Suppression of glutamate synthase genes significantly affects carbon and nitrogen metabolism in rice (Oryza sativa L.)

Identification of Wheat Glutamate Synthetase Gene Family and Expression Analysis under Nitrogen Stress

Nitrogen (N), as the main component of biological macromolecules, maintains the basic process of plant growth and development. GOGAT, as a key enzyme in the N assimilation process, catalyzes α-ketoglutaric acid and glutamine to form glutamate. In this study, six GOGAT genes in wheat (Triticum aestivum L.) were identified and classified into two subfamilies, Fd-GOGAT (TaGOGAT2s) and NADH-GOGAT (TaGOGAT3s), according to the type of electron donor. Subcellular localization prediction showed that TaGOGAT3-D was localized in mitochondria and that the other five TaGOGATs were localized in chloroplasts. Via the analysis of promoter elements, many binding sites related to growth and development, hormone regulation and plant stress resistance regulations were found on the TaGOGAT promoters. The tissue-specificity expression analysis showed that TaGOGAT2s were mainly expressed in wheat leaves and flag leaves, while TaGOGAT3s were highly expressed in roots and leaves. The expression level of TaGOGATs and the enzyme activity of TaGOGAT3s in the leaves and roots of wheat seedlings were influenced by the treatment of N deficiency. This study conducted a systematic analysis of wheat GOGAT genes, providing a theoretical basis not only for the functional analysis of TaGOGATs, but also for the study of wheat nitrogen use efficiency (NUE).

Effects of Different Nitrogen Forms on Blackberry Fruit Quality

To study the optimal form of nitrogen (N) application and to determine the best harvest date for blackberries, different N fertilizers were applied during the critical growth period of blackberry plants. The results showed that NH₄⁺-N significantly improved the appearance of blackberry fruits, including their size, firmness, and color, and promoted the accumulation of soluble solids, sugars, anthocyanin, ellagic acid, and vitamin C (VC), while fruit treated with NO₃^--N accumulated more flavonoids and organic acids and had improved antioxidant capacity. In addition, the fruit size, firmness, and color brightness decreased with the harvest period. While the contents of sugars, anthocyanin, ellagic acid, flavonoids, and VC were higher in the early harvests and then decreased as the season progressed, the total antioxidant capacity and DPPH radical scavenging capacity increased. In all, application of NH₄⁺-N is recommended, as it is more beneficial to fruit appearance, taste, and nutritional quality. Harvests in the early stage help to obtain a good fruit appearance, while harvests in the middle and later stages are more beneficial to fruit taste and quality. This study may help growers to determine the best fertilization scheme for blackberries and choose the appropriate harvest time according to their needs.

Exogenous γ-aminobutyric acid (GABA) improves salt-inhibited nitrogen metabolism and the anaplerotic reaction of the tricarboxylic acid cycle by regulating GABA-shunt metabolism in maize seedlings

Salinity stress hampers the growth of most crop plants and reduces yield considerably. In addition to its role in metabolism, γ-aminobutyric acid (GABA) plays a special role in the regulation of salinity stress tolerance in plants, though the underlying physiological mechanism remains poorly understood. In order to study the physiological mechanism of GABA pathway regulated carbon and nitrogen metabolism and tis relationship with salt resistance of maize seedlings, we supplemented seedlings with exogenous GABA under salt stress. In this study, we showed that supplementation with 0.5 mmol·L^-1 (0.052 mg·g^-1) GABA alleviated salt toxicity in maize seedling leaves, ameliorated salt-induced oxidative stress, and increased antioxidant enzyme activity. Applying exogenous GABA maintained chloroplast structure and relieved chlorophyll degradation, thus improving the photosynthetic performance of the leaves. Due to the improvement in photosynthesis, sugar accumulation also increased. Endogenous GABA content and GABA transaminase (GABA-T) and succinate semialdehyde dehydrogenase (SSADH) activity were increased, while glutamate decarboxylase (GAD) activity was decreased, via the exogenous application of GABA under salt stress. Meanwhile, nitrogen metabolism and the tricarboxylic acid (TCA) cycle were activated by the supply of GABA. In general, through the regulation of GABA-shunt metabolism, GABA activated enzymes related to nitrogen metabolism and replenished the key substrates of the TCA cycle, thereby improving the balance of carbon and nitrogen metabolism of maize and improving salt tolerance.

