Metabolite and light regulation of metabolism in plants: lessons from the study of a single biochemical pathway

Metabolome Profiling of Heat Priming Effects, Senescence, and Acclimation of Bread Wheat Induced by High Temperatures at Different Growth Stages

Our previous study described stage-specific responses of ‘Norin 61’ bread wheat to high temperatures from seedling to tillering (GS1), tillering to flowering (GS2), flowering to full maturity stage (GS3), and seedling to full maturity stage (GS1–3). The grain development phase lengthened in GS1 plants; source tissue decreased in GS2 plants; rapid senescence occurred in GS3 plants; all these effects occurred in GS1–3 plants. The present study quantified 69 flag leaf metabolites during early grain development to reveal the effects of stage-specific high-temperature stress and identify markers that predict grain weight. Heat stresses during GS2 and GS3 showed the largest shifts in metabolite contents compared with the control, followed by GS1–3 and GS1. The GS3 plants accumulated nucleosides related to the nucleotide salvage pathway, beta-alanine, and serotonin. Accumulation of these compounds in GS1 plants was significantly lower than in the control, suggesting that the reduction related to the high-temperature priming effect observed in the phenotype (i.e., inhibition of senescence). The GS2 plants accumulated a large quantity of free amino acids, indicating residual effects of the previous high-temperature treatment and recovery from stress. However, levels in GS1–3 plants tended to be close to those in the control, indicating an acclimation response. Beta-alanine, serotonin, tryptophan, proline, and putrescine are potential molecular markers that predict grain weight due to their correlation with agronomic traits.

Nitrogen use plasticity in response to light intensity in neotropical tree species of distinct functional groups

Environmental conditions influence the use of different nitrogen (N) sources by plants. We hypothesized that an increase in light intensity favors the use of nitrate (NO₃ ^- ) relative to ammonium (NH₄ ⁺ ) by seedlings of neotropical tree species from different functional groups, that is, Cecropia pachystachya (a shade-intolerant species), Cariniana estrellensis (a shade-tolerant canopy species), and Guarea kunthiana (a shade-tolerant understory species). We analyzed the growth and N metabolism in seedlings simultaneously provided with NH₄ ⁺ and NO₃ ^- , under lower (LL) and higher (HL) light intensity. ¹⁵ N incorporation into amino acids was monitored after incubation with ¹⁵ N-labeled NH₄ ⁺ or NO₃ ^- . Under HL, all species showed decreased leaf area ratio, and increased growth, nitrate reductase activity and assimilated N content. Cecropia pachystachya increased the use of both N sources under HL, with substantial increases in ¹⁵ N-amino acids derived from ¹⁵ NO₃ ^- (12.5- and 4.0-fold in roots and leaves, respectively) and ¹⁵ NH₄ ⁺ (4.5- and 3.0-fold in roots and leaves, respectively). Guarea kunthiana showed the greatest plasticity in N use, as the assimilation of ¹⁵ NO₃ ^- in roots and leaves increased substantially under HL (11.2- and 17.0-fold, respectively). Cariniana estrellensis increased the assimilation of ¹⁵ NH₄ ⁺ in roots and ¹⁵ NO₃ ^- in leaves under HL. Therefore, the responses of N use strategies to light intensity varied with the species according to their ecological characteristics.

Gluconate enhanced the water uptake and improved the growth of rice seedlings under PEG-induced osmotic stress

