Non-foliar photosynthesis and nitrogen assimilation influence grain yield in durum wheat regardless of water conditions

There is a need to generate improved crop varieties adapted to the ongoing changes in the climate. We studied durum wheat canopy and central metabolism of six different photosynthetic organs in two yield-contrasting varieties. The aim was to understand the mechanisms associated with the water stress response and yield performance. Water stress strongly reduced grain yield, plant biomass and leaf photosynthesis, and downregulated C/N-metabolism genes and key protein levels, which occurred mainly in leaf blades. By contrast, higher yield was associated with high ear dry weight and lower biomass and ears per area, highlighting the advantage of reduced tillering and its consequent improvement in sink strength that promoted C/N metabolism at the whole plant level. An improved C metabolism in blades and ear bracts and N assimilation in all photosynthetic organs facilitated C/N remobilisation to the grain and promoted yield. Therefore, we propose that further yield gains in Mediterranean conditions could be achieved by considering the source-sink dynamics and the contribution of non-foliar organs, particularly N assimilation and remobilisation during the late growth stages. We highlight the power of linking phenotyping with plant metabolism to identify novel traits at the whole plant level to support breeding programmes.

Singlet Oxygen and Superoxide Anion Radical Detection by EPR Spin Trapping in Thylakoid Preparations

Reactive oxygen species (ROS) are produced by energy transfer and electron transport in plant chloroplast thylakoids at non-toxic levels under normal growth conditions, but at threatening levels under adverse or fluctuating environmental conditions. Among chloroplast ROS, singlet oxygen and superoxide anion radical, respectively, produced by photosystem II (PSII) and PSI, are known to be the major ROS under several stress conditions. Both are very unlikely to diffuse out of chloroplasts, but they are instead capable of triggering ROS-mediated chloroplast operational retrograde signalling to activate defence gene expression in concert with hormones and other molecular compounds. Therefore, their detection, identification and localization in vivo or in biological preparations is a priority for a deeper understanding of their role in (concurrent) regulation of plant growth and defence responses. Here, we present two EPR spin traps, abbreviated as TEMPD-HCl and DEPMPO, to detect and identify ROS in complex systems, such as isolated thylakoids, together with some hints and cautions to perform reliable spin trapping experiments.

Analysis of durum wheat photosynthetic organs during grain filling reveals the ear as a water stress-tolerant organ and the peduncle as the largest pool of primary metabolites

The pool of carbon- and nitrogen-rich metabolites is quantitatively relevant in non-foliar photosynthetic organs during grain filling, which have a better response to water limitation than flag leaves. The response of durum wheat to contrasting water regimes has been extensively studied at leaf and agronomic level in previous studies, but the water stress effects on source-sink dynamics, particularly non-foliar photosynthetic organs, is more limited. Our study aims to investigate the response of different photosynthetic organs to water stress and to quantify the pool of carbon and nitrogen metabolites available for grain filling. Five durum wheat varieties were grown in field trials in the Spanish region of Castile and León under irrigated and rainfed conditions. Water stress led to a significant decrease in yield, biomass, and carbon and nitrogen assimilation, improved water use efficiency, and modified grain quality traits in the five varieties. The pool of carbon (glucose, glucose-6-phosphate, fructose, sucrose, starch, and malate) and nitrogen (glutamate, amino acids, proteins and chlorophylls) metabolites in leaf blades and sheaths, peduncles, awns, glumes and lemmas were also analysed. The results showed that the metabolism of the blades and peduncles was the most susceptible to water stress, while ear metabolism showed higher stability, particularly at mid-grain filling. Interestingly, the total metabolite content per organ highlighted that a large source of nutrients, which may be directly involved in grain filling, are found outside the blades, with the peduncles being quantitatively the most relevant. We conclude that yield improvements in our Mediterranean agro-ecosystem are highly linked to the success of shoots in producing ears and a higher number of grains, while grain filling is highly dependent on the capacity of non-foliar organs to fix CO₂ and N. The ear organs show higher stress resilience than other organs, which deserves our attention in future breeding programmes.

Source-Sink Dynamics in Field-Grown Durum Wheat Under Contrasting Nitrogen Supplies: Key Role of Non-Foliar Organs During Grain Filling

The integration of high-throughput phenotyping and metabolic approaches is a suitable strategy to study the genotype-by-environment interaction and identify novel traits for crop improvement from canopy to an organ level. Our aims were to study the phenotypic and metabolic traits that are related to grain yield and quality at canopy and organ levels, with a special focus on source-sink coordination under contrasting N supplies. Four modern durum wheat varieties with contrasting grain yield were grown in field conditions under two N fertilization levels in north-eastern Spain. We evaluated canopy vegetation indices taken throughout the growing season, physiological and metabolic traits in different photosynthetic organs (flag leaf blade, sheath, peduncle, awn, glume, and lemma) at anthesis and mid-grain filling stages, and agronomic and grain quality traits at harvest. Low N supply triggered an imbalance of C and N coordination at the whole plant level, leading to a reduction of grain yield and nutrient composition. The activities of key enzymes in C and N metabolism as well as the levels of photoassimilates showed that each organ plays an important role during grain filling, some with a higher photosynthetic capacity, others for nutrient storage for later stages of grain filling, or N assimilation and recycling. Interestingly, the enzyme activities and sucrose content of the ear organs were positively associated with grain yield and quality, suggesting, together with the regression models using isotope signatures, the potential contribution of these organs during grain filling. This study highlights the use of holistic approaches to the identification of novel targets to improve grain yield and quality in C₃ cereals and the key role of non-foliar organs at late-growth stages.

Screening for Higher Grain Yield and Biomass among Sixty Bread Wheat Genotypes Grown under Elevated CO2 and High-Temperature Conditions

Global warming will inevitably affect crop development and productivity, increasing uncertainty regarding food production. The exploitation of genotypic variability can be a promising approach for selecting improved crop varieties that can counteract the adverse effects of future climate change. We investigated the natural variation in yield performance under combined elevated CO₂ and high-temperature conditions in a set of 60 bread wheat genotypes (59 of the 8TH HTWSN CIMMYT collection and Gazul). Plant height, biomass production, yield components and phenological traits were assessed. Large variations in the selected traits were observed across genotypes. The CIMMYT genotypes showed higher biomass and grain yield when compared to Gazul, indicating that the former performed better than the latter under the studied environmental conditions. Principal component and hierarchical clustering analyses revealed that the 60 wheat genotypes employed different strategies to achieve final grain yield, highlighting that the genotypes that can preferentially increase grain and ear numbers per plant will display better yield responses under combined elevated levels of CO₂ and temperature. This study demonstrates the success of the breeding programs under warmer temperatures and the plants' capacity to respond to the concurrence of certain environmental factors, opening new opportunities for the selection of widely adapted climate-resilient wheat genotypes.