Multi-omics analysis reveals the influence of tetracycline on the growth of ryegrass root

Environmental factors, including antibiotics such as tetracycline, can alter biological processes in plants. To ascertain how cell/tissue response to tetracycline, a multi-omic analysis was implemented to explore the molecular mechanism of tetracycline influencing the growth of ryegrass root. Tetracycline induced extensive changes in the root metabolome in plants, particularly impacting metabolites of flavonoid metabolic pathways, which were supported through consistent differences between transcriptome and proteome. Cross-comparison between mRNA and protein contents considered the authentication of congruence with related metabolites and revealed changes of several biological processes under tetracycline stress. Overall, we present an undemanding multi-omic strategy to survey the significant influence on the root under tetracycline stress.

Nanoscale zero-valent iron alters physiological, biochemical, and transcriptomic response of nonylphenol-exposed algae (Dictyosphaerium sp.)

Nanoparticles and organic pollutants are two major contaminants found in aquatic environments. Algae are regarded as the model organism for the risk assessment of pollutants in water. In our previous study, we investigated the toxic effects of nonylphenol (NP), a typical organic water pollutant, on algae; however, it remains unclear how algae respond to the coexistence of NP and nanoparticles. In this study, a concentration gradient of nanoscale zero-valent iron (nZVI; 10, 50, 100, and 200 mg/L) was added to NP-exposed Dictyosphaerium sp. to investigate both the toxic effects of this combination and the potential for NP removal. nZVI had a dose-dependent effect on NP-exposed algae, with high nZVI concentrations significantly decreasing algal biomass and pigment content, as well as severely damaging algal cellular ultrastructure. In addition, genes involved in antioxidant response, photosynthesis, and ribosome synthesis were significantly altered when NP-exposed algae were incubated with nZVI. In contrast to high nZVI concentrations, adding a small concentration of nZVI led to reduced toxicity in NP-exposed algae, while significantly enhancing the NP removal rate. This study improves our understanding of algal responses to various pollutants and suggests that nZVI may assist in the remediation of NP in aquatic ecosystems.

Physiological and transcriptome analyses for assessing the effects of exogenous uniconazole on drought tolerance in hemp (Cannabis sativa L.)

Uniconazole (S-(+)-uniconazole), a plant growth retardant, exerts key roles in modulating growth and development and increasing abiotic stress tolerance in plants. However, the underlying mechanisms by which uniconazole regulates drought response remain largely unknown. Here, the effects of exogenous uniconazole on drought tolerance in hemp were studied via physiological and transcriptome analyses of the drought-sensitive industrial hemp cultivar Hanma No. 2 grown under drought stress. Exogenous uniconazole treatment increased hemp tolerance to drought-induced damage by enhancing chlorophyll content and photosynthesis capacity, regulating activities of enzymes involved in carbon and nitrogen metabolism, and altering endogenous hormone levels. Expression of genes associated with porphyrin and chlorophyll metabolism, photosynthesis-antenna proteins, photosynthesis, starch and sucrose metabolism, nitrogen metabolism, and plant hormone signal transduction were significantly regulated by uniconazole compared with that by control (distilled water) under drought stress. Numerous genes were differentially expressed to increase chlorophyll content, enhance photosynthesis, regulate carbon-nitrogen metabolism-related enzyme activities, and alter endogenous hormone levels. Thus, uniconazole regulated physiological and molecular characteristics of photosynthesis, carbon-nitrogen metabolism, and plant hormone signal transduction to enhance drought resistance in industrial hemp.

