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Determining how the sequence of a protein effects its function and physical properties builds the base of a foundation needed to investigate how a protein interacts with substrates and other proteins, to predict the functional effects of variants, understand disease phenotypes, and to improve rational drug and protein design. In my thesis, I describe contributions to understanding how we can understand the molecular basis for nonsynonymous disease mutations in the human metabolic enzyme glutamine synthetase and how we can leverage both experimental and computational approaches to find secondary mutations that can rescue the functional defects of a disease variant, termed compensatory mutations. In chapter one, I developed a computational pipeline to identify potential protein targets in which a human disease mutation is present as the wild type residue in other genetic contexts, called compensated pathogenic deviations (CPD), as well as identify potential compensatory sites in those protein targets. I then chose one target, the human metabolic enzyme glutamine synthetase (GS), and experimentally tested every possible single secondary mutation in the background of the clinically validated R341C disease variant to map the compensatory landscape. We found several sites of compensation that were able to rescue the defects induced by R341C. Interestingly, most of them were far from both the active site and the residue 341, pointing to a potentially more complex method of compensation involving long-range interactions or alteration of the conformational landscape of GS. In chapter two, we aimed investigated if human glutamine synthetase (hGS) activity was regulated by formation of higher order oligomeric assemblies, as is common with some metabolic enzymes, and if this balance could be biased through addition of metal cofactors or through mutation. There has been previous evidence that GS in both e.coli and s. cerevisiae form filamentous assemblies, with the ring structure stacking back-to-back in times of cellular stress as a way to store catalytic potential. We utilized to complementary structural methods to visualize and quantify the oligomeric form of hGS: negative stain electron microscopy and size exclusion chromatography coupled small angle x-ray scattering (SEC-SAXS). We perturbed hGS by increasing the concentration of Mg2+ or Mn2+, varying pH, and single amino acid mutation (including the hGS disease variants) and saw no evidence of higher order oligomers. We did however observe an equilibrium between the pentamer and decamer that existed across all conditions, with the equilibrium shifted more towards the pentamer state than previously expected. While we have concluded that hGS does not regulate catalytic activity through formation of filaments, as do glutamine synthetases in other species, the delicate balance we probed between pentamer and decamer is useful in characterizing the biology of the native hGS and informs future purification and kinetic studies.

BackgroundSalicornia neei is a halophyte plant that has been proposed for use in the phytoremediation of the saline wastewater generated by land-based aquaculture, which usually contains elevated concentrations of ammonium resulting from protein metabolism. To identify the molecular mechanisms related to ammonium response, we analyzed the transcriptome of S. neei in response to growth in saline water containing 3 mM ammonium and the Michaelis–Menten ammonium removal biokinetics.ResultsThe RNA sequencing generated a total of 14,680,108 paired-end reads from the control and stressed conditions. De novo assembly using the CLC Genomic Workbench produced 86,020 transcripts and a reference transcriptome with an N50 of 683 bp.A total of 45,327 genes were annotated, representing 51.2% of the contig predicted from de novo assembly. As regards DEGs, a total of 9,140 genes were differentially expressed in response to ammonium in saline water; of these, 7,396 could be annotated against functional databases. The upregulated genes were mainly involved in cell wall biosynthesis, transmembrane transport and antiporter activities, including biological KEGG pathways linked to the biosynthesis of secondary metabolites, plant hormone signal transduction, autophagy, and nitrogen metabolism. In addiction, a set of 72 genes was directly involved in ammonium metabolism, including glutamine synthetase 1 (GLN1), glutamate synthase 1 (GLT1), and ferredoxin-dependent glutamate synthase chloroplastic (Fd-GOGAT). Finally, we observed that the ammonium uptake rate increased with increasing ammonium concentrations, and tended toward saturation in the range of 3 to 4 mM.ConclusionOur results support the hypothesis that an ammonium detoxification system mediated by glutamine and glutamate synthase was activated in S. neei when exposed to ammonium and saline water. The present transcriptome profiling method could be useful when investigating the response of halophyte plants to saline wastewater from land-based aquaculture.

Glutamine synthetase (GS) is a decameric enzyme that plays a key role in nitrogen metabolism. Acetylation of the N-terminal degron (N-degron) of GS is essential for ubiquitylation and subsequent GS degradation. The full-length GS structure showed that the N-degron is buried inside the GS decamer and is inaccessible to the acetyltransferase. The structure of N-degron-truncated GS reported here reveals that the N-degron is not essential for GS decamer formation. It is also shown that the N-degron can be exposed to a solvent region through a series of conformational adjustments upon ligand binding. In summary, this study elucidated the dynamic movement of the N-degron and the possible effect of glutamine in enhancing the acetylation process.

Melatonin (MT) and salicylic acid (SA) are known to improve plant tolerance to environmental stresses; however, no reports have evaluated the effect of their combined treatment on plants under both normal and stressful conditions. For the first time, the present study aimed to investigate MT and SA’s potential role in regulating polyamine and nitrogen metabolism in wheat plants subjected to salty soils, and counterbalancing oxidative damage induced by salt stress. Moreover, this research aimed to elucidate a possible link between melatonin, salicylic acid, nitrogen and polyamine levels. Wheat (Triticum aestivum L. cv. Sids 14) plants were grown under non-saline or saline conditions (6.0 and 12.0 dS m–1) and were foliar sprayed with 70 µM MT and/or 75 mg l−1 SA. The injury impacts of salt stress on wheat growth and production were significantly alleviated by exogenous MT and/or SA treatments. This was evidenced by increasing polyamines content through accelerating the metabolic flow from the precursor amino acids arginine and methionine to polyamines, decreasing the polyamines degradation, and enhancing the polyamines biosynthesis. Furthermore, MT and/or SA are involved in promoting nitrogen metabolism through up-regulating the activities of N uptake and metabolism related enzymes (nitrate reductase, nitrite reductase, glutamine synthetase, glutamate synthase) as well as enhancing the content of nitrogen, nitrate and protein in salt-stressed plants. The mitigation was also detected in reduced lipid peroxidation, hydrogen peroxide content, carbonyl content, and protease activity in stressed treated plants. Notably, the best response was registered for the combined treatment of MT and SA. Therefore, the co-application of MT and SA is a promising way for ameliorating salt toxicity in sustainable agricultural systems.