Genotypic Variability on Grain Yield and Grain Nutritional Quality Characteristics of Wheat Grown under Elevated CO2 and High Temperature

The progressive rise in atmospheric CO2 concentrations and temperature associated with climate change is predicted to have a major impact on the productivity and quality of food crops. Therefore, food security is highly dependent on climate change. Following a survey with 60 bread wheat genotypes, here we investigated the genetic variation in grain yield and nutritional quality among 10 of these genotypes grown under elevated CO2 and temperature. With this purpose, the biomass production, grain yield-related traits, the grain concentration of starch, total protein, phenolic compounds, and mineral nutrients, together with the total antioxidant capacity, were determined. Variation among genotypes was found for almost all the studied traits. Higher grain and ear numbers were associated with increased grain yield but decreased grain total protein concentration and minerals such as Cu, Fe, Mg, Na, P, and Zn. Mineral nutrients were mainly associated with wheat biomass, whereas protein concentration was affected by plant biomass and yield-related traits. Associations among different nutrients and promising nutrient concentrations in some wheat genotypes were also found. This study demonstrates that the exploration of genetic diversity is a powerful approach, not only for selecting genotypes with improved quality, but also for dissecting the effect of the environment on grain yield and nutritional composition.

Differential Flag Leaf and Ear Photosynthetic Performance Under Elevated (CO2) Conditions During Grain Filling Period in Durum Wheat

Elevated concentrations of CO₂ (CO₂) in plants with C₃ photosynthesis metabolism, such as wheat, stimulate photosynthetic rates. However, photosynthesis tends to decrease as a function of exposure to high (CO₂) due to down-regulation of the photosynthetic machinery, and this phenomenon is defined as photosynthetic acclimation. Considerable efforts are currently done to determine the effect of photosynthetic tissues, such us spike, in grain filling. There is good evidence that the contribution of ears to grain filling may be important not only under good agronomic conditions but also under high (CO₂). The main objective of this study was to compare photoassimilate production and energy metabolism between flag leaves and glumes as part of ears of wheat (Triticum turgidum L. subsp. durum cv. Amilcar) plants exposed to ambient [a(CO₂)] and elevated [e(CO₂)] (CO₂) (400 and 700 μmol mol^-1, respectively). Elevated CO₂ had a differential effect on the responses of flag leaves and ears. The ears showed higher gross photosynthesis and respiration rates compared to the flag leaves. The higher ear carbohydrate content and respiration rates contribute to increase the grain dry mass. Our results support the concept that acclimation of photosynthesis to e(CO₂) is driven by sugar accumulation, reduction in N concentrations and repression of genes related to photosynthesis, glycolysis and the tricarboxylic acid cycle, and that these were more marked in glumes than leaves. Further, important differences are described on responsiveness of flag leaves and ears to e(CO₂) on genes linked with carbon and nitrogen metabolism. These findings provide information about the impact of e(CO₂) on ear development during the grain filling stage and are significant for understanding the effects of increasing (CO₂) on crop yield.

Surfing the Hyperbola Equations of the Steady-State Farquhar-von Caemmerer-Berry C3 Leaf Photosynthesis Model: What Can a Theoretical Analysis of Their Oblique Asymptotes and Transition Points Tell Us?

The asymptotes and transition points of the net CO2 assimilation (A/Ci) rate curves of the steady-state Farquhar-von Caemmerer-Berry (FvCB) model for leaf photosynthesis of C3 plants are examined in a theoretical study, which begins from the exploration of the standard equations of hyperbolae after rotating the coordinate system. The analysis of the A/Ci quadratic equations of the three limitation states of the FvCB model-abbreviated as Ac, Aj and Ap-allows us to conclude that their oblique asymptotes have a common slope that depends only on the mesophyll conductance to CO2 diffusion (gm). The limiting values for the transition points between any two states of the three limitation states c, j and p do not depend on gm, and the results are therefore valid for rectangular and non-rectangular hyperbola equations of the FvCB model. The analysis of the variation of the slopes of the asymptotes with gm casts doubts about the fulfilment of the steady-state conditions, particularly, when the net CO2 assimilation rate is inhibited at high CO2 concentrations. The application of the theoretical analysis to extended steady-state FvCB models, where the hyperbola equations of Ac, Aj and Ap are modified to accommodate nitrogen assimilation and amino acids export via the photorespiratory pathway, is also discussed.

De Novo Transcriptome Analysis of Durum Wheat Flag Leaves Provides New Insights Into the Regulatory Response to Elevated CO2 and High Temperature

Global warming is becoming a significant problem for food security, particularly in the Mediterranean basin. The use of molecular techniques to study gene-level responses to environmental changes in non-model organisms is increasing and may help to improve the mechanistic understanding of durum wheat response to elevated CO2 and high temperature. With this purpose, we performed transcriptome RNA sequencing (RNA-Seq) analyses combined with physiological and biochemical studies in the flag leaf of plants grown in field chambers at ear emergence. Enhanced photosynthesis by elevated CO2 was accompanied by an increase in biomass and starch and fructan content, and a decrease in N compounds, as chlorophyll, soluble proteins, and Rubisco content, in association with a decline of nitrate reductase and initial and total Rubisco activities. While high temperature led to a decline of chlorophyll, Rubisco activity, and protein content, the glucose content increased and starch decreased. Furthermore, elevated CO2 induced several genes involved in mitochondrial electron transport, a few genes for photosynthesis and fructan synthesis, and most of the genes involved in secondary metabolism and gibberellin and jasmonate metabolism, whereas those related to light harvesting, N assimilation, and other hormone pathways were repressed. High temperature repressed genes for C, energy, N, lipid, secondary, and hormone metabolisms. Under the combined increases in atmospheric CO2 and temperature, the transcript profile resembled that previously reported for high temperature, although elevated CO2 partly alleviated the downregulation of primary and secondary metabolism genes. The results suggest that there was a reprogramming of primary and secondary metabolism under the future climatic scenario, leading to coordinated regulation of C-N metabolism towards C-rich metabolites at elevated CO2 and a shift away from C-rich secondary metabolites at high temperature. Several candidate genes differentially expressed were identified, including protein kinases, receptor kinases, and transcription factors.

C and N metabolism in barley leaves and peduncles modulates responsiveness to changing CO2

Balancing of leaf carbohydrates is a key process for maximising crop performance in elevated CO2 environments. With the aim of testing the role of the carbon sink-source relationship under different CO2 conditions, we performed two experiments with two barley genotypes (Harrington and RCSL-89) exposed to changing CO2. In Experiment 1, the genotypes were exposed to 400 and 700 ppm CO2. Elevated CO2 induced photosynthetic acclimation in Harrington that was linked with the depletion of Rubisco protein. In contrast, a higher peduncle carbohydrate-storage capacity in RSCL-89 was associated with a better balance of leaf carbohydrates that could help to maximize the photosynthetic capacity under elevated CO2. In Experiment 2, plants that were grown at 400 ppm or 700 ppm CO2 for 5 weeks were switched to 700 ppm or 400 ppm CO2, respectively. Raising CO2 to 700 ppm increased photosynthetic rates with a reduction in leaf carbohydrate content and an improvement in N assimilation. The increase in nitrate content was associated with up-regulation of genes of protein transcripts of photosynthesis and N assimilation that favoured plant performance under elevated CO2. Finally, decreasing the CO2 from 700 ppm to 400 ppm revealed that both stomatal closure and inhibited expression of light-harvesting proteins negatively affected photosynthetic performance and plant growth.

