Functional assembly of nitrous oxide reductase provides insights into copper site maturation

Sustained bacterial N2O reduction at acidic pH

Nitrous oxide (N2O) is a climate-active gas with emissions predicted to increase due to agricultural intensification. Microbial reduction of N2O to dinitrogen (N2) is the major consumption process but microbial N2O reduction under acidic conditions is considered negligible, albeit strongly acidic soils harbor nosZ genes encoding N2O reductase. Here, we study a co-culture derived from acidic tropical forest soil that reduces N2O at pH 4.5. The co-culture exhibits bimodal growth with a Serratia sp. fermenting pyruvate followed by hydrogenotrophic N2O reduction by a Desulfosporosinus sp. Integrated omics and physiological characterization revealed interspecies nutritional interactions, with the pyruvate fermenting Serratia sp. supplying amino acids as essential growth factors to the N2O-reducing Desulfosporosinus sp. Thus, we demonstrate growth-linked N2O reduction between pH 4.5 and 6, highlighting microbial N2O reduction potential in acidic soils.

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.

A novel mechanism for dissimilatory nitrate reduction to ammonium in Acididesulfobacillus acetoxydans

The biological route of nitrate reduction has important implications for the bioavailability of nitrogen within ecosystems. Nitrate reduction via nitrite, either to ammonium (ammonification) or to nitrous oxide or dinitrogen (denitrification), determines whether nitrogen is retained within the system or lost as a gas. The acidophilic sulfate-reducing bacterium (aSRB) Acididesulfobacillus acetoxydans can perform dissimilatory nitrate reduction to ammonium (DNRA). While encoding a Nar-type nitrate reductase, A. acetoxydans lacks recognized nitrite reductase genes. In this study, A. acetoxydans was cultivated under conditions conducive to DNRA. During cultivations, we monitored the production of potential nitrogen intermediates (nitrate, nitrite, nitric oxide, hydroxylamine, and ammonium). Resting cell experiments were performed with nitrate, nitrite, and hydroxylamine to confirm their reduction to ammonium, and formed intermediates were tracked. To identify the enzymes involved in DNRA, comparative transcriptomics and proteomics were performed with A. acetoxydans growing under nitrate- and sulfate-reducing conditions. Nitrite is likely reduced to ammonia by the previously undescribed nitrite reductase activity of the NADH-linked sulfite reductase AsrABC, or by a putatively ferredoxin-dependent homolog of the nitrite reductase NirA (DEACI_1836), or both. We identified enzymes and intermediates not previously associated with DNRA and nitrosative stress in aSRB. This increases our knowledge about the metabolism of this type of bacteria and helps the interpretation of (meta)genome data from various ecosystems on their DNRA potential and the nitrogen cycle.IMPORTANCENitrogen is crucial to any ecosystem, and its bioavailability depends on microbial nitrogen-transforming reactions. Over the recent years, various new nitrogen-transforming reactions and pathways have been identified, expanding our view on the nitrogen cycle and metabolic versatility. In this study, we elucidate a novel mechanism employed by Acididesulfobacillus acetoxydans, an acidophilic sulfate-reducing bacterium, to reduce nitrate to ammonium. This finding underscores the diverse physiological nature of dissimilatory reduction to ammonium (DNRA). A. acetoxydans was isolated from acid mine drainage, an extremely acidic environment where nitrogen metabolism is poorly studied. Our findings will contribute to understanding DNRA potential and variations in extremely acidic environments.

Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential

Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%-50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.

IMPORTANCE

Archaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.

