Okadaic Acid Mimics Nitrogen-Stimulated Transcription of the NADH-Glutamate Synthase Gene in Rice Cell Cultures

Coregulation of glutamine synthetase1;2 (GLN1;2) and NADH-dependent glutamate synthase (GLT1) gene expression in Arabidopsis roots in response to ammonium supply

Ammonium absorbed by roots is assimilated into amino acids. The glutamine synthetase/glutamate synthase (glutamine 2-oxoglutarate aminotransferase) (GS/GOGAT) cycle is essential to this biological process. In Arabidopsis thaliana, GLN1;2 and GLT1 are the GS and GOGAT isoenzymes induced in response to ammonium supply and playing key roles in ammonium utilization. Although recent studies suggest gene regulatory networks involved in transcriptional regulation of ammonium-responsive genes, direct regulatory mechanisms for ammonium-induced expression of GS/GOGAT remain unclear. In this study, we revealed that the expression of GLN1;2 and GLT1 in Arabidopsis is not directly induced by ammonium but is regulated by glutamine or post-glutamine metabolites produced by ammonium assimilation. Previously, we identified a promoter region required for ammonium-responsive expression of GLN1;2. In this study, we further dissected the ammonium-responsive region of the GLN1;2 promoter and also performed a deletion analysis of the GLT1 promoter, which led to the identification of a conserved ammonium-responsive region. Yeast one-hybrid screening using the ammonium-responsive region of the GLN1;2 promoter as a decoy sequence revealed a trihelix family transcription factor DF1 that binds to this region. A putative DF1 binding site was also found in the ammonium-responsive region of the GLT1 promoter.

Genome-Wide Comprehensive Analysis of the Nitrogen Metabolism Toolbox Reveals Its Evolution and Abiotic Stress Responsiveness in Rice (Oryza sativa L.)

Nitrogen metabolism (NM) plays an essential role in response to abiotic stresses for plants. Enzyme activities have been extensively studied for nitrogen metabolism-associated pathways, but the knowledge of nitrogen metabolism-associated genes involved in stress response is still limited, especially for rice. In this study, we performed the genome-wide characterization of the genes putatively involved in nitrogen metabolism. A total of 1110 potential genes were obtained to be involved in nitrogen metabolism from eight species (Arabidopsis thaliana (L.) Heynh., Glycine max (L.) Merr., Brassica napus L., Triticum aestivum L., Sorghum bicolor L., Zea mays L., Oryza sativa L. and Amborella trichopoda Baill.), especially 104 genes in rice. The comparative phylogenetic analysis of the superfamily revealed the complicated divergence of different NM genes. The expression analysis among different tissues in rice indicates the NM genes showed diverse functions in the pathway of nitrogen absorption and assimilation. Distinct expression patterns of NM genes were observed in rice under drought stress, heat stress, and salt stress, indicating that the NM genes play a curial role in response to abiotic stress. Most NM genes showed a down-regulated pattern under heat stress, while complicated expression patterns were observed for different genes under salt stress and drought stress. The function of four representative NM genes (OsGS2, OsGLU, OsGDH2, and OsAMT1;1) was further validated by using qRT-PCR analysis to confirm their responses to these abiotic stresses. Based on the predicted transcription factor binding sites (TFBSs), we built a co-expression regulatory network containing transcription factors (TFs) and NM genes, of which the constructed ERF and Dof genes may act as the core genes to respond to abiotic stresses. This study provides novel sights to the interaction between nitrogen metabolism and the response to abiotic stresses.

