Nitrate reductase induction and molecular characterization in rice (Oryza sativa L.)

Decreasing nitrogen assimilation under drought stress by suppressing DST-mediated activation of Nitrate Reductase 1.2 in rice

Nitrogen is an essential nutrient for plant growth and development, and plays vital roles in crop yield. Assimilation of nitrogen is thus fine-tuned in response to heterogeneous environments. However, the regulatory mechanism underlying this essential process remains largely unknown. Here, we report that a zinc-finger transcription factor, drought and salt tolerance (DST), controls nitrate assimilation in rice by regulating the expression of OsNR1.2. We found that loss of function of DST results in a significant decrease of nitrogen use efficiency (NUE) in the presence of nitrate. Further study revealed that DST is required for full nitrate reductase activity in rice and directly regulates the expression of OsNR1.2, a gene showing sequence similarity to nitrate reductase. Reverse genetics and biochemistry studies revealed that OsNR1.2 encodes an NADH-dependent nitrate reductase that is required for high NUE of rice. Interestingly, the DST-OsNR1.2 regulatory module is involved in the suppression of nitrate assimilation under drought stress, which contributes to drought tolerance. Considering the negative role of DST in stomata closure, as revealed previously, the positive role of DST in nitrogen assimilation suggests a mechanism coupling nitrogen metabolism and stomata movement. The discovery of this coupling mechanism will aid the engineering of drought-tolerant crops with high NUE in the future.

Transporters and transcription factors gene families involved in improving nitrogen use efficiency (NUE) and assimilation in rice (Oryza sativa L.)

Nitrogen (N) as a macronutrient is an important determinant of plant growth. The excessive usage of chemical fertilizers is increasing environmental pollution; hence, the improvement of crop's nitrogen use efficiency (NUE) is imperative for sustainable agriculture. N uptake, transportation, assimilation, and remobilization are four important determinants of plant NUE. Oryza sativa L. (rice) is a staple food for approximately half of the human population, around the globe and improvement in rice yield is pivotal for rice breeders. The N transporters, enzymes indulged in N assimilation, and several transcription factors affect the rice NUE and subsequent yield. Although, a couple of improvements have been made regarding rice NUE, the knowledge about regulatory mechanisms operating NUE is scarce. The current review provides a precise knowledge of how rice plants detect soil N and how this detection is translated into the language of responses that regulate the growth. Additionally, the transcription factors that control N-associated genes in rice are discussed in detail. This mechanistic insight will help the researchers to improve rice yield with minimized use of chemical fertilizers.

DIFFERENT NITRATE AND AMMONIUM LEVELS MEDIA ON CHANGES OF NITROGEN ASSIMILATION ENZYMES IN RICE

Nitrogen (N) is an important nutrient for the growth and development of rice plants, required in large quantity and often limiting factor of rice yields. The research was to understand the different sources and levels of nitrogen in rice plant on the activity of N assimilation enzymes, including nitrate reductase (NR), glutamine synthase (GS) content, glutamate synthase (Gogat) content, content, ammonium (NH4+) and nitrate (NO3-) content on the leaves. Paddy (Ciherang variety) was grown in sand media containing Hoagland solution with different sources (ammonium and nitrate) and levels (0.4, 0.8, 1.6, 3.2, 6.4, and 12.8 mM) of nitrogen. Nitrogen assimilation was observed from leaves at one month of age. The NR activity increased on both Nitrogen sources, it was a higher activity in media contained nitrate. Also, the activity of GS showed higher in media contains nitrate, but its activity was decreased after application 1.6 mM of nitrate and 3.2 mM of ammonium. Western blot analysis of GS1 and GS2 showed that the band pattern of protein was similar to these enzyme activities. Nitrate content in leaves gradually increased in both sources of nitrogen and higher than 3.2 mM ammonium application caused an increase in ammonium content in leaves, but the nitrate content decreased. This research resulted that the available source of N for rice was in nitrate form, easily by the rice plants during the growth stage.

Nitrogen-dependent regulation of de novo cytokinin biosynthesis in rice: the role of glutamine metabolism as an additional signal

Cytokinin activity in plants is closely related to nitrogen availability, and an Arabidopsis gene for adenosine phosphate-isopentenyltransferase (IPT), IPT3, is regulated by inorganic nitrogen sources in a nitrate-specific manner. In this study, we have identified another regulatory system of cytokinin de novo biosynthesis in response to nitrogen status. In rice, OsIPT4, OsIPT5, OsIPT7 and OsIPT8 were up-regulated in response to exogenously applied nitrate and ammonium, with accompanying accumulation of cytokinins. Pre-treatment of roots with l-methionine sulfoximine, a potent inhibitor of glutamine synthetase, abolished the nitrate- and ammonium-dependent induction of OsIPT4 and OsIPT5, while glutamine application induced their expression. Thus, neither nitrate nor ammonium, but glutamine or a related metabolite, is essential for the induction of these IPT genes in rice. On the other hand, glutamine-dependent induction of IPT3 occurs in Arabidopsis, at least to some extent. In transgenic lines repressing the expression of OsIPT4, which is the dominant IPT in rice roots, the nitrogen-dependent increase of cytokinin in the xylem sap was significantly reduced, and seedling shoot growth was retarded despite sufficient nitrogen. We conclude that plants possess multiple regulation systems for nitrogen-dependent cytokinin biosynthesis to modulate growth in response to nitrogen availability.

