Effect and potential mechanism of nitrite reductase B on nitrite degradation by Limosilactobacillus fermentum RC4

Nitrite has the potential risk of hypoxic poisoning or cancer in pickled food. In our previous study, Limosilactobacillus fermentum (L. fermentum) RC4 is effective in nitrite degradation by producing nitrite reductase B (NirB). To investigate the detailed mechanism from the genome, response, and regulation of NirB, the whole-genome sequence of L. fermentum RC4 was analyzed, the L. fermentum-EGFP-nirB with enhanced green fluorescent protein (EGFP) labeled the nitrite reductase large subunit nirB, and the recombined L. fermentum-NirB with overexpression NirB strain was conducted. The key genes within the dominant metabolism pathways may be involved in stress tolerance to regulate the degrading process. The green fluorescence density of EGFP indicated that NirB activity has a threshold and peaked under 300 mg/L nitrite concentration. NirB overexpressed in L. fermentum RC4 boosted the enzyme activity by 39.6% and the degradation rate by 10.5%, when fermented in 300 mg/L for 40 h, compared to the control group. RNA-seq detected 248 differential genes mainly enriched in carbohydrate, amino acid, and energy metabolism. The ackA gene for pyruvate metabolism and the mtnN gene for cysteine metabolism were up-regulated. NirB regulates these genes to produce acid and improve stress resistance for L. fermentum RC4 to accelerate nitrite degradation.

Response of nitrite accumulation to elevated C/NO- 3-N ratio during partial denitrification process: Insights of extracellular polymeric substance, microbial community and metabolic function

This study investigated the response of nitrite accumulation to elevated COD/NO₃^--N ratio (C/N) during partial denitrification (PD). Results indicated nitrite was gradually accumulated and remained stable (C/N = 1.5 ∼ 3.0), while that rapidly declined after reaching the peak (C/N = 4.0 ∼ 5.0). The polysaccharide (PS) and protein (PN) content of tightly-bound extracellular polymeric substances (TB-EPS) reached the maximum at C/N of 2.5 ∼ 3.0, which might be stimulated by high level of nitrite. Illumina MiSeq sequencing showed Thauera and OLB8 were dominated denitrifying genera at C/N of 1.5 ∼ 3.0, while Thauera was further enriched with fading OLB8 at C/N of 4.0 ∼ 5.0. Meanwhile, the highly-enriched Thauera might enhance the activity of nitrite reductase (nirK) promoting further nitrite reduction. Redundancy analysis (RDA) showed positive correlations between nitrite production and PN content of TB-EPS, denitrifying bacteria (Thauera and OLB8) and nitrate reductases (narG/H/I) in low C/N. Finally, their synergistic effects for driving nitrite accumulation were comprehensively elucidated.

Molecular and kinetic properties of copper nitrite reductase from Sinorhizobium meliloti 2011 upon substituting the interfacial histidine ligand coordinated to the type 2 copper active site for glycine

A copper-containing nitrite reductase catalyzes the reduction of nitrite to nitric oxide in the denitrifier Sinorhizobium meliloti 2011 (SmNirK), a microorganism used as bioinoculant in alfalfa seeds. Wild type SmNirK is a homotrimer that contains two copper centers per monomer, one of type 1 (T1) and other of type 2 (T2). T2 is at the interface of two monomers in a distorted square pyramidal coordination bonded to a water molecule and three histidine side chains, H171 and H136 from one monomer and H342 from the other. We report the molecular, catalytic, and spectroscopic properties of the SmNirK variant H342G, in which the interfacial H342 T2 ligand is substituted for glycine. The molecular properties of H342G are similar to those of wild type SmNirK. Fluorescence-based thermal shift assays and FTIR studies showed that the structural effect of the mutation is only marginal. However, the kinetic reaction with the physiological electron donor was significantly affected, which showed a ∼ 100-fold lower turnover number compared to the wild type enzyme. UV-Vis, EPR and FTIR studies complemented with computational calculations indicated that the drop in enzyme activity are mainly due to the void generated in the protein substrate channel by the point mutation. The main structural changes involve the filling of the void with water molecules, the direct coordination to T2 copper ion of the second sphere aspartic acid ligand, a key residue in catalysis and nitrite sensing in NirK, and to the loss of the 3 N-O coordination of T2.

Fumarate and nitrite reduction by Prevotella nigrescens and Prevotella buccae isolated from Chronic Periodontitis patients

OBJECTIVE

This study is an investigation of anaerobic nitrite and fumarate reduction/respiration abilities of two characterised Prevotella species namely Prevotella nigrescens (SS6B) and Prevotella buccae (GS6B) isolated from the periodontal pockets of chronic periodontitis (ChP) patients.

METHODS

Isolation and identification of the periodontal bacteria from 20 patients showing clinical symptoms of ChP. Characterisation of anaerobic nitrite and fumarate reduction was done in P. nigrescens (SS6B) and P. buccae (GS6B) using reduction assays, inhibition assays with use of specific inhibitors, growth assays and enzyme activity assays. Degenerate PCR was used to detect and amplify nitrite reductase (nrfA) and fumarate reductase (frdA) gene sequences in these Prevotella isolates. In addition, molecular and in silico analysis of the amplified anaerobic reductase gene sequences was performed using NCBI conserved domain analysis, Interpro database and MegaX.

RESULTS

We provided experimental evidence for presence of active nitrite and fumarate reductase activities through enzyme activity, reduction, inhibitor and growth assays. Moreover, we were able to detect presence of 505 bps nrfA gene fragment and 400 bps frdA gene fragment in these Prevotella spp. These fragments show similarity to multiheme ammonia forming cytochrome c nitrite reductases and fumarate reductases flavoprotein subunit, respectively.

CONCLUSION

Anaerobic nitrite and fumarate respiration abilities in P. nigrescens and P. buccae isolates appear to be important for detoxification process and growth, respectively.

Chronic high-dose silver nanoparticle exposure stimulates N2O emissions by constructing anaerobic micro-environment

Silver nanoparticles (Ag-NPs) were found to be responsible for nitrous oxide (N₂O) generation; however, the mechanism of Ag-NP induced N₂O production remains controversial and needs to be elucidated. In this study, chronic Ag-NP exposure experiments were conducted in five independent sequencing batch biofilm reactors to systematically assess the effects of Ag-NPs on N₂O emission. The results indicated that a low dose of Ag-NPs (< 1 mg/L) slightly suppressed N₂O generation by less than 22.99% compared with the no-Ag-NP control method. In contrast, a high dose (5 mg/L) of Ag-NPs stimulated N₂O emission by 67.54%. ICP-MS and SEM-EDS together revealed that high Ag-NP content accumulated on the biofilm surface when exposed to 5 mg/L Ag-NPs. N₂O and DO microelectrodes, as well as N₂O isotopic composition analyses, further demonstrated that the accumulated Ag-NPs construct the anaerobic zone in the biofilm, which is the primary factor for the stimulation of the nitrite reduction pathway to release N₂O. A metagenomic analysis further attributed the higher N₂O emissions under exposure to a high dose of Ag-NPs to the higher relative abundance of narB and nirK genes (i.e. 1.52- and 1.29-fold higher, respectively). These findings collectively suggest that chronic exposure to high doses of Ag-NPs could enhance N₂O emissions by forming anaerobic micro-environments in biofilms.

Myoglobin mutant with enhanced nitrite reductase activity regulates intracellular oxidative stress in human breast cancer cells

Heme proteins play vital roles in regulating the reactive oxygen/nitrogen species (ROS/RNS) levels in cells. In this study, we overexpressed human wild-type (WT) myoglobin (Mb) and its double mutant, F43H/H64A Mb with enhanced nitrite reductase (NIR) activity, in the typical representative triple-negative breast cancer cell, MDA-MB-231 cells. The results showed that the overexpression of F43H/H64A Mb increased the level of nitric oxide (NO) and the degree of oxidative stress, and then activated Akt/MAPK mediated apoptotic cascade, whereas WT Mb showed the opposite effect. This study indicates that Mb plays an important role in maintaining the balance of the cellular redox system and could thus be a valuable target for cancer therapy.

