Evidence for an iron center in the ammonia monooxygenase from Nitrosomonas europaea

The effects of electric field assisted composting on ammonia and nitrous oxide emissions varied with different electrolytes

Enhancing electron transfer through directly elevating electric potential has been verified to reduce gaseous emissions from composting. Reducing electric resistance of composting biomass might be a choice to further strengthening electron transfer. Here, the effects of chemical electrolytes addition on gaseous Nitrogen emission in electric field assistant composting were investigated. Results suggest that adding acidic electrolyte (ferric chloride) significantly reduced ammonia (NH3) emission by 72.1% but increased nitrous oxide (N2O) emission (by 24-fold) (P < 0.05), because of a dual effect on nitrifier activity: i) an elevated abundance and proportion of ammonia oxidizing bacteria Nitrosomonadaceae, and ii) delayed growth of nitrite oxidizing bacteria. Neutral and alkaline electrolytes had no negative or positive effect on N2O or NH3 emission. Hence, there is a potential trade-off between NH3 and N2O mitigation if using ferric chloride as acidic electrolyte, and electrolyte addition should aim to enhance electron production promote N2O mitigation.

Copper-Catalyzed Electrosynthesis of Nitrite and Nitrate from Ammonia: Tuning the Selectivity via an Interplay Between Homogeneous and Heterogeneous Catalysis

Electrocatalytic oxidation of ammonia is an appealing, low-temperature process for the sustainable production of nitrites and nitrates that avoids the formation of pernicious N₂ O and can be fully powered by renewable electricity. Currently, however, the number of known efficient catalysts for such a reaction is limited. The present work demonstrates that copper-based electrodes exhibit high electrocatalytic activity and selectivity for the NH₃ oxidation to NO₂ ^- and NO₃ ^- in alkaline solutions. Systematic investigation of the effects of pH and potential on the kinetics of the reaction using voltammetric analysis andin situ Raman spectroscopy suggest that ammonia electrooxidation on copper occurrs via two primary catalytic mechanisms. In the first pathway, NH₃ is converted to NO₂ ^- via a homogeneous electrocatalytic process mediated by redox transformations of aqueous [Cu(OH)₄ ]^-/2- species, which dissolve from the electrode. The second pathway is the heterogeneous catalytic oxidation of NH₃ on the electrode surface favoring the formation of NO₃ ^- . By virtue of its nature, the homogeneous-mediated pathway enables higher selectivity and was less affected by electrode poisoning with the strongly adsorbed "N" intermediates that have plagued the electrocatalytic ammonia oxidation field. Thus, the selectivity of the Cu-catalyzed NH₃ oxidation towards either nitrite or nitrate can be achieved through balancing the kinetics of the two mechanisms by adjusting the pH of the electrolyte medium and potential.

The Chemistry, Biology, and Modulation of Ammonium Nitrification in Soil

Approximately two percent of the world's energy is consumed in the production of ammonia from hydrogen and nitrogen gas. Ammonia is used as a fertilizer ingredient for agriculture and distributed in the environment on an enormous scale to promote crop growth in intensive farming. Only 30-50 % of the nitrogen applied is assimilated by crop plants; the remaining 50-70 % goes into biological processes such as nitrification by microbial metabolism in the soil. This leads to an imbalance in the global nitrogen cycle and higher nitrous oxide emissions (a potent and significant greenhouse gas) as well as contamination of ground and surface waters by nitrate from the nitrogen-fertilized farmland. This Review gives a critical overview of the current knowledge of soil microbes involved in the chemistry of ammonia nitrification, the structures and mechanisms of the enzymes involved, and phytochemicals capable of inhibiting ammonia nitrification.

