Chemical modification of Arthrobacter sarcosine oxidase by N-methylisothiazolinone reduces reactivity toward oxygen

N-Methylisothiazolinone (MIT) is a thiol group modifier and antimicrobial agent. Arthrobacter sarcosine oxidase (SoxA), a diagnostic enzyme for assaying creatinine, loses its activity upon the addition of MIT, and its inactivation mechanism remains unclear. In this study, SoxA was chemically modified using MIT (mo-SoxA), and its structural and chemical properties were characterized. Spectral analysis data, oxygen consumption rates, and reactions were compared between intact SoxA and mo-SoxA. These demonstrate that the oxidative half-reaction toward oxygen is inhibited by MIT modification. The oxidase activity of mo-SoxA was approximately 2.1% of that of intact SoxA, and its dehydrogenase activity was approximately 4.2 times higher. The C-to-S mutants revealed that cooperative modification of 2 specific cysteine residues caused a drastic change in the enzyme reaction mode. Based on the modeled tertiary structures, the putative entrance for oxygen uptake is predicted to be blocked by the chemical modification of the 2 cysteine residues.

Structural enzymology studies with the substrate 3S-hydroxybutanoyl-CoA: bifunctional MFE1 is a less efficient dehydrogenase than monofunctional HAD

Multifunctional enzyme, type-1 (MFE1) catalyzes the second and third step of the β-oxidation cycle, being, respectively, the 2E-enoyl-CoA hydratase (ECH) reaction (N-terminal part, crotonase fold) and the NAD+-dependent, 3S-hydroxyacyl-CoA dehydrogenase (HAD) reaction (C-terminal part, HAD fold). Structural enzymological properties of rat MFE1 (RnMFE1) as well as of two of its variants, namely the E123A variant (a glutamate of the ECH active site is mutated into alanine) and the BCDE variant (without domain A of the ECH part), were studied, using as substrate 3S-hydroxybutanoyl-CoA. Protein crystallographic binding studies show the hydrogen bond interactions of 3S-hydroxybutanoyl-CoA as well as of its 3-keto, oxidized form, acetoacetyl-CoA, with the catalytic glutamates in the ECH active site. Pre-steady state binding experiments with NAD+ and NADH show that the kon and koff rate constants of the HAD active site of monomeric RnMFE1 and the homologous human, dimeric 3S-hydroxyacyl-CoA dehydrogenase (HsHAD) for NAD+ and NADH are very similar, being the same as those observed for the E123A and BCDE variants. However, steady state and pre-steady state kinetic data concerning the HAD-catalyzed dehydrogenation reaction of the substrate 3S-hydroxybutanoyl-CoA show that, respectively, the kcat and kchem rate constants for conversion into acetoacetyl-CoA by RnMFE1 (and its two variants) are about 10 fold lower as when catalyzed by HsHAD. The dynamical properties of dehydrogenases are known to be important for their catalytic efficiency, and it is discussed that the greater complexity of the RnMFE1 fold correlates with the observation that RnMFE1 is a slower dehydrogenase than HsHAD.

Biocatalytic Hydrogen-Borrowing Cascade in Organic Synthesis

Biocatalytic hydrogen borrowing represents an environmentally friendly and highly efficient synthetic method. This innovative approach involves converting various substrates into high-value-added products, typically via a one-pot, two/three-step sequence encompassing dehydrogenation (intermediate transformation) and hydrogenation processes employing the hydride shuffling between NAD(P)+ and NAD(P)H. Represented key transformations in hydrogen borrowing include stereoisomer conversion within alcohols, conversion between alcohols and amines, conversion of allylic alcohols to saturated carbonyl counterparts, and α,β-unsaturated aldehydes to saturated carboxylic acids, etc. The direct transformation methodology and environmentally benign characteristics of hydrogen borrowing have contributed to its advancements in fine chemical synthesis or drug developments. Over the past decades, the hydrogen borrowing strategy in biocatalysis has led to the creation of diverse catalytic systems, demonstrating substantial potential for straightforward synthesis as well as asymmetric transformations. This perspective serves as a detailed exposition of the recent advancements in biocatalytic reactions employing the hydrogen borrowing strategy. It provides insights into the potential of this approach for future development, shedding light on its promising prospects in the field of biocatalysis.

Recent Advances in 2-Keto-l-gulonic Acid Production Using Mixed-Culture Fermentation and Future Prospects

Vitamin C, also known as ascorbic acid, is an essential vitamin that cannot be synthesized by the human body and must be acquired through our diet. At present, the precursor of vitamin C, 2-keto-l-gulonic acid (2-KGA), is typically produced via a two-step fermentation process utilizing three bacterial strains. The second step of this traditional two-step fermentation method involves mixed-culture fermentation employing 2-KGA-producing bacteria (Ketogulonicigenium vulgare) along with associated bacteria. Because K. vulgare has defects in various metabolic pathways, associated bacteria are needed to provide key substances to promote K. vulgare growth and 2-KGA production. Unlike previous reviews where the main focus was the interaction between associated bacteria and K. vulgare, this Review presents the latest scientific research from the perspective of the metabolic pathways associated with 2-KGA production by K. vulgare and the mechanism underlying the interaction between K. vulgare and the associated bacteria. In addition, the dehydrogenases that are responsible for 2-KGA production, the 2-KGA synthesis pathway, strategies for simplifying 2-KGA production via a one-step fermentation route, and, finally, future prospects and research goals in vitamin C production are also presented.

High-Resolution Structural Proteomics of Mitochondria Using the 'Build and Retrieve' Methodology

The application of integrated systems biology to the field of structural biology is a promising new direction, although it is still in the infant stages of development. Here we report the use of single particle cryo-EM to identify multiple proteins from three enriched heterogeneous fractions prepared from human liver mitochondrial lysate. We simultaneously identify and solve high-resolution structures of nine essential mitochondrial enzymes with key metabolic functions, including fatty acid catabolism, reactive oxidative species clearance, and amino acid metabolism. Our methodology also identified multiple distinct members of the acyl-CoA dehydrogenase family. This work highlights the potential of cryo-EM to explore tissue proteomics at the atomic level.

Kinetic and structural characterization of carboxyspermidine dehydrogenase of polyamine biosynthesis

Polyamines are positively charged alkylamines ubiquitous among eukaryotes, prokaryotes, and archaea. Humans obtain polyamines through dietary intake, metabolic production, or uptake of polyamines made by gut microbes. The polyamine biosynthetic pathway used by most gut microbes differs from that used by human cells. This alternative pathway employs carboxyspermidine dehydrogenase (CASDH), an enzyme with limited characterization. Here, we solved a 1.94 Å X-ray crystal structure of Bacteroides fragilis CASDH by molecular replacement. BfCASDH is composed of three domains with a fold similar to saccharopine dehydrogenase but with a distinct active site arrangement. Using steady-state methods, we determined kcat and kcat/Km for BfCASDH and Clostridium leptum CASDH using putrescine, diaminopropane, aspartate semi-aldehyde, NADH, and NADPH as substrates. These data revealed evidence of cooperativity in BfCASDH. Putrescine is the likely polyamine substrate and NADPH is the coenzyme used to complete the reaction, forming carboxyspermidine as a product. These data provide the first kinetic characterization of CASDH-a key enzyme in the production of microbial polyamines.

Influence of Intensive and Super-Intensive Olive Grove Management on Soil Quality-Nutrients Content and Enzyme Activities

Agricultural soil quality is an issue that has been widely debated in the literature in recent decades. Three olive grove areas (one in Lisbon and the others in Santarém, Portugal) with different management techniques (intensive and super-intensive) were selected. Nutrient concentrations and enzyme activities of soils were determined, as well as the C and N of litter and pruning waste (mulch) to estimate the influence of management techniques on the quality of olive grove soils and to assess the extent to which they are affected by organic covers and different cultivation intensities. Organic C and total N concentrations in soils of the intensive olive grove in Lisbon were the highest when compared with those in the intensive and super-intensive olive groves soils of Santarém. The concentrations of Ca, Mg, Na, and K were the main differences between the Lisbon olive groves and the other two from Santarém. Phosphatase, cellulase, and urease activities were related to the Na, extractable K, extractable P, Zn, Mn, organic C, and total N soil concentrations. Soil management and agricultural practices are determining factors for these enzymatic activities of Santarém olive groves, although climate conditions and soil properties play an important role in the soil enzymatic activities.