Bilirubin oxidase as a single enzymatic oxygen scavenger for the development of reductase-based biosensors in the open air and its application on a nitrite biosensor

The commercialization of amperometric or voltammetric biosensors that operate at potentials lower than -0.2 V vs SHE has been hindered by the need for anoxic working conditions due to the interference of molecular oxygen, whose electrochemical reduction can potentially mask other redox processes and generate reactive oxygen species (ROS). A deoxygenation step must be thus integrated into the analytical process. To this end, several (bio)chemical oxygen scavenging systems have been proposed, such as the bi-enzyme system, glucose oxidase/catalase. Still, a few issues persist owing to enzyme impurities and the formation of oxygen reactive species. Here in, we propose a new mono-enzymatic oxygen scavenging system composed of a multicopper oxidase as a single biocatalytic oxygen reducer. As a model, we used bilirubin oxidase (BOD), which catalyzes the direct reduction of oxygen to water in the presence of an electron donor substrate, without releasing hydrogen peroxide. Both the direct electron transfer and mediated electrochemical approach using different co-substrates were screened for the ability to promote the enzymatic reduction of oxygen. An optimal combination of BOD with sodium ascorbate proved to be quick (5 min) and effective. It was subsequently employed, as a proof-of-concept, in a voltammetric biosensor based on a multiheme cytochrome c nitrite reductase, which performs the reduction of nitrite to ammonia at potentials below -0.3 V vs SHE. The nitrite biosensor performed well under ambient air, with no need for a second enzyme to account for the build-up of oxygen reactive intermediaries.

Nitrite is reduced by nitrite reductase NirB without small subunit NirD in Escherichia coli

The assimilatory nitrite reductase enzyme NirB and small subunit NirD genes encoded in nir operon in Escherichia coli were cloned into the pET28a vector, and the recombinant enzyme was characterized for the first time. Docking of NirB with NirD, NADH, NO₂^-, NO₃^-, and CHO₂^- was performed using docking modeling programs. Methyl viologen and sodium dithionite were used as electron couples, and the amount of reduced nitrite was measured to calculate enzyme activity. NirB is the main enzyme and shows high activity with or without NirD. However, the inclusion of NirD into the enzyme solution at a ratio of 1NirD:2NirB resulted in 10% higher nitrite reductase activity. The enzyme tends to aggregate in the absence of β-mercaptoethanol, which causes the conversion of tetrameric NirB to monomeric form, and the NirB enzyme shows its highest activity in monomeric form. The optimum temperature for enzyme activity was 37 °C and the optimum pH was found to be 7.0. K_m and V_max values of NirB were calculated as 9833 μM and 416.67 μmol NO₂^- reduced min^-1 mg^-1. Enzyme activity decreased by 55% and 50% in the presence of 100 mM nitrate and formate, respectively. The presence of 25 mM Cd²⁺ protected the enzyme at room temperature and the enzyme showed 10% higher activity in the presence of cadmium.

Nitrite reductase activity within an antiparallel de novo scaffold

Copper nitrite reductase (CuNiR) is a copper enzyme that converts nitrite to nitric oxide and is an important part of the global nitrogen cycle in bacteria. The relatively simple CuHis₃ binding site of the CuNiR active site has made it an enticing target for small molecule modeling and de novo protein design studies. We have previously reported symmetric CuNiR models within parallel three stranded coiled coil systems, with activities that span a range of three orders of magnitude. In this report, we investigate the same CuHis₃ binding site within an antiparallel three helical bundle scaffold, which allows the design of asymmetric constructs. We determine that a simple CuHis₃ binding site can be designed within this scaffold with enhanced activity relative to the comparable construct in parallel coiled coils. Incorporating more complex designs or repositioning this binding site can decrease this activity as much as 15 times. Comparing these constructs, we reaffirm a previous result in which a blue shift in the 1s to 4p transition energy determined by Cu(I) X-ray absorption spectroscopy is correlated with an enhanced activity within imidazole-based constructs. With this step and recent successful electron transfer site designs within this scaffold, we are one step closer to a fully functional de novo designed nitrite reductase.

Resequencing and transcriptomic analysis reveal differences in nitrite reductase in jujube fruit (Ziziphus jujuba Mill.)

BACKGROUND

Jujube is a typical fruit tree species from China. 'Muzao', a cracking-susceptible cultivar, and 'Linhuang No. 1', a cracking-resistant cultivar, were selected in a previous study as contrasting research materials. Whole-genome resequencing and transcriptomic analysis of 'Linhuang No. 1' and 'Muzao' allowed the identification of differentially expressed genes with different gene structures between the two cultivars and could be helpful in explaining the differences and similarities between the two cultivars.

RESULTS

Resequencing identified 664,129 polymorphic variable sites between 'Linhuang No. 1' and 'Muzao'. To determine the genetic relationship among 'Linhuang No. 1', 'Muzao' and the jujube genome reference cultivar 'Dongzao', the characteristic polymorphic variable sites were analysed by principal component analysis. The genetic relationship between 'Linhuang No. 1' and 'Muzao' was closer than that of either variety and 'Dongzao'. Nineteen differentially expressed genes were identified by combining transcriptomic analysis with resequencing analysis. LOC107427052 (encoding a nitrite reductase) was identified by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis for further study. The identified insertion was not in the domain region of the LOC107427052 gene coding sequence (CDS) region and was verified by the finding that the insertion did not affect translation of the protein. The LOC107427052 gene expression levels, nitrite reductase activities and nitrite contents of 'Muzao' were significantly higher than the corresponding values of 'Linhuang No. 1' at the young fruit stage. There was no significant difference in the quantity of the product of nitrite reductase, namely, ammonia, between the two cultivars.

CONCLUSIONS

The present study was the first to explore the differences between different jujube cultivars ('Linhuang No. 1' and 'Muzao') by combining genome resequencing and transcriptomics. LOC107427052 (encoding a nitrite reductase) was characterized by KEGG enrichment analysis. The insertion in the CDS region of the LOC107427052 gene provides a new direction for the study of nitrogen metabolism in jujube. Our study has laid a foundation for the comparative analysis of nitrite metabolism between the jujube cultivars 'Linhuang No. 1' and 'Muzao'.

Comparative genomics in "Candidatus Kuenenia stuttgartiensis" reveal high genomic plasticity in the overall genome structure, CRISPR loci and surface proteins

Background

Anaerobic ammonium oxidizing bacteria (anammox bacteria) are contributing significantly to the nitrogen cycle and are successfully used in wastewater treatment. Due to the lack of complete genomes in the databases, little is known about the stability and variability of their genomes and how the genomes evolve in response to changing environments.

Results

Here we report the complete genome of the anammox bacterium “Candidatus Kuenenia stuttgartiensis” strain CSTR1 which was enriched planktonically in a semi-continuous stirred-tank reactor. A comparison of the genome of strain CSTR1 with the genome of “Ca. Kuenenia stuttgartiensis” MBR1 and the draft genome of KUST showed > 99% average nucleotide identity among all. Rearrangements of large genomic regions were observed, most of which were associated with transposase genes. Phylogenetic analysis suggests that strain MBR1 is more distantly related to the other two strains. Proteomic analysis of actively growing cells of strain CSTR1 (growth rate ~ 0.33 d^− 1) failed to detect the annotated cytochrome cd₁-type nitrite reductase (NirS) although in total 1189 proteins were found in the proteome. Yet, this NirS was expressed when strain CSTR1 was under stress or starvation (growth rate < 0.06 d^− 1). We also observed large sequence shifts in the strongly expressed S-layer protein compared to other “Ca. Kuenenia” strains, indicating the formation of hybrids of genes encoding the surface proteins.

Conclusions

“Ca. Kuenenia” strains appear to be relatively stable in their basic physiological traits, but show high variability in overall genome structure and surface proteins.

