Engineering A-type Dye-Decolorizing Peroxidases by Modification of a Conserved Glutamate Residue

Dye-decolorizing peroxidases (DyPs) are recently identified microbial enzymes that have been used in several Biotechnology applications from wastewater treatment to lignin valorization. However, their properties and mechanism of action still have many open questions. Their heme-containing active site is buried by three conserved flexible loops with a putative role in modulating substrate access and enzyme catalysis. Here, we investigated the role of a conserved glutamate residue in stabilizing interactions in loop 2 of A-type DyPs. First, we did site saturation mutagenesis of this residue, replacing it with all possible amino acids in bacterial DyPs from Bacillus subtilis (BsDyP) and from Kitasatospora aureofaciens (KaDyP1), the latter being characterized here for the first time. We screened the resulting libraries of variants for activity towards ABTS and identified variants with increased catalytic efficiency. The selected variants were purified and characterized for activity and stability. We furthermore used Molecular Dynamics simulations to rationalize the increased catalytic efficiency and found that the main reason is the electron channeling becoming easier from surface-exposed tryptophans. Based on our findings, we also propose that this glutamate could work as a pH switch in the wild-type enzyme, preventing intracellular damage.

Biochemical Characterization of Laccase from Spirulina CPCC-695 and Their Role in Estrone Degradation

The addition of exogenous endocrine disrupting compounds (EDCs) like estrone, in the food chain through the aquatic system, disrupts steroid biosynthesis and metabolism by altering either the genomic or non-genomic pathway that eventually results in various diseases. Thus, bioremediation of these compounds is urgently required to prevent their addition and persistence in the environment. Enzymatic degradation has proven to be a knight in shining armour as it is safe and generates no toxic products. The multicopper oxidases (E.C. 1.10.3.2 benzenediol: oxygen oxidoreductase), laccase with the potential to degrade both phenolic and non-phenolic substrates has recently gained attention. In this study, the laccase was purified, characterized, and used to study estrone degradation. The culture filtrate (crude laccase) was concentrated and precipitated using cold-acetone and dialyzed against tris buffer (50 mM) giving a four-fold partially purified form, with 45.56% yield and 204.14 U/mg as specific activity and a single peak at 250-300 nm. The partially purified laccase was approximately 80 kDa as estimated by SDS-PAGE preferred ABTS as substrate. Both crude and partially purified laccase showed maximum activity at pH 3.0, 40 °C, and 4 mM ABTS. Kinetic constants (Km, Vmax) of crude and partially purified laccase were found to be 0.83 mM; 494.31 mM/min, and 0.58 mM; 480.54 mM/min respectively. Iron sulphate and sodium azide inhibited laccase maximally. Crude and partially purified laccase degradation efficiency was 87.55 and 91.35% respectively. Spirulina CPCC-695 laccase with efficient estrone degradation ability renders them promising candidates for EDCs bioremediation.

A wide array of lignin-related phenolics are oxidized by an evolved bacterial dye-decolourising peroxidase

Lignin is the second most abundant natural polymer next to cellulose and by far the largest renewable source of aromatic compounds on the planet. Dye-decolourising peroxidases (DyPs) are biocatalysts with immense potential in lignocellulose biorefineries to valorize emerging lignin building blocks for environmentally friendly chemicals and materials. This work investigates the catalytic potential of the engineered PpDyP variant 6E10 for the oxidation of 24 syringyl, guaiacyl and hydroxybenzene lignin-phenolic derivatives. Variant 6E10 exhibited up to 100-fold higher oxidation rates at pH 8 for all the tested phenolic substrates compared to the wild-type enzyme and other acidic DyPs described in the literature. The main products of reactions were dimeric isomers with molecular weights of (2 × MWsubstrate - 2 H). Their structure depends on the substitution pattern of the aromatic ring of substrates, i.e., of the coupling possibilities of the primarily formed radicals upon enzymatic oxidation. Among the dimers identified were syringaresinol, divanillin and diapocynin, important sources of structural scaffolds exploitable in medicinal chemistry, food additives and polymers.

Chemoenzymatic approach towards the synthesis of the antitumor and antileishmanial marine metabolite (+)-Harzialactone A via the stereoselective, biocatalyzed reduction of a prochiral ketone

As a rich source of biological active compounds, marine natural products have been increasingly screened as candidates for developing new drugs. Among the several marine products and metabolites, (+)-Harzialactone A has drawn considerable attention for its antitumor and antileishmanial activity. In this work a chemoenzymatic approach has been implemented for the preparation of the marine metabolite (+)-Harzialactone A. The synthesis involved a stereoselective, biocatalyzed reduction of the prochiral ketone 4-oxo-5-phenylpentanoic acid or the corresponding esters, all generated by chemical reactions. A collection of different promiscuous oxidoreductases (both wild-type and engineered) and diverse microorganism strains were investigated to mediate the bioconversions. After co-solvent and co-substrate investigation in order to enhance the bioreduction performance, T. molischiana in presence of NADES (choline hydrochloride-glucose) and ADH442 were identified as the most promising biocatalysts, allowing the obtainment of the (S)-enantiomer with excellent ee (97% to > 99% respectively) and good to excellent conversion (88% to 80% respectively). The successful attempt in this study provides a new chemoenzymatic approach for the synthesis of (+)-Harzialactone A.

Probing the mechanism of flavin action in the oxidative decarboxylation catalyzed by salicylate hydroxylase

Salicylate hydroxylase (NahG) is a FAD-dependent monooxygenase in which the reduced flavin activates O₂ coupled to the oxidative decarboxylation of salicylate to catechol or uncoupled from substrate oxidation to afford H₂O₂. This chapter presents different methodologies in equilibrium studies, steady-state kinetics, and identification of reaction products, which were important to understand the S_EAr mechanism of catalysis in NahG, the role of the different FAD parts for ligand binding, the extent of uncoupled reaction, and the catalysis of salicylate's oxidative decarboxylation. These features are likely familiar to many other FAD-dependent monooxygenases and offer a potential asset for developing new tools and strategies in catalysis.

Eco-friendly detoxification of hazardous Congo red dye using novel fungal strain Trametes flavida WTFP2: Deduced enzymatic biomineralization process through combinatorial in-silico and in-vitro studies

Growing textile industry is a major global concern, owing to the presence of recalcitrant hazardous pollutants, like synthetic dyes in discharged effluents. To explore new bioresources for mycoremediation, a high laccase-producing novel white-rot fungus (WRF), Trametes flavida WTFP2, was employed. T. flavida is an underexplored member of Polyporales. Using bioinformatic tools, 8 different cis-acting RNA elements were identified in the 5.8 S ITS gene sequence, where CRISPR (CRISPR-DR15), sRNA (RUF1), and snoRNA (ceN111) are uniquely present. Molecular docking was adopted to predict the catalytic interaction of chosen toxic diazo colorant, Congo red (CR), with four dye-degrading enzymes (laccase, lignin peroxidase, azoreductase, and aryl alcohol oxidase). With 376.41 × 10³ U/L laccase production, novel WRF exhibited dye-decolorization potential. WTFP2 effectively removed 99.48 ± 0.04% CR (100 mg/L) and demonstrated remarkable recyclability and persistence in consecutive remediation trials. Mycelial dye adsorption was not only substantial driver of colorant elimination; decolorization using active T. flavida was regulated by enzymatic catalysis, as outlined by in-vitro growth, induction of extracellular enzymes, and FESEM. Fifteen metabolites were identified using HRLCMS-QTOF, and novel CR degradation pathway was proposed. Furthermore, microbial and phyto-toxicity tests of metabolites suggested complete detoxification of toxic dye, making the process clean, green, and economically sustainable.