Sulfur compounds are known to play crucial roles in plants facilitating tolerance to heavy metal stress. Previous studies have shown the protective role of exogenous cysteine (Cys) to improve chromium (Cr) tolerance. In the present study, we aimed to evaluate the capability of Cys (0.5 mM) to reduce chromium toxicity (100 μM) in rapeseed by physiological and proteomic analyses. Seedlings treated with Cr showed reduced growth and activities of antioxidant enzymes, and increased malondialdehyde (MDA) content. Exogenous application of Cys reduced Cr accumulation and MDA content, restored catalase (CAT) and peroxidase (POD) activities, and caused significant enhancements in seedling growth. 2-DE gel electrophoresis and mass spectrometry were performed to investigate changes in the root proteome in response to Cys and Cr. The Cr-induced down-regulations of glycine-rich RNA-binding protein, lactoylglutathione lyase, fructose-bisphosphate aldolase, and glutamine synthetase were restored with Cys. Additionally, Cys removed the Cr-induced up-regulation of some proteins including pathogenesis-related protein, major latex protein (MLP) like proteins, 22.0 kDa HSP, triosephosphate isomerase, glyceraldehyde-3-phosphate dehydrogenase, glutamine amidotransferase, cysteine synthase, and L-lactate dehydrogenase. Taken together, proteomic analysis revealed that exogenous Cys helps plants to overcome Cr stress by modulating energy metabolism, amino acid metabolism, and defense mechanism.

Abstract— The possible nitrogen sources for Osc. trichoides DG6, a typical strain of the Oscillochloridaceae family, are ammonium, N2, glutamate, asparagine, glycine, and glutamine. The assimilation of molecular nitrogen occurs with the participation of nitrogenase, the structural gene of which, nifH, is located in the gene cluster which also includes the genes of the nifD and nifK nitrogenase subunits and the auxiliary nifB gene. Considering that nifHBDK clusters have been also annotated in the genomes of other members of the Oscillochloridaceae family, including uncultured and candidate taxa, it can be assumed that the ability to fix nitrogen is a property immanent for this entire family. The pathways for assimilating ammonium in the cells grown using different nitrogen sources may differ. Osc. trichoides DG6 growing in a medium containing ammonium assimilated it with the participation of glutamate dehydrogenase, which is determined by a single gene. The expression product of this gene has dual functionality and can be used to implement the reaction with both NAD and NADP. With the growth of Osc. trichoides DG6 on a medium with glutamate as the only nitrogen source all the enzymes necessary for the implementation of the GS‑GOGAT pathway were found in the cells. However, for the glutamine synthetase reaction, ammonium, which was absent in the growth medium, was required. The source of ammonium may be glutamate metabolized through glutamate dehydrogenase.

Glutamine synthetase (GS) plays an important role in nitrogen (N) metabolism in cucumber. In this study, we cloned and sequenced the CsGS1 gene, and analyzed the expression patterns and subcellular localization of the GS1 protein in response to different N conditions in order to determine its role in low-nitrogen (LN) tolerance. CsGS1 was abundantly expressed in the leaves of the low N-requiring cultivar D0328, while the high N-requiring cultivar D0422 showed similar expression levels across different tissues including leaves, shoots and roots. Furthermore, the GS1 protein was primarily localized in the cytoplasm of plant cells. Both cultivars were then transformed with the CsGS1 coding sequence or antisense sequence via Agrobacterium tumefaciens in order to overexpress and silence GS1 expression, respectively. Overexpression of CsGS1 significantly improved LN tolerance and photosynthetic parameters, and increased chlorophyll b content, biomass, plant height, root length, N accumulation and GS activity under LN condition compared to the control. CsGS1 silencing on the other hand significantly reduced the above indices. Taken together, CsGS1 is crucial for maintaining N metabolism in cucumber plants during N deprivation, and is a promising target for generating novel transgenic breeds with increasing nitrogen utilization efficiency.

Because it is the precursor for various essential cellular components, the amino acid serine is indispensable for every living organism. In plants, serine is synthesized by two major pathways: photorespiration and the phosphorylated pathway of serine biosynthesis (PPSB). However, the importance of these pathways in providing serine for plant development is not fully understood. In this study, we examine the relative contributions of photorespiration and PPSB to providing serine for growth and metabolism in the C3 model plant Arabidopsis thaliana. Our analyses of cell proliferation and elongation reveal that PPSB-derived serine is indispensable for plant growth and its loss cannot be compensated by photorespiratory serine biosynthesis. Using isotope labeling, we show that PPSB-deficiency impairs the synthesis of proteins and purine nucleotides in plants. Furthermore, deficiency in PPSB-mediated serine biosynthesis leads to a strong accumulation of metabolites related to nitrogen metabolism. This result corroborates 15N-isotope labeling in which we observed an increased enrichment in labeled amino acids in PPSB-deficient plants. Expression studies indicate that elevated ammonium uptake and higher glutamine synthetase/glutamine oxoglutarate aminotransferase (GS/GOGAT) activity causes this phenotype. Metabolic analyses further show that elevated nitrogen assimilation and reduced amino acid turnover into proteins and nucleotides are the most likely driving forces for changes in respiratory metabolism and amino acid catabolism in PPSB-deficient plants. Accordingly, we conclude that even though photorespiration generates high amounts of serine in plants, PPSB-derived serine is more important for plant growth and its deficiency triggers the induction of nitrogen assimilation, most likely as an amino acid starvation response.

This study aimed to investigate the impact of the herbicide monuron on various aspects of photosynthesis and diazotrophy in the cyanobacterium Nostoc muscorum Meg 1 isolated from a rice field in Cherrapunji, Meghalaya, India. The consequences of monuron exposure on various photosynthetic pigments, functioning of PSII, RuBisCO, nitrogenase and glutamine synthetase enzyme activities, heterocyst frequency, and on production of proteins and carbohydrates in the cyanobacterium were studied in a range of monuron doses (20–100 ppm) to gauge the herbicide’s effect on CO2 and N2 fixation and on net biomass production. The total amount of D1 protein (the host for PSII complex), RuBisCO (the key enzyme for CO2 fixation), nitrogenase (the enzyme responsible for the reduction of atmospheric nitrogen to ammonia), and ammonia assimilating enzyme glutamine synthetase (GS) contents under western blot analysis indicated interruption of new protein synthesis and breakdown of their existing enzyme molecules when exposed to higher monuron concentrations. All parameters studied showed enhanced expression under low dose monuron treatment (20 ppm) indicating a hormetic effect in the exposed organism. The expression of monuron toxicity on various parameters of CO2 and N2 fixation in a dose-dependent manner was immediately visible when cultures were treated with higher doses (40–100 ppm). Scanning and transmission electron microscopic studies further uncovered several undesirable changes in the morphology and ultrastructure of the organism due to herbicide treatment that could be correlated to compromised CO2 and N2 fixation.