Induction of class-1 non-symbiotic hemoglobin genes by nitrate, nitrite and nitric oxide in cultured rice cells

Non-symbiotic hemoglobins (ns-Hbs) are found in all plants, although their physiological function remains to be determined. The present study was undertaken to explore the mode of induction of ns-Hb genes by metabolites of nitrate assimilation using cultured rice (Oryza sativa L.) cells. Two class-1 ns-Hb genes, ORYsa GLB1a and ORYsa GLB1b, were strongly induced by nitrate, nitrite and nitric oxide (NO) donors, S-nitroso-N-acetylpenicillamine and sodium nitroprusside. The rapid and transient accumulation of ORYsa GLB1a and ORYsa GLB1b transcripts in response to nitrate, nitrite and NO donors was similar to that of nia1, which encodes NADH-nitrate reductase (NR), although repression by glutamine and asparagines was significant only for nia1. In the mutants defective in NR mRNA expression, nitrate, nitrite and NO donors failed to induce not only nia1 but also ORYsa GLB1a and ORYsa GLB1b transcripts, indicating that the induction of ns-Hb genes is closely associated with that of the NR gene. Although the kinetics of induction by nitrate, nitrite and NO donors are similar for the two ns-Hb genes, an inhibitor study demonstrated that de novo synthesis of the protein in cytoplasm is essential for inducing ORYsa GLB1b. In contrast, ORYsa GLB1a, like nia1, can be induced in the primary response to these signals without de novo protein synthesis. The role of nitrate, nitrite and NO in the induction of ns-Hb gene expression in rice cells and the possible cellar function of ns-Hbs were discussed in relation to nitrate reduction pathways.

Molecular evolution of nitrate reductase genes

To understand the evolutionary mechanisms and relationships of nitrate reductases (NRs), the nucleotide sequences encoding 19 nitrate reductase (NR) genes from 16 species of fungi, algae, and higher plants were analyzed. The NR genes examined show substantial sequence similarity, particularly within functional domains, and large variations in GC content at the third codon position and intron number. The intron positions were different between the fungi and plants, but conserved within these groups. The overall and nonsynonymous substitution rates among fungi, algae, and higher plants were estimated to be 4.33 x 10(-10) and 3.29 x 10(-10) substitutions per site per year. The three functional domains of NR genes evolved at about one-third of the rate of the N-terminal and the two hinge regions connecting the functional domains. Relative rate tests suggested that the nonsynonymous substitution rates were constant among different lineages, while the overall nucleotide substitution rates varied between some lineages. The phylogenetic trees based on NR genes correspond well with the phylogeny of the organisms determined from systematics and other molecular studies. Based on the nonsynonymous substitution rate, the divergence time of monocots and dicots was estimated to be about 340 Myr when the fungi-plant or algae-higher plant divergence times were used as reference points and 191 Myr when the rice-barley divergence time was used as a reference point. These two estimates are consistent with other estimates of divergence times based on these reference points. The lack of consistency between these two values appears to be due to the uncertainty of the reference times.

Integration of photosynthetic carbon and nitrogen metabolism in higher plants

Concomitant assimilation of C and N in illuminated leaves requires the regulated partitioning of reductant and photosynthate to sustain the demands of amino acid and carbohydrate biosynthesis. The short-term responses of photosynthesis and photosynthate partitioning to N enrichment in wheat (Triticum aestivum, L.) and maize (Zea mays L.) leaves were studied in order to understand the regulatory strategy employed in higher plants. Transgenic tobacco plants (Tobacco plumbaginifolia) over-expressing NR or with poor NR expression were used to compare plants differing in their capacities for NO3 (-) assimilation. Similar regulatory responses to NO3 (-) were observed in leaves having C4- and C3-type photosynthesis. It was shown that the extra- C needed in the short-term to sustain amino acid synthesis was not provided by an increase in photosynthetic CO2 fixation but rather by a rapid shift in the partitioning of photosynthetic C to amino acid at the expense of sucrose biosynthesis. The modulation of three enzymes was shown to be important in this C and N interaction, namely PEPCase (EC 4.1.1.31), SPS (EC 2.4.1.14) and NADH/NR (EC 1.6.6.1). The first two enzymes were shown to share the common feature of regulatory post-transcriptional NO3 (-)-dependent phosphorylation of their proteins on a seryl-residue. While PEPCase is activated, SPS activity is decreased. In contrast the NR phosphorylation state is unchanged and all N-dependent control of NR activity is regulated at the protein level. A number of arguments support the hypothesis that Gln, the primary product of NO3 (-) assimilation, is the metabolite effector for short-term modulation of PEPCase, and SPS in response to N enrichment. Since a major effect of NO3 (-) on the PEPCase-protein kinase activity in concentrated wheat leaf extracts was demonstrated, the hypothesis is put forward that protein phosphorylation is the primary event allowing the short-term adaptation of leaf C metabolism to changes in N supply.

