The identification of new cytosolic glutamine synthetase and asparagine synthetase genes in barley (Hordeum vulgare L.), and their expression during leaf senescence

Integrative omics analyses of tea (Camellia sinensis) under glufosinate stress reveal defense mechanisms: A trade-off with flavor loss

Extensively applied glufosinate (GLU) will trigger molecular alterations in nontarget tea plants (Camellia sinensis), which inadvertently disturbs metabolites and finally affects tea quality. The mechanistic response of tea plants to GLU remains unexplored. This study investigated GLU residue behavior, the impact on photosynthetic capacity, specialized metabolites, secondary pathways, and transcript levels in tea seedlings. Here, GLU mainly metabolized to MPP and accumulated more in mature leaves than in tender ones. GLU catastrophically affected photosynthesis, leading to leaf chlorosis, and decreased Fv/Fm and chlorophyll content. Physiological and biochemical, metabolomics, and transcriptomics analyses were integrated. Showing that GLU disrupted the photosynthetic electron transport chain, triggered ROS and antioxidant system, and inhibited photosynthetic carbon fixation. GLU targeted glutamine synthetase (GS) leading to the accumulation of ammonium and the inhibition of key umami L-theanine, causing a disorder in nitrogen metabolism, especially for amino acids synthesis. Interestingly, biosynthesis of primary flavonoids was sacrificed for defensive phenolic acids and lignin formulation, leading to possible losses in nutrition and tenderness in leaves. This study revealed the defense intricacies and potential quality deterioration of tea plants responding to GLU stress. Valuable insights into detoxification mechanisms for non-target crops post-GLU exposure were offered.

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.

Multilayered regulation of developmentally programmed pre-anthesis tip degeneration of the barley inflorescence

Leaf and floral tissue degeneration is a common feature in plants. In cereal crops such as barley (Hordeum vulgare L.), pre-anthesis tip degeneration (PTD) starts with growth arrest of the inflorescence meristem dome, which is followed basipetally by the degeneration of floral primordia and the central axis. Due to its quantitative nature and environmental sensitivity, inflorescence PTD constitutes a complex, multilayered trait affecting final grain number. This trait appears to be highly predictable and heritable under standardized growth conditions, consistent with a developmentally programmed mechanism. To elucidate the molecular underpinnings of inflorescence PTD, we combined metabolomic, transcriptomic, and genetic approaches to show that barley inflorescence PTD is accompanied by sugar depletion, amino acid degradation, and abscisic acid responses involving transcriptional regulators of senescence, defense, and light signaling. Based on transcriptome analyses, we identified GRASSY TILLERS1 (HvGT1), encoding an HD-ZIP transcription factor, as an important modulator of inflorescence PTD. A gene-edited knockout mutant of HvGT1 delayed PTD and increased differentiated apical spikelets and final spikelet number, suggesting a possible strategy to increase grain number in cereals. We propose a molecular framework that leads to barley PTD, the manipulation of which may increase yield potential in barley and other related cereals.

Uncovering genomic and transcriptional variations facilitates utilization of wild resources in cotton disease resistance improvement

BACKGROUND

Upland cotton wild/landraces represent a valuable resource for disease resistance alleles. Genetic differentiation between genotypes, as well as variation in Verticillium wilt (VW) resistance, has been poorly characterized for upland cotton accessions on the domestication spectrum (from wild/landraces to elite lines).

RESULTS

To illustrate the effects of modern breeding on VW resistance in upland cotton, 37 wild/landraces were resequenced and phenotyped for VW resistance. Genomic patterns of differentiation were identified between wild/landraces and improved upland cotton, and a significant decline in VW resistance was observed in association with improvement. Four genotypes representing different degrees of improvement were used in a full-length transcriptome analysis to study the genetic basis of VW resistance. ROS signaling was highly conserved at the transcriptional level, likely providing the basis for VW resistance in upland cotton. ASN biosynthesis and HSP90-mediated resistance moderated the response to VW in wild/landraces, and loss of induction activity of these genes resulted in VW susceptibility. The observed genomic differentiation contributed to the loss of induction of some important VW resistance genes such as HSP90.4 and PR16.

CONCLUSIONS

Besides providing new insights into the evolution of upland cotton VW resistance, this study also identifies important resistance pathways and genes for both fundamental research and cotton breeding.

Magnesium promotes tea plant growth via enhanced glutamine synthetase-mediated nitrogen assimilation

Acidic tea (Camellia sinensis) plantation soil usually suffers from magnesium (Mg) deficiency, and as such, application of fertilizer containing Mg can substantially increase tea quality by enhancing the accumulation of nitrogen (N)-containing chemicals such as amino acids in young tea shoots. However, the molecular mechanisms underlying the promoting effects of Mg on N assimilation in tea plants remain unclear. Here, both hydroponic and field experiments were conducted to analyze N, Mg, metabolite contents, and gene expression patterns in tea plants. We found that N and amino acids accumulated in tea plant roots under Mg deficiency, while metabolism of N was enhanced by Mg supplementation, especially under a low N fertilizer regime. 15N tracing experiments demonstrated that assimilation of N was induced in tea roots following Mg application. Furthermore, weighted gene correlation network analysis (WGCNA) analysis of RNA-seq data suggested that genes encoding glutamine synthetase isozymes (CsGSs), key enzymes regulating N assimilation, were markedly regulated by Mg treatment. Overexpression of CsGS1.1 in Arabidopsis (Arabidopsis thaliana) resulted in a more tolerant phenotype under Mg deficiency and increased N assimilation. These results validate our suggestion that Mg transcriptionally regulates CsGS1.1 during the enhanced assimilation of N in tea plant. Moreover, results of a field experiment demonstrated that high Mg and low N had positive effects on tea quality. This study deepens our understanding of the molecular mechanisms underlying the interactive effects of Mg and N in tea plants while also providing both genetic and agronomic tools for future improvement of tea production.

Variability and limits of nitrogen and phosphorus resorption during foliar senescence

Foliar nutrient resorption (NuR) plays a key role in ecosystem functioning and plant nutrient economy. Most of this recycling occurs during the senescence of leaves and is actively addressed by cells. Here, we discuss the importance of cell biochemistry, physiology, and subcellular anatomy to condition the outcome of NuR at the cellular level and to explain the existence of limits to NuR. Nutrients are transferred from the leaf in simple metabolites that can be loaded into the phloem. Proteolysis is the main mechanism for mobilization of N, whereas P mobilization requires the involvement of different catabolic pathways, making the dynamics of P in leaves more variable than those of N before, during, and after foliar senescence. The biochemistry and fate of organelles during senescence impose constraints that limit NuR. The efficiency of NuR decreases, especially in evergreen species, as soil fertility increases, which is attributed to the relative costs of nutrient acquisition from soil decreasing with increasing soil nutrient availability, while the energetic costs of NuR from senescing leaves remain constant. NuR is genetically determined, with substantial interspecific variability, and is environmentally regulated in space and time, with nutrient availability being a key driver of intraspecific variability in NuR.

Transcriptome Analysis Reveals the Genes Related to Water-Melon Fruit Expansion under Low-Light Stress

Watermelon is one of people's favorite fruits globally. Fruit size is one of the important characteristics of fruit quality. Low light can seriously affect fruit development, but there have been no reports concerning molecular mechanism analysis in watermelons involved in fruit expansion under low-light stress. To understand this mechanism, the comparative transcriptomic file of watermelon fruit flesh at four different developmental stages under different light levels was studied. The results showed that the fruit size and content of soluble sugar and amino acids at low-light stress significantly decreased compared to the control. In addition, 0-15 DAP was the rapid expansion period of watermelon fruit affected by shading. In total, 8837 differentially expressed genes (DEGs) were identified and 55 DEGs were found to play a role in the four different early fruit development stages. We also found that genes related to oxidation-reduction, secondary metabolites, carbohydrate and amino acid metabolism and transcriptional regulation played a key role in watermelon fruit expansion under low-light stress. This study provides a foundation to investigate the functions of low-light stress-responsive genes and the molecular mechanism of the effects of low-light stress on watermelon fruit expansion.