Cellular glutamine synthesis is thought to be an important resistance factor in protecting cells from nutrient deprivation and may also contribute to drug resistance. The application of ‟targeted stable isotope resolved metabolomics” allowed to directly measure the activity of glutamine synthetase in the cell. With the help of this method, the fate of glutamine derived nitrogen within the biochemical network of the cells was traced. The application of stable isotope labelled substrates and analyses of isotope enrichment in metabolic intermediates allows the determination of metabolic activity and flux in biological systems. In our study we used stable isotope labelled substrates of glutamine synthetase to demonstrate its role in the starvation response of cancer cells. We applied 13C labelled glutamate and 15N labelled ammonium and determined the enrichment of both isotopes in glutamine and nucleotide species. Our results show that the metabolic compensatory pathways to overcome glutamine depletion depend on the ability to synthesise glutamine via glutamine synthetase. We demonstrate that the application of dual-isotope tracing can be used to address specific reactions within the biochemical network directly. Our study highlights the potential of concurrent isotope tracing methods in medical research.

Heterosis refers to the improved agronomic performance of F1 hybrids relative to their parents. Although this phenomenon is widely employed to increase biomass, yield, and stress tolerance of plants, the underlying molecular mechanisms remain unclear. To dissect the metabolic fluctuations derived from genomic and/or environmental differences contributing to the improved biomass of F1 hybrids relative to their parents, we optimized the growth condition for Arabidopsis thaliana F1 hybrids and their parents. Modest but statistically significant increase in the biomass of F1 hybrids was observed. Plant samples grown under the optimized condition were also utilized for integrated omics analysis to capture specific changes in the F1 hybrids. Metabolite profiling of F1 hybrids and parent plants was performed using gas chromatography-mass spectrometry. Among the detected 237 metabolites, 2-oxoglutarate (2-OG) and malate levels were lower and the level of aspartate was higher in the F1 hybrids than in each parent. In addition, microarray analysis revealed that there were 44 up-regulated and 12 down-regulated genes with more than 1.5-fold changes in expression levels in the F1 hybrid compared to each parent. Gene ontology (GO) analyses indicated that genes up-regulated in the F1 hybrids were largely related to organic nitrogen (N) process. Quantitative PCR verified that glutamine synthetase 2 (AtGLN2) was upregulated in the F1 hybrids, while other genes encoding enzymes in the GS-GOGAT cycle showed no significant differences between the hybrid and parent lines. These results suggested the existence of metabolic regulation that coordinates biomass and N metabolism involving AtGLN2 in F1 hybrids.

There is little information on metabolism in developing cerebellum despite the known importance of this region in cognition and motor tasks. Ex vivo 1 H- and 13 C-NMR spectroscopy were used to determine metabolism during late postnatal development in cerebellum and cerebrum from 18-day-old rat pups after intraperitoneal (i.p.) injection of [1,6-13 C]glucose. The concentration of several metabolites in cerebellum was distinctly different than cerebrum; alanine, glutamine, creatine and myo-inositol were higher in cerebellum than cerebrum, the concentrations of lactate, GABA, aspartate and N-acetylaspartate (NAA) were lower in cerebellum than in cerebrum, and levels of glutamate, succinate, choline and taurine were similar in both brain regions. The incorporation of label from the metabolism of [1,6-13 C]glucose into most isotopomers of glutamate (GLU), glutamine (GLN), GABA and aspartate was lower in cerebellum than in cerebrum. Incorporation of label into the C2 position of lactate via the pyruvate recycling pathway was found in both brain regions. The ratio of newly synthesized GLN/GLU was significantly higher in cerebellum than in cerebrum indicating relatively active metabolism via glutamine synthetase in cerebellar astrocytes at postnatal day 18. This is the first study to determine metabolism in the cerebellum and cerebrum of male and female rat brain.

Soil bacteria from the genus Streptomyces, phylum Actinobacteria, feature a complex metabolism and diverse adaptations to environmental stress. These characteristics are consequences of variable nutrition availability in the soil and allow survival under changing nitrogen conditions. Streptomyces coelicolor is a model organism for Actinobacteria and is able to use nitrogen from a variety of sources including unusual compounds originating from the decomposition of dead plant and animal material, such as polyamines or monoamines (like ethanolamine). Assimilation of nitrogen from these sources in S. coelicolor remains largely unstudied. Using microbiological, biochemical and in silico approaches, it was recently possible to postulate polyamine and monoamine (ethanolamine) utilization pathways in S. coelicolor. Glutamine synthetase-like enzymes (GS-like) play a central role in these pathways. Extensive studies have revealed that these enzymes are able to detoxify polyamines or monoamines and allow the survival of S. coelicolor in soil containing an excess of these compounds. On the other hand, at low concentrations, polyamines and monoamines can be utilized as nitrogen and carbon sources. It has been demonstrated that the first step in poly-/monoamine assimilation is catalyzed by GlnA3 (a γ-glutamylpolyamine synthetase) and GlnA4 (a γ-glutamylethanolamide synthetase), respectively. First insights into the regulation of polyamine and ethanolamine metabolism have revealed that the expression of the glnA3 and the glnA4 gene are controlled on the transcriptional level.

