Rieske business: structure-function of Rieske non-heme oxygenases

Model of the MitoNEET [2Fe-2S] Cluster Shows Proton Coupled Electron Transfer

MitoNEET is an outer membrane protein whose exact function remains unclear, though a role of this protein in redox and iron sensing as well as in controlling maximum mitochondrial respiratory rates has been discussed. It was shown to contain a redox active and acid labile [2Fe-2S] cluster which is ligated by one histidine and three cysteine residues. Herein we present the first synthetic analogue with biomimetic {SN/S2} ligation which could be structurally characterized in its diferric form, 52-. In addition to being a high fidelity structural model for the biological cofactor, the complex is shown to mediate proton coupled electron transfer (PCET) at the {SN} ligated site, pointing at a potential functional role of the enzyme's unique His ligand. Full PCET thermodynamic square schemes for the mitoNEET model 52- and a related homoleptic {SN/SN} capped [2Fe-2S] cluster 42- are established, and kinetics of PCET reactivity are investigated by double-mixing stopped-flow experiments for both complexes. While the N-H bond dissociation free energy (BDFE) of 5H2- (230 ± 4 kJ mol-1) and the free energy ΔG°PCET for the reaction with TEMPO (-48.4 kJ mol-1) are very similar to values for the homoleptic cluster 4H2- (232 ± 4 kJ mol-1, -46.3 kJ mol-1) the latter is found to react significantly faster than the mitoNEET model (data for 5H2-: k = 135 ± 27 M-1 s-1, ΔH‡ = 17.6 ± 3.0 kJ mol-1, ΔS‡ = -143 ± 11 J mol-1 K-1, and ΔG‡ = 59.8 kJ mol-1 at 293 K). Comparison of the PCET efficiency of these clusters emphasizes the relevance of reorganization energy in this process.

Dioxygen activation by nonheme iron enzymes with the 2-His-1-carboxylate facial triad that generate high-valent oxoiron oxidants

The 2-His-1-carboxylate facial triad is a widely used scaffold to bind the iron center in mononuclear nonheme iron enzymes for activating dioxygen in a variety of oxidative transformations of metabolic significance. Since the 1990s, over a hundred different iron enzymes have been identified to use this platform. This structural motif consists of two histidines and the side chain carboxylate of an aspartate or a glutamate arranged in a facial array that binds iron(II) at the active site. This triad occupies one face of an iron-centered octahedron and makes the opposite face available for the coordination of O₂ and, in many cases, substrate, allowing the tailoring of the iron-dioxygen chemistry to carry out a plethora of diverse reactions. Activated dioxygen-derived species involved in the enzyme mechanisms include iron(III)-superoxo, iron(III)-peroxo, and high-valent iron(IV)-oxo intermediates. In this article, we highlight the major crystallographic, spectroscopic, and mechanistic advances of the past 20 years that have significantly enhanced our understanding of the mechanisms of O₂ activation and the key roles played by iron-based oxidants.

Biochemical and Genetic Bases of Indole-3-Acetic Acid (Auxin Phytohormone) Degradation by the Plant-Growth-Promoting Rhizobacterium Paraburkholderia phytofirmans PsJN

Several bacteria use the plant hormone indole-3-acetic acid (IAA) as a sole carbon and energy source. A cluster of genes (named iac) encoding IAA degradation has been reported in Pseudomonas putida 1290, but the functions of these genes are not completely understood. The plant-growth-promoting rhizobacterium Paraburkholderia phytofirmans PsJN harbors iac gene homologues in its genome, but with a different gene organization and context than those of P. putida 1290. The iac gene functions enable P. phytofirmans to use IAA as a sole carbon and energy source. Employing a heterologous expression system approach, P. phytofirmans iac genes with previously undescribed functions were associated with specific biochemical steps. In addition, two uncharacterized genes, previously unreported in P. putida and found to be related to major facilitator and tautomerase superfamilies, are involved in removal of an IAA metabolite called dioxindole-3-acetate. Similar to the case in strain 1290, IAA degradation proceeds through catechol as intermediate, which is subsequently degraded by ortho-ring cleavage. A putative two-component regulatory system and a LysR-type regulator, which apparently respond to IAA and dioxindole-3-acetate, respectively, are involved in iac gene regulation in P. phytofirmans These results provide new insights about unknown gene functions and complex regulatory mechanisms in IAA bacterial catabolism.

IMPORTANCE

This study describes indole-3-acetic acid (auxin phytohormone) degradation in the well-known betaproteobacterium P. phytofirmans PsJN and comprises a complete description of genes, some of them with previously unreported functions, and the general basis of their gene regulation. This work contributes to the understanding of how beneficial bacteria interact with plants, helping them to grow and/or to resist environmental stresses, through a complex set of molecular signals, in this case through degradation of a highly relevant plant hormone.

Distinguishing the Protonation State of the Histidine Ligand to the Oxidized Iron-Sulfur Cluster from the MitoNEET Family of Proteins

The iron-sulfur cluster located in the recently discovered human mitoNEET protein (and related proteins) is structurally similar to the more well-known ferredoxin and Rieske clusters. Although its biological function is uncertain, the iron-sulfur cluster in mitoNEET has been proposed to undergo proton-coupled electron transfer involving the histidine ligand to the cluster. The cluster is also released from the protein at low pH. This contribution reports density functional calculations to model the structures, vibrations, and Heisenberg coupling constants (J) for high-spin (HS), broken symmetry (BS) singlet, and extended broken symmetry (EBS) singlet states of the oxidized iron-sulfur cluster from mitoNEET. This work suggests that J values or ¹⁵ N isotopic frequency shifts may provide methods for determining experimentally whether the histidine ligand to the oxidized iron-sulfur cluster in human mitoNEET and mitoNEET-related proteins is protonated or deprotonated.