The effect of hydrophobic immobilization

The Met80Ala and Met80Ala/Tyr67Ala variants of S. cerevisiae iso-1 cytochrome c (ycc) and their adducts with cardiolipin immobilized onto a gold electrode coated with a hydrophobic self-assembled monolayer (SAM) of decane-1-thiol were studied through cyclic voltammetry and surface-enhanced resonance Raman spectroscopy (SERRS). The electroactive species - containing a six-coordinate His/His axially ligated heme and a five-coordinate His/- heme stable in the oxidized and reduced state, respectively - and the pseudoperoxidase activity match those found previously for the wt species and are only slightly affected by CL binding. Most importantly, the reduced His/- ligated form of these variants is able to catalytically reduce the nitrite ion, while electrode-immobilized wt ycc and other His/Met heme ligated variants under a variety of conditions are not. Besides the pseudoperoxidase and nitrite reductase functions, which are the most physiologically relevant abilities of these constructs, also axial heme ligation and the equilibria between conformers are strongly affected by the nature - hydrophobic vs. electrostatic - of the non-covalent interactions determining protein immobilization. Also affected are the catalytic activity changes induced by a given mutation as well as those due to partial unfolding due to CL binding. It follows that under the same solution conditions the structural and functional properties of immobilized ycc are surface-specific and therefore cannot be transferred from an immobilized system to another involving different interfacial protein-SAM interactions.

Community Composition of Nitrite Reductase Gene Sequences in an Acid Mine Drainage Environment

Denitrifying microbial communities play a central role in the nitrogen cycle, contribute to greenhouse gas production, and provide ecosystem services through the mitigation of nitrogen pollution. The impacts of human-induced acid mine drainage (AMD) and naturally occurring acid rock drainage (ARD), both characterized by low pH and high metal concentrations, on denitrifying microbial communities is not well understood. This study examined denitrifying microbes within sediments impacted by acidic and metal-rich AMD or ARD in the Iron Springs Mining District (10 sites across four regions over four time points) located in Southwest Colorado, USA. Denitrification functional gene sequences (nirS and nirK coding for nitrite reductase) had a high number of observed OTUs (260 for nirS and 253 for nirK) and were observed at sites with pH as low as 3.5 and metals > 2 mg/L (including aluminum, iron, manganese, strontium, and zinc). A majority of the nirK and nirS OTUs (> 60%) were present in only one sampling region. Approximately 8% of the nirK and nirS OTUs had a more cosmopolitan distribution with presence in three or more regions. Phylogenetically related OTUs were found across sites with very different chemistry. The overall community structure for nirK and nirS genes was correlated to conductivity and calcium (respectively), which may suggest that conductivity may play an important role in shaping the distribution of nirK- and nirS-type denitrifiers. Overall, these findings improve upon our understanding of the potential for denitrification within an ecosystem impacted by AMD or ARD and provide a foundation for future research to understand the rates and physiology of denitrifying organisms in these systems.

Changes in the Potential Activity of Nitrite Reducers and the Microbial Community Structure After Sediment Dredging and Plant Removal in the Empuriabrava FWS-CW

In constructed wetlands (CW), denitrification usually accounts for > 60% of nitrogen removal and is supposedly affected by wetland management practices, such as dredging (and plant removal). These practices cause an impact in sediment properties and microbial communities living therein. We have quantified the effects of a sediment dredging event on dissimilatory nitrite reduction by analysing the structure and activities of the microbial community before and after the event. Potential rates for nitrate reduction to ammonia and denitrification were in accordance with changes in the physicochemical conditions. Denitrification was the predominant pathway for nitrite removal (> 60%) and eventually led to the complete removal of nitrate. On the contrary, dissimilatory nitrite reduction to ammonia (DNRA) increased from 5 to 18% after the dredging event. Both actual activities and abundances of 16S rRNA, nirK and nirS significantly decreased after sediment dredging. However, genetic potential for denitrification (qnirS + qnirK/q16S rRNA) remained unchanged. Analyses of the 16S rRNA gene sequences revealed the importance of vegetation in shaping microbial community structures, selecting specific phylotypes potentially contributing to the nitrogen cycle. Overall, we confirmed that sediment dredging and vegetation removal exerted a measurable effect on the microbial community, but not on potential nitrite + nitrate removal rates. According to redundancy analysis, nitrate concentration and pH were the main variables affecting sediment microbial communities in the Empuriabrava CWs. Our results highlight a high recovery of the functionality of an ecosystem service after a severe intervention and point to metabolic redundancy of denitrifiers. We are confident these results will be taken into account in future management strategies in CWs.

Characterization of Denitrifying Community for Application in Reducing Nitrogen: a Comparison of nirK and nirS Gene Diversity and Abundance

Studies have shown that the addition of biochar to agricultural soils has the potential to mitigate climate change by decreasing nitrous oxide (N₂O) emissions resulting from denitrification. Rice paddy field soils have been known to have strong denitrifying activity, but the response of microbes to biochar for weakening denitrification in rice paddy field soils is not well known. In this work, compared with the chemical fertilizer alone, the chemical fertilizer + 20 t hm^-2 biochar fertilizer slightly decreased denitrifying the nitrite reductase activity (S-NiR) and N₂O emission without statistic difference, whereas the chemical fertilizer + 40 t hm^-2 biochar significantly boosted them. The abundance of nir-denitrifiers contributed to S-NiR and N₂O emission, especially nirS-denitrifiers, rather than the variation of community structure. Pearson correlation analysis showed that NO₂^--N was a key factor for controlling the abundance of nir-denitrifiers, S-NiR and N₂O emission. The biochar addition fertilization treatments strongly shaped the community structure of nirK-denitrifiers, while the community structure of nirS-denitrifiers remained relatively stable. In addition, Paracoccus and Sinorhizobium were revealed to be as the predominant lineage of nirS- and nirK-containing denitrifiers, respectively. Distance-based redundancy analysis (db-RDA) showed that changes in the nir-denitrifier community structure were significantly related to soil organic carbon, NO₃^--N, and total phosphorus. Our findings suggest that, although the nirS- and nirK-denitrifiers are both controlling nitrite reductase, their responses to biochar addition fertilization treatments showed significant discrepancies of diversity, abundance, and contribution to N₂O and S-NiR in a paddy soil.

Biochar counteracts nitrification inhibitor DMPP-mediated negative effect on spinach (Spinacia oleracea L.) growth

The use of nitrification inhibitors (NIs) such as 3,4-dimethylpyrazole phosphate (DMPP) has been suggested to diminish agricultural soil nitrate (NO₃^-) loss and increase nitrogen (N) use efficiency (NUE). However, the yield of ammonium (NH₄⁺)-sensitive plants such as spinach (Spinacia oleracea L.) may be adversely affected by the application of NIs at high N levels and, on the other hand, the efficiency of the NIs may also be affected by soil amendments such as biochar. These two issues are still not adequately addressed. The aim of this study was to evaluate the effect of different N levels including DMPP or not in a calcareous soil with and without amendment of wheat straw biochar on spinach yield, NUE, nitrate concentration of spinach leaf, activity of enzymes nitrate reductase (NR) and nitrite reductase (NiR), and soil ammonium (NH₄⁺) and NO₃^- concentration under greenhouse conditions. This experiment was carried out with different N rates factor at seven levels (un-fertilized, N0; fertilized with 50 mg N kg^-1 soil, N50; fertilized with 75 mg N kg^-1 soil, N75; fertilized with 100 mg N kg^-1 soil, N100; fertilized with N50 + DMPP; fertilized with N75 + DMPP; and fertilized with N100 + DMPP) and biochar (BC) factor at two levels (0, 0%BC; and 2% (w/w), 2%BC) with six replications over a 56-day cultivation period of spinach. Results showed that the application of DMPP had no significant effect on the yield of spinach plant at low and medium levels of N (50 and 75 mg N kg^-1 soil), but decreased the yield of this plant at the higher level of N (100 mg N kg^-1 soil). However, application of BC decreased the negative effect of DMPP on spinach yield as the yield in spinach plants fertilized with N75 + DMPP and N100 + DMPP significantly increased. Both application of DMPP and addition of BC to soil decreased leaf NO₃^- concentration by 29.2% and 16.3% compared to control, respectively. Biochar compared to control decreased NR activity by 46.3%. With increasing N rate, NR and NiR activities increased, but DMPP decreased the activities of both enzymes. Biochar reduced the efficiency of DMPP as soil NH₄⁺ concentration was higher in the treatments containing DMPP without BC at 56 days after planting. Biochar and DMPP could increase the quality of spinach plant through decreasing the leaf NO₃^- concentration. In general, wheat straw biochar counteracted DMPP-mediated negative effect on growth of spinach plant at high level of N by decreasing the efficiency of this inhibitor. These results provide the useful information for managing the application rate of N fertilizers including DMPP in biochar-amended soil.

