Analysis of metabolic alterations in Arabidopsis following changes in the carbon dioxide and oxygen partial pressures

Glycolate oxidase-dependent H2O2 production regulates IAA biosynthesis in rice

BACKGROUND

Glycolate oxidase (GLO) is not only a key enzyme in photorespiration but also a major engine for H₂O₂ production in plants. Catalase (CAT)-dependent H₂O₂ decomposition has been previously reported to be involved in the regulation of IAA biosynthesis. However, it is still not known which mechanism contributed to the H₂O₂ production in IAA regulation.

RESULTS

In this study, we found that in glo mutants of rice, as H₂O₂ levels decreased IAA contents significantly increased, whereas high CO₂ abolished the difference in H₂O₂ and IAA contents between glo mutants and WT. Further analyses showed that tryptophan (Trp, the precursor for IAA biosynthesis in the Trp-dependent biosynthetic pathway) also accumulated due to increased tryptophan synthetase β (TSB) activity. Moreover, expression of the genes involved in Trp-dependent IAA biosynthesis and IBA to IAA conversion were correspondingly up-regulated, further implicating that both pathways contribute to IAA biosynthesis as mediated by the GLO-dependent production of H₂O₂.

CONCLUSION

We investigated the function of GLO in IAA signaling in different levels from transcription, enzyme activities to metabolic levels. The results suggest that GLO-dependent H₂O₂ signaling, essentially via photorespiration, confers regulation over IAA biosynthesis in rice plants.

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.

Leaf-age dependent response of carotenoid accumulation to elevated CO2 in Arabidopsis

Carotenoids contribute to photosynthesis, photoprotection, phytohormone and apocarotenoid biosynthesis in plants. Carotenoid-derived metabolites control plant growth, development and signalling processes and their accumulation can depend upon changes in the environment. Elevated carbon dioxide (eCO₂) often enhances carbon assimilation, early growth patterns and overall plant biomass, and may increase carotenoid accumulation due to higher levels of precursors from isoprenoid biosynthesis. Variable effects of eCO₂ on carotenoid accumulation in leaves have been observed for different plant species. Here, we determined whether the variable response of carotenoids to eCO₂ was potentially a function of leaf age and the impact of eCO₂ on leaf development by growing Arabidopsis in ambient CO₂ (400 ppm) and eCO₂ (800 ppm). eCO₂ increased plant leaf number, rosette area, biomass, seed yield and net photosynthesis. In addition, eCO₂ increased carotenoid content by 10-20% in younger emerging leaves, but not in older mature leaves. Older leaves contained approximately 60% less total carotenoids compared to younger leaves. The age-dependent effect on carotenoid content was observed for cotyledon, juvenile and adult phase leaves. We conclude that younger leaves utilize additional carbon from enhanced photosynthesis in eCO₂ to increase carotenoid content, yet older leaves have less capacity to store additional carbon into carotenoids.

Leaf day respiration: low CO2 flux but high significance for metabolism and carbon balance

Contents 986 I. 987 II. 987 III. 988 IV. 991 V. 992 VI. 995 VII. 997 VIII. 998 References 998 SUMMARY: It has been 75 yr since leaf respiratory metabolism in the light (day respiration) was identified as a low-flux metabolic pathway that accompanies photosynthesis. In principle, it provides carbon backbones for nitrogen assimilation and evolves CO₂ and thus impacts on plant carbon and nitrogen balances. However, for a long time, uncertainties have remained as to whether techniques used to measure day respiratory efflux were valid and whether day respiration responded to environmental gaseous conditions. In the past few years, significant advances have been made using carbon isotopes, 'omics' analyses and surveys of respiration rates in mesocosms or ecosystems. There is substantial evidence that day respiration should be viewed as a highly dynamic metabolic pathway that interacts with photosynthesis and photorespiration and responds to atmospheric CO₂ mole fraction. The view of leaf day respiration as a constant and/or negligible parameter of net carbon exchange is now outdated and it should now be regarded as a central actor of plant carbon-use efficiency.

