatomical, physiological and biochemical) plasticity in well-watered, drought-stressed and re-watered plants of two populations of Platanus orientalis, an endangered species in the west of the Mediterranean area. The two populations originated in contrasting climate (drier and warmer, Italy (IT) population; more humid and colder, Bulgaria (BG) population). The IT control plants had thicker leaves, enabling them to maintain higher leaf water content in the dry environment, and more spongy parenchyma, which could improve water conductivity of these plants and may result in easier CO2 diffusion than in BG plants. Control BG plants were also characterized by higher photorespiration and leaf antioxidants compared to IT plants. BG plants responded to drought with greater leaf thickness shrinkage. Drought also caused substantial reduction in photosynthetic parameters of both IT and BG plants. After re-watering, photosynthesis did not fully recover in either of the two populations. However, IT leaves became thicker, while photorespiration in BG plants further increased, perhaps indicating sustained activation of defensive mechanisms. Overall, our hypothesis, that plants with a fragmented habitat (i.e., the IT population) lose phenotypic plasticity but acquire traits allowing better resistance to the climate where they became adapted, remains confirmed.

Phosphomimetic T335D Mutation of Hydroxypyruvate Reductase 1 Modifies Cofactor Specificity and Impacts Arabidopsis Growth in Air

Photorespiration is an essential process in oxygenic photosynthetic organisms triggered by the oxygenase activity of Rubisco. In peroxisomes, photorespiratory HYDROXYPYRUVATE REDUCTASE1 (HPR1) catalyzes the conversion of hydroxypyruvate to glycerate together with the oxidation of a pyridine nucleotide cofactor. HPR1 regulation remains poorly understood; however, HPR1 phosphorylation at T335 has been reported. By comparing the kinetic properties of phosphomimetic (T335D), nonphosphorylatable (T335A), and wild-type recombinant Arabidopsis (Arabidopsis thaliana) HPR1, it was found that HPR1-T335D exhibits reduced NADH-dependent hydroxypyruvate reductase activity while showing improved NADPH-dependent activity. Complementation of the Arabidopsis hpr1-1 mutant by either wild-type HPR1 or HPR1-T335A fully complemented the photorespiratory growth phenotype of hpr1-1 in ambient air, whereas HPR1-T335D-containing hpr1-1 plants remained smaller and had lower photosynthetic CO₂ assimilation rates. Metabolite analyses indicated that these phenotypes were associated with subtle perturbations in the photorespiratory cycle of HPR1-T335D-complemented hpr1-1 rosettes compared to all other HPR1-containing lines. Therefore, T335 phosphorylation may play a role in the regulation of HPR1 activity in planta, although it was not required for growth under ambient air controlled conditions. Furthermore, improved NADP-dependent HPR1 activities in peroxisomes could not compensate for the reduced NADH-dependent HPR1 activity.

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.

Peroxisomes: versatile organelles with diverse roles in plants

Peroxisomes are small, ubiquitous organelles that are delimited by a single membrane and lack genetic material. However, these simple-structured organelles are highly versatile in morphology, abundance and protein content in response to various developmental and environmental cues. In plants, peroxisomes are essential for growth and development and perform diverse metabolic functions, many of which are carried out coordinately by peroxisomes and other organelles physically interacting with peroxisomes. Recent studies have added greatly to our knowledge of peroxisomes, addressing areas such as the diverse proteome, regulation of division and protein import, pexophagy, matrix protein degradation, solute transport, signaling, redox homeostasis and various metabolic and physiological functions. This review summarizes our current understanding of plant peroxisomes, focusing on recent discoveries. Current problems and future efforts required to better understand these organelles are also discussed. An improved understanding of peroxisomes will be important not only to the understanding of eukaryotic cell biology and metabolism, but also to agricultural efforts aimed at improving crop performance and defense.

Cyanobacterial carboxysomes contain an unique rubisco-activase-like protein

In plants, rubisco activase (Rca) regulates rubisco by removing inhibitory molecules such as ribulose-1,5-bisphosphate (RuBP). In cyanobacteria, a homologous protein (activase-like cyanobacterial protein, ALC), contains a distinctive C-terminal fusion resembling the small-subunit of rubisco. Although cyanobacterial rubisco is believed to be less sensitive to RuBP inhibition, the ALC is widely distributed among diverse cyanobacteria. Using microscopy, biochemistry and molecular biology, the cellular localization of the ALC, its effect on carboxysome/cell ultrastructure in Fremyella diplosiphon, and its function in vitro were studied. Bioinformatic analysis uncovered evolutionary relationships between the ALC and rubisco. ALC localizes to carboxysomes and exhibits ATPase activity. Furthermore, the ALC induces rubisco aggregation in a manner similar to that of another carboxysomal protein, M35, and this activity is affected by ATP. An alc deletion mutant showed modified cell morphology when grown under enriched CO₂ and impaired regulation of carboxysome biogenesis, without affecting growth rate. Carbamylation of Fremyella recombinant rubisco was inhibited by RuBP, but this inhibition was not relieved by the ALC. The ALC does not appear to function like a canonical Rca; instead, it exerts an effect on the response to CO₂ availability at the level of a metabolic module, the carboxysome, through rubisco network formation, and carboxysome organization.