THP9 enhances seed protein content and nitrogen-use efficiency in maize

Teosinte, the wild ancestor of maize (Zea mays subsp. mays), has three times the seed protein content of most modern inbreds and hybrids, but the mechanisms that are responsible for this trait are unknown^1,2. Here we use trio binning to create a contiguous haplotype DNA sequence of a teosinte (Zea mays subsp. parviglumis) and, through map-based cloning, identify a major high-protein quantitative trait locus, TEOSINTE HIGH PROTEIN 9 (THP9), on chromosome 9. THP9 encodes an asparagine synthetase 4 enzyme that is highly expressed in teosinte, but not in the B73 inbred, in which a deletion in the tenth intron of THP9-B73 causes incorrect splicing of THP9-B73 transcripts. Transgenic expression of THP9-teosinte in B73 significantly increased the seed protein content. Introgression of THP9-teosinte into modern maize inbreds and hybrids greatly enhanced the accumulation of free amino acids, especially asparagine, throughout the plant, and increased seed protein content without affecting yield. THP9-teosinte seems to increase nitrogen-use efficiency, which is important for promoting a high yield under low-nitrogen conditions.

Glutamine synthetase: an unlikely case of functional redundancy in Arabidopsis thaliana

Glutamine synthetase (GS, EC 6.3.1.2) is an essential enzyme in plant metabolism, catalysing the assimilation of inorganic nitrogen into the amino acid glutamine. GS is a key enzyme in plant growth and has received special attention due to its recognized roles in plant nitrogen use efficiency and crop productivity. It occurs in plants as a collection of isoenzymes, located in the cytosol (GS1) and plastids (GS2), consistent with the multiplicity of roles played in plant metabolism. It is considered that the different isoenzymes, involved in a wide variety of physiological processes throughout the plant life cycle, perform non-redundant and non-overlapping roles. In fact, specific and non-redundant roles of GS isoenzymes in nitrogen metabolism were observed in species like Oryza sativa and Zea mays. However, in A. thaliana the GS isoenzymes, five cytosolic and one plastidic, are suggested to have functional redundancy and an isoenzyme compensation mechanism, specific to this species, was described. This review integrates analyses on the likely roles of the distinct cytosol- and plastid-located GS isoenzymes in A. thaliana, highlighting the redundancy of the GS gene family specifically occurring in this model plant.

Understanding the Relationships between Free Asparagine in Grain and Other Traits to Breed Low-Asparagine Wheat

Since the discovery of acrylamide in food, and the identification of free asparagine as the key determinant of acrylamide concentration in wheat products, our understanding of how grain asparagine content is regulated has improved greatly. However, the targeted reduction in grain asparagine content has not been widely implemented in breeding programmes so far. Here we summarise how free asparagine concentration relates to other quality and agronomic traits and show that these relationships are unlikely to pose major issues for the breeding of low-asparagine wheat. We also outline the strategies that are possible for the breeding of low-asparagine wheat, using both natural and induced variation.

Genotypic Variation of Nitrogen Use Efficiency and Amino Acid Metabolism in Barley

Owing to the large genetic diversity of barley and its resilience under harsh environments, this crop is of great value for agroecological transition and the need for reduction of nitrogen (N) fertilizers inputs. In the present work, we investigated the diversity of a North African barley genotype collection in terms of growth under limiting N (LN) or ample N (HN) supply and in terms of physiological traits including amino acid content in young seedlings. We identified a Moroccan variety, Laanaceur, accumulating five times more lysine in its leaves than the others under both N nutritional regimes. Physiological characterization of the barley collection showed the genetic diversity of barley adaptation strategies to LN and highlighted a genotype x environment interaction. In all genotypes, N limitation resulted in global biomass reduction, an increase in C concentration, and a higher resource allocation to the roots, indicating that this organ undergoes important adaptive metabolic activity. The most important diversity concerned leaf nitrogen use efficiency (LNUE), root nitrogen use efficiency (RNUE), root nitrogen uptake efficiency (RNUpE), and leaf nitrogen uptake efficiency (LNUpE). Using LNUE as a target trait reflecting barley capacity to deal with N limitation, this trait was positively correlated with plant nitrogen uptake efficiency (PNUpE) and RNUpE. Based on the LNUE trait, we determined three classes showing high, moderate, or low tolerance to N limitation. The transcriptomic approach showed that signaling, ionic transport, immunity, and stress response were the major functions affected by N supply. A candidate gene encoding the HvNRT2.10 transporter was commonly up-regulated under LN in the three barley genotypes investigated. Genes encoding key enzymes required for lysine biosynthesis in plants, dihydrodipicolinate synthase (DHPS) and the catabolic enzyme, the bifunctional Lys-ketoglutarate reductase/saccharopine dehydrogenase are up-regulated in Laanaceur and likely account for a hyperaccumulation of lysine in this genotype. Our work provides key physiological markers of North African barley response to low N availability in the early developmental stages.

The Evolution of Leaf Function during Development Is Reflected in Profound Changes in the Metabolic Composition of the Vacuole

During its development, the leaf undergoes profound metabolic changes to ensure, among other things, its growth. The subcellular metabolome of tomato leaves was studied at four stages of leaf development, with a particular emphasis on the composition of the vacuole, a major actor of cell growth. For this, leaves were collected at different positions of the plant, corresponding to different developmental stages. Coupling cytology approaches to non-aqueous cell fractionation allowed to estimate the subcellular concentrations of major compounds in the leaves. The results showed major changes in the composition of the vacuole across leaf development. Thus, sucrose underwent a strong allocation, being mostly located in the vacuole at the beginning of development and in the cytosol at maturity. Furthermore, these analyses revealed that the vacuole, rather rich in secondary metabolites and sugars in the growth phases, accumulated organic acids thereafter. This result suggests that the maintenance of the osmolarity of the vacuole of mature leaves would largely involve inorganic molecules.

Structural property, molecular regulation, and functional diversity of glutamine synthetase in higher plants: a data-mining bioinformatics approach

Glutamine synthetase (GS; E.C.6.3.1.2) is a key enzyme in higher plants with two isozymes, cytosolic GS1 and plastidic GS2, and involves in the assimilation and recycling of NH₄⁺ ions and maintenance of complex traits such as crop nitrogen-use efficiency and yield. Our present understanding of crop nitrogen-use efficiency and its correlation with the functional role of the GS family genes is inadequate, which delays harnessing the benefit of this key enzyme in crop improvement. In this report, we performed a comprehensive investigation on the phylogenetic relationship, structural properties, complex multilevel gene regulation, and expression patterns of the GS genes to enrich present understanding about the enzyme. Our Gene Ontology and protein-protein interactions analysis revealed the functional aspects of GS isozymes in stress mitigation, aging, nucleotide biosynthesis/transport, DNA repair and response to metals. The insight gained here contributes to the future research strategies in developing climate-smart crops for global sustainability.

