Localization, Gene Expression, and Functions of Glutamine Synthetase Isozymes in Wheat Grain (Triticum aestivum L.)

Cell-type proteomic and metabolomic resolution of early and late grain filling stages of wheat endosperm

The nutritional value of wheat grains, particularly their protein and metabolite composition, is a result of the grain-filling process, especially in the endosperm. Here, we employ laser microdissection (LMD) combined with shotgun proteomics and metabolomics to generate a cell type-specific proteome and metabolome inventory of developing wheat endosperm at the early (15 DAA) and late (26 DAA) grain-filling stages. We identified 1803 proteins and 41 metabolites from four different cell types (aleurone (AL), sub-aleurone (SA), starchy endosperm (SE) and endosperm transfer cells (ETCs). Differentially expressed proteins were detected, 67 in the AL, 31 in the SA, 27 in the SE and 50 in the ETCs between these two-time points. Cell-type accumulation of specific SUT and GLUT transporters, sucrose converting and starch biosynthesis enzymes correlate well with the respective sugar metabolites, suggesting sugar upload and starch accumulation via nucellar projection and ETC at 15 DAA in contrast to the later stage at 26 DAA. Changes in various protein levels between AL, SA and ETC support this metabolic switch from 15 to 26 DAA. The distinct spatial and temporal abundances of proteins and metabolites revealed a contrasting activity of nitrogen assimilation pathways, e.g. for GOGAT, GDH and glutamic acid, in the different cell types from 15 to 26 DAA, which can be correlated with specific protein accumulation in the endosperm. The integration of cell-type specific proteome and metabolome data revealed a complex metabolic interplay of the different cell types and a functional switch during grain development and grain-filling processes.

Identifying and Characterizing Candidate Genes Contributing to a Grain Yield QTL in Wheat

The current study focuses on identifying the candidate genes of a grain yield QTL from a double haploid population, Westonia × Kauz. The QTL region spans 20 Mbp on the IWGSC whole-genome sequence flank with 90K SNP markers. The IWGSC gene annotation revealed 16 high-confidence genes and 41 low-confidence genes. Bioinformatic approaches, including functional gene annotation, ontology investigation, pathway exploration, and gene network study using publicly available gene expression data, enabled the short-listing of four genes for further confirmation. Complete sequencing of those four genes demonstrated that only two genes are polymorphic between the parental cultivars, which are the ferredoxin-like protein gene and the tetratricopeptide-repeat (TPR) protein gene. The two genes were selected for downstream investigation. Two SNP variations were observed in the exon for both genes, with one SNP resulting in changes in amino acid sequence. qPCR-based gene expression showed that both genes were highly expressed in the high-yielding double haploid lines along with the parental cultivar Westonia. In contrast, their expression was significantly lower in the low-yielding lines in the other parent. It can be concluded that these two genes are the contributing genes to the grain yield QTL.

The Role of Glutamine Synthetase (GS) and Glutamate Synthase (GOGAT) in the Improvement of Nitrogen Use Efficiency in Cereals

Cereals are the most broadly produced crops and represent the primary source of food worldwide. Nitrogen (N) is a critical mineral nutrient for plant growth and high yield, and the quality of cereal crops greatly depends on a suitable N supply. In the last decades, a massive use of N fertilizers has been achieved in the desire to have high yields of cereal crops, leading to damaging effects for the environment, ecosystems, and human health. To ensure agricultural sustainability and the required food source, many attempts have been made towards developing cereal crops with a more effective nitrogen use efficiency (NUE). NUE depends on N uptake, utilization, and lastly, combining the capability to assimilate N into carbon skeletons and remobilize the N assimilated. The glutamine synthetase (GS)/glutamate synthase (GOGAT) cycle represents a crucial metabolic step of N assimilation, regulating crop yield. In this review, the physiological and genetic studies on GS and GOGAT of the main cereal crops will be examined, giving emphasis on their implications in NUE.

Multi-scale analysis provides insights into the roles of ureide permeases in wheat nitrogen use efficiency

