The pathway of nitrogen and reductive enzymes of denitrification

Some recent studies on the pathway of nitrogen and the reductases of denitrification are reviewed. The available evidence suggests that while the intermediates of denitrification can remain enzyme-bound (presumably to nitrite reductase) prior to formation of N₂O, NO and nitroxyl (HNO) can be released in part by certain bacteria. Release of NO is recognized by a nitrite/NO?¹⁵N exchange reaction and isotopic scrambling in product N₂O; release of nitroxyl by Pseudomonas stutzeri is recognized by isotopic scrambling of nitrite and NO in product N₂O in absence of exchange and affords evidence that the first N?N bond forms in denitrification at the N¹⁺ redox level. The recent purification and partial characterization of nitrous oxide reductase are described. The ability of the dissimilatory nitrite reductase to activate nitrite for nitrosyl transfer affords a new chemical probe into the mechanism of action of this central enzyme. It would appear that reduction of nitrite is subject to electrophilic catalysis. ¹⁸O studies show that dissociation of nitrite from nitrite reductase can be slow relative to competing reduction or nitrosyl transfer.     

Substrate binding and activation in the active site of cytochrome <Emphasis Type="Italic">c</Emphasis> nitrite reductase: a density functional study

Cytochrome c nitrite reductase is a homodimeric enzyme, containing five covalently attached c-type hemes per subunit. Four of the heme irons are bishistidine-ligated, whereas the fifth, the active site of the protein, has an unusual lysine coordination and calcium site nearby. A fascinating feature of this enzyme is that the full six-electron reduction of the nitrite is achieved without release of any detectable reaction intermediate. Moreover, the enzyme is known to work over a wide pH range. Both findings suggest a unique flexibility of the active site in the complicated six-electron, seven-proton reduction process. In the present work, we employed density functional theory to study the energetics and kinetics of the initial stages of nitrite reduction. The possible role of second-sphere active-site amino acids as proton donors was investigated by taking different possible protonation states and geometrical conformations into account. It was found that the most probable proton donor is His₂₇₇, whose spatial orientation and fine-tuned acidity lead to energetically feasible, low-barrier protonation reactions. However, substrate protonation may also be accomplished by Arg₁₁₄. The calculated barriers for this pathway are only slightly higher than the experimentally determined value of 15.2 kcal/mol for the rate-limiting step. Hence, having proton-donating side chains of different acidity within the active site may increase the operational pH range of the enzyme. Interestingly, Tyr₂₁₈, which was proposed to play an important role in the overall mechanism, appears not to take part in the reaction during the initial stage.     

Hydrogenase mediated nitrite reduction in chlorella

The assay of the hydrogenase of glucose-grown cells of Chlorella pyrenoidosa, strain 7-11-05 by means of nitrite reduction with molecular hydrogen is described. The hydrogenase of Chlorella shows maximum activity immediately after equilibration in the hydrogen atmosphere. The hydrogenase mediated reduction of nitrite to ammonia requires the presence of CO₂. However, at pH 6.4. when the reaction proceeds optimally, there is apparently sufficient retention of metabolic CO₂ to support the reaction, which goes to completion, at near maximum rates.

Reduction of nitrite in the hydrogenase system when CO₂ is present results in the uptake of 3 moles of H₂ per mole of nitrite and ammonia is the product. When CO₂ is absent or limiting, ammonia is also formed from nitrite but with the uptake of less than the stoichiometric amount of H₂. It is concluded that CO₂ is essential for the uptake of H₂, and that in the absence of CO₂ internal hydrogen donors support nitrite reduction.

The possibility that CO₂ exerts a catalytic effect in all reductions mediated by hydrogenase in algae is considered, and a further hypothesis, that hydrogenase arises from that portion of the photosynthetic machinery which also shows a catalytic requirement for CO₂, is proposed.