Exploration of nitrate-to-glutamate assimilation in non-photosynthetic roots of higher plants by studies of 15N-tracing, enzymes involved, reductant supply, and nitrate signaling: A review and synthesis

Roots of the higher plants can assimilate inorganic nitrogen by an enzymatic reduction of the most oxidized form (+6) nitrate to the reduced form (-2) glutamate. For such reactions, the substrates (originated from photosynthates) must be imported to supply energy through the reductant-generating systems within the root cells. Intensive studies over last 70 years (reviewed here) revealed the precise mechanisms of nitrate-to-glutamate transformation in roots with elaborate searches of ¹⁵N-tracing, enzymes involved, the reductant-supplying system, and nitrate signaling. In the 1970s, the tracing of ¹⁵N-labeled nitrate and ammonia in the roots demonstrated the sequential reduction and assimilation of nitrate to nitrite, ammonia, glutamine amide, and then glutamate. These reactions involve nitrate reductase (NADH-NR, EC 1.7.1.1) in the cytosol, nitrite reductase (ferredoxin [Fd]-NiR, EC 1.7.7.1), glutamine synthetase (GS2, EC 6.3.1.2), and glutamate synthase (Fd-GOGAT, EC 1.4.7.1) in the plastids. NADH for NR is generated by glycolysis in the cytosol, and NADPH for Fd-NIR and Fd-GOGAT are produced by the oxidative pentose phosphate pathway (OPPP). Electrons from NADPH are conveyed to reduce NIR and Fd-GOGAT through Fd-NADP⁺ reductase (FNR, EC 1.6.7.1) specifically in the roots. Physiological and molecular analyses showed the parallel inductions of NR, NIR, GS2, Fd-GOGAT, OPPP enzymes, FNR, and Fd in response to a short-term nitrate supply. Recent studies proposed a molecular mechanism of nitrate-induction of these genes and proteins. Roots can also assimilate the reduced form of inorganic ammonia by the combination of cytosolic GS1 and plastidic NADH-GOGAT.

Regulatory role of indeterminate domain 10 (IDD10) in ammonium-dependent gene expression in rice roots

One of the strategies that plants utilize to adapt to fluctuating soil nutrient levels is rapid reprogramming of transcriptional regulation via cell signaling mechanisms. Higher plants exposed to ammonium undergo modulation of a broad spectrum of gene expression. However, regulation of the transcriptional mechanisms underlying ammonium-mediated gene expression is poorly understood. We identified a transcriptional regulator, indeterminate domain 10 (IDD10), whose mutants exhibited an ammonium-hypersensitive root growth defect. To elucidate the molecular relationship between IDD10 and ammonium-mediated gene expression, ammonium-responsive genes were examined in mutants and overexpressors of IDD10. Among the key ammonium uptake and assimilation genes, AMT1;2 (ammonium transporter 1;2) and GDH2 (glutamate dehydrogenase 2) significantly depend on IDD10 expression levels for ammonium-mediated induction. Extensive molecular analysis revealed that IDD10 directly binds to the promoter of AMT1;2 and the fifth intron of GDH2 genes via the core sequence TTTGTC(C)/(G). Transcriptome analysis with root tissues identified many ammonium-inducible genes whose expression was increased by IDD10. Half of them contained potential IDD10-binding motifs in their promoters. This study determined that IDD10 is a transcriptional activator involved in nitrogen regulatory circuits that control a broad spectrum of gene expression, which might influence root growth in rice.

Indeterminate domain 10 regulates ammonium-mediated gene expression in rice roots

Indeterminate domain (IDD) genes are a family of plant transcriptional regulators that function in the control of development and metabolism during growth. Here, the function of Oryza sativa indeterminate domain 10 (OsIDD10) has been explored in rice plants. Compared with wild-type roots, idd10 mutant roots are hypersensitive to exogenous ammonium. This work aims to define the action of IDD10 on gene expression involved in ammonium uptake and nitrogen (N) metabolism. The ammonium induction of key ammonium uptake and assimilation genes was examined in the roots of idd10 mutants and IDD10 overexpressors. Molecular studies and transcriptome analysis were performed to identify target genes and IDD10 binding cis-elements. IDD10 activates the transcription of AMT1;2 and GDH2 by binding to a cis-element motif present in the promoter region of AMT1;2 and in the fifth intron of GDH2. IDD10 contributes significantly to the induction of several genes involved in N-linked metabolic and cellular responses, including genes encoding glutamine synthetase 2, nitrite reductases and trehalose-6-phosphate synthase. Furthermore, the possibility that IDD10 might influence the N-mediated feedback regulation of target genes was examined. This study demonstrates that IDD10 is involved in regulatory circuits that determine N-mediated gene expression in plant roots.

