Molecular analyses of the rice glutamate dehydrogenase gene family and their response to nitrogen and phosphorous deprivation

Legume-type glutamate dehydrogenase: Structure, activity, and inhibition studies

Glutamate dehydrogenases (GDHs) are key enzymes at the crossroads of N and C metabolism in plants. Legumes, whose N metabolism is particularly intricate, possess a unique type of GDH. This study presents an analysis of a legume-type GDH (isoform 2) from Medicago truncatula (MtGDH2). We measured MtGDH2 activity in both the Glu → 2-oxoglutarate (2OG) and 2OG → Glu reaction directions and obtained kinetic parameters for Glu, 2OG, NAD+, and NADH. Inhibition assays revealed that compounds possessing di- or tricarboxylates act as inhibitors of plant GDHs. Interestingly, 2,6-pyridinedicarboxylate (PYR) weakly inhibits MtGDH2 compared to Arabidopsis thaliana homologs. Furthermore, we explored tetrazole derivatives to discover 3-(1H-tetrazol-5-yl)benzoic acid (TBA) as an MtGDH2 inhibitor. The kinetic experiments are supported by six crystal structures, solved as: (i) unliganded enzyme, (ii) trapping the reaction intermediate 2-amino-2-hydroxyglutarate and NAD+, and also complexed with NAD+ and inhibitors such as (iii) citrate, (iv) PYR, (v) isophthalate, and (vi) TBA. The complex with TBA revealed a new mode of action that, in contrast to other inhibitors, prevents domain closure. This discovery points to TBA as a starting point for the development of novel GDH inhibitors to study the functions of GDH in plants and potentially boost biomass production.

Glutamate dehydrogenase in "Liverworld"-A study in selected species to explore a key enzyme of plant primary metabolism in Marchantiophyta

In plants, glutamate dehydrogenase (GDH) is an ubiquitous enzyme that catalyzes the reversible amination of 2-oxoglutarate in glutamate. It contributes to both the amino acid homeostasis and the management of intracellular ammonium, and it is regarded as a key player at the junction of carbon and nitrogen assimilation pathways. To date, information about the GDH of terrestrial plants refers to a very few species only. We focused on selected species belonging to the division Marchantiophyta, providing the first panoramic overview of biochemical and functional features of GDH in liverworts. Native electrophoretic analyses showed an isoenzymatic profile less complex than what was reported for Arabidposis thaliana and other angiosperms: the presence of a single isoform corresponding to an α-homohexamer, differently prone to thermal inactivation on a species- and organ-basis, was found. Sequence analysis conducted on amino acid sequences confirmed a high similarity of GDH in modern liverworts with the GDH2 protein of A. thaliana, strengthening the hypothesis that the duplication event that gave origin to GDH1-homolog gene from GDH2 occurred after the evolutionary bifurcation that separated bryophytes and tracheophytes. Experiments conducted on Marchantia polymorpha and Calypogeia fissa grown in vitro and compared to A. thaliana demonstrated through in gel activity detection and monodimensional Western Blot that the aminating activity of GDH resulted in strongly enhanced responses to ammonium excess in liverworts as well, even if at a different extent compared to Arabidopsis and other vascular species. The comparative analysis by bi-dimensional Western Blot suggested that the regulation of the enzyme could be, at least partially, untied from the protein post-translational pattern. Finally, immuno-electron microscopy revealed that the GDH enzyme localizes at the subcellular level in both mitochondria and chloroplasts of parenchyma and is specifically associated to the endomembrane system in liverworts.

Structural and functional studies of Arabidopsis thaliana glutamate dehydrogenase isoform 2 demonstrate enzyme dynamics and identify its calcium binding site

Glutamate dehydrogenase (GDH) is an enzyme at the crossroad of plant nitrogen and carbon metabolism. GDH catalyzes the conversion of 2-oxoglutarate into glutamate (2OG → Glu), utilizing ammonia as cosubstrate and NADH as coenzyme. The GDH reaction is reversible, meaning that the NAD+-dependent reaction (Glu → 2OG) releases ammonia. In Arabidopsis thaliana, three GDH isoforms exist, AtGDH1, AtGDH2, and AtGDH3. The subject of this work is AtGDH2. Previous reports have suggested that enzymes homologous to AtGDH2 contain a calcium-binding EF-hand motif located in the coenzyme binding domain. Here, we show that while AtGDH2 indeed does bind calcium, the binding occurs elsewhere and the region predicted to be the EF-hand motif has a completely different structure. As the true calcium binding site is > 20 Å away from the active site, it seems to play a structural, rather than catalytic role. We also performed comparative kinetic characterization of AtGDH1 and AtGDH2 using spectroscopic methods and isothermal titration calorimetry, to note that the isoenzymes generally exhibit similar behavior, with calcium having only a minor effect. However, the spatial and temporal changes in the gene expression profiles of the three AtGDH genes point to AtGDH2 as the most prevalent isoform.

The Key Role of Glutamate Dehydrogenase 2 (GDH2) in the Control of Kernel Production in Maize (Zea mays L.)

The agronomic potential of glutamate dehydrogenase 2 (GDH2) in maize kernel production was investigated by examining the impact of a mutation on the corresponding gene. Mu-insertion homozygous and heterozygous mutant lines lacking GDH2 activity were isolated and characterized at the biochemical, physiological and agronomic levels. In comparison to the wild type and to the homozygous ghd2 mutants, the heterozygous gdh2 mutant plants were characterized by a decrease in the root amino acid content, whereas in the leaves an increase of a number of phenolic compounds was observed. On average, a 30 to 40% increase in kernel yield was obtained only in the heterozygous gdh2 mutant lines when plants were grown in the field over two years. The importance of GDH2 in the control of plant productivity is discussed in relation to the physiological impact of the mutation on amino acid content, with primary carbon metabolism mostly occurring in the roots and secondary metabolism occurring in the leaves.

