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Sample records for 2-oxoglutarate-dependent dioxygenase ectd

  1. Synthesis of 5-hydroxyectoine from ectoine: crystal structure of the non-heme iron(II and 2-oxoglutarate-dependent dioxygenase EctD.

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    Klaus Reuter

    Full Text Available As a response to high osmolality, many microorganisms synthesize various types of compatible solutes. These organic osmolytes aid in offsetting the detrimental effects of low water activity on cell physiology. One of these compatible solutes is ectoine. A sub-group of the ectoine producer's enzymatically convert this tetrahydropyrimidine into a hydroxylated derivative, 5-hydroxyectoine. This compound also functions as an effective osmostress protectant and compatible solute but it possesses properties that differ in several aspects from those of ectoine. The enzyme responsible for ectoine hydroxylation (EctD is a member of the non-heme iron(II-containing and 2-oxoglutarate-dependent dioxygenases (EC 1.14.11. These enzymes couple the decarboxylation of 2-oxoglutarate with the formation of a high-energy ferryl-oxo intermediate to catalyze the oxidation of the bound organic substrate. We report here the crystal structure of the ectoine hydroxylase EctD from the moderate halophile Virgibacillus salexigens in complex with Fe(3+ at a resolution of 1.85 A. Like other non-heme iron(II and 2-oxoglutarate dependent dioxygenases, the core of the EctD structure consists of a double-stranded beta-helix forming the main portion of the active-site of the enzyme. The positioning of the iron ligand in the active-site of EctD is mediated by an evolutionarily conserved 2-His-1-carboxylate iron-binding motif. The side chains of the three residues forming this iron-binding site protrude into a deep cavity in the EctD structure that also harbours the 2-oxoglutarate co-substrate-binding site. Database searches revealed a widespread occurrence of EctD-type proteins in members of the Bacteria but only in a single representative of the Archaea, the marine crenarchaeon Nitrosopumilus maritimus. The EctD crystal structure reported here can serve as a template to guide further biochemical and structural studies of this biotechnologically interesting enzyme family.

  2. Synthesis of 5-hydroxyectoine from ectoine: crystal structure of the non-heme iron(II) and 2-oxoglutarate-dependent dioxygenase EctD.

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    Reuter, Klaus; Pittelkow, Marco; Bursy, Jan; Heine, Andreas; Craan, Tobias; Bremer, Erhard

    2010-05-14

    As a response to high osmolality, many microorganisms synthesize various types of compatible solutes. These organic osmolytes aid in offsetting the detrimental effects of low water activity on cell physiology. One of these compatible solutes is ectoine. A sub-group of the ectoine producer's enzymatically convert this tetrahydropyrimidine into a hydroxylated derivative, 5-hydroxyectoine. This compound also functions as an effective osmostress protectant and compatible solute but it possesses properties that differ in several aspects from those of ectoine. The enzyme responsible for ectoine hydroxylation (EctD) is a member of the non-heme iron(II)-containing and 2-oxoglutarate-dependent dioxygenases (EC 1.14.11). These enzymes couple the decarboxylation of 2-oxoglutarate with the formation of a high-energy ferryl-oxo intermediate to catalyze the oxidation of the bound organic substrate. We report here the crystal structure of the ectoine hydroxylase EctD from the moderate halophile Virgibacillus salexigens in complex with Fe(3+) at a resolution of 1.85 A. Like other non-heme iron(II) and 2-oxoglutarate dependent dioxygenases, the core of the EctD structure consists of a double-stranded beta-helix forming the main portion of the active-site of the enzyme. The positioning of the iron ligand in the active-site of EctD is mediated by an evolutionarily conserved 2-His-1-carboxylate iron-binding motif. The side chains of the three residues forming this iron-binding site protrude into a deep cavity in the EctD structure that also harbours the 2-oxoglutarate co-substrate-binding site. Database searches revealed a widespread occurrence of EctD-type proteins in members of the Bacteria but only in a single representative of the Archaea, the marine crenarchaeon Nitrosopumilus maritimus. The EctD crystal structure reported here can serve as a template to guide further biochemical and structural studies of this biotechnologically interesting enzyme family.

  3. Ascorbate as a co-factor for fe- and 2-oxoglutarate dependent dioxygenases: physiological activity in tumor growth and progression.

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    Kuiper, Caroline; Vissers, Margreet C M

    2014-01-01

    Ascorbate is a specific co-factor for a large family of enzymes known as the Fe- and 2-oxoglutarate-dependent dioxygenases. These enzymes are found throughout biology and catalyze the addition of a hydroxyl group to various substrates. The proline hydroxylase that is involved in collagen maturation is well known, but in recent times many new enzymes and functions have been uncovered, including those involved in epigenetic control and hypoxia-inducible factor (HIF) regulation. These discoveries have provided crucial mechanistic insights into how ascorbate may affect tumor biology. In particular, there is growing evidence that HIF-1-dependent tumor progression may be inhibited by increasing tumor ascorbate levels. However, rigorous clinical intervention studies are lacking. This review will explore the physiological role of ascorbate as an enzyme co-factor and how this mechanism relates to cancer biology and treatment. The use of ascorbate in cancer should be informed by clinical studies based on such mechanistic hypotheses.

  4. Characterization of the fungal gibberellin desaturase as a 2-oxoglutarate-dependent dioxygenase and its utilization for enhancing plant growth.

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    Bhattacharya, Anjanabha; Kourmpetli, Sofia; Ward, Dennis A; Thomas, Stephen G; Gong, Fan; Powers, Stephen J; Carrera, Esther; Taylor, Benjamin; de Caceres Gonzalez, Francisco Nuñez; Tudzynski, Bettina; Phillips, Andrew L; Davey, Michael R; Hedden, Peter

    2012-10-01

    The biosynthesis of gibberellic acid (GA(3)) by the fungus Fusarium fujikuroi is catalyzed by seven enzymes encoded in a gene cluster. While four of these enzymes are characterized as cytochrome P450 monooxygenases, the nature of a fifth oxidase, GA(4) desaturase (DES), is unknown. DES converts GA(4) to GA(7) by the formation of a carbon-1,2 double bond in the penultimate step of the pathway. Here, we show by expression of the des complementary DNA in Escherichia coli that DES has the characteristics of a 2-oxoglutarate-dependent dioxygenase. Although it has low amino acid sequence homology with known 2-oxoglutarate-dependent dioxygenases, putative iron- and 2-oxoglutarate-binding residues, typical of such enzymes, are apparent in its primary sequence. A survey of sequence databases revealed that homologs of DES are widespread in the ascomycetes, although in most cases the homologs must participate in non-gibberellin (GA) pathways. Expression of des from the cauliflower mosaic virus 35S promoter in the plant species Solanum nigrum, Solanum dulcamara, and Nicotiana sylvestris resulted in substantial growth stimulation, with a 3-fold increase in height in S. dulcamara compared with controls. In S. nigrum, the height increase was accompanied by a 20-fold higher concentration of GA(3) in the growing shoots than in controls, although GA(1) content was reduced. Expression of des was also shown to partially restore growth in plants dwarfed by ectopic expression of a GA 2-oxidase (GA-deactivating) gene, consistent with GA(3) being protected from 2-oxidation. Thus, des has the potential to enable substantial growth increases, with practical implications, for example, in biomass production.

  5. Unity in diversity, a systems approach to regulating plant cell physiology by 2-oxoglutarate-dependent dioxygenases.

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    Kundu, Siddhartha

    2015-01-01

    Could a disjoint group of enzymes synchronize their activities and execute a complex multi-step, measurable, and reproducible response? Here, I surmise that the alpha-ketoglutarate dependent superfamily of non-haem iron (II) dioxygenases could influence cell physiology as a cohesive unit, and that the broad spectra of substrates transformed is an absolute necessity to this portrayal. This eclectic group comprises members from all major taxa, and participates in pesticide breakdown, hypoxia signaling, and osmotic stress neutralization. The oxidative decarboxylation of 2-oxoglutarate to succinate is coupled with a concomitant substrate hydroxylation and, in most cases, is followed by an additional specialized conversion. The domain profile of a protein sequence was used as an index of miscellaneous reaction chemistry and interpreted alongside existent kinetic data in a linear model of integrated function. Statistical parameters were inferred by the creation of a novel, empirically motivated flat-file database of over 3800 sequences (DB2OG) with putative 2-oxoglutarate dependent activity. The collated information was categorized on the basis of existing annotation schema. The data suggests that 2OG-dependent enzymes incorporate several desirable features of a systems level player. DB2OG, is free, accessible without a login to all users, and available at the following URL (http://comp-biol.theacms.in/DB2OG.html).

  6. Molecular cloning of hyoscyamine 6 beta-hydroxylase, a 2-oxoglutarate-dependent dioxygenase, from cultured roots of Hyoscyamus niger.

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    Matsuda, J; Okabe, S; Hashimoto, T; Yamada, Y

    1991-05-25

    Roots of several solanaceous plants produce anticholinergic alkaloids, hyoscyamine and scopolamine. Hyoscyamine 6 beta-hydroxylase, a 2-oxoglutarate-dependent dioxygenase (EC 1.14.11.11), catalyzes hydroxylation of hyoscyamine in the biosynthetic pathway leading to scopolamine. We report here on the isolation of cDNA clones encoding the hydroxylase from a cDNA library made from mRNA of the cultured roots of Hyoscyamus niger. The library was screened with three synthetic oligonucleotides that encode amino acid sequences of internal peptide fragments of the purified hydroxylase. Nucleotide sequence analysis of the cloned cDNA revealed an open reading frame that encodes 344 amino acids (Mr = 38,999). All 12 internal peptide fragments determined in the purified enzyme were found in the amino acid sequence deduced from the cDNA. With computer-aided comparison to other proteins we found that the hydroxylase is homologous to two synthases involved in the biosynthesis of beta-lactam antibiotics in some microorganisms and the gene products of tomato pTOM13 cDNA and maize A2 locus which had been proposed to catalyze oxidative reactions in the biosynthesis of ethylene and anthocyan, respectively. RNA blotting hybridization showed that mRNA of the hydroxylase is abundant in cultured roots and present in plant roots, but absent in leaves, stems, and cultured cells of H. niger.

  7. Hydroxylation of aspartic acid in domains homologous to the epidermal growth factor precursor is catalyzed by a 2-oxoglutarate-dependent dioxygenase.

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    Stenflo, J; Holme, E; Lindstedt, S; Chandramouli, N; Huang, L H; Tam, J P; Merrifield, R B

    1989-01-01

    3-Hydroxyaspartic acid and 3-hydroxyasparagine are two rare amino acids that are present in domains homologous to the epidermal growth factor precursor in vitamin K-dependent plasma proteins as well as in proteins that do not require vitamin K for normal biosynthesis. They are formed by posttranslational hydroxylation of aspartic acid and asparagine, respectively. The first epidermal growth factor-like domain in factor IX (residues 45-87) was synthesized with aspartic acid in position 64, replacing 3-hydroxyaspartic acid. It was used as substrate in a hydroxylase assay with rat liver microsomes as the source of enzyme and reaction conditions that satisfy the requirements of 2-oxoglutarate-dependent dioxygenases. The synthetic peptide stimulated the 2-oxoglutarate decarboxylation in contrast to synthetic, modified epidermal growth factor (Met-21 and His-22 deleted and Glu-24 replaced by Asp) and synthetic peptides corresponding to residues 60-71 in human factor IX. This indicates that the hydroxylase is a 2-oxoglutarate-dependent dioxygenase with a selective substrate requirement. Images PMID:2492106

  8. 丹参2-酮戊二酸依赖性双加氧酶基因克隆及表达分析%Cloning and Expression Analysis of 2-oxoglutarate-dependent Dioxygenase from Salvia miltiorrhiza Bunge

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    刘文超; 王东浩; 王喆之; 李翠芹

    2012-01-01

    以商洛紫花丹参为材料,对其转录组序列SRA020132进行Blast分析,采用PCR技术克隆得到丹参2-酮戊二酸依赖性双加氧酶基因Sm2-ODD1,GenBank登录号为JN935923.Sm2-ODD1基因全长1365 bp,包含3个外显子和2个内含子;cDNA全长1189 bp,读码框951 bp,编码316个氨基酸残基;预测的编码蛋白具有2-酮戊二酸依赖性双加氧酶中结合2-酮戊二酸和亚铁离子的“H-T-D”、“H-X”和“R-Y-S”保守基序以及“果冻状”空间结构.表达分析显示,Sm2-ODD1在丹参各个器官都表达,但表达水平具有组织特异性,在根中表达量最高,在叶中表达量最低;该基因表达明显受到MeJA、GA3和ABA的诱导,可能参与了丹参萜类代谢下游途径.%By analyzing Transcriptome (SRA020132) sequences of Salvia miltiorrhiza from Shangluo and using the techniques of PCR,a new 2-oxoglutarate-dependent dioxygenase gene was cloned from Salvia miltiorrhiza for the first time and named as Sm2-ODD1 (GenBank accession number JN935923). SmZ-ODD1 DNA consisted of 1 365 bp including 3 exons and 2 introns. The full-length cDNA of Sm2-ODDl was 1 189 bp, containing a single 951 bp opening reading frame and encoding a 316 amino-acid residues. Bioinformatics analysis showed that SmZ-ODD1 contained a 2-oxoglutarate-dependent dioxygenase super-family containing "distorted jelly roll" domain and "H-T-D","H-X" and "R-Y-S" motifs to bind 2-oxoglut-arate and Fe2+. Quantitative RT-PCR analysis revealed that the gene expressed in different organs. The expression in roots was observably higher than in flowers, stems and leaves. The gene could be induced by methyl jasmonate,GA3 and ABA. The results indicated that the Sm2-ODDl might be involved in the biosynthesis of terpene in Salvia miltiorrhiza.

  9. A 2-oxoglutarate-dependent dioxygenase from Ruta graveolens L. exhibits p-coumaroyl CoA 2'-hydroxylase activity (C2'H): a missing step in the synthesis of umbelliferone in plants.

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    Vialart, Guilhem; Hehn, Alain; Olry, Alexandre; Ito, Kyoko; Krieger, Celia; Larbat, Romain; Paris, Cedric; Shimizu, Bun-Ichi; Sugimoto, Yukihiro; Mizutani, Masaharu; Bourgaud, Frederic

    2012-05-01

    Coumarins are important compounds that contribute to the adaptation of plants to biotic or abiotic stresses. Among coumarins, umbelliferone occupies a pivotal position in the plant phenylpropanoid network. Previous studies indicated that umbelliferone is derived from the ortho-hydroxylation of p-coumaric acid by an unknown biochemical step to yield 2,4-dihydroxycinnamic acid, which then undergoes spontaneous lactonization. Based on a recent report of a gene encoding a 2-oxoglutarate-dependent dioxygenase from Arabidopsis thaliana that exhibited feruloyl CoA 6'-hydroxylase activity (Bourgaud et al., 2006), we combined a bioinformatic approach and a cDNA library screen to identify an orthologous ORF (Genbank accession number JF799117) from Ruta graveolens L. This ORF shares 59% amino acid identity with feruloyl CoA 6'-hydroxylase, was functionally expressed in Escherichia coli, and converted feruloyl CoA into scopoletin and p-coumaroyl CoA into umbelliferone with equal activity. Its bi-functionality was further confirmed in planta: transient expression of JF799117 in Nicotiana benthamiana yielded plants with leaves containing high levels of umbelliferone and scopoletin when compared to control plants, which contained barely detectable traces of these compounds. The expression of JF799117 was also tightly correlated to the amount of umbelliferone that was found in UV-elicited R. graveolens leaves. Therefore, JF799117 encodes a p-coumaroyl CoA 2'-hydroxylase in R. graveolens, which represents a previously uncharacterized step in the synthesis of umbelliferone in plants. Psoralen, which is an important furanocoumarin in R. graveolens, was found to be a competitive inhibitor of the enzyme, and it may exert this effect through negative feedback on the enzyme at an upstream position in the pathway.

  10. The function and catalysis of 2-oxoglutarate-dependent oxygenases involved in plant flavonoid biosynthesis.

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    Cheng, Ai-Xia; Han, Xiao-Juan; Wu, Yi-Feng; Lou, Hong-Xiang

    2014-01-15

    Flavonoids are secondary metabolites derived from phenylalanine and acetate metabolism. They fulfil a variety of functions in plants and have health benefits for humans. During the synthesis of the tricyclic flavonoid natural products in plants, oxidative modifications to the central C ring are catalyzed by four of FeII and 2-oxoglutarate dependent (2-ODD) oxygenases, namely flavone synthase I (FNS I), flavonol synthase (FLS), anthocyanidin synthase (ANS) and flavanone 3β-hydroxylase (FHT). FNS I, FLS and ANS are involved in desaturation of C2-C3 of flavonoids and FHT in hydroxylation of C3. FNS I, which is restricted to the Apiaceae species and in rice, is predicted to have evolved from FHT by duplication. Due to their sequence similarity and substrate specificity, FLS and ANS, which interact with the α surface of the substrate, belong to a group of dioxygenases having a broad substrate specificity, while FNS I and FHT are more selective, and interact with the naringenin β surface. Here, we summarize recent findings regarding the function of the four 2-ODD oxygenases and the relationship between their catalytic activity, their polypeptide sequence and their tertiary structure.

  11. The Function and Catalysis of 2-Oxoglutarate-Dependent Oxygenases Involved in Plant Flavonoid Biosynthesis

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    Ai-Xia Cheng

    2014-01-01

    Full Text Available Flavonoids are secondary metabolites derived from phenylalanine and acetate metabolism. They fulfil a variety of functions in plants and have health benefits for humans. During the synthesis of the tricyclic flavonoid natural products in plants, oxidative modifications to the central C ring are catalyzed by four of FeII and 2-oxoglutarate dependent (2-ODD oxygenases, namely flavone synthase I (FNS I, flavonol synthase (FLS, anthocyanidin synthase (ANS and flavanone 3β-hydroxylase (FHT. FNS I, FLS and ANS are involved in desaturation of C2–C3 of flavonoids and FHT in hydroxylation of C3. FNS I, which is restricted to the Apiaceae species and in rice, is predicted to have evolved from FHT by duplication. Due to their sequence similarity and substrate specificity, FLS and ANS, which interact with the α surface of the substrate, belong to a group of dioxygenases having a broad substrate specificity, while FNS I and FHT are more selective, and interact with the naringenin β surface. Here, we summarize recent findings regarding the function of the four 2-ODD oxygenases and the relationship between their catalytic activity, their polypeptide sequence and their tertiary structure.

  12. Spectroscopic and magnetic studies of wild-type and mutant forms of the Fe(II)- and 2-oxoglutarate-dependent decarboxylase ALKBH4.

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    Bjørnstad, Linn G; Zoppellaro, Giorgio; Tomter, Ane B; Falnes, Pål Ø; Andersson, K Kristoffer

    2011-03-15

    The Fe(II)/2OG (2-oxoglutarate)-dependent dioxygenase superfamily comprises proteins that couple substrate oxidation to decarboxylation of 2OG to succinate. A member of this class of mononuclear non-haem Fe proteins is the Escherichia coli DNA/RNA repair enzyme AlkB. In the present work, we describe the magnetic and optical properties of the yet uncharacterized human ALKBH4 (AlkB homologue). Through EPR and UV-visible spectroscopy studies, we address the Fe-binding environment of the proposed catalytic centre of wild-type ALKBH4 and an Fe(II)-binding mutant. We could observe a novel unusual Fe(III) high-spin EPR-active species in the presence of sulfide with a g(max) of 8.2. The Fe(II) site was probed with NO. An intact histidine-carboxylate site is necessary for productive Fe binding. We also report the presence of a unique cysteine-rich motif conserved in the N-terminus of ALKBH4 orthologues, and investigate its possible Fe-binding ability. Furthermore, we show that recombinant ALKBH4 mediates decarboxylation of 2OG in absence of primary substrate. This activity is dependent on Fe as well as on residues predicted to be involved in Fe(II) co-ordination. The present results demonstrate that ALKBH4 represents an active Fe(II)/2OG-dependent decarboxylase and suggest that the cysteine cluster is involved in processes other than Fe co-ordination.

  13. Identification of a unique 2-oxoglutarate-dependent flavone 7-O-demethylase completes the elucidation of the lipophilic flavone network in basil.

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    Berim, Anna; Kim, Min-Jeong; Gang, David R

    2015-01-01

    Small molecule demethylation is considered unusual in plants. Of the studied instances, the N-demethylation of nicotine is catalyzed by a Cyt P450 monooxygenase, while the O-dealkylation of alkaloids in Papaver somniferum is mediated by 2-oxoglutarate-dependent dioxygenases (2-ODDs). This report describes a 2-ODD regiospecifically catalyzing the 7-O-demethylation of methoxylated flavones in peltate trichomes of sweet basil (Ocimum basilicum L.). Three candidate 2-ODDs were identified in the basil trichome transcriptome database. Only the candidate designated ObF7ODM1 was found to be active with and highly specific for the proposed natural substrates, gardenin B and 8-hydroxysalvigenin. Of the characterized 2-ODDs, ObF7ODM1 is most closely related to O-demethylases from Papaver. The demethylase activity in trichomes from four basil chemotypes matches well with the abundance of ObF7ODM1 peptides and transcripts in the same trichome preparations. Treatment of basil plants with a 2-ODD inhibitor prohexadione-calcium significantly reduced the accumulation of 7-O-demethylated flavone nevadensin, confirming the involvement of a 2-ODD in its formation. Notably, the full-length open reading frame of ObF7ODM1 contains a second in-frame AUG codon 57 nucleotides downstream of the first translation initiation codon. Both AUG codons are recognized by bacterial translation machinery during heterologous gene expression. The N-truncated ObF7ODM1 is nearly inactive. The N-terminus essential for activity is unique to ObF7ODM1 and does not align with the sequences of other 2-ODDs. Further studies will reveal whether alternative translation initiation plays a role in regulating the O-demethylase activity in planta. Molecular identification of the flavone 7-O-demethylase completes the biochemical elucidation of the lipophilic flavone network in basil.

  14. Co-operative intermolecular kinetics of 2-oxoglutarate dependent dioxygenases may be essential for system-level regulation of plant cell physiology

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    Siddhartha eKundu

    2015-07-01

    Full Text Available Chlorosis, a common manifestation of Fe-deficiency in plants occurs in soils with an alkaline pH and/or a high concentration of calcium carbonate (calcareous, and is an important cause of depressed yield. The core premise of this work is the notion that the response to waning ferrous iron in the cytosol of graminaceous root cells is a well orchestrated pathophysiological event, wherein the principal co-ordinator is not restricted to a single protein, but is an assortment of enzymes. The 2OG-dependent sequences comprise members present in all major kingdoms of life, and catalyze the release of carbon dioxide and succinic acid from 2-oxoglutarate, and the hydroxylation of a substrate molecule. This generic reaction is, in most cases accompanied by a specialized conversion of the product. Here, I present a model of iron deficiency sensing and response actuation in the root cells of graminaceous crops. This hypothesis is centered on the rationale that, iron is an essential co-factor for the catalytic process, and therefore, declining cytosolic levels of this micronutrient could trigger compensatory measures. Regression models of empirically available kinetic data for iron and alpha-ketoglutarate were formulated, analysed, and compared. The results, when viewed in the context of the superfamily responding as a unit to this abiotic stressor, suggest that the 2OG-sequences can indeed, work together to mitigate the effects of this noxious stimulus.

  15. The ectD Gene, Which Is Involved in the Synthesis of the Compatible Solute Hydroxyectoine, Is Essential for Thermoprotection of the Halophilic Bacterium Chromohalobacter salexigens

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    García-Estepa, Raúl; Argandoña, Montserrat; Reina-Bueno, Mercedes; Capote, Nieves; Iglesias-Guerra, Fernando; Nieto, Joaquín J.; Vargas, Carmen

    2006-01-01

    The halophilic bacterium Chromohalobacter salexigens synthesizes and accumulates compatible solutes in response to salt and temperature stress. 13C-nuclear magnetic resonance analysis of cells grown in minimal medium at the limiting temperature of 45°C revealed the presence of hydroxyectoine, ectoine, glutamate, trehalose (not present in cells grown at 37°C), and the ectoine precursor, Nγ-acetyldiaminobutyric acid. High-performance liquid chromatography analyses showed that the levels of ectoine and hydroxyectoine were maximal during the stationary phase of growth. Accumulation of hydroxyectoine was up-regulated by salinity and temperature, whereas accumulation of ectoine was up-regulated by salinity and down-regulated by temperature. The ectD gene, which is involved in the conversion of ectoine to hydroxyectoine, was isolated as part of a DNA region that also contains a gene whose product belongs to the AraC-XylS family of transcriptional activators. Orthologs of ectD were found within the sequenced genomes of members of the proteobacteria, firmicutes, and actinobacteria, and their products were grouped into the ectoine hydroxylase subfamily, which was shown to belong to the superfamily of Fe(II)- and 2-oxoglutarate-dependent oxygenases. Analysis of the ectoine and hydroxyectoine contents of an ectABC ectD mutant strain fed with 1 mM ectoine or hydroxyectoine demonstrated that ectD is required for the main ectoine hydroxylase activity in C. salexigens. Although in minimal medium at 37°C the wild-type strain grew with 0.5 to 3.0 M NaCl, with optimal growth at 1.5 M NaCl, at 45°C it could not cope with the lowest (0.75 M NaCl) or the highest (3.0 M NaCl) salinity, and it grew optimally at 2.5 M NaCl. The ectD mutation caused a growth defect at 45°C in minimal medium with 1.5 to 2.5 M NaCl, but it did not affect growth at 37°C at any salinity tested. With 2.5 M NaCl, the ectD mutant synthesized 38% (at 37°C) and 15% (at 45°C) of the hydroxyectoine produced

  16. Ab initio structural modeling of and experimental validation for Chlamydia trachomatis protein CT296 reveal structural similarity to Fe(II) 2-oxoglutarate-dependent enzymes

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    Kemege, Kyle E.; Hickey, John M.; Lovell, Scott; Battaile, Kevin P.; Zhang, Yang; Hefty, P. Scott (Michigan); (Kansas); (HWMRI)

    2012-02-13

    Chlamydia trachomatis is a medically important pathogen that encodes a relatively high percentage of proteins with unknown function. The three-dimensional structure of a protein can be very informative regarding the protein's functional characteristics; however, determining protein structures experimentally can be very challenging. Computational methods that model protein structures with sufficient accuracy to facilitate functional studies have had notable successes. To evaluate the accuracy and potential impact of computational protein structure modeling of hypothetical proteins encoded by Chlamydia, a successful computational method termed I-TASSER was utilized to model the three-dimensional structure of a hypothetical protein encoded by open reading frame (ORF) CT296. CT296 has been reported to exhibit functional properties of a divalent cation transcription repressor (DcrA), with similarity to the Escherichia coli iron-responsive transcriptional repressor, Fur. Unexpectedly, the I-TASSER model of CT296 exhibited no structural similarity to any DNA-interacting proteins or motifs. To validate the I-TASSER-generated model, the structure of CT296 was solved experimentally using X-ray crystallography. Impressively, the ab initio I-TASSER-generated model closely matched (2.72-{angstrom} C{alpha} root mean square deviation [RMSD]) the high-resolution (1.8-{angstrom}) crystal structure of CT296. Modeled and experimentally determined structures of CT296 share structural characteristics of non-heme Fe(II) 2-oxoglutarate-dependent enzymes, although key enzymatic residues are not conserved, suggesting a unique biochemical process is likely associated with CT296 function. Additionally, functional analyses did not support prior reports that CT296 has properties shared with divalent cation repressors such as Fur.

  17. The structure at 2.4 Å resolution of the protein from gene locus At3g21360, a putative Fe{sup II}/2-oxoglutarate-dependent enzyme from Arabidopsis thaliana

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    Bitto, Eduard; Bingman, Craig A.; Allard, Simon T. M.; Wesenberg, Gary E.; Aceti, David J.; Wrobel, Russell L.; Frederick, Ronnie O.; Sreenath, Hassan; Vojtik, Frank C.; Jeon, Won Bae; Newman, Craig S.; Primm, John; Sussman, Michael R.; Fox, Brian G.; Markley, John L.; Phillips, George N. Jr, E-mail: phillips@biochem.wisc.edu [Center for Eukaryotic Structural Genomics, Department of Biochemistry, University of Wisconsin-Madison (United States)

    2005-05-01

    The crystal structure of the 37.2 kDa At3g21360 gene product from A. thaliana was determined at 2.4 Å resolution. The structure establishes that this protein binds a metal ion and is a member of a clavaminate synthase-like superfamily in A. thaliana. The crystal structure of the gene product of At3g21360 from Arabidopsis thaliana was determined by the single-wavelength anomalous dispersion method and refined to an R factor of 19.3% (R{sub free} = 24.1%) at 2.4 Å resolution. The crystal structure includes two monomers in the asymmetric unit that differ in the conformation of a flexible domain that spans residues 178–230. The crystal structure confirmed that At3g21360 encodes a protein belonging to the clavaminate synthase-like superfamily of iron(II) and 2-oxoglutarate-dependent enzymes. The metal-binding site was defined and is similar to the iron(II) binding sites found in other members of the superfamily.

  18. Overexpression, crystallization and preliminary X-ray crystallographic analysis of the ectoine hydroxylase from Sphingopyxis alaskensis.

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    Hoeppner, Astrid; Widderich, Nils; Bremer, Erhard; Smits, Sander H J

    2014-04-01

    The ectoine hydroxylase (EctD) is a member of the non-haem-containing iron(II)- and 2-oxoglutarate-dependent dioxygenase superfamily. Its mononuclear iron centre is a prerequisite for the activity of this enzyme and promotes the O2-dependent oxidative decarboxylation of 2-oxoglutarate, which is coupled to a two-electron oxidation of the substrate ectoine to yield 5-hydroxyectoine. An expression and purification protocol for the EctD enzyme from Sphingopyxis alaskensis was developed and the protein was crystallized using the sitting-drop vapour-diffusion method. This resulted in two different crystal forms, representing the apo and iron-bound forms of the enzyme.

  19. Crystal structure of the ectoine hydroxylase, a snapshot of the active site.

    Science.gov (United States)

    Höppner, Astrid; Widderich, Nils; Lenders, Michael; Bremer, Erhard; Smits, Sander H J

    2014-10-24

    Ectoine and its derivative 5-hydroxyectoine are compatible solutes that are widely synthesized by bacteria to cope physiologically with osmotic stress. They also serve as chemical chaperones and maintain the functionality of macromolecules. 5-Hydroxyectoine is produced from ectoine through a stereo-specific hydroxylation, an enzymatic reaction catalyzed by the ectoine hydroxylase (EctD). The EctD protein is a member of the non-heme-containing iron(II) and 2-oxoglutarate-dependent dioxygenase superfamily and is evolutionarily well conserved. We studied the ectoine hydroxylase from the cold-adapted marine ultra-microbacterium Sphingopyxis alaskensis (Sa) and found that the purified SaEctD protein is a homodimer in solution. We determined the SaEctD crystal structure in its apo-form, complexed with the iron catalyst, and in a form that contained iron, the co-substrate 2-oxoglutarate, and the reaction product of EctD, 5-hydroxyectoine. The iron and 2-oxoglutarate ligands are bound within the EctD active site in a fashion similar to that found in other members of the dioxygenase superfamily. 5-Hydroxyectoine, however, is coordinated by EctD in manner different from that found in high affinity solute receptor proteins operating in conjunction with microbial import systems for ectoines. Our crystallographic analysis provides a detailed view into the active site of the ectoine hydroxylase and exposes an intricate network of interactions between the enzyme and its ligands that collectively ensure the hydroxylation of the ectoine substrate in a position- and stereo-specific manner.

  20. Osmotically induced synthesis of the compatible solute hydroxyectoine is mediated by an evolutionarily conserved ectoine hydroxylase.

    Science.gov (United States)

    Bursy, Jan; Pierik, Antonio J; Pica, Nathalie; Bremer, Erhard

    2007-10-26

    By using natural abundance (13)C NMR spectroscopy, we investigated the types of compatible solutes synthesized in a variety of Bacilli under high salinity growth conditions. Glutamate, proline, and ectoine were the dominant compatible solutes synthesized by the various Bacillus species. The majority of the inspected Bacilli produced the tetrahydropyrimidine ectoine in response to high salinity stress, and a subset of these also synthesized a hydroxylation derivative of ectoine, 5-hydroxyectoine. In Salibacillus salexigens, a representative of the ectoine- and 5-hydroxyectoine-producing species, ectoine production was linearly correlated with the salinity of the growth medium and dependent on an ectABC biosynthetic operon. The formation of 5-hydroxyectoine was primarily a stationary growth phase phenomenon. The enzyme responsible for ectoine hydroxylation (EctD) was purified from S. salexigens to apparent homogeneity. The EctD protein was shown in vitro to directly hydroxylate ectoine in a reaction dependent on iron(II), molecular oxygen, and 2-oxoglutarate. We identified the structural gene (ectD) for the ectoine hydroxylase in S. salexigens. Northern blot analysis showed that the transcript levels of the ectABC and ectD genes increased as a function of salinity. Many EctD-related proteins can be found in data base searches in various Bacteria. Each of these bacterial species also contains an ectABC ectoine biosynthetic gene cluster, suggesting that 5-hydroxyectoine biosynthesis strictly depends on the prior synthesis of ectoine. Our data base searches and the biochemical characterization of the EctD protein from S. salexigens suggest that the EctD-related ectoine hydroxylases are members of a new subfamily within the non-heme-containing, iron(II)- and 2-oxoglutarate-dependent dioxygenase superfamily (EC 1.14.11).

  1. Molecular dynamics simulations and structure-guided mutagenesis provide insight into the architecture of the catalytic core of the ectoine hydroxylase.

    Science.gov (United States)

    Widderich, Nils; Pittelkow, Marco; Höppner, Astrid; Mulnaes, Daniel; Buckel, Wolfgang; Gohlke, Holger; Smits, Sander H J; Bremer, Erhard

    2014-02-06

    Many bacteria amass compatible solutes to fend-off the detrimental effects of high osmolarity on cellular physiology and water content. These solutes also function as stabilizers of macromolecules, a property for which they are referred to as chemical chaperones. The tetrahydropyrimidine ectoine is such a compatible solute and is widely synthesized by members of the Bacteria. Many ectoine producers also synthesize the stress protectant 5-hydroxyectoine from the precursor ectoine, a process that is catalyzed by the ectoine hydroxylase (EctD). The EctD enzyme is a member of the non-heme-containing iron(II) and 2-oxoglutarate-dependent dioxygenase superfamily. A crystal structure of the EctD protein from the moderate halophile Virgibacillus salexigens has previously been reported and revealed the coordination of the iron catalyst, but it lacked the substrate ectoine and the co-substrate 2-oxoglutarate. Here we used this crystal structure as a template to assess the likely positioning of the ectoine and 2-oxoglutarate ligands within the active site by structural comparison, molecular dynamics simulations, and site-directed mutagenesis. Collectively, these approaches suggest the positioning of the iron, ectoine, and 2-oxoglutarate ligands in close proximity to each other and with a spatial orientation that will allow the region-selective and stereo-specific hydroxylation of (4S)-ectoine to (4S,5S)-5-hydroxyectoine. Our study thus provides a view into the catalytic core of the ectoine hydroxylase and suggests an intricate network of interactions between the three ligands and evolutionarily highly conserved residues in members of the EctD protein family.

  2. Indoleamine 2,3-dioxygenase vaccination

    DEFF Research Database (Denmark)

    Andersen, Mads Hald; Svane, Inge Marie

    2015-01-01

    Indoleamine 2,3-dioxygenase (IDO) is an immunoregulatory enzyme. Remarkably, we discovered IDO-specific T cells that can influence adaptive immune reactions in patients with cancer. Further, a recent phase I clinical trial demonstrated long-lasting disease stabilization without toxicity in patien...... with non-small-cell lung cancer (NSCLC) who were vaccinated with an IDO-derived HLA-A2-restricted epitope....

  3. Heme-containing dioxygenases involved in tryptophan oxidation.

    Science.gov (United States)

    Millett, Elizabeth S; Efimov, Igor; Basran, Jaswir; Handa, Sandeep; Mowat, Christopher G; Raven, Emma Lloyd

    2012-04-01

    Heme iron is often used in biology for activation of oxygen. The mechanisms of oxygen activation by heme-containing monooxygenases (the cytochrome P450s) are well known, and involve formation of a Compound I species, but information on the heme-containing dioxygenase enzymes involved in tryptophan oxidation lags far behind. In this review, we gather together information emerging recently from structural, mechanistic, spectroscopic, and computational approaches on the heme dioxygenase enzymes involved in tryptophan oxidation. We explore the subtleties that differentiate various heme enzymes from each other, and use this to piece together a developing picture for oxygen activation in this particular class of heme-containing dioxygenases.

  4. 2-Hydrazinobenzothiazole-based etheno-adduct repair protocol (HERP): a method for quantitative determination of direct repair of etheno-bases.

    Science.gov (United States)

    Shivange, Gururaj; Kodipelli, Naveena; Anindya, Roy

    2015-04-01

    Etheno-DNA adducts are mutagenic and lead to genomic instability. Enzymes belonging to Fe(II)/2-oxoglutarate-dependent dioxygenase family repair etheno-DNA adducts by directly removing alkyl chain as glyoxal. Presently there is no simple method to assess repair reaction of etheno-adducts. We have developed a rapid and sensitive assay for studying etheno-DNA adduct repair by Fe(II)/2-oxoglutarate-dependent dioxygenases. Using AlkB as model Fe(II)/2-oxoglutarate-dependent dioxygenases, we performed in vitro repair of etheno-adducts containing DNA and detected glyoxal by reacting with 2-hydrazinobenzothiazole which forms complex yellow color compound with distinct absorption spectrum with a peak absorption at 365 nm. We refer this method as 2-hydrazinobenzothiazole-based etheno-adduct repair protocol or HERP. Our novel approach for determining repair of etheno-adducts containing DNA overcomes several drawbacks of currently available radioisotope-based assay.

  5. Molecular characterization of the gallate dioxygenase from Pseudomonas putida KT2440. The prototype of a new subgroup of extradiol dioxygenases.

    Science.gov (United States)

    Nogales, Juan; Canales, Angeles; Jiménez-Barbero, Jesús; García, José Luis; Díaz, Eduardo

    2005-10-21

    In this work we have characterized the galA gene product from Pseudomonas putida KT2440, a ring-cleavage dioxygenase that acts specifically on gallate to produce 4-oxalomesaconate. The protein is a trimer composed by three identical subunits of 47.6 kDa (419 amino acids) that uses Fe2+ as the main cofactor. The gallate dioxygenase showed maximum activity at pH 7.0, and the Km and Vmax values for gallate were 144 microM and 53.2 micromol/min/mg of protein, respectively. A phylogenetic study suggests that the gallate dioxygenase from P. putida KT2440 is the prototype of a new subgroup of type II extradiol dioxygenases that share a common ancestor with protocatechuate 4,5-dioxygenases and whose two-domain architecture might have evolved from the fusion of the large and small subunits of the latter. A three-dimensional model for the N-terminal domain (residues 1-281) and C-terminal domain (residues 294-420) of the gallate dioxygenase from P. putida KT2440 was generated by comparison with the crystal structures of the large (LigB) and small (LigA) subunits of the protocatechuate 4,5-dioxygenase from Sphingomonas paucimobilis SYK-6. The expression of the galA gene was specifically induced when P. putida KT2440 cells grew in the presence of gallate. A P. putida KT2440 galA mutant strain was unable to use gallate as the sole carbon source and it did not show gallate dioxygenase activity, suggesting that the GalA protein is the only dioxygenase involved in gallate cleavage in this bacterium. This work points to the existence of a new pathway that is devoted to the catabolism of gallic acid and that remained unknown in the paradigmatic P. putida KT2440 strain.

  6. Energy Sensing versus 2-Oxoglutarate Dependent ATPase Switch in the Control of Synechococcus PII Interaction with Its Targets NAGK and PipX.

    Directory of Open Access Journals (Sweden)

    Jan Lüddecke

    Full Text Available PII proteins constitute a superfamily of highly conserved signaling devices, common in all domains of life. Through binding of the metabolites ATP, ADP and 2-oxoglutarate (2-OG, they undergo conformational changes which allow them to regulate a variety of target proteins including enzymes, transport proteins and transcription factors. But, in reverse, these target proteins also modulate the metabolite sensing properties of PII, as has been recently shown. We used this effect to refine our PII based Förster resonance energy transfer (FRET sensor and amplify its sensitivity towards ADP. With this enhanced sensor setup we addressed the question whether the PII protein from the model organism Synechococcus elongatus autonomously switches into the ADP conformation through ATPase activity as proposed in a recently published model. The present study disproves ATPase activity as a relevant mechanism for the transition of PII into the ADP state. In the absence of 2-OG, only the ATP/ADP ratio and concentration of ADP directs the competitive interaction of PII with two targets, one of which preferentially binds PII in the ATP-state, the other in the ADP-state.

  7. Biochemical and Spectroscopic Characterization of the Non-Heme Fe(II)- and 2-Oxoglutarate-Dependent Ethylene-Forming Enzyme from Pseudomonas syringae pv. phaseolicola PK2.

    Science.gov (United States)

    Martinez, Salette; Hausinger, Robert P

    2016-11-01

    The ethylene-forming enzyme (EFE) from Pseudomonas syringae pv. phaseolicola PK2 is a member of the mononuclear non-heme Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenase superfamily. This enzyme is reported to simultaneously catalyze the conversion of 2OG into ethylene and three CO2 molecules and the Cδ hydroxylation of l-arginine (l-Arg) while oxidatively decarboxylating 2OG to form succinate and carbon dioxide. A new plasmid construct for expression in recombinant Escherichia coli cells allowed for the purification of large amounts of EFE with activity greater than that previously recorded. A variety of assays were used to quantify and confirm the identity of the proposed products, including the first experimental demonstration of l-Δ(1)-pyrroline-5-carboxylate and guanidine derived from 5-hydroxyarginine. Selected l-Arg derivatives could induce ethylene formation without undergoing hydroxylation, demonstrating that ethylene production and l-Arg hydroxylation activities are not linked. Similarly, EFE utilizes the alternative α-keto acid 2-oxoadipate as a cosubstrate (forming glutaric acid) during the hydroxylation of l-Arg, with this reaction unlinked from ethylene formation. Kinetic constants were determined for both ethylene formation and l-Arg hydroxylation reactions. Anaerobic UV-visible difference spectra were used to monitor the binding of Fe(II) and substrates to the enzyme. On the basis of our results and what is generally known about EFE and Fe(II)- and 2OG-dependent oxygenases, an updated model for the reaction mechanism is presented.

  8. Biochemical properties of ectoine hydroxylases from extremophiles and their wider taxonomic distribution among microorganisms.

    Directory of Open Access Journals (Sweden)

    Nils Widderich

    Full Text Available Ectoine and hydroxyectoine are well-recognized members of the compatible solutes and are widely employed by microorganisms as osmostress protectants. The EctABC enzymes catalyze the synthesis of ectoine from the precursor L-aspartate-β-semialdehyde. A subgroup of the ectoine producers can convert ectoine into 5-hydroxyectoine through a region-selective and stereospecific hydroxylation reaction. This compatible solute possesses stress-protective and function-preserving properties different from those of ectoine. Hydroxylation of ectoine is carried out by the EctD protein, a member of the non-heme-containing iron (II and 2-oxoglutarate-dependent dioxygenase superfamily. We used the signature enzymes for ectoine (EctC and hydroxyectoine (EctD synthesis in database searches to assess the taxonomic distribution of potential ectoine and hydroxyectoine producers. Among 6428 microbial genomes inspected, 440 species are predicted to produce ectoine and of these, 272 are predicted to synthesize hydroxyectoine as well. Ectoine and hydroxyectoine genes are found almost exclusively in Bacteria. The genome context of the ect genes was explored to identify proteins that are functionally associated with the synthesis of ectoines; the specialized aspartokinase Ask_Ect and the regulatory protein EctR. This comprehensive in silico analysis was coupled with the biochemical characterization of ectoine hydroxylases from microorganisms that can colonize habitats with extremes in salinity (Halomonas elongata, pH (Alkalilimnicola ehrlichii, Acidiphilium cryptum, or temperature (Sphingopyxis alaskensis, Paenibacillus lautus or that produce hydroxyectoine very efficiently over ectoine (Pseudomonas stutzeri. These six ectoine hydroxylases all possess similar kinetic parameters for their substrates but exhibit different temperature stabilities and differ in their tolerance to salts. We also report the crystal structure of the Virgibacillus salexigens EctD protein in its

  9. Biochemical properties of ectoine hydroxylases from extremophiles and their wider taxonomic distribution among microorganisms.

    Science.gov (United States)

    Widderich, Nils; Höppner, Astrid; Pittelkow, Marco; Heider, Johann; Smits, Sander H J; Bremer, Erhard

    2014-01-01

    Ectoine and hydroxyectoine are well-recognized members of the compatible solutes and are widely employed by microorganisms as osmostress protectants. The EctABC enzymes catalyze the synthesis of ectoine from the precursor L-aspartate-β-semialdehyde. A subgroup of the ectoine producers can convert ectoine into 5-hydroxyectoine through a region-selective and stereospecific hydroxylation reaction. This compatible solute possesses stress-protective and function-preserving properties different from those of ectoine. Hydroxylation of ectoine is carried out by the EctD protein, a member of the non-heme-containing iron (II) and 2-oxoglutarate-dependent dioxygenase superfamily. We used the signature enzymes for ectoine (EctC) and hydroxyectoine (EctD) synthesis in database searches to assess the taxonomic distribution of potential ectoine and hydroxyectoine producers. Among 6428 microbial genomes inspected, 440 species are predicted to produce ectoine and of these, 272 are predicted to synthesize hydroxyectoine as well. Ectoine and hydroxyectoine genes are found almost exclusively in Bacteria. The genome context of the ect genes was explored to identify proteins that are functionally associated with the synthesis of ectoines; the specialized aspartokinase Ask_Ect and the regulatory protein EctR. This comprehensive in silico analysis was coupled with the biochemical characterization of ectoine hydroxylases from microorganisms that can colonize habitats with extremes in salinity (Halomonas elongata), pH (Alkalilimnicola ehrlichii, Acidiphilium cryptum), or temperature (Sphingopyxis alaskensis, Paenibacillus lautus) or that produce hydroxyectoine very efficiently over ectoine (Pseudomonas stutzeri). These six ectoine hydroxylases all possess similar kinetic parameters for their substrates but exhibit different temperature stabilities and differ in their tolerance to salts. We also report the crystal structure of the Virgibacillus salexigens EctD protein in its apo

  10. Hemoglobin: A Nitric-Oxide Dioxygenase

    Directory of Open Access Journals (Sweden)

    Paul R. Gardner

    2012-01-01

    Full Text Available Members of the hemoglobin superfamily efficiently catalyze nitric-oxide dioxygenation, and when paired with native electron donors, function as NO dioxygenases (NODs. Indeed, the NOD function has emerged as a more common and ancient function than the well-known role in O2 transport-storage. Novel hemoglobins possessing a NOD function continue to be discovered in diverse life forms. Unique hemoglobin structures evolved, in part, for catalysis with different electron donors. The mechanism of NOD catalysis by representative single domain hemoglobins and multidomain flavohemoglobin occurs through a multistep mechanism involving O2 migration to the heme pocket, O2 binding-reduction, NO migration, radical-radical coupling, O-atom rearrangement, nitrate release, and heme iron re-reduction. Unraveling the physiological functions of multiple NODs with varying expression in organisms and the complexity of NO as both a poison and signaling molecule remain grand challenges for the NO field. NOD knockout organisms and cells expressing recombinant NODs are helping to advance our understanding of NO actions in microbial infection, plant senescence, cancer, mitochondrial function, iron metabolism, and tissue O2 homeostasis. NOD inhibitors are being pursued for therapeutic applications as antibiotics and antitumor agents. Transgenic NOD-expressing plants, fish, algae, and microbes are being developed for agriculture, aquaculture, and industry.

  11. Structure and mechanism of mouse cysteine dioxygenase

    Science.gov (United States)

    McCoy, Jason G.; Bailey, Lucas J.; Bitto, Eduard; Bingman, Craig A.; Aceti, David J.; Fox, Brian G.; Phillips, George N.

    2006-01-01

    Cysteine dioxygenase (CDO) catalyzes the oxidation of l-cysteine to cysteine sulfinic acid. Deficiencies in this enzyme have been linked to autoimmune diseases and neurological disorders. The x-ray crystal structure of CDO from Mus musculus was solved to a nominal resolution of 1.75 Å. The sequence is 91% identical to that of a human homolog. The structure reveals that CDO adopts the typical β-barrel fold of the cupin superfamily. The NE2 atoms of His-86, -88, and -140 provide the metal binding site. The structure further revealed a covalent linkage between the side chains of Cys-93 and Tyr-157, the cysteine of which is conserved only in eukaryotic proteins. Metal analysis showed that the recombinant enzyme contained a mixture of iron, nickel, and zinc, with increased iron content associated with increased catalytic activity. Details of the predicted active site are used to present and discuss a plausible mechanism of action for the enzyme. PMID:16492780

  12. Synthesis and uptake of the compatible solutes ectoine and 5-hydroxyectoine by Streptomyces coelicolor A3(2) in response to salt and heat stresses.

    Science.gov (United States)

    Bursy, Jan; Kuhlmann, Anne U; Pittelkow, Marco; Hartmann, Holger; Jebbar, Mohamed; Pierik, Antonio J; Bremer, Erhard

    2008-12-01

    Streptomyces coelicolor A3(2) synthesizes ectoine and 5-hydroxyectoine upon the imposition of either salt (0.5 M NaCl) or heat stress (39 degrees C). The cells produced the highest cellular levels of these compatible solutes when both stress conditions were simultaneously imposed. Protection against either severe salt (1.2 M NaCl) or heat stress (39 degrees C) or a combination of both environmental cues could be accomplished by adding low concentrations (1 mM) of either ectoine or 5-hydroxyectoine to S. coelicolor A3(2) cultures. The best salt and heat stress protection was observed when a mixture of ectoine and 5-hydroxyectoine (0.5 mM each) was provided to the growth medium. Transport assays with radiolabeled ectoine demonstrated that uptake was triggered by either salt or heat stress. The most effective transport and accumulation of [(14)C]ectoine by S. coelicolor A3(2) were achieved when both environmental cues were simultaneously applied. Our results demonstrate that the accumulation of the compatible solutes ectoine and 5-hydroxyectoine allows S. coelicolor A3(2) to fend off the detrimental effects of both high salinity and high temperature on cell physiology. We also characterized the enzyme (EctD) required for the synthesis of 5-hydroxyectoine from ectoine, a hydroxylase of the superfamily of the non-heme-containing iron(II)- and 2-oxoglutarate-dependent dioxygenases (EC 1.14.11). The gene cluster (ectABCD) encoding the enzymes for ectoine and 5-hydroxyectoine biosynthesis can be found in the genome of S. coelicolor A3(2), Streptomyces avermitilis, Streptomyces griseus, Streptomyces scabiei, and Streptomyces chrysomallus, suggesting that these compatible solutes play an important role as stress protectants in the genus Streptomyces.

  13. Enzymatic activity of catechol 1,2-dioxygenase and catechol 2,3-dioxygenase produced by Gordonia polyisoprenivorans

    Directory of Open Access Journals (Sweden)

    Andréa Scaramal Silva

    2012-01-01

    Full Text Available This study aimed to evaluate the environmental conditions for enzyme activity of catechol 1,2-dioxygenase (C1,2O and catechol 2,3-dioxygenase (C2,3O produced by Gordonia polyisoprenivorans in cell-free and immobilized extracts. The optimum conditions of pH, temperature, time course and effect of ions for enzyme activity were determined. Peak activity of C1,2O occurred at pH 8.0. The isolate exhibited the highest activity of C2,3O at pH 7.0 and 8.0 for the cell-free extract and immobilized extract, respectively. This isolate exhibited important characteristics such as broad range of pH, temperature and time course for enzyme activity.

  14. INDOLEAMINE 2,3-DIOXYGENASE (IDO AND IMMUNE TOLERANCE

    Directory of Open Access Journals (Sweden)

    Coma-del-Corral MJ

    2013-09-01

    Full Text Available SUMMARY: Indoleamine 2,3-dioxygenase (IDO is an intracellular and extrahepatic enzyme predominantly found in many cells, especially macrophages. Tryptophan degradation generates kynurenine, and this pathway of tryptophan metabolism is an effective mechanism for modulating the immune response. The IDO facilitates immune tolerance and is one of the main actors involved in the inhibition of cell proliferation, including activated T cells. IDO induces production of reactive oxygen species (ROS and nitric oxide (NO radicals. Several pathways involved in the regulation of immune response are regulated by redox mechanisms. Reactive oxygen and nitrogen species (ROS-RNS and other redox active molecules play key roles in immunity.

  15. A novel non-heme iron-containing dioxygenase. Chloridazon-catechol dioxygenase from Phenylobacterium immobilis DSM 1986.

    Science.gov (United States)

    Müller, R; Schmitt, S; Lingens, F

    1982-07-01

    Previously we purified an enzyme from Phenylobacterium immobilis DSM 1986, which cleaves the catechol derivative of the herbicide Chloridazon [5-amino-4-chloro-2-phenyl-3 (2H)-pyridazinone] in the meta position. The enzyme, which could be crystallized, proved in Ouchterlony double-diffusion tests to consist of a single protein species. No cross-reaction was observed with other meta-cleaving enzymes. Its light absorption spectrum showed a maximum at 279 nm (epsilon = 310 mM -1 cm -1), shoulders at 289 nm and 275 nm and a very weak band at around 430 nm (epsilon = 1.14 mM -1 cm -1). The amino acid analysis showed a slight excess of acidic amino acids, in agreement with the pl of 4.5. Surprisingly the enzyme per se is completely inactive, although it contains one non-dialysable iron atom per submit. It has to be activated by preincubation with ferrous ions or ascorbate. The enzyme activated this way is autoxidizable and returns to its non-activated state in the presence of oxygen. During the reaction with the substrate, this inactivation seems to be enhanced about 100 times. Since this kind of activation and inactivation is not observed in other meta-cleaving enzymes, this enzyme seems to represent a new type of a non-heme iron dioxygenase. We tentatively propose the name Chloridazon-catechol dioxygenase for this enzyme.

  16. Chemical components from Aloe and their inhibition of indoleamine 2, 3-dioxygenase

    Directory of Open Access Journals (Sweden)

    Ya Nan Sun

    2017-01-01

    Abbreviation used: IDO: inhibit indoleamine 2, 3-dioxygenase, TMS: tetramethylsilane, HMQC: heteronuclear multiple quantum correlation, HMBC: heteronuclear multiple bond correlation, COSY: 1H-1H correlation spectroscopy, ESI-MS: Electrospray ionization mass spectrometry, DMSO: dimethyl sulfoxide

  17. Trichloroethylene degradation by Escherichia coli containing the cloned Pseudomonas putida F1 toluene dioxygenase genes.

    OpenAIRE

    Zylstra, G J; Wackett, L P; Gibson, D T

    1989-01-01

    Toluene dioxygenase from Pseudomonas putida F1 has been implicated as an enzyme capable of degrading trichloroethylene. This has now been confirmed with Escherichia coli JM109(pDTG601) that contains the structural genes (todC1C2BA) of toluene dioxygenase under the control of the tac promoter. The extent of trichloroethylene degradation by the recombinant organism depended on the cell concentration and the concentration of trichloroethylene. A linear rate of trichloroethylene degradation was o...

  18. Conversion of 3-chlorocatechol by various catechol 2,3-dioxygenases and sequence analysis of the chlorocatechol dioxygenase region of Pseudomonas putida GJ31

    NARCIS (Netherlands)

    Mars, Astrid E.; Kingma, Jaap; Kaschabek, Stefan R.; Reineke, Walter; Janssen, Dick B.

    1999-01-01

    Pseudomonas putida GJ31 contains an unusual catechol 2,3-dioxygenase that converts 3-chlorocatechol and 3-methylcatechol, which enables the organism to use both chloroaromatics and methylaromatics for growth, A 3.1-kb region of genomic DNA of strain GJ31 containing the gene for this chlorocatechol 2

  19. Engineering Non-Heme Mono- and Dioxygenases for Biocatalysis

    Directory of Open Access Journals (Sweden)

    Adi Dror

    2012-09-01

    Full Text Available Oxygenases are ubiquitous enzymes that catalyze the introduction of one or two oxygen atoms to unreactive chemical compounds. They require reduction equivalents from NADH or NADPH and comprise metal ions, metal ion complexes, or coenzymes in their active site. Thus, for industrial purposes, oxygenases are most commonly employed using whole cell catalysis, to alleviate the need for co-factor regeneration. Biotechnological applications include bioremediation, chiral synthesis, biosensors, fine chemicals, biofuels, pharmaceuticals, food ingredients and polymers. Controlling activity and selectivity of oxygenases is therefore of great importance and of growing interest to the scientific community. This review focuses on protein engineering of non-heme monooxygenases and dioxygenases for generating improved or novel functionalities. Rational mutagenesis based on x-ray structures and sequence alignment, as well as random methods such as directed evolution, have been utilized. It is concluded that knowledge-based protein engineering accompanied with targeted libraries, is most efficient for the design and tuning of biocatalysts towards novel substrates and enhanced catalytic activity while minimizing the screening efforts.

  20. Structure of the human 4-hydroxyphenylpyruvic acid dioxygenase gene (HPD)

    Energy Technology Data Exchange (ETDEWEB)

    Awata, H.; Endo, F.; Matsuda, I. [Kumamoto Univ. (Japan)

    1994-10-01

    4-Hydroxyphenylpyruvic acid dioxygenase (HPD) is an important enzyme in tyrosine catabolism in most organisms. The activity of this enzyme is expressed mainly in the liver and developmentally regulated in mammals, and a genetic deficiency in this enzyme in humans and mice leads to hereditary tyrosinemia type 3. Using human HPD cDNA as a probe, a chromosomal gene related to HPD was isolated from human gene libraries. The human HPD gene is over 30 kb long and is split into 14 exons. The extract sizes and boundaries of exon blocks were determined, and all of the splice donor and acceptor sites conformed to the GT/AG rule. Analysis of the 5{prime} flanking sequence of the gene suggests that expression of the gene is regulated by hepatocyte-specific and liver-enriched transcription factors, as well as by hormones. These features of the 5{prime} flanking region of the gene are similar to those of other genes that are specifically expressed in hepatocytes and that are developmentally regulated. 41 refs., 2 figs., 1 tab.

  1. Chloridazon-catechol dioxygenases, a distinct group of meta-cleaving enzymes.

    Science.gov (United States)

    Schmitt, S; Müller, R; Wegst, W; Lingens, F

    1984-02-01

    We previously described a new meta-cleaving enzyme, termed chloridazon-catechol dioxygenase. The present paper describes the comparison of this enzyme with the meta-cleaving enzymes of eighteen strains of soil bacteria isolated with various aromatic compounds. Four of these strains were isolated with the herbicide chloridazon, six with the analgeticum aminopyrine and one with the analgeticum antipyrine as sole carbon source. These strains all belonged to a new type of bacteria, called Phenylobacteria. The seven other strains were isolated with aromatic compounds such as toluene, 3-phenylpropionate, benzoate, papaverine and 4-chlorobenzoate, and belonged to various species including Pseudomonas, Acinetobacter and Nocardia. In double diffusion experiments with antibodies, prepared against chloridazon-catechol dioxygenase, extracts from the eleven strains of Phenylobacteria gave a cross reaction, whereas the extracts of the seven other strains showed no reaction. The enzymes of the eleven positive strains showed the same characteristic kinetic behaviour as the previously described enzyme. In contrast to catechol 2, 3-dioxygenase they needed the addition of exogenous Fe2+ ions for activity. On ion-exchange chromatography they emerged at the same buffer concentration as chloridazon-catechol dioxygenase. In polyacrylamide electrophoresis they migrated identically. The linkage map derived from the activities of the various enzymes with 10 different substrates revealed an identity of more than 80% for these eleven enzymes. So the meta-cleaving enzymes of the Phenylobacteria seem to form a distinct group among the non-heme iron-containing dioxygenases.

  2. Expression, purification and kinetic characterization of recombinant benzoate dioxygenase from Rhodococcus ruber UKMP-5M

    Directory of Open Access Journals (Sweden)

    Arezoo Tavakoli

    2016-09-01

    Full Text Available In this study, benzoate dioxygenase from Rhodococcus ruber UKMP-5M was catalyzed by oxidating the benzene ring to catechol and other derivatives. The benzoate dioxygenase (benA gene from Rhodococcus ruber UKMP-5M was then expressed, purified, characterized, The benA gene was amplified (642 bp, and the product was cloned into a pGEM-T vector.The recombinant plasmid pGEMT-benA was digested by double restriction enzymes BamHI and HindIII to construct plasmid pET28b-benA and was then ligated into Escherichia coli BL21 (DE3. The recombinant E. coli was induced with 0.5 mM isopropyl β-D-thiogalactoside (IPTG at 22˚C to produce benzoate dioxygenase. The enzyme was then purified by ion exchange chromatography after 8 purification folds. The resulting product was 25 kDa, determined by sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE and western blotting. Benzoate dioxygenase activity was found to be 6.54 U/mL and the optimal pH and temperature were 8.5 and 25°C, respectively. Maximum velocity (Vmax and Michaelis constant (Km were 7.36 U/mL and 5.58 µM, respectively. The end metabolite from the benzoate dioxygenase reaction was cyclohexane dione, which was determined by gas chromatography mass spectrometry (GC-MS.

  3. Substrate Oxidation by Indoleamine 2,3-Dioxygenase: EVIDENCE FOR A COMMON REACTION MECHANISM.

    Science.gov (United States)

    Booth, Elizabeth S; Basran, Jaswir; Lee, Michael; Handa, Sandeep; Raven, Emma L

    2015-12-25

    The kynurenine pathway is the major route of L-tryptophan (L-Trp) catabolism in biology, leading ultimately to the formation of NAD(+). The initial and rate-limiting step of the kynurenine pathway involves oxidation of L-Trp to N-formylkynurenine. This is an O2-dependent process and catalyzed by indoleamine 2,3-dioxygenase and tryptophan 2,3-dioxygenase. More than 60 years after these dioxygenase enzymes were first isolated (Kotake, Y., and Masayama, I. (1936) Z. Physiol. Chem. 243, 237-244), the mechanism of the reaction is not established. We examined the mechanism of substrate oxidation for a series of substituted tryptophan analogues by indoleamine 2,3-dioxygenase. We observed formation of a transient intermediate, assigned as a Compound II (ferryl) species, during oxidation of L-Trp, 1-methyl-L-Trp, and a number of other substrate analogues. The data are consistent with a common reaction mechanism for indoleamine 2,3-dioxygenase-catalyzed oxidation of tryptophan and other tryptophan analogues.

  4. Development of catechol 2,3-dioxygenase-specific primers for monitoring bioremediation by competitive quantitative PCR

    Energy Technology Data Exchange (ETDEWEB)

    Mesarch, M.B.; Nakatsu, C.H.; Nies, L.

    2000-02-01

    Benzene, toluene, xylenes, phenol, naphthalene, and biphenyl are among a group of compounds that have at least one reported pathway for biodegradation involving catechol 2,3-dioxygenase enzymes. Thus, detection of the corresponding catechol 2,3-dioxygenase genes can serve as a basis for identifying and quantifying bacteria that have these catabolic abilities. Primes that can successfully amplify a 238-bp catechol 2,3-dioxygenase gene fragment from eight different bacteria are described. The identities of the amplicons were confirmed by hybridization with a 238-bp catechol 2,3-dioxygenase probe. The detection limit was 10{sup 2} to 10{sup 3} gene copies, which was lowered to 10{sup 0} to 10{sup 1} gene copies of hybridization. Using the dioxygenase-specific primers, an increase in catechol 2,3-dioxygenase genes was detected in petroleum-amended soils. The dioxygenase genes were enumerated by competitive quantitative PCR and a 163-bp competitor that was amplified using the same primers. Target and competitor sequences had identical amplification kinetics. Potential PCR inhibitors that could coextract with DNA, nonamplifying DNA, soil factors (humics), and soil pollutants (toluene) did not impact enumeration. Therefore, this technique can be used to accurately and reproducibly quantify catechol 2,3-dioxygenase genes in complex environments such as petroleum-contaminated soil. Direct, non-cultivation-based molecular techniques for detecting and enumerating microbial pollutant-biodegrading genes in environmental samples are powerful tools for monitoring bioremediation and developing field evidence in support of natural attenuation.

  5. Crystal structure of thermostable catechol 2,3-dioxygenase determined by multiwavelength anomalous dispersion method

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The selenomethionyl derivative of the thermostable catechol 2,3-dioxygenase (SeMet-TC23O) is expressed,purified and crystallized. By using multiwave length anomalous dispersion (MAD) phasing techniques, the crystal structure of TC23O at 0.3 nm resolutions is determined.TC23O is a homotetramer. Each monomer is composed of N-terminal and C-terminal domains (residues 1~153 and 153~319, respectively). The two domains are proximately symmetric by a non-crystallographic axis. Each domain contains two characteristic motifs which are found in almost all of extradial dioxygenases.Kevwords: multiwavelength anomalous dispersion (MAD), X-ray diffraction, thermostable catechol 2,3-dioxygenase, crystal structure,synchrotron light source.

  6. Crystal Structures of Fe2+ Dioxygenase Superoxo, Alkylperoxo, and Bound Product Intermediates

    OpenAIRE

    Kovaleva, Elena G.; Lipscomb, John D.

    2007-01-01

    We report the structures of three intermediates in the O2 activation and insertion reactions of an extradiol ring-cleaving dioxygenase. A crystal of Fe2+-containing homoprotocatechuate 2,3-dioxygenase was soaked in the slow substrate 4-nitrocatechol in a low O2 atmosphere. The X-ray crystal structure shows that three different intermediates reside in different subunits of a single homotetrameric enzyme molecule. One of these is the key substrate-alkylperoxo-Fe2+ intermediate, which has been p...

  7. Cloning and Characterization of a Sulfonate/α-Ketoglutarate Dioxygenase from Saccharomyces cerevisiae

    OpenAIRE

    Hogan, Deborah A; Auchtung, Thomas A.; Hausinger, Robert P.

    1999-01-01

    The Saccharomyces cerevisiae open reading frame YLL057c is predicted to encode a gene product with 31.5% amino acid sequence identity to Escherichia coli taurine/α-ketoglutarate dioxygenase and 27% identity to Ralstonia eutropha TfdA, a herbicide-degrading enzyme. Purified recombinant yeast protein is shown to be an Fe(II)-dependent sulfonate/α-ketoglutarate dioxygenase. Although taurine is a poor substrate, a variety of other sulfonates are utilized, with the best natural substrates being is...

