Ferredoxin-nitrite reductase from spinach

Rieske Oxygenases and Other Ferredoxin-Dependent Enzymes: Electron Transfer Principles and Catalytic Capabilities

Enzymes that depend on sophisticated electron transfer via ferredoxins (Fds) exhibit outstanding catalytic capabilities, but despite decades of research, many of them are still not well understood or exploited for synthetic applications. This review aims to provide a general overview of the most important Fd-dependent enzymes and the electron transfer processes involved. While several examples are discussed, we focus in particular on the family of Rieske non-heme iron-dependent oxygenases (ROs). In addition to illustrating their electron transfer principles and catalytic potential, the current state of knowledge on structure-function relationships and the mode of interaction between the redox partner proteins is reviewed. Moreover, we highlight several key catalyzed transformations, but also take a deeper dive into their engineerability for biocatalytic applications. The overall findings from these case studies highlight the catalytic capabilities of these biocatalysts and could stimulate future interest in developing additional Fd-dependent enzyme classes for synthetic applications.

Kinetic Analysis of Nitrite Reduction Reactions by Nitrite Reductase Derived from Spinach in the Presence of One-Electron Reduced Riboflavin

The development of methods for converting nitrogen oxides in water into valuable resources such as ammonia and hydrazine has been given some attention. By utilizing the nitrite-reducing catalytic activity of nitrite reductase (NiR), nitrite in water can be converted into ammonium. However, there are few reports in the research that synthesized ammonium from nitrite using nitrite reductase. Therefore, we aimed to investigate the effect of temperature on the nitrite-reducing catalytic activity of NiR from spinach in the presence of one-electron reduced riboflavin by kinetic analysis to find the optimum temperature conditions. The results of this study showed that the reaction temperature does not need to be higher than 296.15 K in order to improve the efficiency of ammonium production from nitrite using NiR.

Regulation of Phagotrophy by Prey, Low Nutrients, and Low Light in the Mixotrophic Haptophyte Isochrysis galbana

Mixotrophy combines autotrophy and phagotrophy in the same cell. However, it is not known to what extent the phagotrophy influences metabolism, cell composition, and growth. In this work, we assess, on the one hand (first test), the role of phagotrophy on the elemental and biochemical composition, cell metabolism, and enzymes related to C, N, and S metabolism of Isochrysis galbana Parke, 1949. On the other hand, we study how a predicted increase of phagotrophy under environmental conditions of low nutrients (second test) and low light (third test) can affect its metabolism and growth. Our results for the first test revealed that bacterivory increased the phosphorous and iron content per cell, accelerating cell division and improving the cell fitness; in addition, the stimulation of some C and N enzymatic routes help to maintain, to some degree, compositional homeostasis. Under nutrient or light scarcity, I. galbana grew more slowly despite greater bacterial consumption, and the activities of key enzymes involved in C, N, and S metabolism changed according to a predominantly phototrophic strategy of nutrition in this alga. Contrary to recent studies, the stimulation of phagotrophy under low nutrient and low irradiance did not imply greater and more efficient C flux.

NirA Is an Alternative Nitrite Reductase from Pseudomonas aeruginosa with Potential as an Antivirulence Target

The emergence of widespread antimicrobial resistance has led to the need for development of novel therapeutic interventions. Antivirulence strategies are an attractive alternative to classic antimicrobial therapy; however, they require identification of new specific targets which can be exploited in drug discovery programs.

The opportunistic pathogen Pseudomonas aeruginosa produces an arsenal of virulence factors causing a wide range of diseases in multiple hosts and is difficult to eradicate due to its intrinsic resistance to antibiotics. With the antibacterial pipeline drying up, antivirulence therapy has become an attractive alternative strategy to the traditional use of antibiotics to treat P. aeruginosa infections. To identify P. aeruginosa genes required for virulence in multiple hosts, a random library of Tn5 mutants in strain PAO1-L was previously screened in vitro for those showing pleiotropic effects in the production of virulence phenotypes. Using this strategy, we identified a Tn5 mutant with an insertion in PA4130 showing reduced levels of a number of virulence traits in vitro. Construction of an isogenic mutant in this gene presented results similar to those for the Tn5 mutant. Furthermore, the PA4130 isogenic mutant showed substantial attenuation in disease models of Drosophila melanogaster and Caenorhabditis elegans as well as reduced toxicity in human cell lines. Mice infected with this mutant demonstrated an 80% increased survival rate in acute and agar bead lung infection models. PA4130 codes for a protein with homology to nitrite and sulfite reductases. Overexpression of PA4130 in the presence of the siroheme synthase CysG enabled its purification as a soluble protein. Methyl viologen oxidation assays with purified PA4130 showed that this enzyme is a nitrite reductase operating in a ferredoxin-dependent manner. The preference for nitrite and production of ammonium revealed that PA4130 is an ammonia:ferredoxin nitrite reductase and hence was named NirA.