Biological functions of nirS in Pseudomonas aeruginosa ATCC 9027 under aerobic conditions

Through our previous study, we found an up-regulation in the expression of nitrite reductase (nirS) in the isothiazolone-resistant strain of Pseudomonas aeruginosa. However, the definitive molecular role of nirS in ascribing the resistance remained elusive. In the present study, the nirS gene was deleted from the chromosome of P. aeruginosa ATCC 9027 and the resulting phenotypic changes of ΔnirS were studied alongside the wild-type (WT) strain under aerobic conditions. The results demonstrated a decline in the formations of biofilms but not planktonic growth by ΔnirS as compared to WT, especially in the presence of benzisothiazolinone (BIT). Meanwhile, the deletion of nirS impaired swimming motility of P. aeruginosa under the stress of BIT. To assess the influence of nirS on the transcriptome of P. aeruginosa, RNA-seq experiments comparing the ΔnirS with WT were also performed. A total of 694 genes were found to be differentially expressed in ΔnirS, of which 192 were up-regulated, while 502 were down-regulated. In addition, these differently expressed genes were noted to significantly enrich the carbon metabolism along with glyoxylate and dicarboxylate metabolisms. Meanwhile, results from RT-PCR suggested the contribution of mexEF-oprN to the development of BIT resistance by ΔnirS. Further, c-di-GMP was less in ΔnirS than in WT, as revealed by HPLC. Taken together, our results confirm that nirS of P. aeruginosa ATCC 9027 plays a role in BIT resistance along with biofilm formation and further affects several metabolic patterns under aerobic conditions.

The role of the NADH-dependent nitrite reductase, Nir, from Escherichia coli in fermentative ammonification

Nitrate and nitrite reduction are of paramount importance for nitrogen assimilation and anaerobic metabolism, and understanding the specific roles of each participating reductase is necessary to describe the biochemical balance that dictates cellular responses to their environments. The soluble, cytoplasmic siroheme NADH-nitrite reductase (Nir) in Escherichia coli is necessary for nitrate/nitrite assimilation but has also been reported to either "detoxify" nitrite, or to carry out fermentative ammonification in support of anaerobic catabolism. Theoretically, nitrite detoxification would be important for anaerobic growth on nitrate, during which excess nitrite would be reduced to ammonium. Fermentative ammonification by Nir would be important for maximization of non-respiratory ATP production during anaerobic growth in the presence of nitrite. Experiments reported here were designed to test the potential role of Nir in fermentative ammonification directly by growing E. coli along with mutant strains lacking Nir or the respiratory nitrite reductase (Nrf) under anaerobic conditions in defined media while monitoring nitrogen utilization and fermentation metabolites. To focus on the role of Nir in fermentative ammonification, pH control was used in most experiments to eliminate nitrite toxicity due to nitric acid formation. Our results demonstrate that Nir confers a significant benefit during fermentative growth that reflects fermentative ammonification rather than detoxification. We conclude that fermentative ammonification by Nir allows for the energetically favorable fermentation of glucose to formate and acetate. These results and conclusions are discussed in light of the roles of Nir in other bacteria and in plants.

The role of the NADH-dependent nitrite reductase, Nir, from Escherichia coli in fermentative ammonification

Nitrate and nitrite reduction are of paramount importance for nitrogen assimilation and anaerobic metabolism, and understanding the specific roles of each participating reductase is necessary to describe the biochemical balance that dictates cellular responses to their environments. The soluble, cytoplasmic siroheme NADH-nitrite reductase (Nir) in Escherichia coli is necessary for nitrate/nitrite assimilation but has also been reported to either "detoxify" nitrite, or to carry out fermentative ammonification in support of anaerobic catabolism. Theoretically, nitrite detoxification would be important for anaerobic growth on nitrate, during which excess nitrite would be reduced to ammonium. Fermentative ammonification by Nir would be important for maximization of non-respiratory ATP production during anaerobic growth in the presence of nitrite. Experiments reported here were designed to test the potential role of Nir in fermentative ammonification directly by growing E. coli along with mutant strains lacking Nir or the respiratory nitrite reductase (Nrf) under anaerobic conditions in defined media while monitoring nitrogen utilization and fermentation metabolites. To focus on the role of Nir in fermentative ammonification, pH control was used in most experiments to eliminate nitrite toxicity due to nitric acid formation. Our results demonstrate that Nir confers a significant benefit during fermentative growth that reflects fermentative ammonification rather than detoxification. We conclude that fermentative ammonification by Nir allows for the energetically favorable fermentation of glucose to formate and acetate. These results and conclusions are discussed in light of the roles of Nir in other bacteria and in plants.

Leaf nitrogen assimilation and partitioning differ among subtropical forest plants in response to canopy addition of nitrogen treatments

Global increases in nitrogen deposition may alter forest structure and function by interfering with plant nitrogen metabolism (e.g., assimilation and partitioning) and subsequent carbon assimilation, but it is unclear how these responses to nitrogen deposition differ among species. In this study, we conducted a 2-year experiment to investigate the effects of canopy addition of nitrogen (CAN) on leaf nitrogen assimilation and partitioning in three subtropical forest plants (Castanea henryi, Ardisia quinquegona, and Blastus cochinchinensis). We hypothesized that responses of leaf nitrogen assimilation and partitioning to CAN differ among subtropical forest plants. CAN increased leaf nitrate reductase (NR) activity, and leaf nitrogen and chlorophyll contents but reduced leaf maximum photosynthetic rate (A_max), photosynthetic nitrogen use efficiency (PNUE), ribulose-1,5-bisphosphate carboxylase (Rubisco) activity, and metabolic protein content of an overstory tree species C. henryi. In an understory tree A. quinquegona, CAN increased NR activity and glutamine synthetase activity and therefore increased metabolic protein synthesis (e.g., Rubisco) in leaves. In the shrub B. cochinchinensis, CAN increased A_max, PNUE, Rubisco content, metabolic protein content, and Rubisco activity in leaves. Leaf nitrogen assimilation and partitioning results indicated that A. quinquegona and B. cochinchinensis may better acclimate to CAN than C. henryi and that the acclimation mechanism differs among the species. Results from this study suggest that long-term elevated atmospheric nitrogen deposition has contributed to the ongoing transformation of subtropical forests into communities dominated by small trees and shrubs.

Oxidative stress in autoimmune rheumatic diseases

The management of patients with autoimmune rheumatic diseases such as rheumatoid arthritis (RA) remains a significant challenge. Often the rheumatologist is restricted to treating and relieving the symptoms and consequences and not the underlying cause of the disease. Oxidative stress occurs in many autoimmune diseases, along with the excess production of reactive oxygen species (ROS) and reactive nitrogen species (RNS). The sources of such reactive species include NADPH oxidases (NOXs), the mitochondrial electron transport chain, nitric oxide synthases, nitrite reductases, and the hydrogen sulfide producing enzymes cystathionine-β synthase and cystathionine-γ lyase. Superoxide undergoes a dismutation reaction to generate hydrogen peroxide which, in the presence of transition metal ions (e.g. ferrous ions), forms the hydroxyl radical. The enzyme myeloperoxidase, present in inflammatory cells, produces hypochlorous acid, and in healthy individuals ROS and RNS production by phagocytic cells is important in microbial killing. Both low molecular weight antioxidant molecules and antioxidant enzymes, such as superoxide dismutase, catalase, glutathione peroxidase, and peroxiredoxin remove ROS. However, when ROS production exceeds the antioxidant protection, oxidative stress occurs. Oxidative post-translational modifications of proteins then occur. Sometimes protein modifications may give rise to neoepitopes that are recognized by the immune system as 'non-self' and result in the formation of autoantibodies. The detection of autoantibodies against specific antigens, might improve both early diagnosis and monitoring of disease activity. Promising diagnostic autoantibodies include anti-carbamylated proteins and anti-oxidized type II collagen antibodies. Some of the most promising future strategies for redox-based therapeutic compounds are the activation of endogenous cellular antioxidant systems (e.g. Nrf2-dependent pathways), inhibition of disease-relevant sources of ROS/RNS (e.g. isoform-specific NOX inhibitors), or perhaps specifically scavenging disease-related ROS/RNS via site-specific antioxidants.