O2 Activation by Non-Heme Iron Enzymes

The non-heme Fe enzymes are ubiquitous in nature and perform a wide range of functions involving O₂ activation. These had been difficult to study relative to heme enzymes; however, spectroscopic methods that provide significant insight into the correlation of structure with function have now been developed. This Current Topics article summarizes both the molecular mechanism these enzymes use to control O₂ activation in the presence of cosubstrates and the oxygen intermediates these reactions generate. Three types of O₂ activation are observed. First, non-heme reactivity is shown to be different from heme chemistry where a low-spin Fe^III-OOH non-heme intermediate directly reacts with substrate. Also, two subclasses of non-heme Fe enzymes generate high-spin Fe^IV═O intermediates that provide both σ and π frontier molecular orbitals that can control selectivity. Finally, for several subclasses of non-heme Fe enzymes, binding of the substrate to the Fe^II site leads to the one-electron reductive activation of O₂ to an Fe^III-superoxide capable of H atom abstraction and electrophilic attack.

Safety assessment of dicamba mono-oxygenases that confer dicamba tolerance to various crops

Dicamba tolerant (DT) soybean, cotton and maize were developed through constitutive expression of dicamba mono-oxygenase (DMO) in chloroplasts. DMO expressed in three DT crops exhibit 91.6-97.1% amino acid sequence identity to wild type DMO. All DMO forms maintain the characteristics of Rieske oxygenases that have a history of safe use. Additionally, they are all functionally similar in vivo since the three DT crops are all tolerant to dicamba treatment. None of these DMO sequences were found to have similarity to any known allergens or toxins. Herein, to further understand the safety of these DMO variants, a weight of evidence approach was employed. Each purified DMO protein was found to be completely deactivated in vitro by heating at temperatures 55 °C and above, and all were completely digested within 30 s or 5 min by pepsin and pancreatin, respectively. Mice orally dosed with each of these DMO proteins showed no adverse effects as evidenced by analysis of body weight gain, food consumption and clinical observations. Therefore, the weight of evidence from all these protein safety studies support the conclusion that the various forms of DMO proteins introduced into DT soybean, cotton and maize are safe for food and feed consumption, and the small amino acid sequence differences outside the active site of DMO do not raise any additional safety concerns.

Electron Transport in a Dioxygenase-Ferredoxin Complex: Long Range Charge Coupling between the Rieske and Non-Heme Iron Center

Dioxygenase (dOx) utilizes stereospecific oxidation on aromatic molecules; consequently, dOx has potential applications in bioremediation and stereospecific oxidation synthesis. The reactive components of dOx comprise a Rieske structure Cys₂[2Fe-2S]His₂ and a non-heme reactive oxygen center (ROC). Between the Rieske structure and the ROC, a universally conserved Asp residue appears to bridge the two structures forming a Rieske-Asp-ROC triad, where the Asp is known to be essential for electron transfer processes. The Rieske and ROC share hydrogen bonds with Asp through their His ligands; suggesting an ideal network for electron transfer via the carboxyl side chain of Asp. Associated with the dOx is an itinerant charge carrying protein Ferredoxin (Fdx). Depending on the specific cognate, Fdx may also possess either the Rieske structure or a related structure known as 4-Cys-[2Fe-2S] (4-Cys). In this study, we extensively explore, at different levels of theory, the behavior of the individual components (Rieske and ROC) and their interaction together via the Asp using a variety of density function methods, basis sets, and a method known as Generalized Ionic Fragment Approach (GIFA) that permits setting up spin configurations manually. We also report results on the 4-Cys structure for comparison. The individual optimized structures are compared with observed spectroscopic data from the Rieske, 4-Cys and ROC structures (where information is available). The separate pieces are then combined together into a large Rieske-Asp-ROC (donor/bridge/acceptor) complex to estimate the overall coupling between individual components, based on changes to the partial charges. The results suggest that the partial charges are significantly altered when Asp bridges the Rieske and the ROC; hence, long range coupling through hydrogen bonding effects via the intercalated Asp bridge can drastically affect the partial charge distributions compared to the individual isolated structures. The results are consistent with a proton coupled electron transfer mechanism.

Cyclization of polyketides and non-ribosomal peptides on and off their assembly lines

Modular polyketide synthases (PKSs) and non-ribosomal peptide synthetases (NRPSs) are multifunctional megaenzymes that serve as templates to program the assembly of short carboxylic acids and amino acids in a primarily co-linear manner. The variation, combination, permutation and evolution of their functional units (e.g., modules, domains and proteins) along with their association with external enzymes have resulted in the generation of numerous versions of templates, the roles of which have not been fully recognized in the structural diversification of polyketides, non-ribosomal peptides and their hybrids present in nature. In this Highlight, we focus on the assembly-line enzymology and associated chemistry by providing examples of some newly characterized cyclization reactions that occur on and off the assembly lines during and after chain elongation for the purpose of elucidating the template effects of PKSs and NRPSs. A fundamental understanding of the underlying biosynthetic logic would facilitate the elucidation of chemical information contained within the PKS or NRPS templates and benefit the development of strategies for genome mining, biosynthesis-inspired chemical synthesis and combinatorial biosynthesis.

Hydrogen Isotope Fractionation As a Tool to Identify Aerobic and Anaerobic PAH Biodegradation

Aerobic and anaerobic polycyclic aromatic hydrocarbon (PAH) biodegradation was characterized by compound specific stable isotope analysis (CSIA) of the carbon and hydrogen isotope effects of the enzymatic reactions initiating specific degradation pathways, using naphthalene and 2-methylnaphtalene as model compounds. Aerobic activation of naphthalene and 2-methylnaphthalene by Pseudomonas putida NCIB 9816 and Pseudomonas fluorescens ATCC 17483 containing naphthalene dioxygenases was associated with moderate carbon isotope fractionation (εC = -0.8 ± 0.1‰ to -1.6 ± 0.2‰). In contrast, anaerobic activation of naphthalene by a carboxylation-like mechanism by strain NaphS6 was linked to negligible carbon isotope fractionation (εC = -0.2 ± 0.2‰ to -0.4 ± 0.3‰). Notably, anaerobic activation of naphthalene by strain NaphS6 exhibited a normal hydrogen isotope fractionation (εH = -11 ± 2‰ to -47 ± 4‰), whereas an inverse hydrogen isotope fractionation was observed for the aerobic strains (εH = +15 ± 2‰ to +71 ± 6‰). Additionally, isotope fractionation of NaphS6 was determined in an overlaying hydrophobic carrier phase, resulting in more reliable enrichment factors compared to immobilizing the PAHs on the bottle walls without carrier phase. The observed differences especially in hydrogen fractionation might be used to differentiate between aerobic and anaerobic naphthalene and 2-methylnaphthalene biodegradation pathways at PAH-contaminated field sites.

