How Biology Handles Nitrite

Metal-free Transformations of Nitrogen-Oxyanions to Ammonia via Oxoammonium Salt

Transformations of nitrogen-oxyanions (NO_x ^- ) to ammonia impart pivotal roles in sustainable biogeochemical processes. While metal-mediated reductions of NO_x ^- are relatively well known, this report illustrates proton-assisted transformations of NO_x ^- anions in the presence of electron-rich aromatics such as 1,3,5-trimethoxybenzene (TMB-H, 1 a) leading to the formation of diaryl oxoammonium salt [(TMB)₂ N⁺ =O][NO₃ ^- ] (2 a) via the intermediacy of nitrosonium cation (NO⁺ ). Detailed characterizations including UV/Vis, multinuclear NMR, FT-IR, HRMS, X-ray analyses on a set of closely related metastable diaryl oxoammonium [Ar₂ N⁺ =O] species disclose unambiguous structural and spectroscopic signatures. Oxoammonium salt 2 a exhibits 2 e^- oxidative reactivity in the presence of oxidizable substrates such as benzylamine, thiol, and ferrocene. Intriguingly, reaction of 2 a with water affords ammonia. Perhaps of broader significance, this work reveals a new metal-free route germane to the conversion of NO_x  to NH₃ .

Complete genome sequence of a nitrate reducing bacteria, Algoriphagus sp. Y33 isolated from the water of the Indian Ocean

Algoriphagus sp. Y33, is a nitrate-reducing bacterium isolated from the water of Indian Ocean. Here, we present the complete genome sequence of strain Y33. The genome has one circular chromosome of 6,378,979 bp, with an average GC content of 41.86%, and 5757 coding sequences. According to the annotation analysis, strain Y33 encodes 32 proteins related to nitrogen metabolism. To our knowledge, this is the first report of Algoriphagus sp. isolated from the Indian Ocean with the capacity of nitrate reduction, which will provide insights into regulatory mechanisms of nitrate uptake by heterotrophic bacteria and the global nitrogen cycling.

Bayesian Modeling and Intrabacterial Drug Metabolism Applied to Drug-Resistant Staphylococcus aureus

We present the application of Bayesian modeling to identify chemical tools and/or drug discovery entities pertinent to drug-resistant Staphylococcus aureus infections. The quinoline JSF-3151 was predicted by modeling and then empirically demonstrated to be active against in vitro cultured clinical methicillin- and vancomycin-resistant strains while also exhibiting efficacy in a mouse peritonitis model of methicillin-resistant S. aureus infection. We highlight the utility of an intrabacterial drug metabolism (IBDM) approach to probe the mechanism by which JSF-3151 is transformed within the bacteria. We also identify and then validate two mechanisms of resistance in S. aureus: one mechanism involves increased expression of a lipocalin protein, and the other arises from the loss of function of an azoreductase. The computational and experimental approaches, discovery of an antibacterial agent, and elucidated resistance mechanisms collectively hold promise to advance our understanding of therapeutic regimens for drug-resistant S. aureus.

Physiological Roles of Nitrite and Nitric Oxide in Bacteria: Similar Consequences from Distinct Cell Targets, Protection, and Sensing Systems

Nitrite and nitric oxide (NO) are two active nitrogen oxides that display similar biochemical properties, especially when interacting with redox-sensitive proteins (i.e., hemoproteins), an observation serving as the foundation of the notion that the antibacterial effect of nitrite is largely attributed to NO formation. However, a growing body of evidence suggests that they are largely treated as distinct molecules by bacterial cells. Although both nitrite and NO are formed and decomposed by enzymes participating in the transformation of these nitrogen species, NO can also be generated via amino acid metabolism by bacterial NO synthetase and scavenged by flavohemoglobin. NO seemingly interacts with all hemoproteins indiscriminately, whereas nitrite shows high specificity to heme-copper oxidases. Consequently, the homeostasis of redox-sensitive proteins may be responsible for the substantial difference in NO-targets identified to date among different bacteria. In addition, most protective systems against NO damage have no significant role in alleviating inhibitory effects of nitrite. Furthermore, when functioning as signal molecules, nitrite and NO are perceived by completely different sensing systems, through which they are linked to different biological processes.

Mechanism of O-Atom Transfer from Nitrite: Nitric Oxide Release at Copper(II)

Nitric oxide (NO) is a key signaling molecule in health and disease. While nitrite acts as a reservoir of NO activity, mechanisms for NO release require further understanding. A series of electronically varied β-diketiminatocopper(II) nitrite complexes [Cu^II](κ²-O₂N) react with a range of electronically tuned triarylphosphines PAr^Z₃ that release NO with the formation of O═PAr^Z₃. Second-order rate constants are largest for electron-poor copper(II) nitrite and electron-rich phosphine pairs. Computational analysis reveals a transition-state structure energetically matched with experimentally determined activation barriers. The production of NO follows a pathway that involves nitrite isomerization at Cu^II from κ²-O₂N to κ¹-NO₂ followed by O-atom transfer (OAT) to form O═PAr^Z₃ and [Cu^I]-NO that releases NO upon PAr^Z₃ binding at Cu^I to form [Cu^I]-PAr^Z₃. These findings illustrate important mechanistic considerations involved in NO formation from nitrite via OAT.