Hyperammonemia is a dangerous life-threatening metabolic complication characterized by markedly elevated ammonia levels that can lead to irreversible brain damage if not carefully monitored. Current pharmacological treatment strategies available for hyperammonemia patients are suboptimal and associated with major side effects. In this study, we focus on developing and evaluating the

Indigoidine is a dark-blue natural pigment with application prospect and synthesized from glutamine (Gln) by series of indigoidine synthetases (IndCs). Indigoidine production can be improved by enhancing Gln pool via supplementing Gln directly or converting metabolism glutamate (Glu) to Gln by glutamine synthetase (GlnA). But, Gln is expensive, and excess Gln inhibits indigoidine production of the recombinant strain. Supplementing Glu instead of Gln may improve the productive and economic efficiency of indigoidine, but the local activities and positions of the indigoidine pathway enzymes GlnA, Sc-IndC, and the helper protein of Sc-IndC (IndB) should be well arranged. We identified the Streptomyces chromofuscus ATCC 49982 derived IndC (Sc-IndC) as an more efficient IndC compared to other IndCs applied for constructing indigoidine-producting strains, and designed series of protein scaffold complexes with architectures of PDZ, SH3, and GBD domains (PxSyG1) to arrange the pathway enzymes. The strain recruiting GlnA, Sc-IndC, and IndB on the PDZ, SH3, and GBD domains of scaffold P1S2G1, respectively, was the most efficient. In the strain, the GlnA supplied sufficient local Gln for Sc-IndC from Glu, and the generated Gln was immediately consumed by Sc-IndC to relieve cell growth inhibition caused by Gln. The optimum Glu concentration (6 g/L) for the strain was higher than those of the strains recruiting Sc-IndC on the GBD domain, which was away from the PDZ domain recruiting GlnA. The highest titer of indigoidine was 12 g/L, which was two folds of the control without scaffold (5.8 g/L). The titer is 5 g/L higher than the control without Glu supplemented (6.9 g/L), meaning that 97% of the supplemented Glu was transformed into indigoidine. The batch fermentation with the optimum strain in a 5-L reactor achieved an indigoidine titer of 14 g/L in 60 h. To our knowledge, this was the most efficient indigoidine productivity achieved so far. The optimization strategies by protein scaffold should be applicative to other pathways with complex substrate demands. •Protein scaffold systems were designed to arrange the indigoidine synthetic pathway. •The scaffold system improved supplement of Gln for indigoidine production from Glu. •The inhibition caused by excess Gln was relieved by proper designed scaffold. •The yield and titer of indigoidine was improved by arranging the pathway enzymes.

Dopamine plays numerous physiological roles in plants. We explored its role in the regulation of growth, nutrient absorption, and response to nitrogen (N) deficiency in Malus hupehensis Rehd. Under low N condition, plant growth slowed, and the net photosynthetic rates, chlorophyll contents, and maximal quantum yield of PSII (Fv/Fm) decreased significantly. However, the application of 100 μmol L−1 exogenous dopamine significantly reduced the inhibition of low N stress on plant growth. In addition to modifying root system architecture under low N supply, exogenous dopamine also changed the uptake, transport, and distribution of N, P, and K. Furthermore, exogenous dopamine enhances the tolerance to low nitrogen stress by increasing the activity of enzymes (nitrate reductase, nitrite reductase, glutamic acid synthase and glutamine synthetase) involved in N metabolism. We also found that exogenous dopamine promoted the expression of ethylene signaling genes (ERF1, ERF2, EIL1, ERS2, ETR1, and EIN4) under low N stress. Therefore, we hypothesized that ethylene might be involved in dopamine response to low N stress in M. hupehensis. Our results suggest that exogenous dopamine can mitigate low N stress by regulating the absorption of mineral nutrients, possibly through the regulation of the ethylene signaling pathway.

Optimizing the supply of biosynthetic precursors and cofactors is usually an effective metabolic strategy to improve the production of target compounds. Here, the combination of optimizing precursor synthesis and balancing cofactor metabolism was adopted to improve tryptophan production in Escherichia coli. First, glutamine synthesis was improved by expressing heterologous glutamine synthetase from Bacillus subtilis and Bacillus megaterium in the engineered Escherichia coli strain KW001, resulting in the best candidate strain TS-1. Then icd and gdhA were overexpressed in TS-1, which led to the accumulation of 1.060 g/L tryptophan. Subsequently, one more copy of prs was introduced on the chromosome to increase the flux of 5-phospho-α- d -ribose 1-diphosphate followed by the expression of mutated serA and thrA to increase the precursor supply of serine, resulting in the accumulation of 1.380 g/L tryptophan. Finally, to maintain cofactor balance, sthA and pntAB, encoding transhydrogenase, were overexpressed. With sufficient amounts of precursors and balanced cofactors, the engineered strain could produce 1.710 g/L tryptophan after 48 h of shake-flask fermentation, which was 2.76-times higher than the titer of the parent strain. Taken together, our results demonstrate that the combination of optimizing precursor supply and regulating cofactor metabolism is an effective approach for high-level production of tryptophan. Similar strategies could be applied to the production of other amino acids or related derivatives.

Background l-Alanyl-l-glutamine (AQ) is a functional dipeptide with high water solubility, good thermal stability and high bioavailability. It is widely used in clinical treatment, post-operative rehabilitation, sports health care and other fields. AQ is mainly produced via chemical synthesis which is complicated, time-consuming, labor-intensive, and have a low yield accompanied with the generation of by-products. It is therefore highly desirable to develop an efficient biotechnological process for the industrial production of AQ. Results A metabolically engineered E. coli strain for AQ production was developed by over-expressing l-amino acid α-ligase (BacD) from Bacillus subtilis, and inactivating the peptidases PepA, PepB, PepD, and PepN, as well as the dipeptide transport system Dpp. In order to use the more readily available substrate glutamic acid, a module for glutamine synthesis from glutamic acid was constructed by introducing glutamine synthetase (GlnA). Additionally, we knocked out glsA–glsB to block the first step in glutamine metabolism, and glnE–glnB involved in the ATP-dependent addition of AMP/UMP to a subunit of glutamine synthetase, which resulted in increased glutamine supply. Then the glutamine synthesis module was combined with the AQ synthesis module to develop the engineered strain that uses glutamic acid and alanine for AQ production. The expression of BacD and GlnA was further balanced to improve AQ production. Using the final engineered strain p15/AQ10 as a whole-cell biocatalyst, 71.7 mM AQ was produced with a productivity of 3.98 mM/h and conversion rate of 71.7%. Conclusion A metabolically engineered strain for AQ production was successfully developed via inactivation of peptidases, screening of BacD, introduction of glutamine synthesis module, and balancing the glutamine and AQ synthesis modules to improve the yield of AQ. This work provides a microbial cell factory for efficient production of AQ with industrial potential.