Improved responses to elevated CO2 in durum wheat at a low nitrate supply associated with the upregulation of photosynthetic genes and the activation of nitrate assimilation

Elevated CO₂ often leads to photosynthetic acclimation, and N availability may alter this response. We investigated whether the coordination of shoot-root N assimilation by elevated CO₂ may help to optimize the whole-plant N allocation and maximize photosynthesis in hydroponically-grown durum wheat at two NO₃^- supplies in interaction with plant development. Transcriptional and biochemical analyses were performed on flag leaves and roots. At anthesis, the improved photosynthetic acclimation response to elevated CO₂ at low N was associated with increased Rubisco, chlorophyll and amino acid contents, and upregulation of genes related to their biosynthesis, light reactions and Calvin-Benson cycle, while a decrease was recorded at high N. Despite the decrease in carbohydrates with elevated CO₂ at low N and the increase at high N, a stronger upward trend in leaf NR activity was found at low rather than high N. The induction of N recycling-related genes was accompanied by an amino acids decline at high N. At the grain-filling stage, the photosynthetic acclimation to elevated CO₂ at high N was associated with the downregulation of both N assimilation, mainly in roots, and photosynthetic genes. At low N, enhanced root N assimilation partly compensated for slower shoot N assimilation and maximized photosynthetic capacity.

The Combination of Trichoderma harzianum and Chemical Fertilization Leads to the Deregulation of Phytohormone Networking, Preventing the Adaptive Responses of Tomato Plants to Salt Stress

Plants have evolved effective mechanisms to avoid or reduce the potential damage caused by abiotic stresses. In addition to biocontrol abilities, Trichoderma genus fungi promote growth and alleviate the adverse effects caused by saline stress in plants. Morphological, physiological, and molecular changes were analyzed in salt-stressed tomato plants grown under greenhouse conditions in order to investigate the effects of chemical and biological fertilizations. The application of Trichoderma harzianum T34 to tomato seeds had very positive effects on plant growth, independently of chemical fertilization. The application of salt stress significantly changed the parameters related to growth and gas-exchange rates in tomato plants subject to chemical fertilization. However, the gas-exchange parameters were not affected in unfertilized plants under the same moderate saline stress. The combined application of T34 and salt significantly reduced the fresh and dry weights of NPK-fertilized plants, while the opposite effects were detected when no chemical fertilization was applied. Decaying symptoms were observed in salt-stressed and chemically fertilized plants previously treated with T34. This damaged phenotype was linked to significantly higher intercellular CO2 and slight increases in stomatal conductance and transpiration, and to the deregulation of phytohormone networking in terms of significantly lower expression levels of the salt overlay sensitivity 1 (SOS1) gene, and the genes involved in signaling abscisic acid-, ethylene-, and salicylic acid-dependent pathways and ROS production, in comparison with those observed in salt-challenged NPK-fertilized plants.

Metabolic and Transcriptional Analysis of Durum Wheat Responses to Elevated CO2 at Low and High Nitrate Supply

Elevated [CO₂] (eCO₂) can lead to photosynthetic acclimation and this is often intensified by low nitrogen (N). Despite intensive studies of plant responses to eCO₂, the regulation mechanism of primary metabolism at the whole-plant level in interaction with [Formula: see text] supply remains unclear. We examined the metabolic and transcriptional responses triggered by eCO₂ in association with physiological-biochemical traits in flag leaves and roots of durum wheat grown hydroponically in ambient and elevated [CO₂] with low (LN) and high (HN) [Formula: see text] supply. Multivariate analysis revealed a strong interaction between eCO₂ and [Formula: see text] supply. Photosynthetic acclimation induced by eCO₂ in LN plants was accompanied by an increase in biomass and carbohydrates, and decreases of leaf organic N per unit area, organic acids, inorganic ions, Calvin-Benson cycle intermediates, Rubisco, nitrate reductase activity, amino acids and transcripts for N metabolism, particularly in leaves, whereas [Formula: see text] uptake was unaffected. In HN plants, eCO₂ did not decrease photosynthetic capacity or leaf organic N per unit area, but induced transcripts for N metabolism, especially in roots. In conclusion, the photosynthetic acclimation in LN plants was associated with an inhibition of leaf [Formula: see text] assimilation, whereas up-regulation of N metabolism in roots could have mitigated the acclimatory effect of eCO₂ in HN plants.

Temporal kinetics of the transcriptional response to carbon depletion and sucrose readdition in Arabidopsis seedlings

To investigate whether the transcriptional response to carbon (C) depletion and sucrose resupply depends on the duration and severity of the C depletion, Arabidopsis seedlings were grown in liquid culture and harvested 3, 6, 12, 24, 48 and 72 h after removing sucrose from the medium and 30 min after resupplying sucrose at each time. Expression profiling revealed early transcriptional inhibition of cell wall synthesis and remodelling of signalling, followed by induction of C recycling and photosynthesis and general inhibition of growth. The temporal sequence differed from the published response to progressive exhaustion of C during a night and extended night in vegetatively growing plants. The response to sucrose readdition was conserved across the C-depletion time course. Intriguingly, the vast majority of rapidly responding transcripts decreased rather than increased. The majority of transcripts that respond rapidly to sucrose and many transcripts that respond during C depletion also decrease after treating seedlings with the transcriptional inhibitor cordycepin A. Comparison with published responses to overexpression of otsA, AKIN10 and bZIP11 revealed that many genes that respond to C depletion, and especially sucrose resupply, respond to one or more of these C-signalling components. Thus, multiple factors contribute to C responsiveness, including many signalling components, transcriptional regulation and transcript turnover.

Functional and transcriptional characterization of a barley mutant with impaired photosynthesis

Chemical mutagenesis induces variations that may assist in the identification of targets for adaptation to growth under atmospheric CO2 enrichment. The aim of this work was to characterize the limitations causing reduced photosynthetic capacity in G132 mutagenized barley (Hordeum vulgare L. cv. Graphic) grown in a glasshouse. Compared to the wild type (WT) G132 showed increased transcript levels for the PSII light harvesting complex, but lower levels of chlorophyll, transcripts for protochlorophyllide oxidoreductase A and psbQ, and PSII quantum efficiency in young leaves. Rubisco limitation had an overriding influence on G132 photosynthesis, and was due to strong and selective decreases in Rubisco protein and activity. These reductions were accompanied by enhanced Rubisco transcripts, but increased levels of a Rubisco degradation product. G132 showed lower levels of carbohydrates, amino acids and corresponding transcripts, and proteins, but not of nitrate. Many of the measured parameters recovered in the mutant as development progressed, or decreased less than in the WT, indicating that senescence was delayed. G132 had a longer growth period than the WT and similar final plant dry matter. The reduced resource investment in Rubisco of G132 may prove useful for studies on barley adaptation to elevated CO2 and climate change.