A Kinetic Investigation of the Early Steps in Cytochrome c Nitrite Reductase (ccNiR)-Catalyzed Reduction of Nitrite

The decaheme enzyme cytochrome c nitrite reductase (ccNiR) catalyzes reduction of nitrite to ammonium in a six-electron, eight-proton process. With a strong reductant as the electron source, ammonium is the sole product. However, intermediates accumulate when weaker reductants are employed, facilitating study of the ccNiR mechanism. Herein, the early stages of Shewanella oneidensis ccNiR-catalyzed nitrite reduction were investigated by using the weak reductants N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD) and ferrocyanide. In stopped-flow experiments, reduction of nitrite-loaded ccNiR by TMPD generated a transient intermediate, identified as Fe_H1^II(NO₂^-), where Fe_H1 represents the ccNiR active site. Fe_H1^II(NO₂^-) accumulated rapidly and was then more slowly converted to the two-electron-reduced moiety {Fe_H1NO}⁷; ccNiR was not reduced beyond the {Fe_H1NO}⁷ state. The midpoint potentials for sequential reduction of Fe_H1^III(NO₂^-) to Fe_H1^II(NO₂^-) and then to {Fe_H1NO}⁷ were estimated to be 130 and 370 mV versus the standard hydrogen electrode, respectively. Fe_H1^II(NO₂^-) does not accumulate at equilibrium because its reduction to {Fe_H1NO}⁷ is so much easier than the reduction of Fe_H1^III(NO₂^-) to Fe_H1^II(NO₂^-). With weak reductants, free NO• was released from nitrite-loaded ccNiR. The release of NO• from {Fe_H1NO}⁷ is exceedingly slow (k ∼ 0.001 s^-1), but it is somewhat faster (k ∼ 0.050 s^-1) while Fe_H1^III(NO₂^-) is being reduced to {Fe_H1NO}⁷; then, the release of NO• from the undetectable transient {Fe_H1NO}⁶ can compete with reduction of {Fe_H1NO}⁶ to {Fe_H1NO}⁷. CcNiR appears to be optimized to capture nitrite and minimize the release of free NO•. Nitrite capture is achieved by reducing bound nitrite with even weak electron donors, while NO• release is minimized by stabilizing the substitutionally inert {Fe_H1NO}⁷ over the more labile {Fe_H1NO}⁶.

Headspace Solid-Phase Microextraction Following Chemical Vapor Generation for Ultrasensitive, Matrix Effect-Free Detection of Nitrite by Microplasma Optical Emission Spectrometry

A new chemical vapor generation method coupled with headspace solid-phase microextraction miniaturized point discharge optical emission spectrometry (HS-SPME-μPD-OES) for the sensitive and matrix effect-free detection of nitrite in complex samples is described. In an acidic medium, the volatile cyclohexene was generated from cyclamate in the presence of nitrite, which was volatilized to the headspace of the container, efficiently separated, and preconcentrated by HS-SPME. Consequently, the SPME fiber was transferred to a laboratory-constructed thermal desorption chamber wherein the cyclohexene was thermally desorbed and swept into μPD-OES for its sensitive quantification via monitoring the carbon atomic emission line at 193.0 nm. As a result, the quantification of nitrite was accomplished through the determination of cyclohexene. The application of HS-SPME as a sampling technique not only simplifies the experimental setup of μPD-OES but it also preconcentrates and separates cyclohexene from N₂ and sample matrices, thus eliminating the interference from water vapor and N₂ and significantly improving the analytical performance on the determination of nitrite. Under the optimum experimental conditions, a limit of detection of 0.1 μg L^-1 was obtained, which is much better than that obtained by conventional methods. The precision, expressed as relative standard deviation, was better than 3.0% at a concentration of 10 μg L^-1. The proposed method provides several advantages of portability, simplicity, high sensitivity, and low energy consumption and eliminates expensive instruments and matrix interference, thus retaining a promising potential for the rapid, sensitive, and field analysis of nitrite in various samples.

Nanoscale Metal-Organic Frameworks as Fluorescence Sensors for Food Safety

Food safety has attracted attention worldwide, and how to detect various kinds of hazardous substances in an efficient way has always been a focus. Metal-Organic Frameworks (MOFs) are a class of hybrid porous materials formed by organic ligand and metal ions. Nanoscale MOFs (NMOFs) exhibit great potential in serving as fluorescence sensors for food safety due to their superior properties including high accuracy, great stability, fast response, etc. In this review, we focus on the recent development of NMOFs sensing for food safety. Several typical methods of NMOFs synthesis are presented. NMOFs-based fluorescence sensors for contaminants and adulterants, such as antibiotics, food additives, ions and mycotoxin etc. are summarized, and the sensing mechanisms are also presented. We explore these challenges in detail and provide suggestions about how they may be surmounted. This review could help the exploration of NMOFs sensors in food related work.

Grand challenges in the nitrogen cycle

In this Viewpoint, we address some of the limitations within our current understanding of the complex chemistry of the enzymes used in the Nitrogen Cycle. Further understanding of these chemical processes will play a large role in limiting the anthropogenic effects on our environment.

Molecular understanding of heteronuclear active sites in heme-copper oxidases, nitric oxide reductases, and sulfite reductases through biomimetic modelling

Heme-copper oxidases (HCO), nitric oxide reductases (NOR), and sulfite reductases (SiR) catalyze the multi-electron and multi-proton reductions of O2, NO, and SO32-, respectively. Each of these reactions is important to drive cellular energy production through respiratory metabolism and HCO, NOR, and SiR evolved to contain heteronuclear active sites containing heme/copper, heme/nonheme iron, and heme-[4Fe-4S] centers, respectively. The complexity of the structures and reactions of these native enzymes, along with their large sizes and/or membrane associations, make it challenging to fully understand the crucial structural features responsible for the catalytic properties of these active sites. In this review, we summarize progress that has been made to better understand these heteronuclear metalloenzymes at the molecular level though study of the native enzymes along with insights gained from biomimetic models comprising either small molecules or proteins. Further understanding the reaction selectivity of these enzymes is discussed through comparisons of their similar heteronuclear active sites, and we offer outlook for further investigations.