Roles of ammonia-oxidizing bacteria in improving metabolism and cometabolism of trace organic chemicals in biological wastewater treatment processes: A review

While there has been a significant recent improvement in the removal of pollutants in natural and engineered systems, trace organic chemicals (TrOCs) are posing a major threat to aquatic environments and human health. There is a critical need for developing potential strategies that aim at enhancing metabolism and/or cometabolism of these compounds. Recently, knowledge regarding biodegradation of TrOCs by ammonia-oxidizing bacteria (AOB) has been widely developed. This review aims to delineate an up-to-date version of the ecophysiology of AOB and outline current knowledge related to biodegradation efficiencies of the frequently reported TrOCs by AOB. The paper also provides an insight into biodegradation pathways by AOB and transformation products of these compounds and makes recommendations for future research of AOB. In brief, nitrifying WWTFs (wastewater treatment facilities) were superior in degrading most TrOCs than non-nitrifying WWTFs due to cometabolic biodegradation by the AOB. To fully understand and/or enhance the cometabolic biodegradation of TrOCs by AOB, recent molecular research has focused on numerous crucial factors including availability of the compounds to AOB, presence of growth substrate (NH₄-N), redox potentials, microorganism diversity (AOB and heterotrophs), physicochemical properties and operational parameters of the WWTFs, molecular structure of target TrOCs and membrane-based technologies, may all significantly impact the cometabolic biodegradation of TrOCs. Still, further exploration is required to elucidate the mechanisms involved in biodegradation of TrOCs by AOB and the toxicity levels of formed products.

Sulfide inhibition of nitrite oxidation in activated sludge depends on microbial community composition

Increasingly, technologies that use sulfide as an electron donor are being considered for nitrogen removal; however, our understanding of how sulfide affects microbial communities in nitrifying treatment processes is limited. In this study, we used batch experiments to quantify sulfide inhibition of both ammonium oxidizing bacteria (AOB) and nitrite oxidizing bacteria (NOB) using activated sludge from two full-scale treatment plants with distinct treatment processes. The batch experiments showed that NOB were more vulnerable to sulfide inhibition than AOB, and that inhibition constants (K_I) for NOB were distinct between the two treatment plants, which also had distinct nitrite oxidizing microbial communities. A Nitrospira-rich, less diverse NOB community was inhibited more by sulfide than a more diverse community rich in Nitrotoga and Nitrobacter. Therefore, sulfide-induced nitritation may be more successful in less diverse, Nitrospira-rich communities. Additionally, sulfide significantly influenced the activity of non-nitrifying microbial community members, as measured by 16S rRNA cDNA sequencing. Overall, these results indicate that sulfide has a strong impact on both nitrification and the activity of the underlying microbial communities, and that the response is community-specific.

The role of natural polyphenols in cell signaling and cytoprotection against cancer development

The cytoprotective and anticancer action of dietary in-taken natural polyphenols has for long been attributed only to their direct radical scavenging activities. Currently it is well supported that those compounds display a broad spectrum of biological and pharmacological outcomes mediated by their complex metabolism, interaction with gut microbiota as well as direct interactions of their metabolites with key cellular signaling proteins. The beneficial effects of natural polyphenols and their synthetic derivatives are extensively studied in context of cancer prophylaxis and therapy. Herein we focus on cell signaling to explain the beneficial role of polyphenols at the three stages of cancer development: we review the recent proceedings about the impact of polyphenols on the cytoprotective antioxidant response and their proapoptotic action at the premalignant stage, and finally we present data showing how phenolic acids (e.g., caffeic, chlorogenic acids) and flavonols (e.g., quercetin) hamper the development of metastatic cancer.

The geochemical record of the ancient nitrogen cycle, nitrogen isotopes, and metal cofactors

The nitrogen (N) cycle is the only global biogeochemical cycle that is driven by biological functions involving the interaction of many microorganisms. The N cycle has evolved over geological time and its interaction with the oxygen cycle has had profound effects on the evolution and timing of Earth's atmosphere oxygenation (Falkowski and Godfrey, 2008). Almost every enzyme that microorganisms use to manipulate N contains redox-sensitive metals. Bioavailability of these metals has changed through time as a function of varying redox conditions, and likely influenced the biological underpinnings of the N cycle. It is possible to construct a record through geological time using N isotopes and metal concentrations in sediments to determine when the different stages of the N cycle evolved and the role metal availability played in the development of key enzymes. The same techniques are applicable to understanding the operation and changes in the N cycle through geological time. However, N and many of the redox-sensitive metals in some of their oxidation states are mobile and the isotopic composition or distribution can be altered by subsequent processes leading to erroneous conclusions. This chapter reviews the enzymology and metal cofactors of the N cycle and describes proper utilization of methods used to reconstruct evolution of the N cycle through time.