Low-molecular-weight organic acid not only serves as a nutrient of plants or as a source of energy metabolism but also a bioactive molecule, which can be linked with hormones, nitrogen (N), and other signals to participate in regulating gene expression, stress response, growth, and development of plants via mechanisms that remain poorly understood. We investigated how the supply of gluconate and sulfate affects rice plant growth and water absorption at the same N supply under osmotic stress. Using a greenhouse hydroponic experimental approach, we assessed the physiology of rice seedlings supplied with C₆H₁₁O₇NH₄ (AG) and (NH₄)₂SO₄ (AS) over multiple weeks. The root xylem sap rate in rice roots treated with AG increased significantly compared with AS treatment and the control under osmotic stress. The length of roots between 0.5 and 1.5 mm in diameter was obtained after treatment with polyethylene glycol (PEG) solutions containing AG, which was lower than those treated with PEG alone and PEG solutions containing AS. Compared with PEG alone and PEG solutions containing AS, AG induced a significant increase in root lignin under PEG-induced osmotic stress. However, relative to AS supply characteristics, the markedly reduced aerenchyma and porosity of roots, as well as higher root activity, increased fine root tips and length, and higher aquaporins and glutamate synthase (GS) activity in AG supply resulted in increased water uptake under osmotic stress. In addition, AG supply markedly increased leaf area and chlorophyll content. These results suggested that gluconate can enhance the water absorption capacity of the root system by promoting the growth and development of the root system, increasing the activity of aquaporin and GS and reducing the aeration tissue and porosity of the root system under osmotic stress.

A proteomic approach identifies novel proteins and metabolites for lesion mimic formation and disease resistance enhancement in rice

Lesion mimic mutants are ideal genetic materials to study programmed cell death and defense signaling in plants. However, the molecular basis of lesion mimic formation remains largely unknown. Here, we first used a proteomic approach to identify differentially expressed proteins during dynamic lesion mimic formation in the rice oscul3a mutant, then electron microscope observation and physiological assays were used to analyze the mutant. The oscul3a mutant had disrupted cell metabolism balance, and the identified differentially expressed proteins were mainly located in the chloroplast and cytoplasm, which caused enhanced lipid metabolism, but suppressed carbon/nitrogen metabolism with reduced growth and grain quality. The oscul3a mutant had higher salicylic acid (SA) concentration in leaves, and H₂O₂ was shown to accumulate late in the formation of lesions. The secondary metabolite coumarin induced reactive oxygen species (ROS) and had rice blast resistance activity. Moreover, the cell death initiated lesion mimic formation of oscul3a mutant was light-sensitive, which might be associated with metabolite biosynthesis and accumulation. This study sheds light on the metabolic transition associated with cell death and defense response, which is under tight regulation by OsCUL3a and metabolism-related proteins, and the newly identified chemicals in the secondary metabolic pathway can potentially be used to control disease in crop plants.

OsASN1 Plays a Critical Role in Asparagine-Dependent Rice Development

Asparagine is one of the important amino acids for long-distance transport of nitrogen (N) in plants. However, little is known about the effect of asparagine on plant development, especially in crops. Here, a new T-DNA insertion mutant, asparagine synthetase 1 (asn1), was isolated and showed a different plant height, root length, and tiller number compared with wild type (WT). In asn1, the amount of asparagine decreased sharply while the total nitrogen (N) absorption was not influenced. In later stages, asn1 showed reduced tiller number, which resulted in suppressed tiller bud outgrowth. The relative expression of many genes involved in the asparagine metabolic pathways declined in accordance with the decreased amino acid concentration. The CRISPR/Cas9 mutant lines of OsASN1 showed similar phenotype with asn1. These results suggest that OsASN1 is involved in the regulation of rice development and is specific for tiller outgrowth.

Formation and Change of Chloroplast-Located Plant Metabolites in Response to Light Conditions

Photosynthesis is the central energy conversion process for plant metabolism and occurs within mature chloroplasts. Chloroplasts are also the site of various metabolic reactions involving amino acids, lipids, starch, and sulfur, as well as where the production of some hormones takes place. Light is one of the most important environmental factors, acting as an essential energy source for plants, but also as an external signal influencing their growth and development. Plants experience large fluctuations in the intensity and spectral quality of light, and many attempts have been made to improve or modify plant metabolites by treating them with different light qualities (artificial lighting) or intensities. In this review, we discuss how changes in light intensity and wavelength affect the formation of chloroplast-located metabolites in plants.