     

Time-Resolved Resonance Raman Investigation of Oxygen Reduction Mechanism of Bovine Cytochrome c Oxidase

Six oxygen-associated resonance Raman bands were identified for intermediates in the reaction of bovine cytochrome c oxidase with O₂ at room temperature. The primary intermediate, corresponding to Compound A of cryogenic measurements, is an O₂ adduct of heme a ₃ and its isotope frequency shifts for ¹⁶O¹⁸O have established that the binding is of an end-on type. This is followed by two oxoheme intermediates, and the final intermediate appearing around 3 ms is the Fe–OH heme. The reaction rate between the two oxoheme intermediates is significantly slower in D₂O than in H₂O, suggesting that the electron transfer is regulated by proton translocations at this step. It is noted that the reaction intermediates of oxidized enzyme with hydrogen peroxide yield the same three sets of oxygen isotope-sensitive bands as those of oxoheme intermediates seen for O₂ reduction and that the O–O bond has already been cleaved in the so-called peroxy form (or 607 nm form).     

Loss of Ammonia Monooxygenase Activity in Nitrosomonas europaea upon Exposure to Nitrite

Nitrosomonas europaea, an obligate ammonia-oxidizing bacterium, lost an increasing amount of ammonia oxidation activity upon exposure to increasing concentrations of nitrite, the primary product of ammonia-oxidizing metabolism. The loss of activity was specific to the ammonia monooxygenase (AMO) enzyme, as confirmed by a decreased rate of NH₄⁺-dependent O₂ consumption, some loss of active AMO molecules observed by polypeptide labeling with ¹⁴C₂H₂, the protection of activity by substrates of AMO, and the requirement for copper. The loss of AMO activity via nitrite occurred under both aerobic and anaerobic conditions, and more activity was lost under alkaline than under acidic conditions except in the presence of large concentrations (20 mM) of nitrite. These results indicate that nitrite toxicity in N. europaea is mediated by a unique mechanism that is specific for AMO.     

Ammonia Formation By The Reduction Of Nitrite/Nitrate By Fes: Ammonia Formation Under Acidic Conditions

One issue for the origin of life under a non-reducing atmosphere is the availability of the reduced nitrogen necessary for amino acids, nucleic acids, etc. One possible source of this nitrogen is the formation of ammonia from the reduction of nitrates and nitrites produced by the shock heating of the atmosphere and subsequent chemistry. Ferrous ions will reduce these species to ammonium, but not under acidic conditions. We wish to report results on the reduction of nitrite and nitrate by another source of iron (II), ferrous sulfide, FeS. FeS reduces nitrite to ammonia at lower pHs than the corresponding reduction by aqueous Fe^{+ 2}. The reduction follows a first order decay, in nitrite concentration, with a half-life of about 150 min (room temperature, CO₂, pH 6.25). The highest product yield of ammonia measured was 53%. Under CO₂, the product yield decreases from pH 5.0 to pH 6.9. The increasing concentration of bicarbonate, at higher pH, interferes with the reaction. Comparing experiments under N₂ CO₂ shows the interference of bicarbonate. The reaction proceeds well in the presence of such species as chloride, sulfate, and phosphate, though the yield drops significantly with phosphate. FeS also reduces nitrate and, unlike with Fe^{+ 2}, the reduction shows more reproducibility. Again, the product yield decreases with increasing pH, from 7% at pH 4.7 to 0% at pH 6.9. It appears that nitrate is much more sensitive to the presence of added species, perhaps not competing as well for binding sites on the FeS surface. This may be the cause of the lack of reproducibility of nitrate reduction by Fe^{+ 2} (which also can be sensitive to binding by certain species)     

Analysis of Proteins Binding to the ITAM Motif of the β-Subunit of the High-Affinity Receptor for IgE (FcεRI)

Aggregation of the multichain (α β γ₂) high-affinity IgE receptor (Fcε RI) initiates a signaling cascade that results in the release of allergic mediators. The cytoplasmic tails of the Fcε RI-β and -γ subunits contain immunoreceptor tyrosine-based activation motifs (ITAMs). Phosphorylation of the γ ITAM mediates activation of Syk kinase and is sufficient for triggering the responses induced by Fcε RI crosslinking. Phosphorylation of the β ITAM is insufficient to mediate cell activation. The rat β ITAM contains three tyrosines (Tyr²¹⁸, Tyr²²⁴, and Tyr²²⁸) with an intermediate noncanonical tyrosine. Synthetic peptides based on the ITAM of the Fcε RI-β subunit were used to investigate the role of each phosphotyrosine in the binding of signaling proteins to this motif. Among the proteins that bind to phosphorylated β ITAM are Syk, Grb2, Shc, SHIP, and SHP-1, and binding does not depend on previous cell activation. Nonphosphorylated peptides do not bind these proteins. Syk binding to β -peptides is dependent on the number and position of phosphotyrosines in the ITAM. Phosphorylation of Tyr²¹⁸ seems to be most important for Syk binding. Recruitment of Syk and other signaling proteins to the β -subunit might be important for its amplifier role.     