Histamine Dehydrogenase through Protein Engineering for Food Quality Applications

Histamine is a biogenic amine found in fish-derived and fermented food products with physiological relevance since its concentration is proportional to food spoilage and health risk for sensitive consumers. There are various analytical methods for histamine quantification from food samples; however, a simple and quick enzymatic detection and quantification method is highly desirable. Histamine dehydrogenase (HDH) is a candidate for enzymatic histamine detection; however, other biogenic amines can change its activity or produce false positive results with an observed substrate inhibition at higher concentrations. In this work, we studied the effect of site saturation mutagenesis in Rhizobium sp. Histamine Dehydrogenase (Rsp HDH) in nine amino acid positions selected through structural alignment analysis, substrate docking, and proximity to the proposed histamine-binding site. The resulting libraries were screened for histamine and agmatine activity. Variants from two libraries (positions 72 and 110) showed improved histamine/agmatine activity ratio, decreased substrate inhibition, and maintained thermal resistance. In addition, activity characterization of the identified Phe72Thr and Asn110Val HDH variants showed a clear substrate inhibition curve for histamine and modified kinetic parameters. The observed maximum velocity (V_max) increased for variant Phe72Thr at the cost of an increased value for the Michaelis-Menten constant (K_m) for histamine. The increased K_m value, decreased substrate inhibition, and biogenic amine interference observed for variant Phe72Thr support a tradeoff between substrate affinity and substrate inhibition in the catalytic mechanism of HDHs. Considering this tradeoff for future enzyme engineering of HDH could lead to breakthroughs in performance increases and understanding of this enzyme class.

Staphylococcus aureus FadB is a dehydrogenase that mediates cholate resistance and survival under human colonic conditions

Staphylococcus aureus is a common colonizer of the human gut and in doing so it must be able to resist the actions of the host's innate defences. Bile salts are a class of molecules that possess potent antibacterial activity that control growth. Bacteria that colonize and survive in that niche must be able to resist the action of bile salts, but the mechanisms by which S. aureus does so are poorly understood. Here we show that FadB is a bile-induced oxidoreductase which mediates bile salt resistance and when heterologously expressed in Escherichia coli renders them resistant. Deletion of fadB attenuated survival of S. aureus in a model of the human distal colon.

Domiciliation of Trichoderma asperellum Suppresses Globiosporangium ultimum and Promotes Pea Growth, Ultrastructure, and Metabolic Features

The beneficial microorganisms represent a new and hopeful solution for a sustainable environment and development. In this investigation, Trichoderma asperellum ZNW, isolated from seeds, was domiciliated within the pea plant for improving growth, disease management, and enhancement of productivity. Globisporangium ultimum NZW was isolated from deformed pea seeds, representing the first record of the pathogen caused by pea damping-off. Both fungi were molecularly identified. T. asperellum ZNW produced several lytic enzymes and bioactive metabolites as detected by GC-MC. The SEM illustrated the mycoparasitic behavior of T. asperellum ZNW on G. ultimum NZW mycelia. In the pot experiment, T. asperellum domiciliated the root and grew as an endophytic fungus, leading to root vessel lignification. Under soil infection, T. asperellum reduced damping-off, by enhancing peroxidase, polyphenol, total phenols, and photosynthetic pigments content. The vegetative growth, yield, and soil dehydrogenase activity were improved, with an enhancement in the numerical diversity of the microbial rhizosphere. This work may enable more understanding of the plant-fungal interaction, yet, working on domiciliation is recommended as a new approach to plant protection and growth promotion under various ecological setups.

Non-Aerated Common Nettle (Urtica dioica L.) Extract Enhances Green Beans (Phaseolus vulgaris L.) Growth and Soil Enzyme Activity

One of the limiting factors in organic farming is the scarcity of allowed fertilizers and chemicals for plant protection. Plant and compost extracts are a promising solution for fertilization because of their positive effect on plant growth and soil microbial activity. Nettle extract was already successfully applied to some vegetables. Not-aerated nettle extract, obtained from dry nettle leaves, was applied in experiments with green beans in a quantity of 1 L per pot at two-day intervals was studied. A three-factorial experimental design was applied with two soil types (brown-Calcic Gleysol and red-Eutric Cambisol), soil disinfection with dazomet or not, and irrigated with nettle extract or water. Nettle extract application increased all above-ground traits; plant height, leaf area, flower buds, shoot dry weight at flowering, pod length, pod diameter, and shoot dry weight at harvest by 49%, 66%, 43%, 36%, 11%, 9%, and 37%, respectively, the root length at harvest by 59%, total yield by 48%, soil respiration by 91% and 74% in two soil types, and alkaline phosphatase by 30%. Dehydrogenase activity was enhanced by nettle extract application on red soil, while nettle extract application had no effect on root nodulation. The nettle extract application benefits in green bean organic production were attributed to the nutrients and other components present in the extract and not to nitrogen fixation. The optimization of the dose of the extract and experiments in real conditions of green bean production would be the next step toward the implementation of nettle extract as an organic fertilizer.

Nickel (ii) effects on Anammox reaction: reactor performance, dehydrogenase, sludge morphology and microbial community changes

Nickel (ii) (Ni²⁺) is considered as one of the necessary trace elements in the process of Anammox culture, but it may have toxic effects at high concentration. This study explored the long-term influence of Ni²⁺ on the denitrification efficiency of Anammox bioreactors. The results showed that when the concentration of Ni²⁺ was 0.5 mg/L, the bioreactor had the highest denitrification efficiency, while the removal efficiency of ammonia nitrogen and nitrite nitrogen gradually decreased at concentrations higher than 2 mg/L, and the removal rates of ammonia nitrogen and nitrite nitrogen were 26% and 39.81% at the end of the experiment, respectively. The NRR was decreased from 7.47 kg N/m³ d to 3.28 kg N/m³ d during the whole process. The highest concentration of microbial dehydrogenase was attained in about 40 days; in the meantime, its ability to consume organic matter was also maximized. The sludge morphology was changed from granular cluster to loose flocculant with a small number of spherical and filamentous bacteria and bacilli distributed on the surface. At the end of the experiment, both species richness and community diversity were reduced, and the proportion of the dominant bacteria Candidatus Kuenenia was also decreased from 59.89% to 36.72%.

Structure of lactate oxidase from Enterococcus hirae revealed new aspects of active site loop function: Product-inhibition mechanism and oxygen gatekeeper

l-Lactate oxidase (LOx) is a flavin mononucleotide (FMN)-dependent triose phosphate isomerase (TIM) barrel fold enzyme that catalyzes the oxidation of l-lactate using oxygen as a primary electron acceptor. Although reductive half-reaction mechanism of LOx has been studied by structure-based kinetic studies, oxidative half-reaction and substrate/product-inhibition mechanisms were yet to be elucidated. In this study, the structure and enzymatic properties of wild-type and mutant LOxs from Enterococcus hirae (EhLOx) were investigated. EhLOx structure showed the common TIM-barrel fold with flexible loop region. Noteworthy observations were that the EhLOx crystal structures prepared by co-crystallization with product, pyruvate, revealed the complex structures with "d-lactate form ligand," which was covalently bonded with a Tyr211 side chain. This observation provided direct evidence to suggest the product-inhibition mode of EhLOx. Moreover, this structure also revealed a flip motion of Met207 side chain, which is located on the flexible loop region as well as Tyr211. Through a saturation mutagenesis study of Met207, one of the mutants Met207Leu showed the drastically decreased oxidase activity but maintained dye-mediated dehydrogenase activity. The structure analysis of EhLOx Met207Leu revealed the absence of flipping in the vicinity of FMN, unlike the wild-type Met207 side chain. Together with the simulation of the oxygen-accessible channel prediction, Met207 may play as an oxygen gatekeeper residue, which contributes oxygen uptake from external enzyme to FMN. Three clades of LOxs are proposed based on the difference of the Met207 position and they have different oxygen migration pathway from external enzyme to active center FMN.

Supported Pt Enabled Proton-Driven NAD(P)+ Regeneration for Biocatalytic Oxidation

The utilization of biocatalytic oxidations has evolved from the niche applications of the early 21st century to a widely recognized tool for general chemical synthesis. One of the major drawbacks that hinders commercialization is the dependence on expensive nicotinamide adenine dinucleotide (NAD(P)⁺) cofactors, and so, their regeneration is essential. Here, we report the design of carbon-supported Pt catalysts that can regenerate NAD(P)⁺ by proton-driven NAD(P)H oxidation with concurrent hydrogen formation. The carbon support was modified to tune the electronic nature of the Pt nanoparticles, and it was found that the best catalyst for NAD(P)⁺ regeneration (TOF = 581 h^-1) was electron-rich Pt on carbon. Finally, the heterogeneous Pt catalyst was applied in the biocatalytic oxidation of a variety of alcohols catalyzed by different alcohol dehydrogenases. The Pt catalyst exhibited good compatibility with the biocatalytic system. Its NAD(P)⁺ regeneration function successfully supported biocatalytic conversion from alcohols to corresponding ketone or lactone products. This work provides a promising strategy for chemical synthesis via NAD(P)⁺-dependent pathways utilizing a cooperative inorganic-enzymatic catalytic system.