Metabolite pools and carbon flow during C4 photosynthesis in maize: 13CO2 labeling kinetics and cell type fractionation

Worldwide efforts to engineer C4 photosynthesis into C3 crops require a deep understanding of how this complex pathway operates. CO2 is incorporated into four-carbon metabolites in the mesophyll, which move to the bundle sheath where they are decarboxylated to concentrate CO2 around RuBisCO. We performed dynamic 13CO2 labeling in maize to analyze C flow in C4 photosynthesis. The overall labeling kinetics reflected the topology of C4 photosynthesis. Analyses of cell-specific labeling patterns after fractionation to enrich bundle sheath and mesophyll cells revealed concentration gradients to drive intercellular diffusion of malate, but not pyruvate, in the major CO2-concentrating shuttle. They also revealed intercellular concentration gradients of aspartate, alanine, and phosphenolpyruvate to drive a second phosphoenolpyruvate carboxykinase (PEPCK)-type shuttle, which carries 10-14% of the carbon into the bundle sheath. Gradients also exist to drive intercellular exchange of 3-phosphoglycerate and triose-phosphate. There is rapid carbon exchange between the Calvin-Benson cycle and the CO2-concentrating shuttle, equivalent to ~10% of carbon gain. In contrast, very little C leaks from the large pools of metabolites in the C concentration shuttle into respiratory metabolism. We postulate that the presence of multiple shuttles, alongside carbon transfer between them and the Calvin-Benson cycle, confers great flexibility in C4 photosynthesis.

The Transcriptional Responses and Metabolic Consequences of Acclimation to Elevated Light Exposure in Grapevine Berries

An increasing number of field studies that focus on grapevine berry development and ripening implement systems biology approaches; the results are highlighting not only the intricacies of the developmental programming/reprogramming that occurs, but also the complexity of how profoundly the microclimate influences the metabolism of the berry throughout the different stages of development. In a previous study we confirmed that a leaf removal treatment to Sauvignon Blanc grapes, grown in a highly characterized vineyard, primarily affected the level of light exposure to the berries throughout their development. A full transcriptomic analysis of berries from this model vineyard details the underlying molecular responses of the berries in reaction to the exposure and show how the berries acclimated to the imposing light stress. Gene expression involved in the protection of the photosynthetic machinery through rapid protein-turnover and the expression of photoprotective flavonoid compounds were most significantly affected in green berries. Overall, the transcriptome analysis showed that the berries implemented multiple stress-mitigation strategies in parallel and metabolite analysis was used to support the main findings. Combining the transcriptome data and amino acid profiling provided evidence that amino acid catabolism probably contributed to the mitigation of a likely energetic deficit created by the upregulation of (energetically) costly stress defense mechanisms. Furthermore, the rapid turnover of essential proteins involved in the maintenance of primary metabolism and growth in the photosynthetically active grapes appeared to provide precursors for the production of protective secondary metabolites such as apocarotenoids and flavonols in the ripening stages of the berries. Taken together, these results confirmed that the green grape berries responded to light stress much like other vegetative organs and were able to acclimate to the increased exposure, managing their metabolism and energy requirements to sustain the developmental cycle toward ripening. The typical metabolic consequences of leaf removal on grape berries can therefore now be linked to increased light exposure through mechanisms of photoprotection in green berries that leads toward acclimation responses that remain intact until ripening.

Mass spectrometry as a quantitative tool in plant metabolomics

Metabolomics is a research field used to acquire comprehensive information on the composition of a metabolite pool to provide a functional screen of the cellular state. Studies of the plant metabolome include the analysis of a wide range of chemical species with very diverse physico-chemical properties, and therefore powerful analytical tools are required for the separation, characterization and quantification of this vast compound diversity present in plant matrices. In this review, challenges in the use of mass spectrometry (MS) as a quantitative tool in plant metabolomics experiments are discussed, and important criteria for the development and validation of MS-based analytical methods provided.This article is part of the themed issue 'Quantitative mass spectrometry'.

Unravelling the in vivo regulation and metabolic role of the alternative oxidase pathway in C3 species under photoinhibitory conditions

The mitochondrial alternative oxidase pathway (AOP) has been suggested to act as a sink for excess reducing power generated in the chloroplast under high-light (HL) stress and thus may reduce photoinhibition. The aim of this study was to compare different species to investigate the in vivo regulation and role of AOP under HL stress. The in vivo activities of AOP (νalt ) and the cytochrome oxidase pathway, chlorophyll fluorescence, metabolite profiles, alternative oxidase (AOX) capacity and protein amount were determined in leaves of five C3 species under growth light and after HL treatment. Differences in respiration and metabolite levels were observed among species under growth light conditions. The HL response of νalt was highly species dependent, correlated with the AOP capacity and independent of AOX protein content. Nevertheless, significant correlations were observed between νalt , levels of key metabolites and photosynthetic parameters. The results show that the species-specific response of νalt is caused by the differential post-translational regulation of AOX. Significant correlations between respiration, metabolites and photosynthetic performance across species suggest that AOP may permit stress-related amino acid synthesis, whilst maintaining photosynthetic activity under HL stress.

