N2O binding at a [4Cu:2S] copper–sulphur cluster in nitrous oxide reductase

Future directions in microbial nitrogen cycling in wastewater treatment

Discoveries in the past decade of novel reactions, processes, and micro-organisms have altered our understanding of microbial nitrogen cycling in wastewater treatment systems. These advancements pave the way for a transition toward more sustainable and energy-efficient wastewater treatment systems that also minimize greenhouse gas emissions. This review highlights these innovative directions in microbial nitrogen cycling within the context of wastewater treatment. Processes such as comammox, Feammox, electro-anammox, and nitrous oxide mitigation offer innovative approaches for sustainable, energy-efficient nitrogen removal. However, while these emerging processes show promise, advancing from laboratory research to practical applications, particularly in decentralized systems, remains a critical next step toward a sustainable and efficient wastewater management.

Enhancing agroecosystem nitrogen management: microbial insights for improved nitrification inhibition

Nitrification is a key microbial process in the nitrogen (N) cycle that converts ammonia to nitrate. Excessive nitrification, typically occurring in agroecosystems, has negative environmental impacts, including eutrophication and greenhouse gas emissions. Nitrification inhibitors (NIs) are widely used to manage N in agricultural systems by reducing nitrification rates and improving N use efficiency. However, the effectiveness of NIs can vary depending on the soil conditions, which, in turn, affect the microbial community and the balance between different functional groups of nitrifying microorganisms. Understanding the mechanisms underlying the effectiveness of NIs, and how this is affected by the soil microbial communities or abiotic factors, is crucial for promoting sustainable fertilizer practices. Therefore, this review examines the different types of NIs and how abiotic parameters can influence the nitrifying community, and, therefore, the efficacy of NIs. By discussing the latest research in this field, we provide insights that could facilitate the development of more targeted, efficient, or complementary NIs that improve the application of NIs for sustainable management practices in agroecosystems.

Impact of aerobic granular sludge sizes and dissolved oxygen concentration on greenhouse gas N2O emission

Aerobic granular sludge (AGS) at wastewater treatment plants (WWTPs) are known to produce nitrous oxide (N2O), a greenhouse gas which has a ∼300 times higher global warming potential than carbon dioxide. In this research, we studied N2O emissions from different sizes of AGS developed at a dissolved oxygen (DO) level of 2 mgO2/L while exposing them to disturbances at various DO concentrations ranging from 1 to 4 mgO2/L. Five different AGS size classes were studied: 212-600 µm, 600-1000 µm, 1000-1400 µm, 1400-2000 µm, and > 2000 µm. Metagenomic data showed N2O reductase genes (nosZ) were more abundant in the smaller AGS sizes which aligned with the observation of higher N2O reduction rates in small AGS under anaerobic conditions. However, when oxygen was present, the activity measurements of N2O emission showed an opposite trend compared to metagenomic data, smaller AGS (212 to 1000 µm) emitted significantly higher N2O (p < 0.05) than larger AGS (1000 µm to >2000 µm) at DO of 2, 3, and 4 mgO2/L. The N2O emission rate showed positive correlation with both oxygen levels and nitrification rate. This pattern indicates a connection between N2O emission and nitrification. In addition, the data suggested the penetration of oxygen into the anoxic zone of granules might have hindered nitrous oxide reduction, resulting in incomplete denitrification stopping at N2O and consequently contributing to an increase in N2O emissions. This work sets the stage to better understand the impacts of AGS size on N2O emissions in WWTPs under different disturbance of DO conditions, and thus ensure that wastewater treatment will comply with possible future regulations demanding lowering greenhouse gas emissions in an effort to combat climate change.

Revisiting the metal sites of nitrous oxide reductase in a low-dose structure from Marinobacter nauticus

Copper-containing nitrous oxide reductase catalyzes a 2-electron reduction of the green-house gas N2O to yield N2. It contains two metal centers, the binuclear electron transfer site CuA, and the unique, tetranuclear CuZ center that is the site of substrate binding. Different forms of the enzyme were described previously, representing variations in oxidation state and composition of the metal sites. Hypothesizing that many reported discrepancies in the structural data may be due to radiation damage during data collection, we determined the structure of anoxically isolated Marinobacter nauticus N2OR from diffraction data obtained with low-intensity X-rays from an in-house rotating anode generator and an image plate detector. The data set was of exceptional quality and yielded a structure at 1.5 Å resolution in a new crystal form. The CuA site of the enzyme shows two distinct conformations with potential relevance for intramolecular electron transfer, and the CuZ cluster is present in a [4Cu:2S] configuration. In addition, the structure contains three additional types of ions, and an analysis of anomalous scattering contributions confirms them to be Ca2+, K+, and Cl-. The uniformity of the present structure supports the hypothesis that many earlier analyses showed inhomogeneities due to radiation effects. Adding to the earlier description of the same enzyme with a [4Cu:S] CuZ site, a mechanistic model is presented, with a structurally flexible CuZ center that does not require the complete dissociation of a sulfide prior to N2O binding.

Natural chalcopyrite mitigates nitrous oxide emissions in sediment from coastal wetlands

Coastal wetlands are one of the most important natural sources of nitrous oxide (N2O). Previous studies have shown that copper-containing chemicals are able to reduce N2O emissions from these ecosystems. However, these chemicals may harm organisms present in coastal waters and sediment, and disturb the ecological balance of these areas. Here, we first investigated the physiological characteristics and genetic potential of denitrifying bacteria isolated from coastal wetlands. Based on an isolated denitrifier carrying a complete denitrification pathway, we tested the effect of the natural mineral chalcopyrite on N2O production by the bacteria. The results demonstrated that chalcopyrite addition lowers N2O emissions from the bacteria while increasing its N2 production rate. Among the four denitrification genes of the isolate, only nosZ gene expression was significantly upregulated following the addition of 2 mg L-1 chalcopyrite. Furthermore, chalcopyrite was applied to coastal wetland sediments. The N2O flux was significantly reduced in 50-100 mg L-1 chalcopyrite-amended sets relative to the controls. Notably, the dissolved Cu concentration in chalcopyrite-amended sediment remained within the limit set by the National Sewage Treatment Discharge Standard. qPCR and metagenomic analysis revealed that the abundance of N2O-reducing bacteria with the nosZ or nirK + nosZ genotype increased significantly in the chalcopyrite-amended groups relative to the controls, suggesting their active involvement in the reduction of N2O emissions. Our findings offer valuable insights for the use of natural chalcopyrite in large-scale field applications to reduce N2O emissions.

What can molecular assembly learn from catalysed assembly in living organisms?