Cell-Free Biosynthesis of ω-Hydroxy Acids Boosted by a Synergistic Combination of Alcohol Dehydrogenases

The activity orchestration of an unprecedented cell-free enzyme system with self-sufficient cofactor recycling enables the stepwise transformation of aliphatic diols into ω-hydroxy acids at the expense of molecular oxygen as electron acceptor. The efficiency of the biosynthetic route was maximized when two compatible alcohol dehydrogenases were selected as specialist biocatalysts for each one of the oxidative steps required for the oxidative lactonization of diols. The cell-free system reached up to 100 % conversion using 100 mM of linear C₅ diols and performed the desymmetrization of prochiral branched diols into the corresponding ω-hydroxy acids with an exquisite enantioselectivity (ee>99 %). Green metrics demonstrate superior sustainability of this system compared to traditional metal catalysts and even to whole cells for the synthesis of 5-hydroxypetanoic acid. Finally, the cell-free system was assembled into a consortium of heterogeneous biocatalysts that allowed the enzyme reutilization. This cascade illustrates the potential of systems biocatalysis to access new heterofunctional molecules such as ω-hydroxy acids.

Unidirectional mannitol synthesis of Acinetobacter baumannii MtlD is facilitated by the helix-loop-helix-mediated dimer formation

Mannitol biosynthesis is essential for Acinetobacter baumannii to cope with osmotic stress. Currently, only Pseudomonas putida, Acinetobacter baylyi, and A. baumannii are able to de novo synthesize mannitol by a structurally unique bifunctional mannitol-1-phosphate dehydrogenase/phosphatase (AbMtlD). The molecular mechanism of reduction and dephosphorylation of fructose-6-phosphate to mannitol is highly dependent on the substrate shuffling from one protomer to the other protomer by a unique helix–loop–helix domain–mediated dimer formation, thus ensuring unidirectional and efficient biosynthesis of mannitol. These observations support an evolutionary adaptation of AbMtlD by fusion of dehydrogenase and phosphatase domains to facilitate efficient unidirectional enzymatic production of mannitol, unifying regulatory control and minimizing the intracellular concentration of toxic mannitol-1-phosphate during salt stress.

Persistence of Acinetobacter baumannii in environments with low water activity is largely attributed to the biosynthesis of compatible solutes. Mannitol is one of the key compatible solutes in A. baumannii, and it is synthesized by a bifunctional mannitol-1-phosphate dehydrogenase/phosphatase (AbMtlD). AbMtlD catalyzes the conversion of fructose-6-phosphate to mannitol in two consecutive steps. Here, we report the crystal structure of dimeric AbMtlD, constituting two protomers each with a dehydrogenase and phosphatase domain. A proper assembly of AbMtlD dimer is facilitated by an intersection comprising a unique helix–loop–helix (HLH) domain. Reduction and dephosphorylation catalysis of fructose-6-phosphate to mannitol is dependent on the transient dimerization of AbMtlD. AbMtlD presents as a monomer under lower ionic strength conditions and was found to be mainly dimeric under high-salt conditions. The AbMtlD catalytic efficiency was markedly increased by cross-linking the protomers at the intersected HLH domain via engineered disulfide bonds. Inactivation of the AbMtlD phosphatase domain results in an intracellular accumulation of mannitol-1-phosphate in A. baumannii, leading to bacterial growth impairment upon salt stress. Taken together, our findings demonstrate that salt-induced dimerization of the bifunctional AbMtlD increases catalytic dehydrogenase and phosphatase efficiency, resulting in unidirectional catalysis of mannitol production.

Dehydrogenase reductase 9 (SDR9C4) and related homologs recognize a broad spectrum of lipid mediator oxylipins as substrates

Bioactive oxylipins play multiple roles during inflammation and in the immune response, with termination of their actions partly dependent on the activity of yet-to-be characterized dehydrogenases. Here, we report that human microsomal dehydrogenase reductase 9 (DHRS9, also known as SDR9C4 of the short-chain dehydrogenase/reductase (SDR) superfamily) exhibits a robust oxidative activity toward oxylipins with hydroxyl groups located at carbons C9 and C13 of octadecanoids, C12 and C15 carbons of eicosanoids, and C14 carbon of docosanoids. DHRS9/SDR9C4 is also active toward lipid inflammatory mediator dihydroxylated Leukotriene B₄ and proresolving mediators such as tri-hydroxylated Resolvin D1 and Lipoxin A₄, although notably, with lack of activity on the 15-hydroxyl of prostaglandins. We also found that the SDR enzymes phylogenetically related to DHRS9, i.e., human SDR9C8 (or retinol dehydrogenase 16), the rat SDR9C family member known as retinol dehydrogenase 7, and the mouse ortholog of human DHRS9 display similar activity toward oxylipin substrates. Mice deficient in DHRS9 protein are viable, fertile, and display no apparent phenotype under normal conditions. However, the oxidative activity of microsomal membranes from the skin, lung, and trachea of Dhrs9^−/− mice toward 1 μM Leukotriene B₄ is 1.7- to 6-fold lower than that of microsomes from wild-type littermates. In addition, the oxidative activity toward 1 μM Resolvin D1 is reduced by about 2.5-fold with DHRS9-null microsomes from the skin and trachea. These results strongly suggest that DHRS9 might play an important role in the metabolism of a wide range of bioactive oxylipins in vivo.

Antibacterial and Antibiofilm Effect of Ultrasound and Mild Heat Against a Multidrug-Resistant Klebsiella pneumoniae Stain Isolated from Meat of Yellow-Feathered Chicken

Klebsiella pneumoniae is an important foodborne pathogen with high biofilm-forming ability, which is continuously detected in food products in recent years. The antibacterial and antibiofilm activities and mechanism of ultrasonication in combination with heat treatment against K. pneumoniae were studied. K. pneumoniae planktonic and biofilm cells were treated with ultrasound (US), mild heat treatment (HT50, HT60, and HT70), and combinations of US and mild heat treatment (UH50, UH60, and UH70) for 5, 10, 20, 30, and 60 min. Results showed that the combination of US and mild heat treatment was more effective in inactivating K. pneumoniae planktonic and biofilm cells than the single treatment by counting viable bacteria. In addition, confocal laser scanning microscopy, scanning electron microscopy, and analysis of leakage of intracellular substances have revealed that the combination treatment effectively damaged the integrity of bacterial cell membrane and increased cell permeability, which led to the quick release of adenosine triphosphate (ATP) and macromolecular substances of nucleic acids and proteins. Moreover, the activities of respiratory chain dehydrogenase in planktonic and biofilm cells significantly decreased after UH treatment. The results indicated that ultrasonication and mild heat treatment had a synergistic effect on the inactivation of K. pneumoniae planktonic and biofilm cells by damaging the cell membrane and inhibiting intercellular cell respiration.

A Specialized Dehydrogenase Provides l-Phenyllactate for FR900359 Biosynthesis

d‐Phenyllactate (PLA) is a component of the selective Gq protein inhibitor and nonribosomal cyclic depsipeptide FR900359 (FR). Here we report a detailed biochemical investigation of pla biosynthesis and its incorporation into the natural product FR. The enzyme FrsC, member of the lactate/malate dehydrogenase superfamily, was shown to catalyze the formation of l‐PLA from phenylpyruvate. FrsC was kinetically characterized and its substrate specificity determined. Incorporation of l‐PLA was probed by assaying the adenylation domain FrsE‐A3 and feeding studies with a Chromobacterium vaccinii ΔfrsC mutant, confirming preferred activation of l‐PLA followed by on‐line epimerization to d‐pla. Finally, detailed bioinformatic analyses of FrsC revealed its close relation to malate dehydrogenases from primary metabolism and suggest extensions in the substrate binding loop to be responsible for its adaptation to accepting larger aromatic substrates with high specificity.

Substituted Aryl Benzylamines as Potent and Selective Inhibitors of 17β-Hydroxysteroid Dehydrogenase Type 3

17β-Hydroxysteroid dehydrogenase type 3 (17β-HSD3) is expressed at high levels in testes and seminal vesicles; it is also present in prostate tissue and involved in gonadal and non-gonadal testosterone biosynthesis. The enzyme is membrane-bound, and a crystal structure is not yet available. Selective aryl benzylamine-based inhibitors were designed and synthesised as potential agents for prostate cancer therapeutics through structure-based design, using a previously built homology model with docking studies. Potent, selective, low nanomolar IC₅₀ 17β-HSD3 inhibitors were discovered using N-(2-([2-(4-chlorophenoxy)phenylamino]methyl)phenyl)acetamide (1). The most potent compounds have IC₅₀ values of approximately 75 nM. Compound 29, N-[2-(1-Acetylpiperidin-4-ylamino)benzyl]-N-[2-(4-chlorophenoxy)phenyl]acetamide, has an IC₅₀ of 76 nM, while compound 30, N-(2-(1-[2-(4-chlorophenoxy)-phenylamino]ethyl)phenyl)acetamide, has an IC₅₀ of 74 nM. Racemic C-allyl derivative 26 (IC₅₀ of 520 nM) was easily formed from 1 in good yield and, to determine binding directionality, its enantiomers were separated by chiral chromatography. Absolute configuration was determined using single crystal X-ray crystallography. Only the S-(+)-enantiomer (32) was active with an IC₅₀ of 370 nM. Binding directionality was predictable through our in silico docking studies, giving confidence to our model. Importantly, all novel inhibitors are selective over the type 2 isozyme of 17β-HSD2 and show <20% inhibition when tested at 10 µM. Lead compounds from this series are worthy of further optimisation and development as inhibitors of testosterone production by 17β-HSD3 and as inhibitors of prostate cancer cell growth.