Electrocatalysis by Heme Enzymes—Applications in Biosensing

Heme proteins take part in a number of fundamental biological processes, including oxygen transport and storage, electron transfer, catalysis and signal transduction. The redox chemistry of the heme iron and the biochemical diversity of heme proteins have led to the development of a plethora of biotechnological applications. This work focuses on biosensing devices based on heme proteins, in which they are electronically coupled to an electrode and their activity is determined through the measurement of catalytic currents in the presence of substrate, i.e., the target analyte of the biosensor. After an overview of the main concepts of amperometric biosensors, we address transduction schemes, protein immobilization strategies, and the performance of devices that explore reactions of heme biocatalysts, including peroxidase, cytochrome P450, catalase, nitrite reductase, cytochrome c oxidase, cytochrome c and derived microperoxidases, hemoglobin, and myoglobin. We further discuss how structural information about immobilized heme proteins can lead to rational design of biosensing devices, ensuring insights into their efficiency and long-term stability.

Biochemical and artificial pathways for the reduction of carbon dioxide, nitrite and the competing proton reduction: effect of 2nd sphere interactions in catalysis

Reduction of oxides and oxoanions of carbon and nitrogen are of great contemporary importance as they are crucial for a sustainable environment.

The Metaphosphite (PO2 - ) Anion as a Ligand

The utilization of monomeric, lower phosphorous oxides and oxoanions, such as metaphosphite (PO2 - ), which is the heavier homologue of the common nitrite anion but previously only observed in the gas phase and by matrix isolation, requires new synthetic strategies. Herein, a series of rhenium(I-III) complexes with PO2 - as ligand is reported. Synthetic access was enabled by selective oxygenation of a terminal phosphide complex. Spectroscopic and computational examination revealed slightly stronger σ-donor and comparable π-acceptor properties of PO2 - compared to homologous NO2 - , which is one of the archetypal ligands in coordination chemistry.

Atomic-scale evidence for highly selective electrocatalytic N-N coupling on metallic MoS2

Molybdenum sulfide (MoS₂) is the most studied two-dimensional (2D) material bar graphene. Current research on crystal-phase engineering focuses almost exclusively on the improvement of catalytic activity. However, the potential advantages of phase engineering toward regulation of selectivity control during multistep catalytic processes remain unexplored. Here, we report atomic-scale evidence on how metallic MoS₂ shows significantly higher selectivity compared to the semiconducting phase during multielectron reduction of nitrite to nitrous oxide. Namely, a reaction intermediate specific to metallic MoS₂ increases the selectivity by decoupling the proton and electron transfer steps. This has previously been shown to be a universal mechanism to enhance selectivity, and therefore, our work opens directions of the application of 2D materials toward selective electrocatalysis.

Molybdenum sulfide (MoS₂) is the most widely studied transition-metal dichalcogenide (TMDs) and phase engineering can markedly improve its electrocatalytic activity. However, the selectivity toward desired products remains poorly explored, limiting its application in complex chemical reactions. Here we report how phase engineering of MoS₂ significantly improves the selectivity for nitrite reduction to nitrous oxide, a critical process in biological denitrification, using continuous-wave and pulsed electron paramagnetic resonance spectroscopy. We reveal that metallic 1T-MoS₂ has a protonation site with a pK_a of ∼5.5, where the proton is located ∼3.26 Å from redox-active Mo site. This protonation site is unique to 1T-MoS₂ and induces sequential proton−electron transfer which inhibits ammonium formation while promoting nitrous oxide production, as confirmed by the pH-dependent selectivity and deuterium kinetic isotope effect. This is atomic-scale evidence of phase-dependent selectivity on MoS₂, expanding the application of TMDs to selective electrocatalysis.

Geochemical and isotopic study of abiotic nitrite reduction coupled to biologically produced Fe(II) oxidation in marine environments

Estuarine sediments are often characterized by abundant iron oxides, organic matter, and anthropogenic nitrogen compounds (e.g., nitrate and nitrite). Anoxic dissimilatory iron reducing bacteria (e.g., Shewanella loihica) are ubiquitous in these environments where they can catalyze the reduction of Fe(III) (oxyhydr)oxides, thereby releasing aqueous Fe(II). The biologically produced Fe(II) can later reduce nitrite to form nitrous oxide. The effect on nitrite reduction by both biologically produced and artificially amended Fe(II) was examined experimentally. Ferrihydrite was reduced by Shewanella loihica in a batch reaction with an anoxic synthetic sea water medium. Some of the Fe(II) released by S. loihica adsorbed onto ferrihydrite, which was involved in the transformation of ferrihydrite to magnetite. In a second set of experiments with identical medium, no microorganism was present, instead, Fe(II) was amended. The amount of solid-bound Fe(II) in the experiments with bioproduced Fe(II) increased the rate of abiotic NO₂^- reduction with respect to that with synthetic Fe(II), yielding half-lives of 0.07 and 0.47 d, respectively. The δ¹⁸O and δ¹⁵N of NO₂^- was measured through time for both the abiotic and innoculated experiments. The ratio of ε¹⁸O/ε¹⁵N was 0.6 for the abiotic experiments and 3.1 when NO₂^- was reduced by S. loihica, thus indicating two different mechanisms for the NO₂^- reduction. Notably, there is a wide range of the ε¹⁸O/ε¹⁵N values in the literature for abiotic and biotic NO₂^- reduction, as such, the use of this ratio to distinguish between reduction mechanisms in natural systems should be taken with caution. Therefore, we suggest an additional constraint to identify the mechanisms (i.e. abiotic/biotic) controlling NO₂^- reduction in natural settings through the correlation of δ¹⁵N-NO₂^- and the aqueous Fe(II) concentration.