Biocatalysis for biorefineries: The case of dye-decolorizing peroxidases

Dye-decolorizing Peroxidases (DyPs) are heme-containing enzymes in fungi and bacteria that catalyze the reduction of hydrogen peroxide to water with concomitant oxidation of various substrates, including anthraquinone dyes, lignin-related phenolic and non-phenolic compounds, and metal ions. Investigation of DyPs has shed new light on peroxidases, one of the most extensively studied families of oxidoreductases; still, details of their microbial physiological role and catalytic mechanisms remain to be fully disclosed. They display a distinctive ferredoxin-like fold encompassing anti-parallel β-sheets and α-helices, and long conserved loops surround the heme pocket with a role in catalysis and stability. A tunnel routes H₂O₂ to the heme pocket, whereas binding sites for the reducing substrates are in cavities near the heme or close to distal aromatic residues at the surface. Variations in reactions, the role of catalytic residues, and mechanisms were observed among different classes of DyP. They were hypothetically related to the presence or absence of distal H₂O molecules in the heme pocket. The engineering of DyPs for improved properties directed their biotechnological applications, primarily centered on treating textile effluents and degradation of other hazardous pollutants, to fields such as biosensors and valorization of lignin, the most abundant renewable aromatic polymer. In this review, we track recent research contributions that furthered our understanding of the activity, stability, and structural properties of DyPs and their biotechnological applications. Overall, the study of DyP-type peroxidases has significant implications for environmental sustainability and the development of new bio-based products and materials with improved end-of-life options via biodegradation and chemical recyclability, fostering the transition to a sustainable bio-based industry in the circular economy realm.

Expansion of the Catalytic Repertoire of Alcohol Dehydrogenases in Plant Metabolism

Medium-chain alcohol dehydrogenases (ADHs) comprise a highly conserved enzyme family that catalyse the reversible reduction of aldehydes. However, recent discoveries in plant natural product biosynthesis suggest that the catalytic repertoire of ADHs has been expanded. Here we report the crystal structure of dihydroprecondylocarpine acetate synthase (DPAS), an ADH that catalyses the non-canonical 1,4-reduction of an α,β-unsaturated iminium moiety. Comparison with structures of plant-derived ADHs suggest the 1,4-iminium reduction does not require a proton relay or the presence of a catalytic zinc ion in contrast to canonical 1,2-aldehyde reducing ADHs that require the catalytic zinc and a proton relay. Furthermore, ADHs that catalysed 1,2-iminium reduction required the presence of the catalytic zinc and the loss of the proton relay. This suggests how the ADH active site can be modified to perform atypical carbonyl reductions, providing insight into how chemical reactions are diversified in plant metabolism.

Biological oxidation methods for the removal of organic and inorganic contaminants from wastewater: A comprehensive review

Enzyme-based bioremediation is a simple, cost-effective, and environmentally friendly method for isolating and removing a wide range of environmental pollutants. This study is a comprehensive review of recent studies on the oxidation of pollutants by biological oxidation methods, performed individually or in combination with other methods. The main bio-oxidants capable of removing all types of pollutants, such as organic and inorganic molecules, from fungi, bacteria, algae, and plants, and different types of enzymes, as well as the removal mechanisms, were investigated. The use of mediators and modification methods to improve the performance of microorganisms and their resistance under harsh real wastewater conditions was discussed, and numerous case studies were presented and compared. The advantages and disadvantages of conventional and novel immobilization methods, and the development of enzyme engineering to adjust the content and properties of the desired enzymes, were also explained. The optimal operating parameters such as temperature and pH, which usually lead to the best performance, were presented. A detailed overview of the different combination processes was also given, including bio-oxidation in coincident or consecutive combination with adsorption, advanced oxidation processes, and membrane separation. One of the most important issues that this study has addressed is the removal of both organic and inorganic contaminants, taking into account the actual wastewaters and the economic aspect.

Oxalate Oxidase for In Situ H2 O2 -Generation in Unspecific Peroxygenase-Catalysed Drug Oxyfunctionalisations

H₂ O₂ -driven enzymes are of great interest for industrial biotransformations. Herein, we show for the first time that oxalate oxidase (OXO) is an efficient in situ source of H₂ O₂ for one of these biocatalysts, which is known as unspecific peroxygenase (UPO). OXO is reasonably robust, produces only CO₂ as a by-product and uses oxalate as a cheap sacrificial electron donor. UPO has significant potential as an industrial catalyst for selective C-H oxyfunctionalisations, as we confirm herein by testing a diverse drug panel using miniaturised high-throughput assays and mass spectrometry. 33 out of 64 drugs were converted in 5 μL-scale reactions by the UPO with OXO (conversion >70 % for 11 drugs). Furthermore, oxidation of the drug tolmetin was achieved on a 50 mg scale (TON_UPO 25 664) with 84 % yield, which was further improved via enzyme immobilization. This one-pot approach ensures adequate H₂ O₂ levels, enabling rapid access to industrially relevant molecules that are difficult to obtain by other routes.

The Deconstruction of the Lignocellulolytic Structure of Sugarcane Bagasse by Laccases Improves the Production of H2 and Organic Acids

The production of biofuels using sugarcane bagasse (SCB) as substrate can be considered an environmentally friendly approach, due to the possibility of combining energy production with the reuse of agroindustrial wastes. This study was undertaken to explore the applicability of a new extract with the enzymes (Lac_mix) isolated from Chaetomium cupreum for SCB pretreatment. Lac_mix was more active at pH of 2.2 to 4 and 50 to 60 °C. Further, the individual and mutual effects of SCB concentration (6.6 to 23.4 g L^- 1), enzyme concentration (0.066 to 0.234 U L^- 1), and incubation time of the SCB with Lac_mix (19 to 221 min) on SCB pretreatment were evaluated using a response surface methodology and central composite design. The optimized conditions were 23.4 g L^- 1 SCB, 0.234 U mL^- 1 laccases, and 2.44 h resulting in 547 ± 108 mg L^- 1 of total sugars. This value agrees with the predicted value (455 ± 41 mg L^- 1) by the statistical model. Through the SCB pretreated with Lac_mix fermentation, 96.1% more H₂ and 22.5% more organic acids were observed compared to SCB without pretreatment. Therefore, laccases improve delignification, maximizing biomass fermentation for biofuel production.

