Denitrification by the fungus Cylindrocarpon tonkinense: anaerobic cell growth and two isozyme forms of cytochrome P-450nor

Climate warming, but not Spartina alterniflora invasion, enhances wetland soil HONO and NOx emissions

Climate warming and invasive plant growth (plant invasion) may aggravate air pollution by affecting soil nitrogen (N) cycling and the emissions of reactive N gases, such as nitrous acid (HONO) and nitrogen oxides (NO_x). However, little is known about the response of soil NO_y (HONO + NO_x) emissions and microbial functional genes to the interaction of climate warming and plant invasion. Here, we found that experimental warming (approximately 1.5 °C), but not Spartina alterniflora invasion, increased NO_y emissions (0-140 ng N m^-2 s^-1) of treated wetland soils by 4-10 fold. Warming also decreased soil archaeal and fungal richness and diversity, shifted their community structure (e.g., decreased the archaeal classes Thermoplasmata and Iainarchaeia, and increased the archaeal genus Candidatus Nitrosoarchaeum, and the fungal classes Saccharomycetes and Tritirachiomycetes), and decreased the overall abundance of soil N cycling genes. Structural equation modeling revealed that warming-associated changes in edaphic factors and the microbial N cycling potential are responsible for the observed increase in soil NO_y emissions. Collectively, the results showed that climate warming accelerates soil N cycling by stimulating large soil HONO and NO_x emissions, and influences air quality by contributing to atmospheric reactive N and ozone cycling.

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.

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.

Metabolic preference of nitrate over oxygen as an electron acceptor in foraminifera from the Peruvian oxygen minimum zone

Benthic foraminifera populate a diverse range of marine habitats. Their ability to use alternative electron acceptors-nitrate (NO₃ ^-) or oxygen (O₂)-makes them important mediators of benthic nitrogen cycling. Nevertheless, the metabolic scaling of the two alternative respiration pathways and the environmental determinants of foraminiferal denitrification rates are yet unknown. We measured denitrification and O₂ respiration rates for 10 benthic foraminifer species sampled in the Peruvian oxygen minimum zone (OMZ). Denitrification and O₂ respiration rates significantly scale sublinearly with the cell volume. The scaling is lower for O₂ respiration than for denitrification, indicating that NO₃ ^- metabolism during denitrification is more efficient than O₂ metabolism during aerobic respiration in foraminifera from the Peruvian OMZ. The negative correlation of the O₂ respiration rate with the surface/volume ratio is steeper than for the denitrification rate. This is likely explained by the presence of an intracellular NO₃ ^- storage in denitrifying foraminifera. Furthermore, we observe an increasing mean cell volume of the Peruvian foraminifera, under higher NO₃ ^- availability. This suggests that the cell size of denitrifying foraminifera is not limited by O₂ but rather by NO₃ ^- availability. Based on our findings, we develop a mathematical formulation of foraminiferal cell volume as a predictor of respiration and denitrification rates, which can further constrain foraminiferal biogeochemical cycling in biogeochemical models. Our findings show that NO₃ ^- is the preferred electron acceptor in foraminifera from the OMZ, where the foraminiferal contribution to denitrification is governed by the ratio between NO₃ ^- and O₂.

Fungal Cytochrome P450s and the P450 Complement (CYPome) of Fusarium graminearum

Cytochrome P450s (CYPs), heme-containing monooxygenases, play important roles in a wide variety of metabolic processes important for development as well as biotic/trophic interactions in most living organisms. Functions of some CYP enzymes are similar across organisms, but some are organism-specific; they are involved in the biosynthesis of structural components, signaling networks, secondary metabolisms, and xenobiotic/drug detoxification. Fungi possess more diverse CYP families than plants, animals, or bacteria. Various fungal CYPs are involved in not only ergosterol synthesis and virulence but also in the production of a wide array of secondary metabolites, which exert toxic effects on humans and other animals. Although few studies have investigated the functions of fungal CYPs, a recent systematic functional analysis of CYP genes in the plant pathogen Fusarium graminearum identified several novel CYPs specifically involved in virulence, asexual and sexual development, and degradation of xenobiotics. This review provides fundamental information on fungal CYPs and a new platform for further metabolomic and biochemical studies of CYPs in toxigenic fungi.

Expression and Purification of Cytochrome P450 55B1 from Chlamydomonas reinhardtii and Its Application in Nitric Oxide Biosensing

Cytochrome P450 55B1 from Chlamydomonas reinhardtii is reported to function as a nitric oxide reductase (NOR). Here, we expressed the cytochrome P450 55B1 gene with an HIS-tag in E scherichia coli using a pET28a vector. The native protein was produced at a level of 1.59 μmol/g of total protein, with approximately 85% of the P450 being soluble. The CYP55B1 protein was characterized spectrally and purified by a HIS-trap column. This procedure allowed recovery of 45% of the expressed protein and CYP55B1 with a specific content of 0.70 μmol/g of the total protein, which showed a single band on a SDS-PAGE and Western blot. The direct electrochemistry of CYP55B1 in dihexadecylphosphate (DHP) film was realized with an electric potential at -0.47 V at the scan rate of 1 V s^-1. We studied the in vitro interaction between P450 55B1 and NO by the fluorescence spectrometric method. The results show that the fluorescence intensity of iron-porphyrin in P450 55B1 changes gradually with the addition of NO. The fluorescence intensity change values against NO concentrations were plotted, and it showed a linear range of NO from 0 to 22.5 μM with a sensitivity of 0.15 μM/AU and a detection limit of 0.15 μM.