A soluble form of ammonia monooxygenase in Nitrosomonas europaea

Ammonia monooxygenase (AMO) ofNitrosomonas europaeais a metalloenzyme that catalyzes the oxidation of ammonia to hydroxylamine. This study shows that AMO resides in the cytoplasm of the bacteria in addition to its location in the membrane and is distributed approximately equally in both subcellular fractions. AMO in both fractions catalyzes the oxidation of ammonia and binds [14C]acetylene, a mechanism-based inhibitor which specifically interacts with catalytically active AMO. Soluble AMO was purified 12-fold to electrophoretic homogeneity with a yield of 8%. AMO has a molecular mass of approximately 283 kDa with subunits of ca. 27 kDa (α-subunit, AmoA), ca. 42 kDa (β-subunit, AmoB), and ca. 24 kDa (γ-subunit, cytochromec1) in an α3β3γ3sub-unit structure. Different from the β-subunit of membrane-bound AMO, AmoB of soluble AMO possesses an N-terminal signal sequence. AMO contains Cu (9.4±0.6 mol per mol AMO), Fe (3.9±0.3 mol per mol AMO), and Zn (0.5 to 2.6 mol per mol AMO). Upon reduction the visible absorption spectrum of AMO reveals absorption bands characteristic of cytochromec. Electron para-magnetic resonance spectroscopy of air-oxidized AMO at 50 K shows a paramagnetic signal originating from Cu2+and at 10 K a paramagnetic signal characteristic of heme-Fe.

Interaction of the mechanism-based inactivator acetylene with ammonia monooxygenase of Nitrosomonas europaea

The ammonia monooxygenase (AMO) of Nitrosomonas europaea is a metalloenzyme that catalyses the oxidation of ammonia to hydroxylamine. We have identified histidine 191 of AmoA as the binding site for the oxidized mechanism-based inactivator acetylene. Binding of acetylene changed the molecular mass of His-191 from 155.15 to 197.2 Da (+42.05), providing evidence that acetylene was oxidized to ketene (CH2CO; 42.04 Da) which binds specifically to His-191. It must be assumed that His-191 is part of the acetylene-activating site in AMO or at least directly neighbours this site.

Metabolism of Inorganic N Compounds by Ammonia-Oxidizing Bacteria

Ammonia oxidizing bacteria extract energy for growth from the oxidation of ammonia to nitrite. Ammonia monooxygenase, which initiates ammonia oxidation, remains enigmatic given the lack of purified preparations. Genetic and biochemical studies support a model for the enzyme consisting of three subunits and metal centers of copper and iron. Knowledge of hydroxylamine oxidoreductase, which oxidizes hydroxylamine formed by ammonia monooxygenase to nitrite, is informed by a crystal structure and detailed spectroscopic and catalytic studies. Other inorganic nitrogen compounds, including NO, N2O, NO2, and N2 can be consumed and/or produced by ammonia-oxidizing bacteria. NO and N2O can be produced as byproducts of hydroxylamine oxidation or through nitrite reduction. NO2 can serve as an alternative oxidant in place of O2 in some ammonia-oxidizing strains. Our knowledge of the diversity of inorganic N metabolism by ammonia-oxidizing bacteria continues to grow. Nonetheless, many questions remain regarding the enzymes and genes involved in these processes and the role of these pathways in ammonia oxidizers.