Effect of glycine nitrogen on lettuce growth under soilless culture: a metabolomics approach to identify the main changes occurred in plant primary and secondary metabolism

BACKGROUND

Lettuce is a significant source of antioxidants and bioactive compounds. Nitrate is a cardinal fertilizer in horticulture and influences vegetable yield and quality; however, the negative effects of nitrate on the biosynthesis of flavonoids require further study. It is expected that using fertilizers containing organic nitrogen (N) could promote the synthesis of health-promoting compounds.

RESULTS

Lettuces were hydroponically cultured in media containing 9 mmol L-1 nitrate or 9 mmol L-1 glycine for 4 weeks. Primary and secondary metabolites were analyzed using gas chromatography/mass spectrometry (GC/MS) and ultra-performance liquid chromatography/ion mobility spectrometry/quadrupole time-of-flight mass spectrometry (UPLC/IMS/QTOF-MS). Data analysis revealed that 29 metabolites were significantly altered between nitrate and glycine treatments. Metabolites were tentatively identified by comparison with online databases, literature and standards and using collision cross-section values. Significant differences in flavonoid biosynthesis, phenolic biosynthesis and the tricarboxylic acid (TCA) cycle response were observed between N sources. Compared with nitrate, glycine promoted accumulation of glycosylated flavonoids (quercetin 3-glucoside, quercetin 3-(6″-malonyl-glucoside), luteolin 7-glucuronide, luteolin 7-glucoside), ascorbic acid and amino acids (l-valine, l-leucine, l-glutamine, asparagine, l-serine, l-ornithine, 4-aminobutanoic acid, l-phenylalanine) but reduced phenolic acids (dihydroxybenzoic acid hexose isomers 1 and 2, chicoric acid, chicoric acid isomer 1) and TCA intermediates (fumaric, malic, citric and succinic acids).

CONCLUSION

The novel methodology applied in this study can be used to characterize metabolites in lettuce. Accumulation of glycosylated flavonoids, amino acids and ascorbic acid in response to glycine supply provides strong evidence supporting the idea that using amino acids as an N source alters the nutritional value of vegetable crops. © 2017 Society of Chemical Industry.

Comparative transcriptome profiling of upland (VS16) and lowland (AP13) ecotypes of switchgrass

KEY MESSAGE

Transcriptomes of two switchgrass genotypes representing the upland and lowland ecotypes will be key tools in switchgrass genome annotation and biotic and abiotic stress functional genomics. Switchgrass (Panicum virgatum L.) is an important bioenergy feedstock for cellulosic ethanol production. We report genome-wide transcriptome profiling of two contrasting tetraploid switchgrass genotypes, VS16 and AP13, representing the upland and lowland ecotypes, respectively. A total of 268 million Illumina short reads (50 nt) were generated, of which, 133 million were obtained in AP13 and the rest 135 million in VS16. More than 90% of these reads were mapped to the switchgrass reference genome (V1.1). We identified 6619 and 5369 differentially expressed genes in VS16 and AP13, respectively. Gene ontology and KEGG pathway analysis identified key genes that regulate important pathways including C4 photosynthesis, photorespiration and phenylpropanoid metabolism. A series of genes (33) involved in photosynthetic pathway were up-regulated in AP13 but only two genes showed higher expression in VS16. We identified three dicarboxylate transporter homologs that were highly expressed in AP13. Additionally, genes that mediate drought, heat, and salinity tolerance were also identified. Vesicular transport proteins, syntaxin and signal recognition particles were seen to be up-regulated in VS16. Analyses of selected genes involved in biosynthesis of secondary metabolites, plant-pathogen interaction, membrane transporters, heat, drought and salinity stress responses confirmed significant variation in the relative expression reflected in RNA-Seq data between VS16 and AP13 genotypes. The phenylpropanoid pathway genes identified here are potential targets for biofuel conversion.