Distinguishing Protonation States of Histidine Ligands to the Oxidized Rieske Iron-Sulfur Cluster through (15) N Vibrational Frequency Shifts

The Rieske [2Fe-2S] cluster is a vital component of many oxidoreductases, including mitochondrial cytochrome bc1; its chloroplast equivalent, cytochrome b6f; one class of dioxygenases; and arsenite oxidase. The Rieske cluster acts as an electron shuttle and its reduction is believed to couple with protonation of one of the cluster's His ligands. In cytochromes bc1 and b6f, for example, the Rieske cluster acts as the first electron acceptor in a modified Q cycle. The protonation states of the cluster's His ligands determine its ability to accept a proton and possibly an electron through a hydrogen bond to the electron carrier, ubiquinol. Experimental determination of the protonation states of a Rieske cluster's two His ligands by NMR spectroscopy is difficult, due to the close proximity of the two paramagnetic iron atoms of the cluster. Therefore, this work reports density functional calculations and proposes that difference vibrational spectroscopy with (15) N isotopic substitution may be used to assign the protonation states of the His ligands of the oxidized Rieske [2Fe-2S] complex.

Metabolic Pathways for Degradation of Aromatic Hydrocarbons by Bacteria

The aim of this review was to build an updated collection of information focused on the mechanisms and elements involved in metabolic pathways of aromatic hydrocarbons by bacteria. Enzymes as an expression of the genetic load and the type of electron acceptor available, as an environmental factor, were highlighted. In general, the review showed that both aerobic routes and anaerobic routes for the degradation of aromatic hydrocarbons are divided into two pathways. The first, named the upper pathways, entails the route from the original compound to central intermediate compounds still containing the aromatic ring but with the benzene nucleus chemically destabilized. The second, named the lower pathway, begins with ring de-aromatization and subsequent cleavage, resulting in metabolites that can be used by bacteria in the production of biomass. Under anaerobic conditions the five mechanisms of activation of the benzene ring described show the diversity of chemical reactions that can take place. Obtaining carbon and energy from an aromatic hydrocarbon molecule is a process that exhibits the high complexity level of the metabolic apparatus of anaerobic microorganisms. The ability of these bacteria to express enzymes that catalyze reactions, known only in non-biological conditions, using final electron acceptors with a low redox potential, is a most interesting topic. The discovery of phylogenetic and functional characteristics of cultivable and noncultivable hydrocarbon degrading bacteria has been made possible by improvements in molecular research techniques such as SIP (stable isotope probing) tracing the incorporation of (13)C, (15)N and (18)O into nucleic acids and proteins. Since many metabolic pathways in which enzyme and metabolite participants are still unknown, much new research is required. Therefore, it will surely allow enhancing the known and future applications in practice.

Rate-Determining Attack on Substrate Precedes Rieske Cluster Oxidation during Cis-Dihydroxylation by Benzoate Dioxygenase

Rieske dearomatizing dioxygenases utilize a Rieske iron-sulfur cluster and a mononuclear Fe(II) located 15 Å across a subunit boundary to catalyze O2-dependent formation of cis-dihydrodiol products from aromatic substrates. During catalysis, O2 binds to the Fe(II) while the substrate binds nearby. Single-turnover reactions have shown that one electron from each metal center is required for catalysis. This finding suggested that the reactive intermediate is Fe(III)-(H)peroxo or HO-Fe(V)═O formed by O-O bond scission. Surprisingly, several kinetic phases were observed during the single-turnover Rieske cluster oxidation. Here, the Rieske cluster oxidation and product formation steps of a single turnover of benzoate 1,2-dioxygenase are investigated using benzoate and three fluorinated analogues. It is shown that the rate constant for product formation correlates with the reciprocal relaxation time of only the fastest kinetic phase (RRT-1) for each substrate, suggesting that the slower phases are not mechanistically relevant. RRT-1 is strongly dependent on substrate type, suggesting a role for substrate in electron transfer from the Rieske cluster to the mononuclear iron site. This insight, together with the substrate and O2 concentration dependencies of RRT-1, indicates that a reactive species is formed after substrate and O2 binding but before electron transfer from the Rieske cluster. Computational studies show that RRT-1 is correlated with the electron density at the substrate carbon closest to the Fe(II), consistent with initial electrophilic attack by an Fe(III)-superoxo intermediate. The resulting Fe(III)-peroxo-aryl radical species would then readily accept an electron from the Rieske cluster to complete the cis-dihydroxylation reaction.

Oxidized and reduced [2Fe-2S] clusters from an iron(I) synthon

Synthetic [2Fe-2S] clusters are often used to elucidate ligand effects on the reduction potentials and spectroscopy of natural electron-transfer sites, which can have anionic Cys ligands or neutral His ligands. Current synthetic routes to [2Fe-2S] clusters are limited in their feasibility with a range of supporting ligands. Here, we report a new synthetic route to synthetic [2Fe-2S] clusters, through oxidation of an iron(I) source with elemental sulfur. This method yields a neutral diketiminate-supported [2Fe-2S] cluster in the diiron(III)-oxidized form. The oxidized [2Fe-2S] cluster can be reduced to a mixed valent iron(II)-iron(III) compound. Both the diferric and reduced mixed valent clusters are characterized using X-ray crystallography, Mössbauer spectroscopy, EPR spectroscopy and cyclic voltammetry. The reduced compound is particularly interesting because its X-ray crystal structure shows a difference in Fe-S bond lengths to one of the iron atoms, consistent with valence localization. The valence localization is also evident from Mössbauer spectroscopy.

Draft Genome Sequence of a Papaverine-Degrading, Gram-positive Arthrobacter sp., Isolated from Soil Near Hohenheim, Germany

We present the 4.8-Mb draft genome of a soil bacterium identified as Arthrobacter sp. This Gram-positive soil bacterium is able to use the aromatic compound papaverine as sole carbon source and will be examined for novel oxygenases.