Unravelling Rubber Tree Growth by Integrating GWAS and Biological Network-Based Approaches

Hevea brasiliensis (rubber tree) is a large tree species of the Euphorbiaceae family with inestimable economic importance. Rubber tree breeding programs currently aim to improve growth and production, and the use of early genotype selection technologies can accelerate such processes, mainly with the incorporation of genomic tools, such as marker-assisted selection (MAS). However, few quantitative trait loci (QTLs) have been used successfully in MAS for complex characteristics. Recent research shows the efficiency of genome-wide association studies (GWAS) for locating QTL regions in different populations. In this way, the integration of GWAS, RNA-sequencing (RNA-Seq) methodologies, coexpression networks and enzyme networks can provide a better understanding of the molecular relationships involved in the definition of the phenotypes of interest, supplying research support for the development of appropriate genomic based strategies for breeding. In this context, this work presents the potential of using combined multiomics to decipher the mechanisms of genotype and phenotype associations involved in the growth of rubber trees. Using GWAS from a genotyping-by-sequencing (GBS) Hevea population, we were able to identify molecular markers in QTL regions with a main effect on rubber tree plant growth under constant water stress. The underlying genes were evaluated and incorporated into a gene coexpression network modelled with an assembled RNA-Seq-based transcriptome of the species, where novel gene relationships were estimated and evaluated through in silico methodologies, including an estimated enzymatic network. From all these analyses, we were able to estimate not only the main genes involved in defining the phenotype but also the interactions between a core of genes related to rubber tree growth at the transcriptional and translational levels. This work was the first to integrate multiomics analysis into the in-depth investigation of rubber tree plant growth, producing useful data for future genetic studies in the species and enhancing the efficiency of the species improvement programs.

Glutamate dehydrogenase isogenes CsGDHs cooperate with glutamine synthetase isogenes CsGSs to assimilate ammonium in tea plant (Camellia sinensis L.)

Glutamate dehydrogenase (GDH) is a central enzyme in nitrogen metabolism, assimilating ammonia into glutamine or deaminating glutamate into α-oxoglutarate. Tea (Camellia sinensis L.) plants assimilate ammonium efficiently, but the role of CsGDH in ammonium assimilation remains unclear. We confirmed that tea has three GDH isogenes: CsGDH1-3. Bioinformatic analysis showed that CsGDH1 encodes the β-GDH subunit, CsGDH2/3 encode the α-GDH subunit, and their proteins all feature an NADH-specific motif. CsGDH1 is mainly expressed in mature leaves and roots, CsGDH3 is mainly expressed in new shoots and roots, and CsGDH2 has the highest expression level in flowers compared to the other five tissues. Expression patterns of CsGDHs and glutamine synthetase isogenes (CsGSs) under different ammonium concentrations suggested that CsGDHs cooperate with CsGSs to assimilate ammonium, especially under high ammonium conditions. Inhibition of GS and its isogenes resulted in significant induction of CsGDH3 in roots and CsGDH2 in leaves, indicating their potential roles in ammonium assimilation. Moreover, CsGDHs transcripts were highly abundant in chlorotic tea leaves, in constrast to those of CsGSs, suggesting that CsGDHs play a vital role in ammonium assimilation in chlorotic tea mutant. Altogether, our circumstantial evidence that CsGDHs cooperate with CsGSs in ammonium assimilation provides a basis for unveiling their functions in tea plants.

Heterologous expression of fungal AcGDH alleviates ammonium toxicity and suppresses photorespiration, thereby improving drought tolerance in rice

Drought stress can significantly affect plant growth and agricultural productivity. Thus, it is essential to explore and identify the optimal genes for the improvement of crop drought tolerance. Here, a fungal NADP(H)-dependent glutamate dehydrogenase gene (AcGDH) was isolated from Aspergillus candidus, and heterologously expressed in rice. AcGDH has a high affinity for NH₄⁺ and increases the ammonium assimilation in rice. AcGDH transgenic plants exhibited a tolerance to drought and alkali stresses, and their photorespiration was significantly suppressed. Our findings demonstrate that AcGDH alleviates ammonium toxicity and suppresses photorespiration by assimilating excess NH₄⁺ and disturbing the delicate balance of carbon and nitrogen metabolism, thereby improving drought tolerance in rice. Moreover, AcGDH not only improved drought tolerance at the seedling stage but also increased the grain yield under drought stress. Thus, AcGDH is a promising candidate gene for maintaining rice grain yield, and offers an opportunity for improving crop yield under drought stress.

How to easily detect plant NADH-glutamate dehydrogenase (GDH) activity? A simple and reliable in planta procedure suitable for tissues, extracts and heterologous microbial systems

Plant NADH glutamate dehydrogenase (GDH) is an intriguing enzyme, since it is involved in different metabolic processes owing to its reversible (anabolic/catabolic) activity and due to the oligomeric nature of the enzyme, that gives rise to several isoforms. The complexity of GDH isoenzymes pattern and the variability of the spatial and temporal localization of the different isoforms have limited our comprehension of the physiological role of GDH in plants. Genetics, immunological, and biochemical approaches have been used until now in order to shed light on the regulatory mechanism that control GDH expression in different plant systems and environmental conditions. We describe here the validation of a simple in planta GDH activity staining procedure, providing evidence that it might be used, with different purposes, to determine GDH expression in plant organs, tissues, extracts and also heterologous systems.