Variation of nitrate reductase genes in selected grass species

In order to study the variation of nitrate reductase (NR) genes among grass species, gene number, intron size and number, and the heme-hinge fragment sequence of 25 grass species were compared. Genomic DNA cut with six restriction enzymes and hybridized with the barley NAD(P)H and NADH NR gene probes revealed a single NAD(P)H NR gene copy and two or more NADH NR gene copies per haploid genome in most of the species examined. Major exceptions were Hordeum vulgare, H. vulgare ssp. spontaneum, and Avena strigosa, which appeared to have a single NADH NR gene copy. The NADH NR gene intron number and lengths were examined by polymerase chain reaction amplification. Introns I and III appeared to be absent in at least one of the NADH NR genes in the grass species, while intron II varied from 0.8 to 2.4 kilobases in length. The NADH NR gene heme-hinge regions were amplified and sequenced. The estimated average overall nucleotide substitution rate in the sequenced region was 7.8 x 10(-10) substitutions/site per year. The synonymous substitution rate was 2.11 x 10(-9) substitutions/synonymous site per year and the nonsynonymous substitution rate was 4.10 x 10(-10) substitutions/nonsynonymous site per year. Phylogenetic analyses showed that all of the wild Hordeum species examined clustered in a group separate from H. vulgare and H. vulgare ssp. spontaneum.

Expression of nitrate assimilation related genes in Chlamydomonas reinhardtii

The mRNA accumulation pattern of the Chlamydomonas reinhardtii nitrate assimilation-related gene cluster has been elucidated. In ammonium-grown wild-type cells, nit-1 (nitrate reductase, NR), nar-1, nar-2 and nar-3 (nitrate transporter) genes showed very similar kinetics of expression when transferred to nitrate medium. Transcripts of all these genes accumulated transiently in ammonium-grown wild-type cells after a one-hour incubation in nitrogen-free medium, and practically disappeared at about 2 hours. Mutant strains lacking functional nitrate reductase showed similar accumulation kinetics of these transcripts during both nitrate induction and derepression in nitrogen-free media. In contrast to the other nar transcripts, that nar-4, a gene sharing similar sequences with nar-3, accumulated in small amounts in wild-type cells, and only increased after a long nitrate induction period. Nitrate and light showed a strong positive effect on the accumulation of nit-1 gene transcripts. Acetate as a carbon source allowed accumulation of nit-1 mRNA in the dark, indicating the existence of interactions between light and carbon metabolism in nit-1 gene expression. Our data strongly suggest that NR negatively autoregulates its own expression and that of nar genes.

Characterization of a rice (Oryza sativa L.) mutant deficient in the heme domain of nitrate reductase

Biochemical and genetical characterization of a rice nitrate reductase (NR)-deficient mutant, M819, which had been isolated as a chlorate-resistant mutant, was carried out. In M819, leaf NADH-NR activity was found to be about 10% of that of the wild-type cv 'Norin 8', while NADPH-NR activity was higher than that in the wild-type; FMNH2-NR and MV-NR activities were also 10% of those of the wild type; BPB-NR activity was higher than that of the wild type; and xanthine dehydrogenase activity was revealed to be present in both. These results suggest that the mutant line M819 lacks the functional heme domain of the NADH-NR polypeptide due to a point mutation or a small deletion within the coding region of the structural gene. Chlorate resistance in M819 was transmitted by a single recessive nuclear gene.

Analysis of barley nitrate reductase cDNA and genomic clones

Barley nitrate reductase cDNA and genomic clones were isolated by homology with the barley nitrate reductase cDNA clone bNRp10 and sequenced. This is the first reported analysis of a full-length nitrate reductase gene and its corresponding cDNA in the same species. The longest cDNA clone extends to within 9 bp of the ATG start codon and the sequence is similar to that reported for the higher plant NR sequences. As expected, the amino acid sequence of barley nitrate reductase is more related closely to the rice (84% homology) than to the Arabidopsis (62%) sequence. Four different polyA addition sites were identified from sequence analysis of nine barley NR cDNA clones. A 7.3 kb region of a genomic recombinant lambda clone was subcloned as two contiguous BamHI fragments into p Bluescript, designated pMJ7 and pMJ8, and sequenced. These clones include the entire nitrate reductase coding region, one large intron, 2.7 kb of untranslated sequence 5' to the translation start codon and 0.25 kb 3' to the translation termination codon. The mRNA cap site was identified as a cytosine, 111 bases upstream of the ATG translation start codon. The putative CAAT and TATA boxes were identified at -115 and -33 bp, respectively, with the mRNA cap site designated as +1. The barley nitrate reductase gene coding region strongly favors G or C in the third codon position.