The role of remote flavin adenine dinucleotide pieces in the oxidative decarboxylation catalyzed by salicylate hydroxylase

Salicylate hydroxylase (NahG) has a single redox site in which FAD is reduced by NADH, the O₂ is activated by the reduced flavin, and salicylate undergoes an oxidative decarboxylation by a C(4a)-hydroperoxyflavin intermediate to give catechol. We report experimental results that show the contribution of individual pieces of the FAD cofactor to the observed enzymatic activity for turnover of the whole cofactor. A comparison of the kinetic parameters and products for the NahG-catalyzed reactions of FMN and riboflavin cofactor fragments reveal that the adenosine monophosphate (AMP) and ribitol phosphate pieces of FAD act to anchor the flavin to the enzyme and to direct the partitioning of the C(4a)-hydroperoxyflavin reaction intermediate towards hydroxylation of salicylate. The addition of AMP or ribitol phosphate pieces to solutions of the truncated flavins results in a partial restoration of the enzymatic activity lost upon truncation of FAD, and the pieces direct the reaction of the C(4a)-hydroperoxyflavin intermediate towards hydroxylation of salicylate.

Biocatalytic remediation of pharmaceutically active micropollutants for environmental sustainability

The discharge of an alarming number of recalcitrant pollutants from various industrial activities presents a serious threat to environmental sustainability and ecological integrity. Bioremediation has gained immense interest around the world due to its environmentally friendly and cost-effective nature. In contrast to physical and chemical methods, the use of microbial enzymes, particularly immobilized biocatalysts, has been demonstrated as a versatile approach for the sustainable mitigation of environmental pollution. Considerable attention is now devoted to developing novel enzyme engineering approaches and state-of-the-art bioreactor design for ameliorating the overall bio-catalysis and biodegradation performance of enzymes. This review discusses the contemporary and state of the art technical and scientific progress regarding applying oxidoreductase enzyme-based biocatalytic systems to remediate a vast number of pharmaceutically active compounds from water and wastewater bodies. A comprehensive insight into enzyme immobilization, the role of mediators, bioreactors designing, and transformation products of pharmaceuticals and their associated toxicity is provided. Additional studies are necessary to elucidate enzymatic degradation mechanisms, monitor the toxicity levels of the resulting degraded metabolites and optimize the entire bio-treatment strategy for technical and economical affordability.

Methyl and Isopropyl N-Methylanthranilates Affect Primary Macrophage Function - an Insight into the Possible Immunomodulatory Mode of Action

To complement the knowledge on the anti-inflammatory activity of methyl and isopropyl N -methylanthranilates, two natural products with panacea-like properties, we investigated their effects on thioglycolate-elicited macrophages by evaluating macrophage ability to metabolize MTT, macrophage membrane function, and macrophage myeloperoxidase and phagocytic activities. Moreover, two additional aspects of the inflammatory response of these compounds, their inhibitory activity on xanthine oxidase and catalase, were studied. It was found that these two compounds regulate elicited macrophage functions, most probably by interfering with the function of cell membranes and changing the reducing cellular capacity or enzyme activity of macrophages. Nonetheless, no significant inhibitory action either towards xanthine oxidase or catalase was found, suggesting that the inhibition of these enzymes is not involved in the anti-inflammatory mode of action of these two esters.

High pressure homogenization with a cooling circulating system: The effect on physiochemical and rheological properties, enzymes, and carotenoid profile of carrot juice

The influence of high pressure homogenization (HPH) at 100-150 MPa performed by multiple passes below 35 °C on carrot juice quality and stability was studied. The highest reduction in microorganisms (by 2.47 log) was noted at 150 MPa with 5 passes of the juice through the homogenizer. The PPO and POD's residual activity increased after HPH; PG was at the same level, while PME activity increased or decreased depending on the process parameters used. HPH treatment resulted in a decrease in the apparent dynamic viscosity, turbidity and colour parameters. Five passes at 150 MPa caused an increase in the carotenoid content, especially 9-Z-β-carotene (by 154%) while the TPC did not change significantly. Carrot juice treatment at 150 MPa with 5 passes may extend its shelf-life by 3 days when stored at 4 °C.

Synthesis and analysis of 4-oxothiazolidines as potential dual inhibitors of deoxyribonuclease I and xanthine oxidase

In this study, seven new 4-oxothiazolidine derivatives were synthesized and assayed, along 7 known derivatives, for inhibitory properties against deoxyribonuclease I (DNase I) and xanthine oxidase (XO) in vitro. Among tested compounds, (5Z)-Ethyl-2-(2-(cyanomethylene)-4-oxothiazolidin-5-yliden)acetate (6) exhibited inhibitory activity against both enzymes (DNase I IC₅₀ = 67.94 ± 5.99 μM; XO IC₅₀ = 98.98 ± 13.47 μM), therefore being the first reported dual inhibitor of DNase I and XO. Observed DNase I inhibition qualifies compound 6 as the most potent small organic DNase I inhibitor reported so far. Derivatives of 2-alkyliden-4-oxothiazolidinone (1) inhibited DNase I below 200 μM, while the other tested 4-oxothiazolidine derivatives remained inactive against both enzymes. The molecular docking and molecular dynamics simulations into the binding sites of DNase I and XO enzyme allowed us to clarify the binding modes of this 4-oxothiazolidine derivative, which might aid future development of dual DNase I and XO.

Laccase as an efficacious approach to remove anticancer drugs: A study of doxorubicin degradation, kinetic parameters, and toxicity assessment

The degradation of an anticancer drug by laccase was investigated for the first time, bringing a new approach to treat these hazardous substances through the direct enzymatic application. Degradations of doxorubicin by laccase were performed in different enzymatic concentrations, pH values and temperatures through kinetic studies. The highest enzymatic degradation of doxorubicin was achieved at pH 7 and 30 ºC, which resembles effluent characteristics from wastewater treatment plants. Assays were carried out in different doxorubicin concentrations to comprehend the enzymatic kinetics of degradation. Michaelis-Menten kinetic parameters obtained were maximum velocity obtained (V_max) of 702.8 µg_DOX h^-1 L^-1 and Michaelis-Menten constant (K_M) of 4.05 µM, which showed a good affinity for the substrate. The toxicity was evaluated against L-929 cell line, and the degraded doxorubicin solution did not show a reduction in cell viability in the concentration of 250 µg L^-1. In contrast, the doxorubicin shows a reduction of 27% in cell viability. Furthermore, in the highest tested concentration (1000 µg L^-1), enzymatic degradation reduced in up 41.4% the toxicity of doxorubicin, which indicates laccase degrades doxorubicin to non-toxic compounds. In conclusion, this study provides a new application to laccase since the results showed great potential to remove anticancer drugs from effluents.