Effect of ZnO Nanoparticles on Growth and Biochemical Responses of Wheat and Maize

Zinc is an essential element that is also renowned for widespread contamination and toxicity at high concentrations. The present study was carried out to analyze the responses induced by lower, as well as higher, doses of zinc (0-200 mg/L), in the form of zinc oxide nanoparticles (ZnO NPs) in wheat and maize, for a period of 21 days. Accumulation of zinc increases with increasing Zn doses in both wheat and maize, with higher doses being in wheat (121 mg/kg in root and 66 mg/kg in shoot) than in maize (95 mg/kg in root and 48 mg/kg in shoot). The activity of alpha-amylase showed increase, while that of dehydrogenase decline, in response to ZnO NPs. The length and biomass of plants and photosynthetic pigments increased slightly upon ZnO NPs supply. Malondialdehyde content showed a progressive increase in root and shoot of both plants. However, in response, antioxidant enzymes (superoxide dismutase, ascorbate peroxidase, guaiacol peroxidase, and catalase) showed increase up to lower concentrations (100 mg/L) of ZnO NPs but decline variably at higher levels (150-200 mg/L) in wheat and maize. The results suggest that lower supply of ZnO NPs (100 mg/L) could be stimulatory to the growth of plants and can be recommended as a Zn fertilizer source for crop production.

Synergistic Antibiofilm Effects of Ultrasound and Phenyllactic Acid against Staphylococcus aureus and Salmonella enteritidis

This study evaluated the effect of the combination of ultrasound and phenyllactic acid (PLA) on inactivating Staphylococcus aureus and Salmonella enteritidis biofilm cells and determined the possible antibiofilm mechanism. S. aureus and S. enteritidis biofilm cells were separately treated with ultrasound (US, 270 W), phenyllactic acid (PLA, 0.5% and 1%), and their combination (US + 0.5% PLA, and US + 1% PLA) for 5, 10, 20, 30, and 60 min. Biofilm inactivation, polysaccharide, and respiratory chain dehydrogenase assays were conducted. US and PLA had a synergistic effect on inactivating bacterial cells in S. aureus and S. enteritidis biofilms. The combination of US and PLA significantly decreased the contents of soluble and insoluble polysaccharides and the activity of respiratory chain dehydrogenase in the biofilm cells compared to the single treatment. Confocal laser scanning microscopy, scanning electron microscopy, and intracellular adenosine-triphosphate (ATP) analyses indicated that the combination of US and PLA seriously destroyed the cell membrane integrity of the S. aureus and S. enteritidis biofilms and caused the leakage of intracellular ATP. These findings demonstrated the synergistic antibiofilm effect of US combined with PLA and offered a research basis for its application in the food industry.

Contrasting Effects of Forest Type and Stand Age on Soil Microbial Activities: An Analysis of Local Scale Variability

Simple Summary

The potentially important role of forests in climate change mitigation suggests a strong need for a more detailed understanding of these ecosystems. Besides climatic conditions, diverse forest vegetation creates varied conditions for the activity of soil microorganisms, and particular attention should be focused on a comprehensive study on the influence of different forest types on microbial activities. We conducted an experiment on six different forest soils (two coniferous, two deciduous, and two mixed sites comprising trees of different ages) collected from the same region (Lublin Upland, Poland) to assess the relationship between forest type and seasonal changes in microbial parameters. The annual mean values of the soil microbial indicators suggest that the mature deciduous stand was the most sustainable in microbial activities among the forest soils investigated. The diversity of the forest environment and the multifactorial dependence of the microbiological activity of forest soils necessitates further research in this field, especially using the same soil types. An understanding of forest ecosystem functioning can also be useful for forest management.

Abstract

Understanding the functioning of different forest ecosystems is important due to their key role in strategies for climate change mitigation, especially through soil C sequestration. In controlled laboratory conditions, we conducted a preliminary study on six different forest soils (two coniferous, two deciduous, and two mixed sites comprising trees of different ages) collected from the same region. The aim was to explore any differences and assess seasonal changes in soil microbial parameters (basal respiration BR, microbial biomass C_mic, metabolic quotient qCO₂, dehydrogenase activity DHA, and C_mic:C_org ratio). Indicator- and forest-specific seasonality was assessed. In addition to litter input, soil parameters (pH, nutrient content, texture and moisture) strongly regulated the analyzed microbial indicators. PCA analysis indicated similarity between mature mixed and deciduous forests. Among annual mean values, high C_mic and DHA with simultaneously low qCO₂ suggest that the mature deciduous stand was the most sustainable in microbial activities among the investigated forest soils. Research on the interrelationship between soil parameters and forest types with different tree ages needs to be continued and extended to analyze a greater number of forest and soil types.

Responses of oil degrader enzyme activities, metabolism and degradation kinetics to bean root exudates during rhizoremediation of crude oil contaminated soil

During rhizoremediation process, plant roots secrete the specific exudates which enhance or stimulate growth and activity of microbial community in the rhizosphere resulting in effective degradation of pollutants. The present study characterized cowpea (CP) and mung bean (MB) root exudates and examined their influences on the degradation of total petroleum hydrocarbons (TPHs) and polycyclic aromatic hydrocarbons (PAHs) by the two oil degraders Micrococcus luteus WN01 and Bacillus cereus W2301. The effects of root exudates on soil microbial population dynamic and their enzymes dehydrogenase (DHA), and catechol 2,3 dioxygenase (C23O) activities were assessed. Both root exudates enhanced the degradation by both oil degraders. Cowpea root exudates maximized the removal of TPHs and PAHs by M. luteus WN01. Both bacterial population and DHA increased significantly in the presence of both root exudates. However, the C23O activities were significantly higher in WN01 treated. No significant influence of root exudates was observed on the C23O activities of W2301 treated. By using gas chromatography -mass spectroscopy, the dominant compounds found in cowpea and mung bean root exudates were 4-methoxy-cinnamic acid and terephthalic acid. Found in lower amount were propionic, malonic acid, and citric acid which were associated with enhanced PAHs desorption from soil and subsequent degradation. Novelty statement This is the first study to characterize the low molecular weight organic acids from root exudates of cowpea and mung bean and their influences on hydrocarbon desorption and hence enhancing the biodegradation process. The findings of the present study will greatly contribute to a better understanding of plant-microbe interaction in total petroleum hydrocarbons contaminated soil.

[Progress in vitamin C biosynthesis related dehydrogenases]

Vitamin C is an essential vitamin for human beings. It has a huge market in the fields of food and pharmaceuticals. 2-keto-L-gulonic acid is an important precursor to produce vitamin C by microbial fermentation in industrial. In microbial fermentations, the L-sorbose pathway and the D-gluconate pathway have been the focus of research because of high yield. This article aims at stating recent research progress in dehydrogenases related to biosynthesis of vitamin C in the L-sorbose pathway and the D-gluconate pathway. The properties of dehydrogenase in terms of localization, substrate specificity, cofactors, and electron transport carrier are elaborated. And then, the main problems and strategies are reviewed in the L-sorbose pathway and in the D-gluconate pathway. Finally, future research on the dehydrogenases in the biosynthesis of vitamin C through L-sorbose pathway and D-gluconate pathway is discussed.

Strain Chol11 Acts as Circuit Breaker During Growth With Toxic Bile Salts

In contrast to many steroid hormones and cholesterol, mammalian bile salts are 5β-steroids, which leads to a bent structure of the steroid core. Bile salts are surface-active steroids excreted into the environment in large amounts, where they are subject to bacterial degradation. Bacterial steroid degradation is initiated by the oxidation of the A-ring leading to canonical Δ⁴-3-keto steroids with a double bond in the A-ring. For 5β-bile salts, this Δ⁴-double bond is introduced into 3-keto-bile salts by a 5β-Δ⁴-ketosteroid dehydrogenase (5β-Δ⁴-KSTD). With the Nov2c019 protein from bile-salt degrading Sphingobium sp. strain Chol11, a novel 5β-Δ⁴-KSTD for bile-salt degradation belonging to the Old Yellow Enzyme family was identified and named 5β-Δ⁴-KSTD1. By heterologous production in Escherichia coli, 5β-Δ⁴-KSTD function could be shown for 5β-Δ⁴-KSTD1 as well as the homolog CasH from bile-salt degrading Rhodococcus jostii RHA1. The deletion mutant of 5β-Δ⁴-kstd1 had a prolonged lag-phase with cholate as sole carbon source and, in accordance with the function of 5β-Δ⁴-KSTD1, showed delayed 3-ketocholate transformation. Purified 5β-Δ⁴-KSTD1 was specific for 5β-steroids in contrast to 5α-steroids and converted steroids with a variety of hydroxy groups regardless of the presence of a side chain. 5β-Δ⁴-KSTD1 showed a relatively low K _m for 3-ketocholate, a very high specific activity and pronounced substrate inhibition. With respect to the toxicity of bile salts, these kinetic properties indicate that 5β-Δ⁴-KSTD1 can achieve fast detoxification of the detergent character as well as prevention of an overflow of the catabolic pathway in presence of increased bile-salt concentrations.