Unraveling Curcumin Degradation: AUTOXIDATION PROCEEDS THROUGH SPIROEPOXIDE AND VINYLETHER INTERMEDIATES EN ROUTE TO THE MAIN BICYCLOPENTADIONE*

Curcumin is a dietary anti-inflammatory and chemopreventive agent consisting of two methoxyphenol rings connected by a conjugated heptadienedione chain. Curcumin is unstable at physiological pH and rapidly degrades in an autoxidation reaction to a major bicyclopentadione product in which the 7-carbon chain has undergone oxygenation and double cyclization. Early degradation products (but not the final bicyclopentadione) mediate topoisomerase poisoning and possibly many other activities of curcumin, but it is not known how many and what autoxidation products are formed, nor their mechanism of formation. Here, using [¹⁴C₂]curcumin as a tracer, seven novel autoxidation products, including two reaction intermediates, were isolated and identified using one- and two-dimensional NMR and mass spectrometry. The unusual spiroepoxide and vinylether reaction intermediates are precursors to the final bicyclopentadione product. A mechanism for the autoxidation of curcumin is proposed that accounts for the addition and exchange of oxygen that have been determined using ¹⁸O₂ and H₂¹⁸O. Several of the by-products are formed from an endoperoxide intermediate via reactions that are well precedented in lipid peroxidation. The electrophilic spiroepoxide intermediate formed a stable adduct with N-acetylcysteine, suggesting that oxidative transformation is required for biological effects mediated by covalent adduction to protein thiols. The spontaneous autoxidation distinguishes curcumin among natural polyphenolic compounds of therapeutic interest; the formation of chemically diverse reactive and electrophilic products provides a novel paradigm for understanding the polypharmacological effects of curcumin.     

Interrelationship between hydrogen peroxide,ammonia, glutamine,hydroxylamine and nitrite metabolism in the cyanobacterium Phormidium uncinatum

On transition from nitrogen starvation to ammonia or ammonia/glutamine sufficiency Phormidium uncinatum produces high amounts of H₂O₂, which is consumed by several oxidative reactions catalyzed by thylakoid membrane bound enzymes. These include: oxidation of glutamine to free hydroxylamine, of ammonia to nitrite, of bound hydroxylamine to nitrite, and dismutation of free hydroxylamine to ammonia and nitrite. A possible role of these transformations for detoxification is discussed.Non-standard abbreviations FCCP p-trifluormethoxy carbonylcyanide phenylhydrazone - DCMU dichloromethyl urea     

Reply to: Comment on ‘neutron imaging reveals internal plant water dynamics’

Background

Our recent publication (Warren et al., Plant Soil 366:683–693, 2013) described how pulses of deuterium oxide (D₂O) or H₂O combined with neutron radiography can be used to indicate root water uptake and hydraulic redistribution in maize. This technique depends on the large inherent differences in neutron cross-section between D and H atoms resulting in strong image contrast.

Scope and Conclusions

However, as illustrated by Carminati and Zarebanadkouki (2013) there can be a change in total water content without a change in contrast simply by a change in the relative proportions of D₂O and H₂O. We agree with their premise and detailed calculations (Zarebanadkouki at al. 2012, 2013), and present further evidence that mixing of D₂O and H₂O did not confound evidence of hydraulic redistribution in our study.     