Functional diversity of prokaryotic HdrA(BC) modules: Role in flavin-based electron bifurcation processes and beyond

In methanogenic archaea, the archetypical complex of heterodisulfide reductase (HdrABC) and hydrogenase (MvhAGD) couples the endergonic reduction of CO₂ by H₂ to the exergonic reduction of the CoB-S-S-CoM heterodisulfide by H₂ via flavin-based electron bifurcation. Presently known enzymes containing HdrA(BC)-like components play key roles in methanogenesis, acetogenesis, respiratory sulfate reduction, lithotrophic reduced sulfur compound oxidation, aromatic compound degradation, fermentations, and probably many further processes. This functional diversity is achieved by a modular architecture of HdrA(BC) enzymes, where a big variety of electron input/output modules may be connected either directly or via adaptor modules to the HdrA(BC) components. Many, but not all HdrA(BC) complexes are proposed to catalyse a flavin-based electron bifurcation/confurcation. Despite the availability of HdrA(BC) crystal structures, fundamental questions of electron transfer and energy coupling processes remain. Here, we address the common properties and functional diversity of HdrA(BC) core modules integrated into electron-transfer machineries of outstanding complexity.

Glial cells in the posterior sub-esophageal mass of the brain in Sepia officinalis (Linnaeus, 1758) (decapodiformes-sepiida): ultrastructure and cytochemical studies

Electron microscopy revealed that glial cells in the posterior sub-esophageal mass of the brain in Sepia officinalis had a well-developed rough endoplasmic reticulum formed by long coverslips with rectilinear or curvilinear arrangements. The coverslips appeared dilated and have a large amount of adhered polysomes. Vesicular lamellae coexisted with the elongated lamellae of RER and dictyosomes of Golgi apparatus. Endocytosis was evidenced through the pale vesicles which were appeared next to the apical border of microvilli in some glial cells. Sub-cellular features of endocytosis, predominantly the fluid phase, were observed in the apical glial cell cytoplasm. Glial cells were related to phagocytosis of apoptotic neurons, endocytosis, pinocytosis and adsorption. These functions were proposed based on their ultrastructure characteristics and a significant number of vesicles with different shapes (oval to polygonal), sizes 0.052-0.67 µm and contents. Glycogen, MPS and lipid were detected in the glial cells. Alkaline phosphatase was not observed, while an activity of acid phosphatase was bound to lysosomes. ATPases were present in the glial cells along the lateral and basal plasma lemma as well as on the membranes of cell organelles. Unspecific esterase was clearly recognizable by electron microscopy. The monoamine and cytochrome oxidase activities were demonstrated, while the succinate dehydrogenase showed a weak enzyme activity.

Protein-protein interaction of Rv0148 with Htdy and its predicted role towards drug resistance in Mycobacterium tuberculosis

BACKGROUND

Mycobacterium tuberculosis resides inside host macrophages during infection and adapts to resilient stresses generated by the host immune system. As a response, M. tuberculosis codes for short-chain dehydrogenases/reductases (SDRs). These SDRs are nicotinamide adenine dinucleotide-reliant oxidoreductases involved in cell homeostasis. The precise function of oxidoreductases in bacteria especially M. tuberculosis were not fully explored. This study aimed to know the detail functional role of one of the oxidoreductase Rv0148 in M. tuberculosis.

RESULTS

In silico analysis revealed that Rv0148 interacts with Htdy (Rv3389) and the protein interactions were confirmed using far western blot. Gene knockout mutant of Rv0148 in M. tuberculosis was constructed by specialized transduction. Macrophage cell line infection with this knockout mutant showed increased expression of pro-inflammatory cytokines. This knockout mutant is sensitive to oxidative, nitrogen, redox and electron transport inhibitor stress agents. Drug susceptibility testing of the deletion mutant showed resistance to first-line drugs such as streptomycin and ethambutol and second-line aminoglycosides such as amikacin and kanamycin. Based on interactorme analysis for Rv0148 using STRING database, we identified 220 most probable interacting partners for Htdy protein. In the Rv0148 knockout mutants, high expression of htdy was observed and we hypothesize that this would have perturbed the interactome thus resulting in drug resistance. Finally, we propose that Rv0148 and Htdy are functionally interconnected and involved in drug resistance and cell homeostasis of M. tuberculosis.

CONCLUSIONS

Our study suggests that Rv0148 plays a significant role in various functional aspects such as intermediatory metabolism, stress, homeostasis and also in drug resistance.

Biotransformation and toxicity effect of monoanthraquinone dyes during Bjerkandera adusta CCBAS 930 cultures

The aim of this study was to evaluate of possibility of biotransformation and toxicity effect of monoanthraquinone dyes in cultures of Bjerkandera adusta CCBAS 930. Phenolic compounds, free radicals, phytotoxicity (Lepidium sativum L.), ecotoxicity (Vibrio fischeri) and cytotoxicity effect were evaluated to determine the toxicity of anthraquinone dyes before and after the treatment with B. adusta CCBAS 930. More than 80% of ABBB and AB129 was removed by biodegradation (decolorization) and biosorption, but biodegradation using oxidoreductases was the main dye removing mechanism. Secondary products toxic to plants and bacteria were formed in B. adusta strain CCBAS 930 cultures, despite efficient decolorization. ABBB and AB129 metabolites increased reactive oxygen species (ROS) production in human fibroblasts, but did not increase LDH release, did not affect the resazurine reduction assay and did not change caspase-9 or caspase-3 activity.

Protein Quality Control in the Endoplasmic Reticulum

The site of protein folding and maturation for the majority of proteins that are secreted, localized to the plasma membrane or targeted to endomembrane compartments is the endoplasmic reticulum (ER). It is essential that proteins targeted to the ER are properly folded in order to carry out their function, as well as maintain protein homeostasis, as accumulation of misfolded proteins could lead to the formation of cytotoxic aggregates. Because protein folding is an error-prone process, the ER contains protein quality control networks that act to optimize proper folding and trafficking of client proteins. If a protein is unable to reach its native state, it is targeted for ER retention and subsequent degradation. The protein quality control networks of the ER that oversee this evaluation or interrogation process that decides the fate of maturing nascent chains is comprised of three general types of families: the classical chaperones, the carbohydrate-dependent system, and the thiol-dependent system. The cooperative action of these families promotes protein quality control and protein homeostasis in the ER. This review will describe the families of the ER protein quality control network and discuss the functions of individual members.

Circulating biomarkers of antioxidant status and oxidative stress in people with cystic fibrosis: A systematic review and meta-analysis

Introduction

Oxidative stress may play an important role in the pathophysiology of cystic fibrosis (CF). This review aimed to quantify CF-related redox imbalances.

Methods

Systematic searches of the Medline, CINAHL, CENTRAL and PsycINFO databases were conducted. Mean content of blood biomarkers from people with clinically-stable CF and non-CF controls were used to calculate the standardized mean difference (SMD) and 95% confidence intervals (95% CI).