The putative Escherichia coli dehydrogenase YjhC metabolises two dehydrated forms of N-acetylneuraminate produced by some sialidases

Homologues of the putative dehydrogenase YjhC are found in operons involved in the metabolism of N-acetylneuraminate (Neu5Ac) or related compounds. We observed that purified recombinant YjhC forms Neu5Ac from two dehydrated forms of this compound, 2,7-anhydro-N-acetylneuraminate (2,7-AN) and 2-deoxy-2,3-didehydro-N-acetylneuraminate (2,3-EN) that are produced during the degradation of sialoconjugates by some sialidases. The conversion of 2,7-AN into Neu5Ac is reversible and reaches its equilibrium when the ratio of 2,7-AN to Neu5Ac is ≈1/6. The conversion of 2,3-EN is irreversible, leading to a mixture of Neu5Ac and 2,7-AN. NMR analysis of the reaction catalysed by YjhC on 2,3-EN indicated that Neu5Ac was produced as the α-anomer. All conversions require NAD⁺ as a cofactor, which is regenerated in the reaction. They appear to involve the formation of keto (presumably 4-keto) intermediates of 2,7-AN, 2,3-EN and Neu5Ac, which were detected by liquid chromatography-mass spectrometry (LC-MS). The proposed reaction mechanism is reminiscent of the one catalysed by family 4 β-glycosidases, which also use NAD⁺ as a cofactor. Both 2,7-AN and 2,3-EN support the growth of Escherichia coli provided the repressor NanR, which negatively controls the expression of the yjhBC operons, has been inactivated. Inactivation of either YjhC or YjhB in NanR-deficient cells prevents the growth on 2,7-AN and 2,3-EN. This confirms the role of YjhC in 2,7-AN and 2,3-EN metabolism and indicates that transport of 2,7-AN and 2,3-EN is carried out by YjhB, which is homologous to the Neu5Ac transporter NanT.

Characterization of the sorbitol dehydrogenase SmoS from Sinorhizobium meliloti 1021

Sinorhizobium meliloti 1021 is a Gram-negative alphaproteobacterium with a robust capacity for carbohydrate metabolism. The enzymes that facilitate these reactions assist in the survival of the bacterium across a range of environmental niches, and they may also be suitable for use in industrial processes. SmoS is a dehydrogenase that catalyzes the oxidation of the commonly occurring sugar alcohols sorbitol and galactitol to fructose and tagatose, respectively, using NAD⁺ as a cofactor. The main objective of this study was to evaluate SmoS using biochemical techniques. The nucleotide sequence was codon-optimized for heterologous expression in Escherichia coli BL21 (DE3) Gold cells and the protein was subsequently overexpressed and purified. Size-exclusion chromatography and X-ray diffraction experiments suggest that SmoS is a tetramer. SmoS was crystallized, and crystals obtained in the absence of substrate diffracted to 2.1 Å resolution and those of a complex with sorbitol diffracted to 2.0 Å resolution. SmoS was characterized kinetically and shown to have a preference for sorbitol despite having a higher affinity for galactitol. Computational ligand-docking experiments suggest that tagatose binds the protein in a more energetically favourable complex than fructose, which is retained in the active site over a longer time frame following oxidation and reduces the rate of the reaction. These results supplement the inventory of biomolecules with potential for industrial applications and enhance the understanding of metabolism in the model organism S. meliloti.

NAD(H) phosphates mediate tetramer assembly of human C-terminal binding protein (CtBP)

C-terminal binding proteins (CtBPs) are cotranscriptional factors that play key roles in cell fate. We have previously shown that NAD(H) promotes the assembly of similar tetramers from either human CtBP1 and CtBP2 and that CtBP2 tetramer destabilizing mutants are defective for oncogenic activity. To assist structure-based design efforts for compounds that disrupt CtBP tetramerization, it is essential to understand how NAD(H) triggers tetramer assembly. Here, we investigate the moieties within NAD(H) that are responsible for triggering tetramer formation. Using multiangle light scattering (MALS), we show that ADP is able to promote tetramer formation of both CtBP1 and CtBP2, whereas AMP promotes tetramer assembly of CtBP1, but not CtBP2. Other NAD(H) moieties that lack the adenosine phosphate, including adenosine and those incorporating nicotinamide, all fail to promote tetramer assembly. Our crystal structures of CtBP1 with AMP reveal participation of the adenosine phosphate in the tetrameric interface, pinpointing its central role in NAD(H)-linked assembly. CtBP1 and CtBP2 have overlapping but unique roles, suggesting that a detailed understanding of their unique structural properties might have utility in the design of paralog-specific inhibitors. We investigated the different responses to AMP through a series of site-directed mutants at 13 positions. These mutations reveal a central role for a hinge segment, which we term the 120s hinge that connects the substrate with coenzyme-binding domains and influences nucleotide binding and tetramer assembly. Our results provide insight into suitable pockets to explore in structure-based drug design to interfere with cotranscriptional activity of CtBP in cancer.

Changes in retinoid metabolism and signaling associated with metabolic remodeling during fasting and in type I diabetes

Liver is the central metabolic hub that coordinates carbohydrate and lipid metabolism. The bioactive derivative of vitamin A, retinoic acid (RA), was shown to regulate major metabolic genes including phosphoenolpyruvate carboxykinase, fatty acid synthase, carnitine palmitoyltransferase 1, and glucokinase among others. Expression levels of these genes undergo profound changes during adaptation to fasting or in metabolic diseases such as type 1 diabetes (T1D). However, it is unknown whether the levels of hepatic RA change during metabolic remodeling. This study investigated the dynamics of hepatic retinoid metabolism and signaling in the fed state, in fasting, and in T1D. Our results show that fed-to-fasted transition is associated with significant decrease in hepatic retinol dehydrogenase (RDH) activity, the rate-limiting step in RA biosynthesis, and downregulation of RA signaling. The decrease in RDH activity correlates with the decreased abundance and altered subcellular distribution of RDH10 while Rdh10 transcript levels remain unchanged. In contrast to fasting, untreated T1D is associated with upregulation of RA signaling and an increase in hepatic RDH activity, which correlates with the increased abundance of RDH10 in microsomal membranes. The dynamic changes in RDH10 protein levels in the absence of changes in its transcript levels imply the existence of posttranscriptional regulation of RDH10 protein. Together, these data suggest that the downregulation of hepatic RA biosynthesis, in part via the decrease in RDH10, is an integral component of adaptation to fasting. In contrast, the upregulation of hepatic RA biosynthesis and signaling in T1D might contribute to metabolic inflexibility associated with this disease.

Establishing Interfacial Charge-Transfer Transitions on Ferroelectric Perovskites: An Efficient Route for Photoelectrochemical Bioanalysis

This work presents the concept of establishing interfacial charge-transfer transitions (ICTT) on ferroelectric perovskites for efficient photoelectrochemical (PEC) bioanalysis. The model system was exemplified by using representative lead titanate (PbTiO₃) and an enzyme tandem consisting of the isocitrate dehydrogenase (ICDH) and p-hydroxybenzoate hydroxylase (PHBH). The enzymatic generation of protocatechuic acid (PCA) can coordinate onto the surface of the PbTiO₃ and hence form the ICTT that enables direct ligand-to-metal charge transfer from the highest occupied molecular orbital (HOMO) of PCA to the conduction band (CB) of PbTiO₃ under light irradiation. Due to the ferroelectric polarization induced electric field of PbTiO₃ and the surface polarity of PCA modification, enhanced charge separation of the ICTT contributes to the generation of anodic photocurrent and thus underlies a unique route for detecting the enzymatic activity or its substrate. For dehydrogenase detection, this strategy has better performance than some classical methodologies in terms of high sensitivity and improved selectivity. This work not only features ICTT establishment on ferroelectric perovskites for unique bioanalysis but also provides new insights into the utilization of ferroelectric perovskites for advanced PEC bioanalysis.