Production of reactive oxygen species in decoupled, Ca2+-depleted PSII and their use in assigning a function to chloride on both sides of PSII

Extraction of Ca²⁺ from the oxygen-evolving complex of photosystem II (PSII) in the absence of a chelator inhibits O₂ evolution without significant inhibition of the light-dependent reduction of the exogenous electron acceptor, 2,6-dichlorophenolindophenol (DCPIP) on the reducing side of PSII. The phenomenon is known as “the decoupling effect” (Semin et al. Photosynth Res 98:235–249, 2008). Extraction of Cl^? from Ca²⁺-depleted membranes (PSII[–Ca]) suppresses the reduction of DCPIP. In the current study we investigated the nature of the oxidized substrate and the nature of the product(s) of the substrate oxidation. After elimination of all other possible donors, water was identified as the substrate. Generation of reactive oxygen species HO, H₂O₂, and O ₂ ^·? , as possible products of water oxidation in PSII(–Ca) membranes was examined. During the investigation of O ₂ ^·? production in PSII(–Ca) samples, we found that (i) O ₂ ^·? is formed on the acceptor side of PSII due to the reduction of O₂; (ii) depletion of Cl^? does not inhibit water oxidation, but (iii) Cl^? depletion does decrease the efficiency of the reduction of exogenous electron acceptors. In the absence of Cl^? under aerobic conditions, electron transport is diverted from reducing exogenous acceptors to reducing O₂, thereby increasing the rate of O ₂ ^·? generation. From these observations we conclude that the product of water oxidation is H₂O₂ and that Cl^? anions are not involved in the oxidation of water to H₂O₂ in decoupled PSII(–Ca) membranes. These results also indicate that Cl^? anions are not directly involved in water oxidation by the Mn cluster in the native PSII membranes, but possibly provide access for H₂O molecules to the Mn₄CaO₅ cluster and/or facilitate the release of H⁺ ions into the lumenal space.     

The reduction of nitrate, nitrite and hydroxylamine to ammonia by enzymes from Cucurbita pepo L. in the presence of reduced benzyl viologen as electron donor

1. Enzyme systems from Cucurbita pepo have been shown to catalyse the reduction of nitrite and hydroxylamine to ammonia in yields about 90–100%. 2. Reduced benzyl viologen serves as an efficient electron donor for both systems. Activity of the nitrite-reductase system is directly related to degree of dye reduction when expressed in terms of the function for oxidation–reduction potentials, but appears to decrease to negligible activity below about 9% dye reduction. 3. NADH and NADPH alone produce negligible nitrite loss, but NADPH can be linked to an endogenous diaphorase system to reduce nitrite to ammonia in the presence of catalytic amounts of benzyl viologen. 4. The NADH– or NADPH–nitrate-reductase system that is also present can accept electrons from reduced benzyl viologen, but shows relationships opposite to that for the nitrite-reductase system with regard to effect of degree of dye reduction on activity. The product of nitrate reduction may be nitrite alone, or nitrite and ammonia, or ammonia alone, according only to the degree of dye reduction. 5. The relative activities of nitrite-reductase and hydroxylamine-reductase systems show different relationships with degree of dye reduction and may become reversed in magnitude when effects of degree of dye reduction are tested over a suitable range. 6. Nitrite severely inhibits the rate of reduction of hydroxylamine without affecting the yield of ammonia as a percentage of total substrate loss, but hydroxylamine has a negligible effect on the activity of the nitrite-reductase system. 7. The apparent K_m for nitrite (1 μm) is substantially less than that for hydroxylamine, for which variable values between 0·05 and 0·9mm (mean 0·51 mm) have been observed. 8. The apparent K_m values for reduced benzyl viologen differ for the nitrite-reductase and hydroxylamine-reductase systems: 60 and 7·5 μm respectively. 9. It is concluded that free hydroxylamine may not be an intermediate in the reduction of nitrite to ammonia by plants, and a possible mechanism for reduction of both compounds by the same enzyme system is discussed in the light of current ideas relating to other organisms.     