  8. Enzymology of the carotenoid cleavage dioxygenases: reaction mechanisms, inhibition and biochemical roles.

    Science.gov (United States)

    Harrison, Peter J; Bugg, Timothy D H

    2014-02-15

    Carotenoid cleavage dioxygenases (CCDs) are a large family of non-heme iron (II) dependent enzymes. CCDs catalyse the selective oxidative cleavage of carotenoids to produce apocarotenoids. Apocarotenoid derived molecules form important signalling molecules in plants in the form of abscisic acid and strigolactone and in mammals in the form of retinal. Very little is known biochemically about the CCDs and only a handful of CCDs have been biochemically characterised. Mechanistically, debate surrounds whether CCDs utilise a mono or dioxygenase mechanism. Here, we review the biochemical roles of CCDs, discuss the mechanisms by which CCD cleavage is proposed to occur, and discuss recent reports of selective CCD enzyme inhibitors.

  9. Structures of aminophenol dioxygenase in complex with intermediate, product and inhibitor.

    Science.gov (United States)

    Li, De Feng; Zhang, Jia Yue; Hou, Yan Jie; Liu, Lei; Hu, Yonglin; Liu, Shuang Jiang; Wang, Da Cheng; Liu, Wei

    2013-01-01

    Dioxygen activation by nonhaem Fe(II) enzymes containing the 2-His-1-carboxylate facial triad has been extensively studied in recent years. Here, crystal structures of 2-aminophenol 1,6-dioxygenase, an enzyme that represents a minor group of extradiol dioxygenases and that catalyses the ring opening of 2-aminophenol, in complex with the lactone intermediate (4Z,6Z)-3-iminooxepin-2(3H)-one and the product 2-aminomuconic 6-semialdehyde and in complex with the suicide inhibitor 4-nitrocatechol are reported. The Fe-ligand binding schemes observed in these structures revealed some common geometrical characteristics that are shared by the published structures of extradiol dioxygenases, suggesting that enzymes that catalyse the oxidation of noncatecholic compounds are very likely to utilize a similar strategy for dioxygen activation and the fission of aromatic rings as the canonical mechanism. The Fe-ligation arrangement, however, is strikingly enantiomeric to that of all other 2-His-1-carboxylate enzymes apart from protocatechuate 4,5-dioxygenase. This structural variance leads to the generation of an uncommon O(-)-Fe(2+)-O(-) species prior to O(2) binding, which probably forms the structural basis on which APD distinguishes its specific substrate and inhibitor, which share an analogous molecular structure.

  10. EXPRESSION AND POST-TRANSLATIONAL MODIFICATION OF HUMAN 4-HYDROXY-PHENYLPYRUVATE DIOXYGENASE

    DEFF Research Database (Denmark)

    Aarenstrup, Lene; Falch, Anne-Marie; Jakobsen, Kirsten K.;

    2002-01-01

    4-hydroxyphenylpyruvate dioxygenase (HPD) (EC 1.13.11.27) is a key enzyme involved in tyrosine catabolism. Congenital HPD deficiency is a rare, relatively benign condition known as hereditary type III tyrosinemia. The severe type I tyrosinemia, caused by a deficiency of fumarylacetoacetate hydrol...

  11. Natural CD4+ T-cell responses against indoleamine 2,3-dioxygenase

    DEFF Research Database (Denmark)

    Munir, Shamaila; Larsen, Stine Kiaer; Iversen, Trine Zeeberg;

    2012-01-01

    The enzyme indoleamine 2,3-dioxygenase (IDO) contributes to immune tolerance in a variety of settings. In cancer IDO is expressed within the tumor itself as well as in antigen-presenting cells in tumor-draining lymph nodes, where it endorses the establishment of peripheral immune tolerance to tumor...

  12. Spontaneous cytotoxic T-Cell reactivity against indoleamine 2,3-dioxygenase-2

    DEFF Research Database (Denmark)

    Sørensen, Rikke Bæk; Køllgaard, Tania; Andersen, Rikke Sick;

    2011-01-01

    Several lines of data have suggested a possible link between the indoleamine 2,3-dioxygenase (IDO)-like protein IDO2 and cancer. First, IDO2 expression has been described in human tumors, including renal, gastric, colon, and pancreatic tumors. Second, the apparent selective inhibition of IDO2...

  13. An iron-oxygen intermediate formed during the catalytic cycle of cysteine dioxygenase.

    Science.gov (United States)

    Tchesnokov, E P; Faponle, A S; Davies, C G; Quesne, M G; Turner, R; Fellner, M; Souness, R J; Wilbanks, S M; de Visser, S P; Jameson, G N L

    2016-07-07

    Cysteine dioxygenase is a key enzyme in the breakdown of cysteine, but its mechanism remains controversial. A combination of spectroscopic and computational studies provides the first evidence of a short-lived intermediate in the catalytic cycle. The intermediate decays within 20 ms and has absorption maxima at 500 and 640 nm.

  14. A biological pathway linking inflammation and depression: activation of indoleamine 2,3-dioxygenase

    Directory of Open Access Journals (Sweden)

    Christmas DM

    2011-07-01

    Full Text Available David M Christmas, JP Potokar, Simon JC DaviesAcademic Unit of Psychiatry, School of Social and Community Medicine, University of Bristol, Bristol, UK A presentation relating to this manuscript was made by Dr David Christmas at the 9th International Meeting on Clinical Pharmacology in Psychiatry (9th IMCPP in Copenhagen, Denmark in September 2010Abstract: This article highlights the evidence linking depression to increased inflammatory drive and explores putative mechanisms for the association by reviewing both preclinical and clinical literature. The enzyme indoleamine 2,3-dioxygenase is induced by proinflammatory cytokines and may form a link between immune functioning and altered neurotransmission, which results in depression. Increased indoleamine 2,3-dioxygenase activity may cause both tryptophan depletion and increased neurotoxic metabolites of the kynurenine pathway, two alterations which have been hypothesized to cause depression. The tryptophan-kynurenine pathway is comprehensively described with a focus on the evidence linking metabolite alterations to depression. The use of immune-activated groups at high risk of depression have been used to explore these hypotheses; we focus on the studies involving chronic hepatitis C patients receiving interferon-alpha, an immune activating cytokine. Findings from this work have led to novel strategies for the future development of antidepressants including inhibition of indoleamine 2,3-dioxygenase, moderating the cytokines which activate it, or addressing other targets in the kynurenine pathway.Keywords: depression, inflammation, indoleamine 2,3-dioxygenase, kynurenine, serotonin, tryptophan

  15. 4-Nitrocatechol as a colorimetric probe for non-heme iron dioxygenases.

    Science.gov (United States)

    Tyson, C A

    1975-03-10

    4-Nitrocatechol is examined as an active site probe for non-heme iron dioxygenases and found to be of value, particularly with those containing iron in the Fe(II) oxidation state. 4-Nitrocatechol is astrong competitive inhibitor of substrate oxygenation by protocatechuate 3,4-dioxygenase, forming a reversible complex with this enzyme, and by pyrocatechase. The number of binding sites per enzyme molecule titrated spectrophotometrically with 4-nitrocatechol agrees with results from previous studies with either the principal substrate or other analogues, as expected of an effective probe. Despite these facts and the observation that both enzymes cleave the same substrates at the same carbon-carbon bond, the optical and electron paramagnetic resonance (EPR) spectra of their 4-nitrocatechol complexes are remarkably different. The 4-nitocatechol-protocatechuate 3,4-dioxygenase optical spectra resemble that of the 4-nitrocatecholate ion shifted 20 to 30 nm to longer wavelength. Concomitant with this change the EPR signal centered at g equal 4.28 shows increased rhombicity (g values at 4.74, 4.28, and 3.74). In contrast, the spectrum of the 4-nitrocatechol-pyrocatechase complex has a maximum at the same wavelength as that of a 1:1 solution of free Fe(II) and 4-nitrocatechol in the absence of enzyme after titration of the catecholic protons with base and the g equal 4.28 EPR signal is not resolved at liquid N-2 temperature. These changes are interpreted as resulting in part from a pronounced change in the ligand fields about the irons at the active sites which in the case of protocatechuate 3,4-dioxygenase leads to enzyme inactivation. The results also are the first indication that substrate analogues change their ionization form upon complexation with Fe (III) dioxygenases. The interaction of the probe with metapyrocatechase, an Fe(III) containing dioxygenase, and with several additional oxygenases and hydroperoxidases is also briefly examined. The probe is not specific

  16. Cloning, expression, and characterization of catechol 1,2-dioxygenase from a phenol-degrading Candida tropicalis JH8 strain.

    Science.gov (United States)

    Long, Yan; Yang, Sheng; Xie, Zhixiong; Cheng, Li

    2016-10-02

    The sequence cato encoding catechol 1,2-dioxygenase from Candida tropicalis JH8 was cloned, sequenced, and expressed in Escherichia coli. The sequence cato contained an ORF of 858 bp encoding a polypeptide of 285 amino acid residues. The recombinant catechol 1,2-dioxygenase exists as a homodimer structure with a subunit molecular mass of 32 KD. Recombinant catechol 1,2-dioxygenase was unstable below pH 5.0 and stable from pH 7.0 to 9.0; its optimum pH was at 7.5. The optimum temperature for the enzyme was 30°C, and it possessed a thermophilic activity within a broad temperature range. Under the optimal conditions with catechol as substrate, the Km and Vmax of recombinant catechol 1,2-dioxygenase were 9.2 µM and 0.987 µM/min, respectively. This is the first article presenting cloning and expressing in E. coli of catechol 1,2-dioxygenase from C. tropicalis and characterization of the recombinant catechol 1,2-dioxygenase.

  17. Characterization of catechol 2,3-dioxygenase from Planococcus sp. strain S5 induced by high phenol concentration.

    Science.gov (United States)

    Hupert-Kocurek, Katarzyna; Guzik, Urszula; Wojcieszyńska, Danuta

    2012-01-01

    This study aimed at characterization of a new catechol 2,3-dioxygenase isolated from a Gram-positive bacterium able to utilize phenol as the sole carbon and energy source. Planococcus sp. strain S5 grown on 1 or 2 mM phenol showed activity of both a catechol 1,2- and catechol 2,3-dioxygenase while at a higher concentrations of phenol only catechol 2,3-dioxygenase activity was observed. The enzyme was optimally active at 60°C and pH 8.0. Kinetic studies showed that the K(m) and V(max) of the enzyme were 42.70 µM and 329.96 mU, respectively. The catechol 2,3-dioxygenase showed the following relative meta-cleavage activities for various catechols tested: catechol (100%), 3-methylcatechol (13.67%), 4-methylcatechol (106.33%) and 4-chlorocatechol (203.80%). The high reactivity of this enzyme towards 4-chlorocatechol is different from that observed for other catechol 2,3-dioxygenases. Nucleotide sequencing and homology search revealed that the gene encoding the S5 catechol 2,3-dioxygenase shared the greatest homology with the known genes encoding isoenzymes from Gram-negative Pseudomonas strains.

  18. A two-electron shell game: Intermediates of the extradiol-cleaving catechol dioxygenases

    Science.gov (United States)

    Fielding, Andrew J.

    2014-01-01

    Extradiol catechol ring-cleaving dioxygenases function by binding both the organic substrate and O2 at a divalent metal center in the active site. They have proven to be a particularly versatile group of enzymes with which to study the O2 activation process. Here, recent studies of homoprotocatechuate 2,3-dioxygenase (HPCD) are summarized with the objective of showing how Nature can utilize the enzyme structure and the properties of the metal and the substrate to select among many possible chemical paths to achieve both specificity and efficiency. Possible intermediates in the mechanism have been trapped by swapping active site metals, introducing active site amino acid substituted variants, and using substrates with different electron donating capacities. While each of these intermediates could form part of a viable reaction pathway, kinetic measurements significantly limit the likely candidates. Structural, kinetic, spectroscopic and computational analysis of the various intermediates shed light on how catalytic efficiency can be achieved. PMID:24615282

  19. Discovery of Key Dioxygenases that Diverged the Paraherquonin and Acetoxydehydroaustin Pathways in Penicillium brasilianum.

    Science.gov (United States)

    Matsuda, Yudai; Iwabuchi, Taiki; Fujimoto, Takayuki; Awakawa, Takayoshi; Nakashima, Yu; Mori, Takahiro; Zhang, Huiping; Hayashi, Fumiaki; Abe, Ikuro

    2016-09-28

    Paraherquonin (1), a fungal meroterpenoid produced by Penicillium brasilianum NBRC 6234, possesses a unique, highly congested hexacyclic molecular architecture. Here we identified the biosynthetic gene cluster of 1 (the prh cluster) and elucidated the pathway up to berkeleydione (2), which serves as the key intermediate for the biosynthesis of 1 as well as many other meroterpenoids. Interestingly, the nonheme iron and α-ketoglutarate-dependent dioxygenase PrhA constructs the cycloheptadiene moiety to afford 2 from preaustinoid A1 (6), probably via the homoallyl-homoallyl radical rearrangement. Additionally, another fungal strain, P. brasilianum MG11, which produces acetoxydehydroaustin instead of 1, was found to have a gene cluster nearly identical to the prh cluster. The dioxygenase encoded by the cluster shares 92% sequence identity with PrhA, and also accepts 6 but produces preaustinoid A3 (17) with a spiro-lactone system, generating a diverging point for the two different meroterpenoid pathways in the same species.

  20. Ring-hydroxylating dioxygenases involved in PAH biodegradation : structure, function, biodiversity

    OpenAIRE

    Jouanneau, Yves; Martin, Florence; Krivobok, Serge; Willison, John Christopher

    2011-01-01

    International audience; The first step in the biodegradation of PAHs by aerobic bacteria is catalyzed by metalloenzymes known as ring-hydroxylating dioxygenases (RHDs). Because of the hydrophobic nature and chemical resistance of PAHs, their initial attack by RHDs is a difficult reaction, which is critical to the whole degradation process. This chapter gives an overview of the current knowledge on the genetics, structure, catalytic mechanism and diversity of RHDs involved in PAH degradation. ...

  1. 4-Hydroxyphenylpyruvate dioxygenase inhibitors in combination with safeners: solutions for modern and sustainable agriculture.

    Science.gov (United States)

    Ahrens, Hartmut; Lange, Gudrun; Müller, Thomas; Rosinger, Chris; Willms, Lothar; van Almsick, Andreas

    2013-09-01

    Inhibitors of 4-hydroxyphenylpyruvate dioxygenase (HPPD) prevent plant carotenoid pigment formation, which in turn leads to chlorophyll degradation. This "bleaching" herbicide mode of action provides weed-control products for various crops, such as rice, corn, and cereals. Combinations with suitable safeners allow the full exploitation of the potential of this compound class to selectively control major weed problems, including rapidly increasing cases of resistance against other important herbicide classes.

  2. Novel carotenoid cleavage dioxygenase catalyzes the first dedicated step in saffron crocin biosynthesis

    KAUST Repository

    Frusciante, Sarah

    2014-08-05

    Crocus sativus stigmas are the source of the saffron spice and accumulate the apocarotenoids crocetin, crocins, picrocrocin, and safranal, responsible for its color, taste, and aroma. Through deep transcriptome sequencing, we identified a novel dioxygenase, carotenoid cleavage dioxygenase 2 (CCD2), expressed early during stigma development and closely related to, but distinct from, the CCD1 dioxygenase family. CCD2 is the only identified member of a novel CCD clade, presents the structural features of a bona fide CCD, and is able to cleave zeaxanthin, the presumed precursor of saffron apocarotenoids, both in Escherichia coli and in maize endosperm. The cleavage products, identified through high-resolution mass spectrometry and comigration with authentic standards, are crocetin dialdehyde and crocetin, respectively. In vitro assays show that CCD2 cleaves sequentially the 7,8 and 7′,8′ double bonds adjacent to a 3-OH-β-ionone ring and that the conversion of zeaxanthin to crocetin dialdehyde proceeds via the C30 intermediate 3-OH-β-apo-8′-carotenal. In contrast, zeaxanthin cleavage dioxygenase (ZCD), an enzyme previously claimed to mediate crocetin formation, did not cleave zeaxanthin or 3-OH-β-apo-8′-carotenal in the test systems used. Sequence comparison and structure prediction suggest that ZCD is an N-truncated CCD4 form, lacking one blade of the β-propeller structure conserved in all CCDs. These results constitute strong evidence that CCD2 catalyzes the first dedicated step in crocin biosynthesis. Similar to CCD1, CCD2 has a cytoplasmic localization, suggesting that it may cleave carotenoids localized in the chromoplast outer envelope.

  3. [Isolation, charcaterization of an anthracene degrading bacterium Martelella sp. AD-3 and cloning of dioxygenase gene].

    Science.gov (United States)

    Cui, Chang-Zheng; Feng, Tian-Cai; Yu, Ya-Qi; Dong, Fei; Yang, Xin-Mei; Feng, Yao-Yu; Liu, Yong-Di; Lin, Han-Ping

    2012-11-01

    Anthracene, among the 16 US EPA polycyclic aromatic hydrocarbons (PAHs), is a typical low molecular weight environmental contaminant, which gains concern on its biodegradation under hypersaline condition. In this study, an anthracene-degrading bacterial strain was isolated from highly saline petroleum-contaminated soil. Based on its physiological, biochemical characteristics and 16S rDNA sequence analysis, the bacteria was preliminary identified and named as Martelella sp. AD-3. The strain was able to utilize anthracene as sole carbon source for growth and the degradation occurred under broad salinities (0.1% to 10%) and varying pHs (6.0 to 10.0). The optimized degradation conditions were initial concentration 25 mg x L(-1), culture temperature 30 degrees C, pH 9.0 and salinity 3%. And 94.6% of anthracene was degraded by strain AD-3 under the optimal conditions within 6 days. Degenerate primers design was performed with a reported dioxygenase alpha subunit homologous gene. A length of 307 bp fragment of the partial dioxygenase gene sequences (GenBank accession: JF823991.1) was amplified by nested PCR. The clones amino acid sequence from strain AD-3 showed 95% identity to that of the partial naphthalene dioxygenase large-subunit from Marinobacter sp. NCE312 (AF295033). The results lay a foundation for the further study of molecular mechanism involved in the PAHs biodegradation by strain AD-3.

  4. Characterization of an indoleamine 2,3-dioxygenase-like protein found in humans and mice.

    Science.gov (United States)

    Ball, Helen J; Sanchez-Perez, Angeles; Weiser, Silvia; Austin, Christopher J D; Astelbauer, Florian; Miu, Jenny; McQuillan, James A; Stocker, Roland; Jermiin, Lars S; Hunt, Nicholas H

    2007-07-01

    Indoleamine 2,3-dioxygenase (INDO) and tryptophan 2,3-dioxygenase (TDO) each catalyze the first step in the kynurenine pathway of tryptophan metabolism. We describe the discovery of another enzyme with this activity, indoleamine 2,3-dioxygenase-like protein (INDOL1), which is closely related to INDO and is expressed in mice and humans. The corresponding genes have a similar genomic structure and are situated adjacent to each other on human and mouse chromosome 8. They are likely to have arisen by gene duplication before the origin of the tetrapods. The expression of INDOL1 is highest in the mouse kidney, followed by epididymis, and liver. Expression of mouse INDOL1 was further localized to the tubular cells in the kidney and the spermatozoa. INDOL1 was assigned its name because of its structural similarity to INDO. We demonstrate that INDOL1 catalyses the conversion of tryptophan to kynurenine therefore a more appropriate nomenclature for the enzymes might be INDO-1 and INDO-2, or the more commonly-used abbreviations, IDO-1 and IDO-2. Although the two proteins have similar enzymatic activities, their different expression patterns within tissues and during malaria infection, suggests a distinct role for each protein. This identification of INDOL1 may help to explain the regulation of the diversity of physiological and patho-physiological processes in which the kynurenine pathway is involved.

  5. Loss of ETHE1, a mitochondrial dioxygenase, causes fatal sulfide toxicity in ethylmalonic encephalopathy.

    Science.gov (United States)

    Tiranti, Valeria; Viscomi, Carlo; Hildebrandt, Tatjana; Di Meo, Ivano; Mineri, Rossana; Tiveron, Cecilia; Levitt, Michael D; Prelle, Alessandro; Fagiolari, Gigliola; Rimoldi, Marco; Zeviani, Massimo

    2009-02-01

    Ethylmalonic encephalopathy is an autosomal recessive, invariably fatal disorder characterized by early-onset encephalopathy, microangiopathy, chronic diarrhea, defective cytochrome c oxidase (COX) in muscle and brain, high concentrations of C4 and C5 acylcarnitines in blood and high excretion of ethylmalonic acid in urine. ETHE1, a gene encoding a beta-lactamase-like, iron-coordinating metalloprotein, is mutated in ethylmalonic encephalopathy. In bacteria, ETHE1-like sequences are in the same operon of, or fused with, orthologs of TST, the gene encoding rhodanese, a sulfurtransferase. In eukaryotes, both ETHE1 and rhodanese are located within the mitochondrial matrix. We created a Ethe1(-/-) mouse that showed the cardinal features of ethylmalonic encephalopathy. We found that thiosulfate was excreted in massive amounts in urine of both Ethe1(-/-) mice and humans with ethylmalonic encephalopathy. High thiosulfate and sulfide concentrations were present in Ethe1(-/-) mouse tissues. Sulfide is a powerful inhibitor of COX and short-chain fatty acid oxidation, with vasoactive and vasotoxic effects that explain the microangiopathy in ethylmalonic encephalopathy patients. Sulfide is detoxified by a mitochondrial pathway that includes a sulfur dioxygenase. Sulfur dioxygenase activity was absent in Ethe1(-/-) mice, whereas it was markedly increased by ETHE1 overexpression in HeLa cells and Escherichia coli. Therefore, ETHE1 is a mitochondrial sulfur dioxygenase involved in catabolism of sulfide that accumulates to toxic levels in ethylmalonic encephalopathy.

  6. Crystal structure of the terminal oxygenase component of cumene dioxygenase from Pseudomonas fluorescens IP01.

    Science.gov (United States)

    Dong, Xuesong; Fushinobu, Shinya; Fukuda, Eriko; Terada, Tohru; Nakamura, Shugo; Shimizu, Kentaro; Nojiri, Hideaki; Omori, Toshio; Shoun, Hirofumi; Wakagi, Takayoshi

    2005-04-01

    The crystal structure of the terminal component of the cumene dioxygenase multicomponent enzyme system of Pseudomonas fluorescens IP01 (CumDO) was determined at a resolution of 2.2 A by means of molecular replacement by using the crystal structure of the terminal oxygenase component of naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4 (NphDO). The ligation of the two catalytic centers of CumDO (i.e., the nonheme iron and Rieske [2Fe-2S] centers) and the bridging between them in neighboring catalytic subunits by hydrogen bonds through a single amino acid residue, Asp231, are similar to those of NphDO. An unidentified external ligand, possibly dioxygen, was bound at the active site nonheme iron. The entrance to the active site of CumDO is different from the entrance to the active site of NphDO, as the two loops forming the lid exhibit great deviation. On the basis of the complex structure of NphDO, a biphenyl substrate was modeled in the substrate-binding pocket of CumDO. The residues surrounding the modeled biphenyl molecule include residues that have already been shown to be important for its substrate specificity by a number of engineering studies of biphenyl dioxygenases.

  7. Expression Pattern and Clinicopathological Relevance of the Indoleamine 2,3-Dioxygenase 1/Tryptophan 2,3-Dioxygenase Protein in Colorectal Cancer

    Directory of Open Access Journals (Sweden)

    I-Chien Chen

    2016-01-01

    Full Text Available Aims. Cancer cells use the indoleamine 2,3-dioxygenase 1 (IDO1 pathway to suppress the host’s immune response in order to facilitate survival, growth, invasion, and metastasis of malignant cells. Higher IDO1 expression was shown to be involved in colorectal cancer (CRC progression and to be correlated with impaired clinical outcome. However, the potential correlation between the expression of IDO1 in a CRC population with a low mutation rate of the APC gene remains unknown. Material and Methods. Tissues and blood samples were collected from 192 CRC patients. The expressions of IDO1, tryptophan 2,3-dioxygenase (TDO2, and beta-catenin proteins were analyzed by immunohistochemistry. Microsatellite instability (MSI was determined by PCR amplification of microsatellite loci. Results. The results showed that high IDO1 or TDO2 protein expression was associated with characteristics of more aggressive phenotypes of CRC. For the first time, they also revealed a positive correlation between the abnormal expression of beta-catenin and IDO1 or TDO2 proteins in a CRC population with a low mutation rate of APC. Conclusion. We concluded that an IDO1-regulated molecular pathway led to abnormal expression of beta-catenin in the nucleus/cytoplasm of CRC patients with low mutation rate of APC, making IDO1 an interesting target for immunotherapy in CRC.

  8. Diversity of 16S rRNA and dioxygenase genes detected in coal-tar-contaminated site undergoing active bioremediation

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, M.; Khanna, S. [NIIT Univ, Neemrana (India). Dept. of Biotechnology & Bioinformation

    2010-04-15

    In order to develop effective bioremediation strategies for polyaromatic hydrocarbons (PAHs) degradation, the composition and metabolic potential of microbial communities need to be better understood, especially in highly PAH contaminated sites in which little information on the cultivation-independent communities is available. Coal-tar-contaminated soil was collected, which consisted of 122-122.5 mg g{sup -1} total extractable PAH compounds. Biodegradation studies with this soil indicated the presence of microbial community that is capable of degrading the model PAH compounds viz naphthalene, phenanthrene and pyrene at 50 ppm each. PCR clone libraries were established from the DNA of the coal-tar-contaminated soil, targeting the 16S rRNA to characterize (I) the microbial communities, (ii) partial gene fragment encoding the Rieske iron sulfur center {alpha}-subunit) common to all PAH dioxygenase enzymes and (iii) {beta}-subunit of dioxygenase. Phylotypes related to Proteobacteria ({Alpha}-, {Epsilon}- and Gammaproteobacteria), Acidobacteria, Actinobacteria, Firmicutes, Gemmatimonadetes and Deinococci were detected in 16S rRNA derived clone libraries. Many of the gene fragment sequences of alpha-subunit and beta-subunit of dioxygenase obtained from the respective clone libraries fell into clades that are distinct from the reference dioxygenase gene sequences. Presence of consensus sequence of the Rieske type (2Fe2S) cluster binding site suggested that these gene fragments encode for {alpha}-subunit of dioxygenase gene. Sequencing of the cloned libraries representing {alpha}-subunit gene fragments (Rf1) and beta-subunit of dioxygenase showed the presence of hitherto unidentified dioxygenase in coal-tar-contaminated soil.

  9. Anaerobic enzyme·substrate structures provide insight into the reaction mechanism of the copper-dependent quercetin 2,3-dioxygenase

    NARCIS (Netherlands)

    Steiner, Roberto A.; Kalk, Kor H.; Dijkstra, Bauke W.

    2002-01-01

    Quercetin 2,3-dioxygenase (2,3QD) is the only firmly established copper dioxygenase known so far. Depending solely on a mononuclear Cu center, it catalyzes the breakage of the O-heterocycle of flavonols, producing more easily degradable phenolic carboxylic acid ester derivatives. In the enzymatic pr

  10. Anaerobic enzyme-substrate structures provide insight into the reaction mechanism of the copper-dependent quercetin 2,3-dioxygenase

    NARCIS (Netherlands)

    Steiner, RA; Kalk, KH; Dijkstra, BW

    2002-01-01

    Quercetin 2,3-dioxygenase (2,3QD) is the only firmly established copper dioxygenase known so far. Depending solely on a mononuclear Cu center, it catalyzes the breakage of the O-heterocycle of flavonols, producing more easily degradable phenolic carboxylic acid ester derivatives. In the enzymatic pr

  11. Oxidation of chlorinated olefins by Escherichia coli transformed with dimethyl sulfide monooxygenase genes or cumene dioxygenase genes.

    Science.gov (United States)

    Takami, Wako; Yoshida, Takako; Nojiri, Hideaki; Yamane, Hisakazu; Omori, Toshio

    1999-04-01

    In the present work, it was shown that the dimethyl sulfide (DMS) monooxygenase and the cumene dioxygenase catalyzed oxidation of various chlorinated ethenes, propenes, and butenes. The specific activities of these oxygenases were determined for C(2) to C(4) chlorinated olefins, and the oxidation rates ranged from 0.19 to 4.18 nmol.min(-1).mg(-1) of dry cells by the DMS monooxygenase and from 0.19 to 1.29 nmol.min(-1).mg(-1) of dry cells by the cumene dioxygenase. The oxidation products were identified by gas chromatography-mass spectrometry. Most chlorinated olefins were monooxygenated by the DMS monooxygenase to yield chlorinated epoxides. In the case of the cumene dioxygenase, the substrates lacking any chlorine atom on double-bond carbon atoms were dioxygenated, and those with chlorine atoms attaching to double-bond carbon atoms were monooxygenated to yield allyl alcohols.

  12. Mechanism of S-oxygenation by a cysteine dioxygenase model complex

    Science.gov (United States)

    Sastry, G. Narahari

    2012-01-01

    In this work we present the first computational study on a biomimetic cysteine dioxygenase model complex, [FeII(LN3S)]+ where LN3S is a tetradentate ligand with a bis(imino)pyridyl scaffold and a pendant arylthiolate group. The reaction mechanism of sulfur dioxygenation with O2 was examined by density functional theory (DFT) methods, and compared to results obtained for cysteine dioxygenase. The reaction proceeds via multistate reactivity patterns on competing singlet, triplet and quintet spin state surfaces. The reaction mechanism is analogous to that found for cysteine dioxygenase enzymes [Kumar, D.; Thiel, W.; de Visser, S. P. J. Am. Chem. Soc. 2011, 133, 3869–3882], hence the computations indicate that this complex can closely mimic the enzymatic process. The catalytic mechanism starts from an iron(III)-superoxo complex and the attack of the terminal oxygen atom of the superoxo group on the sulfur atom of the ligand. Subsequently, the dioxygen bond breaks to form an iron(IV)-oxo complex with a bound sulfenato group. After reorganization the second oxygen atom is transferred to the substrate to give a sulfinic acid product. An alternative mechanism involving the direct attack of dioxygen on the sulfur, without involving any iron-oxygen intermediates, was also examined. Importantly, a significant energetic preference for dioxygen coordinating to the iron center prior to attack at sulfur was discovered and serves to elucidate the function of the metal ion in the reaction process. The computational results are in good agreement with experimental observations, and the differences and similarities of the biomimetic complex and the enzymatic CDO center are highlighted. PMID:22091701

  13. Compound-Specific Isotope Analysis of Nitroaromatic Contaminant Transformations by Nitroarene Dioxygenases

    Science.gov (United States)

    Pati, Sarah G.; Kohler, Hans-Peter E.; Hofstetter, Thomas B.

    2014-05-01

    Dioxygenation is an important biochemical reaction that often initiates the mineralization of recalcitrant organic contaminants such as nitroaromatic explosives, chlorinated benzenes, and polycyclic aromatic hydrocarbons. However, to assess the extent of dioxygenation in contaminated environments is difficult because of competing transformation processes and further reactions of the dioxygenation products. Compound-specific isotope analysis (CSIA) offers a new approach to reliably quantify biodegradation initiated by dioxygenation based on changes in stable isotope ratios of the pollutant. For CSIA it is essential to know the kinetic isotope effects (KIEs) pertinent to the dioxygenation mechanism of organic contaminants. Unfortunately, the range of KIEs of such reactions is poorly constrained although many dioxygenase enzymes with a broad substrate specificity have been reported. Dioxygenase enzymes usually exhibit complex reaction kinetics involving multiple substrates and substrate-specific binding modes which makes the determination of KIEs challenging. The goal of this study was to explore the magnitude and variability of 13C-, 2H-, and 15N-KIEs for the dioxygenation of one contaminant class, that is nitroaromatic contaminants (NACs). To this end, we investigated the C, H, and N isotope fractionation during the dioxygenation of nitrobenzene (NB), 2-nitrotoluene (2-NT), and 3-nitrotoluene (3-NT) by pure cultures, E. coli clones, cell extracts, and purified enzymes. From isotope fractionations measured in the substrates and reaction products, we determined dioxygenation KIEs for different combinations of the three substrates with nitrobenzene dioxygenase (NBDO) and 2-nitrotoluene dioxygenase (2NTDO). The 13C-, 2H-, and 15N-KIEs for the dioxygenation of NB by NBDO were consistent for all experimental systems considered (i.e., Comamonas sp. Strain JS765, E. coli clones, cell extracts of E. coli clones, and purified NBDO). This observation suggests that the isotope

  14. Iron(III) complexes of certain tetradentate phenolate ligands as functional models for catechol dioxygenases

    Indian Academy of Sciences (India)

    Mallayan Palaniandavar; Marappan Velusamy; Ramasamy Mayilmurugan

    2006-11-01

    Catechol 1,2-dioxygenase (CTD) and protocatechuate 3,4-dioxygenase (PCD) are bacterial non-heme iron enzymes, which catalyse the oxidative cleavage of catechols to cis, cis-muconic acids with the incorporation of molecular oxygen via a mechanism involving a high-spin ferric centre. The iron(III) complexes of tripodal phenolate ligands containing N3O and N2O2 donor sets represent the metal binding region of the iron proteins. In our laboratory iron(III) complexes of mono- and bisphenolate ligands have been studied successfully as structural and functional models for the intradiol-cleaving catechol dioxygenase enzymes. The single crystal X-ray crystal structures of four of the complexes have been determined. One of the bis-phenolato complexes contains a FeN2O2Cl chromophore with a novel trigonal bipyramidal coordination geometry. The Fe-O-C bond angle of 136.1° observed for one of the iron(III) complex of a monophenolate ligand is very similar to that in the enzymes. The importance of the nearby sterically demanding coordinated -NMe2 group has been established and implies similar stereochemical constraints from the other ligated amino acid moieties in the 3,4-PCD enzymes, the enzyme activity of which is traced to the difference in the equatorial and axial Fe-O(tyrosinate) bonds (Fe-O-C, 133, 148°). The nature of heterocyclic rings of the ligands and the methyl substituents on them regulate the electronic spectral features, FeIII/FeII redox potentials and catechol cleavage activity of the complexes. Upon interacting with catecholate anions, two catecholate to iron(III) charge transfer bands appear and the low energy band is similar to that of catechol dioxygenase-substrate complex. Four of the complexes catalyze the oxidative cleavage of H2DBC by molecular oxygen to yield intradiol cleavage products. Remarkably, the more basic N-methylimidazole ring in one of the complexes facilitates the rate-determining productreleasing phase of the catalytic reaction. The present

  15. Structure of the 2, 4′-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP

    Energy Technology Data Exchange (ETDEWEB)

    Keegan, R.; Lebedev, A. [RAL, Harwell Oxford, Didcot OX11 0FA (United Kingdom); Erskine, P.; Guo, J.; Wood, S. P. [UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF (United Kingdom); Hopper, D. J. [Aberystwyth University, Penglais, Aberystwyth SY23 3DA Wales (United Kingdom); Rigby, S. E. J. [University of Manchester, 131 Princess Street, Manchester M1 7DN (United Kingdom); Cooper, J. B., E-mail: jon.cooper@ucl.ac.uk [UCL Division of Medicine (Royal Free Campus), Rowland Hill Street, London NW3 2PF (United Kingdom); RAL, Harwell Oxford, Didcot OX11 0FA (United Kingdom)

    2014-09-01

    The first X-ray structure of a 2, 4′-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP at a resolution of 2.2 Å is reported. This structure establishes that the enzyme adopts the cupin-fold, forming compact dimers with a pronounced hydrophobic interface between the monomers. Each monomer possesses a catalytic ferrous iron that is coordinated by three histidines (76, 78 and 114) and an additional ligand which has been putatively assigned as a carbonate, although formate and acetate are possibilities. The enzyme 2, 4′-dihydroxyacetophenone dioxygenase (DAD) catalyses the conversion of 2, 4′-dihydroxyacetophenone to 4-hydroxybenzoic acid and formic acid with the incorporation of molecular oxygen. Whilst the vast majority of dioxygenases cleave within the aromatic ring of the substrate, DAD is very unusual in that it is involved in C—C bond cleavage in a substituent of the aromatic ring. There is evidence that the enzyme is a homotetramer of 20.3 kDa subunits, each containing nonhaem iron, and its sequence suggests that it belongs to the cupin family of dioxygenases. In this paper, the first X-ray structure of a DAD enzyme from the Gram-negative bacterium Alcaligenes sp. 4HAP is reported, at a resolution of 2.2 Å. The structure establishes that the enzyme adopts a cupin fold, forming dimers with a pronounced hydrophobic interface between the monomers. The catalytic iron is coordinated by three histidine residues (76, 78 and 114) within a buried active-site cavity. The iron also appears to be tightly coordinated by an additional ligand which was putatively assigned as a carbonate dianion since this fits the electron density optimally, although it might also be the product formate. The modelled carbonate is located in a position which is highly likely to be occupied by the α-hydroxyketone group of the bound substrate during catalysis. Modelling of a substrate molecule in this position indicates that it will interact with many conserved amino acids in

  16. A synthetic model of the putative Fe(II)-iminobenzosemiquinonate intermediate in the catalytic cycle of o-aminophenol dioxygenases.

    Science.gov (United States)

    Bittner, Michael M; Lindeman, Sergey V; Fiedler, Adam T

    2012-03-28

    The oxidative ring cleavage of aromatic substrates by nonheme Fe dioxygenases is thought to involve formation of a ferrous-(substrate radical) intermediate. Here we describe the synthesis of the trigonal-bipyramdial complex Fe((Ph2)Tp)(ISQ(tBu)) (2), the first synthetic example of an iron(II) center bound to an iminobenzosemiquinonate (ISQ) radical. The unique electronic structure of this S = 3/2 complex and its one-electron oxidized derivative ([3](+)) have been established on the basis of crystallographic, spectroscopic, and computational analyses. These findings further demonstrate the viability of Fe(2+)-ISQ intermediates in the catalytic cycles of o-aminophenol dioxygenases.

  17. The Role of Indoleamine 2,3-Dioxygenase in a Mouse Model of Neuroinflammation-Induced Depression

    NARCIS (Netherlands)

    Dobos, Nikoletta; de Vries, Erik F. J.; Kema, Ido P.; Patas, Konstantinos; Prins, Marloes; Nijholt, Ingrid M.; Dierckx, Rudi A.; Korf, Jakob; den Boer, Johan A.; Luiten, Paul G. M.; Eisel, Ulrich L. M.; Borsello, Tiziana

    2012-01-01

    Indoleamine 2,3-dioxygenase (IDO), an enzyme which is activated by pro-inflammatory cytokines, has been suggested as a potential link between neuroinflammatory processes in neurodegenerative diseases (like Alzheimer's disease) and depression. The present study aimed to determine whether neuroinflamm

  18. Characterization of catechol 1,2-dioxygenase from cell extracts of Sphingomonas xenophaga QYY

    Institute of Scientific and Technical Information of China (English)

    GOU Min; QU YuanYuan; ZHOU JiTi; LI Ang; M.Salah Uddin

    2009-01-01

    Sphingomonas xenophaga QYY, capable of growing significantly on more than ten kinds of aromatic compounds as sole carbon source, was used to study characterization of catechol 1,2-dioxygenase (C120) in cell extracts. Characterization of the crude C120 showed that the maximum activity was obtained at 40-70℃ and pH 7.8-8.8. Metal ions had different influences on the activity of crude C120. It was suggested that strain QYY possessed an inducible and ferric-dependent C120. Kinetic studies showed that the value of Vmax and Km was 0.25 μmol catechol/L/mg protein/min and 52.85 μmol/L, respectively. In addition, the partial purification of C120 was achieved by a HiTrap Q Sepharose column chromatography.

  19. Characterization of catechol 1,2-dioxygenase from cell extracts of Sphingomonas xenophaga QYY

    Institute of Scientific and Technical Information of China (English)

    M.Salah; Uddin

    2009-01-01

    Sphingomonas xenophaga QYY, capable of growing significantly on more than ten kinds of aromatic compounds as sole carbon source, was used to study characterization of catechol 1,2-dioxygenase (C12O) in cell extracts. Characterization of the crude C12O showed that the maximum activity was obtained at 40-70℃ and pH 7.8-8.8. Metal ions had different influences on the activity of crude C12O. It was suggested that strain QYY possessed an inducible and ferric-dependent C12O. Kinetic studies showed that the value of Vmax and Km was 0.25 μmol catechol/L/mg protein/min and 52.85 μmol/L, respectively. In addition, the partial purification of C12O was achieved by a HiTrap Q Sepharose column chromatography.

  20. Mutations in the 4-hydroxyphenylpyruvate dioxygenase gene (HPD) in patients with tyrosinemia type III.

    Science.gov (United States)

    Rüetschi, U; Cerone, R; Pérez-Cerda, C; Schiaffino, M C; Standing, S; Ugarte, M; Holme, E

    2000-06-01

    Tyrosinemia type III (OMIM 276710) is an autosomal recessive disorder caused by the deficiency of 4-hydroxyphenylpyruvate dioxygenase (HPD), the second enzyme in the tyrosine catabolic pathway. The enzyme deficiency results in an accumulation and increased excretion of tyrosine and phenolic metabolites. Only a few cases with the disorder have been described, and the clinical spectrum of the disorder is unknown. Reported patients have presented with mental retardation or neurological symptoms or have been picked up by neonatal screening. We have identified four presumed pathogenic mutations (two missense and two nonsense mutations) in the HPD gene in three unrelated families encompassing four homozygous individuals and one compound heterozygous individual with tyrosinemia type III. Furthermore, a number of polymorphic mutations have been identified in the HPD gene. No correlation of the severity of the mutation and enzyme deficiency and mental function has been found; neither do the recorded tyrosine levels correlate with the clinical phenotype.

  1. Synthesis and bioevaluation of pyrazole-benzimidazolone hybrids as novel human 4-Hydroxyphenylpyruvate dioxygenase inhibitors.

    Science.gov (United States)

    Xu, Yu-Ling; Lin, Hong-Yan; Ruan, Xu; Yang, Sheng-Gang; Hao, Ge-Fei; Yang, Wen-Chao; Yang, Guang-Fu

    2015-03-06

    4-Hydroxyphenylpyruvate dioxygenase (HPPD), an essential enzyme in tyrosine catabolism, is an important target for treating type I tyrosinemia. Inhibition of HPPD can effectively alleviate the symptoms of type I tyrosinemia. However, only one commercial HPPD inhibitor, 2-(2-nitro-4-trifluoromethylbenzoyl) cyclohexane-1,3-dione (NTBC), has been available for clinical use so far. In the present study, a series of novel pyrazole-benzimidazolone hybrids were designed, synthesized and evaluated as potent human HPPD inhibitors. Most of the new compounds displayed significant inhibitory activity against the recombinant human HPPD. Moreover, compound 9l was identified as the most potent candidate with IC50 value of 0.021 μM against recombinant human HPPD, about 3-fold more potent than NTBC. Thus the pyrazole-benzimidazolone hybrid has great potential to be further developed for the treatment of type I tyrosinemia.

  2. Degradation of phenanthrene and pyrene using genetically engineered dioxygenase producing Pseudomonas putida in soil

    Directory of Open Access Journals (Sweden)

    Mardani Gashtasb

    2016-01-01

    Full Text Available Bioremediation use to promote degradation and/or removal of contaminants into nonhazardous or less-hazardous substances from the environment using microbial metabolic ability. Pseudomonas spp. is one of saprotrophic soil bacterium and can be used for biodegradation of polycyclic aromatic hydrocarbons (PAHs but this activity in most species is weak. Phenanthrene and pyrene could associate with a risk of human cancer development in exposed individuals. The aim of the present study was application of genetically engineered P. putida that produce dioxygenase for degradation of phenanthrene and pyrene in spiked soil using high-performance liquid chromatography (HPLC method. The nahH gene that encoded catechol 2,3-dioxygenase (C23O was cloned into pUC18 and pUC18-nahH recombinant vector was generated and transformed into wild P. putida, successfully. The genetically modified and wild types of P. putida were inoculated in soil and pilot plan was prepared. Finally, degradation of phenanthrene and pyrene by this bacterium in spiked soil were evaluated using HPLC measurement technique. The results were showed elimination of these PAH compounds in spiked soil by engineered P. putida comparing to dishes containing natural soil with normal microbial flora and inoculated autoclaved soil by wild type of P. putida were statistically significant (p0.05 but it was few impact on this process (more than 2%. Additional and verification tests including catalase, oxidase and PCR on isolated bacteria from spiked soil were indicated that engineered P. putida was alive and functional as well as it can affect on phenanthrene and pyrene degradation via nahH gene producing. These findings indicated that genetically engineered P. putida generated in this work via producing C23O enzyme can useful and practical for biodegradation of phenanthrene and pyrene as well as petroleum compounds in polluted environments.

  3. 2,3-Dihydroxybiphenyl dioxygenase gene was first discovered in Arthrobacter sp. strain P J3

    Institute of Scientific and Technical Information of China (English)

    YANG MeiYing; MA PengDa; LI WenMing; LIU JinYing; LI Liang; ZHU XiaoJuan; WANG XingZhi

    2007-01-01

    Bacterium strain PJ3, isolated from wastewater and identified as Arthrobacter sp. bacterium based on its 16S rDNA gene, could use carbazole as the sole carbon, nitrogen and energy source. The genomic libraryof strain PJ3 was constructed and a positive clone JM109 (pUCW402) was screened out for the expression of dioxygenase by the ability to form yellow ring-fission product. A 2,3-dihydroxybiphenyl dioxygenase (23DHBD) gene of 933 bp was found in the 3360 bp exogenous fragment of pUCW402 by GenSCAN software and BLAST analysis. The phylogenetic analysis showed that 23DHBD from strain PJ3 formed a deep branch separate from a cluster containing most known 23DHBD in GenBank.Southern hybridization confirmed for the first time that the 23DHBD gene was from the genomic DNA of Arthrobacter sp. PJ3. In order to test the gene function, recombinant bacterium BL21 (pETW-8) was constructed to express 23DHBD. The expression level in BL21 (pETW-8) was highest compared with the recombinant bacteria JM109 (pUCW402) and strain PJ3. We observed that 23DHBD was not absolute specific. The enzyme activity was higher with 2,3-dihydroxybiphenyl as a substrate than with catechol.The substrate specificity assay suggested that 23DHBD was essential for cleavage of bi-cyclic aromatic compounds during the course of aromatic compound biodegradation in Arthrobacter sp. strain PJ3.

  4. Promotion of Germination Using Hydroxamic Acid Inhibitors of 9-cis-Epoxycarotenoid Dioxygenase

    Science.gov (United States)

    Awan, Sajjad Z.; Chandler, Jake O.; Harrison, Peter J.; Sergeant, Martin J.; Bugg, Timothy D. H.; Thompson, Andrew J.

    2017-01-01

    Abscisic acid (ABA) inhibits seed germination and the regulation of ABA biosynthesis has a role in maintenance of seed dormancy. The key rate-limiting step in ABA biosynthesis is catalyzed by 9-cis-epoxycarotenoid dioxygenase (NCED). Two hydroxamic acid inhibitors of carotenoid cleavage dioxygenase (CCD), D4 and D7, previously found to inhibit CCD and NCED in vitro, are shown to have the novel property of decreasing mean germination time of tomato (Solanum lycopersicum L.) seeds constitutively overexpressing LeNCED1. Post-germination, D4 exhibited no negative effects on tomato seedling growth in terms of height, dry weight, and fresh weight. Tobacco (Nicotiana tabacum L.) seeds containing a tetracycline-inducible LeNCED1 transgene were used to show that germination could be negatively and positively controlled through the chemical induction of gene expression and the chemical inhibition of the NCED protein: application of tetracycline increased mean germination time and delayed hypocotyl emergence in a similar manner to that observed when exogenous ABA was applied and this was reversed by D4 when NCED expression was induced at intermediate levels. D4 also improved germination in lettuce (Lactuca sativa L.) seeds under thermoinhibitory temperatures and in tomato seeds imbibed in high osmolarity solutions of polyethylene glycol. D4 reduced ABA and dihydrophaseic acid accumulation in tomato seeds overexpressing LeNCED1 and reduced ABA accumulation in wild type tomato seeds imbibed on polyethylene glycol. The evidence supports a mode of action of D4 through NCED inhibition, and this molecule provides a lead compound for the design of NCED inhibitors with greater specificity and potency.

  5. Structure of the Dioxygenase AsqJ: Mechanistic Insights into a One-Pot Multistep Quinolone Antibiotic Biosynthesis

    KAUST Repository

    Bräuer, Alois

    2015-11-10

    © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. Multienzymatic cascades are responsible for the biosynthesis of natural products and represent a source of inspiration for synthetic chemists. The FeII/α-ketoglutarate-dependent dioxygenase AsqJ from Aspergillus nidulans is outstanding because it stereoselectively catalyzes both a ferryl-induced desaturation reaction and epoxidation on a benzodiazepinedione. Interestingly, the enzymatically formed spiro epoxide spring-loads the 6,7-bicyclic skeleton for non-enzymatic rearrangement into the 6,6-bicyclic scaffold of the quinolone alkaloid 4′-methoxyviridicatin. Herein, we report different crystal structures of the protein in the absence and presence of synthesized substrates, surrogates, and intermediates that mimic the various stages of the reaction cycle of this exceptional dioxygenase.

  6. The gene coding for the DOPA dioxygenase involved in betalain biosynthesis in Amanita muscaria and its regulation.

    Science.gov (United States)

    Hinz, U G; Fivaz, J; Girod, P A; Zyrd, J P

    1997-09-01

    Genomic and cDNA clones derived from the gene (dodA) coding for DOPA dioxygenase, a key enzyme in the betalain pathway, were obtained from the basidiomycete Amanita muscaria. A cDNA library was established in the phage lambda ZapII and dodA clones were isolated using polyclonal antibodies raised against the purified enzyme. Their identity was confirmed by comparison of the deduced amino acid sequence with the sequence of several tryptic peptide fragments of DOPA dioxygenase. The gene coded for a 228-amino acid protein that showed no homology to published sequences. The coding region was interrupted by five short introns. Regulation was shown to occur at the transcriptional level; the mRNA accumulated to high levels only in the coloured cap tissue. dodA was found to be a single-copy gene in A. muscaria. To our knowledge, this is the first gene from the betalain pathway to be cloned. It encodes a type of aromatic ring-cleaving dioxygenase that has not been previously described.

  7. Crystallization and preliminary crystallographic analysis of the catechol 2,3-dioxygenase PheB from Bacillus stearothermophilus BR219

    Energy Technology Data Exchange (ETDEWEB)

    Sugimoto, Keisuke; Matsufuzi, Kazuki; Ohnuma, Hiroaki [Department of Material Chemistry, Asahikawa National College of Technology, 2-2-1-6 Shunko-dai, Asahikawa, Hokkaido 071-8142 (Japan); Senda, Miki [Japan Biological Information Research Center (JBIRC), Japan Biological Informatics Consortium (JBIC), 2-42 Aomi, Koto-ku, Tokyo 135-0064 (Japan); Fukuda, Masao [Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Niigata 940-2188 (Japan); Senda, Toshiya, E-mail: tsenda@jbirc.aist.go.jp [Biological Information Research Center (BIRC), National Institute of Advanced Industrial Science and Technology (AIST), 2-42 Aomi, Koto-ku, Tokyo (Japan); Department of Material Chemistry, Asahikawa National College of Technology, 2-2-1-6 Shunko-dai, Asahikawa, Hokkaido 071-8142 (Japan)

    2006-02-01

    PheB, an extradiol-cleaving catecholic dioxygenase, was crystallized by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The crystal belongs to the orthorhombic system, space group P2{sub 1}2{sub 1}2{sub 1}, and diffracts to 2.3 Å resolution. Class II extradiol-cleaving catecholic dioxygenase, a key enzyme of aromatic compound degradation in bacteria, cleaves the aromatic ring of catechol by adding two O atoms. PheB is one of the class II extradiol-cleaving catecholic dioxygenases and shows a high substrate specificity for catechol derivatives, which have one aromatic ring. In order to reveal the mechanism of the substrate specificity of PheB, PheB has been crystallized by the hanging-drop vapour-diffusion method using PEG 4000 as a precipitant. The space group of the obtained crystal was P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 65.5, b = 119.2, c = 158.7 Å. The crystal diffracted to 2.3 Å resolution.

  8. Crystallization and preliminary crystallographic analysis of 2-aminophenol 1,6-dioxygenase complexed with substrate and with an inhibitor.

    Science.gov (United States)

    Li, De-Feng; Zhang, Jia-Yue; Hou, Yanjie; Liu, Lei; Liu, Shuang-Jiang; Liu, Wei

    2012-11-01

    Dioxygen activation implemented by nonhaem Fe(II) enzymes containing the 2-His-1-carboxylate facial triad has been extensively studied in recent years. Extradiol dioxygenase is the archetypal member of this superfamily and catalyzes the oxygenolytic ring opening of catechol analogues. Here, the crystallization and preliminary X-ray analysis of 2-aminophenol 1,6-dioxygenase, an enzyme representing a minor subset of extradiol dioxygenases that catalyze the fission of 2-aminophenol rather than catecholic compounds, is reported. Crystals of the holoenzyme with FeII and of complexes with the substrate 2-aminophenol and the suicide inhibitor 4-nitrocatechol were grown using the cocrystallization method under the same conditions as used for the crystallization of the apoenzyme. The crystals belonged to space group C2 and diffracted to 2.3-2.7 Å resolution; the crystal that diffracted to the highest resolution had unit-cell parameters a=270.24, b=48.39, c=108.55 Å, β=109.57°. All X-ray data sets collected from diffraction-quality crystals were suitable for structure determination.

  9. Molecular mechanism of strict substrate specificity of an extradiol dioxygenase, DesB, derived from Sphingobium sp. SYK-6.

    Directory of Open Access Journals (Sweden)

    Keisuke Sugimoto

    Full Text Available DesB, which is derived from Sphingobium sp. SYK-6, is a type II extradiol dioxygenase that catalyzes a ring opening reaction of gallate. While typical extradiol dioxygenases show broad substrate specificity, DesB has strict substrate specificity for gallate. The substrate specificity of DesB seems to be required for the efficient growth of S. sp. SYK-6 using lignin-derived aromatic compounds. Since direct coordination of hydroxyl groups of the substrate to the non-heme iron in the active site is a critical step for the catalytic reaction of the extradiol dioxygenases, the mechanism of the substrate recognition and coordination of DesB was analyzed by biochemical and crystallographic methods. Our study demonstrated that the direct coordination between the non-heme iron and hydroxyl groups of the substrate requires a large shift of the Fe (II ion in the active site. Mutational analysis revealed that His124 and His192 in the active site are essential to the catalytic reaction of DesB. His124, which interacts with OH (4 of the bound gallate, seems to contribute to proper positioning of the substrate in the active site. His192, which is located close to OH (3 of the gallate, is likely to serve as the catalytic base. Glu377' interacts with OH (5 of the gallate and seems to play a critical role in the substrate specificity. Our biochemical and structural study showed the substrate recognition and catalytic mechanisms of DesB.

  10. The Role of 4-Hydroxyphenylpyruvate Dioxygenase in Enhancement of Solid-Phase Electron Transfer by Shewanella oneidensis MR-1

    Energy Technology Data Exchange (ETDEWEB)

    Turick, Charles E. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Beliaev, Alex S. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Zakrajsek, Brian A. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Reardon, Catherine L. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lowy, Daniel A. [Nova Research Inc., Alexandria, VA (United States); Poppy, Tara E. [Univ. of South Carolina, Aiken, SC (United States); Maloney, Andrea [Winthrop Univ., Rock Hill, SC (United States); Ekechukwu, Amy A. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2009-05-01

    ABSTRACT - While mechanistic details of dissimilatory metal reduction are far from being understood, it is postulated that the electron transfer to solid metal oxides is mediated by outer membrane associated c-type cytochromes and electron shuttling compounds. This study focuses on the production of homogensitate in Shewanella oneidensis MR-1, an intermediate of the tyrosine degradation pathway, which is a precursor of a redox cycling metabolite, pyomelanin. We determined that two enzymes involved in this pathway, 4-hydroxyphenylpyruvate dioxygenase (4HPPD) and homogentisate 1,2-dioxygenase are responsible for homogentisate production and oxidation, respectively. Inhibition of 4-HPPD activity with the specific inhibitor sulcotrione ([2-(2- chloro- 4- methane sulfonylbenzoyl)-1,3-cyclohexanedione), and deletion of melA, a gene encoding 4-HPPD, resulted in no pyomelanin production by S. oneidensis MR-1. Conversely, deletion of hmgA, which encodes the putative homogentisate 1,2-dioxygenase, resulted in pyomelanin overproduction. The efficiency and rates at which MR-1 reduces hydrous ferric oxide were directly linked to the ability of mutant strains to produce pyomelanin. Electrochemical studies with whole cells demonstrated that pyomelanin substantially increases the formal potential (E°') of S. oneidensis MR-1. Based on our findings, environmental production of pyomelanin likely contributes to an increased solid-phase metal reduction capacity in S. oneidensis MR-1.

  11. THE ROLE OF 4-HYDROXYPHENYLPYRUVATE DIOXYGENASE IN ENHANCEMENT OF SOLID-PHASE ELECTRON TRANSFER BY SHEWANELLA ONEIDENSIS MR-1

    Energy Technology Data Exchange (ETDEWEB)

    Turick, C; Amy Ekechukwu, A

    2007-06-01

    While mechanistic details of dissimilatory metal reduction are far from being understood, it is postulated that the electron transfer to solid metal oxides is mediated by outer membrane-associated c-type cytochromes and redox active electron shuttling compounds. This study focuses on the production of homogensitate in Shewanella oneidensis MR-1, an intermediate of tyrosine degradation pathway, which is a precursor of a redox cycling metabolite, pyomelanin. In this study, we determined that two enzymes involved in this pathway, 4-hydroxyphenylpyruvate dioxygenase (4HPPD) and homogentisate 1,2-dioxygenase are responsible for homogentisate production and oxidation, respectively. Inhibition of 4-HPPD activity with the specific inhibitor sulcotrione (2-(2-chloro-4-methane sulfonylbenzoyl)-1,3-cyclohexanedione), and deletion of melA, a gene encoding 4-HPPD, resulted in no pyomelanin production by S. oneidensis MR-1. Conversely, deletion of hmgA which encodes the putative homogentisate 1,2-dioxygenase, resulted in pyomelanin overproduction. The efficiency and rates, with which MR-1 reduces hydrous ferric oxide, were directly linked to the ability of mutant strains to produce pyomelanin. Electrochemical studies with whole cells demonstrated that pyomelanin substantially increases the formal potential (E{sup o}{prime}) of S. oneidensis MR-1. Based on this work, environmental production of pyomelanin likely contributes to an increased solid-phase metal reduction capacity in Shewanella oneidensis.

  12. Characterization of arene di-oxygenases involved in polycyclic aromatic hydrocarbons biodegradation in Mycobacterium sp. 6PY1; Caracterisation d'arene dioxygenases impliquees dans la biodegradation des hydrocarbures aromatiques polycycliques chez Mycobacterium sp. 6PY1

    Energy Technology Data Exchange (ETDEWEB)

    Kuony, S.

    2005-06-15

    This thesis deals with the bacterial biodegradation of pollutants called polycyclic aromatic hydrocarbons (PAHs). The bacterium Mycobacterium sp. 6PY1 was isolated from a polluted soil for its ability to use pyrene, a 4-ring PAH, as sole source of carbon and energy. To learn about the pyrene metabolic pathway, the identification of the enzymes involved in this process has been undertaken using a proteomic approach. This approach revealed the occurrence of two ring-hydroxylating di-oxygenases in strain 6PY1, which could catalyze the initial attack of pyrene. The goal of this study was to clone the genes encoding the di-oxygenases identified in Mycobacterium sp. 6PY1, over-express these genes in an heterologous system in order to facilitate the purification of the corresponding enzymes, and determine the biochemical and catalytic properties of these enzymes. The pdoA1B1 genes encoding the terminal component of a di-oxygenase were cloned and over-expressed in Escherichia coli. The catalytic properties of this enzyme, called Pdo1, were determined in vivo by measuring the oxidation products of 2- to 4-ring PAHs by gas chromatography coupled to mass spectrometry (GC-MS). Analysis of the selectivity of the enzyme, as determined using GC-MS, showed that Pdo1 preferentially oxidized 3- or 4-ring PAHs, including phenanthrene and pyrene, but was inactive on di-aromatic compounds such as naphthalene and biphenyl. Pdo1 was unstable and was therefore purified in inactive form. The genes encoding a second di-oxygenase component were found in a locus containing two other catabolic genes. The pdoA2B2 genes encoded an enzyme called Pdo2 showing a narrow specificity towards 2- to 3-ring PAHs, and a high preference for phenanthrene. Pdo2 is an a3{beta}3 hexamer, containing [2Fe-2S] Rieske clusters which confer it a characteristic absorbance spectrum. A third set of genes possibly encoding another di-oxygenase was discovered in the genome of Mycobacterium sp. 6PY1. This set is closely

  13. Indoleamine 2,3 Dioxygenase (IDO Expression and Activity in Relapsing-Remitting Multiple Sclerosis.

    Directory of Open Access Journals (Sweden)

    Roberta Mancuso

    Full Text Available Interferon gamma (IFN-γ production induces the transcription of indoleamine 2,3 dioxygenase (IDO resulting in the reduction of T-cell activation and proliferation through the depletion of tryptophan and the elicitation of Treg lymphocytes. IDO was shown to be involved in the pathogenesis of autoimmune diseases; we investigated whether changes in IDO gene expression and activity could be indicative of onset of relapse in multiple sclerosis (MS patients.IDO and interferon-γ (IFN-γ gene expression, serum IDO activity (Kynurenine/Tryptophan ratio and serum neopterin concentration--a protein released by macrophages upon IFN-γ stimulation--were measured in 51 individuals: 36 relapsing remitting (RR-MS patients (21 in acute phase--AMS, 15 in stable phase--SMS and 15 healthy controls (HC. PBMCs samples in AMS patients were collected before (BT-AMS and during glucocorticoids-based therapy (DT-AMS.IDO expression was increased and IFN-γ was decreased (p<0.001 in BT-AMS compared to SMS patients. Glucocorticoids-induced disease remission resulted in a significant reduction of IDO and IFN-γ gene expression, IDO catalytic activity (p<0.001. Serum neopterin concentration followed the same trend as IDO expression and activity.Measurement of IDO gene expression and activity in blood could be a useful marker to monitor the clinical course of RR-MS. Therapeutic interventions modulating IDO activity may be beneficial in MS.

  14. Nanomedicine and cancer immunotherapy: focus on indoleamine 2,3-dioxygenase inhibitors

    Science.gov (United States)

    Zulfiqar, Bilal; Mahroo, Amnah; Nasir, Kaenat; Farooq, Rai Khalid; Jalal, Nasir; Rashid, Muhammad Usman; Asghar, Kashif

    2017-01-01

    Nanomedicine application in cancer immunotherapy is currently one of the most challenging areas in cancer therapeutic intervention. Innovative solutions have been provided by nanotechnology to deliver cytotoxic agents to the cancer cells partially affecting the healthy cells of the body during the process. Nanoparticle-based drug delivery is an emerging approach to stimulate the immune responses against cancer. The inhibition of indoleamine 2,3-dioxygenase (IDO) is a pivotal area of research in cancer immunotherapy. IDO is a heme-containing immunosuppressive enzyme, which is responsible for the degradation of tryptophan while increasing the concentration of kynurenine metabolites. Various preclinical studies showed that IDO inhibition in certain diseases may result in significant therapeutic effects. Here, we provide a review of the natural and synthetic inhibitors of IDO. These inhibitors are classified according to their source, inhibitory concentrations, the chemical structure, and the mechanism of action. Tumor-targeted chemotherapy is an advanced technique and has more advantages as compared to the conventional chemotherapy. Search for more efficient and less toxic nanoparticles in conjunction with compounds to inhibit IDO is still an area of interest for several research groups worldwide, especially revealing to be an extensive and a promising area in cancer therapeutic innovations. PMID:28176942

  15. Indoleamine 2,3-dioxygenase: First evidence of expression in rainbow trout (Oncorhynchus mykiss).

    Science.gov (United States)

    Cortés, Jimena; Alvarez, Claudio; Santana, Paula; Torres, Elisa; Mercado, Luis

    2016-12-01

    The role of enzymes as active antimicrobial agents of the innate immunity in teleost fish is proposed in diverse works. Secretion of Indoleamine 2,3-dioxygenase (IDO) has been described in higher vertebrates; it degrades l-tryptophan in extracellular environments associated mainly with mucosal organs. The effect of IDO on decreasing amino acid concentration may inhibit the growth of potential pathogens. In fish the study of this molecule is still. Here we report the identification of an Onchorhyncus mykiss IDO homologue (OmIDO). IDO was cloned, sequenced, and the primary structure shows conservation of key functional sites. The constitutive expression is altered when the fish is challenged with LPS as a pathogen-associated molecular pattern (PAMPs). Up-regulation of IDO was shown preferentially in the fish's mucosal cells. In order to obtain evidence of a possible regulation mechanism, an in vitro cell model was used for to show that OmIDO is induced by rIFN. These study has identified a Indoleamine 2,3-dyoxigenase in O. mykiss will contribute to expands our knowledge of the function this protein in fish immune response. These findings allow to propose the use of OmIDO as a molecular indicator of strength of the animal's immune response and wellbeing.

  16. Cysteine dioxygenase type 1 promotes adipogenesis via interaction with peroxisome proliferator-activated receptor gamma

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Peng; Chen, Yi; Ji, Ning; Lin, Yunfeng; Yuan, Quan; Ye, Ling; Chen, Qianming, E-mail: qmchen@scu.edu.cn

    2015-02-27

    Mammalian cysteine dioxygenase type 1 (CDO1) is an essential enzyme for taurine biosynthesis and the biodegradation of toxic cysteine. As previously suggested, Cdo1 may be a marker of liposarcoma progression and adipogenic differentiation, but the role of Cdo1 in adipogenesis has yet been reported. In this study, we found that the expression of Cdo1 is dramatically elevated during adipogenic differentiation of 3T3-L1 pre-adipocytes and mouse bone marrow-derived mesenchymal stem cells (mBMSCs). Conversely, knockdown of Cdo1 inhibited expression of adipogenic specific genes and lipid droplet formation in 3T3-L1 cells and mBMSCs. Mechanistically, we found Cdo1 interacted with Pparγ in response to adipogenic stimulus. Further, depletion of Cdo1 reduced the recruitment of Pparγ to the promoters of C/EBPα and Fabp4. Collectively, our finding indicates that Cdo1 may be a co-activator of Pparγ in adipogenesis, and may contribute to the development of disease associated with excessive adipose tissue. - Highlights: • Cdo1expression is highly up-regulated during adipogenic differentiation of 3T3-L1 and mBMSCs. • Depletion of Cdo1 inhibited expression of adipogenic specific genes and lipid droplet formation. • Cdo1interacts with Pparγ during adipogenesis. • Knockdown of Cdo1 inhibited Pparγ binding to the promoters of C/EBPα and Fabp4.

