Identification and characterization of a nitrate reductase gene from bean (Phaseolus vulgaris) containing four introns

A structural gene encoding nitrate reductase (NR) in bean ( Phaseolus vulgaris ) has been cloned and sequenced. The NR gene encodes a protein of 890 amino acids with a molecular mass of 100 kDa. Comparison to the other known NR gene from bean reveals 76% amino acid identity and comparison to NRs from other species shows amino acid identities ranging from 67 to 77%. At three positions the amino acid sequence displays differences from residues conserved in all other known NR proteins. The coding sequence is interrupted by four introns. Three of them are located at conserved positions in the region encoding the molybdenum cofactor-binding domain. The fourth intron is located in the hinge region between the heme and the FAD domain. This is the only example in which more than three introns have been found in a higher plant NR gene. The mRNA cap site was identified as an adenosine 79 nucleotides (nt) upstream of the ATG translation start codon. Northern analysis shows that the gene is nitrate inducible and highly expressed in trifoliolate leaves of 20-day-old bean plants and only weakly expressed in roots. The gene is also induced by light and sucrose in leaves of dark-adapted plants. The mRNA displays diurnal oscillation under the control of a circadian rhythm. Putative conserved GATA motifs in the promoter are discussed.     

Cloning and expression of a gene encoding a root specific nitrate reductase in bean (Phaseolus vulgaris)

A structural gene encoding nitrate reductase (NR) in the legume Phaseolus vulgaris cv. Saxonia has been cloned and sequenced. The NR gene encodes a protein of 881 amino acids with a MW of 99.2 kDa. The coding sequence is interrupted by three introns, which are located in the molybdopterin cofactor binding domain. In the flanking regions the signals of a functional eukaryotic gene are present. The gene is the smallest NR gene so far identified in higher plants. Comparison to other NRs shows homology ranging from 65 to 74% at the amino acid level. The similarity is highest for the three functional domains, and lowest in the N-terminal end of the protein. mRNA studies demonstrate that the gene is nitrate inducible and expressed exclusively in the roots of bean. Southern blot analysis indicates the presence of a second NR gene in bean. This gene may encode a NR enzyme expressed in leaves.     

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 b₅₅₆ 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.     

Isolation and analysis of a cDNA clone that encodes an alfalfa (Medicago sativa) aspartate aminotransferase

Summary Nitrate reductase (NR) assays revealed a bi-specific NAD(P)H-NR (EC 1.6.6.2.) to be the only nitrate-reducing enzyme in leaves of hydroponically grown birches. To obtain the primary structure of the NAD(P)H-NR, leaf poly(A)⁺ mRNA was used to construct a cDNA library in the lambda gt11 phage. Recombinant clones were screened with heterologous gene probes encoding NADH-NR from tobacco and squash. A 3.0 kb cDNA was isolated which hybridized to a 3.2 kb mRNA whose level was significantly higher in plants grown on nitrate than in those grown on ammonia. The nucleotide sequence of the cDNA comprises a reading frame encoding a protein of 898 amino acids which reveals 67%–77% identity with NADH-nitrate reductase sequences from higher plants. To identify conserved and variable regions of the multicentre electron-transfer protein a graphical evaluation of identities found in NR sequence alignments was carried out. Thirteen well-conserved sections exceeding a size of 10 amino acids were found in higher plant nitrate reductases. Sequence comparisons with related redox proteins indicate that about half of the conserved NR regions are involved in cofactor binding. The most striking difference in the birch NAD(P)H-NR sequence in comparison to NADH-NR sequences was found at the putative pyridine nucleotide binding site. Southern analysis indicates that the bi-specific NR is encoded by a single copy gene in birch. These sequence data appeared in the EMBL/GenBank/DDBJ nucleotide sequence data bases under the accession number X54097     

Effect of light/dark cycles on expression of nitrate assimilatory genes in maize shoots and roots

The level of nitrate reductase (NR) and nitrite reductase (NiR) varied in both shoot and root tissue from nitrate-fed Zea mays L. grown under a 16-hour light/8-hour dark regime over a 10-day period postgermination, with peak activity occurring in days 5 to 6. To study the effect of different light regimes on NR and NiR enzyme activity and mRNA levels, 6-day-old plants were grown in the presence of continuous KNO₃ (10 millimolar). Both shoot NRA and mRNA varied considerably, peaking 4 to 8 hours into the light period. Upon transferring plants to continuous light, the amplitude of the peaks increased, and the peaks moved closer together. In continuous darkness, no NR mRNA or NR enzyme activity could be detected by 8 hours and 12 hours, respectively. In either a light/dark or continuous light regime, root NRA and mRNA did not vary substantially. However, when plants were placed in continuous darkness, both declined steadily in the roots, although some remained after 48 hours. Although there was no obvious cycling of NiR enzyme activity in shoot tissue, changes in mRNA mimicked those seen for NR mRNA. The expression of NR and NiR genes is affected by the light regime adopted, but light does not have a direct effect on the expression of these genes.     