Interaction between tyrosineZ and substrate water in active photosystem II

In the field of photosynthetic water oxidation it has been under debate whether Tyrosine_Z (Tyr_Z) acts as a hydrogen or an electron acceptor from water. In the former concept, direct contact of Tyr_Z with substrate water has been assumed. However, there is no direct evidence for the interaction between Tyr_Z and substrate water in active Photosystem II (PSII), instead most experiments have been performed on inhibited PSII. Here, this problem is tackled in active PSII by combining low temperature EPR measurements and quantum chemistry calculations. EPR measurements observed that the maximum yield of Tyr_Z oxidation at cryogenic temperature in the S₀ and S₁ states was around neutral pH and was essentially pH-independent. The yield of Tyr_Z oxidation decreased at acidic and alkaline pH, with pKs at 4.7-4.9 and 7.7, respectively. The observed pH-dependent parts at low and high values of pH can be explained as due to sample inactivation, rather than active PSII. The reduction kinetics of Tyr_Z^· in the S₀ and S₁ states were pH independent at pH range from 4.5 to 8. Therefore, the change of the pH in bulk solution probably has no effect on the Tyr_Z oxidation and Tyr_Z^· reduction at cryogenic temperature in the S₀ and S₁ states of the active PSII. Theoretical calculations indicate that Tyr_Z becomes more difficult to oxidize when a H₂O molecule interacts directly with it. It is suggested that Tyr_Z is probably located in a hydrophobic environment with no direct interaction with the substrate H₂O in active PSII. These results provide new insights on the function and mechanism of water oxidation in PSII.     

Chloroplast Respiration : A MEANS OF SUPPLYING OXIDIZED PYRIDINE NUCLEOTIDE FOR DARK CHLOROPLASTIC METABOLISM

A spinach (Spinacia oleracia var. America) chloroplast particle fortified with ferredoxin, fructose-1,6-bisphosphate, or ribose-5-phosphate and NADP has been shown to generate NADPH by the oxidation of glyceraldehyde-3 phosphate to glycerate-3-phosphate (PGA) and to reduce ferredoxin with the NADPH. The resulting reduced ferredoxin can reduce O₂ to H₂O₂, nitrite to ammonia, or protons to H₂. Hydrogen production was the result of adding hydrogenase from Chlamydomonas reinhardii to the chloroplast preparation. The predicted stoichiometry of 1 PGA:1 O₂ in the absence of and 2 PGA:1 O₂ in the presence of catalase was observed indicating H₂O₂ as the end product of O₂ reduction. The predicted stoichiometry of 3 PGA:1 nitrite:1 ammonia was also observed. A scheme is presented to account for a sustained generation of NADP and ATP necessary for the dissimilation of starch in the darkened chloroplast. The unifying term chloroplast respiration is introduced to account for those reactions in which reduced ferredoxin interacts with physiological acceptors other than NADP or nitrite, hydrogen, or O₂ respiration when nitrite, protons, or O₂ is the ultimate electron acceptor.     

Unexpected dependence on pH of NO release from Paracoccus pantotrophus cytochrome cd1

A previous study of nitrite reduction by Paracoccus pantotrophus cytochrome cd₁ at pH 7.0 identified early reaction intermediates. The c-heme rapidly oxidised and nitrite was reduced to NO at the d₁-heme. A slower equilibration of electrons followed, forming a stable complex assigned as 55% cFe(III)d₁Fe(II)-NO and 45% cFe(II)d₁Fe(II)-NO⁺. No catalytically competent NO release was observed. Here we show that at pH 6.0, a significant proportion of the enzyme undergoes turnover and releases NO. An early intermediate, which was previously overlooked, is also identified; enzyme immediately following product release is a candidate. However, even at pH 6.0 a considerable fraction of the enzyme remains bound to NO so another component is required for full product release. The kinetically stable product formed at the end of the reaction differs significantly at pH 6.0 and 7.0, as does its rate of formation; thus the reaction is critically dependent on pH.     

Stoichiometry of nitrite reduction catalyzed by Pseudomonas aeruginosa nitrite-reductase

The stoichiometry of the reduction of nitrite catalyzed by Pseudomonas aeruginosa nitrite-reductase (cytochrome cd₁) has been shown to yield nitrous oxide as the final product. Gas chromatography experiments demonstrated that nitric oxide is also formed as a free intermediate. A sequential formation of NO and N₂O is discussed as proposed to the parallel formation of the two products.     