Molecular assembly is the process of organizing individual molecules into larger structures and complex systems. The self-assembly approach is predominantly utilized in creating artificial molecular assemblies, and was believed to be the primary mode of molecular assembly in living organisms as well. However, it has been shown that the assembly of many biological complexes is "catalysed" by other molecules, rather than relying solely on self-assembly. In this review, we summarize these catalysed-assembly (catassembly) phenomena in living organisms and systematically analyse their mechanisms. We then expand on these phenomena and discuss related concepts, including catalysed-disassembly and catalysed-reassembly. Catassembly proves to be an efficient and highly selective strategy for synergistically controlling and manipulating various noncovalent interactions, especially in hierarchical molecular assemblies. Overreliance on self-assembly may, to some extent, hinder the advancement of artificial molecular assembly with powerful features. Furthermore, inspired by the biological catassembly phenomena, we propose guidelines for designing artificial catassembly systems and developing characterization and theoretical methods, and review pioneering works along this new direction. Overall, this approach may broaden and deepen our understanding of molecular assembly, enabling the construction and control of intelligent assembly systems with advanced functionality.

Metagenomic binning analyses of swine manure composting reveal mechanism of nitrogen cycle amendment using kaolin

The efficient control of nitrogen loss in composting and the enhancement of product quality have become prominent concerns in current research. The positive role of varying concentrations kaolin in reducing nitrogen loss during composting was revealed using metagenomic binning combined with reverse transcription quantitative polymerase chain reaction. The results indicated that the addition of 0.5 % kaolin significantly (P < 0.05) up-regulated the expression of nosZ and nifH on day 35, while concurrently reducing norB abundance, resulting in a reduction of NH3 and N2O emissions by 61.4 % and 17.5 %, respectively. Notably, this study represents the first investigation into the co-occurrence of nitrogen functional genes and heavy metal resistance genes within metagenomic assembly genomes during composting. Emerging evidence indicates that kaolin effectively impedes the binding of Cu/Zn to nirK and nosZ gene reductases through passivation. This study offers a novel approach to enhance compost quality and waste material utilization.

Triazenide-supported [Cu4S] structural mimics of CuZ that mediate N2O disproportionation rather than reduction

As part of the nitrogen cycle, environmental nitrous oxide (N2O) undergoes the N2O reduction reaction (N2ORR) catalyzed by nitrous oxide reductase, a metalloenzyme whose catalytic active site is a tetranuclear copper-sulfide cluster (CuZ). On the other hand, heterogeneous Cu catalysts on oxide supports are known to mediate decomposition of N2O (deN2O) by disproportionation. In this study, a CuZ model system supported by triazenide ligands is characterized by X-ray crystallography, NMR and EPR spectroscopies, and electronic structure calculations. Although the triazenide-ligated Cu4(μ4-S) clusters are closely related to previous formamidinate derivatives, which differ only in replacement of a remote N atom for a CH group, divergent reactivity with N2O is observed. Whereas the formamidinate-ligated clusters were previously shown to mediate single-turnover N2ORR, the triazenide-ligated clusters are found to mediate deN2O, behavior that was previously unknown to natural or synthetic copper-sulfide clusters. The reaction pathway for deN2O by this model system, including previously unidentified transition state models for N2O activation in N-O cleavage and O-O coupling steps, are included. The divergent reactivity of these two related but subtly different systems point to key factors influencing behavior of Cu-based catalysts for N2ORR (i.e., CuZ) and deN2O (e.g., CuO/CeO2).

Cooperative small molecule activation by apolar and weakly polar bonds through the lens of a suitable computational protocol

Small molecule activation processes are central in chemical research and cooperativity is a valuable tool for the fine-tuning of the efficiency of these reactions. In this contribution, we discuss recent and remarkable examples in which activation processes are mediated by bimetallic compounds featuring apolar or weakly polar metal-metal bonds. Relevant experimental breakthroughs are thoroughly analyzed from a computational perspective. We highlight how the rational and non-trivial application of selected computational approaches not only allows rationalization of the observed reactivities but also inferring of general principles applicable to activation processes, such as the breakdown of the structure-reactivity relationship in carbon dioxide activation in a cooperative framework. We finally provide a simple yet unbiased computational protocol to study these reactions, which can support experimental advances aimed at expanding the range of applications of apolar and weakly polar bonds as catalysts for small molecule activation.

Electrochemical Reduction of N2O with a Molecular Copper Catalyst

Deoxygenation of nitrous oxide (N2O) has significant environmental implications, as it is not only a potent greenhouse gas but is also the main substance responsible for the depletion of ozone in the stratosphere. This has spurred significant interest in molecular complexes that mediate N2O deoxygenation. Natural N2O reduction occurs via a Cu cofactor, but there is a notable dearth of synthetic molecular Cu catalysts for this process. In this work, we report a selective molecular Cu catalyst for the electrochemical reduction of N2O to N2 using H2O as the proton source. Cyclic voltammograms show that increasing the H2O concentration facilitates the deoxygenation of N2O, and control experiments with a Zn(II) analogue verify an essential role for Cu. Theory and spectroscopy support metal-ligand cooperative catalysis between Cu(I) and a reduced tetraimidazolyl-substituted radical pyridine ligand (MeIm4P2Py = 2,6-(bis(bis-2-N-methylimidazolyl)phosphino)pyridine), which can be observed by Electron Paramagnetic Resonance (EPR) spectroscopy. Comparison with biological processes suggests a common theme of supporting electron transfer moieties in enabling Cu-mediated N2O reduction.

Cu4S Cluster in "0-Hole" and "1-Hole" States: Geometric and Electronic Structure Variations for the Active CuZ* Site of N2O Reductase

The active site of nitrous oxide reductase (N2OR), a key enzyme in denitrification, features a unique μ4-sulfido-bridged tetranuclear Cu cluster (the so-called CuZ or CuZ* site). Details of the catalytic mechanism have remained under debate and, to date, synthetic model complexes of the CuZ*/CuZ sites are extremely rare due to the difficulty in building the unique {Cu4(μ4-S)} core structure. Herein, we report the synthesis and characterization of [Cu4(μ4-S)]n+ (n = 2, 2; n = 3, 3) clusters, supported by a macrocyclic {py2NHC4} ligand (py = pyridine, NHC = N-heterocyclic carbene), in both their 0-hole (2) and 1-hole (3) states, thus mimicking the two active states of the CuZ* site during enzymatic N2O reduction. Structural and electronic properties of these {Cu4(μ4-S)} clusters are elucidated by employing multiple methods, including X-ray diffraction (XRD), nuclear magnetic resonance (NMR), UV/vis, electron paramagnetic resonance (EPR), Cu/S K-edge X-ray emission spectroscopy (XES), and Cu K-edge X-ray absorption spectroscopy (XAS) in combination with time-dependent density functional theory (TD-DFT) calculations. A significant geometry change of the {Cu4(μ4-S)} core occurs upon oxidation from 2 (τ4(S) = 0.46, seesaw) to 3 (τ4(S) = 0.03, square planar), which has not been observed so far for the biological CuZ(*) site and is unprecedented for known model complexes. The single electron of the 1-hole species 3 is predominantly delocalized over two opposite Cu ions via the central S atom, mediated by a π/π superexchange pathway. Cu K-edge XAS and Cu/S K-edge XES corroborate a mixed Cu/S-based oxidation event in which the lowest unoccupied molecular orbital (LUMO) has a significant S-character. Furthermore, preliminary reactivity studies evidence a nucleophilic character of the central μ4-S in the fully reduced 0-hole state.