Draft Genome Sequence of Phenylobacterium immobile Strain E (DSM 1986), Isolated from Uncontaminated Soil in Ecuador

We report the draft genome sequence of 3.3 Mb and the sequence (19.2 kb) of a natural plasmid isolated from Phenylobacterium immobile strain E (DSM 1986), able to degrade xenobiotic compounds as the sole carbon source. The sequences reveal a large number of novel Rieske nonheme iron aromatic ring-hydroxylating oxygenases (RHOs).

Re-evaluation of dioxygenase gene phylogeny for the development and validation of a quantitative assay for environmental aromatic hydrocarbon degraders

Rieske non-heme iron oxygenases enzymes have been widely studied, as they catalyse essential reactions initiating the bacterial degradation of organic compounds, for instance aromatic hydrocarbons. The genes encoding these enzymes offer a potential target for studying aromatic hydrocarbon-degrading organisms in the environment. However, previously reported primer sets that target dioxygenase gene sequences or the common conserved Rieske centre of aromatics dioxygenases have limited specificity and/or target non-dioxygenase genes. In this work, an extensive database of dioxygenase α-subunit gene sequences was constructed, and primer sets targeting the conserved Rieske centre were developed. The high specificity of the primers was confirmed by polymerase chain reaction analysis, agarose gel electrophoresis and sequencing. Quantitative polymerase chain reaction (qPCR) assays were also developed and optimized, following MIQE guidelines (Minimum Information for Publication of Quantitative Real-Time PCR Experiments). Comparison of the qPCR quantification of dioxygenases in spiked sediment samples and in pure cultures demonstrated an underestimation of the Ct value, and the requirement for a correction factor at gene abundances below 10⁸ gene copies per g of sediment. Externally validated qPCR provides a valuable tool to monitor aromatic hydrocarbon degrader population abundances at contaminated sites.

Our study aimed to re-evaluate the phylogeny of Rieske non-heme iron dioxygenases using only retrieved primary nucleic acid sequences for the development of quantitative real-time PCR primers.

Heterologous expression of galbonolide biosynthetic genes in Streptomyces coelicolor

The galbonolide antibiotics are non-glycosylated heptaketide 14-membered macrolides. These antibiotics exhibit broad-spectrum fungicidal activities, including against the human pathogen Cryptococcus neoformans. Previously, galbonolides B and E were isolated from the marine actinomycete Streptomyces sp. LZ35. By bioinformatics analysis, the putative galbonolide biosynthetic gene cluster, gbn, was identified in the genome of strain LZ35. In order to verify that the core genes (gbnA-E) are sufficient for synthesizing the basic structure of galbonolide as previously proposed, we performed the heterologous expression of gbnA-E in a "clean background" host Streptomyces coelicolor ZM12, in which all the native polyketide synthase genes have been deleted. As expected, the production of galbonolide B (1) was detected in the transformant. To the best of our knowledge, this is the first report that demonstrates the essential role of gbnA-E in the biosynthesis of galbonolides by heterologous expression. This heterologous expression system would be helpful to generate novel galbonolide derivatives by co-overexpression of unusual biosynthesis extender units.

Tuning the reactivity of Fe(V)(O) toward C-H bonds at room temperature: effect of water

The presence of an Fe(V)(O) species has been postulated as the active intermediate for the oxidation of both C-H and C═C bonds in the Rieske dioxygenase family of enzymes. Understanding the reactivity of these high valent iron-oxo intermediates, especially in an aqueous medium, would provide a better understanding of these enzymatic reaction mechanisms. The formation of an Fe(V)(O) complex at room temperature in an aqueous CH3CN mixture that contains up to 90% water using NaOCl as the oxidant is reported here. The stability of Fe(V)(O) decreases with increasing water concentration. We show that the reactivity of Fe(V)(O) toward the oxidation of C-H bonds, such as those in toluene, can be tuned by varying the amount of water in the H2O/CH3CN mixture. Rate acceleration of up to 60 times is observed for the oxidation of toluene upon increasing the water concentration. The role of water in accelerating the rate of the reaction has been studied using kinetic measurements, isotope labeling experiments, and density functional theory (DFT) calculations. A kinetic isotope effect of ∼13 was observed for the oxidation of toluene and d8-toluene showing that C-H abstraction was involved in the rate-determining step. Activation parameters determined for toluene oxidation in H2O/CH3CN mixtures on the basis of Eyring plots for the rate constants show a gain in enthalpy with a concomitant loss in entropy. This points to the formation of a more-ordered transition state involving water molecules. To further understand the role of water, we performed a careful DFT study, concentrating mostly on the rate-determining hydrogen abstraction step. The DFT-optimized structure of the starting Fe(V)(O) and the transition state indicates that the rate enhancement is due to the transition state's favored stabilization over the reactant due to enhanced hydrogen bonding with water.

Unexpected roles for ancient proteins: flavone 8-hydroxylase in sweet basil trichomes is a Rieske-type, PAO-family oxygenase

Most elucidated hydroxylations in plant secondary metabolism are catalyzed by oxoglutarate- or cytochrome P450-dependent oxygenases. Numerous hydroxylations still evade clarification, suggesting that they might be performed by alternative enzyme types. Here, we report the identification of the flavone 8-hydroxylase (F8H) in sweet basil (Ocimum basilicum L.) trichomes as a Rieske-type oxygenase. Several features of the F8H activity in trichome protein extracts helped to differentiate it from a cytochrome P450-catalyzed reaction and identify candidate genes in the basil trichome EST database. The encoded ObF8H proteins share approximately 50% identity with Rieske-type protochlorophyllide a oxygenases (PTC52) from higher plants. Homology cloning and DNA blotting revealed the presence of several PTC52-like genes in the basil genome. The transcripts of the candidate gene designated ObF8H-1 are strongly enriched in trichomes compared to whole young leaves, indicating trichome-specific expression. The full-length ObF8H-1 protein possesses a predicted N-terminal transit peptide, which directs green fluorescent protein at least in part to chloroplasts. The F8H activity in crude trichome protein extracts correlates well with the abundance of ObF8H peptides. The purified recombinant ObF8H-1 displays high affinity for salvigenin and is inactive with other tested flavones except cirsimaritin, which is 8-hydroxylated with less than 0.2% relative activity. The efficiency of in vivo 8-hydroxylation by engineered yeast was improved by manipulation of protein subcellular targeting. blast searches showed that occurrence of several PTC52-like genes is rather common in sequenced plant genomes. The discovery of ObF8H suggests that Rieske-type oxygenases may represent overlooked candidate catalysts for oxygenations in specialized plant metabolism.