The metal centers of particulate methane monooxygenase from Methylosinus trichosporium OB3b

Particulate methane monooxygenase (pMMO) is a membrane-bound metalloenzyme that oxidizes methane to methanol in methanotrophic bacteria. The nature of the pMMO active site and the overall metal content are controversial, with spectroscopic and crystallographic data suggesting the presence of a mononuclear copper center, a dinuclear copper center, a trinuclear center, and a diiron center or combinations thereof. Most studies have focused on pMMO from Methylococcus capsulatus (Bath). pMMO from a second organism, Methylosinus trichosporium OB3b, has been purified and characterized by spectroscopic and crystallographic methods. Purified M. trichosporium OB3b pMMO contains approximately 2 copper ions per 100 kDa protomer. Electron paramagnetic resonance (EPR) spectroscopic parameters indicate that type 2 Cu(II) is present as two distinct species. Extended X-ray absorption fine structure (EXAFS) data are best fit with oxygen/nitrogen ligands and reveal a Cu-Cu interaction at 2.52 A. Correspondingly, X-ray crystallography of M. trichosporium OB3b pMMO shows a dinuclear copper center, similar to that observed previously in the crystal structure of M. capsulatus (Bath) pMMO. There are, however, significant differences between the pMMO structures from the two organisms. A mononuclear copper center present in M. capsulatus (Bath) pMMO is absent in M. trichosporium OB3b pMMO, whereas a metal center occupied by zinc in the M. capsulatus (Bath) pMMO structure is occupied by copper in M. trichosporium OB3b pMMO. These findings extend previous work on pMMO from M. capsulatus (Bath) and provide new insight into the functional importance of the different metal centers.

Community Level Analysis: Genetic and Biogeochemical Approaches to Investigate Community Composition and Function in Aerobic Ammonia Oxidation

Aerobic ammonia oxidation is the process that converts ammonium to nitrate and thus links the regeneration of organic nitrogen to fixed nitrogen loss by denitrification. It is performed by a phylogenetically restricted group of Proteobacteria (ammonia-oxidizing bacteria, AOB) that are autotrophic and obligately aerobic. This chapter describes methods for the measurement of ammonia oxidation in the environment, with a focus on seawater systems and stable isotopic tracer methods. It also summarizes the current state of molecular ecological approaches for detection of AOB in the environment and characterization of the composition of AOB assemblages.

The membrane-associated form of methane mono-oxygenase from Methylococcus capsulatus (Bath) is a copper/iron protein

A protocol has been developed which permits the purification of a membrane-associated methane-oxidizing complex from Methylococcus capsulatus (Bath). This complex has approximately 5 fold higher specific activity than any purified particulate methane mono-oxygenase (pMMO) previously reported from M. capsulatus (Bath). This efficiently functioning methane-oxidizing complex consists of the pMMO hydroxylase (pMMOH) and an unidentified component we have assigned as a potential pMMO reductase (pMMOR). The complex was isolated by solubilizing intracytoplasmic membrane preparations containing the high yields of active membrane-bound pMMO (pMMO(m)), using the non-ionic detergent dodecyl-beta-D-maltoside, to yield solubilized enzyme (pMMO(s)). Further purification gave rise to an active complex (pMMO(c)) that could be resolved (at low levels) by ion-exchange chromatography into two components, the pMMOH (47, 27 and 24 kDa subunits) and the pMMOR (63 and 8 kDa subunits). The purified complex contains two copper atoms and one non-haem iron atom/mol of enzyme. EPR spectra of preparations grown with (63)Cu indicated that the copper ion interacted with three or four nitrogenic ligands. These EPR data, in conjunction with other experimental results, including the oxidation by ferricyanide, EDTA treatment to remove copper and re-addition of copper to the depleted protein, verified the essential role of copper in enzyme catalysis and indicated the implausibility of copper existing as a trinuclear cluster. The EPR measurements also demonstrated the presence of a tightly bound mononuclear Fe(3+) ion in an octahedral environment that may well be exchange-coupled to another paramagnetic species.

Proterozoic ocean chemistry and evolution: a bioinorganic bridge?