Inhibition of Methylmercury and Methane Formation by Nitrous Oxide in Arctic Tundra Soil Microcosms

Climate warming causes permafrost thaw predicted to increase toxic methylmercury (MeHg) and greenhouse gas [i.e., methane (CH₄), carbon dioxide (CO₂), and nitrous oxide (N₂O)] formation. A microcosm incubation study with Arctic tundra soil over 145 days demonstrates that N₂O at 0.1 and 1 mM markedly inhibited microbial MeHg formation, methanogenesis, and sulfate reduction, while it slightly promoted CO₂ production. Microbial community analyses indicate that N₂O decreased the relative abundances of methanogenic archaea and microbial clades implicated in sulfate reduction and MeHg formation. Following depletion of N₂O, both MeHg formation and sulfate reduction rapidly resumed, whereas CH₄ production remained low, suggesting that N₂O affected susceptible microbial guilds differently. MeHg formation strongly coincided with sulfate reduction, supporting prior reports linking sulfate-reducing bacteria to MeHg formation in the Arctic soil. This research highlights complex biogeochemical interactions in governing MeHg and CH₄ formation and lays the foundation for future mechanistic studies for improved predictive understanding of MeHg and greenhouse gas fluxes from thawing permafrost ecosystems.

Structural biology of proteins involved in nitrogen cycling

Microbial metabolic processes drive the global nitrogen cycle through sophisticated and often unique metalloenzymes that facilitate difficult redox reactions at ambient temperature and pressure. Understanding the intricacies of these biological nitrogen transformations requires a detailed knowledge that arises from the combination of a multitude of powerful analytical techniques and functional assays. Recent developments in spectroscopy and structural biology have provided new, powerful tools for addressing existing and emerging questions, which have gained urgency due to the global environmental implications of these fundamental reactions. The present review focuses on the recent contributions of the wider area of structural biology to understanding nitrogen metabolism, opening new avenues for biotechnological applications to better manage and balance the challenges of the global nitrogen cycle.

Widening the Landscape of Small Molecule Activation with Gold-Aluminyl Complexes: A Systematic Study of E-H (E=O, N) Bonds, SO2 and N2 O Activation

The electronic features of gold-aluminyl complexes have been thoroughly explored. Their similarity with Group 14 dimetallenes and other metal-aluminyl complexes suggests that their reactivity with small molecules beyond carbon dioxide could be accessed. In this work, the reactivity of the [^t Bu₃ PAuAl(NON)] (NON=4,5-bis(2,6 diisopropylanilido)-2,7-ditert-butyl-9,9-dimethylxanthene) complex towards water, ammonia, sulfur dioxide and nitrous oxide is computationally explored. The reaction mechanisms computed for each substrate strongly suggest that all activation processes are in principle experimentally feasible. Electronic structure analysis highlights that, in all cases, the reactivity is driven by the presence of the poorly polarized electron-sharing gold-aluminyl bond, which induces a radical-like reactivity of the complex towards all the substrates. A flat topology of the potential energy surface (PES) has been found for the reaction with N₂ O, where two almost isoenergetic transition states can be located along the same reaction coordinate with different geometries, suggesting that the N₂ O binding mode may not be a good indicator of the nature of N₂ O activation in a cooperative bimetallic reactivity. In addition, the catalytic potentialities of these complexes have been explored in the framework of nitrous oxide reduction. The study reveals that the [^t Bu₃ PAuAl(NON)] complex might be an efficient catalyst towards oxidation of phosphines (and boranes) via N₂ O reduction. These findings underline recurring trends in the novel chemistry of gold-aluminyl complexes and call for experimental feedbacks.

Pharmaceutical Biotransformation is Influenced by Photosynthesis and Microbial Nitrogen Cycling in a Benthic Wetland Biomat

In shallow, open-water engineered wetlands, design parameters select for a photosynthetic microbial biomat capable of robust pharmaceutical biotransformation, yet the contributions of specific microbial processes remain unclear. Here, we combined genome-resolved metatranscriptomics and oxygen profiling of a field-scale biomat to inform laboratory inhibition microcosms amended with a suite of pharmaceuticals. Our analyses revealed a dynamic surficial layer harboring oxic-anoxic cycling and simultaneous photosynthetic, nitrifying, and denitrifying microbial transcription spanning nine bacterial phyla, with unbinned eukaryotic scaffolds suggesting a dominance of diatoms. In the laboratory, photosynthesis, nitrification, and denitrification were broadly decoupled by incubating oxic and anoxic microcosms in the presence and absence of light and nitrogen cycling enzyme inhibitors. Through combining microcosm inhibition data with field-scale metagenomics, we inferred microbial clades responsible for biotransformation associated with membrane-bound nitrate reductase activity (emtricitabine, trimethoprim, and atenolol), nitrous oxide reduction (trimethoprim), ammonium oxidation (trimethoprim and emtricitabine), and photosynthesis (metoprolol). Monitoring of transformation products of atenolol and emtricitabine confirmed that inhibition was specific to biotransformation and highlighted the value of oscillating redox environments for the further transformation of atenolol acid. Our findings shed light on microbial processes contributing to pharmaceutical biotransformation in open-water wetlands with implications for similar nature-based treatment systems.

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

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

Orchestrating copper binding: structure and variations on the cupredoxin fold

A large number of copper binding proteins coordinate metal ions using a shared three-dimensional fold called the cupredoxin domain. This domain was originally identified in Type 1 "blue copper" centers but has since proven to be a common domain architecture within an increasingly large and diverse group of copper binding domains. The cupredoxin fold has a number of qualities that make it ideal for coordinating Cu ions for purposes including electron transfer, enzyme catalysis, assembly of other copper sites, and copper sequestration. The structural core does not undergo major conformational changes upon metal binding, but variations within the coordination environment of the metal site confer a range of Cu-binding affinities, reduction potentials, and spectroscopic properties. Here, we discuss these proteins from a structural perspective, examining how variations within the overall cupredoxin fold and metal binding sites are linked to distinct spectroscopic properties and biological functions. Expanding far beyond the blue copper proteins, cupredoxin domains are used by a growing number of proteins and enzymes as a means of binding copper ions, with many more likely remaining to be identified.