Trace metal metabolism in plants

Many trace metals are essential micronutrients, but also potent toxins. Due to natural and anthropogenic causes, vastly different trace metal concentrations occur in various habitats, ranging from deficient to toxic levels. Therefore, one focus of plant research is on the response to trace metals in terms of uptake, transport, sequestration, speciation, physiological use, deficiency, toxicity, and detoxification. In this review, we cover most of these aspects for the essential micronutrients copper, iron, manganese, molybdenum, nickel, and zinc to provide a broader overview than found in other recent reviews, to cross-link aspects of knowledge in this very active research field that are often seen in a separated way. For example, individual processes of metal usage, deficiency, or toxicity often were not mechanistically interconnected. Therefore, this review also aims to stimulate the communication of researchers following different approaches, such as gene expression analysis, biochemistry, or biophysics of metalloproteins. Furthermore, we highlight recent insights, emphasizing data obtained under physiologically and environmentally relevant conditions.

A novel microperoxidase activity: methyl viologen-linked nitrite reducing activity of microperoxidase

To investigate the nitrite reducing activity of microperoxidases (mps) in the presence of methyl viologen and dithionite, the fragments C14-K22 (mp9), V11-L32 (mp22), and G1-M65 (mp65) containing heme were prepared by enzymatic hydrolysis of commercially equine heart cytochrome c (Cyt c), in which His is axially coordinated to heme iron, and acts as its fifth ligand. The nitrite reducing activity of mps was measured under anaerobic condition, and the nitrite reducing activity of mps increased with the cutting of the peptide chain. The activity of the shortest nonapeptide mp9 was approximately 120-fold that of Cyt c (104 amino acid residues) and 3.2-fold that of nitrite reductase (EC 1.7.7.1) from Escherichia coli. In the nitrite reduction by mp, nitrite was completely reduced to ammonia. We presumed that ferrous mps reduced NO2- to NO by donating one electron, the NO was completely reduced to NH4+ under anaerobic condition via ferrous-NO complexes as a reaction intermediate using visible spectra and ESR spectra, and this overall reaction was a 6-electron and 8-proton reduction. Sepharose-immobilized mp9 had a nitrite reducing activity similar to that of mp9 in solution, and the resin retained the activity after five uses and even 1-year storage. The mp will be able to use as a substitute for nitrite reductase.

Light-regulated expression of the Arabidopsis thaliana ferredoxin A gene involves both transcriptional and post-transcriptional processes

Ferredoxin is part of the photosynthetic apparatus of the chloroplast and is encoded in the nucleus. In Arabidopsis thaliana expression of the ferredoxin A gene is influenced by both the presence of chloroplasts and light. Tobacco plants transformed with a ferredoxin promoter-GUS fusion gene showed a tissue-specific and light-dependent expression pattern. The effect of light on the expression of the fusion gene in transgenic seedlings was only two- to fourfold, which is less pronounced than the 20-fold effect in Arabidopsis itself. Run-on transcription assays with nuclei isolated from Arabidopsis revealed a twofold modulation of transcriptional activity of the ferredoxin A gene under the influence of light. These results suggest the involvement of post-transcriptional processes in light-regulated gene expression. A ferredoxin promoter deletion series ranging from -1205 to -143 was studied. All but the smallest deletion construct (at position -143 relative to the translation start site) showed comparable expression levels in mature leaves, suggesting the presence of a positive regulating element between -269 and -143. The same pattern of tissue specificity was found in all promoter deletions studied. Expression of the fusion genes is high in all chloroplast-containing cells: mesophyll, chlorenchyma, paravascular tissue, epidermal and stomatal guard cells and trichomes. Transgenic seedlings treated with norflurazon, which blocks the development of green chloroplasts, showed a two- to fourfold reduction in GUS expression for all constructs. In Arabidopsis seedlings the effect of norflurazon on the expression of the ferredoxin A was eightfold. This again can be explained by the need for post-transcriptional processes of the regulated gene expression of Arabidopsis ferredoxin A.