Results

Forty-nine studies were eligible for this review including a total of 1792 people with CF and 1675 controls. Meta-analysis revealed that protein carbonyls (SMD: 1.13, 95% CI: 0.48 to 1.77), total F₂-isoprostane 8-iso-prostaglandin F_2α (SMD: 0.64, 95% CI: 0.23 to 1.05) and malondialdehyde (SMD: 1.34, 95% CI: 0.30 to 2.39) were significantly higher, and vitamins A (SMD: −0.66, 95% CI -1.14 to −0.17) and E (SMD: −0.74, 95% CI: −1.28 to −0.20), β-carotene (SMD: −1.80, 95% CI: −2.92 to −0.67), lutein (SMD: −1.52, 95% CI: −1.83 to −1.20) and albumin (SMD: −0.98, 95% CI: −1.68 to −0.27) were significantly lower in the plasma or serum of people with CF versus controls.

Conclusions

This systematic review and meta-analysis found good evidence for reduced antioxidant capacity and elevated oxidative stress in people with clinically-stable CF.

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Blood biomarkers of oxidative stress were elevated in stable CF vs non-CF controls.

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Lipid peroxidation was positively correlated with age and immune cell count in CF.

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Antioxidants vitamins A & E, β-carotene, lutein and albumin were lower in stable CF.

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Antioxidants were positively correlated with body mass index and lung function in CF.

Highly thermostable carboxylic acid reductases generated by ancestral sequence reconstruction

Carboxylic acid reductases (CARs) are biocatalysts of industrial importance. Their properties, especially their poor stability, render them sub-optimal for use in a bioindustrial pipeline. Here, we employed ancestral sequence reconstruction (ASR) - a burgeoning engineering tool that can identify stabilizing but enzymatically neutral mutations throughout a protein. We used a three-algorithm approach to reconstruct functional ancestors of the Mycobacterial and Nocardial CAR1 orthologues. Ancestral CARs (AncCARs) were confirmed to be CAR enzymes with a preference for aromatic carboxylic acids. Ancestors also showed varied tolerances to solvents, pH and in vivo-like salt concentrations. Compared to well-studied extant CARs, AncCARs had a Tm up to 35 °C higher, with half-lives up to nine times longer than the greatest previously observed. Using ancestral reconstruction we have expanded the existing CAR toolbox with three new thermostable CAR enzymes, providing access to the high temperature biosynthesis of aldehydes to drive new applications in biocatalysis.

Biocatalytic degradation/redefining "removal" fate of pharmaceutically active compounds and antibiotics in the aquatic environment

Recently, the increasing concentration and persistent appearance of antibiotics traces in the water streams are considered an issue of high concern. In this context, an array of antibiotics has been categorized as pollutants of emerging concern due to their complex and highly stable bioactivity, indiscriminate usage with ultimate release into water bodies, and notable persistence in environmental matrices. Moreover, antibiotics traces containing household sewage/drain waste and pharmaceutical wastewater effluents contain a range of bioactive/toxic organic compounds, inorganic salts, pharmaceutically-active ingredients, or a mixture of all, which possesses negative influences ranging from ecological pollution to damage biodiversity. Moreover, their uncontrolled and undesirable bioaccumulation also poses a potential threat to target and non-target organisms in the environment. Aiming to tackle this issue effectively, various detection, quantification, degradation, and redefining "removal" processes have been proposed and investigated based on physical, chemical, and biological strategies. Though both useful and side effects of antibiotics on humans and animals are usually investigated thoroughly following safety and toxicity measures, however, their direct or indirect environmental impacts are not well reviewed yet. Owing to the considerable research gap, the environmental perfectives of antibiotics traces and their effects on target and non-target populations have now become the topic of research interest. Based on literature evidence, over the past several years, numerous individual studies have been performed and published covering various aspects of antibiotics. However, a comprehensive compilation on enzyme-based degradation of antibiotics is still lacking and requires careful consideration. Hence, this review summarizes up-to-date literature on enzymes as biocatalytic systems, explicitly, free as well as immobilized forms and their effective exploitation for the degradation of various antibiotics traces and other pharmaceutically-active compounds present in the water bodies. It is further envisioned that the enzyme-based strategies, for antibiotics degradation or removal, discussed herein, will help readers for a better understanding of antibiotics persistence in the environment along with the associated risks and removal measures. In summary, the current research thrust presented in this review will additionally evoke researcher to engineer robust and sustainable processes to effectively remediate antibiotics-contaminated environmental matrices.

Consensus model of a cyanobacterial light-dependent protochlorophyllide oxidoreductase in its pigment-free apo-form and photoactive ternary complex

Photosynthetic organisms employ two different enzymes for the reduction of the C17 = C18 double bond of protochlorophyllide (Pchlide), yielding the chlorophyll precursor chlorophyllide. First, a nitrogenase-like, light-independent (dark-operative) Pchlide oxidoreductase and secondly, a light-dependent Pchlide oxidoreductase (LPOR). For the latter enzyme, despite decades of research, no structural information is available. Here, we use protein structure modelling, molecular dynamics (MD) simulations combined with multi-wavelength analytical ultracentrifugation (MWA-AUC) and small angle X-ray scattering (SAXS) experiments to derive a consensus model of the LPOR apoprotein and the substrate/cofactor/LPOR ternary complex. MWA-AUC and SAXS experiments independently demonstrate that the apoprotein is monomeric, while ternary complex formation induces dimerization. SAXS-guided modelling studies provide a full-length model of the apoprotein and suggest a tentative mode of dimerization for the LPOR ternary complex, supported by published cross-link constraints. Our study provides a first impression of the LPOR structural organization.

Effects of industrial heat treatments on the kinetics of inactivation of antimicrobial bovine milk xanthine oxidase

Milk is a source of antimicrobial systems such as xanthine oxidoreductase, which has been proposed to modulate the oral and gut microbiota of infants. Heat treatments are applied to milk to ensure its microbial safety, however, the effects of heat on this antimicrobial enzyme are not known. The effects of batch pasteurization (BP), high-temperature short time (HTST), and ultra high temperature (UHT) on kinetics of inactivation of xanthine oxidase and its antimicrobial properties were determined. Xanthine oxidase activity was preserved by HTST (100%). Partial (8%) and nearly complete (95%) enzyme inactivation were observed for BP and UHT milks, respectively. K_m values of 100 μM and V_max values of 6.85, 5.12, 6.31, and 0.40 μmol/min/mg were determined for xanthine oxidase in raw, BP, HTST, and UHT milks, respectively. These results demonstrate that xanthine oxidase maintains apparent affinity and activity for its substrate when milk is treated by BP and HTST and yet the enzyme is inactivated with UHT. To investigate heat treatment-induced alterations in the biological activity of xanthine oxidase, heat treated milks were compared to raw milk for their ability to inhibit the growth of S. aureus. Raw, BP, and HTST milk xanthine oxidase efficiently inhibited S. aureus growth. However, these antibacterial properties were lost when milk was subjected to UHT. These results demonstrate that HTST and BP preserves bovine milk xanthine oxidase activity compared with UHT and that, the judicious selection of thermal treatments could be exploited to preserve the antimicrobial properties of bovine milk.