Global Metabolic Shifts in Age and Alzheimer's Disease Mouse Brains Pivot at NAD+/NADH Redox Sites

Age and Alzheimer’s disease (AD) share some common features such as cognitive impairments, memory loss, metabolic disturbances, bioenergetic deficits, and inflammation. Yet little is known on how systematic shifts in metabolic networks depend on age and AD. In this work, we investigated the global metabolomic alterations in non-transgenic (NTg) and triple-transgenic (3xTg-AD) mouse brain hippocampus as a function of age by using untargeted Ultrahigh Performance Liquid Chromatography-tandem Mass Spectroscopy (UPLC-MS/MS). We observed common metabolic patterns with aging in both NTg and 3xTg-AD brains involved in energy-generating pathways, fatty acids oxidation, glutamate, and sphingolipid metabolism. We found age-related downregulation of metabolites from reactions in glycolysis that consumed ATP and in the TCA cycle, especially at NAD⁺/NADH-dependent redox sites, where age- and AD-associated limitations in the free NADH may alter reactions. Conversely, metabolites increased in glycolytic reactions in which ATP is produced. With age, inputs to the TCA cycle were increased including fatty acid β-oxidation and glutamine. Overall age- and AD-related changes were > 2-fold when comparing the declines of upstream metabolites of NAD⁺/NADH-dependent reactions to the increases of downstream metabolites (p = 10^-5, n = 8 redox reactions). Inflammatory metabolites such as ceramides and sphingosine-1-phosphate also increased with age. Age-related decreases in glutamate, GABA, and sphingolipid were seen which worsened with AD genetic load in 3xTg-AD brains, possibly contributing to synaptic, learning- and memory-related deficits. The data support the novel hypothesis that age- and AD-associated metabolic shifts respond to NAD(P)⁺/NAD(P)H redox-dependent reactions, which may contribute to decreased energetic capacity.

Resistance to Acetylsalicylic Acid in Patients with Coronary Heart Disease Is the Result of Metabolic Activity of Platelets

Sensitivity to acetylsalicylic acid (ASA) is important in the treatment of patients with coronary heart disease (CHD) after coronary artery bypass grafting (CABG). Patients were divided into ASA sensitive (sASA) and ASA resistant (rASA) by the activity of platelet aggregation induced arachidonic acid (ARA) together with ASA. Induced platelet aggregation activity was studied in sASA and rASA patients with CHD before and after CABG. The level of synthesis of primary and secondary reactive oxygen species (ROS) by platelets was determined using chemiluminescent analysis. The activity of NAD- and NADP-dependent dehydrogenases in platelets was determined by the bioluminescent method. It was found that the aggregation activity of platelets depended on the sensitivity of CHD patients to ASA and decreased during postoperative ASA therapy. The most pronounced differences in metabolic parameters of platelets in sASA and rASA patients were detected by Nox2 activity. The synthesis of secondary ROS by platelets of CHD patients did not depend on the sensitivity of patients to ASA but increased during postoperative treatment with ASA. The activity of NAD(P)-dependent dehydrogenases in platelets did not differ in sASA and rASA patients with CHD.

Crystallographic snapshots of UDP-glucuronic acid 4-epimerase ligand binding, rotation, and reduction

UDP-glucuronic acid is converted to UDP-galacturonic acid en route to a variety of sugar-containing metabolites. This reaction is performed by a NAD⁺-dependent epimerase belonging to the short-chain dehydrogenase/reductase family. We present several high-resolution crystal structures of the UDP-glucuronic acid epimerase from Bacillus cereus The geometry of the substrate-NAD⁺ interactions is finely arranged to promote hydride transfer. The exquisite complementarity between glucuronic acid and its binding site is highlighted by the observation that the unligated cavity is occupied by a cluster of ordered waters whose positions overlap the polar groups of the sugar substrate. Co-crystallization experiments led to a structure where substrate- and product-bound enzymes coexist within the same crystal. This equilibrium structure reveals the basis for a "swing and flip" rotation of the pro-chiral 4-keto-hexose-uronic acid intermediate that results from glucuronic acid oxidation, placing the C4' atom in position for receiving a hydride ion on the opposite side of the sugar ring. The product-bound active site is almost identical to that of the substrate-bound structure and satisfies all hydrogen-bonding requirements of the ligand. The structure of the apoenzyme together with the kinetic isotope effect and mutagenesis experiments further outlines a few flexible loops that exist in discrete conformations, imparting structural malleability required for ligand rotation while avoiding leakage of the catalytic intermediate and/or side reactions. These data highlight the double nature of the enzymatic mechanism: the active site features a high degree of precision in substrate recognition combined with the flexibility required for intermediate rotation.

Alteration of Electron Acceptor Preferences in the Oxidative Half-Reaction of Flavin-Dependent Oxidases and Dehydrogenases

In this review, recent progress in the engineering of the oxidative half-reaction of flavin-dependent oxidases and dehydrogenases is discussed, considering their current and future applications in bioelectrochemical studies, such as for the development of biosensors and biofuel cells. There have been two approaches in the studies of oxidative half-reaction: engineering of the oxidative half-reaction with oxygen, and engineering of the preference for artificial electron acceptors. The challenges for engineering oxidative half-reactions with oxygen are further categorized into the following approaches: (1) mutation to the putative residues that compose the cavity where oxygen may be located, (2) investigation of the vicinities where the reaction with oxygen may take place, and (3) investigation of possible oxygen access routes to the isoalloxazine ring. Among these approaches, introducing a mutation at the oxygen access route to the isoalloxazine ring represents the most versatile and effective strategy. Studies to engineer the preference of artificial electron acceptors are categorized into three different approaches: (1) engineering of the charge at the residues around the substrate entrance, (2) engineering of a cavity in the vicinity of flavin, and (3) decreasing the glycosylation degree of enzymes. Among these approaches, altering the charge in the vicinity where the electron acceptor may be accessed will be most relevant.

The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase

NADP-dependent methylene-tetrahydromethanopterin (methylene-H₄MPT) dehydrogenase (MtdA) catalyzes the reversible dehydrogenation of methylene-H₄MPT to form methenyl-H₄MPT⁺ by using NADP⁺ as a hydride acceptor. This hydride transfer reaction is involved in the oxidative metabolism from formaldehyde to CO₂ in methylotrophic and methanotrophic bacteria. Here, we report on the crystal structures of the ternary MtdA-substrate complexes from Methylorubrum extorquens AM1 obtained in open and closed forms. Their conversion is accomplished by opening/closing the active site cleft via a 15° rotation of the NADP, relative to the pterin domain. The 1.08 Å structure of the closed and active enzyme-NADP-methylene-H₄MPT complex allows a detailed geometric analysis of the bulky substrates and a precise prediction of the hydride trajectory. Upon domain closure, the bulky substrate rings become compressed resulting in a tilt of the imidazolidine group of methylene-H₄MPT that optimizes the geometry for hydride transfer. An additional 1.5 Å structure of MtdA in complex with the nonreactive NADP⁺ and methenyl-H₄MPT⁺ revealed an extremely short distance between nicotinamide-C4 and imidazoline-C14a of 2.5 Å, which demonstrates the strong pressure imposed. The pterin-imidazolidine-phenyl butterfly angle of methylene-H₄MPT bound to MtdA is smaller than that in the enzyme-free state but is similar to that in H₂- and F₄₂₀-dependent methylene-H₄MPT dehydrogenases. The concept of compression-driven hydride transfer including quantum mechanical hydrogen tunneling effects, which are established for flavin- and NADP-dependent enzymes, can be expanded to hydride-transferring H₄MPT-dependent enzymes.

Selective enrichment of heterotrophic nitrifiers Alcaligenaceae and Alcanivorax spp. from industrial wastewaters

Removal of nitrogen from wastewaters (WW) represents a global problem. The low nitrification rate during WW treatment is often caused by ecotoxicity. This problem is attributed mostly to the industrial WW. Our study was focused on the testing of industrial WW and activated sludge (AS) with the aim to reveal the abundance of nitrifiers and increase their biomass, thus, providing the additional step, i.e., bioaugmentation, within the technological process of WW treatment. Plating of AS on the selective solidified media designated for the 1st and 2nd nitrification stages, resulted in the shift in bacterial community structure with dominated Alcaligenaceae and Alcanivorax for the 1st stage, and Alcanivorax-for the 2nd stage of nitrification, respectively. Incubation of AS in the presence of real WW and selective nitrification broth resulted in a considerable increase (one or two magnitudes in the presence of the 1st and 2nd stage nitrification broth, respectively) of culturable nitrifiers after 5 days incubation under aerated conditions. The obtained data provide with evidence about a possibility to strengthen the role of heterotrophic nitrifiers in the treatment of industrial WW, where toxicity obstacles inhibited nitrification under conventional conditions.