Photosynthetic electron transport: Emergence of a concept, 1949-59

Historically, two main concepts guided research into possible mechanisms of light-induced atomic rearrangements in oxygenic photosynthesis: Photodecomposition of CO2 and photodecomposition of water. Both concepts envisioned photoinduced transfers of cumbersome whole atoms and not, as is currently held, photoinduced electron transfers. Early proposals for light-induced electron transfers were relegated to obscurity because they were speculative ideas, not supported by meaningful experimental findings and tied to hypothetical and ephemeral schemes. The concept of photoinduced rearrangements of whole atoms rather than electrons was so well entrenched that it was even invoked to explain their findings by the discoverers of the Hill reaction and cyclic photophosphorylation. The light-induced electron flow concept gained acceptance in photosynthesis research only with the discovery of non-cyclic photophosphorylation in which ATP formation is coupled with electron transport to ferredoxin/NADP(+) or to artificial substitutes like ferricyanide.

Regulation of nitrite uptake and nitrite reductase expression in Chlamydomonas reinhardtii

Expression of nitrite uptake and nitrite reductase activities has been studied in Chlamydomonas reinhardtii under different nutritional conditions. Both activities were expressed at a low level in derepressed cells (with no nitrogen source) and at a high level in induced cells (with nitrate or nitrite). Nitrate was required for both activities to be maximally expressed. Ammonium-grown cells did not show nitrite uptake capability and had a basal nitrite reductase activity. Nitrite uptake but not nitrite reductase levels decreased very significantly in nitrate-induced cells subject to cycloheximide treatment, which suggests that protein(s) involved in the uptake are under a rapid turnover. Nitrite uptake expression was strongly inhibited by the presence of the glutamine synthetase inhibitor L-methionine-D,L-sulfoximine under either derepression or induction conditions, whereas that of nitrite reductase was not affected under the same conditions. Our results indicate that nitrite uptake expression is regulated primarily by ammonium, and that of nitrite reductase by both ammonium and ammonium derivative(s).

Photoreduction of NADP+ by isolated reaction centers of photosystem II: requirement for plastocyanin

The carrier of photosynthetically generated reducing power is the iron-sulfur protein ferredoxin, which provides directly, or via NADP+, reducing equivalents needed for CO2 assimilation and other metabolic reactions in the cell. It is now widely held that, in oxygenic photosynthesis, the generation of reduced ferredoxin-NADP+ requires the collaboration in series of two photosystems: photosystem II (PSII), which energizes electrons to an intermediate reducing potential and transfers them to photosystem I (PSI), which in turn is solely competent to energize electrons to the strong reducing potential required for the reduction of ferredoxin-NADP+ (the Z scheme). This investigation tested the premise of an alternative scheme, which envisions that PSII, without the involvement of PSI, is also capable of photoreducing ferredoxin-NADP+. We report here unexpected findings consistent with the alternative scheme. Isolated PSII reaction centers (completely free of PSI components), when supplemented with ferredoxin, ferredoxin-NADP+ oxidoreductase, and a PSII electron donor,1,5-diphenylcarbazide, gave a significant photoreduction of NADP+. A striking feature of this electron transfer from a PSII donor to the perceived terminal acceptor of PSI was its total dependence on catalytic quantities of plastocyanin, a copper-containing electron-transport protein hitherto known only as an electron donor to PSI.

Ammonium regulation of urate uptake in Chlamydomonas reinhardtii

Urate was taken up at a negligible rate by Chlamydomonas reinhardtii cells grown on ammonium and transferred to media containing urate plus ammonium or urate plus chloral hydrate or cycloheximide. Addition of ammonium to cells actively consuming urate produced a rapid inhibition of urate uptake whereas the intracellular oxidation of urate was unaffected. Methylammonium but not glutamine or glutamate inhibited urate uptake. Addition of L-methionine-DL-sulfoximine to cells actively consuming urate provoked ammonium excretion, which was accompanied by a rapid inhibition of urate uptake. In cells growing on urate and exhibiting noticeable levels of nitrite-reductase activity, nitrite caused a sudden inhibition of urate uptake whereas nitrate required a time to induce nitrate reductase and to exert its inhibitory effect on uptake. The urate-uptake system did not require urate for induction since the urate-uptake capacity appeared in nitrogen-starved cells. From these results it is concluded that, in Chlamydomonas reinhardtii, ammonium inhibits urate uptake and also acts as co-repressor of the uptake system.

