Co-ordination of leaf minor amino acid contents in crop species: significance and interpretation

Ascophyllum nodosum Based Extracts Counteract Salinity Stress in Tomato by Remodeling Leaf Nitrogen Metabolism

Biostimulants have rapidly and widely been adopted as growth enhancers and stress protectants in agriculture, however, due to the complex nature of these products, their mechanism of action is not clearly understood. By using two algal based commercial biostimulants in combination with the Solanum lycopersicum cv. MicroTom model system, we assessed how the modulation of nitrogen metabolites and potassium levels could contribute to mediate physiological mechanisms that are known to occur in response to salt/and or osmotic stress. Here we provide evidence that the reshaping of amino acid metabolism can work as a functional effector, coordinating ion homeostasis, osmotic adjustment and scavenging of reactive oxygen species under increased osmotic stress in MicroTom plant cells. The Superfifty biostimulant is responsible for a minor amino acid rich-phenotype and could represent an interesting instrument to untangle nitrogen metabolism dynamics in response to salinity and/or osmotic stress.

Nitrogen Uptake in Plants: The Plasma Membrane Root Transport Systems from a Physiological and Proteomic Perspective

Nitrogen nutrition in plants is a key determinant in crop productivity. The availability of nitrogen nutrients in the soil, both inorganic (nitrate and ammonium) and organic (urea and free amino acids), highly differs and influences plant physiology, growth, metabolism, and root morphology. Deciphering this multifaceted scenario is mandatory to improve the agricultural sustainability. In root cells, specific proteins located at the plasma membrane play key roles in the transport and sensing of nitrogen forms. This review outlines the current knowledge regarding the biochemical and physiological aspects behind the uptake of the individual nitrogen forms, their reciprocal interactions, the influences on root system architecture, and the relations with other proteins sustaining fundamental plasma membrane functionalities, such as aquaporins and H⁺-ATPase. This topic is explored starting from the information achieved in the model plant Arabidopsis and moving to crops in agricultural soils. Moreover, the main contributions provided by proteomics are described in order to highlight the goals and pitfalls of this approach and to get new hints for future studies.

Rice OsLHT1 Functions in Leaf-to-Panicle Nitrogen Allocation for Grain Yield and Quality

Proper allocation of nitrogen (N) from source leaves to grains is essential step for high crop grain yield and N use efficiency. In rice (Oryza sativa) grown in flooding paddy field, amino acids are the major N compounds for N distribution and re-allocation. We have recently identified that Lysine-Histidine-type Transporter 1 (OsLHT1) is the major transporter for root uptake and root-to-shoot allocation of amino acids in rice. In this study, we planted knockout mutant lines of OsLHT1 together wild-type (WT) in paddy field for evaluating OsLHT1 function in N redistribution and grain production. OsLHT1 is expressed in vascular bundles of leaves, rachis, and flowering organs. Oslht1 plants showed lower panicle length and seed setting rate, especially lower grain number per panicle and total grain weight. The concentrations of both total N and free amino acids in the flag leaf were similar at anthesis between Oslht1 lines and WT while significantly higher in the mutants than WT at maturation. The Oslht1 seeds contained higher proteins and most of the essential free amino acids, similar total starch but less amylose with lower paste viscosity than WT seeds. The mutant seeds showed lower germination rate than WT. Knockout of OsLHT1 decreased N uptake efficiency and physiological utilization efficiency (kg-grains/kg-N) by about 55% and 72%, respectively. Taken together, we conclude that OsLHT1 plays critical role in the translocation of amino acids from vegetative to reproductive organs for grain yield and quality of nutrition and functionality.

Diplotaxis tenuifolia (L.) DC. Yield and Quality as Influenced by Cropping Season, Protein Hydrolysates, and Trichoderma Applications

Increasing attention is being given to plant biostimulants as a sustainable farming practice aimed to enhance vegetable crop performance. This research was conducted on greenhouse-grown perennial wall rocket (Diplotaxis tenuifolia (L.) DC.), comparing three biostimulant treatments (legume-derived protein hydrolysates, Trichoderma harzianum T22, and protein hydrolysates + Trichoderma harzianum T22) plus an untreated control, in a factorial combination with three cropping seasons (autumn-winter, winter, winter-spring). Measurements were performed on leaf yield components, colorimetric indicators, mineral composition, bioactive compounds, and antioxidant activity. Leaf marketable yield and mean weight, as well as plant dry weight, showed the highest values in winter crop cycle. Biostimulant treatments resulted in 18.4% and 26.4% increase in leaf yield and number of leaves per rosette, respectively, compared to the untreated control. Protein hydrolysates led to the highest plant dry weight (+34.7% compared to the control). Soil plant analysis development (SPAD) index as well as NO₃, PO₄, SO₄, and Ca contents were influenced more during the winter-spring season than the winter cropping season. The winter production season resulted in a 19.8% increase in the leaf lipophilic antioxidant activity, whereas the hydrophilic antioxidant activity was 34.9% higher during the winter-spring season. SPAD index was the highest with protein hydrolysates + Trichoderma applications, which also increased the colorimetric parameters compared to the untreated control. The treatment with protein hydrolysates + Trichoderma enhanced N, PO₄, Mg, and Na contents, compared to both biostimulants applied singly and to the untreated control. Both biostimulants applied alone or the protein hydrolysates + Trichoderma combination led to the increase of the lipophilic and hydrophilic antioxidant activity, as well as ascorbic acid and chlorophyll b, compared to the untreated control. The present research revealed that protein hydrolysates and Trichoderma single applications, and even more their combination in the case of some nutrients content, represent an effective tool for enhancing the yield and the quality attributes of perennial wall rocket produced under the perspective of sustainable crop system.

Physiological performance of glyphosate and imazamox mixtures on Amaranthus palmeri sensitive and resistant to glyphosate

The herbicides glyphosate and imazamox inhibit the biosynthetic pathway of aromatic amino acids (AAA) and branched-chain amino acids (BCAA), respectively. Both herbicides share several physiological effects in the processes triggered in plants after herbicide application that kills the plant, and mixtures of both herbicides are being used. The aim of this study was to evaluate the physiological effects in the mixture of glyphosate and imazamox in glyphosate-sensitive (GS) and -resistant (GR) populations of the troublesome weed Amaranthus palmeri. The changes detected in the physiological parameters after herbicide mixtures application were similar and even less to the changes detected after individual treatments. This pattern was detected in shikimate, amino acid and carbohydrate content, and it was independent of the EPSPS copy number, as it was detected in both populations. In the case of the transcriptional pattern of the AAA pathway after glyphosate, interesting and contrary interactions with imazamox treatment were detected for both populations; enhancement of the effect in the GS population and alleviation in the GR population. At the transcriptional level, no cross regulation between AAA and BCAA inhibitors was confirmed. This study suggests that mixtures are equally or less toxic than herbicides alone, and would implicate careful considerations when applying the herbicide mixtures.

Biostimulant Application with a Tropical Plant Extract Enhances Corchorus olitorius Adaptation to Sub-Optimal Nutrient Regimens by Improving Physiological Parameters

The emerging role of plant biostimulants in enhancing nutrient efficiency is important for maintaining soil fertility under sub-optimal nutrient regimens. We aimed to elucidate the morpho-physiological and biochemical effects as well as mineral composition changes of greenhouse jute (Corchorus olitorius L.) treated with a commercial vegetal-derived biostimulant from a tropical plant extract (PE; Auxym®, Italpollina, Rivoli Veronese, Italy). Plants were sprayed in weekly intervals with a solution containing 2 mL·L−1 PE. Jute plants were supplied with three nutrient solution concentrations: full-, half-, and quarter-strength. Decreasing macronutrient concentrations in the nutrient solution (NS), especially at quarter-strength, triggered a decrease in several morphological (plant height, leaf number, and dry biomass) and physiological (net CO2 assimilation rate (ACO2) and SPAD (Soil Plant Analysis Development) index) parameters. PE application triggered specific ameliorative effects in terms of fresh yield at both half- and quarter-strength nutrient solution (15.5% and 29.5%, respectively). This was associated with an enhancement in ACO2, SPAD index, and especially the nutritional status (high nitrate, K, and Mg contents, and low Na content). The foliar application of PE, strongly increased chlorophyll b content, enhancing jute plant adaptation to fluctuating light and therefore the efficiency of photosynthesis, positively affecting starch, soluble proteins, and total amino acids content but only when jute plants were irrigated with full-strength NS, compared to the respective control treatment. At lower nutrient strength, PE reprogrammed the nitrogen distribution, allowing its remobilization from glutamate, which was quantitatively the major amino acid under lower nutrient strength, but not from chlorophylls, thus maintaining efficient photosynthesis. We confirmed that PE Auxym® acts in a balanced manner on the main metabolic pathways of the plant, regulating the uptake and transport of mineral nutrients and protein synthesis, increasing the accumulation of essential amino acids under full nutritive solutions, and re-distributing nitrogen from amino acids to allow leaf growth and expansion even under sub-optimal nutrient conditions. Overall, the use of natural plant biostimulants may be a potential solution in low-input conditions, where environmental constraints and restricted use of fertilizers may affect potential crop productivity.