Identification of Differentially Expressed Genes and Pathways Involved in Growth and Development of Mesona chinensis Benth Under Red- and Blue-Light Conditions

Mesona chinensis Benth (MCB) is an important Chinese herbal medicine. The plant factories might be one of the ways to solve the shortage of MCB supply. In this study, the MCB seedlings were treated under the red (R) and blue (B) lights in the plant factory. Results showed that the red light promoted the growth and development of MCB in comparison with the blue light. Under the red-light condition, the biomass, plant height, and root characteristics were significantly higher than those under blue-light condition, while the soil and plant analyzer development (SPAD) under the red-light treatment was significantly lower than that under the blue-light treatment. Red light also significantly promoted the content of soluble sugar and pectin of MCB compared with blue light. Transcriptome analysis showed that a total of 4,165 differentially expressed genes (DEGs) were detected including 2,034 upregulated and 2,131 downregulated. Of these, 1,112 DEGs including 410 upregulated and 702 downregulated genes were associated with 111 pathways. Moreover, a total of 8,723 differentially expressed transcription factors (TFs) were identified in R vs. B, and these TFs were distributed in 56 gene families. Metabonomic results revealed that a total of 184 metabolites and 99 differentially expressed metabolites (DEMs) (42 upregulated and 57 downregulated) were identified in the red- and blue-light treatments. Integrative analysis of transcriptome and metabolome unveiled that a total of 24 pathways included 70 compounds (metabolites) and were associated with 28 unigenes. In particular, these pathways included starch and sucrose metabolism, phenylpropanoid biosynthesis, cysteine and methionine metabolism, glycolysis/gluconeogenesis, and pentose and glucuronate interconversions. The unigenes included asparagine synthetase (AS), thymidine kinase (TK), alpha, alpha-trehalose-phosphate synthase (TPS), phosphatase IMPL1 (IMPL1), dihydroflavonol 4-reductase (D4R), and 4-coumarate-CoA ligase-like 6 (4CL6), bifunctional aspartokinase-homoserine dehydrogenase 1 (thrA), and abscisic acid 8'-hydroxylase 2 isoform X1 (ABA8). It was indicated that these pathways and genes might play important roles in the growth and development of MCB. This study laid a foundation for the future research of MCB.

Ammonium supply induces differential metabolic adaptive responses in tomato according to leaf phenological stage

Nitrate (NO3-) and ammonium (NH4+) are the main inorganic nitrogen sources available to plants. However, exclusive ammonium nutrition may lead to stress characterized by growth inhibition, generally associated with a profound metabolic reprogramming. In this work, we investigated how metabolism adapts according to leaf position in the vertical axis of tomato (Solanum lycopersicum cv. M82) plants grown with NH4+, NO3-, or NH4NO3 supply. We dissected leaf biomass composition and metabolism through an integrative analysis of metabolites, ions, and enzyme activities. Under ammonium nutrition, carbon and nitrogen metabolism were more perturbed in mature leaves than in young ones, overall suggesting a trade-off between NH4+ accumulation and assimilation to preserve young leaves from ammonium stress. Moreover, NH4+-fed plants exhibited changes in carbon partitioning, accumulating sugars and starch at the expense of organic acids, compared with plants supplied with NO3-. We explain such reallocation by the action of the biochemical pH-stat as a mechanism to compensate the differential proton production that depends on the nitrogen source provided. This work also underlines that the regulation of leaf primary metabolism is dependent on both leaf phenological stage and the nitrogen source provided.

Dark-Induced Barley Leaf Senescence - A Crop System for Studying Senescence and Autophagy Mechanisms

This review synthesizes knowledge on dark-induced barley, attached, leaf senescence (DILS) as a model and discusses the possibility of using this crop system for studying senescence and autophagy mechanisms. It addresses the recent progress made in our understanding of DILS. The following aspects are discussed: the importance of chloroplasts as early targets of DILS, the role of Rubisco as the largest repository of recoverable nitrogen in leaves senescing in darkness, morphological changes of these leaves other than those described for chloroplasts and metabolic modifications associated with them, DILS versus developmental leaf senescence transcriptomic differences, and finally the observation that in DILS autophagy participates in the circulation of cell components and acts as a quality control mechanism during senescence. Despite the progression of macroautophagy, the symptoms of degradation can be reversed. In the review, the question also arises how plant cells regulate stress-induced senescence via autophagy and how the function of autophagy switches between cell survival and cell death.

Genetic regulation of the traits contributing to wheat nitrogen use efficiency

High nitrogen application aimed at increasing crop yield is offset by higher production costs and negative environmental consequences. For wheat, only one third of the applied nitrogen is utilized, which indicates there is scope for increasing Nitrogen Use Efficiency (NUE). However, achieving greater NUE is challenged by the complexity of the trait, which comprises processes associated with nitrogen uptake, transport, reduction, assimilation, translocation and remobilization. Thus, knowledge of the genetic regulation of these processes is critical in increasing NUE. Although primary nitrogen uptake and metabolism-related genes have been well studied, the relative influence of each towards NUE is not fully understood. Recent attention has focused on engineering transcription factors and identification of miRNAs acting on expression of specific genes related to NUE. Knowledge obtained from model species needs to be translated into wheat using recently-released whole genome sequences, and by exploring genetic variations of NUE-related traits in wild relatives and ancient germplasm. Recent findings indicate the genetic basis of NUE is complex. Pyramiding various genes will be the most effective approach to achieve a satisfactory level of NUE in the field.

Cereal asparagine synthetase genes

Asparagine synthetase catalyses the transfer of an amino group from glutamine to aspartate to form glutamate and asparagine. The accumulation of free (nonprotein) asparagine in crops has implications for food safety because free asparagine is the precursor for acrylamide, a carcinogenic contaminant that forms during high-temperature cooking and processing. Here we review publicly available genome data for asparagine synthetase genes from species of the Pooideae subfamily, including bread wheat and related wheat species (Triticum and Aegilops spp.), barley (Hordeum vulgare) and rye (Secale cereale) of the Triticeae tribe. Also from the Pooideae subfamily: brachypodium (Brachypodium dIstachyon) of the Brachypodiae tribe. More diverse species are also included, comprising sorghum (Sorghum bicolor) and maize (Zea mays) of the Panicoideae subfamily and rice (Oryza sativa) of the Ehrhartoideae subfamily. The asparagine synthetase gene families of the Triticeae species each comprise five genes per genome, with the genes assigned to four groups: 1, 2, 3 (subdivided into 3.1 and 3.2) and 4. Each species has a single gene per genome in each group, except that some bread wheat varieties (genomes AABBDD) and emmer wheat (Triticum dicoccoides; genomes AABB) lack a group 2 gene in the B genome. This raises questions about the ancestry of cultivated pasta wheat and the B genome donor of bread wheat, suggesting that the hybridisation event that gave rise to hexaploid bread wheat occurred more than once. In phylogenetic analyses, genes from the other species cluster with the Triticeae genes, but brachypodium, sorghum and maize lack a group 2 gene, while rice has only two genes, one group 3 and one group 4. This means that TaASN2, the most highly expressed asparagine synthetase gene in wheat grain, has no equivalent in maize, rice, sorghum or brachypodium. An evolutionary pathway is proposed in which a series of gene duplications gave rise to the five genes found in modern Triticeae species.

Seasonal senescence of leaves and roots of Populus trichocarpa-is the scenario the same or different?

The remobilization and resorption of plant nutrients is considered as a crucial aspect of the seasonal senescence of plant organs. In leaves, the mechanisms responsible for the relocation of valuable compounds are well understood while the related processes in roots are still being debated. Some research indicates that remobilization in roots occurs, while other studies have not found evidence of this process. Considering that the total biomass of fine roots is equal to or greater than that of leaves, clarifying the conflicting reports and ambiguities may provide critical information on the circulation of chemical elements in forest ecosystems. This study provides new information concerning the basis for remobilization processes in roots by combining physiological data with gene expression and protein levels. We suggest that, as in leaves, molecular mechanisms involved in nitrogen (N) resorption are also activated in senescent roots. An analysis of N concentration indicated that N levels decreased during the senescence of both organs. The decrease was associated with an increase in the expression of a glutamine synthetase (GS) gene and a concomitant elevation in the amount of GS-one of the most important enzymes in N metabolism. In addition, significant accumulation of carbohydrates was observed in fine roots, which may represent an adaptation to unfavorable weather conditions that would allow remobilization to occur rather than a rapid death in response to ground frost or cold. Our results provide new insights into the senescence of plant organs and clarify contentious topics related to the remobilization process in fine roots.