Assimilation of exogenous cyanide cross talk in Oryza sativa L. to the key nodes in nitrogen metabolism

Exogenous cyanide (CN^-) effects on nitrogen (N) uptake, transport, and assimilation in rice seedlings were investigated at the biochemical and molecular levels. Seedlings were treated with either a 2-d or 4-d supply of potassium cyanide (KCN) in the nutrient solution containing nitrate (NO₃^-) or ammonium (NH₄⁺). Although a KCN-induced increase was recorded in the activity of β-cyanoalanine synthase (β-CAS) in rice tissues of both NH₄⁺-fed and NO₃^--fed seedlings, the former showed a significantly greater assimilation rate for CN^- than the latter. The addition of KCN decreased NO₃^- uptake and assimilation, whereas a negligible impact was observed in NH₄⁺ treatments. Enzymatic assays showed a marked activities enhancement of glutamine synthetase (GS), glutamate synthase (GOGAT), and glutamate dehydrogenase (GDH) in NH₄⁺-fed seedlings after KCN exposure. Similarly, the rises occurring in nitrate reductase (NR) and GDH activity in NO₃^--fed seedlings were also detected after 2-d exposure to KCN, whereas a significant reduction of GS and GOGAT activities was determined. The results suggest that although exogenous KCN at moderate or high concentrations caused repressively effects on biomass growth of both NH₄⁺-fed and NO₃^--fed rice seedlings, the nontoxic concentration of KCN supplied can serve as a supplemental N source in plant nutrition and N metabolism.

Structural Studies of Glutamate Dehydrogenase (Isoform 1) From Arabidopsis thaliana, an Important Enzyme at the Branch-Point Between Carbon and Nitrogen Metabolism

Glutamate dehydrogenase (GDH) releases ammonia in a reversible NAD(P)⁺-dependent oxidative deamination of glutamate that yields 2-oxoglutarate (2OG). In current perception, GDH contributes to Glu homeostasis and plays a significant role at the junction of carbon and nitrogen assimilation pathways. GDHs are members of a superfamily of ELFV (Glu/Leu/Phe/Val) amino acid dehydrogenases and are subdivided into three subclasses, based on coenzyme specificity: NAD⁺-specific, NAD⁺/NADP⁺ dual-specific, and NADP⁺-specific. We determined in this work that the mitochondrial AtGDH1 isozyme from A. thaliana is NAD⁺-specific. Altogether, A. thaliana expresses three GDH isozymes (AtGDH1-3) targeted to mitochondria, of which AtGDH2 has an extra EF-hand motif and is stimulated by calcium. Our enzymatic assays of AtGDH1 established that its sensitivity to calcium is negligible. In vivo the AtGDH1-3 enzymes form homo- and heterohexamers of varied composition. We solved the crystal structure of recombinant AtGDH1 in the apo-form and in complex with NAD⁺ at 2.59 and 2.03 Å resolution, respectively. We demonstrate also that both in the apo form and in 1:1 complex with NAD⁺, it forms D ₃-symmetric homohexamers. A subunit of AtGDH1 consists of domain I, which is involved in hexamer formation and substrate binding, and of domain II which binds coenzyme. Most of the subunits in our crystal structures, including those in NAD⁺ complex, are in open conformation, with domain II forming a large (albeit variable) angle with domain I. One of the subunits of the AtGDH1-NAD⁺ hexamer contains a serendipitous 2OG molecule in the active site, causing a dramatic (∼25°) closure of the domains. We provide convincing evidence that the N-terminal peptide preceding domain I is a mitochondrial targeting signal, with a predicted cleavage site for mitochondrial processing peptidase (MPP) at Leu17-Leu18 that is followed by an unexpected potassium coordination site (Ser27, Ile30). We also identified several MPD [(+/-)-2-methyl-2,4-pentanediol] binding sites with conserved sequence. Although AtGDH1 is insensitive to MPD in our assays, the observation of druggable sites opens a potential for non-competitive herbicide design.

Identification of novel OsCML16 target proteins and differential expression analysis under abiotic stresses in rice

Calmodulin-like proteins (CMLs) have been shown to play key regulatory roles in calcium signaling in plants. However, few bona-fide CMLs binding proteins have been characterized in rice, a monocot model plant. Here, through large-scale screening of a yeast-two hybrid (Y2H) cDNA library with OsCML16 as a bait, six new putative interacting partners of OsCML16 were discovered and confirmed by both pairwise Y2H and bimolecular fluorescence complementation (BiFC) assays. Interestingly, the in vitro peptide-binding assays manifested that OsERD2 could bind both OsCaM1 and OsCML16 whereas other five target proteins could specifically bind OsCML16 but not OsCaM1. Furthermore, Ca²⁺ and TFP, a calmodulin (CaM) antagonist, were involved in the ABA-induced transcription of OsCML16 and its target genes, and they were also obviously induced by cold, drought, and salt stresses. Taken together, our new findings have provided the basis for the novel signaling pathways of OsCML16 in the abiotic stress response in rice.

Glutamate dehydrogenase is essential in the acclimation of Virgilia divaricata, a legume indigenous to the nutrient-poor Mediterranean-type ecosystems of the Cape Fynbos