Atmospheric emission of nitric oxide and processes involved in its biogeochemical transformation in terrestrial environment

Nitric oxide (NO) is an intra- and intercellular gaseous signaling molecule with a broad spectrum of regulatory functions in biological system. Its emissions are produced by both natural and anthropogenic sources; however, soils are among the most important sources of NO. Nitric oxide plays a decisive role in environmental-atmospheric chemistry by controlling the tropospheric photochemical production of ozone and regulates formation of various oxidizing agents such as hydroxyl radical (OH), which contributes to the formation of acid of precipitates. Consequently, for developing strategies to overcome the deleterious impact of NO on terrestrial ecosystem, it is mandatory to have reliable information about the exact emission mechanism and processes involved in its transformation in soil-atmospheric system. Although the formation process of NO is a complex phenomenon and depends on many physicochemical characteristics, such as organic matter, soil pH, soil moisture, soil temperature, etc., this review provides comprehensive updates about the emission characteristics and biogeochemical transformation mechanism of NO. Moreover, this article will also be helpful to understand the processes involved in the consumption of NO in soils. Further studies describing the functions of NO in biological system are also discussed.

Detection and Diversity of Fungal Nitric Oxide Reductase Genes (p450nor) in Agricultural Soils

Members of the Fungi convert nitrate (NO3 (-)) and nitrite (NO2 (-)) to gaseous nitrous oxide (N2O) (denitrification), but the fungal contributions to N loss from soil remain uncertain. Cultivation-based methodologies that include antibiotics to selectively assess fungal activities have limitations, and complementary molecular approaches to assign denitrification potential to fungi are desirable. Microcosms established with soils from two representative U.S. Midwest agricultural regions produced N2O from added NO3 (-) or NO2 (-) in the presence of antibiotics to inhibit bacteria. Cultivation efforts yielded 214 fungal isolates belonging to at least 15 distinct morphological groups, 151 of which produced N2O from NO2 (-) Novel PCR primers targeting the p450nor gene, which encodes the nitric oxide (NO) reductase responsible for N2O production in fungi, yielded 26 novel p450nor amplicons from DNA of 37 isolates and 23 amplicons from environmental DNA obtained from two agricultural soils. The sequences shared 54 to 98% amino acid identity with reference P450nor sequences within the phylum Ascomycota and expand the known fungal P450nor sequence diversity. p450nor was detected in all fungal isolates that produced N2O from NO2 (-), whereas nirK (encoding the NO-forming NO2 (-) reductase) was amplified in only 13 to 74% of the N2O-forming isolates using two separate nirK primer sets. Collectively, our findings demonstrate the value of p450nor-targeted PCR to complement existing approaches to assess the fungal contributions to denitrification and N2O formation.

IMPORTANCE

A comprehensive understanding of the microbiota controlling soil N loss and greenhouse gas (N2O) emissions is crucial for sustainable agricultural practices and addressing climate change concerns. We report the design and application of a novel PCR primer set targeting fungal p450nor, a biomarker for fungal N2O production, and demonstrate the utility of the new approach to assess fungal denitrification potential in fungal isolates and agricultural soils. These new PCR primers may find application in a variety of biomes to assess the fungal contributions to N loss and N2O emissions.

Nitrate Storage and Dissimilatory Nitrate Reduction by Eukaryotic Microbes

The microbial nitrogen cycle is one of the most complex and environmentally important element cycles on Earth and has long been thought to be mediated exclusively by prokaryotic microbes. Rather recently, it was discovered that certain eukaryotic microbes are able to store nitrate intracellularly and use it for dissimilatory nitrate reduction in the absence of oxygen. The paradigm shift that this entailed is ecologically significant because the eukaryotes in question comprise global players like diatoms, foraminifers, and fungi. This review article provides an unprecedented overview of nitrate storage and dissimilatory nitrate reduction by diverse marine eukaryotes placed into an eco-physiological context. The advantage of intracellular nitrate storage for anaerobic energy conservation in oxygen-depleted habitats is explained and the life style enabled by this metabolic trait is described. A first compilation of intracellular nitrate inventories in various marine sediments is presented, indicating that intracellular nitrate pools vastly exceed porewater nitrate pools. The relative contribution by foraminifers to total sedimentary denitrification is estimated for different marine settings, suggesting that eukaryotes may rival prokaryotes in terms of dissimilatory nitrate reduction. Finally, this review article sketches some evolutionary perspectives of eukaryotic nitrate metabolism and identifies open questions that need to be addressed in future investigations.