Involvement of nitrogen in storage root growth and related gene expression in sweet potato (Ipomoea batatas)

Nitrogen (N) could affect storage root growth and development of sweet potato. To manage external N concentration fluctuations, plants have developed a wide range of strategies, such as growth changes and gene expression. Five sweet potato cultivars were used to analyse the functions of N in regulating storage root growth. Growth responses and physiological indicators were measured to determine the physiological changes regulated by different N concentrations. Expression profiles of related genes were analysed via microarray hybridization data and qRT-PCR analysis to reveal the molecular mechanisms of storage root growth regulated by different N concentrations. The growth responses and physiological indicators of the five cultivars were changed by N concentration. The root fresh weight of two of the sweet potato cultivars, SS19 and GS87, was higher under low N concentrations compared with the other cultivars. SS19 and GS87 were found to be having greater tolerance to low N concentration. The expression of N metabolism and storage root growth related genes was regulated by N concentration in sweet potato. These results reveal that N significantly regulated storage root growth. SS19 and GS87 were more tolerant to low N concentration and produced greater storage root yield (at 30 days). Furthermore, several N response genes were involved in both N metabolism and storage root growth.

Global transcriptome analysis of alfalfa reveals six key biological processes of senescent leaves

Leaf senescence is a complex organized developmental stage limiting the yield of crop plants, and alfalfa is an important forage crop worldwide. However, our understanding of the molecular mechanism of leaf senescence and its influence on biomass in alfalfa is still limited. In this study, RNA sequencing was utilized to identify differentially expressed genes (DEGs) in young, mature, and senescent leaves, and the functions of key genes related to leaf senescence. A total of 163,511 transcripts and 77,901 unigenes were identified from the transcriptome, and 5,133 unigenes were differentially expressed. KEGG enrichment analyses revealed that ribosome and phenylpropanoid biosynthesis pathways, and starch and sucrose metabolism pathways are involved in leaf development and senescence in alfalfa. GO enrichment analyses exhibited that six clusters of DEGs are involved in leaf morphogenesis, leaf development, leaf formation, regulation of leaf development, leaf senescence and negative regulation of the leaf senescence biological process. The WRKY and NAC families of genes mainly consist of transcription factors that are involved in the leaf senescence process. Our results offer a novel interpretation of the molecular mechanisms of leaf senescence in alfalfa.

Manipulating Amino Acid Metabolism to Improve Crop Nitrogen Use Efficiency for a Sustainable Agriculture

In a context of a growing worldwide food demand coupled to the need to develop a sustainable agriculture, it is crucial to improve crop nitrogen use efficiency (NUE) while reducing field N inputs. Classical genetic approaches based on natural allelic variations existing within crops have led to the discovery of quantitative trait loci controlling NUE under low nitrogen conditions; however, the identification of candidate genes from mapping studies is still challenging. Amino acid metabolism is the cornerstone of plant N management, which involves N uptake, assimilation, and remobilization efficiencies, and it is finely regulated during acclimation to low N conditions and other abiotic stresses. Over the last two decades, biotechnological engineering of amino acid metabolism has led to promising results for the improvement of crop NUE, and more recently under low N conditions. This review summarizes current work carried out in crops and provides perspectives on the identification of new candidate genes and future strategies for crop improvement.

Asparagine Synthesis During Tobacco Leaf Curing

Senescence is a genetically controlled mechanism that modifies leaf chemistry. This involves significant changes in the accumulation of carbon- and nitrogen-containing compounds, including asparagine through the activity of asparagine synthetases. These enzymes are required for nitrogen re-assimilation and remobilization in plants; however, their mechanisms are not fully understood. Here, we report how leaf curing—a senescence-induced process that allows tobacco leaves to dry out—modifies the asparagine metabolism. We show that leaf curing strongly alters the concentration of the four main amino acids, asparagine, glutamine, aspartate, and glutamate. We demonstrate that detached tobacco leaf or stalk curing has a different impact on the expression of asparagine synthetase genes and accumulation of asparagine. Additionally, we characterize the main asparagine synthetases involved in the production of asparagine during curing. The expression of ASN1 and ASN5 genes is upregulated during curing. The ASN1-RNAi and ASN5-RNAi tobacco plant lines display significant alterations in the accumulation of asparagine, glutamine, and aspartate relative to wild-type plants. These results support the idea that ASN1 and ASN5 are key regulators of asparagine metabolism during leaf curing.

Acrylamide in food: Progress in and prospects for genetic and agronomic solutions

Acrylamide is a processing contaminant and Group 2a carcinogen that was discovered in foodstuffs in 2002. Its presence in a range of popular foods has become one of the most difficult problems facing the food industry and its supply chain. Wheat, rye and potato products are major sources of dietary acrylamide, with biscuits, breakfast cereals, bread (particularly toasted), crispbread, batter, cakes, pies, French fries, crisps and snack products all affected. Here we briefly review the history of the issue, detection methods, the levels of acrylamide in popular foods and the risk that dietary acrylamide poses to human health. The pathways for acrylamide formation from free (non-protein) asparagine are described, including the role of reducing sugars such as glucose, fructose and maltose and the Maillard reaction. The evolving regulatory situation in the European Union and elsewhere is discussed, noting that food businesses and their suppliers must plan to comply not only with current regulations but with possible future regulatory scenarios. The main focus of the review is on the genetic and agronomic approaches being developed to reduce the acrylamide-forming potential of potatoes and cereals and these are described in detail, including variety selection, plant breeding, biotechnology and crop management. Obvious targets for genetic interventions include asparagine synthetase genes, and the asparagine synthetase gene families of different crop species are compared. Current knowledge on crop management best practice is described, including maintaining optimum storage conditions for potatoes and ensuring sulphur sufficiency and disease control for wheat.

Wheat drought tolerance in the field is predicted by amino acid responses to glasshouse-imposed drought

Water limits crop productivity, so selecting for a minimal yield gap in drier environments is critical to mitigate against climate change and land-use pressure. We investigated the responses of relative water content (RWC), stomatal conductance, chlorophyll content, and metabolites in flag leaves of commercial wheat (Triticum aestivum L.) cultivars to three drought treatments in the glasshouse and in field environments. We observed strong genetic associations between glasshouse-based RWC, metabolites, and yield gap-based drought tolerance (YDT; the ratio of yield in water-limited versus well-watered conditions) across 18 field environments spanning sites and seasons. Critically, RWC response to glasshouse drought was strongly associated with both YDT (r2=0.85, P<8E-6) and RWC under field drought (r2=0.77, P<0.05). Moreover, multiple regression analyses revealed that 98% of genetic YDT variance was explained by drought responses of four metabolites: serine, asparagine, methionine, and lysine (R2=0.98; P<0.01). Fitted coefficients suggested that, for given levels of serine and asparagine, stronger methionine and lysine accumulation was associated with higher YDT. Collectively, our results demonstrate that high-throughput, targeted metabolic phenotyping of glasshouse-grown plants may be an effective tool for selection of wheat cultivars with high field-derived YDT.