  17. Emerging concepts on inhibitors of indoleamine 2,3-dioxygenase in rheumatic diseases.

    Science.gov (United States)

    Filippini, P; Del Papa, N; Sambataro, D; Del Bufalo, A; Locatelli, F; Rutella, S

    2012-01-01

    The enzyme indoleamine 2,3-dioxygenase 1 (IDO1) finely regulates both innate and adaptive immune responses through the degradation of the essential amino acid tryptophan into kynurenine and other downstream metabolites, which suppress effector T-cell function and promote the differentiation of regulatory T cells. A novel role for IDO1 as a signaling molecule and a modifier of innate inflammatory responses is now emerging. In particular, IDO1 can either support or antagonize inflammation in a context- and tissuedependent manner. Studies in experimental arthritis have unravelled a previously unappreciated role for IDO in controlling B-cell activation and autoantibody production. IDO dysregulation has been documented in patients with systemic lupus erythematosus, systemic sclerosis and Sjogren's syndrome, as well as in severe sepsis and chronic kidney disease. This article summarizes the contribution of IDO to the pathophysiology of inflammatory/autoimmune disorders, and discusses whether strategies to restore metabolic equilibrium in the kynurenine pathway might be pursued in diseases states such as rheumatoid arthritis and systemic sclerosis.

  18. Inhibition of indoleamine 2,3-dioxygenase activity accelerates skin wound healing.

    Science.gov (United States)

    Ito, Hiroyasu; Ando, Tatsuya; Ogiso, Hideyuki; Arioka, Yuko; Saito, Kuniaki; Seishima, Mitsuru

    2015-06-01

    Skin wound healing is a complex process involving several stages that include inflammation, proliferation, and remodeling. In the inflammatory phase, pro-inflammatory cytokines and chemokines are induced at the wound site and, they contribute to the development of wound healing. These cytokines also induce indoleamine 2,3-dioxygenase (IDO1) activity; this is the rate-limiting and first enzyme in the l-tryptophan (TRP)-l-kynurenine (KYN) pathway. This study examined the effect of IDO1 on the process of skin wound healing. The expression of the Ido1 mRNA was enhanced after creating a wound in wild-type (WT) mice. TRP concentration was simultaneously reduced at the wound site. The rate of wound healing in IDO1 knockout (IDO-KO) mice was significantly higher than that in WT mice. 1-Methyl-dl-tryptophan (1-MT), a potent inhibitor of IDO1, increased the rate of wound healing in WT mice. The administration of TRP accelerated wound healing in vivo and in an in vitro experimental model, whereas the rate of wound healing was not affected by the administration of KYN. The present study identifies the role of IDO1 in skin wound healing, and indicates that the local administration of 1-MT or TRP may provide an effective strategy for accelerating wound healing.

  19. Suicide inactivation of catechol 2,3-dioxygenase from Pseudomonas putida mt-2 by 3-halocatechols

    Energy Technology Data Exchange (ETDEWEB)

    Bartels, I.; Knackmuss, H.J.; Reineke, W.

    1984-03-01

    The inactivation of catechol 2,3-dioxygenase from Pseudomonas putida mt-2 by 3-chloro- and 3-fluorocatechol and the iron-chelating agent Tiron (catechol-3,5-disulfonate) was studied. Whereas inactivation by Tiron is an oxygen-independent and mostly reversible process, inactivation by the 3-halocatechols was only observed in the presence of oxygen and was largely irreversible. The rate constants for inactivation (K/sub 2/) were 1.62 x 10/sup -3/ sec/sup -1/ for 3-chlorocatechol and 2.38 x 10/sup -3/ sec/sup -1/ for 3-fluorocatechol. The inhibitor constants (K/sub i/) were 23 ..mu..M for 3-chlorocatechol and 17 ..mu..M for 3-fluorocatechol. The kinetic data for 3-fluorocatechol could only be obtained in the presence of 2-mercaptoethanol. Besides inactivated enzyme, some 2-hydroxyhexa-2,4-dienoic acid as the actual suicide product of meta-cleavage. A side product of 3-fluorocatechol cleavage is a yellow compound with the spectral characteristics of a 2-hydroxy-6-oxohexa-2,4-dienoci acid indicating 1,6-cleavage. Rates of inactivation by 3-fluorocatechol were reduced in the presence of superoxide dismutase, catalase, formate, and mannitol, which implies that superoxide anion, hydrogen peroxide, and hydroxyl radical exhibit additional inactivation. 64 references.

  20. Inhibition of Indoleamine-2,3-dioxygenase (IDO in Glioblastoma Cells by Oncolytic Herpes Simplex Virus

    Directory of Open Access Journals (Sweden)

    Bonnie Reinhart

    2012-01-01

    Full Text Available Successful oncolytic virus treatment of malignant glioblastoma multiforme depends on widespread tumor-specific lytic virus replication and escape from mitigating innate immune responses to infection. Here we characterize a new HSV vector, JD0G, that is deleted for ICP0 and the joint sequences separating the unique long and short elements of the viral genome. We observed that JD0G replication was enhanced in certain glioblastoma cell lines compared to HEL cells, suggesting that a vector backbone deleted for ICP0 may be useful for treatment of glioblastoma. The innate immune response to virus infection can potentially impede oncolytic vector replication in human tumors. Indoleamine-2,3-dioxygenase (IDO is expressed in response to interferon γ (IFNγ and has been linked to both antiviral functions and to the immune escape of tumor cells. We observed that IFNγ treatment of human glioblastoma cells induced the expression of IDO and that this expression was quelled by infection with both wild-type and JD0G viruses. The role of IDO in inhibiting virus replication and the connection of this protein to the escape of tumor cells from immune surveillance suggest that IDO downregulation by HSV infection may enhance the oncolytic activity of vectors such as JD0G.

  1. Reaction mechanism of cobalt-substituted homoprotocatechuate 2,3-dioxygenase: a QM/MM study.

    Science.gov (United States)

    Cao, Lili; Dong, Geng; Lai, Wenzhen

    2015-04-01

    The reaction mechanisms of cobalt-substituted homoprotocatechuate 2,3-dioxygenase (Co-HPCD) with electron-rich substrate homoprotocatechuate (HPCA) and electron-poor substrate 4-nitrocatechol (4NC) were investigated by quantum mechanical/molecular mechanical (QM/MM) calculations. Our results demonstrated that the Co-O2 adducts has doublet ground state with a Co(III)-O2(•-) character when 4NC was used as the substrate, in good agreement with the EPR spectroscopic experiment. The reactive oxygen species is the doublet Co(III)-O2(•-) for Co-HPCD/4NC and the quartet SQ(•↑)-Co(II)-O2(•-↓) species for Co-HPCD/HPCA, indicating that the substrate plays important roles in the dioxygen activation by Co-HPCD. B3LYP was found to overestimate the rate-limiting barriers in Co-HPCD. TPSSh predicts barriers of 21.5 versus 12.0 kcal/mol for Co-HPCD/4NC versus Co-HPCD/HPCA, which is consistent with the fact that the rate of the reaction is decreased when the substrate was changed from HPCA to 4NC.

  2. Novel bacterial bioassay for a high-throughput screening of 4-hydroxyphenylpyruvate dioxygenase inhibitors.

    Science.gov (United States)

    Rocaboy-Faquet, Emilie; Noguer, Thierry; Romdhane, Sana; Bertrand, Cédric; Dayan, Franck Emmanuel; Barthelmebs, Lise

    2014-08-01

    Plant 4-hydroxyphenylpyruvate dioxygenase (HPPD) is the molecular target of a range of synthetic β-triketone herbicides that are currently used commercially. Their mode of action is based on an irreversible inhibition of HPPD. Therefore, this inhibitory capacity was used to develop a whole-cell colorimetric bioassay with a recombinant Escherichia coli expressing a plant HPPD for the herbicide analysis of β-triketones. The principle of the bioassay is based on the ability of the recombinant E. coli clone to produce a soluble melanin-like pigment, from tyrosine catabolism through p-hydroxyphenylpyruvate and homogentisate. The addition of sulcotrione, a HPPD inhibitor, decreased the pigment production. With the aim to optimize the assay, the E. coli recombinant clone was immobilized in sol-gel or agarose matrix in a 96-well microplate format. The limit of detection for mesotrione, tembotrione, sulcotrione, and leptospermone was 0.069, 0.051, 0.038, and 20 μM, respectively, allowing to validate the whole-cell colorimetric bioassay as a simple and cost-effective alternative tool for laboratory use. The bioassay results from sulcotrione-spiked soil samples were confirmed with high-performance liquid chromatography.

  3. Exposition of dermatophyte Trichophyton mentagrophytes to L-cystine induces expression and activation of cysteine dioxygenase.

    Science.gov (United States)

    Kasperova, Alena; Cahlikova, Romana; Kunert, Jiri; Sebela, Marek; Novak, Zdenek; Raska, Milan

    2014-11-01

    Cysteine dioxygenase (CDO) is involved in regulation of intracellular cysteine levels by catabolising the cysteine to sulphite and sulphate. In keratinolytic fungi, sulphite is actively excreted to reduce disulphide bridges in keratin before its enzymatic degradation. The pathogenicity role of CDO was confirmed in cysteine-hypersensitive and growth-defective ΔCdo mutant of Arthroderma benhamiae on hair and nails. We analysed the CDO expression regulation in T. mentagrophytes (anamorph of A. benhamiae) mycelia by determining the Cdo mRNA and CDO protein levels and by analysing the proportion of two molecular forms of CDO in response to l-cystine exposure. Cdo mRNA levels in mycelia lysates were detected by reverse-transcription real-time polymerase chain reaction and CDO protein by western blot using mouse CDO-specific hyperimmune serum. The Cdo mRNA level increased gradually 2.5-4.5 h after exposure of the mycelium to l-cystine. The CDO protein, detected as two bands of different mobility, appeared earlier in comparison to mRNA (1 h) and culminated after 24 h. More mobile form prevailed after 4.5 h. The comparison of the dynamics in the Cdo mRNA and CDO protein levels indicates that T. mentagrophytes responds to l-cystine by increased transcription and apparently decreased degradation of the CDO and by changing towards higher mobility molecular form, similar to previous reports describing mammalian analogue.

  4. Salmonella overcomes tumor immune tolerance by inhibition of tumor indoleamine 2, 3-dioxygenase 1 expression.

    Science.gov (United States)

    Kuan, Yu-Diao; Lee, Che-Hsin

    2016-01-05

    Over the past decades, Salmonella has been proven capable of inhibiting tumor growth. It can specifically target tumors and due to its facultative anaerobic property, can be more penetrative than other drug therapies. However, the molecular mechanism by which Salmonella inhibits tumor growth is still incompletely known. The antitumor therapeutic effect mediated by Salmonella is associated with an inflammatory immune response at the tumor site and a T cell-dependent immune response. Many tumors have been proven to have a high expression of indoleamine 2, 3-dioxygenase 1 (IDO), which is a rate-limiting enzyme that catalyzes tryptophan to kynurenine, thus causing immune tolerance within the tumor microenvironment. With decreased expression of IDO, increased immune response can be observed, which might be helpful when developing cancer immunotherapy. The expression of IDO was decreased after tumor cells were infected with Salmonella. In addition, Western blot analysis showed that the expression levels of phospho-protein kinase B (P-AKT), phospho-mammalian targets of rapamycin (P-mTOR), and phospho-p70 ribosomal s6 kinase (P-p70s6K) in tumor cells were decreased after Salmonella infection. In conclusion, our results indicate that Salmonella inhibits IDO expression and plays a crucial role in anti-tumor therapy, which might be a promising strategy combined with other cancer treatments.

  5. Negative Impact of Hypoxia on Tryptophan 2,3-Dioxygenase Function

    Directory of Open Access Journals (Sweden)

    Frank Elbers

    2016-01-01

    Full Text Available Tryptophan is an essential amino acid for hosts and pathogens. The liver enzyme tryptophan 2,3-dioxygenase (TDO provokes, by its ability to degrade tryptophan to N-formylkynurenine, the precursor of the immune-relevant kynurenines, direct and indirect antimicrobial and immunoregulatory states. Up to now these TDO-mediated broad-spectrum effector functions have never been observed under hypoxia in vitro, although physiologic oxygen concentrations in liver tissue are low, especially in case of infection. Here we analysed recombinant expressed human TDO and ex vivo murine TDO functions under different oxygen conditions and show that TDO-induced restrictions of clinically relevant pathogens (bacteria, parasites and of T cell proliferation are abrogated under hypoxic conditions. We pinpointed the loss of TDO efficiency to the reduction of TDO activity, since cell survival and TDO protein levels were unaffected. In conclusion, the potent antimicrobial as well as immunoregulatory effects of TDO were substantially impaired under hypoxic conditions that pathophysiologically occur in vivo. This might be detrimental for the appropriate host immune response towards relevant pathogens.

  6. Tryptophan-2,3-dioxygenase (TDO) inhibition ameliorates neurodegeneration by modulation of kynurenine pathway metabolites

    Science.gov (United States)

    Breda, Carlo; Sathyasaikumar, Korrapati V.; Sograte Idrissi, Shama; Notarangelo, Francesca M.; Estranero, Jasper G.; Moore, Gareth G. L.; Green, Edward W.; Kyriacou, Charalambos P.; Schwarcz, Robert; Giorgini, Flaviano

    2016-01-01

    Metabolites of the kynurenine pathway (KP) of tryptophan (TRP) degradation have been closely linked to the pathogenesis of several neurodegenerative disorders. Recent work has highlighted the therapeutic potential of inhibiting two critical regulatory enzymes in this pathway—kynurenine-3-monooxygenase (KMO) and tryptophan-2,3-dioxygenase (TDO). Much evidence indicates that the efficacy of KMO inhibition arises from normalizing an imbalance between neurotoxic [3-hydroxykynurenine (3-HK); quinolinic acid (QUIN)] and neuroprotective [kynurenic acid (KYNA)] KP metabolites. However, it is not clear if TDO inhibition is protective via a similar mechanism or if this is instead due to increased levels of TRP—the substrate of TDO. Here, we find that increased levels of KYNA relative to 3-HK are likely central to the protection conferred by TDO inhibition in a fruit fly model of Huntington’s disease and that TRP treatment strongly reduces neurodegeneration by shifting KP flux toward KYNA synthesis. In fly models of Alzheimer’s and Parkinson’s disease, we provide genetic evidence that inhibition of TDO or KMO improves locomotor performance and ameliorates shortened life span, as well as reducing neurodegeneration in Alzheimer's model flies. Critically, we find that treatment with a chemical TDO inhibitor is robustly protective in these models. Consequently, our work strongly supports targeting of the KP as a potential treatment strategy for several major neurodegenerative disorders and suggests that alterations in the levels of neuroactive KP metabolites could underlie several therapeutic benefits. PMID:27114543

  7. Tissue distribution, intracellular localization and proteolytic processing of rat 4-hydroxyphenylpyruvate dioxygenase.

    Science.gov (United States)

    Neve, Søren; Aarenstrup, Lene; Tornehave, Ditte; Rahbek-Nielsen, Henrik; Corydon, Thomas Juhl; Roepstorff, Peter; Kristiansen, Karsten

    2003-01-01

    4-hydroxyphenylpyruvate dioxygenase (HPD) is an important enzyme involved in tyrosine catabolism. HPD was shown to be identical to a protein named the F-antigen, exploited by immunologists because of its unique immunological properties. Congenital HPD deficiency is a rare, relatively benign condition known as hereditary type III tyrosinemia. Decreased expression of HPD is often observed in association with the severe type I tyrosinemia, and interestingly, inhibition of HPD activity seems to ameliorate the clinical symptoms of type I tyrosinemia. In this study we present a comprehensive analysis of tissue specific expression and intracellular localization of HPD in the rat. By combined use of in situ hybridization and immunohistochemistry we confirm previously known sites of expression in liver and kidney. In addition, we show that HPD is abundantly expressed in neurons in the cortex, cerebellum and hippocampus. By using immunoelectron microscopy and confocal laser scanning microscopy, we provide evidence that HPD contrary to earlier assumptions specifically localizes to membranes of the endoplasmic reticulum and the Golgi apparatus. Detailed mass spectrometric analyses of HPD purified from rat liver revealed N-terminal and C-terminal processing of HPD, and expression of recombinant HPD suggested that C-terminal processing enhances the enzymatic activity.

  8. Expression and post-translational modification of human 4-hydroxy-phenylpyruvate dioxygenase.

    Science.gov (United States)

    Aarenstrup, Lene; Falch, Anne Marie; Jakobsen, Kirsten K; Neve, Søren; Henriksen L, Linda Ø; Tommerup, Niels; Leffers, Henrik; Kristiansen, Karsten

    2002-01-01

    4-hydroxyphenylpyruvate dioxygenase (HPD) (EC 1.13.11.27) is a key enzyme involved in tyrosine catabolism. Congenital HPD deficiency is a rare, relatively benign condition known as hereditary type III tyrosinemia. The severe type I tyrosinemia, caused by a deficiency of fumarylacetoacetate hydrolase which functions downstream of HPD in the tyrosine degradation pathway, is often associated with decreased expression of HPD, and interestingly, inhibition of HPD activity seems to ameliorate the clinical symptoms of type I tyrosinemia. The HPD gene was previously mapped to the chromosomal region 12q24-->qter. In the present study high-resolution chromosome mapping localized the HPD gene to 12q24.31. DNase I footprinting, revealed that four regions of the HPD promoter were protected by rat liver nuclear proteins. Computer-assisted analyses suggested that these elements might bind Sp1/AP2, HNF4, HNF3/CREB, and C/EBP, respectively. In transient transfection experiments, the proximal 271bp of the promoter conferred basal transcriptional activation in human Chang cells. Sequences in intron 1 were able to enhance the activity of this basal promoter. Finally, vaccinia virus-based expression provided evidence that HPD is subject to phosphorylation, and furthermore, allowed mapping of the HPD protein in the human keratinocyte 2D database.

  9. Mutations in the 4-hydroxyphenylpyruvic acid dioxygenase gene are responsible for tyrosinemia type III and hawkinsinuria.

    Science.gov (United States)

    Tomoeda, K; Awata, H; Matsuura, T; Matsuda, I; Ploechl, E; Milovac, T; Boneh, A; Scott, C R; Danks, D M; Endo, F

    2000-11-01

    The enzyme 4-hydroxyphenylpyruvic acid dioxygenase (HPD) catalyzes the reaction of 4-hydroxyphenylpyruvic acid to homogentisic acid in the tyrosine catabolism pathway. A deficiency in the catalytic activity of HPD may lead to tyrosinemia type III, an autosomal recessive disorder characterized by elevated levels of blood tyrosine and massive excretion of tyrosine derivatives into urine. It has been postulated that hawkinsinuria, an autosomal dominant disorder characterized by the excretion of 'hawkinsin,' may also be a result of HPD deficiency. Hawkinsin is a sulfur amino acid identified as (2-l-cystein-S-yl, 4-dihydroxycyclohex-5-en-1-yl)acetic acid. Patients with hawkinsinuria excrete this metabolite in their urine throughout their life, although symptoms of metabolic acidosis and tyrosinemia improve in the first year of life. We performed analyses of the HPD gene in a patient with tyrosinemia type III and two unrelated patients with hawkinsinuria. A homozygous missense mutation predicting an Ala to Val change at codon 268 (A268V) in the HPD gene was found in the patient with tyrosinemia type III. A heterozygous missense mutation predicting an Ala to Thr change at codon 33 (A33T) was found in the same HPD gene in the two patients with hawkinsinuria. These findings support the hypothesis that alterations in the structure and activity of HPD are causally related to two different metabolic disorders, tyrosinemia type III and hawkinsinuria.

  10. Indoleamine 2,3-dioxygenase attenuates inhibitor development in gene-therapy-treated hemophilia A mice.

    Science.gov (United States)

    Liu, L; Liu, H; Mah, C; Fletcher, B S

    2009-06-01

    A serious impediment to gene and protein replacement therapy in hemophilia A is the development of inhibitors. Mechanisms responsible for inhibitor development include T-cell-dependent adaptive immune responses and the CD28-B7 signaling pathway that eventually leads to the formation of antibodies directed against factor VIII (FVIII). Indoleamine 2,3-dioxygenase (IDO) is a potent immunosuppressive enzyme that can inhibit T-cell responses and induce T-cell apoptosis by regulation of tryptophan metabolism. Kynurenine, one of the metabolites of tryptophan, has been implicated as an immune modulator. Here we hypothesize that co-delivery of the genes for FVIII and IDO can attenuate inhibitor formation. Using transposon-based gene delivery, we observed long-term therapeutic FVIII expression and significantly reduced inhibitor titers when the genes were co-delivered. Co-expression of FVIII and IDO in the liver was associated with increased plasma kynurenine levels, an inhibition of T-cell infiltration and increased apoptosis of T cells within the liver. These experiments suggest that modulation of tryptophan catabolism through IDO expression provides a novel strategy to reduce inhibitor development in hemophilia gene/protein therapy.

  11. Induction of 9-cis-epoxycarotenoid dioxygenase in Arabidopsis thaliana seeds enhances seed dormancy.

    Science.gov (United States)

    Martínez-Andújar, Cristina; Ordiz, M Isabel; Huang, Zhonglian; Nonogaki, Mariko; Beachy, Roger N; Nonogaki, Hiroyuki

    2011-10-11

    Full understanding of mechanisms that control seed dormancy and germination remains elusive. Whereas it has been proposed that translational control plays a predominant role in germination, other studies suggest the importance of specific gene expression patterns in imbibed seeds. Transgenic plants were developed to permit conditional expression of a gene encoding 9-cis-epoxycarotenoid dioxygenase 6 (NCED6), a rate-limiting enzyme in abscisic acid (ABA) biosynthesis, using the ecdysone receptor-based plant gene switch system and the ligand methoxyfenozide. Induction of NCED6 during imbibition increased ABA levels more than 20-fold and was sufficient to prevent seed germination. Germination suppression was prevented by fluridone, an inhibitor of ABA biosynthesis. In another study, induction of the NCED6 gene in transgenic seeds of nondormant mutants tt3 and tt4 reestablished seed dormancy. Furthermore, inducing expression of NCED6 during seed development suppressed vivipary, precocious germination of developing seeds. These results indicate that expression of a hormone metabolism gene in seeds can be a sole determinant of dormancy. This study opens the possibility of developing a robust technology to suppress or promote seed germination through engineering pathways of hormone metabolism.

  12. On the substrate- and stereospecificity of the plant carotenoid cleavage dioxygenase 7

    KAUST Repository

    Bruno, Mark

    2014-05-01

    Strigolactones are phytohormones synthesized from carotenoids via a stereospecific pathway involving the carotenoid cleavage dioxygenases 7 (CCD7) and 8. CCD7 cleaves 9-cis-β-carotene to form a supposedly 9-cis-configured β-apo-10′-carotenal. CCD8 converts this intermediate through a combination of yet undetermined reactions into the strigolactone-like compound carlactone. Here, we investigated the substrate and stereo-specificity of the Arabidopsis and pea CCD7 and determined the stereo-configuration of the β-apo-10′-carotenal intermediate by using Nuclear Magnetic Resonance Spectroscopy. Our data unequivocally demonstrate the 9-cis-configuration of the intermediate. Both CCD7s cleave different 9-cis-carotenoids, yielding hydroxylated 9-cis-apo-10′-carotenals that may lead to hydroxylated carlactones, but show highest affinity for 9-cis-β-carotene. © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  13. Antiparasitic and antiproliferative effects of indoleamine 2,3-dioxygenase enzyme expression in human fibroblasts.

    Science.gov (United States)

    Gupta, S L; Carlin, J M; Pyati, P; Dai, W; Pfefferkorn, E R; Murphy, M J

    1994-01-01

    Studies were carried out to evaluate the proposed role of indoleamine 2,3-dioxygenase (INDO) induction in the antimicrobial and antiproliferative effects of gamma interferon (IFN-gamma) in human fibroblasts. The INDO cDNA coding region was cloned in the pMEP4 expression vector, containing the metallothionein (MTII) promoter in the sense (+ve) or the antisense (-ve) orientation. Human fibroblasts (GM637) stably transfected with the sense construct expressed INDO activity after treatment with CdCl2 or ZnSO4, but cells transfected with the antisense construct did not. The growth of Chlamydia psittaci was strongly inhibited in INDO +ve cells but not in INDO -ve cells after treatment with Cd2+ or Zn2+. The inhibition correlated with the level of INDO activity induced and could be reversed by the addition of excess tryptophan to the medium. The growth of Toxoplasma gondii was also strongly inhibited in INDO +ve cells but not in INDO -ve cells after treatment with Cd2+. Expression of Cd(2+)-induced INDO activity also inhibited thymidine incorporation and led to cytotoxicity in INDO +ve cells but not in INDO -ve cells. Thus, the induction of INDO activity by IFN-gamma may be an important factor in the antimicrobial and antiproliferative effects of IFN-gamma in human fibroblasts. Images PMID:8188349

  14. Indoleamine 2,3-dioxygenase expression in patients with allergic rhinitis: a case-control study

    Directory of Open Access Journals (Sweden)

    Luukkainen Annika

    2011-12-01

    Full Text Available Abstract Background Indoleamine 2,3-dioxygenase (IDO is a tryptophan catalyzing enzyme. It has been suggested that it has a role in lower airway allergic inflammations, but its role in allergic rhinitis has not been investigated. Objective Our aim was to evaluate the expression of IDO in the nasal mucosa of allergic rhinitis patients allergic to birch pollen during peak exposure to birch pollen allergen and compare it to non-atopic patients. Methods IDO expression was immunohistochemically evaluated from nasal specimens obtained in- and off-season from otherwise healthy non-smoking volunteers both allergic to birch pollen (having mild or moderate allergic rhinoconjunctivitis and non-allergic controls. Results: The IDO expression levels were low in healthy controls and remained low also in patients allergic to birch pollen. There were no differences in the expression of IDO in- and off-season in either healthy or allergic subjects. Conclusions There is a controversy in the role of IDO in upper and lower airways during allergic airway disease. It seems that IDO is associated to allergic inflammations of the lower airways, but does not have a local role in the nasal cavity at least in mild or moderate forms of allergic rhinitis.

  15. Substrate Recognition and Catalysis by the Cofactor-Independent Dioxygenase DpgC+

    Energy Technology Data Exchange (ETDEWEB)

    Fielding,E.; Widboom, P.; Bruner, S.

    2007-01-01

    The enzyme DpgC belongs to a small class of oxygenases not dependent on accessory cofactors for activity. DpgC is in the biosynthetic pathway for the nonproteinogenic amino acid 3, 5-dihydroxyphenylglycine in actinomycetes bacteria responsible for the production of the vancomycin/teicoplanin family of antibiotic natural products. The X-ray structure of DpgC confirmed the absence of cofactors and defined a novel hydrophobic dioxygen binding pocket adjacent to a bound substrate analogue. In this paper, the role specific amino acids play in substrate recognition and catalysis is examined through biochemical and structural characterization of site-specific enzyme mutations and alternate substrates. The results establish the importance of three amino acids, Arg254, Glu299, and Glu189, in the chemistry of DpgC. Arg254 and Glu189 join to form a specific contact with one of the phenolic hydroxyls of the substrate, and this interaction plays a key role in both substrate recognition and catalysis. The X-ray crystal structure of Arg254Lys was determined to address the role this residue plays in the chemistry. In addition, characterization of alternate substrate analogues demonstrates the presence and position of phenol groups are necessary for both enzyme recognition and downstream oxidation chemistry. Overall, this work defines the mechanism of substrate recognition and specificity by the cofactor-independent dioxygenase DpgC.

  16. Indoleamine 2, 3-dioxygenase (IDO) is essential for dendritic cell activation and chemotactic responsiveness to chemokines

    Institute of Scientific and Technical Information of China (English)

    Shih Ling HWANG; Nancy Pei-Yee CHUNG; Jacqueline Kwai-Yi CHAN; Chen-Lung Steve LIN

    2005-01-01

    Indoleamine 2, 3-dioxygenase (IDO) is a rate-limiting enzyme for the tryptophan catabolism. In human and murine cells, IDO inhibits antigen-specific T cell proliferation in vitro and suppresses T cell responses to fetal alloantigens during murine pregnancy. In mice, IDO expression is an inducible feature of specific subsets of dendritic cells (DCs),and is important for T cell regulatory properties. However, the effect of IDO and tryptophan deprivation on DC functions remains unknown. We report here that when tryptophan utilization was prevented by a pharmacological inhibitor of IDO, 1-methyl tryptophan (1MT), DC activation induced by pathogenic stimulus lipopolysaccharide (LPS) or inflammatory cytokine TNF-α was inhibited both phenotypically and functionally. Such an effect was less remarkable when DC was stimulated by a physiological stimulus, CD40 ligand. Tryptophan deprivation during DC activation also regulated the expression of CCR5 and CXCR4, as well as DC responsiveness to chemokines. These results suggest that tryptophan usage in the microenvironment is essential for DC maturation, and may also play a role in the regulation of DC migratory behaviors.

  17. Expression Profile of Carotenoid Cleavage Dioxygenase Genes in Summer Squash (Cucurbita pepo L.).

    Science.gov (United States)

    González-Verdejo, Clara I; Obrero, Ángeles; Román, Belén; Gómez, Pedro

    2015-06-01

    Carotenoids are important dietary components that can be found in vegetable crops. The accumulation of these compounds in fruit and vegetables is altered by the activity of carotenoid cleavage dioxygenases (CCDs) enzymes that produce their degradation. The aim of this work was to study the possible implication of CCD genes in preventing carotenoid storage in the horticultural crop summer squash (Cucurbita pepo L.). The relationship between the presence of these compounds and gene expression for CCDs was studied in three varieties showing different peel and flesh colour. Expression analysis for the CCD genes CpNCED1, CpNCED2, CpNCED3, CpNCED9, CpCCD1, CpCCD4a, CpCCD4b and CpCCD8 was carried out on different organs and at several fruit developmental stages. The results showed that the CpCCD4a and CpCCD4b genes were highly expressed in the variety with lowest carotenoid content suggesting a putative role in carotenoid accumulation pattern in summer squash fruit.

  18. A nonsense mutation in the 4-hydroxyphenylpyruvic acid dioxygenase gene (Hpd) causes skipping of the constitutive exon and hypertyrosinemia in mouse strain III

    Energy Technology Data Exchange (ETDEWEB)

    Endo, Fumio; Awata, Hisataka; Matsuda, Ichiro [Kumamoto Univ. (Japan)

    1995-01-01

    4-Hydroxyphenylpyruvic acid dioxygenase (HPD; EC 1.13.11.27) is an important enzyme in tyrosine catabolism in most organisms. Decreased activity of 4-hydroxyphenylpyruvic acid dioxygenase in the liver of mouse strain III is associated with tyrosinemia. We report a nucleotide substitution that generates a termination codon in exon 7 of the 4-hydroxyphenylpyruvic acid dioxygenase gene in III mice. This mutation is associated with partial exon skipping, and most of the mRNA lacks sequences corresponding to exon 7. The partial exon skipping apparently is the result of a nonsense mutation in the exon. Mouse strain III is a model for human tyrosinemia type 3 (McKusick 276710), and this train together with recently established models for tyrosinemia type 1 will facilitate studies of hereditary tyrosinemias.

  19. A nonsense mutation in the 4-hydroxyphenylpyruvic acid dioxygenase gene (Hpd) causes skipping of the constitutive exon and hypertyrosinemia in mouse strain III.

    Science.gov (United States)

    Endo, F; Awata, H; Katoh, H; Matsuda, I

    1995-01-01

    4-Hydroxyphenylpyruvic acid dioxygenase (HPD; EC 1.13.11.27) is an important enzyme in tyrosine catabolism in most organisms. Decreased activity of 4-hydroxyphenylpyruvic acid dioxygenase in the liver of mouse strain III is associated with tyrosinemia. We report a nucleotide substitution that generates a termination codon in exon 7 of the 4-hydroxyphenylpyruvic acid dioxygenase gene in III mice. This mutation is associated with partial exon skipping, and most of the mRNA lacks sequences corresponding to exon 7. The partial exon skipping apparently is the result of a nonsense mutation in the exon. Mouse strain III is a model for human tyrosinemia type 3 (McKusick 276710), and this strain together with recently established models for tyrosinemia type 1 will facilitate studies of hereditary tyrosinemias.

  20. The different catalytic roles of the metal-binding ligands in human 4-hydroxyphenylpyruvate dioxygenase.

    Science.gov (United States)

    Huang, Chih-Wei; Liu, Hsiu-Chen; Shen, Chia-Pei; Chen, Yi-Tong; Lee, Sung-Jai; Lloyd, Matthew D; Lee, Hwei-Jen

    2016-05-01

    4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a non-haem iron(II)-dependent oxygenase that catalyses the conversion of 4-hydroxyphenylpyruvate (HPP) to homogentisate (HG). In the active site, a strictly conserved 2-His-1-Glu facial triad co-ordinates the iron ready for catalysis. Substitution of these residues resulted in about a 10-fold decrease in the metal binding affinity, as measured by isothermal titration calorimetry, and a large reduction in enzyme catalytic efficiencies. The present study revealed the vital role of the ligand Glu(349) in enzyme function. Replacing this residue with alanine resulted in loss of activity. The E349G variant retained 5% activity for the coupled reaction, suggesting that co-ordinating water may be able to support activation of the trans-bound dioxygen upon substrate binding. The reaction catalysed by the H183A variant was fully uncoupled. H183A variant catalytic activity resulted in protein cleavage between Ile(267) and Ala(268) and the production of an N-terminal fragment. The H266A variant was able to produce 4-hydroxyphenylacetate (HPA), demonstrating that decarboxylation had occurred but that there was no subsequent product formation. Structural modelling of the variant enzyme with bound dioxygen revealed the rearrangement of the co-ordination environment and the dynamic behaviour of bound dioxygen in the H266A and H183A variants respectively. These models suggest that the residues regulate the geometry of the reactive oxygen intermediate during the oxidation reaction. The mutagenesis and structural simulation studies demonstrate the critical and unique role of each ligand in the function of HPPD, and which correlates with their respective co-ordination position.

  1. Robust crop resistance to broadleaf and grass herbicides provided by aryloxyalkanoate dioxygenase transgenes.

    Science.gov (United States)

    Wright, Terry R; Shan, Guomin; Walsh, Terence A; Lira, Justin M; Cui, Cory; Song, Ping; Zhuang, Meibao; Arnold, Nicole L; Lin, Gaofeng; Yau, Kerrm; Russell, Sean M; Cicchillo, Robert M; Peterson, Mark A; Simpson, David M; Zhou, Ning; Ponsamuel, Jayakumar; Zhang, Zhanyuan

    2010-11-23

    Engineered glyphosate resistance is the most widely adopted genetically modified trait in agriculture, gaining widespread acceptance by providing a simple robust weed control system. However, extensive and sustained use of glyphosate as a sole weed control mechanism has led to field selection for glyphosate-resistant weeds and has induced significant population shifts to weeds with inherent tolerance to glyphosate. Additional weed control mechanisms that can complement glyphosate-resistant crops are, therefore, urgently needed. 2,4-dichlorophenoxyacetic acid (2,4-D) is an effective low-cost, broad-spectrum herbicide that controls many of the weeds developing resistance to glyphosate. We investigated the substrate preferences of bacterial aryloxyalkanoate dioxygenase enzymes (AADs) that can effectively degrade 2,4-D and have found that some members of this class can act on other widely used herbicides in addition to their activity on 2,4-D. AAD-1 cleaves the aryloxyphenoxypropionate family of grass-active herbicides, and AAD-12 acts on pyridyloxyacetate auxin herbicides such as triclopyr and fluroxypyr. Maize plants transformed with an AAD-1 gene showed robust crop resistance to aryloxyphenoxypropionate herbicides over four generations and were also not injured by 2,4-D applications at any growth stage. Arabidopsis plants expressing AAD-12 were resistant to 2,4-D as well as triclopyr and fluroxypyr, and transgenic soybean plants expressing AAD-12 maintained field resistance to 2,4-D over five generations. These results show that single AAD transgenes can provide simultaneous resistance to a broad repertoire of agronomically important classes of herbicides, including 2,4-D, with utility in both monocot and dicot crops. These transgenes can help preserve the productivity and environmental benefits of herbicide-resistant crops.

  2. The immune system strikes back: cellular immune responses against indoleamine 2,3-dioxygenase.

    Directory of Open Access Journals (Sweden)

    Rikke Baek Sørensen

    Full Text Available BACKGROUND: The enzyme indoleamine 2,3-dioxygenase (IDO exerts an well established immunosuppressive function in cancer. IDO is expressed within the tumor itself as well as in antigen-presenting cells in tumor-draining lymph nodes, where it promotes the establishment of peripheral immune tolerance to tumor antigens. In the present study, we tested the notion whether IDO itself may be subject to immune responses. METHODS AND FINDINGS: The presence of naturally occurring IDO-specific CD8 T cells in cancer patients was determined by MHC/peptide stainings as well as ELISPOT. Antigen specific cytotoxic T lymphocytes (CTL from the peripheral blood of cancer patients were cloned and expanded. The functional capacity of the established CTL clones was examined by chrome release assays. The study unveiled spontaneous cytotoxic T-cell reactivity against IDO in peripheral blood as well as in the tumor microenvironment of different cancer patients. We demonstrate that these IDO reactive T cells are indeed peptide specific, cytotoxic effector cells. Hence, IDO reactive T cells are able to recognize and kill tumor cells including directly isolated AML blasts as well as IDO-expressing dendritic cells, i.e. one of the major immune suppressive cell populations. CONCLUSION: IDO may serve as an important and widely applicable target for anti-cancer immunotherapeutic strategies. Furthermore, as emerging evidence suggests that IDO constitutes a significant counter-regulatory mechanism induced by pro-inflammatory signals, IDO-based immunotherapy holds the promise to boost anti-cancer immunotherapy in general.

  3. In vivo correction with recombinant adenovirus of 4-hydroxyphenylpyruvic acid dioxygenase deficiencies in strain III mice.

    Science.gov (United States)

    Kubo, S; Kiwaki, K; Awata, H; Katoh, H; Kanegae, Y; Saito, I; Yamamoto, T; Miyazaki, J; Matsuda, I; Endo, F

    1997-01-01

    Tyrosinemia type 3, caused by a genetic deficiency of 4-hydroxyphenylpyruvic acid dioxygenase (HPD) in tyrosine catabolism, is characterized by convulsion, ataxia, and mental retardation. The III mouse is a model of tyrosinemia type 3. HPD activity and protein are defective in the liver and its blood tyrosine levels are elevated, the range being between 1,100 and 1,656 microM. We constructed a recombinant adenoviral vector bearing the human HPD cDNA (AdexCAGhHPD), which is expressed under the control of a potent CAG promoter. III mice were injected with 1.0 x 10(8) to 1.0 x 10(9) pfu of AdexCAGhHPD through the tail vein. When 3.0 x 10(8) - 1.0 x 10(9) pfu were injected, blood tyrosine levels decreased within 3 hr, reached a normal range (under 300 microM), and remained at a low level for 2-6 weeks. Hepatic HPD activities also increased as early as 3 hr after the injection of 5.0 x 10(8) pfu, reached the levels comparable to the control mice in 3-7 days, and then decreased, and correlated well to blood tyrosine. Hepatic HPD expression was confirmed by Northern blot and immunoblot analyses. Histology revealed no difference (gross or microscopic) between the liver injected with AdexCAGhHPD and the control. No significant changes in blood tyrosine levels were noted after the second injection of 5.0 x 10(8) pfu of AdexCAGhHPD. Thus, the intravenous administration of the adenoviral vector bearing a foreign gene seems suitable for transient, early gene transfer into the liver.

  4. Structure of 4-hydrophenylpyruvic acid dioxygenase (HPD) gene and its mutation in tyrosinemic mouse strain III

    Energy Technology Data Exchange (ETDEWEB)

    Awata, H.; Endo, F.; Matsuda, I. [Kumamoto Univ. Medical School (Japan)] [and others

    1994-09-01

    4-Hydroxphenylpyruvic acid dioxygenase (HPD) is an important enzyme in tyrosine catabolism in most organisms. The activity of this enzyme is expressed mainly in the liver and is developmentally regulated in mammals. A genetic deficiency of the enzyme in man and mouse leads to hereditary tyrosinemia type 3. Using human HPD cDNA as a probe, a chromosomal gene related to HPD was isolated from human and mouse gene libraries. The human HPD gene is over 30 kilo-bases long and is split into 14 exons. Analysis of the 5{prime} flanking sequence of the gene suggests that expression of the gene is regulated by hepatocyte-specific and liver-enriched transcription factors, as well as by hormones. These features of the 5{prime} flanking region of the gene are similar to those of other genes which are specifically expressed in hepatocytes and which are developmentally regulated. The gene for mouse HPD has a similar structure and we obtained evidence for a nucleotide substitution which generates a termination codon in exon 7 of the HPD gene in III mice. This mutation associates a partial exon skipping and most of the mRNA lacks sequences corresponding to exon 7. The partial exon skipping apparently is the result of a nonsense mutation in the exon. Thus, mouse strain III can serve as a genetic model for human tyrosinemia type 3. Ongoing studies are expected to elucidate the disease process involved in hereditary tyrosinemia type 1 and to shed light on mechanisms that mediate developmental regulation of HPD gene expression. In addition, mouse strain III together with recently established models for tyrosinemia type 1 will facilitate studies on hereditary tyrosinemias.

  5. Resonance Raman study on indoleamine 2,3-dioxygenase: Control of reactivity by substrate-binding

    Energy Technology Data Exchange (ETDEWEB)

    Yanagisawa, Sachiko; Hara, Masayuki [Graduate School of Life Science and Picobiology Institute, University of Hyogo, Koto 3-2-1, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan); Sugimoto, Hiroshi; Shiro, Yoshitsugu [Biometal Science Laboratory, RIKEN SPring-8 Center, Harima Institute, Koto 1-1-1, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan); Ogura, Takashi, E-mail: ogura@sci.u-hyogo.ac.jp [Graduate School of Life Science and Picobiology Institute, University of Hyogo, Koto 3-2-1, Kamigori-cho, Ako-gun, Hyogo 678-1297 (Japan)

    2013-06-20

    Highlights: • Indoleamine 2,3-dioygenase has been studied by resonance Raman spectroscopy. • Trp-binding to the enzyme induces high frequency shift of the Fe–His stretching mode. • Increased imidazolate character of histidine promotes the O–O bond cleavage step. • A fine-tuning of the reactivity of the O–O bond cleavage reaction is identified. • The results are consistent with the sequential oxygen-atom-transfer mechanism. - Abstract: Resonance Raman spectra of ligand-bound complexes including the 4-phenylimidazole complex and of free and L-Trp-bound forms of indoleamine 2, 3-dioxygenase in the ferric state were examined. Effects on the vinyl and propionate substituent groups of the heme were detected in a ligand-dependent fashion. The effects of phenyl group of 4-phenylimidazole on the vinyl and propionate Raman bands were evident when compared with the case of imidazole ligand. Substrate binding to the ferrous protein caused an upshift of the iron–histidine stretching mode by 3 cm{sup −1}, indicating an increase in negativity of the imidazole ring, which favors the O–O bond cleavage. The substrate binding event is likely to be communicated from the heme distal side to the iron–histidine bond through heme substituent groups and the hydrogen-bond network which includes water molecules, as identified in an X-ray structure of a 4-phenylimidazole complex. The results provide evidence for fine-tuning of the reactivity of O–O bond cleavage by the oxygenated heme upon binding of L-Trp.

  6. Novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of Patagonia

    Directory of Open Access Journals (Sweden)

    Ferrero Marcela A

    2008-03-01

    Full Text Available Abstract Background Polycyclic aromatic hydrocarbons (PAHs, widespread pollutants in the marine environment, can produce adverse effects in marine organisms and can be transferred to humans through seafood. Our knowledge of PAH-degrading bacterial populations in the marine environment is still very limited, and mainly originates from studies of cultured bacteria. In this work, genes coding catabolic enzymes from PAH-biodegradation pathways were characterized in coastal sediments of Patagonia with different levels of PAH contamination. Results Genes encoding for the catalytic alpha subunit of aromatic ring-hydroxylating dioxygenases (ARHDs were amplified from intertidal sediment samples using two different primer sets. Products were cloned and screened by restriction fragment length polymorphism analysis. Clones representing each restriction pattern were selected in each library for sequencing. A total of 500 clones were screened in 9 gene libraries, and 193 clones were sequenced. Libraries contained one to five different ARHD gene types, and this number was correlated with the number of PAHs found in the samples above the quantification limit (r = 0.834, p nahAc-like genes, phnAc-like genes as identified in Alcaligenes faecalis AFK2, and phnA1-like genes from marine PAH-degraders from the genus Cycloclasticus. Conclusion These results show the presence of hitherto unidentified ARHD genes in this sub-Antarctic marine environment exposed to anthropogenic contamination. This information can be used to study the geographical distribution and ecological significance of bacterial populations carrying these genes, and to design molecular assays to monitor the progress and effectiveness of remediation technologies.

  7. Structural Basis for Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine-200

    OpenAIRE

    Kovaleva, Elena G.; Rogers, Melanie S.; Lipscomb, John D.

    2015-01-01

    Kinetic and spectroscopic studies have shown that the conserved active site residue His200 of the extradiol ring-cleaving homoprotocatechuate 2,3-dioxygenase (FeHPCD) from Brevibacterium fuscum is critical for efficient catalysis. The roles played by this residue are probed here by analysis of the steady state kinetics, pH dependence, and X-ray crystal structures of the FeHPCD position 200 variants His200Asn, His200Gln, and His200Glu alone and in complex with three catecholic substrates (homo...

  8. Structure and mechanism leading to formation of the cysteine sulfinate product complex of a biomimetic cysteine dioxygenase model.

    Science.gov (United States)

    Sallmann, Madleen; Kumar, Suresh; Chernev, Petko; Nehrkorn, Joscha; Schnegg, Alexander; Kumar, Devesh; Dau, Holger; Limberg, Christian; de Visser, Sam P

    2015-05-11

    Cysteine dioxygenase is a unique nonheme iron enzyme that is involved in the metabolism of cysteine in the body. It contains an iron active site with an unusual 3-His ligation to the protein, which contrasts with the structural features of common nonheme iron dioxygenases. Recently, some of us reported a truly biomimetic model for this enzyme, namely a trispyrazolylborato iron(II) cysteinato complex, which not only has a structure very similar to the enzyme-substrate complex but also represents a functional model: Treatment of the model with dioxygen leads to cysteine dioxygenation, as shown by isolating the cysteine part of the product in the course of the work-up. However, little is known on the conversion mechanism and, so far, not even the structure of the actual product complex had been characterised, which is also unknown in case of the enzyme. In a multidisciplinary approach including density functional theory calculations and X-ray absorption spectroscopy, we have now determined the structure of the actual sulfinato complex for the first time. The Cys-SO2 (-) functional group was found to be bound in an η(2) -O,O-coordination mode, which, based on the excellent resemblance between model and enzyme, also provides the first support for a corresponding binding mode within the enzymatic product complex. Indeed, this is again confirmed by theory, which had predicted a η(2) -O,O-binding mode for synthetic as well as the natural enzyme.

  9. Activity of a Carboxyl-Terminal Truncated Form of Catechol 2,3-Dioxygenase from Planococcus sp. S5

    Directory of Open Access Journals (Sweden)

    Katarzyna Hupert-Kocurek

    2014-01-01

    Full Text Available Catechol 2,3-dioxygenases (C23Os, E.C.1.13.12.2 are two domain enzymes that catalyze degradation of monoaromatic hydrocarbons. The catalytically active C-domain of all known C23Os comprises ferrous ion ligands as well as residues forming active site pocket. The aim of this work was to examine and discuss the effect of nonsense mutation at position 289 on the activity of catechol 2,3-dioxygenase from Planococcus strain. Although the mutant C23O showed the same optimal temperature for activity as the wild-type protein (35°C, it exhibited activity slightly more tolerant to alkaline pH. Mutant enzyme exhibited also higher affinity to catechol as a substrate. Its Km (66.17 µM was approximately 30% lower than that of wild-type enzyme. Interestingly, removal of the C-terminal residues resulted in 1.5- to 1.8-fold (P<0.05 increase in the activity of C23OB61 against 4-methylcatechol and 4-chlorocatechol, respectively, while towards catechol the activity of the protein dropped to about 80% of that of the wild-type enzyme. The results obtained may facilitate the engineering of the C23O for application in the bioremediation of polluted areas.

  10. Molecular basis for catalysis and substrate-mediated cellular stabilization of human tryptophan 2,3-dioxygenase

    Science.gov (United States)

    Lewis-Ballester, Ariel; Forouhar, Farhad; Kim, Sung-Mi; Lew, Scott; Wang, YongQiang; Karkashon, Shay; Seetharaman, Jayaraman; Batabyal, Dipanwita; Chiang, Bing-Yu; Hussain, Munif; Correia, Maria Almira; Yeh, Syun-Ru; Tong, Liang

    2016-01-01

    Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) play a central role in tryptophan metabolism and are involved in many cellular and disease processes. Here we report the crystal structure of human TDO (hTDO) in a ternary complex with the substrates L-Trp and O2 and in a binary complex with the product N-formylkynurenine (NFK), defining for the first time the binding modes of both substrates and the product of this enzyme. The structure indicates that the dioxygenation reaction is initiated by a direct attack of O2 on the C2 atom of the L-Trp indole ring. The structure also reveals an exo binding site for L-Trp, located ~42 Å from the active site and formed by residues conserved among tryptophan-auxotrophic TDOs. Biochemical and cellular studies indicate that Trp binding at this exo site does not affect enzyme catalysis but instead it retards the degradation of hTDO through the ubiquitin-dependent proteasomal pathway. This exo site may therefore provide a novel L-Trp-mediated regulation mechanism for cellular degradation of hTDO, which may have important implications in human diseases. PMID:27762317

  11. Multistep conversion of para-substituted phenols by phenol hydroxylase and 2,3-dihydroxybiphenyl 1,2-dioxygenase.

    Science.gov (United States)

    Qu, Yuanyuan; Shi, Shengnan; Ma, Qiao; Kong, Chunlei; Zhou, Hao; Zhang, Xuwang; Zhou, Jiti

    2013-04-01

    A multistep conversion system of para-substituted phenols by recombinant phenol hydroxylase (PH(IND)) and 2,3-dihydroxybiphenyl 1,2-dioxygenase (BphC(LA-4)) was constructed in this study. Docking studies with different para-substituted phenols and corresponding catechols inside of the active site of PH(IND) and BphC(LA-4) predicted that all the substrates should be transformed. High-performance liquid chromatography-mass spectrometry analysis showed that the products of multistep conversion were the corresponding para-substituted catechols and semialdehydes. For the first-step conversion, the formation rate of 4-fluorocatechol (0.39 μM/min/mg dry weight) by strain PH(IND) hydroxylation was 1.15, 6.50, 3.00, and 1.18-fold higher than the formation of 4-chlorocatechol, 4-bromocatechol, 4-nitrocatechol, and 4-methylcatechol, respectively. For the second-step conversion, the formation rates of semialdehydes by strain BphC(LA-4) were as follows: 5-fluoro-HODA>5-chloro-HODA>2-hydroxy-5-nitro-ODA>5-bromo-HODA>2-hydroxy-5-methyl-ODA. The present study suggested that the multistep conversion by both ring hydroxylase and cleavage dioxygenase should be potential in the synthesis of industrial precursors and provide a novel avenue in the wastewater recycling treatment.

  12. Cloning and mutagenesis of catechol 2,3-dioxygenase gene from the gram-positive Planococcus sp. strain S5.

    Science.gov (United States)

    Hupert-Kocurek, Katarzyna; Stawicka, Agnieszka; Wojcieszyńska, Danuta; Guzik, Urszula

    2013-01-01

    In this study, the catechol 2,3-dioxygenase gene that encodes a 307- amino-acid protein was cloned from Planococcus sp. S5. The protein was identified to be a member of the superfamily I, subfamily 2A of extradiol dioxygenases. In order to study residues and regions affecting the enzyme's catalytic parameters, the c23o gene was randomly mutated by error-prone PCR. The wild-type enzyme and mutants containing substitutions within either the C-terminal or both domains were functionally produced in Escherichia coli and their activity towards catechol was characterized. The C23OB65 mutant with R296Q substitution showed significant tolerance to acidic pH with an optimum at pH 5.0. In addition, it showed activity more than 1.5 as high as that of the wild type enzyme and its Km was 2.5 times lower. It also showed altered sensitivity to substrate inhibition. The results indicate that residue at position 296 plays a role in determining pH dependence of the enzyme and its activity. Lower activity toward catechol was shown for mutants C23OB58 and C23OB81. Despite lower activity, these mutants showed higher affinity to catechol and were more sensitive to substrate concentration than nonmutated enzyme.

  13. NO binding to Mn-substituted homoprotocatechuate 2,3-dioxygenase: relationship to O₂ reactivity.

    Science.gov (United States)

    Hayden, Joshua A; Farquhar, Erik R; Que, Lawrence; Lipscomb, John D; Hendrich, Michael P

    2013-10-01

    Iron(II)-containing homoprotocatechuate 2,3-dioxygenase (FeHPCD) activates O2 to catalyze the aromatic ring opening of homoprotocatechuate (HPCA). The enzyme requires Fe(II) for catalysis, but Mn(II) can be substituted (MnHPCD) with essentially no change in the steady-state kinetic parameters. Near simultaneous O2 and HPCA activation has been proposed to occur through transfer of an electron or electrons from HPCA to O2 through the divalent metal. In O2 reactions with MnHPCD-HPCA and the 4-nitrocatechol (4NC) complex of the His200Asn (H200N) variant of FeHPCD, this transfer has resulted in the detection of a transient M(III)-O2 (·-) species that is not observed during turnover of the wild-type FeHPCD. The factors governing formation of the M(III)-O2 (·-) species are explored here by EPR spectroscopy using MnHPCD and nitric oxide (NO) as an O2 surrogate. Both the HPCA and the dihydroxymandelic substrate complexes of MnHPCD bind NO, thus representing the first reported stable MnNO complexes of a nonheme enzyme. In contrast, the free enzyme, the MnHPCD-4NC complex, and the MnH200N and MnH200Q variants with or without HPCA bound do not bind NO. The MnHPCD-ligand complexes that bind NO are also active in normal O2-linked turnover, whereas the others are inactive. Past studies have shown that FeHPCD and the analogous variants and catecholic ligand complexes all bind NO, and are active in normal turnover. This contrasting behavior may stem from the ability of the enzyme to maintain the approximately 0.8-V difference in the solution redox potentials of Fe(II) and Mn(II). Owing to the higher potential of Mn, the formation of the NO adduct or the O2 adduct requires both strong charge donation from the bound catecholic ligand and additional stabilization by interaction with the active-site His200. The same nonoptimal electronic and structural forces that prevent NO and O2 binding in MnHPCD variants may lead to inefficient electron transfer from the catecholic substrate to

  14. NO Binding to Mn-Substituted Homoprotocatechuate 2,3-Dioxygenase: Relationship to O2 Reactivity

    Science.gov (United States)

    Hayden, Joshua A.; Farquhar, Erik R.; Que, Lawrence; Lipscomb, John D.; Hendrich, Michael P.

    2014-01-01

    Homoprotocatechuate 2,3-dioxygenase (FeHPCD) activates O2 to catalyze the aromatic ring opening of 3,4-dihydroxyphenylacetic acid (HPCA). The enzyme requires FeII for catalysis, but MnII can be substituted (MnHPCD) with essentially no change in the steady-state kinetic parameters. Near simultaneous O2 and HPCA activation has been proposed to occur through transfer of an electron(s) from HPCA to O2 through the divalent metal. In O2 reactions with MnHPCD-HPCA and the 4-nitrocatechol (4NC) complex of the His200Asn (H200N) variant of FeHPCD, this transfer has resulted in the detection of a transient MIII-O2•− species not observed during turnover of the wild type FeHPCD. The factors governing formation of the MIII-O2•− species are explored here with EPR spectroscopy using MnHPCD and nitric oxide (NO) as an O2 surrogate. Both the HPCA and dihydroxymandelic substrate complexes of MnHPCD bind NO, thus representing the first reported stable MnNO complexes of a nonheme enzyme. In contrast, the free enzyme, the MnHPCD-4NC complex, and the MnH200N and MnH200Q variants with or without HPCA bound do not bind NO. The MnHPCD-ligand complexes that bind NO are also active in normal O2-linked turnover, whereas the others are inactive. Past studies have shown that FeHPCD and the analogous variants and catecholic ligand complexes all bind NO, and are active in normal turnover. This contrasting behavior may stem from ability of the enzyme to maintain the ~0.8 V difference in the solution redox potentials of FeII and MnII. Due to the higher potential of Mn, the formation of the NO or O2 adduct requires both strong charge donation from the bound catecholic ligand and additional stabilization by interaction with the active site His200. The same non-optimal electronic and structural forces that prevent NO and O2 binding in MnHPCD variants may lead to inefficient electron transfer from the catecholic substrate to the metal center in variants of FeHPCD during O2-linked turnover

  15. Characterization of metal binding in the active sites of acireductone dioxygenase isoforms from Klebsiella ATCC 8724.

    Science.gov (United States)

    Chai, Sergio C; Ju, Tingting; Dang, Marina; Goldsmith, Rachel Beaulieu; Maroney, Michael J; Pochapsky, Thomas C

    2008-02-26

    The two acireductone dioxygenase (ARD) isozymes from the methionine salvage pathway of Klebsiella ATCC 8724 present an unusual case in which two enzymes with different structures and distinct activities toward their common substrates (1,2-dihydroxy-3-oxo-5-(methylthio)pent-1-ene and dioxygen) are derived from the same polypeptide chain. Structural and functional differences between the two isozymes are determined by the type of M2+ metal ion bound in the active site. The Ni2+-bound NiARD catalyzes an off-pathway shunt from the methionine salvage pathway leading to the production of formate, methylthiopropionate, and carbon monoxide, while the Fe2+-bound FeARD' catalyzes the on-pathway formation of methionine precursor 2-keto-4-methylthiobutyrate and formate. Four potential protein-based metal ligands were identified by sequence homology and structural considerations. Based on the results of site-directed mutagenesis experiments, X-ray absorption spectroscopy (XAS), and isothermal calorimetry measurements, it is concluded that the same four residues, His96, His98, Glu102 and His140, provide the protein-based ligands for the metal in both the Ni- and Fe-containing forms of the enzyme, and subtle differences in the local backbone conformations trigger the observed structural and functional differences between the FeARD' and NiARD isozymes. Furthermore, both forms of the enzyme bind their respective metals with pseudo-octahedral geometry, and both may lose a histidine ligand upon binding of substrate under anaerobic conditions. However, mutations at two conserved nonligand acidic residues, Glu95 and Glu100, result in low metal contents for the mutant proteins as isolated, suggesting that some of the conserved charged residues may aid in transfer of metal from in vivo sources or prevent the loss of metal to stronger chelators. The Glu100 mutant reconstitutes readily but has low activity. Mutation of Asp101 results in an active enzyme that incorporates metal in vivo but

  16. The effects of trace elements, cations, and environmental conditions on protocatechuate 3,4-dioxygenase activity

    Directory of Open Access Journals (Sweden)

    Andréa Scaramal da Silva

    2013-04-01

    Full Text Available Phenanthracene is a highly toxic organic compound capable of contaminating water and soils, and biodegradation is an important tool for remediating polluted environments. This study aimed to evaluate the effects of trace elements, cations, and environmental conditions on the activity of the protocatechol 3,4-dioxygenase (P3,4O enzyme produced by the isolate Leifsonia sp. in cell-free and immobilized extracts. The isolate was grown in Luria Bertani broth medium (LB amended with 250 mg L-1 of phenanthrene. Various levels of pH (4.0-9.0, temperature (5-80 °C, time (0-90 min, trace elements (Cu2+, Hg2+ and Fe3+, and cations (Mg2+, Mn2+, K+ and NH4+ were tested to determine which conditions optimized enzyme activity. In general, the immobilized extract exhibited higher enzyme activity than the cell-free extract in the presence of trace elements and cations. Adding iron yielded the highest relative activity for both cell-free and immobilized extracts, with values of 16 and 99 %, respectively. Copper also increased enzyme activity for both cell-free and immobilized extracts, with values of 8 and 44 %, respectively. Enzyme activity in the phosphate buffer was high across a wide range of pH, reaching 80 % in the pH range between 6.5 and 8.0. The optimum temperatures for enzyme activity differed for cell-free and immobilized extracts, with maximum enzyme activity observed at 35 ºC for the cell-free extract and at 55 ºC for the immobilized extract. The cell-free extract of the P3,4O enzyme exhibited high activity only during the first 3 min of incubation, when it showed 50 % relative activity, and dropped to 0 % after 60 min of incubation. By contrast, activity in the immobilized extract was maintained during 90 min of incubation. This isolate has important characteristics for phenanthrene biodegradation, producing high quantities of the P3,4O enzyme that forms part of the most important pathway for PAH biodegradation.

  17. NUCLEOTIDE SEQUENCING AND TRANSCRIPTIONAL MAPPING OF THE GENES ENCODING BIPHENYL DIOXYGENASE, A MULTICOM- PONENT POLYCHLORINATED-BIPHENYL-DEGRADING ENZYME IN PSEUDOMONAS STRAIN LB400

    Science.gov (United States)

    The DNA region encoding biphenyl dioxygenase, the first enzyme in the biphenyl-polychlorinated biphenyl degradation pathway of Pseudomonas species strain LB400, was sequenced. Six open reading frames were identified, four of which are homologous to the components of toluene dioxy...

  18. Modeling the 2-His-1-Carboxylate Facial Triad: Iron-Catecholato Complexes as Structural and Functional Models of the Extradiol Cleaving Dioxygenases

    NARCIS (Netherlands)

    Bruijnincx, P.C.A.; Lutz, M.; Spek, A.L.; Hagen, W.R.; Weckhuysen, B.M.; van Koten, G.; Klein Gebbink, R.J.M.

    2007-01-01

    Mononuclear iron(II)- and iron(III)-catecholato complexes with three members of a new 3,3-bis(1-alkylimidazol-2-yl)propionate ligand family have been synthesized as models of the active sites of the extradiol cleaving catechol dioxygenases. These enzymes are part of the superfamily of dioxygen-activ

  19. Inflammation-induced activation of the indoleamine 2,3-dioxygenase pathway: Relevance to cancer-related fatigue.

    Science.gov (United States)

    Kim, Sangmi; Miller, Brian J; Stefanek, Michael E; Miller, Andrew H

    2015-07-01

    Cancer-related fatigue (CRF) is a common complication of cancer and its treatment that can significantly impair quality of life. Although the specific mechanisms remain poorly understood, inflammation is now considered to be a distinct component of CRF in addition to effects of depression, anxiety, insomnia, and other factors. One key biological pathway that may link inflammation and CRF is indoleamine 2,3-dioxygenase (IDO). Induced by inflammatory stimuli, IDO catabolizes tryptophan to kynurenine (KYN), which is subsequently converted into neuroactive metabolites. Here we summarize current knowledge concerning the relevance of the IDO pathway to CRF, including activation of the IDO pathway in cancer patients and, as a consequence, accumulation of neurotoxic KYN metabolites and depletion of serotonin in the brain. Because IDO inhibitors are already being evaluated as therapeutic agents in cancer, the elucidation of the relationship between IDO activation and CRF in cancer patients may lead to novel diagnostic and clinical approaches to managing CRF and its debilitating consequences.

  20. Characteristics and biotechnology applications of aliphatic amino acid hydroxylases belonging to the Fe(II)/α-ketoglutarate-dependent dioxygenase superfamily.

    Science.gov (United States)

    Hibi, Makoto; Ogawa, Jun

    2014-05-01

    The asymmetric hydroxylation of inactive carbon atoms is still an important reaction in the industrial synthesis of valuable chiral compounds such as pharmaceuticals and fine chemicals. Applications of monooxygenation enzymes, like cytochrome P450 monooxygenases, flavin-containing monooxygenases, and Fe(II)/α-ketoglutarate-dependent dioxygenases (Fe/αKG-DOs), are strongly desired as hydroxylation biocatalysts because they have great advantages in regio- and stereoselectivity of the reactions. Recently, several novel Fe/αKG-DOs have been found to catalyze the asymmetric hydroxylation of aliphatic amino acids. Depending on their amino acid sequences, these Fe/αKG-DOs catalyze different types of regioselective hydroxylations, or C3-, C4-, and C5-hydroxylation. Additionally, most also have stereoselective sulfoxidation activities. Here, we have reviewed the characterization and process development of this novel functioning group of Fe/αKG-DOs.

  1. Properties of catechol 1,2-dioxygenase in the cell free extract and immobilized extract of Mycobacterium fortuitum

    Directory of Open Access Journals (Sweden)

    A.S. Silva

    2013-01-01

    Full Text Available Polycyclic aromatic hydrocarbons (PAH are carcinogenic compounds which contaminate water and soil, and the enzymes can be used for bioremediation of these environments. This study aimed to evaluate some environmental conditions that affect the production and activity of the catechol 1,2-dioxygenase (C12O by Mycobacterium fortuitum in the cell free and immobilized extract in sodium alginate. The bacterium was grown in mineral medium and LB broth containing 250 mg L-1 of anthracene (PAH. The optimum conditions of pH (4.0-9.0, temperature (5-70 ºC, reaction time (10-90 min and the effect of ions in the enzyme activity were determined. The Mycobacterium cultivated in LB shown higher growth and the C12O activity was two-fold higher to that in the mineral medium. To both extracts the highest enzyme activity was at pH 8.0, however, the immobilized extract promoted the increase in the C12O activity in a pH range between 4.0 and 8.5. The immobilized extract increased the enzymatic activity time and showed the highest C12O activity at 45 ºC, 20 ºC higher than the greatest temperature in the cell free extract. The enzyme activity in both extracts was stimulated by Fe3+, Hg2+ and Mn2+ and inhibited by NH4+ and Cu2+, but the immobilization protected the enzyme against the deleterious effects of K+ and Mg2+ in tested concentrations. The catechol 1,2-dioxygenase of Mycobacterium fortuitum in the immobilized extract has greater stability to the variations of pH, temperature and reaction time, and show higher activity in presence of ions, comparing to the cell free extract.

  2. Cytosolic and plastoglobule-targeted carotenoid dioxygenases from Crocus sativus are both involved in beta-ionone release.

    Science.gov (United States)

    Rubio, Angela; Rambla, José Luís; Santaella, Marcella; Gómez, M Dolores; Orzaez, Diego; Granell, Antonio; Gómez-Gómez, Lourdes

    2008-09-05

    Saffron, the processed stigma of Crocus sativus, is characterized by the presence of several apocarotenoids that contribute to the color, flavor, and aroma of the spice. However, little is known about the synthesis of aroma compounds during the development of the C. sativus stigma. The developing stigma is nearly odorless, but before and at anthesis, the aromatic compound beta-ionone becomes the principal norisoprenoid volatile in the stigma. In this study, four carotenoid cleavage dioxygenase (CCD) genes, CsCCD1a, CsCCD1b, CsCCD4a, and CsCCD4b, were isolated from C. sativus. Expression analysis showed that CsCCD1a was constitutively expressed, CsCCD1b was unique to the stigma tissue, but only CsCCD4a and -b had expression patterns consistent with the highest levels of beta-carotene and emission of beta-ionone derived during the stigma development. The CsCCD4 enzymes were localized in plastids and more specifically were present in the plastoglobules. The enzymatic activities of CsCCD1a, CsCCD1b, and CsCCD4 enzymes were determined by Escherichia coli expression, and subsequent analysis of the volatile products was generated by GC/MS. The four CCDs fell in two phylogenetically divergent dioxygenase classes, but all could cleave beta-carotene at the 9,10(9',10') positions to yield beta-ionone. The data obtained suggest that all four C. sativus CCD enzymes may contribute in different ways to the production of beta-ionone. In addition, the location and precise timing of beta-ionone synthesis, together with its known activity as a fragrance and insect attractant, suggest that this volatile may have a role in Crocus pollination.