Nitrogen Source Affects the Composition of Metabolites in Pepper (Capsicum annuum L.) and Regulates the Synthesis of Capsaicinoids through the GOGAT-GS Pathway

Phytochemical analyses of pepper fruit metabolites have been reported; however, much less is known about the influence of different forms of nitrogen (N), which is critical for plant growth and fruit quality formation. The "Longjiao No. 5" variety (Capsicum annuum L.) grown in Northwestern China was profiled using liquid chromatography-mass spectrometry (LC-MS) coupled with multivariate data analysis to explore the composition of different metabolites in pericarp and placenta, and to investigate the effect of three ammonium (NH4+)-to-nitrate (NO3-) ratios (0:100, 25:75, and 50:50). A total of 215 metabolites were obtained by qualitative analysis, where 31 metabolites were the major differential metabolite components of pepper fruits between placenta and pericarp, and 25 among N treatments. The addition of ammonium up-regulated carbohydrates, such as α-lactose and sucrose, as well as phenylalanine lyase (PAL) of placenta tissue. The supply of 25% NH4+-N and 75% NO3--N exhibited a relatively higher levels of ascorbic acid in pericarp and amino acids, capsaicin, and dihydrocapsaicin in placenta, and led to higher fruit weight among the ammonium-to-nitrate ratios. The expression and activities of glutamic acid synthetase (GOGAT) and glutamine synthetase (GS) that are involved in ammonium assimilation were affected by adjusting the ammonium-N proportion, and they were significantly positively correlated with capsaicin, dihydrocapsaicin contents, capsaicinoid synthetase (CS), as well as the relative expression levels of genes related to capsaicinoid biosynthesis, such as acyltransferase 3 (AT3) and acyl-ACP thioesterase (FatA).

Effect of Dihydroartemisinin on Plasmodium NADH-Dependent Glutamate Synthase: The Implication in Malaria Management

Artemisinin and its analogues (ARTs) are currently the most effective anti-malarial drugs, but the precise mechanism of action is still highly controversial. Effects of ARTs on Plasmodium genes expression are studied in our Lab. The overexpression of an interesting amidotransferase, NADH-dependent glutamate synthase (NADH-GltS) was found in treated by dihydroartemisinin (DHA). The increased expression occurred not only from global transcriptomics analysis on the human malaria parasite Plasmodium falciparum (P. falciparum) 3D7 and gene expression screening on all of iron-sulphur cluster proteins from P.f. 3D7 in vitro but also from Plasmodium berghei (P. berghei) ANKA in mice. Influence of DHA on NADH-GltS was specifically at trophozoite stage of P. falciparum and in a dose-dependent manner below the effective doses. L-glutamine (Gln) and L-glutamate (Glu) are the substrate and product of NADH-GltS respectively. Azaserine (Aza) is specific inhibitor for NADH-GltS. Experimental data showed that Glu levels were significantly decreasing with DHA dose increasing but NADH-GltS enzyme activities were still remained at higher levels in parasites, and appropriate amount of exogenous Glu could significantly reduce anti-malarial action of DHA but excessive amount lost the above effect. Aza alone could inhibit proliferation of P. falciparum and had an additive effect in combination with DHA. Those results could suggest that: Glutamate depletion is one of the anti-malarial actions of DHA; overexpression of NADH-GltS would be a feedback pattern of parasite itself due to glutamate depletion, but not a direct action of DHA; the "feedback pattern" is one of protective strategies of Plasmodium to interfere with the anti-malarial actions of DHA; and specific inhibitor for NADH-GltS as a new type of anti-malarial agents or new partner in ACT might provide a potential.