N2O production, a widespread trait in fungi

N₂O is a powerful greenhouse gas contributing both to global warming and ozone depletion. While fungi have been identified as a putative source of N₂O, little is known about their production of this greenhouse gas. Here we investigated the N₂O-producing ability of a collection of 207 fungal isolates. Seventy strains producing N₂O in pure culture were identified. They were mostly species from the order Hypocreales order—particularly Fusarium oxysporum and Trichoderma spp.—and to a lesser extent species from the orders Eurotiales, Sordariales, and Chaetosphaeriales. The N₂O ¹⁵N site preference (SP) values of the fungal strains ranged from 15.8‰ to 36.7‰, and we observed a significant taxa effect, with Penicillium strains displaying lower SP values than the other fungal genera. Inoculation of 15 N₂O-producing strains into pre-sterilized arable, forest and grassland soils confirmed the ability of the strains to produce N₂O in soil with a significant strain-by-soil effect. The copper-containing nitrite reductase gene (nirK) was amplified from 45 N₂O-producing strains, and its genetic variability showed a strong congruence with the ITS phylogeny, indicating vertical inheritance of this trait. Taken together, this comprehensive set of findings should enhance our knowledge of fungi as a source of N₂O in the environment.

Dissimilatory nitrate reduction by Aspergillus terreus isolated from the seasonal oxygen minimum zone in the Arabian Sea

BACKGROUND

A wealth of microbial eukaryotes is adapted to life in oxygen-deficient marine environments. Evidence is accumulating that some of these eukaryotes survive anoxia by employing dissimilatory nitrate reduction, a strategy that otherwise is widespread in prokaryotes. Here, we report on the anaerobic nitrate metabolism of the fungus Aspergillus terreus (isolate An-4) that was obtained from sediment in the seasonal oxygen minimum zone in the Arabian Sea, a globally important site of oceanic nitrogen loss and nitrous oxide emission.

RESULTS

Axenic incubations of An-4 in the presence and absence of oxygen and nitrate revealed that this fungal isolate is capable of dissimilatory nitrate reduction to ammonium under anoxic conditions. A ¹⁵N-labeling experiment proved that An-4 produced and excreted ammonium through nitrate reduction at a rate of up to 175 nmol ¹⁵NH₄⁺ g⁻¹ protein h⁻¹. The products of dissimilatory nitrate reduction were ammonium (83%), nitrous oxide (15.5%), and nitrite (1.5%), while dinitrogen production was not observed. The process led to substantial cellular ATP production and biomass growth and also occurred when ammonium was added to suppress nitrate assimilation, stressing the dissimilatory nature of nitrate reduction. Interestingly, An-4 used intracellular nitrate stores (up to 6-8 μmol NO₃⁻ g⁻¹ protein) for dissimilatory nitrate reduction.

CONCLUSIONS

Our findings expand the short list of microbial eukaryotes that store nitrate intracellularly and carry out dissimilatory nitrate reduction when oxygen is absent. In the currently spreading oxygen-deficient zones in the ocean, an as yet unexplored diversity of fungi may recycle nitrate to ammonium and nitrite, the substrates of the major nitrogen loss process anaerobic ammonium oxidation, and the potent greenhouse gas nitrous oxide.

Watershed-scale fungal community characterization along a pH gradient in a subsurface environment cocontaminated with uranium and nitrate

The objective of this study was to characterize fungal communities in a subsurface environment cocontaminated with uranium and nitrate at the watershed scale and to determine the potential contribution of fungi to contaminant transformation (nitrate attenuation). The abundance, distribution, and diversity of fungi in subsurface groundwater samples were determined using quantitative and semiquantitative molecular techniques, including quantitative PCR of eukaryotic small-subunit rRNA genes and pyrosequencing of fungal internal transcribed spacer (ITS) regions. Potential bacterial and fungal denitrification was assessed in sediment-groundwater slurries amended with antimicrobial compounds and in fungal pure cultures isolated from the subsurface. Our results demonstrate that subsurface fungal communities are dominated by members of the phylum Ascomycota, and a pronounced shift in fungal community composition occurs across the groundwater pH gradient at the field site, with lower diversity observed under acidic (pH <4.5) conditions. Fungal isolates recovered from subsurface sediments, including cultures of the genus Coniochaeta, which were detected in abundance in pyrosequence libraries of site groundwater samples, were shown to reduce nitrate to nitrous oxide. Denitrifying fungal isolates recovered from the site were classified and found to be distributed broadly within the phylum Ascomycota and within a single genus of the Basidiomycota. Potential denitrification rate assays with sediment-groundwater slurries showed the potential for subsurface fungi to reduce nitrate to nitrous oxide under in situ acidic pH conditions.

Putting the N in dinoflagellates

The cosmopolitan presence of dinoflagellates in aquatic habitats is now believed to be a direct consequence of the different trophic modes they have developed through evolution. While heterotrophs ingest food and photoautotrophs photosynthesize, mixotrophic species are able to use both strategies to harvest energy and nutrients. These different trophic modes are of particular importance when nitrogen nutrition is considered. Nitrogen is required for the synthesis of amino acids, nucleic acids, chlorophylls, and toxins, and thus changes in the concentrations of various nitrogenous compounds can strongly affect both primary and secondary metabolism. For example, high nitrogen concentration is correlated with rampant cell division resulting in the formation of the algal blooms commonly called red tides. Conversely, nitrogen starvation results in cell cycle arrest and induces a series of physiological, behavioral and transcriptomic modifications to ensure survival. This review will combine physiological, biochemical, and transcriptomic data to assess the mechanism and impact of nitrogen metabolism in dinoflagellates and to compare the dinoflagellate responses with those of diatoms.