Response of Arabidopsis primary metabolism and circadian clock to low night temperature in a natural light environment

Plants are exposed to varying irradiance and temperature within a day and from day to day. We previously investigated metabolism in a temperature-controlled greenhouse at the spring equinox on both a cloudy and a sunny day [daily light integral (DLI) of 7 mol m-2 d-1 and 12 mol m-2 d-1]. Diel metabolite profiles were largely captured in sinusoidal simulations at similar DLIs in controlled-environment chambers, except that amino acids were lower in natural light regimes. We now extend the DLI12 study by investigating metabolism in a natural light regime with variable temperature including cool nights. Starch was not completely turned over, anthocyanins and proline accumulated, and protein content rose. Instead of decreasing, amino acid content rose. Connectivity in central metabolism, which decreased in variable light, was not further weakened by variable temperature. We propose that diel metabolism operates better when light and temperature are co-varying. We also compared transcript abundance of 10 circadian clock genes in this temperature-variable regime with the temperature-controlled natural and sinusoidal light regimes. Despite temperature compensation, peak timing and abundance for dawn- and day-phased genes and GIGANTEA were slightly modified in the variable temperature treatment. This may delay dawn clock activity until the temperature rises enough to support rapid metabolism and photosynthesis.

Metabolic Profiling and Chemical-Based Antioxidant Assays of Green and Red Lettuce (Lactuca sativa)

Lettuce ( Lactuca sativa) is an important leaf vegetable crop worldwide. The total phenolic content was higher in the red skirt methanol extracts with a level of 64.9 ± 0.3 mg GA/g, and phenolic content of green skirt was 49.4 ± 0.3 mg GA/g. The total flavonoid content in the methanol extract of red skirt showed the highest concentration (291.6 ± 9.0 mg rutin/g), followed by green skirt (223 ± 9.8 mg rutin/g). The red skirt showed a higher content of anthocyanin (23.7 ± 0.8 mg/100 g) compared to the green skirt (7.4 ± 0.9 mg/100 g). Seven carotenoids i.e., lutein, β–carotene, 9 Z–β–carotene, 13 Z–β–carotene, violaxanthin, zeaxanthin, and α–carotene were detected in both cultivars. The polar metabolites are strongly associated with the metabolites that participate in the TCA cycle. Correlations between primary and secondary metabolites were easily achieved by gas chromatography-time-of-flight mass spectrometry (GC-TOFMS)-based metabolite profiling method. Red skirt methanol extract showed 77.5 ± 0.4% 2,2-diphenyl-1-picrylhydrazyl (DPPH) activity, 50.8 ± 0.8% hydrogen peroxide radical scavenging assay and absorbance value (0.052) reducing power assay at 250 μL/mL, having significantly higher activity than the green skirt extract. The red lettuce extract also showed higher levels of phenolic compounds, flavonoids, and anthocyanins, and it possesses more antioxidant properties compared to the green skirt extract. In this study we compared two cultivars of lettuce, red skirt and green skirt, for various nutritional parameters and to understand the association of secondary metabolites with their corresponding primary metabolites. From the overall analysis, it is confirmed that GC-TOFMS-based metabolite profiling is an appropriate method for determining biochemical reactions and also acts as a combined resource to understand primary and secondary metabolism.

Comparative Metabolomic Analyses of Ipomoea lacunosa Biotypes with Contrasting Glyphosate Tolerance Captures Herbicide-Induced Differential Perturbations in Cellular Physiology

Glyphosate-tolerant Ipomoea lacunosa is emerging as a problematic weed in the southeastern United States. Metabolomic profiling was conducted to examine the innate physiology and the glyphosate induced perturbations in two biotypes of I. lacunosa (WAS and QUI) that had contrasting glyphosate tolerance. Compared to the less tolerant QUI-biotype, the innate metabolism of the more tolerant WAS-biotype was characterized by a higher abundance of amino acids, and pyruvate; whereas the sugar profile of the QUI biotype was dominated by the transport sugar sucrose. Glyphosate application (80 g ae/ha) caused similar shikimate accumulation in both biotypes. Compared to QUI, in WAS, the content of aromatic amino acids was less affected by glyphosate treatment, and the content of Ala, Val, Ile, and Pro increased. However, the total sugars decreased by ∼75% in WAS, compared to ∼50% decrease in QUI. The innate, higher proportional abundance, of the transport-sugar sucrose in QUI coud partly explain the higher translocation and greater sensitivity of this biotype to glyphosate. The decrease in sugars, accompanied by an increase in amino acids could delay feedback regulation of upstream enzymes of the shikimate acid pathway in WAS, which could contribute to a greater glyphosate tolerance. Our study, through a metabolomics approach, provides complementary data that elucidates the cellular physiology of herbicide tolerance in Ipomoea lacunosa biotypes.

Effects of EPSPS Copy Number Variation (CNV) and Glyphosate Application on the Aromatic and Branched Chain Amino Acid Synthesis Pathways in Amaranthus palmeri

A key enzyme of the shikimate pathway, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS; EC 2.5.1.19), is the known target of the widely used herbicide glyphosate. Glyphosate resistance in Amaranthus palmeri, one of the most troublesome weeds in agriculture, has evolved through increased EPSPS gene copy number. The aim of this work was to study the pleiotropic effects of (i) EPSPS increased transcript abundance due to gene copy number variation (CNV) and of (ii) glyphosate application on the aromatic amino acid (AAA) and branched chain amino acid (BCAA) synthesis pathways. Hydroponically grown glyphosate sensitive (GS) and glyphosate resistant (GR) plants were treated with glyphosate 3 days after treatment. In absence of glyphosate treatment, high EPSPS gene copy number had only a subtle effect on transcriptional regulation of AAA and BCAA pathway genes. In contrast, glyphosate treatment provoked a general accumulation of the transcripts corresponding to genes of the AAA pathway leading to synthesis of chorismate in both GS and GR. After chorismate, anthranilate synthase transcript abundance was higher while chorismate mutase transcription showed a small decrease in GR and remained stable in GS, suggesting a regulatory branch point in the pathway that favors synthesis toward tryptophan over phenylalanine and tyrosine after glyphosate treatment. This was confirmed by studying enzyme activities in vitro and amino acid analysis. Importantly, this upregulation was glyphosate dose dependent and was observed similarly in both GS and GR populations. Glyphosate treatment also had a slight effect on the expression of BCAA genes but no general effect on the pathway could be observed. Taken together, our observations suggest that the high CNV of EPSPS in A. palmeri GR populations has no major pleiotropic effect on the expression of AAA biosynthetic genes, even in response to glyphosate treatment. This finding supports the idea that the fitness cost associated with EPSPS CNV in A. palmeri may be limited.