Functional and evolutionary significance of unknown genes from uncultivated taxa

Many of the Earth's microbes remain uncultured and understudied, limiting our understanding of the functional and evolutionary aspects of their genetic material, which remain largely overlooked in most metagenomic studies1. Here we analysed 149,842 environmental genomes from multiple habitats2-6 and compiled a curated catalogue of 404,085 functionally and evolutionarily significant novel (FESNov) gene families exclusive to uncultivated prokaryotic taxa. All FESNov families span multiple species, exhibit strong signals of purifying selection and qualify as new orthologous groups, thus nearly tripling the number of bacterial and archaeal gene families described to date. The FESNov catalogue is enriched in clade-specific traits, including 1,034 novel families that can distinguish entire uncultivated phyla, classes and orders, probably representing synapomorphies that facilitated their evolutionary divergence. Using genomic context analysis and structural alignments we predicted functional associations for 32.4% of FESNov families, including 4,349 high-confidence associations with important biological processes. These predictions provide a valuable hypothesis-driven framework that we used for experimental validatation of a new gene family involved in cell motility and a novel set of antimicrobial peptides. We also demonstrate that the relative abundance profiles of novel families can discriminate between environments and clinical conditions, leading to the discovery of potentially new biomarkers associated with colorectal cancer. We expect this work to enhance future metagenomics studies and expand our knowledge of the genetic repertory of uncultivated organisms.

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.

Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen deficient zones with diverse metabolic potential

Archaea belonging to the DPANN superphylum have been found within an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise 15-26% of the archaeal community within marine oxygen deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes belonging to DPANN phyla Nanoarchaeota, Pacearchaeota, Woesarchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and Arabian Sea. We find these archaea to be permanent, stable residents of all 3 major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25-50% of archaea. ODZ DPANN appear capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.

Aurantibacillus circumpalustris gen. nov., sp. nov., the first characterized representative of the Bacteroidota candidate family env.OPS 17 and proposal of Aurantibacillaceae fam. nov

16S rRNA sequence types associated with the candidate family env.OPS 17 have been reported from various environments, but no representatives have been characterized and validly named. Bacteria of env.OPS 17 are affiliated with the order Sphingobacteriales and were first detected more than two decades ago in the vicinity of a thermal spring in Yellowstone National Park. Strain Swamp196T, isolated from the soil surrounding a swamp in Northern Germany, is the first characterized representative of candidate family env.OPS 17. Cells of strain Swamp196T are rod-shaped, non-motile, non-spore-forming, non-capsulated and stain Gram-negative. Colonies are small and orange-coloured. The strain is mesophilic and grows under aerobic or microaerophilic conditions. It grows chemo-organotrophically over a narrow range of pH and exclusively on proteinaceous substrates. The major cellular fatty acids are iso-C15 : 0, iso-C15 : 1  ω10c, C18 : 1  ω9c and C16 : 1  ω7c and the major polar lipids are two unidentified aminophospholipids, one unidentified aminolipid and one unidentified lipid. The predominant respiratory quinone is MK-7. The DNA G+C content of genomic DNA is 35.5 mol%. Strain Swamp196T is related to Pedobacter cryophilus AR-3-17T, Arcticibacter pallidicorallinus Hh36T and Pedobacter daechungensis Dae 13T with 16S rRNA gene sequence similarity of 84.1, 83.8 and 83.5 %, respectively. Based on our phenotypic, genomic and phylogenetic analysis, we propose the novel species Aurantibacillus circumpalustris sp. nov (type strain Swamp196T=DSM 105849T=CECT 30420T) of the novel genus Aurantibacillus gen. nov. and the novel family Aurantibacillaceae fam. nov.

Oxidoreductases and metal cofactors in the functioning of the earth

Life sustains itself using energy generated by thermodynamic disequilibria, commonly existing as redox disequilibria. Metals are significant players in controlling redox reactions, as they are essential components of the engine that life uses to tap into the thermodynamic disequilibria necessary for metabolism. The number of proteins that evolved to catalyze redox reactions is extraordinary, as is the diversification level of metal cofactors and catalytic domain structures involved. Notwithstanding the importance of the topic, the relationship between metals and the redox reactions they are involved in has been poorly explored. This work reviews the structure and function of different prokaryotic organometallic-protein complexes, highlighting their pivotal role in controlling biogeochemistry. We focus on a specific subset of metal-containing oxidoreductases (EC1 or EC7.1), which are directly involved in biogeochemical cycles, i.e., at least one substrate or product is a small inorganic molecule that is or can be exchanged with the environment. Based on these inclusion criteria, we select and report 59 metalloenzymes, describing the organometallic structure of their active sites, the redox reactions in which they are involved, and their biogeochemical roles.

Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones

Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3- to N2. This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. We assemble genomes from metagenomes spanning the ETNP and Arabian Sea, and map these metagenome-assembled genomes (MAGs) to 56 metagenomes from all three major ODZs to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 MAGs presents the largest collection of pelagic ODZ microorganisms and reveals a clearer picture of the nitrogen cycling community within this environment.