Spectrophotometric activity microassay for pure and recombinant cytochrome P450-type nitric oxide reductase

Nitric oxide reductase (NOR) of the P450 oxidoreductase family accepts electrons directly from its cofactor, NADH, to reduce two nitric oxide (NO) molecules to one nitrous oxide molecule and water. The enzyme plays a key role in the removal of radical NO produced during respiratory metabolism, and applications in bioremediation and biocatalysis have been identified. However, a rapid, accurate, and sensitive enzyme assay has not yet been developed for this enzyme family. In this study, we optimized reaction conditions for the development of a spectrophotometric NOR activity microassay using NOC-5 for the provision of NO in solution. We also demonstrate that the assay is suitable for the quantification and characterization of P450-type NOR. The K(m) and k(cat) kinetic constants obtained by this assay were comparable to the values determined by gas chromatography, but with improved convenience and cost efficiency, effectively by miniaturization. To our knowledge, this is the first study to present the quantification of NOR activity in a kinetic microassay format.

Fungal denitrification and nitric oxide reductase cytochrome P450nor

We have shown that many fungi (eukaryotes) exhibit distinct denitrifying activities, although occurrence of denitrification was previously thought to be restricted to bacteria (prokaryotes), and have characterized the fungal denitrification system. It comprises NirK (copper-containing nitrite reductase) and P450nor (a cytochrome P450 nitric oxide (NO) reductase (Nor)) to reduce nitrite to nitrous oxide (N(2)O). The system is localized in mitochondria functioning during anaerobic respiration. Some fungal systems further contain and use dissimilatory and assimilatory nitrate reductases to denitrify nitrate. Phylogenetic analysis of nirK genes showed that the fungal-denitrifying system has the same ancestor as the bacterial counterpart and suggested a possibility of its proto-mitochondrial origin. By contrast, fungi that have acquired a P450 from bacteria by horizontal transfer of the gene, modulated its function to give a Nor activity replacing the original Nor with P450nor. P450nor receives electrons directly from nicotinamide adenine dinucleotide to reduce NO to N(2)O. The mechanism of this unprecedented electron transfer has been extensively studied and thoroughly elucidated. Fungal denitrification is often accompanied by a unique phenomenon, co-denitrification, in which a hybrid N(2) or N(2)O species is formed upon the combination of nitrogen atoms of nitrite with a nitrogen donor (amines and imines). Possible involvement of NirK and P450nor is suggested.

Molecular Diversity of Fungi from Marine Oxygen-Deficient Environments (ODEs)

Molecular diversity surveys of marine fungi have demonstrated that the species richness known to date is just the tip of the iceberg and that there is a large extent of unknown fungal diversity in marine habitats. Reports of novel fungal lineages at higher taxonomic levels are documented from a large number of marine habitats, including the various marine oxygen-deficient environments (ODEs). In the past few years, a strong focus of eukaryote diversity research has been on a variety of ODEs, as these environments are considered to harbor a large number of organisms, which are highly divergent to known diversity and could provide insights into the early eukaryotic evolution. ODEs that have been targeted so far include shallow water sediments, hydrothermal vent systems, deep-sea basins, intertidal habitats, and fjords. Most, if not all, molecular diversity studies in marine ODEs have shown, that contrary to previous assumptions, fungi contribute significantly to the micro-eukaryotic community in such habitats. In this chapter, we have reanalyzed the environmental fungal sequences obtained from the molecular diversity survey in 14 different sites to obtain a comprehensive picture of fungal diversity in these marine habitats. The phylogenetic analysis of the fungal environmental sequences from various ODEs have grouped these sequences into seven distinct clades (Clade 1-7) clustering with well-known fungal taxa. Apart from this, four environmental clades (EnvClade A, B, C, and D) with exclusive environmental sequences were also identified. This has provided information on the positioning of the environmental sequences at different taxonomic levels within the major fungal phylums. The taxonomic distribution of these environmental fungal sequences into clusters and clades has also shown that they are not restricted by geographical boundaries. The distribution pattern together with the reports on the respiratory abilities of fungi under reduced oxygen conditions shows that they are highly adaptive and may have a huge ecological role in these oxygen deficient habitats.

Diatoms respire nitrate to survive dark and anoxic conditions

Diatoms survive in dark, anoxic sediment layers for months to decades. Our investigation reveals a correlation between the dark survival potential of marine diatoms and their ability to accumulate NO(3)(-) intracellularly. Axenic strains of benthic and pelagic diatoms that stored 11-274 mM NO(3)(-) in their cells survived for 6-28 wk. After sudden shifts to dark, anoxic conditions, the benthic diatom Amphora coffeaeformis consumed 84-87% of its intracellular NO(3)(-) pool within 1 d. A stable-isotope labeling experiment proved that (15)NO(3)(-) consumption was accompanied by the production and release of (15)NH(4)(+), indicating dissimilatory nitrate reduction to ammonium (DNRA). DNRA is an anaerobic respiration process that is known mainly from prokaryotic organisms, and here shown as dissimilatory nitrate reduction pathway used by a eukaryotic phototroph. Similar to large sulfur bacteria and benthic foraminifera, diatoms may respire intracellular NO(3)(-) in sediment layers without O(2) and NO(3)(-). The rapid depletion of the intracellular NO(3)(-) storage, however, implies that diatoms use DNRA to enter a resting stage for long-term survival. Assuming that pelagic diatoms are also capable of DNRA, senescing diatoms that sink through oxygen-deficient water layers may be a significant NH(4)(+) source for anammox, the prevalent nitrogen loss pathway of oceanic oxygen minimum zones.