The mycolic acid reductase Rv2509 has distinct structural motifs and is essential for growth in slow-growing mycobacteria

The final step in mycolic acid biosynthesis in Mycobacterium tuberculosis is catalysed by mycolyl reductase encoded by the Rv2509 gene. Sequence analysis and homology modelling indicate that Rv2509 belongs to the short‐chain fatty acid dehydrogenase/reductase (SDR) family, but with some distinct features that warrant its classification as belonging to a novel family of short‐chain dehydrogenases. In particular, the predicted structure revealed a unique α‐helical C‐terminal region which we demonstrated to be essential for Rv2509 function, though this region did not seem to play any role in protein stabilisation or oligomerisation. We also show that unlike the M. smegmatis homologue which was not essential for growth, Rv2509 was an essential gene in slow‐growing mycobacteria. A knockdown strain of the BCG2529 gene, the Rv2509 homologue in Mycobacterium bovis BCG, was unable to grow following the conditional depletion of BCG2529. This conditional depletion also led to a reduction of mature mycolic acid production and accumulation of intermediates derived from 3‐oxo‐mycolate precursors. Our studies demonstrate novel features of the mycolyl reductase Rv2509 and outline its role in mycobacterial growth, highlighting its potential as a new target for therapies.

Functional Characterization and Structural Analysis of NADH Oxidase Mutants from Thermus thermophilus HB27: Role of Residues 166, 174, and 194 in the Catalytic Properties and Thermostability

The Thermus thermophilus strain HB27 NADH-oxidase (Tt27-NOX) catalyzes the oxidation of nicotinamide adenine dinucleotide (NAD(P)H) by reducing molecular oxygen to hydrogen peroxide in a two-electron transfer mechanism. Surprisingly, Tt27-NOX showed significant differences in catalytic properties compared to its counterpart from the strain HB8 (Tt8-NOX), despite a high degree of sequence homology between both variants. The sequence comparison between both enzymes revealed only three divergent amino acid residues at positions 166, 174, and 194. Motivated with these findings, in this work we performed mutagenesis experiments in the former three positions to study the specific role of these residues in the catalytic properties and thermostability of Tt27-NOX. We subjected five mutants, along with the wild-type enzyme, to biochemical characterization and thermal stability studies. As a result, we identified two more active and more thermostable variants than any Tt8-NOX variant reported in the literature. The most active and thermostable variant K166/H174/Y194 retained 90% of its initial activity after 5 h at pH 7 and 80 °C and an increase in melting temperature of 48.3 °C compared with the least active variant K166/R174/Y194 (inactivated after 15 min of incubation). These results, supported by structural analysis and molecular dynamics simulation studies, suggest that Lys at position 166 may stabilize the loop in which His174 is located, increasing thermal stability.

Staphylopine and pseudopaline dehydrogenase from bacterial pathogens catalyze reversible reactions and produce stereospecific metallophores

Pseudopaline and staphylopine are opine metallophores biosynthesized by Pseudomonas aeruginosa and Staphylococcus aureus, respectively. The final step in opine metallophore biosynthesis is the condensation of the product of a nicotianamine (NA) synthase reaction (i.e. l-HisNA for pseudopaline and d-HisNA for staphylopine) with an α-keto acid (α-ketoglutarate for pseudopaline and pyruvate for staphylopine), which is performed by an opine dehydrogenase. We hypothesized that the opine dehydrogenase reaction would be reversible only for the opine metallophore product with (R)-stereochemistry at carbon C2 of the α-keto acid (prochiral prior to catalysis). A kinetic analysis using stopped-flow spectrometry with (R)- or (S)-staphylopine and kinetic and structural analysis with (R)- and (S)-pseudopaline confirmed catalysis in the reverse direction for only (R)-staphylopine and (R)-pseudopaline, verifying the stereochemistry of these two opine metallophores. Structural analysis at 1.57-1.85 Å resolution captured the hydrolysis of (R)-pseudopaline and allowed identification of a binding pocket for the l-histidine moiety of pseudopaline formed through a repositioning of Phe-340 and Tyr-289 during the catalytic cycle. Transient-state kinetic analysis revealed an ordered release of NADP⁺ followed by staphylopine, with staphylopine release being the rate-limiting step in catalysis. Knowledge of the stereochemistry for opine metallophores has implications for future studies involving kinetic analysis, as well as opine metallophore transport, metal coordination, and the generation of chiral amines for pharmaceutical development.

Gossypol Suppresses Growth of Temozolomide-Resistant Glioblastoma Tumor Spheres

Temozolomide is the current first-line treatment for glioblastoma patients but, because many patients are resistant to it, there is an urgent need to develop antitumor agents to treat temozolomide-resistant glioblastoma. Gossypol, a natural polyphenolic compound, has been studied as a monotherapy or combination therapy for the treatment of glioblastoma. The combination of gossypol and temozolomide has been shown to inhibit glioblastoma, but it is not clear yet whether gossypol alone can suppress temozolomide-resistant glioblastoma. We find that gossypol suppresses the growth of temozolomide-resistant glioblastoma cells in both tumor sphere and adherent culture conditions, with tumor spheres showing the greatest sensitivity. Molecular docking and binding energy calculations show that gossypol has a similar affinity to the Bcl2 (B-cell lymphoma 2) family of proteins and several dehydrogenases. Gossypol reduces mitochondrial membrane potential and cellular ATP levels before cell death, which suggests that gossypol inhibits several dehydrogenases in the cell’s metabolic pathway. Treatment with a Bcl2 inhibitor does not fully explain the effect of gossypol on glioblastoma. Overall, this study demonstrates that gossypol can suppress temozolomide-resistant glioblastoma and will be helpful for the refinement of gossypol treatments by elucidating some of the molecular mechanisms of gossypol in glioblastoma.

Mice lacking the epidermal retinol dehydrogenases SDR16C5 and SDR16C6 display accelerated hair growth and enlarged meibomian glands

Retinol dehydrogenases catalyze the rate-limiting step in the biosynthesis of retinoic acid, a bioactive lipid molecule that regulates the expression of hundreds of genes by binding to nuclear transcription factors, the retinoic acid receptors. Several enzymes exhibit retinol dehydrogenase activities in vitro; however, their physiological relevance for retinoic acid biosynthesis in vivo remains unclear. Here, we present evidence that two murine epidermal retinol dehydrogenases, short-chain dehydrogenase/reductase family 16C member 5 (SDR16C5) and SDR16C6, contribute to retinoic acid biosynthesis in living cells and are also essential for the oxidation of retinol to retinaldehyde in vivo Mice with targeted knockout of the more catalytically active SDR16C6 enzyme have no obvious phenotype, possibly due to functional redundancy, because Sdr16c5 and Sdr16c6 exhibit an overlapping expression pattern during later developmental stages and in adulthood. Mice that lack both enzymes are viable and fertile but display accelerated hair growth after shaving and also enlarged meibomian glands, consistent with a nearly 80% reduction in the retinol dehydrogenase activities of skin membrane fractions from the Sdr16c5/Sdr16c6 double-knockout mice. The up-regulation of hair-follicle stem cell genes is consistent with reduced retinoic acid signaling in the skin of the double-knockout mice. These results indicate that the retinol dehydrogenase activities of murine SDR16C5 and SDR16C6 enzymes are not critical for survival but are responsible for most of the retinol dehydrogenase activity in skin, essential for the regulation of the hair-follicle cycle, and required for the maintenance of both sebaceous and meibomian glands.

Dual Role of gnaA in Antibiotic Resistance and Virulence in Acinetobacter baumannii

Acinetobacter baumannii is an important Gram-negative pathogen in hospital-related infections. However, treatment options for A. baumannii infections have become limited due to multidrug resistance. Bacterial virulence is often associated with capsule genes found in the K locus, many of which are essential for biosynthesis of the bacterial envelope. However, the roles of other genes in the K locus remain largely unknown. From an in vitro evolution experiment, we obtained an isolate of the virulent and multidrug-resistant A. baumannii strain MDR-ZJ06, called MDR-ZJ06^M, which has an insertion by the ISAba16 transposon in gnaA (encoding UDP-N-acetylglucosamine C-6 dehydrogenase), a gene found in the K locus. The isolate showed an increased resistance toward tigecycline, whereas the MIC decreased in the case of carbapenems, cephalosporins, colistin, and minocycline. By using knockout and complementation experiments, we demonstrated that gnaA is important for the synthesis of lipooligosaccharide and capsular polysaccharide and that disruption of the gene affects the morphology, drug susceptibility, and virulence of the pathogen.