Molecular response to nitrogen starvation by Frankia alni ACN14a revealed by transcriptomics and functional analysis with a fosmid library in Escherichia coli

The transcriptome of Frankia alni strain ACN14a was compared between in vitro ammonium-replete (N-replete) and ammonium-free dinitrogen-fixing (N-fixing) conditions using DNA arrays. A Welch-test (p < 0.05) revealed significant upregulation of 252 genes under N-fixing vs. N-replete (fold-change (FC) ≥ 2), as well as significant downregulation of 48 other genes (FC ≤ 0.5). Interestingly, there were 104 Frankia genes upregulated in vitro that were also significantly upregulated in symbiosis with Alnus glutinosa, while the other 148 genes were not, showing that the physiology of in vitro fixation is markedly different from that under symbiotic conditions. In particular,in vitro fixing cells were seen to upregulate genes identified as coding for a nitrite reductase, and amidases that were not upregulated in symbiosis. Confirmatory assays for nitrite reductase showed that Frankia indeed reduced nitrite and used it as a nitrogen source. An Escherichia coli fosmid clone carrying the nirB region was able to grow better in the presence of 5 mM nitrite than without it, confirming the function of the genome region. The physiological pattern that emerges shows that Frankia undergoes nitrogen starvation that induces a molecular response different from that seen in symbiosis.

Carbonic anhydrase II does not exhibit Nitrite reductase or Nitrous Anhydrase Activity

Carbonic anhydrase II (CA II) is a zinc metalloenzyme that catalyzes the reversible interconversion of water and CO₂ to bicarbonate and a proton. CA II is abundant in most cells, and plays a role in numerous processes including gas exchange, epithelial ion transport, respiration, extra- and intracellular pH control, and vascular regulation. Beyond these CO₂ and pH-linked roles, it has been postulated that CA II might also reduce nitrite (NO₂^-) to nitric oxide (NO), as bicarbonate and NO₂^- both exhibit sp² molecular geometry and NO also plays an important role in vasodilation and regulation of blood pressure. Indeed, previous studies by Aamand et al. have shown that bovine CA II (BCA II) possesses nitrite dehydration activity and paradoxically demonstrated that CA inhibitors (CAIs) such as dorzolamide and acetazolamide significantly increased NO production (Aamand et al., 2009; Nielsen and Fago, 2015) [1,2]. Hence, the goal of this work was to revisit these studies using the same experimental conditions as Aamand et al. measuring NO generation by two methods, and to examine the structure of CA II in complex with NO₂^- in the presence and absence of dorzolamide. Our results contradict the previous findings and indicate that CA II does not exhibit nitrite reductase or dehydration activity, and that this is not enhanced in the presence of CA inhibitors. In addition, a structural examination of BCA II in complex with NO₂^- and superimposed with dorzolamide demonstrates that CA inhibitor binding at the active site to the zinc moiety blocks potential NO₂^- binding.

Study of the Cys-His bridge electron transfer pathway in a copper-containing nitrite reductase by site-directed mutagenesis, spectroscopic, and computational methods

The Cys-His bridge as electron transfer conduit in the enzymatic catalysis of nitrite to nitric oxide by nitrite reductase from Sinorhizobium meliloti 2011 (SmNir) was evaluated by site-directed mutagenesis, steady state kinetic studies, UV-vis and EPR spectroscopic measurements as well as computational calculations. The kinetic, structural and spectroscopic properties of the His171Asp (H171D) and Cys172Asp (C172D) SmNir variants were compared with the wild type enzyme. Molecular properties of H171D and C172D indicate that these point mutations have not visible effects on the quaternary structure of SmNir. Both variants are catalytically incompetent using the physiological electron donor pseudoazurin, though C172D presents catalytic activity with the artificial electron donor methyl viologen (k_cat=3.9(4) s^-1) lower than that of wt SmNir (k_cat=240(50) s^-1). QM/MM calculations indicate that the lack of activity of H171D may be ascribed to the N^δ1H…OC hydrogen bond that partially shortcuts the T1-T2 bridging Cys-His covalent pathway. The role of the N^δ1H…OC hydrogen bond in the pH-dependent catalytic activity of wt SmNir is also analyzed by monitoring the T1 and T2 oxidation states at the end of the catalytic reaction of wt SmNir at pH6 and 10 by UV-vis and EPR spectroscopies. These data provide insight into how changes in Cys-His bridge interrupts the electron transfer between T1 and T2 and how the pH-dependent catalytic activity of the enzyme are related to pH-dependent structural modifications of the T1-T2 bridging chemical pathway.

Covalent attachment of the heme to Synechococcus hemoglobin alters its reactivity toward nitric oxide

The cyanobacterium Synechococcus sp. PCC 7002 produces a monomeric hemoglobin (GlbN) implicated in the detoxification of reactive nitrogen and oxygen species. GlbN contains a b heme, which can be modified under certain reducing conditions. The modified protein (GlbN-A) has one heme-histidine C-N linkage similar to the C-S linkage of cytochrome c. No clear functional role has been assigned to this modification. Here, optical absorbance and NMR spectroscopies were used to compare the reactivity of GlbN and GlbN-A toward nitric oxide (NO). Both forms of the protein are capable of NO dioxygenase activity and both undergo heme bleaching after multiple NO challenges. GlbN and GlbN-A bind NO in the ferric state and form diamagnetic complexes (Fe^III-NO) that resist reductive nitrosylation to the paramagnetic Fe^II-NO forms. Dithionite reduction of Fe^III-NO GlbN and GlbN-A, however, resulted in distinct outcomes. Whereas GlbN-A rapidly formed the expected Fe^II-NO complex, NO binding to Fe^II GlbN caused immediate heme loss and, remarkably, was followed by slow heme rebinding and HNO (nitrosyl hydride) production. Additionally, combining Fe^III GlbN, ¹⁵N-labeled nitrite, and excess dithionite resulted in the formation of Fe^II-H¹⁵NO GlbN. Dithionite-mediated HNO production was also observed for the related GlbN from Synechocystis sp. PCC 6803. Although ferrous GlbN-A appeared capable of trapping preformed HNO, the histidine-heme post-translational modification extinguished the NO reduction chemistry associated with GlbN. Overall, the results suggest a role for the covalent modification in Fe^II GlbNs: protection from NO-mediated heme loss and prevention of HNO formation.

Potential for aerobic NO2- reduction and corresponding key enzyme genes involved in Alcaligenes faecalis strain NR

The potential for aerobic NO₂^- removal by Alcaligenes faecalis strain NR was investigated. 35 mg/L of NO₂^--N was removed by strain NR under aerobic conditions in the presence of NH₄⁺. ¹⁵N-labeling experiment demonstrated that N₂O and N₂ were possible products during the aerobic nitrite removal process by strain NR. The key enzyme genes of nirK, norB and nosZ, which regulate the aerobic nitrite denitrification process, were successfully amplified from strain NR. The gene sequence analysis indicates that copper-containing nitrite reductase (NIRK) and periplasmic nitrous oxide reductase (NOSZ) were both hydrophilic protein and the transmembrane structures were absent, while nitric oxide reductase large subunit (NORB) was a hydrophobic and transmembrane protein. According to the three-dimensional structure and binding site analysis, the bulky and hydrophobic methionine residue proximity to the nitrite binding sites of NIRK was speculated to be related to the oxygen tolerance of NIRK from strain NR.