The dual roles of a V(III) centre for substrate binding and oxygen atom abstraction; nitrite reduction mediated by a V(III) complex

A V(iii) complex bearing a tris(thiolato)phoshine derivative mediates the reduction of nitrite without the assistance of external protons or oxophilic substrates. The metal site plays dual roles for nitrite binding and deoxygenation. The reaction is monitored by spectroscopy combined with isotopic labeling experiments. The formed product, a {VNO}4 species, is isolated and characterized.

Genome Analysis of a Marine Bacterium Halomonas sp. and Its Role in Nitrate Reduction under the Influence of Photoelectrons

The solar light response and photoelectrons produced by widespread semiconducting mineral play important roles in biogeochemical cycles on Earth's surface. To explore the potential influence of photoelectrons generated by semiconducting mineral particles on nitrate-reducing microorganisms in the photic zone, a marine heterotrophic denitrifier Halomonas sp. strain 3727 was isolated from seawater in the photic zone of the Yellow Sea, China. This strain was classified as a Halomonadaceae. Whole-genome analysis indicated that this strain possessed genes encoding the nitrogen metabolism, i.e., narG, nasA, nirBD, norZ, nosB, and nxr, which sustained dissimilatory nitrate reduction, assimilatory nitrate reduction, and nitrite oxidation. This strain also possessed genes related to carbon, sulfur, and other metabolisms, hinting at its substantial metabolic flexibility. A series of microcosm experiments in a simulative photoelectron system was conducted, and the results suggested that this bacterial strain could use simulated photoelectrons with different energy for nitrate reduction. Nitrite, as an intermediate product, was accumulated during the nitrate reduction with limited ammonia residue. The nitrite and ammonia productions differed with or without different energy electron supplies. Nitrite was the main product accounting for 30.03% to 68.40% of the total nitrogen in photoelectron supplement systems, and ammonia accounted for 3.77% to 8.52%. However, in open-circuit systems, nitrite and ammonia proportions were 26.77% and 11.17%, respectively, and nitrogen loss in the liquid was not observed. This study reveals that photoelectrons can serve as electron donors for nitrogen transformation mediated by Halomonas sp. strain 3727, which reveals an underlying impact on the nitrogen biogeochemical cycle in the marine photic zone.

Complete denitrification of nitrate and nitrite to N2 gas by samarium(II) iodide

The reduction of nitrogen oxides (NxOyn-) to dinitrogen gas by samarium(ii) iodide is reported. The polyoxoanions nitrate (NO3-) and nitrite (NO2-), as well as nitrous oxide (N2O) and nitric oxide (NO) were all shown to react with stoichiometric amounts of SmI2 in THF for the complete denitrification to N2.

The model structure of the copper-dependent ammonia monooxygenase

Abstract

Ammonia monooxygenase is a copper-dependent membrane-bound enzyme that catalyzes the first step of nitrification in ammonia-oxidizing bacteria to convert ammonia to hydroxylamine, through the reductive insertion of a dioxygen-derived O atom in an N–H bond. This reaction is analogous to that carried out by particulate methane monooxygenase, which catalyzes the conversion of methane to methanol. The enzymatic activity of ammonia monooxygenase must be modulated to reduce the release of nitrogen-based soil nutrients for crop production into the atmosphere or underground waters, a phenomenon known to significantly decrease the efficiency of primary production as well as increase air and water pollution. The structure of ammonia monooxygenase is not available, rendering the rational design of enzyme inhibitors impossible. This study describes a successful attempt to build a structural model of ammonia monooxygenase, and its accessory proteins AmoD and AmoE, from Nitrosomonas europaea, taking advantage of the high sequence similarity with particulate methane monooxygenase and the homologous PmoD protein, for which crystal structures are instead available. The results obtained not only provide the structural details of the proteins ternary and quaternary structures, but also suggest a location for the copper-containing active site for both ammonia and methane monooxygenases, as well as support a proposed structure of a CuA-analogue dinuclear copper site in AmoD and PmoD.

Graphic abstract

Electronic supplementary material

The online version of this article (10.1007/s00775-020-01820-0) contains supplementary material, which is available to authorized users.

The role of porphyrin peripheral substituents in determining the reactivities of ferrous nitrosyl species

Ferrous nitrosyl {FeNO}⁷ species is an intermediate common to the catalytic cycles of Cd₁NiR and CcNiR, two heme-based nitrite reductases (NiR), and its reactivity varies dramatically in these enzymes.

Ferrous nitrosyl {FeNO}⁷ species is an intermediate common to the catalytic cycles of Cd₁NiR and CcNiR, two heme-based nitrite reductases (NiR), and its reactivity varies dramatically in these enzymes. The former reduces NO₂^– to NO in the denitrification pathway while the latter reduces NO₂^– to NH₄⁺ in a dissimilatory nitrite reduction. With very similar electron transfer partners and heme based active sites, the origin of this difference in reactivity has remained unexplained. Differences in the structure of the heme d₁ (Cd₁NiR), which bears electron-withdrawing groups and has saturated pyrroles, relative to heme c (CcNiR) are often invoked to explain these reactivities. A series of iron porphyrinoids, designed to model the electron-withdrawing peripheral substitution as well as the saturation present in heme d₁ in Cd₁NiR, and their NO adducts were synthesized and their properties were investigated. The data clearly show that the presence of electron-withdrawing groups (EWGs) and saturated pyrroles together in a synthetic porphyrinoid (FeDEsC) weakens the Fe–NO bond in {FeNO}⁷ adducts along with decreasing the bond dissociation free energies (BDFE_NH) of the {FeHNO}⁸ species. The EWG raises the E° of the {FeNO}^7/8 process, making the electron transfer (ET) facile, but decreases the pK_a of {FeNO}⁸ species, making protonation (PT) difficult, while saturation has the opposite effect. The weakening of the Fe–NO bonding biases the {FeNO}⁷ species of FeDEsC for NO dissociation, as in Cd₁NiR, which is otherwise set-up for a proton-coupled electron transfer (PCET) to form an {FeHNO}⁸ species eventually leading to its further reduction to NH₄⁺.