Engineering of the Dsb (disulfide bond) proteins - contribution towards understanding their mechanism of action and their applications in biotechnology and medicine

The Dsb protein family in prokaryotes catalyzes the generation of disulfide bonds between thiol groups of cysteine residues in nascent proteins, ensuring their proper three-dimensional structure; these bonds are crucial for protein stability and function. The first Dsb protein, Escherichia coli DsbA, was described in 1991. Since then, many details of the bond-formation process have been described through microbiological, biochemical, biophysical and bioinformatics strategies. Research with the model microorganism E. coli and many other bacterial species revealed an enormous diversity of bond-formation mechanisms. Research using Dsb protein engineering has significantly helped to reveal details of the disulfide bond formation. The first part of this review presents the research that led to understanding the mechanism of action of DsbA proteins, which directly transfer their own disulfide into target proteins. The second part concentrates on the mechanism of electron transport through the cell cytoplasmic membrane. Third and lastly, the review discusses the contribution of this research towards new antibacterial agents.

Enzyme-Based Electrobiotechnological Synthesis

Oxidoreductases are enzymes with a high potential for organic synthesis, as their selectivity often exceeds comparable chemical syntheses. The biochemical cofactors of these enzymes need regeneration during synthesis. Several regeneration methods are available but the electrochemical approach offers an efficient and quasi mass-free method for providing the required redox equivalents. Electron transfer systems involving direct regeneration of natural and artificial cofactors, indirect electrochemical regeneration via a mediator, and indirect electroenzymatic cofactor regeneration via enzyme and mediator have been investigated. This chapter gives an overview of electroenzymatic syntheses with oxidoreductases, structured by the enzyme subclass and their usage of cofactors for electron relay. Particular attention is given to the productivity of electroenzymatic biotransformation processes. Because most electroenzymatic syntheses suffer from low productivity, we discuss reaction engineering concepts to overcome the main limiting factors, with a focus on media conductivity optimization, approaches to prevent enzyme inactivation, and the application of advanced cell designs. Graphical Abstract.

Emerging contaminants of high concern and their enzyme-assisted biodegradation - A review

The widespread occurrence and adverse environmental and health-related impacts of various types of emerging contaminants (ECs) have become an issue of high concern. With ever increasing scientific knowledge, socio-economic awareness, health-related problems and ecological apprehensions, people are more concerned about the widespread ECs, around the globe. Among ECs, biologically active compounds from pharmaceutical, cosmeceutical, biomedical, personal care products (PPCPs), endocrine-disrupting chemicals (EDCs), and flame-retardants are of paramount concern. The presence and persistence of ECs in water bodies are of continued and burning interest, worldwide. Various types of ECs are being discharged knowingly/unknowingly with/without partial treatments into the aquatic environments that pose serious health issues and affects the entire living ecosystem. So far, various approaches have been developed for ECs degradation and removal to diminish their adverse impact. Many previous and/or ongoing studies have focused on contaminants degradation and efficient removal via numerous treatment strategies, i.e. (1) physical, (2) chemical and (3) biological. However, the experimental evidence is lacking to enable specific predictions about ECs mechanistic degradation and removal fate across various in-practice systems. In this context, the deployment oxidoreductases such as peroxidases (lignin peroxidases, manganese-dependent peroxidases, and horseradish peroxidase), aromatic dioxygenases, various oxygenases, laccases, and tyrosinases have received considerable research attention. Immobilization is highlighted as a promising approach to improve enzyme catalytic performance and stabilization, as well as, to protect the three-dimensional structure of the enzyme against the undesirable consequences of harsh reaction environment. This work overviews the current and state-of-the-art critical aspect related to hazardous pollutants at large and ECs in particular by the immobilized oxidoreductase enzymes. The first part of the review focuses on the occurrence, physiochemical behavior, potent sources and significant routes of ECs. Following that, environmentally-related adverse impacts and health-related issues of ECs are discussed in the second part. In the third part, biodegradation and removal strategies with a comparative overview of several conventional vs. non-conventional methods are presented briefly. The fourth part majorly focuses on operational modes of different oxidoreductase enzyme-based biocatalytic processes for the biodegradation and biotransformation of a wide array of harmful environmental contaminants. Finally, the left behind research gaps, concluding remarks as well as future trends and recommendations in the use of carrier-immobilized oxidoreductases for environmental perspective are also discussed.

Dual roles of different redox forms of complement factor H in protecting against age related macular degeneration

Complement Factor H (CFH) is an important inhibitor of the alternate complement pathway in Bruch's membrane (BM), located between the choriocapillaris and the retinal pigment epithelium. Furthermore dysfunction of its activity as occurs with certain polymorphisms is associated with an increased risk of age related macular degeneration (AMD). The retina is a site of high generation of reactive oxygen species (ROS) and dysfunction of redox homeostasis in this milieu also contributes to AMD pathogenesis. In this study we wanted to explore if CFH exists in distinct redox forms and whether these species have unique protective biological functions. CFH can be reduced by the naturally occurring thioredoxin - 1 in CFH domains 1-4, 17-20. We found a duality of function between the oxidised and reduced forms of CFH. The oxidised form was more efficient in binding to C3b and lipid peroxidation by-products that are known to accumulate in the retinae and activate the alternate complement pathway. Oxidised CFH enhances Factor I mediated cleavage of C3 and C3b whereas the reduced form loses this activity. In the setting of oxidative stress (hydrogen peroxide)-mediated death of human retinal pigment epithelial cells as can occur in AMD, the free thiol form of CFH offers a protective function compared to the oxidised form. We found for the first time using a novel ELISA system we have developed for free thiol CFH, that both redox forms of CFH are found in the human plasma. Furthermore there is a distinct ratio of these redox forms in plasma depending if an individual has early or late AMD, with individuals with early AMD having higher levels of the free thiol form compared to late AMD.

Protein biocargo of citrus fruit-derived vesicles reveals heterogeneous transport and extracellular vesicle populations

Cell-derived vesicles are membrane-enclosed organelles that transport material inside and outside the cell. Plant-derived vesicles are receiving more and more attention due to their potential as nanovectors for the delivery of biologically active substances. Here, we studied the heterogeneity and protein biocargo in citrus fruit juice sac cell-derived vesicles populations. Micro- and nano-sized vesicle fractions were isolated from four citrus species, C. sinensis, C. limon, C. paradisi and C. aurantium, characterized using physicochemical methods and protein cargos were compared using label-free quantitative shotgun proteomics. In each sample approximately 600-800 proteins were identified. Orthologues of most of the top-ranking proteins have previously been reported in extracellular vesicles of mammalian origin. High expression levels of patellin-3-like, clathrin heavy chain, heat shock proteins, 14-3-3 protein, glyceraldehyde-3-phosphate dehydrogenase and fructose-bisphosphate aldolase 6 were measured in all samples while aquaporin was highly expressed only in the nanovesicle fractions. Bioinformatics revealed more than hundred protein orthologues potentially implicated in vesicular trafficking. In particular, the presence of CCV, COPI and COPII coat proteins indicates the presence of heterogeneous populations of intracellular transport vesicles. Moreover, a high number of different enzymes including hydrolases and oxidoreductases are ubiquities in citrus fruit sac cell-derived vesicles.