Nitrogen-regulated changes in total amino acid profile of maize genotypes having contrasting response to nitrogen deficit

Sustainable development of cellular organisms depends on a precise coordination between the carbon and nitrogen metabolisms within the living system. Inorganic N is assimilated into amino acids which serve as an important N source for various regulatory metabolic pathways in plants. This study investigates the role of amino acids in C/N balance by examining changes in amino acid profile in the leaves and roots of low-N-tolerant (PHEM-2) and low-N-sensitive (HM-4) maize genotypes grown hydroponically under N-sufficient (4.5 mM), N-deficient (0.05 mM) and N-restoration conditions. N application effectively altered the level of cysteine, methionine, asparagine, arginine, phenylalanine, glycine, glutamine, aspartate and glutamate in both genotypes. Under low N (0.05 mM), the asparagine and glutamine contents increased, while those of glutamate, phenylalanine and aspartate decreased in both genotypes. However, serine content increased in PHEM-2 but decreased in HM-4. Resupply of N to low-N-grown plants of both genotypes restored the amino acids level to that in the control; the restoration was quicker and more consistent in PHEM-2 than in HM-4. Based on alteration of amino acid level, a strategy can be developed to improve the ability of maize to adapt to low-N environments by way of an improved N utilization.

Temporal development of the barley leaf metabolic response to Pi limitation

The response of plants to P_i limitation involves interplay between root uptake of P_i , adjustment of resource allocation to different plant organs and increased metabolic P_i use efficiency. To identify potentially novel, early-responding, metabolic hallmarks of P_i limitation in crop plants, we studied the metabolic response of barley leaves over the first 7 d of P_i stress, and the relationship of primary metabolites with leaf P_i levels and leaf biomass. The abundance of leaf P_i , Tyr and shikimate were significantly different between low Pi and control plants 1 h after transfer of the plants to low P_i . Combining these data with ¹⁵ N metabolic labelling, we show that over the first 48 h of P_i limitation, metabolic flux through the N assimilation and aromatic amino acid pathways is increased. We propose that together with a shift in amino acid metabolism in the chloroplast a transient restoration of the energetic and redox state of the leaf is achieved. Correlation analysis of metabolite abundances revealed a central role for major amino acids in P_i stress, appearing to modulate partitioning of soluble sugars between amino acid and carboxylate synthesis, thereby limiting leaf biomass accumulation when external P_i is low.

Durum wheat seedling responses to simultaneous high light and salinity involve a fine reconfiguration of amino acids and carbohydrate metabolism

Durum wheat plants are extremely sensitive to drought and salinity during seedling and early development stages. Their responses to stresses have been extensively studied to provide new metabolic targets and improving the tolerance to adverse environments. Most of these studies have been performed in growth chambers under low light [300-350 µmol m^-2 s^-1 photosynthetically active radiation (PAR), LL]. However, in nature plants have to face frequent fluctuations of light intensities that often exceed their photosynthetic capacity (900-2000 µmol m^-2 s^-1 ). In this study we investigated the physiological and metabolic changes potentially involved in osmotic adjustment and antioxidant defense in durum wheat seedlings under high light (HL) and salinity. The combined application of the two stresses decreased the water potential and stomatal conductance without reducing the photosynthetic efficiency of the plants. Glycine betaine (GB) synthesis was inhibited, proline and glutamate content decreased, while γ-aminobutyric acid (GABA), amides and minor amino acids increased. The expression level and enzymatic activities of Δ1-pyrroline-5-carboxylate synthetase, asparagine synthetase and glutamate decarboxylase, as well as other enzymatic activities of nitrogen and carbon metabolism, were analyzed. Antioxidant enzymes and metabolites were also considered. The results showed that the complex interplay seen in durum wheat plants under salinity at LL was simplified: GB and antioxidants did not play a main role. On the contrary, the fine tuning of few specific primary metabolites (GABA, amides, minor amino acids and hexoses) remodeled metabolism and defense processes, playing a key role in the response to simultaneous stresses.

Trans-Himalayan Rhodiola imbricata Edgew. root: a novel source of dietary amino acids, fatty acids and minerals

Roots of Rhodiola imbricata Edgew from Indian trans-Himalayan cold desert known for their nutritional and medicinal attributes were evaluated for the dietary amino acids, fatty acids and mineral composition. Nine essential and twelve non-essential amino acids were quantified. The contents ranged between 91.33 and 1640.67 µg/g. Histidine (1434.33 µg/g), lysine (1329.33 µg/g) and threonine (1015.67 μg/g) were dominant essential amino acids, while glycine (1640.67 µg/g), proline (1263.67 µg/g), alanine (1142.33 µg/g), cystine HCL (1136.33 μg/g) and nor leucine (1038.67 μg/g) were major non essential amino acids. The total lipid was found to be rich source of saturated fatty acids such as capric acid (19.91%), caproic acid (10.87%), palmitic acid (9.42%), lignoceric acid (6.16%) and behenic acid (5.71%), which together constituted 52% of the lipid content. Linoleic acid (15.06%), oleic acid (12.38%), arachidonic acid (8.38%), linolelaidic acid (6.11%) and docosadienoic acid (5.99%) were prominent unsaturated fatty acids (UFAs). Mono unsaturated fatty acids (MUFAs) and poly unsaturated fatty acids (PUFAs) were 35.64% and 12.33% of the lipid content respectively. Calcium (11034.17 mg/kg), potassium (2143.25 mg/kg), iron (1441.17 mg/kg), magnesium (581.99 mg/kg), phosphorous (376.72 mg/kg) and sodium (109.75 mg/kg) were detected as the major dietary minerals.

Durum Wheat Roots Adapt to Salinity Remodeling the Cellular Content of Nitrogen Metabolites and Sucrose

Plants are currently experiencing increasing salinity problems due to irrigation with brackish water. Moreover, in fields, roots can grow in soils which show spatial variation in water content and salt concentration, also because of the type of irrigation. Salinity impairs crop growth and productivity by inhibiting many physiological and metabolic processes, in particular nitrate uptake, translocation, and assimilation. Salinity determines an increase of sap osmolality from about 305 mOsmol kg-1 in control roots to about 530 mOsmol kg-1 in roots under salinity. Root cells adapt to salinity by sequestering sodium in the vacuole, as a cheap osmoticum, and showing a rearrangement of few nitrogen-containing metabolites and sucrose in the cytosol, both for osmotic adjustment and oxidative stress protection, thus providing plant viability even at low nitrate levels. Mainly glycine betaine and sucrose at low nitrate concentration, and glycine betaine, asparagine and proline at high nitrate levels can be assumed responsible for the osmotic adjustment of the cytosol, the assimilation of the excess of ammonium and the scavenging of ROS under salinity. High nitrate plants with half of the root system under salinity accumulate proline and glutamine in both control and salt stressed split roots, revealing that osmotic adjustment is not a regional effect in plants. The expression level and enzymatic activities of asparagine synthetase and Δ1-pyrroline-5-carboxylate synthetase, as well as other enzymatic activities of nitrogen and carbon metabolism, are analyzed.

Metabolite transport and associated sugar signalling systems underpinning source/sink interactions

Metabolite transport between organelles, cells and source and sink tissues not only enables pathway co-ordination but it also facilitates whole plant communication, particularly in the transmission of information concerning resource availability. Carbon assimilation is co-ordinated with nitrogen assimilation to ensure that the building blocks of biomass production, amino acids and carbon skeletons, are available at the required amounts and stoichiometry, with associated transport processes making certain that these essential resources are transported from their sites of synthesis to those of utilisation. Of the many possible posttranslational mechanisms that might participate in efficient co-ordination of metabolism and transport only reversible thiol-disulphide exchange mechanisms have been described in detail. Sucrose and trehalose metabolism are intertwined in the signalling hub that ensures appropriate resource allocation to drive growth and development under optimal and stress conditions, with trehalose-6-phosphate acting as an important signal for sucrose availability. The formidable suite of plant metabolite transporters provides enormous flexibility and adaptability in inter-pathway coordination and source-sink interactions. Focussing on the carbon metabolism network, we highlight the functions of different transporter families, and the important of thioredoxins in the metabolic dialogue between source and sink tissues. In addition, we address how these systems can be tailored for crop improvement.