Can cyanobacteria serve as a model of plant photorespiration? - a comparative meta-analysis of metabolite profiles

Photorespiration is a process that is crucial for the survival of oxygenic phototrophs in environments that favour the oxygenation reaction of Rubisco. While photorespiration is conserved among cyanobacteria, algae, and embryophytes, it evolved to different levels of complexity in these phyla. The highest complexity is found in embryophytes, where the pathway involves four cellular compartments and respective transport processes. The complexity of photorespiration in embryophytes raises the question whether a simpler system, such as cyanobacteria, may serve as a model to facilitate our understanding of the common key aspects of photorespiration. In this study, we conducted a meta-analysis of publicly available metabolite profiles from the embryophyte Arabidopsis thaliana and the cyanobacterium Synechocystis sp. PCC 6803 grown under conditions that either activate or suppress photorespiration. The comparative meta-analysis evaluated the similarity of metabolite profiles, the variability of metabolite pools, and the patterns of metabolite ratios. Our results show that the metabolic signature of photorespiration is in part conserved between the compared model organisms under conditions that favour the oxygenation reaction. Therefore, our findings support the claim that cyanobacteria can serve as prokaryotic models of photorespiration in embryophytes.

On the metabolic interactions of (photo)respiration

Given that photorespiration is inextricably linked to the process of photosynthesis by virtue of sharing the common first enzyme Rubisco, the photorespiratory pathway has been less subject to study in isolation than many other metabolic pathways. That said, despite often being described to be linked to reactions of ammonia assimilation, C1 metabolism and respiratory metabolism, the precise molecular mechanisms governing these linkages in land plants remain partially obscure. The application of broad metabolite profiling on mutants with altered levels of metabolic enzymes has facilitated the identification of common and distinct metabolic responses among them. Here we provide an update of the recent findings from such studies, focusing particularly on the interplay between photorespiration and the metabolic reactions of mitochondrial respiration. In order to do so we evaluated (i) changes in organic acids following environmental perturbation of metabolism, (ii) changes in organic acid levels in a wide range of photorespiratory mutants, (iii) changes in levels of photorespiratory metabolites in transgenic tomato lines deficient in the expression of enzymes of the tricarboxylic acid cycle. In addition, we estimated the rates of photorespiration in a complete set of tricarboxylic acid cycle transgenic tomato lines. Finally, we discuss insight concerning the interaction between photorespiration and other pathways that has been attained following the development of (13)CO2-based flux profiling methods.

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.

Response and adaptation of photosynthesis, respiration, and antioxidant systems to elevated CO2 with environmental stress in plants

It is well known that plant photosynthesis and respiration are two fundamental and crucial physiological processes, while the critical role of the antioxidant system in response to abiotic factors is still a focus point for investigating physiological stress. Although one key metabolic process and its response to climatic change have already been reported and reviewed, an integrative review, including several biological processes at multiple scales, has not been well reported. The current review will present a synthesis focusing on the underlying mechanisms in the responses to elevated CO2 at multiple scales, including molecular, cellular, biochemical, physiological, and individual aspects, particularly, for these biological processes under elevated CO2 with other key abiotic stresses, such as heat, drought, and ozone pollution, as well as nitrogen limitation. The present comprehensive review may add timely and substantial information about the topic in recent studies, while it presents what has been well established in previous reviews. First, an outline of the critical biological processes, and an overview of their roles in environmental regulation, is presented. Second, the research advances with regard to the individual subtopics are reviewed, including the response and adaptation of the photosynthetic capacity, respiration, and antioxidant system to CO2 enrichment alone, and its combination with other climatic change factors. Finally, the potential applications for plant responses at various levels to climate change are discussed. The above issue is currently of crucial concern worldwide, and this review may help in a better understanding of how plants deal with elevated CO2 using other mainstream abiotic factors, including molecular, cellular, biochemical, physiological, and whole individual processes, and the better management of the ecological environment, climate change, and sustainable development.