Nitrate Reductases from Wild-Type and nr(1)-Mutant Soybean (Glycine max [L.] Merr.) Leaves : I. Purification, Kinetics, and Physical Properties

Isoform-Specific NO Synthesis by Arabidopsis thaliana Nitrate Reductase

Nitrate reductase (NR) is important for higher land plants, as it catalyzes the rate-limiting step in the nitrate assimilation pathway, the two-electron reduction of nitrate to nitrite. Furthermore, it is considered to be a major enzymatic source of the important signaling molecule nitric oxide (NO), that is produced in a one-electron reduction of nitrite. Like many other plants, the model plant Arabidopsis thaliana expresses two isoforms of NR (NIA1 and NIA2). Up to now, only NIA2 has been the focus of detailed biochemical studies, while NIA1 awaits biochemical characterization. In this study, we have expressed and purified functional fragments of NIA1 and subjected them to various biochemical assays for comparison with the corresponding NIA2-fragments. We analyzed the kinetic parameters in multiple steady-state assays using nitrate or nitrite as substrate and measured either substrate consumption (nitrate or nitrite) or product formation (NO). Our results show that NIA1 is the more efficient nitrite reductase while NIA2 exhibits higher nitrate reductase activity, which supports the hypothesis that the isoforms have special functions in the plant. Furthermore, we successfully restored the physiological electron transfer pathway of NR using reduced nicotinamide adenine dinucleotide (NADH) and nitrate or nitrite as substrates by mixing the N-and C-terminal fragments of NR, thus, opening up new possibilities to study NR activity, regulation and structure.

Nitrite-dependent nitric oxide production pathway: implications for involvement of active nitrogen species in photoinhibition in vivo

Air pollution studies have shown that nitric oxide (NO), a gaseous free radical, is a potent photosynthetic inhibitor that reduces CO2 uptake activity in leaves. It is now recognized that NO is not only an air pollutant but also an endogenously produced metabolite, which may play a role in regulating plant cell functions. Although many studies have suggested the presence of mammalian-type NO synthase (NOS) in plants, the source of NO is still not clear. There has been a number of studies indicating that plant cells possess a nitrite-dependent NO production pathway which can be distinguished from the NOS-mediated reaction. Nitrate reductase (NR) has been recently found to be capable of producing NO through one-electron reduction of nitrite using NAD(P)H as an electron donor. This review focuses on current understanding of the mechanism for the nitrite-dependent NO production in plants. Impacts of NO produced by NR on photosynthesis are discussed in association with photo-oxidative stress in leaves.

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.

Methylammonium-resistant mutants of Nicotiana plumbaginifolia are affected in nitrate transport

This work reports the isolation and preliminary characterization of Nicotiana plumbaginifolia mutants resistant to methylammonium. Nicotiana plumbaginifolia plants cannot grow on low levels of nitrate in the presence of methylammonium. Methylammonium is not used as a nitrogen source, although it can be efficiently taken up by Nicotiana plumbaginifolia cells and converted into methylglutamine, an analog of glutamine. Glutamine is known to repress the expression of the enzymes that mediate the first two steps in the nitrate assimilatory pathway, nitrate reductase (NR) and nitrite reductase (NiR). Methylammonium has therefore been used, in combination with low concentrations of nitrate, as a selective agent in order to screen for mutants in which the nitrate pathway is de-repressed. Eleven semi-dominant mutants, all belonging to the same complementation group, were identified. The mutant showing the highest resistance to methylammonium was not affected either in the utilization of ammonium, accumulation of methylammonium or in glutamine synthase activity. A series of experiments showed that utilization of nitrite by the wild-type and the mutant was comparable, in the presence or the absence of methylammonium, thus suggesting that the mutation specifically affected nitrate transport or reduction. Although NR mRNA levels were less repressed by methylammonium treatment of the wild-type than the mutant, NR activities of the mutant remained comparable with or without methylammonium, leading to the hypothesis that modified expression of NR is probably not responsible for resistance to methylammonium. Methylammonium inhibited nitrate uptake in the wild-type but had only a limited effect in the mutant. The implications of these results are discussed.