The ureides allantoin and allantoate serve as nitrogen (N) transport compounds in plants, and more recently, allantoin has been shown to play a role in signaling. In planta, tissue ureide levels are controlled by the activity of enzymes of the purine degradation pathway and by ureide transporters called ureide permeases (UPS). Little is known about the physiological function of UPS proteins in crop plants, and especially in monocotyledon species. Here, we identified 13 TaUPS genes in the wheat (Triticum aestivum L.) genome. Phylogenetic and genome location analyses revealed a close relationship of wheat UPSs to orthologues in other grasses and a division into TaUPS1, TaUPS2.1, and TaUPS2.2 groups, each consisting of three homeologs, with a total of four tandem duplications. Expression, localization, and biochemical analyses resolved spatio-temporal expression patterns of TaUPS genes, transporter localization at the plasma membrane, and a role for TaUPS2.1 proteins in cellular import of ureides and phloem and seed loading. In addition, positive correlations between TaUPS1 and TaUPS2.1 transcripts and ureide levels were found. Together the data support that TaUPSs function in regulating ureide pools at source and sink, along with source-to-sink transport. Moreover, comparative studies between wheat cultivars grown at low and high N strengthened a role for TaUPS1 and TaUPS2.1 transporters in efficient N use and in controlling primary metabolism. Co-expression, protein-protein interaction, and haplotype analyses further support TaUPS involvement in N partitioning, N use efficiency, and domestication. Overall, this work provides a new understanding on UPS transporters in grasses as well as insights for breeding resilient wheat varieties with improved N use efficiency.

Pine has two glutamine synthetase paralogs, GS1b.1 and GS1b.2, exhibiting distinct biochemical properties

The enzyme glutamine synthetase (EC 6.3.1.2) is mainly responsible for the incorporation of inorganic nitrogen into organic molecules in plants. In the present work, a pine (Pinus pinaster) GS1 (PpGS1b.2) gene was identified, showing a high sequence identity with the GS1b.1 gene previously characterized in conifers. Phylogenetic analysis revealed that the presence of PpGS1b.2 is restricted to the genera Pinus and Picea and is not found in other conifers. Gene expression data suggest a putative role of PpGS1b.2 in plant development, similar to other GS1b genes from angiosperms, suggesting evolutionary convergence. The characterization of GS1b.1 and GS1b.2 at the structural, physicochemical, and kinetic levels has shown differences even though they have high sequence homology. GS1b.2 had a lower optimum pH (6 vs. 6.5) and was less thermally stable than GS1b.1. GS1b.2 exhibited positive cooperativity for glutamate and substrate inhibition for ammonium. However, GS1b.1 exhibited substrate inhibition behavior for glutamate and ATP. Alterations in the kinetic characteristics produced by site-directed mutagenesis carried out in this work strongly suggest an implication of amino acids at positions 264 and 267 in the active center of pine GS1b.1 and GS1b.2 being involved in affinity toward ammonium. Therefore, the amino acid differences between GS1b.1 and GS1b.2 would support the functioning of both enzymes to meet distinct plant needs.

Development and marker-trait relationships of functional markers for glutamine synthetase GS1 and GS2 homoeogenes in bread wheat

GS1 and GS2 genes encode, respectively, the main cytosolic and the plastidic isoforms of glutamine synthetase (GS). In the present study, the wheat GS1 and GS2 homoeogenes located in the A, B and D genome chromosomes have been sequenced in a group of 15 bread wheat varieties including landraces, old commercial varieties and modern cultivars. Phenotypic characterization by multi-environment field trials detected significant effects of specific GS homoeogenes on three of the seven agronomic and grain quality traits analyzed. Based on the gene sequence polymorphisms found, biallelic molecular markers that could facilitate marker-assisted breeding were developed for genes GS1A, GS2A and GS2D. The remaining genes encoding main wheat GS were excluded because of being monomorphic (GS1D) or too polymorphic (GS1B and GS2B) in the sequencing panel varieties. A collection of 187 Spanish bread wheat landraces was genotyped for these gene-based molecular markers. Data analyses conducted with phenotypic records reported for this germplasm collection in López-Fernández et al. (Plants-Basel 10: 620, 2021) have revealed the beneficial influence of some individual alleles on thousand-kernel weight (TKW), kernels per spike (KS) and grain protein content. Furthermore, genetic interactions between GS1A, a cytosolic GS isoform coding gene, and GS2A or GS2D, plastidic GS enzyme coding genes, were found to affect TKW and KS. The finding that some alleles at one locus may mask the effect of positive alleles at hypostatic GS loci should be kept in mind if gene pyramiding strategies are attempted for the improvement of N-use efficiency-related traits.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01354-0.