Glycogen Metabolism Supports Photosynthesis Start through the Oxidative Pentose Phosphate Pathway in Cyanobacteria

Cyanobacteria experience drastic changes in their carbon metabolism under daily light/dark cycles. During the day, the Calvin-Benson cycle fixes CO₂ and diverts excess carbon into glycogen storage. At night, glycogen is degraded to support cellular respiration. The dark/light transition represents a universal environmental stress for cyanobacteria and other photosynthetic lifeforms. Recent studies revealed the essential genetic background necessary for the fitness of cyanobacteria during diurnal growth. However, the metabolic processes underlying the dark/light transition are not well understood. In this study, we observed that glycogen metabolism supports photosynthesis in the cyanobacterium Synechococcus elongatus PCC 7942 when photosynthesis reactions start upon light exposure. Compared with the wild type, the glycogen mutant ∆glgC showed a reduced photosynthetic efficiency and a slower P700⁺ rereduction rate when photosynthesis starts. Proteomic analyses indicated that glycogen is degraded through the oxidative pentose phosphate (OPP) pathway during the dark/light transition. We confirmed that the OPP pathway is essential for the initiation of photosynthesis and further showed that glycogen degradation through the OPP pathway contributes to the activation of key Calvin-Benson cycle enzymes by modulating NADPH levels. This strategy stimulates photosynthesis in cyanobacteria following dark respiration and stabilizes the Calvin-Benson cycle under fluctuating environmental conditions, thereby offering evolutionary advantages for photosynthetic organisms using the Calvin-Benson cycle for carbon fixation.

The plastid phosphorylase as a multiple-role player in plant metabolism

The physiological roles of the plastidial phosphorylase in starch metabolism of higher plants have been debated for decades. While estimated physiological substrate levels favor a degradative role, genetic evidence indicates that the plastidial phosphorylase (Pho1) plays an essential role in starch initiation and maturation of the starch granule in developing rice grains. The plastidial enzyme contains a unique peptide domain, up to 82 residues in length depending on the plant species, not found in its cytosolic counterpart or glycogen phosphorylases. The role of this extra peptide domain is perplexing, as its complete removal does not significantly affect the in vitro catalytic or enzymatic regulatory properties of rice Pho1. This peptide domain may have a regulatory function as it contains potential phosphorylation sites and, in some plant Pho1s, a PEST motif, a substrate for proteasome-mediated degradation. We discuss the potential roles of Pho1 and its L80 domain in starch biosynthesis and photosynthesis.

Tracing metabolic flux through time and space with isotope labeling experiments

Metabolism is dynamic and must function in context-specific ways to adjust to changes in the surrounding cellular and ecological environment. When isotopic tracers are used, metabolite flow (i.e. metabolic flux) can be quantified through biochemical networks to assess metabolic pathway operation. The cellular activities considered across multiple tissues and organs result in the observed phenotype and can be analyzed to discover emergent, whole-system properties of biology and elucidate misconceptions about network operation. However, temporal and spatial challenges remain significant hurdles and require novel approaches and creative solutions. We survey current investigations in higher plant and animal systems focused on dynamic isotope labeling experiments, spatially resolved measurement strategies, and observations from re-analysis of our own studies that suggest prospects for future work. Related discoveries will be necessary to push the frontier of our understanding of metabolism to suggest novel solutions to cure disease and feed a growing future world population.

Faster Removal of 2-Phosphoglycolate through Photorespiration Improves Abiotic Stress Tolerance of Arabidopsis

Photorespiration metabolizes 2-phosphoglyolate (2-PG) to avoid inhibition of carbon assimilation and allocation. In addition to 2-PG removal, photorespiration has been shown to play a role in stress protection. Here, we studied the impact of faster 2-PG degradation through overexpression of 2-PG phosphatase (PGLP) on the abiotic stress-response of Arabidopsis thaliana (Arabidopsis). Two transgenic lines and the wild type were subjected to short-time high light and elevated temperature stress during gas exchange measurements. Furthermore, the same lines were exposed to long-term water shortage and elevated temperature stresses. Faster 2-PG degradation allowed maintenance of photosynthesis at combined light and temperatures stress and under water-limiting conditions. The PGLP-overexpressing lines also showed higher photosynthesis compared to the wild type if grown in high temperatures, which also led to increased starch accumulation and shifts in soluble sugar contents. However, only minor effects were detected on amino and organic acid levels. The wild type responded to elevated temperatures with elevated mRNA and protein levels of photorespiratory enzymes, while the transgenic lines displayed only minor changes. Collectively, these results strengthen our previous hypothesis that a faster photorespiratory metabolism improves tolerance against unfavorable environmental conditions, such as high light intensity and temperature as well as drought. In case of PGLP, the likely mechanism is alleviation of inhibitory feedback of 2-PG onto the Calvin–Benson cycle, facilitating carbon assimilation and accumulation of transitory starch.