Glutamate dehydrogenase (NAD(H)- GDH, EC 1.4.1.2) is an important enzyme in nitrogen (N) metabolism. It serves as a link between C and N metabolism, in its role of assimilating ammonia into glutamine or deaminating glutamate into 2-oxoglutarate and ammonia. GDH may also have a key in the N assimilation of legumes growing in P-poor soils. Virgilia divaricata is such a legume, growing in the nutrient limited soils of the mediterranean-type Cape fynbos ecosystem. In order to understand the role of GDH in the nitrogen nutrition of V. divaricata, the aim of this study was to identify the GDH gene transcripts, their relative expressions and enzyme activity in P-stressed roots and nodules during N metabolism. During P deficiency there was a reduction in total plant biomass as well as total plant P concentration. The analysis of the GDH cDNA sequences in V. divaricata revealed the presence of GHD1 and GHD2 subunits, these corresponding to the GDH1, GDH-B and GDH3 genes of legumes and non-legume plants. The relative expression of GDH1 and GDH2 genes in the roots and nodules, indicates that two the subunits were differently regulated depending on the organ type, rather than P supply. Although both transcripts appeared to be ubiquitously expressed in the roots and nodules, the GDH2 transcript evidently predominated over those of GDH1. Furthermore, the higher expression of both GDH transcripts in the roots than nodules, suggests that roots are more reliant on on GDH in P-poor soils, than nodules. With regards to GHD activity, both aminating and deaminating GDH activities were differently affected by P deficiency in roots and nodules. This may function to assimilate N and regulate internal C and N in the roots and nodules. The variation in GDH1 and GDH2 transcript expression and GDH enzyme activities, indicate that the enzyme may be regulated by post-translational modification, instead of by gene expression during P deficiency in V. divaricata.

Generation of semi-dwarf rice (Oryza sativa L.) lines by CRISPR/Cas9-directed mutagenesis of OsGA20ox2 and proteomic analysis of unveiled changes caused by mutations

Plant height (PH) is one of the most important agronomic traits of rice, as it directly affects the yield potential and lodging resistance. Here, semi-dwarf mutant lines were developed through CRISPR/Cas9-based editing of OsGA20ox2 in an indica rice cultivar. Total 24 independent lines were obtained in T₀ generation with the mean mutation rate of 73.5% including biallelic (29.16%), homozygous (47.91%) and heterozygous (16.66%) mutations, and 16 T-DNA-free lines (50%) were obtained in T₁ generation without off-target effect in four most likely sites. Mutations resulted in a changed amino acid sequence of mutant plants and reduced gibberellins (GA) level and PH (22.2%), flag leaf length (FLL) and increased yield per plant (YPP) (6.0%), while there was no effect on other agronomic traits. Mutants restored their PH to normal by exogenous GA₃ treatment. The expression of the OsGA20ox2 gene was significantly suppressed in mutant plants, while the expression level was not affected for other GA biosynthesis (OsGA2ox3 and OsGA3ox2) and signaling (D1, GIDI and SLR1) genes. The mutant lines showed decreased cell length and width, abnormal cell elongation, while increased cell numbers in the second internode sections at mature stage. Total 30 protein spots were exercised, and 24 proteins were identified, and results showed that OsGA20ox2 editing altered protein expression. Five proteins including, glyceraldehyde-3-phosphate dehydrogenase, putative ATP synthase, fructose-bisphosphate aldolase 1, S-adenosyl methionine synthetase 1 and gibberellin 20 oxidase 2, were downregulated in dwarf mutant lines which may affect the plant growth. Collectively, our results provide the insights into the role of OsGA20ox2 in PH and confirmed that CRISPR-Cas9 is a powerful tool to understand the gene functions.

Overexpression of an NADP(H)-dependent glutamate dehydrogenase gene, TrGDH, from Trichurus improves nitrogen assimilation, growth status and grain weight per plant in rice

As glutamate dehydrogenases (GDHs) of microorganisms usually have higher affinity for NH₄ ⁺ than do those of higher plants, it is expected that ectopic expression of these GDHs can improve nitrogen assimilation in higher plants. Here, a novel NADP(H)-GDH gene (TrGDH) was isolated from the fungus Trichurus and introduced into rice (Oryza sativa L.). Investigation of kinetic properties in vitro showed that, compared with the rice GDH (OsGDH4), TrGDH exhibited higher affinity for NH₄ ⁺ (K _m = 1.48 ± 0.11 mM). Measurements of the NH₄ ⁺ assimilation rate demonstrated that the NADP(H)-GDH activities of TrGDH transgenic lines were significantly higher than those of the controls. Hydroponic experiments revealed that the fresh weight, dry weight and nitrogen content significantly increased in the TrGDH transgenic lines. Field trials further demonstrated that the number of effective panicles, 1,000-grain weight and grain weight per plant of the transgenic lines were significantly higher than those of the controls, especially under low-nitrogen levels. Moreover, glutelin and prolamine were found to be markedly increased in seeds from the transgenic rice plants. These results sufficiently confirm that overexpression of TrGDH in rice can improve the growth status and grain weight per plant by enhancing nitrogen assimilation. Thus, TrGDH is a promising candidate gene for maintaining yields in crop plants via genetic engineering.

Interaction of cyanate uptake by rice seedlings with nitrate assimilation: gene expression analysis

Cyanate (CNO^-) has been produced in the environment through either natural or anthropogenic sources. However, due to industrialization, it has been led more over-loads. In this study, interaction of CNO^- uptake by rice seedlings with nitrate assimilation was investigated using gene expression analysis after an acute phytotoxicity assay. Our results showed that CNO^- exposure caused inhibition on relative growth rates of plants. CNO^- analysis demonstrated that rice seedlings had higher potential for CNO^- uptake and the removal rates showed a zero-order kinetic. PCR analysis exposed that OsCYN transcript was not significantly induced by CNO^- treatments in rice tissues and CNO^- exposure also repressed gene expression of the collaborative enzyme carbonic anhydrase (CA), suggesting that assimilation of CNO^- initiated by the enzyme cyanase (CYN) in rice seedlings was an enzyme-limitation reaction. Gene expression of other enzymes involved in nitrate metabolism was tissue-specific under CNO^- exposure, suggesting that rice seedlings were able to trigger its intrinsic regulative and responsive mechanisms to cope up with uneven N conditions. Significant upregulation of three OsGDH isogenes, except for OsGDH1 in roots, was detected in both rice materials with enhancing CNO^- concentrations, suggesting that GDH may play a primary role to maintain the balance of C and N in plants under CNO^- exposure. In conclusion, because the innate pool of CYN activity was non-sufficient to degrade exogenous CNO^- by rice seedlings, CNO-derived ammonium only can serve as a supporting N source to support growth of rice seedling under non-effective doses of CNO^- exposure.