Cytochrome P450 enzymes in the fungal kingdom

Cytochrome P450 monooxygenases of fungi are involved in many essential cellular processes and play diverse roles. The enzymes catalyze the conversion of hydrophobic intermediates of primary and secondary metabolic pathways, detoxify natural and environmental pollutants and allow fungi to grow under different conditions. Fungal genome sequencing projects have enabled the annotation of several thousand novel cytochromes P450, many of which constitute new families. This review presents the characteristics of fungal cytochrome P450 systems and updates information on the functions of characterized fungal P450 monooxygenases as well as outlines the currently used strategies for determining the function of the many putative P450 enzymes.

Cloning and characterization of two flavohemoglobins from Aspergillus oryzae

Two flavohemoglobin (FHb) genes, fhb1 and fhb2, were cloned from Aspergillus oryzae. The amino acid sequences of the deduced FHb1 and FHb2 showed high identity to other FHbs except for the predicted mitochondrial targeting signal in the N-terminus of FHb2. The recombinant proteins displayed absorption spectra similar to those of other FHbs. FHb1 and FHb2 were estimated to be a monomer and a dimer in solution, respectively. Both of the isozymes exhibit high NO dioxygenase (NOD) activity. FHb1 utilizes either NADH or NADPH as an electron donor, whereas FHb2 can only use NADH. These results suggest that FHb1 and FHb2 are fungal counterparts of bacterial FHbs and act as NO detoxification enzymes in the cytosol and mitochondria, respectively. This study is the first to show that a microorganism contains two isozymes of FHb and that intracellular localization of the isozymes could differ.

Spectroscopic and kinetic studies of Nor1, a cytochrome P450 nitric oxide reductase from the fungal pathogen Histoplasma capsulatum

The fungal respiratory pathogen Histoplasma capsulatum evades the innate immune response and colonizes macrophages during infection. Although macrophage production of the antimicrobial effector nitric oxide (NO) restricts H. capsulatum growth, the pathogen is able to establish a persistent infection. H. capsulatum contains a P450 nitric oxide reductase homologue (NOR1) that may be important for detoxifying NO during infection. To characterize the activity of this putative P450 enzyme, a 404 amino acid fragment of Nor1p was expressed in Escherichia coli and purified to homogeneity. Spectral characterization of Nor1p indicated that it was similar to other fungal P450 nitric oxide reductases. Nor1p catalyzed the reduction of NO to N2O using NADH as the direct reductant. The K(M) for NO was determined to be 20 microM and the k(cat) to be 5000 min(-1). Together, these results provide evidence for a protective role of a P450 nitric oxide reductase against macrophage-derived NO.

Genetic and functional variation in denitrifier populations along a short-term restoration chronosequence

Complete removal of plants and soil to exposed bedrock, in order to eradicate the Hole-in-the-Donut (HID) region of the Everglades National Park, FL, of exotic invasive plants, presented the opportunity to monitor the redevelopment of soil and the associated microbial communities along a short-term restoration chronosequence. Sampling plots were established for sites restored in 1989, 1997, 2000, 2001, and 2003. The goal of this study was to characterize the activity and diversity of denitrifying bacterial populations in developing HID soils in an effort to understand changes in nitrogen (N) cycling during short-term primary succession. Denitrifying enzyme activity (DEA) was detected in soils from all sites, indicating a potential for N loss via denitrification. However, no correlation between DEA and time since disturbance was observed. Diversity of bacterial denitrifiers in soils was characterized by sequence analysis of nitrite reductase genes (nirK and nirS) in DNA extracts from soils ranging in nitrate concentrations from 1.8 to 7.8 mg kg(-1). High levels of diversity were observed in both nirK and nirS clone libraries. Statistical analyses of clone libraries suggest a different response of nirS- and nirK-type denitrifiers to factors associated with soil redevelopment. nirS populations demonstrated a linear pattern of succession, with individual lineages represented at each site, while multiple levels of analysis suggest nirK populations respond in a grouped pattern. These findings suggest that nirK communities are more sensitive than nirS communities to environmental gradients in these soils.

Purification and functional analysis of fungal nitric oxide reductase cytochrome P450nor

Cytochrome P450nor (P450nor) is a nitric oxide (NO) reductase involved in fungal denitrification. Denitrification is a biological process in which nitrate or nitrite is reduced to gaseous nitrogen, the reverse reaction of nitrogen fixation. It therefore plays an important role in maintaining global environmental homeostasis. The involvement of P450nor in fungal denitrification indicates that denitrification not only occurs in prokaryotic bacteria, but also in eukaryotic fungi. In addition, the reduction of NO to nitrous oxide catalyzed by P450nor has added new insight into the function of cytochrome P450s, which are usually monooxygenases. Currently, five isozymes of P450nor have been isolated from the subdivisions of eumycota, and studies on the function and structure of P450nor have provided important information for both molecular mechanisms of P450 reactions and wastewater treatment. This chapter describes the screening of NO reductase activities, cloning, purification, and functional analysis of P450nor.