Reducing expression of a nitrate-responsive bZIP transcription factor increases grain yield and N use in wheat

Nitrogen (N) plays critical role in plant growth; manipulating N assimilation could be a target to increase grain yield and N use. Here, we show that ABRE-binding factor (ABF)-like leucine zipper transcription factor TabZIP60 mediates N use and growth in wheat. The expression of TabZIP60 is repressed when the N-deprived wheat plants is exposed to nitrate. Knock down of TabZIP60 through RNA interference (RNAi) increases NADH-dependent glutamate synthase (NADH-GOGAT) activity, lateral root branching, N uptake and spike number, and improves grain yield more than 25% under field conditions, while overexpression of TabZIP60-6D had the opposite effects. Further investigation shows TabZIP60 binds to ABRE-containing fragment in the promoter of TaNADH-GOGAT-3B and negatively regulates its expression. Genetic analysis reveals that TaNADH-GOGAT-3B overexpression overcomes the spike number and yield reduction caused by overexpressing TabZIP60-6D. As such, TabZIP60-mediated wheat growth and N use is associated with its negative regulation on TaNADH-GOGAT expression. These findings indicate that TabZIP60 and TaNADH-GOGAT interaction plays important roles in mediating N use and wheat growth, and provides valuable information for engineering N use efficiency and yield in wheat.

Candidate genes and genome-wide association study of grain protein content and protein deviation in durum wheat

Stable QTL for grain protein content co-migrating with nitrogen-related genes have been identified by the candidate genes and genome-wide association mapping approaches useful for marker-assisted selection. Grain protein content (GPC) is one of the most important quality traits in wheat, defining the nutritional and end-use properties and rheological characteristics. Over the years, a number of breeding programs have been developed aimed to improving GPC, most of them having been prevented by the negative correlation with grain yield. To overcome this issue, a collection of durum wheat germplasm was evaluated for both GPC and grain protein deviation (GPD) in seven field trials. Fourteen candidate genes involved in several processes related to nitrogen metabolism were precisely located on two high-density consensus maps of common and durum wheat, and six of them were found to be highly associated with both traits. The wheat collection was genotyped using the 90 K iSelect array, and 11 stable quantitative trait loci (QTL) for GPC were detected in at least three environments and the mean across environments by the genome-wide association mapping. Interestingly, seven QTL were co-migrating with N-related candidate genes. Four QTL were found to be significantly associated to increases of GPD, indicating that selecting for GPC could not affect final grain yield per spike. The combined approaches of candidate genes and genome-wide association mapping led to a better understanding of the genetic relationships between grain storage proteins and grain yield per spike, and provided useful information for marker-assisted selection programs.

Water impacts nutrient dose responses genome-wide to affect crop production

Changes in nutrient dose have dramatic effects on gene expression and development. One outstanding question is whether organisms respond to changes in absolute nutrient amount (moles) vs. its concentration in water (molarity). This question is particularly relevant to plants, as soil drying can alter nutrient concentration, without changing its absolute amount. To compare the effects of amount vs. concentration, we expose rice to a factorial matrix varying the dose of nitrogen (N) and water (W) over a range of combinations, and quantify transcriptome and phenotype responses. Using linear models, we identify distinct dose responses to either N-moles, W-volume, N-molarity (N/W), or their synergistic interaction (N×W). Importantly, genes whose expression patterns are best explained by N-dose and W interactions (N/W or N×W) in seedlings are associated with crop outcomes in replicated field trials. Such N-by-W responsive genes may assist future efforts to develop crops resilient to increasingly arid, low nutrient soils.

Glutamate synthase MoGlt1-mediated glutamate homeostasis is important for autophagy, virulence and conidiation in the rice blast fungus

Glutamate homeostasis plays a vital role in central nitrogen metabolism and coordinates several key metabolic functions. However, its function in fungal pathogenesis and development has not been investigated in detail. In this study, we identified and characterized a glutamate synthase gene MoGLT1 in the rice blast fungus Magnaporthe oryzae that was important to glutamate homeostasis. MoGLT1 was constitutively expressed, but showed the highest expression level in appressoria. Deletion of MoGLT1 resulted in a significant reduction in conidiation and virulence. The ΔMoglt1 mutants were defective in appressorial penetration and the differentiation and spread of invasive hyphae in penetrated plant cells. The addition of exogenous glutamic acid partially rescued the defects of the ΔMoglt1 mutants in conidiation and plant infection. Assays for MoAtg8 expression and localization showed that the ΔMoglt1 mutants were defective in autophagy. The ΔMoglt1 mutants were delayed in the mobilization of glycogens and lipid bodies from conidia to developing appressoria. Taken together, our results show that glutamate synthase MoGlt1-mediated glutamate homeostasis is important for pathogenesis and development in the rice blast fungus, possibly via the regulation of autophagy.