Clarifying Microbial Nitrous Oxide Reduction under Aerobic Conditions: Tolerant, Intolerant, and Sensitive

One of the major challenges for the bioremediation application of microbial nitrous oxide (N2O) reduction is its oxygen sensitivity. While a few strains were reported capable of reducing N2O under aerobic conditions, the N2O reduction kinetics of phylogenetically diverse N2O reducers are not well understood. Here, we analyzed and compared the kinetics of clade I and clade II N2O-reducing bacteria in the presence or absence of oxygen (O2) by using a whole-cell assay with N2O and O2 microsensors. Among the seven strains tested, N2O reduction of Stutzerimonas stutzeri TR2 and ZoBell was not inhibited by oxygen (i.e., oxygen tolerant). Paracoccus denitrificans, Azospirillum brasilense, and Gemmatimonas aurantiaca reduced N2O in the presence of O2 but slower than in the absence of O2 (i.e., oxygen sensitive). N2O reduction of Pseudomonas aeruginosa and Dechloromonas aromatica did not occur when O2 was present (i.e., oxygen intolerant). Amino acid sequences and predicted structures of NosZ were highly similar among these strains, whereas oxygen-tolerant N2O reducers had higher oxygen consumption rates. The results suggest that the mechanism of O2 tolerance is not directly related to NosZ structure but is rather related to the scavenging of O2 in the cells and/or accessory proteins encoded by the nos cluster. IMPORTANCE Some bacteria can reduce N2O in the presence of O2, whereas others cannot. It is unclear whether this trait of aerobic N2O reduction is related to the phylogeny and structure of N2O reductase. The understanding of aerobic N2O reduction is critical for guiding emission control, due to the common concurrence of N2O and O2 in natural and engineered systems. This study provided the N2O reduction kinetics of various bacteria under aerobic and anaerobic conditions and classified the bacteria into oxygen-tolerant, -sensitive, and -intolerant N2O reducers. Oxygen-tolerant N2O reducers rapidly consumed O2, which could help maintain the low O2 concentration in the cells and keep their N2O reductase active. These findings are important and useful when selecting N2O reducers for bioremediation applications.

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.

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.

Complex and flexible catabolism in Aromatoleum aromaticum pCyN1

Large quantities of organic matter are continuously deposited, and (a)biotic gradients intersect in the soil-rhizosphere, where biodegradation contributes to the global cycles of elements. The betaproteobacterial genus Aromatoleum comprises cosmopolitan, facultative denitrifying degradation specialists. A. aromaticum pCyN1 stands out for anaerobically decomposing plant-derived monoterpenes in addition to monoaromatic hydrocarbons, polar aromatics and aliphatics. The catabolic network's structure and flexibility in A. aromaticum pCyN1 was studied across 34 growth conditions by superimposing proteome profiles onto the manually annotated 4.37 Mbp genome. Strain pCyN1 employs three fundamentally different enzymes for C-H-bond cleavage at the methyl groups of p-cymene/4-ethyltoluene, toluene and p-cresol, respectively. Regulation of degradation modules displayed substrate specificities ranging from narrow (toluene and cyclohexane carboxylate) via medium-wide (one module shared by p-cymene, 4-ethyltoluene, α-phellandrene, α-terpinene, γ-terpinene and limonene) to broad (central benzoyl-CoA pathway serving 16 aromatic substrates). Remarkably, three variants of ATP-dependent (class I) benzoyl-CoA reductase and four different β-oxidation routes establish a degradation hub that accommodates the substrate diversity. The respiratory system displayed several conspicuous profiles, e.g., the presence of nitrous oxide reductase under oxic and of low-affinity oxidase under anoxic conditions. Overall, nutritional versatility in conjunction with network regulation endow A. aromaticum pCyN1 with broad adaptability. This article is protected by copyright. All rights reserved.

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.