Regulation of Mo-cofactor, NADH- and NAD(P)H-specific nitrate reductase activities in the wild type and two nar-mutant lines of barley (Hordeum vulgare L.)

Seedlings of three genotypes of barley, Hordeum vulgare L.,cv. Winer, were grown in nutrient solutions for 12 d: (a) Wt,the wild type; (b) Chlo19 and (c) Chlo29, two nitrate reductase(NR) deficient nar-mutants. Nar-mutant plants grown in nitratedeveloped about 5–24% of NADH-NR (EC 1.6.6.1 [EC] .) activitylevel characteristic of the Wt. The NR in vitro assays in whichNADH or NADPH were used as electron donors showed that the twomutant lines contained a mixture of NADH-specific and NAD(P)H-bispecific(EC 1.6.6.2 [EC] .) NRs. Chlo19 had a very low level of MoCo activityas compared to Chlo29 and Wt. Chlo19 appeared to be mutatedin a MoCo gene rather than in the genes coding for the nitrateNR apoenzyme. NAD(P)H-NR was found in the shoots and roots of both mutantsbut only in the roots of Wt. Several aspects of the regulationof NADH and NAD(P)H specific NRs in plants of the barley cv.Winer genotypes are discussed. MoCo was a strong limiting factorfor NR biosynthesis in nitrate-fed plants of Chlo19, but lesslimited in N-starved and ammonium-fed plants. Biomass productionby the three genotypes was similar during first 12 d after germination,regardless of the level of NR detected in vitro. Mutant plantsmay be able to supply the nitrogen required for growth withonly 5–24% of the NR level of the WT. Key words: Hordeum vulgare, mutants, nitrate, nitrate reductase, molybdenum cofactor     

Relationship between Soil Nitrate Content and Activities of NADH: and NAD(P)H:Nitrate Reductases in Indian Mustard

The pattern of NADH- and NAD(P)H-specific nitrate reductase (NRs) activities in Indian mustard (Brassica juncea L. Czern. and Coss.) was monitored throughout growth stages. NAD(P)H:NR (EC 1.6.6.2) activity was maximum at early stages of growth (30 days after sowing, DAS), then declined gradually reaching to almost zero at 90 DAS. Contrary to this, NADH:NR (EC 1.6.6.1) activity was low at 30 DAS, then gradually increased till 90 DAS and thereafter, it became constant. The decrease in NAD(P)H:NR activity and increase in the NADH:NR activity were associated with the seasonal decrease in nitrate content in the soil. This revised version was published online in July 2006 with corrections to the Cover Date.     

The activation state of nitrate reductase is not always correlated with total nitrate reductase activity in leaves

The relation between nitrate reductase (NR; EC 1.6.6.1) activity, activation state and NR protein in leaves of barley (Hordeum vulgare L.) seedlings was investigated. Maximum NR activity (NRA_max) and NR protein content (Western blotting) were modified by growing plants hydroponically at low (0.3 mM) or high (10 mM) nitrate supply. In addition, plants were kept under short-day (8 h light/16 h dark) or long-day (16 h light/8 h dark) conditions in order to manipulate the concentration of nitrate stored in the leaves during the dark phase, and the concentrations of sugars and amino acids accumulated during the light phase, which are potential signalling compounds. Plants were also grown under phosphate deficiency in order to modify their glucose-6-phosphate content. In high-nitrate/long-day conditions, NRA_max and NR protein were almost constant during the whole light period. Low-nitrate/long-day plants had only about 30% of the NRA_max and NR protein of high-nitrate plants. In low-nitrate/long-day plants, NRA_max and NR protein decreased strongly during the second half of the light phase. The decrease was preceded by a strong decrease in the leaf nitrate content. Short daylength generally led to higher nitrate concentrations in leaves. Under short-day/low-nitrate conditions, NRA_max was slightly higher than under long-day conditions and remained almost constant during the day. This correlated with maintenance of higher nitrate concentrations during the short light period. The NR activation state in the light was very similar in high-nitrate and low-nitrate plants, but dark inactivation was twice as high in the high-nitrate plants. Thus, the low NRA_max in low-nitrate/long-day plants was slightly compensated by a higher activation state of NR. Such a partial compensation of a low NR_max by a higher dark activation state was not observed with phosphate-depleted plants. Total leaf concentrations of sugars, of glutamine and glutamate and of glucose-6-phosphate did not correlate with the NR activation state nor with NRA_max. Received: 24 March 1999 / Accepted: 31 May 1999     

Nitrate assimilation in the forage legume Lotus japonicus L.