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.

Regulation of the inducible nitrate reductase isoform from soybeans

The activity of the pH 7.5 NADH-linked nitrate reductase isoform from soybeans is termed inducible. Activity can be observed only in seedlings which have been supplied nitrate. Steady-state levels of mRNA for this isoform also show an absolute requirement for nitrate. Nitrate reductase specific mRNA can be observed within 2 h after nitrate treatment. Levels peaked 48 h after nitrate treatment, while the addition of glutamine to nitrate diminished amounts of nitrate reductase specific mRNA. Using nuclear runoff transcription assays, we have shown that one level of control of nitrate reductase synthesis is transcriptional.

Comparison between NO(x) Evolution Mechanisms of Wild-Type and nr(1) Mutant Soybean Leaves

The nr(1) soybean (Glycine max [L.] Merr.) mutant does not contain the two constitutive nitrate reductases, one of which is responsible for enzymic conversion of nitrite to NO(x) (NO + NO(2)). It was tested for possible nonenzymic NO(x) formation and evolution because of known chemical reactions between NO(2) (-) and plant metabolites and the instability of nitrous acid. It did not evolve NO(x) during the in vivo NR assay, but intact leaves did evolve small amounts of NO(x) under dark, anaerobic conditions. Experiments were conducted to compare NO(3) (-) reduction, NO(2) (-) accumulation, and the NO(x) evolution processes of the wild type (cv Williams) and the nr(1) mutant. In vivo NR assays showed that wild-type leaves had three times more NO(3) (-) reducing capacity than the nr(1) mutant. NO(x) evolution from intact, anerobic nr(1) leaves was approximately 10 to 20% that from wild-type leaves. Nitrite content of the nr(1) mutant leaves was usually higher than wild type due to low NO(x) evolution. Lag times and threshold NO(2) (-) concentrations for NO(x) evolution were similar for the two genotypes. While only 1 to 2% of NO(x) from wild type is NO(2), the nr(1) mutant evolved 15 to 30% NO(2). The kinetic patterns of NO(x) evolution with time weré completely different for the mutant and wild type. Comparisons of light and heat treatments also gave very different results. It is generally accepted that the NO(x) evolution by wild type is primarily an enzymic conversion of NO(2) (-) to NO. However, this report concludes that NO(x) evolution by the nr(1) mutant was due to nonenzymic, chemical reactions between plant metabolites and accumulated NO(2) (-) and/or decomposition of nitrous acid. Nonenzymic NO(x) evolution probably also occurs in wild type to a degree but could be easily masked by high rates of the enzymic process.

Nitrate transport is independent of NADH and NAD(P)H nitrate reductases in barley seedlings

Barley (Hordeum vulgare L.) has NADH-specific and NAD(P)H-bispecific nitrate reductase isozymes. Four isogenic lines with different nitrate reductase isozyme combinations were used to determine the role of NADH and NAD(P)H nitrate reductases on nitrate transport and assimilation in barley seedlings. Both nitrate reductase isozymes were induced by nitrate and were required for maximum nitrate assimilation in barley seedlings. Genotypes lacking the NADH isozyme (Az12) or the NAD(P)H isozyme (Az70) assimilated 65 or 85%, respectively, as much nitrate as the wild type. Nitrate assimilation by genotype (Az12;Az70) which is deficient in both nitrate reductases, was only 13% of the wild type indicating that the NADH and NAD(P)H nitrate reductase isozymes are responsible for most of the nitrate reduction in barley seedlings. For all genotypes, nitrate assimilation rates in the dark were about 55% of the rates in light. Hypotheses that nitrate reductase has direct or indirect roles in nitrate uptake were not supported by this study. Induction of nitrate transporters and the kinetics of net nitrate uptake were the same for all four genotypes indicating that neither nitrate reductase isozyme has a direct role in nitrate uptake in barley seedlings.