Whole-Plant Dynamic System of Nitrogen Use for Vegetative Growth and Grain Filling in Rice Plants (Oryza sativa L.) as Revealed through the Production of 350 Grains from a Germinated Seed Over 150 Days: A Review and Synthesis

A single germinated rice (Oryza sativa L) seed can produce 350 grains with the sequential development of 15 leaves on the main stem and 7-10 leaves on four productive tillers (forming five panicles in total), using nitrogen (N) taken up from the environment over a 150-day growing season. Nitrogen travels from uptake sites to the grain through growing organ-directed cycling among sequentially developed organs. Over the past 40 years, the dynamic system for N allocation during vegetative growth and grain filling has been elucidated through studies on N and (15)N transport as well as enzymes and transporters involved. In this review, we synthesize the information obtained in these studies along the following main points: (1) During vegetative growth before grain-filling, about half of the total N in the growing organs, including young leaves, tillers, root tips and differentiating panicles is supplied via phloem from mature source organs such as leaves and roots, after turnover and remobilization of proteins, whereas the other half is newly taken up and supplied via xylem, with an efficient xylem-to-phloem transfer at stem nodes. Thus, the growth of new organs depends equally on both N sources. (2) A large fraction (as much as 80%) of the grain N is derived largely from mature organs such as leaves and stems by degradation, including the autophagy pathway of chloroplast proteins (e.g., Rubisco). (3) Mobilized proteinogenic amino acids (AA), including arginine, lysine, proline and valine, are derived mainly from protein degradation, with AA transporters playing a role in transferring these AAs across cell membranes of source and sink organs, and enabling their efficient reutilization in the latter. On the other hand, AAs such as glutamine, glutamic acid, γ-amino butyric acid, aspartic acid, and alanine are produced by assimilation of newly taken up N by roots and and transported via xylem and phloem. The formation of 350 filled grains over 50 days during the reproductive stage is ascribed mainly to degradation and remobilization of the reserves, previously accumulated over 100 days in the sequentially developed vegetative organs.

Connecting Source with Sink: The Role of Arabidopsis AAP8 in Phloem Loading of Amino Acids

Allocation of large amounts of nitrogen to developing organs occurs in the phloem and is essential for plant growth and seed development. In Arabidopsis (Arabidopsis thaliana) and many other plant species, amino acids represent the dominant nitrogen transport forms in the phloem, and they are mainly synthesized in photosynthetically active source leaves. Following their synthesis, a broad spectrum of the amino nitrogen is actively loaded into the phloem of leaf minor veins and transported within the phloem sap to sinks such as developing leaves, fruits, or seeds. Controlled regulation of the source-to-sink transport of amino acids has long been postulated; however, the molecular mechanism of amino acid phloem loading was still unknown. In this study, Arabidopsis AMINO ACID PERMEASE8 (AAP8) was shown to be expressed in the source leaf phloem and localized to the plasma membrane, suggesting its function in phloem loading. This was further supported by transport studies with aap8 mutants fed with radiolabeled amino acids and by leaf exudate analyses. In addition, biochemical and molecular analyses revealed alterations in leaf nitrogen pools and metabolism dependent on the developmental stage of the mutants. Decreased amino acid phloem loading and partitioning to sinks led to decreased silique and seed numbers, but seed protein levels were unchanged, demonstrating the importance of AAP8 function for sink development rather than seed quality. Overall, these results show that AAP8 plays an important role in source-to-sink partitioning of nitrogen and that its function affects source leaf physiology and seed yield.

The Regulation of Essential Amino Acid Synthesis and Accumulation in Plants

Although amino acids are critical for all forms of life, only proteogenic amino acids that humans and animals cannot synthesize de novo and therefore must acquire in their diets are classified as essential. Nine amino acids-lysine, methionine, threonine, phenylalanine, tryptophan, valine, isoleucine, leucine, and histidine-fit this definition. Despite their nutritional importance, several of these amino acids are present in limiting quantities in many of the world's major crops. In recent years, a combination of reverse genetic and biochemical approaches has been used to define the genes encoding the enzymes responsible for synthesizing, degrading, and regulating these amino acids. In this review, we describe recent advances in our understanding of the metabolism of the essential amino acids, discuss approaches for enhancing their levels in plants, and appraise efforts toward their biofortification in crop plants.

Profiling of spatial metabolite distributions in wheat leaves under normal and nitrate limiting conditions

The control and interaction between nitrogen and carbon assimilatory pathways is essential in both photosynthetic and non-photosynthetic tissue in order to support metabolic processes without compromising growth. Physiological differences between the basal and mature region of wheat (Triticum aestivum) primary leaves confirmed that there was a change from heterotrophic to autotrophic metabolism. Fourier Transform Infrared (FT-IR) spectroscopy confirmed the suitability and phenotypic reproducibility of the leaf growth conditions. Principal Component-Discriminant Function Analysis (PC-DFA) revealed distinct clustering between base, and tip sections of the developing wheat leaf, and from plants grown in the presence or absence of nitrate. Gas Chromatography-Time of Flight/Mass Spectrometry (GC-TOF/MS) combined with multivariate and univariate analyses, and Bayesian network (BN) analysis, distinguished different tissues and confirmed the physiological switch from high rates of respiration to photosynthesis along the leaf. The operation of nitrogen metabolism impacted on the levels and distribution of amino acids, organic acids and carbohydrates within the wheat leaf. In plants grown in the presence of nitrate there was reduced levels of a number of sugar metabolites in the leaf base and an increase in maltose levels, possibly reflecting an increase in starch turnover. The value of using this combined metabolomics analysis for further functional investigations in the future are discussed.

The Arabidopsis TUMOR PRONE5 gene encodes an acetylornithine aminotransferase required for arginine biosynthesis and root meristem maintenance in blue light

Arginine is an essential amino acid necessary for protein synthesis and is also a nitrogen storage compound. The genes encoding the enzymes of arginine biosynthesis in plants are not well characterized and have mainly been predicted from homologies to bacterial and fungal genes. We report the cloning and characterization of the TUMOR PRONE5 (TUP5) gene of Arabidopsis (Arabidopsis thaliana) encoding an acetylornithine aminotransferase (ACOAT), catalyzing the fourth step of arginine biosynthesis. The free arginine content was strongly reduced in the chemically induced recessive mutant tup5-1, root growth was restored by supplementation with arginine and its metabolic precursors, and a yeast (Saccharomyces cerevisiae) ACOAT mutant was complemented by TUP5. Two null alleles of TUP5 caused a reduced viability of gametes and embryo lethality, possibly caused by insufficient Arg supply from maternal tissue. TUP5 expression is positively regulated by light, and a TUP5-green fluorescent protein was localized in chloroplasts. tup5-1 has a unique light-dependent short root phenotype. Roots of light-grown tup5-1 seedlings switch from indeterminate growth to determinate growth with arresting cell production and an exhausted root apical meristem. The inhibitory activity was specific for blue light, and the inhibiting light was perceived by the root. Thus, tup5-1 reveals a novel role of amino acids and blue light in regulating root meristem function.

Metabolomics of forage plants: a review

BACKGROUND

Forage plant breeding is under increasing pressure to deliver new cultivars with improved yield, quality and persistence to the pastoral industry. New innovations in DNA sequencing technologies mean that quantitative trait loci analysis and marker-assisted selection approaches are becoming faster and cheaper, and are increasingly used in the breeding process with the aim to speed it up and improve its precision. High-throughput phenotyping is currently a major bottle neck and emerging technologies such as metabolomics are being developed to bridge the gap between genotype and phenotype; metabolomics studies on forages are reviewed in this article.

SCOPE

Major challenges for pasture production arise from the reduced availability of resources, mainly water, nitrogen and phosphorus, and metabolomics studies on metabolic responses to these abiotic stresses in Lolium perenne and Lotus species will be discussed here. Many forage plants can be associated with symbiotic microorganisms such as legumes with nitrogen fixing rhizobia, grasses and legumes with phosphorus-solubilizing arbuscular mycorrhizal fungi, and cool temperate grasses with fungal anti-herbivorous alkaloid-producing Neotyphodium endophytes and metabolomics studies have shown that these associations can significantly affect the metabolic composition of forage plants. The combination of genetics and metabolomics, also known as genetical metabolomics can be a powerful tool to identify genetic regions related to specific metabolites or metabolic profiles, but this approach has not been widely adopted for forages yet, and we argue here that more studies are needed to improve our chances of success in forage breeding.