Transcriptional downregulation of rice rpL32 gene under abiotic stress is associated with removal of transcription factors within the promoter region

BACKGROUND

The regulation of ribosomal proteins in plants under stress conditions has not been well studied. Although a few reports have shown stress-specific post-transcriptional and translational mechanisms involved in downregulation of ribosomal proteins yet stress-responsive transcriptional regulation of ribosomal proteins is largely unknown in plants.

METHODOLOGY/PRINCIPAL FINDINGS

In the present work, transcriptional regulation of genes encoding rice 60S ribosomal protein L32 (rpL32) in response to salt stress has been studied. Northern and RT-PCR analyses showed a significant downregulation of rpL32 transcripts under abiotic stress conditions in rice. Of the four rpL32 genes in rice genome, the gene on chromosome 8 (rpL32_8.1) showed a higher degree of stress-responsive downregulation in salt sensitive rice variety than in tolerant one and its expression reverted to its original level upon withdrawal of stress. The nuclear run-on and promoter:reporter assays revealed that the downregulation of this gene is transcriptional and originates within the promoter region. Using in vivo footprinting and electrophoretic mobility shift assay (EMSA), cis-elements in the promoter of rpL32_8.1 showing reduced binding to proteins in shoots of salt stressed rice seedlings were identified.

CONCLUSIONS

The present work is one of the few reports on study of stress downregulated genes. The data revealed that rpL32 gene is transcriptionally downregulated under abiotic stress in rice and that this transcriptional downregulation is associated with the removal of transcription factors from specific promoter elements.

Cyclobutane pyrimidine dimer (CPD) photolyase repairs ultraviolet-B-induced CPDs in rice chloroplast and mitochondrial DNA

Plants use sunlight as energy for photosynthesis; however, plant DNA is exposed to the harmful effects of ultraviolet-B (UV-B) radiation (280-320 nm) in the process. UV-B radiation damages nuclear, chloroplast and mitochondrial DNA by the formation of cyclobutane pyrimidine dimers (CPDs), which are the primary UV-B-induced DNA lesions, and are a principal cause of UV-B-induced growth inhibition in plants. Repair of CPDs is therefore essential for plant survival while exposed to UV-B-containing sunlight. Nuclear repair of the UV-B-induced CPDs involves the photoreversal of CPDs, photoreactivation, which is mediated by CPD photolyase that monomerizes the CPDs in DNA by using the energy of near-UV and visible light (300-500 nm). To date, the CPD repair processes in plant chloroplasts and mitochondria remain poorly understood. Here, we report the photoreactivation of CPDs in chloroplast and mitochondrial DNA in rice. Biochemical and subcellular localization analyses using rice strains with different levels of CPD photolyase activity and transgenic rice strains showed that full-length CPD photolyase is encoded by a single gene, not a splice variant, and is expressed and targeted not only to nuclei but also to chloroplasts and mitochondria. The results indicate that rice may have evolved a CPD photolyase that functions in chloroplasts, mitochondria and nuclei, and that contains DNA to protect cells from the harmful effects of UV-B radiation.

Comparative proteomics analysis of differentially expressed proteins in chickpea extracellular matrix during dehydration stress