Polyamines - A New Metabolic Switch: Crosstalk With Networks Involving Senescence, Crop Improvement, and Mammalian Cancer Therapy

Polyamines (PAs) are low molecular weight organic cations comprising biogenic amines that play multiple roles in plant growth and senescence. PA metabolism was found to play a central role in metabolic and genetic reprogramming during dark-induced barley leaf senescence (DILS). Robust PA catabolism can impact the rate of senescence progression in plants. We opine that deciphering senescence-dependent polyamine-mediated multidirectional metabolic crosstalks is important to understand regulation and involvement of PAs in plant death and re-mobilization of nutrients during senescence. This will involve optimizing the use of PA biosynthesis inhibitors, robust transgenic approaches to modulate PA biosynthetic and catabolic genes, and developing novel germplasm enriched in pro- and anti-senescence traits to ensure sustained crop productivity. PA-mediated delay of senescence can extend the photosynthesis capacity, thereby increasing grain starch content in malting grains such as barley. On the other hand, accelerating the onset of senescence can lead to increases in mineral and nitrogen content in grains for animal feed. Unraveling the "polyamine metabolic switch" and delineating the roles of PAs in senescence should further our knowledge about autophagy mechanisms involved in plant senescence as well as mammalian systems. It is noteworthy that inhibitors of PA biosynthesis block cell viability in animal model systems (cell tumor lines) to control some cancers, in this instance, proliferative cancer cells were led toward cell death. Likewise, PA conjugates work as signal carriers for slow release of regulatory molecule nitric oxide in the targeted cells. Taken together, these and other outcomes provide examples for developing novel therapeutics for human health wellness as well as developing plant resistance/tolerance to stress stimuli.

Functional Research on Three Presumed Asparagine Synthetase Family Members in Poplar

Asparagine synthetase (AS), a key enzyme in plant nitrogen metabolism, plays an important role in plant nitrogen assimilation and distribution. Asparagine (Asn), the product of asparagine synthetase, is one of the main compounds responsible for organic nitrogen transport and storage in plants. In this study, we performed complementation experiments using an Asn-deficient Escherichia coli strain to demonstrate that three putative asparagine synthetase family members in poplar (Populussimonii× P.nigra) function in Asn synthesis. Quantitative real-time PCR revealed that the three members had high expression levels in different tissues of poplar and were regulated by exogenous nitrogen. PnAS1 and PnAS2 were also affected by diurnal rhythm. Long-term dark treatment resulted in a significant increase in PnAS1 and PnAS3 expression levels. Under long-term light conditions, however, PnAS2 expression decreased significantly in the intermediate region of leaves. Exogenous application of ammonium nitrogen, glutamine, and a glutamine synthetase inhibitor revealed that PnAS3 was more sensitive to exogenous glutamine, while PnAS1 and PnAS2 were more susceptible to exogenous ammonium nitrogen. Our results suggest that the various members of the PnAS gene family have distinct roles in different tissues and are regulated in different ways.

Plant-Mediated Interactions between Two Cereal Aphid Species: Promotion of Aphid Performance and Attraction of More Parasitoids by Infestation of Wheat with Phytotoxic Aphid Schizaphis graminum

Here, we investigated changes in physiological characteristics in wheat affected by phytotoxic-aphid Schizaphis graminum feeding and nonphytotoxic-aphid Sitobion avenae feeding. We also determined whether shared host-mediated interspecific interactions occur between S. graminum and S. avenae. S. graminum feeding but not S. avenae feeding induced significant chlorophyll loss and hydrogen peroxide accumulation in wheat. Gene-expression analysis and GC/MS metabonomic results indicated that S. graminum infestation induced stronger salicylic acid mediated defense responses than S. avenae did and significantly increased the contents of several amino acids in wheat leaves. Feeding on wheat preinfested with S. graminum significantly increased the reproduction of both aphids and shortened the development time of S. graminum. However, olfactometer bioassays showed that the parasitoid wasp Aphidius gifuensis was more attracted to the odors of S. graminum infested wheat than to those of control and S. avenae infested wheat. This study demonstrates that S. graminum and S. avenae feeding induced different defense responses and changes in plant nutritional quality. Additionally, plant-mediated interactions occurred between these cereal aphids.

Effects of different nitrogen fertilizers on two wheat cultivars: An integrated approach

Investigation of cultivated plant physiology grown under low energy input plays an important role to indicate their fitness to the new environmental conditions. The durum-wheat cultivars Creso and Dylan were tested to evaluate the growth, production, and proteomic and transcriptomic profiles of the crop under different synthetic and organic nitrogen fertilization regimes. In this work, a two-dimensional gel electrophoresis (2-DE) approach combined with liquid chromatography-mass spectrometry (LC-MS) was used to investigate the protein changes induced by the use of different nitrogen sources (hydrolysate of proteins 1 and 2, rhizovit, synthesis, leather) on wheat plants. Proteomic studies were integrated with qPCR analysis of genes related to glutamine synthetase/glutamine-2-oxoglutarate aminotransferase (GS-GOGAT) and tricarboxylic acid (TCA) metabolic pathways because most relevant for nitrogen-dependent plants growth. The proteomic analysis lead to the isolation of 23 spots that were able to distinguish the analyzed samples. These spots yielded the identification of 60 proteins involved in photosynthesis, glycolysis, and nitrogen metabolism. As an example, the quinone oxidoreductase-like protein and probable glutathione S-transferase GSTU proteins were identified in two spots that represents the most statistically significant ones in Dylan samples. Transcript analysis indicated that related genes exhibited different expression trends; the heat map also revealed the different behaviors of the hydrolysates of the proteins 1 and 2 nitrogen sources. The effects of nitrogenous fertilizers at the proteomic and agronomic levels revealed that plants fertilized with synthesis or rhizovit gave the best results concerning yield, whereas rhizovit and protein hydrolysates were most effective for proteins content in the grain (% of dry weight). Therefore, all parameters measured in this study indicated that different kinds of nitrogen fertilization used have a relevant impact on plant growth and production.

Physio-Genetic Dissection of Dark-Induced Leaf Senescence and Timing Its Reversal in Barley

Barley crop model was analyzed for early and late events during the dark-induced leaf senescence (DILS) as well as for deciphering critical time limit for reversal of the senescence process. Chlorophyll fluorescence vitality index Rfd was determined as the earliest parameter that correlated well with the cessation of photosynthesis prior to microautophagy symptoms, initiation of DNA degradation, and severalfold increase in the endonuclease BNUC1. DILS was found characterized by up-regulation of processes that enable recycling of degraded macromolecules and metabolites, including increased NH4 + remobilization, gluconeogenesis, glycolysis, and partial up-regulation of glyoxylate and tricarboxylate acid cycles. The most evident differences in gene medleys between DILS and developmental senescence included hormone-activated signaling pathways, lipid catabolic processes, carbohydrate metabolic processes, low-affinity ammonia remobilization, and RNA methylation. The mega-autophagy symptoms were apparent much later, specifically on day 10 of DILS, when disruption of organelles-nucleus and mitochondria -became evident. Also, during this latter-stage programmed cell death processes, namely, shrinking of the protoplast, tonoplast interruption, and vacuole breakdown, chromatin condensation, more DNA fragmentation, and disintegration of the cell membrane were prominent. Reversal of DILS by re-exposure of the plants from dark to light was possible until but not later than day 7 of dark exposure and was accompanied by regained photosynthesis, increase in chlorophyll, and reversal of Rfd, despite activation of macro-autophagy-related genes.