Molecular interplay of an assembly machinery for nitrous oxide reductase

Emissions of the critical ozone-depleting and greenhouse gas nitrous oxide (N₂O) from soils and industrial processes have increased considerably over the last decades^1-3. As the final step of bacterial denitrification, N₂O is reduced to chemically inert N₂ (refs. ^1,4) in a reaction that is catalysed by the copper-dependent nitrous oxide reductase (N₂OR) (ref. ⁵). The assembly of its unique [4Cu:2S] active site cluster Cu_Z requires both the ATP-binding-cassette (ABC) complex NosDFY and the membrane-anchored copper chaperone NosL (refs. ^4,6). Here we report cryo-electron microscopy structures of Pseudomonas stutzeri NosDFY and its complexes with NosL and N₂OR, respectively. We find that the periplasmic NosD protein contains a binding site for a Cu⁺ ion and interacts specifically with NosL in its nucleotide-free state, whereas its binding to N₂OR requires a conformational change that is triggered by ATP binding. Mutually exclusive structures of NosDFY in complex with NosL and with N₂OR reveal a sequential metal-trafficking and assembly pathway for a highly complex copper site. Within this pathway, NosDFY acts as a mechanical energy transducer rather than as a transporter. It links ATP hydrolysis in the cytoplasm to a conformational transition of the NosD subunit in the periplasm, which is required for NosDFY to switch its interaction partner so that copper ions are handed over from the chaperone NosL to the enzyme N₂OR.

Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere

Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.

Cryptic Sulfur and Oxygen Cycling Potentially Reduces N2O-Driven Greenhouse Warming: Underlying Revision Need of the Nitrogen Cycle

Increasing global deoxygenation has widely formed oxygen-limited biotopes, altering the metabolic pathways of numerous microbes and causing a large greenhouse effect of nitrous oxide (N₂O). Although there are many sources of N₂O, denitrification is the sole sink that removes N₂O from the biosphere, and the low-level oxygen in waters has been classically thought to be the key factor regulating N₂O emissions from incomplete denitrification. However, through microcosm incubations with sandy sediment, we demonstrate here for the first time that the stress from oxygenated environments does not suppress, but rather boosts the complete denitrification process when the sulfur cycle is actively ongoing. This study highlights the potential of reducing N₂O-driven greenhouse warming and fills a gap in pre-cognitions on the nitrogen cycle, which may impact our current understanding of greenhouse gas sinks. Combining molecular techniques and kinetic verification, we reveal that dominant inhibitions in oxygen-limited environments can interestingly undergo triple detoxification by cryptic sulfur and oxygen cycling, which may extensively occur in nature but have been long neglected by researchers. Furthermore, reviewing the present data and observations from natural and artificial ecosystems leads to the necessary revision needs of the global nitrogen cycle.

Structural basis for an unprecedented enzymatic alkylation in cylindrocyclophane biosynthesis

The cyanobacterial enzyme CylK assembles the cylindrocyclophane natural products by performing two unusual alkylation reactions, forming new carbon–carbon bonds between aromatic rings and secondary alkyl halide substrates. This transformation is unprecedented in biology, and the structure and mechanism of CylK are unknown. Here, we report X-ray crystal structures of CylK, revealing a distinctive fusion of a Ca²⁺-binding domain and a β-propeller fold. We use a mutagenic screening approach to locate CylK’s active site at its domain interface, identifying two residues, Arg105 and Tyr473, that are required for catalysis. Anomalous diffraction datasets collected with bound bromide ions, a product analog, suggest that these residues interact with the alkyl halide electrophile. Additional mutagenesis and molecular dynamics simulations implicate Asp440 in activating the nucleophilic aromatic ring. Bioinformatic analysis of CylK homologs from other cyanobacteria establishes that they conserve these key catalytic amino acids, but they are likely associated with divergent reactivity and altered secondary metabolism. By gaining a molecular understanding of this unusual biosynthetic transformation, this work fills a gap in our understanding of how alkyl halides are activated and used by enzymes as biosynthetic intermediates, informing enzyme engineering, catalyst design, and natural product discovery.

Organic carbon determines nitrous oxide consumption activity of clade I and II nosZ bacteria: Genomic and biokinetic insights

Harnessing nitrous oxide (N2O)-reducing bacteria is a promising strategy to reduce the N2O footprint of engineered systems. Applying a preferred organic carbon source as an electron donor accelerates N2O consumption by these bacteria. However, their N2O consumption potential and activity when fed different organic carbon species remain unclear. Here, we systematically compared the effects of various organic carbon sources on the activity of N2O-reducing bacteria via investigation of their biokinetic properties and genomic potentials. Five organic carbon sources-acetate, succinate, glycerol, ethanol, and methanol-were fed to four N2O-reducing bacteria harboring either clade I or clade II nosZ gene. Respirometric analyses were performed with four N2O-reducing bacterial strains, identifying distinct shifts in DO- and N2O-consumption biokinetics in response to the different feeding schemes. Regardless of the N2O-reducing bacteria, higher N2O consumption rates, accompanied by higher biomass yields, were obtained with acetate and succinate. The biomass yield (15.45 ± 1.07 mg-biomass mmol-N2O-1) of Azospira sp. strain I13 (clade II nosZ) observed under acetate-fed condition was significantly higher than those of Paracoccus denitrificans and Pseudomonas stutzeri, exhibiting greater metabolic efficiency. However, the spectrum of the organic carbon species utilizable to Azospira sp. strain I13 was limited, as demonstrated by the highly variable N2O consumption rates observed with different substrates. The potential to metabolize the supplemented carbon sources was investigated by genomic analysis, the results of which corroborated the N2O consumption biokinetics results. Moreover, electron donor selection had a substantial impact on how N2O consumption activities were recovered after oxygen exposure. Collectively, our findings highlight the importance of choosing appropriate electron donor additives for increasing the N2O sink capability of biological nitrogen removal systems.

The copper-linked Escherichia coli AZY operon: Structure, metal binding, and a possible physiological role in copper delivery

The Escherichia coli yobA-yebZ-yebY (AZY) operon encodes the proteins YobA, YebZ, and YebY. YobA and YebZ are homologs of the CopC periplasmic copper-binding protein and the CopD putative copper importer, respectively, whereas YebY belongs to the uncharacterized Domain of Unknown Function 2511 family. Despite numerous studies of E. coli copper homeostasis and the existence of the AZY operon in a range of bacteria, the operon's proteins and their functional roles have not been explored. In this study, we present the first biochemical and functional studies of the AZY proteins. Biochemical characterization and structural modeling indicate that YobA binds a single Cu2+ ion with high affinity. Bioinformatics analysis shows that YebY is widespread and encoded either in AZY operons or in other genetic contexts unrelated to copper homeostasis. We also determined the 1.8 Å resolution crystal structure of E. coli YebY, which closely resembles that of the lantibiotic self-resistance protein MlbQ. Two strictly conserved cysteine residues form a disulfide bond, consistent with the observed periplasmic localization of YebY. Upon treatment with reductants, YebY binds Cu+ and Cu2+ with low affinity, as demonstrated by metal-binding analysis and tryptophan fluorescence. Finally, genetic manipulations show that the AZY operon is not involved in copper tolerance or antioxidant defense. Instead, YebY and YobA are required for the activity of the copper-related NADH dehydrogenase II. These results are consistent with a potential role of the AZY operon in copper delivery to membrane proteins.