Structure-function analysis of NEET proteins uncovers their role as key regulators of iron and ROS homeostasis in health and disease

A novel family of 2Fe-2S proteins, the NEET family, was discovered during the last decade in numerous organisms, including archea, bacteria, algae, plant and human; suggesting an evolutionary-conserved function, potentially mediated by their CDGSH Iron-Sulfur Domain. In human, three NEET members encoded by the CISD1-3 genes were identified. The structures of CISD1 (mitoNEET, mNT), CISD2 (NAF-1), and the plant At-NEET uncovered a homodimer with a unique "NEET fold", as well as two distinct domains: a beta-cap and a 2Fe-2S cluster-binding domain. The 2Fe-2S clusters of NEET proteins were found to be coordinated by a novel 3Cys:1His structure that is relatively labile compared to other 2Fe-2S proteins and is the reason of the NEETs' clusters could be transferred to apo-acceptor protein(s) or mitochondria. Positioned at the protein surface, the NEET's 2Fe-2S's coordinating His is exposed to protonation upon changes in its environment, potentially suggesting a sensing function for this residue. Studies in different model systems demonstrated a role for NAF-1 and mNT in the regulation of cellular iron, calcium and ROS homeostasis, and uncovered a key role for NEET proteins in critical processes, such as cancer cell proliferation and tumor growth, lipid and glucose homeostasis in obesity and diabetes, control of autophagy, longevity in mice, and senescence in plants. Abnormal regulation of NEET proteins was consequently found to result in multiple health conditions, and aberrant splicing of NAF-1 was found to be a causative of the neurological genetic disorder Wolfram Syndrome 2. Here we review the discovery of NEET proteins, their structural, biochemical and biophysical characterization, and their most recent structure-function analyses. We additionally highlight future avenues of research focused on NEET proteins and propose an essential role for NEETs in health and disease. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.

Metabolic engineering of Arabidopsis for remediation of different polycyclic aromatic hydrocarbons using a hybrid bacterial dioxygenase complex

The widespread presence of polycyclic aromatic hydrocarbons (PAHs) and their potential harm to various organisms has generated interest in efficiently eliminating these compounds from the environment. Phytoremediation is an efficient technology for cleaning up pollutants. However, unlike microorganisms, plants lack the catabolic pathway for complete degradation of these dangerous groups of compounds. One way to enhance the potential of plants for remediation of these compounds is by transferring genes involved in xenobiotic degradation from microbes to plants. In this paper, four genes, namely nidA and nidB (encoding the large and small subunits of naphthalene dioxygenase of Mycobacterium vanbaalenii PYR-1) as well as NahAa and NahAb (encoding flavoprotein reductase and ferredoxin of the electron-transport chain of the Pseudomonas putida G7 naphthalene dioxygenase system), were transferred and ectopically expressed in Arabidopsis thaliana. Transgenic Arabidopsis plants overexpressing the heterozygous naphthalene dioxygenase system exhibited enhanced tolerance toward 2-4 rings PAHs. Transgenic plants assimilated PAHs from the culture media faster and accumulated less in vivo than wild-type plants. Furthermore, examination of metabolic intermediates by gas chromatography-mass spectrometry revealed that the naphthalene metabolic pathway in transgenic plants mainly involves the dioxygenase pathway. Taken together, our findings suggest that grafting the naphthalene dioxygenase complex into plants is a possible strategy to breed PAH-tolerant plants to efficiently degrade PAHs in the environment.

Substrate specificities and conformational flexibility of 3-ketosteroid 9α-hydroxylases

KshA is the oxygenase component of 3-ketosteroid 9α-hydroxylase, a Rieske oxygenase involved in the bacterial degradation of steroids. Consistent with its role in bile acid catabolism, KshA1 from Rhodococcus rhodochrous DSM43269 had the highest apparent specificity (kcat/Km) for steroids with an isopropyl side chain at C17, such as 3-oxo-23,24-bisnorcholesta-1,4-diene-22-oate (1,4-BNC). By contrast, the KshA5 homolog had the highest apparent specificity for substrates with no C17 side chain (kcat/Km >10(5) s(-1) M(-1) for 4-estrendione, 5α-androstandione, and testosterone). Unexpectedly, substrates such as 4-androstene-3,17-dione (ADD) and 4-BNC displayed strong substrate inhibition (Ki S ∼100 μM). By comparison, the cholesterol-degrading KshAMtb from Mycobacterium tuberculosis had the highest specificity for CoA-thioesterified substrates. These specificities are consistent with differences in the catabolism of cholesterol and bile acids, respectively, in actinobacteria. X-ray crystallographic structures of the KshAMtb·ADD, KshA1·1,4-BNC-CoA, KshA5·ADD, and KshA5·1,4-BNC-CoA complexes revealed that the enzymes have very similar steroid-binding pockets with the substrate's C17 oriented toward the active site opening. Comparisons suggest Tyr-245 and Phe-297 are determinants of KshA1 specificity. All enzymes have a flexible 16-residue "mouth loop," which in some structures completely occluded the substrate-binding pocket from the bulk solvent. Remarkably, the catalytic iron and α-helices harboring its ligands were displaced up to 4.4 Å in the KshA5·substrate complexes as compared with substrate-free KshA, suggesting that Rieske oxygenases may have a dynamic nature similar to cytochrome P450.