Characterization of natural leaf senescence in tobacco (Nicotiana tabacum) plants grown in vitro

Leaf senescence is a highly regulated final phase of leaf development preceding massive cell death. It results in the coordinated degradation of macromolecules and the subsequent nutrient relocation to other plant parts. Very little is still known about early stages of leaf senescence during normal leaf ontogeny that is not triggered by stress factors. This paper comprises an integrated study of natural leaf senescence in tobacco plants grown in vitro, using molecular, structural, and physiological information. We determined the time sequence of ultrastructural changes in mesophyll cells during leaf senescence, showing that the degradation of chloroplast ultrastructure fully correlated with changes in chlorophyll content. The earliest degenerative changes in chloroplast ultrastructure coinciding with early chromatin condensation were observed already in mature green leaves. A continuum of degradative changes in chloroplast ultrastructure, chromatin condensation and aggregation, along with progressive decrease in cytoplasm organization and electron density were observed in the course of mesophyll cells ageing. Although the total amounts of endogenous cytokinins gradually increased during leaf ontogenesis, the proportion of bioactive cytokinin forms, as well as their phosphate precursors, in total cytokinin content rapidly declined with ageing. Endogenous indole-3-acetic acid (IAA) levels were strongly reduced in senescent leaves, and a decreasing tendency was also observed for abscisic acid (ABA) levels. Senescence-associated tobacco cysteine proteases (CP, E.C. 3.4.22) CP1 and CP23 genes were induced in the initial phase of senescence. Genes encoding glutamate dehydrogenase (GDH, E.C. 1.4.1.2) and one isoform of cytosolic glutamine synthetase (GS1, E.C. 6.3.1.2) were induced in the late stage of senescence, while chloroplastic GS (GS2) gene showed a continuous decrease with leaf ageing.

Regulation of amino acid metabolic enzymes and transporters in plants

Amino acids play several critical roles in plants, from providing the building blocks of proteins to being essential metabolites interacting with many branches of metabolism. They are also important molecules that shuttle organic nitrogen through the plant. Because of this central role in nitrogen metabolism, amino acid biosynthesis, degradation, and transport are tightly regulated to meet demand in response to nitrogen and carbon availability. While much is known about the feedback regulation of the branched biosynthesis pathways by the amino acids themselves, the regulation mechanisms at the transcriptional, post-transcriptional, and protein levels remain to be identified. This review focuses mainly on the current state of our understanding of the regulation of the enzymes and transporters at the transcript level. Current results describing the effect of transcription factors and protein modifications lead to a fragmental picture that hints at multiple, complex levels of regulation that control and coordinate transport and enzyme activities. It also appears that amino acid metabolism, amino acid transport, and stress signal integration can influence each other in a so-far unpredictable fashion.

Modulating plant primary amino acid metabolism as a necrotrophic virulence strategy: the immune-regulatory role of asparagine synthetase in Botrytis cinerea-tomato interaction

The fungal plant pathogen Botrytis cinerea is the causal agent of the "gray mold" disease on a broad range of hosts. As an archetypal necrotroph, B. cinerea has evolved multiple virulence strategies for inducing cell death in its host. Moreover, progress of B. cinerea colonization is commonly associated with induction of senescence in the host tissue, even in non-invaded regions. In a recent study, we showed that abscisic acid deficiency in the sitiens tomato mutant culminates in an anti-senescence defense mechanism which effectively contributes to resistance against B. cinerea infection. Conversely, in susceptible wild-type tomato a strong induction of senescence could be observed following B. cinerea infection. Building upon this earlier work, we here discuss the immune-regulatory role of a key senescence-associated protein, asparagine synthetase. We found that infection of wild-type tomato leads to a strong transcriptional upregulation of asparagine synthetase, followed by a severe depletion of asparagine titers. In contrast, resistant sitiens plants displayed a strong induction of asparagine throughout the course of infection. We hypothesize that rapid activation of asparagine synthetase in susceptible tomato may play a dual role in promoting Botrytis cinerea pathogenesis by providing a rich source of N for the pathogen, on the one hand, and facilitating pathogen-induced host senescence, on the other.