Improving yield and quality of rice under acid rain stress by regulating nitrogen assimilation with exogenous Ca2

Acid rain threatens crop yield and nutritional quality, and Ca²⁺ can regulate plant responses to abiotic stresses. To improve the yield and nutritional quality of crops under acid rain stress, we applied exogenous Ca²⁺ to regulate nitrogen assimilation in rice seedlings under simulated acid rain stress (pH 4.5 or 3.0), taking yield and nutritional quality of rice as evaluation criteria. We found that Ca²⁺ (5 mM) maintained the total nitrogen content of rice at the seedling and booting stages to alleviate the inhibitory effect of simulated acid rain on rice yield. Meanwhile, Ca²⁺ improved the activity of glutamate synthase to eliminate the disruption of glutamine synthetase/glutamate synthase balance under simulated acid rain. It decreased the efficiency of nitrogen assimilation, thereby reducing the inhibition of essential amino acid content in rice. The mitigation effect on simulated acid rain at pH 4.5 was better than that of simulated acid rain at pH 3.0. Overall, Ca²⁺ may reduce the negative effect of acid rain on the yield and nutritional quality of crops.

Breeding for Higher Yields of Wheat and Rice through Modifying Nitrogen Metabolism

Wheat and rice produce nutritious grains that provide 32% of the protein in the human diet globally. Here, we examine how genetic modifications to improve assimilation of the inorganic nitrogen forms ammonium and nitrate into protein influence grain yield of these crops. Successful breeding for modified nitrogen metabolism has focused on genes that coordinate nitrogen and carbon metabolism, including those that regulate tillering, heading date, and ammonium assimilation. Gaps in our current understanding include (1) species differences among candidate genes in nitrogen metabolism pathways, (2) the extent to which relative abundance of these nitrogen forms across natural soil environments shape crop responses, and (3) natural variation and genetic architecture of nitrogen-mediated yield improvement. Despite extensive research on the genetics of nitrogen metabolism since the rise of synthetic fertilizers, only a few projects targeting nitrogen pathways have resulted in development of cultivars with higher yields. To continue improving grain yield and quality, breeding strategies need to focus concurrently on both carbon and nitrogen assimilation and consider manipulating genes with smaller effects or that underlie regulatory networks as well as genes directly associated with nitrogen metabolism.

Nitrogen starvation induces genome-wide activation of transposable elements in Arabidopsis

Nitrogen (N) availability is a major limiting factor for plant growth and agricultural productivity. Although the gene regulation network in response to N starvation has been extensively studied, it remains unknown whether N starvation has an impact on the activity of transposable elements (TEs). Here, we report that TEs can be transcriptionally activated in Arabidopsis under N starvation conditions. Through genetic screening of idm1-14 suppressors, we cloned GLU1, which encodes a glutamate synthase that catalyzes the synthesis of glutamate in the primary N assimilation pathway. We found that glutamate synthase 1 (GLU1) and its functional homologs GLU2 and glutamate transport 1 (GLT1) are redundantly required for TE silencing, suggesting that N metabolism can regulate TE activity. Transcriptome and methylome analyses revealed that N starvation results in genome-wide TE activation without inducing obvious alteration of DNA methylation. Genetic analysis indicated that N starvation-induced TE activation is also independent of other well-established epigenetic mechanisms, including histone methylation and heterochromatin decondensation. Our results provide new insights into the regulation of TE activity under stressful environments in planta.

Wheat NAM genes regulate the majority of early monocarpic senescence transcriptional changes including nitrogen remobilization genes

Senescence enables the remobilization of nitrogen and micronutrients from vegetative tissues of wheat (Triticum aestivum L.) into the grain. Understanding the molecular players in this process will enable the breeding of wheat lines with tailored grain nutrient content. The NAC transcription factor NAM-B1 is associated with earlier senescence and higher levels of grain protein, iron, and zinc contents due to increased nutrient remobilization. To investigate how related NAM genes control nitrogen remobilization at the molecular level, we carried out a comparative transcriptomic study using flag leaves at 7 time points (3, 7, 10, 13, 15, 19, and 26 days after anthesis) in wild type and NAM RNA interference lines with reduced NAM gene expression. Approximately 2.5 times more genes were differentially expressed in wild type than NAM RNA interference plants during this early senescence time course (6,508 vs 2,605 genes). In both genotypes, differentially expressed genes were enriched for gene ontology terms related to photosynthesis, hormones, amino acid transport, and nitrogen metabolism. However, nitrogen metabolism genes including glutamine synthetase (GS1 and GS2), glutamate decarboxylase (GAD), glutamate dehydrogenase (GDH), and asparagine synthetase (ASN1) showed stronger or earlier differential expression in wild-type than in NAM RNA interference plants, consistent with higher nitrogen remobilization. The use of time course data identified the dynamics of NAM-regulated and NAM-independent gene expression changes during senescence and provides an entry point to functionally characterize the pathways regulating senescence and nutrient remobilization in wheat.