NosZ gene cloning, reduction performance and structure of Pseudomonas citronellolis WXP-4 nitrous oxide reductase

Nitrous oxide reductase (N₂OR) is the only known enzyme that can reduce the powerful greenhouse gas nitrous oxide (N₂O) to harmless nitrogen at the final step of bacterial denitrification. To alleviate the N₂O emission, emerging approaches aim at microbiome biotechnology. In this study, the genome sequence of facultative anaerobic bacteria Pseudomonas citronellolis WXP-4, which efficiently degrades N₂O, was obtained by de novo sequencing for the first time, and then, four key reductase structure coding genes related to complete denitrification were identified. The single structural encoding gene nosZ with a length of 1914 bp from strain WXP-4 was cloned in Escherichia coli BL21(DE3), and the N₂OR protein (76 kDa) was relatively highly efficiently expressed under the optimal inducing conditions of 1.0 mM IPTG, 5 h, and 30 °C. Denitrification experiment results confirmed that recombinant E. coli had strong denitrification ability and reduced 10 mg L⁻¹ of N₂O to N₂ within 15 h under the optimal conditions of pH 7.0 and 40 °C, its corresponding N₂O reduction rate was almost 2.3 times that of Alcaligenes denitrificans strain TB, but only 80% of that of wild strain WXP-4, meaning that nos gene cluster auxiliary gene deletion decreased the activity of N₂OR. The 3D structure of N₂OR predicted on the basis of sequence homology found that electron transfer center CuA had only five amino acid ligands, and the S2 of the catalytically active center CuZ only bound one Cu_I atom. The unique 3D structure was different from previous reports and may be closely related to the strong N₂O reduction ability of strain WXP-4 and recombinant E. coli. The findings show a potential application of recombinant E. coli in alleviating the greenhouse effect and provide a new perspective for researching the relationship between structure and function of N₂OR.

Nitrous oxide reductase (N₂OR) is the only known enzyme that can reduce the powerful greenhouse gas nitrous oxide (N₂O) to harmless nitrogen at the final step of bacterial denitrification. The recombinant E. coli and wild strain WXP-4 demonstrate strong N₂O reduction ability.

The Biologically Relevant Coordination Chemistry of Iron and Nitric Oxide: Electronic Structure and Reactivity

Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological and pathological events in biology. Metal coordination chemistry, especially with iron, is at the heart of many biological transformations involving NO. A series of heme proteins, nitric oxide synthases (NOS), soluble guanylate cyclase (sGC), and nitrophorins, are responsible for the biosynthesis, sensing, and transport of NO. Alternatively, NO can be generated from nitrite by heme- and copper-containing nitrite reductases (NIRs). The NO-bearing small molecules such as nitrosothiols and dinitrosyl iron complexes (DNICs) can serve as an alternative vehicle for NO storage and transport. Once NO is formed, the rich reaction chemistry of NO leads to a wide variety of biological activities including reduction of NO by heme or non-heme iron-containing NO reductases and protein post-translational modifications by DNICs. Much of our understanding of the reactivity of metal sites in biology with NO and the mechanisms of these transformations has come from the elucidation of the geometric and electronic structures and chemical reactivity of synthetic model systems, in synergy with biochemical and biophysical studies on the relevant proteins themselves. This review focuses on recent advancements from studies on proteins and model complexes that not only have improved our understanding of the biological roles of NO but also have provided foundations for biomedical research and for bio-inspired catalyst design in energy science.

The Copper Chaperone NosL Forms a Heterometal Site for Cu Delivery to Nitrous Oxide Reductase

The final step of denitrification is the reduction of nitrous oxide (N2 O) to N2 , mediated by Cu-dependent nitrous oxide reductase (N2 OR). Its metal centers, CuA and CuZ , are assembled through sequential provision of twelve CuI ions by a metallochaperone that forms part of a nos gene cluster encoding the enzyme and its accessory factors. The chaperone is the nosL gene product, an 18 kDa lipoprotein predicted to reside in the outer membrane of Gram-negative bacteria. In order to better understand the assembly of N2 OR, we have produced NosL from Shewanella denitrificans and determined the structure of the metal-loaded chaperone by X-ray crystallography. The protein assembled a heterodinuclear metal site consisting of ZnII and CuI , as evidenced by anomalous X-ray scattering. While only CuI is delivered to the enzyme, the stabilizing presence of ZnII is essential for the functionality and structural integrity of the chaperone.

K fertilizer alleviates N2O emissions by regulating the abundance of nitrifying and denitrifying microbial communities in the soil-plant system

Potassium (K) fertilizer additions can result in high crop yields of good quality and low nitrogen (N) loss; however, the interaction between K and N fertilizer and its effect on N₂O emissions and associated microbes remain unclear. We investigated this in a pot experiment with six fertilizer treatments involving K and two sources of N, using agricultural soil from the suburbs of Wuhan, central China. The aim was to determine the effects of the interaction between K and different forms of N on the N₂O flux and the abundance of nitrifying and denitrifying microbial communities, using static chamber-gas chromatography and high-throughput sequencing methods. Compared with no fertilizer control (CK), the addition of nitrate fertilizer (NN) or ammonia fertilizer (AN) or K fertilizer significantly increased N₂O emissions. However, the combined application (NNK) of K and NN significantly reduced the average N₂O emissions by 28.3%, while the combined application (ANK) of K and AN increased N₂O emissions by 22.7%. The abundance of nitrifying genes amoA in ammonia oxidizing archaea (AOA) and ammonia oxidizing bacteria (AOB) changed in response to N and/or K fertilization, but the denitrifying genes narG, nirK and norl were strongly correlated with N₂O emissions. This suggests that N or K fertilizer and their interaction affect N₂O emissions mainly by altering the abundance of functional genes of denitrifying microbes in the soil-plant system. The genera Paracoccus, Rubrivivax and Geobacter as well as Streptomyces and Hyphomicrobium play an important role in N₂O emissions during denitrification with the combined application of N and K.