The effect of processing medium on the 2 H/1 H of carbon-bound hydrogen in α-cellulose extracted from higher plants

RATIONALE

Although the ² H/¹ H ratio of the carbon-bound hydrogens (C-Hs) in α-cellulose extracted from higher plants has long been used successfully for climate, environmental and metabolic studies, the assumption that bleaching with acidified NaClO₂ to remove lignin before pure α-cellulose can be obtained does not alter the ² H/¹ H ratio of α-cellulose C-Hs has nonetheless not been tested.

METHODS

For reliable application of the ² H/¹ H ratio of α-cellulose C-H, we processed plant materials representing different phytochemistries and photosynthetic carbon assimilation modes in isotopically contrasting bleaching media (with an isotopic difference of 273 mUr). All the isotope ratios were measured by elemental analyzer/isotope ratio mass spectrometry (EA/IRMS).

RESULTS

Our results show that H from the bleaching medium does appear in the final pure α-cellulose product, although the isotopic alteration to the C-H in α-cellulose due to the incorporation of processing H from the medium is small if isotopically "natural" water is used to prepare the processing medium. However, under prolonged bleaching such an isotope effect can be significant, implying that standardizing the bleaching process is necessary for reliable ² H/¹ H measurement.

CONCLUSIONS

The currently adopted method for removing lignin for α-cellulose extraction from higher plant materials with acidified NaClO₂ bleaching is considered acceptable in terms of preserving the isotopic fidelity if isotopically "natural" water is used to prepare the bleaching solution.

Nitrite modulates aminoglycoside tolerance by inhibiting cytochrome heme-copper oxidase in bacteria

As a bacteriostatic agent, nitrite has been used in food preservation for centuries. When used in combination with antibiotics, nitrite is reported to work either cooperatively or antagonistically. However, the mechanism underlying these effects remains largely unknown. Here we show that nitrite mediates tolerance to aminoglycosides in both Gram-negative and Gram-positive bacteria, but has little interaction with other types of antibiotics. Nitrite directly and mainly inhibits cytochrome heme-copper oxidases (HCOs), and by doing so, the membrane potential is compromised, blocking uptake of aminoglycosides. In contrast, reduced respiration (oxygen consumption rate) resulting from nitrite inhibition is not critical for aminoglycoside tolerance. While our data indicate that nitrite is a promising antimicrobial agent targeting HCOs, cautions should be taken when used with other antibiotics, aminoglycosides in particular.

Reduction of Substrates by Nitrogenases

Nitrogenase is the enzyme that catalyzes biological N₂ reduction to NH₃. This enzyme achieves an impressive rate enhancement over the uncatalyzed reaction. Given the high demand for N₂ fixation to support food and chemical production and the heavy reliance of the industrial Haber-Bosch nitrogen fixation reaction on fossil fuels, there is a strong need to elucidate how nitrogenase achieves this difficult reaction under benign conditions as a means of informing the design of next generation synthetic catalysts. This Review summarizes recent progress in addressing how nitrogenase catalyzes the reduction of an array of substrates. New insights into the mechanism of N₂ and proton reduction are first considered. This is followed by a summary of recent gains in understanding the reduction of a number of other nitrogenous compounds not considered to be physiological substrates. Progress in understanding the reduction of a wide range of C-based substrates, including CO and CO₂, is also discussed, and remaining challenges in understanding nitrogenase substrate reduction are considered.

Nitrate from diet might fuel gut microbiota metabolism: Minding the gap between redox signaling and inter-kingdom communication

The gut microbiota has been recently interpreted in terms of a metabolic organ that influences the host through reciprocal interactions, encompassing metabolic and immune pathways, genetic and epigenetic programming in host mammal tissues in a diet-depended manner, that shape virtually all aspects of host physiology. In this scenario, dietary nitrate, a major component of leafy green vegetables known for their health benefits, might fuel microbiota metabolism with ensued consequences for microbiota-host interaction. Cumulating evidence support that nitrate shapes oral microbiome communities with impact on the kinetics and systemic levels of both nitrate and nitrite. However, the impact of nitrate, which is steadily delivered into the lower gastrointestinal tract after a vegetable-rich meal, in the intestinal microbiome communities and their functional capacity remains largely elusive. Several mechanisms reinforce the notion that nitrate may be a nutrient for the lower microbiome and might participate in local redox interactions with relevance for bacteria-host interactions, among these nitric oxide-dependent mechanisms along the nitrate-nitrite-nitric oxide pathway. Also, by allowing bacteria to thrive, either by increasing microbial biomass or by acting as a respiratory substrate for the existing communities, nitrate ensures the production of bacterial metabolites (e.g., pathogen-associated molecular patterns, PAMP, short chain fatty acids, among other) that are recognised by host receptors (such as toll-like, TLR, and formyl peptide receptors, FPR) thereby activating local signalling pathways. Here, we elaborate on the notion that via modulation of intestinal microbiota metabolism, dietary nitrate impacts on host-microbiota metabolic and redox interactions, thereby contributing as an essential nutrient to optimal health.