Abiotic nitrate incorporation, anaerobic microsites, and the ferrous wheel

Nitrate has long been thought to be chemically unreactive in soil. This view was challenged by the report of an apparently abiotic process whereby nitrate (NO₃ ^?) is incorporated into organic compounds (Dail et al. 2001). In Colman et al. (2007), we examined how common this process might be by testing for it in 45 soils collected from across a range of ecosystem types. We found no evidence of this process occurring in any of the soils, but found evidence of an analytical artifact that creates the appearance of incorporation. We suggested that prior evidence of this process might be due in part or in total to this analytical artifact. Davidson et al. (2008), however, challenged our results and conclusions, suggesting that we failed to observe the abiotic incorporation because we eliminated the anaerobic microsites they argue are necessary for the process. We address the criticisms, and show that they actually raise questions about the robustness of the only study to have reported abiotic NO₃ ^? incorporation in sterile soils. We argue that this area of research needs new artifact-free experiments if the controversy is going to be resolved.     

Oxidative and hydrolytic transformations of hydroxylamine compounds in cyanobacteria

Ammonia-incubated cyanobacteria liberated H₂O₂, accumulated hydroxylamine compounds and nitrite and catalyzed dismutation of hydroxylamine as well as oxidations of ammonia, glutamine, and oximes. Ethyl acetohydroximate-adapted Phormidium released excess H₂O₂ and phototrophically metabolized the oxime via hydrolysis and dismutation to nitrite and ammonia, which were consumed by nitrite reductase and glutamine synthetase. Added ammonia stimulated H₂O₂ production and oxime metabolism via glutamate dehydrogenase pathway.Abbreviations EAH Ethyl acetohydroximate - GDH glutamate dehydrogenase - GS glutamine synthetase - NiR nitrite reductase     

A proposed role for inorganic carbon in water oxidation

This is an article on the peroxydicarbonic acid (PODCA) hypothesis of photosynthetic water oxidation, which follows our first article in this general area (Castelfranco et al., Photosynth Res 94:235–246, 2007). In this article I have expanded on the idea of a protein-bound intermediate containing inorganic carbon in some chemically bound form. PODCA is conceived in this article as constituting a bridge between two proteins of the oxygen-evolving complex (OEC) that are essential for the evolution of O₂. Presumably, these are two proteins which have been shown to possess Mn-dependent carbonic anhydrase activity (Lu et al., Plant Cell Physiol 46:1944–1953, 2005; Shitov et al., Biochemistry (Moscow) 74:509–517, 2009). One of these proteins may be the D_I of the OEC core and the other may be the PsbO extrinsic protein. I attempt to relate briefly the PODCA hypothesis to the role of two cofactors for O₂ evolution: Ca²⁺ and inorganic carbon. In this scheme, inorganic carbon (HCO₃ ^?) mediates the oxidation of peroxide to dioxygen, thus avoiding the homolytic cleavage of the peroxide into two free radicals. I visualize the role of Ca²⁺ in the binding of PODCA to two essential photosystem II proteins. I propose that PODCA alternates between two Phases. In Phase 1, PODCA is broken down with the production of O₂. In Phase 2, PODCA is regenerated.     

Lithotrophic growth ofSulfurospirillum deleyianum with sulfide as electron donor coupled to respiratory reduction of nitrate to ammonia

Sulfurospirillum deleyianum grew in batch culture under anoxic conditions with sulfide (up to 5 mM) as electron donor, nitrate as electron acceptor, and acetate as carbon source. Nitrate was reduced to ammonia via nitrite, a quantitatively liberated intermediate. Four moles of sulfide were oxidized to elemental sulfur per mole nitrate converted to ammonia. The molar growth yield per mole sulfide consumed, Y_m, was 1.5 ± 0.2 g mol^–1 for the reduction of nitrate to ammonia. By this type of metabolism, S. deleyianum connected the biogeochemical cycles of sulfur and nitrogen. The sulfur reductase activity in S. deleyianum was inducible, as the activity depended on the presence of sulfide or elemental sulfur during cultivation with nitrate or fumarate as electron acceptor. Hydrogenase activity was always high, indicating that the enzyme is constitutively expressed. The ammonia-forming nitrite reductase was an inducible enzyme, expressed when cells were cultivated with nitrate, nitrite, or elemental sulfur, but repressed after cultivation with fumarate. Received: 13 March 1995 / Accepted: 29 May 1995