CONCLUSIONS

Metabolomics combined with other '-omics' technologies and genome sequencing can be invaluable tools for large-scale geno- and phenotyping of breeding populations, although the implementation of these approaches in forage breeding programmes still lags behind. The majority of studies using metabolomics approaches have been performed with model species or cereals and findings from these studies are not easily translated to forage species. To be most effective these approaches should be accompanied by whole-plant physiology and proof of concept (modelling) studies. Wider considerations of possible consequences of novel traits on the fitness of new cultivars and symbiotic associations need also to be taken into account.

Maize source leaf adaptation to nitrogen deficiency affects not only nitrogen and carbon metabolism but also control of phosphate homeostasis

Crop plant development is strongly dependent on the availability of nitrogen (N) in the soil and the efficiency of N utilization for biomass production and yield. However, knowledge about molecular responses to N deprivation derives mainly from the study of model species. In this article, the metabolic adaptation of source leaves to low N was analyzed in maize (Zea mays) seedlings by parallel measurements of transcriptome and metabolome profiling. Inbred lines A188 and B73 were cultivated under sufficient (15 mM) or limiting (0.15 mM) nitrate supply for up to 30 d. Limited availability of N caused strong shifts in the metabolite profile of leaves. The transcriptome was less affected by the N stress but showed strong genotype- and age-dependent patterns. N starvation initiated the selective down-regulation of processes involved in nitrate reduction and amino acid assimilation; ammonium assimilation-related transcripts, on the other hand, were not influenced. Carbon assimilation-related transcripts were characterized by high transcriptional coordination and general down-regulation under low-N conditions. N deprivation caused a slight accumulation of starch but also directed increased amounts of carbohydrates into the cell wall and secondary metabolites. The decrease in N availability also resulted in accumulation of phosphate and strong down-regulation of genes usually involved in phosphate starvation response, underlining the great importance of phosphate homeostasis control under stress conditions.

Different accumulation of free amino acids during short- and long-term osmotic stress in wheat

The effect of wheat chromosome 5A on free amino acid accumulation induced by osmotic stress was compared in chromosome 5A substitution lines with different freezing tolerance. Treatment with 15% polyethylene glycol (PEG) resulted in greater total free amino acid content even after 3 days compared to the controls. The ratio of amino acids belonging to various amino acid families differed after 3-week treatment in the control and PEG-treated plants only in the case of the freezing-sensitive substitution line. There was a transient increase with a maximum after 3 days in the amounts of several amino acids, after which their concentrations exhibited a more gradual increase. During the first days of osmotic stress the Glu, Gln, Asp, Asn, Thr, Ser, Leu, and His concentrations were greater in the tolerant substitution line than in the sensitive one, while the opposite relationship was observed at the end of the PEG treatment. The coordinated changes in the levels of individual amino acids indicated that they are involved in both the short- and long-term responses to osmotic stress. The alterations differed in the two chromosome 5A substitution lines, depending on the stress tolerance of the chromosome donor genotype.

Photosynthesis, photorespiration and productivity of wheat and soybean genotypes

The results of the numerous measurements obtained during the last 40 years on gas exchange rate, photosynthetic carbon metabolism by exposition in ¹⁴CO₂ and activities of primary carbon fixation enzyme, ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPC/O), in various wheat and soybean genotypes grown over a wide area in the field and contrasting in photosynthetic traits and productivity are presented in this article. It was established that high productive wheat genotypes (7-9 t ha⁻¹) with the optimal architectonics possess higher rate of CO₂ assimilation during the leaf ontogenesis. Along with the high rate of photosynthesis, high values of photorespiration are characteristic for the high productive genotypes. Genotypes with moderate (4-5 t ha⁻¹) and low (3 t ha⁻¹) grain yield are characterized by relatively low rates of both CO₂ assimilation and photorespiration. A value of photorespiration constitutes 28-35% of photosynthetic rate in contrasting genotypes. The activities of RuBPC and RuBPO were changing in a similar way in the course of the flag leaf and ear elements development. High productive genotypes are also characterized by a higher rate of biosynthesis and total value of glycine-serine and a higher photosynthetic rate. Therefore, contrary to conception arisen during many years on the wastefulness of photorespiration, taking into account the versatile investigations on different aspects of photorespiration, it was proved that photorespiration is one of the evolutionarily developed vital metabolic processes in plants and the attempts to reduce this process with the purpose of increasing the crop productivity are inconsistent.

Untargeted metabolic quantitative trait loci analyses reveal a relationship between primary metabolism and potato tuber quality

Recent advances in -omics technologies such as transcriptomics, metabolomics, and proteomics along with genotypic profiling have permitted dissection of the genetics of complex traits represented by molecular phenotypes in nonmodel species. To identify the genetic factors underlying variation in primary metabolism in potato (Solanum tuberosum), we have profiled primary metabolite content in a diploid potato mapping population, derived from crosses between S. tuberosum and wild relatives, using gas chromatography-time of flight-mass spectrometry. In total, 139 polar metabolites were detected, of which we identified metabolite quantitative trait loci for approximately 72% of the detected compounds. In order to obtain an insight into the relationships between metabolic traits and classical phenotypic traits, we also analyzed statistical associations between them. The combined analysis of genetic information through quantitative trait locus coincidence and the application of statistical learning methods provide information on putative indicators associated with the alterations in metabolic networks that affect complex phenotypic traits.

An engineered pathway for glyoxylate metabolism in tobacco plants aimed to avoid the release of ammonia in photorespiration

BACKGROUND

The photorespiratory nitrogen cycle in C₃ plants involves an extensive diversion of carbon and nitrogen away from the direct pathways of assimilation. The liberated ammonia is re-assimilated, but up to 25% of the carbon may be released into the atmosphere as CO₂. Because of the loss of CO₂ and high energy costs, there has been considerable interest in attempts to decrease the flux through the cycle in C₃ plants. Transgenic tobacco plants were generated that contained the genes gcl and hyi from E. coli encoding glyoxylate carboligase (EC 4.1.1.47) and hydroxypyruvate isomerase (EC 5.3.1.22) respectively, targeted to the peroxisomes. It was presumed that the two enzymes could work together and compete with the aminotransferases that convert glyoxylate to glycine, thus avoiding ammonia production in the photorespiratory nitrogen cycle.

RESULTS

When grown in ambient air, but not in elevated CO₂, the transgenic tobacco lines had a distinctive phenotype of necrotic lesions on the leaves. Three of the six lines chosen for a detailed study contained single copies of the gcl gene, two contained single copies of both the gcl and hyi genes and one line contained multiple copies of both gcl and hyi genes. The gcl protein was detected in the five transgenic lines containing single copies of the gcl gene but hyi protein was not detected in any of the transgenic lines. The content of soluble amino acids including glycine and serine, was generally increased in the transgenic lines growing in air, when compared to the wild type. The content of soluble sugars, glucose, fructose and sucrose in the shoot was decreased in transgenic lines growing in air, consistent with decreased carbon assimilation.

CONCLUSIONS

Tobacco plants have been generated that produce bacterial glyoxylate carboligase but not hydroxypyruvate isomerase. The transgenic plants exhibit a stress response when exposed to air, suggesting that some glyoxylate is diverted away from conversion to glycine in a deleterious short-circuit of the photorespiratory nitrogen cycle. This diversion in metabolism gave rise to increased concentrations of amino acids, in particular glutamine and asparagine in the leaves and a decrease of soluble sugars.