Polyamines in the Context of Metabolic Networks

Polyamines (PAs) are essential biomolecules that are known to be involved in the regulation of many plant developmental and growth processes as well as their response to different environmental stimuli. Maintaining the cellular pools of PAs or their metabolic precursors and by-products is critical to accomplish their normal functions. Therefore, the titre of PAs in the cells must be under tight regulation to enable cellular PA homeostasis. Polyamine homeostasis is hence achieved by the regulation of their input into the cellular PA pool, their conversion into secondary metabolites, their transport to other issues/organs, and their catabolism or turnover. The major contributors of input to the PA pools are their in vivo biosynthesis, interconversion between different PAs, and transport from other tissues/organs; while the output or turnover of PAs is facilitated by transport, conjugation and catabolism. Polyamine metabolic pathways including the biosynthesis, catabolism/turnover and conjugation with various organic molecules have been widely studied in all kingdoms. Discoveries on the molecular transporters facilitating the intracellular and intercellular translocation of PAs have also been reported. Numerous recent studies using transgenic approaches and mutagenesis have shown that plants can tolerate quite large concentrations of PAs in the cells; even though, at times, high cellular accumulation of PAs is quite detrimental, and so is high rate of catabolism. The mechanism by which plants tolerate such large quantities of PAs is still unclear. Interestingly, enhanced PA biosynthesis via manipulation of the PA metabolic networks has been suggested to contribute directly to increased growth and improvements in plant abiotic and biotic stress responses; hence greater biomass and productivity. Genetic manipulation of the PA metabolic networks has also been shown to improve plant nitrogen assimilation capacity, which may in turn lead to enhanced carbon assimilation. These potential benefits on top of the widely accepted role of PAs in improving plants' tolerance to biotic and abiotic stressors are invaluable tools for future plant improvement strategies.

Rice Ferredoxin-Dependent Glutamate Synthase Regulates Nitrogen-Carbon Metabolomes and Is Genetically Differentiated between japonica and indica Subspecies

Plants assimilate inorganic nitrogen absorbed from soil into organic forms as Gln and Glu through the glutamine synthetase/glutamine:2-oxoglutarate amidotransferase (GS/GOGAT) cycle. Whereas GS catalyzes the formation of Gln from Glu and ammonia, GOGAT catalyzes the transfer of an amide group from Gln to 2-oxoglutarate to produce two molecules of Glu. However, the regulatory role of the GS/GOGAT cycle in the carbon-nitrogen balance is not well understood. Here, we report the functional characterization of rice ABNORMAL CYTOKININ RESPONSE 1 (ABC1) gene that encodes a ferredoxin-dependent (Fd)-GOGAT. The weak mutant allele abc1-1 mutant shows a typical nitrogen-deficient syndrome, whereas the T-DNA insertional mutant abc1-2 is seedling lethal. Metabolomics analysis revealed the accumulation of an excessive amount of amino acids with high N/C ratio (Gln and Asn) and several intermediates in the tricarboxylic acid cycle in abc1-1, suggesting that ABC1 plays a critical role in nitrogen assimilation and carbon-nitrogen balance. Five non-synonymous single-nucleotide polymorphisms were identified in the ABC1 coding region and characterized as three distinct haplotypes, which have been highly and specifically differentiated between japonica and indica subspecies. Collectively, these results suggest that ABC1/OsFd-GOGAT is essential for plant growth and development by modulating nitrogen assimilation and the carbon-nitrogen balance.