Recent data imply that for much of the Proterozoic Eon (2500 to 543 million years ago), Earth's oceans were moderately oxic at the surface and sulfidic at depth. Under these conditions, biologically important trace metals would have been scarce in most marine environments, potentially restricting the nitrogen cycle, affecting primary productivity, and limiting the ecological distribution of eukaryotic algae. Oceanic redox conditions and their bioinorganic consequences may thus help to explain observed patterns of Proterozoic evolution.

Kinetic characterization of the inactivation of ammonia monooxygenase in Nitrosomonas europaea by alkyne, aniline and cyclopropane derivatives

The kinetic mechanisms of seven inactivators of ammonia oxidation activity in cells of the nitrifying bacterium, Nitrosomonas europaea were investigated. The effects of the inactivators were specific for ammonia monooxygenase (AMO) which oxidizes ammonia to hydroxylamine. The aniline derivatives, 1,3-phenylenediamine and p-anisidine, were potent inactivators of AMO while other derivatives were ineffective as inactivators. Two cyclopropane derivatives, 1, 2-dimethylcyclopropane and cyclopropyl bromide, were inactivators while cyclopropane was not an inactivator. The mechanisms of three alkynes, 1-hexyne, 3-hexyne, and acetylene, were also examined. For all seven compounds, the inactivation of AMO was irreversible, time-dependent, first-order, and dependent on catalytic turnover. Saturation of the rate of inactivation was indicated for p-anisidine (kinact=2.85 min-1; KI=1.0 mM) and cyclopropyl bromide (kinact=4.4 min-1; KI=97 microM), but not for any of the remaining five inactivators, including acetylene. Ammonia slowed the rate of inactivation for acetylene and cyclopropyl bromide, but enhanced the rate of inactivation for the remaining inactivators. All seven compounds appear to be mechanism-based inactivators of AMO.

Loss of ammonia monooxygenase activity in nitrosomonas europaea upon exposure to nitrite

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

Copper-binding compounds from Methylosinus trichosporium OB3b

Two copper-binding compounds/cofactors (CBCs) were isolated from the spent media of both the wild type and a constitutive soluble methane monooxygenase (sMMOC) mutant, PP319 (P. A. Phelps et al., Appl. Environ. Microbiol. 58:3701-3708, 1992), of Methylosinus trichosporium OB3b. Both CBCs are small polypeptides with molecular masses of 1,218 and 779 Da for CBC-L1 and CBC-L2, respectively. The amino acid sequence of CBC-L1 is S?MYPGS?M, and that of CBC-L2 is SPMP?S. Copper-free CBCs showed absorption maxima at 204, 275, 333, and 356 with shoulders at 222 and 400 nm. Copper-containing CBCs showed a broad absorption maximum at 245 nm. The low-temperature electron paramagnetic resonance (EPR) spectra of copper-containing CBC-L1 showed the presence of a copper center with an EPR splitting constant between those of type 1 and type 2 copper centers (g = 2.087, g = 2.42 G, A = 128 G). The EPR spectrum of CBC-L2 was more complex and showed two spectrally distinct copper centers. One signal can be attributed to a type 2 Cu2+ center (g = 2.073, g = 2.324 G, A = 144 G) which could be saturated at higher powers, while the second shows a broad, nearly isotropic signal near g = 2.063. In wild-type strains, the concentrations of CBCs in the spent media were highest in cells expressing the pMMO and stressed for copper. In contrast to wild-type strains, high concentrations of CBCs were observed in the extracellular fraction of the sMMOC mutants PP319 and PP359 regardless of the copper concentration in the culture medium.

Nitrogen cycle enzymology

The minimal nitrogen cycle involves five reduction reactions and three oxidation reactions, each of which poses interesting problems in bioinorganic chemistry, energy transduction and protein structure/function relationships. Many of the major recent developments in this field have depended on the acquisition of protein crystal structures, including structures of enzymes with bound substrates or products and in protein-protein complexes. These enzymes include nitrogenase, nitrite reductases, hydroxylamine oxidoreductase and a fungal nitric oxide reductase.