  3. Localization of the human indoleamine 2,3-dioxygenase (IDO) gene to the pericentromeric region of human chromosome 8

    Energy Technology Data Exchange (ETDEWEB)

    Burkin, D.J.; Jones, C. (Eleanor Roosevelt Institute for Cancer Research, Denver, CO (United States)); Kimbro, K.S.; Taylor, M.W. (Indiana Univ., Bloomington, IN (United States)); Barr, B.L.; Gupta, S.L. (Hipple Cancer Research Center, Dayton, OH (United States))

    1993-07-01

    Indoleamine 2,3-dioxygenase (IDO) is the first enzyme in the catabolic pathway for tryptophan. This extrahepatic enzyme differs from the hepatic enzyme, tryptophan 2,3-dioxygenase (TDO), in molecular as well as enzymatic characteristics, although both enzymes catalyze the same reaction: cleavage of tryptophan into N-formylkynurenine. The induction of IDO by IFN-[gamma] plays a role in the antigrowth effect of IFN-[gamma] in cell cultures and in the inhibition of intracellular pathogens, e.g., Toxoplasma gondii and Chlamydia psittaci. Tryptophan is also the precursor for the synthesis of serotonin, and reduced levels of tryptophan and serotonin found in AIDS patients have been correlated with the presence of IFN-[gamma] and consequent elevation of IDO activity. The IDO enzyme has been purified and characterized, and its cDNA and genomic DNA clones have been isolated and analyzed. DNA from hybrid cells containing fragments of human chromosome 8 was used to determine the regional localization of the IDO gene on chromosome 8. The hybrids R30-5B and R30-2A contain 8p11 [yields] qter and 8q13 [yields] qter, respectively. Hybrid 229-3A contains the 8pter [yields] q11. The hybrid R30-2A was negative for the IDO gene, whereas R30-5B and 229-3A were positive as analyzed by PCR and verified by Southern blotting. Only the region close to the centromere is shared by R30-5B and 229-3A hybrids. The results indicate that the IDO gene is located on chromosome 8p11 [yields] q11.

  4. Redox proteins of hydroxylating bacterial dioxygenases establish a regulatory cascade that prevents gratuitous induction of tetralin biodegradation genes

    Science.gov (United States)

    Ledesma-García, Laura; Sánchez-Azqueta, Ana; Medina, Milagros; Reyes-Ramírez, Francisca; Santero, Eduardo

    2016-01-01

    Bacterial dioxygenase systems are multicomponent enzymes that catalyze the initial degradation of many environmentally hazardous compounds. In Sphingopyxis granuli strain TFA tetralin dioxygenase hydroxylates tetralin, an organic contaminant. It consists of a ferredoxin reductase (ThnA4), a ferredoxin (ThnA3) and a oxygenase (ThnA1/ThnA2), forming a NAD(P)H–ThnA4–ThnA3–ThnA1/ThnA2 electron transport chain. ThnA3 has also a regulatory function since it prevents expression of tetralin degradation genes (thn) in the presence of non-metabolizable substrates of the catabolic pathway. This role is of physiological relevance since avoids gratuitous and wasteful production of catabolic enzymes. Our hypothesis for thn regulation implies that ThnA3 exerts its action by diverting electrons towards the regulator ThnY, an iron-sulfur flavoprotein that together with the transcriptional activator ThnR is necessary for thn gene expression. Here we analyze electron transfer among ThnA4, ThnA3 and ThnY by using stopped-flow spectrophotometry and determination of midpoint reduction potentials. Our results indicate that when accumulated in its reduced form ThnA3 is able to fully reduce ThnY. In addition, we have reproduced in vitro the regulatory circuit in the proposed physiological direction, NAD(P)H–ThnA4–ThnA3–ThnY. ThnA3 represents an unprecedented way of communication between a catabolic pathway and its regulatory system to prevent gratuitous induction. PMID:27030382

  5. Crystal Structure and Mechanism of Tryptophan 2,3-Dioxygenase, a Heme Enzyme Involved in Tryptophan Catabolism and in Quinolinate Biosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Zhang,Y.; Kang, S.; Mukherjee, T.; Bale, S.; Crane, B.; Begley, T.; Ealick, S.

    2007-01-01

    The structure of tryptophan 2,3-dioxygenase (TDO) from Ralstonia metallidurans was determined at 2.4 {angstrom}. TDO catalyzes the irreversible oxidation of L-tryptophan to N-formyl kynurenine, which is the initial step in tryptophan catabolism. TDO is a heme-containing enzyme and is highly specific for its substrate L-tryptophan. The structure is a tetramer with a heme cofactor bound at each active site. The monomeric fold, as well as the heme binding site, is similar to that of the large domain of indoleamine 2,3-dioxygenase, an enzyme that catalyzes the same reaction except with a broader substrate tolerance. Modeling of the putative (S)-tryptophan hydroperoxide intermediate into the active site, as well as substrate analogue and mutagenesis studies, are consistent with a Criegee mechanism for the reaction.

  6. Blockage of indoleamine 2,3-dioxygenase regulates Japanese encephalitis via enhancement of type I/II IFN innate and adaptive T-cell responses

    OpenAIRE

    2016-01-01

    Background Japanese encephalitis (JE), a leading cause of viral encephalitis, is characterized by extensive neuroinflammation following infection with neurotropic JE virus (JEV). Indoleamine 2,3-dioxygenase (IDO) has been identified as an enzyme associated with immunoregulatory function. Although the regulatory role of IDO in viral replication has been postulated, the in vivo role of IDO activity has not been fully addressed in neurotropic virus-caused encephalitis. Methods Mice in which IDO ...

  7. Analysis of multi-domain hypothetical proteins containing iron-sulphur clusters and fad ligands reveal rieske dioxygenase activity suggesting their plausible roles in bioremediation.

    Science.gov (United States)

    Sathyanarayanan, Nitish; Nagendra, Holenarasipur Gundurao

    2012-01-01

    'Conserved hypothetical' proteins pose a challenge not just for functional genomics, but also to biology in general. As long as there are hundreds of conserved proteins with unknown function in model organisms such as Escherichia coli, Bacillus subtilis or Saccharomyces cerevisiae, any discussion towards a 'complete' understanding of these biological systems will remain a wishful thinking. Insilico approaches exhibit great promise towards attempts that enable appreciating the plausible roles of these hypothetical proteins. Among the majority of genomic proteins, two-thirds in unicellular organisms and more than 80% in metazoa, are multi-domain proteins, created as a result of gene duplication events. Aromatic ring-hydroxylating dioxygenases, also called Rieske dioxygenases (RDOs), are class of multi-domain proteins that catalyze the initial step in microbial aerobic degradation of many aromatic compounds. Investigations here address the computational characterization of hypothetical proteins containing Ferredoxin and Flavodoxin signatures. Consensus sequence of each class of oxidoreductase was obtained by a phylogenetic analysis, involving clustering methods based on evolutionary relationship. A synthetic sequence was developed by combining the consensus, which was used as the basis to search for their homologs via BLAST. The exercise yielded 129 multidomain hypothetical proteins containing both 2Fe-2S (Ferredoxin) and FNR (Flavodoxin) domains. In the current study, 40 proteins with N-terminus 2Fe-2S domain and C-terminus FNR domain are characterized, through homology modelling and docking exercises which suggest dioxygenase activity indicating their plausible roles in degradation of aromatic moieties.

  8. A murine model for type III tyrosinemia: lack of immunologically detectable 4-hydroxyphenylpyruvic acid dioxygenase enzyme protein in a novel mouse strain with hypertyrosinemia.

    Science.gov (United States)

    Endo, F; Katoh, H; Yamamoto, S; Matsuda, I

    1991-04-01

    We have characterized a new mutant strain of mouse that has hypertyrosinemia. The blood tyrosine level was persistently high, and increased amounts of 4-hydroxyphenylpyruvic acid and its derivatives were excreted into the urine. Succinylacetone was not detected in urine samples from these mice. All the animals were apparently healthy, and there was no evidence of hepatorenal dysfunction. The hypertyrosinemia was transmitted through an autosomal recessive inheritance. Analyses of hepatic enzymes related to tyrosine metabolism revealed that 4-hydroxyphenylpyruvic acid dioxygenase activity was virtually absent, while fumarylacetoacetase and tyrosine aminotransferases (cytosolic and mitochondrial forms) were normal in these mutant mice. Immunoblot analysis of 4-hydroxyphenylpyruvic acid dioxygenase protein in the liver indicated that the subunit protein of the enzyme was absent. It would appear that hypertyrosinemia in this mutant strain was caused by a genetic defect in 4-hydroxyphenylpyruvic acid dioxygenase. These features are similar to type III tyrosinemia in humans. Analysis of this mutant strain of mouse is expected to provide valuable information on the pathogenesis of human type III tyrosinemia and can also serve as a useful system for studies on tyrosine metabolism.

  9. The mitochondrial sulfur dioxygenase ETHYLMALONIC ENCEPHALOPATHY PROTEIN1 is required for amino acid catabolism during carbohydrate starvation and embryo development in Arabidopsis.

    Science.gov (United States)

    Krüßel, Lena; Junemann, Johannes; Wirtz, Markus; Birke, Hannah; Thornton, Jeremy D; Browning, Luke W; Poschet, Gernot; Hell, Rüdiger; Balk, Janneke; Braun, Hans-Peter; Hildebrandt, Tatjana M

    2014-05-01

    The sulfur dioxygenase ETHYLMALONIC ENCEPHALOPATHY PROTEIN1 (ETHE1) catalyzes the oxidation of persulfides in the mitochondrial matrix and is essential for early embryo development in Arabidopsis (Arabidopsis thaliana). We investigated the biochemical and physiological functions of ETHE1 in plant metabolism using recombinant Arabidopsis ETHE1 and three transfer DNA insertion lines with 50% to 99% decreased sulfur dioxygenase activity. Our results identified a new mitochondrial pathway catalyzing the detoxification of reduced sulfur species derived from cysteine catabolism by oxidation to thiosulfate. Knockdown of the sulfur dioxygenase impaired embryo development and produced phenotypes of starvation-induced chlorosis during short-day growth conditions and extended darkness, indicating that ETHE1 has a key function in situations of high protein turnover, such as seed production and the use of amino acids as alternative respiratory substrates during carbohydrate starvation. The amino acid profile of mutant plants was similar to that caused by defects in the electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase complex and associated dehydrogenases. Thus, in addition to sulfur amino acid catabolism, ETHE1 also affects the oxidation of branched-chain amino acids and lysine.

  10. Tryptophan 2,3-dioxygenase (TDO)-reactive T cells differ in their functional characteristics in health and cancer

    Science.gov (United States)

    Hjortsø, Mads Duus; Larsen, Stine Kiaer; Kongsted, Per; Met, Özcan; Frøsig, Thomas Mørch; Andersen, Gitte Holmen; Ahmad, Shamaila Munir; Svane, Inge Marie; Becker, Jürgen C; Straten, Per thor; Andersen, Mads Hald

    2015-01-01

    Tryptophan-2,3-dioxygenase (TDO) physiologically regulates systemic tryptophan levels in the liver. However, numerous studies have linked cancer with activation of local and systemic tryptophan metabolism. Indeed, similar to other heme dioxygenases TDO is constitutively expressed in many cancers. In the present study, we detected the presence of both CD8+ and CD4+ T-cell reactivity toward TDO in peripheral blood of patients with malignant melanoma (MM) or breast cancer (BC) as well as healthy subjects. However, TDO-reactive CD4+ T cells constituted distinct functional phenotypes in health and disease. In healthy subjects these cells predominately comprised interferon (IFN)γ and tumor necrosis factor (TNF)-α producing Th1 cells, while in cancer patients TDO-reactive CD4+ T-cells were more differentiated with release of not only IFNγ and TNFα, but also interleukin (IL)-17 and IL-10 in response to TDO-derived MHC-class II restricted peptides. Hence, in healthy donors (HD) a Th1 helper response was predominant, whereas in cancer patients CD4+ T-cell responses were skewed toward a regulatory T cell (Treg) response. Furthermore, MM patients hosting a TDO-specific IL-17 response showed a trend toward an improved overall survival (OS) compared to MM patients with IL-10 producing, TDO-reactive CD4+ T cells. For further characterization, we isolated and expanded both CD8+ and CD4+ TDO-reactive T cells in vitro. TDO-reactive CD8+ T cells were able to kill HLA-matched tumor cells of different origin. Interestingly, the processed and presented TDO-derived epitopes varied between different cancer cells. With respect to CD4+ TDO-reactive T cells, in vitro expanded T-cell cultures comprised a Th1 and/or a Treg phenotype. In summary, our data demonstrate that the immune modulating enzyme TDO is a target for CD8+ and CD4+ T cell responses both in healthy subjects as well as patients with cancer; notably, however, the functional phenotype of these T-cell responses differ

  11. Expression of tryptophan 2,3-dioxygenase in mature granule cells of the adult mouse dentate gyrus

    Directory of Open Access Journals (Sweden)

    Ohira, Koji

    2010-09-01

    Full Text Available Abstract New granule cells are continuously generated in the dentate gyrus of the adult hippocampus. During granule cell maturation, the mechanisms that differentiate new cells not only describe the degree of cell differentiation, but also crucially regulate the progression of cell differentiation. Here, we describe a gene, tryptophan 2,3-dioxygenase (TDO, whose expression distinguishes stem cells from more differentiated cells among the granule cells of the adult mouse dentate gyrus. The use of markers for proliferation, neural progenitors, and immature and mature granule cells indicated that TDO was expressed in mature cells and in some immature cells. In mice heterozygous for the alpha-isoform of calcium/calmodulin-dependent protein kinase II, in which dentate gyrus granule cells fail to mature normally, TDO immunoreactivity was substantially downregulated in the dentate gyrus granule cells. Moreover, a 5-bromo-2'-deoxyuridine labeling experiment revealed that new neurons began to express TDO between 2 and 4 wk after the neurons were generated, when the axons and dendrites of the granule cells developed and synaptogenesis occurred. These findings indicate that TDO might be required at a late-stage of granule cell development, such as during axonal and dendritic growth, synaptogenesis and its maturation.

  12. 4-hydroxyphenylpyruvate dioxygenase catalysis: identification of catalytic residues and production of a hydroxylated intermediate shared with a structurally unrelated enzyme.

    Science.gov (United States)

    Raspail, Corinne; Graindorge, Matthieu; Moreau, Yohann; Crouzy, Serge; Lefèbvre, Bertrand; Robin, Adeline Y; Dumas, Renaud; Matringe, Michel

    2011-07-22

    4-Hydroxyphenylpyruvate dioxygenase (HPPD) catalyzes the conversion of 4-hydroxyphenylpyruvate (HPP) into homogentisate. HPPD is the molecular target of very effective synthetic herbicides. HPPD inhibitors may also be useful in treating life-threatening tyrosinemia type I and are currently in trials for treatment of Parkinson disease. The reaction mechanism of this key enzyme in both plants and animals has not yet been fully elucidated. In this study, using site-directed mutagenesis supported by quantum mechanical/molecular mechanical theoretical calculations, we investigated the role of catalytic residues potentially interacting with the substrate/intermediates. These results highlight the following: (i) the central role of Gln-272, Gln-286, and Gln-358 in HPP binding and the first nucleophilic attack; (ii) the important movement of the aromatic ring of HPP during the reaction, and (iii) the key role played by Asn-261 and Ser-246 in C1 hydroxylation and the final ortho-rearrangement steps (numbering according to the Arabidopsis HPPD crystal structure 1SQD). Furthermore, this study reveals that the last step of the catalytic reaction, the 1,2 shift of the acetate side chain, which was believed to be unique to the HPPD activity, is also catalyzed by a structurally unrelated enzyme.

  13. P-HYDROXYPHENYLPYRUVATE DIOXYGENASE from Medicago sativa is involved in vitamin E biosynthesis and abscisic acid-mediated seed germination

    Science.gov (United States)

    Jiang, Jishan; Chen, Zhihong; Ban, Liping; Wu, Yudi; Huang, Jianping; Chu, Jinfang; Fang, Shuang; Wang, Zan; Gao, Hongwen; Wang, Xuemin

    2017-01-01

    P-HYDROXYPHENYLPYRUVATE DIOXYGENASE (HPPD) is the first committed enzyme involved in the biosynthesis of vitamin E, and is characterized by catalyzing the conversion of p-hydroxyphenyl pyruvate (HPP) to homogentisic acid (HGA). Here, an HPPD gene was cloned from Medicago sativa L. and designated MsHPPD, which was expressed at high levels in alfalfa leaves. PEG 6000 (polyethylene glycol), NaCl, abscisic acid and salicylic acid were shown to significantly induce MsHPPD expression, especially in the cotyledons and root tissues. Overexpression of MsHPPD was found to significantly increase the level of β-tocotrienol and the total vitamin E content in Arabidopsis seeds. Furthermore, these transgenic Arabidopsis seeds exhibited an accelerated germination time, compared with wild-type seeds under normal conditions, as well as under NaCl and ABA treatments. Meanwhile, the expression level of several genes associated with ABA biosynthesis (NCED3, NCED5 and NCED9) and the ABA signaling pathway (RAB18, ABI3 and ABI5) were significantly down-regulated in MsHPPD-overexpressing transgenic lines, as well as the total free ABA content. Taken together, these results demonstrate that MsHPPD functions not only in the vitamin E biosynthetic pathway, but also plays a critical role in seed germination via affecting ABA biosynthesis and signaling. PMID:28084442

  14. Reaction mechanism of homoprotocatechuate 2,3-dioxygenase with 4-nitrocatechol: implications for the role of substrate.

    Science.gov (United States)

    Dong, Geng; Lai, Wenzhen

    2014-02-20

    The reaction mechanism of the dioxygen activation by homoprotocatechuate 2,3-dioxygenase (HPCD) with the substrate 4-nitrocatechol was investigated by quantum mechanical/molecular mechanical calculations. Our results demonstrated that the experimentally determined side-on iron-oxygen complex in crystallo is a semiquinone substrate radical (SQ(•))-Fe(III)-hydroperoxo species, which could not act as the reactive species. In fact, the Fe(III)-superoxo species with a hydrogen bond between His200 and the proximal oxygen is the reactive oxygen species. The second-sphere His200 residue was found to play an important role in manipulating the orientation of the superoxide in the Fe-O2 adduct for the further reaction. The rate-limiting step is the attack of the superoxo group on the substrate with a barrier of 17.2 kcal/mol, in good agreement with the experimental value of 16.8 kcal/mol. The reaction mechanism was then compared with the one for HPCD with its native substrate homoprotocatechuate studied recently by the same methods, in which a hybrid SQ(•)-Fe(II)-O2(•-)/Fe(III)-O2(•-) was suggested to be the reactive species. Therefore, our studies suggested that the substrate plays important roles in the dioxygen activation by HPCD.

  15. Absolute configuration-dependent epoxide formation from isoflavan-4-ol stereoisomers by biphenyl dioxygenase of Pseudomonas pseudoalcaligenes strain KF707.

    Science.gov (United States)

    Seo, Jiyoung; Kang, Su-Il; Won, Dongho; Kim, Mihyang; Ryu, Ji-Young; Kang, Suk-Woo; Um, Byung-Hun; Pan, Cheol-Ho; Ahn, Joong-Hoon; Chong, Youhoon; Kanaly, Robert A; Han, Jaehong; Hur, Hor-Gil

    2011-03-01

    Biphenyl dioxygenase from Pseudomonas pseudoalcaligenes strain KF707 expressed in Escherichia coli was found to exhibit monooxygenase activity toward four stereoisomers of isoflavan-4-ol. LC-MS and LC-NMR analyses of the metabolites revealed that the corresponding epoxides formed between C2' and C3' on the B-ring of each isoflavan-4-ol substrate were the sole products. The relative reactivity of the stereoisomers was found to be in the order: (3S,4S)-cis-isoflavan-4-ol > (3R,4S)-trans-isoflavan-4-ol > (3S,4R)-trans-isoflavan-4-ol > (3R,4R)-cis-isoflavan-4-ol and this likely depended upon the absolute configuration of the 4-OH group on the isoflavanols, as explained by an enzyme-substrate docking study. The epoxides produced from isoflavan-4-ols by P. pseudoalcaligenes strain KF707 were further abiotically transformed into pterocarpan, the molecular structure of which is commonly found as part of plant-protective phytoalexins, such as maackiain from Cicer arietinum and medicarpin from Medicago sativa.

  16. Transgenic Leucaena leucocephala expressing the Rhizobium gene pydA encoding a meta-cleavage dioxygenase shows reduced mimosine content.

    Science.gov (United States)

    Jube, Sandro L R; Borthakur, Dulal

    2010-04-01

    The use of the tree-legume Leucaena leucocephala (leucaena), which contains high levels of proteins in its foliage, is limited due to the presence of the toxic free amino acid mimosine. The goal of this research was to develop transgenic leucaena with reduced mimosine content. Two genes, pydA and pydB, encoding a meta-cleavage dioxygenase (EC 1.13.11.2) and a pyruvate hydrolase (EC 3.7.1.6), respectively, from the mimosine-degrading leucaena symbiont Rhizobium sp. strain TAL1145, were used to transform leucaena. These bacterial genes were sequence-optimized for expression in leucaena and cloned into the plant binary vector pCAMBIA3201 for Agrobacterium tumefaciens-mediated transformation. Using immature zygotic embryos as the start explant material, six pydA and three pydB transgenic lines were developed. The presence and expression of the bacterial genes in the transgenic lines were verified by PCR, reverse transcriptase PCR, and Southern analyses. HPLC analyses of the transgenic plants determined that the mimosine contents of the pydA-expressing lines were reduced up to 22.5% in comparison to the wild-type. No significant reduction in mimosine content was observed in the pydB-expressing lines. This is the first example of using a gene from a bacterial symbiont to reduce the toxicity of a tree-legume.

  17. Eucalyptus ESTs involved in the production of 9-cis epoxycarotenoid dioxygenase, a regulatory enzyme of abscisic acid production

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    Iraê A. Guerrini

    2005-01-01

    Full Text Available Abscisic acid (ABA regulates stress responses in plants, and genomic tools can help us to understand the mechanisms involved in that process. FAPESP, a Brazilian research foundation, in association with four private forestry companies, has established the FORESTs database (https://forests.esalq.usp.br. A search was carried out in the Eucalyptus expressed sequence tag database to find ESTs involved with 9-cis epoxycarotenoid dioxygenase (NCED, the regulatory enzyme for ABA biosynthesis, using the basic local BLAST alignment tool. We found four clusters (EGEZLV2206B11.g, EGJMWD2252H08.g, EGBFRT3107F10.g, and EGEQFB1200H10.g, which represent similar sequences of the gene that produces NCED. Data showed that the EGBFRT3107F10.g cluster was similar to the maize (Zea mays NCED enzyme, while EGEZLV2206B11.g and EGJMWD2252H08.g clusters were similar to the avocado (Persea americana NCED enzyme. All Eucalyptus clusters were expressed in several tissues, especially in flower buds, where ABA has a special participation during the floral development process.

  18. Structural characterization of Pandoraea pnomenusa B-356 biphenyl dioxygenase reveals features of potent polychlorinated biphenyl-degrading enzymes.

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    Christopher L Colbert

    Full Text Available The oxidative degradation of biphenyl and polychlorinated biphenyls (PCBs is initiated in Pandoraea pnomenusa B-356 by biphenyl dioxygenase (BPDO(B356. BPDO(B356, a heterohexameric (αβ(3 Rieske oxygenase (RO, catalyzes the insertion of dioxygen with stereo- and regioselectivity at the 2,3-carbons of biphenyl, and can transform a broad spectrum of PCB congeners. Here we present the X-ray crystal structures of BPDO(B356 with and without its substrate biphenyl 1.6-Å resolution for both structures. In both cases, the Fe(II has five ligands in a square pyramidal configuration: H233 Nε2, H239 Nε2, D386 Oδ1 and Oδ2, and a single water molecule. Analysis of the active sites of BPDO(B356 and related ROs revealed structural features that likely contribute to the superior PCB-degrading ability of certain BPDOs. First, the active site cavity readily accommodates biphenyl with minimal conformational rearrangement. Second, M231 was predicted to sterically interfere with binding of some PCBs, and substitution of this residue yielded variants that transform 2,2'-dichlorobiphenyl more effectively. Third, in addition to the volume and shape of the active site, residues at the active site entrance also apparently influence substrate preference. Finally, comparison of the conformation of the active site entrance loop among ROs provides a basis for a structure-based classification consistent with a phylogeny derived from amino acid sequence alignments.

  19. Scavenging properties of neutrophil 4-hydroxyphenylpyruvate dioxygenase are based on a hypothesis that does not stand up to scrutiny.

    Science.gov (United States)

    Salerno, Costantino; Zicari, Alessandra; Mari, Emanuela; D'Eufemia, Patrizia

    2014-10-01

    It was previously reported by D'Eufemia et al. [9] that neutrophil preparations from a patient with tyrosinemia type III, i.e. with inherited deficiency of 4-hydroxyphenylpyruvate dioxygenase (HPPD), exhibited a far higher NO release than controls, when NO was estimated in terms of nitrite content in the suspending media. It was hypothesized that HPPD might participate to NO sequestration in neutrophils and that excessive NO release might reflect the lack of the scavenging action in defective cells. In recent control experiments, we found that HPPD activity in neutrophils preparations from healthy subjects is below the detection limit of the enzymatic assay (less than 3nmol product/h per mg protein). This indicates that HPPD concentration in neutrophils is very low, if any, confirming what was already suggested in literature, and rules out the possibility of a prominent role of HPPD as NO scavenger in these cells. Moreover, we found that 500μM l-tyrosine increases nitrite release and accumulation in suspending media of U-937 cells, a human monoblast-like lymphoma cell line which displays many characteristics of macrophages, including the expression of inducible and endothelial nitric oxide synthases. We hypothesize that the increase of nitrite release by patient's neutrophils might be related to the presence of high l-tyrosine concentrations in the blood samples (426μmol/L instead of 52.1±10.9μmol/L as healthy subjects), rather than to HPPD deficiency of in these cells.

  20. Triterpenoids isolated from the rhizomes and roots of Gentiana scabra and their inhibition of indoleamine 2,3-dioxygenase.

    Science.gov (United States)

    Li, Wei; Li, Lin Ying; Zhou, Wei; Hwang, Inkyu; Ma, Jin Yeul; Kim, Young Ho

    2015-12-01

    Gentiana scabra Bunge (Gentianaceae) is an important traditional Chinese medicine commonly used as a stomachic or appetite stimulant. In this study, 21 triterpenoids (1-21) were isolated from a methanol extract of the rhizomes and roots of G. scabra. Their structures were elucidated by comparing spectroscopic data with reported values. Among the isolated triterpenoids, scabanol (2) was firstly isolated from natural sources. All isolated compounds were evaluated for their inhibitory activity against indoleamine 2,3-dioxygenase (IDO), which catalyzes the rate limiting reaction for the conversion of tryptophan to kynurenine. Compounds 10 and 11 showed significant inhibitory activities, with IC(50) values of 12.5 and 9.5 μM, respectively. Compound 12 showed a moderate inhibitory effect, with an IC(50) value of 18.7 μM. Compounds 2 and 13 showed weaker inhibitory effects, with IC(50) values of 56.8 and 60.6 μM, respectively. Kynurenine is a potent immune modulator to suppress the functions of a variety of immune cells including T cells and natural killer cells. Given that, our results that a few selected triterpenoids inhibit IDO warrant further studies on their effects on the host immune system as natural immune stimulators.

  1. New insight into the cleavage reaction of Nostoc sp. strain PCC 7120 carotenoid cleavage dioxygenase in natural and nonnatural carotenoids.

    Science.gov (United States)

    Heo, Jinsol; Kim, Se Hyeuk; Lee, Pyung Cheon

    2013-06-01

    Carotenoid cleavage dioxygenases (CCDs) are enzymes that catalyze the oxidative cleavage of carotenoids at a specific double bond to generate apocarotenoids. In this study, we investigated the activity and substrate preferences of NSC3, a CCD of Nostoc sp. strain PCC 7120, in vivo and in vitro using natural and nonnatural carotenoid structures. NSC3 cleaved β-apo-8'-carotenal at 3 positions, C-13 C-14, C-15 C-15', and C-13' C-14', revealing a unique cleavage pattern. NSC3 cleaves the natural structure of carotenoids 4,4'-diaponeurosporene, 4,4'-diaponeurosporen-4'-al, 4,4'-diaponeurosporen-4'-oic acid, 4,4'-diapotorulene, and 4,4'-diapotorulen-4'-al to generate novel cleavage products (apo-14'-diaponeurosporenal, apo-13'-diaponeurosporenal, apo-10'-diaponeurosporenal, apo-14'-diapotorulenal, and apo-10'-diapotorulenal, respectively). The study of carotenoids with natural or nonnatural structures produced by using synthetic modules could provide information valuable for understanding the cleavage reactions or substrate preferences of other CCDs in vivo and in vitro.

  2. Ring-hydroxylating dioxygenase (RHD) expression in a microbial community during the early response to oil pollution.

    Science.gov (United States)

    Paissé, Sandrine; Goñi-Urriza, Marisol; Stalder, Thibault; Stadler, Thibault; Budzinski, Hélène; Duran, Robert

    2012-04-01

    The early functional response of a bacterial community from the sediments of a chronically oil-polluted retention basin located at the Etang de Berre (France) was investigated just after petroleum addition. After removing hydrocarbon compounds by natural abiotic and biotic processes, the sediments were maintained in microcosms and Vic Bilh petroleum was added. The diversity and the expression of genes encoding ring-hydroxylating dioxygenases (RHD) were examined just after the petroleum addition until 14 days focussing on the first hours following the contamination. RHD gene copy numbers and diversity were maintained throughout all the incubation period; however, transcripts were detected only during the first 2 days. One dominant RHD gene, immediately and specifically expressed in response to petroleum contamination, was related to RHD gene carried by a plasmid found in Pseudomonas spp. The expression of the RHD genes was correlated with high biodegradation levels observed for low molecular weight PAHs at 7 days of incubation. The study shows that the bacterial metabolism induced just after the oil input is a key stage that could determine the bacterial community structure changes. Monitoring the expression of RHD genes, key genes involved in hydrocarbon degradation, may provide useful information for managing bioremediation processes.

  3. The carotenoid cleavage dioxygenase CCD2 catalysing the synthesis of crocetin in spring crocuses and saffron is a plastidial enzyme.

    Science.gov (United States)

    Ahrazem, Oussama; Rubio-Moraga, Angela; Berman, Judit; Capell, Teresa; Christou, Paul; Zhu, Changfu; Gómez-Gómez, Lourdes

    2016-01-01

    The apocarotenoid crocetin and its glycosylated derivatives, crocins, confer the red colour to saffron. Crocetin biosynthesis in saffron is catalysed by the carotenoid cleavage dioxygenase CCD2 (AIG94929). No homologues have been identified in other plant species due to the very limited presence of crocetin and its derivatives in the plant kingdom. Spring Crocus species with yellow flowers accumulate crocins in the stigma and tepals. Four carotenoid CCDs, namely CaCCD1, CaCCD2 and CaCCD4a/b and CaCCD4c were first cloned and characterized. CaCCD2 was localized in plastids, and a longer CCD2 version, CsCCD2L, was also localized in this compartment. The activity of CaCCD2 was assessed in Escherichia coli and in a stable rice gene function characterization system, demonstrating the production of crocetin in both systems. The expression of all isolated CCDs was evaluated in stigma and tepals at three key developmental stages in relation with apocarotenoid accumulation. CaCCD2 expression parallels crocin accumulation, but C14 apocarotenoids most likely are associated to the CaCCD1 activity in Crocus ancyrensis flowers. The specific CCD2 localization and its membrane interaction will contribute to the development of a better understanding of the mechanism of crocetin biosynthesis and regulation in the chromoplast.

  4. Altering substrate specificity of catechol 2,3-dioxygenase from Planococcus sp. strain S5 by random mutagenesis.

    Science.gov (United States)

    Hupert-Kocurek, Katarzyna; Wojcieszyńska, Danuta; Guzik, Urszula

    2014-01-01

    c23o gene, encoding catechol 2,3-dioxygenase from Planococcus sp. strain S5 was randomly mutagenized to generate variant forms of the enzyme with higher degradation activity. Additionally, the effect of introduced mutations on the enzyme structure was analyzed based on the putative 3D models the wild-type and mutant enzymes. C23OB58 and C23OB81 mutant proteins with amino acid substitutions in close proximity to the enzyme surface or at the interface and in the vicinity of the enzyme active site respectively showed the lowest activity towards all catecholic substrates. The relative activity of C23OC61 mutant towards para-substituted catechols was 20-30% lower of the wild-type enzyme. In this mutant all changes: F191I, C268R, Y272H, V280A and Y293D were located within the conserved regions of C-terminal domain. From these F191I seems to have significant implications for enzyme activity. The highest activity towards different catechols was found for mutant C23OB65. R296Q mutation improved the activity of C23O especially against 4-chlorocatechol. The relative activity of above-mentioned mutant detected against this substrate was almost 6-fold higher than the wild-type enzyme. These results should facilitate future engineering of the enzyme for bioremediation.

  5. Dynamic changes in bacterial community structure and in naphthalene dioxygenase expression in vermicompost-amended PAH-contaminated soils.

    Science.gov (United States)

    Di Gennaro, Patrizia; Moreno, Beatriz; Annoni, Emanuele; García-Rodríguez, Sonia; Bestetti, Giuseppina; Benitez, Emilio

    2009-12-30

    The aim of the present study was to explore the potential for using vermicompost from olive-mill waste as an organic amendment for enhanced bioremediation of polycyclic aromatic hydrocarbons (PAHs)-contaminated soils. The focus was to analyse the genetic potential and the naphthalene dioxygenase (NDO) expression of the bacterial communities involved in the degradation of naphthalene, as chemical model for the degradation of PAH. The structure of the metabolically active bacterial population was evidenced in the RNA-based denaturing gradient gel electrophoresis (DGGE) profiles. The relative expression of NDO was determined with real-time PCR in both the soil and the vermicompost cDNA. Naphthalene changed the structure of the metabolically active bacterial community in the vermicompost when this was artificially contaminated. When used as amendment, naphthalene-free vermicompost modified the bacterial population in the PAH-contaminated soil, evidenced in the DGGE gels after 1 month of incubation. In the amended soil, the vermicompost enhanced the NDO enzyme expression with a concomitant biodegradation of naphthalene. The effect of the vermicompost was to induce the expression of biodegradation indicator genes in the autochthonous bacterial community and/or incorporate new bacterial species capable of degrading PAH. The results indicated that vermicompost from olive-mill wastes could be considered a suitable technology to be used in PAH bioremediation.

  6. Diazotization of kynurenine by acidified nitrite secreted from indoleamine 2,3-dioxygenase-expressing myeloid dendritic cells.

    Science.gov (United States)

    Hara, Toshiaki; Yamakura, Fumiyuki; Takikawa, Osamu; Hiramatsu, Rie; Kawabe, Tsutomu; Isobe, Ken-Ichi; Nagase, Fumihiko

    2008-03-20

    Indoleamine 2,3-dioxygenase (IDO)-initiated tryptophan metabolism along the kynurenine (Kyn) pathway regulates T-cell responses in some dendritic cells (DC) such as plasmacytoid DC. A Kyn assay using HPLC showed that samples were frequently deproteinized with trichloroacetic acid (TCA). In the present study, bone marrow-derived myeloid DC (BMDC) were differentiated from mouse bone marrow cells with GM-CSF. CpG oligodeoxynucleotides (CpG) induced the expression of IDO protein with NO production in BMDC cultured for 24 h. The concentrations of Kyn in the culture supernatants were not increased by stimulation with CpG but rather decreased by based on the Kyn assay after deproteinization with TCA. The level of Kyn exogenously added into the cell-free culture supernatant of BMDC stimulated with CpG was severely decreased by deproteinization with TCA but not methanol, and the decrease was prevented when BMDC was stimulated with CpG in the presence of a NOS inhibitor. Under acidic conditions, Kyn reacted with nitrite produced by BMDC, and generated a new compound that was not detected by Ehrlich reagent reacting with the aromatic amino residue of Kyn. An analysis by mass spectrometry showed the new compound to be a diazotization form of Kyn. In conclusion, the deproteinization of samples by acidic treatment should be avoided for the Kyn assay when NO is produced.

  7. Relationship of Abortion and the Expression of Indoleamine 2,3- dioxygenase (IDO) in Villus and Syncytiotrophoblasts

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Objective To study the relationship of abortion and the expression of indoleamine 2,3- dioxygenase (IDO) in villus and syncytiotrophoblast in vitro.Methods RT-PCR was applied to analyze the mRNA transcription of IDO in villus of normal pregnancy and inevitable abortion and JAR cells as well. Immunohistochemistry was applied to analyze the expression of IDO protein in villus. Western blot was applied to determinate the expression of IDO protein on cultured syncytiotrophoblast. Highperformance liquid chromatography was applied to determinate whether there was kynurenine in cell culture medium of syncytiotrophoblast.Results The expression of IDO mRNA and protein in villus of inevitable abortion was lower than that of normal pregnancy; IDO mRNA did not express in JAR cells. IDO protein expressed on cultured syncytiotrophoblast, and there was kynurenine in cell culture medium of syncytiotrophoblast.Conclusion Appropriate expression of IDO in villus is necessary for maintenance of normal pregnancy and an active IDO protein expresses in syncytiotrophoblast.

  8. Eosinophil Granulocytes Account for Indoleamine 2,3-Dioxygenase-Mediated Immune Escape in Human Non Small Cell Lung Cancer

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    Simonetta Astigiano

    2005-04-01

    Full Text Available Indoleamine 2,3-dioxygenase (IDO, a catabolizing enzyme of tryptophan, is supposed to play a role in tumor immune escape. Its expression in solid tumors has not yet been well elucidated: IDO can be expressed by the tumor cells themselves, or by ill-defined infiltrating cells, possibly depending on tumor type. We have investigated IDO expression in 25 cases of non small cell lung cancer (NSCLC. Using histochemistry and immunohistochemistry, we found that IDO was expressed not by tumor cells, but by normal cells infiltrating the peritumoral stroma. These cells were neither macrophages nor dendritic cells, and were identified as eosinophil granulocytes. The amount of IDO-positive eosinophils varied in different cases, ranging from a few cells to more than 50 per field at x200 magnification. IDO protein in NSCLC was enzymatically active. Therefore, at least in NSCLC cases displaying a large amount of these cells in the inflammatory infiltrate, IDO-positive eosinophils could exert an effective immunosuppressive action. On analyzing the 17 patients with adequate follow-up, a significant relationship was found between the amount of IDO-positive infiltrate and overall survival. This finding suggests that the degree of IDO-positive infiltrate could be a prognostic marker in NSCLC.

  9. Patchwork assembly of nag-like nitroarene dioxygenase genes and the 3-chlorocatechol degradation cluster for evolution of the 2-chloronitrobenzene catabolism pathway in Pseudomonas stutzeri ZWLR2-1.

    Science.gov (United States)

    Liu, Hong; Wang, Shu-Jun; Zhang, Jun-Jie; Dai, Hui; Tang, Huiru; Zhou, Ning-Yi

    2011-07-01

    Pseudomonas stutzeri ZWLR2-1 utilizes 2-chloronitrobenzene (2CNB) as a sole source of carbon, nitrogen, and energy. To identify genes involved in this pathway, a 16.2-kb DNA fragment containing putative 2CNB dioxygenase genes was cloned and sequenced. Of the products from the 19 open reading frames that resulted from this fragment, CnbAc and CnbAd exhibited striking identities to the respective α and β subunits of the Nag-like ring-hydroxylating dioxygenases involved in the metabolism of nitrotoluene, nitrobenzene, and naphthalene. The encoding genes were also flanked by two copies of insertion sequence IS6100. CnbAa and CnbAb are similar to the ferredoxin reductase and ferredoxin for anthranilate 1,2-dioxygenase from Burkholderia cepacia DBO1. Escherichia coli cells expressing cnbAaAbAcAd converted 2CNB to 3-chlorocatechol with concomitant nitrite release. Cell extracts of E. coli/pCNBC exhibited chlorocatechol 1,2-dioxygenase activity. The cnbCDEF gene cluster, homologous to a 3-chlorocatechol degradation cluster in Sphingomonas sp. strain TFD44, probably contains all of the genes necessary for the conversion of 3-chlorocatechol to 3-oxoadipate. The patchwork-like structure of this catabolic cluster suggests that the cnb cluster for 2CNB degradation evolved by recruiting two catabolic clusters encoding a nitroarene dioxygenase and a chlorocatechol degradation pathway. This provides another example to help elucidate the bacterial evolution of catabolic pathways in response to xenobiotic chemicals.

  10. The Ternary Complex of PrnB (the Second Enzyme in the Pyrrolnitrin Biosynthesis Pathway), Tryptophan, and Cyanide Yields New Mechanistic Insights into the Indolamine Dioxygenase Superfamily*

    Science.gov (United States)

    Zhu, Xiaofeng; van Pée, Karl-Heinz; Naismith, James H.

    2010-01-01

    Pyrrolnitrin (3-chloro-4-(2′-nitro-3′-chlorophenyl)pyrrole) is a broad-spectrum antifungal compound isolated from Pseudomonas pyrrocinia. Four enzymes (PrnA, PrnB, PrnC, and PrnD) are required for pyrrolnitrin biosynthesis from tryptophan. PrnB rearranges the indole ring of 7-Cl-l-tryptophan and eliminates the carboxylate group. PrnB shows robust activity in vivo, but in vitro activity for PrnB under defined conditions remains undetected. The structure of PrnB establishes that the enzyme belongs to the heme b-dependent indoleamine 2,3-dioxygenase (IDO) and tryptophan 2,3-dioxygenase (TDO) family. We report the cyanide complex of PrnB and two ternary complexes with both l-tryptophan or 7-Cl-l-tryptophan and cyanide. The latter two complexes are essentially identical and mimic the likely catalytic ternary complex that occurs during turnover. In the cyanide ternary complexes, a loop previously disordered becomes ordered, contributing to the binding of substrates. The conformations of the bound tryptophan substrates are changed from that seen previously in the binary complexes. In l-tryptophan ternary complex, the indole ring now adopts the same orientation as seen in the PrnB binary complexes with other tryptophan substrates. The amide and carboxylate group of the substrate are orientated in a new conformation. Tyr321 and Ser332 play a key role in binding these groups. The structures suggest that catalysis requires an l-configured substrate. Isothermal titration calorimetry data suggest d-tryptophan does not bind after cyanide (or oxygen) coordinates with the distal (or sixth) site of heme. This is the first ternary complex with a tryptophan substrate of a member of the tryptophan dioxygenase superfamily and has mechanistic implications. PMID:20421301

  11. Purification and Characterization of Catechol 1,2-Dioxygenase from Acinetobacter sp. Y64 Strain and Escherichia coli Transformants.

    Science.gov (United States)

    Lin, J; Milase, R N

    2015-12-01

    This study intends to purify and characterize catechol 1,2-dioxygenase (C1,2O) of phenol-degrading Acinetobacter sp. Y64 and of E. coli transformant. Acinetobacter sp. Y64 was capable of degrading 1000 mg/L of phenol within 14 ± 2 h at 30 °C, 160 rpm and pH of 7. One C1,2O of 36 kDa was purified using ammonium sulphate precipitation and Hitrap QFF column chromatograph with 49% recovery and a 10.6-fold increase in purity. Purified Y64 C1,2O had temperature and pH optimum at 37 °C and pH 7.7 respectively with the Michaelis constant of 17.53 µM and the maximal velocity of 1.95 U/mg, respectively. The presence of Fe(3+) or Fe(2+) enhanced the activity of Y64 C1,2O while other compounds such as Ca(2+), and EDTA had an inhibitory effect. 80% of C1,2O activity remained using 4-nitrocatechol as substrate while 2% remained using 3-methylcatechol compared with that using catechol. Y64 catA gene encoding C1,2O was amplified using PCR cloned into pET22b vector and expressed in Escherichia coli BL21 DE3 (pLysS) after transformation. Purified and cloned Y64 C1,2O show no significant differences in the biochemical properties. The phylogenetic tree based on the protein sequences indicates that these C1,2Os possess a common ancestry.

  12. Structural Basis for Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine-200

    Science.gov (United States)

    Kovaleva, Elena G.; Rogers, Melanie S.; Lipscomb, John D.

    2015-01-01

    Kinetic and spectroscopic studies have shown that the conserved active site residue His200 of the extradiol ring-cleaving homoprotocatechuate 2,3-dioxygenase (FeHPCD) from Brevibacterium fuscum is critical for efficient catalysis. The roles played by this residue are probed here by analysis of the steady state kinetics, pH dependence, and X-ray crystal structures of the FeHPCD position 200 variants His200Asn, His200Gln, and His200Glu alone and in complex with three catecholic substrates (homoprotocatechuate, 4-sulfonylcatechol, and 4-nitrocatechol) possessing substituents with different inductive capacity. Structures solved at 1.35 –1.75 Å resolution show that there is essentially no change in overall active site architecture or substrate binding mode for these variants when compared to the structures of the wild type enzyme and its analogous complexes. This shows that the maximal 50-fold decrease in kcat for ring cleavage, the dramatic changes in pH dependence, and the switch from ring cleavage to ring oxidation of 4-nitrocatechol by the FeHPCD variants can be attributed specifically to the properties of the altered second sphere residue and the substrate. The results suggest that proton transfer is necessary for catalysis, and that it occurs most efficiently when the substrate provides the proton and His200 serves as a catalyst. However, in the absence of an available substrate proton, a defined proton-transfer pathway in the protein can be utilized. Changes in steric bulk and charge of the residue at position 200 appear capable of altering the rate-limiting step in catalysis, and perhaps, the nature of the reactive species. PMID:26267790

  13. Structural Basis for Substrate and Oxygen Activation in Homoprotocatechuate 2,3-Dioxygenase: Roles of Conserved Active Site Histidine 200.

    Science.gov (United States)

    Kovaleva, Elena G; Rogers, Melanie S; Lipscomb, John D

    2015-09-01

    Kinetic and spectroscopic studies have shown that the conserved active site residue His200 of the extradiol ring-cleaving homoprotocatechuate 2,3-dioxygenase (FeHPCD) from Brevibacterium fuscum is critical for efficient catalysis. The roles played by this residue are probed here by analysis of the steady-state kinetics, pH dependence, and X-ray crystal structures of the FeHPCD position 200 variants His200Asn, His200Gln, and His200Glu alone and in complex with three catecholic substrates (homoprotocatechuate, 4-sulfonylcatechol, and 4-nitrocatechol) possessing substituents with different inductive capacity. Structures determined at 1.35-1.75 Å resolution show that there is essentially no change in overall active site architecture or substrate binding mode for these variants when compared to the structures of the wild-type enzyme and its analogous complexes. This shows that the maximal 50-fold decrease in kcat for ring cleavage, the dramatic changes in pH dependence, and the switch from ring cleavage to ring oxidation of 4-nitrocatechol by the FeHPCD variants can be attributed specifically to the properties of the altered second-sphere residue and the substrate. The results suggest that proton transfer is necessary for catalysis, and that it occurs most efficiently when the substrate provides the proton and His200 serves as a catalyst. However, in the absence of an available substrate proton, a defined proton-transfer pathway in the protein can be utilized. Changes in the steric bulk and charge of the residue at position 200 appear to be capable of altering the rate-limiting step in catalysis and, perhaps, the nature of the reactive species.

  14. Prognostic Significance of Promoter DNA Hypermethylation of cysteine dioxygenase 1 (CDO1 Gene in Primary Breast Cancer.

    Directory of Open Access Journals (Sweden)

    Naoko Minatani

    Full Text Available Using pharmacological unmasking microarray, we identified promoter DNA methylation of cysteine dioxygenase 1 (CDO1 gene in human cancer. In this study, we assessed the clinicopathological significance of CDO1 methylation in primary breast cancer (BC with no prior chemotherapy. The CDO1 DNA methylation was quantified by TaqMan methylation specific PCR (Q-MSP in 7 BC cell lines and 172 primary BC patients with no prior chemotherapy. Promoter DNA of the CDO1 gene was hypermethylated in 6 BC cell lines except SK-BR3, and CDO1 gene expression was all silenced at mRNA level in the 7 BC cell lines. Quantification of CDO1 methylation was developed using Q-MSP, and assessed in primary BC. Among the clinicopathologic factors, CDO1 methylation level was not statistically significantly associated with any prognostic factors. The log-rank plot analysis elucidated that the higher methylation the tumors harbored, the poorer prognosis the patients exhibited. Using the median value of 58.0 as a cut-off one, disease specific survival in BC patients with CDO1 hypermethylation showed significantly poorer prognosis than those with hypomethylation (p = 0.004. Multivariate Cox proportional hazards model identified that CDO1 hypermethylation was prognostic factor as well as Ki-67 and hormone receptor status. The most intriguingly, CDO1 hypermethylation was of robust prognostic relevance in triple negative BC (p = 0.007. Promoter DNA methylation of CDO1 gene was robust prognostic indicator in primary BC patients with no prior chemotherapy. Prognostic relevance of the CDO1 promoter DNA methylation is worthy of being paid attention in triple negative BC cancer.

  15. High activity of indoleamine 2,3 dioxygenase enzyme predicts disease severity and case fatality in bacteremic patients.

    Science.gov (United States)

    Huttunen, Reetta; Syrjänen, Jaana; Aittoniemi, Janne; Oja, Simo S; Raitala, Annika; Laine, Janne; Pertovaara, Marja; Vuento, Risto; Huhtala, Heini; Hurme, Mikko

    2010-02-01

    Indoleamine 2,3-dioxygenase (IDO), which is the rate-limiting enzyme for tryptophan (trp) catabolism, may play a critical role in various inflammatory disorders. Recent studies on trauma patients have suggested that the degradation of trp is associated with the development of sepsis. The role of IDO activity in bacteremic patients is unclear. We studied IDO activity in 132 patients with bacteremia caused by Staphylococcus aureus, Streptococcus pneumoniae, beta-hemolytic streptococcae, or Eschericia coli. The serum concentrations of trp and its metabolite kynurenine (kyn) were measured by reverse-phase high-performance liquid chromatography 1 to 4 days after the positive blood culture and on recovery. The kyn-to-trp ratio (kyn/trp), reflecting the activity of the IDO enzyme, was calculated. The maximum value in the ratio for every patient during 1 to 4 days after positive blood culture was used in analysis. The maximum kyn/trp ratio was significantly higher in nonsurvivors versus those who survived (193.7 vs. 82.4 micromol/mmol; P = 0.001). The AUC(ROC) of maximal kyn/trp in the prediction of case fatality was 0.75 (95% confidence interval, 0.64-0.87), and the kyn/trp ratio at a cutoff level of 120 micromol/mmol showed 83% sensitivity and 69% specificity for fatal disease. A kyn/trp ratio greater than 120 micromol/mmol was associated with increased risk of death versus low (

  16. The cystine/glutamate antiporter regulates indoleamine 2,3-dioxygenase protein levels and enzymatic activity in human dendritic cells.

    Science.gov (United States)

    Mattox, Mildred L; D'Angelo, June A; Grimes, Zachary M; Fiebiger, Edda; Dickinson, Bonny L

    2012-11-30

    Indoleamine 2,3-dioxygenase (IDO) is the rate-limiting enzyme in the tryptophan-catabolizing pathway and a key regulator of peripheral immune tolerance. As the suppressive effects of IDO are predominantly mediated by dendritic cells (DCs) and IDO-competent DCs promote long-term immunologic tolerance, a detailed understanding of how IDO expression and activity is regulated in these cells is central to the rational design of therapies to induce robust immune tolerance. We previously reported that the cystine/glutamate antiporter modulates the functional expression of IDO in human monocyte-derived DCs. Specifically, we showed that blocking antiporter uptake of cystine significantly increased both IDO mRNA and IDO enzymatic activity and that this correlated with impaired DC presentation of exogenous antigen to T cells via MHC class II and the cross-presentation pathway. The antiporter regulates intracellular and extracellular redox by transporting cystine into the cell in exchange for glutamate. Intracellular cystine is reduced to cysteine to support biosynthesis of the major cellular antioxidant glutathione and cysteine is exported from the cell where it functions as an extracellular antioxidant. Here we show that antiporter control of IDO expression in DCs is reversible, independent of interferon-γ, regulated by redox, and requires active protein synthesis. These findings highlight a role for antiporter regulation of cellular redox as a critical control point for modulating IDO expression and activity in DCs. Thus, systemic disease and aging, processes that perturb redox homeostasis, may adversely affect immunity by promoting the generation of IDO-competent DCs.

  17. Respiratory Syncytial Virus-Infected Mesenchymal Stem Cells Regulate Immunity via Interferon Beta and Indoleamine-2,3-Dioxygenase

    Science.gov (United States)

    Cheung, Michael B.; Sampayo-Escobar, Viviana; Green, Ryan; Moore, Martin L.; Mohapatra, Subhra; Mohapatra, Shyam S.

    2016-01-01

    Respiratory syncytial virus (RSV) has been reported to infect human mesenchymal stem cells (MSCs) but the consequences are poorly understood. MSCs are present in nearly every organ including the nasal mucosa and the lung and play a role in regulating immune responses and mediating tissue repair. We sought to determine whether RSV infection of MSCs enhances their immune regulatory functions and contributes to RSV-associated lung disease. RSV was shown to replicate in human MSCs by fluorescence microscopy, plaque assay, and expression of RSV transcripts. RSV-infected MSCs showed differentially altered expression of cytokines and chemokines such as IL-1β, IL6, IL-8 and SDF-1 compared to epithelial cells. Notably, RSV-infected MSCs exhibited significantly increased expression of IFN-β (~100-fold) and indoleamine-2,3-dioxygenase (IDO) (~70-fold) than in mock-infected MSCs. IDO was identified in cytosolic protein of infected cells by Western blots and enzymatic activity was detected by tryptophan catabolism assay. Treatment of PBMCs with culture supernatants from RSV-infected MSCs reduced their proliferation in a dose dependent manner. This effect on PBMC activation was reversed by treatment of MSCs with the IDO inhibitors 1-methyltryptophan and vitamin K3 during RSV infection, a result we confirmed by CRISPR/Cas9-mediated knockout of IDO in MSCs. Neutralizing IFN-β prevented IDO expression and activity. Treatment of MSCs with an endosomal TLR inhibitor, as well as a specific inhibitor of the TLR3/dsRNA complex, prevented IFN-β and IDO expression. Together, these results suggest that RSV infection of MSCs alters their immune regulatory function by upregulating IFN-β and IDO, affecting immune cell proliferation, which may account for the lack of protective RSV immunity and for chronicity of RSV-associated lung diseases such as asthma and COPD. PMID:27695127

  18. Indoleamine 2,3-dioxygenase 1 (IDO1 activity correlates with immune system abnormalities in multiple myeloma

    Directory of Open Access Journals (Sweden)

    Bonanno Giuseppina

    2012-12-01

    Full Text Available Abstract Background Multiple myeloma (MM is a plasma cell malignancy with a multifaceted immune dysfunction. Indoleamine 2,3-dioxygenase 1 (IDO1 degrades tryptophan into kynurenine (KYN, which inhibits effector T cells and promote regulatory T-cell (Treg differentiation. It is presently unknown whether MM cells express IDO1 and whether IDO1 activity correlates with immune system impairment. Methods We investigated IDO1 expression in 25 consecutive patients with symptomatic MM and in 7 patients with either monoclonal gammopathy of unknown significance (MGUS; n=3 or smoldering MM (SMM; n=4. IDO1-driven tryptophan breakdown was correlated with the release of hepatocyte growth factor (HGF and with the frequency of Treg cells and NY-ESO-1-specific CD8+ T cells. Results KYN was increased in 75% of patients with symptomatic MM and correlated with the expansion of CD4+CD25+FoxP3+ Treg cells and the contraction of NY-ESO-1-specific CD8+ T cells. In vitro, primary MM cells promoted the differentiation of allogeneic CD4+ T cells into bona fide CD4+CD25hiFoxP3hi Treg cells and suppressed IFN-γ/IL-2 secretion, while preserving IL-4 and IL-10 production. Both Treg expansion and inhibition of Th1 differentiation by MM cells were reverted, at least in part, by d,l-1-methyl-tryptophan, a chemical inhibitor of IDO. Notably, HGF levels were higher within the BM microenvironment of patients with IDO+ myeloma disease compared with patients having IDO- MM. Mechanistically, the antagonism of MET receptor for HGF with SU11274, a MET inhibitor, prevented HGF-induced AKT phosphorylation in MM cells and translated into reduced IDO protein levels and functional activity. Conclusions These data suggest that IDO1 expression may contribute to immune suppression in patients with MM and possibly other HGF-producing cancers.

  19. Role of 9-Lipoxygenase and α-Dioxygenase Oxylipin Pathways as Modulators of Local and Systemic Defense

    Institute of Scientific and Technical Information of China (English)

    Jorge Vicente; Tomás Cascón; Begonya Vicedo; Pilar García-Agustín; Mats Hamberg; Carmen Castresana

    2012-01-01

    Plant 9-lipoxygenases(9-LOX)and α-dioxygenases(α-DOX)initiate the synthesis of oxylipins after bacterial infection.Here,the role of these enzymes in plants' defense was investigated using individual Arabidopsis thaliana lox1 and dox1 mutants and a double lox1 dox1 mutant.Studies with Pseudomonas syringae pv.tomato(Pst)revealed the enhanced susceptibility of lox1 to the virulent strain Pst DC3000 and the partial impairment of lox1 and dox1 mutants to activate systemic acquired resistance.Notably,both defects were enhanced in the lox1 dox1 plants as compared with individual mutants.We found that pre-treatment with 9-LOX- and α-DOX-generated oxylipins protected plant tissues against bacterial infection.The strongest effect in this respect was exerted by 9-ketooctadecatrienoic acid(9-KOT),which is produced from linolenic acid by 9-LOX.Quantification of 9-KOT revealed its accumulation after bacterial infection.The levels were reduced in lox1 and lox1 dox1 plants but strongly increased in the dox1 mutant due to metabolic interaction of the two pathways.Transcriptional analyses indicated that 9-KOT pre-treatment modifies hormone homeostasis during bacterial infection.The nature of the changes detected suggested that 9-KOT interferes with the hormonal changes caused by bacterial effectors.This notion was substantiated by the finding that 9-KOT failed to reduce the growth of PstDC3000hrpA,a mutant compromised in effector secretion,and of the avirulent strain Pst DC3000 avrRpm1.Further support for the action of the 9-LOX- and α-DOX-oxylipin pathways as modulators of hormone homeostasis was the observation that lox1 dox1 seedlings are hypersensitive to the growth-inhibitory effect of ABA and showed enhanced activation of ABA-inducible marker genes as compared with wild-type plants.

  20. An ancient relative of cyclooxygenase in cyanobacteria is a linoleate 10S-dioxygenase that works in tandem with a catalase-related protein with specific 10S-hydroperoxide lyase activity.

    Science.gov (United States)

    Brash, Alan R; Niraula, Narayan P; Boeglin, William E; Mashhadi, Zahra

    2014-05-09

    In the course of exploring the scope of catalase-related hemoprotein reactivity toward fatty acid hydroperoxides, we detected a novel candidate in the cyanobacterium Nostoc punctiforme PCC 73102. The immediate neighboring upstream gene, annotated as "cyclooxygenase-2," appeared to be a potential fatty acid heme dioxygenase. We cloned both genes and expressed the cDNAs in Escherichia coli, confirming their hemoprotein character. Oxygen electrode recordings demonstrated a rapid (>100 turnovers/s) reaction of the heme dioxygenase with oleic and linoleic acids. HPLC, including chiral column analysis, UV, and GC-MS of the oxygenated products, identified a novel 10S-dioxygenase activity. The catalase-related hemoprotein reacted rapidly and specifically with linoleate 10S-hydroperoxide (>2,500 turnovers/s) with a hydroperoxide lyase activity specific for the 10S-hydroperoxy enantiomer. The products were identified by NMR as (8E)10-oxo-decenoic acid and the C8 fragments, 1-octen-3-ol and 2Z-octen-1-ol, in ∼3:1 ratio. Chiral HPLC analysis established strict enzymatic control in formation of the 3R alcohol configuration (99% enantiomeric excess) and contrasted with racemic 1-octen-3-ol formed in reaction of linoleate 10S-hydroperoxide with hematin or ferrous ions. The Nostoc linoleate 10S-dioxygenase, the sequence of which contains the signature catalytic sequence of cyclooxygenases and fungal linoleate dioxygenases (YRWH), appears to be a heme dioxygenase ancestor. The novel activity of the lyase expands the known reactions of catalase-related proteins and functions in Nostoc in specific transformation of the 10S-hydroperoxylinoleate.

  1. Identification and characterization of genes encoding polycyclic aromatic hydrocarbon dioxygenase and polycyclic aromatic hydrocarbon dihydrodiol dehydrogenase in Pseudomonas putida OUS82.

    OpenAIRE

    Takizawa, N; Kaida, N; Torigoe, S; Moritani,T.; Sawada, T.; Satoh, S.; Kiyohara, H

    1994-01-01

    Naphthalene and phenanthrene are transformed by enzymes encoded by the pah gene cluster of Pseudomonas putida OUS82. The pahA and pahB genes, which encode the first and second enzymes, dioxygenase and cis-dihydrodiol dehydrogenase, respectively, were identified and sequenced. The DNA sequences showed that pahA and pahB were clustered and that pahA consisted of four cistrons, pahAa, pahAb, pahAc, and pahAd, which encode ferredoxin reductase, ferredoxin, and two subunits of the iron-sulfur prot...

  2. Spectroscopic and computational studies of NTBC bound to the non-heme iron enzyme (4-hydroxyphenyl)pyruvate dioxygenase: active site contributions to drug inhibition.

    Science.gov (United States)

    Neidig, Michael L; Decker, Andrea; Kavana, Michael; Moran, Graham R; Solomon, Edward I

    2005-12-01

    (4-Hydroxyphenyl)pyruvate dioxygenase (HPPD) is an alpha-keto-acid-dependent dioxygenase which catalyzes the conversion of (4-hydroxyphenyl)pyruvate (HPP) to homogentisate as part of tyrosine catabolism. While several di- and tri-ketone alkaloids are known as inhibitors of HPPD and used commercially as herbicides, one such inhibitor, [2-nitro-4-(trifluoromethyl)benzoyl]-1,3-cyclohexanedione (NTBC), has also been used therapeutically to treat type I tyrosinemia and alkaptonuria in humans. To gain further insight into the mechanism of inhibition by NTBC, a combination of CD/MCD spectroscopy and DFT calculations of HPPD/Fe(II)/NTBC has been performed to evaluate the contribution of the Fe(II)-NTBC bonding interaction to the high affinity of this drug for the enzyme. The results indicate that the bonding of NTBC to Fe(II) is very similar to that for HPP, both involving similar pi-backbonding interactions between NTBC/HPP and Fe(II). Combined with the result that the calculated binding energy of NTBC is, in fact, approximately 3 kcal/mol less than that for HPP, the bidentate coordination of NTBC to Fe(II) is not solely responsible for its extremely high affinity for the enzyme. Thus, the pi-stacking interactions between the aromatic rings of NTBC and two phenyalanine residues, as observed in the crystallography of the HPPD/Fe(II)/NTBC complex, appear to be responsible for the observed high affinity of drug binding.

  3. Cysteine dioxygenase and cysteine sulfinate decarboxylase genes of the deep-sea mussel Bathymodiolus septemdierum: possible involvement in hypotaurine synthesis and adaptation to hydrogen sulfide.

    Science.gov (United States)

    Nagasaki, Toshihiro; Hongo, Yuki; Koito, Tomoko; Nakamura-Kusakabe, Ikumi; Shimamura, Shigeru; Takaki, Yoshihiro; Yoshida, Takao; Maruyama, Tadashi; Inoue, Koji

    2015-03-01

    It has been suggested that invertebrates inhabiting deep-sea hydrothermal vent areas use the sulfinic acid hypotaurine, a precursor of taurine, to protect against the toxicity of hydrogen sulfide contained in the seawater from the vent. In this protective system, hypotaurine is accumulated in the gill, the primary site of sulfide exposure. However, the pathway for hypotaurine synthesis in mollusks has not been identified. In this study, we screened for the mRNAs of enzymes involved in hypotaurine synthesis in the deep-sea mussel Bathymodiolus septemdierum and cloned cDNAs encoding cysteine dioxygenase and cysteine sulfinate decarboxylase. As mRNAs encoding cysteamine dioxygenase and cysteine lyase were not detected, the cysteine sulfinate pathway is suggested to be the major pathway of hypotaurine and taurine synthesis. The two genes were found to be expressed in all the tissues examined, but the gill exhibited the highest expression. The mRNA level in the gill was not significantly changed by exposure to sulfides or thiosulfate. These results suggests that the gill of B. septemdierum maintains high levels of expression of the two genes regardless of ambient sulfide level and accumulates hypotaurine continuously to protect against sudden exposure to high level of sulfide.

  4. Molecular Cloning and Characterization of a New Cold-active Extradiol Dioxygenase from a Metagenomic Library Derived from Polychlorinated Biphenyl-contaminated Soil

    Institute of Scientific and Technical Information of China (English)

    REN He-jun; LU Yang; ZHOU Rui; DAI Chun-yan; WANG Yan; ZHANG Lan-ying

    2012-01-01

    To find new extradiol dioxygenases(EDOs,EC 1.13.11.2),a metagenomics library was constructed from polychlorinated biphenyl-contaminated soil and was screened for some dioxygenase with aromatic ring cleavage activity.A novel EDO,designated as BphC_A,was identified and heterologously expressed in Escherichia coli.The deduced amino acid sequence of BphC_A exhibited a homology of less than 60% with other known EDOs.Phylogenetic analysis of BphC_A suggests that the protein is a novel member of the EDO family.The enzyme exhibits higher substrate affinity and catalytic efficiency toward 3-methylcatechol than toward 2,3-dihydroxybiphenyl or catechol,the preferred substrate of other known EDOs.The optimum activity of purified BphC_A occurred at pH=8.5 and 35 ℃,and BphC_A showed more than 40% of its initial activity at 5 ℃.The activity of purified BphC_A was significantly induced by Mn2+ and slightly reduced bv Al3+,Cu2+ and Zn2+.