Linking meta-omics to the kinetics of denitrification intermediates reveals pH-dependent causes of N2O emissions and nitrite accumulation in soil

Soil pH is a key controller of denitrification. We analysed the metagenomics/transcriptomics and phenomics of two soils from a long-term liming experiment, SoilN (pH 6.8) and un-limed SoilA (pH 3.8). SoilA had severely delayed N2O reduction despite early transcription of nosZ (mainly clade I), encoding N2O reductase, by diverse denitrifiers. This shows that post-transcriptionally hampered maturation of the NosZ apo-protein at low pH is a generic phenomenon. Identification of transcript reads of several accessory genes in the nos cluster indicated that enzymes for NosZ maturation were present across a range of organisms, eliminating their absence as an explanation for the failure to produce a functional enzyme. nir transcript abundances (for NO2- reductase) in SoilA suggest that low NO2- concentrations in acidic soils, often ascribed to abiotic degradation, are primarily due to biological activity. The accumulation of NO2- in neutral soil was ascribed to high nar expression (nitrate reductase). The -omics results revealed dominance of nirK over nirS in both soils while qPCR showed the opposite, demonstrating that standard primer pairs only capture a fraction of the nirK pool. qnor encoding NO reductase was strongly expressed in SoilA, implying an important role in controlling NO. Production of HONO, for which some studies claim higher, others lower, emissions from NO2- accumulating soil, was estimated to be ten times higher from SoilA than from SoilN. The study extends our understanding of denitrification-driven gas emissions and the diversity of bacteria involved and demonstrates that gene and transcript quantifications cannot always reliably predict community phenotypes.

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.

Bacterial nitric oxide metabolism: Recent insights in rhizobia

Nitric oxide (NO) is a reactive gaseous molecule that has several functions in biological systems depending on its concentration. At low concentrations, NO acts as a signaling molecule, while at high concentrations, it becomes very toxic due to its ability to react with multiple cellular targets. Soil bacteria, commonly known as rhizobia, have the capacity to establish a N₂-fixing symbiosis with legumes inducing the formation of nodules in their roots. Several reports have shown NO production in the nodules where this gas acts either as a signaling molecule which regulates gene expression, or as a potent inhibitor of nitrogenase and other plant and bacteria enzymes. A better understanding of the sinks and sources of NO in rhizobia is essential to protect symbiotic nitrogen fixation from nitrosative stress. In nodules, both the plant and the microsymbiont contribute to the production of NO. From the bacterial perspective, the main source of NO reported in rhizobia is the denitrification pathway that varies significantly depending on the species. In addition to denitrification, nitrate assimilation is emerging as a new source of NO in rhizobia. To control NO accumulation in the nodules, in addition to plant haemoglobins, bacteroids also contribute to NO detoxification through the expression of a NorBC-type nitric oxide reductase as well as rhizobial haemoglobins. In the present review, updated knowledge about the NO metabolism in legume-associated endosymbiotic bacteria is summarized.

Competition for electrons favours N2 O reduction in denitrifying Bradyrhizobium isolates

Bradyrhizobia are common members of soil microbiomes and known as N₂ -fixing symbionts of economically important legumes. Many are also denitrifiers, which can act as sinks or sources for N₂ O. Inoculation with compatible rhizobia is often needed for optimal N₂ -fixation, but the choice of inoculant may have consequences for N₂ O emission. Here, we determined the phylogeny and denitrification capacity of Bradyrhizobium strains, most of them isolated from peanut-nodules. Analyses of genomes and denitrification end-points showed that all were denitrifiers, but only ~1/3 could reduce N₂ O. The N₂ O-reducing isolates had strong preference for N₂ O- over NO₃ ^- -reduction. Such preference was also observed in a study of other bradyrhizobia and tentatively ascribed to competition between the electron pathways to Nap (periplasmic NO₃ ^- reductase) and Nos (N₂ O reductase). Another possible explanation is lower abundance of Nap than Nos. Here, proteomics revealed that Nap was instead more abundant than Nos, supporting the hypothesis that the electron pathway to Nos outcompetes that to Nap. In contrast, Paracoccus denitrificans, which has membrane-bond NO₃ ^- reductase (Nar), reduced N₂ O and NO₃ ^- simultaneously. We propose that the control at the metabolic level, favouring N₂ O reduction over NO₃ ^- reduction, applies also to other denitrifiers carrying Nos and Nap but lacking Nar.

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.

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.

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.