Genetic Diversity in Nitrogen Fertiliser Responses and N Gas Emission in Modern Wheat

Crops assimilate nitrogen (N) as ammonium via the glutamine synthetase/glutamate synthase (GS/GOGAT) pathway which is of central importance for N uptake and potentially represents a bottle neck for N fertiliser-use efficiency. The aim of this study was to assess whether genetic diversity for N-assimilation capacity exists in wheat and could be exploited for breeding. Wheat plants rapidly, within 6 h, responded to N application with an increase in GS activity. This was not accompanied by an increase in GS gene transcript abundance and a comparison of GS1 and GS2 protein models revealed a high degree of sequence conservation. N responsiveness amongst ten wheat varieties was assessed by measuring GS enzyme activity, leaf tissue ammonium, and by a leaf-disc assay as a proxy for apoplastic ammonia. Based on these data, a high-GS group showing an overall positive response to N could be distinguished from an inefficient, low-GS group. Subsequent gas emission measurements confirmed plant ammonia emission in response to N application and also revealed emission of N2O when N was provided as nitrate, which is in agreement with our current understanding that N2O is a by-product of nitrate reduction. Taken together, the data suggest that there is scope for improving N assimilation capacity in wheat and that further investigations into the regulation and role of GS-GOGAT in NH3 emission is justified. Likewise, emission of the climate gas N2O needs to be reduced, and future research should focus on assessing the nitrate reductase pathway in wheat and explore fertiliser management options.

Cytosolic Glutamine Synthetase GS1;3 Is Involved in Rice Grain Ripening and Germination

Ammonium is combined with glutamate to form glutamine. This reaction is catalyzed by glutamine synthetase (GS or GLN). Plants harbor several isoforms of cytosolic GS (GS1). Rice GS1;3 is highly expressed in seeds during grain filling and germination, suggesting a unique role in these processes. This study aimed to investigate the role of GS1;3 for rice growth and yield. Tos17 insertion lines for GS1;3 were isolated, and the nitrogen (N), amino acid, and ammonium contents of GS1;3 mutant grains were compared to wild-type grains. The spatiotemporal expression of GS1;3 and the growth and yield of rice plants were evaluated in hydroponic culture and the paddy field. Additionally, the stable isotope of N was used to trace the foliar N flux during grain filling. Results showed that the loss of GS1;3 retarded seed germination. Seeds of GS1;3 mutants accumulated glutamate but did not show a marked change in the level of phytohormones. The expression of GS1;3 was detected at the beginning of germination, with limited promoter activity in seeds. GS1;3 mutants showed a considerably decreased ripening ratio and decreased N efflux in the 12th leaf blade under N deficient conditions. The β-glucuronidase gene expression under control of the GS1;3 promoter was detected in the vascular tissue and aleurone cell layer of developing grains. These data suggest unique physiological roles of GS1;3 in the early stage of seed germination and grain filling under N deficient conditions in rice.

A Mathematical Model for Characterizing the Biomass and the Physiological/Biochemical Indicators of Salvia miltiorrhiza Based on Growth-Defense Tradeoff

Carbon(C) and nitrogen(N) metabolisms are important for plant growth and defense, and enzymes play a major role in these two metabolisms. Current studies show that the enzymes of N Metabolism, C Metabolism, and defense are correlated with biomass. Then, we conducted this research under the assumption that enzymes could characterize the relationship based on growth-defense tradeoff, and some of the enzymes could be used to represent the plant growth. From the mechanism model, we picked out 18 physiological/biochemical indicators and obtained the data from 24 tissue culture seedlings of Salvia miltiorrhiza (S.miltiorrhiza) which were grafted with 11 endophytic fungi. Then, the relationship between the biomass and the physiological/biochemical indicators was investigated by using statistical analysis, such as correlation analysis, variable screening, and regression analysis. The results showed that many physiological/biochemical indicators, especially enzyme activities, were related to biomass accumulation. Through a rigorous logical reasoning process, we established a mathematical model of the biomass and 6 key physiological/biochemical indicators, including glutamine synthetase (GS), glutamate synthase (GLS), glutamate dehydrogenase (GDH), peroxidase (POD), catalase (CAT), and soluble protein from Cobb-Douglas production function. This model had high prediction accuracy, and it could simplify the measurement of biomass. During the artificial cultivation of S.miltiorrhiza, we can monitor the biomass accumulation by scaling the key physiological/biochemical indicators in the leaves. Interestingly, the coefficients of Lasso regression during our analysis were consistent with the mechanism of growth-defense tradeoff. Perhaps, the key physiological/biochemical indicators obtained in the statistical analysis are related to the indicators affecting biomass accumulation in practice.