Leaf Amino Acid Supply Affects Photosynthetic and Plant Nitrogen Use Efficiency under Nitrogen Stress

The coordinated distribution of nitrogen to source leaves and sinks is essential for supporting leaf metabolism while also supplying sufficient nitrogen to seeds for development. This study aimed to understand how regulated amino acid allocation to leaves affects photosynthesis and overall plant nitrogen use efficiency in Arabidopsis (Arabidopsis thaliana) and how soil nitrogen availability influences these processes. Arabidopsis plants with a knockout of AAP2, encoding an amino acid permease involved in xylem-to-phloem transfer of root-derived amino acids, were grown in low-, moderate-, and high-nitrogen environments. We analyzed nitrogen allocation to shoot tissues, photosynthesis, and photosynthetic and plant nitrogen use efficiency in these knockout plants. Our results demonstrate that, independent of nitrogen conditions, aap2 plants allocate more nitrogen to leaves than wild-type plants. Increased leaf nitrogen supply positively affected chlorophyll and Rubisco levels, photosynthetic nitrogen use efficiency, and carbon assimilation and transport to sinks. The aap2 plants outperformed wild-type plants with respect to growth, seed yield and carbon storage pools, and nitrogen use efficiency in both high and deficient nitrogen environments. Overall, this study demonstrates that increasing nitrogen allocation to leaves represents an effective strategy for improving carbon fixation and photosynthetic nitrogen use efficiency. The results indicate that an optimized coordination of nitrogen and carbon partitioning processes is critical for high oilseed production in Arabidopsis, including in plants exposed to limiting nitrogen conditions.

Three cytosolic glutamine synthetase isoforms localized in different-order veins act together for N remobilization and seed filling in Arabidopsis

Glutamine synthetase (GS) is central for ammonium assimilation and consists of cytosolic (GS1) and chloroplastic (GS2) isoenzymes. During plant ageing, GS2 protein decreases due to chloroplast degradation, and GS1 activity increases to support glutamine biosynthesis and N remobilization from senescing leaves. The role of the different Arabidopsis GS1 isoforms in nitrogen remobilization was examined using 15N tracing experiments. Only the gln1;1-gln1;2-gln1;3 triple-mutation affecting the three GLN1;1, GLN1;2, and GLN1;3 genes significantly reduced N remobilization, total seed yield, individual seed weight, harvest index, and vegetative biomass. The triple-mutant accumulated a large amount of ammonium that could not be assimilated by GS1. Alternative ammonium assimilation through asparagine biosynthesis was increased and was related to higher ASN2 asparagine synthetase transcript levels. The GS2 transcript, protein, and activity levels were also increased to compensate for the lack of GS1-related glutamine biosynthesis. Localization of the different GLN1 genes showed that they were all expressed in the phloem companion cells but in veins of different order. Our results demonstrate that glutamine biosynthesis for N-remobilization occurs in veins of all orders (major and minor) in leaves, it is mainly catalysed by the three major GS1 isoforms (GLN1;1, GLN1;2, and GLN1;3), and it is alternatively supported by AS2 in the veins and GS2 in the mesophyll cells.

Nitrogen Supply and Leaf Age Affect the Expression of TaGS1 or TaGS2 Driven by a Constitutive Promoter in Transgenic Tobacco

Glutamine synthetase (GS) plays a key role in nitrogen metabolism. Here, two types of tobacco transformants, overexpressing Triticum aestivum GS1 (TaGS1) or GS2 (TaGS2), were analysed. Four independent transformed lines, GS1-TR1, GS1-TR2, GS2-TR1 and GS2-TR2, were used for the nitrogen treatment. Under nitrogen-sufficient conditions, the leaves of GS2-TR showed high accumulation of the TaGS2 transcript, while those of GS1-TR showed a low TaGS1 transcript levels. However, compared with nitrogen-sufficient conditions, the TaGS1 transcript level increased in the leaves under nitrogen starvation, but the TaGS2 transcript level decreased. In addition, the TaGS1 and TaGS2 transcript levels were highest in the middle leaves under nitrogen-sufficient and starvation conditions. These results show that nitrogen supply and leaf age regulate TaGS expression, even when they are driven by a super-promoter. Additionally, in regard to nitrogen metabolism level, the lower leaves of the GS1-TR exhibited lower NH₄⁺ and higher amino acid contents, while the upper leaves exhibited higher amino acid, soluble protein and chlorophyll contents. The leaves of the GS2-TR exhibited lower NH₄⁺ but higher amino acid, soluble protein and chlorophyll contents. Given the role that GS isoforms play in nitrogen metabolism, these data suggest that TaGS1 overexpression may improve nitrogen transport, and that TaGS2 overexpression may improve nitrogen assimilation under nitrogen stress.

Expression Analysis of Nitrogen Metabolism-Related Genes Reveals Differences in Adaptation to Low-Nitrogen Stress between Two Different Barley Cultivars at Seedling Stage

The excess use of nitrogen fertilizers causes many problems, including higher costs of crop production, lower nitrogen use efficiency, and environmental damage. Crop breeding for low-nitrogen tolerance, especially molecular breeding, has become the major route to solving these issues. Therefore, in crops such as barley (Hordeum vulgare L.), it is crucial to understand the mechanisms of low-nitrogen tolerance at the molecule level. In the present study, two barley cultivars, BI-04 (tolerant to low nitrogen) and BI-45 (sensitive to low nitrogen), were used for gene expression analysis under low-nitrogen stress, including 10 genes related to primary nitrogen metabolism. The results showed that the expressions of HvNIA2 (nitrite reductase), HvGS2 (chloroplastic glutamine synthetase), and HvGLU2 (ferredoxin-dependent glutamate synthase) were only induced in shoots of BI-04 under low-nitrogen stress, HvGLU2 was also only induced in roots of BI-04, and HvGS2 showed a rapid response to low-nitrogen stress in the roots of BI-04. The expression of HvASN1 (asparagine synthetase) was reduced in both cultivars, but it showed a lower reduction in the shoots of BI-04. In addition, gene expression and regulation differences in the shoots and roots were also compared between the barley cultivars. Taken together, the results indicated that the four above-mentioned genes might play important roles in low-nitrogen tolerance in barley.

Changes in nitrogen availability lead to a reprogramming of pyruvate metabolism

BACKGROUND

Low availability of nitrogen (N) severely affects plant growth at different levels, which can be reverted by the resupply of N. To unravel the critical steps in primary metabolism underlying the growth adjustment in response to changes in N availability, transcriptomic and comprehensive metabolite analyses were performed in barley using primary leaves at early and later stages of N deprivation, and after N resupply to N-deficient plants.

RESULT

N deficiency in leaves caused differential regulation of 1947 genes, mostly belonging to the functional classes photosynthesis, cell wall degradation, lipid degradation, amino acid degradation, transcription factors, phytohormone metabolism and receptor-like kinases. Interestingly, 62% of the genes responding to low N were regulated in the opposite direction after two days of N resupply. Reprogramming of gene transcription was linked to metabolic rearrangements and affected the metabolism of amino acids and sugars. The levels of major amino acids, including Glu, Asp, Ser, Gln, Gly, Thr, Ala, and Val, decreased during primary leaf age and, more pronounced, during low N-induced senescence, which was efficiently reverted after resupply of N. A significant decrease was observed for pyruvate and metabolites involved in the TCA cycle under low N, and this was reverted to initial levels after 5 days of N resupply. Correspondingly, transcript levels of genes coding for pyruvate kinase, pyruvate dehydrogenase, and pyruvate orthophosphate dikinase followed the same trend as related metabolites.

CONCLUSION

Our results show that upon N limitation a specific pathway for remobilization at the link between glycolysis and TCA cycle in barley is established that is at least partly regulated by a strict reprogramming of the gene coding for pyruvate orthophosphate dikinase. Further analysis of this pathway, its regulatory levels and biochemical changing of pyruvate metabolism enzymes in response to N availability is needed to determine the link between N status and primary metabolism.