The Glutamate Dehydrogenase Pathway and Its Roles in Cell and Tissue Biology in Health and Disease

Glutamate dehydrogenase (GDH) is a hexameric enzyme that catalyzes the reversible conversion of glutamate to α-ketoglutarate and ammonia while reducing NAD(P)⁺ to NAD(P)H. It is found in all living organisms serving both catabolic and anabolic reactions. In mammalian tissues, oxidative deamination of glutamate via GDH generates α-ketoglutarate, which is metabolized by the Krebs cycle, leading to the synthesis of ATP. In addition, the GDH pathway is linked to diverse cellular processes, including ammonia metabolism, acid-base equilibrium, redox homeostasis (via formation of fumarate), lipid biosynthesis (via oxidative generation of citrate), and lactate production. While most mammals possess a single GDH1 protein (hGDH1 in the human) that is highly expressed in the liver, humans and other primates have acquired, via duplication, an hGDH2 isoenzyme with distinct functional properties and tissue expression profile. The novel hGDH2 underwent rapid evolutionary adaptation, acquiring unique properties that enable enhanced enzyme function under conditions inhibitory to its ancestor hGDH1. These are thought to provide a biological advantage to humans with hGDH2 evolution occurring concomitantly with human brain development. hGDH2 is co-expressed with hGDH1 in human brain, kidney, testis and steroidogenic organs, but not in the liver. In human cerebral cortex, hGDH1 and hGDH2 are expressed in astrocytes, the cells responsible for removing and metabolizing transmitter glutamate, and for supplying neurons with glutamine and lactate. In human testis, hGDH2 (but not hGDH1) is densely expressed in the Sertoli cells, known to provide the spermatids with lactate and other nutrients. In steroid producing cells, hGDH1/2 is thought to generate reducing equivalents (NADPH) in the mitochondria for the biosynthesis of steroidal hormones. Lastly, up-regulation of hGDH1/2 expression occurs in cancer, permitting neoplastic cells to utilize glutamine/glutamate for their growth. In addition, deregulation of hGDH1/2 is implicated in the pathogenesis of several human disorders.

Increase of Fungal Pathogenicity and Role of Plant Glutamine in Nitrogen-Induced Susceptibility (NIS) To Rice Blast

Highlight  Modifications in glutamine synthetase OsGS1-2 expression and fungal pathogenicity underlie nitrogen-induced susceptibility to rice blast. Understanding why nitrogen fertilization increase the impact of many plant diseases is of major importance. The interaction between Magnaporthe oryzae and rice was used as a model for analyzing the molecular mechanisms underlying Nitrogen-Induced Susceptibility (NIS). We show that our experimental system in which nitrogen supply strongly affects rice blast susceptibility only slightly affects plant growth. In order to get insights into the mechanisms of NIS, we conducted a dual RNA-seq experiment on rice infected tissues under two nitrogen fertilization regimes. On the one hand, we show that enhanced susceptibility was visible despite an over-induction of defense gene expression by infection under high nitrogen regime. On the other hand, the fungus expressed to high levels effectors and pathogenicity-related genes in plants under high nitrogen regime. We propose that in plants supplied with elevated nitrogen fertilization, the observed enhanced induction of plant defense is over-passed by an increase in the expression of the fungal pathogenicity program, thus leading to enhanced susceptibility. Moreover, some rice genes implicated in nitrogen recycling were highly induced during NIS. We further demonstrate that the OsGS1-2 glutamine synthetase gene enhances plant resistance to M. oryzae and abolishes NIS and pinpoint glutamine as a potential key nutrient during NIS.

Laser microdissection-based gene expression analysis in the aleurone layer and starchy endosperm of developing rice caryopses in the early storage phase

BACKGROUND

Rice endosperm is composed of aleurone cells in the outermost layers and starchy endosperm cells in the inner part. The aleurone layer accumulates lipids, whereas starchy endosperm mainly accumulates starch. During the ripening stage, the starch accumulation rate is known to be asynchronous, depending on the position of the starchy endosperm. Different physiological and molecular mechanisms are hypothesized to underlie the qualitative and quantitative differences in storage products among developing rice endosperm tissues.

RESULTS

Target cells in aleurone layers and starchy endosperm were isolated by laser microdissection (LM), and RNAs were extracted from each endosperm tissue in the early storage phase. Genes important for carbohydrate metabolism in developing endosperm were analyzed using qRT-PCR, and some of the genes showed specific localization in either tissue of the endosperm. Aleurone layer-specific gene expression of a sucrose transporter, OsSUT1, suggested that the gene functions in sucrose uptake into aleurone cells. The expression levels of ADP-glucose pyrophosphorylase (AGPL2 and AGPS2b) in each endosperm tissue spatially corresponded to the distribution of starch granules differentially observed among endosperm tissues. By contrast, expressions of genes for sucrose cleavage-hexokinase, UDP-glucose pyrophosphorylase, and phosphoglucomutase-were observed in all endosperm tissues tested. Aleurone cells predominantly expressed mRNAs for the TCA cycle and oxidative phosphorylation. This finding was supported by the presence of oxygen (8 % concentration) and large numbers of mitochondria in the aleurone layers. In contrast, oxygen was absent and only a few mitochondria were observed in the starchy endosperm. Genes for carbon fixation and the GS/GOGAT cycle were expressed highly in aleurone cells compared to starchy endosperm.