The Conversion of Nitrite to Nitrogen Oxide(s) by the Constitutive NAD(P)H-Nitrate Reductase Enzyme from Soybean

A two-step purification protocol was used in an attempt to separate the constitutive NAD(P)H-nitrate reductase [NAD(P)H-NR, pH 6.5; EC 1.6.6.2] activity from the nitric oxide and nitrogen dioxide (NO((x))) evolution activity extracted from soybean (Glycine max [L.] Merr.) leaflets. Both of these activities were eluted with NADPH from Blue Sepharose columns loaded with extracts from either wild-type or LNR-5 and LNR-6 (lack constitutive NADH-NR [pH 6.5]) mutant soybean plants regardless of nutrient growth conditions. Fast protein liquid chromatography-anion exchange (Mono Q column) chromatography following Blue Sepharose affinity chromatography was also unable to separate the two activities. These data provide strong evidence that the constitutive NAD(P)H-NR (pH 6.5) in soybean is the enzyme responsible for NO((x)) formation. The Blue Sepharose-purified soybean enzyme has a pH optimum of 6.75, an apparent K(m) for nitrite of 0.49 millimolar, and an apparent K(m) for NADPH and NADH of 7.2 and 7.4 micromolar, respectively, for the NO((x)) evolution activity. In addition to NAD(P)H, reduced flavin mononucleotide (FMNH(2)) and reduced methyl viologen (MV) can serve as electron donors for NO((x)) evolution activity. The NADPH-, FMNH(2)-, and reduced MV-NO((x)) evolution activities were all inhibited by cyanide. The NADPH activity was also inhibited by p-hydroxymer-curibenzoate, whereas, the FMNH(2) and MV activities were relatively insensitive to inhibition. These data indicate that the terminal molybdenum-containing portion of the enzyme is involved in the reduction of nitrite to NO((x)). NADPH eluted both NR and NO((x)) evolution activities from Blue Sepharose columns loaded with extracts of either nitrate- or zero N-grown winged bean (Psophocarpus tetragonolobus [L.]), whereas NADH did not elute either type of activity. Winged bean appears to contain only one type of NR enzyme that is similar to the constitutive NAD(P)H-NR (pH 6.5) enzyme of soybean.

Transcriptional control of the inducible nitrate reductase isoform from soybeans

The activity of the pH 7.5 NADH-linked nitrate reductase isoform from soybean seedlings is termed inducible. Activity is present only in the leaves of seedlings which have been supplied nitrate. A cDNA clone that encoded part of the mRNA for squash nitrate reductase hybridized specifically with mRNA for this inducible nitrate reductase isoform. Nitrate induction resulted in an increase in the steady-state levels of mRNA for this isoform after 24 hours, while the addition of glutamine to the nitrate diminished steady-steady state levels of this mRNA.

A method for the separation and partial purification of the three forms of nitrate reductase present in wild-type soybean leaves

A rapid and simple purification method was used to separate and purify nitrate reductases (NR) from Williams soybean leaves. Blue Sepharose columns were sequentially eluted with 50 millimolar NADPH and 50 millimolar NADH, thus separating NAD(P)H:NR from NADH:NRs. Subsequent purification of the collected peaks on a fast protein liquid chromatography-Mono Q column enabled separation of two NADH:NRs. Sodium dodecyl sulfate polyacrylamide gel electrophoresis revealed that the subunit relative molecular mass for all three NR forms (constitutive NAD(P)H:NR [pH 6.5], EC 1.6.6.2; constitutive NADH:NR [pH 6.5], EC not assigned; and inducible NADH:NR [pH 7.5], EC 1.6.6.1) was approximately 107 to 109 kilodaltons. All three NRs showed similar spectra with absorption maxima at 413 and 273 nanometers in the oxidized state, and with the characteristics of a cytochrome b type heme upon reduction with NADH (absorption maxima at 556, 527, and 424 nanometers). The technique developed provides an improved separation of the three NR forms from soybean leaves. The similarity of the NRs with regard to their cytochrome b(556) type heme content and in relative molecular mass indicated that other differences must exist to account for the different kinetic and physical properties previously reported.