Nitrogen assimilation in plants: current status and future prospects

Nitrogen (N) is the driving force for crop yields, however, excessive N application in agriculture not only increases production cost, but also causes severe environmental problems. Therefore, comprehensively understanding the molecular mechanisms of N use efficiency (NUE) and breeding crops with higher NUE is essential to tackle these problems. NUE of crops is determined by N uptake, transport, assimilation, and remobilization. In the process of N assimilation, nitrate reductase (NR), nitrite reductase (NiR), glutamine synthetase (GS), and glutamine-2-oxoglutarate aminotransferase (GOGAT, also known as glutamate synthase) are the major enzymes. NR and NiR mediate the initiation of inorganic N utilization, and GS/GOGAT cycle converts inorganic N to organic N, playing a vital role in N assimilation and the final NUE of crops. Besides, asparagine synthetase (ASN), glutamate dehydrogenase (GDH), and carbamoylphosphate synthetase (CPSase) are also involved. In this review, we summarize the function and regulation of these enzymes reported in three major crops, rice, maize, wheat, also in the model plant Arabidopsis, and we highlight their application in improving NUE of crops via manipulating N assimilation. Anticipated challenges and prospects toward fully understanding the function of N assimilation and further exploring the potential for NUE improvement are discussed.

Ammonium transporter PsAMT1.2 from Populus simonii functions in nitrogen uptake and salt resistance

Ammonium (NH4+) is a primary nitrogen (N) source for many species, and NH4+ uptake is mediated by various transporters. However, the effects of NH4+ transporters on N uptake and metabolism under salt stress remain unclear. In the present study, we investigated the expression characteristics and transport function of PsAMT1.2 in Populus simonii and its role in ammonium uptake and metabolism under salt stress. PsAMT1.2 was localized in the plasma membrane highly expressed in the roots. Heterologous functionality tests demonstrated that PsAMT1.2 mediates NH4+ permeation across the plasma membrane in yeast mutants, restoring growth. A short-term NH4+ uptake experiment showed that PsAMT1.2 is a high-affinity NH4+ transporter with a Km value of 80.603 μM for NH4+. Compared with the wild type (WT, Populus tremula × Populus alba INRA 717-IB4 genotype), PsAMT1.2-overexpressing transgenic poplar grew better, with higher increases in stem height and relative chlorophyll content under both control and salt-stress conditions. PsAMT1.2 overexpression significantly increased the total NH4+ concentration and total N of whole plants under salt stress. The glutamate synthase (GS), glutamine synthetase (GOGAT) and glutamate dehydrogenase (GDH) activities and the total amino acids largely increased in the roots of PsAMT1.2-overexpressing transgenic plants compared with the WT plants under control conditions, suggesting that PsAMT1.2 overexpression promotes NH4+ assimilation and metabolism in poplar roots. Consistent with the increased total amino acid content, GS1.3, GS2 and Fd-GOGAT expression was upregulated in the roots and leaves of the PsAMT1.2-overexpressing transgenic plants compared with the WT plants under salt stress. Collectively, PsAMT1.2 encodes a high-affinity NH4+ transporter crucial to NH4+ uptake and metabolism under salt stress.

A New Perspective on the Role of Glutamine Synthetase in Nitrogen Remobilization in Wheat (Triticum aestivum L.)

Glutamine synthetase (GS), a key enzyme in plant nitrogen metabolism, is closely related to nitrogen remobilization. However, how GS isoforms participate in nitrogen remobilization remains unclear. Here, the spatiotemporal expression of the TaGS gene family after anthesis was investigated, and the results showed that TaGS1;1 was mainly encoded by TaGS1;1-6A, while the other isozymes were mainly encoded by TaGS localized on the A and D subgenomes. TaGS1;2-4A/4D had the highest expression level, especially in rachis and peduncle. Furthermore, immunofluorescence showed TaGS1;2 was located in the phloem of rachis and peduncle. GUS (β-glucuronidase) staining confirmed that ProTaGS1;2-4A/4D::GUS activity was mainly present in the vascular system of leaves, roots, and petal of Arabidopsis. Ureides, an important transport form of nitrogen, were mainly synthesized in flag leaves and transported to grains through the phloem of peduncle and rachis during grain filling. TaAAH, which encodes the enzyme that degrades ureides to release NH₄⁺, had a higher expression in rachis and peduncle and was synchronized with the increase in NH₄⁺ concentration in phloem, indicating that NH₄⁺ in phloem is from ureide degradation. Taking the above into account, TaGS1;2, which is highly expressed in the phloem of peduncle and rachis, may participate in N remobilization by assimilating NH₄⁺ released from ureide degradation.