Nitrogen-source preference in blueberry (Vaccinium sp.): Enhanced shoot nitrogen assimilation in response to direct supply of nitrate

Blueberry (Vaccinium sp.) is thought to display a preference for the ammonium (NH₄⁺) form over the nitrate (NO₃^-) form of inorganic nitrogen (N). This N-source preference has been associated with a generally low capacity to assimilate the NO₃^- form of N, especially within the shoot tissues. Nitrate assimilation is mediated by nitrate reductase (NR), a rate limiting enzyme that converts NO₃^- to nitrite (NO₂^-). We investigated potential limitations of NO₃^- assimilation in two blueberry species, rabbiteye (Vaccinium ashei) and southern highbush (Vaccinium corymbosum) by supplying NO₃^- to the roots, leaf surface, or through the cut stem. Both species displayed relatively low but similar root uptake rates for both forms of inorganic N. Nitrate uptake through the roots transiently increased NR activity by up to 3.3-fold and root NR gene expression by up to 4-fold. However, supplying NO₃^- to the roots did not increase its transport in the xylem, nor did it increase NR activity in the leaves, indicating that the acquired N was largely assimilated or stored within the roots. Foliar application of NO₃^- increased leaf NR activity by up to 3.5-fold, but did not alter NO₃^- metabolism-related gene expression, suggesting that blueberries are capable of post translational regulation of NR activity in the shoots. Additionally, supplying NO₃^- to the cut ends of stems resulted in around a 5-fold increase in NR activity, a 10-fold increase in NR transcript accumulation, and up to a 195-fold increase in transcript accumulation of NITRITE REDUCTASE (NiR1) which codes for the enzyme catalyzing the conversion of NO₂^- to NH₄⁺. These data indicate that blueberry shoots are capable of assimilating NO₃^- when it is directly supplied to these tissues. Together, these data suggest that limitations in the uptake and translocation of NO₃^- to the shoots may limit overall NO₃^- assimilation capacity in blueberry.

Nitrate and Nitrogen Oxides: Sources, Health Effects and Their Remediation

Increased use of nitrogenous (N) fertilizers in agriculture has significantly altered the global N-cycle because they release nitrogenous gases of environmental concerns. The emission of nitrous oxide (N2O) contributes to the global greenhouse gas accumulation and the stratospheric ozone depletion. In addition, it causes nitrate leaching problem deteriorating ground water quality. The nitrate toxicity has been reported in a number of studies showing the health hazards like methemoglobinemia in infants and is a potent cause of cancer. Despite these evident negative environmental as well as health impacts, consumption of N fertilizer cannot be reduced in view of the food security for the teeming growing world population. Various agronomic and genetic modifications have been practiced to tackle this problem. Some agronomic techniques adopted include split application of N, use of slow-release fertilizers, nitrification inhibitors and encouraging the use of organic manure over chemical fertilizers. As a matter of fact, the use of chemical means to remediate nitrate from the environment is very difficult and costly. Particularly, removal of nitrate from water is difficult task because it is chemically non-reactive in dilute aqueous solutions. Hence, the use of biological means for nitrate remediation offers a promising strategy to minimize the ill effects of nitrates and nitrites. One of the important goals to reduce N-fertilizer application can be effectively achieved by choosing N-efficient genotypes. This will ensure the optimum uptake of applied N in a balanced manner and exploring the molecular mechanisms for their uptake as well as metabolism in assimilatory pathways. The objectives of this paper are to evaluate the interrelations which exist in the terrestrial ecosystems between the plant type and characteristics of nutrient uptake and analyze the global consumption and demand for fertilizer nitrogen in relation to cereal production, evaluate the various methods used to determine nitrogen use efficincy (NUE), determine NUE for the major cereals grown across large agroclimatic regions, determine the key factors that control NUE, and finally analyze various strategies available to improve the use efficiency of fertilizer nitrogen.

Heterologous expression and biochemical characterization of assimilatory nitrate and nitrite reductase reveals adaption and potential of Bacillus megaterium NCT-2 in secondary salinization soil

Large accumulation of nitrate in soil has resulted in "salt stress" and soil secondary salinization. Bacillus megaterium NCT-2 which was isolated from secondary salinization soil showed high capability of nitrate reduction. The genes encoding assimilatory nitrate and nitrite reductase from NCT-2 were cloned and over-expressed in Escherichia coli. The optimum co-expression condition was obtained with E. coli BL21 (DE3) and 0.1mM IPTG for 10h when expression was carried out at 20°C and 120rpm in Luria-Bertani (LB) medium. The molecular mass of nitrate reductase was 87.3kDa and 80.5kDa for electron transfer and catalytic subunit, respectively. The large and small subunit of nitrite reductase was 88kDa and 11.7kDa, respectively. The purified recombinant enzymes showed broad activity range of temperature and pH. The maximum activities were obtained at 35°C and 30°C, pH 6.2 and 6.5, which was similar to the condition of greenhouse soils. Maximum stimulation of the enzymes occurred with addition of Fe³⁺, while Cu²⁺ caused the maximum inhibition. The optimum electron donor was MV+Na₂S₂O₄+EDTA and MV+Na₂S₂O₄, respectively. Kinetic parameters of K_m and V_max were determined to be 670μM and 58U/mg for nitrate reductase, and 3100μM and 5.2U/mg for nitrite reductase. Results of quantitative real-time PCR showed that the maximum expression levels of nitrate and nitrite reductase were obtained at 50mM nitrate for 8h and 12h, respectively. These results provided information on novel assimilatory nitrate and nitrite reductase and their properties presumably revealed adaption of B. megaterium NCT-2 to secondary salinization condition. This study also shed light on the role played by the nitrate assimilatory pathway in B. megaterium NCT-2.

Dissecting the role of NtrC and RpoN in the expression of assimilatory nitrate and nitrite reductases in Bradyrhizobium diazoefficiens

Bradyrhizobium diazoefficiens, a nitrogen-fixing endosymbiont of soybeans, is a model strain for studying rhizobial denitrification. This bacterium can also use nitrate as the sole nitrogen (N) source during aerobic growth by inducing an assimilatory nitrate reductase encoded by nasC located within the narK-bjgb-flp-nasC operon along with a nitrite reductase encoded by nirA at a different chromosomal locus. The global nitrogen two-component regulatory system NtrBC has been reported to coordinate the expression of key enzymes in nitrogen metabolism in several bacteria. In this study, we demonstrate that disruption of ntrC caused a growth defect in B. diazoefficiens cells in the presence of nitrate or nitrite as the sole N source and a decreased activity of the nitrate and nitrite reductase enzymes. Furthermore, the expression of narK-lacZ or nirA-lacZ transcriptional fusions was significantly reduced in the ntrC mutant after incubation under nitrate assimilation conditions. A B. diazoefficiens rpoN 1/2 mutant, lacking both copies of the gene encoding the alternative sigma factor σ54, was also defective in aerobic growth with nitrate as the N source as well as in nitrate and nitrite reductase expression. These results demonstrate that the NtrC regulator is required for expression of the B. diazoefficiens nasC and nirA genes and that the sigma factor RpoN is also involved in this regulation.

The combined nitrate reductase and nitrite-dependent route of NO synthesis in potato immunity to Phytophthora infestans

In contrast to the in-depth knowledge concerning nitric oxide (NO) function, our understanding of NO synthesis in plants is still very limited. In view of the above, this paper provides a step by step presentation of the reductive pathway for endogenous NO generation involving nitrate reductase (NR) activity and nitrite implication in potato defense to Phytophthora infestans. A biphasic character of NO emission, peaking mainly at 3 and then at 24 hpi, was detected during the hypersensitive response (HR). In avr P. infestans potato leaves enhanced NR gene and protein expression was tuned with the depletion of nitrate contents and the increase in nitrite supply at 3 hpi. In the same time period a temporary down-regulation of nitrite reductase (NiR) and activity was found. The study for the link between NO signaling and HR revealed an up-regulation of used markers of effective defense, i.e. Nonexpressor of PR genes (NPR1), thioredoxins (Thx) and PR1, at early time-points (1-3 hpi) upon inoculation. In contrast to the resistant response, in the susceptible one a late overexpression (24-48 hpi) of NPR1 and PR1 mRNA levels was observed. Presented data confirmed the importance of nitrite processed by NR in NO generation in inoculated potato leaves. However, based on the pharmacological approach the potential formation of NO from nitrite bypassing the NR activity during HR response to P. infestans has also been discussed.