Respiration and nitrogen assimilation: targeting mitochondria-associated metabolism as a means to enhance nitrogen use efficiency

Considerable advances in our understanding of the control of mitochondrial metabolism and its interactions with nitrogen metabolism and associated carbon/nitrogen interactions have occurred in recent years, particularly highlighting important roles in cellular redox homeostasis. The tricarboxylic acid (TCA) cycle is a central metabolic hub for the interacting pathways of respiration, nitrogen assimilation, and photorespiration, with components that show considerable flexibility in relation to adaptations to the different functions of mitochondria in photosynthetic and non-photosynthetic cells. By comparison, the operation of the oxidative pentose phosphate pathway appears to represent a significant limitation to nitrogen assimilation in non-photosynthetic tissues. Valuable new insights have been gained concerning the roles of the different enzymes involved in the production of 2-oxoglutarate (2-OG) for ammonia assimilation, yielding an improved understanding of the crucial role of cellular energy balance as a broker of co-ordinate regulation. Taken together with new information on the mechanisms that co-ordinate the expression of genes involved in organellar functions, including energy metabolism, and the potential for exploiting the existing flexibility for NAD(P)H utilization in the respiratory electron transport chain to drive nitrogen assimilation, the evidence that mitochondrial metabolism and machinery are potential novel targets for the enhancement of nitrogen use efficiency (NUE) is explored.

Plant glutathione biosynthesis: diversity in biochemical regulation and reaction products

In plants, exposure to temperature extremes, heavy metal-contaminated soils, drought, air pollutants, and pathogens results in the generation of reactive oxygen species that alter the intracellular redox environment, which in turn influences signaling pathways and cell fate. As part of their response to these stresses, plants produce glutathione. Glutathione acts as an anti-oxidant by quenching reactive oxygen species, and is involved in the ascorbate-glutathione cycle that eliminates damaging peroxides. Plants also use glutathione for the detoxification of xenobiotics, herbicides, air pollutants (sulfur dioxide and ozone), and toxic heavy metals. Two enzymes catalyze glutathione synthesis: glutamate-cysteine ligase, and glutathione synthetase. Glutathione is a ubiquitous protective compound in plants, but the structural and functional details of the proteins that synthesize it, as well as the potential biochemical mechanisms of their regulation, have only begun to be explored. As discussed here, the core reactions of glutathione synthesis are conserved across various organisms, but plants have diversified both the regulatory mechanisms that control its synthesis and the range of products derived from this pathway. Understanding the molecular basis of glutathione biosynthesis and its regulation will expand our knowledge of this component in the plant stress response network.

Histidine biosynthesis

Histidine (His) is one of the standard amino acids in proteins, and plays a critical role in plant growth and development. The chemical properties of the imidazole side group allow His to participate in acid-base catalysis, and in the co-ordination of metal ions. Despite the biological importance of this molecule, His biosynthesis has been somewhat neglected in plants, in stark contrast to micro-organisms where the study of this pathway was fundamental in the discovery of operon structure and regulation by attenuation. With the recent isolation of histidinol-phosphate phosphatase, all the enzymes of His biosynthesis have now been identified in Arabidopsis, and several lines of evidence have implicated ATP-phosphoribosyl transferase (which catalyses the first committed step of the pathway) as playing an important role in the regulation of this pathway. However, little is known about the transcriptional regulation of the His biosynthetic genes, nor how demand for this amino acid is balanced with other metabolic requirements in plants. Similarly, the pathway of His catabolism has yet to be determined.

A novel approach for determining environment-specific protein costs: the case of Arabidopsis thaliana

Motivation: Comprehensive understanding of cellular processes requires development of approaches which consider the energetic balances in the cell. The existing approaches that address this problem are based on defining energy-equivalent costs which do not include the effects of a changing environment. By incorporating these effects, one could provide a framework for integrating ‘omics’ data from various levels of the system in order to provide interpretations with respect to the energy state and to elicit conclusions about putative global energy-related response mechanisms in the cell.

Results: Here we define a cost measure for amino acid synthesis based on flux balance analysis of a genome-scale metabolic network, and develop methods for its integration with proteomics and metabolomics data. This is a first measure which accounts for the effect of different environmental conditions. We applied this approach to a genome-scale network of Arabidopsis thaliana and calculated the costs for all amino acids and proteins present in the network under light and dark conditions. Integration of function and process ontology terms in the analysis of protein abundances and their costs indicates that, during the night, the cell favors cheaper proteins compared with the light environment. However, this does not imply that there is squandering of resources during the day. The results from the association analysis between the costs, levels and well-defined expenses of amino acid synthesis, indicate that our approach not only captures the adjustment made at the switch of conditions, but also could explain the anticipation of resource usage via a global energy-related regulatory mechanism of amino acid and protein synthesis.

Contact:nikoloski@mpimp-golm.mpg.de

Supplementary information:Supplementary data are available at Bioinformatics online.

Proteomic analysis of shoot tissue during photoperiod induced growth cessation in V. riparia Michx. grapevines

BACKGROUND

Growth cessation, cold acclimation and dormancy induction in grapevines and other woody perennial plants native to temperate continental climates is frequently triggered by short photoperiods. The early induction of these processes by photoperiod promotes winter survival of grapevines in cold temperate zones. Examining the molecular processes, in particular the proteomic changes in the shoot, will provide greater insight into the signaling cascade that initiates growth cessation and dormancy induction. To begin understanding transduction of the photoperiod signal, Vitis riparia Michx. grapevines that had grown for 35 days in long photoperiod (long day, LD, 15 h) were subjected to either a continued LD or a short photoperiod (short day, SD, 13 h) treatment. Shoot tips (4-node shoot terminals) were collected from each treatment at 7 and 28 days of LD and SD for proteomic analysis via two-dimensional (2D) gel electrophoresis.

RESULTS

Protein profiles were characterized in V. riparia shoot tips during active growth or SD induced growth cessation to examine physiological alterations in response to differential photoperiod treatments. A total of 1054 protein spots were present on the 2D gels. Among the 1054 proteins, 216 showed differential abundance between LD and SD (>/= two-fold ratio, p-value

CONCLUSIONS

The proteomics analysis uncovered a portion of the signal transduction involved in V. riparia grapevine growth cessation and dormancy induction. Different enzymes of the Calvin-Benson cycle and glutamate synthetase isoforms were more abundant either in LD or SD treatments. In LD tissues the significantly differentially more abundant proteins included flavonoid biosynthesis and polyphenol enzymes, cinnamyl alcohol dehydrogenase, and TCP-1 complexes. In the SD tissue photorespiratory proteins were more abundant than in the LD. The significantly differentially more abundant proteins in SD were involved in ascorbate biosynthesis, photosystem II and photosystem I subunits, light harvesting complexes, and carboxylation enzymes.

Collapse

Key Words Collapse

MESH Headings Collapse

Grants Collapse

Affiliation(s)

Kim J Victor Department of Horticulture, Forestry, Landscape, & Parks, Box 2140A, South Dakota State University, Brookings, SD 57007, USA
Anne Y Fennell Department of Horticulture, Forestry, Landscape, & Parks, Box 2140A, South Dakota State University, Brookings, SD 57007, USA
Jérôme Grimplet Department of Horticulture, Forestry, Landscape, & Parks, Box 2140A, South Dakota State University, Brookings, SD 57007, USA Instituto de Ciencias de la Vid y del Vino (CSIC, Universidad de La Rioja, Gobierno de La Rioja) Longroño, 26006, Spain

Collapse

Conditional modulation of NAD levels and metabolite profiles in Nicotiana sylvestris by mitochondrial electron transport and carbon/nitrogen supply

Environmental controls on leaf NAD status remain poorly understood. Here, we analyzed the effects of two key environmental variables, CO(2) and nitrogen, on leaf metabolite profiles, NAD status and the abundance of key transcripts involved in de novo NAD synthesis in wild-type (WT) Nicotiana sylvestris and the CMSII mutant that lacks respiratory complex I. High CO(2) and increased N supply both significantly enhanced NAD(+) and NADH pools in WT leaves. In nitrogen-sufficient conditions, CMSII leaves were enriched in NAD(+) and NADH compared to the WT, but the differences in NADH were smaller at high CO(2) than in air because high CO(2) increased WT NADH/NAD(+). The CMSII-linked increases in NAD(+) and NADH status were abolished by growth with limited nitrogen, which also depleted the nicotine and nicotinic acid pools in the CMSII leaves. Few statistically significant genotype and N-dependent differences were detected in NAD synthesis transcripts, with effects only on aspartate oxidase and NAD synthetase mRNAs. Non-targeted metabolite profiling as well as quantitative amine analysis showed that NAD(+) and NADH contents correlated tightly with leaf amino acid contents across all samples. The results reveal considerable genotype- and condition-dependent plasticity in leaf NAD(+) and NADH contents that is not linked to modified expression of NAD synthesis genes at the transcript level and show that NAD(+) and NADH contents are tightly integrated with nitrogen metabolism. A regulatory two-way feedback circuit between nitrogen and NAD in the regulation of N assimilation is proposed that potentially links the nutritional status to NAD-dependent signaling pathways.