Water deficit or dehydration is the most crucial environmental factor that limits crop productivity and influences geographical distribution of many crop plants. It is suggested that dehydration-responsive changes in expression of proteins may lead to cellular adaptation against water deficit conditions. Most of the earlier understanding of dehydration-responsive cellular adaptation has evolved from transcriptome analyses. By contrast, comparative analysis of dehydration-responsive proteins, particularly proteins in the subcellular fraction, is limiting. In plants, cell wall or extracellular matrix (ECM) serves as the repository for most of the components of the cell signaling process and acts as a frontline defense. Thus, we have initiated a proteomics approach to identify dehydration-responsive ECM proteins in a food legume, chickpea. Several commercial chickpea varieties were screened for the status of dehydration tolerance using different physiological and biochemical indexes. Dehydration-responsive temporal changes of ECM proteins in JG-62, a relatively tolerant variety, revealed 186 proteins with variance at a 95% significance level statistically. The comparative proteomics analysis led to the identification of 134 differentially expressed proteins that include predicted and novel dehydration-responsive proteins. This study, for the first time, demonstrates that over a hundred ECM proteins, presumably involved in a variety of cellular functions, viz. cell wall modification, signal transduction, metabolism, and cell defense and rescue, impinge on the molecular mechanism of dehydration tolerance in plants.

ACT Domain Repeat Protein 7, ACR7, Interacts with a Chaperone HSP18.0-CII in Rice Nuclei

The regulatory ACT domains serve as amino acid-binding sites in some amino acid metabolic enzymes and transcriptional regulators in bacteria. To elucidate the molecular roles of the glutamine (Gln)-sensing system in nitrogen (N) metabolism in plants, we isolated six genes encoding ACT domain repeat proteins (ACR1, and ACR5-ACR9) from rice (Oryza sativa L.) using genomic information on the primary structure composed of four copies of the domain homologous to those of bacterial Gln sensor GLND. Since expression of ACR7 was the most abundant of the six ACR orthologous genes, we focused on this ACR in the current study. Gene products of ACR7 were most abundant in young developing leaf blades of rice, and ACR7 protein is specifically localized in the nucleus of the parenchyma cells of phloem and xylem in the vascular bundles. A yeast two-hybrid screen identified a small heat stress protein (HSP18.0-CII) as a protein interacting with ACR7. Transient expression analysis of HSP18.0-CII:sGFP in cultured rice cells, followed by co-immunoprecipitation, suggests that the nuclear ACR7 indeed interacted with nucleocytoplasmic HSP18.0-CII in vivo. The potential ability of nuclear protein ACR7 to bind Gln and the possibility of the protein acting as a Gln sensor in rice leaves is discussed.

Glutamate synthase: structural, mechanistic and regulatory properties, and role in the amino acid metabolism

Ammonium ion assimilation constitutes a central metabolic pathway in many organisms, and glutamate synthase, in concert with glutamine synthetase (GS, EC 6.3.1.2), plays the primary role of ammonium ion incorporation into glutamine and glutamate. Glutamate synthase occurs in three forms that can be distinguished based on whether they use NADPH (NADPH-GOGAT, EC 1.4.1.13), NADH (NADH-GOGAT, EC 1.4.1.14) or reduced ferredoxin (Fd-GOGAT, EC 1.4.7.1) as the electron donor for the (two-electron) conversion of L-glutamine plus 2-oxoglutarate to L-glutamate. The distribution of these three forms of glutamate synthase in different tissues is quite specific to the organism in question. Gene structures have been determined for Fd-, NADH- and NADPH-dependent glutamate synthases from different organisms, as shown by searches in nucleic acid sequence data banks. Fd-glutamate synthase contains two electron-carrying prosthetic groups, the redox properties of which are discussed. A description of the ferredoxin binding by Fd-glutamate synthase is also presented. In plants, including nitrogen-fixing legumes, Fd-glutamate synthase and NADH-glutamate synthase supply glutamate during the nitrogen assimilation and translocation. The biological functions of Fd-glutamate synthase and NADH-glutamate synthase, which show a highly tissue-specific distribution pattern, are tightly related to the regulation by the light and metabolite sensing systems. Analysis of mutants and transgenic studies have provided insights into the primary individual functions of Fd-glutamate synthase and NADH-glutamate synthase. These studies also provided evidence that glutamate dehydrogenase (NADH-GDH, EC 1.4.1.2) does not represent a significant alternate route for glutamate formation in plants. Taken together, biochemical analysis and genetic and molecular data imply that Fd-glutamate synthase incorporates photorespiratory and non-photorespiratory ammonium and provides nitrogen for transport to maintain nitrogen status in plants. Fd-glutamate synthase also plays a role that is redundant, in several important aspects, to that played by NADH-glutamate synthase in ammonium assimilation and nitrogen transport.