Asparagine Metabolic Pathways in Arabidopsis

Inorganic nitrogen in the form of ammonium is assimilated into asparagine via multiple steps involving glutamine synthetase (GS), glutamate synthase (GOGAT), aspartate aminotransferase (AspAT) and asparagine synthetase (AS) in Arabidopsis. The asparagine amide group is liberated by the reaction catalyzed by asparaginase (ASPG) and also the amino group of asparagine is released by asparagine aminotransferase (AsnAT) for use in the biosynthesis of amino acids. Asparagine plays a primary role in nitrogen recycling, storage and transport in developing and germinating seeds, as well as in vegetative and senescence organs. A small multigene family encodes isoenzymes of each step of asparagine metabolism in Arabidopsis, except for asparagine aminotransferase encoded by a single gene. The aim of this study is to highlight the structure of the genes and encoded enzyme proteins involved in asparagine metabolic pathways; the regulation and role of different isogenes; and kinetic and physiological properties of encoded enzymes in different tissues and developmental stages.

Structural analysis of the wheat genes encoding NADH-dependent glutamine-2-oxoglutarate amidotransferases and correlation with grain protein content

BACKGROUND

Nitrogen uptake and the efficient absorption and metabolism of nitrogen are essential elements in attempts to breed improved cereal cultivars for grain or silage production. One of the enzymes related to nitrogen metabolism is glutamine-2-oxoglutarate amidotransferase (GOGAT). Together with glutamine synthetase (GS), GOGAT maintains the flow of nitrogen from NH4 (+) into glutamine and glutamate, which are then used for several aminotransferase reactions during amino acid synthesis.

RESULTS

The aim of the present work was to identify and analyse the structure of wheat NADH-GOGAT genomic sequences, and study the expression in two durum wheat cultivars characterized by low and high kernel protein content. The genomic sequences of the three homoeologous A, B and D NADH-GOGAT genes were obtained for hexaploid Triticum aestivum and the tetraploid A and B genes of Triticum turgidum ssp. durum. Analysis of the gene sequences indicates that all wheat NADH-GOGAT genes are composed of 22 exons and 21 introns. The three hexaploid wheat homoeologous genes have high conservation of sequence except intron 13 which shows differences in both length and sequence. A comparative analysis of sequences among di- and mono-cotyledonous plants shows both regions of high conservation and of divergence. qRT-PCR performed with the two durum wheat cvs Svevo and Ciccio (characterized by high and low protein content, respectively) indicates different expression levels of the two NADH-GOGAT-3A and NADH-GOGAT-3B genes.

CONCLUSION

The three hexaploid wheat homoeologous NADH-GOGAT gene sequences are highly conserved - consistent with the key metabolic role of this gene. However, the dicot and monocot amino acid sequences show distinctive patterns, particularly in the transit peptide, the exon 16-17 junction, and the C-terminus. The lack of conservation in the transit peptide may indicate subcellular differences between the two plant divisions - while the sequence conservation within enzyme functional domains remains high. Higher expression levels of NADH-GOGAT are associated with higher grain protein content in two durum wheats.

Engineering nitrogen use efficient crop plants: the current status

In the last 40 years the amount of synthetic nitrogen (N) applied to crops has risen drastically, resulting in significant increases in yield but with considerable impacts on the environment. A requirement for crops that require decreased N fertilizer levels has been recognized in the call for a 'Second Green Revolution' and research in the field of nitrogen use efficiency (NUE) has continued to grow. This has prompted a search to identify genes that improve the NUE of crop plants, with candidate NUE genes existing in pathways relating to N uptake, assimilation, amino acid biosynthesis, C/N storage and metabolism, signalling and regulation of N metabolism and translocation, remobilization and senescence. Herein is a review of the approaches taken to determine possible NUE candidate genes, an overview of experimental study of these genes as effectors of NUE in both cereal and non-cereal plants and the processes of commercialization of enhanced NUE crop plants. Patents issued regarding increased NUE in plants as well as gene pyramiding studies are also discussed as well as future directions of NUE research.