  5. Searching iron sensors in plants by exploring the link among 2’-OG-dependent dioxygenases, the iron deficiency response and metabolic adjustments occurring under iron deficiency

    Directory of Open Access Journals (Sweden)

    GIANPIERO eVIGANI

    2013-05-01

    Full Text Available Knowledge accumulated on the regulation of iron (Fe homeostasis, its intracellular trafficking and transport across various cellular compartments and organs in plants; storage proteins, transporters and transcription factors involved in Fe metabolism have been analysed in detail in recent years. However, the key sensor(s of cellular plant Fe status triggering the long-distance shoot-root signalling and leading to the root Fe-deficiency responses is (are still unknown. Local Fe sensing is also a major task for roots, for adjusting the internal Fe requirements to external Fe availability: how such sensing is achieved and how it leads to metabolic adjustments in case of nutrient shortage, is mostly unknown. Two proteins belonging to the 2′-OG dependent dioxygenases family accumulate several folds in Fe-deficient Arabidopsis roots. Such proteins require Fe(II as enzymatic cofactor; one of their subgroups, the HIF-P4H (Hypoxia Inducible Factor- Prolyl 4-Hydroxylase, is an effective oxygen sensor in animal cells. We envisage here the possibility that some members of the 2′-OG dioxygenase family may be involved in the Fe-deficiency response and in the metabolic adjustments to Fe deficiency or even in sensing Fe, in plant cells.

  6. Effects of polycyclic aromatic hydrocarbons on microbial community structure and PAH ring hydroxylating dioxygenase gene abundance in soil.

    Science.gov (United States)

    Sawulski, Przemyslaw; Clipson, Nicholas; Doyle, Evelyn

    2014-11-01

    Development of successful bioremediation strategies for environments contaminated with recalcitrant pollutants requires in-depth knowledge of the microorganisms and microbial processes involved in degradation. The response of soil microbial communities to three polycyclic aromatic hydrocarbons, phenanthrene (3-ring), fluoranthene (4-ring) and benzo(a)pyrene (5-ring), was examined. Profiles of bacterial, archaeal and fungal communities were generated using molecular fingerprinting techniques (TRFLP, ARISA) and multivariate statistical tools were employed to interpret the effect of PAHs on community dynamics and composition. The extent and rate of PAH removal was directly related to the chemical structure, with the 5-ring PAH benzo(a)pyrene degraded more slowly than phenathrene or fluoranthene. Bacterial, archaeal and fungal communities were all significantly affected by PAH amendment, time and their interaction. Based on analysis of clone libraries, Actinobacteria appeared to dominate in fluoranthene amended soil, although they also represented a significant portion of the diversity in phenanthrene amended and unamended soils. In addition there appeared to be more γ-Proteobacteria and less Bacteroidetes in soil amended with either PAH compared to the control. The soil bacterial community clearly possessed the potential to degrade PAHs as evidenced by the abundance of PAH ring hydroxylating (PAH-RHDα) genes from both gram negative (GN) and gram positive (GP) bacteria in PAH-amended and control soils. Although the dioxygenase gene from GP bacteria was less abundant in soil than the gene associated with GN bacteria, significant (p PAH-RHDα gene were observed during phenanthrene and fluoranthene degradation, whereas there was no significant difference in the abundance of the GN PAH-RHDα gene during the course of the experiment. Few studies to-date have examined the effect of pollutants on more than one microbial community in soil. The current study provides

  7. 3,4-Dihydroxyphenylacetate 2,3-dioxygenase from Pseudomonas aeruginosa: An Fe(II)-containing enzyme with fast turnover

    Science.gov (United States)

    Kamutira, Philaiwarong; Watthaisong, Pratchaya; Thotsaporn, Kittisak; Tongsook, Chanakan; Juttulapa, Maneerat; Nijvipakul, Sarayut; Chaiyen, Pimchai

    2017-01-01

    3,4-dihydroxyphenylacetate (DHPA) dioxygenase (DHPAO) from Pseudomonas aeruginosa (PaDHPAO) was overexpressed in Escherichia coli and purified to homogeneity. As the enzyme lost activity over time, a protocol to reactivate and conserve PaDHPAO activity has been developed. Addition of Fe(II), DTT and ascorbic acid or ROS scavenging enzymes (catalase or superoxide dismutase) was required to preserve enzyme stability. Metal content and activity analyses indicated that PaDHPAO uses Fe(II) as a metal cofactor. NMR analysis of the reaction product indicated that PaDHPAO catalyzes the 2,3-extradiol ring-cleavage of DHPA to form 5-carboxymethyl-2-hydroxymuconate semialdehyde (CHMS) which has a molar absorptivity of 32.23 mM-1cm-1 at 380 nm and pH 7.5. Steady-state kinetics under air-saturated conditions at 25°C and pH 7.5 showed a Km for DHPA of 58 ± 8 μM and a kcat of 64 s-1, indicating that the turnover of PaDHPAO is relatively fast compared to other DHPAOs. The pH-rate profile of the PaDHPAO reaction shows a bell-shaped plot that exhibits a maximum activity at pH 7.5 with two pKa values of 6.5 ± 0.1 and 8.9 ± 0.1. Study of the effect of temperature on PaDHPAO activity indicated that the enzyme activity increases as temperature increases up to 55°C. The Arrhenius plot of ln(k’cat) versus the reciprocal of the absolute temperature shows two correlations with a transition temperature at 35°C. Two activation energy values (Ea) above and below the transition temperature were calculated as 42 and 14 kJ/mol, respectively. The data imply that the rate determining steps of the PaDHPAO reaction at temperatures above and below 35°C may be different. Sequence similarity network analysis indicated that PaDHPAO belongs to the enzyme clusters that are largely unexplored. As PaDHPAO has a high turnover number compared to most of the enzymes previously reported, understanding its biochemical and biophysical properties should be useful for future applications in biotechnology

  8. Indoleamine 2,3-dioxygenases with very low catalytic activity are well conserved across kingdoms: IDOs of Basidiomycota.

    Science.gov (United States)

    Yuasa, Hajime J; Ball, Helen J

    2013-07-01

    Indoleamine 2,3-dioxygenase (IDO) is a tryptophan-degrading enzyme and is found in animals, fungi and bacteria. In fungi, its primary role is to supply nicotinamide adenine dinucleotide (NAD(+)) via the kynurenine pathway. A number of organisms possess more than one IDO gene, for example, mammals have IDO1 and IDO2 genes. We previously reported that the Pezizomycotina fungi commonly possess three types of IDO genes, IDOα, IDOβ and IDOγ. In this study, we surveyed the nature of IDO genes from Basidiomycota fungi, which are categorized into three subphyla (Agaricomycotina, Pucciniomycotina and Ustilaginomycotina). The Agaricomycotina fungi generally have three types of IDO genes (IDOa, IDOb and IDOc), which are distinct from Pezizomycotina three isozymes. Pucciniomycotina and Ustilaginomycotina species possess two types of IDO; one forms a monophyletic clade with Agaricomycotina IDOs in the phylogenetic tree, these IDOs are referred to as "typical Basidiomycota IDOs". The other is IDOγ, which showed more than 40% identity with Pezizomycotina and ciliate IDOγ. We previously demonstrated that IDO2 in mammals and IDOγ in Perzizomycotina fungi have much lower catalytic efficiencies in an in vitro assay, compared with the other IDO isoforms found in the respective species. We have developed a functional assay to determine whether particular IDO enzymes have sufficient enzymatic activity to rescue a yeast strain where IDO-deletion has rendered it auxotrophic for nicotinic acid. IDOα and IDOβ showed comparable catalytic efficiency, both of them could function in the Pezizomycotina fungal L-Trp metabolism. The catalytic efficiency and functional capacity of the Basidiomycota IDOa and IDOb were similar to Pezizomycotina IDOα/IDOβ. We found that Basidiomycota IDOc could not rescue the nicotinic acid auxotroph, similar to other IDO enzymes with low catalytic efficiency (mammalian IDO2 and most fungal IDOγ). Our study suggests that some fungal IDO enzymes function in

  9. Staphylococcus aureus CstB is a novel multidomain persulfide dioxygenase-sulfurtransferase involved in hydrogen sulfide detoxification

    Science.gov (United States)

    Shen, Jiangchuan; Keithly, Mary E.; Armstrong, Richard N.; Higgins, Khadine A.; Edmonds, Katherine A.; Giedroc, David P.

    2016-01-01

    Hydrogen sulfide (H2S) is both a lethal gas and an emerging gasotransmitter in humans, suggesting that cellular H2S level must be tightly regulated. CstB is encoded by the cst operon of the major human pathogen Staphylococcus aureus (S. aureus) and is under the transcriptional control of the persulfide sensor CstR and H2S. Here we show that CstB is a multifunctional Fe(II)-containing persulfide dioxygenase (PDO), analogous to the vertebrate protein ETHE1 (Ethylmalonic Encephalopathy Protein 1). Chromosomal deletion of ethe1 is fatal in vertebrates. In the presence of molecular oxygen (O2), hETHE1 oxidizes glutathione persulfide (GSSH) to generate sulfite and reduced glutathione. In contrast, CstB oxidizes major cellular low molecular weight (LMW) persulfide substrates from S. aureus, coenzyme A persulfide (CoASSH) and bacillithiol persulfide (BSSH), directly to generate thiosulfate (TS) and reduced thiols, thereby avoiding the cellular toxicity of sulfite. Both Cys201 in the N-terminal PDO domain (CstBPDO) and Cys408 in the C-terminal rhodanese domain (CstBRhod) strongly enhance the TS generating activity of CstB. CstB also possesses persulfide transferase (PT; reverse rhodanese) activity which generates TS when provided with LMW persulfides and sulfite, as well as conventional thiosulfate transferase (TST; rhodanese) activity; both activities require Cys408. CstB protects S. aureus against H2S toxicity with C201S and C408S cstB genes unable to rescue a NaHS-induced ΔcstB growth phenotype. Induction of the cst operon by NaHS reveals that functional CstB impacts the cellular TS concentrations. These data collectively suggest that CstB may have evolved to facilitate the clearance of LMW persulfides that occur upon the elevation of the level of cellular H2S and hence may have an impact on bacterial viability under H2S stress, in concert with the other enzymes encoded by the cst operon. PMID:26177047

  10. Recent Advances in Developing Inhibitors for Hypoxia-Inducible Factor Prolyl Hydroxylases and Their Therapeutic Implications

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    So Yeon Kim

    2015-11-01

    Full Text Available Hypoxia-inducible factor (HIF prolyl hydroxylases (PHDs are members of the 2-oxoglutarate dependent non-heme iron dioxygenases. Due to their physiological roles in regulation of HIF-1α stability, many efforts have been focused on searching for selective PHD inhibitors to control HIF-1α levels for therapeutic applications. In this review, we first describe the structure of PHD2 as a molecular basis for structure-based drug design (SBDD and various experimental methods developed for measuring PHD activity. We further discuss the current status of the development of PHD inhibitors enabled by combining SBDD approaches with high-throughput screening. Finally, we highlight the clinical implications of small molecule PHD inhibitors.

  11. Variation of glucosinolates and quinone reductase activity among different varieties of Chinese kale and improvement of glucoraphanin by metabolic engineering.

    Science.gov (United States)

    Qian, Hongmei; Sun, Bo; Miao, Huiying; Cai, Congxi; Xu, Chaojiong; Wang, Qiaomei

    2015-02-01

    The variation of glucosinolates and quinone reductase (QR) activity in fourteen varieties of Chinese kale (Brassica oleracea var. alboglabra Bailey) was investigated in the present study. Results showed that gluconapin (GNA), instead of glucoraphanin (GRA), was the most predominant glucosinolate in all varieties, and QR activity was remarkably positively correlated with the glucoraphanin level. AOP2, a tandem 2-oxoglutarate-dependent dioxygenase, catalyzes the conversion of glucoraphanin to gluconapin in glucosinolate biosynthesis. Here, antisense AOP2 was transformed into Gailan-04, the variety with the highest gluconapin content and ratio of GNA/GRA. The glucoraphanin content and corresponding QR activity were notably increased in transgenic plants, while no significant difference at the level of other main nutritional compounds (total phenolics, vitamin C, carotenoids and chlorophyll) was observed between the transgenic lines and the wide-type plants. Taken together, metabolic engineering is a good practice for improvement of glucoraphanin in Chinese kale.

  12. HIF hydroxylase pathways in cardiovascular physiology and medicine.

    Science.gov (United States)

    Bishop, Tammie; Ratcliffe, Peter J

    2015-06-19

    Hypoxia inducible factors (HIFs) are α/β heterodimeric transcription factors that direct multiple cellular and systemic responses in response to changes in oxygen availability. The oxygen sensitive signal is generated by a series of iron and 2-oxoglutarate-dependent dioxygenases that catalyze post-translational hydroxylation of specific prolyl and asparaginyl residues in HIFα subunits and thereby promote their destruction and inactivation in the presence of oxygen. In hypoxia, these processes are suppressed allowing HIF to activate a massive transcriptional cascade. Elucidation of these pathways has opened several new fields of cardiovascular research. Here, we review the role of HIF hydroxylase pathways in cardiac development and in cardiovascular control. We also consider the current status, opportunities, and challenges of therapeutic modulation of HIF hydroxylases in the therapy of cardiovascular disease.

  13. Safety, immune and clinical responses in metastatic melanoma patients vaccinated with a long peptide derived from indoleamine 2,3-dioxygenase in combination with ipilimumab

    DEFF Research Database (Denmark)

    Bjoern, Jon; Iversen, Trine Zeeberg; Nitschke, Nikolaj Juul;

    2016-01-01

    BACKGROUND AIM: Indoleamine 2,3-dioxygenase (IDO) is an emerging new target in cancer therapy that can be targeted with active immunotherapy (e.g. through peptide vaccination). Furthermore, IDO has been identified as a key mechanism underlying resistance to treatment with the checkpoint blocking...... antibody ipilimumab (ipi). METHODS: Ten patients with metastatic melanoma participated in a phase I first-in-human clinical study assessing safety of combining ipi with a 21-mer synthetic peptide vaccine from IDO denoted IDOlong. Secondary and tertiary end points included vaccine and clinical response....... RESULTS: Treatment was generally safe and well tolerated. Vaccine related adverse reactions included grade I and II erythema, oedema and pruritus at the vaccination site, which were manageable with mild topical corticosteroids. One patient developed presumed ipi-induced colitis. It initially responded...

  14. Remarkable Role of Indoleamine 2,3-Dioxygenase and Tryptophan Metabolites in Infectious Diseases: Potential Role in Macrophage-Mediated Inflammatory Diseases

    Directory of Open Access Journals (Sweden)

    Yuki Murakami

    2013-01-01

    Full Text Available Indoleamine 2,3-dioxygenase 1 (IDO1, the L-tryptophan-degrading enzyme, plays a key role in the immunomodulatory effects on several types of immune cells. Originally known for its regulatory function during pregnancy and chronic inflammation in tumorigenesis, the activity of IDO1 seems to modify the inflammatory state of infectious diseases. The pathophysiologic activity of L-tryptophan metabolites, kynurenines, is well recognized. Therefore, an understanding of the regulation of IDO1 and the subsequent biochemical reactions is essential for the design of therapeutic strategies in certain immune diseases. In this paper, current knowledge about the role of IDO1 and its metabolites during various infectious diseases is presented. Particularly, the regulation of type I interferons (IFNs production via IDO1 in virus infection is discussed. This paper offers insights into new therapeutic strategies in the modulation of viral infection and several immune-related disorders.

  15. Interferon-γ regulates the proliferation and differentiation of mesenchymal stem cells via activation of indoleamine 2,3 dioxygenase (IDO.

    Directory of Open Access Journals (Sweden)

    Juliana Croitoru-Lamoury

    Full Text Available The kynurenine pathway (KP of tryptophan metabolism is linked to antimicrobial activity and modulation of immune responses but its role in stem cell biology is unknown. We show that human and mouse mesenchymal and neural stem cells (MSCs and NSCs express the complete KP, including indoleamine 2,3 dioxygenase 1 (IDO and IDO2, that it is highly regulated by type I (IFN-β and II interferons (IFN-γ, and that its transcriptional modulation depends on the type of interferon, cell type and species. IFN-γ inhibited proliferation and altered human and mouse MSC neural, adipocytic and osteocytic differentiation via the activation of IDO. A functional KP present in MSCs, NSCs and perhaps other stem cell types offers novel therapeutic opportunities for optimisation of stem cell proliferation and differentiation.

  16. Comparative quantitative prevalence of mycobacteria and functionally abundant nidA, nahAc, and nagAc Dioxygenase genes in coal tar contaminated sediments

    Energy Technology Data Exchange (ETDEWEB)

    Jennifer M. DeBruyn; Christopher S. Chewning; Gary S. Sayler [University of Tennessee, Knoxville, TN (United States). Department of Ecology and Evolutionary Biology

    2007-08-01

    The Chattanooga Creek Superfund site is heavily contaminated with metals, pesticides, and coal tar with sediments exhibiting high concentrations of polycyclic aromatic hydrocarbons (PAHs). High molecular weight PAHs are of concern because of their toxicity and recalcitrance in the environment; as such, there is great interest in microbes, such as fast-growing Mycobacterium spp., capable of degradation of these compounds. Real-time quantitative PCR assays were developed targeting multiple dioxygenase genes to assess the ecology and functional diversity of PAH-degrading communities. These assays target the Mycobacterium nidA, {beta}-proteobacteria nagAc, and {gamma}-proteobacteria nahAc with the specific goal of testing the hypothesis that Mycobacteria catabolic genes are enriched and may be functionally associated with high molecular weight PAH biodegradation in Chattanooga Creek. Dioxygenase gene abundances were quantitatively compared to naphthalene and pyrene mineralization, and temporal and spatial PAH concentrations. nidA abundances ranged from 5.69 x 10{sup 4} to 4.92 x 10{sup 6} copies per gram sediment; nagAc from 2.42 x 10{sup 3} to 1.21 x 10{sup 7}, and nahAc from below detection to 4.01 x 10{sup 6} copies per gram sediment. There was a significantly greater abundance of nidA and nagAc at sites with the greatest concentrations of PAHs. In addition, nidA and nagAc were significantly positively correlated, indicating a coexistence of organisms carrying these genes. A positive relationship was also observed between nidA and nagAc and pyrene mineralization indicating that these genes serve as biomarkers for pyrene degradation. A 16S rDNA clone library of fast-growing Mycobacteria indicated that the population is very diverse and likely plays an important role in attenuation of high molecular weight PAHs from Chattanooga Creek. 35 refs., 5 figs., 1 tab.

  17. Acireductone dioxygenase- (ARD-) type reactivity of a nickel(II) complex having monoanionic coordination of a model substrate: product identification and comparisons to unreactive analogues.

    Science.gov (United States)

    Szajna-Fuller, Ewa; Rudzka, Katarzyna; Arif, Atta M; Berreau, Lisa M

    2007-07-09

    A mononuclear Ni(II) complex ([(6-Ph2TPA)Ni(PhC(O)C(OH)C(O)Ph)]ClO4 (1)), supported by the 6-Ph2TPA chelate ligand (6-Ph2TPA = N,N-bis((6-phenyl-2-pyridyl)methyl)-N-((2-pyridyl)methyl)amine) and containing a cis-beta-keto-enolate ligand having a C2 hydroxyl substituent, undergoes reaction with O2 to produce a Ni(II) monobenzoate complex ([(6-Ph2TPA)Ni(O2CPh)]ClO4 (3)), CO, benzil (PhC(O)C(O)Ph), benzoic acid, and other minor unidentified phenyl-containing products. Complex 3 has been identified through independent synthesis and was characterized by X-ray crystallography, 1H NMR, FAB-MS, FTIR, and elemental analysis. A series of cis-beta-keto-enolate Ni(II) complexes supported by the 6-Ph2TPA ligand ([(6-Ph2TPA)Ni(PhC(O)CHC(O)Ph)]ClO4 (4), [(6-Ph2TPA)Ni(CH3C(O)CHC(O)CH3)]ClO4 (5), and [(6-Ph2TPA)Ni(PhC(O)CHC(O)C(O)Ph) (6)) have been prepared and characterized. While these complexes exhibit structural and/or spectroscopic similarity to 1, all are unreactive with O2. The results of this study are discussed in terms of relevance to Ni(II)-containing acireductone dioxygenase enzymes, as well as in the context of recently reported cofactor-free, quercetin, and beta-diketone dioxygenases.

  18. Purification and some properties of component B of the 4-chlorophenylacetate 3,4-dioxygenase from Pseudomonas species strain CBS 3.

    Science.gov (United States)

    Schweizer, D; Markus, A; Seez, M; Ruf, H H; Lingens, F

    1987-07-05

    4-Chlorophenylacetate 3,4-dioxygenase system from Pseudomonas sp. CBS 3 consists of two protein components, a red-brown iron-sulfur protein (component A) which functions as dioxygenase and an orange-colored reductase (component B). Component B was purified by a five-step procedure. Criterion of purity was sodium dodecyl sulfate-polyacrylamide gel electrophoresis, which also showed that the protein consists of one polypeptide species with a molecular weight of 35,000. With gel chromatography on Sephadex G-100 also, a molecular weight of 35,000 was found for the native enzyme, suggesting a monomeric structure for the reductase enzyme. The isoelectric point was determined as pH 4.8. The visible absorption spectrum of the homogeneous protein exhibits maxima at 336, 394, and 458 nm. One mol of FMN, 2.1 mol of iron, and 1.7 mol of acid-labile sulfide were found in one mol of component B. The EPR-spectrum of the reduced form of the enzyme (with NADH) showed two types of signals. The signal at g values of 2.03, 1.94, and 1.90 was assigned to an iron-sulfur cluster of the [2Fe-2S]-type. The properties of the other signal type at g = 2.004 are characteristic of flavosemiquinone radical which does not show coupling to an other paramagnetic center. The apparent Km values for 2,6-dichlorophenolindophenol, cytochrome c, and NADH were calculated from Lineweaver-Burk plots as 6.3, 2.3, and 32 microM, respectively. Inhibitors of the reductase are metal-chelating reagents and sulfhydryl-inhibiting compounds. Component B reduces several redox compounds: 2,6-dichlorophenolindophenol, potassium hexacyanoferrat III, cytochrome c, methylene blue, and nitro blue tetrazolium.

  19. Abundance of Dioxygenase Genes Similar to Ralstonia sp. Strain U2 nagAc Is Correlated with Naphthalene Concentrations in Coal Tar-Contaminated Freshwater Sediments

    Science.gov (United States)

    Dionisi, Hebe M.; Chewning, Christopher S.; Morgan, Katherine H.; Menn, Fu-Min; Easter, James P.; Sayler, Gary S.

    2004-01-01

    We designed a real-time PCR assay able to recognize dioxygenase large-subunit gene sequences with more than 90% similarity to the Ralstonia sp. strain U2 nagAc gene (nagAc-like gene sequences) in order to study the importance of organisms carrying these genes in the biodegradation of naphthalene. Sequencing of PCR products indicated that this real-time PCR assay was specific and able to detect a variety of nagAc-like gene sequences. One to 100 ng of contaminated-sediment total DNA in 25-μl reaction mixtures produced an amplification efficiency of 0.97 without evident PCR inhibition. The assay was applied to surficial freshwater sediment samples obtained in or in close proximity to a coal tar-contaminated Superfund site. Naphthalene concentrations in the analyzed samples varied between 0.18 and 106 mg/kg of dry weight sediment. The assay for nagAc-like sequences indicated the presence of (4.1 ± 0.7) × 103 to (2.9 ± 0.3) × 105 copies of nagAc-like dioxygenase genes per μg of DNA extracted from sediment samples. These values corresponded to (1.2 ± 0.6) × 105 to (5.4 ± 0.4) × 107 copies of this target per g of dry weight sediment when losses of DNA during extraction were taken into account. There was a positive correlation between naphthalene concentrations and nagAc-like gene copies per microgram of DNA (r = 0.89) and per gram of dry weight sediment (r = 0.77). These results provide evidence of the ecological significance of organisms carrying nagAc-like genes in the biodegradation of naphthalene. PMID:15240274

  20. Mechanism of repair of acrolein- and malondialdehyde-derived exocyclic guanine adducts by the α-ketoglutarate/Fe(II) dioxygenase AlkB.

    Science.gov (United States)

    Singh, Vipender; Fedeles, Bogdan I; Li, Deyu; Delaney, James C; Kozekov, Ivan D; Kozekova, Albena; Marnett, Lawrence J; Rizzo, Carmelo J; Essigmann, John M

    2014-09-15

    The structurally related exocyclic guanine adducts α-hydroxypropano-dG (α-OH-PdG), γ-hydroxypropano-dG (γ-OH-PdG), and M1dG are formed when DNA is exposed to the reactive aldehydes acrolein and malondialdehyde (MDA). These lesions are believed to form the basis for the observed cytotoxicity and mutagenicity of acrolein and MDA. In an effort to understand the enzymatic pathways and chemical mechanisms that are involved in the repair of acrolein- and MDA-induced DNA damage, we investigated the ability of the DNA repair enzyme AlkB, an α-ketoglutarate/Fe(II) dependent dioxygenase, to process α-OH-PdG, γ-OH-PdG, and M1dG in both single- and double-stranded DNA contexts. By monitoring the repair reactions using quadrupole time-of-flight (Q-TOF) mass spectrometry, it was established that AlkB can oxidatively dealkylate γ-OH-PdG most efficiently, followed by M1dG and α-OH-PdG. The AlkB repair mechanism involved multiple intermediates and complex, overlapping repair pathways. For example, the three exocyclic guanine adducts were shown to be in equilibrium with open-ring aldehydic forms, which were trapped using (pentafluorobenzyl)hydroxylamine (PFBHA) or NaBH4. AlkB repaired the trapped open-ring form of γ-OH-PdG but not the trapped open-ring of α-OH-PdG. Taken together, this study provides a detailed mechanism by which three-carbon bridge exocyclic guanine adducts can be processed by AlkB and suggests an important role for the AlkB family of dioxygenases in protecting against the deleterious biological consequences of acrolein and MDA.

  1. Expression of tryptophan 2,3-dioxygenase and production of kynurenine pathway metabolites in triple transgenic mice and human Alzheimer's disease brain.

    Directory of Open Access Journals (Sweden)

    Wei Wu

    Full Text Available To assess the role of the kynurenine pathway in the pathology of Alzheimer's disease (AD, the expression and localization of key components of the kynurenine pathway including the key regulatory enzyme tryptophan 2,3 dioxygenase (TDO, and the metabolites tryptophan, kynurenine, kynurenic acid, quinolinic acid and picolinic acid were assessed in different brain regions of triple transgenic AD mice. The expression and cell distribution of TDO and quinolinic acid, and their co-localization with neurofibrillary tangles and senile β amyloid deposition were also determined in hippocampal sections from human AD brains. The expression of TDO mRNA was significantly increased in the cerebellum of AD mouse brain. Immunohistochemistry demonstrated that the density of TDO immuno-positive cells was significantly higher in the AD mice. The production of the excitotoxin quinolinic acid strongly increased in the hippocampus in a progressive and age-dependent manner in AD mice. Significantly higher TDO and indoleamine 2,3 dioxygenase 1 immunoreactivity was observed in the hippocampus of AD patients. Furthermore, TDO co-localizes with quinolinic acid, neurofibrillary tangles-tau and amyloid deposits in the hippocampus of AD. These results show that the kynurenine pathway is over-activated in AD mice. This is the first report demonstrating that TDO is highly expressed in the brains of AD mice and in AD patients, suggesting that TDO-mediated activation of the kynurenine pathway could be involved in neurofibrillary tangles formation and associated with senile plaque. Our study adds to the evidence that the kynurenine pathway may play important roles in the neurodegenerative processes of AD.

  2. 4-nitrocatechol as a probe of a Mn(II)-dependent extradiol-cleaving catechol dioxygenase (MndD): comparison with relevant Fe(II) and Mn(II) model complexes.

    Science.gov (United States)

    Reynolds, Mark F; Costas, Miquel; Ito, Masami; Jo, Du-Hwan; Tipton, A Alex; Whiting, Adam K; Que, Lawrence

    2003-02-01

    Mn(II)-dependent 3,4-dihydroxyphenylacetate 2,3-dioxygenase (MndD) is an extradiol-cleaving catechol dioxygenase from Arthrobacter globiformis that has 82% sequence identity to and cleaves the same substrate (3,4-dihydroxyphenylacetic acid) as Fe(II)-dependent 3,4-dihydroxyphenylacetate 2,3-dioxygenase (HPCD) from Brevibacterium fuscum. We have observed that MndD binds the chromophoric 4-nitrocatechol (4-NCH(2)) substrate as a dianion and cleaves it extremely slowly, in contrast to the Fe(II)-dependent enzymes which bind 4-NCH(2) mostly as a monoanion and cleave 4-NCH(2) 4-5 orders of magnitude faster. These results suggest that the monoanionic binding state of 4-NC is essential for extradiol cleavage. In order to address the differences in 4-NCH(2) binding to these enzymes, we synthesized and characterized the first mononuclear monoanionic and dianionic Mn(II)-(4-NC) model complexes as well as their Fe(II)-(4-NC) analogs. The structures of [(6-Me(2)-bpmcn)Fe(II)(4-NCH)](+), [(6-Me(3)-TPA)Mn(II)(DBCH)](+), and [(6-Me(2)-bpmcn)Mn(II)(4-NCH)](+) reveal that the monoanionic catecholate is bound in an asymmetric fashion (Delta r(metal-O(catecholate))=0.25-0.35 A), as found in the crystal structures of the E(.)S complexes of extradiol-cleaving catechol dioxygenases. Acid-base titrations of [(L)M(II)(4-NCH)](+) complexes in aprotic solvents show that the p K(a) of the second catecholate proton of 4-NCH bound to the metal center is half a p K(a) unit higher for the Mn(II) complexes than for the Fe(II) complexes. These results are in line with the Lewis acidities of the two divalent metal ions but are the opposite of the trend observed for 4-NCH(2) binding to the Mn(II)- and Fe(II)-catechol dioxygenases. These results suggest that the MndD active site decreases the second p K(a) of the bound 4-NCH(2) relative to the HPCD active site.

  3. Biodegradation of phenanthrene, spatial distribution of bacterial populations and dioxygenase expression in the mycorrhizosphere of Lolium perenne inoculated with Glomus mosseae.

    Science.gov (United States)

    Corgié, S C; Fons, F; Beguiristain, T; Leyval, C

    2006-05-01

    Interactions between the plant and its microbial communities in the rhizosphere control microbial polycyclic aromatic hydrocarbons (PAH) biodegradation processes. Arbuscular mycorrhizal (AM) fungi can influence plant survival and PAH degradation in polluted soil. This work was aimed at studying the contribution of the mycorrhizosphere to PAH biodegradation in the presence of ryegrass (Lolium perenne L., cv. Barclay) inoculated with Glomus mosseae (BEG 69) by taking into account the structure and activity of bacterial communities, PAH degrading culturable bacteria as a function of the distance from roots. Ryegrass was grown in compartmentalized systems designed to harvest successive sections of rhizosphere in lateral compartments polluted or not with phenanthrene (PHE). Colonization of roots by G. mosseae (BEG 69) modified the structure and density of bacterial populations in the mycorrhizosphere, compared to the rhizosphere of non-mycorrhizal plants. G. mosseae increased the density of culturable heterotrophic and PAH degrading bacteria beyond the immediate rhizosphere in the presence of PHE, and increased the density of PAH degraders in the absence of the pollutant. Biodegradation was not significantly increased in the mycorrhizosphere, compared to control non-mycorrhizal plants, where PHE biodegradation already reached 92% after 6 weeks. However, dioxygenase transcriptional activity was found to be higher in the immediate mycorrhizosphere in the presence of G. mosseae (BEG 69).

  4. Genomic analysis and gene structure of the plant carotenoid dioxygenase 4 family: a deeper study in Crocus sativus and its allies.

    Science.gov (United States)

    Ahrazem, Oussama; Trapero, Almudena; Gómez, M Dolores; Rubio-Moraga, Angela; Gómez-Gómez, Lourdes

    2010-10-01

    The plastoglobule-targeted enzyme carotenoid cleavage dioxygenase (CCD4) mediates the formation of volatile C13 ketones, such as β-ionone, by cleaving the C9-C10 and C9'-C10' double bonds of cyclic carotenoids. Here, we report the isolation and analysis of CCD4 genomic DNA regions in Crocus sativus. Different CCD4 alleles have been identified: CsCCD4a which is found with and without an intron and CsCCD4b that showed the presence of a unique intron. The presence of different CCD4 alleles was also observed in other Crocus species. Furthermore, comparison of the locations of CCD4 introns within the coding region with CCD4 genes from other plant species suggests that independent gain/losses have occurred. The comparison of the promoter region of CsCCD4a and CsCCD4b with available CCD4 gene promoters from other plant species highlighted the conservation of cis-elements involved in light response, heat stress, as well as the absence and unique presence of cis-elements involved in circadian regulation and low temperature responses, respectively. Functional characterization of the Crocus sativus CCD4a promoter using Arabidopsis plants stably transformed with a DNA fragment of 1400 base pairs (P-CsCCD4a) fused to the β-glucuronidase (GUS) reporter gene showed that this sequence was sufficient to drive GUS expression in the flower, in particular high levels were detected in pollen.

  5. Developmental and stress regulation of gene expression for a 9-cis-epoxycarotenoid dioxygenase, CstNCED, isolated from Crocus sativus stigmas.

    Science.gov (United States)

    Ahrazem, Oussama; Rubio-Moraga, Angela; Trapero, Almudena; Gómez-Gómez, Lourdes

    2012-01-01

    Oxidative cleavage of cis-epoxycarotenoids by 9-cis-epoxycarotenoid dioxygenase (NCED) is the critical step in the regulation of abscisic acid (ABA) synthesis in higher plants. ABA has been associated with dormancy and flower senescence, while also regulating plant adaptive responses to various environmental stresses. An NCED gene, CstNCED, was cloned from Crocus sativus stigmas. The deduced amino acid sequence of the CstNCED protein shared high identity with other monocot NCEDs, and was closely related to the liliopsida enzymes. At the N-terminus of CstNCED a chloroplast transit peptide sequence is located. However, its expression in chloroplast-free tissues suggested localization in other plastid types. The relationship between expression of CstNCED and the endogenous ABA level was investigated in the stigma and corms, where it was developmentally regulated. The senescence of the unpollinated stigma is preceded by an increase in ABA levels and CstNCED expression. In corms, a correlation was observed between CstNCED expression and dormancy. Furthermore, CstNCED expression was correlated with the presence of zeaxanthin in the dormant corms. When detached C. sativus leaves and stigmas were water and salt stressed, increases in CstNCED mRNA were observed. The results provided evidence of the involvement of CstNCED in the regulation of ABA-associated processes such as flower senescence and corm dormancy in monocotyledonous saffron.

  6. Oral Probiotic VSL#3 Prevents Autoimmune Diabetes by Modulating Microbiota and Promoting Indoleamine 2,3-Dioxygenase-Enriched Tolerogenic Intestinal Environment

    Directory of Open Access Journals (Sweden)

    Jayashree Dolpady

    2016-01-01

    Full Text Available The gut microbiota modulates the autoimmune pathogenesis of type 1 diabetes (T1D via mechanisms that remain largely unknown. The inflammasome components are innate immune sensors that are highly influenced by the gut environment and play pivotal roles in maintaining intestinal immune homeostasis. In this study we show that modifications of the gut microbiota induced by oral treatment with Lactobacillaceae-enriched probiotic VSL#3, alone or in combination with retinoic acid (RA, protect NOD mice from T1D by affecting inflammasome at the intestinal level. In particular, we show that VSL#3 treatment inhibits IL-1β expression while enhancing release of protolerogenic components of the inflammasome, such as indoleamine 2,3-dioxygenase (IDO and IL-33. Those modifications of the intestinal microenvironment in VSL#3-treated NOD mice modulate gut immunity by promoting differentiation of tolerogenic CD103+ DCs and reducing differentiation/expansion of Th1 and Th17 cells in the intestinal mucosa and at the sites of autoimmunity, that is, within the pancreatic lymph nodes (PLN of VSL#3-treated NOD mice. Our data provide a link between dietary factors, microbiota composition, intestinal inflammation, and immune homeostasis in autoimmune diabetes and could pave the way for new therapeutic approaches aimed at changing the intestinal microenvironment with probiotics to counterregulate autoimmunity and prevent T1D.

  7. Engineering catechol 1, 2-dioxygenase by design for improving the performance of the cis, cis-muconic acid synthetic pathway in Escherichia coli

    Science.gov (United States)

    Han, Li; Liu, Pi; Sun, Jixue; Wu, Yuanqing; Zhang, Yuanyuan; Chen, Wujiu; Lin, Jianping; Wang, Qinhong; Ma, Yanhe

    2015-01-01

    Regulating and ameliorating enzyme expression and activity greatly affects the performance of a given synthetic pathway. In this study, a new synthetic pathway for cis, cis-muconic acid (ccMA) production was reconstructed without exogenous induction by regulating the constitutive expression of the important enzyme catechol 1,2-dioxygenase (CatA). Next, new CatAs with significantly improved activities were developed to enhance ccMA production using structure-assisted protein design. Nine mutations were designed, simulated and constructed based on the analysis of the CatA crystal structure. These results showed that mutations at Gly72, Leu73 and/or Pro76 in CatA could improve enzyme activity, and the activity of the most effective mutant was 10-fold greater than that of the wild-type CatA from Acinetobacter sp. ADP1. The most productive synthetic pathway with a mutated CatA increased the titer of ccMA by more than 25%. Molecular dynamic simulation results showed that enlarging the entrance of the substrate-binding pocket in the mutants contributed to their increased enzyme activities and thus improved the performance of the synthetic pathway. PMID:26306712

  8. Identification of 11 Novel Homogentisate 1,2 Dioxygenase Variants in Alkaptonuria Patients and Establishment of a Novel LOVD-Based HGD Mutation Database.

    Science.gov (United States)

    Zatkova, Andrea; Sedlackova, Tatiana; Radvansky, Jan; Polakova, Helena; Nemethova, Martina; Aquaron, Robert; Dursun, Ismail; Usher, Jeannette L; Kadasi, Ludevit

    2012-01-01

    Enzymatic loss in alkaptonuria (AKU), an autosomal recessive disorder, is caused by mutations in the homogentisate 1,2 dioxygenase (HGD) gene, which decrease or completely inactivate the function of the HGD protein to metabolize homogentisic acid (HGA). AKU shows a very low prevalence (1:100,000-250,000) in most ethnic groups, but there are countries with much higher incidence, such as Slovakia and the Dominican Republic. In this work, we report 11 novel HGD mutations identified during analysis of 36 AKU patients and 41 family members from 27 families originating from 9 different countries, mainly from Slovakia and France. In Slovak patients, we identified two additional mutations, thus a total number of HGD mutations identified in this small country is 12. In order to record AKU-causing mutations and variants of the HGD gene, we have created a HGD mutation database that is open for future submissions and is available online ( http://hgddatabase.cvtisr.sk/ ). It is founded on the Leiden Open (source) Variation Database (LOVD) system and includes data from the original AKU database ( http://www.alkaptonuria.cib.csic.es ) and also all so far reported variants and AKU patients. Where available, HGD-haplotypes associated with the mutations are also presented. Currently, this database contains 148 unique variants, of which 115 are reported pathogenic mutations. It provides a valuable tool for information exchange in AKU research and care fields and certainly presents a useful data source for genotype-phenotype correlations and also for future clinical trials.

  9. Detailed analysis and follow-up studies of a high-throughput screening for indoleamine 2,3-dioxygenase 1 (IDO1) inhibitors.

    Science.gov (United States)

    Röhrig, Ute F; Majjigapu, Somi Reddy; Chambon, Marc; Bron, Sylvian; Pilotte, Luc; Colau, Didier; Van den Eynde, Benoît J; Turcatti, Gerardo; Vogel, Pierre; Zoete, Vincent; Michielin, Olivier

    2014-09-12

    Indoleamine 2,3-dioxygenase 1 (IDO1) is a key regulator of immune responses and therefore an important therapeutic target for the treatment of diseases that involve pathological immune escape, such as cancer. Here, we describe a robust and sensitive high-throughput screen (HTS) for IDO1 inhibitors using the Prestwick Chemical Library of 1200 FDA-approved drugs and the Maybridge HitFinder Collection of 14,000 small molecules. Of the 60 hits selected for follow-up studies, 14 displayed IC50 values below 20 μM under the secondary assay conditions, and 4 showed an activity in cellular tests. In view of the high attrition rate we used both experimental and computational techniques to identify and to characterize compounds inhibiting IDO1 through unspecific inhibition mechanisms such as chemical reactivity, redox cycling, or aggregation. One specific IDO1 inhibitor scaffold, the imidazole antifungal agents, was chosen for rational structure-based lead optimization, which led to more soluble and smaller compounds with micromolar activity.

  10. Early carcinogenesis involves the establishment of immune privilege via intrinsic and extrinsic regulation of Indoleamine 2,3-dioxygenase-1: Translational implications in cancer immunotherapy

    Directory of Open Access Journals (Sweden)

    Alisha eHoltzhausen

    2014-10-01

    Full Text Available Although prolonged genetic pressure has been conjectured to be necessary for the eventual development of tumor immune evasion mechanisms, recent work is demonstrating that early genetic mutations are capable of moonlighting as both intrinsic and extrinsic modulators of the tumor immune microenvironment. The indoleamine 2,3-dioxygenase-1 (IDO immunoregulatory enzyme is emerging as a key player in tumor-mediated immune tolerance. While loss of the tumor suppressor, BIN-1, and the over-expression of cyclooxygenase-2 (COX-2 have been implicated in intrinsic regulation of IDO, recent findings have demonstrated the loss of TβRIII and the upregulation of Wnt5a by developing cancers to play a role in the extrinsic control of IDO activity by local dendritic cell populations residing within tumor and tumor-draining lymph node tissues. Together, these genetic changes are capable of modulating paracrine signaling pathways in the early stages of carcinogenesis to establish a site of immune privilege by promoting the differentiation and activation of local regulatory T cells. Additional investigation of these immune evasion pathways promises to provide opportunities for the development of novel strategies to synergistically enhance the efficacy of the evolving class of T cell-targeted ‘checkpoint’ inhibitors.

  11. Effects of various phytochemicals on indoleamine 2,3-dioxygenase 1 activity: galanal is a novel, competitive inhibitor of the enzyme.

    Directory of Open Access Journals (Sweden)

    Rie Yamamoto

    Full Text Available Indoleamine 2,3-dioxygenase (IDO 1, that catalyzes the first and rate-limiting step in the degradation of L-tryptophan, has an important immunomodulatory function. The activity of IDO1 increases in various inflammatory diseases, including tumors, autoimmune diseases, and different kinds of inflammation. We evaluated the suppressive effect of plant extracts or phytochemicals on IDO1 induction and activity; sixteen kinds of plants extracts and fourteen kinds of phytochemicals were examined. As a result, the methanol extracts of Myoga flower buds, which are traditional Japanese foods, and labdane-type diterpene galanal derived from Myoga flowers significantly suppressed IDO1 activity. The Lineweaver-Burk plot analysis indicated that galanal is a competitive inhibitor. Galanal attenuated L-kynurenine formation with an IC₅₀ value of 7.7 µM in the assay system using recombinant human IDO1, and an IC₅₀ value of 45 nM in the cell-based assay. Further, mechanistic analysis revealed that galanal interfered with the transcriptional function of the nuclear factor-κB and the interferon-γ signaling pathway. These effects of galanal are important for immune response. Because the inhibitory effect of galanal on IDO1 activity was stronger than that of 1-methyl tryptophan, a tryptophan analog, galanal may have great potential as the novel drug for various immune-related diseases.

  12. Intracerebroventricular Administration of Streptozotocin as an Experimental Approach to Depression: Evidence for the Involvement of Proinflammatory Cytokines and Indoleamine-2,3-Dioxygenase.

    Science.gov (United States)

    Souza, Leandro Cattelan; Jesse, Cristiano R; de Gomes, Marcelo Gomes; Viana, Cristini Escobar; Mattos, Etiara; Silva, Neici Cáceres; Boeira, Silvana Peterini

    2017-02-02

    There is a lack of information about the molecular events underlying the depressive-like effect of an intracerebroventricular injection of streptozotocin (ICV-STZ) in mice. Elevated activity of the tryptophan-degrading enzyme indoleamine-2,3-dioxygenase (IDO) has been proposed to mediate depression in inflammatory disorders. In this study, we report that ICV-STZ activates IDO in the hippocampus of mice and culminates in depressive-like behaviors, measured by an increased duration in immobility time in the forced swimming test and decreased total time of grooming in the splash test. Indirect blockade of IDO activation with the cytokine inhibitor minocycline prevents the development of depressive-like behaviors and attenuates STZ-induced upregulation of proinflammatory cytokines in the hippocampus. Minocycline abrogates the increase in tryptophan and kynurenine levels as well as prevents serotonin dysfunction in the hippocampus of STZ-injected mice. These results suggest that hippocampal IDO activation in STZ-associated depressive-like behavior is mediated by proinflammatory cytokine-dependent mechanisms. Our study not only extends the evidence that IDO has a critical role in mediating inflammation-induced depression but also supports the notion that neuroinflammation and the kynurenine pathway are important targets of novel therapeutic drugs for depression. In addition, our study provides new insights into the neurobiological mechanisms underlying ICV-STZ and indicates that this model could be employed in the preclinical research of depression.

  13. para-Nitrophenol 4-monooxygenase and hydroxyquinol 1,2-dioxygenase catalyze sequential transformation of 4-nitrocatechol in Pseudomonas sp. strain WBC-3.

    Science.gov (United States)

    Wei, Min; Zhang, Jun-Jie; Liu, Hong; Zhou, Ning-Yi

    2010-11-01

    Pseudomonas sp. strain WBC-3 utilizes para-nitrophenol (PNP) as a sole source of carbon, nitrogen and energy. PnpA (PNP 4-monooxygenase) and PnpB (para-benzoquinone reductase) were shown to be involved in the initial steps of PNP catabolism via hydroquinone. We demonstrated here that PnpA also catalyzed monooxygenation of 4-nitrocatechol (4-NC) to hydroxyquinol, probably via hydroxyquinone. It was the first time that a single-component PNP monooxygenase has been shown to catalyze this conversion. PnpG encoded by a gene located in the PNP degradation cluster was purified as a His-tagged protein and identified as a hydroxyquinol dioxygenase catalyzing a ring-cleavage reaction of hydroxyquinol. Although all the genes necessary for 4-NC metabolism seemed to be present in the PNP degradation cluster in strain WBC-3, it was unable to grow on 4-NC as a sole source of carbon, nitrogen and energy. This was apparently due to the substrate's inability to trigger the expression of genes involved in degradation. Nevertheless, strain WBC-3 could completely degrade both PNP and 4-NC when PNP was used as the inducer, demonstrating its potential in bioremediation of the environment polluted by both 4-NC and PNP.

  14. Tomato carotenoid cleavage dioxygenases 1A and 1B: Relaxed double bond specificity leads to a plenitude of dialdehydes, mono-apocarotenoids and isoprenoid volatiles

    KAUST Repository

    Ilg, Andrea

    2014-06-25

    The biosynthetic processes leading to many of the isoprenoid volatiles released by tomato fruits are still unknown, though previous reports suggested a clear correlation with the carotenoids contained within the fruit. In this study, we investigated the activity of the tomato (Solanum lycopersicum) carotenoid cleavage dioxygenase (SlCCD1B), which is highly expressed in fruits, and of its homolog SlCCD1A. Using in vitro assays performed with purified recombinant enzymes and by analyzing products formed by the two enzymes in carotene-accumulating Escherichia coli strains, we demonstrate that SlCCD1A and, to a larger extent, SlCCD1B, have a very relaxed specificity for both substrate and cleavage site, mediating the oxidative cleavage of cis- and all-. trans-carotenoids as well as of different apocarotenoids at many more double bonds than previously reported. This activity gives rise to a plenitude of volatiles, mono-apocarotenoids and dialdehyde products, including cis-pseudoionone, neral, geranial, and farnesylacetone. Our results provide a direct evidence for a carotenoid origin of these compounds and point to CCD1s as the enzymes catalyzing the formation of the vast majority of tomato isoprenoid volatiles, many of which are aroma constituents. © 2014 The Authors.

  15. Membrane-type 1 matrix metalloproteinase cytoplasmic tail binding protein-1 (MTCBP-1) acts as an eukaryotic aci-reductone dioxygenase (ARD) in the methionine salvage pathway.

    Science.gov (United States)

    Hirano, Wakako; Gotoh, Isamu; Uekita, Takamasa; Seiki, Motoharu

    2005-06-01

    MTCBP-1 was identified as a protein that binds the cytoplasmic tail of membrane-type 1 matrix metalloproteinase (MT1-MMP/MMP-14). Since MTCBP-1 has a putative beta-barrel structure, it is presumably a member of the recently proposed cupin superfamily that contains tremendously diverged functions of proteins in spite of their well-conserved beta-barrel structure. MTCBP-1 shows significant homology to the bacterial aci-reductone dioxygenase (ARD) in the cupin family, which is an enzyme in the methionine salvage pathway (MTA cycle). Since it is difficult to speculate the functions of cupin proteins simply based on their sequence homology, we examined whether the eukaryotic ARD homologs surely function in the methionine metabolism. Under sulfur-depleted conditions, yeast could grow when substrate of MTA cycle was provided. Disruption of the yeast ARD homolog, YMR009w gene, abolished ability of the cells to grow in this culture condition. Re-expression of either the YMR009w or MTCBP-1 gene restored the cell growth. Mutation analysis revealed that the glutamic acid residue in the beta-barrel fold and the N-terminal extension from the beta-barrel fold were found to be important for the activity to restore the growth. Thus, MTCBP-1 isolated as a binding protein for MT1-MMP was demonstrated to function as an ARD-like enzyme in the MTA cycle in yeast.

  16. St. John's Wort increases brain serotonin synthesis by inhibiting hepatic tryptophan 2, 3 dioxygenase activity and its gene expression in stressed rats.

    Science.gov (United States)

    Bano, Samina; Ara, Iffat; Saboohi, Kausar; Moattar, Tariq; Chaoudhry, Bushra

    2014-09-01

    We aimed to investigate the effects of herbal St. John's Wort (SJW) on transcriptional regulation of hepatic tryptophan 2, 3 - dioxygenase (TDO) enzyme activity and brain regional serotonin (5-HT) levels in rats exposed to forced swim test (FST). TDO mRNA expression was quantified using real-time reverse transcription polymerase chain (RT-PCR) reaction and brain regional indoleamines were determined by high performance liquid chromatography coupled to fluorescence detector. Behavioral analysis shows significant reduction in immobility time in SJW (500mg/kg/ml) administered rats. It was found that pretreatment of SJW to rats did not prevent stress-induced elevation in plasma corticosterone levels however it increases serotonin synthesis by virtue of inhibiting hepatic TDO enzyme activity and its gene expression, ascertaining the notion that there exists an inverse relationship between hepatic TDO enzyme activity and brain 5-HT. The drug also decreases serotonin turnover in all the brain areas (hypothalamus, hippocampus amygdala) in stressed rats endorsing its monoamine oxidase inhibition property. Inhibition of TDO enzyme activity and its gene expression by the drug provides new insights for the development of therapeutic interventions for stress related mental illnesses.

  17. Primary hepatocytes from mice lacking cysteine dioxygenase show increased cysteine concentrations and higher rates of metabolism of cysteine to hydrogen sulfide and thiosulfate.

    Science.gov (United States)

    Jurkowska, Halina; Roman, Heather B; Hirschberger, Lawrence L; Sasakura, Kiyoshi; Nagano, Tetsuo; Hanaoka, Kenjiro; Krijt, Jakub; Stipanuk, Martha H

    2014-05-01

    The oxidation of cysteine in mammalian cells occurs by two routes: a highly regulated direct oxidation pathway in which the first step is catalyzed by cysteine dioxygenase (CDO) and by desulfhydration-oxidation pathways in which the sulfur is released in a reduced oxidation state. To assess the effect of a lack of CDO on production of hydrogen sulfide (H2S) and thiosulfate (an intermediate in the oxidation of H2S to sulfate) and to explore the roles of both cystathionine γ-lyase (CTH) and cystathionine β-synthase (CBS) in cysteine desulfhydration by liver, we investigated the metabolism of cysteine in hepatocytes isolated from Cdo1-null and wild-type mice. Hepatocytes from Cdo1-null mice produced more H2S and thiosulfate than did hepatocytes from wild-type mice. The greater flux of cysteine through the cysteine desulfhydration reactions catalyzed by CTH and CBS in hepatocytes from Cdo1-null mice appeared to be the consequence of their higher cysteine levels, which were due to the lack of CDO and hence lack of catabolism of cysteine by the cysteinesulfinate-dependent pathways. Both CBS and CTH appeared to contribute substantially to cysteine desulfhydration, with estimates of 56 % by CBS and 44 % by CTH in hepatocytes from wild-type mice, and 63 % by CBS and 37 % by CTH in hepatocytes from Cdo1-null mice.

  18. Oral Probiotic VSL#3 Prevents Autoimmune Diabetes by Modulating Microbiota and Promoting Indoleamine 2,3-Dioxygenase-Enriched Tolerogenic Intestinal Environment.

    Science.gov (United States)

    Dolpady, Jayashree; Sorini, Chiara; Di Pietro, Caterina; Cosorich, Ilaria; Ferrarese, Roberto; Saita, Diego; Clementi, Massimo; Canducci, Filippo; Falcone, Marika

    2016-01-01

    The gut microbiota modulates the autoimmune pathogenesis of type 1 diabetes (T1D) via mechanisms that remain largely unknown. The inflammasome components are innate immune sensors that are highly influenced by the gut environment and play pivotal roles in maintaining intestinal immune homeostasis. In this study we show that modifications of the gut microbiota induced by oral treatment with Lactobacillaceae-enriched probiotic VSL#3, alone or in combination with retinoic acid (RA), protect NOD mice from T1D by affecting inflammasome at the intestinal level. In particular, we show that VSL#3 treatment inhibits IL-1β expression while enhancing release of protolerogenic components of the inflammasome, such as indoleamine 2,3-dioxygenase (IDO) and IL-33. Those modifications of the intestinal microenvironment in VSL#3-treated NOD mice modulate gut immunity by promoting differentiation of tolerogenic CD103(+) DCs and reducing differentiation/expansion of Th1 and Th17 cells in the intestinal mucosa and at the sites of autoimmunity, that is, within the pancreatic lymph nodes (PLN) of VSL#3-treated NOD mice. Our data provide a link between dietary factors, microbiota composition, intestinal inflammation, and immune homeostasis in autoimmune diabetes and could pave the way for new therapeutic approaches aimed at changing the intestinal microenvironment with probiotics to counterregulate autoimmunity and prevent T1D.

  19. The potato carotenoid cleavage dioxygenase 4 catalyzes a single cleavage of β-ionone ring-containing carotenes and non-epoxidated xanthophylls

    KAUST Repository

    Bruno, Mark

    2015-04-01

    Down-regulation of the potato carotenoid cleavage dioxygenase 4 (StCCD4) transcript level led to tubers with altered morphology and sprouting activity, which also accumulated higher levels of violaxanthin and lutein leading to elevated carotenoid amounts. This phenotype indicates a role of this enzyme in tuber development, which may be exerted by a cleavage product. In this work, we investigated the enzymatic activity of StCCD4, by expressing the corresponding cDNA in carotenoid accumulating Escherichia coli strains and by performing in vitro assays with heterologously expressed enzyme. StCCD4 catalyzed the cleavage of all-. trans-β-carotene at the C9\\'-C10\\' double bond, leading to β-ionone and all-. trans-β-apo-10\\'-carotenal, both in vivo and in vitro. The enzyme also cleaved β,β-cryptoxanthin, zeaxanthin and lutein either at the C9\\'-C10\\' or the C9-C10 double bond in vitro. In contrast, we did not observe any conversion of violaxanthin and only traces of activity with 9-. cis-β-carotene, which led to 9-. cis-β-apo-10\\'-carotenal. Our data indicate that all-. trans-β-carotene is the likely substrate of StCCD4 in planta, and that this carotene may be precursor of an unknown compound involved in tuber development.

  20. DNA双加氧酶TET在中枢神经系统的研究进展%Research progress of DNA dioxygenase TET in the central nervous system

    Institute of Scientific and Technical Information of China (English)

    刘洁; 米亚静

    2015-01-01

    DNA双加氧酶TET家族是新发现的一类表观遗传修饰蛋白,能够将DNA的5-甲基胞嘧啶氧化为5-羟甲基胞嘧啶,进而调控基因的表达。多项研究显示,TET1-3在中枢神经系统表达丰富,其潜在的生物功能也被广泛关注。本文从TET蛋白结构功能概述、TET蛋白在中枢神经系统的表达及功能以及针对TET家族的基因敲除小鼠实验三方面作一综述。%DNA dioxygenase TET family is a recently discovered proteins involved epigenetic modification, which can oxidize the 5-methylcytosine of DNA into 5-hydroxymethylcytosine and thereby regulate gene expression. Accumulative studies have shown that TET1-3 was abundantly expressed in the central nervous system, and its poten-tial functions were beginning to be studied. This paper gives an overview of the structure and functions of TET, its po-tential roles in the central nervous system, and also the TET gene knockout experiments.

  1. Effect of surfactant-induced cell surface modifications on electron transport system and catechol 1,2-dioxygenase activities and phenanthrene biodegradation by Citrobacter sp. SA01.

    Science.gov (United States)

    Li, Feng; Zhu, Lizhong

    2012-11-01

    In order to better understand how surfactants affect biodegradation of hydrophobic organic compounds (HOCs), Tween 80 and sodium dodecyl benzene sulfonate (SDBS), were selected to investigate effects on cell surface hydrophobicity (CSH), electron transport system (ETS) activities and phenanthrene biodegradation by Citrobacter sp. SA01. Tween 80 and SDBS increased CSH by 19.8-25.2%, ETS activities by 352.1-376.0μmol/gmin, catechol 1,2-dioxygenase (C12) activities by 50.8-52.7U/L, and phenanthrene biodegradation by 8.9-17.2% separately in the presence of 50mg/L of surfactants as compared to in their absence. Lipopolysaccharide (LPS) release was 334.7μg/mg in the presence of both surfactants whereas in their absence only 8.6-44.4μg/mg of LPS was released. Thus, enhanced LPS release probably increased ETS and C12 activities as well as phenanthrene biodegradation by increasing CSH. The results demonstrate that surfactant-enhanced CSH provides a simple, yet effective strategy for field applications of surfactant-enhanced bioremediation of HOCs.

  2. Prognostic significance of Tet methylcytosine dioxygenase 2 (TET2) gene mutations in adult patients with acute myeloid leukemia: a meta-analysis.

    Science.gov (United States)

    Liu, Wen-Jian; Tan, Xiao-Hong; Luo, Xiu-Ping; Guo, Bao-Ping; Wei, Zhou-Ji; Ke, Qing; He, Sha; Cen, Hong

    2014-12-01

    Tet methylcytosine dioxygenase 2 (TET2) gene mutations have recently been recognized in acute myeloid leukemia (AML). We performed a meta-analysis to evaluate the controversial prognostic significance of TET2 mutations in AML. Eight studies, covering 2552 patients with AML, were included in this analysis. Pooled hazard ratios (HRs) indicated that TET2 mutations had a poor prognostic impact on the survival of patients with AML. The combined HR for overall survival (OS) was 1.53 and the summary HR for event-free survival (EFS) was 1.64. Additionally, TET2 mutations appeared to be an adverse prognostic indicator in both patients with cytogenetically normal (CN)-AML (HR for OS: 1.43 and HR for EFS: 1.76) and subgroups of patients with favorable-risk genotypes (HR for EFS: 2.35) and intermediate-I-risk genotypes (HR for EFS: 1.57). These findings indicate that TET2 mutations have an adverse impact on prognosis and may help to justify risk-adapted therapeutic strategies for patients with AML.

  3. Enhanced tolerance and remediation to mixed contaminates of PCBs and 2,4-DCP by transgenic alfalfa plants expressing the 2,3-dihydroxybiphenyl-1,2-dioxygenase.

    Science.gov (United States)

    Wang, Yan; Ren, Hejun; Pan, Hongyu; Liu, Jinliang; Zhang, Lanying

    2015-04-01

    Polychlorinated biphenyls (PCBs) and 2,4-dichlorophenol (2,4-DCP) generally led to mixed contamination of soils as a result of commercial and agricultural activities. Their accumulation in the environment poses great risks to human and animal health. Therefore, the effective strategies for disposal of these pollutants are urgently needed. In this study, genetic engineering to enhance PCBs/2,4-DCP phytoremediation is a focus. We cloned the 2,3-dihydroxybiphenyl-1,2-dioxygenase (BphC.B) from a soil metagenomic library, which is the key enzyme of aerobic catabolism of a variety of aromatic compounds, and then it was expressed in alfalfa driven by CaMV 35S promoter using Agrobacterium-mediated transformation. Transgenic line BB11 was selected out through PCR, Western blot analysis and enzyme activity assays. Its disposal and tolerance to both PCBs and 2,4-DCP were examined. The tolerance capability of transgenic line BB11 towards complex contaminants of PCBs/2,4-DCP significantly increased compared with non-transgenic plants. Strong dissipation of PCBs and high removal efficiency of 2,4-DCP were exhibited in a short time. It was confirmed expressing BphC.B would be a feasible strategy to help achieving phytoremediation in mixed contaminated soils with PCBs and 2,4-DCP.

  4. Tryptamine and dimethyltryptamine inhibit indoleamine 2,3 dioxygenase and increase the tumor-reactive effect of peripheral blood mononuclear cells.

    Science.gov (United States)

    Tourino, Melissa Cavalheiro; de Oliveira, Edson Mendes; Bellé, Luziane Potrich; Knebel, Franciele Hinterholz; Albuquerque, Renata Chaves; Dörr, Felipe Augusto; Okada, Sabrina Sayori; Migliorini, Silene; Soares, Irene Silva; Campa, Ana

    2013-07-01

    Indoleamine 2,3-dioxygenase (IDO) is an interferon-γ (IFN-γ)-induced tryptophan-degrading enzyme, producing kynurenine (KYN) that participates in the mechanism of tumor immune tolerance. Thus, IDO inhibition has been considered a strategy for anticancer therapy. The aim of this study was to identify whether the metabolites originated from the competitive routes of tryptophan metabolism, such as the serotonergic or N, N-dimethyltryptamine (DMT) pathways, have inhibitory effects on recombinant human IDO (rhIDO) activity. Serotonin and melatonin had no effect; on the other hand, tryptamine (TRY) and DMT modulated the activity of rhIDO as classical non-competitive inhibitors, with Ki values of 156 and 506 μM, respectively. This inhibitory effect was also observed on constitutively expressed or IFN-γ-induced IDO in the A172 human glioma cell line. TRY and DMT increased the cytotoxic activity of peripheral blood mononuclear cells (PBMCs) in co-culture assays. We conclude that the IDO inhibition by TRY and DMT contributed to a more effective tumor-reactive response by the PBMCs.

  5. The Fe-heme structure of met-indoleamine 2,3-dioxygenase-2 determined by X-ray absorption fine structure

    Energy Technology Data Exchange (ETDEWEB)

    Aitken, Jade B. [School of Chemistry, The University of Sydney, NSW 2006 (Australia); Australian Synchrotron, Clayton, Victoria 3168 (Australia); Institute of Materials Structure Science, KEK, Tsukuba, Ibaraki 305-0801 (Japan); Austin, Christopher J.D. [School of Chemistry, The University of Sydney, NSW 2006 (Australia); Department of Pathology and Bosch Institute, The University of Sydney, Camperdown, NSW 2006 (Australia); Hunt, Nicholas H.; Ball, Helen J. [Department of Pathology and Bosch Institute, The University of Sydney, Camperdown, NSW 2006 (Australia); Lay, Peter A., E-mail: peter.lay@sydney.edu.au [School of Chemistry, The University of Sydney, NSW 2006 (Australia)

    2014-07-18

    Highlights: • IDO2 is a newly discovered tryptophan metabolising enzyme with a role in immunity. • IDO2’s active site contains a heme moiety for tryptophan binding and catabolism. • EXAFS/XANES analysis provides the first data of an IDO2 Fe-heme environment. • IDO2 Fe-heme exists as a low spin bis(His) form at 10 K; mixed spin-state at RT. - Abstract: Multiple-scattering (MS) analysis of EXAFS data on met-indoleamine 2,3-dioxygenase-2 (IDO2) and analysis of XANES have provided the first direct structural information about the axial donor ligands of the iron center for this recently discovered protein. At 10 K, it exists in a low-spin bis(His) form with Fe–N{sub p}(av) = 1.97 Å, the Fe–N{sub Im} bond lengths of 2.11 Å and 2.05 Å, which is in equilibrium with a high-spin form at room temperature. The bond distances in the low-spin form are consistent with other low-spin hemeproteins, as is the XANES spectrum, which is closer to that of the low-spin met-Lb than that of the high-spin met-Mb. The potential physiological role of this spin equilibrium is discussed.

  6. High-affinity uptake of kynurenine and nitric oxide-mediated inhibition of indoleamine 2,3-dioxygenase in bone marrow-derived myeloid dendritic cells.

    Science.gov (United States)

    Hara, Toshiaki; Ogasawara, Nanako; Akimoto, Hidetoshi; Takikawa, Osamu; Hiramatsu, Rie; Kawabe, Tsutomu; Isobe, Ken-Ichi; Nagase, Fumihiko

    2008-02-15

    Indoleamine 2,3-dioxygenase (IDO)-initiated tryptophan metabolism along the kynurenine (Kyn) pathway in some dendritic cells (DC) such as plasmacytoid DC (pDC) regulates T-cell responses. It is unclear whether bone marrow-derived myeloid DC (BMDC) express functional IDO. The IDO expression was examined in CD11c(+)CD11b(+) BMDC differentiated from mouse bone marrow cells using GM-CSF. CpG oligodeoxynucleotides (CpG) induced the expression of IDO protein with the production of nitric oxide (NO) in BMDC in cultures for 24h. In the enzyme assay using cellular extracts of BMDC, the IDO activity of BMDC stimulated with CpG was enhanced by the addition of a NO synthase (NOS) inhibitor, suggesting that IDO activity was suppressed by NO production. On the other hand, the concentration of Kyn in the culture supernatant of BMDC was not increased by stimulation with CpG. Exogenously added Kyn was taken up by BMDC independently of CpG stimulation and NO production, and the uptake of Kyn was inhibited by a transport system L-specific inhibitor or high concentrations of tryptophan. The uptake of tryptophan by BMDC was markedly lower than that of Kyn. In conclusion, IDO activity in BMDC is down-regulated by NO production, whereas BMDC strongly take up exogenous Kyn.

