Flavin oxidation in flavin‐dependent N‐monooxygenases

Siderophore A (SidA) from Aspergillus fumigatus is a flavin‐containing monooxygenase that hydroxylates ornithine (Orn) at the amino group of the side chain. Lysine (Lys) also binds to the active site of SidA; however, hydroxylation is not efficient and H₂O₂ is the main product. The effect of pH on steady‐state kinetic parameters was measured and the results were consistent with Orn binding with the side chain amino group in the neutral form. From the pH dependence on flavin oxidation in the absence of Orn, a pK_a value >9 was determined and assigned to the FAD‐N5 atom. In the presence of Orn, the pH dependence displayed a pK_a value of 6.7 ±0.1 and of 7.70 ±0.10 in the presence of Lys. Q102 interacts with NADPH and, upon mutation to alanine, leads to destabilization of the C4a‐hydroperoxyflavin (FAD_OOH). Flavin oxidation with Q102A showed a pK_a value of ~8.0. The data are consistent with the pK_a of the FAD N5‐atom being modulated to a value >9 in the absence of Orn, which aids in the stabilization of FAD_OOH. Changes in the FAD‐N5 environment lead to a decrease in the pK_a value, which facilitates elimination of H₂O₂ or H₂O. These findings are supported by solvent kinetic isotope effect experiments, which show that proton transfer from the FAD N5‐atom is rate limiting in the absence of a substrate, however, is significantly less rate limiting in the presence of Orn and or Lys.     

Biodegradation of polycyclic aromatic hydrocarbons

The intent of this review is to provide an outline of the microbial degradation of polycyclic aromatic hydrocarbons. A catabolically diverse microbial community, consisting of bacteria, fungi and algae, metabolizes aromatic compounds. Molecular oxygen is essential for the initial hydroxylation of polycyclic aromatic hydrocarbons by microorganisms. In contrast to bacteria, filamentous fungi use hydroxylation as a prelude to detoxification rather than to catabolism and assimilation. The biochemical principles underlying the degradation of polycyclic aromatic hydrocarbons are examined in some detail. The pathways of polycyclic aromatic hydrocarbon catabolism are discussed. Studies are presented on the relationship between the chemical structure of the polycyclic aromatic hydrocarbon and the rate of polycyclic aromatic hydrocarbon biodegradation in aquatic and terrestrial ecosystems.     

Structural and chemical trapping of flavin‐oxide intermediates reveals substrate‐directed reaction multiplicity

Though reactive flavin‐N5/C4α‐oxide intermediates can be spectroscopically profiled for some flavin‐assisted enzymatic reactions, their exact chemical configurations are hardly visualized. Structural systems biology and stable isotopic labelling techniques were exploited to correct this stereotypical view. Three transition‐like complexes, the α‐ketoacid…N5‐FMN_ox complex ( I ), the FMN_ox‐N5‐aloxyl‐C′α^?‐C4α⁺ zwitterion ( II ), and the FMN‐N5‐ethenol‐N5‐C4α‐epoxide ( III ), were determined from mandelate oxidase (Hmo) or its mutant Y128F (monooxygenase) crystals soaked with monofluoropyruvate (a product mimic), establishing that N5 of FMN_ox an alternative reaction center can polarize to an ylide‐like mesomer in the active site. In contrast, four distinct flavin‐C4α‐oxide adducts ( IV – VII ) from Y128F crystals soaked with selected substrates materialize C4α of FMN an intrinsic reaction center, witnessing oxidation, Baeyer–Villiger/peroxide‐assisted decarboxylation, and epoxidation reactions. In conjunction with stopped‐flow kinetics, the multifaceted flavin‐dependent reaction continuum is physically dissected at molecular level for the first time.     