Global warming has reached an alarming situation, which led to a dangerous climatic condition. The irregular rainfalls and land degradation are the significant consequences of these climatic changes causing a decrease in crop productivity. The effect of drought and its tolerance mechanism, a comparative roots proteomic analysis of chickpea seedlings grown under hydroponic conditions for three weeks, performed at different time points using 2-Dimensional gel electrophoresis (2-DE). After PD-Quest analysis, 110 differentially expressed spots subjected to MALDI-TOF/TOF and 75 spots identified with a significant score. These identified proteins classified into eight categories based on their functional annotation. Proteins involved in carbon and energy metabolism comprised 23% of total identified proteins include mainly glyceraldehyde-3-phosphate dehydrogenase, malate dehydrogenase, transaldolase, and isocitrate dehydrogenase. Proteins related to stress response (heat-shock protein, CS domain protein, and chitinase 2-like) contributed 16% of total protein spots followed by 13% involved in protein metabolism (adenosine kinase 2, and protein disulfide isomerase). ROS metabolism contributed 13% (glutathione S-transferase, ascorbate peroxidase, and thioredoxin), and 9% for signal transduction (actin-101, and 14-3-3-like protein B). Five percent protein identified for secondary metabolism (cinnamoyl-CoA reductase-1 and chalcone-flavononeisomerase 2) and 7% for nitrogen (N) and amino acid metabolism (glutamine synthetase and homocysteine methyltransferase). The abundance of some proteins validated by using Western blotting and Real-Time-PCR. The detailed information for drought-responsive root protein(s) through comparative proteomics analysis can be utilized in the future for genetic improvement programs to develop drought-tolerant chickpea lines.

Glufosinate inhibits glutamine synthetase (GS), a key enzyme for amino acid metabolism and photorespiration. Protoporphyrinogen oxidase (PPO) inhibitors block chlorophyll biosynthesis and cause protoporphyrin accumulation, a highly photodynamic intermediate. Both herbicides ultimately lead to plant death by a massive accumulation of reactive oxygen species (ROS) through different mechanisms. We investigated a potential synergistic effect by the mixture of the two herbicide mechanisms of action (MoAs). The tank mix between a low rate of glufosinate (280 g ai ha−1) with an ultra-low dose of saflufenacil (1 g ha−1) provided enhanced herbicidal activity compared with the products applied individually on Palmer amaranth (Amaranthus palmeriS. Watson). The synergism between the two herbicides was also confirmed by isobole analysis and field trials. The herbicide combination provided high levels of efficacy when applied at low temperature and low humidity. Mechanistically, glufosinate caused a transient accumulation of glutamate, the building block for chlorophyll biosynthesis. Consequently, inhibition of both GS and PPO resulted in greater accumulation of protoporphyrin and ROS, forming the physiological basis for the synergism between glufosinate and PPO inhibitors. While the synergy between the two herbicide MoAs provided excellent efficacy on weeds, it caused low injury to PPO-resistant waterhemp [Amaranthus tuberculatus(Moq.) Sauer] and high injury to both glufosinate-resistant and glufosinate-susceptible soybean [Glycine max(L.) Merr.]. Glufosinate enhances the activity of PPO inhibitors through glutamate and protoporphyrin accumulation, leading to increased levels of ROS and lipid peroxidation. The synergism between the two herbicide MoAs can help to overcome environmental effects limiting the efficacy of glufosinate. Future research is needed to optimize the uses for this herbicidal composition across different cropping systems.

Low light intensity is always the important factor that influences the growth and development of Brassica pekinesis during winter seasons. We have found out that appropriate ammonium/nitrate ratio mitigated low light intensity in the previous study. In the present study, the nitrogen metabolism and proteomic responses of Brassica pekinensis to light intensities and ammonium/nitrate were further investigated to find out the mitigation mechanism. The activities of nitrate reductase (NR) and glutamine synthetase (GS) and the relative expression of GS1 as well as the content of nitric oxide (NO) were significantly higher in the NH4+:NO3− (15:85) treatment than in the NH4+:NO3− (0:100) treatment under normal light intensity. However, under low light intensity condition, the activities of NR and GS and relative expression of NR as well as the NO level in seedlings fertilized with NH4+:NO3− (10:90) were significantly higher compared with those fertilized with NH4+:NO3− (0:100). In addition, we found thirty-six protein spots, which exhibited significant changes in abundance using similarity searches across the uniprot database of Brassica. The proteins identified were classified into ten functional groups including photosynthesis, carbon and energy metabolism, stress/defense, protein folding, and modification and degradation response. We concluded that appropriate ammonium nitrate ratio improves the tolerance of mini Chinese cabbage seedlings to low light intensity by regulating the nitrogen metabolism and expression levels of some key proteins.

Glutamine synthetase is an essential enzyme in ammonium assimilation and glutamine biosynthesis. The Haloferax mediterranei genome has two other glnA-type genes (glnA2 and glnA3) in addition to the glutamine synthetase gene glnA. To determine whether the glnA2 and glnA3 genes can replace glnA in nitrogen metabolism, we generated deletion mutants of glnA. The glnA deletion mutants could not be generated in a medium without glutamine, and thus, glnA is an essential gene in H. mediterranei. The glnA deletion mutant was achieved by adding 40 mM glutamine to the selective medium. This conditional HM26-ΔglnA mutant was characterised with different approaches in the presence of distinct nitrogen sources and nitrogen starvation. Transcriptomic analysis was performed to compare the expression profiles of the strains HM26-ΔglnA and HM26 under different growth conditions. The glnA deletion did not affect the expression of glnA2, glnA3 and nitrogen assimilation genes under nitrogen starvation. Moreover, the results showed that glnA, glnA2 and glnA3 were not expressed under the same conditions. These results indicated that glnA is an essential gene for H. mediterranei and, therefore, glnA2 and glnA3 cannot replace glnA in the conditions analysed. This work was funded by MICINN Grant Number BIO2013-42921P (to MJB), Generalitat Valenciana Grant Number ACIF/2018/200 (to GP) and Universidad de Alicante (VIGROB-016).