Anaerobically fermented spent mushroom substrates improve nitrogen removal and lead (II) adsorption

In this study, spent mushroom substrates (SMSs) were fermented anaerobically at room temperature to gain liquid SMSs (LSMSs) that were used to remove nitrogen from the piggery wastewater with a low C/N ratio in a sequencing batch reactor (SBR) and solid SMSs (SSMSs) that were utilized to adsorb Pb²⁺ from Pb²⁺-containing wastewater in a fixed-bed reactor (FBR). After LSMSs supplement, the removal efficiency of both total nitrogen (TN) and NH⁺₄-N increased from around 50% to 60-80%. High-throughput sequencing results presented an obvious change in microbial diversity, and some functional microorganisms like Zoogloea and Hydrogenophaga predominated to promote nitrogen removal. Pb²⁺ did not emerge from the effluent until 240 min with the corresponding concentration being less than 3 mg/L when using 30-day SSMSs as adsorbents, and it was demonstrated to be appropriate to use the Thomas model to predict Pb²⁺ sorption on SSMSs. Although various functional groups played a role in binding ions, the carboxyl group was proved to contribute most to Pb²⁺ adsorption. These results certified that the anaerobically fermented SMSs are decidedly suitable for wastewater treatment.

Side-on Coordination in Isostructural Nitrous Oxide and Carbon Dioxide Complexes of Nickel

A nickel complex incorporating an N₂ O ligand with a rare η² -N,N'-coordination mode was isolated and characterized by X-ray crystallography, as well as by IR and solid-state NMR spectroscopy augmented by ¹⁵ N-labeling experiments. The isoelectronic nickel CO₂ complex reported for comparison features a very similar solid-state structure. Computational studies revealed that η² -N₂ O binds to nickel slightly stronger than η² -CO₂ in this case, and comparably to or slightly stronger than η² -CO₂ to transition metals in general. Comparable transition-state energies for the formation of isomeric η² -N,N'- and η² -N,O-complexes, and a negligible activation barrier for the decomposition of the latter likely account for the limited stability of the N₂ O complex.

Coordination chemistry of the CuZ site in nitrous oxide reductase and its synthetic mimics

Atmospheric nitrous oxide (N2O) has garnered significant attention recently due to its dual roles as an ozone depletion agent and a potent greenhouse gas. Anthropogenic N2O emissions occur primarily through agricultural disruption of nitrogen homeostasis causing N2O to build up in the atmosphere. The enzyme responsible for N2O fixation within the geochemical nitrogen cycle is nitrous oxide reductase (N2OR), which catalyzes 2H+/2e- reduction of N2O to N2 and H2O at a tetranuclear active site, CuZ. In this review, the coordination chemistry of CuZ is reviewed. Recent advances in the understanding of biological CuZ coordination chemistry is discussed, as are significant breakthroughs in synthetic modeling of CuZ that have emerged in recent years. The latter topic includes both structurally faithful, synthetic [Cu4(µ4-S)] clusters that are able to reduce N2O, as well as dicopper motifs that shed light on reaction pathways available to the critical CuI-CuIV cluster edge of CuZ. Collectively, these advances in metalloenzyme studies and synthetic model systems provide meaningful knowledge about the physiologically relevant coordination chemistry of CuZ but also open new questions that will pose challenges in the near future.

Biological Reduction of Nitric Oxide for Efficient Recovery of Nitrous Oxide as an Energy Source

Chemical absorption-biological reduction based on Fe(II)EDTA is a promising technology to remove nitric oxide (NO) from flue gases. However, limited effort has been made to enable direct energy recovery from NO through production of nitrous oxide (N₂O) as a potential renewable energy rather than greenhouse gas. In this work, the enhanced energy recovery in the form of N₂O via biological NO reduction was investigated by conducting short-term and long-term experiments at different Fe(II)EDTA-NO and organic carbon levels. The results showed both NO reductase and N₂O reductase were inhibited at Fe(II)EDTA-NO concentration up to 20 mM, with the latter being inhibited more significantly, thus facilitating N₂O accumulation. Furthermore, N₂O accumulation was enhanced under carbon-limiting conditions because of electron competition during short-term experiments. Up to 47.5% of NO-N could be converted to gaseous N₂O-N, representing efficient N₂O recovery. Fe(II)EDTA-NO reduced microbial diversity and altered the community structure toward Fe(II)EDTA-NO-reducing bacteria-dominated culture during long-term experiments. The most abundant bacterial genus Pseudomonas, which was able to resist the toxicity of Fe(II)EDTA-NO, was significantly enriched, with its relative abundance increased from 1.0 to 70.3%, suggesting Pseudomonas could be the typical microbe for the energy recovery technology in NO-based denitrification.

A [3Cu:2S] cluster provides insight into the assembly and function of the CuZ site of nitrous oxide reductase

Nitrous oxide reductase (N₂OR) is the only known enzyme reducing environmentally critical nitrous oxide (N₂O) to dinitrogen (N₂) as the final step of bacterial denitrification. The assembly process of its unique catalytic [4Cu:2S] cluster Cu_Z remains scarcely understood. Here we report on a mutagenesis study of all seven histidine ligands coordinating this copper center, followed by spectroscopic and structural characterization and based on an established, functional expression system for Pseudomonas stutzeri N₂OR in Escherichia coli. While no copper ion was found in the Cu_Z binding site of variants H129A, H130A, H178A, H326A, H433A and H494A, the H382A variant carried a catalytically inactive [3Cu:2S] center, in which one sulfur ligand, S_Z2, had relocated to form a weak hydrogen bond to the sidechain of the nearby lysine residue K454. This link provides sufficient stability to avoid the loss of the sulfide anion. The UV-vis spectra of this cluster are strikingly similar to those of the active enzyme, implying that the flexibility of S_Z2 may have been observed before, but not recognized. The sulfide shift changes the metal coordination in Cu_Z and is thus of high mechanistic interest.

Variants of all seven histidine ligands of the [4Cu:2S] active site of nitrous oxide reductase mostly result in loss of the metal site. However, a H382A variant retains a [3Cu:2S] cluster that hints towards a structural flexibility also present in the intact site.