Photosynthesis-dependent/independent control of stomatal responses to CO2 in mutant barley with surplus electron transport capacity and reduced SLAH3 anion channel transcript

The mechanisms of stomatal sensitivity to CO2 are yet to be fully understood. The role of photosynthetic and non-photosynthetic factors in stomatal responses to CO2 was investigated in wild-type barley (Hordeum vulgare var. Graphic) and in a mutant (G132) with decreased photochemical and Rubisco capacities. The CO2 and DCMU responses of stomatal conductance (gs), gas exchange, chlorophyll fluorescence and levels of ATP, with a putative transcript for stomatal opening were analysed. G132 had greater gs than the wild-type, despite lower photosynthesis rates and higher intercellular CO2 concentrations (Ci). The mutant had Rubisco-limited photosynthesis at very high CO2 levels, and higher ATP contents than the wild-type. Stomatal sensitivity to CO2 under red light was lower in G132 than in the wild-type, both in photosynthesizing and DCMU-inhibited leaves. Under constant Ci and red light, stomatal sensitivity to DCMU inhibition was higher in G132. The levels of a SLAH3-like slow anion channel transcript, involved in stomatal closure, decreased sharply in G132. The results suggest that stomatal responses to CO2 depend partly on the balance of photosynthetic electron transport to carbon assimilation capacities, but are partially regulated by the CO2 signalling network. High gs can improve the adaptation to climate change in well-watered conditions.

Quantitative RT-PCR Platform to Measure Transcript Levels of C and N Metabolism-Related Genes in Durum Wheat: Transcript Profiles in Elevated [CO2] and High Temperature at Different Levels of N Supply

Only limited public transcriptomics resources are available for durum wheat and its responses to environmental changes. We developed a quantitative reverse transcription-PCR (qRT-PCR) platform for analysing the expression of primary C and N metabolism genes in durum wheat in leaves (125 genes) and roots (38 genes), based on available bread wheat genes and the identification of orthologs of known genes in other species. We also assessed the expression stability of seven reference genes for qRT-PCR under varying environments. We therefore present a functional qRT-PCR platform for gene expression analysis in durum wheat, and suggest using the ADP-ribosylation factor as a reference gene for qRT-PCR normalization. We investigated the effects of elevated [CO(2)] and temperature at two levels of N supply on C and N metabolism by combining gene expression analysis, using our qRT-PCR platform, with biochemical and physiological parameters in durum wheat grown in field chambers. Elevated CO(2) down-regulated the photosynthetic capacity and led to the loss of N compounds, including Rubisco; this effect was exacerbated at low N. Mechanistically, the reduction in photosynthesis and N levels could be associated with a decreased transcription of the genes involved in photosynthesis and N assimilation. High temperatures increased stomatal conductance, and thus did not inhibit photosynthesis, even though Rubisco protein and activity, soluble protein, leaf N, and gene expression for C fixation and N assimilation were down-regulated. Under a future scenario of climate change, the extent to which C fixation capacity and N assimilation are down-regulated will depend upon the N supply.

Transcriptome and metabolome analysis of plant sulfate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulfur, nitrogen and phosphorus nutritional responses in Arabidopsis

Sulfur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulfur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulfate starvation have been studied in the past, knowledge of the regulation of sulfur metabolism is still fragmentary. This work focuses on the discovery of candidates for regulatory genes such as transcription factors (TFs) using 'omics technologies. For this purpose a short term sulfate-starvation/re-supply approach was used. ATH1 microarray studies and metabolite determinations yielded 21 TFs which responded more than 2-fold at the transcriptional level to sulfate starvation. Categorization by response behaviors under sulfate-starvation/re-supply and other nutrient starvations such as nitrate and phosphate allowed determination of whether the TF genes are specific for or common between distinct mineral nutrient depletions. Extending this co-behavior analysis to the whole transcriptome data set enabled prediction of putative downstream genes. Additionally, combinations of transcriptome and metabolome data allowed identification of relationships between TFs and downstream responses, namely, expression changes in biosynthetic genes and subsequent metabolic responses. Effect chains on glucosinolate and polyamine biosynthesis are discussed in detail. The knowledge gained from this study provides a blueprint for an integrated analysis of transcriptomics and metabolomics and application for the identification of uncharacterized genes.

Transcriptome and metabolome analysis of plant sulfate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulfur, nitrogen and phosphorus nutritional responses in Arabidopsis

Sulfur is an essential macronutrient for plant growth and development. Reaching a thorough understanding of the molecular basis for changes in plant metabolism depending on the sulfur-nutritional status at the systems level will advance our basic knowledge and help target future crop improvement. Although the transcriptional responses induced by sulfate starvation have been studied in the past, knowledge of the regulation of sulfur metabolism is still fragmentary. This work focuses on the discovery of candidates for regulatory genes such as transcription factors (TFs) using 'omics technologies. For this purpose a short term sulfate-starvation/re-supply approach was used. ATH1 microarray studies and metabolite determinations yielded 21 TFs which responded more than 2-fold at the transcriptional level to sulfate starvation. Categorization by response behaviors under sulfate-starvation/re-supply and other nutrient starvations such as nitrate and phosphate allowed determination of whether the TF genes are specific for or common between distinct mineral nutrient depletions. Extending this co-behavior analysis to the whole transcriptome data set enabled prediction of putative downstream genes. Additionally, combinations of transcriptome and metabolome data allowed identification of relationships between TFs and downstream responses, namely, expression changes in biosynthetic genes and subsequent metabolic responses. Effect chains on glucosinolate and polyamine biosynthesis are discussed in detail. The knowledge gained from this study provides a blueprint for an integrated analysis of transcriptomics and metabolomics and application for the identification of uncharacterized genes.

Involvement of nitrogen and cytokinins in photosynthetic acclimation to elevated CO₂ of spring wheat

Acclimation of photosynthetic capacity to elevated CO₂ involves a decrease of the leaf Rubisco content. In the present study, it was hypothesized that nitrogen uptake and partitioning within the leaf and among different aboveground organs affects the down-regulation of Rubisco. Given the interdependence of nitrogen and cytokinin signals at the whole plant level, it is also proposed that cytokinins affect the nitrogen economy of plants under elevated CO₂, and therefore the acclimatory responses. Spring wheat received varying levels of nitrogen and cytokinin in field chambers with ambient (370 μmol mol⁻¹) or elevated (700 μmol mol⁻¹) atmospheric CO₂. Gas exchange, Rubisco, soluble protein and nitrogen contents were determined in the top three leaves in the canopy, together with total nitrogen contents per shoot. Growth in elevated CO₂ induced decreases in photosynthetic capacity only when nitrogen supply was low. However, the leaf contents of Rubisco, soluble protein and total nitrogen on an area basis declined in elevated CO₂ regardless of nitrogen supply. Total nitrogen in the shoot was no lower in elevated than ambient CO₂, but the fraction of this nitrogen located in flag and penultimate leaves was lower in elevated CO₂. Decreased Rubisco: chlorophyll ratios accompanied losses of leaf Rubisco with CO₂ enrichment. Cytokinin applications increased nitrogen content in all leaves and nitrogen allocation to senescing leaves, but decreased Rubisco contents in flag leaves at anthesis and in all leaves 20 days later, together with the amount of Rubisco relative to soluble protein in all leaves at both growth stages. The results suggest that down regulation of Rubisco in leaves at elevated CO₂ is linked with decreased allocation of nitrogen to the younger leaves and that cytokinins cause a fractional decrease of Rubisco and therefore do not alleviate acclimation to elevated CO₂.