A recently evolved diflavin-containing monomeric nitrate reductase is responsible for highly efficient bacterial nitrate assimilation

Nitrate is one of the major inorganic nitrogen sources for microbes. Many bacterial and archaeal lineages have the capacity to express assimilatory nitrate reductase (NAS), which catalyzes the rate-limiting reduction of nitrate to nitrite. Although a nitrate assimilatory pathway in mycobacteria has been proposed and validated physiologically and genetically, the putative NAS enzyme has yet to be identified. Here, we report the characterization of a novel NAS encoded by Mycolicibacterium smegmatis Msmeg_4206, designated NasN, which differs from the canonical NASs in its structure, electron transfer mechanism, enzymatic properties, and phylogenetic distribution. Using sequence analysis and biochemical characterization, we found that NasN is an NADPH-dependent, diflavin-containing monomeric enzyme composed of a canonical molybdopterin cofactor-binding catalytic domain and an FMN-FAD/NAD-binding, electron-receiving/transferring domain, making it unique among all previously reported hetero-oligomeric NASs. Genetic studies revealed that NasN is essential for aerobic M. smegmatis growth on nitrate as the sole nitrogen source and that the global transcriptional regulator GlnR regulates nasN expression. Moreover, unlike the NADH-dependent heterodimeric NAS enzyme, NasN efficiently supports bacterial growth under nitrate-limiting conditions, likely due to its significantly greater catalytic activity and oxygen tolerance. Results from a phylogenetic analysis suggested that the nasN gene is more recently evolved than those encoding other NASs and that its distribution is limited mainly to Actinobacteria and Proteobacteria. We observed that among mycobacterial species, most fast-growing environmental mycobacteria carry nasN, but that it is largely lacking in slow-growing pathogenic mycobacteria because of multiple independent genomic deletion events along their evolution.

Phenol Reduces Nitrite to NO at Copper(II): Role of a Proton-Responsive Outer Coordination Sphere in Phenol Oxidation

In the view of physiological significance, the transition-metal-mediated routes for nitrite (NO₂^-) to nitric oxide (NO) conversion and phenol oxidation are of prime importance. Probing the reactivity of substituted phenols toward the nitritocopper(II) cryptate complex [mC]Cu(κ²-O₂N)(ClO₄) (1a), this report illustrates NO release from nitrite at copper(II) following a proton-coupled electron transfer (PCET) pathway. Moreover, a different protonated state of 1a with a proton hosted in the outer coordination sphere, [mCH]Cu(κ²-O₂N)(ClO₄)₂ (3), also reacts with substituted phenols via primary electron transfer from the phenol. Intriguingly, the alternative mechanism operative because of the presence of a proton at the remote site in 3 facilitates an unusual anaerobic pathway for phenol nitration.

(Hydr)oxo-bridged heme complexes: From structure to reactivity

Iron–porphyrins ([Formula: see text] hemes) are present throughout the biosphere and perform a wide range of functions, particularly those that involve complex multiple-electron redox processes. Some common heme enzymes involved in these processes include cytochrome P450, heme/copper oxidase or heme/non-heme diiron nitric oxide reductase. Consequently, the (hydr)oxo-bridged heme species have been studied for the important roles that they play in many life processes or for their application for catalysis and preparation of new functional materials. This review encompasses important synthetic, structural and reactivity aspects of the (hydr)oxo-bridged heme constructs that govern their function and application. The properties and reactivity of the bridging (hydr)oxo moieties are directly dictated by the coordination environment of the heme core, the nature and ligation of the second metal center attached to the (hydr)oxo group, the presence or absence of a linker, and the degree of flexibility around that linker within the scaffold. Here, we summarize the structural features of all known (hydr)oxo-bridged heme constructs and use those to categorize and thus, provide a more comprehensive picture of structure–function relationships.

Conversion of NOx1− (x = 2, 3) to NO using an oxygen-deficient polyoxovanadate–alkoxide cluster

We report the activation of nitrogen-containing oxyanions using an oxygen-deficient polyoxovanadate–alkoxide cluster.

A water-stable terbium metal–organic framework as a highly sensitive fluorescent sensor for nitrite

A terbium metal–organic framework was synthesized for highly sensitive nitrite detection. The mechanism of the quenching process was also studied in detail.

Effects of cobalt-histidine absorbent on aerobic denitrification by Paracoccus versutus LYM

To overcome the problem that ferrous complexes are easily oxidized by O₂ and then lose NO binding ability in the chemical absorption-biological reduction (CABR) process, cobalt(II)-histidine [Co(II)His] was proposed as an alternative. To evaluate the applicability of Co(II)His, the effects of CoHis absorbent on the aerobic denitrification by Paracoccus versutus LYM were investigated. Results indicated that His significantly promoted nitrite reduction. The inhibition effects of CoHis absorbent could be substantially alleviated by increasing the initial His/Co²⁺ to 4 or higher. CoHis with concentrations of 4, 8, 12, 16 and 20 mM presented no distinct effect on nitrite reduction, but slightly inhibited the reduction of nitrate, resulting in longer lag of nitrate reduction, and obviously promoted the growth of strain LYM. In the presence of 5, 10, 15 and 20 mM CoHis absorbent, the main denitrification product was N₂ (not less than 95.0%). This study is of significance in verifying the applicability of Co(II)His in the CABR process, and provides a referable CoHis absorbent concentration as 20 mM with an initial His/Co²⁺ of 4 for the future experiments.