The possible role of quinate in the mode of action of glyphosate and acetolactate synthase inhibitors

BACKGROUND

The herbicide glyphosate inhibits the biosynthesis of aromatic amino acids by blocking the shikimate pathway. Imazethapyr and chlorsulfuron are two herbicides that act by inhibiting branched-chain amino acid biosynthesis. These herbicides stimulate secondary metabolism derived from the aromatic amino acids. The aim of this study was to test if they cause any cross-effect in the amino acid content and if they have similar effects on the shikimate pathway.

RESULTS

The herbicides inhibiting two different amino acid biosynthesis pathways showed a common pattern in general content of free amino acids. There was a general increase in total free amino acid content, with a transient decrease in the proportion of amino acids whose pathways were specifically inhibited. Afterwards, an increase in these inhibited amino acids was detected; this was probably related to proteolysis. All herbicides caused quinate accumulation. Exogenous application of quinate arrested growth, decreased net photosynthesis and stomatal conductance and was ultimately lethal, similarly to glyphosate and imazethapyr.

CONCLUSIONS

Quinate accumulation was a common effect of the two different classes of herbicide. Moreover, exogenous quinate application had phytotoxic effects, showing that this plant metabolite can trigger the toxic effects of the herbicides. This ability to mimic the herbicide effects suggests a possible link between the mode of action of these herbicides and the potential role of quinate as a natural herbicide.

Uptake of organic nitrogen by plants

Languishing for many years in the shadow of plant inorganic nitrogen (N) nutrition research, studies of organic N uptake have attracted increased attention during the last decade. The capacity of plants to acquire organic N, demonstrated in laboratory and field settings, has thereby been well established. Even so, the ecological significance of organic N uptake for plant N nutrition is still a matter of discussion. Several lines of evidence suggest that plants growing in various ecosystems may access organic N species. Many soils display amino acid concentrations similar to, or higher than, those of inorganic N, mainly as a result of rapid hydrolysis of soil proteins. Transporters mediating amino acid uptake have been identified both in mycorrhizal fungi and in plant roots. Studies of endogenous metabolism of absorbed amino acids suggest that L- but not D-enantiomers are efficiently utilized. Dual labelled amino acids supplied to soil have provided strong evidence for plant uptake of organic N in the field but have failed to provide information on the quantitative importance of this process. Thus, direct evidence that organic N contributes significantly to plant N nutrition is still lacking. Recent progress in our understanding of the mechanisms underlying plant organic N uptake may open new avenues for the exploration of this subject.

Phytochemical diversity in tubers of potato cultivars and landraces using a GC-MS metabolomics approach

Phytochemical diversity with respect to a range of polar (including amino acids, organic acids, sugars, and sugar alcohols) and nonpolar (including fatty acids, alkanols, and sterols) metabolites was examined within tubers from a total of 29 genetically diverse potato cultivars and Chilean landraces using a metabolomics approach by gas chromatography-mass spectrometry. From principal component analysis of the polar and nonpolar metabolite data there was insufficient variation to differentiate the majority of cultivars and landraces. Analysis of all polar metabolite profiles revealed separation of two cultivars (Glenna and Morag) from the other cultivars and landraces and a separate cluster of one landrace line, largely due to higher levels of sugars. Pentland Javelin was distinct in containing high levels of many amino acids. The two Solanum tuberosum group phureja cultivars (Inca Sun and Mayan Gold) were not particularly similar and were not separated from the S. tuberosum group tuberosum cultivars. Analysis of the nonpolar metabolite data revealed partial separation of two landrace lines and, on the basis of some minor fatty acids, Mayan Gold was distinct. The differences in metabolite profiles are considered in terms of the taxonomy and breeding history of the cultivars and possible influences from other factors such as developmental stage of the tuber. With a view to exploring biosynthetic links between metabolites, a pairwise correlation analysis was performed on all metabolites. The significance of high correlations between many amino acids and between several nonpolar metabolites is discussed.

Time-resolved metabolomics reveals metabolic modulation in rice foliage

BACKGROUND

To elucidate the interaction of dynamics among modules that constitute biological systems, comprehensive datasets obtained from "omics" technologies have been used. In recent plant metabolomics approaches, the reconstruction of metabolic correlation networks has been attempted using statistical techniques. However, the results were unsatisfactory and effective data-mining techniques that apply appropriate comprehensive datasets are needed.

RESULTS

Using capillary electrophoresis mass spectrometry (CE-MS) and capillary electrophoresis diode-array detection (CE-DAD), we analyzed the dynamic changes in the level of 56 basic metabolites in plant foliage (Oryza sativa L. ssp. japonica) at hourly intervals over a 24-hr period. Unsupervised clustering of comprehensive metabolic profiles using Kohonen's self-organizing map (SOM) allowed classification of the biochemical pathways activated by the light and dark cycle. The carbon and nitrogen (C/N) metabolism in both periods was also visualized as a phenotypic linkage map that connects network modules on the basis of traditional metabolic pathways rather than pairwise correlations among metabolites. The regulatory networks of C/N assimilation/dissimilation at each time point were consistent with previous works on plant metabolism. In response to environmental stress, glutathione and spermidine fluctuated synchronously with their regulatory targets. Adenine nucleosides and nicotinamide coenzymes were regulated by phosphorylation and dephosphorylation. We also demonstrated that SOM analysis was applicable to the estimation of unidentifiable metabolites in metabolome analysis. Hierarchical clustering of a correlation coefficient matrix could help identify the bottleneck enzymes that regulate metabolic networks.

CONCLUSION

Our results showed that our SOM analysis with appropriate metabolic time-courses effectively revealed the synchronous dynamics among metabolic modules and elucidated the underlying biochemical functions. The application of discrimination of unidentified metabolites and the identification of bottleneck enzymatic steps even to non-targeted comprehensive analysis promise to facilitate an understanding of large-scale interactions among components in biological systems.

The role of JAR1 in Jasmonoyl-L: -isoleucine production during Arabidopsis wound response

The Arabidopsis thaliana (L.) Heynh. JASMONATE RESISTANT 1( JAR1) locus is essential for pathogen defense, but its role in wound response has not been investigated. JAR1 encodes an enzyme that conjugates jasmonic acid (JA) to isoleucine, which was recently shown to function directly in CORONATINE INSENSITIVE 1 (COI1)-mediated signal transduction. Leaf wounding rapidly increased the level of JA-Ile by about 60-fold to a peak of 279 pmole/g FW at 40 min after wounding. Conjugates with Leu, Val and Phe remained near basal level or were not detected. Kinetic analysis showed that JAR1 had a K (m) of 0.03 mM for Ile, which was 60-80-fold lower than for Leu, Val and Phe. JA-Ile accumulated mostly near the wound site with a minor increase in unwounded portions of wounded leaves. JAR1 transcript also increased dramatically in wounded tissue, reaching a maximum after about 1 h. In the jar1-1 mutant JA-Ile was only about 10% of the WT level at 40 min after leaf wounding, and reached a maximum of 47 pmole/g FW at 2 h. However, the reduced accumulation of JA-Ile had little or no effect on several jasmonate-dependent wound-induced genes. Wound induction of the VSP2 transcript was only slightly delayed while transcripts for LOX2, PDF1.2, WRKY33, TAT3 and CORI3 were unaffected. These results suggest that the rapid increase in JA-Ile mediated by the JAR1 enzyme plays only a minor role in transcriptional modulation of genes induced by mechanical wounding.