Nitrate assimilation in the model legume, Lotus japonicus, has been investigated using a variety of approaches. A gene encoding a nitrate-inducible nitrate reductase (NR) has been cloned and appears to be the only NR gene present in the genome. Most of the nitrate reductase activity (NRA) is found in the roots and the plant assimilates the bulk of its nitrogen in that tissue. We calculate that the observed rates of nitrate reduction are compatible with the growth requirement for reduced nitrogen. The NR mRNA, NRA and the nitrate content do not show a strong diurnal rhythm in the roots and assimilation continues during the dark period although export of assimilated N to the shoot is lower during this time. In shoots, the previous low NR activity may be further inactivated during the dark either by a phosphorylation mechanism or due to reduced nitrate flux coincident with a decreased delivery through the transpiration stream. From nitrate-sufficient conditions, the removal of nitrate from the external medium causes a rapid drop in hydraulic conductivity and a decline in nitrate and reduced-N export. Root nitrate content, NR and nitrate transporter (NRT2) mRNA decline over a period of 2 days to barely detectable levels. On resupply, a coordinated increase of NR and NRT2 mRNA, and NRA is seen within hours.     

Nitrate-independent expression of plant nitrate reductase in Lotus japonicus root nodules

Nitrate-independent nitrate reductase (NR) activity is generally found in legume root nodules. Therefore, the effects of nitrate on plant NR activity and mRNA were investigated in the root nodules of Lotus japonicus (L. japonicus). Both NR activity and mRNA levels in roots and root nodules were up-regulated by the addition of nitrate. In the absence of nitrate, NR activity and mRNA were detected in root nodules but not in roots. Southern blotting analysis indicates that NR is encoded by a single gene in L. japonicus. No nitrate was detected in the root nodules or roots of plants grown in the absence of nitrate, while its accumulation was observed in plants supplied with exogenous nitrate. These results indicate that inducible-type NR can be expressed in root nodules in the absence of nitrate. The activation state of the nitrate-independent activity of NR was as high as that of NR activity induced by nitrate. NR mRNA expressed independently of nitrate in root nodules without nitrate was localized in the infected regions of the root nodules. Thus, the expression could be related to the specific structure and environment of root nodules.     

The roles of nitrate and ammonium in the regulation of the development of nitrate reductase in Chlamydomonas reinhardii

The regulation of the development of nitrate reductase (NR) activity in Chlamydomonas reinhardii has been compared in a wild-type strain and in a mutant (nit-A) which possesses a modified nitrate reductase enzyme that is non-functional in vivo. The modified enzyme cannot use NAD(P)H as an electron donor for nitrate reduction and it differs from wild-type enzyme in that NR activity is not inactivated in vitro by incubation with NAD(P)H and small quantities of cyanide; it is inactivated when reduced benzyl viologen or flavin mononucleotide is present. After short periods of nitrogen starvation mutant organisms contain much higher levels of terminal-NR activity than do similarly treated wild-type ones. Despite the inability of the mutant to utilize nitrate, no nitrate or nitrite was found in nitrogen-starved cultures; it is therefore concluded that the appearance of NR activity is not a consequence of nitrification. After prolonged nitrogen starvation (22 h) the NR level in the mutant is low. It increases rapidly if nitrate is then added and this increase in activity does not occur in the presence of ammonium, tungstate or cycloheximide. Disappearance of preformed NR activity is stimulated by addition of tungstate and even more by addition of ammonium. The results are interpreted as evidence for a continuous turnover of NR in cells of the mutant with ammonium both stimulating NR breakdown and stopping NR synthesis. Nitrate protects the enzyme from breakdown. Reversible inactivation of NR activity is thought to play an insignificant rôle in the mutant.Abbreviations NR nitrate reductase - BV benzyl viologen     

Preparation of Monoclonal Antibodies against NADH: Nitrate Reductase from the Red Alga Porphyra yezoensis

Twenty-two monoclonal antibodies were raised against the nativeform of nitrate reductase (NR) from Porphyra yezoensis, a marinered alga. All the antibodies were able to bind to NR from P.yezoensis, with resultant inhibition of full (NADH:NR) and/orpartial (NADH:FR, NADH:CR, FMNH₂:NR, and MV:NR) enzymatic activity.Fifteen of the antibodies recognized the denatured form of theenzyme. Size-exclusion gel nitration and immunoblotting of theproducts of the limited proteolysis of NR from P. yezoensisby trypsin or Staphylococcus aureus V8 protease revealed that2 out of the 15 subunit-recognizing antibodies bound to theFAD domain, 6 bound to the heme domain, and 7 bound to the Mo-pterindomain. The products of limited proteolysis of NR from P. yezoensisalso revealed that the sites of proteolytic cleavage that encompassedthe heme domain were inverted as compared to the analogous sitesin NRs of higher plants. Some of the monoclonal antibodies cross-reactedwith NRs from plants belonged to different phyla. From threeto five of the antibodies bound subunits of NR from multicellularred algae, but failed to bind NRs from unicellular red algae.Three or four of the antibodies crossreacted with NRs from higherplants, such as tobacco and spinach. One of the antibodies boundNRs from several types of plant, namely, members of Cryptophyta,Chromophyta, and Chlorophyta. All of the monoclonal antibodiesthat cross-reacted with NRs from plants other than the red algaewere specific for the Mo-pterin domain of NR from P. yezoensis. (Received May 10, 1994; Accepted September 7, 1994)