Engineering of the redox imbalance of Fusarium oxysporum enables anaerobic growth on xylose

Dissimilatory nitrate reduction metabolism, of the natural xylose-fermenting fungus Fusarium oxysporum, was used as a strategy to achieve anaerobic growth and ethanol production from xylose. Beneficial alterations of the redox fluxes and thereby of the xylose metabolism were obtained by taking advantage of the regeneration of the cofactor NAD(+) during the denitrification process. In batch cultivations, nitrate sustained growth under anaerobic conditions (1.21 g L(-1) biomass) and simultaneously a maximum yield of 0.55 moles of ethanol per mole of xylose was achieved, whereas substitution of nitrate with ammonium limited the growth significantly (0.15 g L(-1) biomass). Using nitrate, the maximum acetate yield was 0.21 moles per mole of xylose and no xylitol excretion was observed. Furthermore, the network structure in the central carbon metabolism of F. oxysporum was characterized in steady state. F. oxysporum grew anaerobically on [1-(13)C] labelled glucose and unlabelled xylose in chemostat cultivation with nitrate as nitrogen source. The use of labelled substrate allowed the precise determination of the glucose and xylose contribution to the carbon fluxes in the central metabolism of this poorly described microorganism. It was demonstrated that dissimilatory nitrate reduction allows F. oxysporum to exhibit typical respiratory metabolic behaviour with a highly active TCA cycle and a large demand for NADPH.

Denitrification by the mix-culturing of fungi and bacteria with shell

Denitrification by pure and mixed culture of Fusarium oxysporum and Pseudomonas stutzeri in different mineral medium and in synthetic wastewater were examined. The results obtained revealed that a rapid N2 evolution by F. oxysporum and P. stutzeri in mineral medium and synthetic wastewater was observed. In co-cultures of F. oxysporum and P. stutzeri, N2O produced by F. oxysporum was rapidly consumed by P. stutzeri. This indicated that mixed culture of F. oxysporum and P. stutzeri could be used for efficient nitrate and nitrite removal. Using synthetic wastewater, about 87% of nitrate was reduced by co-denitrification of F. oxysporum and P. stutzeri after incubation for 6 days. In the further denitrification tests, the interaction of shell and mixed culture of F. oxysporum and P. stutzeri was investigated. The dinitrogen was rapidly evolved (442.48 micromol N2 produced from 1.0 mmol of NO3(-) in 36 h). These results clearly showed that shell provide a suitable microenvironment for P. stutzeri, which is beneficial to the denitrification.

Dissimilatory nitrate reduction metabolisms and their control in fungi

Most fungi grow under aerobic conditions by generating ATP through oxygen respiration. However, they alternatively express two pathways of dissimilatory nitrate reduction in response to environmental oxygen tension when the oxygen supply is insufficient. The fungus Fusarium oxysporum expressed the pathway of respiratory nitrate denitrification that is catalyzed by the sequential reactions of nitrate reductase and nitrite reductase. These enzymes are coupled with ATP generation through the respiratory chain and produce nitric oxide. Fungal nitric oxide reductase uses NADH as the direct electron donor in contrast to bacterial systems and thus might function in regeneration of NAD+ and detoxification of the toxic radical, nitric oxide. Another pathway of nitrate dissimilation by fungi reduces nitrate to ammonium and couples acetogenic reaction with substrate-level phosphorylation. This metabolic mechanism is also in feature of a variety of fungi and it is called ammonia fermentation. Thus, fungi adapt to various aerated conditions using these pathways of nitrate dissimilation in addition to conventional oxygen respiration.

Study ofTrichoderma viridemetabolism under conditions of the restriction of oxidative processes

Trichoderma viride was capable of growth and conidiation in the presence of high concentrations of the uncoupler 3,3′,4′,5-tetrachlorosalicylanilide (up to 100 µmol·L–1) and of the respiration inhibitor mucidin (up to 100 µmol·L–1) in both submerged and surface cultivation. When vegetative mycelia were cultivated on the solid Czapek-Dox medium with yeast autolysate under an anaerobic and CO2-containing atmosphere, the growth was observed only rarely but the microorganism survived as long as 3 months under these conditions. Major products of metabolism of both aerobic and anaerobic submerged mycelia were identified by means of1H-NMR measurements. Major products excreted to the medium under aerobic conditions were succinic and citric acids. Major metabolites present in the submerged mycelia were γ-aminobutyric (and glutamic) acid and alanine. Under anaerobic conditions, citric acid was not excreted into the medium but ethanol appeared. Its production could not be increased upon increasing the sugar concentration. The appearance of secondary metabolites was found to be modified by oxygen availability during the mycelial growth. Results suggest that the vegetative form of T. viride is capable of fermentative metabolism characterized by the production of ethanol and succinate and that the excretion of carboxylic acids is developmentally regulated and modified by oxygen availability.Key words: Trichoderma, mycelia, anaerobiosis, citrate, succinate, ethanol, GABA.

Nitrous oxide-forming codenitrification catalyzed by cytochrome P450nor

Intact cells of the denitrifying fungus Fusarium oxysporum were previously shown to catalyze codenitrification to form a hybrid nitrous oxide (N2O) species from nitrite and other nitrogen compounds such as azide and ammonia. Here we show that cytochrome P450nor can catalyze the codenitrification reaction to form N2O from nitric oxide (NO) but not nitrite, and azide or ammonia. The results show that the direct substrate of the codenitrification by intact cells should not be nitrite but NO, which is formed from nitrite by the reaction of a dissimilatory nitrite reductase.