CONCLUSIONS

The transcript level of AGPL2 and AGPS2b encoding ADP-glucose pyrophosphorylase appears to regulate the asynchronous development of starch granules in developing caryopses. Aleurone cells appear to generate, at least partially, ATP via aerobic respiration as observed from specific expression of identified genes and large numbers of mitochondria. The LM-based expression analysis and physiological experiments provide insight into the molecular basis of the spatial and nutritional differences between rice aleurone cells and starchy endosperm cells.

Enhanced expression of OsSPL14 gene and its association with yield components in rice (Oryza sativa) under low nitrogen conditions

Nitrogen use efficiency (NUE) in rice crop is the need of the hour for reduction of nitrous oxide emission resulting from excess nitrogen (N) fertilizer application and also in reduction of cost of cultivation. Ten rice genotypes were grown under low and recommended dose of N application and characterized in terms of parameters related to yield, yield related components and NUE indicators. Wide genetic variability under low N conditions was observed with significant variation for 15 yield related parameters in interactions of genotypes and treatment. Limitation of N has led to the decrease of all yield and yield related parameters, but for grain filling % and 1000 grain weight. Two genotypes, Rasi and Varadhan have shown minimum differences between low and recommended N conditions. Correlation analysis of various yield components showed the importance of the secondary branches for the total grains under low N. Expression analysis of OsSPL14 (LOC_Os08g39890) gene reported to be associated with increased panicle branching and higher grain yield through real time PCR in leaf and three stages of panicle has shown differential temporal expression and its association with yield and yield related components across the genotypes. The expression of OsSPL14 at panicle stage 3, has shown correlation (P<0.05) with N% in grain. Since OsSPL14 is a functional transcription activator, its association of expression in leaf and three panicle stages with yield components as observed in the present study suggests the role of nitrogen metabolism related genes in plant growth and development and its conversion into yield components in rice.

Silicon induces resistance to the brown spot fungus Cochliobolus miyabeanus by preventing the pathogen from hijacking the rice ethylene pathway

Although numerous studies have shown the ability of silicon (Si) to mitigate a wide variety of abiotic and biotic stresses, relatively little is known about the underlying mechanism(s). Here, we have investigated the role of hormone defense pathways in Si-induced resistance to the rice brown spot fungus Cochliobolus miyabeanus. To delineate the involvement of multiple hormone pathways, a multidisciplinary approach was pursued, combining exogenous hormone applications, pharmacological inhibitor experiments, time-resolved hormone measurements, and bioassays with hormone-deficient and/or -insensitive mutant lines. Contrary to other types of induced resistance, we found Si-induced brown spot resistance to function independently of the classic immune hormones salicylic acid and jasmonic acid. Our data also rule out a major role of the abscisic acid (ABA) and cytokinin pathways, but suggest that Si mounts resistance to C. miyabeanus by preventing the fungus from hijacking the rice ethylene (ET) machinery. Interestingly, rather than suppressing rice ET signaling per se, Si probably interferes with the production and/or action of fungal ET. Together our findings favor a scenario whereby Si induces brown spot resistance by disarming fungal ET and argue that impairment of pathogen virulence factors is a core resistance mechanism underpinning Si-induced plant immunity.

Plant exomics: concepts, applications and methodologies in crop improvement

Molecular breeding has a crucial role in improvement of crops. Conventional breeding techniques have failed to ameliorate food production. Next generation sequencing has established new concepts of molecular breeding. Exome sequencing has proven to be a significant tool for assessing natural evolution in plants, studying host pathogen interactions and betterment of crop production as exons assist in interpretation of allelic variation with respect to their phenotype. This review covers the platforms for exome sequencing, next generation sequencing technologies that have revolutionized exome sequencing and led toward development of third generation sequencing. Also discussed in this review are the uses of these sequencing technologies to improve wheat, rice and cotton yield and how these technologies are used in exploring the biodiversity of crops, providing better understanding of plant-host pathogen interaction and assessing the process of natural evolution in crops and it also covers how exome sequencing identifies the gene pool involved in symbiotic and other co-existential systems. Furthermore, we conclude how integration of other methodologies including whole genome sequencing, proteomics, transcriptomics and metabolomics with plant exomics covers the areas which are left untouched with exomics alone and in the end how these integration will transform the future of crops.

Comprehensive Expression Profiling of Rice Tetraspanin Genes Reveals Diverse Roles During Development and Abiotic Stress

Tetraspanin family is comprised of evolutionarily conserved integral membrane proteins. The incredible ability of tetraspanins to form 'micro domain complexes' and their preferential targeting to membranes emphasizes their active association with signal recognition and communication with neighboring cells, thus acting as key modulators of signaling cascades. In animals, tetraspanins are associated with multitude of cellular processes. Unlike animals, the biological relevance of tetraspanins in plants has not been well investigated. In Arabidopsis tetraspanins are known to contribute in important plant development processes such as leaf morphogenesis, root, and floral organ formation. In the present study we investigated the genomic organization, chromosomal distribution, phylogeny and domain structure of 15 rice tetraspanin proteins (OsTETs). OsTET proteins had similar domain structure and signature 'GCCK/R' motif as reported in Arabidopsis. Comprehensive expression profiling of OsTET genes suggested their possible involvement during rice development. While OsTET9 and 10 accumulated predominantly in flowers, OsTET5, 8, and 12 were preferentially expressed in root tissues. Noticeably, seven OsTETs exhibited more than twofold up regulation at early stages of flag leaf senescence in rice. Furthermore, several OsTETs were differentially regulated in rice seedlings exposed to abiotic stresses, exogenous treatment of hormones and nutrient deprivation. Transient subcellular localization studies of eight OsTET proteins in tobacco epidermal cells showed that these proteins localized in plasma membrane. The present study provides valuable insights into the possible roles of tetraspanins in regulating development and defining response to abiotic stresses in rice. Targeted proteomic studies would be useful in identification of their interacting partners under different conditions and ultimately their biological function in plants.