Biochemical and microbiological activity of soil contaminated with o-cresol and biostimulated with Perna canaliculus mussel meal

The choice of the study subject was a consequence of the growing interest in volatile organic compounds which are strongly dispersed in the environment. The knowledge of o-cresol's capability for being broken down by bacteria should be supplemented by studies aimed at determining the biochemical and microbiological activity of soils. o-Cresol was applied at the following rates: 0, 0.1, 1, 10, and 50 mg of o-cresol kg^-1 d.m. of soil to determine its effect on the biological properties of soil. The activity of dehydrogenases, catalase, urease, acid phosphatase, alkaline phosphatase, arylsulfatase, and β-glucosidase, the eight groups of microorganism counts, was determined in soil samples after 45 days and the barley yield was determined. Preventive biostimulation with Perna canaliculus mussel meal, illustrated by means of the index of fertility (IF), was conducted in order to eliminate the adverse effect of o-cresol. The soil and crop resistance index (RS) was used to illustrate the response of barley, and R:S-the rhizosphere effect index was used to determine the effect of the crop on the enzymatic activity of soil. o-Cresol had a beneficial effect on the biological activity of soil at an acceptable rate of 0.1 and 1 mg kg^-1 d.m. of soil, and it became its inhibitor after being applied at 10 and 50 mg kg^-1 d.m. of soil, which also brought about a decrease in the resistance of spring barley. Dehydrogenases are the most sensitive, and catalase is the least sensitive, to the pressure of o-cresol in soil. Mussel meal can be recommended as a biostimulator of soil fertility. It also eliminated the negative effect of o-cresol on its biological activity.

Sequence-Based In-silico Discovery, Characterisation, and Biocatalytic Application of a Set of Imine Reductases

Imine reductases (IREDs) have recently become a primary focus of research in biocatalysis, complementing other classes of amine-forming enzymes such as transaminases and amine dehydrogenases. Following in the footsteps of other research groups, we have established a set of IRED biocatalysts by sequence-based in silico enzyme discovery. In this study, we present basic characterisation data for these novel IREDs and explore their activity and stereoselectivity using a panel of structurally diverse cyclic imines as substrates. Specific activities of >1 U/mg and excellent stereoselectivities (ee>99 %) were observed in many cases, and the enzymes proved surprisingly tolerant towards elevated substrate loadings. Co-expression of the IREDs with an alcohol dehydrogenase for cofactor regeneration led to whole-cell biocatalysts capable of efficiently reducing imines at 100 mM initial concentration with no need for the addition of extracellular nicotinamide cofactor. Preparative biotransformations on gram scale using these 'designer cells' afforded chiral amines in good yield and excellent optical purity.

Developments in support materials for immobilization of oxidoreductases: A comprehensive review

Bioremediation, a biologically mediated transformation or degradation of persistent chemicals into nonhazardous or less-hazardous substances, has been recognized as a key strategy to control levels of pollutants in water and soils. The use of enzymes, notably oxidoreductases such as laccases, tyrosinases, various oxygenases, aromatic dioxygenases, and different peroxidases (all of EC class 1) is receiving significant research attention in this regard. It should be stated that immobilization is emphasized as a powerful tool for enhancement of enzyme activity and stability as well as for protection of the enzyme proteins against negative effects of harsh reaction conditions. As proper selection of support materials for immobilization and their performance is overlooked when it comes to comparing performance of immobilized enzyme in academic studies, this review summarizes the current state of knowledge regarding the materials used for enzyme immobilization of these oxidoreductase enzymes for environmental applications. In the presented study, thorough physicochemical characteristics of the support materials was presented. Moreover, various types of reactions and notably operational modes of enzymatic processes for biodegradation of harmful pollutants are summarized, and future trends in use of immobilized oxidoreductases for environmental applications are discussed. Our goal is to provide an improved foundation on which new technological advancements can be made to achieve efficient enzyme-assisted bioremediation.

Enzyme Nicotinamide Cofactor Specificity Reversal Guided by Automated Structural Analysis and Library Design

The specificity of enzymes for nicotinamide adenine dinucleotide (NAD) or nicotinamide adenine dinucleotide phosphate (NADP) as redox carriers can pose a significant hurdle for metabolic engineering and synthetic biology applications, where switching the specificity might be beneficial. We have developed an easy-to-use computational tool (CSR-SALAD) for the design of mutant libraries to simplify the process of reversing the cofactor specificity of an enzyme. Here, we describe the optimal use of this tool and present methods for its application in a laboratory setting.

Comparative study of eco- and cytotoxicity during biotransformation of anthraquinone dye Alizarin Blue Black B in optimized cultures of microscopic fungi

The aim of this study was to select optimal conditions (C and N sources, initial pH and temperature) for biodecolorization of 0.03% anthraquinone dye Alizarin Blue Black B (ABBB) by microscopic fungi: Haematonectria haematococca BwIII43, K37 and Trichoderma harzianum BsIII33. The phenolic compounds, phytotoxicity (Lepidium sativum L.), biotoxicity (Microtox), cytotoxicity and yeast viability assay were performed to determine the extent of ABBB detoxification. Biodecolorization and detoxification of 0.03% ABBB in H. haematococca BwIII43 and T. harzianum BsIII33 cultures was correlated with extracellular oxidoreductases activity. In turn, secondary products, toxic to human fibroblasts and respiring sod1 Saccharomyces cerevisiae cells, were formed in H. haematococca K37 strain cultures, despite efficient decolorization.

The genome of Pleurotus eryngii provides insights into the mechanisms of wood decay

Pleurotus eryngii (DC.) Quél. is widely used for bioconverting lignocellulosic byproducts into biofuel and value added products. Sequencing and annotating the genome of a monokaryon strain P. eryngii 183 allows us to gain a better understanding of carbohydrate-active enzymes (CAZymes) and oxidoreductases for degradation of lignocellulose in white-rot fungi. The genomic data provides insights into genomic basis of degradation mechanisms of lignin and cellulose and may pave new avenues for lignocellulose bioconversion.