Molecular Dynamics Simulation of Nitrobenzene Dioxygenase Using AMBER Force Field

Molecular dynamics simulation of the oxygenase component of nitrobenzene dioxygenase (NBDO) system, a member of the naphthalene family of Rieske nonheme iron dioxygenases, has been carried out using the AMBER force field combined with a new set of parameters for the description of the mononuclear nonheme iron center and iron-sulfur Rieske cluster. Simulation results provide information on the structure and dynamics of nitrobenzene dioxygenase in an aqueous environment and shed light on specific interactions that occur in its catalytic center. The results suggest that the architecture of the active site is stabilized by key hydrogen bonds, and Asn258 positions the substrate for oxidation. Analysis of protein-water interactions reveal the presence of a network of solvent molecules at the entrance to the active site, which could be of potential catalytic importance.

Characterization and genetic analyses of a carbazole-degrading gram-positive marine isolate, Janibacter sp. strain OC11

Strain OC11 was isolated from seawater sampled at the coast of Chiba, Japan, in artificial seawater medium with carbazole (CAR) as the sole carbon source. Its 16S ribosomal RNA gene sequence suggested that strain OC11 belongs to the genus Janibacter. The CAR-degradation genes (car genes) of strain OC11 were PCR amplified, using degenerate primers designed based on the car gene sequences of other CAR-degrading bacteria. Complete nucleotide sequences encoding six complete open reading frames were determined, and the first known ferredoxin reductase gene (carAd) was found from a CAR-degrading bacterium isolated from the marine environment. An experiment using a mutant strain suggested that the car genes of strain OC11 are functional in CAR degradation. Southern hybridization indicated that strain OC11 had one car gene cluster in vivo. RT-PCR revealed that transcription of carOC11 constitutes an operon.

Gentisate 1,2-Dioxygenase fromXanthobacter polyaromaticivorans127W

A putative gentisate 1,2-dioxygenase was encoded in the dibenzothiophene degradation gene cluster (dbd) from Xanthobacter polyaromaticivorans 127W. The deduced amino acid sequence showed high sequence similarity with gentisate dioxygenases from Pseudomonas alcaligenes (AAD49427, 65% identical), Bradyrhizobium japonicum (NP_766750, 64%), and P. aeruginosa (ZP_00135722, 54%), and moderate similarity with 1-hydroxy-2-naphthoate dioxygenase from Nocardioides sp. KP7 (BAA31235, 33%) and salicylate dioxygenase from Pseudaminobacter salicylatoxidans (AAQ91293, 33%). The enzyme, GDOxp, was heterologously produced in Escherichia coli and purified to homogeneity. GDOxp formed a tetramer and exhibited high dioxygenase activity against 1,4-dihydroxy 2-naphthoate as well as gentisate, suggesting unusually broad substrate specificity. GDOxp easily released ferrous ion under unfavorable temperature and pH conditions to become an inactive monomer protein. An inactive monomer protein can reconstitute a tetramer structure and restore enzyme activity in a cooperative manner upon the addition of ferrous ion. Chymotryptic digestion and protein truncation experiments suggested that the N-terminal region is important for the tetramerization of GDOxp.

3-Ketosteroid 9α-hydroxylase enzymes: Rieske non-heme monooxygenases essential for bacterial steroid degradation

Various micro-organisms are able to use sterols/steroids as carbon- and energy sources for growth. 3-Ketosteroid 9α-hydroxylase (KSH), a two component Rieske non-heme monooxygenase comprised of the oxygenase KshA and the reductase KshB, is a key-enzyme in bacterial steroid degradation. It initiates opening of the steroid polycyclic ring structure. The enzyme has industrial relevance in the synthesis of pharmaceutical steroids. Deletion of KSH activity in sterol degrading bacteria results in blockage of steroid ring opening and is used to produce valuable C19-steroids such as 4-androstene-3,17-dione and 1,4-androstadiene-3,17-dione. Interestingly, KSH activity is essential for the pathogenicity of Mycobacterium tuberculosis. Detailed information about KSH thus is of medical relevance, and KSH inhibitory compounds may find application in combatting tuberculosis. In recent years, the 3D structure of the KshA protein of M. tuberculosis H37Rv has been elucidated and various studies report biochemical characteristics and possible physiological roles of KSH. The current knowledge is reviewed here and forms a solid basis for further studies on this highly interesting enzyme. Future work may result in the construction of KSH mutants capable of production of specific bioactive steroids. Furthermore, KSH provides an promising target for drugs against the pathogenic agent M. tuberculosis.

A DFT study of the cis-dihydroxylation of nitroaromatic compounds catalyzed by nitrobenzene dioxygenase

The mechanism of cis-dihydroxylation of nitrobenzene and 2-nitrotoluene catalyzed by nitrobenzene 1,2-dioxygenase (NBDO), a member of the naphthalene family of Rieske non-heme iron dioxygenases, was studied by means of the density functional theory method using four models of the enzyme active site. Different possible reaction pathways for the substrate dioxygenation initiated either by the Fe^III–OOH or HO–Fe^V=O attack on the aromatic ring were considered and the computed activation barriers compared with the Gibbs free energy of activation for the oxygen–oxygen cleavage leading to the formation of the iron(V)–oxo species from its ferric hydroperoxo precursor. The mechanism of the substrate cis-dihydroxylation leading to the formation of a cis-dihydrodiol was then investigated, and the most feasible mechanism was found to be starting with the attack of the high-valent iron–oxo species on the substrate ring yielding a radical intermediate, which further evolves toward the final product.

Electron transfer and proton-coupled electron transfer reactivity and self-exchange of synthetic [2Fe-2S] complexes: models for Rieske and mitoNEET clusters