Short-term nitrate (nitrite) inhibition of nitrogen fixation in Azotobacter chroococcum

Nitrate-grown Azotobacter chroococcum ATCC 4412 cells lack the ability to fix N2. Nitrogenase activity developed after the cells were suspended in a combined nitrogen-free medium and was paralleled by a concomitant decrease in nitrate assimilation capacity. In such treated cells exhibiting transitory nitrate assimilation and N2-fixation capacity, nitrate or nitrite caused a short-term inhibitory effect on nitrogenase activity which ceased once the anion was exhausted from the medium. The analog L-methionine-DL-sulfoximine, an inhibitor of glutamine synthetase, prevented inhibition of nitrogenase activity by nitrate or nitrite without affecting the uptake of these antions, which were reduced and stoichiometrically released into the external medium as ammonium. Inhibition of nitrogenase by nitrate (nitrite) did not take place in A. chroococcum MCD1, which is unable to assimilate either. We conclude that the short-term inhibitory effect of nitrate (nitrite) on nitrogenase activity is due to some organic product(s) formed during the assimilation of the ammonium resulting from nitrate (nitrite) reduction.

Regulation of the nitrate-reducing system enzymes in wild-type and mutant strains of Chlamydomonas reinhardii

Six mutant strains (301, 102, 203, 104, 305, and 307) affected in their nitrate assimilation capability and their corresponding parental wild-type strains (6145c and 21gr) from Chlamydomonas reinhardii have been studied on different nitrogen sources with respect to NAD(P)H-nitrate reductase and its associated activities (NAD(P)H-cytochrome c reductase and reduced benzyl viologen-nitrate reductase) and to nitrite reductase activity. The mutant strains lack NAD(P)H-nitrate reductase activity in all the nitrogen sources. Mutants 301, 102, 104, and 307 have only NAD(P)H-cytochrome c reductase activity whereas mutant 305 solely has reduced benzyl viologen-nitrate reductase activity. Both activities are repressible by ammonia but, in contrast to the nitrate reductase complex of wild-type strains, require neither nitrate nor nitrite for their induction. Moreover, the enzyme from mutant 305 is always obtained in active form whereas nitrate reductase from wild-types needs to be reactivated previously with ferricyanide to be fully detected. Wild-type strains and mutants 301, 102, 104, and 307, when properly induced, exhibit an NAD(P)H-cytochrome c reductase distinguishable electrophoretically from constitutive diaphorases as a rapidly migrating band. Nitrite reductase from wild-type and mutant strains is also repressible by ammonia and does not require nitrate or nitrite for its synthesis. These facts are explained in terms of a regulation of nitrate reductase synthesis by the enzyme itself.

Kinetics of leaf nitrite reductase with Methyl Viologen and ferredoxin under controlled redox conditions

Some factors that influence the activity of nitrite reductase (EC 1.7.7.1) were investigated, the enzyme from Curcurbita pepo (vegetable marrow) being used. The activity with ferredoxin or Methyl Viologen as electron donor was inhibited by certain salts, including NaCl. The steady-state kinetic parameters measured in a commonly used open-tube (aerobic) system were compared with a closed-cell (anaerobic) system in which the redox potential, and thus the concentrations of oxidized and reduced donor, could be controlled. This showed that in the open-tube system the apparent Km values determined were overestimated (by a factor of 10 for reduced Methyl Viologen), owing to incomplete mediator reduction and competitive inhibition by the oxidized form of the mediator.

The effect of kinetin on the photosynthetic apparatus of Sinapis alba

The influence of kinetin during the development of primary leaves of Sinapis alba was investigated. Kinetin treatment (6 ppm) induced an increase of dry weight, of soluble reducing sugars, soluble protein, chlorophylls, carotenoids and cytochrome f; a higher ratio of chlorophyll a to chlorophyll b, higher rates of CO2 fixation per fresh weight and higher activity of nitrite reductase, were also found. These effects are comparable with strong and blue light adaptations. On the other hand, the Hill activity with ferricyanide as the electron acceptor, the rates of CO2 fixation per chlorophyll, the ratios of chlorophyll to cytochrome f and of protein to chlorophyll did not change. Therefore we assume that the kinetin induced and the light induced adaptations are brought about by different causal reaction chains.