Glutamate dehydrogenase isoenzyme 3 (GDH3) of Arabidopsis thaliana is regulated by a combined effect of nitrogen and cytokinin

In higher plants, NAD(H)-glutamate dehydrogenase (GDH; EC 1.4.1.2) is an abundant enzyme that exists in different isoenzymic forms. In Arabidopsis thaliana, three genes (Gdh1, Gdh2 and Gdh3) encode three different GDH subunits (β, α and γ) that randomly associate to form a complex array of homo- and heterohexamers. The modification of the GDH isoenzyme pattern and its regulation was studied during the development of A. thaliana in the gdh1, gdh2 single mutants and the gdh1-2 double mutant, with particular emphasis on GDH3. Investigations showed that the GDH3 isoenzyme could not be detected in closely related Arabidopsis species. The induction and regulation of GDH3 activity in the leaves and roots was investigated following nitrogen deprivation in the presence or absence of sucrose or kinetin. These experiments indicate that GDH3 is likely to play an important role during senescence and nutrient remobilization.

Gene expression studies for the analysis of domoic acid production in the marine diatom Pseudo-nitzschia multiseries

BACKGROUND

Pseudo-nitzschia multiseries Hasle (Hasle) (Ps-n) is distinctive among the ecologically important marine diatoms because it produces the neurotoxin domoic acid. Although the biology of Ps-n has been investigated intensely, the characterization of the genes and biochemical pathways leading to domoic acid biosynthesis has been limited. To identify transcripts whose levels correlate with domoic acid production, we analyzed Ps-n under conditions of high and low domoic acid production by cDNA microarray technology and reverse-transcription quantitative PCR (RT-qPCR) methods. Our goals included identifying and validating robust reference genes for Ps-n RNA expression analysis under these conditions.

RESULTS

Through microarray analysis of exponential- and stationary-phase cultures with low and high domoic acid production, respectively, we identified candidate reference genes whose transcripts did not vary across conditions. We tested eleven potential reference genes for stability using RT-qPCR and GeNorm analyses. Our results indicated that transcripts encoding JmjC, dynein, and histone H3 proteins were the most suitable for normalization of expression data under conditions of silicon-limitation, in late-exponential through stationary phase. The microarray studies identified a number of genes that were up- and down-regulated under toxin-producing conditions. RT-qPCR analysis, using the validated controls, confirmed the up-regulation of transcripts predicted to encode a cycloisomerase, an SLC6 transporter, phosphoenolpyruvate carboxykinase, glutamate dehydrogenase, a small heat shock protein, and an aldo-keto reductase, as well as the down-regulation of a transcript encoding a fucoxanthin-chlorophyll a-c binding protein, under these conditions.

CONCLUSION

Our results provide a strong basis for further studies of RNA expression levels in Ps-n, which will contribute to our understanding of genes involved in the production and release of domoic acid, an important neurotoxin that affects human health as well as ecosystem function.

Further insights into the isoenzyme composition and activity of glutamate dehydrogenase in Arabidopsis thaliana

Following the discovery that in Arabidopsis, a third isoenzyme of NADH-dependent glutamate dehydrogenase (GDH) is expressed in the mitochondria of the root companion cells, we have re-examined the GDH isoenzyme composition. By analyzing the NADH-GDH isoenzyme composition of single, double and triple mutants deficient in the expression of the three genes encoding the enzyme, we have found that the α, β and γ polypeptides that comprise the enzyme can be assembled into a complex combination of heterohexamers in roots. Moreover, we observed that when one or two of the three root isoenzymes were missing from the mutants, the remaining isoenzymes compensated for this deficiency. The significance of such complexity is discussed in relation to the metabolic and signaling function of the NADH-GDH enzyme. Although it has been shown that a fourth gene encoding a NADPH-dependent enzyme is present in Arabidopsis, we were not able to detect corresponding enzyme activity, even in the triple mutant totally lacking NADH-GDH activity.

Novel glutamate dehydrogenase genes show increased transcript and protein abundances in mature tomato fruits

NAD(P)H-glutamate dehydrogenase (GDH, EC 1.4.1.3) contributes to the control of glutamate homeostasis in all living organisms. In bacteria and animals, GDH is a homohexamer allosterically regulated, whereas in plants NADH-GDH (EC 1.4.1.2) is also found as heterohexamer of α- and β-subunits, but its regulation remains undefined. In tomato (Solanum lycopersicum), GDH activity increases during the fruit ripening along with the content of free glutamate, the most abundant amino acid of ripe fruit involved in conferring the genuine tomato flavour. In this work, novel Slgdh-NAD genes were identified in the recently deciphered tomato genome: three encoding the α-subunit (Slgdh-NAD;A1-3) and one additional gene encoding the β-subunit of GDH (Slgdh-NAD;B1) isolated from a genomic library. These genes are located in different chromosomes. Slgdh-NAD;A1-3 show conserved structures, whereas Slgdh-NAD;B1 includes a novel 5'-untranslated exon. Slgdh-NAD;A1-3 transcripts were detected in all tomato tissues examined, showing the highest levels in mature green fruits, contrasting with Slgdh-NAD;B1 transcripts which were detected mainly in roots or in mature fruits when treated with glutamate, NaCl or salicylic acid. Analyses of GDH activity and protein distribution in different tissues of the Micro-Tom cultivar showed that only the active homohexamer of GDH β-subunits was detected in roots while heterohexamers of GDH α- and β-subunits were found in fruits. These results indicate that GDH β-subunit could modulate the heteromeric isoforms of GDH in response to the environment and physiology of the tomato fruit. This information is relevant to manipulate glutamate contents in tomato fruits genetically.