This report describes the thermochemistry, proton-coupled electron transfer (PCET) reactions and self-exchange rate constants for a set of bis-benzimidazolate-ligated [2Fe–2S] clusters. These clusters serve as a model for the chemistry of biological Rieske and mitoNEET clusters. PCET from [Fe₂S₂(^Prbbim)(^PrbbimH)]^2– (4) and [Fe₂S₂(^Prbbim)(^PrbbimH₂)]^1– (5) to TEMPO occurs via concerted proton–electron transfer (CPET) mechanisms (^PrbbimH₂ = 4,4-bis-(benzimidazol-2-yl)heptane). Intermolecular electron transfer (ET) self-exchange between [Fe₂S₂(^Prbbim)₂]^2– (1) and [Fe₂S₂(^Prbbim)₂]^3– (2) occurs with a rate constant of (1.20 ± 0.06) × 10⁵ M^–1 s^–1 at 26 °C. A similar self-exchange rate constant is found for the related [2Fe–2S] cluster [Fe₂S₂(SArO)₂]^2–/3–, SArO^2– = thiosalicylate. These are roughly an order of magnitude slower than that reported for larger [4Fe–4S] clusters and 1 order of magnitude faster than that reported for N-ligated high-spin iron complexes. These results suggest that the rate of intermolecular ET to/from [Fe–S] clusters is modulated by cluster size. The measured PCET self-exchange rate constant for 1 and 4 at −30 °C is (3.8 ± 0.7) × 10⁴ M^–1 s^–1. Analysis of rate constants using the Marcus cross-relation suggests that this process likely occurs via a concerted proton–electron transfer (CPET) mechanism. The implications of these findings to biological systems are also discussed, including the conclusion that histidine-ligated [2Fe–2S] clusters should not have a strong bias to undergo concerted e^–/H⁺ transfers.

[Fe₂S₂(^Prbbim)(^PrbbimH_x)]^y- clusters have been generated in multiple redox and protonation states. Their PCET and ET thermochemistry and reactivity are described. The PCET self-exchange reaction occurs by concerted e⁻/H⁺ exchange, and the ET self-exchange barriers for different clusters are shown to scale with [Fe−S] cluster size. The implications of these results for the reactivity of biochemical imidazole-ligated clusters is discussed.

Carnitine metabolism to trimethylamine by an unusual Rieske-type oxygenase from human microbiota

Dietary intake of L-carnitine can promote cardiovascular diseases in humans through microbial production of trimethylamine (TMA) and its subsequent oxidation to trimethylamine N-oxide by hepatic flavin-containing monooxygenases. Although our microbiota are responsible for TMA formation from carnitine, the underpinning molecular and biochemical mechanisms remain unclear. In this study, using bioinformatics approaches, we first identified a two-component Rieske-type oxygenase/reductase (CntAB) and associated gene cluster proposed to be involved in carnitine metabolism in representative genomes of the human microbiota. CntA belongs to a group of previously uncharacterized Rieske-type proteins and has an unusual "bridging" glutamate but not the aspartate residue, which is believed to facilitate intersubunit electron transfer between the Rieske center and the catalytic mononuclear iron center. Using Acinetobacter baumannii as the model, we then demonstrate that cntAB is essential in carnitine degradation to TMA. Heterologous overexpression of cntAB enables Escherichia coli to produce TMA, confirming that these genes are sufficient in TMA formation. Site-directed mutagenesis experiments have confirmed that this unusual "bridging glutamate" residue in CntA is essential in catalysis and neither mutant (E205D, E205A) is able to produce TMA. Taken together, the data in our study reveal the molecular and biochemical mechanisms underpinning carnitine metabolism to TMA in human microbiota and assign the role of this novel group of Rieske-type proteins in microbial carnitine metabolism.

Structural basis of the divergent oxygenation reactions catalyzed by the rieske nonheme iron oxygenase carbazole 1,9a-dioxygenase

Carbazole 1,9a-dioxygenase (CARDO), a Rieske nonheme iron oxygenase (RO), is a three-component system composed of a terminal oxygenase (Oxy), ferredoxin, and a ferredoxin reductase. Oxy has angular dioxygenation activity against carbazole. Previously, site-directed mutagenesis of the Oxy-encoding gene from Janthinobacterium sp. strain J3 generated the I262V, F275W, Q282N, and Q282Y Oxy derivatives, which showed oxygenation capabilities different from those of the wild-type enzyme. To understand the structural features resulting in the different oxidation reactions, we determined the crystal structures of the derivatives, both free and complexed with substrates. The I262V, F275W, and Q282Y derivatives catalyze the lateral dioxygenation of carbazole with higher yields than the wild type. A previous study determined the crystal structure of Oxy complexed with carbazole and revealed that the carbonyl oxygen of Gly178 hydrogen bonds with the imino nitrogen of carbazole. In these derivatives, the carbazole was rotated approximately 15, 25, and 25°, respectively, compared to the wild type, creating space for a water molecule, which hydrogen bonds with the carbonyl oxygen of Gly178 and the imino nitrogen of carbazole. In the crystal structure of the F275W derivative complexed with fluorene, C-9 of fluorene, which corresponds to the imino nitrogen of carbazole, was oriented close to the mutated residue Trp275, which is on the opposite side of the binding pocket from the carbonyl oxygen of Gly178. Our structural analyses demonstrate that the fine-tuning of hydrophobic residues on the surface of the substrate-binding pocket in ROs causes a slight shift in the substrate-binding position that, in turn, favors specific oxygenation reactions toward various substrates.

Fast proton-coupled electron transfer observed for a high-fidelity structural and functional [2Fe-2S] Rieske model

Rieske cofactors have a [2Fe–2S] cluster with unique {His₂Cys₂} ligation and distinct Fe subsites. The histidine ligands are functionally relevant, since they allow for coupling of electron and proton transfer (PCET) during quinol oxidation in respiratory and photosynthetic ET chains. Here we present the highest fidelity synthetic analogue for the Rieske [2Fe–2S] cluster reported so far. This synthetic analogue 5^x– emulates the heteroleptic {His₂Cys₂} ligation of the [2Fe–2S] core, and it also serves as a functional model that undergoes fast concerted proton and electron transfer (CPET) upon reaction of the mixed-valent (ferrous/ferric) protonated 5H^2– with TEMPO. The thermodynamics of the PCET square scheme for 5^x– have been determined, and three species (diferric 5^2–, protonated diferric 5H^–, and mixed-valent 5^3–) have been characterized by X-ray diffraction. pK_a values for 5H^– and 5H^2– differ by about 4 units, and the reduction potential of 5H^– is shifted anodically by about +230 mV compared to that of 5^2–. While the N–H bond dissociation free energy of 5H^2– (60.2 ± 0.5 kcal mol^–1) and the free energy, ΔG°_CPET, of its reaction with TEMPO (−6.3 kcal mol^–1) are similar to values recently reported for a homoleptic {N₂/N₂}-coordinated [2Fe–2S] cluster, CPET is significantly faster for 5H^2– with biomimetic {N₂/S₂} ligation (k = (9.5 ± 1.2) × 10⁴ M^–1 s^–1, ΔH^‡ = 8.7 ± 1.0 kJ mol^–1, ΔS^‡ = −120 ± 40 J mol^–1 K^–1, and ΔG^‡ = 43.8 ± 0.3 kJ mol^–1 at 293 K). These parameters, and the comparison with homoleptic analogues, provide important information and new perspectives for the mechanistic understanding of the biological Rieske cofactor.