Mechanism of action of nitrification inhibitors based on dimethylpyrazole: A matter of chelation

In agriculture, the applied nitrogen (N) can be lost in the environment in different forms because of microbial transformations. It is of special concern the nitrate (NO₃^-) leaching and the nitrous oxide (N₂O) emissions, due to their negative environmental impacts. Nitrification inhibitors (NIs) based on dimethylpyrazole (DMP) are applied worldwide in order to reduce N losses. These compounds delay ammonium (NH₄⁺) oxidation by inhibiting ammonia-oxidizing bacteria (AOB) growth. However, their mechanism of action has not been demonstrated, which represent an important lack of knowledge to use them correctly. In this work, through chemical and biological analysis, we unveil the mechanism of action of the commonly applied 3,4-dimethyl-1H-pyrazole dihydrogen phosphate (DMPP) and the new DMP-based NI, 2-(3,4-dimethyl-1H-pyrazol-1-yl)-succinic acid (DMPSA). Our results show that DMP and DMPSA form complexes with copper (Cu²⁺) cations, an indispensable cofactor in the nitrification pathway. Three coordination compounds namely [Cu(DMP)₄Cl₂] (CuDMP1), [Cu(DMP)₄SO₄]_n (CuDMP2) and [Cu(DMPSA)₂]·H₂O (CuDMPSA) have been synthesized and chemical and structurally characterized. The CuDMPSA complex is more stable than those containing DMP ligands; however, both NIs show the same nitrification inhibition efficiency in soils with different Cu contents, suggesting that the active specie in both cases is DMP. Our soil experiment reveals that the usual application dose is enough to inhibit nitrification within the range of Cu and Zn contents present in agricultural soils, although their effects vary depending on the content of these elements. As a result of AOB inhibition by these NIs, N₂O-reducing bacteria seem to be beneficed in Cu-limited soils due to a reduction in the competence. This opens up the possibility to induce N₂O reduction to N₂ through Cu fertilization. On the other hand, when fertilizing with micronutrients such as Cu and Zn, the use of NIs could be beneficial to counteract the increase of nitrification derived from their application.

Temperature and oxygen level determine N2 O respiration activities of heterotrophic N2 O-reducing bacteria: Biokinetic study

Nitrous oxide (N₂ O), a potent greenhouse gas, is reduced to N₂ gas by N₂ O-reducing bacteria (N₂ ORB), a process which represents an N₂ O sink in natural and engineered ecosystems. The N₂ O sink activity by N₂ ORB depends on temperature and O₂ exposure, yet the specifics are not yet understood. This study explores the effects of temperature and oxygen exposure on biokinetics of pure culture N₂ ORB. Four N₂ ORB, representing either clade I type nosZ (Pseudomonas stutzeri JCM5965 and Paracoccus denitrificans NBRC102528) or clade II type nosZ (Azospira sp. strains I09 and I13), were individually tested. The higher activation energy for N₂ O by Azospira sp. strain I13 (114.0 ± 22.6 kJ mol^-1 ) compared with the other tested N₂ ORB (38.3-60.1 kJ mol^-1 ) indicates that N₂ ORB can adapt to different temperatures. The O₂ inhibition constants (K_I ) of Azospira sp. strain I09 and Ps. stutzeri JCM5965 increased from 0.06 ± 0.05 and 0.05 ± 0.02 μmol L^-1 to 0.92 ± 0.24 and 0.84 ± 0.31 μmol L^-1 , respectively, as the temperature increased from 15°C to 35°C, while that of Azospira sp. strain I13 was temperature-independent (p = 0.106). Within the range of temperatures examined, Azospira sp. strain I13 had a faster recovery after O₂ exposure compared with Azospira sp. strain I09 and Ps. stutzeri JCM5965 (p < 0.05). These results suggest that temperature and O₂ exposure result in the growth of ecophysiologically distinct N₂ ORB as N₂ O sinks. This knowledge can help develop a suitable N₂ O mitigation strategy according to the physiologies of the predominant N₂ ORB.

A Series of Homoleptic Linear Trimethylsilylchalcogenido Cuprates, Argentates and Aurates Cat[Me3SiE-M-ESiMe3] (M = Cu, Ag, Au; E = S, Se)

The syntheses and XRD molecular structures of a complete series of silylsulfido metalates Cat[M(SSiMe₃)₂] (M = Cu, Ag, Au) and corresponding silylselenido metalates Cat[M(SeSiMe₃)₂] (M = Cu, Ag, Au) comprising lattice stabilizing organic cations (Cat = Ph₄P⁺ or PPN⁺) are reported. Much to our surprise these homoleptic cuprates, argentates, and aurates are stable enough to be isolated even in the absence of any strongly binding phosphines or N-heterocyclic carbenes as coligands. Their metal atoms are coordinated by two silylchalcogenido ligands in a linear fashion. The silyl moieties of all anions show an unexpected gauche conformation of the silyl substituents with respect to the central axis Si-[E-M-E]-Si in the solid state. The energetic preference for the gauche conformation is confirmed by quantum chemical calculations and amounts to about 2-6 kJ/mol, thus revealing a rather shallow potential mainly depending on electronic effects of the metal. Furthermore, 2D HMQC methods were applied to detect the otherwise nonobservable NMR shifts of the ²⁹Si and ⁷⁷Se nuclei of the silylselenido compounds. Preliminary investigations reveal that these thermally and protolytically labile chalcogenido metalates are valuable precursors for the precipitation of binary coinage metal chalcogenide nanoparticles from organic solution and for coinage metal cluster syntheses.

Cu(II) nonspecifically binding chromate reductase NfoR promotes Cr(VI) reduction

Cu(II)-enhanced microbial Cr(VI) reduction is common in the environment, yet its mechanism is unknown. The specific activity of chromate reductase, NfoR, from Staphylococcus aureus sp. LZ-01 was augmented 1.5-fold by Cu(II). Isothermal titration calorimetry and spectral data show that Cu(II) binds to NfoR nonspecifically. Further, Cu(II) stimulates the nitrobenzene reduction of NfoR, indicating that Cu(II) promotes electron transfer. The crystal structure of NfoR in complex with CuSO₄ (1.46 Å) was determined. The overall structure of NfoR-Cu(II) complex is a dimer that covalently binds with FMN and Cu(II)-binding pocket is located at the interface of the NfoR dimer. Structural superposition revealed that NfoR resembles the structure of class II chromate reductase. Site-directed mutagenesis revealed that Leu⁴⁶ and Phe¹²³ were involved in NADH binding, whereas Trp⁷⁰ and Ser⁴⁵ were the key residues for nitrobenzene binding. Furthermore, His¹⁰⁰ and Asp¹⁷¹ were preferential affinity sites for Cu(II) and that Cys¹⁶³ is an active site for FMN binding. Attenuation reductase activity in C163S can be partially restored to 54% wild type by increasing Cu(II) concentration. Partial restoration indicates dual-channel electron transfer of NfoR via Cu(II) and FMN. We propose a catalytic mechanism for Cu(II)-enhanced NfoR activity in which Cu(I) is formed transiently. Together, the current results provide an insight on Cu (II)-induced enhancement and benefit of Cr(VI) bioremediation.