Design of Redox-Active Peptides: Towards Functional Materials

In nature, the majority of processes that occur in the cell involve the cycling of electrons and protons, changing the reduction and oxidation state of substrates to alter their chemical reactivity and usefulness in vivo. One of the most relevant examples of these processes is the electron transport chain, a series of oxidoreductase proteins that shuttle electrons through well-defined pathways, concurrently moving protons across the cell membrane. Inspired by these processes, researchers have sought to develop materials to mimic natural systems for a number of applications, including fuel production. The most common cofactors found in proteins to carry out electron transfer are iron sulfur clusters and porphyrin-like molecules. Both types have been studied within natural proteins, such as in photosynthetic machinery or soluble electron carriers; in parallel, an extensive literature has developed over recent years attempting to model and study these cofactors within peptide-based materials. This chapter will focus on major designs that have significantly advanced the field.

A survey of synthetic nicotinamide cofactors in enzymatic processes

Synthetic nicotinamide cofactors are analogues of the natural cofactors used by oxidoreductases as redox intermediates. Their ability to be fine-tuned makes these biomimetics an attractive alternative to the natural cofactors in terms of stability, reactivity, and cost. The following mini-review focuses on the current state of the art of those biomimetics in enzymatic processes.

Effect of Aptamer Binding on the Electron-Transfer Properties of Redox Cofactors

In vitro selection or SELEX has allowed for the identification of functional nucleic acids (FNAs) that can potentially mimic and replace protein enzymes. These FNAs likely interact with cofactors, just like enzymes bind cofactors in their active sites. Investigating how FNA binding affects cofactor properties is important for understanding how an active site is formed and for developing useful enzyme mimics. Oxidoreductase enzymes contain cofactors in their active sites that allow the enzymes to do redox chemistry. In certain applications, these redox cofactors act as electron-transfer shuttles that transport electrons between the enzymes' active sites and electrode surfaces. Three redox cofactors commonly found in oxidoreductases are flavin adenine dinucleotide, nicotinamide adenine dinucleotide (NAD(+)), and pyrroloquinoline quinone (PQQ). We are interested in investigating how DNA aptamers that bind these cofactors influence the cofactors' redox abilities and if these aptamer-cofactor complexes could serve as redox catalysts. We employed cyclic voltammetry and amperometry to study the electrochemical properties of NAD(+) and PQQ when bound to DNA aptamers. Our results suggest that the aptamers provide a stable environment for the cofactor to participate in redox reactions, although enhanced redox activity was not observed. This work provides a foundation for the development of new FNAs capable of redox activity.

Nature-inspired enzymatic cascades to build valuable compounds

Biocatalysis currently is focusing on enzymatic and multi-enzymatic cascade processes instead of single steps imbedded into chemical pathways. Alongside this scientific revolution, this review provides an overview on multi-enzymatic cascades that are responsible for the biosynthesis of some terpenes, alkaloids and polyethers, which are important classes of natural products. Herein, we illustrate the development of studies inspired by multi- and chemo-enzymatic approaches to build the core moieties of polyethers, polypeptide alkaloids, piperidines and pyrrolidines promoted by the joint action of oxidoreductases, hydrolases, cyclases, transaminases and imine reductases.

Quorum quenching enzymes

Bacteria use cell-to-cell communication systems based on chemical signal molecules to coordinate their behavior within the population. These quorum sensing systems are potential targets for antivirulence therapies, because many bacterial pathogens control the expression of virulence factors via quorum sensing networks. Since biofilm maturation is also usually influenced by quorum sensing, quenching these systems may contribute to combat biofouling. One possibility to interfere with quorum sensing is signal inactivation by enzymatic degradation or modification. Such quorum quenching enzymes are wide-spread in the bacterial world and have also been found in eukaryotes. Lactonases and acylases that hydrolyze N-acyl homoserine lactone (AHL) signaling molecules have been investigated most intensively, however, different oxidoreductases active toward AHLs or 2-alkyl-4(1H)-quinolone signals as well as other signal-converting enzymes have been described. Several approaches have been assessed which aim at alleviating virulence, or biofilm formation, by reducing the signal concentration in the bacterial environment. These involve the application or stimulation of signal-degrading bacteria as biocontrol agents in the protection of crop plants against soft-rot disease, the use of signal-degrading bacteria as probiotics in aquaculture, and the immobilization or entrapment of quorum quenching enzymes or bacteria to control biofouling in membrane bioreactors. While most approaches to use quorum quenching as antivirulence strategy are still in the research phase, the growing number of organisms and enzymes known to interfere with quorum sensing opens up new perspectives for the development of innovative antibacterial strategies.

Strategies for regeneration of nicotinamide coenzymes emphasizing self-sufficient closed-loop recycling systems

Biocatalytic reduction reactions depending on nicotinamide coenzymes require an additional reaction to regenerate the consumed cofactor. For preparative application the preferred method is the simultaneous coupling of an in situ regeneration reaction. There are different strategically advantageous routes to achieve this goal. The standard method uses a second enzyme and a second co-substrate, for example formate and formate dehydrogenase or glucose and glucose dehydrogenase. Alternatively, a second substrate is employed which is converted by the same enzyme used for the primary reaction. For example, alcohol dehydrogenase catalyzed reactions are often coupled with excess 2-propanol which is oxidized to acetone during the regeneration of NAD(P)H. A third method utilizes a reaction-internal sequence by the direct coupling of an oxidizing and a reducing enzyme reaction. Neither an additional substrate nor a further regenerating enzyme are required for the recycling reaction. This kind of "closed-loop" or "self-sufficient" redox process for cofactor regeneration has been used rarely so far. Its most intriguing advantage is that even redox reactions with unstable precursors can be realized provided that this compound is produced in situ by an opposite redox reaction. This elegant method is applicable in special cases only but increasing numbers of examples have been published during the last years.

Identification of Genes Differentially Expressed Between Ochratoxin-Producing and Non-Producing Strains of Aspergillus westerdijkiae

Approximately 70 % of Aspergillus westerdijkiae strains are able to produce ochratoxin A (OTA), a nephrotoxic and carcinogenic mycotoxin which have been found in cereal and food commodities. Despite of its importance there is, up to now, no information available about which genes are differentially expressed between A. westerdijkiae ochratoxin-producing and non-producing strains. Using cDNA RDA approach we successfully sequenced 231 raw ESTs expected to be enriched in the ochratoxin-producing strain. BLASTX searches against the public databases showed that of these, 205 ESTs (79 %) exhibited significant similarities with proteins of known functions, 28 ESTs (11 %) had matches to hypothetical proteins, and the remaining 27 ESTs (10 %) had no significant hits. EST alignment resulted in a total of 14 non-redundant consensus sequences. Three putative genes encoding oxidoreductases were validated as up-expressed in the OTA producer strain using RT-qPCR approach. The expression of the putative genes encoding a cytochrome P450 family protein, 3-hydroxyphenylacetate-6-hydroxylase, and endoplasmic reticulum oxidoreductin were higher (32-, 2.8- and 20-fold respectively) in the OTA producer strain compared to the non-producer strain.