Functional interactions between nitrite reductase and nitric oxide reductase from Paracoccus denitrificans

Denitrification is a microbial pathway that constitutes an important part of the nitrogen cycle on earth. Denitrifying organisms use nitrate as a terminal electron acceptor and reduce it stepwise to nitrogen gas, a process that produces the toxic nitric oxide (NO) molecule as an intermediate. In this work, we have investigated the possible functional interaction between the enzyme that produces NO; the cd₁ nitrite reductase (cd₁NiR) and the enzyme that reduces NO; the c-type nitric oxide reductase (cNOR), from the model soil bacterium P. denitrificans. Such an interaction was observed previously between purified components from P. aeruginosa and could help channeling the NO (directly from the site of formation to the side of reduction), in order to protect the cell from this toxic intermediate. We find that electron donation to cNOR is inhibited in the presence of cd₁NiR, presumably because cd₁NiR binds cNOR at the same location as the electron donor. We further find that the presence of cNOR influences the dimerization of cd₁NiR. Overall, although we find no evidence for a high-affinity, constant interaction between the two enzymes, our data supports transient interactions between cd₁NiR and cNOR that influence enzymatic properties of cNOR and oligomerization properties of cd₁NiR. We speculate that this could be of particular importance in vivo during metabolic switches between aerobic and denitrifying conditions.

Porpholactone Chemistry: An Emerging Approach to Bioinspired Photosensitizers with Tunable Near-Infrared Photophysical Properties

Chlorophylls, known as the key building blocks of natural light-harvesting antennae, are essential to utilize solar energy from visible to near-infrared (NIR) region during the photosynthesis process. The fundamental studies for the relationship between structure and photophysical properties of chlorophylls disclosed the importance of β-peripheral modification and thus boosted the fast growth of NIR absorbing/emissive porphyrinoids via altering the extent of π-conjugation and the degree of distortion from the planarity of macrocycle. Despite the tremendous progress made in various porphyrin-based synthetic models, it still remains a challenge to precisely modulate photophysical properties through fine-tuning of β-peripheral structures in the way natural chlorophylls do. With this in mind, we initiated a program and focused on meso-C₆F₅-substituted porpholactone (F₂₀TPPL), in which one β-pyrrolic double bond was replaced by a lactone moiety, as an attractive platform to construct the bioinspired library of NIR porphyrinoids. In this Account, we summarize our recent contributions to the bioinspired design, synthesis, photophysical characterization, and applications of porpholactones and their derivatives. We have developed a general, convenient method to directly prepare porpholactones in large scale up to gram, which forms the chemical basis of porpholactone chemistry. By modulation of the saturation level and in particular regioisomerization of β-dilactone moieties, a synthetic library constituted by a series of porpholactones and their derivatives has been established. Thanks to the electron-withdrawing nature of lactone moiety, derivation of the saturation levels gives help to build stable models for chlorin, bacteriochlorin, and tunichlorin. It is worth noting that regioisomerization of dilactone moieties mimics the relative orientation of β-substituents in natural chlorophylls and hemes, which was considered as the key factor to tune NIR absorption and reactivity. Porpholactones can illustrate the capability of fine-tuning photophysical properties including the excited triplet states by subtle alteration of β-peripheral structures in the presence of transition metals and lanthanides (Ln). Furthermore, they can serve as efficient photosensitizers for singlet oxygen and NIR Ln, showing potential applications in cell imaging and photocytotoxicity studies. The high luminescence, tunable structures, high cellular uptake, and intense NIR absorption render them as promising and competitive candidates for theranostics in vitro and in vivo. Therefore, extending the studies of "porpholactone chemistry" not only tests the fundamental understanding of the structure-function relationship that governs NIR photophysical properties of natural tetrapyrrole cofactors such as chlorophylls but also provides the guiding principles for the bioinspired design of NIR luminescent molecular probes with various applications. Taken together, as a new synthetic porphyrin derivative, porpholactone chemistry shines light on synthetic porphyrin, bioinorganic, and lanthanide chemistry.

Long-range electron-electron interaction and charge transfer in protein complexes: a numerical approach

With application to the nitrite reductase hexameric protein complex of Desulfovibrio vulgaris, NrfH2A4, we suggest a strategy to compute the energy landscape of electron transfer in large systems of biochemical interest. For small complexes, the energy of all electronic configurations can be scanned completely on the level of a numerical solution of the Poisson-Boltzmann equation. In contrast, larger systems have to be treated using a pair approximation, which is verified here. Effective Coulomb interactions between neighbouring sites of excess electron localization may become as large as 200 meV, and they depend in a nontrivial manner on the intersite distance. We discuss the implications of strong Coulomb interactions on the thermodynamics and kinetics of charging and decharging a protein complex. Finally, we turn to the effect of embedding the system into a biomembrane.

Nitrite reductase activity of heme and copper bound Aβ peptides

A significant abundance of copper (Cu) and iron in amyloid β (Aβ) plaques, and several heme related metabolic disorders are directly correlated with Alzheimer's disease (AD), and these together with co-localization of Aβ plaques with heme rich deposits in the brains of AD sufferers indicates a possible association of the said metals with the disease. Recently, the Aβ peptides have been found to bind heme and Cu individually as well as simultaneously. Another significant finding relevant to this is the lower levels of nitrite and nitrate found in the brains of patients suffering from AD. In this study, a combination of absorption and electron paramagnetic resonance spectroscopy and kinetic assays have been used to study the interaction of nitrite with the metal bound Aβ complexes. The data indicate that heme(III)-Cu(i)-Aβ, heme(II)-Cu(i)-Aβ, heme(II)-Aβ and Cu(i)-Aβ can reduce nitrite to nitric oxide (NO), an important biological messenger also related to AD, and thus behave as nitrite reductases. However these complexes reduce nitrite at different rates with heme(III)-Cu(i)-Aβ being the fastest following an inner sphere electron transfer mechanism. The rest of the metal-Aβ adducts follow an outer sphere electron transfer mechanism during nitrite reduction. Protonation from the Arg5 residue triggering the N-O bond heterolysis in heme(III) bound nitrite with a simultaneous electron transfer from the Cu(i) center to produce NO is the rate determining step, indicating a proton transfer followed by electron transfer (PTET) mechanism.