Structural evidence for direct hydride transfer from NADH to cytochrome P450nor

Nitric oxide reductase cytochrome P450nor catalyzes an unusual reaction, direct electron transfer from NAD(P)H to bound heme. Here, we succeeded in determining the crystal structure of P450nor in a complex with an NADH analogue, nicotinic acid adenine dinucleotide, which provides conclusive evidence for the mechanism of the unprecedented electron transfer. Comparison of the structure with those of dinucleotide-free forms revealed a global conformational change accompanied by intriguing local movements caused by the binding of the pyridine nucleotide. Arg64 and Arg174 fix the pyrophosphate moiety upon the dinucleotide binding. Stereo-selective hydride transfer from NADH to NO-bound heme was suggested from the structure, the nicotinic acid ring being fixed near the heme by the conserved Thr residue in the I-helix and the upward-shifted propionate side-chain of the heme. A proton channel near the NADH channel is formed upon the dinucleotide binding, which should direct continuous transfer of the hydride and proton. A salt-bridge network (Glu71-Arg64-Asp88) was shown to be crucial for a high catalytic turnover.

D88A mutant of cytochrome P450nor provides kinetic evidence for direct complex formation with electron donor NADH

The haem-distal pocket of nitric oxide reductase cytochrome P450 contains many Arg and Lys residues that are clustered to form a putative access channel for NADH. Asp88 is the sole negatively charged amino acid in this positive charge cluster, and thus it would be interesting to know its functional role. Here we found the intriguing phenomenon that mutation at this site of P450nor (D88A or D88V) considerably decreased the overall nitric oxide reductase activity without blocking the reducing half reaction in which the ferric enzyme-NO complex is reduced with NADH to yield a specific intermediate (I). The results indicate that the catalytic turnover subsequent to the I formation was blocked by such mutation. This property of the mutants made it possible to perform kinetic analysis of the reduction step, which is impossible with the wild-type P450nor. These results are the first kinetic evidence for direct complex formation between P450nor and an electron donor (NADH or NADPH). The kinetic analysis also showed that the inhibition by chloride ions (Cl(-)) is competitive with respect to NAD(P)H, which highlights the importance of the binding site for Cl(-) (the anion hole) in the interaction with NAD(P)H. We also characterized another mutant (D393A) of P450nor. The results demonstrated that both Asp residues play important roles in the interaction with NADH, whereas the role of Asp88 is unique in that it must be essential for the release of NAD(+) rather than binding to NADH.

A possible role of NADPH-dependent cytochrome P450nor isozyme in glycolysis under denitrifying conditions

The denitrifying fungus Cylindrocarpon tonkinense contains two isozymes of cytochrome P450nor. One isozyme, P450nor1, uses NADH specifically as its electron donor whereas the other isozyme P450nor2 prefers NADPH to NADH. Here we show that P450nor1 is localized in both cytosol and mitochondria, like P450nor of Fusarium oxysporum, while P450nor2 is exclusively in cytosol. We also found that the addition of glucose as a carbon source to the culture media leads to the production of much more P450nor2 in the fungal cells than a non-fermentable substrate (glycerol or acetate) does. These results suggest that the NADP-dependent pentose phosphate cycle acts predominantly in C. tonkinense as the glycolysis pathway under the denitrifying conditions, which was confirmed by the observation that glucose induced enzyme activities involved in the cycle. These results showed that P450nor2 should act as the electron sink under anaerobic, denitrifying conditions to regenerate NADP+ for the pentose phosphate cycle.

Denitrification of nitrate by the fungus Cylindrocarpon tonkinense

The denitrifying fungus Cylindrocarpon tonkinense was thought to be able to denitrify only nitrite (NO2-) but not nitrate (NO3-) to form nitrous oxide (N2O). Here we found, however, that C. tonkinense can denitrify NO3- under certain conditions. Presence of ammonium (NH3+) in addition to NO3- and the use of a fermentable sugar as an electron donor were key conditions for inducing the denitrifying activity. Such induction accompanied a remarkable increase in the intracellular level of the enzyme activities related to NO3- metabolism. These activities contained assimilatory type NADPH (or NADH)-dependent NO3- reductase (aNar), dissimilatory nitrite reductase (dNir), and nitric oxide reductase (P450nor), but did not contain ubiquinol-dependent, dissimilatory NO3- reductase (dNar). The denitrification was inhibited by tungstate, an inhibitor of Nar. These results demonstrated occurrence of a novel type of denitrification in C. tonkinense, in which assimilatory type Nar is possibly involved.

Formate-forming fungal catabolic pathway to supply electrons to nitrate respiration

Pyruvate was catabolized anaerobically by resting cells of Fusarium oxysporum to form formate and acetate. Addition of nitrate decreased the accumulation of formate in the medium with concomitant formation of nitrite and N2O. The results suggested a unique metabolic pathway that occurs in fungi mediated by pyruvate-formate lyase to supply electrons via formate to fungal denitrification.