  7. Chronic lymphocytic leukemia nurse-like cells express hepatocyte growth factor receptor (c-MET) and indoleamine 2,3-dioxygenase and display features of immunosuppressive type 2 skewed macrophages

    Science.gov (United States)

    Giannoni, Paolo; Pietra, Gabriella; Travaini, Giorgia; Quarto, Rodolfo; Shyti, Genti; Benelli, Roberto; Ottaggio, Laura; Mingari, Maria Cristina; Zupo, Simona; Cutrona, Giovanna; Pierri, Ivana; Balleari, Enrico; Pattarozzi, Alessandra; Calvaruso, Marco; Tripodo, Claudio; Ferrarini, Manlio; de Totero, Daniela

    2014-01-01

    Hepatocyte growth factor, produced by stromal and follicular dendritic cells, and present at high concentrations in the sera of patients with chronic lymphocytic leukemia, prolongs the survival of leukemic B cells by interacting with their receptor, c-MET. It is, however, unknown whether hepatocyte growth factor influences microenvironmental cells, such as nurse-like cells, which deliver survival signals to the leukemic clone. We evaluated the expression of c-MET on nurse-like cells and monocytes from patients with chronic lymphocytic leukemia and searched for phenotypic/functional features supposed to be influenced by the hepatocyte growth factor/c-MET interaction. c-MET is expressed at high levels on nurse-like cells and at significantly higher levels than normal on monocytes from patients. Moreover, the hepatocyte growth factor/c-MET interaction activates STAT3TYR705 phosphorylation in nurse-like cells. Indoleamine 2,3-dioxygenase, an enzyme modulating T-cell proliferation and induced on normal monocytes after hepatocyte growth factor treatment, was detected together with interleukin-10 on nurse-like cells, and on freshly-prepared patients’ monocytes. Immunohistochemical/immunostaining analyses demonstrated the presence of c-MET+ and indoleamine 2,3-dioxygenase+ cells in lymph node biopsies, co-expressed with CD68 and vimentin. Furthermore nurse-like cells and chronic lymphocytic monocytes significantly inhibited T-cell proliferation, prevented by anti-transforming growth factor beta and interleukin-10 antibodies and indoleamine 2,3-dioxygenase inhibitors, and supported CD4+CD25high+/FOXP3+ T regulatory cell expansion. We suggest that nurse-like cells display features of immunosuppressive type 2 macrophages: higher hepatocyte growth factor levels, produced by leukemic or other microenvironmental surrounding cells, may cooperate to induce M2 polarization. Hepatocyte growth factor may thus have a dual pathophysiological role: directly through enhancement of

  8. [Degradation of L-phenylalanine and of aromatic carboxylic acids by chloridazon-degrading bacteria. Combination of side chain degradation and dioxygenase pathway].

    Science.gov (United States)

    Wegst, W; Lingens, F

    1981-09-01

    Strain N of Chloridazon-degrading bacteria degrades phenylalanine via cis-2,3-dihydro-2,3-dihydroxyphenylalanine,2,3-dihydroxyphenylalanine aspartate and 4-hydroxy-2-oxovalerate [Hoppe-Seyler's Z. Physiol. Chem. 360, 957--969, (1979); Biochem. J. 194, 679--684 (1981)]. cis-2,3-Dihydro-2,3-dihydroxyphenylalanine and 2,3-dihydroxyphenylalanine as well as phenylpyruvate, cis-2,3-dihydro-2,3-dihydroxyphenylpyruvate, 2,3-dihydroxyphenylpyruvate, cis-2,3-dihydro-2,3-dihydroxyphenylacetate, 2,3-dihydroxyphenylacetate and 2,3-dihydroxybenzaldehyde are detectable in the medium of strain E during growth on phenylalanine. Incubation with phenylacetate, 3-phenylpropionate or 4-phenylbutyrate leads to the accumulation of the corresponding cis-2,3-dihydro-2,3-dihydroxyphenyl derivatives. These compounds are transformed with dihydrodiol dehydrogenase to 2,3-dihydroxyphenylacetate, 3-(2,3-dihydroxyphenyl)propionate and 4-(2,3-dihydroxyphenyl)-butyrate, 3-(2,3-dihydroxyphenyl)propionate is attacked by a catechol 2,3-dioxygenase and the meta-cleavage product is again cleaved by a hydrolase yielding succinate. In a similar reaction sequence the degradation of 4-phenylbutyrate leads to the formation of glutarate. From the growth medium of strain E on phenylacetate also small amounts of 2-, 3- and 4-hydroxyphenylacetate were isolated. Resting cells were shown to metabolize 3- and 4-hydroxyphenylacetate via homogentisate and 3,4-dihydroxyphenylacetate. In the culture medium of strain K2AP benzoate could be detected. Pathways for the degradation of phenylalanine and aromatic carboxylic acids in chloridazon degrading bacteria are proposed.

  9. Homogentisate 1-2-Dioxygenase Downregulation in the Chronic Persistence of Pseudomonas aeruginosa Australian Epidemic Strain-1 in the CF Lung.

    Directory of Open Access Journals (Sweden)

    Christopher J Harmer

    Full Text Available Some Pseudomonas aeruginosa strains including Australian Epidemic Strain-1 (AES-1 or AUS-01 cause persistent chronic infection in cystic fibrosis (CF patients, with greater morbidity and mortality. Factors conferring persistence are largely unknown. Previously we analysed the transcriptomes of AES-1 grown in Luria broth, nematode growth medium for Caenorhabditis elegans assay (both aerobic and artificial sputum medium (mainly hypoxic. Transcriptional comparisons included chronic AES-1 strains against PAO1 and acute AES-1 (AES-1R against its chronic isogen (AES-1M, isolated 10.5 years apart from a CF patient and not eradicated in the meantime. Prominent amongst genes downregulated in AES-1M in all comparisons was homogentisate-1-2-dioxygenase (hmgA; an oxygen-dependent gene known to be mutationally deactivated in many chronic infection strains of P. aeruginosa. To investigate if hmgA downregulation and deactivation gave similar virulence persistence profiles, a hmgA mutant made in UCBPP-PA14 utilising RedS-recombinase and AES-1M were assessed in the C. elegans virulence assay, and the C57BL/6 mouse for pulmonary colonisation and TNF-α response. In C. elegans, hmgA deactivation resulted in significantly increased PA14 virulence while hmgA downregulation reduced AES-1M virulence. AES-1M was significantly more persistent in mouse lung and showed a significant increase in TNF-α (p<0.0001, sustained even with no detectable bacteria. PA14ΔhmgA did not show increased TNF-α. This study suggests that hmgA may have a role in P. aeruginosa persistence in chronic infection and the results provide a starting point for clarifying the role of hmgA in chronic AES-1.

  10. Lipopolysaccharide-induced brain activation of the indoleamine 2,3-dioxygenase and depressive-like behavior are impaired in a mouse model of metabolic syndrome.

    Science.gov (United States)

    Dinel, Anne-Laure; André, Caroline; Aubert, Agnès; Ferreira, Guillaume; Layé, Sophie; Castanon, Nathalie

    2014-02-01

    Although peripheral low-grade inflammation has been associated with a high incidence of mood symptoms in patients with metabolic syndrome (MetS), much less is known about the potential involvement of brain activation of cytokines in that context. Recently we showed in a mouse model of MetS, namely the db/db mice, an enhanced hippocampal inflammation associated with increased anxiety-like behavior (Dinel et al., 2011). However, depressive-like behavior was not affected in db/db mice. Based on the strong association between depressive-like behavior and cytokine-induced brain activation of indoleamine 2,3-dioxygenase (IDO), the enzyme that metabolizes tryptophan along the kynurenine pathway, these results may suggest an impairment of brain IDO activation in db/db mice. To test this hypothesis, we measured the ability of db/db mice and their healthy db/+ littermates to enhance brain IDO activity and depressive-like behavior after a systemic immune challenge with lipopolysaccharide (LPS). Here we show that LPS (5 μg/mouse) significantly increased depressive-like behavior (increased immobility time in a forced-swim test, FST) 24h after treatment in db/+ mice, but not in db/db mice. Interestingly, db/db mice also displayed after LPS treatment blunted increase of brain kynurenine/tryptophan ratio compared to their db/+ counterparts, despite enhanced induction of hippocampal cytokine expression (interleukin-1β, tumor necrosis factor-α). Moreover, this was associated with an impaired effect of LPS on hippocampal expression of the brain-derived neurotrophic factor (BDNF) that contributes to mood regulation, including under inflammatory conditions. Collectively, these data indicate that the rise in brain tryptophan catabolism and depressive-like behavior induced by innate immune system activation is impaired in db/db mice. These findings could have relevance in improving the management and treatment of inflammation-related complications in MetS.

  11. Overexpression of Crocus carotenoid cleavage dioxygenase, CsCCD4b, in Arabidopsis imparts tolerance to dehydration, salt and oxidative stresses by modulating ROS machinery.

    Science.gov (United States)

    Baba, Shoib Ahmad; Jain, Deepti; Abbas, Nazia; Ashraf, Nasheeman

    2015-09-15

    Apocarotenoids modulate vital physiological and developmental processes in plants. These molecules are formed by the cleavage of carotenoids, a reaction catalyzed by a family of enzymes called carotenoid cleavage dioxygenases (CCDs). Apocarotenoids like β-ionone and β-cyclocitral have been reported to act as stress signal molecules during high light stress in many plant species. In Crocus sativus, these two apocarotenoids are formed by enzymatic cleavage of β-carotene at 9, 10 and 7, 8 bonds by CsCCD4 enzymes. In the present study three isoforms of CsCCD4 were subjected to molecular modeling and docking analysis to determine their substrate specificity and all the three isoforms displayed high substrate specificity for β-carotene. Further, expression of these three CsCCD4 isoforms investigated in response to various stresses revealed that CsCCD4a and CsCCD4b exhibit enhanced expression in response to dehydration, salt and methylviologen, providing a clue towards their role in mediating plant defense response. This was confirmed by overexpressing CsCCD4b in Arabidopsis. The transgenic plants developed longer roots and possessed higher number of lateral roots. Further, overexpression of CsCCD4b imparted enhanced tolerance to salt, dehydration and oxidative stresses as was evidenced by higher survival rate, increased relative root length and biomass in transgenic plants as compared to wild type. Transgenic plants also displayed higher activity and expression of reactive oxygen species (ROS) metabolizing enzymes. This indicates that β-ionone and β-cyclocitral which are enzymatic products of CsCCD4b may act as stress signals and mediate reprogramming of stress responsive genes which ultimately leads to plant defense.

  12. The tryptophan derivative, tranilast, and conditioned medium with indoleamine 2,3-dioxygenase-expressing cells inhibit the proliferation of lymphoid malignancies.

    Science.gov (United States)

    Suwa, Shihoko; Kasubata, Aya; Kato, Miyu; Iida, Megumi; Watanabe, Ken; Miura, Osamu; Fukuda, Tetsuya

    2015-03-01

    Indoleamine 2,3-dioxygenase (IDO) is an enzyme that catalyzes tryptophan degradation and induces immunosuppression. Although IDO is an important factor that allows tumors to escape from immunological attack, its effect on lymphoid malignancies has not been fully revealed. We evaluated the expression of IDO in samples from patients with B-cell malignancies. The IDO expression in the tumor samples was comparable to those in peripheral blood mononuclear cells from healthy donors and had mainly originated from non-B cell populations. We introduced IDO gene into Chinese hamster ovary (CHO) cells. We then cultured various cell lines using CHO- or CHO-IDO-conditioned medium. Compared with the CHO medium (CHO-CM), the CHO-IDO medium (IDO-CM) decreased the viability of lymphoid cell lines but not those of the non-lymphoid lines. Next, we examined the effects of tryptophan metabolites on lymphoid tumors, and revealed that the drug N-[3',4'-dimethoxycinnamoyl] anthranilic acid (tranilast), a synthetic derivative of the tryptophan metabolite, was able to repress proliferation and dose-dependently induce cell death of lymphoid cell lines. Tranilast induced the activation of the c-Jun N-terminal kinase, which is activated by cellular stress, in lymphoid cells. The effect of tranilast on lymphoid cells was independent of the aryl hydrocarbon receptor (AhR) although tranilast has been reported to be an AhR agonist. Finally, the administration of tranilast decreased murine lymphoid tumor progression in vivo. These results indicated that IDO and tryptophan derivatives, particularly tranilast, can be tools for the therapy for lymphoid malignancies.

  13. New target carotenoids for CCD4 enzymes are revealed with the characterization of a novel stress-induced carotenoid cleavage dioxygenase gene from Crocus sativus.

    Science.gov (United States)

    Rubio-Moraga, Angela; Rambla, José Luis; Fernández-de-Carmen, Asun; Trapero-Mozos, Almudena; Ahrazem, Oussama; Orzáez, Diego; Granell, Antonio; Gómez-Gómez, Lourdes

    2014-11-01

    Apocarotenoid compounds play diverse communication functions in plants, some of them being as hormones, pigments and volatiles. Apocarotenoids are the result of enzymatic cleavage of carotenoids catalyzed by carotenoid cleavage dioxygenase (CCD). The CCD4 family is the largest family of plant CCDs, only present in flowering plants, suggesting a functional diversification associated to the adaptation for specific physiological capacities unique to them. In saffron, two CCD4 genes have been previously isolated from the stigma tissue and related with the generation of specific volatiles involved in the attraction of pollinators. The aim of this study was to identify additional CCD4 members associated with the generation of other carotenoid-derived volatiles during the development of the stigma. The expression of CsCCD4c appears to be restricted to the stigma tissue in saffron and other Crocus species and was correlated with the generation of megastigma-4,6,8-triene. Further, CsCCD4c was up-regulated by wounding, heat, and osmotic stress, suggesting an involvement of its apocarotenoid products in the adaptation of saffron to environmental stresses. The enzymatic activity of CsCCD4c was determined in vivo in Escherichia coli and subsequently in Nicotiana benthamiana by analyzing carotenoids by HPLC-DAD and the volatile products by GC/MS. β-Carotene was shown to be the preferred substrate, being cleaved at the 9,10 (9',10') bonds and generating β-ionone, although β-cyclocitral resulting from a 7,8 (7',8') cleavage activity was also detected at lower levels. Lutein, neoxanthin and violaxanthin levels in Nicotiana leaves were markedly reduced when CsCCD4c is over expressed, suggesting that CsCCD4c recognizes these carotenoids as substrates.

  14. Haemophilus ducreyi lipooligosaccharides induce expression of the immunosuppressive enzyme indoleamine 2,3-dioxygenase via type I interferons and tumor necrosis factor alpha in human dendritic cells.

    Science.gov (United States)

    Li, Wei; Katz, Barry P; Spinola, Stanley M

    2011-08-01

    Haemophilus ducreyi causes chancroid, a genital ulcer disease. In human inoculation experiments, most volunteers fail to clear the bacteria despite the infiltration of innate and adaptive immune cells to the infected sites. The immunosuppressive protein indoleamine 2,3-dioxygenase (IDO) is a rate-limiting enzyme in the L-tryptophan-kynurenine metabolic pathway. Tryptophan depletion and tryptophan metabolites contribute to pathogen persistence by inhibiting T cell proliferation, inducing T cell apoptosis, and promoting the expansion of FOXP3(+) regulatory T (Treg) cells. We previously found that FOXP3(+) Treg cells are enriched in experimental lesions and that H. ducreyi induced IDO transcription in dendritic cells (DC) derived from blood of infected volunteers who developed pustules. Here, we showed that enzymatically active IDO was induced in DC by H. ducreyi. Neutralizing antibodies against interferon alpha/beta receptor 2 chain (IFNAR2) and tumor necrosis factor alpha (TNF-α) inhibited IDO induction. Inhibitors of the mitogen-activated protein kinase (MAPK) p38 and nuclear factor-κB (NF-κB) also inhibited IDO expression. Neither bacterial contact with nor uptake by DC was required for IDO activation. H. ducreyi culture supernatant and H. ducreyi lipooligosaccharides (LOS) induced IDO expression, which required type I interferons, TNF-α, and the three MAPK (p38, c-Jun N-terminal kinase, and extracellular signal regulated kinase) and NF-κB pathways. In addition, LOS-induced IFN-β activated the JAK-STAT pathway. Blocking the LOS/Toll-like receptor 4 (TLR4) signaling pathway greatly reduced H. ducreyi-induced IDO production. These findings indicate that H. ducreyi-induced IDO expression in DC is largely mediated by LOS via type I interferon- and TNF-α-dependent mechanisms and the MAPK, NF-κB, and JAK-STAT pathways.

  15. A "White" Anthocyanin-less Pomegranate (Punica granatum L.) Caused by an Insertion in the Coding Region of the Leucoanthocyanidin Dioxygenase (LDOX; ANS) Gene.

    Science.gov (United States)

    Ben-Simhon, Zohar; Judeinstein, Sylvie; Trainin, Taly; Harel-Beja, Rotem; Bar-Ya'akov, Irit; Borochov-Neori, Hamutal; Holland, Doron

    2015-01-01

    Color is an important determinant of pomegranate fruit quality and commercial value. To understand the genetic factors controlling color in pomegranate, chemical, molecular and genetic characterization of a "white" pomegranate was performed. This unique accession is lacking the typical pomegranate color rendered by anthocyanins in all tissues of the plant, including flowers, fruit (skin and arils) and leaves. Steady-state gene-expression analysis indicated that none of the analyzed "white" pomegranate tissues are able to synthesize mRNA corresponding to the PgLDOX gene (leucoanthocyanidin dioxygenase, also called ANS, anthocyanidin synthase), which is one of the central structural genes in the anthocyanin-biosynthesis pathway. HPLC analysis revealed that none of the "white" pomegranate tissues accumulate anthocyanins, whereas other flavonoids, corresponding to biochemical reactions upstream of LDOX, were present. Molecular analysis of the "white" pomegranate revealed the presence of an insertion and an SNP within the coding region of PgLDOX. It was found that the SNP does not change amino acid sequence and is not fully linked with the "white" phenotype in all pomegranate accessions from the collection. On the other hand, genotyping of pomegranate accessions from the collection and segregating populations for the "white" phenotype demonstrated its complete linkage with the insertion, inherited as a recessive single-gene trait. Taken together, the results indicate that the insertion in PgLDOX is responsible for the "white" anthocyanin-less phenotype. These data provide the first direct molecular, genetic and chemical evidence for the effect of a natural modification in the LDOX gene on color accumulation in a fruit-bearing woody perennial deciduous tree. This modification can be further utilized to elucidate the physiological role of anthocyanins in protecting the tree organs from harmful environmental conditions, such as temperature and UV radiation.

  16. A "White" Anthocyanin-less Pomegranate (Punica granatum L. Caused by an Insertion in the Coding Region of the Leucoanthocyanidin Dioxygenase (LDOX; ANS Gene.

    Directory of Open Access Journals (Sweden)

    Zohar Ben-Simhon

    Full Text Available Color is an important determinant of pomegranate fruit quality and commercial value. To understand the genetic factors controlling color in pomegranate, chemical, molecular and genetic characterization of a "white" pomegranate was performed. This unique accession is lacking the typical pomegranate color rendered by anthocyanins in all tissues of the plant, including flowers, fruit (skin and arils and leaves. Steady-state gene-expression analysis indicated that none of the analyzed "white" pomegranate tissues are able to synthesize mRNA corresponding to the PgLDOX gene (leucoanthocyanidin dioxygenase, also called ANS, anthocyanidin synthase, which is one of the central structural genes in the anthocyanin-biosynthesis pathway. HPLC analysis revealed that none of the "white" pomegranate tissues accumulate anthocyanins, whereas other flavonoids, corresponding to biochemical reactions upstream of LDOX, were present. Molecular analysis of the "white" pomegranate revealed the presence of an insertion and an SNP within the coding region of PgLDOX. It was found that the SNP does not change amino acid sequence and is not fully linked with the "white" phenotype in all pomegranate accessions from the collection. On the other hand, genotyping of pomegranate accessions from the collection and segregating populations for the "white" phenotype demonstrated its complete linkage with the insertion, inherited as a recessive single-gene trait. Taken together, the results indicate that the insertion in PgLDOX is responsible for the "white" anthocyanin-less phenotype. These data provide the first direct molecular, genetic and chemical evidence for the effect of a natural modification in the LDOX gene on color accumulation in a fruit-bearing woody perennial deciduous tree. This modification can be further utilized to elucidate the physiological role of anthocyanins in protecting the tree organs from harmful environmental conditions, such as temperature and UV

  17. Comparative study of putative 9-cis-epoxycarotenoid dioxygenase and abscisic acid accumulation in the responses of Sunki mandarin and Rangpur lime to water deficit.

    Science.gov (United States)

    Neves, D M; Filho, M A Coelho; Bellete, B S; Silva, M F G F; Souza, D T; Dos S Soares Filho, W; Costa, M G C; Gesteira, A S

    2013-09-01

    Abscisic acid is a plant hormone that participates in essential plant physiological processes, especially during adaptation to many environmental stresses, such as water deficit. The relationship between ABA accumulation and the expression of putative carotenoid cleavage dioxygenase (CCD) genes was investigated in the pot-cultivated leaves and roots of the 'Rangpur' lime and 'Sunki Maravilha' mandarin plants. Transpiration, stomatal resistance and leaf growth were evaluated when these genotypes were subjected to continuous water deficit. Under water deficit conditions, the 'Rangpur' lime extracts used greater amounts of water when compared to the 'Sunki Maravilha' plants, which reached the greatest stomatal resistance 5 days before 'Rangpur' lime. When subjected to water deficit, the roots and leaves of 'Sunki Maravilha' showed a progressive increase in ABA accumulation; however, in 'Rangpur' lime, alternations between high and low ABA concentrations were observed. These results suggest a retroactive feeding regulation by ABA. In 'Rangpur' lime the NCED2, NCED3 and CCD4a genes were expressed at the highest levels in the roots, and NCED5 was highly expressed in the leaves; in 'Sunki Maravilha', the NCED2 and NCED5 genes were most highly expressed in the roots, and NCED2 was most highly expressed in the leaves. However, for both genotypes, the transcription of these genes only correlated with ABA accumulation during the most severe water deficit conditions. The 'Rangpur' lime behaved as a vigorous rootstock; the leaf growth remained unaltered even when water was scarce. However, 'Sunki Maravilha' adaptation was based on the equilibrium of the response between the root and the aerial tissues due to water restriction. The use of the Sunki mandarin in combination with a scion with similar characteristics as its own, which responds to water deficit stress by accumulating ABA in the leaves, may display good drought tolerance under field conditions.

  18. Strong Correlation of Indoleamine 2,3-Dioxygenase 1 Expression with Basal-Like Phenotype and Increased Lymphocytic Infiltration in Triple-Negative Breast Cancer

    Science.gov (United States)

    Kim, Sewha; Park, Sanghui; Cho, Min Sun; Lim, Woosung; Moon, Byung-In; Sung, Sun Hee

    2017-01-01

    Indoleamine 2,3-dioxygenase 1 (IDO1) is an immunosuppressive enzyme involved in tumor immune escape. Blockade of the IDO1 pathway is an emerging modality of cancer immunotherapy. Triple-negative breast cancer (TNBC) lacks established therapeutic targets and may be a good candidate for this novel immunotherapeutic agent. The purpose of this study was to evaluate the clinicopathologic characteristics of the IDO1-expressing TNBC subset. A tissue microarray was constructed from 200 patients with TNBC. Immunohistochemistry (IHC) for IDO1 and TNBC molecular subtype-surrogate markers (AR, GCDFP-15, claudin-3, E-cadherin, CK5/6, and EGFR) was performed using this tissue microarray. Real-time polymerase chain reaction was performed to confirm the IDO1 mRNA expression level in 16 fresh-frozen TNBC samples. Two hundred TNBCs were classified into four subtypes based on surrogate IHC results: 22 luminal androgen receptor type (11.0%), 23 claudin-low type (11.4%), 103 basal-like type (51.5%), and 52 mixed type (26.0%). IDO1 positivity (defined as expression of >10% tumor cells) was observed in 37% of all TNBCs. IDO1 IHC expression was well correlated with mRNA expression. IDO1 positivity was significantly associated with smaller tumor size, dense stromal lymphocytic infiltration, and basal-like phenotype; however, it did not affect the patients' prognosis. IDO1 expression in basal-like TNBCs is considered an immune inhibitory signal that counterbalances active immunity and may reflect the high mutational load of these tumors. Our results suggest which patients with TNBC would be more efficaciously treated with IDO1 blockade. PMID:28123606

  19. Replacement of two amino acids of 9R-dioxygenase-allene oxide synthase of Aspergillus niger inverts the chirality of the hydroperoxide and the allene oxide.

    Science.gov (United States)

    Sooman, Linda; Wennman, Anneli; Hamberg, Mats; Hoffmann, Inga; Oliw, Ernst H

    2016-02-01

    The genome of Aspergillus niger codes for a fusion protein (EHA25900), which can be aligned with ~50% sequence identity to 9S-dioxygenase (DOX)-allene oxide synthase (AOS) of Fusarium oxysporum, homologues of the Fusarium and Colletotrichum complexes and with over 62% sequence identity to homologues of Aspergilli, including (DOX)-9R-AOS of Aspergillus terreus. The aims were to characterize the enzymatic activities of EHA25900 and to identify crucial amino acids for the stereospecificity. Recombinant EHA25900 oxidized 18:2n-6 sequentially to 9R-hydroperoxy-10(E),12(Z)-octadecadienoic acid (9R-HPODE) and to a 9R(10)-allene oxide. 9S- and 9R-DOX-AOS catalyze abstraction of the pro-R hydrogen at C-11, but the direction of oxygen insertion differs. A comparison between twelve 9-DOX domains of 9S- and 9R-DOX-AOS revealed conserved amino acid differences, which could contribute to the chirality of products. The Gly616Ile replacement of 9R-DOX-AOS (A. niger) increased the biosynthesis of 9S-HPODE and the 9S(10)-allene oxide, whereas the Phe627Leu replacement led to biosynthesis of 9S-HPODE and the 9S(10)-allene oxide as main products. The double mutant (Gly616Ile, Phe627Leu) formed over 90% of the 9S stereoisomer of HPODE. 9S-HPODE was formed by antarafacial hydrogen abstraction and oxygen insertion, i.e., the original H-abstraction was retained but the product chirality was altered. We conclude that 9R-DOX-AOS can be altered to 9S-DOX-AOS by replacement of two amino acids (Gly616Ile, Phe627Leu) in the DOX domain.

  20. Implication of Tryptophan 2,3-Dioxygenase and its Novel Variants in the Hippocampus and Cerebellum During the Developing and Adult Brain

    Directory of Open Access Journals (Sweden)

    Masaaki Kanai

    2010-07-01

    Full Text Available Tryptophan 2,3-dioxygenase (TDO is a first and rate-limiting enzyme for the kynurenine pathway of tryptophan metabolism. Using Tdo-/-mice, we have recently shown that TDO plays a pivotal role in systemic tryptophan metabolism and brain serotonin synthesis as well as emotional status and adult neurogenesis. However, the expression of TDO in the brain has not yet been well characterized, in contrast to its predominant expression in the liver. To further examine the possible role of local TDO in the brain, we quantified the levels of tdo mRNA in various nervous tissues, using Northern blot and quantitative real-time RT-PCR. Higher levels of tdo mRNA expression were detected in the cerebellum and hippocampus. We also identified two novel variants of the tdo gene, termed tdo variant1 and variant2, in the brain. Similar to the known TDO form (TDO full-form, tetramer formation and enzymatic activity were obtained when these variant forms were expressed in vitro. While quantitative real-time RT-PCR revealed that the tissue distribution of these variants was similar to that of tdo full-form, the expression patterns of these variants during early postnatal development in the hippocampus and cerebellum differed. Our findings indicate that in addition to hepatic TDO, TDO and its variants in the brain might function in the developing and adult nervous system. Given the previously reported associations of tdo gene polymorphisms in the patients with autism and Tourette syndrome, the expression of TDO in the brain suggests the possible influence of TDO on psychiatric status. Potential functions of TDOs in the cerebellum, hippocampus and cerebral cortex under physiological and pathological conditions are discussed.

  1. Mononuclear non-heme iron(III) complexes of linear and tripodal tridentate ligands as functional models for catechol dioxygenases: Effect of -alkyl substitution on regioselectivity and reaction rate

    Indian Academy of Sciences (India)

    Mallayan Palaniandavar; Kusalendiran Visvaganesan

    2011-03-01

    Catechol dioxygenases are responsible for the last step in the biodegradation of aromatic molecules in the environment. The iron(II) active site in the extradiol-cleaving enzymes cleaves the C-C bond adjacent to the hydroxyl group, while the iron(III) active site in the intradiol-cleaving enzymes cleaves the C-C bond in between two hydroxyl groups. A series of mononuclear iron(III) complexes of the type [Fe(L)Cl3], where L is the linear -alkyl substituted bis(pyrid-2-ylmethyl)amine, -alkyl substituted -(pyrid-2-ylmethyl)ethylenediamine, linear tridentate 3N ligands containing imidazolyl moieties and tripodal ligands containing pyrazolyl moieties have been isolated and studied as structural and functional models for catechol dioxygenase enzymes. All the complexes catalyse the cleavage of catechols using molecular oxygen to afford both intra- and extradiol cleavage products. The rate of oxygenation depends on the solvent and the Lewis acidity of iron(III) center as modified by the sterically demanding -alkyl groups. Also, our studies reveal that stereo-electronic factors like the Lewis acidity of the iron(III) center and the steric demand of ligands, as regulated by the -alkyl substituents, determine the regioselectivity and the rate of dioxygenation. In sharp contrast to all these complexes, the pyrazole-containing tripodal ligand complexes yield mainly the oxidized product benzoquinone.

  2. Betalain production is possible in anthocyanin-producing plant species given the presence of DOPA-dioxygenase and L-DOPA

    Directory of Open Access Journals (Sweden)

    Harris Nilangani N

    2012-03-01

    Full Text Available Abstract Background Carotenoids and anthocyanins are the predominant non-chlorophyll pigments in plants. However, certain families within the order Caryophyllales produce another class of pigments, the betalains, instead of anthocyanins. The occurrence of betalains and anthocyanins is mutually exclusive. Betalains are divided into two classes, the betaxanthins and betacyanins, which produce yellow to orange or violet colours, respectively. In this article we show betalain production in species that normally produce anthocyanins, through a combination of genetic modification and substrate feeding. Results The biolistic introduction of DNA constructs for transient overexpression of two different dihydroxyphenylalanine (DOPA dioxygenases (DODs, and feeding of DOD substrate (L-DOPA, was sufficient to induce betalain production in cell cultures of Solanum tuberosum (potato and petals of Antirrhinum majus. HPLC analysis showed both betaxanthins and betacyanins were produced. Multi-cell foci with yellow, orange and/or red colours occurred, with either a fungal DOD (from Amanita muscaria or a plant DOD (from Portulaca grandiflora, and the yellow/orange foci showed green autofluorescence characteristic of betaxanthins. Stably transformed Arabidopsis thaliana (arabidopsis lines containing 35S: AmDOD produced yellow colouration in flowers and orange-red colouration in seedlings when fed L-DOPA. These tissues also showed green autofluorescence. HPLC analysis of the transgenic seedlings fed L-DOPA confirmed betaxanthin production. Conclusions The fact that the introduction of DOD along with a supply of its substrate (L-DOPA was sufficient to induce betacyanin production reveals the presence of a background enzyme, possibly a tyrosinase, that can convert L-DOPA to cyclo-DOPA (or dopaxanthin to betacyanin in at least some anthocyanin-producing plants. The plants also demonstrate that betalains can accumulate in anthocyanin-producing species. Thus, introduction

  3. Synthesis and characterization of Fe(II) β-diketonato complexes with relevance to acetylacetone dioxygenase: insights into the electronic properties of the 3-histidine facial triad.

    Science.gov (United States)

    Park, Heaweon; Baus, Jacob S; Lindeman, Sergey V; Fiedler, Adam T

    2011-12-05

    A series of high-spin iron(II) β-diketonato complexes have been prepared and characterized with the intent of modeling the substrate-bound form of the enzyme acetylacetone dioxygenase (Dke1). The Dke1 active site features an Fe(II) center coordinated by three histidine residues in a facial geometry--a departure from the standard 2-histidine-1-carboxylate (2H1C) facial triad dominant among nonheme monoiron enzymes. The deprotonated β-diketone substrate binds to the Fe center in a bidentate fashion. To better understand the implications of subtle changes in coordination environment for the electronic structures of nonheme Fe active sites, synthetic models were prepared with three different supporting ligands (L(N3)): the anionic (Me2)Tp and (Ph2)Tp ligands ((R2)Tp = hydrotris(pyrazol-1-yl)borate substituted with R-groups at the 3- and 5-pyrazole positions) and the neutral (Ph)TIP ligand ((Ph)TIP = tris(2-phenylimidazol-4-yl)phosphine). The resulting [(L(N3))Fe(acac(X))](0/+) complexes (acac(X) = substituted β-diketonates) were analyzed with a combination of experimental and computational methods, namely, X-ray crystallography, cyclic voltammetry, spectroscopic techniques (UV-vis absorption and (1)H NMR), and density functional theory (DFT). X-ray diffraction results for complexes with the (Me2)Tp ligand revealed six-coordinate Fe(II) centers with a bound MeCN molecule, while structures of the (Ph2)Tp and (Ph)TIP complexes generally exhibited five-coordinate geometries. Each [(L(N3))Fe(acac(X))](0/+) complex displays two broad absorption features in the visible region that arise from Fe(II)→acac(X) charge transfer and acac(X)-based transitions, consistent with UV-vis data reported for Dke1. These absorption bands, along with the Fe redox potentials, are highly sensitive to the identity of L(N3) and substitution of the β-diketonates. By interpreting the experimental results in conjunction with DFT calculations, detailed electronic-structure descriptions of the

  4. LPS-induced NF-{kappa}B expression in THP-1Blue cells correlates with neopterin production and activity of indoleamine 2,3-dioxygenase

    Energy Technology Data Exchange (ETDEWEB)

    Schroecksnadel, Sebastian [Division of Biological Chemistry, Innsbruck Medical University, Innsbruck (Austria); Jenny, Marcel [Division of Biological Chemistry, Innsbruck Medical University, Innsbruck (Austria); Division of Medical Biochemistry, Biocenter, Innsbruck Medical University, Innsbruck (Austria); Kurz, Katharina [Department of Internal Medicine, Innsbruck Medical University, Innsbruck (Austria); Klein, Angela [Division of Medical Biochemistry, Biocenter, Innsbruck Medical University, Innsbruck (Austria); Ledochowski, Maximilian [Department of Internal Medicine, Innsbruck Medical University, Innsbruck (Austria); Uberall, Florian [Division of Medical Biochemistry, Biocenter, Innsbruck Medical University, Innsbruck (Austria); Fuchs, Dietmar, E-mail: dietmar.fuchs@i-med.ac.at [Division of Biological Chemistry, Innsbruck Medical University, Innsbruck (Austria)

    2010-09-03

    Research highlights: {yields} LPS induces NF-{kappa}B, neopterin formation and tryptophan degradation in THP-1 cells. {yields} Close dose- and time-dependent correlations exist between these biochemical events. {yields} Data provides some evidence for a parallel induction of them upon TLR stimulation. {yields} Results can be of considerable relevance also in vivo. -- Abstract: Neopterin production is induced in human monocyte-derived macrophages and dendritic cells upon stimulation with Th1-type cytokine interferon-{gamma} (IFN-{gamma}). In parallel, IFN-{gamma} induces the tryptophan-(trp)-degrading enzyme indoleamine 2,3-dioxygenase (IDO) and triggers the formation of reactive oxygen species (ROS). Translocation of the signal transduction element nuclear factor-{kappa}B (NF-{kappa}B) is induced by ROS and accelerates the pro-inflammatory response by activation of other pro-inflammatory pathways. Therefore, a close relationship between NF-{kappa}B expression, the production of neopterin and the degradation of trp can be assumed, although this has not been demonstrated so far. In the present in vitro study we compared the influence of lipopolysaccharide (LPS) on NF-{kappa}B activation, neopterin formation and the degradation of trp in THP-1Blue cells, which represent the human myelomonocytic cell line THP-1 stably transfected with an NF-{kappa}B inducible reporter system. In cells stimulated with LPS, a significant induction of NF-{kappa}B was observed, and this was paralleled by an increase of kynureunine (kyn) and neopterin concentrations and a decline of trp. The increase of the kyn to trp quotient indicates accelerated IDO activity. Higher LPS concentrations and longer incubation of cells were associated with higher activities of all three biochemical pathways and significant correlations existed between NF-{kappa}B activation, neopterin release and trp degradation (all p < 0.001). We conclude that there is a parallel induction of NF-{kappa}B, neopterin

  5. HIV-1 Tat activates indoleamine 2,3 dioxygenase in murine organotypic hippocampal slice cultures in a p38 mitogen-activated protein kinase-dependent manner

    Directory of Open Access Journals (Sweden)

    Kelley Keith W

    2011-08-01

    Full Text Available Abstract Background We have established that activation of the tryptophan degrading enzyme indoleamine 2,3 dioxygenase (IDO mediates the switch from cytokine-induced sickness behavior to depressive-like behavior. Because human immunodeficiency virus type 1 (HIV-1 Tat protein causes depressive-like behavior in mice, we investigated its ability to activate IDO in organotypic hippocampal slice cultures (OHSCs derived from neonatal C57BL/6 mice. Methods Depressive-like behavior in C57BL/6J mice was assessed by the forced swim test. Expression of cytokines and IDO mRNA in OHSCs was measured by real-time RT-PCR and cytokine protein was measured by enzyme-linked immunosorbent assays (ELISAs. p38 MAPK phosphorylation was analyzed by western blot. Results Intracerebroventricular (i.c.v. administration of Tat (40 ng induced depressive-like behavior in the absence of sickness. Addition of Tat (40 ng/slice to the medium of OHSCs induced IDO steady-state mRNA that peaked at 6 h. This effect was potentiated by pretreatment with IFNγ. Tat also induced the synthesis and release of TNFα and IL-6 protein in the supernatant of the slices and increased expression of the inducible isoform of nitric oxide synthase (iNOS and the serotonin transporter (SERT. Tat had no effect on endogenous synthesis of IFNγ. To explore the mechanisms of Tat-induced IDO expression, slices were pretreated with the p38 mitogen-activated protein kinase (MAPK inhibitor SB 202190 for 30 min before Tat treatment. SB 202190 significantly decreased IDO expression induced by Tat, and this effect was accompanied by a reduction of Tat-induced expression of TNFα, IL-6, iNOS and SERT. Conclusion These data establish that Tat induces IDO expression via an IFNγ-independent mechanism that depends upon activation of p38 MAPK. Targeting IDO itself or the p38 MAPK signaling pathway could provide a novel therapy for comorbid depressive disorders in HIV-1-infected patients.

  6. Central Administration of Lipopolysaccharide Induces Depressive-like Behavior in Vivo and Activates Brain Indoleamine 2,3 Dioxygenase In Murine Organotypic Hippocampal Slice Cultures

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    Kavelaars Annemieke

    2010-08-01

    Full Text Available Abstract Background Transient stimulation of the innate immune system by an intraperitoneal injection of lipopolysaccharide (LPS activates peripheral and central expression of the tryptophan degrading enzyme indoleamine 2,3 dioxygenase (IDO which mediates depressive-like behavior. It is unknown whether direct activation of the brain with LPS is sufficient to activate IDO and induce depressive-like behavior. Methods Sickness and depressive-like behavior in C57BL/6J mice were assessed by social exploration and the forced swim test, respectively. Expression of cytokines and IDO mRNA was measured by real-time RT-PCR and cytokine protein was measured by enzyme-linked immunosorbent assays (ELISAs. Enzymatic activity of IDO was estimated as the amount of kynurenine produced from tryptophan as determined by high pressure liquid chromatography (HPLC with electrochemical detection. Results Intracerebroventricular (i.c.v. administration of LPS (100 ng increased steady-state transcripts of TNFα, IL-6 and the inducible isoform of nitric oxide synthase (iNOS in the hippocampus in the absence of any change in IFNγ mRNA. LPS also increased IDO expression and induced depressive-like behavior, as measured by increased duration of immobility in the forced swim test. The regulation of IDO expression was investigated using in situ organotypic hippocampal slice cultures (OHSCs derived from brains of newborn C57BL/6J mice. In accordance with the in vivo data, addition of LPS (10 ng/ml to the medium of OHSCs induced steady-state expression of mRNA transcripts for IDO that peaked at 6 h and translated into increased IDO enzymatic activity within 8 h post-LPS. This activation of IDO by direct application of LPS was preceded by synthesis and secretion of TNFα and IL-6 protein and activation of iNOS while IFNγ expression was undetectable. Conclusion These data establish that activation of the innate immune system in the brain is sufficient to activate IDO and induce

  7. Targeting Oxidative Stress, Cytokines and Serotonin Interactions Via Indoleamine 2, 3 Dioxygenase by Coenzyme Q10: Role in Suppressing Depressive Like Behavior in Rats.

    Science.gov (United States)

    Abuelezz, Sally A; Hendawy, Nevien; Magdy, Yosra

    2016-10-11

    Depression is a major health problem in which oxidative stress and inflammation are inextricably connected in its pathophysiology. Coenzyme Q10 (CoQ10) is an important anti-oxidant compound with anti-inflammatory and neuro-protective properties. This study was designed to investigate the hypothesis that CoQ10 by its anti-oxidant and anti-inflammatory potentials can alleviate depressive- like behavior by restoring the balance of the tryptophan catabolites kynurenine/serotonin toward the serotonin pathway by down-regulation of hippocampal indoleamine 2,3-dioxygenase 1 (IDO-1). Depressive-like behavior was induced by chronic unpredictable mild stress (CUMS) protocol including food or water deprivation, cage tilting, reversed light cycle etc. Male Wistar rats were randomly divided into five groups; Control, CUMS, CUMS and CoQ10 (50,100 and 200 mg/kg/day i.p. respectively) groups. CoQ10 effects on different behavioral and biochemical tests were analyzed. CoQ10 showed significant antidepressant efficacy, as evidenced by significantly decreased stress induced changes to forced swimming challenge and open field test, as well as attenuating raised corticosterone level and adrenal glands weight. The anti-oxidant effect of CoQ10 was exhibited by its ability to significantly reduce hippocampal elevated malondialdehyde and 4-hydroxynonenal levels and elevate the reduced glutathione and catalase levels. CoQ10 significantly reduced different pro-inflammatory cytokines levels including interleukin (IL)-1β, IL-2, IL-6 and tumor necrosis factor-α. It suppressed hippocampal IDO-1 and subsequent production of kynurenine and enhanced the hippocampal contents of tryptophan and serotonin. Immunohistochemical analysis revealed that CoQ10 was able to attenuate the elevated microglial CD68 and elevate the astrocyte glial fibrillary acidic protein compared to CUMS group. CoQ10 exhibited antidepressant-like effects on rats exposed to CUMS. This could be attributed to its ability to reduce

  8. 细菌芳烃外二醇双加氧酶研究进展%Advance in Research on Bacterial Aromatic Extradiol Dioxygenase

    Institute of Scientific and Technical Information of China (English)

    许炳雯; 李诗阳; 张强; 曲媛媛; 马桥; 李新亮; 周集体; 张旭旺; 周豪

    2012-01-01

    As a type of bacterial aromatic ring-cleavage enzymes with versatile functions, extradiol dioxygenases (EDOs) have broad application in the field of environmental protection, chemical synthesis and biotechnologies. This paper reviewed the achievements of EDOs researches including the studies on their classification, catalytic mechanism, the application in biodegradation, biosynthesis, biotechnologies and the novel methods for extracting and modify EDOs. EDOs belong to three evolutionarily independent families, which utilize Fe(II) or Mn(II) as metal ions to catalyze the oxygenolytic fission of aromatic compounds via iron-alkylperoxo intermediates by the incorporation of substrates and O2. Through this mechanism, EDOs possess broad substrates spectra, and often take part in the biosynthesis of active compounds. Meanwhile, EDOs play an important role in the biotechnology such as biosensors. Recently, combined with the technology of metagenomic, hybrid enzymes, more and more EDOs were extracted and modified to provide a general message for the in depth study of EDOs. Fig 5, Ref32%外二醇双加氧酶(EDOs)是一种多功能细菌芳烃开环氧化酶,在环境保护、化工合成及生物技术等领域中有着巨大的应用潜力.本文综述了EDOs自开发以来的研究成果,包括分类学研究,酶的催化机制,在生物降解、生物合成、生物技术中的应用及其开发改造新技术.EDOs属于3个进化关系相互独立的酶家族,它们利用活性位点金属离子Fe/Mn(Ⅱ)与底物和氧气结合,通过形成一种烷基过氧化中间产物,使芳香化合物开环断裂.利用这一催化机制,EDOs可以广泛地降解多种环境污染物,同时,某些EDOs还能够参与生物活性物质的合成,并且在生物传感器等生物技术中也有着广泛的应用.近年来,结合宏基因组、杂交酶等技术手段,研究人员开发改造出更多的EDOs资源,旨在为EDOs的深入研究提供更全面的信息.

  9. Iron(III) complexes of tripodal tetradentate 4N ligands as functional models for catechol dioxygenases: the electronic vs. steric effect on extradiol cleavage.

    Science.gov (United States)

    Balamurugan, Mani; Vadivelu, Prabha; Palaniandavar, Mallayan

    2014-10-21

    A few mononuclear iron(iii) complexes of the type [Fe(L)Cl2]Cl , where L is a tetradentate tripodal 4N ligand such as N,N-dimethyl-N',N'-bis(pyrid-2-ylmethyl)ethane-1,2-diamine (), N,N-diethyl-N',N'-bis(pyrid-2-ylmethyl)ethane-1,2-diamine (), N,N-dimethyl-N',N'-bis-(6-methylpyrid-2-ylmethyl)ethane-1,2-diamine (), N,N-dimethyl-N'-(pyrid-2-ylmethyl)-N'-(1-methyl-1H-imidazol-2-ylmethyl)ethane-1,2-diamine (), N,N-dimethyl-N',N'-bis(1-methyl-1H-imidazol-2-ylmethyl)ethane-1,2-diamine () and N,N-dimethyl-N',N'-bis(quinolin-2-ylmethyl)ethane-1,2-diamine (), have been isolated and characterized by CHN analysis, UV-Visible spectroscopy and electrochemical methods. The complex cation [Fe(H)Cl3](+) possesses a distorted octahedral geometry in which iron is coordinated by the monoprotonated 4N ligand in a tridentate fashion and the remaining three sites of the octahedron are occupied by chloride ions. The DFT optimized octahedral geometries of , and contain iron(iii) with a high-spin (S = 5/2) ground state. The catecholate adducts [Fe(L)(DBC)](+), where H2DBC is 3,5-di-tert-butylcatechol, of all the complexes have been generated in situ in acetonitrile solution and their spectral and redox properties and dioxygenase activities have been studied. The DFT optimized geometries of the catecholate adducts [Fe()(DBC)](+), [Fe()(DBC)](+) and [Fe()(DBC)](+) have also been generated to illustrate the ability of the complexes to cleave H2DBC in the presence of molecular oxygen to afford varying amounts of intra- (I) and extradiol (E) cleavage products. The extradiol to intradiol product selectivity (E/I, 0.1-2.0) depends upon the asymmetry in bidentate coordination of catecholate, as determined by the stereoelectronic properties of the ligand donor functionalities. While the higher E/I value obtained for [Fe()(DBC)](+) is on account of the steric hindrance of the quinolyl moiety to coordination the lower value observed for [Fe()(DBC)](+) and [Fe()(DBC)](+) is on account of the electron

  10. ITC Methods for Assessing Buffer/Protein Interactions from the Perturbation of Steady-State Kinetics: A Reactivity Study of Homoprotocatechuate 2,3-Dioxygenase.

    Science.gov (United States)

    Henderson, Kate L; Boyles, Delta K; Le, Vu H; Lewis, Edwin A; Emerson, Joseph P

    2016-01-01

    -hydroxymuconic semialdehyde by the nonheme iron(II) metalloenzyme, homoprotocatechuate 2,3-dioxygenase. Several buffers were observed to engage in buffer/enzyme interactions within the active site pocket. These enzyme-buffer interactions were shown to inhibit substrate turnover and to contribute additional enthalpy terms to the overall heat of reaction observed for substrate turnover (and for substrate binding).

  11. Structural insight into the substrate- and dioxygen-binding manner in the catalytic cycle of rieske nonheme iron oxygenase system, carbazole 1,9a-dioxygenase

    Directory of Open Access Journals (Sweden)

    Ashikawa Yuji

    2012-06-01

    Full Text Available Abstract Background Dihydroxylation of tandemly linked aromatic carbons in a cis-configuration, catalyzed by multicomponent oxygenase systems known as Rieske nonheme iron oxygenase systems (ROs, often constitute the initial step of aerobic degradation pathways for various aromatic compounds. Because such RO reactions inherently govern whether downstream degradation processes occur, novel oxygenation mechanisms involving oxygenase components of ROs (RO-Os is of great interest. Despite substantial progress in structural and physicochemical analyses, no consensus exists on the chemical steps in the catalytic cycles of ROs. Thus, determining whether conformational changes at the active site of RO-O occur by substrate and/or oxygen binding is important. Carbazole 1,9a-dioxygenase (CARDO, a RO member consists of catalytic terminal oxygenase (CARDO-O, ferredoxin (CARDO-F, and ferredoxin reductase. We have succeeded in determining the crystal structures of oxidized CARDO-O, oxidized CARDO-F, and both oxidized and reduced forms of the CARDO-O: CARDO-F binary complex. Results In the present study, we determined the crystal structures of the reduced carbazole (CAR-bound, dioxygen-bound, and both CAR- and dioxygen-bound CARDO-O: CARDO-F binary complex structures at 1.95, 1.85, and 2.00 Å resolution. These structures revealed the conformational changes that occur in the catalytic cycle. Structural comparison between complex structures in each step of the catalytic mechanism provides several implications, such as the order of substrate and dioxygen bindings, the iron-dioxygen species likely being Fe(III-(hydroperoxo, and the creation of room for dioxygen binding and the promotion of dioxygen binding in desirable fashion by preceding substrate binding. Conclusions The RO catalytic mechanism is proposed as follows: When the Rieske cluster is reduced, substrate binding induces several conformational changes (e.g., movements of the nonheme iron and the ligand

  12. Role of dioxygenase α-DOX2 and SA in basal response and in hexanoic acid-induced resistance of tomato (Solanum lycopersicum) plants against Botrytis cinerea.

    Science.gov (United States)

    Angulo, Carlos; de la O Leyva, María; Finiti, Ivan; López-Cruz, Jaime; Fernández-Crespo, Emma; García-Agustín, Pilar; González-Bosch, Carmen

    2015-03-01

    Resistance of tomato (Solanum Lycopersicum) to the fungal pathogen Botrytis cinerea requires complex interplay between hormonal signalling. In this study, we explored the involvement of new oxylipins in the tomato basal and induced response to this necrotroph through the functional analysis of the tomato α-dioxygenase2 (α-DOX2)-deficient mutant divaricata. We also investigated the role of SA in the defence response against this necrotrophic fungus using SA-deficient tomato nahG plants. The plants lacking dioxigenase α-DOX2, which catalyses oxylipins production from fatty acids, were more susceptible to Botrytis, and hexanoic acid-induced resistance (Hx-IR) was impaired; hence α-DOX2 is required for both tomato defence and the enhanced protection conferred by natural inducer hexanoic acid (Hx) against B. cinerea. The divaricata plants accumulated less pathogen-induced callose and presented lower levels of jasmonic acid (JA) and 12-oxo-phytodienoic acid (OPDA) upon infection if compared to the wild type. Glutathion-S-transferase (GST) gene expression decreased and ROS production significantly increased in Botrytis-infected divaricata plants. These results indicate that absence of α-DOX2 influences the hormonal changes, oxidative burst and callose deposition that occur upon Botrytis infection in tomato. The study of SA-deficient nahG tomato plants showed that the plants with low SA levels displayed increased resistance to Botrytis, but were unable to display Hx-IR. This supports the involvement of SA in Hx-IR. NaghG plants displayed reduced callose and ROS accumulation upon infection and an increased GST expression. This reflects a positive relationship between SA and these defensive mechanisms in tomato. Finally, Hx boosted the pathogen-induced callose in nahG plants, suggesting that this priming mechanism is SA-independent. Our results support the involvement of the oxylipins pathway and SA in tomato response to Botrytis, probably through complex crosstalk of

  13. Interaction of (4-hydroxyphenyl)pyruvate dioxygenase with the specific inhibitor 2-[2-nitro-4-(trifluoromethyl)benzoyl]-1,3-cyclohexanedione.

    Science.gov (United States)

    Kavana, Michael; Moran, Graham R

    2003-09-01

    (4-Hydroxyphenyl)pyruvate dioxygenase (HPPD) is a non-heme Fe(II) enzyme that catalyzes the conversion of (4-hydroxyphenyl)pyruvate (HPP) to homogentisate as part of the tyrosine catabolism pathway. Inhibition of HPPD by the triketone 2-[2-nitro-4-(trifluoromethyl)benzoyl]-1,3-cyclohexanedione (NTBC) is used to treat type I tyrosinemia, a rare but fatal defect in tyrosine catabolism. Although triketones have been used for many years as HPPD inhibitors for both medical and herbicidal purposes, the mechanism of inhibition is not well understood. The following work provides mechanistic insight into NTBC binding. The tautomeric population of NTBC in aqueous solution is dominated by a single enol as determined by NMR spectroscopy. NTBC preferentially binds to the complex of HPPD and FeII [HPPD.Fe(II)] as evidenced by a visible absorbance feature centered at 450 nm. The binding of NTBC to HPPD.Fe(II) was observed using a rapid mixing method and was shown to occur in two phases and comprise three steps. A hyperbolic dependence of the first observable process with NTBC concentration indicates a pre-equilibrium binding step followed by a limiting rate (K(1) = 1.25 +/- 0.08 mM, k(2) = 8.2 +/- 0.2 s(-1)), while the second phase (k(3) = 0.76 +/- 0.02 s(-1)) had no dependence on NTBC concentration. Neither K(1),k(2), nor k(3) was influenced by pH in the range of 6.0-8.0. Isotope effects on both k(2) and k(3) were observed when D(2)O is used as the solvent (for k(2), k(h)/k(d) = 1.3; for k(3), k(h)/k(d) = 3.2). It is therefore proposed that the bidentate association of NTBC with the active site metal ion (k(2)) precedes the Lewis acid-assisted conversion of the bound enol to the enolate (k(3)). Although the native enzyme without substrate reacts with molecular oxygen to form the oxidized holoenzyme, the HPPD.Fe(II).NTBC complex does not. When the complex is exposed to atmospheric oxygen, the absorbance feature associated with NTBC binding does not diminish over the course of 2

  14. Isolation and Expression of 9-cis Epoxycarotenoid Dioxygenase Gene in Tree Peony%牡丹NCED基因的克隆和表达分析

    Institute of Scientific and Technical Information of China (English)

    王晓庆; 张超; 王彦杰; 董丽

    2012-01-01

    A full-length cDNA(temporarily name it Ps-NCED1)encoding 9-cis-epoxycarotenoid (NCED)was isolated with the techniques of RT-PCR and RACE from petals of tree peony flower and characterized. Phylogenetic tree analysis revealed that amino acids sequence of Ps-NCED1 shared more than 70% identity with the sequence of NCED from plants such as Vitis vinifera,Solanum tuberosum, Daucus carota and so on. Ps-NCED1 also had the highest amino acids sequence identity with At-NCED3 of CCD(carotenoid cleavage dioxygenase)family in Arabidopsis. Cut flowers during full open stage had the lowest endogenous ABA levels,to the contrary,flowers during primary and senescent stages had higher ABA levels. The relative real-time PCR analysis was used to identify the expression of Ps-NCED1 in different parts of tree peony at blooming stage. The expression in root and stamen presented the highest,while that in leaf and sepal the lowest. The expression of Ps-NCED1 in the petals from ABA treated flowers during vasing increased with cut flowers opening and senescence,coincided with the ABA content increase,resulted in the assumption that it might be the main member in regulation the ABA biosynthesis in tree peony responding to the postharvest stress during opening and senescence process.%通过RT-PCR和RACE技术克隆得到了牡丹(Paeonia suffruticosa Andr.)中编码9–顺式–环氧类胡萝卜素加双氧酶蛋白(NCED)的一条cDNA基因全长(暂命名为Ps-NCED1)。进化树分析显示Ps-NCED1的氨基酸序列与葡萄、马铃薯、胡萝卜等植物中的NCED一致性均达到了70%以上。通过与拟南芥中CCD(类胡萝卜素分解加双氧酶)家族氨基酸序列比对后发现,Ps-NCED1与调控ABA合成的At-NCED3一致性最高。对花朵中内源ABA的研究发现,ABA在花朵蕾期及衰老期含量较高,盛开期时含量较低,表明ABA对于植物的开放衰老具有促进作用。相对荧光定量PCR分析发现:在花朵完全

  15. Protein engineering of the archetypal nitroarene dioxygenase of Ralstonia sp. strain U2 for activity on aminonitrotoluenes and dinitrotoluenes through alpha-subunit residues leucine 225, phenylalanine 350, and glycine 407.

    Science.gov (United States)

    Keenan, Brendan G; Leungsakul, Thammajun; Smets, Barth F; Mori, Masa-aki; Henderson, David E; Wood, Thomas K

    2005-05-01

    Naphthalene dioxygenase (NDO) from Ralstonia sp. strain U2 has not been reported to oxidize nitroaromatic compounds. Here, saturation mutagenesis of NDO at position F350 of the alpha-subunit (NagAc) created variant F350T that produced 3-methyl-4-nitrocatechol from 2,6-dinitrotoluene (26DNT), that released nitrite from 23DNT sixfold faster than wild-type NDO, and that produced 3-amino-4-methyl-5-nitrocatechol and 2-amino-4,6-dinitrobenzyl alcohol from 2-amino-4,6-dinitrotoluene (2A46DNT) (wild-type NDO has no detectable activity on 26DNT and 2A46DNT). DNA shuffling identified the beneficial NagAc mutation G407S, which when combined with the F350T substitution, increased the rate of NDO oxidation of 26DNT, 23DNT, and 2A46DNT threefold relative to variant F350T. DNA shuffling of NDO nagAcAd also generated the NagAc variant G50S/L225R/A269T with an increased rate of 4-amino-2-nitrotoluene (4A2NT; reduction product of 2,4-dinitrotoluene) oxidation; from 4A2NT, this variant produced both the previously uncharacterized oxidation product 4-amino-2-nitrocresol (enhanced 11-fold relative to wild-type NDO) as well as 4-amino-2-nitrobenzyl alcohol (4A2NBA; wild-type NDO does not generate this product). G50S/L225R/A269T also had increased nitrite release from 23DNT (14-fold relative to wild-type NDO) and generated 2,3-dinitrobenzyl alcohol (23DNBA) fourfold relative to wild-type NDO. The importance of position L225 for catalysis was confirmed through saturation mutagenesis; relative to wild-type NDO, NDO variant L225R had 12-fold faster generation of 4-amino-2-nitrocresol and production of 4A2NBA from 4A2NT as well as 24-fold faster generation of nitrite and 15-fold faster generation of 23DNBA from 23DNT. Hence, random mutagenesis discovered two new residues, G407 and L225, that influence the regiospecificity of Rieske non-heme-iron dioxygenases.

  16. Probiotics Differently Affect Gut-Associated Lymphoid Tissue Indolamine-2,3-Dioxygenase mRNA and Cerebrospinal Fluid Neopterin Levels in Antiretroviral-Treated HIV-1 Infected Patients: A Pilot Study

    Science.gov (United States)

    Scagnolari, Carolina; Corano Scheri, Giuseppe; Selvaggi, Carla; Schietroma, Ivan; Najafi Fard, Saeid; Mastrangelo, Andrea; Giustini, Noemi; Serafino, Sara; Pinacchio, Claudia; Pavone, Paolo; Fanello, Gianfranco; Ceccarelli, Giancarlo; Vullo, Vincenzo; d’Ettorre, Gabriella

    2016-01-01

    Recently the tryptophan pathway has been considered an important determinant of HIV-1 infected patients’ quality of life, due to the toxic effects of its metabolites on the central nervous system (CNS). Since the dysbiosis described in HIV-1 patients might be responsible for the microbial translocation, the chronic immune activation, and the altered utilization of tryptophan observed in these individuals, we speculated a correlation between high levels of immune activation markers in the cerebrospinal fluid (CSF) of HIV-1 infected patients and the over-expression of indolamine-2,3-dioxygenase (IDO) at the gut mucosal surface. In order to evaluate this issue, we measured the levels of neopterin in CSF, and the expression of IDO mRNA in gut-associated lymphoid tissue (GALT), in HIV-1-infected patients on effective combined antiretroviral therapy (cART), at baseline and after six months of probiotic dietary management. We found a significant reduction of neopterin and IDO mRNA levels after the supplementation with probiotic. Since the results for the use of adjunctive therapies to reduce the levels of immune activation markers in CSF have been disappointing so far, our pilot study showing the efficacy of this specific probiotic product should be followed by a larger confirmatory trial. PMID:27689995

  17. A mathematical model of tryptophan metabolism via the kynurenine pathway provides insights into the effects of vitamin B-6 deficiency, tryptophan loading, and induction of tryptophan 2,3-dioxygenase on tryptophan metabolites.

    Science.gov (United States)

    Rios-Avila, Luisa; Nijhout, H Frederik; Reed, Michael C; Sitren, Harry S; Gregory, Jesse F

    2013-09-01

    Vitamin B-6 deficiency is associated with impaired tryptophan metabolism because of the coenzyme role of pyridoxal 5'-phosphate (PLP) for kynureninase and kynurenine aminotransferase. To investigate the underlying mechanism, we developed a mathematical model of tryptophan metabolism via the kynurenine pathway. The model includes mammalian data on enzyme kinetics and tryptophan transport from the intestinal lumen to liver, muscle, and brain. Regulatory mechanisms and inhibition of relevant enzymes were included. We simulated the effects of graded reduction in cellular PLP concentration, tryptophan loads and induction of tryptophan 2,3-dioxygenase (TDO) on metabolite profiles and urinary excretion. The model predictions matched experimental data and provided clarification of the response of metabolites in various extents of vitamin B-6 deficiency. We found that moderate deficiency yielded increased 3-hydroxykynurenine and a decrease in kynurenic acid and anthranilic acid. More severe deficiency also yielded an increase in kynurenine and xanthurenic acid and more pronounced effects on the other metabolites. Tryptophan load simulations with and without vitamin B-6 deficiency showed altered metabolite concentrations consistent with published data. Induction of TDO caused an increase in all metabolites, and TDO induction together with a simulated vitamin B-6 deficiency, as has been reported in oral contraceptive users, yielded increases in kynurenine, 3-hydroxykynurenine, and xanthurenic acid and decreases in kynurenic acid and anthranilic acid. These results show that the model successfully simulated tryptophan metabolism via the kynurenine pathway and can be used to complement experimental investigations.

  18. Identification of differentially expressed genes associated with flower color in peach using genome-wide transcriptional analysis.

    Science.gov (United States)

    Zhou, Y; Wu, X X; Zhang, Z; Gao, Z H

    2015-05-11

    Flower color is an important trait of the ornamental peach (Prunus persica L.). However, the mechanism responsible for the different colors that appear in the same genotype remains unclear. In this study, red samples showed higher anthocyanins content (0.122 ± 0.009 mg/g), which was significantly different from that in white samples (0.066 ± 0.010 mg/g). Similarly to carotenoids content, red extract (0.058 ± 0.004 mg/L) was significantly higher in white extract (0.015 ± 0.004 mg/L). We estimated gene expression using Illumina sequencing technology in libraries from white and red flower buds. A total of 3,599,960 and 3,464,141 tags were sequenced from the 2 libraries, respectively. Moreover, we identified 106 significantly differentially expressed genes between the 2 libraries. Among these, 78 and 28 represented transcripts with a higher or lower abundance of more than 2-fold than in the white flower library, respectively. GO annotation indicated that highly ranked genes were involved in the pigment biosynthetic process. Expression patterns of 11 genes were verified using quantitative reverse transcription-polymerase chain reaction assays. The results suggest that hydroxycinnamoyl-coenzyme A shikimate/quinate hydroxycinnamoyltransferase, 2-oxoglutarate-dependent dioxygenase, isoflavone reductase, riboflavin kinase, zeta-carotene desaturase, and ATP binding cassette transporter may be associated with the flower color formation. Our results may be useful for scientists focusing on Prunus persica floral development and biotechnology.

  19. Krebs cycle intermediates regulate DNA and histone methylation: epigenetic impact on the aging process.

    Science.gov (United States)

    Salminen, Antero; Kauppinen, Anu; Hiltunen, Mikko; Kaarniranta, Kai

    2014-07-01

    Many aging theories have proposed that mitochondria and energy metabolism have a major role in the aging process. There are recent studies indicating that Krebs cycle intermediates can shape the epigenetic landscape of chromatin by regulating DNA and histone methylation. A growing evidence indicates that epigenetics plays an important role in the regulation of healthspan but also is involved in the aging process. 2-Oxoglutarate (α-ketoglutarate) is a key metabolite in the Krebs cycle but it is also an obligatory substrate for 2-oxoglutarate-dependent dioxygenases (2-OGDO). The 2-OGDO enzyme family includes the major enzymes of DNA and histone demethylation, i.e. Ten-Eleven Translocation (TETs) and Jumonji C domain containing (JmjC) demethylases. In addition, 2-OGDO members can regulate collagen synthesis and hypoxic responses in a non-epigenetical manner. Interestingly, succinate and fumarate, also Krebs cycle intermediates, are potent inhibitors of 2-OGDO enzymes, i.e. the balance of Krebs cycle reactions can affect the level of DNA and histone methylation and thus control gene expression. We will review the epigenetic mechanisms through which Krebs cycle intermediates control the DNA and histone methylation. We propose that age-related disturbances in the Krebs cycle function induce stochastic epigenetic changes in chromatin structures which in turn promote the aging process.

  20. Krebs cycle dysfunction shapes epigenetic landscape of chromatin: novel insights into mitochondrial regulation of aging process.

    Science.gov (United States)

    Salminen, Antero; Kaarniranta, Kai; Hiltunen, Mikko; Kauppinen, Anu

    2014-07-01

    Although there is a substantial literature that mitochondria have a crucial role in the aging process, the mechanism has remained elusive. The role of reactive oxygen species, mitochondrial DNA injuries, and a decline in mitochondrial quality control has been proposed. Emerging studies have demonstrated that Krebs cycle intermediates, 2-oxoglutarate (also known as α-ketoglutarate), succinate and fumarate, can regulate the level of DNA and histone methylation. Moreover, citrate, also a Krebs cycle metabolite, can enhance histone acetylation. Genome-wide screening studies have revealed that the aging process is linked to significant epigenetic changes in the chromatin landscape, e.g. global demethylation of DNA and histones and increase in histone acetylation. Interestingly, recent studies have revealed that the demethylases of DNA (TET1-3) and histone lysines (KDM2-7) are members of 2-oxoglutarate-dependent dioxygenases (2-OGDO). The 2-OGDO enzymes are activated by oxygen, iron and the major Krebs cycle intermediate, 2-oxoglutarate, whereas they are inhibited by succinate and fumarate. Considering the endosymbiont origin of mitochondria, it is not surprising that Krebs cycle metabolites can control the gene expression of host cell by modifying the epigenetic landscape of chromatin. It seems that age-related disturbances in mitochondrial metabolism can induce epigenetic reprogramming, which promotes the appearance of senescent phenotype and degenerative diseases.