Expression, purification and substrate specificities of 3-nitrotoluene dioxygenase from Diaphorobacter sp. strain DS2

3-Nitotoluene dioxygenase (3-NTDO) is the first enzyme in the degradation pathway of 3-nitrotoluene (3-NT) by Diaphorobacter sp. strain DS2. The complete gene sequences of 3-NTDO were PCR amplified from genomic DNA of Diaphorobacter sp., cloned, sequenced and expressed. The 3-NTDO gene revealed a multi component structure having a reductase, a ferredoxin and two oxygenase subunits. Clones expressing the different subunits were constructed in pET21a expression vector system and overexpressed in E. coli BL21(DE3) host. Each subunit was individually purified separately to homogeneity. The active recombinant enzyme was reconstituted in vitro by mixing all three purified subunits. The reconstituted recombinant enzyme could catalyse biotransformations on a variety of organic aromatics.

Novel insight into the genetic context of the cadAB genes from a 4-chloro-2-methylphenoxyacetic acid-degrading Sphingomonas

The 2-methyl-4-chlorophenoxyacetic (MCPA) acid-degrader Sphingomonas sp. ERG5 has recently been isolated from MCPA-degrading bacterial communities. Using Illumina-sequencing, the 5.7 Mb genome of this isolate was sequenced in this study, revealing the 138 kbp plasmid pCADAB1 harboring the 32.5 kbp composite transposon Tn6228 which contains genes encoding proteins for the removal of 2,4-dichlorophenoxyacetic acid (2,4-D) and MCPA, as well as the regulation of this pathway. Transposon Tn6228 was confirmed by PCR to be situated on the plasmid and also exist in a circular intermediate state - typical of IS3 elements. The canonical tfdAα-gene of group III 2,4-D degraders, encoding the first step in degradation of 2,4-D and related compounds, was not present in the chromosomal contigs. However, the alternative cadAB genes, also providing the initial degradation step, were found in Tn6228, along with the 2,4-D-degradation-associated genes tfdBCDEFKR and cadR. Putative reductase and ferredoxin genes cadCD of Rieske non-heme iron oxygenases were also present in close proximity to cadAB, suggesting that these might have an unknown role in the initial degradation reaction. Parts of the composite transposon contain sequence displaying high similarity to previously analyzed 2,4-D degradation genes, suggesting rapid dissemination and high conservation of the chlorinated-phenoxyacetic acid (PAA)-degradation genotype among the sphingomonads.

Crustacean oxi-reductases protein sequences derived from a functional genomic project potentially involved in ecdysteroid hormones metabolism - a starting point for function examination

A transcriptomic assembly originated from hypodermis and Y organ of the crustacean Pontastacus leptodactylus is used here for in silico characterization of oxi-reductase enzymes potentially involved in the metabolism of ecdysteroid molting hormones. RNA samples were extracted from male Y organ and its neighboring hypodermis in all stages of the molt cycle. An equimolar RNA mix from all stages was sequenced using next generation sequencing technologies and de novo assembled, resulting with 74,877 unique contigs. These transcript sequences were annotated by examining their resemblance to all GenBank translated transcripts, determining their Gene Ontology terms and their characterizing domains. Based on the present knowledge of arthropod ecdysteroid metabolism and more generally on steroid metabolism in other taxa, transcripts potentially related to ecdysteroid metabolism were identified and their longest possible conceptual protein sequences were constructed in two stages, correct reading frame was deduced from BLASTX resemblances, followed by elongation of the protein sequence by identifying the correct translation frame of the original transcript. The analyzed genes belonged to several oxi-reductase superfamilies including the Rieske non heme iron oxygenases, cytochrome P450s, short-chained hydroxysteroid oxi-reductases, aldo/keto oxireductases, lamin B receptor/sterol reductases and glucose-methanol-cholin oxi-reductatses. A total of 68 proteins were characterized and the most probable participants in the ecdysteroid metabolism where indicated. The study provides transcript and protein structural information, a starting point for further functional studies, using a variety of gene-specific methods to demonstrate or disprove the roles of these proteins in relation to ecdysteroid metabolism in P. leptodactylus.

3-Nitrotoluene dioxygenase from Diaphorobacter sp. strains: cloning, sequencing and evolutionary studies

The first step in the degradation of 3-nitrotoluene by Diaphorobacter sp. strain DS2 is the dihydroxylation of the benzene ring with the concomitant removal of nitro group. This is catalyzed by a dioxygenase enzyme system. We report here the cloning and sequencing of the complete dioxygenase gene with its putative regulatory sequence from the genomic DNA of Diaphorobacter sp. strains DS1, DS2 and DS3. Analysis of the 5 kb DNA stretch that was cloned, revealed five complete open reading frames (ORFs) encoding for a reductase, a ferredoxin and two dioxygenase subunits with predicted molecular weights (MW) of 35, 12, 50 and 23 kDa respectively. A regulatory protein was also divergently transcribed from the reductase subunit and has a predicated MW of 34 kDa. Presence of parts of two functional ORFs in between the reductase and the ferredoxin subunits reveals an evolutionary route from a naphthalene dioxygenase like system of Ralstonia sp. strain U2. Further a 100 % identity of its ferredoxin subunit reveals its evolution via dinitrotoluene dioxygenase like system present in Burkholderia cepacia strain R34. A modeled structure of oxygenase3NT from strain DS2 was generated using nitrobenzene dioxygenase as a template. The modeled structure only showed minor changes at its active site. Comparison of growth patterns of strains DS1, DS2 and DS3 revealed that Diaphorobacter sp. strain DS1 has been evolved to degrade 4-nitrotoluene better by an oxidative route amongst all three strains.