Does ear C sink strength contribute to overcoming photosynthetic acclimation of wheat plants exposed to elevated CO2?

Wheat plants (Triticum durum Desf., cv. Regallo) were grown in the field to study the effects of contrasting [CO(2)] conditions (700 versus 370 μmol mol(-1)) on growth, photosynthetic performance, and C management during the post-anthesis period. The aim was to test whether a restricted capacity of sink organs to utilize photosynthates drives a loss of photosynthetic capacity in elevated CO(2). The ambient (13)C/(12)C isotopic composition (δ(13)C) of air CO(2) was changed from -10.2‰ in ambient [CO(2)] to -23.6‰ under elevated [CO(2)] between the 7th and the 14th days after anthesis in order to study C assimilation and partitioning between leaves and ears. Elevated [CO(2)] had no significant effect on biomass production and grain filling, and caused an accumulation of C compounds in leaves. This was accompanied by up-regulation of phosphoglycerate mutase and ATP synthase protein content, together with down-regulation of adenosine diphosphate glucose pyrophosphatase protein. Growth in elevated [CO(2)] negatively affected Rubisco and Rubisco activase protein content and induced photosynthetic down-regulation. CO(2) enrichment caused a specific decrease in Rubisco content, together with decreases in the amino acid and total N content of leaves. The C labelling revealed that in flag leaves, part of the C fixed during grain filling was stored as starch and structural C compounds whereas the rest of the labelled C (mainly in the form of soluble sugars) was completely respired 48 h after the end of labelling. Although labelled C was not detected in the δ(13)C of ear total organic matter and respired CO(2), soluble sugar δ(13)C revealed that a small amount of labelled C reached the ear. The (12)CO(2) labelling suggests that during the beginning of post-anthesis the ear did not contribute towards overcoming flag leaf carbohydrate accumulation, and this had a consequent effect on protein expression and photosynthetic acclimation.

Acclimation to future atmospheric CO2 levels increases photochemical efficiency and mitigates photochemistry inhibition by warm temperatures in wheat under field chambers

A study was conducted over 2 years to determine whether growth under elevated CO(2) (700 μmol mol(-1) ) and temperature (ambient + 4 °C) conditions modifies photochemical efficiency or only the use of electron transport products in spring wheat grown in field chambers. Elevated atmospheric CO(2) concentrations increased crop dry matter at maturity by 12-17%, while above-ambient temperatures did not significantly affect dry matter yield. In measurements with ambient CO(2) at ear emergence and after anthesis, growth at elevated CO(2) concentrations decreased flag leaf light-saturated carbon assimilation. The quantum yield of electron transport (Φ(PSII) ) measured at ambient CO(2) and higher irradiances increased at ear emergence and decreased after anthesis in plants grown at elevated CO(2) . At higher light intensities, but not in low light, photochemical quenching (qP) decreased after growth in elevated CO(2) conditions. Growth under CO(2) enrichment increased dark- (Fv:Fm) and light-adapted (Fv':Fm') photochemical efficiencies, and decreased the chlorophyll a:b ratio, suggesting an increase in light-harvesting complexes relative to PSII reaction centres. A relatively higher decrease in carbon assimilation than the decrease in Φ(PSII) pointed to a sink other than CO(2) assimilation for electron transport products at defined growth stages. With higher light intensities, warmer temperatures increased Φ(PSII) and Fv':Fm' at ear emergence and decreased Φ(PSII) after anthesis; in ambient-but not elevated-CO(2) , warmer temperatures also decreased qP after anthesis. CO(2) fixation increased or did not change with temperature, depending on the growth stage and year. We conclude that elevated CO(2) decreases the carbon assimilation capacity, but increases photochemistry and resource allocation to light harvesting, and that elevated levels of CO(2) can mitigate photochemistry inhibition as a result of warm temperatures.

Acclimation to future atmospheric CO2 levels increases photochemical efficiency and mitigates photochemistry inhibition by warm temperatures in wheat under field chambers

A study was conducted over 2 years to determine whether growth under elevated CO(2) (700 μmol mol(-1) ) and temperature (ambient + 4 °C) conditions modifies photochemical efficiency or only the use of electron transport products in spring wheat grown in field chambers. Elevated atmospheric CO(2) concentrations increased crop dry matter at maturity by 12-17%, while above-ambient temperatures did not significantly affect dry matter yield. In measurements with ambient CO(2) at ear emergence and after anthesis, growth at elevated CO(2) concentrations decreased flag leaf light-saturated carbon assimilation. The quantum yield of electron transport (Φ(PSII) ) measured at ambient CO(2) and higher irradiances increased at ear emergence and decreased after anthesis in plants grown at elevated CO(2) . At higher light intensities, but not in low light, photochemical quenching (qP) decreased after growth in elevated CO(2) conditions. Growth under CO(2) enrichment increased dark- (Fv:Fm) and light-adapted (Fv':Fm') photochemical efficiencies, and decreased the chlorophyll a:b ratio, suggesting an increase in light-harvesting complexes relative to PSII reaction centres. A relatively higher decrease in carbon assimilation than the decrease in Φ(PSII) pointed to a sink other than CO(2) assimilation for electron transport products at defined growth stages. With higher light intensities, warmer temperatures increased Φ(PSII) and Fv':Fm' at ear emergence and decreased Φ(PSII) after anthesis; in ambient-but not elevated-CO(2) , warmer temperatures also decreased qP after anthesis. CO(2) fixation increased or did not change with temperature, depending on the growth stage and year. We conclude that elevated CO(2) decreases the carbon assimilation capacity, but increases photochemistry and resource allocation to light harvesting, and that elevated levels of CO(2) can mitigate photochemistry inhibition as a result of warm temperatures.

Future CO2 concentrations, though not warmer temperatures, enhance wheat photosynthesis temperature responses

The temperature dependence of C3 photosynthesis is known to vary according to the growth environment. Atmospheric CO2 concentration and temperature are predicted to increase with climate change. To test whether long-term growth in elevated CO2 and temperature modifies photosynthesis temperature response, wheat (Triticum aestivum L.) was grown in ambient CO2 (370 micromol mol(-1)) and elevated CO2 (700 micromol mol(-1)) combined with ambient temperatures and 4 degrees C warmer ones, using temperature gradient chambers in the field. Flag leaf photosynthesis was measured at temperatures ranging from 20 to 35 degrees C and varying CO2 concentrations between ear emergence and anthesis. The maximum rate of carboxylation was determined in vitro in the first year of the experiment and from the photosynthesis-intercellular CO2 response in the second year. With measurement CO2 concentrations of 330 micromol mol(-1) or lower, growth temperature had no effect on flag leaf photosynthesis in plants grown in ambient CO2, while it increased photosynthesis in elevated growth CO2. However, warmer growth temperatures did not modify the response of photosynthesis to measurement temperatures from 20 to 35 degrees C. A central finding of this study was that the increase with temperature in photosynthesis and the photosynthesis temperature optimum were significantly higher in plants grown in elevated rather than ambient CO2. In association with this, growth in elevated CO2 increased the temperature response (activation energy) of the maximum rate of carboxylation. The results provide field evidence that growth under CO2 enrichment enhances the response of Rubisco activity to temperature in wheat.

Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings

Arabidopsis seedlings were subjected to 2 days of carbon starvation, and then resupplied with 15 mm sucrose. The transcriptional and metabolic response was analyzed using ATH1 arrays, real-time quantitative (q)RT-PCR analysis of >2000 transcription regulators, robotized assays of enzymes from central metabolism and metabolite profiling. Sucrose led within 30 min to greater than threefold changes of the transcript levels for >100 genes, including 20 transcription regulators, 15 ubiquitin-targeting proteins, four trehalose phosphate synthases, autophagy protein 8e, several glutaredoxins and many genes of unknown function. Most of these genes respond to changes of endogenous sugars in Arabidopsis rosettes, making them excellent candidates for upstream components of sugar signaling pathways. Some respond during diurnal cycles, consistent with them acting in signaling pathways that balance the supply and utilization of carbon in normal growth conditions. By 3 h, transcript levels change for >1700 genes. This includes a coordinated induction of genes involved in carbohydrate synthesis, glycolysis, respiration, amino acid and nucleotide synthesis, DNA, RNA and protein synthesis and protein folding, and repression of genes involved in amino acid and lipid catabolism, photosynthesis and chloroplast protein synthesis and folding. The changes of transcripts are followed by a delayed activation of central metabolic pathways and growth processes, which use intermediates from these pathways. Sucrose and reducing sugars accumulate during the first 3-8 h, and starch for 24 h, showing that there is a delay until carbon utilization for growth recommences. Gradual changes of enzyme activities and metabolites are found for many metabolic pathways, including glycolysis, nitrate assimilation, the shikimate pathway and myoinositol, proline and fatty acid metabolism. After 3-8 h, there is a decrease of amino acids, followed by a gradual increase of protein.

Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus

Affymetrix ATH1 arrays, large-scale real-time reverse transcription PCR of approximately 2200 transcription factor genes and other gene families, and analyses of metabolites and enzyme activities were used to investigate the response of Arabidopsis to phosphate (Pi) deprivation and re-supply. Transcript data were analysed with MapMan software to identify coordinated, system-wide changes in metabolism and other cellular processes. Phosphorus (P) deprivation led to induction or repression of > 1000 genes involved in many processes. A subset, including the induction of genes involved in P uptake, the mobilization of organic Pi, the conversion of phosphorylated glycolytic intermediates to carbohydrates and organic acids, the replacement of P-containing phospholipids with galactolipids and the repression of genes involved in nucleotide/nucleic acid synthesis, was reversed within 3 h after Pi re-supply. Analyses of 22 enzyme activities revealed that changes in transcript levels often, but not always, led to changes in the activities of the encoded enzymes in P-deprived plants. Analyses of metabolites confirmed that P deprivation leads to a shift towards the accumulation of carbohydrates, organic acids and amino acids, and that Pi re-supply leads to use of the latter. P-deprived plants also showed large changes in the expression of many genes involved in, for example, secondary metabolism and photosynthesis. These changes were not reversed rapidly upon Pi re-supply and were probably secondary in origin. Differentially expressed and highly P-specific putative regulator genes were identified that presumably play central roles in coordinating the complex responses of plants to changes in P nutrition. The specific responses to Pi differ markedly from those found for nitrate, whereas the long-term responses during P and N deprivation share common and non-specific features.

Sugar-induced increases in trehalose 6-phosphate are correlated with redox activation of ADPglucose pyrophosphorylase and higher rates of starch synthesis in Arabidopsis thaliana

Tre6P (trehalose 6-phosphate) is implicated in sugar-signalling pathways in plants, but its exact functions in vivo are uncertain. One of the main obstacles to discovering these functions is the difficulty of measuring the amount of Tre6P in plant tissues. We have developed a highly specific assay, using liquid chromatography coupled to MS-Q3 (triple quadrupole MS), to measure Tre6P in the femto-picomole range. The Tre6P content of sucrose-starved Arabidopsis thaliana seedlings in axenic culture increased from 18 to 482 pmol x g(-1) FW (fresh weight) after adding sucrose. Leaves from soil-grown plants contained 67 pmol x g(-1) FW at the end of the night, which rose to 108 pmol x g(-1)FW after 4 h of illumination. Even greater changes in Tre6P content were seen after a 6 h extension of the dark period, and in the starchless mutant, pgm. The intracellular concentration of Tre6P in wild-type leaves was estimated to range from 1 to 15 microM. It has recently been reported that the addition of Tre6P to isolated chloroplasts leads to redox activation of AGPase (ADPglucose pyrophosphorylase) [Kolbe, Tiessen, Schluepmann, Paul, Ulrich and Geigenberger (2005) Proc. Natl. Acad. Sci. U.S.A. 102, 11118-11123]. Using the new assay for Tre6P, we found that rising sugar levels in plants are accompanied by increases in the level of Tre6P, redox activation of AGPase and the stimulation of starch synthesis in vivo. These results indicate that Tre6P acts as a signalling metabolite of sugar status in plants, and support the proposal that Tre6P mediates sucrose-induced changes in the rate of starch synthesis.

Effect of sulfur availability on the integrity of amino acid biosynthesis in plants

Amino acid levels in plants are regulated by a complex interplay of regulatory circuits at the level of enzyme activities and gene expression. Despite the diversity of precursors involved in amino acid biosynthesis as providing the carbon backbones, the amino groups and, for the amino acids methionine and cysteine, the sulfhydryl group and despite the involvement of amino acids as substrates in various downstream metabolic processes, the plant usually manages to provide relatively constant levels of all amino acids. Here we collate data on how amino acid homeostasis is shifted upon depletion of one of the major biosynthetic constituents, i.e., sulfur. Arabidopsis thaliana seedlings exposed to sulfate starvation respond with a set of adaptation processes to achieve a new balance of amino acid metabolism. First, metabolites containing reduced sulfur (cysteine, glutathione, S-adenosylmethionine) are reduced leading to a number of downstream effects. Second, the relative excess accumulation of N over S triggers processes to dump nitrogen in asparagine, glutamine and further N-rich compounds like ureides. Third, the depletion of glutathione affects the redox and stress response system of the glutathione-ascorbate cycle. Thus, biosynthesis of aromatic compounds is triggered to compensate for this loss, leading to an increased flux and accumulation of aromatic amino acids, especially tryptophan. Despite sulfate starvation, the homeostasis is kept, though shifted to a new state. This adaptation process keeps the plant viable even under an adverse nutritional status.

Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis

The diurnal cycle strongly influences many plant metabolic and physiological processes. Arabidopsis thaliana rosettes were harvested six times during 12-h-light/12-h-dark treatments to investigate changes in gene expression using ATH1 arrays. Diagnostic gene sets were identified from published or in-house expression profiles of the response to light, sugar, nitrogen, and water deficit in seedlings and 4 h of darkness or illumination at ambient or compensation point [CO(2)]. Many sugar-responsive genes showed large diurnal expression changes, whose timing matched that of the diurnal changes of sugars. A set of circadian-regulated genes also showed large diurnal changes in expression. Comparison of published results from a free-running cycle with the diurnal changes in Columbia-0 (Col-0) and the starchless phosphoglucomutase (pgm) mutant indicated that sugars modify the expression of up to half of the clock-regulated genes. Principle component analysis identified genes that make large contributions to diurnal changes and confirmed that sugar and circadian regulation are the major inputs in Col-0 but that sugars dominate the response in pgm. Most of the changes in pgm are triggered by low sugar levels during the night rather than high levels in the light, highlighting the importance of responses to low sugar in diurnal gene regulation. We identified a set of candidate regulatory genes that show robust responses to alterations in sugar levels and change markedly during the diurnal cycle.

Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis

The diurnal cycle strongly influences many plant metabolic and physiological processes. Arabidopsis thaliana rosettes were harvested six times during 12-h-light/12-h-dark treatments to investigate changes in gene expression using ATH1 arrays. Diagnostic gene sets were identified from published or in-house expression profiles of the response to light, sugar, nitrogen, and water deficit in seedlings and 4 h of darkness or illumination at ambient or compensation point [CO(2)]. Many sugar-responsive genes showed large diurnal expression changes, whose timing matched that of the diurnal changes of sugars. A set of circadian-regulated genes also showed large diurnal changes in expression. Comparison of published results from a free-running cycle with the diurnal changes in Columbia-0 (Col-0) and the starchless phosphoglucomutase (pgm) mutant indicated that sugars modify the expression of up to half of the clock-regulated genes. Principle component analysis identified genes that make large contributions to diurnal changes and confirmed that sugar and circadian regulation are the major inputs in Col-0 but that sugars dominate the response in pgm. Most of the changes in pgm are triggered by low sugar levels during the night rather than high levels in the light, highlighting the importance of responses to low sugar in diurnal gene regulation. We identified a set of candidate regulatory genes that show robust responses to alterations in sugar levels and change markedly during the diurnal cycle.

Fructan synthesis is inhibited by phosphate in warm-grown, but not in cold-treated, excised barley leaves

The inhibition of fructan accumulation by phosphate was investigated in warm-grown and cold-treated barley (Hordeum vulgare) plants. Detached leaves were incubated in water or phosphate for 24 h under lighting or in darkness. Fructosyltransferase, sucrose phosphate synthase (SPS) and cytosolic fructose-1,6-bisphosphatase (FBPase) activities were subsequently analysed, as well as the content of carbohydrates, hexose-phosphates, phosphate, amino acids and protein. In warm-grown leaves, phosphate decreased fructan accumulation and total carbon in carbohydrates and did not affect protein content. Phosphate increased hexose-phosphates, phosphate and amino acids. Fructosyltransferase and FBPase activities were not affected by phosphate feeding, while SPS activity was inhibited by phosphate in incubations in both light and darkness. In cold-treated leaves, which before incubation had higher SPS activities than warm-grown leaves, phosphate had no inhibitory effect on fructan accumulation, carbohydrate content or total C in carbohydrates. The activities of SPS and FBPase were unaffected by phosphate. The results indicate that phosphate decreases fructan accumulation through an inhibition of SPS whenever this activity is not high before a rise in phosphate content.

Extension of the visualization tool MapMan to allow statistical analysis of arrays, display of corresponding genes, and comparison with known responses

MapMan is a user-driven tool that displays large genomics datasets onto diagrams of metabolic pathways or other processes. Here, we present new developments, including improvements of the gene assignments and the user interface, a strategy to visualize multilayered datasets, the incorporation of statistics packages, and extensions of the software to incorporate more biological information including visualization of corresponding genes and horizontal searches for similar global responses across large numbers of arrays.

Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen

Transcriptome analysis, using Affymetrix ATH1 arrays and a real-time reverse transcription-PCR platform for >1,400 transcription factors, was performed to identify processes affected by long-term nitrogen-deprivation or short-term nitrate nutrition in Arabidopsis. Two days of nitrogen deprivation led to coordinate repression of the majority of the genes assigned to photosynthesis, chlorophyll synthesis, plastid protein synthesis, induction of many genes for secondary metabolism, and reprogramming of mitochondrial electron transport. Nitrate readdition led to rapid, widespread, and coordinated changes. Multiple genes for the uptake and reduction of nitrate, the generation of reducing equivalents, and organic acid skeletons were induced within 30 min, before primary metabolites changed significantly. By 3 h, most genes assigned to amino acid and nucleotide biosynthesis and scavenging were induced, while most genes assigned to amino acid and nucleotide breakdown were repressed. There was coordinate induction of many genes assigned to RNA synthesis and processing and most of the genes assigned to amino acid activation and protein synthesis. Although amino acids involved in central metabolism increased, minor amino acids decreased, providing independent evidence for the activation of protein synthesis. Specific genes encoding expansin and tonoplast intrinsic proteins were induced, indicating activation of cell expansion and growth in response to nitrate nutrition. There were rapid responses in the expression of many genes potentially involved in regulation, including genes for trehalose metabolism and hormone metabolism, protein kinases and phosphatases, receptor kinases, and transcription factors.

Nitrate is a negative signal for fructan synthesis, and the fructosyltransferase-inducing trehalose inhibits nitrogen and carbon assimilation in excised barley leaves

•  Fructan biosynthesis in barley (Hordeum vulgare) has been shown to be upregulated by sugar signalling and downregulated by nitrogen. The relationship between these two regulations is investigated. •  Excised third-leaves of barley were fed nitrate or glutamine under two light intensities. Other leaf blades were supplied in the dark for 24 h with nitrate and trehalose in the presence of validamycin A, a trehalase inhibitor. •  In the light, nitrate, but not glutamine, decreased fructan contents and sucrose:fructan 6-fructosyltransferase protein without affecting the levels of sucrose and other carbohydrates. In darkened leaves, trehalose increased and nitrate decreased the fructan contents and total sucrose:fructosyltransferase activity without altering the concentration of sucrose. The effect on fructan contents of trehalose disappeared, whereas that of nitrate remained in subsequent incubations in water under light. Trehalose decreased and nitrate increased the light- and CO₂ -saturated rate of photosynthesis without significantly affecting the initial Rubisco (ribulose-1,5-bisphosphate carboxylase oxygenase) activity. Trehalose feeding decreased the activation of nitrate reductase and amino acid levels, and blocked the positive effect of nitrate on the maximal activity of this enzyme. •  The results indicate that nitrate, and not a downstream metabolite, is a negative signal for fructan synthesis, independent from the positive sugar signalling and overriding it. Trehalose signalling inhibits nitrogen and carbon assimilation, at the same time, inducing fructosyltransferase activity.