Cu Homeostasis in Bacteria: The Ins and Outs

Copper (Cu) is an essential trace element for all living organisms and used as cofactor in key enzymes of important biological processes, such as aerobic respiration or superoxide dismutation. However, due to its toxicity, cells have developed elaborate mechanisms for Cu homeostasis, which balance Cu supply for cuproprotein biogenesis with the need to remove excess Cu. This review summarizes our current knowledge on bacterial Cu homeostasis with a focus on Gram-negative bacteria and describes the multiple strategies that bacteria use for uptake, storage and export of Cu. We furthermore describe general mechanistic principles that aid the bacterial response to toxic Cu concentrations and illustrate dedicated Cu relay systems that facilitate Cu delivery for cuproenzyme biogenesis. Progress in understanding how bacteria avoid Cu poisoning while maintaining a certain Cu quota for cell proliferation is of particular importance for microbial pathogens because Cu is utilized by the host immune system for attenuating pathogen survival in host cells.

nosX is essential for whole-cell N2O reduction in Paracoccus denitrificans but not for assembly of copper centres of nitrous oxide reductase

Nitrous oxide (N₂O) is a potent greenhouse gas that is produced naturally as an intermediate during the process of denitrification carried out by some soil bacteria. It is consumed by nitrous oxide reductase (N₂OR), the terminal enzyme of the denitrification pathway, which catalyses a reduction reaction to generate dinitrogen. N₂OR contains two important copper cofactors (Cu_A and Cu_Z centres) that are essential for activity, and in copper-limited environments, N₂OR fails to function, contributing to rising levels of atmospheric N₂O and a major environmental challenge. Here we report studies of nosX, one of eight genes in the nos cluster of the soil dwelling α-proteobaterium Paraccocus denitrificans. A P. denitrificans ΔnosX deletion mutant failed to reduce N₂O under both copper-sufficient and copper-limited conditions, demonstrating that NosX plays an essential role in N₂OR activity. N₂OR isolated from nosX-deficient cells was found to be unaffected in terms of the assembly of its copper cofactors, and to be active in in vitro assays, indicating that NosX is not required for the maturation of the enzyme; in particular, it plays no part in the assembly of either of the Cu_A and Cu_Z centres. Furthermore, quantitative Reverse Transcription PCR (qRT-PCR) studies showed that NosX does not significantly affect the expression of the N₂OR-encoding nosZ gene. NosX is a homologue of the FAD-binding protein ApbE from Pseudomonas stutzeri, which functions in the flavinylation of another N₂OR accessory protein, NosR. Thus, it is likely that NosX is a system-specific maturation factor of NosR, and so is indirectly involved in maintaining the reaction cycle of N₂OR and cellular N₂O reduction.

The effect of pH on Marinobacter hydrocarbonoclasticus denitrification pathway and nitrous oxide reductase

Increasing atmospheric concentration of N₂O has been a concern, as it is a potent greenhouse gas and promotes ozone layer destruction. In the N-cycle, release of N₂O is boosted upon a drop of pH in the environment. Here, Marinobacter hydrocarbonoclasticus was grown in batch mode in the presence of nitrate, to study the effect of pH in the denitrification pathway by gene expression profiling, quantification of nitrate and nitrite, and evaluating the ability of whole cells to reduce NO and N₂O. At pH 6.5, accumulation of nitrite in the medium occurs and the cells were unable to reduce N₂O. In addition, the biochemical properties of N₂O reductase isolated from cells grown at pH 6.5, 7.5 and 8.5 were compared for the first time. The amount of this enzyme at acidic pH was lower than that at pH 7.5 and 8.5, pinpointing to a post-transcriptional regulation, though pH did not affect gene expression of N₂O reductase accessory genes. N₂O reductase isolated from cells grown at pH 6.5 has its catalytic center mainly as CuZ(4Cu1S), while that from cells grown at pH 7.5 or 8.5 has it as CuZ(4Cu2S). This study evidences that an in vivo secondary level of regulation is required to maintain N₂O reductase in an active state.

A critical review of aerobic denitrification: Insights into the intracellular electron transfer

Aerobic denitrification is a novel biological nitrogen removal technology, which has been widely investigated as an alternative to the conventional denitrification and for its unique advantages. To fully comprehend aerobic denitrification, it is essential to clarify the regulatory mechanisms of intracellular electron transfer during aerobic denitrification. However, reports on intracellular electron transfer during aerobic denitrification are rather limited. Thus, the purpose of this review is to discuss the molecular mechanism of aerobic denitrification from the perspective of electron transfer, by summarizing the advancements in current research on electron transfer based on conventional denitrification. Firstly, the implication of aerobic denitrification is briefly discussed, and the status of current research on aerobic denitrification is summarized. Then, the occurring foundation and significance of aerobic denitrification are discussed based on a brief review of the key components involved in the electron transfer of denitrifying enzymes. Moreover, a strategy for enhancing the efficiency of aerobic denitrification is proposed on the basis of the regulatory mechanisms of denitrification enzymes. Finally, scientific outlooks are given for further investigation on aerobic denitrification in the future. This review could help clarify the mechanism of aerobic denitrification from the perspective of electron transfer.

Biological and Bioinspired Inorganic N-N Bond-Forming Reactions

The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.

Impact of Electronic and Steric Changes of Ligands on the Assembly, Stability, and Redox Activity of Cu4(μ4-S) Model Compounds of the CuZ Active Site of Nitrous Oxide Reductase (N2OR)

Model compounds have been widely utilized in understanding the structure and function of the unusual Cu₄(μ₄-S) active site (Cu_Z) of nitrous oxide reductase (N₂OR). However, only a limited number of model compounds that mimic both structural and functional features of Cu_Z are available, limiting insights about Cu_Z that can be gained from model studies. Our aim has been to construct Cu₄(μ₄-S) clusters with tailored redox activity and chemical reactivity via modulating the ligand environment. Our synthetic approach uses dicopper(I) precursor complexes (Cu₂L₂) that assemble into a Cu₄(μ₄-S)L₄ cluster with the addition of an appropriate sulfur source. Here, we summarize the features of the ligands L that stabilize precursor and Cu₄(μ₄-S) clusters, along with the alternative products that form with inappropriate ligands. The precursors are more likely to rearrange to Cu₄(μ₄-S) clusters when the Cu(I) ions are supported by bidentate ligands with 3-atom bridges, but steric and electronic features of the ligand also play crucial roles. Neutral phosphine donors have been found to stabilize Cu₄(μ₄-S) clusters in the 4Cu(I) oxidation state, while neutral nitrogen donors could not stabilize Cu₄(μ₄-S) clusters. Anionic formamidinate ligands have been found to stabilize Cu₄(μ₄-S) clusters in the 2Cu(I):2Cu(II) and 3Cu(I):1Cu(II) states, with both the formation of the dicopper(I) precursors and subsequent assembly of clusters being governed by the steric factor at the ortho positions of the N-aryl substituents. Phosphaamidinates, which combine a neutral phosphine donor and an anionic nitrogen donor in the same ligand, form multinuclear Cu(I) clusters unless the negative charge is valence-trapped on nitrogen, in which case the resulting dicopper precursor is unable to rearrange to a multinuclear cluster. Taken together, the results presented in this study provide design criteria for successful assembly of synthetic model clusters for the Cu_Z active site of N₂OR, which should enable future insights into the chemical behavior of Cu_Z.