Exome sequencing and advances in crop improvement

Next-generation sequencing strategies have opened new vistas for molecular plant breeding. The sequence information obtained by the advent of next-generation sequencing provides a valuable tool not only for improving domesticated crops but also for investigating the natural evolution of crops. Such information provides an enormous potential for sustainable agriculture. In this review, we discuss how such sequencing approaches have transformed exome sequencing into a practical utility that has enormous potential for crop improvement in agriculture. Furthermore, we also describe the future of crop improvement beyond the exome sequencing strategies.

A novel rice gene, NRR responds to macronutrient deficiency and regulates root growth

To better understand the response of rice to nutrient stress, we have taken a systematic approach to identify rice genes that respond to deficiency of macronutrients and affect rice growth. We report here the expression and biological functions of a previously uncharacterized rice gene that we have named NRR (nutrition response and root growth). NRR is alternatively spliced, producing two 5'-coterminal transcripts, NRRa and NRRb, encoding two proteins of 308 and 223 aa, respectively. Compared to NRRb, NRRa possesses an additional CCT domain at the C-terminus. Expression of NRR in rice seedling roots was significantly influenced by deficiency of macronutrients. Knock-down of expression of NRRa or NRRb by RNA interference resulted in enhanced rice root growth. By contrast, overexpression of NRRa in rice exhibited significantly retarded root growth. These results revealed that both NRRa and NRRb played negative regulatory roles in rice root growth. Our findings suggest that NRRa and NRRb, acting as the key components, modulate the rice root architecture with the availability of macronutrients.

L-aspartate dehydrogenase: features and applications

L-amino acid dehydrogenases are a group of enzymes that catalyze the reversible oxidative deamination of L-amino acids to their corresponding 2-oxoacids, using either nicotinamide adenine dinucleotide (NAD(+)) or nicotinamide adenine dinucleotide phosphate (NADP(+)) as cofactors. These enzymes have been studied widely because of their potential applications in the synthesis of amino acids for use in production of pharmaceutical peptides, herbicides and insecticides, in biosensors or diagnostic kits, and development of coenzyme regeneration systems for industrial processes. This article presents a review of the currently available data about the recently discovered amino acid dehydrogenase superfamily member L-aspartate dehydrogenase (L-AspDH), their relevant catalytic properties and speculated physiological roles, and potential for biotechnological applications. The proposed classification of L-AspDH on the basis of bioinformatic information and potential role in vivo into NadB (NAD biosynthesis-related) and non-NadB type is unique. In particular, the mesophilic non-NadB type L-AspDH is a novel group of amino acid dehydrogenases with great promise as potential industrial biocatalysts owing to their relatively high catalytic properties at room temperature. Considering that only a few L-AspDH homologs have been characterized so far, identification and prodigious enzymological research of the new members will be necessary to shed light on the gray areas pertaining to these enzymes.

Combined noninvasive imaging and modeling approaches reveal metabolic compartmentation in the barley endosperm

The starchy endosperm of cereals is a priori taken as a metabolically uniform tissue. By applying a noninvasive assay based on (13)C/(1)H-magnetic resonance imaging (MRI) to barley (Hordeum vulgare) grains, we uncovered metabolic compartmentation in the endosperm. (13)C-Suc feeding during grain filling showed that the primary site of Ala synthesis was the central region of the endosperm, the part of the caryopsis experiencing the highest level of hypoxia. Region-specific metabolism in the endosperm was characterized by flux balance analysis (FBA) and metabolite profiling. FBA predicts that in the central region of the endosperm, the tricarboxylic acid cycle shifts to a noncyclic mode, accompanied by elevated glycolytic flux and the accumulation of Ala. The metabolic compartmentation within the endosperm is advantageous for the grain's carbon and energy economy, with a prominent role being played by Ala aminotransferase. An investigation of caryopses with a genetically perturbed tissue pattern demonstrated that Ala accumulation is a consequence of oxygen status, rather than being either tissue specific or dependent on the supply of Suc. Hence the (13)C-Ala gradient can be used as an in vivo marker for hypoxia. The combination of MRI and metabolic modeling offers opportunities for the noninvasive analysis of metabolic compartmentation in plants.

Organ-specific expression of glutamate dehydrogenase (GDH) subunits in yellow lupine

Glutamate dehydrogenase (GDH, EC 1.4.2-4) is present in yellow lupine (Lupinus luteus cv. Juno) in many isoforms. The number and banding pattern of isoenzymes varies with respect to plant organ and developmental stage. To better understand the complex nature of GDH regulation in plants, the levels of GDH transcripts, enzyme activity and isoenzyme patterns in germinating seeds and roots of yellow lupine were examined. The analysis of GDH cDNA sequences in lupine revealed three mRNA types, of which two encoded the β-GDH subunit and one encoded the α-GDH subunit (corresponding to the GDH1(GDH3) and GDH2 genes, respectively). The relative expression of GDH1 and GDH2 genes was analyzed in various lupine organs by using quantitative real-time PCR. Our results indicate that different mRNA types were differently regulated depending on organ type. Although both genes appeared to be ubiquitously expressed in all lupine tissues, the GDH1 transcripts evidently predominated over those of GDH2. Immunochemical analyses confirmed that, during embryo development, varied expression of two GDH subunits takes place. The α-GDH subunit (43kDa) predominated in the early stages of germinating seeds, while the β-GDH subunit (44kDa) was the only GDH polypeptide present in lupine roots. These results firmly support the hypothesis that isoenzyme variability of GDH in yellow lupine is associated with the varied expression of α and β subunits into the complexes of hexameric GDH forms. The presence of several isogenes of GDH in yellow lupine may explain the high number (over 20) of its molecular forms in germinating lupine.