Nitrogen (N) deficiency is one of the factors limiting crop productivity worldwide. As major forms of N, nitrate (NO3−) and ammonium (NH4+) regulate plant growth as signals. Although there are abundant studies on the response of many plants to N stress, the mechanism by which wheat (Triticum aestivum L.) roots adapt to low N, especially to low-NH4+ stress, has not been fully elucidated. In this study, wheat seedlings were planted in 1/2-strength Hoagland’s solution containing 5 mM NO3−, 0.1 mM NO3−, or 0.1 mM NH4+ to characterize root physiological responses to N deficit. Under low-N stress, root fresh weight, lateral root number increased compared with those under control conditions. Moreover, the concentrations of indole-3-acetic acid (IAA), cytokinins (CKs), gibberellin (GA3), and jasmonic acid (JA) increased, while the salicylic acid (SA) concentration decreased under low-N stress. Assays using enzyme-linked immunosorbent assay (ELISA) and non-invasive micro-test technology (NMT) showed that H+-ATPase activity, the H+ efflux, and the IAA influx increased, while N influx decreased under low-N stress. Further study revealed that low-NO3− stress increased nitrate reductase and glutamine synthetase activities, while low-NH4+ stress increased the activities of glutamine synthetase and glutamate synthase. In conclusion, low-N stress altered root IAA, CKs, GA3, JA, and SA concentrations; increased H+-ATPase activity and H+ efflux; promoted an increase in lateral root number and thus N absorption area. Besides, low-N stress increased the activities of key enzymes related to N assimilation, promoted protein biosynthesis, and ultimately enhanced root growth.

It is an integral property of sorghum (Sorghum bicolor L.) to extensively release biological nitrification inhibitors (BNIs) under NH4+ nutrition, in comparison to NO3− nutrition. Our previous research indicated that plasma membrane (PM) H+-ATPase activity was stimulated by NH4+ and low rhizosphere pH, which in turn provided the driving force for BNIs release from sorghum roots. However, the regulatory mechanism of PM H+-ATPase itself in this regard is not fully elucidated. The present study thus aims at post-translational regulation of PM H+-ATPase via phosphorylation in response to NH4+ nutrition and its functional link to the release of BNIs from sorghum roots. A hydroponic system is used to grow sorghum with 1 mM NH4+ or NO3− as N source at pH 3.0 or pH 7.0 in root medium for the analysis of PM H+-ATPase and BNIs release. The effect of NH4+ on the regulation of PM H+-ATPase was further evaluated by the treatment of NO3−cultivated sorghum roots with different NH4+ concentrations (0.1~1 mM). In addition, fusicoccin (a stimulator of PM H+-ATPase) and vanadate (an inhibitor of PM H+-ATPase) were added to check the effect of PM H+-ATPase phosphorylation on BNIs release. Further, methionine sulphoximine (MSX), which inhibits glutamine synthetase, is used to analyze the effect of ammonium transport/assimilation process on the PM H+-ATPase and BNIs release. Microsomal membrane protein isolated from these roots was used for the test of PM H+-ATPase phosphorylation level by western blot technique. Meanwhile, the root exudates were collected for the analysis of BNIs. Higher amount of PM H+-ATPase protein with higher phosphorylation level were detected in sorghum roots in response to NH4+ and low rhizosphere pH, as compared to NO3− and high pH. Further, PM H+-ATPase protein amount and phosporylation level were dependent on the local supplement of NH4+ (from 0.1 ~ 1 mM) to roots. Nevertheless, the enhanced posphorylation level under all of these treatments was significantly higher than the enhanced protein level of PM H+ ATPase. Unlike protein level, phosphorylation level is closely correlated to the release of BNIs from sorghum roots. In addition, phosphorylation level of PM H+-ATPase adjusted by fusicoccin or vanadate directly affected the release of BNIs, irrespective of the protein level. In addition, ammonium assimilation inhibitor MSX caused decreased phosphorylation level of PM H+-ATPase without affecting the protein level, meanwhile inhibited the release of BNIs from sorghum roots. Our research suggests that phosphorylation of PM H+-ATPase is one of the important regulation mechanisms involved in the release of BNIs from sorghum roots. NH4+ stimulated PM H+-ATPase phosphorylation via excessive H+ generated by NH4+ assimilation in cytoplasm. The up regulation of PM H+-ATPase at post-translational level thus activated the H+ pumping activity to provide the driving force for BNIs release. A new hypothesis is proposed to elucidate the interplay of these functionally inter-linked processes involving ammonium-uptake, −assimilation, and H+-pumps activation in PM on the release of BNIs from sorghum roots.

Nitrogen (N) is the essential nutrient for wheat growth and development, its accumulation and metabolism controlled by many other elements. Zinc (Zn) is one of the important elements which tends to have effects on plant N homeostasis. Here in our study, 0 μM and 5 μM Zn was applied to the wheat seedlings culturing in 5 mM (+N) and 0.5 mM (-N) N treatments, respectively. The results showed that the shoot and root length growth performance, total N, NO3−, and amino acid concentrations, glutamine synthetase (GS) activity of wheat were facilitated by 5 μM Zn application under + N and –N conditions. Quantitative real-time PCR (qRT-PCR) analysis indicated that several NO3− transporters genes (TaNRT2.1, TaNPF7.1 and TaNPF7.2) and the genes encoding GS (TaGS1 and TaGS2) were induced by 5 μM Zn. In addition, transcriptional changes in wheat shoots and roots with Zn application were tested by RNA-seq techniques. A total of 147/551 induced and 36/2162 reduced differentially expression genes (DEGs) was detected in wheat shoots/roots, respectively. GO and KEGG enrichment analyses showed that 5 μM Zn mainly affected the glutathione (GSH) metabolism, phenylpropanoid biosynthesis and amino acid metabolism, involving in N homeostasis. Furthermore, the relative expression of genes related to phenylalanine, cysteine and methionine metabolism was induced by 5 μM Zn to promote the amino acid accumulation. Overall, these results highlight the facilitating of N accumulation by low level Zn, and provide an insight into the effects of Zn on N metabolism in wheat.

Hepatic encephalopathy (HE) is a debilitating neurological complication of chronic liver disease (CLD). Hyperammonemia plays an important role in HE's pathogenesis, acting synergistically with systemic oxidative stress. During CLD, muscle plays a compensatory role in detoxifying ammonia, and therefore muscle loss leads to an increase in the risk of developing HE. With most animal studies involving males, sex's impact on the development of CLD and associated complications such as HE and muscle loss remains unknown. Therefore, we aimed to identify the impact of sex on CLD, HE, and muscle mass loss in a rodent model of CLD. Liver injury markers, hyperammonemia, oxidative stress, muscle mass, and ammonia clearance were measured in female and male bile-duct ligated (BDL) rats. In addition, covert HE was assessed in females while ammonia-precipitated severe HE was assessed in female and male BDL rats, and male BDL rats treated with allopurinol (100 mg/kg), an antioxidant (xanthine oxidase inhibitor). Female BDL developed CLD and HE (impaired motor coordination and night activity) compared to respective SHAM. Hyperammonemia and muscle ammonia clearance were similar between female and male BDL. However, only female BDL rats did not develop muscle loss, brain edema, and short-term memory impairment (vs. female SHAM) and systemic oxidative stress and decreased albumin levels (vs. male BDL). Furthermore, both female BDL and allopurinol-treated male BDL rats were protected against ammonia-induced overt HE. In conclusion, female and male BDL rats develop distinct features of CLD and HE, with systemic oxidative stress playing a pivotal role in the susceptibility to ammonia-precipitated overt HE.