Construction of a network describing asparagine metabolism in plants and its application to the identification of genes affecting asparagine metabolism in wheat under drought and nutritional stress

A detailed network describing asparagine metabolism in plants was constructed using published data from Arabidopsis (Arabidopsis thaliana) maize (Zea mays), wheat (Triticum aestivum), pea (Pisum sativum), soybean (Glycine max), lupin (Lupus albus), and other species, including animals. Asparagine synthesis and degradation is a major part of amino acid and nitrogen metabolism in plants. The complexity of its metabolism, including limiting and regulatory factors, was represented in a logical sequence in a pathway diagram built using yED graph editor software. The network was used with a Unique Network Identification Pipeline in the analysis of data from 18 publicly available transcriptomic data studies. This identified links between genes involved in asparagine metabolism in wheat roots under drought stress, wheat leaves under drought stress, and wheat leaves under conditions of sulfur and nitrogen deficiency. The network represents a powerful aid for interpreting the interactions not only between the genes in the pathway but also among enzymes, metabolites and smaller molecules. It provides a concise, clear understanding of the complexity of asparagine metabolism that could aid the interpretation of data relating to wider amino acid metabolism and other metabolic processes.

Improving Plant Nitrogen Use Efficiency through Alteration of Amino Acid Transport Processes

Improving the efficiency of nitrogen (N) uptake and utilization in plants could potentially increase crop yields while reducing N fertilization and, subsequently, environmental pollution. Within most plants, N is transported primarily as amino acids. In this study, pea (Pisum sativum) plants overexpressing AMINO ACID PERMEASE1 (AAP1) were used to determine if and how genetic manipulation of amino acid transport from source to sink affects plant N use efficiency. The modified plants were grown under low, moderate, or high N fertilization regimes. The results showed that, independent of the N nutrition, the engineered plants allocate more N via the vasculature to the shoot and seeds and produce more biomass and higher seed yields than wild-type plants. Dependent on the amount of N supplied, the AAP1-overexpressing plants displayed improved N uptake or utilization efficiency, or a combination of the two. They also showed significantly increased N use efficiency in N-deficient as well as in N-rich soils and, impressively, required half the amount of N to produce as many fruits and seeds as control plants. Together, these data support that engineering N allocation from source to sink presents an effective strategy to produce crop plants with improved productivity as well as N use efficiency in a range of N environments.

The role of glutamine synthetase isozymes in enhancing nitrogen use efficiency of N-efficient winter wheat

Glutamine synthetase (GS) isozymes play critical roles in nitrogen (N) metabolism. However, the exact relationship between GS and nitrogen use efficiency (NUE) remain unclear. We have selected and compared two wheat cultivars, YM49 and XN509, which were identified as the N-efficient and N-inefficient genotypes, respectively. In this study, agronomical, morphological, physiological and biochemical approaches were performed. The results showed that TaGS1 was high expressed post-anthesis, and TaGS2 was highly expressed pre-anthesis in N-efficient genotype compared to N-inefficient genotype. GS1 and GS2 isozymes were also separated by native-PAGE and found that the spatial and temporal distribution of GS isozymes, their expression of gene and protein subunits in source-sink-flow organs during development periods triggered the pool strength and influenced the N flow. According to the physiological role of GS isozymes, we illustrated four metabolic regulation points, by which acting collaboratively in different organs, accelerating the transport of nutrients to the grain. It suggested that the regulation of GS isozymes may promote flow strength and enhance NUE by a complex C-N metabolic mechanism. The relative activity or amount of GS1 and GS2 isozymes could be a potential marker to predict and select wheat genotypes with enhanced NUE.

Acceleration of leaf senescence is slowed down in transgenic barley plants deficient in the DNA/RNA-binding protein WHIRLY1

WHIRLY1 in barley was isolated as a potential regulator of the senescence-associated gene HvS40. In order to investigate whether the plastid-nucleus-located DNA/RNA-binding protein WHIRLY1 plays a role in regulation of leaf senescence, primary foliage leaves from transgenic barley plants with an RNAi-mediated knockdown of the WHIRLY1 gene were characterized by typical senescence parameters, namely pigment contents, function and composition of the photosynthetic apparatus, as well as expression of selected genes known to be either down- or up-regulated during leaf senescence. When the plants were grown at low light intensity, senescence progression was similar between wild-type and RNAi-W1 plants. Likewise, dark-induced senescence of detached leaves was not affected by reduction of WHIRLY1. When plants were grown at high light intensity, however, senescence was induced prematurely in wild-type plants but was delayed in RNAi-W1 plants. This result suggests that WHIRLY1 plays a role in light sensing and/or stress communication between chloroplasts and the nucleus.

Genomic, Biochemical, and Modeling Analyses of Asparagine Synthetases from Wheat

Asparagine synthetase activity in cereals has become an important issue with the discovery that free asparagine concentration determines the potential for formation of acrylamide, a probably carcinogenic processing contaminant, in baked cereal products. Asparagine synthetase catalyses the ATP-dependent transfer of the amino group of glutamine to a molecule of aspartate to generate glutamate and asparagine. Here, asparagine synthetase-encoding polymerase chain reaction (PCR) products were amplified from wheat (Triticum aestivum) cv. Spark cDNA. The encoded proteins were assigned the names TaASN1, TaASN2, and TaASN3 on the basis of comparisons with other wheat and cereal asparagine synthetases. Although very similar to each other they differed slightly in size, with molecular masses of 65.49, 65.06, and 66.24 kDa, respectively. Chromosomal positions and scaffold references were established for TaASN1, TaASN2, and TaASN3, and a fourth, more recently identified gene, TaASN4. TaASN1, TaASN2, and TaASN4 were all found to be single copy genes, located on chromosomes 5, 3, and 4, respectively, of each genome (A, B, and D), although variety Chinese Spring lacked a TaASN2 gene in the B genome. Two copies of TaASN3 were found on chromosome 1 of each genome, and these were given the names TaASN3.1 and TaASN3.2. The TaASN1, TaASN2, and TaASN3 PCR products were heterologously expressed in Escherichia coli (TaASN4 was not investigated in this part of the study). Western blot analysis identified two monoclonal antibodies that recognized the three proteins, but did not distinguish between them, despite being raised to epitopes SKKPRMIEVAAP and GGSNKPGVMNTV in the variable C-terminal regions of the proteins. The heterologously expressed TaASN1 and TaASN2 proteins were found to be active asparagine synthetases, producing asparagine and glutamate from glutamine and aspartate. The asparagine synthetase reaction was modeled using SNOOPY^® software and information from the BRENDA database to generate differential equations to describe the reaction stages, based on mass action kinetics. Experimental data from the reactions catalyzed by TaASN1 and TaASN2 were entered into the model using Copasi, enabling values to be determined for kinetic parameters. Both the reaction data and the modeling showed that the enzymes continued to produce glutamate even when the synthesis of asparagine had ceased due to a lack of aspartate.