Comparison of three seemingly similar lytic polysaccharide monooxygenases from Neurospora crassa suggests different roles in plant biomass degradation

Many fungi produce multiple lytic polysaccharide monooxygenases (LPMOs) with seemingly similar functions, but the biological reason for this multiplicity remains unknown. To address this question, here we carried out comparative structural and functional characterizations of three cellulose-active C4-oxidizing family AA9 LPMOs from the fungus Neurospora crassa, NcLPMO9A (NCU02240), NcLPMO9C (NCU02916), and NcLPMO9D (NCU01050). We solved the three-dimensional structure of copper-bound NcLPMO9A at 1.6-Å resolution and found that NcLPMO9A and NcLPMO9C, containing a CBM1 carbohydrate-binding module, bind cellulose more strongly and were less susceptible to inactivation than NcLPMO9D, which lacks a CBM. All three LPMOs were active on tamarind xyloglucan and konjac glucomannan, generating similar products but clearly differing in activity levels. Importantly, in some cases, the addition of phosphoric acid-swollen cellulose (PASC) had a major effect on activity: NcLPMO9A was active on xyloglucan only in the presence of PASC, and PASC enhanced NcLPMO9D activity on glucomannan. Interestingly, the three enzymes also exhibited large differences in their interactions with enzymatic electron donors, which could reflect that they are optimized to act with different reducing partners. All three enzymes efficiently used H₂O₂ as a cosubstrate, yielding product profiles identical to those obtained in O₂-driven reactions with PASC, xyloglucan, or glucomannan. Our results indicate that seemingly similar LPMOs act preferentially on different types of copolymeric substructures in the plant cell wall, possibly because these LPMOs are functionally adapted to distinct niches differing in the types of available reductants.

Addition of formate dehydrogenase increases the production of renewable alkane from an engineered metabolic pathway

An engineered metabolic pathway consisting of reactions that convert fatty acids to aldehydes and eventually alkanes would provide a means to produce biofuels from renewable energy sources. The enzyme aldehyde-deformylating oxygenase (ADO) catalyzes the conversion of aldehydes and oxygen to alkanes and formic acid and uses oxygen and a cellular reductant such as ferredoxin (Fd) as co-substrates. In this report, we aimed to increase ADO-mediated alkane production by converting an unused by-product, formate, to a reductant that can be used by ADO. We achieved this by including the gene (fdh), encoding formate dehydrogenase from Xanthobacter sp. 91 (XaFDH), into a metabolic pathway expressed in Escherichia coli Using this approach, we could increase bacterial alkane production, resulting in a conversion yield of ∼50%, the highest yield reported to date. Measuring intracellular nicotinamide concentrations, we found that E. coli cells harboring XaFDH have a significantly higher concentration of NADH and a higher NADH/NAD⁺ ratio than E. coli cells lacking XaFDH. In vitro analysis disclosed that ferredoxin (flavodoxin):NADP⁺ oxidoreductase could use NADH to reduce Fd and thus facilitate ADO-mediated alkane production. As formic acid can decrease the cellular pH, the addition of formate dehydrogenase could also maintain the cellular pH in the neutral range, which is more suitable for alkane production. We conclude that this simple, dual-pronged approach of increasing NAD(P)H and removing extra formic acid is efficient for increasing the production of renewable alkanes via synthetic biology-based approaches.

An in silico Workflow that Yields Experimentally Comparable Inhibitors for Human Dihydroorotate Dehydrogenase

INTRODUCTION

Rheumatoid Arthritis [RA] is an autoimmune disease that can cause chronic inflammation of the joints. Human DiHydroOrotate DeHydrogenase [DHODH] is a clinically validated drug target for the treatment of Rheumatoid Arthritis. DHODH inhibition results in beneficial immunosuppressant and anti-proliferative effects.

MATERIALS AND METHODS

Leflunomide [LEF] and Brequinar Sodium [BREQ], drugs used in the treatment of RA, suppresses the immune cells responsible for inflammation but has several side-effects, most predominant being symptomatic liver damage and toxicity. An existing scaffold based on structural analogies with LEF and BREQ was used to screen out potent inhibitors of DHODH, in ZINC Database using 2D binary fingerprint. 10 structures similar to the scaffold were shortlisted due to their Tanimoto similarity coefficient. Selected structures were docked using the tools AutoDock, Ligand fit and iGEMDOCK with target human DHODH. High scoring compounds having similar interactions as that of scaffold were checked to evaluate their Drug-Likeliness.

RESULTS

The five shortlisted compounds were then subjected to Molecular Dynamics Simulation studies for 50ns using GROMACS. Measures of structural similarity based on 2D Fingerprint Screening and Molecular Dynamics Simulation studies can suggest good leads for drug designing. The novelty of this study is that the workflow used here yields the same results that are at par with the experimental data.

CONCLUSION

This suggests the use of the 2D fingerprint similarity search in various databases, followed by multiple docking algorithms and dynamics as a workflow that will lead to finding novel compounds that a structurally and functionally similar to LEF and BREQ.

Chemoenzymatic Hydrogen Production from Methanol through the Interplay of Metal Complexes and Biocatalysts

Microbial methylotrophic organisms can serve as great inspiration in the development of biomimetic strategies for the dehydrogenative conversion of C₁ molecules under ambient conditions. In this Concept article, a concise personal perspective on the recent advancements in the field of biomimetic catalytic models for methanol and formaldehyde conversion, in the presence and absence of enzymes and co-factors, towards the formation of hydrogen under ambient conditions is given. In particular, formaldehyde dehydrogenase mimics have been introduced in stand-alone C₁ -interconversion networks. Recently, coupled systems with alcohol oxidase and dehydrogenase enzymes have been also developed for in situ formation and decomposition of formaldehyde and/or reduced/oxidized nicotinamide adenine dinucleotide (NADH/ NAD⁺ ). Although C₁ molecules are already used in many industries for hydrogen production, these conceptual bioinspired low-temperature energy conversion processes may lead one day to more efficient energy storage systems enabling renewable and sustainable hydrogen generation for hydrogen fuel cells under ambient conditions using C₁ molecules as fuels for mobile and miniaturized energy storage solutions in which harsh conditions like those in industrial plants are not applicable.

Characterization of the recombinant (R)- and (S)-hydroxypropyl-coenzyme M dehydrogenases: A case study to augment the teaching of enzyme kinetics and stereoselectivity

A homologous pair of stereospecific NAD-dependent enzymes, (R)- and (S)-hydroxypropyl-coenzyme M dehydrogenase, are part of a bacterial pathway of short-chain alkene and epoxide metabolism. Their discovery and study, which spans multiple publications over more than a decade, is a data rich story that combines both classical and contemporary experimental biochemistry. A subset of the data for characterization of the recombinant enzymes was used as a case study to augment the teaching of enzyme kinetics and stereoselectivity in an undergraduate biochemistry course at California State University-Chico. © 2018 International Union of Biochemistry and Molecular Biology, 47(2): 124-132, 2019.

Enzymology of monoterpene functionalization in glandular trichomes

The plant kingdom supports an extraordinary chemical diversity, with terpenoids representing a particularly diversified class of secondary (or specialized) metabolites. Volatile and semi-volatile terpenoids in the C10-C20 range are often formed in specialized cell types and secretory structures. In the angiosperm lineage, glandular trichomes play an important role in enabling the biosynthesis and storage (or in some cases secretion) of functionalized terpenoids. The 'decoration' of a terpenoid scaffold with functional groups changes its physical and chemical properties, and can therefore affect the perception of a specific metabolite by other organisms. Because of the ecological implications (e.g. plant-herbivore interactions) and commercial relevance (e.g. volatiles used in the flavor and fragrance industries), terpenoid functionalization has been researched extensively. Recent successes in the cloning and functional evaluation of genes as well as the structural and biochemical characterization of enzyme catalysts have laid the foundation for an improved understanding of how pathways toward functionalized monoterpenes may have evolved. In this review, we will focus on an up-to-date account of functionalization reactions present in glandular trichomes.

Architecture of Microcin B17 Synthetase: An Octameric Protein Complex Converting a Ribosomally Synthesized Peptide into a DNA Gyrase Poison

The introduction of azole heterocycles into a peptide backbone is the principal step in the biosynthesis of numerous compounds with therapeutic potential. One of them is microcin B17, a bacterial topoisomerase inhibitor whose activity depends on the conversion of selected serine and cysteine residues of the precursor peptide to oxazoles and thiazoles by the McbBCD synthetase complex. Crystal structures of McbBCD reveal an octameric B₄C₂D₂ complex with two bound substrate peptides. Each McbB dimer clamps the N-terminal recognition sequence, while the C-terminal heterocycle of the modified peptide is trapped in the active site of McbC. The McbD and McbC active sites are distant from each other, which necessitates alternate shuttling of the peptide substrate between them, while remaining tethered to the McbB dimer. An atomic-level view of the azole synthetase is a starting point for deeper understanding and control of biosynthesis of a large group of ribosomally synthesized natural products.

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Azole synthetase McbBCD is co-crystallized with its product, microcin B17

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Crystal structure of McbBCD reveals an octameric assembly of B₄C₂D₂

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Two McbB subunits within each asymmetric unit interact to recognize a peptide

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Formation of each azole ring requires shuttling of peptide between two active centers