Glutamine synthetase (GS), which catalyzes the ATP-dependent synthesis of L-glutamine from L-glutamate and ammonia, is a ubiquitous and conserved enzyme that plays a pivotal role in nitrogen metabolism across all life domains. In vertebrates, GS is highly expressed in astrocytes, where its activity sustains the glutamate-glutamine cycle at glutamatergic synapses and is thus essential for maintaining brain homeostasis. In fact, decreased GS levels or activity have been associated with neurodegenerative diseases, with these alterations attributed to oxidative post-translational modifications of the protein, in particular tyrosine nitration. In this study, we expressed and purified human GS (HsGS) and performed an in-depth analysis of its oxidative inactivation by peroxynitrite (ONOO−) in vitro. We found that ONOO− exposure led to a dose-dependent loss of HsGS activity, the oxidation of cysteine, methionine, and tyrosine residues and also the nitration of tryptophan and tyrosine residues. Peptide mapping by LC-MS/MS through combined H216O/H218O trypsin digestion identified up to 10 tyrosine nitration sites and five types of dityrosine cross-links; these modifications were further scrutinized by structural analysis. Tyrosine residues 171, 185, 269, 283, and 336 were the main nitration targets; however, tyrosine-to-phenylalanine HsGS mutants revealed that their sole nitration was not responsible for enzyme inactivation. In addition, we observed that ONOO− induced HsGS aggregation and activity loss. Thiol oxidation was a key modification to elicit aggregation, as it was also induced by hydrogen peroxide treatment. Taken together, our results indicate that multiple oxidative events at various sites are responsible for the inactivation and aggregation of human GS.

Chromium (Cr) is a dangerous metal that has been found in the environment in high amounts as the result of numerous human activities, with proven negative effects on various organisms, including plants. The exposure of some plant species to this metal resulted in reduced growth, impaired nutrient uptake, and led to an overproduction of reactive oxygen species (ROS), ultimately causing oxidative damage. Nevertheless, studies regarding the impact of Cr on nitrogen (N) metabolism, the main limiting factor for plant growth, either directly or through the occurrence of oxidative stress, are scarce. Thus, this work aimed to explore the interplay between ammonia (NH4+) assimilation, redox homeostasis and antioxidant (AOX) system of tomato plants exposed to increased concentrations of Cr (VI) (0, 5 and 10 µM). The results revealed that Cr (VI) induced biometric damages, with roots being the most affected organ. Glutamine synthetase (GS) was differentially influenced by the metal at the gene expression, protein and activity levels, whereas glutamate dehydrogenase (GDH) activity was enhanced. Moreover, in Cr (VI)-treated plants, the observed oxidative damage was dependent on metal concentration and plant organ, with a differential accumulation of ROS and a generalized increase of lipid peroxidation (LP) recorded, being paired with an overall failure of the enzymatic antioxidant (AOX) system. Still, the non-enzymatic AOX component had a relevant role in the protection of plants against Cr (VI). Overall, the obtained results suggest that Cr (VI)-mediated plant growth reduction resulted from the occurrence of oxidative stress, coupled with the lack of enzymatic AOX defense, which, consequently, affected the NH4+ assimilatory route.

The adverse effects of arsenic (As) contamination are well known. Rice is a staple food for 50% of the world population but the accumulation of As into rice hampers the food security and safety. Thus the amelioration of As stress and reduction of As levels in rice are needed. In this study, transcriptome (Illumina sequencing) and proteome (2D gel electrophoresis) explored mechanisms of consortium (P. putida+C. vulgaris) mediated growth promotion and As amelioration in rice. The rice seedlings grown hydroponically in the Hewitt nutrient medium and after acclimatization, exposed to 50 µM As alone as well as with microbial consortium to observe the impact at morphological and molecular level. The inoculation of microbial consortium significantly ameliorated the As toxicity, improved growth of root hairs and maintained cellular integrity of the epidermis, exodermis and the stele region during As exposure. Several genes showed differential expression in As and As+P. putida. Down-regulation of As transporters (OsPIP2;2 and OsPIP2;3, OsTIP2;1) and higher expression of WRKY gene (WRKY28) during As+P. putida+C.vulgaris suggested reduction of As uptake in rice. The up-regulation of nutrient elements transporters (OsZIFL9, OsZIFL5, OsZIFL12 and OsZIP2, OsYSL15 and OsCOPT6) in the presence of consortium indicated the improved nutrient status of rice. Higher expression of regulatory elements like auxin/indole 3 acetic acid (AUX/IAA), WRKY and myeloblastosis (MYB) TFs and down-regulation of defense responsive genes such Glutathione-S-transferase, Peroxidase and Glutaredoxinduring As+P. putida+C.vulgaris exposure was also observed. Proteome profiling demonstrated differential abundance of proteins involved in photosynthesis (chlorophyll a/b binding protein, photosystem I Fe-S centre), energy metabolism (ATP synthase subunit beta) transport, signaling (tubulin 1, actin 1), defense (glutathione S-transferase, phenylalanine ammonia lyase) and amino acid metabolism (cysteine synthase, glutamine synthetase), which supported the As ameliorative and growth-promoting potential of microbial consortium during As stress in rice plants. The study gives comprehensive information about gene and protein changes in rice plants in As+consortium exposure.