Ammonium formation and assimilation in P(SARK)∷IPT tobacco transgenic plants under low N

Wild Type (WT) and transgenic tobacco plants expressing isopentenyltransferase (IPT), a gene encoding the enzyme regulating the rate-limiting step in cytokinins (CKs) synthesis, were grown under limited nitrogen (N) conditions. We analyzed nitrogen forms, nitrogen metabolism related-enzymes, amino acids and photorespiration related-enzymes in WT and P(SARK)∷IPT tobacco plants. Our results indicate that the WT plants subjected to N deficiency displayed reduced nitrate (NO₃⁻) assimilation. However, an increase in the production of ammonium (NH₄⁺), by the degradation of proteins and photorespiration led to an increase in the glutamine synthetase/glutamate synthase (GS/GOGAT) cycle in WT plants. In these plants, the amounts of amino acids decreased with N deficiency, although the relative amounts of glutamate and glutamine increased with N deficiency. Although the transgenic plants expressing P(SARK)∷IPT and growing under suboptimal N conditions displayed a significant decline in the N forms in the leaf, they maintained the GS/GOGAT cycle at control levels. Our results suggest that, under N deficiency, CKs prevented the generation and assimilation of NH₄⁺ by increasing such processes as photorespiration, protein degradation, the GS/GOGAT cycle, and the formation of glutamine.

Amino acid export in plants: a missing link in nitrogen cycling

The export of nutrients from source organs to parts of the body where they are required (e.g. sink organs) is a fundamental biological process. Export of amino acids, one of the most abundant nitrogen species in plant long-distance transport tissues (i.e. xylem and phloem), is an essential process for the proper distribution of nitrogen in the plant. Physiological studies have detected the presence of multiple amino acid export systems in plant cell membranes. Yet, surprisingly little is known about the molecular identity of amino acid exporters, partially due to the technical difficulties hampering the identification of exporter proteins. In this short review, we will summarize our current knowledge about amino acid export systems in plants. Several studies have described plant amino acid transporters capable of bi-directional, facilitative transport, reminiscent of activities identified by earlier physiological studies. Moreover, recent expansion in the number of available amino acid transporter sequences have revealed evolutionary relationships between amino acid exporters from other organisms with a number of uncharacterized plant proteins, some of which might also function as amino acid exporters. In addition, genes that may regulate export of amino acids have been discovered. Studies of these putative transporter and regulator proteins may help in understanding the elusive molecular mechanisms of amino acid export in plants.

Quality traits of conventional and transgenic lettuce (Lactuca sativa L.) at harvesting by NMR metabolic profiling

Metabolism of genetically modified (GM) lettuce (Lactuca sativa L.) leaves was investigated by comparing NMR metabolic profiles of three lines (T(3)B12, T(7)B7, and T(7)B14) overexpressing the E. coli asparagine synthetase A gene with those of the wild type (WT) at 24, 56, and 64 days after sowing (DAS). Statistical analyses based on hydro-soluble compound profiles significantly and maximally discriminated the WT from GM-lines at optimal harvest time (56 DAS). The T(7)B14 metabolic variations were opposite to those of both T(3)B12/T(7)B7 lines, suggesting that unexpected effects of transgenesis had occurred. Compared to controls, the T(3)B12/T(7)B7 plants shared the leaf mass increase, higher amino acid (asparagine, glutamine, valine, and isoleucine) and protein levels, and lower nitrate contents, accompanied by a modest sink of organic acids (alpha-chetoglutarate, succinate, fumarate, and malate), sucrose, fructose, and inulins. Incongruously, the T(7)B14 butter heads were less leafy than the controls and showed lowered amino acid/protein contents and overstored inulin. To further investigate the metabolic discrepancies among the GM-lines, a set of key nitrogen and inulin genes was monitored. The T(3)B12/T(7)B7 lines shared comparable gene expression changes, including the induction of the endogenous asparagine synthetase1 and nitrate reductase1 that supported the targeted enhancement of nitrogen status. Transgene product malfunctioning and T-DNA rearrangements throughout generations were proposed to explain the decreased asparagine content and the complex expression pattern of N genes in T(7)B14 leaves. In the latter, the inulin accumulation was associated with the upregulation of fructan biosynthesis genes and the intense repression of fructan hydrolases.