  1. Vitamin C facilitates dopamine neuron differentiation in fetal midbrain through TET1- and JMJD3-dependent epigenetic control manner.

    Science.gov (United States)

    He, Xi-Biao; Kim, Mirang; Kim, Seon-Young; Yi, Sang-Hoon; Rhee, Yong-Hee; Kim, Taeho; Lee, Eun-Hye; Park, Chang-Hwan; Dixit, Shilpy; Harrison, Fiona E; Lee, Sang-Hun

    2015-04-01

    Intracellular Vitamin C (VC) is maintained at high levels in the developing brain by the activity of sodium-dependent VC transporter 2 (Svct2), suggesting specific VC functions in brain development. A role of VC as a cofactor for Fe(II)-2-oxoglutarate-dependent dioxygenases has recently been suggested. We show that VC supplementation in neural stem cell cultures derived from embryonic midbrains greatly enhanced differentiation toward midbrain-type dopamine (mDA) neurons, the neuronal subtype associated with Parkinson's disease. VC induced gain of 5-hydroxymethylcytosine (5hmC) and loss of H3K27m3 in DA phenotype gene promoters, which are catalyzed by Tet1 and Jmjd3, respectively. Consequently, VC enhanced DA phenotype gene transcriptions in the progenitors by Nurr1, a transcription factor critical for mDA neuron development, to be more accessible to the gene promoters. Further mechanism studies including Tet1 and Jmjd3 knockdown/inhibition experiments revealed that both the 5hmC and H3K27m3 changes, specifically in the progenitor cells, are indispensible for the VC-mediated mDA neuron differentiation. We finally show that in Svct2 knockout mouse embryos, mDA neuron formation in the developing midbrain decreased along with the 5hmC/H3k27m3 changes. These findings together indicate an epigenetic role of VC in midbrain DA neuron development.

  2. Regulation of BZR1 in fruit ripening revealed by iTRAQ proteomics analysis

    Science.gov (United States)

    Liu, Lihong; Liu, Haoran; Li, Shuo; Zhang, Xin; Zhang, Min; Zhu, Ning; Dufresne, Craig P.; Chen, Sixue; Wang, Qiaomei

    2016-01-01

    Fruit ripening is a complex and genetically programmed process. Brassinosteroids (BRs) play an essential role in plant growth and development, including fruit ripening. As a central component of BR signaling, the transcription factor BZR1 is involved in fruit development in tomato. However, the transcriptional network through which BZR1 regulates fruit ripening is mostly unknown. In this study, we use isobaric tags for relative and absolute quantitation (iTRAQ) labeling technology to explore important proteins regulated by BZR1 in two independent tomato transgenic lines over-expressing BZR1-1D at four ripening stages, identifying 411 differentially expressed proteins. These proteins were implicated in light reaction, plant hormone pathways and cell-wall-related metabolism, etc. The ‘light reaction’ metabolic pathway was identified as a markedly enhanced pathway by BZR1 during tomato fruit ripening. The protein level of a probable 2-oxoglutarate-dependent dioxygenase 2-ODD2, involved in gibberellin biosynthesis was significantly increased at all four developmental and ripening stages. The results reveal molecular links between BR signaling pathway and downstream components involved in multiple ripening-associated events during tomato fruit ripening, which will provide new insights into the molecular mechanisms underlying tomato ripening regulatory networks, and be potential in understanding BR-regulated fruit ripening. PMID:27680870

  3. Comparative proteomics reveals that a saxitoxin-producing and a nontoxic strain of Anabaena circinalis are two different ecotypes.

    Science.gov (United States)

    D'Agostino, Paul M; Song, Xiaomin; Neilan, Brett A; Moffitt, Michelle C

    2014-03-01

    In Australia, saxitoxin production is restricted to the cyanobacterial species Anabaena circinalis and is strain-dependent. We aimed to characterize a saxitoxin-producing and nontoxic strain of A. circinalis at the proteomic level using iTRAQ. Seven proteins putatively involved in saxitoxin biosynthesis were identified within our iTRAQ experiment for the first time. The proteomic profile of the toxic A. circinalis was significantly different from the nontoxic strain, indicating that each is likely to inhabit a unique ecological niche. Under control growth conditions, the saxitoxin-producing A. circinalis displayed a higher abundance of photosynthetic, carbon fixation and nitrogen metabolic proteins. Differential abundance of these proteins suggests a higher intracellular C:N ratio and a higher concentration of intracellular 2-oxoglutarate in our toxic strain compared with the nontoxic strain. This may be a novel site for posttranslational regulation because saxitoxin biosynthesis putatively requires a 2-oxoglutarate-dependent dioxygenase. The nontoxic A. circinalis was more abundant in proteins, indicating cellular stress. Overall, our study has provided the first insight into fundamental differences between a toxic and nontoxic strain of A. circinalis, indicating that they are distinct ecotypes.

  4. Hypoxia-inducible Factor Prolyl 4-Hydroxylase Inhibition A TARGET FOR NEUROPROTECTION IN THE CENTRAL NERVOUS SYSTEM*

    Science.gov (United States)

    Siddiq, Ambreena; Ayoub, Issam A.; Chavez, Juan C.; Aminova, Leila; Shah, Sapan; LaManna, Joseph C.; Patton, Stephanie M.; Connor, James R.; Cherny, Robert A.; Volitakis, Irene; Bush, Ashley I.; Langsetmo, Ingrid; Seeley, Todd; Gunzler, Volkmar; Ratan, Rajiv R.

    2008-01-01

    Hypoxia-inducible factor (HIF) prolyl 4-hydroxylases are a family of iron- and 2-oxoglutarate-dependent dioxygenases that negatively regulate the stability of several proteins that have established roles in adaptation to hypoxic or oxidative stress. These proteins include the transcriptional activators HIF-1α and HIF-2α. The ability of the inhibitors of HIF prolyl 4-hydroxylases to stabilize proteins involved in adaptation in neurons and to prevent neuronal injury remains unclear. We reported that structurally diverse low molecular weight or peptide inhibitors of the HIF prolyl 4-hydroxylases stabilize HIF-1α and up-regulate HIF-dependent target genes (e.g. enolase, p21waf1/cip1, vascular endothelial growth factor, or erythropoietin) in embryonic cortical neurons in vitro or in adult rat brains in vivo. We also showed that structurally diverse HIF prolyl 4-hydroxylase inhibitors prevent oxidative death in vitro and ischemic injury in vivo. Taken together these findings identified low molecular weight and peptide HIF prolyl 4-hydroxylase inhibitors as novel neurological therapeutics for stroke as well as other diseases associated with oxidative stress. PMID:16227210

  5. Cellular Oxygen Sensing: Crystal Structure of Hypoxia-Inducible Factor Prolyl Hydroxylase (PHD2)

    Energy Technology Data Exchange (ETDEWEB)

    McDonough,M.; Li, V.; Flashman, E.; Chowdhury, R.; Mohr, C.; Lienard, B.; Zondlo, J.; Oldham, N.; Clifton, I.; et al.

    2006-01-01

    Cellular and physiological responses to changes in dioxygen levels in metazoans are mediated via the posttranslational oxidation of hypoxia-inducible transcription factor (HIF). Hydroxylation of conserved prolyl residues in the HIF-{alpha} subunit, catalyzed by HIF prolyl-hydroxylases (PHDs), signals for its proteasomal degradation. The requirement of the PHDs for dioxygen links changes in dioxygen levels with the transcriptional regulation of the gene array that enables the cellular response to chronic hypoxia; the PHDs thus act as an oxygen-sensing component of the HIF system, and their inhibition mimics the hypoxic response. We describe crystal structures of the catalytic domain of human PHD2, an important prolyl-4-hydroxylase in the human hypoxic response in normal cells, in complex with Fe(II) and an inhibitor to 1.7 Angstroms resolution. PHD2 crystallizes as a homotrimer and contains a double-stranded {beta}-helix core fold common to the Fe(II) and 2-oxoglutarate-dependant dioxygenase family, the residues of which are well conserved in the three human PHD enzymes (PHD 1-3). The structure provides insights into the hypoxic response, helps to rationalize a clinically observed mutation leading to familial erythrocytosis, and will aid in the design of PHD selective inhibitors for the treatment of anemia and ischemic disease.

  6. Expression and role of indoleamine-2 , 3-dioxygenase and Treg cells in breast cancer%乳腺癌中吲哚胺2,3-双加氧酶和调节性T细胞的表达

    Institute of Scientific and Technical Information of China (English)

    苏宝霞

    2012-01-01

    [Objective] To study the expression of indoleamine-2, 3-dioxygenase (IDO) and Treg cells in breast cancer and tumor draining lymph nodes(TDLNs), then to seek the relationship between them. [Methods] RT-PCR and immunohistochemistry was used to detect the mRNA of IDO and the expression of IDO and Foxp3 proteins in breast cancer, TDLNs and benign diseases. [ Results] The mRNA of IDO in TDLNs was higher than breast cancer (P < 0.05) and breast cancer was higher than benign diseases (P < 0.05). Immunohistochemistry results showed that the expression level of IDO in TDLNs was higher than breast cancer (P < 0.05), the breast cancer was higher than benign diseases (P < 0.05). The expression level of IDO protein in breast cancer was associated with clinical stage and pathological type. The positive ratio of Foxp3* Treg cells in breast cancer was higher than the benign diseases( P < 0.05) and the TDLNs was higher than breast cancer (P < 0.05). The expression of IDO in breast cancer was positive correlation with the distribution of Treg cells in breast primary cancer (r2=0.413, P< 0.05 )and in TDLNs (r2=0.528, P < 0.05). [Conclusion] IDO and Treg cells may participate the immune tolerance in breast cancer.%[目的]通过研究在乳腺癌和引流淋巴结中吲哚胺2,3-双加氧酶(indoleamine-2,3-dioxygenase,IDO)和调节性T细胞(Treg cells)的表达,探讨两者之间的关系.[方法]采用半定量RT-PCR法和免疫组织化学检测IDO mRNA和蛋白及Foxp3蛋白在乳腺癌、淋巴结和乳腺良性病变中表达情况.[结果]乳腺癌引流淋巴结中IDO的mRNA水平高于乳腺癌组织(P<0.05),乳腺癌组织中IDO的mRNA水平高于乳腺良性病变组织(P<0.05).免疫组化结果显示示乳腺癌引流淋巴结内IDO表达水平高于原发癌(P<0.05),乳腺癌组织中IDO表达水平高于乳腺良性病变组织(P<0.05).乳腺癌中IDO的表达与病理类型和临床分期相关(P<0.05).乳腺癌中Treg细胞Foxp3+比例高于乳腺良性

  7. A gene expression study of the activities of aromatic ring-cleavage dioxygenases in Mycobacterium gilvum PYR-GCK to changes in salinity and pH during pyrene degradation.

    Directory of Open Access Journals (Sweden)

    Abimbola Comfort Badejo

    Full Text Available Polycyclic aromatic hydrocarbons (PAHs are toxic pollutants found in the environment which can be removed through the use of physical and biological agents. The rate of PAH biodegradation is affected by environmental conditions of pH, salinity and temperature. Adaptation of the pyrene degrading bacteria, Mycobacterium gilvum PYR-GCK, to fluctuating environmental conditions during pyrene biodegrading activity was studied using the quantitative real time - Polymerase Chain Reaction (qRT-PCR technique. Four aromatic ring-cleavage dioxygenase genes: phdF, phdI, pcaG and pcaH; critical to pyrene biodegradation, were studied in pH states of 5.5, 6.5, 7.5 and NaCl concentrations 0 M, 0.17 M, 0.5 M, 0.6 M, 1 M. First, we conducted a residual pyrene study using gas chromatography and flame ionization technologies. Central to a gene expression study is the use of a valid endogenous reference gene, making its determination our next approach, using the geNorm/NormFinder algorithms. Armed with a valid control gene, rpoB, we applied it to a gene expression study, using the comparative critical threshold (2(ΔΔCT quantification method. The pyrene degrading activity of the strain was strongly functional in all the NaCl concentration states, with the least activity found at 1M (∼70% degraded after 48 hours of cultivation. The transcripts quantification of three genes backed this observation with high expression levels. The gene expression levels also revealed pH 6.5 as optimal for pyrene degradation and weak degradation activity at pH of 5.5, corroborating the residual pyrene analysis. The expression of these genes as proteins has already been studied in our laboratory using proteomics techniques and this validates our current study.

  8. The Crystal Structure of a Quercetin 2,3-Dioxygenase from Bacillus subtilis Suggests Modulation of Enzyme Activity by a Change in the Metal Ion at the Active Site(s)

    Energy Technology Data Exchange (ETDEWEB)

    Gopal, B.; Madan, Lalima L.; Betz, Stephen F.; Kossiakoff, Anthony A. (Indian); (UC); (GeneFormatics)

    2010-11-10

    Common structural motifs, such as the cupin domains, are found in enzymes performing different biochemical functions while retaining a similar active site configuration and structural scaffold. The soil bacterium Bacillus subtilis has 20 cupin genes (0.5% of the total genome) with up to 14% of its genes in the form of doublets, thus making it an attractive system for studying the effects of gene duplication. There are four bicupins in B. subtilis encoded by the genes yvrK, yoaN, yxaG, and ywfC. The gene products of yvrK and yoaN function as oxalate decarboxylases with a manganese ion at the active site(s), whereas YwfC is a bacitracin synthetase. Here we present the crystal structure of YxaG, a novel iron-containing quercetin 2,3-dioxygenase with one active site in each cupin domain. Yxag is a dimer, both in solution and in the crystal. The crystal structure shows that the coordination geometry of the Fe ion is different in the two active sites of YxaG. Replacement of the iron at the active site with other metal ions suggests modulation of enzymatic activity in accordance with the Irving-Williams observation on the stability of metal ion complexes. This observation, along with a comparison with the crystal structure of YvrK determined recently, has allowed for a detailed structure-function analysis of the active site, providing clues to the diversification of function in the bicupin family of proteins.

  9. The ectD Gene, Which Is Involved in the Synthesis of the Compatible Solute Hydroxyectoine, Is Essential for Thermoprotection of the Halophilic Bacterium Chromohalobacter salexigens

    OpenAIRE

    2006-01-01

    The halophilic bacterium Chromohalobacter salexigens synthesizes and accumulates compatible solutes in response to salt and temperature stress. 13C-nuclear magnetic resonance analysis of cells grown in minimal medium at the limiting temperature of 45°C revealed the presence of hydroxyectoine, ectoine, glutamate, trehalose (not present in cells grown at 37°C), and the ectoine precursor, N')'-acetyldiaminobutyric acid. High-performance liquid chromatography analyses showed that the levels of ec...

  10. Effects of pentoxifylline, 7-nitroindazole, and imipramine on tumor necrosis factor-α and indoleamine 2,3-dioxygenase enzyme activity in the hippocampus and frontal cortex of chronic mild-stress-exposed rats

    Directory of Open Access Journals (Sweden)

    Mohamed BMSA

    2013-05-01

    Full Text Available Bassim MSA Mohamed,1,6 Sawsan Aboul-Fotouh,2,5 Eman A Ibrahim,3 Hanan Shehata,4 Amal A Mansour,4 Nemat AZ Yassin,1 Wafaa El-Eraky,1 Ahmed M Abdel-Tawab2,5 1Department of Pharmacology, National Research Centre, Cairo, Egypt; 2Department of Pharmacology, 3Department of Pathology, 4Department of Medical Biochemistry and Molecular Biology, 5Clinical Pharmacology Unit, Ain Shams University, Cairo, Egypt; 6Atlantic Veterinary College, University of Prince Edward Island, Charlottetown, PE, Canada Objectives: This study aimed to investigate the role of tumor necrosis factor (TNF-α and the neuronal nitric oxide synthase enzyme in dysregulation of indoleamine 2,3-dioxygenase (IDO enzyme, and hence serotonin availability in chronic mild stress (CMS, an animal model of depression. Methods: Rats were divided into five groups: two control and CMS-exposed for 6 weeks, and another three groups exposed to CMS and administered pentoxifylline 50 mg/kg/day intraperitoneally, 7-nitroindazole 40 mg/kg/day subcutaneously, or imipramine 20 mg/kg/day intraperitoneally for the previous 3 CMS weeks. Rats were assessed for neurochemical and immunohistochemical abnormalities. Results: Pentoxifylline-, 7-nitroindazole-, and imipramine-treated rats showed amelioration of CMS-induced behavioral deficits that was accompanied by significant reduction in kynurenine/serotonin molar ratio and nitrates/nitrites in frontal cortex and hippocampus. In the pentoxifylline and 7-nitroindazole groups, serum TNF-α was reduced relative to the CMS group (18.54 ± 0.85 and 19.16 ± 1.54 vs 26.20 ± 1.83 pg/mL, respectively; P < 0.05. Exposure to CMS increased TNF-α and IDO immunohistochemical staining scores in both hippocampus and midbrain raphe nuclei. 7-Nitroindazole and pentoxifylline significantly (P < 0.05 reduced TNF-α immunostaining in hippocampus and raphe nuclei, with significant (P < 0.01 reduction of IDO immunostaining in raphe nuclei. Likewise, imipramine reduced TNF

  11. Isolation,Charcaterization of an Anthracene Degrading Bacterium Martelella sp. AD-3 and Cloning of Dioxygenase Gene%降解蒽嗜盐菌AD-3的筛选、降解特性及加氧酶基因的研究

    Institute of Scientific and Technical Information of China (English)

    崔长征; 冯天才; 于亚琦; 董婓; 杨昕梅; 冯耀宇; 刘勇弟; 林汉平

    2012-01-01

    Anthracene,among the 16 US EPA polycyclic aromatic hydrocarbons(PAHs),is a typical low molecular weight environmental contaminant,which gains concern on its biodegradation under hypersaline condition.In this study,an anthracene-degrading bacterial strain was isolated from highly saline petroleum-contaminated soil.Based on its physiological,biochemical characteristics and 16S rDNA sequence analysis,the bacteria was preliminary identified and named as Martelella sp. AD-3.The strain was able to utilize anthracene as sole carbon source for growth and the degradation occurred under broad salinities(0.1% to 10%) and varying pHs(6.0 to 10.0).The optimized degradation conditions were initial concentration 25 mg·L^-1,culture temperature 30℃,pH 9.0 and salinity 3%.And 94.6% of anthracene was degraded by strain AD-3 under the optimal conditions within 6 days.Degenerate primers design was performed with a reported dioxygenase α subunit homologous gene.A length of 307 bp fragment of the partial dioxygenase gene sequences(GenBank accession: JF823991.1) was amplified by nested PCR.The clones amino acid sequence from strain AD-3 showed 95% identity to that of the partial naphthalene dioxygenase large-subunit from Marinobacter sp. NCE312(AF295033).The results lay a foundation for the further study of molecular mechanism involved in the PAHs biodegradation by strain AD-3.%蒽是典型的多环芳烃类环境污染物,属于美国EPA优先控制的16种多环芳烃类化合物,其在高盐环境下的生物降解备受关注.本研究从某石油污染的高盐土壤中成功筛选出了1株高效降解蒽的菌株,经过对其生理生化特征和16S rDNA序列分析,初步鉴定并命名该菌株为Martelella sp.AD-3.该菌株在0.1%~10%的盐度和6.0~10.0的pH范围内,均能够降解蒽.其生长和降解蒽的优化条件是:蒽初始浓度25 mg·L^-1、温度30℃、pH值9.0和盐度3%,在优化条件下培养6 d,蒽的降解率可达到94.6%.根据已报道的双

  12. Isolation, degradation characteristics and catechol 1,2 dioxygenase gene expression level of 1,2,4-TCB degrading bacterium under low temperature%低温1,2,4-TCB降解菌的选育、降解特性及邻苯二酚1,2-双加氧酶基因表达水平

    Institute of Scientific and Technical Information of China (English)

    胡日查; 孙立波

    2013-01-01

    从长期受l,2,4-三氯苯(1,2,4-TCB)污染的地下水中筛选出一株低温寡营养降解菌A2,对A2菌进行革兰氏染色鉴定和16S rDNA鉴定,研究了不同pH、温度、盐度等因素对A2菌降解l,2,4-TCB效果以及对邻苯二酚l,2-双加氧酶基因表达的影响,并进行了正交实验.结果表明,A2菌为革兰氏阴性短杆细菌,初步鉴定为假单胞菌;在pH值为7、培养温度30℃、盐度0.8%、培养时间6d时,A2菌对1,2,4-TCB降解效果最好,降解率达到88.14%,同时该条件下邻苯二酚1,2-双加氧酶基因相对表达水平最高;培养温度为10℃时,A2菌对1,2,4-TCB降解率可达到85.3%,同时邻苯二酚l,2-双加氧酶基因也有较高的相对表达水平 以上结果说明,将A2菌应用于低温寡营养地下水的生物修复是可能的.%An oligotrophic degrading bacterium named strain A2 was screened from groundwater long-term contaminated by 1 , 2 , 4-TCB under low temperature condition, strain A2 was identified by gram stain and 16S rDNA sequence, the impacts of different pH, temperature, salinity on degradation effect and catechol 1 ,2 dioxyge-nase gene expression level were studied, and orthogonality experiment was carried out. The results showed that strain A2 was gram negative short rods, and was identified as pseudomonas preliminarily. The degrading effect of strain A2 on 1 ,2,4-TCB and catechol 1 ,2 dioxygenase gene expression level showed best under the conditions; pH of 7, cultivation temperature of 30℃ , salinity of 0.8% , cultivation time of 6 days, and the degrading rate could reach 88. 14% . The degrading rate of 1 ,2,4-TCB by strain A2 could reach 85.3% at 10℃ , and catechol 1 ,2 dioxygenase gene expression level also showed a relative high expression level. This research demonstrated that it is possible to apply strain A2 in the bioremediation of oligotrophic groundwater under low temperature condition.

  13. Prolyl hydroxylase domain enzymes: important regulators of cancer metabolism

    Directory of Open Access Journals (Sweden)

    Yang M

    2014-08-01

    , hypoxia-inducible factor (HIF, metabolism, mouse models, hydroxylation, 2-oxoglutarate-dependent dioxygenases

  14. Evolution of flavone synthase I from parsley flavanone 3beta-hydroxylase by site-directed mutagenesis.

    Science.gov (United States)

    Gebhardt, Yvonne Helen; Witte, Simone; Steuber, Holger; Matern, Ulrich; Martens, Stefan

    2007-07-01

    Flavanone 3beta-hydroxylase (FHT) and flavone synthase I (FNS I) are 2-oxoglutarate-dependent dioxygenases with 80% sequence identity, which catalyze distinct reactions in flavonoid biosynthesis. However, FNS I has been reported exclusively from a few Apiaceae species, whereas FHTs are more abundant. Domain-swapping experiments joining the N terminus of parsley (Petroselinum crispum) FHT with the C terminus of parsley FNS I and vice versa revealed that the C-terminal portion is not essential for FNS I activity. Sequence alignments identified 26 amino acid substitutions conserved in FHT versus FNS I genes. Homology modeling, based on the related anthocyanidin synthase structure, assigned seven of these amino acids (FHT/FNS I, M106T, I115T, V116I, I131F, D195E, V200I, L215V, and K216R) to the active site. Accordingly, FHT was modified by site-directed mutagenesis, creating mutants encoding from one to seven substitutions, which were expressed in yeast (Saccharomyces cerevisiae) for FNS I and FHT assays. The exchange I131F in combination with either M106T and D195E or L215V and K216R replacements was sufficient to confer some FNS I side activity. Introduction of all seven FNS I substitutions into the FHT sequence, however, caused a nearly complete change in enzyme activity from FHT to FNS I. Both FHT and FNS I were proposed to initially withdraw the beta-face-configured hydrogen from carbon-3 of the naringenin substrate. Our results suggest that the 7-fold substitution affects the orientation of the substrate in the active-site pocket such that this is followed by syn-elimination of hydrogen from carbon-2 (FNS I reaction) rather than the rebound hydroxylation of carbon-3 (FHT reaction).

  15. The Identification of Maize and Arabidopsis Type I FLAVONE SYNTHASEs Links Flavones with Hormones and Biotic Interactions.

    Science.gov (United States)

    Falcone Ferreyra, María Lorena; Emiliani, Julia; Rodriguez, Eduardo José; Campos-Bermudez, Valeria Alina; Grotewold, Erich; Casati, Paula

    2015-10-01

    Flavones are a major group of flavonoids with diverse functions and are extensively distributed in land plants. There are two different classes of FLAVONE SYNTHASE (FNS) enzymes that catalyze the conversion of the flavanones into flavones. The FNSI class comprises soluble Fe(2+)/2-oxoglutarate-dependent dioxygenases, and FNSII enzymes are oxygen- and NADPH-dependent cytochrome P450 membrane-bound monooxygenases. Here, we describe the identification and characterization of FNSI enzymes from maize (Zea mays) and Arabidopsis (Arabidopsis thaliana). In maize, ZmFNSI-1 is expressed at significantly higher levels in silks and pericarps expressing the 3-deoxy flavonoid R2R3-MYB regulator P1, suggesting that ZmFNSI-1 could be the main enzyme for the synthesis of flavone O-glycosides. We also show here that DOWNY MILDEW RESISTANT6 (AtDMR6), the Arabidopsis homologous enzyme to ZmFNSI-1, has FNSI activity. While dmr6 mutants show loss of susceptibility to Pseudomonas syringae, transgenic dmr6 plants expressing ZmFNSI-1 show similar susceptibility to wild-type plants, demonstrating that ZmFNSI-1 can complement the mutant phenotype. AtDMR6 expression analysis showed a tissue- and developmental stage-dependent pattern, with high expression in cauline and senescing leaves. Finally, we show that Arabidopsis cauline and senescing leaves accumulate apigenin, demonstrating that Arabidopsis plants have an FNSI activity involved in the biosynthesis of flavones. The results presented here also suggest cross talk between the flavone and salicylic acid pathways in Arabidopsis; in this way, pathogens would induce flavones to decrease salicylic acid and, hence, increase susceptibility.

  16. The gene pat-2, which induces natural parthenocarpy, alters the gibberellin content in unpollinated tomato ovaries.

    Science.gov (United States)

    Fos, M; Nuez, F; García-Martínez, J L

    2000-02-01

    We investigated the role of gibberellins (GAs) in the effect of pat-2, a recessive mutation that induces facultative parthenocarpic fruit development in tomato (Lycopersicon esculentum Mill.) using near-isogenic lines with two different genetic backgrounds. Unpollinated wild-type Madrigal (MA/wt) and Cuarenteno (CU/wt) ovaries degenerated, but GA(3) application induced parthenocarpic fruit growth. On the contrary, parthenocarpic growth of MA/pat-2 and CU/pat-2 fruits, which occurs in the absence of pollination and hormone application, was not affected by GA(3). Pollinated MA/wt and parthenocarpic MA/pat-2 ovary development was negated by paclobutrazol, and this inhibitory effect was counteracted by GA(3). The main GAs of the early-13-hydroxylation pathway (GA(1), GA(3), GA(8), GA(19), GA(20), GA(29), GA(44), GA(53), and, tentatively, GA(81)) and two GAs of the non-13-hydroxylation pathway (GA(9) and GA(34)) were identified in MA/wt ovaries by gas chromatography-selected ion monitoring. GAs were quantified in unpollinated ovaries at flower bud, pre-anthesis, and anthesis. In unpollinated MA/pat-2 and CU/pat-2 ovaries, the GA(20) content was much higher (up to 160 times higher) and the GA(19) content was lower than in the corresponding non-parthenocarpic ovaries. The application of an inhibitor of 2-oxoglutarate-dependent dioxygenases suggested that GA(20) is not active per se. The pat-2 mutation may increase GA 20-oxidase activity in unpollinated ovaries, leading to a higher synthesis of GA(20), the precursor of an active GA.

  17. Kinetic analysis of FTO (fat mass and obesity-associated) reveals that it is unlikely to function as a sensor for 2-oxoglutarate.

    Science.gov (United States)

    Ma, Marcella; Harding, Heather P; O'Rahilly, Stephen; Ron, David; Yeo, Giles S H

    2012-06-01

    Genomewide-association studies have revealed that SNPs (single nucleotide polymorphisms) in FTO (fat mass and obesity-associated) are robustly associated with BMI (body mass index) and obesity. FTO is an Fe(II) 2-OG (2-oxoglutarate)-dependent dioxygenase that can demethylate 3-meT (3-methylthymine) in single-stranded DNA, as well as 3-meU (3-methyluracil) and N6-methyl adenosine in RNA. In the present paper we describe the development of an RNase-cleavage assay measuring the demethylation activity of FTO on 3-meU. RNase A cleaves at the 3'-end of pyrimidines, including uracil, and a methyl group at position three of uracil inhibits cleavage. An oligonucleotide probe was designed consisting of a DNA stem, an RNA loop containing a single 3-meU as the only RNase A-cleavage site, a fluorescent reporter on one end and a quencher at the other end. FTO demethylation of the unique 3-meU enables RNase A cleavage, releasing the quencher and enabling a fluorescent signal. In the presence of excess RNase A, FTO activity is limiting to the development of fluorescent signal, which can be read continuously and is able to discriminate between wild-type and the catalytically dead R316Q FTO. 2-OG is a co-substrate of FTO and, as a metabolite in the citric acid cycle, is a marker of intracellular nutritional status. The assay described in the present paper was used to measure, for the first time, the K(m) of FTO for 2-OG. The K(m) of 2.88 μM is up to 10-fold lower than the estimated intracellular concentrations of 2-OG, rendering it unlikely that FTO functions as a sensor for 2-OG levels.

  18. Effects of the tryptophan 2,3-dioxygenase in tryptophan metabolism and immunoregulation%色氨酸2,3-双加氧酶在色氨酸分解代谢及免疫调节中的作用

    Institute of Scientific and Technical Information of China (English)

    李善宝; 徐军明

    2016-01-01

    Tryptophan 2,3-dioxygenase (TDO)is the rate-limiting enzyme in the catabolism of Trp along the kynurenine pathway.Trp is mainly catabilized by the TDO in the liver,which could not only regulate the concentration of the Trp and suppress the T cells proliferation,but also participate in antibacterial action and inflammatory response.The metabolin kynurenines as an endogenous ligand of the AhR receptor,the TDO enzymes,Kyn and AhR form the TDO-Kyn-AhR pathway have effects of regulatory the growth of tumor.With the research of the mechanism of immune regulation goes futher,it is expected to be a promising prospect in cancer therapy and the immune tolerance of transplantation.We reviewed in the article,which summarized the TDO mediated catabolism of Trp and immunomodulatory effect.%色氨酸2,3-双加氧酶(TDO)是催化色氨酸由犬尿氨酸(Kyn)途径分解代谢的限速酶.TDO主要在肝内降解色氨酸,调整体内色氨酸水平,能够抑制T细胞增殖,参与抗菌及炎性反应.代谢产物Kyn为芳烃受体(AhR)的内源性配体,TDO-Kyn-AhR通路具有调节肿瘤生长作用.随着对TDO介导色氨酸代谢免疫机制研究的不断积累,其在肿瘤治疗及移植免受耐受领域的应用前景令人期待.本文就TDO介导的色氨酸分解代谢及免疫调节作用进行综述.

  19. Materials for depollution based on the model of manganese dioxygenase

    OpenAIRE

    Chaignon, Jérémy

    2013-01-01

    La utilización intensiva de pesticidas ha traído consigo la presencia de una gran cantidad de moléculas contaminantes en aguas y suelos. Los tratamientos para degradar estas moléculas son caros, por lo que es de gran interés la búsqueda de soluciones más baratas. En el caso de los catecoles, existen enzimas, las catecol-dioxigenasas, que abren el ciclo aromático por oxidación con dioxígeno. Las condiciones suaves y la gran disponibilidad de este oxidante podrían ofrecer una solución para esos...

  20. Oxygenase-Catalyzed Desymmetrization of N,N-Dialkyl-piperidine-4-carboxylic Acids**

    Science.gov (United States)

    Rydzik, Anna M; Leung, Ivanhoe K H; Kochan, Grazyna T; McDonough, Michael A; Claridge, Timothy D W; Schofield, Christopher J

    2014-01-01

    γ-Butyrobetaine hydroxylase (BBOX) is a 2-oxoglutarate dependent oxygenase that catalyzes the final hydroxylation step in the biosynthesis of carnitine. BBOX was shown to catalyze the oxidative desymmetrization of achiral N,N-dialkyl piperidine-4-carboxylates to give products with two or three stereogenic centers. PMID:25164544

  1. Biosynthesis of 8-O-methylated benzoxazinoid defense compounds in maize

    Science.gov (United States)

    Benzoxazinoids are important defense compounds in grasses. Here, we investigated the biosynthesis and biological roles of the 8-O-methylated benzoxazinoids, DIM2BOA-Glc and HDM2BOA-Glc. Using quantitative trait locus mapping and heterologous expression, we identified a 2-oxoglutarate-dependent dioxy...

  2. Cloning of parsley flavone synthase I.

    Science.gov (United States)

    Martens, S; Forkmann, G; Matern, U; Lukacin, R

    2001-09-01

    A cDNA encoding flavone synthase I was amplified by RT-PCR from leaflets of Petroselinum crispum cv. Italian Giant seedlings and functionally expressed in yeast cells. The identity of the recombinant, 2-oxoglutarate-dependent enzyme was verified in assays converting (2S)-naringenin to apigenin.

  3. Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins

    Directory of Open Access Journals (Sweden)

    Edler Stefanie

    2008-06-01

    Full Text Available Abstract Background The jumonji C (JmjC domain containing gene 6 (Jmjd6, previously known as phosphatidylserine receptor has misleadingly been annotated to encode a transmembrane receptor for the engulfment of apoptotic cells. Given the importance of JmjC domain containing proteins in controlling a wide range of diverse biological functions, we undertook a comparative genomic analysis to gain further insights in Jmjd6 gene organisation, evolution, and protein function. Results We describe here a semiautomated computational pipeline to identify and annotate JmjC domain containing proteins. Using a sequence segment N-terminal of the Jmjd6 JmjC domain as query for a reciprocal BLAST search, we identified homologous sequences in 62 species across all major phyla. Retrieved Jmjd6 sequences were used to phylogenetically analyse corresponding loci and their genomic neighbourhood. This analysis let to the identification and characterisation of a bi-directional transcriptional unit compromising the Jmjd6 and 1110005A03Rik genes and to the recognition of a new, before overseen Jmjd6 exon in mammals. Using expression studies, two novel Jmjd6 splice variants were identified and validated in vivo. Analysis of the Jmjd6 neighbouring gene 1110005A03Rik revealed an incident deletion of this gene in two out of three earlier reported Jmjd6 knockout mice, which might affect previously described conflicting phenotypes. To determine potentially important residues for Jmjd6 function a structural model of the Jmjd6 protein was calculated based on sequence conservation. This approach identified a conserved double-stranded β-helix (DSBH fold and a HxDxnH facial triad as structural motifs. Moreover, our systematic annotation in nine species identified 313 DSBH fold-containing proteins that split into 25 highly conserved subgroups. Conclusion We give further evidence that Jmjd6 most likely has a function as a nonheme-Fe(II-2-oxoglutarate-dependent dioxygenase as

  4. The GA5 locus of Arabidopsis thaliana encodes a multifunctional gibberellin 20-oxidase: Molecular cloning and functional expression

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Yun-Ling; Li, Li; Wu, Keqiang [Michigan State Univ., East Lansing, MI (United States)] [and others

    1995-07-03

    The biosynthesis of gibberellins (GAs) after GA{sub 12}-aldehyde involves a series of oxidative steps that lead to the formation of bioactive GAs. Previously, a cDNA clone encoding a GA 20-oxidase [gibberellin, 2-oxoglutarate:oxygen oxidoreductase (20-hydroxylating, oxidizing), EC 1.14.11-] was isolated by immunoscreening a cDNA library from liquid endosperm of pumpkin (Cucurbita maxima L.) with antibodies against partially purified GA 20-oxidase. Here, we report isolation of a genomic clone for GA 20-oxidase from a genomic library of the long-day species Arabidopsis thaliana Heynh., strain Columbia, by using the pumpkin cDNA clone as a heterologous probe. This genomic clone contains a GA 20-oxidase gene that consists of three exons and two introns. The three exons are 1131-bp long and encode 377 amino acid residues. A cDNA clone corresponding to the putative GA 20-oxidase genomic sequence was constructed with the reverse transcription-PCR method, and the identity of the cDNA clone was confirmed by analyzing the capability of the fusion protein expressed in Escherichia coli to convert GA{sub 53} to GA{sub 44} and GA{sub 19} to GA{sub 20}. The Arabidopsis GA 20-oxidase shares 55% identity and >80% similarity with the pumpkin GA 20-oxidase at the derived amino acid level. Both GA 20-oxidases share high homology with other 2-oxoglutarate-dependent dioxygenases (2-ODDs), but the highest homology was found between the two GA 20-oxidases. Mapping results indicated tight linkage between the cloned GA 20-oxidase and the GA locus of Arabidopsis. The ga5 semidwarf mutant contains a G {yields} A point mutation that inserts a translational stop codon in the protein-coding sequence, thus confirming that the GA5 locus encodes GA 20-oxidase. Expression of the GA5 gene in Arabidopsis leaves was enhanced after plants were transferred from short to long days; it was reduced by GA{sub 4} treatment, suggesting end-product repression in the GA biosynthetic pathway. 28 refs., 6 figs.

  5. 吲哚胺2,3双加氧酶在诊断肝移植急性排斥中的作用%Role of indoleamine 2, 3-dioxygenase in diagnosing rat's acute rejection after liver transplantation

    Institute of Scientific and Technical Information of China (English)

    翁明哲; 徐军明; 张金彦; 张寅; 许勇刚; 王兆文; 孙星; 彭志海

    2011-01-01

    目的 探讨外周血吲哚胺2,3双加氧酶(IDO)基因表达对大鼠肝移植急性排斥反应(AR)的诊断价值.方法 建立大鼠原位肝移植模型,分为4组:A组:同基因移植组(Wistar-Wistar,n=32);B组:异基因移植组(SD-Wistar,n=32);C组:异基因移植+长期环孢素A组(CsA,n=32);D组:异基因移植+短期CsA组(用药剂量同C组,第3天起停药,n=32).应用实时聚合酶链反应(Real-time PCR)方法 分别检测术后第0、1、2、3、4、5、7、9天外周血IDO mRNA值,同时检测各时间点血清谷草转氨酶(AST)、总胆红素(T-BIL)、碱性磷酸酶(ALP)水平,并取肝脏病理切片.结果 A组外周血IDO mRNA呈持续低水平,AST、T-BIL、ALP逐渐降至正常,病理无排斥反应.C组检测结果 与A组相似.B组IDO mRNA显著上升为术后第2天(P<0.05),AST、T-BIL、ALP值显著上升为术后4d(P<0.01),病理切片判断轻度排斥为术后5d(χ2=4.8,P<0.05).D组IDO mRNA显著上升为术后第4天(P<0.05),AST、T-BIL、ALP值显著上升为术后5d(P<0.01),病理切片判断轻度排斥为术后7d(χ2=4.8,P<0.05).结论 外周血IDO mRNA检测可较病理检查更早诊断大鼠肝移植AR的发生,且方法 简单、安全.%Objective To study the diagnostic value of indoleamine 2, 3-dioxygenase (IDO) gene expression in acute liver rejection in rat orthotopic liver transplantation model. Methods The rat orthotopic liver transplantation models were divided into four groups: group A, isograft transplantation group (Wistar to Wistar); group B, allograft transplantation (SD to Wistar); group C, allograft transplantation and cyclosporine; Group D, allograft transplantation and cyclosporine (the drug was withdrawn on the 3rd day after the operation). The samples (peripheral blood and liver tissue) were obtained on the operation day, 1st, 2nd, 3rd, 4th, 5th, 7th and 9th day post-operation. Luorescent quantitative polymerase chain reaction (PCR), pathological study and serum test were performed on each sample

  6. Dynamic observation of the expression of indoleamine 2,3-dioxygenase on the surface of dendritic cells induced by Echinococcus granulosus antigens%细粒棘球蚴抗原诱导树突状细胞表达吲哚胺2,3-双加氧酶的动态观察

    Institute of Scientific and Technical Information of China (English)

    单骄宇; 李海涛; 吐尔洪江·吐逊; 肖晋; 李亮; 林仁勇; 温浩

    2012-01-01

    Objective To dynamically observe the expression of indoleamine 2, 3-dioxygenase(IDO) on the surface of dendritic cells (DCs) using different Echinococcus granulosus antigens. Methods Bone marrow DCs (BMDCs) from C57BL/6 mice were obtained in vitro. BMDCs were then treated with 15 μg/ml rAgB, 5 mg/ml MHF or 1 000 U/ml IFN-γ (as a positive control. The relative expression of IDO mRNA and IL-10 mRNA was dynamically measured with FQ-RT-PCR and the expression of IDO protein was determined with Western blot at 6 , 18, 24, 48, and 60 h. Results FQ-RT-PCR analysis showed that IDO was up-regulated 26. 8-fold at 24 h while IL-10 was markedly up-regulated 65. 1-fold at 48 h in rAgB-treated DCs. In MHF-treated DCs, IDO and IL-10 were up-regulated 12. 6-fold and 3. 9-fold at 24 h, respectively. In IDO protein detection, the expression of IDO increased in DCs treated with rAgB and MHF. In rAgB-treated DCs, the expression of IDO became evident at 24 h; in MHF-treated DCs, the expression of IDO became evident at 48 h. Conclusion rAgB and MHF up-regulate the expression of IDO. rAgB was better able to up-regulate IDO than was MHF. IDO is a molecule that regulates the immune response and can play a key role in the Th2 immune responsc. Results suggest that IDO may be involved in immune evasion and inhibition of the inflammatory response by echinococco-sis.%目的 动态检测细粒棘球蚴不同抗原体外诱导树突状细胞表达吲哚胺2,3-双加氧酶(IDO). 方法 在体外实验的条件下,获得C57BL/6小鼠骨髓来源的树突状细胞(BMDCs),分别应用15 μg/ml重组抗原B(rAgB)、5 mg/ml小鼠囊型包虫囊液(MHF)、1 000 U/ml IFN-γ(阳性对照)刺激BMDCs,在6、18、24、48、60h采用实时荧光定量RT-PCR动态监测IDO、IL-10 mRNA相对表达情况;在不同时间点收集各组DCs,应用Western blot检测IDO蛋白的表达.结果 FQ-RT-PCR显示,rAgB处理组IDO mRNA在24 h时上调26.8倍,IL-10 mRNA在48 h时上调65.1倍,MHF处理组干预24 h

  7. 78 FR 10181 - Documents To Support Submission of an Electronic Common Technical Document; Availability

    Science.gov (United States)

    2013-02-13

    ... versions of technical documentation in the Federal Register of August 6, 2012 (77 FR 46763). FDA has... Technical Document; Availability AGENCY: Food and Drug Administration, HHS. ACTION: Notice. SUMMARY: The... electronic Common Technical Document (eCTD) specifications: ``The eCTD Backbone Files Specification...

  8. 77 FR 46763 - Documents to Support Submission of an Electronic Common Technical Document; Availability

    Science.gov (United States)

    2012-08-06

    ... available draft technical documentation for public comment in a Federal Register notice dated October 26... Technical Document; Availability AGENCY: Food and Drug Administration, HHS. ACTION: Notice. SUMMARY: The... Technical Document (eCTD) specifications: ``The eCTD Backbone Files Specification for Module 1, version...

  9. 78 FR 52776 - Documents to Support Submission of an Electronic Common Technical Document; Availability

    Science.gov (United States)

    2013-08-26

    ... final versions of technical documentation in a Federal Register notice dated February 13, 2013 (Docket... Technical Document; Availability AGENCY: Food and Drug Administration, HHS. ACTION: Notice. SUMMARY: The... format using the electronic Common Technical Document (eCTD) specifications: ``The eCTD Backbone...

  10. Different Echinococcus granulosus Antigens Induced Indoleamine 2,3-dioxygenase Expression in Dendritic Cells%不同棘球蚴抗原诱导树突状细胞表达吲哚胺2,3-双加氧酶的实验研究

    Institute of Scientific and Technical Information of China (English)

    单骄宇; 李海涛; 李春燕; 肖晋; 李亮; 张雪; 林仁勇; 温浩

    2013-01-01

    Objective To observe the expression of indoleamine 2,3-dioxygenase (IDO) in dendritic cells (DCs) via different Echinococcus granulosus antigens in vitro.Methods Bone Marrow DCs generated from bone marrow precursor cells of C57BL/6 mice and cultured in the presence of recombinant mouse GM-CSF (rmGM-CSF).Then,DCs were induced with 15 μg/ml recombinant antigen B (rAgB),5 mg/ml mouse hydatid fluid (MHF),1 000 U/ml IFN-γ (as positive control),and RPMI 1640 complete medium (as negative control),respectively.Meanwhile,the treated DCs and cell supernatants were collected at 18,24 and 48 h after induction.The positive expressions of D40,CD80,CD86 and I-A/I-E on DCs were determined by flow cytometry.By real-time fluorescent quantitative reverse-transcription polymerase chain reaction (FQ-RT-PCR),the expression level of IDO mRNA in DCs was measured.Concentrations of tryptophan (Try) were tested by high-performance liquid chromatography (HPLC) assay in cell supernatant.Results The data from flow cytometry showed that the positive expressions of CD40,CD80,CD86,I-A/I-E were decreased after stimulated by rAgB and MHF.At 24 h after induction,there was significant difference in the level of CD40,CD86 and I-A/I-E among rAgB-treated group [(22.60±2.69)%,(35.50±4.38)%,(57.30±4.38)%],MHF-treated group [(38.00±3.54)%,(53.00± 3.39)%,(77.10±1.70)%] and negative control [(37.95±3.61) %,(19.55±1.06) % and (85.45±1.63) %](P<0.05).At 18,24 and 48h after induction,the levels of IDO mRNA in rAgB-treated group [(9.20t0.01),(29.44±0.02),(16.48±0.04)] and MHF-treated group [(9.67±0.02),(17.52±0.01),(16.81±0.01)] was higher than that of negative control group[(2.46±0.01),(7.77±0.01),and(10.56±0.01)] (P<0.01).And significant difference was found between rAgB-treated group and MHF-treated group (P<0.05).At 18,24 and 48 h after induction,the concentrations of Try were lowest in rAgB-treated group [(23.65±0.64),(13.95±1.06),(19.05±0.64) μmol/L].At 24h

  11. 吲哚胺2,3双加氧酶与乙肝病毒不同感染状态T淋巴细胞亚群及病毒载量的相关性研究%Investigation of the correlation between indoleamine 2,3-dioxygenase and T cell subsets,viral load in different hepatitis B virus infection status

    Institute of Scientific and Technical Information of China (English)

    曾道炳; 卢实春; 李军峰; 胡冬; 周育森

    2012-01-01

    目的 探讨乙肝病毒(HBV)不同感染状态下,吲哚胺2,3双加氧酶(indoleamine 2,3-dioxygenase,IDO)表达水平及其与T淋巴细胞亚群及病毒载量的相关性.方法 检测受检者外周静脉血IDO mRNA、IDO蛋白、IDO活性,T淋巴细胞亚群及病毒载量(对照组除外);进行各组间均数比较及相关性分析.结果 IDO mRNA、IDO蛋白及IDO活性从高到低依次为急性乙型肝炎组(acute hepatitis B,AHB)、肝硬化组(HBV-related liver cirrhosis,LC)、慢性乙型肝炎组(chronic hepatitis B,CHB)、肝癌组(HBV-related hepatocellular carcinoma,HCC)、对照组.HCC组及对照组均明显低于其他3组(P<0.01),其余各组间两两比较,差异有统计学意义(P<0.05).CD3+、CD4+T淋巴细胞在AHB组最高,对照组次之,LC组最低;AHB组、对照组及CHB组均明显高于LC组(P< 0.05);AHB组、对照组明显高于HCC组(P<0.05).CD8+T淋巴细胞在对照组最高,AHB组次之,LC组最低;但仅AHB组、对照组明显高于LC组(P<0.05).AHB组CD4+/CD8+明显高于其他组(P<0.01).CHB及LC组病毒载量最高,均明显高于HCC及AHB组(P<0.05).CD3+、CD4+、CD8+T淋巴细胞与病毒载量、IDO蛋白及IDO活性均呈负相关,CD8+T淋巴细胞与IDO mRNA呈负相关(r=-0.287,P=0.039);CD4+/CD8+与IDO蛋白及IDO活性均呈正相关(r=0.470,P=0.000;r=0.285,P=0.040),病毒载量与IDO mRNA、IDO蛋白及IDO活性均呈正相关(r=0.530,P=0.001;r=0.416,P=0.002;r=0.649,P=0.000).结论 HBV感染者IDO表达明显增强,与病毒载量呈正相关,与T淋巴细胞呈负相关,其早期升高有利于病毒清除,但持续升高会导致HBV特异性T淋巴细胞功能抑制,使HBV慢性化.%Objective To investigate the expression levels of indoleamine 2,3-dioxygenase(IDO) and the correlation between IDO level, T cell subsets and viral load in hepatitis B related liver disease subjects. Methods Peripheral blood samples were collected, and the the expression level of IDO Mrna and IDO protein in PBMC

  12. Indoleamine 2,3-dioxygenase specific, cytotoxic T cells as immune regulators

    DEFF Research Database (Denmark)

    Sørensen, Rikke Bæk; Hadrup, Sine Reker; Svane, Inge Marie;

    2011-01-01

    , this caused an increase in the production of the proinflammatory cytokines IL-6 and tumor necrosis factor-alpha while decreasing the IL-10 production. Finally, the addition of IDO-inducing agents (ie, the TLR9 ligand cytosine-phosphate- guanosine, soluble cytotoxic T lymphocyte-associated antigen 4...... show that the presence of such IDO-specific CD8(+) T cells boosted T-cell immunity against viral or tumor-associated antigens by eliminating IDO+ suppressive cells. This had profound effects on the balance between interleukin-17 (IL-17)-producing CD4(+) T cells and regulatory T cells. Furthermore...

  13. The immune system strikes back: cellular immune responses against indoleamine 2,3-dioxygenase

    DEFF Research Database (Denmark)

    Sørensen, Rikke Baek; Berge-Hansen, Linda; Junker, Niels;

    2009-01-01

    of the major immune suppressive cell populations. CONCLUSION: IDO may serve as an important and widely applicable target for anti-cancer immunotherapeutic strategies. Furthermore, as emerging evidence suggests that IDO constitutes a significant counter-regulatory mechanism induced by pro-inflammatory signals...

  14. Characterization of oxylipins and dioxygenase genes in the asexual fungus Aspergillus niger

    NARCIS (Netherlands)

    Wadman, Mayken W; de Vries, Ronald P; Kalkhove, Stefanie I C; Veldink, Gerrit A; Vliegenthart, Johannes F G

    2009-01-01

    BACKGROUND: Aspergillus niger is an ascomycetous fungus that is known to reproduce through asexual spores, only. Interestingly, recent genome analysis of A. niger has revealed the presence of a full complement of functional genes related to sexual reproduction 1. An example of such genes are the dio

  15. The Targeting of Indoleamine 2,3 Dioxygenase -Mediated Immune Escape in Cancer

    DEFF Research Database (Denmark)

    Iversen, Trine Zeeberg; Andersen, Mads Hald; Svane, Inge Marie

    2015-01-01

    The era of immunotherapies was unleashed in 2010 with the Food and Drug Administration (FDA) approval of the first therapeutic vaccine sipuleucel-T as a standard treatment for metastatic prostate cancer. Next, the first immune-activating anticytotoxic lymphocyte antigen-4 (CTLA-4) antibody...... investigation in metastatic melanoma (MM) and non-small-cell lung cancer (NSCLC), and impressive clinical results are anticipated. Despite these successes, only a fraction of patients become clinical responders to therapy. Thus, to improve the selection of patients likely to respond, scrutinizing different...... immune parameters during treatment is essential. In the summary of this PhD thesis, we investigated changes in immune parameters and their possible correlation with clinical efficacy in patients with MM during treatments with the standard chemo- and immunotherapies, temozolomide (TMZ) and interferon-α2b...

  16. Investigating the Role of Indoleamine 2,3- dioxygenase (IDO) in Breast Cancer Metastasis

    Science.gov (United States)

    2012-09-01

    influencing immune cell maturation. Specifically, these cytokines regulate divergence into Th1, Th2 or Th17 cell lineages. It is generally...accepted that a Th1 environment suppresses tumor outgrowth while a Th2 environment promotes immune escape. The cytokine profile for Th1/Th2/ Th17 showed no...inflammation in the lung and included IL-6, IL-10, MCP-1, IFN-, TNF and IL-12p70. Samples were collected and analyzed similarly to the Th1/Th2/ Th17

  17. Spontaneous cytotoxic T-Cell reactivity against indoleamine 2,3-dioxygenase-2

    DEFF Research Database (Denmark)

    Sørensen, Rikke Bæk; Køllgaard, Tania; Andersen, Rikke Sick;

    2011-01-01

    by the D stereoisomer of the IDO blocker 1-methyl-tryptophan (1MT), which tends to be more active than the L-isomer in a variety of biological assays for IDO function, suggests that IDO2 may be important to sustain immune escape and growth of tumors. Especially, D-1MT heightens chemotherapeutic efficacy...... in mouse models of cancer in a nontoxic fashion. Here, we describe the immunogenicity of IDO2 by showing the presence of spontaneous cytotoxic T-cell reactivity against IDO2 in peripheral blood of both healthy donors and cancer patients. Furthermore, we show that these IDO2-specific T cells are cytotoxic...

  18. Jmjd6, a JmjC Dioxygenase with Many Interaction Partners and Pleiotropic Functions

    Science.gov (United States)

    Kwok, Janice; O’Shea, Marie; Hume, David A.; Lengeling, Andreas

    2017-01-01

    Lysyl hydroxylation and arginyl demethylation are post-translational events that are important for many cellular processes. The jumonji domain containing protein 6 (JMJD6) has been reported to catalyze both lysyl hydroxylation and arginyl demethylation on diverse protein substrates. It also interacts directly with RNA. This review summarizes knowledge of JMJD6 functions that have emerged in the last 15 years and considers how a single Jumonji C (JmjC) domain-containing enzyme can target so many different substrates. New links and synergies between the three main proposed functions of Jmjd6 in histone demethylation, promoter proximal pause release of polymerase II and RNA splicing are discussed. The physiological context of the described molecular functions is considered and recently described novel roles for JMJD6 in cancer and immune biology are reviewed. The increased knowledge of JMJD6 functions has wider implications for our general understanding of the JmjC protein family of which JMJD6 is a member. PMID:28360925

  19. Buffer management optimization strategy for satellite ATM

    Institute of Scientific and Technical Information of China (English)

    Lu Rong; Cao Zhigang

    2006-01-01

    ECTD (erroneous cell tail drop), a buffer management optimization strategy is suggested which can improve the utilization of buffer resources in satellite ATM (asynchronous transfer mode) networks. The strategy, in which erroneous cells caused by satellite channel and the following cells that belong to the same PDU (protocol data Unit) are discarded, concerns non-real-time data services that use higher layer protocol for retransmission. Based on EPD (early packet drop) policy, mathematical models are established with and without ECTD. The numerical results show that ECTD would optimize buffer management and improve effective throughput (goodput), and the increment of goodput is relative to the CER (cell error ratio) and the PDU length. The higher their values are, the greater the increment. For example,when the average PDU length values are 30 and 90, the improvement of goodput are respectively about 4% and 10%.

  20. CAROTENOID CLEAVAGE DIOXYGENASE 7 modulates plant growth, reproduction, senescence, and determinate nodulation in the model legume Lotus japonicas

    NARCIS (Netherlands)

    Liu, J.; Novero, M.; Charnikhova, T.; Ferrandino, A.; Schubert, A.; Ruyter-Spira, C.P.; Biofante, P.; Lovisolo, C.; Bouwmeester, H.J.

    2013-01-01

    Strigolactones (SLs) are newly identified hormones that regulate multiple aspects of plant development, infection by parasitic weeds, and mutualistic symbiosis in the roots. In this study, the role of SLs was studied for the first time in the model plant Lotus japonicus using transgenic lines silenc

  1. 3D-QSAR Study of Indol-2-yl Ethanones Derivatives as Novel Indoleamine 2,3-Dioxygenase (IDO Inhibitors

    Directory of Open Access Journals (Sweden)

    Kamlendra S. Bhadoriya

    2012-01-01

    Full Text Available 3D-QSAR approach using kNN-MFA was applied to a series of Indol-2-yl ethanones derivatives as novel IDO inhibitors. For the purpose, 22 compounds were used to develop models. To elucidate the structural properties required for IDO inhibitory activity, we report here k-nearest neighbor molecular field analysis (kNN-MFA-based 3D-QSAR model for Indol-2-yl ethanones derivatives as novel IDO inhibitors. Overall model classification accuracy was 76.27% (q2 = 0.7627, representing internal validation in training set and 79.35% (pred_r2 = 0.7935, representing external validation in test set using sphere exclusion and forward as a method of data selection and variable selection, respectively. Contour maps using this approach showed that hydrophobic and steric effects dominantly determine binding affinities. The information rendered by 3D-QSAR model may lead to a better understanding of structural requirements of IDO inhibitors and can help in the design of novel potent molecules.

  2. Indoleamine 2,3 Dioxygenase (IDO) as a Mediator of Myeloid Derived Suppressor Cell Function in Breast Cancer

    Science.gov (United States)

    2009-10-31

    Ronca, R., Serafini , P ., Zam boni, P., Restifo, N. P., and Zanovello, P. Identification of a CD11b(+)/Gr-1(+)/CD31(+) myeloid progenitor capable...of activating or suppressing CD8(+) T cells. Blood, 96: 3838-3846, 2000. 6. Serafini , P., De Santo, C., Marigo, I. , Cingarlini, S., Dolcetti, L

  3. Metabolomic and genetic analyses of flavonol synthesis in Arabidopsis thaliana support the in vivo involvement of leucoanthocyanidin dioxygenase

    NARCIS (Netherlands)

    Stracke, R.; Vos, de R.C.H.; Bartelniewoehner, L.; Ishihara, H.; Sagasser, M.; Martens, S.; Weisshaar, B.

    2009-01-01

    Flavonol synthase (FLS) (EC-number 1.14.11.23), the enzyme that catalyses the conversion of flavonols into dihydroflavonols, is part of the flavonoid biosynthesis pathway. In Arabidopsis thaliana, this activity is thought to be encoded by several loci. In addition to the FLAVONOL SYNTHASE1 (FLS1) lo

  4. Indoleamine 2,3-Dioxygenase: Expressing Cells in Inflammatory Bowel Disease—A Cross-Sectional Study

    Directory of Open Access Journals (Sweden)

    Janette Furuzawa-Carballeda

    2013-01-01

    Full Text Available Aim. To characterise and enumerate IDO+ cells, Tregs, and T cell subsets in patients with ulcerative colitis (UC and Crohn’s disease (CD with regard to their clinical activity. Methods. Ten active UC (aUC, 10 inactive UC (iUC, 6 aCD, and 8 iCD patients and 10 healthy individuals were included in the study. Circulating Foxp3-, IDO-, IL-17A-, IL-4-, IFN-γ-, and IL-10-expressing CD4+ T cells were quantitated by flow cytometry. Interleukin-17-expressing cells, CD25+/Foxp3+ Tregs, and CD123+/IDO+ plasmacytoid dendritic cells were evaluated in intestinal biopsies from 10 aUC, 6 aCD, and 10 noninflamed tissues. Results. All CD4+ T subsets were increased in aIBD patients compared with healthy donors. Meanwhile, frequency of CD8α+/CD16+/IDO+, CD8α+/CD56+/IDO+, CD8α+/CD80+/IDO+, CD8α+/CD123+/IDO+ large granular nonlymphoid cells, and CCR6+/CD123+/IDO+ plasmacytoid dendritic cells was higher in aIBD patients versus healthy donors or iIBD patients. Tissue IL-17A+ cells were present in higher amounts in aIBD versus noninflamed controls. IDO- and Foxp3-expressing cells were increased in aUC versus aCD patients and noninflamed tissues. Conclusions. The findings represent an original work in Mexican Mestizo patients with IBD. It shows that Tregs and IDO-expressing cells are increased with regard to disease activity. These cells could significantly shape inflammatory bowel disease pathophysiology, severity, and tolerance loss.

  5. A Calculus of Macro-Events: Progress Report

    Science.gov (United States)

    2000-01-01

    1410, USA iliano@itd.nrl.navy.mil Angelo Montanari Dipartimento di Matematica e Informatica Universita di Udine Via delle Scienze, 206 { 33100 Udine...nition of ECTD-structure only by the following points: M MT is a set of macro-events over T . The codomain of [jji and hjj] are rede ned to be

  6. GenBank blastx search result: AK062096 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK062096 001-044-H12 AB075242.1 Terrabacter sp. YK3 plasmid pYK3 genes for alpha subunit of dibenzofuran... dioxygenase, beta subunit of dibenzofuran dioxygenase, ferredoxin component of dibenzofuran... dioxygenase, ferredoxin reductase component of dibenzofuran dioxygenase, complete cds.|BCT BCT 3e-17 +3 ...

  7. GenBank blastx search result: AK062096 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK062096 001-044-H12 M86348.1 Pseudomonas sp. LB400 biphenyl dioxygenase (bphA), biphenyl dioxygenase (bph...E), biphenyl dioxygenase (bphF) and biphenyl dioxygenase (bphG)s, complete cds, and dihydrodiol dehydrogenase (bphB), partial cds.|BCT BCT 1e-14 +3 ...

  8. Protein (Cyanobacteria): 175247 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available sistance protein/dioxygenase Gloeocapsa sp. PCC 7428 MKFGYTIFYVPDVSAAVSFYEQAFGLSRRFVHESSQYAEMETGSTILAFASEEMAKSNGLTITPHRLENNAAAVEVAFITETIEEAFNQAIKAGAVAVKPIEVKPWGQTVGYVRDLNGVVVELCTPVL ...

  9. Protozoan ALKBH8 Oxygenases Display both DNA Repair and tRNA Modification Activities

    DEFF Research Database (Denmark)

    Zdżalik, Daria; Vågbø, Cathrine B; Kirpekar, Finn;

    2014-01-01

    1-8 and FTO. Mammalian and plant ALKBH8 are tRNA hydroxylases targeting 5-methoxycarbonylmethyl-modified uridine (mcm5U) at the wobble position of tRNAGly(UCC). In contrast, the genomes of some bacteria encode a protein with strong sequence homology to ALKBH8, and robust DNA repair activity......, interestingly, two protozoan ALKBH8s also catalyzed wobble uridine modification of tRNA, thus displaying a dual in vitro activity. Also, we found the modification status of tRNAGly(UCC) to be unaltered in an ALKBH8 deficient mutant of Agrobacterium tumefaciens, indicating that bacterial ALKBH8s have a function......The ALKBH family of Fe(II) and 2-oxoglutarate dependent oxygenases comprises enzymes that display sequence homology to AlkB from E. coli, a DNA repair enzyme that uses an oxidative mechanism to dealkylate methyl and etheno adducts on the nucleobases. Humans have nine different ALKBH proteins, ALKBH...

  10. The structure at 2.4 Å resolution of the protein from gene locus At3g21360, a putative FeII/2-oxo­glutarate-dependent enzyme from Arabidopsis thaliana

    Science.gov (United States)

    Bitto, Eduard; Bingman, Craig A.; Allard, Simon T. M.; Wesenberg, Gary E.; Aceti, David J.; Wrobel, Russell L.; Frederick, Ronnie O.; Sreenath, Hassan; Vojtik, Frank C.; Jeon, Won Bae; Newman, Craig S.; Primm, John; Sussman, Michael R.; Fox, Brian G.; Markley, John L.; Phillips, George N.

    2005-01-01

    The crystal structure of the gene product of At3g21360 from Arabidopsis thaliana was determined by the single-wavelength anomalous dispersion method and refined to an R factor of 19.3% (R free = 24.1%) at 2.4 Å resolution. The crystal structure includes two monomers in the asymmetric unit that differ in the conformation of a flexible domain that spans residues 178–230. The crystal structure confirmed that At3g21360 encodes a protein belonging to the clavaminate synthase-like superfamily of iron(II) and 2-oxoglutarate-dependent enzymes. The metal-binding site was defined and is similar to the iron(II) binding sites found in other members of the superfamily. PMID:16511070

  11. Transcriptional regulation of 9-cis-epoxycarotenoid dioxygenase (NCED) gene by putrescine accumulation positively modulates ABA synthesis and drought tolerance in Lotus tenuis plants.

    Science.gov (United States)

    Espasandin, Fabiana D; Maiale, Santiago J; Calzadilla, Pablo; Ruiz, Oscar A; Sansberro, Pedro A

    2014-03-01

    The accumulation of putrescine (Put) and increased arginine decarboxylase (ADC, EC 4.1.1.19) activity levels in response to osmotic stress has been reported; however, the biological meaning of this increase remains unclear. To obtain new insights into these questions, we studied the drought response of a transgenic Lotus tenuis line that expresses the oat ADC gene, which is driven by the stress-inducible pRD29A promoter. This line contains high levels of Put with no changes in spermidine and spermine contents, even under water deficits. Our results indicate that the biochemical and morphological responses to dehydration correlate with the Put level and provide evidence that Put controls the ABA content in response to drought by modulating ABA biosynthesis at the transcriptional level.

  12. A new iron(III) complex of glycine derivative of amine-chloro substituted phenol ligand: Synthesis, characterization and catechol dioxygenase activity

    Science.gov (United States)

    Saberikia, Iraj; Safaei, Elham; Kowsari, Mohammad Hossein; Lee, Yong-Ill; Cotic, Patricia; Bruno, Giuseppe; Rudbari, Hadi Amiri

    2012-12-01

    A new iron(III) complex of the glycine derivative of amine-chloro substituted phenol ligand (H3LGDC) has been prepared and characterized by IR, 1H NMR, UV-Vis spectroscopic techniques, cyclic voltammetry, ESI-MS and magnetic susceptibility studies. X-ray analysis reveals that in iron complex of FeLGDC the iron(III) center has a distorted trigonal bipyramidal coordination sphere and is surrounded by an amine nitrogen, a carboxylate, a water and two phenolate oxygen atoms. The DFT calculations with the UB3LYP/6-311++G** level optimized structure of the complex are in good agreement with experimental X-ray structural data. The variable-temperature magnetic susceptibility indicates that FeLGDC is the paramagnetic high spin iron(III) complex. It has been shown that electrochemical oxidation of this complex is ligand-centered due to the oxidation of phenolate to the phenoxyl radicals. This enzyme mimic utilized molecular oxygen in carrying out the oxidative cleavage of catechols with complete conversion at room temperature.