Long‐term intake of phenolic compounds attenuates age‐related cardiac remodeling

With the onset of advanced age, cardiac‐associated pathologies have increased in prevalence. The hallmarks of cardiac aging include cardiomyocyte senescence, fibroblast proliferation, inflammation, and hypertrophy. The imbalance between levels of reactive oxygen species (ROS) and antioxidant enzymes is greatly enhanced in aging cells, promoting cardiac remodeling. In this work, we studied the long‐term impact of phenolic compounds (PC) on age‐associated cardiac remodeling. Three‐month‐old Wistar rats were treated for 14 months till middle‐age with either 2.5, 5, 10, or 20 mg kg^?1 day^?1 of PC. PC treatment showed a dose‐dependent preservation of cardiac ejection fraction and fractional shortening as well as decreased hypertrophy reflected by left ventricular chamber diameter and posterior wall thickness as compared to untreated middle‐aged control animals. Analyses of proteins from cardiac tissue showed that PC attenuated several hypertrophic pathways including calcineurin/nuclear factor of activated T cells (NFATc3), calcium/calmodulin‐dependent kinase II (CAMKII), extracellular regulated kinase 1/2 (ERK1/2), and glycogen synthase kinase 3ß (GSK 3ß). PC‐treated groups exhibited reduced plasma inflammatory and fibrotic markers and revealed as well ameliorated extracellular matrix remodeling and interstitial inflammation by a downregulated p38 pathway. Myocardia from PC‐treated middle‐aged rats presented less fibrosis with suppression of profibrotic transforming growth factor‐ß1 (TGF‐ß1) Smad pathway. Additionally, reduction of apoptosis and oxidative damage in the PC‐treated groups was reflected by elevated antioxidant enzymes and reduced RNA/DNA damage markers. Our findings pinpoint that a daily consumption of phenolic compounds could preserve the heart from the detrimental effects of aging storm.     

Expression and metabolic activity of flavin‐containing monooxygenase 1 in cynomolgus macaque kidney

Flavin‐containing monooxygenase 1 (FMO1) largely remains to be characterized in cynomolgus macaque kidney. Immunoblotting showed expression of cynomolgus FMO1 in kidneys where activities of FMO1 (benzydamine N‐oxygenation) were detected. No sex differences were observed in their contents or activities. These results suggest the functional role of cynomolgus FMO1 in kidney.     

Role of inflammation and oxidative stress in post‐menopausal oestrogen‐dependent breast cancer

Weight gain and obesity are among the most important risk factors for post-menopausal oestrogen-dependent breast cancer (EDBC). Weight gain is associated with oxidative stress, which in turn promotes breast cancer progression. We carried out a prospective study in 216 consecutive post-menopausal breast cancer patients aiming to examine the correlations between traditional prognostic factors (tumour size, T, nodal, N, grading, G, and metastasis status, M), and body mass index (BMI), leptin, pro-inflammatory cytokines (Interleukin, IL,-6 and tumour necrosis factor-alpha, TNF-α), and oxidative stress (reactive oxygen species, ROS, glutathione peroxidase, GPx, superoxide dismutase, SOD) among patients with oestrogen receptor (ER)+ and ER− breast cancers. Distribution of T, N and M categories did not differ between ER+ and ER− breast cancer patients. ER− patients showed a higher incidence of G3 tumours. Weight, BMI, leptin, IL-6 and ROS were higher in ER+ compared with ER− patients. Among ER+ patients, BMI, leptin, IL-6 and ROS correlated with T and M. Leptin, IL-6 and ROS were positively correlated also with N. Among ER− patients, BMI and leptin did not correlate with any of prognostic parameters, whereas a positive correlation between IL-6, ROS and M was found. Multivariate regression analysis showed that BMI, leptin, IL-6 and ROS were predictive for T, N and M in ER+ patients. Weight gain, inflammation and oxidative stress are involved in EDBC prognosis. Their modulation through antidiabetic, anti-inflammatory and antioxidants drugs combined with endocrine therapy may constitute a targeted approach in post-menopausal EDBC.     

Abscisic acid is involved in the response of grape (Vitis vinifera L.) cv. Malbec leaf tissues to ultraviolet-B radiation by enhancing ultraviolet-absorbing compounds, antioxidant enzymes and membrane sterols

We investigated the interactions of abscisic acid (ABA) in the responses of grape leaf tissues to contrasting ultraviolet (UV)-B treatments. One-year-old field-grown plants of Vitis vinifera L. were exposed to photosynthetically active radiation (PAR) where solar UV-B was eliminated by using polyester filters, or where PAR was supplemented with UV-B irradiation. Treatments combinations included weekly foliar sprays of ABA or a water control. The levels of UV-B absorbing flavonols, quercetin and kaempferol were significantly decreased by filtering out UV-B, while applied ABA increased their content. Concentration of two hydroxycinnamic acids, caffeic and ferulic acids, were also increased by ABA, but not affected by plus UV-B (+UV-B) treatments. Levels of carotenoids and activities of the antioxidant enzymes, catalase, ascorbate peroxidase and peroxidase were elevated by +ABA treatments, but only if +UV-B was given. Cell membrane β -sitosterol was enhanced by ABA independently of +UV-B. Changes in photoprotective compounds, antioxidant enzymatic activities and sterols were correlated with lessened membrane harm by UV-B, as assessed by ion leakage. Oxidative damage expressed as malondialdehyde content was increased under +UV-B treatments. Our results suggest that the defence system of grape leaf tissues against UV-B is activated by UV-B irradiation with ABA acting downstream in the signalling pathway.     