Leaf development and the role of NADP-malate dehydrogenase in C3 plants

The activity of NADP-malate dehydrogenase (NADP-MDH) was determined in the developing first leaf of the C3 plants wheat, barley and pea. Light dependent activation of the enzyme was observed in all three species following rapid extraction and immediate assay. Maximum activity was obtained following extraction from preilluminated leaves and incubation on ice for 45 min in the presence of dithiothreitol. In all three species, maximum activity was obtained in the young leaf 4 days after emergence of the seedling (about 2.5 to 3 μmoles per milligram chlorophyll per min in wheat and barley, and 6 μmoles per milligram chlorophyll per min in pea). On a chlorophyll basis there was an approximate five-fold decrease in NADP-MDH activity as the leaf matured. A similar pattern was found for phospho-enolpyruvate carboxylase and NADP-malic enzyme which had maximum activity in younger leaf tissue. Similarly, the activity of nitrate reductase in wheat and barley was high in the young leaf and it rapidly declined as the leaf matured. In contrast, the capacity for photosynthesis was relatively low in the young leaf, reaching a maximum 6 to 8 days after seedling emergence. The pattern of change in activity of phosphoribulokinase, an enzyme of the reductive pentose phosphate pathway, was similar to that of photosynthesis. The results suggest NADP-MDH and phospho-enolpyruvate carboxylase have important function(s) in the young leaf, which are not directly linked to C3 photosynthesis, and which, in part, may be linked to nitrate assimilation and provision of malate to mitochondria.

Nitric Oxide and Nitrous Oxide Production by Soybean and Winged Bean during the in Vivo Nitrate Reductase Assay

This study was conducted to determine by gas chromatography (GC) and mass spectrometry (MS) the identity and the quantity of volatile N products produced during the helium-purged in vivo NR assay of soybean (Glycine max [L.] Merr. cv Williams) and winged bean (Psophocarpus tetragonolobus [L.] DC. cv Lunita) leaflets. Gaseous material for identification and quantitation was collected by cryogenic trapping of volatile compounds carried in the He-purge gas stream. As opposed to an earlier report, acetaldehyde oxime production was not detected by our GC method, and acetaldehyde oxime was shown to be much more soluble in water than the compound(s) evolved from soybean leaflets. Nitric oxide (NO) and nitrous oxide (N(2)O) were identified by GC and GC/MS as the main N products formed. NO and N(2)O produced from soybean leaflets were both labeled with (15)N when (15)N-nitrate was used in the assay medium, demonstrating that both were produced from nitrate during nitrate reduction. Other compounds co-trapped with NO and N(2)O were identified as air (N(2), O(2)), CO(2), methanol, acetaldehyde, and ethanol. Leaves of winged bean, subjected to the purged in vivo NR assay, evolved greater quantities of NO and N(2)O (13.9 and 0.37 micromole per gram fresh weight per 30 minutes, respectively) than did the soybean cv Williams (1.67 and 0.09 micromole per gram fresh weight per 30 minutes, respectively). In both species NO production was dominant. In contrast, with similar assays, NO and N(2)O were not evolved from leaves of the nr(1) soybean mutant which lacks the constitutive NR enzymes. In addition to soybean cv Williams, six other Glycine sp. examined evolved significant quantities of NO((x)) (NO and NO(2)). Other species including Neonotonia wightii (Arn.) Lackey comb. nov., Pueraria montana (Lour.) Merr., and Pueraria thunbergiana Benth. evolved lower levels of NO((x)).

NADH Nitrate Reductase and NAD(P)H Nitrate Reductase in Genetic Variants and Regenerating Callus of Maize