Dissecting the Metabolic Role of Mitochondria during Developmental Leaf Senescence

The functions of mitochondria during leaf senescence, a type of programmed cell death aimed at the massive retrieval of nutrients from the senescing organ to the rest of the plant, remain elusive. Here, combining experimental and analytical approaches, we showed that mitochondrial integrity in Arabidopsis (Arabidopsis thaliana) is conserved until the latest stages of leaf senescence, while their number drops by 30%. Adenylate phosphorylation state assays and mitochondrial respiratory measurements indicated that the leaf energy status also is maintained during this time period. Furthermore, after establishing a curated list of genes coding for products targeted to mitochondria, we analyzed in isolation their transcript profiles, focusing on several key mitochondrial functions, such as the tricarboxylic acid cycle, mitochondrial electron transfer chain, iron-sulfur cluster biosynthesis, transporters, as well as catabolic pathways. In tandem with a metabolomic approach, our data indicated that mitochondrial metabolism was reorganized to support the selective catabolism of both amino acids and fatty acids. Such adjustments would ensure the replenishment of α-ketoglutarate and glutamate, which provide the carbon backbones for nitrogen remobilization. Glutamate, being the substrate of the strongly up-regulated cytosolic glutamine synthase, is likely to become a metabolically limiting factor in the latest stages of developmental leaf senescence. Finally, an evolutionary age analysis revealed that, while branched-chain amino acid and proline catabolism are very old mitochondrial functions particularly enriched at the latest stages of leaf senescence, auxin metabolism appears to be rather newly acquired. In summation, our work shows that, during developmental leaf senescence, mitochondria orchestrate catabolic processes by becoming increasingly central energy and metabolic hubs.

Changes in Free Amino Acid Concentration in Rye Grain in Response to Nitrogen and Sulfur Availability, and Expression Analysis of Genes Involved in Asparagine Metabolism

Free asparagine plays a central role in nitrogen storage and transport in many plant species due to its relatively high ratio of nitrogen to carbon. However, it is also a precursor for acrylamide, a Class 2a carcinogen that forms during high-temperature processing and cooking. The concentration of free asparagine was shown to increase by approximately 70% in rye grain in response to severe sulfur deficiency (F-test, p = 0.004), while the concentration of both free asparagine and free glutamine increased (by almost threefold and approximately 62%, respectively) in response to nitrogen application (F-test, p < 0.001 for free asparagine; p = 0.004 for free glutamine). There were also effects of nutrient supply on other free amino acids: The concentration of free proline, for example, showed a significant (F-test, p = 0.019) effect of nitrogen interacting with sulfur, with the highest concentration occurring when the plants were deprived of both nitrogen and sulfur. Polymerase chain reaction products for several genes involved in asparagine metabolism and its regulation were amplified from rye grain cDNA. These genes were asparagine synthetase-1 (ScASN1), glutamine synthetase-1 (ScGS1), potassium-dependent asparaginase (ScASP), aspartate kinase (ScASK), and general control non-derepressible-2 (ScGCN2). The expression of these genes and of a previously described sucrose non-fermenting-1-related protein kinase-1 gene (ScSnRK1) was analyzed in flag leaf and developing grain in response to nitrogen and sulfur supply, revealing a significant (F-test, p < 0.05) effect of nitrogen supply on ScGS1 expression in the grain at 21 days post-anthesis. There was also evidence of an effect of sulfur deficiency on ScASN1 gene expression. However, although this effect was large (almost 10-fold) it was only marginally statistically significant (F-test, 0.05 < p < 0.10). The study reinforced the conclusion that nutrient availability can have a profound impact on the concentrations of different free amino acids, something that is often overlooked by plant physiologists but which has important implications for flavor, color, and aroma development during cooking and processing, as well as the production of undesirable contaminants such as acrylamide.

Effect of post-silking drought on nitrogen partitioning and gene expression patterns of glutamine synthetase and asparagine synthetase in two maize (Zea mays L.) varieties

Glutamine synthetase (GS) and asparagine synthetase (AS) are proposed to have important function in plant nitrogen (N) remobilization, but their roles under drought stress are not well defined. In this study, the expression dynamics of GS and AS genes were analyzed in two maize varieties (ZD958 and NH101) in relation to post-silking drought stress induced nitrogen partitioning. ZD958 was a 'stay-green' variety with 5% nitrogen harvest index (NHI) lower than NH101. From silking to maturity, the amount of nitrogen remobilized from ear-leaves in ZD958 was evidently lower than NH101, and post-silking drought stress increased the nitrogen remobilization for both varieties. In ear-leaves, the expression of ZmGln1-3 was enhanced under drought stress. Three AS genes (ZmAS1, ZmAS2 and ZmAS3) were differentially regulated by post-silking drought treatment, of which the expression of ZmAS3 was stimulated at late stage of leaf senescence. In NH101, the expression level of ZmAS3 was markedly higher than that in ZD958. In developing grains, there were no significant differences in expression patterns of GS and AS genes between well water and drought treated plants. Drought stress altered maize N partitioning at the whole-plant level, and the up-regulation of GS and AS genes may contribute to the higher leaf nitrogen remobilization when exposed to drought treatments.

Decreased glycolate oxidase activity leads to altered carbon allocation and leaf senescence after a transfer from high CO2 to ambient air in Arabidopsis thaliana

Metabolic and physiological analyses of Arabidopsis thaliana glycolate oxidase (GOX) mutant leaves were performed to understand the development of the photorespiratory phenotype after transfer from high CO2 to air. We show that two Arabidopsis genes, GOX1 and GOX2, share a redundant photorespiratory role. Air-grown single gox1 and gox2 mutants grew normally and no significant differences in leaf metabolic levels and photosynthetic activities were found when compared with wild-type plants. To study the impact of a highly reduced GOX activity on plant metabolism, both GOX1 and GOX2 expression was knocked-down using an artificial miRNA strategy. Air-grown amiRgox1/2 plants with a residual 5% GOX activity exhibited a severe growth phenotype. When high-CO2-grown adult plants were transferred to air, the photosynthetic activity of amiRgox1/2 was rapidly reduced to 50% of control levels, and a high non-photochemical chlorophyll fluorescence quenching was maintained. (13)C-labeling revealed that daily assimilated carbon accumulated in glycolate, leading to reduced carbon allocation to sugars, organic acids, and amino acids. Such changes were not always mirrored in leaf total metabolite levels, since many soluble amino acids increased after transfer, while total soluble protein, RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase), and chlorophyll amounts decreased in amiRgox1/2 plants. The senescence marker, SAG12, was induced only in amiRgox1/2 rosettes after transfer to air. The expression of maize photorespiratory GOX in amiRgox1/2 abolished all observed phenotypes. The results indicate that the inhibition of the photorespiratory cycle negatively impacts photosynthesis, alters carbon allocation, and leads to early senescence in old rosette leaves.

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.

Food safety: Structure and expression of the asparagine synthetase gene family of wheat

Asparagine is an important nitrogen storage and transport molecule, but its accumulation as a free amino acid in crops has implications for food safety because free asparagine is a precursor for acrylamide formation during cooking and processing. Asparagine synthesis occurs by the amidation of aspartate, catalysed by asparagine synthetase, and this study concerned the expression of asparagine synthetase (TaASN) genes in wheat. The expression of three genes, TaASN1-3, was studied in different tissues and in response to nitrogen and sulphur supply. The expression of TaASN2 in the embryo and endosperm during mid to late grain development was the highest of any of the genes in any tissue. Both TaASN1 and TaASN2 increased in expression through grain development, and in the grain of field-grown plants during mid-development in response to sulphur deprivation. However, only TaASN1 was affected by nitrogen or sulphur supply in pot-based experiments, showing complex tissue-specific and developmentally-changing responses. A putative N-motif or GCN4-like regulatory motif was found in the promoter of TaASN1 genes from several cereal species. As the study was completed, a fourth gene, TaASN4, was identified from recently available genome data. Phylogenetic analysis showed that other cereal species have similar asparagine synthetase gene families to wheat.

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Three wheat asparagine synthetase genes show differential regulation.

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TaASN2 is highly expressed specifically in the grain.

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TaASN2 is a target for reducing the acrylamide-forming potential of wheat.

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A GCN4-like motif is present in the promoter of TaASN1 genes from multiple species.

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A fourth gene, TaASN4, is identifiable from wheat genome data.