The nitrate-reducing enzyme system of Chlamydomonas reinhardii

In Chlamydomonas reinhardii the reduction of nitrate to ammonia occurs in two independent enzymatic steps: 1. the two-electrons reduction of nitrate to nitrite catalyzed by NADH-nitrate reductase, and, 2. the six-electrons reduction of nitrite to ammonia catalyzed by ferredoxin-nitrite reductase. Both enzymes have been purified and characterized, and some of their properties have been studied.

Photosynthesis and the induction of nitrate reductase and nitrite reductase in bean leaves

In laaves of Phaseolus vulgaris L. cv. Prelude, the light-induced increase in activity of NADH-nitrate oxidoreductase (E.C.1.6.6.2; NAR) and reduced benzylviologennitrite oxidoreductase (E.C.1.6.6.4; NIR) starts at a certain stage in the development of the chloroplasts. In leaves with completely developed chloroplasts, a higher increase in activity of NAR and NIR is observed, after induction by the addition of nitrate, in the light than in the dark. DCMU inhibits the increase in activity of the two enzymes in the light. Both in the light in the presence of DCMU, and in the dark the increase in activity reaches a higher level by the addition of sucrose.Induction of NAR, but not of NIR, can be observed in excised etiolated leaves. No induction is found in leaves of intact etiolated seedlings.The relation between photosynthetic reactions and the increase in activity of NAR and NIR is discussed. It is suggested that NADH, indirectly formed by photosynthesis, protects NAR and affects in this way the balance between synthesis and breakdown of the enzyme. The increase in activity of NIR is possibly influenced by the presence of reduced ferredoxin.

Effect of chloramphenicol and cycloheximide on the induction of nitrate reductase and nitrite reductase in bean leaves

In etiolated leaves of Phaseolus vulgaris L. cv. Prelude only low levels of NADH-nitrate oxidoreductase (E.C. 1.6.6.2; NAR) and reduced benzyl viologen-nitrite oxidoreductase (E.C. 1.6.6.4; NIR) could be detected, even in the presence of nitrate. When nitrate was available illumination of leaves of 10-day-old etiolated seedlings resulted in an induction of both NAR and NIR. In the absence of nitrate no induction of the enzymes took place, although greening of the leaves was normal. Chloramphenicol (CAP) and cycloheximide (CHI), applied at the beginning of the light period, inhibited the induction of both NAR and NIR. Administered after 24 h of illumination CHI still inhibited the induction of both enzymes whereas CAP was no longer inhibitory. The induction of NAR and NIR by nitrate in green leaves in light was inhibited by CHI but not by CAP. From these results it seems likely that both the enzymes NAR and NIR are synthesized on cytoplasmic ribosomes. Before the enzymes can be manufactured in the cytoplasm some chloroplast development is required.

Reduced nicotinamide-adenine dinucleotide-nitrite reductase from Azotobacter chroococcum

1. The assimilatory nitrite reductase of the N(2)-fixing bacterium Azotobacter chroococcum was prepared in a soluble form from cells grown aerobically with nitrate as the nitrogen source, and some of its properties have been studied. 2. The enzyme is a FAD-dependent metalloprotein (mol.wt. about 67000), which stoicheiometrically catalyses the direct reduction of nitrite to NH(3) with NADH as the electron donor. 3. NADH-nitrite reductase can exist in two either active or inactive interconvertible forms. Inactivation in vitro can be achieved by preincubation with NADH. Nitrite can specifically protect the enzyme against this inactivation and reverse the process once it has occurred. 4. A. chroococcum nitrite reductase is an adaptive enzyme whose formation depends on the presence of either nitrate or nitrite in the nutrient solution. 5. Tungstate inhibits growth of the microorganism very efficiently, by competition with molybdate, when nitrate is the nitrogen source, but does not interfere when nitrite or NH(3) is substituted for nitrate. The addition of tungstate to the culture media results in the loss of nitrate reductase activity but does not affect nitrite reductase.