Exogenous ammonium inhibits petal pigmentation and expansion in Gerbera hybrida

Petal pigmentation is the most important aspect in natural flower coloration. In the present study, the inhibition of petal pigmentation by exogenous ammonium was investigated. Ray floret petals detached from inflorescences of Gerbera hybrida (Shenzhen No. 5) were cultured in vitro on media supplied with different forms of nitrogen and its assimilated compounds. The expression of a set of genes involved in anthocyanin biosynthesis and regulation was determined by Northern blotting assay. It was found that ammonium (NH4+), not nitrate (NO3-), in millimolar concentrations inhibited anthocyanin accumulation. The expressions of Gerbera chalcone synthase 1 (GCHS1), Gerbera chalcone synthase 2 (GCHS2) and Gerbera dihydroflavonol-4-reductase (GDFR) decreased, while six other related genes showed no significant changes after NH4+ treatment. Further studies on NH4+ function indicated that glutamine (Gln) acted as a downstream factor of NH4+ to suppress petal pigmentation. Both exogenous Gln and NH4+ were found to inhibit anthocyanin accumulation in the petals, and the application of Gln was also found to inhibit the expressions of GCHS1, GCHS2 and GDFR. The application of NH4+ also resulted in an increase in the activity of Gerbera glutamine synthetase (EC 6.3.1.2) along with a rapid increase of Gln content. When methionine sulfoximine, an inhibitor of glutamine synthetase (GS), was added, it was found to block the NH4+-induced inhibition of pigmentation. From these experiments, we conclude that the NH4+-induced suppression of petal pigmentation is not because of NH4+ toxicity, and the inhibition of pigmentation caused by the addition of exogenous NH4+ is the result of its assimilation into Gln.

Life-cycle and genome of OtV5, a large DNA virus of the pelagic marine unicellular green alga Ostreococcus tauri

Large DNA viruses are ubiquitous, infecting diverse organisms ranging from algae to man, and have probably evolved from an ancient common ancestor. In aquatic environments, such algal viruses control blooms and shape the evolution of biodiversity in phytoplankton, but little is known about their biological functions. We show that Ostreococcus tauri, the smallest known marine photosynthetic eukaryote, whose genome is completely characterized, is a host for large DNA viruses, and present an analysis of the life-cycle and 186,234 bp long linear genome of OtV5. OtV5 is a lytic phycodnavirus which unexpectedly does not degrade its host chromosomes before the host cell bursts. Analysis of its complete genome sequence confirmed that it lacks expected site-specific endonucleases, and revealed the presence of 16 genes whose predicted functions are novel to this group of viruses. OtV5 carries at least one predicted gene whose protein closely resembles its host counterpart and several other host-like sequences, suggesting that horizontal gene transfers between host and viral genomes may occur frequently on an evolutionary scale. Fifty seven percent of the 268 predicted proteins present no similarities with any known protein in Genbank, underlining the wealth of undiscovered biological diversity present in oceanic viruses, which are estimated to harbour 200Mt of carbon.