Nitrogen (N) is one of the abundant and essential elements for plant growth and development, and N deficiency (ND) affects plants at both physiological and transcriptomic levels. Neolamarckia cadamba is a fast-growing woody plant from the Rubiaceae family. However, the physiological and molecular impacts of ND on this species have not been well investigated. Here, we studied how N. cadamba responds to ND under hydroponic conditions. In a physiological aspect, ND led to a reduction in biomass, chlorophyll content, and photosynthetic capacity. ND also impaired the assimilation of N as the activities of glutamine synthetase (GS) and nitrate reductase (NR) were decreased in the root. Interestingly, the lignin content of stem increased progressively during the ND stress. The main transcription factors, the transcription factors that are important to N regulation has been found to be upregulated, including Nodule inception-like protein 7 (NLP7), TGACG motif-binding factor 1 (TGA1), basic helix-loop-helix protein 45 (BHLH45), NAM, ATAF1,2, CUC2 (NAC) transcription factor 43 (NAC43), and basic leucine zipper pattern 44 (bZIP44). The expression of N transporters, such as nitrate transporter 2.4 (NRT2.4), ammonium transporter 3 (AMT3), and amino acid transporter protein 3 (AAP3), was also upregulated. In addition, phosphorus- and calcium-related genes such as phosphate starvation response 2 (PHR2) and cyclic nucleotide-gated ion channel 15 (CNGC15) were expressed more abundantly in response to ND stress. Our results reveal the physiological and molecular mechanisms by which woody plants respond to ND.

Theanine (N-ethyl-γ-l-glutamine) is a special nonprotein amino acid that contributes to the umami taste and health function of tea. Although recent studies on tea breeding have focused on albino tea because of its umami taste, a factor of higher theanine concentration, the mechanism of biosynthesis of l-theanine is still unclear. In this study, four glutamine synthetase genes (CsGSs) were obtained and functionally characterized by overexpressing them in Arabidopsis. The enzyme activities of the purified CsGS proteins from Escherichia coli were detected. The results showed that CsGSs have a dual function in the synthesis of glutamine and theanine in vivo and in vitro. Interestingly, l-theanine was abundantly synthesized in the tender shoots of "Huabai 1". In the white tender shoots, the cytosol CsGS1.2 might exhibit increased expression to compensate for decreasing levels of chloroplast CsGS2, which plays a vital role in high accumulation of theanine in "Huabai 1". In addition, CsGS2 was most likely the key l-theanine synthases in green tissues of tea. The present findings will provide basis for and considerably broaden the scope of understanding the function of CsGSs and the mechanism of l-theanine accumulation in the tender shoots of "Huabai 1", and will be useful for breeding and screening tea with high l-theanine content.

Glutamine is the most abundant amino acid in the body, and adipose tissue is one of the glutamine-producing organs. Glutamine has important and unique metabolic functions; however, its effects in adipocytes are still unclear. 3T3-L1 adipocytes produced and secreted glutamine dependent on glutamine synthetase, but preadipocytes did not. The inhibition of glutamine synthetase by methionine sulfoximine (MSO) impaired the differentiation of preadipocytes to mature adipocytes, and this inhibitory effect of MSO was rescued by exogenous glutamine supplementation. Glutamine concentrations were low, and Atgl gene expression was high in epididymal white adipose tissues of fasting mice in vivo. In 3T3-L1 adipocytes, glutamine deprivation induced Atgl expression and increased glycerol concentration in culture medium. Atgl expression is regulated by FoxO1, and glutamine deprivation reduced FoxO1 phosphorylation (Ser256), indicating the activation of FoxO1. These results demonstrate that glutamine is necessary for the differentiation of preadipocytes and regulates lipolysis through FoxO1 in mature adipocytes.

Paper mulberry, a vigorous pioneer species used for ecological reclamation and a high-protein forage plant for economic development, has been widely planted in China. To further develop its potential value, it is necessary to explore the regulatory mechanism of nitrogen metabolism for rational nitrogen utilization. In this study, we investigated the morphology, physiology and transcriptome of a paper mulberry hybrid (Broussonetia kazinoki × B. papyrifera) in response to different nitrogen concentrations. Moderate nitrogen promoted plant growth and biomass accumulation. Photosynthetic characteristics, concentration of nitrogenous compounds and activities of enzymes were stimulated under nitrogen treatment. However, these enhancements were slightly or severely inhibited under excessive nitrogen supply. Nitrite reductase and glutamate synthase were more sensitive than nitrate reductase and glutamine synthetase and more likely to be inhibited under high nitrogen concentrations. Transcriptome analysis of the leaf transcriptome identified 161,961 unigenes. The differentially expressed genes associated with metabolism of nitrogen, alanine, aspartate, glutamate and glycerophospholipid showed high transcript abundances after nitrogen application, whereas those associated with glycerophospholipid, glycerolipid, amino sugar and nucleotide sugar metabolism were down-regulated. Combined with weighted gene coexpression network analysis, we uncovered 16 modules according to similarity in expression patterns. Asparagine synthetase and inorganic pyrophosphatase were considered two hub genes in two modules, which were associated with nitrogen metabolism and phosphorus metabolism, respectively. The expression characteristics of these genes may explain the regulation of morphological, physiological and other related metabolic strategies harmoniously. This multifaceted study provides valuable insights to further understand the mechanism of nitrogen metabolism and to guide utilization of paper mulberry.

Scytonemin acts as a natural photoprotectant against high-intensity solar photosynthetically active radiation and harmful ultraviolet radiation, which has been reported in several cyanobacteria, and gets accumulated in their extracellular polysaccharide sheath. UV-B radiation (280–315 nm) has detrimental effect on physiological and biochemical processes of living organisms. In this study, scytonemin was extracted from dried cyanobacterial mats collected from the bark of mango trees and was partially characterized using high-performance liquid chromatography and electrospray ionization–mass spectrometry (retention time: 1.7 min; UVλmax: 386 nm; [M + H]+m/z: 545.1). Thereafter, photoprotective capabilities of scytonemin against UV-B radiation in a non-sheathed cyanobacterium Nostoc sp. strain HKAR-2 were assessed followed by studying its role in the recovery process. We found that UV-B radiation inhibited growth, survival, Chl a content and total protein concentration and caused an increase in total carotenoid content. The activities of nitrogen-assimilating enzymes, glutamine synthetase and nitrate reductase, were also affected. In vivo nitrate reductase activity exhibited a stimulatory response, while in vivo glutamine synthetase activity was adversely inhibited after UV-B exposure. Scytonemin with different concentrations exhibited efficient photoprotective ability by nullifying the deleterious effects of UV-B and also enhanced the recovery process. UV-screening effects of scytonemin in terms of growth, pigmentation, survival and nitrogen metabolism enzymes in the cyanobacterial strain have been reported for the first time in the present study. Our results suggest that scytonemin aids in the better survival and adaptability of cyanobacteria in stressed habitats facing harsh environmental conditions.