Comparative bioavailability of ammonium, nitrate, nitrite and urea to typically harmful cyanobacterium Microcystis aeruginosa

Phosphorus is generally considered as the prime limiting nutrient responsible for cyanobacterial blooms. However, recent research is drawing attention to the importance of bioavailable nitrogen (N) in freshwater eutrophication. This study investigated the bioavailability of NO3(-)-N, NO2(-)-N, NH4(+)-N and Urea-N under different concentrations of 1.2, 3.6 and 6.0mgL(-1) to Microcystis aeruginosa. Overall, Urea-N ranked the first in promoting M. aeruginosa growth, followed by NO3(-)-N and NO2(-)-N. However, the algal growth cultured in NH4(+)-N was depressed under test N levels. The bioavailability of N to M. aeruginosa was seriously influenced by both N forms and N concentrations (p<0.01). Total N concentrations in Urea-N treatment decreased the fastest, which were corresponding with the μ values of M. aeruginosa. The high enzymic activities of nitrate reductase, nitrite reductase and glutamine synthetase indicated that the decomposition process for urea is effective, which contributed in N assimilation and utilization in M. aeruginosa cells.

Molybdenum-containing nitrite reductases: Spectroscopic characterization and redox mechanism

OBJECTIVES

This review summarizes the spectroscopic results, which will provide useful suggestions for future research. In addition, the fields that urgently need more information are also advised.

BACKGROUND

Nitrite-NO-cGMP has been considered as an important signaling pathway of NO in human cells. To date, all the four known human molybdenum-containing enzymes, xanthine oxidase, aldehyde oxidase, sulfite oxidase, and mitochondrial amidoxime-reducing component, have been shown to function as nitrite reductases under hypoxia by biochemical, cellular, or animal studies. Various spectroscopic techniques have been applied to investigate the structure and catalytic mechanism of these enzymes for more than 20 years.

METHODS

We summarize the published data on the applications of UV-vis and EPR spectroscopies, and X-ray crystallography in studying nitrite reductase activity of the four human molybdenum-containing enzymes.

RESULTS

UV-vis has provided useful information on the redox active centers of these enzymes. The utilization of EPR spectroscopy has been critical in determining the coordination and redox status of the Mo center during catalysis. Despite the lack of substrate-bound crystal structures of these nitrite reductases, valuable structural information has been obtained by X-ray crystallography.

CONCLUSIONS

To fully understand the catalytic mechanisms of these physiologically/pathologically important nitrite reductases, structural studies on substrate-redox center interaction are needed.

Exogenously applied nitrate improves the photosynthetic performance and nitrogen metabolism in tomato (Solanumlycopersicum L. cv Pusa Rohini) under arsenic (V) toxicity

Tomato (Solanum lycopersicum L.) being a widespread and most commonly consumed vegetable all over the world has an important economic value for its producers and related food industries. It is a serious matter of concern as its production is affected by arsenic present in soil. So, the present study, investigated the toxicity of As(V) on photosynthetic performance along with nitrogen metabolism and its alleviation by exogenous application of nitrate. Plants were grown under natural conditions using soil spiked with 25 mg and 20 mM, As(V) and nitrate, respectively. Our results revealed that plant growth indices, photosynthetic pigments, and other major photosynthetic parameters like net photosynthetic rate and maximum quantum efficiency (F_v/F_m ) of photosystem II (PSII) were significantly (P ≤ 0.05) reduced under As(V) stress. However, nitrate application significantly (P ≤ 0.05) alleviated As(V) toxicity by improving the aforesaid plant responses and also restored the abnormal shape of guard cells. Nitrogen metabolism was assessed by studying the key nitrogen-metabolic enzymes. Exogenous nitrate revamped nitrogen metabolism through a major impact on activities of NR, NiR, GS and GOGAT enzymes and also enhanced the total nitrogen and NO content while malondialdehyde content, and membrane electrolytic leakage were remarkably reduced. Our study suggested that exogenous nitrate application could be considered as a cost effective approach in ameliorating As(V) toxicity.

Regulating the nitrite reductase activity of myoglobin by redesigning the heme active center

Heme proteins perform diverse functions in living systems, of which nitrite reductase (NIR) activity receives much attention recently. In this study, to better understand the structural elements responsible for the NIR activity, we used myoglobin (Mb) as a model heme protein and redesigned the heme active center, by introducing one or two distal histidines, and by creating a channel to the heme center with removal of the native distal His64 gate (His to Ala mutation). UV-Vis kinetic studies, combined with EPR studies, showed that a single distal histidine with a suitable position to the heme iron, i.e., His43, is crucial for nitrite (NO2(-)) to nitric oxide (NO) reduction. Moreover, creation of a water channel to the heme center significantly enhanced the NIR activity compared to the corresponding mutant without the channel. In addition, X-ray crystallographic studies of F43H/H64A Mb and its complexes with NO2(-) or NO revealed a unique hydrogen-bonding network in the heme active center, as well as unique substrate and product binding models, providing valuable structural information for the enhanced NIR activity. These findings enriched our understanding of the structure and NIR activity relationship of heme proteins. The approach of creating a channel in this study is also useful for rational design of other functional heme proteins.

Nitrate metabolism in tobacco leaves overexpressing Arabidopsis nitrite reductase

Primary nitrogen assimilation in plants includes the reduction of nitrite to ammonium in the chloroplasts by the enzyme nitrite reductase (NiR EC:1.7.7.1) or in the plastids of non-photosynthetic organs. Here we report on a study overexpressing the Arabidopsis thaliana NiR (AtNiR) gene in tobacco plants under the control of a constitutive promoter (CERV - Carnation Etched Ring Virus). The aim was to overexpress AtNiR in an attempt to alter the level of residual nitrite in the leaf which can act as precursor to the formation of nitrosamines. The impact of increasing the activity of AtNiR produced an increase in leaf protein and a stay-green phenotype in the primary transformed AtNiR population. Investigation of the T1 homozygous population demonstrated elevated nitrate reductase (NR) activity, reductions in leaf nitrite and nitrate and the amino acids proline, glutamine and glutamate. Chlorophyl content of the transgenic lines was increased, as evidenced by the stay-green phenotype. This reveals the importance of NiR in primary nitrogen assimilation and how modification of this key enzyme affects both the nitrogen and carbon metabolism of tobacco plants.

Nitrate reductase and nitrite as additional components of defense system in pigeonpea (Cajanus cajan L.) against Helicoverpa armigera herbivory

Amylase inhibitors serve as attractive candidates of defense mechanisms against insect attack. Therefore, the impediment of Helicoverpa armigera digestion can be the effective way of controlling this pest population. Nitrite was found to be a potent mixed non-competitive competitive inhibitor of partially purified α-amylase of H. armigera gut. This observation impelled us to determine the response of nitrite and nitrate reductase (NR) towards H. armigera infestation in nine pigeonpea genotypes (four moderately resistant, three intermediate and two moderately susceptible). The significant upregulation of NR in moderately resistant genotypes after pod borer infestation suggested NR as one of the factors that determine their resistance status against insect attack. The pod borer attack caused greater reduction of nitrate and significant accumulation of nitrite in moderately resistant genotypes. The activity of nitrite reductase (NiR) was also enhanced more in moderately resistant genotypes than moderately susceptible genotypes on account of H. armigera herbivory. Expression of resistance to H. armigera was further revealed when significant negative association between NR, NiR, nitrite and percent pod damage was observed. This is the first report that suggests nitrite to be a potent inhibitor of H. armigera α-amylase and also the involvement of nitrite and NR in providing resistance against H. armigera herbivory.