Water‐soluble calix[4]resorcinarenes as chiral NMR solvating agents for bicyclic aromatic compounds

Water‐soluble calix[4]resorcinarenes with proline, 3‐hydroxyproline, and 4‐hydroxyproline substituent groups are evaluated as chiral NMR solvating agents on a series of bicyclic aromatic compounds with naphthyl, indole, dihydroindole, and indane rings. The substrates interact with the calixresorcinarene through insertion of the aromatic ring into the cavity. Most of the substrates are analyzed as cationic species, although one anionic species is analyzed. All of the substrates exhibit enantiomeric discrimination in the ¹H‐NMR spectrum with one or more of the calixresorcinarenes. In most cases, the hydroxyproline derivatives are more effective at causing enantiodifferentiation than the corresponding proline derivative. Presumably, the hydroxyl group on the proline moieties is involved in interactions with the substituent groups of the substrate that are important in creating chiral recognition. The enantiomeric discrimination in the ¹H‐NMR spectrum is large enough for many resonances to permit the analysis of enantiomeric purity. Chirality 2009. © 2009 Wiley‐Liss, Inc.     

Utilization of aromatic compounds by phototrophic purple nonsulfur bacteria

Biodegradation of aromatic compounds byRhodopseudomonas blastica andRhodospirillum rubrum appears to be lacking in the literature. The above species grew phototrophically (illuminated anaerobic conditions) on a variety of organic compounds. They were found to degrade benzoate, benzyl alcohol, 4-hydroxy-3,5-dimethoxybenzoate (Syringate) and 4-hydroxy-3-methoxybenzoate (vanillate). The ability of the above species to photocatabolize aromatic compounds indicates that these organisms may be ecologically significant as scavengers of aromatic derivatives in illuminated anaerobic habitats in nature.     

A selectivity study of sodium‐dependent glucose cotransporter 2/sodium‐dependent glucose cotransporter 1 inhibitors by molecular modeling

Sodium‐dependent glucose cotransporters (SGLTs) play an important role in glucose reabsorption in the kidney and have been identified as promising targets to treat diabetes. Because of the side effects like glucose and galactose malabsorption by targeting SGLT1, highly selective SGLT2 inhibitors are more promising in the treatment of diabetes. To understand the mechanism of selectivity, we conducted selectivity‐based three‐dimensional quantitative structure–activity relationship studies to highlight the structure requirements for highly selective SGLT2 inhibitors. The best comparative molecular field analysis and comparative molecular similarity indices analysis models showed the noncross‐validated coefficient (r²) of 0.967 and 0.943, respectively. The predicted correlation coefficients (r²_pred) of 0.974 and 0.938 validated the reliability and predictability of these models. Besides, homology models of SGLT2 and SGLT1 were also constructed to investigate the selective mechanism from structure‐based perspective. Molecular dynamics simulation and binding free energy calculation were performed on the systems of a potent and selective compound interacting with SGLT2 and SGLT1 to compare the different binding modes. The simulation results showed that the stretch of the methylthio group on Met241 had an essential effect on the different binding modes between SGLT1 and SGLT2, which was consistent with the three‐dimensional quantitative structure–activity relationship analysis. Hydrogen bond analysis and binding free energy calculation revealed that SGLT2 binding complex was more stable and favorable than SGLT1 complex, which was highly correlated with the experimental results. Our obtained results give useful information for the investigation of the inhibitors' selectivity between SGLT2 and SGLT1 and will help for further development of highly selective SGLT2 inhibitors. Copyright © 2015 John Wiley & Sons, Ltd.     