Steps towards an integrated view of nitrogen metabolism

This article discusses how nitrate assimilation is integrated with nitrate uptake, with ammonium assimilation and amino acid synthesis, with pH regulation, and with the sugar supply in tobacco leaves. During the first part of the light period, nitrate assimilation exceeds nitrate uptake by 2-fold and ammonium assimilation by 50%, leading to rapid depletion of nitrate and accumulation of ammonium, glutamine, glycine and serine. NIA, NII and PPC expression show a shared maximum early in the diurnal cycle to direct carbon towards malate synthesis for pH regulation. Later in the diurnal cycle an orchestrated increase of GLN2, PKc, CS, and ICDH-1 expression re-establishes a balance between nitrate assimilation and ammonium metabolism. Nitrate uptake continues throughout the night, replenishing the leaf nitrate pool. These diurnal changes are attenuated or abolished in mutants with low NIA activity, and modified in wild-type plants growing on different nitrogen sources or elevated [CO(2)]. Comparison across genotypes and conditions reveals that NIA transcript levels are always closely related to the balance between nitrate influx and assimilation, but are unrelated to changes of glutamine or 2-oxoglutarate. In a systematic search for other downstream regulators, a wide range of downstream metabolites was fed to detached leaves and glutamate, cysteine, asparagine, and malate identified as candidates. Low sugars totally inhibit nitrate assimilation, overriding signals from nitrogen metabolism. Moderate changes act post-transcriptionally, and larger changes lead to a collapse of the NIA transcript. Low sugars also lead to a collapse of minor amino acids and a dramatic decrease of phenylpropanoids and nicotine. Consequently, wild-type plants growing in unfavourable light regimes and antisense RBCS transformants are simultaneously carbon- and nitrogen-limited.

Contrasting responses of photosynthesis and carbon metabolism to low temperatures in tall fescue and clovers

Growth, photosynthesis and carbohydrate metabolism in plants of two grassland species, clover (Trifolium subterraneum L. cv. Areces and Gaitan) and tall fescue (Festuca arundinacea Schreb.), shifted from 25 to 12 degrees C for 1 day or developed at 12 degrees C were compared with controls kept at 25 degrees C. Cold development produced a larger inhibition of growth in fescue than in clovers. In contrast, transferring plants from high to low temperature inhibited photosynthesis to a lesser extent in fescue than in clovers, this difference being associated with an increase in the activation state of Calvin cycle enzymes in fescue, but not in the clovers, a decreased cytosolic fructose-1,6-bisphosphatase (cFBPase, EC 3.1.3.11) activity in clovers, and an accumulation of hexose phosphates only in fescue. Development at 12 degrees C partly relieved the inhibition of photosynthesis in clovers, in contrast with fescue, which correlated with increases in total ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco, EC 4.1.1.39) activity only in clovers, and with greater increases in total stromal FBPase (sFBPase) activity in clovers than in fescue. The activity of sucrose synthesis enzymes was increased in the two clovers and fescue developed in the cold, while carbohydrate accumulation was much bigger in cold-developed fescue than in clovers because of a 5-fold increase in fructan contents in the former. The contents of phosphorylated intermediates increased in clovers but decreased in fescue grown at 12 degrees C. Our results suggest that restricted ribulose-1,5-bisphosphate (RuBP) regeneration limited the recovery of photosynthetic capacity in cold-developed fescue.

Tobacco mutants with a decreased number of functional nia genes compensate by modifying the diurnal regulation of transcription, post-translational modification and turnover of nitrate reductase

Although nitrate reductase (NR. EC 1.6.6.1) is thought to control the rate of nitrate assimilation, mutants with 40-45% of wildtype (WT) NR activity (NRA) grow as fast as the WT. We have investigated how tobacco (Nicotiana tabacum L. cv. Gatersleben) mutants with one or two instead of four functional nia genes compensate. (i) The nia transcript was higher in the leaves of the mutants. However, the diurnal rhythm was retained in the mutants, with a maximum at the end of the night and a strong decline during the photoperiod. (ii) Nitrate reductase protein and NRA rose to a maximum after 3-4 h light in WT leaves, and then decreased by 50-60% during the second part of the photoperiod and the first part of the night. Leaves of mutants contained 40-60% less NR protein and NRA after 3-4 h illumination, but NR did not decrease during the photoperiod. At the end of the photoperiod the WT and the mutants contained similar levels of NR protein and NRA. (iii) Darkening led to a rapid inactivation of NR in the WT and the mutants. However, in the mutants, this inactivation was reversed after 1-3 h darkness. Calyculin A prevented this reversal. When magnesium was included in the assay to distinguish between the active and inactive forms of NR, mutants contained 50% more activity than the WT during the night. Conversion of [15N]-nitrate to organic compounds in leaves in the first 6 h of the night was 60% faster in the mutants than in the WT. (iv) Growth of WT plants in enhanced carbon dioxide prevented the decline of NRA during the second part of the photoperiod, and led to reactivation of NR in the dark. (v) Increased stability of NR in the light and reversal of dark-inactivation correlated with decreased levels of glutamine in the leaves. When glutamine was supplied to detached leaves it accelerated the breakdown of NR, and led to inactivation of NR, even in the light. (vi) Diurnal changes were also investigated in roots. In the WT, the amount of nia transcript rose to a maximum after 4 h illumination and then gradually decreased. The amplitude of the changes in transcript amount was smaller in roots than in leaves, and there were no diurnal changes in NRA. In mutants, nia transcript levels were high through the photoperiod and the first part of the night. The NRA was 50% lower during the day but rose during the night to an activity almost as high as in the WT. The rate of [15N]-nitrate assimilation in the roots of the mutants resembled that in the WT during the first 6 h of the night. (vii) Diurnal changes were also compared in Nia30(145) transformants with very low NRA, and in nitrate-deficient WT plants. Both sets of plants had similar low growth rates. Nitrate reductase did not show a diurnal rhythm in leaves or roots of Nia30(145), the leaves contained very low glutamine, and NR did not inactivate in the dark. Nitrate-deficient WT plants were watered each day with 0.2 mM nitrate. After watering, there was a small peak of nia transcript NR protein and NRA and, slightly later, a transient increase of glutamine and other amino acids in the leaves. During the night glutamine was low, and NR did not inactivate. In the roots, there was a very marked increase of nitrate, nia transcript and NRA 2-3 h after the daily watering with 0.2 mM nitrate. (viii) It is concluded that WT plants have excess capacity for nitrate assimilation. They only utilise this potential capacity for a short time each day, and then down-regulate nitrate assimilation in response, depending on the conditions, to accumulation of the products of nitrate assimilation or exhaustion of external nitrate. Genotypes with a lower capacity for nitrate assimilation compensate by increasing expression of NR and weakening the feedback regulation, to allow assimilation to continue for a longer period each day.