Does the stromal concentration of Pi control chloroplast ATP synthase protein amount in contrasting growth environments?

Changes in the growth environment can generate imbalances in chloroplast photosynthetic metabolism. Under water deficit, stomatal closure limits CO2 availability such that the production of ATP and NADPH by the thylakoid membrane-localized electron transport chain may not match the consumption of these energy intermediates by the stroma-localized Calvin-Benson cycle, thus challenging energy balance. Alternatively, in an elevated CO2 atmosphere, carbon fixation by the Calvin-Benson cycle may outpace the activity of downstream carbohydrate-utilizing processes, thus challenging carbon balance. Our previous studies have shown that, in both of the above scenarios, a mitochondrial alternative oxidase contributes to maintaining energy or carbon balance, highlighting the importance of photosynthesis-respiration interactions in optimizing photosynthesis in different growth environments. In these previous studies, we observed aberrant amounts of chloroplast ATP synthase protein across the different transgenic plant lines and growth conditions, compared to wild-type. Based on these observations, we develop here the hypothesis that an important determinant of chloroplast ATP synthase protein amount is the stromal concentration of inorganic phosphate. ATP synthase is a master regulator of photosynthesis. Coarse control of ATP synthase protein amount by the stromal inorganic phosphate status could provide a means to coordinate the electron transport and carbon fixation reactions of photosynthesis.

Redox-Regulation of Photorespiration through Mitochondrial Thioredoxin o1

Photorespiration sustains photosynthesis in the presence of oxygen due to rapid metabolization of 2-phosphoglycolate, the major side-product of the oxygenase activity of Rubisco that also directly impedes carbon assimilation and allocation. Despite the fact that both the biochemical reactions and the underlying genetics are well characterized, information concerning the regulatory mechanisms that adjust photorespiratory flux is rare. Here, we studied the impact of mitochondrial-localized thioredoxin o1 (TRXo1) on photorespiratory metabolism. The characterization of an Arabidopsis (Arabidopsis thaliana) transfer DNA insertional line (trxo1-1) revealed an increase in the stoichiometry of photorespiratory CO2 release and impaired Gly-to-Ser turnover after a shift from high-to-low CO2 without changes in Gly decarboxylase (GDC) gene or protein expression. These effects were distinctly pronounced in a double mutant, where the TRXo1 mutation was combined with strongly reduced GDC T-protein expression. The double mutant (TxGT) showed reduced growth in air but not in high CO2, decreased photosynthesis, and up to 54-fold more Gly alongside several redox-stress-related metabolites. Given that GDC proteins are potential targets for redox-regulation, we also examined the in vitro properties of recombinant GDC l-proteins (lipoamide dehydrogenase) from plants and the cyanobacterium Synechocystis species strain PCC6803 and observed a redox-dependent inhibition by either artificial reducing agents or TRXo1 itself. Collectively, our results demonstrate that TRXo1 potentially adjusts photorespiration via redox-regulation of GDC in response to environmental changes.

Transcriptional Regulation of the Glucose-6-Phosphate/Phosphate Translocator 2 Is Related to Carbon Exchange Across the Chloroplast Envelope

The exchange of reduced carbon across the inner chloroplast envelope has a large impact on photosynthesis and growth. Under steady-state conditions it is thought that glucose 6-phosphate (G6P) does not cross the chloroplast membrane. However, growth at high CO₂, or disruption of starch metabolism can result in the GPT2 gene for a G6P/P_i translocator to be expressed presumably allowing G6P exchange across the chloroplast envelope. We found that after an increase in light, the transcript for GPT2 transiently increases several 100-fold within 2 h in both the Col-0 and WS ecotypes of Arabidopsis thaliana. The increase in transcript for GPT2 is preceded by an increase in transcript for many transcription factors including Redox Responsive Transcription Factor 1 (RRTF1). The increase in GPT2 transcript after exposure to high light is suppressed in a mutant lacking the RRTF1 transcription factor. The GPT2 response was also suppressed in a mutant with a T-DNA insert in the gene for the triose-phosphate/P_i translocator (TPT). However, plants lacking TPT still had a robust rise in RRTF1 transcript in response to high light. From this, we conclude that both RRTF1 (and possibly other transcription factors) and high amounts of cytosolic triose phosphate are required for induction of the expression of GPT2. We hypothesize that transient GPT2 expression and subsequent translation is adaptive, allowing G6P to move into the chloroplast from the cytosol. The imported G6P can be used for starch synthesis or may flow directly into the Calvin-Benson cycle via an alternative pathway (the G6P shunt), which could be important for regulating and stabilizing photosynthetic electron transport and carbon metabolism.