Interaction of N-acetylglutamate kinase with a PII-like protein in rice

PII protein in bacteria is a sensor for 2-oxoglutarate and a transmitter for glutamine signaling. We identified an OsGlnB gene that encoded a bacterial PII-like protein in rice. Yeast two-hybrid analysis showed that an OsGlnB gene product interacted with N-acetylglutamate kinase 1 (OsNAGK1) and PII-like protein (OsGlnB) itself in rice. In cyanobacteria, NAGK is a key enzyme in arginine biosynthesis. Transient expression of OsGlnB cDNA or OsNAGK1 cDNA fused with sGFP in rice leaf blades strongly suggested that the PII-like protein as well as OsNAGK1 protein is located in chloroplasts. Both OsGlnB and OsNAGK1 genes were expressed in roots, leaf blades, leaf sheaths and spikelets of rice, and these two genes were coordinately expressed in leaf blades during the life span. Thus, PII-like protein in rice plants is potentially able to interact with OsNAGK1 protein in vivo. This finding will provide a clue to the precise physiological function of PII-like protein in rice.

Induction of SULTR1;1 sulfate transporter in Arabidopsis roots involves protein phosphorylation/dephosphorylation circuit for transcriptional regulation

SULTR1;1 high-affinity sulfate transporter is highly regulated by sulfur deficiency (-S) in the epidermis and cortex of Arabidopsis roots. The regulatory mechanism of SULTR1;1 expression was studied using inhibitors for transcription, translation, protein phosphorylation and dephosphorylation. The induction of SULTR1;1 mRNA during -S was blocked by the addition of actinomycin D in the medium, suggesting that SULTR1;1 is transcriptionally regulated. Cycloheximide repressed the -S induction of SULTR1;1, but enhanced the basal mRNA level of SULTR1;1 under sulfur replete (+S) condition. In addition, the induction of SULTR1;1 by -S was significantly blocked by okadaic acid (OKA) and calyculin A (CalyA). Regulation of SULTR1;1 was further confirmed in transgenic plants expressing green fluorescent protein (GFP) under the control of SULTR1;1 promoter. Accumulation of GFP during -S was dependent to SULTR1;1 promoter, and the effects of OKA and CalyA were reproducible in the SULTR1;1 promoter-GFP plants. These results suggested that the up-regulation of SULTR1;1 by -S requires protein phosphatase as an upstream regulatory factor.

Arabidopsis glt1-T mutant defines a role for NADH-GOGAT in the non-photorespiratory ammonium assimilatory pathway

The physiological role of the NADH-dependent glutamine-2-oxoglutarate aminotransferase (NADH-GOGAT) enzyme was addressed in Arabidopsis using gene expression analysis and by the characterization of a knock-out T-DNA insertion mutant (glt1-T) in the single NADH-GOGAT GLT1 gene. The NADH-GOGAT GLT1 mRNA is expressed at higher levels in roots than in leaves. This expression pattern contrasts with GLU1, the major gene encoding Fd-GOGAT, which is most highly expressed in leaves and is involved in photorespiration. These distinct organ-specific expression patterns suggested a non-redundant physiological role for the NADH-GOGAT and Fd-GOGAT gene products. To test the in vivo function of NADH-GOGAT, we conducted molecular and physiological analysis of the glt1-T mutant, which is null for NADH-GOGAT, as judged by mRNA level and enzyme activity. Metabolic analysis showed that the glt1-T mutant has a specific defect in growth and glutamate biosynthesis when photorespiration was repressed by 1% CO2. Under these conditions, the glt1-T mutant displayed a 20% decrease in growth and a dramatic 70% reduction in glutamate levels. Herein, we discuss the significance of NADH-GOGAT in non-photorespiratory ammonium assimilation and in glutamate synthesis required for plant development.