Overlapped and differential expression of cAMP‐dependent kinase‐inhibitor isoforms during avian organogenesis period

Although cAMP‐dependent kinase (PKA) has been known to regulate many biological systems, including patterning, cell differentiation and proliferation, it is not well understood how the spatial‐temporal specificity of the PKA signaling is generated. While the PKA signal activation is regulated in many ways, a direct visualization of PKA activity in situ is not possible. Thus, examinations of PKA regulators will provide indirect, but nonetheless important information to elucidate the distribution of PKA activity. In the present study, three isoforms of PKA‐inhibitor (PKI) genes were identified from avian genome, and their expression patterns were examined during the organogenesis period. PKI genes were strongly expressed in muscle, liver, and nervous system primordia, suggesting their inhibitory roles on the PKA signaling in the development of these tissues.     

Evolution and diversity of the 2–oxoglutarate‐dependent dioxygenase superfamily in plants

The 2–oxoglutarate‐dependent dioxygenase (2OGD) superfamily is the second largest enzyme family in the plant genome, and its members are involved in various oxygenation/hydroxylation reactions. Despite their biochemical significance in metabolism, a systematic analysis of plant 2OGDs remains to be accomplished. We present a phylogenetic classification of 479 2OGDs in six plant models, ranging from green algae to angiosperms. These were classified into three classes – DOXA, DOXB and DOXC – based on amino acid sequence similarity. The DOXA class includes plant homologs of Escherichia coli AlkB, which is a prototype of 2OGD involved in the oxidative demethylation of alkylated nucleic acids and histones. The DOXB class is conserved across all plant taxa and is involved in proline 4–hydroxylation in cell wall protein synthesis. The DOXC class is involved in specialized metabolism of various phytochemicals, including phytohormones and flavonoids. The vast majority of 2OGDs from land plants were classified into the DOXC class, but only seven from Chlamydomonas, suggesting that this class has diversified during land plant evolution. Phylogenetic analysis assigned DOXC‐class 2OGDs to 57 phylogenetic clades. 2OGD genes involved in gibberellin biosynthesis were conserved among vascular plants, and those involved in flavonoid and ethylene biosynthesis were shared among seed plants. Several angiosperm‐specific clades were found to be involved in various lineage‐specific specialized metabolisms, but 31 of the 57 DOXC‐class clades were only found in a single species. Therefore, the evolution and diversification of DOXC‐class 2OGDs is partly responsible for the diversity and complexity of specialized metabolites in land plants.     

Identification of a flavin‐containing S‐oxygenating monooxygenase involved in alliin biosynthesis in garlic

S‐Alk(en)yl‐l ‐cysteine sulfoxides are cysteine‐derived secondary metabolites highly accumulated in the genus Allium. Despite pharmaceutical importance, the enzymes that contribute to the biosynthesis of S‐alk‐(en)yl‐l ‐cysteine sulfoxides in Allium plants remain largely unknown. Here, we report the identification of a flavin‐containing monooxygenase, AsFMO1, in garlic (Allium sativum), which is responsible for the S‐oxygenation reaction in the biosynthesis of S‐allyl‐l ‐cysteine sulfoxide (alliin). Recombinant AsFMO1 protein catalyzed the stereoselective S‐oxygenation of S‐allyl‐l ‐cysteine to nearly exclusively yield (R_CS_S)‐S‐allylcysteine sulfoxide, which has identical stereochemistry to the major natural form of alliin in garlic. The S‐oxygenation reaction catalyzed by AsFMO1 was dependent on the presence of nicotinamide adenine dinucleotide phosphate (NADPH) and flavin adenine dinucleotide (FAD), consistent with other known flavin‐containing monooxygenases. AsFMO1 preferred S‐allyl‐l ‐cysteine to γ‐glutamyl‐S‐allyl‐l ‐cysteine as the S‐oxygenation substrate, suggesting that in garlic, the S‐oxygenation of alliin biosynthetic intermediates primarily occurs after deglutamylation. The transient expression of green fluorescent protein (GFP) fusion proteins indicated that AsFMO1 is localized in the cytosol. AsFMO1 mRNA was accumulated in storage leaves of pre‐emergent nearly sprouting bulbs, and in various tissues of sprouted bulbs with green foliage leaves. Taken together, our results suggest that AsFMO1 functions as an S‐allyl‐l ‐cysteine S‐oxygenase, and contributes to the production of alliin both through the conversion of stored γ‐glutamyl‐S‐allyl‐l ‐cysteine to alliin in storage leaves during sprouting and through the de novo biosynthesis of alliin in green foliage leaves.