Systems approach identifies an organic nitrogen-responsive gene network that is regulated by the master clock control gene CCA1

Understanding how nutrients affect gene expression will help us to understand the mechanisms controlling plant growth and development as a function of nutrient availability. Nitrate has been shown to serve as a signal for the control of gene expression in Arabidopsis. There is also evidence, on a gene-by-gene basis, that downstream products of nitrogen (N) assimilation such as glutamate (Glu) or glutamine (Gln) might serve as signals of organic N status that in turn regulate gene expression. To identify genome-wide responses to such organic N signals, Arabidopsis seedlings were transiently treated with ammonium nitrate in the presence or absence of MSX, an inhibitor of glutamine synthetase, resulting in a block of Glu/Gln synthesis. Genes that responded to organic N were identified as those whose response to ammonium nitrate treatment was blocked in the presence of MSX. We showed that some genes previously identified to be regulated by nitrate are under the control of an organic N-metabolite. Using an integrated network model of molecular interactions, we uncovered a subnetwork regulated by organic N that included CCA1 and target genes involved in N-assimilation. We validated some of the predicted interactions and showed that regulation of the master clock control gene CCA1 by Glu or a Glu-derived metabolite in turn regulates the expression of key N-assimilatory genes. Phase response curve analysis shows that distinct N-metabolites can advance or delay the CCA1 phase. Regulation of CCA1 by organic N signals may represent a novel input mechanism for N-nutrients to affect plant circadian clock function.

The sucrose regulated transcription factor bZIP11 affects amino acid metabolism by regulating the expression of ASPARAGINE SYNTHETASE1 and PROLINE DEHYDROGENASE2

Translation of the transcription factor bZIP11 is repressed by sucrose in a process that involves a highly conserved peptide encoded by the 5' leaders of bZIP11 and other plant basic region leucine zipper (bZip) genes. It is likely that a specific signaling pathway operating at physiological sucrose concentrations controls metabolism via a feedback mechanism. In this paper bZIP11 target processes are identified using transiently increased nuclear bZIP11 levels and genome-wide expression analysis. bZIP11 affects the expression of hundreds of genes with proposed functions in biochemical pathways and signal transduction. The expression levels of approximately 80% of the genes tested are not affected by bZIP11 promoter-mediated overexpression of bZIP11. This suggests that <20% of the identified genes appear to be physiologically relevant targets of bZIP11. ASPARAGINE SYNTHETASE1 and PROLINE DEHYDROGENASE2 are among the rapidly activated bZIP11 targets, whose induction is independent of protein translation. Transient expression experiments in Arabidopsis protoplasts show that the bZIP11-dependent activation of the ASPARAGINE SYNTHETASE1 gene is dependent on a G-box element present in the promoter. Increased bZIP11 expression leads to decreased proline and increased phenylalanine levels. A model is proposed in which sugar signals control amino acid levels via the bZIP11 transcription factor.

Salinity-induced tissue-specific diurnal changes in nitrogen assimilatory enzymes in tomato seedlings grown under high or low nitrate medium

We studied the salt stress (100 mM NaCl) effects on the diurnal changes in N metabolism enzymes in tomato seedlings (Lycopersicon esculentum Mill. cv. Chibli F1) that were grown under high nitrogen (HN, 5 mM NO(3)(-)) or low nitrogen (LN, 0.1 mM NO(3)(-)). NaCl stress led to a decrease in plant DW production and leaf surface to higher extent in HN than in LN plants. Total leaf chlorophyll (Chl) content was decreased by salinity in HN plants, but unchanged in LN plants. Soluble protein content was decreased by salt in the leaves from HN and LN plants, but increased in the stems-petioles from LN plants. Nitrate reductase (NR, EC 1.6.1.6) showed an activity peak during first part of the light period, but no diurnal changes were observed for the nitrite reductase (NiR, EC 1.7.7.1) activity. Glutamine synthetase (GS, EC 6.3.1.2) and glutamate synthase (Fd-GOGAT, EC 1.4.7.1) activities increased in HN plant leaves during the second part of the light period, probably when enough ammonium is produced by nitrate reduction. NR and NiR activities in the leaves were more decreased by NaCl in LN than in HN plants, whereas the opposite response was obtained for the GS activity. Fd-GOGAT activity was inhibited by NaCl in HN plant leaves, while salinity did not shift the peak of the NR and Fd-GOGAT activities during a diurnal cycle. The induction by NaCl stress occurred for the NR and GS activities in the roots of both HN and LN plants. Glutamate dehydrogenase (GDH, EC 1.4.1.2) activity shifted from the deaminating activity to the aminating activity in all tissues of HN plants. In LN plants, both aminating and deaminating activities were increased by salinity in the leaves and roots. The differences in the sensitivity to NaCl between HN and LN plants are discussed in relation to the N metabolism status brought on by salt stress.