The B' helix determines cytochrome P450nor specificity for the electron donors NADH and NADPH

Nitric oxide reductase (Nor) cytochrome P450nor (P450nor) is unique because it is catalytically self-sufficient, receiving electrons directly from NADH or NADPH. However, little is known about the direct binding of NADH to cytochrome. Here, we report that oxidized pyridine nucleotides (NAD(+) and NADP(+)) and an analogue induce a spectral perturbation in bound heme when mixed with P450nor. The P450nor isoforms are classified according to electron donor specificity for NADH or NADPH. One type (Fnor, a P450nor of Fusarium oxysporum) utilizes only NADH. We found that NAD(+) induced a type I spectral change in Fnor, whereas NADP(+) induced a reverse type I spectral change, although the K(d) values for both were comparable. In contrast, NADP(+) as well as NAD(+) caused a type I spectral change in Tnor, a P450nor isozyme from Trichosporon cutaneum that utilizes both NADH and NADPH as electron donors. The B' helix region of Tnor ((73)SAGGKAAA(80)) contains some Ala and Gly residues, whereas the sequence is replaced at a few sites with more bulky amino acid residues in Fnor ((73)SASGKQAA(80)). A single mutation (S75G) significantly improved the NADPH- dependent Nor activity of Fnor, and the overall activity was accelerated via the NADPH-enhanced reduction step. These results showed that pyridine nucleotide cofactors can bind P450nor and that only a few residues in the B' helix region determine cofactor specificity. We further showed that a poor electron donor (NADPH) could also bind Fnor, but an appropriate configuration for electron transfer is blocked by steric hindrance mainly by Ser(75) against the 2'-phosphate moiety. The present results along with previous observations together revealed a novel motif for cofactor binding.

Codenitrification and denitrification are dual metabolic pathways through which dinitrogen evolves from nitrate in Streptomyces antibioticus

We screened actinomycete strains for dinitrogen (N(2))-producing activity and discovered that Streptomyces antibioticus B-546 evolves N(2) and some nitrous oxide (N(2)O) from nitrate (NO(3)(-)). Most of the N(2) that evolved from the heavy isotope ([(15)N]NO(3)(-)) was (15)N(14)N, indicating that this nitrogen species consists of two atoms, one arising from NO(3)(-) and the other from different sources. This phenomenon is similar to codenitrification in fungi. The strain also evolved less, but significant, amounts of (15)N(15)N from [(15)N]NO(3)(-) in addition to (15)N(15)NO with concomitant cell growth. Prior to the production of N(2) and N(2)O, NO(3)(-) was rapidly reduced to nitrite (NO(2)(-)) accompanied by distinct cell growth, showing that the actinomycete strain is a facultative anaerobe that depends on denitrification and nitrate respiration for anoxic growth. The cell-free activities of denitrifying enzymes could be reconstituted, supporting the notion that the (15)N(15)N and (15)N(15)NO species are produced by denitrification from NO(3)(-) via NO(2)(-). We therefore demonstrated a unique system in an actinomycete that produces gaseous nitrogen (N(2) and N(2)O) through both denitrification and codenitrification. The predominance of codenitrification over denitrification along with oxygen tolerance is the key feature of nitrate metabolism in this actinomycete.

Purification and cDNA cloning of nitric oxide reductase cytochrome P450nor (CYP55A4) from Trichosporon cutaneum

Cytochrome P450nor is involved in fungal denitrification as nitric oxide (NO) reductase. Although the heme protein has been known to occur in restricted species of fungi that belong to ascomycotina, we have previously suggested that it would also occur in the yeast Trichosporon cutaneum, which is phylogenetically far from those P450nor-producing ascomycetous fungi. Here we isolated and characterized the heme protein from the basidiomycetous yeast T. cutaneum. P450nor of the yeast (TcP450nor) exhibited properties in terms of catalysis, absorption spectrum and molecular mass that are almost identical to those of its counterparts in ascomycetous fungi. We also isolated and sequenced its cDNA. The predicted primary structure of TcP450nor showed high sequence identities (around 65%) to those of other P450nors, indicating that they belong to the same family. TcP450nor protein cofractionated with cytochrome c oxidase by subcellular fractionation and its predicted primary structure contained an extension on its amino terminus that is characteristic of a mitochondrial-targeting signal, indicating that it is a mitochondrial protein like some of the isoforms of other fungi. On the other hand, TcP450nor was unique in that inducers such as nitrate, nitrite, or NO were not required for its production in the cells. The occurrence of P450nor across the subdivisions of eumycota suggests that P450nor and denitrification are distributed more universally among fungi than was previously thought.

Purification of a soluble cytochrome P450 from Trichosporon montevideense

The yeast Trichosporon montevideense CBS 6721 expressed large amounts of cytochrome P450 after cultivation in a glucose-peptone medium. The P450, which could be detected in the cytosolic fraction after cell breakage and ultracentrifugation, was purified to electrophoretic homogeneity and migrated in SDS-PAGE with a M(r) of 43,000. As indicated by IEF, the preparation consisted of two different P450 isoforms with pI-values of 5.9 and 6.2, which were named P450MS1 and P450MS2 respectively. Both isoforms had a characteristic maximum at 446 nm in the reduced carbon monoxide difference spectra. Partial N-terminal sequencing of P450MS1 and P450MS2 demonstrated a high degree of sequence homology between the soluble P450 enzymes of T. montevideense CBS 6721 and their close relationship to the soluble P450 forms of Trichosporon spec. SBUG 752, T. cutaneum ATCC 58094 and to the P450s of the CYP55 family of Fusarium oxysporum and Cylindrocarpon tonkinense.