Different organs of maize seedlings are known to contain different complements of NADH and NAD(P)H nitrate reductase (NR) activity. The study of the genetic programming that gives rise to such differences can be initiated by looking for genetic variants exhibiting different patterns of distribution of the above enzymes. We demonstrate in this work that scutella of very young maize seedlings contain NADH NR almost exclusively and that this activity is gradually replaced, as the seedling ages, with NAD(P)H NR. Leaves in the seedlings contain exclusively the NADH NR activity. A genetic variant is described that contains much reduced levels of NAD(P)H NR activity but not of NADH NR activity in the scutellum. This same variant exhibits a relatively low level of NAD(P)H NR but normal NADH NR activity in seedling root tips. These observations suggest that the genetic program used to specify the scutellar complement of NR activity shares some common components with the genetic program used to determine the young root tip complement of NR activities. Parts of regenerating callus at different stages of differentiation were examined to determine when the differences in NR complement begin to appear. The same pattern of NADH NR and NAD(P)H NR activities was found in unorganized as well as in organized callus, in recognizable root-like and even in green shoot-like material, both activities being present in all these tissues. An examination of the NR complement in different organs of a number of siblings originating from a cross involving transposon Mu-containing parents and having different levels of leaf NADH NR activity shows that the leaf NADH NR activity content and the scutellum NAD(P)H NR activity content are relatively independent of each other, indicating that the genetic programs specifying the NR content of these organs are not tightly coupled, if at all.

Biochemical Characterization of Soybean Mutants Lacking Constitutive NADH:Nitrate Reductase

Two nitrate reductase (NR) mutants were selected for low nitrate reductase (LNR) activity by in vivo NR microassays of M(2) seedlings derived from nitrosomethylurea-mutagenized soybean (Glycine max [L.] Merr. cv Williams) seeds. The mutants (LNR-5 and LNR-6) appeared to have normal nitrate-inducible NR activity. Both mutants, however, showed decreased NR activity in vivo and in vitro compared with the wild-type. In vitro FMNH(2)-dependent nitrate reduction and Cyt c reductase activity of nitrate-grown plants, and nitrogenous gas evolution during in vivo NR assays of urea-grown plants, were also decreased in the mutants. The latter observation was due to insufficient generation of nitrite substrate, rather than some inherent difference in enzyme between mutant and wild-type plants. When grown on urea, crude extracts of LNR-5 and LNR-6 lines had similar NADPH:NR activities to that of the wild type, but both mutants had very little NADH:NR activity, relative to the wild type. Blue Sepharose columns loaded with NR extract of urea-grown mutants and sequentially eluted with NADPH and NADH yielded a NADPH:NR peak only, while the wild-type yielded both NADPH: and NADH:NR peaks. Activity profiles confirmed the lack of constitutive NADH:NR in the mutants throughout development. The results provide additional support to our claim that wild-type soybean contains three NR isozymes, namely, constitutive NADPH:NR (c(1)NR), constitutive NADH:NR (c(2)NR), and nitrate-inducible NR (iNR).

Nitrate Reductases from Wild-Type and nr(1)-Mutant Soybean (Glycine max [L.] Merr.) Leaves : II. Partial Activity, Inhibitor, and Complementation Analyses

Soybean (Glycine max [L.] Merr.) leaves have been shown to contain three forms of nitrate reductase (NR). Two of the forms, which are present in leaves of wild-type (cv. Williams) plants grown in the absence of NO(3) (-), are termed constitutive and designated c(1)NR and c(2)NR. The third form, which is present in NO(3) (-)-grown mutant (nr(1)) plants lacking the constitutive forms, is termed inducible and designated iNR. Samples of c(1)NR, c(2)NR, and iNR obtained from appropriately treated plants were analyzed for the presence of partial activities, response to inhibitors, and ability to complement a barley NR which lacks the molybdenum cofactor (MoCo) but is otherwise active.The three forms were similar to most assimilatory NR enzymes in that they (a) exhibited NADH-cytochrome c reductase, reduced flavin mononucleotide-NR, and reduced methyl viologen-NR partial activities; (b) were inhibited by p-hydroxymercuribenzoate at the site of initial electron transport through each enzyme; (c) were more inhibited by CN(-) in their reduced enzyme state as compared with their oxidized state; and (d) complemented a MoCo-defective NR (e.g. contained cofactors with characteristics similar to the MoCo found in barley NR and commercial xanthine oxidase). However, among themselves, they showed dissimilarities in their response to treatment with HCO(3) (-) and CN(-), and in their absolute ability to complement the barley NR. The site of effect for these treatments was the terminal cofactor-containing portion of each enzyme. This indicated that, although a terminal cofactor (presumably a MoCo) was present in each form, structural or conformational differences existed in the terminal cofactor-protein complex of each form.