Slowly released molasses barrier system for controlling nitrate plumes in groundwater: a pilot-scale tank study

A well-type barrier system containing solidified molasses as a reactive medium was developed to promote the indigenous denitrifying activity and to treat nitrate plumes in groundwater. Three slowly released molasses (SRM) barrier systems harboring 60, 120, and 120 SRM rods, which were named System A, B, and C, respectively, were operated to examine nitrate removal efficiency in a pilot-scale sandy tank. These SRM systems induced a consistent removal of nitrate without pore clogging and hydraulic disturbance during the test period. The initial nitrate concentration was 142mgL(-1), and the concentrations decreased by 80%, 84%, and 79% in System A, B, and C, respectively. In particular, System C was inoculated with heterotrophic denitrifiers, but the nitrate removal efficiency was not enhanced compared to System B, probably due to the prior existence of indigenous denitrifiers in the sandy tank. The presence of nitrite reductase-encoding gene (i.e. nirK) at the site was confirmed by denatured gradient gel electrophoresis analysis.

Effects of quinoid redox mediators on the activity of anammox biomass

This study first explored the relationship between the activity of anammox biomass/key enzymes and quinoid redox mediators, which were anthraquinone-2,6-disulfonate (AQDS), 2-hydroxy-1,4-napthoquinone (LAW) and anthraquinone-2-carboxylic acid (AQC). Experimental results demonstrated that the total nitrogen removal performance showed a downward trend with all three redox mediators (RMs) dosage increasing. For instance, when the AQC addition increased to 0.8 mM, the TN removal rate sharply reduced to 17.2 mg-N/gVSS/h, only about 20% of the control. This phenomenon might be caused by microbial poisoning with the extracellular RMs additions. Nevertheless, the crude hydrazine dehydrogenase, nitrite reductase, and nitrate reductase activities were enhanced with RMs addition, about 0.6-3 folds compared to the control experiments without RMs addition. The RMs was inferred to play the role as ubiquinol/ubiquinone (Q/QH2) during the anammox process. Furthermore, the specific ladderane membrane structure could block the contacting between RMs and the key enzymes inside anammoxosome. This might be the main reason for the contrary effects of RMs on anammox biomass and the key enzymes.

Protein disulfide isomerase may facilitate the efflux of nitrite derived S-nitrosothiols from red blood cells

Protein disulfide isomerase (PDI) is an abundant protein primarily found in the endoplasmic reticulum and also secreted into the blood by a variety of vascular cells. The evidence obtained here, suggests that PDI could directly participate in the efflux of NO⁺ from red blood cells (RBC). PDI was detected both in RBC membranes and in the cytosol. PDI was S-nitrosylated when RBCs were exposed to nitrite under ∼50% oxygen saturation but not under ∼100% oxygen saturation. Furthermore, it was observed that hemoglobin (Hb) could promote PDI S-nitrosylation in the presence of ∼600 nM nitrite. In addition, three lines of evidence were obtained for PDI–Hb interactions: (1) Hb co-immunoprecipitated with PDI; (2) Hb quenched the intrinsic PDI fluorescence in a saturable manner; and (3) Hb–Fe(II)–NO absorption spectrum decreased in a [PDI]-dependent manner. Finally, PDI was detected on the surface RBC under ∼100% oxygen saturation and released as soluble under ∼50% oxygen saturation. The soluble PDI detected under ∼50% oxygen saturation was S-nitrosylated. Based on these data it is proposed that PDI is taken up by RBC and forms a complex with Hb. Hb–Fe(II)–NO that is formed from nitrite reduction under ∼50% O₂, then transfers NO⁺ to either Hb–Cys β93 or directly to PDI resulting in S-nitroso-PDI which transverses the RBC membrane and attaches to the RBC surface. When RBCs enter tissues the S-nitroso-PDI is released from the RBC-surface into the blood where its NO⁺ is transferred into the endothelium thereby inducing vasodilation, suggesting local oxygen-dependent dynamic interplays between nitrite, NO and S-nitrosylation.

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Red blood cells (RBC) contain protein disulfide isomerase (PDI) that can associate with hemoglobin.

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Formation of S-nitroso-PDI is an oxygen- and Hb-dependent process.

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S-nitroso-PDI associates with RBC surface in an oxygen dependent manner that facilitates its release under hypoxia.

Expression patterns and adaptive functional diversity of vertebrate myoglobins

Recent years have witnessed a new round of research on one of the most studied proteins - myoglobin (Mb), the oxygen (O2) carrier of skeletal and heart muscle. Two major discoveries have stimulated research in this field: 1) that Mb has additional protecting functions, such as the regulation of in vivo levels of the signaling molecule nitric oxide (NO) by scavenging and generating NO during normoxia and hypoxia, respectively; and 2) that Mb in vertebrates (particularly fish) is expressed as tissue-specific isoforms in other tissues than heart and skeletal muscle, such as vessel endothelium, liver and brain, as found in cyprinid fish. Furthermore, Mb has also been found to protect against oxidative stress after hypoxia and reoxygenation and to undergo allosteric, O2-linked S-nitrosation, as in rainbow trout. Overall, the emerging evidence, particularly from fish species, indicates that Mb fulfills a broader array of physiological functions in a wider range of different tissues than hitherto appreciated. This new knowledge helps to better understand how variations in Mb structure and function may correlate with differences in animals' lifestyles and hypoxia-tolerance. This review integrates old and new results on Mb expression patterns and functional properties amongst vertebrates and discusses how these may relate to adaptive variations in different species. This article is part of a special issue entitled: Oxygen Binding and Sensing Proteins.

Is methemoglobin an inert bystander, biomarker or a mediator of oxidative stress--The example of anemia?

Acute anemia increases the risk for perioperative morbidity and mortality in critically ill patients who experience blood loss and fluid resuscitation (hemodilution). Animal models of acute anemia suggest that neuronal nitric oxide synthase (nNOS)-derived nitric oxide (NO) is adaptive and protects against anemia-induced mortality. During acute anemia, we have observed a small but consistent increase in methemoglobin (MetHb) levels that is inversely proportional to the acute reduction in Hb observed during hemodilution in animals and humans. We hypothesize that this increase in MetHb may be a biomarker of anemia-induced tissue hypoxia. The increase in MetHb may occur by at least two mechanisms: (1) direct hemoglobin oxidation by increased nNOS-derived NO within the perivascular tissue and (2) by increased deoxyhemoglobin (DeoxyHb) nitrite reductase activity within the vascular compartment. Both mechanisms reflect a potential increase in NO signaling from the tissue and vascular compartments during anemia. These responses are thought to be adaptive; as deletion of nNOS results in increased mortality in a model of acute anemia. Finally, it is possible that prolonged activation of these mechanisms may lead to maladaptive changes in redox signaling. We hypothesize, increased MetHb in the vascular compartment during acute anemia may reflect activation of adaptive mechanisms which augment NO signaling. Understanding the link between anemia, MetHb and its treatments (transfusion of stored blood) may help us to develop novel treatment strategies to reduce the risk of anemia-induced morbidity and mortality.

Nitrate assimilatory enzymes of Spirulina (Arthospira) platensis are more thermotolerant than those of rice

In order to assess the potential of Spirulina (Arthospira) platensis as a source of abundant, thermostable nitrate assimilatory enzymes, the specific activities and thermal tolerance of nitrate reductase (NR), nitrite reductase (NiR) and glutamine synthetase (GS) were compared with those of rice in crude extracts in vitro. The results show that Spirulina enzymes have relatively higher thermotolerance. When the extracts were pre-exposed to 80 °C for 1 hr, Spirulina enzymes retained higher activities by 3.4, 1.7 and 3.7 fold, respectively than corresponding enzymes in rice. This property was not due to salts and other small proteins/molecules, as their removal by gel filtration (G-25) did not affect their thermotolerance.

Spirulina nitrate-assimilating enzymes (NR, NiR, GS) have higher specific activities and are more stable than those of rice

Spirulina platensis, a cyanobacterium whose N-metabolic pathway is similar to that of higher plants like rice (Oryza sativa), produces tenfold more protein, indicating a higher capacity for nitrate utilization/removal. Our in vitro analyses in crude extracts revealed that this can be attributed, at least in part, to the higher specific activities (3-6 fold) and half lives (1.2-4.4 fold) of the N-assimilating enzymes, nitrate reductase (NR), nitrite reductase (NiR) and glutamine synthetase (GS) in Spirulina.