Metabolic profiles of Lolium perenne are differentially affected by nitrogen supply, carbohydrate content, and fungal endophyte infection

Lolium perenne cultivars differing in their capacity to accumulate water soluble carbohydrates (WSCs) were infected with three strains of fungal Neotyphodium lolii endophytes or left uninfected. The endophyte strains differed in their alkaloid profiles. Plants were grown at two different levels of nitrogen (N) supply in a controlled environment. Metabolic profiles of blades were analyzed using a variety of analytical methods. A total of 66 response variables were subjected to a principle components analysis and factor rotation. The first three rotated factors (46% of the total variance) were subsequently analyzed by analysis of variance. At high N supply nitrogenous compounds, organic acids and lipids were increased; WSCs, chlorogenic acid (CGA), and fibers were decreased. The high-sugar cultivar 'AberDove' had reduced levels of nitrate, most minor amino acids, sulfur, and fibers compared to the control cultivar 'Fennema', whereas WSCs, CGA, and methionine were increased. In plants infected with endophytes, nitrate, several amino acids, and, magnesium were decreased; WSCs, lipids, some organic acids, and CGA were increased. Regrowth of blades was stimulated at high N, and there was a significant endophyte x cultivar interaction on regrowth. Mannitol, a fungal specific sugar alcohol, was significantly correlated with fungal biomass. Our findings suggest that effects of endophytes on metabolic profiles of L. perenne can be considerable, depending on host plant characteristics and nutrient supply, and we propose that a shift in carbon/N ratios and in secondary metabolite production as seen in our study is likely to have impacts on herbivore responses.

Differences in the metabolite profiles of spinach (Spinacia oleracea L.) leaf in different concentrations of nitrate in the culture solution

The nitrogen (N) status of a plant determines the composition of its major components (amino acids, proteins, carbohydrates and organic acids) and, directly or indirectly, affects the quality of agricultural products in terms of their calorific value and taste. Although these effects are guided by changes in metabolic pathways, no overall metabolic analysis has previously been conducted to demonstrate such effects. Here, metabolite profiling using gas chromatography-mass spectrometry (GC-MS) was used to evaluate the effect of N levels on spinach tissue, comparing two cultivars that differed in their ability to use N. Wide variation in N content was observed without any distinct inhibition of growth in either cultivar. Principal component analysis (PCA) and self-organizing mapping (SOM) were undertaken to describe changes in the metabolites of mature spinach leaves. In PCA, the first component accounted for 44.5% of the total variance, the scores of which was positively correlated with the plant's N content, and a close relationship between metabolite profiles and N status was observed. Both PCA and SOM revealed that metabolites could be broadly divided into two types, correlating either positively or negatively with plant N content. The simple and co-coordinated metabolic stream, containing both general and spinach-specific aspects of plant N content, will be useful in future research on such topics as the detection of environmental effects on spinach through comprehensive metabolic profiling.

Getting to grips with the plant metabolic network

Research into plant metabolism has a long history, and analytical approaches of ever-increasing breadth and sophistication have been brought to bear. We now have access to vast repositories of data concerning enzymology and regulatory features of enzymes, as well as large-scale datasets containing profiling information of transcripts, protein and metabolite levels. Nevertheless, despite this wealth of data, we remain some way off from being able to rationally engineer plant metabolism or even to predict metabolic responses. Within the past 18 months, rapid progress has been made, with several highly informative plant network interrogations being discussed in the literature. In the present review we will appraise the current state of the art regarding plant metabolic network analysis and attempt to outline what the necessary steps are in order to further our understanding of network regulation.

Capacities and constraints of amino acid utilization in Arabidopsis

Various amino acids, including both L- and D-enantiomers, may be present in soils, and recent studies have indicated that plants may access such nitrogen (N) forms. Here, the capacity of Arabidopsis to utilize different L- and D-amino acids is investigated and the constraints on this process are explored. Mutants defective in the lysine histidine transporter 1 (LHT1) and transgenic plants overexpressing LHT1 as well as plants expressing D-amino acid-metabolizing enzymes, were used in studies of uptake and growth on various N forms. Arabidopsis absorbed all tested N-forms, but D-enantiomers at lower rates than L-forms. Several L- but no D-forms were effective as N sources. Plants deficient in LHT1 displayed strong growth reductions and plants overexpressing LHT1 showed strong growth enhancement when N was supplied as amino acids, in particular when these were supplied at low concentrations. Several D- amino acids inhibited growth of wild-type plants, while transgenic Arabidopsis-expressing genes encoding D-amino acid-metabolizing enzymes could efficiently utilize such compounds for growth. These results suggest that several amino acids, and in particular L-Gln and L-Asn, promote growth of Arabidopsis, and increased expression of specific amino acid transporters enhances growth on amino acids. The efficiency by which transgenic plants exploit D-amino acids illustrates how plants can be engineered to utilize specific N sources otherwise inaccessible to them.

Altered amino Acid metabolism in glutamine dumper1 plants

Amino acid metabolism lies at the crossroad between nitrogen assimilation, carbon fixation and secondary metabolism. Because of this central position in plant metabolism, amino acid metabolism is tightly regulated by numerous factors to match both demand from the organs and availability of reduced carbon and inorganic nitrogen. While the amino acid biosynthesis enzymes have been shown to be regulated at the transcriptional and protein levels, the genes involved in amino acid sensing, signal transduction and regulation have not yet been identified. The overexpression of Glutamine Dumper1 leads to a large increase in the amino acid content of the plant and, as we show here, to insensitivity to externally applied amino acids. This phenotype is reminiscent of that of the pig1-1 mutant proposed to display a deregulated metabolism. These data suggest that GDU1 is involved in the regulation of amino acid metabolism and transport. As published previously, the analysis of deletion mutants proves that GDU1's VIMAG domain is important for the function of the protein. The present data show furthermore that other regions participate to this function.

Impact of the C-N status on the amino acid profile in tobacco source leaves

This paper investigates the influence of the carbon (C) and nitrogen (N) status on the amino acid profile in tobacco source leaves. Treatments used included growing plants at different light intensities, using an antisense RBCS (small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase) construct to inhibit Rubisco activity, growing plants on 12 or 0.5 mM nitrate, comparing wild-types with genotypes that have small and large decreases in nitrate reductase (NIA) activity, and sampling plants at different times during the diurnal cycle. This combination of experiments provides information on how amino acid levels respond to several inputs including the C and N status, nitrate, excess light and light-dark transitions. The data set was analysed using principal component analysis, regression analysis and by normalizing the level of each individual amino acid on the total amino acid pool. Most amino acids show a downward trend when the C or the N status is decreased, and rise during day and fall at night during the diurnal cycle. However, individual amino acids often showed deviating responses. Furthermore, no evidence was found for feedback inhibition of minor amino acid synthesis, either within or between pathways, when 18 individual amino acids were supplied to detached leaves. Results indicate that regulation of amino acid metabolism, for example by the C and N status, leads to qualitatively similar responses of many amino acids, but homeostatic mechanisms involving feedback inhibition within or between individual amino acid biosynthesis pathways are not stringent. All of the above inputs affect the level of phenylalanine, an amino acid that is also the substrate for an important sector of secondary metabolism. The levels of glutamate were remarkably constant, indicating that unknown mechanisms stabilize the concentration of this key central amino acid. Analyses of metabolite levels and feeding experiments indicated that 2-oxoglutarate plays an important role in regulating glutamate levels. Glutamate was the most effective inhibitor of NIA activity when 18 individual amino acids were supplied to detached leaves. Feeding glutamate, and other downstream amino acids, led to an increase of glutamine, indicating glutamate exerts feedback regulation on ammonium metabolism.

Histidine biosynthesis in plants

The study of histidine metabolism has never been at the forefront of interest in plant systems despite the significant role that the analysis of this pathway has played in development of the field of molecular genetics in microbes. With the advent of methods to analyze plant gene function by complementation of microbial auxotrophic mutants and the complete analysis of plant genome sequences, strides have been made in deciphering the histidine pathway in plants. The studies point to a complex evolutionary origin of genes for histidine biosynthesis. Gene regulation studies have indicated novel regulatory networks involving histidine. In addition, physiological studies have indicated novel functions for histidine in plants as chelators and transporters of metal ions. Recent investigations have revealed intriguing connections of histidine in plant reproduction. The exciting new information suggests that the study of plant histidine biosynthesis has finally begun to flower.