Integrative analysis of transcript and metabolite profiling data sets to evaluate the regulation of biochemical pathways during photomorphogenesis

One of the key developmental processes during photomorphogenesis is the differentiation of prolamellar bodies of proplastids into thylakoid membranes containing the photosynthetic pigment-protein complexes of chloroplasts. To study the regulatory events controlling pigment-protein complex assembly, including the biosynthesis of metabolic precursors and pigment end products, etiolated Arabidopsis thaliana seedlings were irradiated with continuous red light (Rc), which led to rapid greening, or continuous far-red light (FRc), which did not result in visible greening, and subjected to analysis by oligonucleotide microarrays and targeted metabolite profiling. An analysis using BioPathAt, a bioinformatic tool that allows the visualization of post-genomic data sets directly on biochemical pathway maps, indicated that in Rc-treated seedlings mRNA expression and metabolite patterns were tightly correlated (e.g., Calvin cycle, biosynthesis of chlorophylls, carotenoids, isoprenoid quinones, thylakoid lipids, sterols, and amino acids). K-means clustering revealed that gene expression patterns across various biochemical pathways were very similar in Rc- and FRc-treated seedlings (despite the visible phenotypic differences), whereas a principal component analysis of metabolite pools allowed a clear distinction between both treatments (in accordance with the visible phenotype). Our results illustrate the general importance of integrative approaches to correlate post-genomic data sets with phenotypic outcomes.

Expression and transcriptional regulation of amino acid transporters in plants

Recent studies have shown that there are more than 50 amino acid transporter genes in the Arabidopsis genome. This abundance of amino acid transporters implies that they play a multitude of fundamental roles in plant growth and development. Current research on the expression and regulation (i.e., tissue-specific expression and regulation of expression in response to nutrient and environmental changes) of these genes has provided useful information about the functional significance of plant amino acid transport systems.

The role of glutamine synthetase and glutamate dehydrogenase in nitrogen assimilation and possibilities for improvement in the nitrogen utilization of crops

This short review outlines the central role of glutamine synthetase (GS) in plant nitrogen metabolism and discusses some possibilities for crop improvement. GS functions as the major assimilatory enzyme for ammonia produced from N fixation, and nitrate or ammonia nutrition. It also reassimilates ammonia released as a result of photorespiration and the breakdown of proteins and nitrogen transport compounds. GS is distributed in different subcellular locations (chloroplast and cytoplasm) and in different tissues and organs. This distribution probably changes as a function of the development of the tissue, for example, GS1 appears to play a key role in leaf senescence. The enzyme is the product of multiple genes with complex promoters that ensure the expression of the genes in an organ- and tissue-specific manner and in response to a number of environmental variables affecting the nutritional status of the cell. GS activity is also regulated post-translationally in a manner that involves 14-3-3 proteins and phosphorylation. GS and plant nitrogen metabolism is best viewed as a complex matrix continually changing during the development cycle of plants. Along with GS, a number of other enzymes play key roles in maintaining the balance of carbon and nitrogen. It is proposed that one of these is glutamate dehydrogenase (GDH). There is considerable evidence for a GDH shunt to return the carbon in amino acids back into reactions of carbon metabolism and the tri-carboxylic acid cycle. Results with transgenic plants containing transferred GS genes suggest that there may be ways in which it is possible to improve the efficiency with which crop plants use nitrogen. Marker-assisted breeding may also bring about such improvements.