Crystal structure of catena-poly[[(μ-6-{[bis-(pyridin-2-ylmeth-yl)amino]-meth-yl}pyridine-2-carboxyl-ato)copper(II)] perchlorate aceto-nitrile monosolvate]

The crystal structure of the title compound, {[Cu(C19H17N4O2)]ClO4·C2H3N} n , is reported and compared to similar structures in the literature. The compound crystallizes in the monoclinic space group P21. The unit cell contains one complex mol-ecule in addition to perchlorate as the counter-ion and solvent (aceto-nitrile). The crystal packing evinces extended chains whereby the carboxyl-ate moiety on the 6-carboxyl-ato-2-(pyridyl-meth-yl)bis-(pyridin-2-ylmeth-yl)amine ligand bridges between two different copper centers in adjacent mol-ecules. This packing arrangement for the title compound appears to be unique when compared to allied structures in the literature. The perchlorate anion showed signs of disorder and its oxygen atoms were modelled over two sets of partially occupied sites, the occupancy of which was competitively refined to 0.564 (12)/0.436 (12). The crystal studied was refined as a two-component inversion twin.

NOx- anion recognition by bimetallic cryptates: selectivity for nitrite over nitrate

Nitrate and nitrite anions have multifaceted impacts on the environment and human health. We herein report selective recognition of nitrite over nitrate anion inside the cavity of bimetallic azacryptates having p-xylyl spacers. This work reveals a number of binding interactions which play pivotal roles in nitrite anion recognition by rigid metal cryptates.

One metal is enough: a nickel complex reduces nitrate anions to nitrogen gas

A stepwise reduction sequence from nitrate to dinitrogen gas at a single nickel center was discovered. A PNP nickel scaffold (PNP- = N[2-P i Pr2-4-Me-C6H3]2) emerged as a universal platform for the deoxygenation of NO x substrates. In these reactions carbon monoxide acts as the oxygen acceptor and forms CO2 to provide the necessary chemical driving force. Whereas the first two oxygens are removed from the Ni-nitrate and Ni-nitrite complexes with CO, the deoxygenation of NO requires a disproportionation reaction with another NO molecule to form NO2 and N2O. The final deoxygenation of nitrous oxide is accomplished by the Ni-NO complex and generates N2 and Ni-NO2 in a relatively slow, but clean reaction. This sequence of reactions is the first example of the complete denitrification of nitrate at a single metal-site and suggests a new paradigm of connecting CO and NO x as an effective reaction pair for NO x removal.

Computational analysis of non-heme iron-oxo formation by direct NO release in nitrite reduction

A direct NO-releasing reaction of nitrite catalyzed by [N(afa^Cy)₃Fe(OTf)]⁺ (afa (azafulvene-amine); OTf (trifluoromethanesulfonate); Cy (cyclohexyl)) was investigated using density functional theory (DFT) with D3 dispersion correction. The complex featured a secondary coordination sphere that facilitated the formation of the iron-oxo product [N(afa^Cy)₃FeO]⁺ with three (Fe)OH-N hydrogen bonds. As a high-spin iron(ii), the O-binding initial intermediate Fe(O)-nitrito was thermodynamically favorable in the S = 2 state. The cleavage of the (Fe)O-NO bond was performed by a β-electron shift to produce Fe(iii)-O by electron rearrangement in the S = 5/2 state. The different electron configurations are responsible for the structural properties, the valence of iron in the complexes, and the pathways of the reactions. Moreover, the two different H-bonds, (Fe)OH-N and (Fe)O-HN (by O-protonation), in the product complexes played a role in determining the reaction channels by impacting the N-H bond rotation. Thus, an exothermic sequence of conversions Fe(ii) → Fe(iii)-O → Fe(iii)-OH → Fe(iii)-O was established for the targeted product formation. This process provided a clue to build two key intermediates, iron-oxo and iron-hydroxo, in a variety of biological and synthetic systems. The results of this study are in agreement with experimental observations and describe the roles of H-bonding in nitrite reduction catalyzed by the non-heme iron complex.

Myoglobinopathy is an adult-onset autosomal dominant myopathy with characteristic sarcoplasmic inclusions

Myoglobin, encoded by MB, is a small cytoplasmic globular hemoprotein highly expressed in cardiac myocytes and oxidative skeletal myofibers. Myoglobin binds O_2, facilitates its intracellular transport and serves as a controller of nitric oxide and reactive oxygen species. Here, we identify a recurrent c.292C>T (p.His98Tyr) substitution in MB in fourteen members of six European families suffering from an autosomal dominant progressive myopathy with highly characteristic sarcoplasmic inclusions in skeletal and cardiac muscle. Myoglobinopathy manifests in adulthood with proximal and axial weakness that progresses to involve distal muscles and causes respiratory and cardiac failure. Biochemical characterization reveals that the mutant myoglobin has altered O₂ binding, exhibits a faster heme dissociation rate and has a lower reduction potential compared to wild-type myoglobin. Preliminary studies show that mutant myoglobin may result in elevated superoxide levels at the cellular level. These data define a recognizable muscle disease associated with MB mutation.

Myoglobin is a hemeprotein that reversibly binds oxygen and gives muscle its red color. Here, the authors report a genetic variant in the MB gene that associates with myoglobinopathy, an autosomal dominant progressive myopathy, and altered oxygen binding properties of the mutant protein.