  13. 邻苯二酚双加氧酶传感器的研究%Studies on the Catechol Dioxygenase sensor

    Institute of Scientific and Technical Information of China (English)

    吕鹏; 史建国; 冯东; 庄重; 王建传; 凌建亚; 张长铠

    2005-01-01

    洋葱伯克霍尔德氏菌L68的细胞裂解液经硫酸铵分级沉淀后,依次经DEAE-Sepharose Fast Flow柱层析,Hydroxyapatite柱层析和Sephadex G-150 凝胶过滤分离,提取到邻苯二酚双加氧酶.经SDS-PAGE检测,达到电泳纯.将酶反应与氧电极偶联,研究了检测水体中邻苯二酚的邻苯二酚双加氧酶传感器.以100mmol/L磷酸钠标准缓冲液(pH7.24)作为该酶传感器的的工作介质,在25℃条件下测得传感器对邻苯二酚标准液的工作曲线线性范围为0.2~3mmol/L,检测限为0.05mmol/L,响应时间为1min,平均回收率达到1.03%.

  14. Intracerebroventricular administration of HIV-1 Tat induces brain cytokine and indoleamine 2,3-dioxygenase expression: a possible mechanism for AIDS comorbid depression.

    Science.gov (United States)

    Lawson, Marcus A; Kelley, Keith W; Dantzer, Robert

    2011-11-01

    Human immunodeficiency virus (HIV) remains a major public health concern despite a large education effort during the past 25 years. A persistent problem with HIV infection is the high comorbity rate of clinical depression. We previously established that increasing proinflammatory cytokines within the brain of mice induces sickness that can culminate in depressive-like behavior. Here we investigated the role of the HIV transactivator of transcription (Tat) protein in activation of brain cytokine signaling and subsequent induction of depressive-like behavior in a murine model. Adult Balb/c mice were administered a single intracerebroventricular (ICV) injection of Tat (40 ng). Social investigation of a novel juvenile was measured at 2, 4, 8 and 24 h post-treatment. Mice treated with Tat did not display signs of sickness, as measured by either decreased social investigation or loss of body weight. At 24 h post-injection, mice were subjected to the forced swim test (FST). ICV administration of Tat to Balb/c mice increased immobility in the FST at 24 h post injection. A different strain of mice, C57BL/6J, responded similarly in the FST. Furthermore, adult C57BL/6J mice injected with Tat and tested in a two-bottle 1% sucrose preference test displayed reduced preference for sucrose during the 24 h post-injection period. Subsequently, brain tissues from Tat-treated and control C57BL/6J mice were collected at 4 and 24 h post injection. CNS tissue from Tat-treated mice had increased expression of IL-1β, TNF-α, IL-6, and IDO mRNAs at 4 h post injection. These data demonstrate that a single exposure to Tat in the brain is sufficient to induce brain cytokine signaling that culminates in depressive-like behavior. The results reveal a potential role for Tat in the development of comorbid depression in HIV-infected individuals.

  15. Long-lasting Disease Stabilization in the Absence of Toxicity in Metastatic Lung Cancer Patients Vaccinated with an Epitope Derived from Indoleamine 2,3 Dioxygenase

    DEFF Research Database (Denmark)

    Iversen, Trine Zeeberg; Engell-Noerregaard, Lotte; Ellebaek, Eva;

    2014-01-01

    significant improved OS (P = 0.03) when compared with the group of patients excluded because of HLA-A2 negativity. IDO-specific CD8(+) T-cell immunity was demonstrated by IFN-γ Elispot and Tetramer staining. Fluorescence-activated cell sorting analyses demonstrated a significant reduction of the Treg...... population (P = 0.03) after the sixth vaccine (2.5 months) compared with pretreatment levels. Furthermore, expression of IDO was detected in nine of ten tumor biopsies by immunohistochemistry. High-performance liquid chromatography analyses of kynurenine/tryptophan (Kyn/Trp) ratio in sera were performed....... In long-term analyses of two clinical responding patients, the ratio of Kyn/Trp remained stable. CONCLUSIONS: The vaccine was well tolerated with no severe toxicity occurring. A median OS of 25.9 months was demonstrated and long-lasting PR+SD was seen in 47% of the patients....

  16. Hydrogen Peroxide-induced Cell Death in Arabidopsis : Transcriptional and Mutant Analysis Reveals a Role of an Oxoglutarate-dependent Dioxygenase Gene in the Cell Death Process

    NARCIS (Netherlands)

    Gechev, Tsanko S.; Minkov, Ivan N.; Hille, Jacques

    2005-01-01

    Hydrogen peroxide is a major regulator of plant programmed cell death (PCD) but little is known about the downstream genes from the H2O2-signaling network that mediate the cell death. To address this question, a novel system for studying H2O2-induced programmed cell death in Arabidopsis thaliana was

  17. EST Table: FY036659 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available FY036659 rbmte13c09 11/12/09 GO hit GO:0047800(cysteamine dioxygenase activity)|GO:...f|XP_974899.1| PREDICTED: similar to 2-aminoethanethiol (cysteamine) dioxygenase [Tribolium castaneum] FY036659 bmte ...

  18. Arabidopsis CDS blastp result: AK120176 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK120176 J013033B20 At4g19170.1 9-cis-epoxycarotenoid dioxygenase, putative / neoxa...nthin cleavage enzyme, putative / carotenoid cleavage dioxygenase, putative similar to 9-cis-epoxycarotenoid

  19. Arabidopsis CDS blastp result: AK064824 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK064824 J013000F03 At4g19170.1 9-cis-epoxycarotenoid dioxygenase, putative / neoxa...nthin cleavage enzyme, putative / carotenoid cleavage dioxygenase, putative similar to 9-cis-epoxycarotenoid

  20. Arabidopsis CDS blastp result: AK099580 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK099580 J013040C20 At4g19170.1 9-cis-epoxycarotenoid dioxygenase, putative / neoxa...nthin cleavage enzyme, putative / carotenoid cleavage dioxygenase, putative similar to 9-cis-epoxycarotenoid

  1. Arabidopsis CDS blastp result: AK119780 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK119780 002-173-D12 At1g78390.1 9-cis-epoxycarotenoid dioxygenase, putative / neox...anthin cleavage enzyme, putative / carotenoid cleavage dioxygenase, putative similar to 9-cis-epoxycarotenoid

  2. GenBank blastx search result: AK058470 [KOME

    Lifescience Database Archive (English)

    Full Text Available hnC, trpB, orf7, phnA4, phnA3 and phnD genes for hypothetical protein, aromatic dioxygenase large subunit, PAH dioxygenase iron sulfe...r protein large subunit, PAH dioxygenase iron sulfer protein small subunit, extradi

  3. GenBank blastx search result: AK058605 [KOME

    Lifescience Database Archive (English)

    Full Text Available hnC, trpB, orf7, phnA4, phnA3 and phnD genes for hypothetical protein, aromatic dioxygenase large subunit, PAH dioxygenase iron sulfe...r protein large subunit, PAH dioxygenase iron sulfer protein small subunit, extradi

  4. GenBank blastx search result: AK060205 [KOME

    Lifescience Database Archive (English)

    Full Text Available hnC, trpB, orf7, phnA4, phnA3 and phnD genes for hypothetical protein, aromatic dioxygenase large subunit, PAH dioxygenase iron sulfe...r protein large subunit, PAH dioxygenase iron sulfer protein small subunit, extradi

  5. Arabidopsis CDS blastp result: AK107649 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK107649 002-131-F10 At1g30100.1 9-cis-epoxycarotenoid dioxygenase, putative / neox...anthin cleavage enzyme, putative / carotenoid cleavage dioxygenase, putative similar to 9-cis-epoxycarotenoid dioxygenase GI:6715257 from [Phaseolus vulgaris] 2e-94 ...

  6. GenBank blastx search result: AK062096 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK062096 001-044-H12 AF060489.1 Sphingomonas sp. CB3 initial dioxygenase large subu...nit (carAa) gene, partial cds; and initial dioxygenase small subunit (carAb), initial dioxygenase ferredoxin subunit (carAc), initial

  7. Ectoine and 5-hydroxyectoine accumulation in the halophile Virgibacillus halodenitrificans PDB-F2 in response to salt stress.

    Science.gov (United States)

    Tao, Ping; Li, Hui; Yu, Yunjiang; Gu, Jidong; Liu, Yongdi

    2016-08-01

    The moderately halophilic bacterium Virgibacillus halodenitrificans PDB-F2 copes with salinity by synthesizing or taking up compatible solutes. The main compatible solutes in this strain were ectoine and hydroxyectoine, as determined by (1)H nuclear magnetic resonance spectroscopy ((1)H-NMR). A high-performance liquid chromatography (HPLC) analysis showed that ectoine was the major solute that was synthesized in response to elevated salinity, while hydroxyectoine was a minor solute. However, the hydroxyectoine/ectoine ratio increased from 0.04 at 3 % NaCl to 0.45 at 15 % NaCl in the late exponential growth phase. A cluster of ectoine biosynthesis genes was identified, including three genes in the order of ectA, ectB, and ectC. The hydroxyectoine biosynthesis gene ectD was not part of the ectABC gene cluster. Reverse transcription-quantitative polymerase chain reactions (RT-qPCR) showed that the expression of the ect genes was salinity dependent. The expression of ectABC reached a maximum at 12 % NaCl, while ectD expression increased up to 15 % NaCl. Ectoine and hydroxyectoine production was growth phase dependent. The hydroxyectoine/ectoine ratio increased from 0.018 in the early exponential phase to 0.11 in the stationary phase at 5 % NaCl. Hydroxyectoine biosynthesis started much later than ectoine biosynthesis after osmotic shock, and the temporal expression of the ect genes differed under these conditions, with the ectABC genes being expressed first, followed by ectD gene. Increased culture salinity triggered ectoine or hydroxyectoine uptake when they were added to the medium. Hydroxyectoine was accumulated preferentially when both ectoine and hydroxyectoine were provided exogenously.

  8. International Conference on Harmonisation; guidance on electronic common technical document specification; availability. Notice.

    Science.gov (United States)

    2003-04-02

    The Food and Drug Administration (FDA) is announcing the availability of a guidance entitled "M2 eCTD: Electronic Common Technical Document Specification." The guidance was prepared under the auspices of the International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). The guidance defines the means for industry-to-agency transfer of regulatory information that will facilitate the creation, review, life cycle management, and archiving of the electronic submission. The guidance is intended to assist industry in transferring electronically their marketing applications for human drug and biological products to a regulatory authority.

  9. Cloning and Sequence Analysis of 1, 2, 4-Trichlorobenzene Dioxygenase and Dehydrogenase Genes%1,2,4-三氯苯双加氧酶和脱氢酶基因克隆与序列分析

    Institute of Scientific and Technical Information of China (English)

    姜健; 王慧; 高静思; 宋蕾; 宁大亮

    2008-01-01

    通过PseudomonasnitroreducensJ5-1对不同氯苯类底物的降解实验,发现其降解能力大小顺序为:1,2,4-三氯苯,1,3-二氯苯,1,2-=氯苯,氯苯,与已报道的1,2,4-三氯苯降解菌株在底物利用的特性方面存在差异.采用PCR技术从J5-1中扩增获得氯苯降解过程中的关键酶--氯苯双加氧酶和脱氢酶的基因序列,分别命名为tcbA和tcbB,序列比对发现其与Burkholderia sp-PS12的氯苯双加氧酶和脱氢酶的基因序列同源性最高.通过J5-1的氯苯双加氧酶.亚基(TcbAa)与PS12的氯苯双加氧酶a亚基(TecAl)的氨基酸序列比对发现,在307-310位置有连续4个氨基酸残基的差异(1307L、M308T、1309V、Q310E),这可能是造成2株菌对1,2,4,5-四氯苯降解偏好性差异的原因.此外,通过催化芳香化合物降解的双力D氧酶a亚基的系统进化分析,认为TcbAa属于甲苯/联苯亚科,且与多取代氯苯双加氧酶e亚基的同源性最大.

  10. Cloning of 9-cis-epoxycarotenoid dioxygenase (NCED) gene encoding a key enzyme during abscisic acid (ABA) biosynthesis and ABA-regulated ethylene production in detached young persimmon calyx

    Institute of Scientific and Technical Information of China (English)

    LENG Ping; ZHANG GuangLian; LI XiangXin; WANG LiangHe; ZHENG ZhongMing

    2009-01-01

    Unlike the typical climacteric fruits,persimmons (Diospyros kaki Thunb.) produce higher levels of ethylene when they are detached from trees at a younger stage.In order to obtain detailed information on the role of abscisic acid (ABA) in ripening,we cloned the DKNCED1,DKACS2,and DKAC01 genes from the calyx.Water loss was first noted in the calyx lobe,and DKNCED1 was highly expressed 1 d after the fruits were detached,coinciding with an increase in the ABA content.Then,the DKACS2 and DKAC01 genes were expressed after some delay.In the calyx,the ABA peak was observed 2 d after the fruits were harvested,and this peak preceded the ethylene peak observed on day 3.The fruit firmness rapidly decreased on day 4,and the fruits softened completely 6 d after they were harvested.The increases in the expressions of ABA,ethylene,and the genes in the calyxes occurred earlier than the corresponding increases in the pulp,although the 3 increases occurred on different days.Exogenous ABA treatment increased ABA concentration,induced expression of both ACS and ACO,and promoted ethylene synthesis and young-fruit softening;by contrast,treatment with NDGA inhibited the gene expressions and ethylene synthesis and delayed young-fruit softening.These results indicate that ethylene biosynthesis in the detached young persimmon fruits is initially triggered by ABA,which is induced by water loss in the calyx,through the induction of DKACS2 and DKAC01 expressions.The ethylene produced in the calyx subsequently diffuses into the pulp tissue,where it induces autocatalytic ethylene biosynthesis,resulting in an abrupt increase in ethylene production.

  11. Posttranslational oxidative modification of (R)-2-(2,4-dichlorophenoxy)propionate/α-ketoglutarate-dependent dioxygenases (RdpA) leads to improved degradation of 2,4-dichlorophenoxyacetate (2,4-D)

    NARCIS (Netherlands)

    Leibeling, S.; Maeß, M.B.; Centler, F.; Kleinsteuber, S.; von Bergen, M.; Thullner, M.; Harms, H.; Müller, R.H.

    2013-01-01

    Microbial activities and the versatility gained through adaptation to xenobiotic compounds are the main biological forces to counteract environmental pollution. The current results present a new adaptive mechanism that is mediated through posttranslational modifications. Strains of Delftia acidovora

  12. 山葡萄无色花色素双加氧酶基因(LDOX)cDNA的克隆与表达%Cloning and Analysis of Leucoanthocyanidin Dioxygenase (LDOX) in Vitis amurensis Rupr

    Institute of Scientific and Technical Information of China (English)

    李娟; 刘海峰; 曹芳芳

    2016-01-01

    为获得山葡萄LDOX基因的全长序列,采用RT-PCR与SMART RACE技术克隆LDOX基因,并对该基因进行生物信息学分析.结果显示,山葡萄LDOX基因全长1 353 bp,其中开放阅读框(ORF)为1 068 bp,编码355个氨基酸,氨基酸序列的分子质量为40.19 ku,等电点为5.61;VAmLDOX基因(GenBank登陆号:FJ645769)属于双加氧酶基因家族,不含信号肽,VAmLDOX蛋白属于不稳定亲水蛋白,二级结构中随机卷曲含量最高;山葡萄VAmLDOX氨基酸序列与欧亚种葡萄、苹果、大豆、三花龙胆和紫苏等的同源性系数分别为99%、81%、80%、77%和75%;半定量RT-PCR分析显示,在山葡萄果实着色过程中,VAmLDOX在不同时期的果皮中均有表达,在转色期的叶片、茎、果肉中也均有表达,且表达量相近.

  13. Cloning and characterisation of a maize carotenoid cleavage dioxygenase (ZmCCD1) and its involvement in the biosynthesis of apocarotenoids with various roles in mutualistic and parasitic interactions

    NARCIS (Netherlands)

    Sun, Z.; Hans, J.; Walter, M.H.; Matusova, R.; Beekwilder, M.J.; Verstappen, F.W.A.; Ming, Z.; Echteld, van E.; Strack, D.; Bisseling, T.; Bouwmeester, H.J.

    2008-01-01

    Colonisation of maize roots by arbuscular mycorrhizal (AM) fungi leads to the accumulation of apocarotenoids (cyclohexenone and mycorradicin derivatives). Other root apocarotenoids (strigolactones) are involved in signalling during early steps of the AM symbiosis but also in stimulation of germinati

  14. Intracellular ascorbate enhances hypoxia-inducible factor (HIF)-hydroxylase activity and preferentially suppresses the HIF-1 transcriptional response.

    Science.gov (United States)

    Kuiper, Caroline; Dachs, Gabi U; Currie, Margaret J; Vissers, Margreet C M

    2014-04-01

    Hypoxia-inducible factor (HIF)-1 drives the transcription of hundreds of genes to support cell survival under conditions of microenvironmental and metabolic stress. HIF-1 is downregulated by iron-containing 2-oxoglutarate-dependent enzymes that require ascorbate as a cofactor. The HIF hydroxylases control both protein stability and the formation of an active transcription complex and, consequently, ascorbate could affect HIF-1α stabilization and/or gene expression, but the relative effect of ascorbate on these separate processes has not been well characterized. In this study we examined the effects of known intracellular ascorbate concentrations on both processes in response to various means of hydroxylase inhibition, including CoCl2, NiCl2, desferrioxamine, dimethyloxalylglycine, and hypoxia. Ascorbate inhibited HIF-1 activity most dramatically with all mechanisms of iron competition. In addition, HIF-1-dependent gene expression was effectively prevented by ascorbate and was inhibited even under conditions that allowed HIF-1α protein stabilization. This suggests that (1) ascorbate acts primarily to stabilize and reduce the iron atom in the hydroxylase active site and (2) the asparagine hydroxylase controlling HIF-1 transcriptional activity is particularly susceptible to fluctuations in intracellular ascorbate. These findings suggest that ascorbate plays a significant role in supporting HIF-hydroxylase function and that it could thereby modulate the cell survival response.

  15. The fat mass and obesity associated gene FTO functions in the brain to regulate postnatal growth in mice.

    Directory of Open Access Journals (Sweden)

    Xue Gao

    Full Text Available FTO (fat mass and obesity associated was identified as an obesity-susceptibility gene by several independent large-scale genome association studies. A cluster of SNPs (single nucleotide polymorphism located in the first intron of FTO was found to be significantly associated with obesity-related traits, such as body mass index, hip circumference, and body weight. FTO encodes a protein with a novel C-terminal α-helical domain and an N-terminal double-strand β-helix domain which is conserved in Fe(II and 2-oxoglutarate-dependent oxygenase family. In vitro, FTO protein can demethylate single-stranded DNA or RNA with a preference for 3-methylthymine or 3-methyluracil. Its physiological substrates and function, however, remain to be defined. Here we report the generation and analysis of mice carrying a conditional deletion allele of Fto. Our results demonstrate that Fto plays an essential role in postnatal growth. The mice lacking Fto completely display immediate postnatal growth retardation with shorter body length, lower body weight, and lower bone mineral density than control mice, but their body compositions are relatively normal. Consistent with the growth retardation, the Fto mutant mice have reduced serum levels of IGF-1. Moreover, despite the ubiquitous expression of Fto, its specific deletion in the nervous system results in similar phenotypes as the whole body deletion, indicating that Fto functions in the central nerve system to regulate postnatal growth.

  16. Arabidopsis CDS blastp result: AK065189 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK065189 J013002E07 At5g54080.2 homogentisate 1,2-dioxygenase / homogentisicase/hom...(EC 1.13.11.5) (Homogentisicase) (Homogentisate oxygenase) (Homogentisic acid oxidase) {Arabidopsis thaliana}; contains Pfam profile PF04209: homogentisate 1,2-dioxygenase 0.0 ... ...ogentisate oxygenase / homogentisic acid oxidase (HGO) identical to SP|Q9ZRA2 Homogentisate 1,2-dioxygenase

  17. Gclust Server: 50744 [Gclust Server

    Lifescience Database Archive (English)

    Full Text Available 50744 Mtu_Rv3568c=bphC Cluster Sequences Related Sequences(4) 300 PROBABLE BIPHENYL...-2,3-DIOL 1,2-DIOXYGENASE BPHC (23OHBP OXYGENASE) (2,3-DIHYDROXYBIPHENYL DIOXYGENASE) (2,3-DIHYDROXYBIPHENYL... 1,2-DIOXYGENASE) (DHBD) 2 1.00e-31 0.0 0.0 0.0 0.0 6.45 0.0 Show 50744 Cluster ID 50744 Sequence ID Mtu_Rv3568c=bph...elated Sequences(4) Sequence length 300 Representative annotation PROBABLE BIPHENYL-2,3-DIOL 1,2-DIOXYGENASE BPH

  18. Protein (Viridiplantae): 302824020 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 750 3244:750 3245:750 3246:750 88036:750 2-oxoacid-dependent dioxygenase Selaginella moellendorffii MYGKCSSL...PDAWSVFHDLVHKNAFSCNIMISTLCANGQSAQAIHLFLALASDSVVRPTHVSFVAAKRVLGLFSESLGLESGALEEAFGGERHAMRMNYYPPCPEPELTIGLDAHAD

  19. Protein (Viridiplantae): 302824008 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 750 3244:750 3245:750 3246:750 88036:750 2-oxoacid-dependent dioxygenase Selaginella moellendorffii MYGKCSSL...PDAWSVFHDLVHKNAFSCNIVISTLCANGQSAQAIHLFLALASDSVVRPTHVSFVAAKRVLGLFSESLGLESGALEEAFGGERHAMRMNYYPPCAEPELTIGLDAHAD

  20. Protein (Viridiplantae): 302824016 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 750 3244:750 3245:750 3246:750 88036:750 2-oxoacid-dependent dioxygenase Selaginella moellendorffii MYGKCSSL...PDAWSVFHDLVHKNAFSCNIVISTLCANGQSAQAIHLFLALASDSVVRPTHVSFVAAKRVLGLFSESLGLESGALEEAFGGERHAMRMNYYPPCPEPELTIGLDAHAD

  1. Protein (Viridiplantae): 302824022 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 750 3244:750 3245:750 3246:750 88036:750 2-oxoacid-dependent dioxygenase Selaginella moellendorffii MYGKCSSL...PDAWSVFHDLVHKNAFSCNIMISTLCANGQSAQAIHLFLALASDSVVRPTHVSFVAAKRVLGLFSESLGLESGALEEAFEGERHAMRMNYYPPCPEPELTILDAHADP

  2. Protein (Viridiplantae): 302798721 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 750 3244:750 3245:750 3246:750 88036:750 2-oxoacid-dependent dioxygenase Selaginella moellendorffii MYGKCSGL...PDAWSVFHDLVHKNAFSCNIMISTLCANGQSAQAIDLFLALASDSVVRPTHVSFVAAKRVLGLFSESLGLESGALEEAFGGERHAMRMNYYPPCPEPELTIGLDAHAD

  3. Protein (Viridiplantae): 302824018 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 750 3244:750 3245:750 3246:750 88036:750 2-oxoacid-dependent dioxygenase Selaginella moellendorffii MYGKCSSL...PDAWSVFHDLVHKNAFSCNIMISTLCANGQSAQAIHLFLALASDSVVRPTHVSFVAAKRVLGLFSESLGLESGALEEAFEGERHAMRMNYYPPCPEPELTILDAHADP

  4. Protein (Viridiplantae): 302798723 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available 750 3244:750 3245:750 3246:750 88036:750 2-oxoacid-dependent dioxygenase Selaginella moellendorffii MYGKCSSL...PDAWSVFHDLVHKNAFSCNIMISTLCANGQSAQAIHLFLALASDSVVRPTHVSFVAAKRVLGLFSESLGLESGALEEAFGGERHAMRMNYYPPCPEPELTILDAHADP

  5. Metabolism of aromatic compounds by Caulobacter crescentus

    Energy Technology Data Exchange (ETDEWEB)

    Chatterjee, D.K.; Bourquin, A.W.

    1987-05-01

    Cultures of Caulobacter crescentus were found to grow on a variety of aromatic compounds. Degradation of benzoate, p-hydroxybenzoate, and phenol was found to occur via ..beta..-ketoadipate. The induction of degradative enzymes such as benzoate 1,2-dioxygenase, the ring cleavage enzyme catechol 1,2-dioxygenase, and cis,cis-muconate lactonizing enzyme appeared similar to the control mechanism present in Pseudomonas spp. Both benzoate 1,2-dioxygenase and catechol 1,2-dioxygenase had stringent specificities, as revealed by their action toward substituted benzoates and substituted catechols, respectively.

  6. EST Table: FS920530 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available FS920530 E_FL_fufe_50K23_F_0 11/12/09 GO hit GO:0047800(cysteamine dioxygenase acti...090992|ref|XP_974899.1| PREDICTED: similar to 2-aminoethanethiol (cysteamine) dioxygenase [Tribolium castaneum] FS920530 fufe ...

  7. Sequence Classification: 509427 [

    Lifescience Database Archive (English)

    Full Text Available g-cleavage dioxygenase:Catechol dioxygenase, N-terminal || http://www.ncbi.nlm.nih.gov/protein/73539675 ... ...TMB Non-TMH Non-TMB TMB Non-TMB Non-TMB >gi|73539675|ref|YP_300042.1| Intradiol rin

  8. NCBI nr-aa BLAST: CBRC-XTRO-01-3800 [SEVENS

    Lifescience Database Archive (English)

    Full Text Available CBRC-XTRO-01-3800 ref|ZP_02006305.1| 2-nitropropane dioxygenase, NPD [Ralstonia pick...ettii 12D] gb|EDN42447.1| 2-nitropropane dioxygenase, NPD [Ralstonia pickettii 12D] ZP_02006305.1 0.32 25% ...

  9. Arabidopsis CDS blastp result: AK062144 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK062144 001-045-G08 At5g54080.2 homogentisate 1,2-dioxygenase / homogentisicase/ho... (EC 1.13.11.5) (Homogentisicase) (Homogentisate oxygenase) (Homogentisic acid oxidase) {Arabidopsis thaliana}; contains Pfam profile PF04209: homogentisate 1,2-dioxygenase 1e-155 ...

  10. SwissProt search result: AK107236 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK107236 002-125-E12 (Q924Y0) Gamma-butyrobetaine dioxygenase (EC 1.14.11.1) (Gamma-butyrobetaine...,2-oxoglutarate dioxygenase) (Gamma-butyrobetaine hydroxylase) (Gamma-BBH) BODG_MOUSE 7e-33 ...

  11. SwissProt search result: AK107236 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK107236 002-125-E12 (Q9QZU7) Gamma-butyrobetaine dioxygenase (EC 1.14.11.1) (Gamma-butyrobetaine...,2-oxoglutarate dioxygenase) (Gamma-butyrobetaine hydroxylase) (Gamma-BBH) BODG_RAT 6e-34 ...

  12. SwissProt search result: AK110314 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK110314 002-164-B12 (Q98KK0) Probable gamma-butyrobetaine dioxygenase (EC 1.14.11.1) (Gamma-butyrobetaine...,2-oxoglutarate dioxygenase) (Gamma-butyrobetaine hydroxylase) (Gamma-BBH) BODG_RHILO 1e-20 ...

  13. SwissProt search result: AK107236 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK107236 002-125-E12 (Q19000) Probable gamma-butyrobetaine dioxygenase (EC 1.14.11.1) (Gamma-butyrobetaine...,2-oxoglutarate dioxygenase) (Gamma-butyrobetaine hydroxylase) (Gamma-BBH) BODG_CAEEL 1e-14 ...

  14. SwissProt search result: AK107236 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK107236 002-125-E12 (O75936) Gamma-butyrobetaine dioxygenase (EC 1.14.11.1) (Gamma-butyrobetaine...,2-oxoglutarate dioxygenase) (Gamma-butyrobetaine hydroxylase) (Gamma-BBH) BODG_HUMAN 7e-32 ...

  15. SwissProt search result: AK110314 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK110314 002-164-B12 (Q9QZU7) Gamma-butyrobetaine dioxygenase (EC 1.14.11.1) (Gamma-butyrobetaine...,2-oxoglutarate dioxygenase) (Gamma-butyrobetaine hydroxylase) (Gamma-BBH) BODG_RAT 2e-11 ...

  16. SwissProt search result: AK107236 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK107236 002-125-E12 (P80193) Gamma-butyrobetaine dioxygenase (EC 1.14.11.1) (Gamma-butyrobetaine...,2-oxoglutarate dioxygenase) (Gamma-butyrobetaine hydroxylase) (Gamma-BBH) BODG_PSESK 1e-34 ...

  17. SwissProt search result: AK110314 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK110314 002-164-B12 (O75936) Gamma-butyrobetaine dioxygenase (EC 1.14.11.1) (Gamma-butyrobetaine...,2-oxoglutarate dioxygenase) (Gamma-butyrobetaine hydroxylase) (Gamma-BBH) BODG_HUMAN 3e-12 ...

  18. SwissProt search result: AK110314 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK110314 002-164-B12 (P80193) Gamma-butyrobetaine dioxygenase (EC 1.14.11.1) (Gamma-butyrobetaine...,2-oxoglutarate dioxygenase) (Gamma-butyrobetaine hydroxylase) (Gamma-BBH) BODG_PSESK 4e-18 ...

  19. SwissProt search result: AK110314 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK110314 002-164-B12 (Q924Y0) Gamma-butyrobetaine dioxygenase (EC 1.14.11.1) (Gamma-butyrobetaine...,2-oxoglutarate dioxygenase) (Gamma-butyrobetaine hydroxylase) (Gamma-BBH) BODG_MOUSE 2e-11 ...

  20. SwissProt search result: AK107236 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK107236 002-125-E12 (Q98KK0) Probable gamma-butyrobetaine dioxygenase (EC 1.14.11.1) (Gamma-butyrobetaine...,2-oxoglutarate dioxygenase) (Gamma-butyrobetaine hydroxylase) (Gamma-BBH) BODG_RHILO 7e-33 ...

  1. Alternative primer sets for PCR detection of genotypes involved in bacterial aerobic BTEX degradation : Distribution of the genes in BTEX degrading isolates and in subsurface soils of a BTEX contaminated industrial site

    NARCIS (Netherlands)

    Hendrickx, B; Junca, H; Vosahlova, J; Lindner, A; Ruegg, [No Value; Bucheli-Witschel, M; Faber, F; Egli, T; Mau, M; Schlomann, M; Brennerova, M; Brenner, [No Value; Pieper, DH; Top, EM; Dejonghe, W; Bastiaens, L; Springael, D

    2006-01-01

    Eight new primer sets were designed for PCR detection of (i) mono-oxygenase and dioxygenase gene sequences involved in initial attack of bacterial aerobic BTEX degradation and of (ii) catechol 2,3-dioxygenase gene sequences responsible for metacleavage of the aromatic ring. The new primer sets allow

  2. Arabidopsis CDS blastp result: AK066766 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK066766 J013088L06 At3g63520.1 9-cis-epoxycarotenoid dioxygenase / neoxanthin cleavage enzyme / NCED1 / car...otenoid cleavage dioxygenase 1 (CCD1) identical to putative 9-cis-epoxy-carotenoid

  3. Arabidopsis CDS blastp result: AK241374 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK241374 J065155A15 At3g63520.1 68416.m07155 9-cis-epoxycarotenoid dioxygenase / ne...oxanthin cleavage enzyme / NCED1 / carotenoid cleavage dioxygenase 1 (CCD1) identical to putative 9-cis-epoxy-carotenoid

  4. InterProScan Result: FS936940 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available FS936940 FS936940_1_ORF2 666B71608D2EC1C9 PANTHER PTHR11959 4-HYDROXYPHENYLPYRUVATE DIO...XYGENASE 6e-117 T IPR005956 4-hydroxyphenylpyruvate dioxygenase Molecular Function: 4-hydroxyphenylpyruvate dio

  5. InterProScan Result: FS936940 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available FS936940 FS936940_2_ORF2 E86957CEA24E174E PANTHER PTHR11959 4-HYDROXYPHENYLPYRUVATE DIO...XYGENASE 1.7e-06 T IPR005956 4-hydroxyphenylpyruvate dioxygenase Molecular Function: 4-hydroxyphenylpyruvate dio

  6. Molecular characterization and expression analysis of fat mass and obesity-associated gene in rabbit

    Indian Academy of Sciences (India)

    Jinyi Xing; Wenqian Jing; Yunliang Jiang

    2013-12-01

    Fat mass and obesity-associated (FTO) gene codes for a nuclear protein of the AlkB related nonhaem iron and 2-oxoglutarate-dependent oxygenase superfamily, and is involved in animal fat deposition and human obesity. In this work, the molecular characterization and expression features of rabbit (Oryctolagus cuniculus) FTO cDNA were analysed. The rabbit FTO cDNA with a size of 2158 bp was cloned, including 1515 bp of the open reading frame that encoded a basic protein of 504 amino acids. Homologous comparison indicated that the rabbit FTO shared 36.36–91.88% identity with those from other species and phylogenetic analysis showed that the rabbit FTO is closely related to human, but more distantly related to zebrafish. The New Zealand rabbit FTO mRNA was detected in all tissues examined, with the highest levels found in the spleen and the lowest found in the kidney. However, no significant differences were seen in cerebellum, corpora quadrigemina, medulla oblongata and cerebral cortex of commercial adult rabbits. Moreover, mRNA levels of FTO in liver tissues were significantly increased in lactating New Zealand rabbits compared with 70-day-old, 90-day-old and gestating rabbits $(P \\lt 0.05)$. In contrast, FTO mRNA levels were significantly lower in longissimus dorsi muscle of 90-day-old New Zealand rabbits than in 70-day-old rabbits $(P \\lt 0.05)$. However, the expression levels of FTO in mammary gland and ovary of gestating and lactating rabbits were not significantly different $(P \\gt 0.05)$.

  7. Quantitative high-throughput screening identifies 8-hydroxyquinolines as cell-active histone demethylase inhibitors.

    Directory of Open Access Journals (Sweden)

    Oliver N F King

    Full Text Available BACKGROUND: Small molecule modulators of epigenetic processes are currently sought as basic probes for biochemical mechanisms, and as starting points for development of therapeutic agents. N(ε-Methylation of lysine residues on histone tails is one of a number of post-translational modifications that together enable transcriptional regulation. Histone lysine demethylases antagonize the action of histone methyltransferases in a site- and methylation state-specific manner. N(ε-Methyllysine demethylases that use 2-oxoglutarate as co-factor are associated with diverse human diseases, including cancer, inflammation and X-linked mental retardation; they are proposed as targets for the therapeutic modulation of transcription. There are few reports on the identification of templates that are amenable to development as potent inhibitors in vivo and large diverse collections have yet to be exploited for the discovery of demethylase inhibitors. PRINCIPAL FINDINGS: High-throughput screening of a ∼236,000-member collection of diverse molecules arrayed as dilution series was used to identify inhibitors of the JMJD2 (KDM4 family of 2-oxoglutarate-dependent histone demethylases. Initial screening hits were prioritized by a combination of cheminformatics, counterscreening using a coupled assay enzyme, and orthogonal confirmatory detection of inhibition by mass spectrometric assays. Follow-up studies were carried out on one of the series identified, 8-hydroxyquinolines, which were shown by crystallographic analyses to inhibit by binding to the active site Fe(II and to modulate demethylation at the H3K9 locus in a cell-based assay. CONCLUSIONS: These studies demonstrate that diverse compound screening can yield novel inhibitors of 2OG dependent histone demethylases and provide starting points for the development of potent and selective agents to interrogate epigenetic regulation.

  8. Impaired mitochondrial energy metabolism in Alzheimer's disease: Impact on pathogenesis via disturbed epigenetic regulation of chromatin landscape.

    Science.gov (United States)

    Salminen, Antero; Haapasalo, Annakaisa; Kauppinen, Anu; Kaarniranta, Kai; Soininen, Hilkka; Hiltunen, Mikko

    2015-08-01

    The amyloid cascade hypothesis for the pathogenesis of Alzheimer's disease (AD) was proposed over twenty years ago. However, the mechanisms of neurodegeneration and synaptic loss have remained elusive delaying the effective drug discovery. Recent studies have revealed that amyloid-β peptides as well as phosphorylated and fragmented tau proteins accumulate within mitochondria. This process triggers mitochondrial fission (fragmentation) and disturbs Krebs cycle function e.g. by inhibiting the activity of 2-oxoglutarate dehydrogenase. Oxidative stress, hypoxia and calcium imbalance also disrupt the function of Krebs cycle in AD brains. Recent studies on epigenetic regulation have revealed that Krebs cycle intermediates control DNA and histone methylation as well as histone acetylation and thus they have fundamental roles in gene expression. DNA demethylases (TET1-3) and histone lysine demethylases (KDM2-7) are included in the family of 2-oxoglutarate-dependent oxygenases (2-OGDO). Interestingly, 2-oxoglutarate is the obligatory substrate of 2-OGDO enzymes, whereas succinate and fumarate are the inhibitors of these enzymes. Moreover, citrate can stimulate histone acetylation via acetyl-CoA production. Epigenetic studies have revealed that AD is associated with changes in DNA methylation and histone acetylation patterns. However, the epigenetic results of different studies are inconsistent but one possibility is that they represent both coordinated adaptive responses and uncontrolled stochastic changes, which provoke pathogenesis in affected neurons. Here, we will review the changes observed in mitochondrial dynamics and Krebs cycle function associated with AD, and then clarify the mechanisms through which mitochondrial metabolites can control the epigenetic landscape of chromatin and induce pathological changes in AD.

  9. Ectoine production from lignocellulosic biomass-derived sugars by engineered Halomonas elongata.

    Science.gov (United States)

    Tanimura, Kosuke; Nakayama, Hideki; Tanaka, Tsutomu; Kondo, Akihiko

    2013-08-01

    In this study, the water-retaining cyclic amino acid ectoine was produced from a variety of sugars, including glucose, xylose, cellobiose, and glucose/xylose mixture using engineered Halomonas elongata. When grown on xylose as the sole carbon source, H. elongata produced 333 mmol/kg fresh cell weight (FW) of ectoine, which was 1.4-fold higher than that produced from glucose. To improve ectoine production, an ectD deficient H. elongata mutant was constructed. The engineered H. elongata produced 377 mmol/kg FW of ectoine from a glucose/xylose mixture. Ectoine was also produced from rice straw hydrolysate. These results show that H. elongata can produce ectoine from a variety of sugars derived from lignocellulosic biomass and thus has tremendous potential as a host for producing useful compounds from biomass resources.

  10. Aeromonas sp.XJ-6双加氧酶基因的克隆、表达及对酪氨酸的降解%Cloning and Expression of Dioxygenase Gene from Aeromonas sp.XJ-6 and Promoting Degradation of Tyr

    Institute of Scientific and Technical Information of China (English)

    杨杨; 杨江科; 熊炜; 梁建芳; 段魏魏; 晁群芳

    2016-01-01

    目的:从Aeromonas sp.XJ-6中克隆双加氧酶基因,初步探索该酶的功能,为芳香烃化合物的生物降解提供基因资源.方法:PCR扩增双加氧酶基因dio6,并实现该基因在大肠杆菌(Escherichia coli)中的诱导表达.产物经Ni-NTA柱纯化后,通过薄层层析(TLC)和HPLC检测双加氧酶dio6对Tyr的降解效果,再结合LC-MS检测降解产物,并分析其可能的降解途径.结果:Aeromonas sp.XJ-6双加氧酶基因dio6大小为1 194bp;通过金属鳌合亲和层析(MCAC)纯化后dio6表达产物的大小为44.9kDa.双加氧酶dio6对Tyr具有较强的降解作用.TLC和HPLC检测表明,在60μl酶量和30℃反应温度等条件下,Tyr降解较快;Mg2、Ca2略微抑制酶促反应,Mn2+、Zn2、Cu2+、Fe2+、Ca2+促进底物降解,其中Mn2+对双加氧酶影响最大.LC-MS分析表明,在双加氧酶dio6作用下,Tyr被降解为延胡索酸.结论:Aeromonas sp.XJ-6双加氧酶dio6是一种苯环开环酶,为芳香烃化合物的生物降解提供了良好的基因资源.

  11. Protein (Cyanobacteria): 175290 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007131221.1 1117:3496 52604:2952 102115:797 102116:797 111780:797 Glyoxalase/bleomycin resistan...ce protein/dioxygenase Stanieria cyanosphaera PCC 7437 MINNQIIFHLAIPINDLAKAKEFYAQGLGCQIGRENST

  12. Protein (Cyanobacteria): 143489 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007131876.1 1117:2878 52604:682 102115:1231 102116:1231 111780:1231 glyoxalase/bleomycin resistan...ce protein/dioxygenase Stanieria cyanosphaera PCC 7437 MSFFCHDALVTIAALEYQKVIDFYRKLLSQEPQPYI

  13. Protein (Cyanobacteria): 175756 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007131410.1 1117:3497 52604:2652 102115:934 102116:934 111780:934 Glyoxalase/bleomycin resistan...ce protein/dioxygenase Stanieria cyanosphaera PCC 7437 MMHHVSIRTANIHRAIAFYEQLGFTVNERFTTGYTLAC

  14. Protein (Cyanobacteria): 175683 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007132840.1 1117:3497 52604:2654 102115:393 102116:393 111780:393 Glyoxalase/bleomycin resistan...ce protein/dioxygenase Stanieria cyanosphaera PCC 7437 MTDIGLTHIALPVSNLERSIKFYSTYAKMRVVHRRIDA

  15. Protein (Cyanobacteria): 175437 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007130757.1 1117:3496 52604:2653 102115:394 102116:394 111780:394 Glyoxalase/bleomycin resistan...ce protein/dioxygenase Stanieria cyanosphaera PCC 7437 MTVKPEIKSNSLRPGSLRKVHHIALNVKDMAASRHFYG

  16. Protein (Cyanobacteria): 175681 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007134225.1 1117:3497 52604:2654 102115:393 102116:393 111780:393 Glyoxalase/bleomycin resistan...ce protein/dioxygenase Stanieria cyanosphaera PCC 7437 MQITRLLHTAILVSDLAKAEHFYGEVLGLVKAEGRTSN

  17. Protein (Cyanobacteria): 175438 [PGDBj - Ortholog DB

    Lifescience Database Archive (English)

    Full Text Available YP_007131651.1 1117:3496 52604:2653 102115:394 102116:394 111780:394 Glyoxalase/bleomycin resistan...ce protein/dioxygenase Stanieria cyanosphaera PCC 7437 MNLSKIHHIAIICSNYQVSKHFYTEILGLKIIQETYRE

  18. InterProScan Result: BY940643 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available ogentisate 1,2-dioxygenase Biological Process: L-phenylalanine catabolic process (GO:0006559)|Biological Process...: tyrosine metabolic process (GO:0006570)|Biological Process: oxidation reduction (GO:0055114) ...

  19. InterProScan Result: FS863249 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available mogentisate 1,2-dioxygenase Biological Process: L-phenylalanine catabolic process (GO:0006559)|Biological Process...: tyrosine metabolic process (GO:0006570)|Biological Process: oxidation reduction (GO:0055114) ...

  20. Cloning and Sequence Analysis of Lipoxygenase Gene cDNA from Cucumber Fruit (Cucumis sativus L.)

    Institute of Scientific and Technical Information of China (English)

    Z.K. Wang; Z.W. Qin; X.Y. Zhou; D.Y. Song

    2007-01-01

    @@ Lipoxygenases are nonheme-iron-containing dioxygenases that catalyze the hydroperoxidation of unsatrated fatty acids containing a cis, cis-1,4-pentadiene structure producing hydroperoxy acids with conjugated dienes.

  1. Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis

    DEFF Research Database (Denmark)

    Rasmussen, Kasper D; Jia, Guangshuai; Johansen, Jens V

    2015-01-01

    DNA methylation is tightly regulated throughout mammalian development, and altered DNA methylation patterns are a general hallmark of cancer. The methylcytosine dioxygenase TET2 is frequently mutated in hematological disorders, including acute myeloid leukemia (AML), and has been suggested...

  2. Disease: H00163 [KEGG MEDICUS

    Lifescience Database Archive (English)

    Full Text Available ,2-dioxygenase that leads to the widespread deposition of polymeric homogentisic acid, and clinical symptoms from degeneration of joi...nts and the aortic valve. Inherited metabolic disease hsa00350(3081+C00544) Tyrosin

  3. Disease: H00926 [KEGG MEDICUS

    Lifescience Database Archive (English)

    Full Text Available tercurrent infection or unidentified cause in these patients. Congenital disorder...e dioxygenase-encoding FTO gene causes severe growth retardation and multiple malformations. Am J Hum Genet 85:106-11 (2009) ...

  4. Bacterial Degradation of DNT and TNT Mixtures

    Science.gov (United States)

    2005-10-31

    hydroxylating dioxygenase and salicylate hydroxylase genes from JS180. Figure III-5. Conversion of 3M4NC to HNOHA by DniB. Figure III-6. Extradiol ring...cycloisomerases (tautomerases) from various lower pathways and fumarylacetoacetate (FAA) hydrolases from the phenylalanine /tyrosine degradation pathway...the salicylate hydroxylase from the naphthalene pathway, are functional (labeled G and H in Figure III- 3). Although the dioxygenase from JS180

  5. New metabolic pathway for N,N-dimethyltryptamine

    Energy Technology Data Exchange (ETDEWEB)

    Hryhorczuk, L.M.; Rainey, J.M. Jr.; Frohman, C.E.; Novak, E.A.

    1986-01-01

    N,N-Dimethyltryptamine (DMT) undergoes a major structural alteration when added to whole human blood or its red blood cells in vitro. A new high-pressure liquid chromatography (HPLC) peak is present in extracts of these treated tissues. The compound responsible for this peak has been identified by ultraviolet spectrophotometry and by mass spectrometry as dimethylkynuramine (DMK). The enzyme responsible for this appears to be different from tryptophan 2,3-dioxygenase and also from indoleamine 2,3-dioxygenase.

  6. Determination of biodegradation potential by two culture-independent methods in PAH-contaminated soils.

    Science.gov (United States)

    Moon, H S; Kahng, H-Y; Kim, J Y; Kukor, J J; Nam, K

    2006-04-01

    Biodegradation potentials of polycyclic aromatic hydrocarbons (PAHs) were determined with soil samples collected from various depths of a PAH-contaminated site and of a site nearby where PAHs were not found. Putative dioxygenase genes were amplified by a primer set specific for initial dioxygenases and identified by web-based database homology search. They were further categorized into several groups of which four dioxygenases were selected as probes for DNA hybridization. The hybridization signals according to the presence of putative dioxygenases were positively related to the extent of PAH contamination. However, the signal intensities varied depending on the probes hybridized and moreover were not consistent with PAH biodegradation activities determined by CO2 evolution. Despite widely accepted advantages of molecular biodegradation assessment, our data clearly present the variations of assessment results depending on the genetic information used and suggest that the methodology may tend to underestimate the real biodegradation capacity of a site probably due to the limited dioxygenase database available at the moment. Therefore, the molecular assessment of biodegradation potential should involve a very careful primer and probe design and an extensive microbiological examination of a site of interest to accurately delineate the biodegradation potential of the site.

  7. Metabolic Engineering to Develop a Pathway for the Selective Cleavage of Carbon-Nitrogen Bonds

    Energy Technology Data Exchange (ETDEWEB)

    John J. Kilbane II

    2005-10-01

    The objective of the project is to develop a biochemical pathway for the selective cleavage of C-N bonds in molecules found in petroleum. Specifically a novel biochemical pathway will be developed for the selective cleavage of C-N bonds in carbazole. The cleavage of the first C-N bond in carbazole is accomplished by the enzyme carbazole dioxygenase, that catalyzes the conversion of carbazole to 2-aminobiphenyl-2,3-diol. The genes encoding carbazole dioxygenase were cloned from Sphingomonas sp. GTIN11 and from Pseudomonas resinovorans CA10. The selective cleavage of the second C-N bond has been challenging, and efforts to overcome that challenge have been the focus of recent research in this project. Enrichment culture experiments succeeded in isolating bacterial cultures that can metabolize 2-aminobiphenyl, but no enzyme capable of selectively cleaving the C-N bond in 2-aminobiphenyl has been identified. Aniline is very similar to the structure of 2-aminobiphenyl and aniline dioxygenase catalyzes the conversion of aniline to catechol and ammonia. For the remainder of the project the emphasis of research will be to simultaneously express the genes for carbazole dioxygenase and for aniline dioxygenase in the same bacterial host and then to select for derivative cultures capable of using carbazole as the sole source of nitrogen.

  8. Degradation of Benzene by Pseudomonas veronii 1YdBTEX2 and 1YB2 Is Catalyzed by Enzymes Encoded in Distinct Catabolism Gene Clusters

    Science.gov (United States)

    de Lima-Morales, Daiana; Chaves-Moreno, Diego; Wos-Oxley, Melissa L.; Jáuregui, Ruy; Vilchez-Vargas, Ramiro

    2015-01-01

    Pseudomonas veronii 1YdBTEX2, a benzene and toluene degrader, and Pseudomonas veronii 1YB2, a benzene degrader, have previously been shown to be key players in a benzene-contaminated site. These strains harbor unique catabolic pathways for the degradation of benzene comprising a gene cluster encoding an isopropylbenzene dioxygenase where genes encoding downstream enzymes were interrupted by stop codons. Extradiol dioxygenases were recruited from gene clusters comprising genes encoding a 2-hydroxymuconic semialdehyde dehydrogenase necessary for benzene degradation but typically absent from isopropylbenzene dioxygenase-encoding gene clusters. The benzene dihydrodiol dehydrogenase-encoding gene was not clustered with any other aromatic degradation genes, and the encoded protein was only distantly related to dehydrogenases of aromatic degradation pathways. The involvement of the different gene clusters in the degradation pathways was suggested by real-time quantitative reverse transcription PCR. PMID:26475106

  9. Tearing down to build up: Metalloenzymes in the biosynthesis lincomycin, hormaomycin and the pyrrolo [1,4]benzodiazepines.

    Science.gov (United States)

    Colabroy, Keri L

    2016-06-01

    The metabolic pathways for the production of lincomycin, hormaomycin and the antitumor pyrrolo [1,4] benzodiazepines share a vinyl substituted pyrroline carboxylic acid (3-vinyl-2,3-pyrroline-5-carboxylic acid, VPCA) as a common intermediate. Biosynthesis of this vinyl substituted pyrroline carboxylic acid intermediate requires a short, three-enzyme pathway containing two metalloenzymes: a heme-dependent l-tyrosine hydroxylase and a non-heme Fe(2+) dependent l-DOPA dioxygenase. The l-tyrosine hydroxylase is an unprecedented type of peroxidase that specifically monohydroxylates tyrosine, while the l-DOPA extradiol cleaving enzyme is a single-domain vicinal-oxygen-chelate (VOC) dioxygenase. The dioxygenase product subsequently undergoes an, as yet uncharacterized, C-C bond cleavage reaction. This mini-pathway demonstrates the use of metal-dependent chemistry typically associated with natural product degradation in order to build a compact, functionalized building block for larger, bioactive molecules.

  10. Key enzymes of the protocatechuate branch of the β-ketoadipate pathway for aromatic degradation in Corynebacterium glutamicum

    Institute of Scientific and Technical Information of China (English)

    SHEN; Xihui; LIU; Shuangjiang

    2005-01-01

    Although the protocatechuate branch of the β-ketoadipate pathway in Gram bacteria has been well studied, this branch is less understood in Gram+ bacteria. In this study,Corynebacterium glutamicum was cultivated with protocatechuate, p-cresol, vanillate and 4-hydroxybenzoate as sole carbon and energy sources for growth. Enzymatic assays indicated that growing cells on these aromatic compounds exhibited protocatechuate 3,4-dioxygenase activities. Data-mining of the genome of this bacterium revealed that the genetic locus ncg12314-ncg12315 encoded a putative protocatechuate 3,4-dioxygenase. The genes,ncg12314 and ncg12315, were amplified by PCR technique and were cloned into plasmid (pET21aP34D). Recombinant Escherichia coli strain harboring this plasmid actively expressed protocatechuate 3,4-dioxygenase activity. Further, when this locus was disrupted in C. glutamicum, the ability to degrade and assimilate protocatechuate, p-cresol, vanillate or 4-hydroxybenzoate was lost and protocatechuate 3,4-dioxygenase activity was disappeared. The ability to grow with these aromatic compounds and protocatechuate 3,4-dioxygenase activity of C.glutamicum mutant could be restored by gene complementation. Thus, it is clear that the key enzyme for ring-cleavage, protocatechuate 3,4-dioxygenase, was encoded by ncg12314 and ncg12315. The additional genes involved in the protocatechuate branch of the β-ketoadipate pathway were identified by mining the genome data publically available in the GenBank. The functional identification of genes and their unique organization in C. glutamicum provided new insight into the genetic diversity of aromatic compound degradation.

  11. Main: 1YGE [RPSD[Archive

    Lifescience Database Archive (English)

    Full Text Available 1YGE 大豆 Soybean Glycine max (L.) Merrill Seed Lipoxygenase-1 Name=Lox1.1; Synonyms=Lox1; Glycin...e Max Molecule: Lipoxygenase-1; Chain: Null; Synonym: L-1; Dioxygenase 1.13.11.12 (Lipoxygenase-1) W.Min...or, J.Steczko, B.Stec, Z.Otwinowski, J.T.Bolin, R.Walter, B.Axelrod W.Minor, J.Steczko, B.Stec, Z.Otwinowski, J.T.Bolin...e L-1 At 1.4 A Resolution Biochemistry V. 35 10687 1996 Dioxygenase, Lipoxygenase, Metalloprotein, Fatty Aci

  12. Tyrosinemia type III: diagnosis and ten-year follow-up.

    Science.gov (United States)

    Cerone, R; Holme, E; Schiaffino, M C; Caruso, U; Maritano, L; Romano, C

    1997-09-01

    Tyrosinemia type III, caused by deficiency of 4-hydroxyphenylpyruvate dioxygenase, is a rare disorder of tyrosine catabolism. Primary 4-hydroxyphenylpyruvate dioxygenase deficiency has been described in only three patients. The biochemical phenotype shows hypertyrosinemia and elevated urinary excretion of 4-hydroxyphenyl derivatives. We report the clinical and biochemical findings and the results of long-term follow-up in a new patient with this disorder presenting with severe mental retardation and neurological abnormalities. The clinical phenotype is compared with those reported in the three previously described patients.

  13. Synthesis and release of the bacterial compatible solute 5-hydroxyectoine in Hansenula polymorpha.

    Science.gov (United States)

    Eilert, Eva; Kranz, Andreas; Hollenberg, Cornelis P; Piontek, Michael; Suckow, Manfred

    2013-08-20

    Ectoine and 5-hydroxyectoine belong to the family of compatible solutes which are known to mainly contribute to the adaptation of the cell to osmotic stress by mediation of a constant turgor. In addition the cell's essential functions are maintained under stress conditions like high salinity, heat or aridity stress. Hansenula polymorpha was engineered to catalyze the transformation of monomeric substrates to 5-hydroxyectoine. For this purpose four genes encoding the enzymes of the 5-hydroxyectoine biosynthesis pathway of Halomonas elongata, EctA, EctB, EctC, and EctD, were inserted into the genome of H. polymorpha. Subsequently the syntheses of ectoine and 5-hydroxyectoine were analyzed and optimized. We showed that H. polymorpha is a suitable system for recombinant 5-hydroxyectoine synthesis in gram per liter scale (2.8 g L⁻¹ culture supernatant, 365 μmol/g dcw) in which almost 100% conversion of ectoine to 5-hydroxyectoine without necessity of high salinity were achieved.

  14. Estimating Influence of Crystallizing Latent Heat on Cooling-Crystallizing Process of a Granitic Melt and Its Geological Implications

    Institute of Scientific and Technical Information of China (English)

    ZHANG Bangtong; WU Junqi; LING Hongfei; CHEN Peirong

    2008-01-01

    Based on the theory of thermal conductivity, in this paper we derived a formula to estimate the prolongation period (AtL) of cooling-crystallization process of a granitic melt caused by latent heat of crystallization as follows: △t=QL×△tcol/TM-TC×CP where TM is initial temperature of the granite melt, Tc crystallization temperature of the granite melt,CP specific heat, △tcol cooling period of a granite melt from its initial temperature (TM) to its crystallization temperature (TC), QL latent heat of the granite melt. The cooling period of the melt for the Fanshan granodiorite from its initial temperature (900℃) to crystallization temperature (600℃) could be estimated ~210,000 years if latent heat was not considered. Calculation for the Fanshan melt using the above formula yields a AtL value of~190,000 years, which implies that the actual cooling period within the temperature range of 900℃-600℃ should be 400,000 years. This demonstrates that the latent heat produced from crystallization of the granitic melt is a key factor influencing the cooling-crystallization process of a granitic melt, prolongating the period of crystallization and resulting in the large emplacement-crystallization time difference (ECTD) in granite batholith.

  15. Identification of Metabolic Intermediates in Microbial Degradation of Chrysene by Armillaria sp. F022

    Directory of Open Access Journals (Sweden)

    Tony Hadibarata

    2015-11-01

    Full Text Available To degrade chrysene, a polycyclic aromatic hydrocarbon (PAH, Armillaria sp. F022, a fungus collected from a soil, was used. Maximal degradation (77% was obtained when Armillaria sp. F022 was incubated in cultures agitated at 120 rpm for 30 days, as compared to just 41% degradation in stationary culture. Furthermore, the degradation of chrysene was affected by the addition of surfactants. The mechanism of degradation was determined through identification of the intermediates. Several enzymes (manganese peroxidase, lignin peroxidase, laccase, 1,2-dioxygenase and 2,3-dioxygenase produced by Armillaria sp. F022 were detected in the culture. The highest level of activity was shown by 1,2-dioxygenase after 20 days (143.6 U l-1. Theseligninolytic and dioxygenase enzymes played an important role in the oxidation of chrysene. Chrysene was indeed degraded by Armillaria sp. F022 through several intermediates, chrysenequinone, 2-((1E,3E-4-carboxy-3-hydroxybuta-1,3-dien-1-yl-1-naphthoic acid , 1-hydroxy-2-naphthoic acid, and gentisic acid.Keywords : Biodegradation, Chrysene, Metabolites, Armillaria sp. F022

  16. The rhizosphere and PAH amendment mediate impacts on functional and structural bacterial diversity in sandy peat soil

    Energy Technology Data Exchange (ETDEWEB)

    Yrjaelae, Kim, E-mail: kim.yrjala@helsinki.f [Department of Biological and Environmental Sciences, General Microbiology, University of Helsinki, P.O. Box 56, (Biocenter 1C), 00014 Helsinki (Finland); Keskinen, Anna-Kaisa; Akerman, Marja-Leena; Fortelius, Carola [METROPOLIA University of Applied Science, Vantaa (Finland); Sipilae, Timo P. [Department of Biological and Environmental Sciences, General Microbiology, University of Helsinki, P.O. Box 56, (Biocenter 1C), 00014 Helsinki (Finland)

    2010-05-15

    To reveal the degradation capacity of bacteria in PAH polluted soil and rhizosphere we combined bacterial extradiol ring-cleavage dioxygenase and 16S rRNA analysis in Betula pubescens rhizoremediation. Characterisation of the functional bacterial community by RFLP revealed novel environmental dioxygenases, and their putative hosts were studied by 16S rRNA amplification. Plant rhizosphere and PAH amendment effects were detected by the RFLP/T-RFLP analysis. Functional species richness increased in the birch rhizosphere and PAH amendment impacted the compositional diversity of the dioxygenases and the structural 16S rRNA community. A shift from an Acidobacteria and Verrucomicrobia dominated to an Alpha- and Betaproteobacteria dominated community structure was detected in polluted soil. Clone sequence analysis indicated catabolic significance of Burkholderia in PAH polluted soil. These results advance our understanding of rhizoremediation and unveil the extent of uncharacterized functional bacteria to benefit bioremediation by facilitating the development of the molecular tool box to monitor bacterial populations in biodegradation. - The bacterial community analysis using 16S rRNA and extradiol dioxygenase marker genes in rhizoremediation revealed both a rhizosphere and a PAH-pollution effect.

  17. Proteomic characterization of plasmid pLA1 for biodegradation of polycyclic aromatic hydrocarbons in the marine bacterium, Novosphingobium pentaromativorans US6-1.

    Science.gov (United States)

    Yun, Sung Ho; Choi, Chi-Won; Lee, Sang-Yeop; Lee, Yeol Gyun; Kwon, Joseph; Leem, Sun Hee; Chung, Young Ho; Kahng, Hyung-Yeel; Kim, Sang Jin; Kwon, Kae Kyoung; Kim, Seung Il

    2014-01-01

    Novosphingobium pentaromativorans US6-1 is a halophilic marine bacterium able to degrade polycyclic aromatic hydrocarbons (PAHs). Genome sequence analysis revealed that the large plasmid pLA1 present in N. pentaromativorans US6-1 consists of 199 ORFs and possess putative biodegradation genes that may be involved in PAH degradation. 1-DE/LC-MS/MS analysis of N. pentaromativorans US6-1 cultured in the presence of different PAHs and monocyclic aromatic hydrocarbons (MAHs) identified approximately 1,000 and 1,400 proteins, respectively. Up-regulated biodegradation enzymes, including those belonging to pLA1, were quantitatively compared. Among the PAHs, phenanthrene induced the strongest up-regulation of extradiol cleavage pathway enzymes such as ring-hydroxylating dioxygenase, putative biphenyl-2,3-diol 1,2-dioxygenase, and catechol 2,3-dioxygenase in pLA1. These enzymes lead the initial step of the lower catabolic pathway of aromatic hydrocarbons through the extradiol cleavage pathway and participate in the attack of PAH ring cleavage, respectively. However, N. pentaromativorans US6-1 cultured with p-hydroxybenzoate induced activation of another extradiol cleavage pathway, the protocatechuate 4,5-dioxygenase pathway, that originated from chromosomal genes. These results suggest that N. pentaromativorans US6-1 utilizes two different extradiol pathways and plasmid pLA1 might play a key role in the biodegradation of PAH in N. pentaromativorans US6-1.

  18. Main: 1SP9 [RPSD[Archive

    Lifescience Database Archive (English)

    Full Text Available 11.27 (4-Hydroxyphenylpyruvate Dioxygenase) I.M.Fritze, L.Linden, J.Freigang, G.Auerbach,... R.Huber, S.Steinbacher I.M.Fritze, L.Linden, J.Freigang, G.Auerbach, R.Huber, S.Steinbacher The Cry

  19. EST Table: FS904141 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available ar to 2-aminoethanethiol (cysteamine) dioxygenase [Tribolium castaneum] gb|EFA09634.1| hypothetical protein ...10 33 %/248 aa gnl|Amel|GB12350-PA 10/09/10 35 %/238 aa gi|91090992|ref|XP_974899.1| PREDICTED: similar to 2-aminoethanethiol (cystea

  20. Characterization of Phenol Biodegradation by Comamonas testosteroni ZD4-1 and Pseudomonas aeruginosa ZD4-3

    Institute of Scientific and Technical Information of China (English)

    YING-XU CHEN; HE LIU; HUA-LIN CHEN

    2003-01-01

    Objective To investigate the characteristic and biochemical mechanism about the phenolbiodegradation by bacterial strains ZD 4-1 and ZD 4-3. Methods Bacterial strains ZD 4-1 and ZD4-3 were isolated by using phenol as the sole source of carbon and energy, and identified by 16SrDNA sequence analysis. The concentrations of phenol and total organic carbon (TOC) weremonitored to explore the degradation mechanism. The biodegradation intermediates were scanned at375 nm by using a uv-vis spectrophotometer. The enzyme assays were performed to detect theactivities of dioxygenases. Results Bacterial strains ZD 4-1 and ZD 4-3 were identified asComamonas testosteroni and Pseudomonas aeruginosa by 16S rDNA sequence analysis, respectively.The growth of the two strains was observed on a variety of aromatic hydrocarbons. The strains ZD 4-1and ZD 4-3 metabolized phenol via ortho-pathways and meta-pathways, respectively. In addition, theresults of enzyme assays showed that the biodegradation efficiency of phenol by meta-pathways washigher than that by ortho-pathways. Finally, the results of induction experiment indicated that thecatechol dioxygenases, both catechol 1,2-dioxygenase (C120) and catechol 2,3-dioxygenase (C230),were all inducible. Conclusion The strains ZD 4-1 and ZD 4-3 metabolize phenol throughortho-pathways and meta-pathway, respectively. Furthermore, the biodegradation efficiency of phenolby meta-pathways is higher than that by ortho-pathways.

  1. Structure and function of para-hydroxybenzoate hydroxylase

    NARCIS (Netherlands)

    Bolt, van der F.J.T.

    1999-01-01

    Enzymes which utilize molecular oxygen to either hydroxylate or cleave an aromatic ring are known as monooxygenases and dioxygenases, respectively. These enzymes contain a non-protein group such as heme, flavin, pterin or a transition metal ion in their active site, for oxygen activation. In his the

  2. LOX1 inhibition with small molecules

    DEFF Research Database (Denmark)

    Gousiadou, Chryssoula; Kouskoumvekaki, Irene

    2016-01-01

    Lipoxygenases (LOXs) are nonheme, iron-containing dioxygenases that catalyze the dioxygenation of polyunsaturated fatty acids and are widely distributed among plant and animal species. Human LOXs, now identified as key enzymes in the pathogenesis of major disorders, have increasingly drawn the at...

  3. Delaying aging and the aging-associated decline in protein homeostasis by inhibition of tryptophan degradation

    NARCIS (Netherlands)

    van der Goot, Annemieke T.; Zhu, Wentao; Vazquez-Manrique, Rafael P.; Seinstra, Renee I.; Dettmer, Katja; Michels, Helen; Farina, Francesca; Krijnen, Jasper; Melki, Ronald; Buijsman, Rogier C.; Silva, Mariana Ruiz; Thijssen, Karen L.; Kema, Ido P.; Neri, Christian; Oefner, Peter J.; Nollen, Ellen A. A.

    2012-01-01

    Toxicity of aggregation-prone proteins is thought to play an important role in aging and age-related neurological diseases like Parkinson and Alzheimer's diseases. Here, we identify tryptophan 2,3-dioxygenase (tdo-2), the first enzyme in the kynurenine pathway of tryptophan degradation, as a metabol

  4. PhnY and PhnZ comprise a new oxidative pathway for enzymatic cleavage of a carbon-phosphorus bond

    DEFF Research Database (Denmark)

    McSorley, Fern R.; Wyatt, Peter W.; Martinez, Ascuncion;

    2012-01-01

    The sequential activities of PhnY, an α-ketoglutarate/Fe(II)-dependent dioxygenase, and PhnZ, a Fe(II)-dependent enzyme of the histidine-aspartate motif hydrolase family, cleave the carbon-phosphorus bond of the organophosphonate natural product 2-aminoethylphosphonic acid. PhnY adds a hydroxyl g...

  5. Total synthesis of exiguamines A and B inspired by catecholamine chemistry.

    Science.gov (United States)

    Sofiyev, Vladimir; Lumb, Jean-Philip; Volgraf, Matthew; Trauner, Dirk

    2012-04-16

    The evolution of a total synthesis of the exiguamines, two structurally unusual natural products that are highly active inhibitors of indolamine-2,3-dioxygenase (IDO), is described. The ultimately successful strategy involves advanced cross-coupling methodology and features a potentially biosynthetic tautomerization/electrocyclization cascade reaction that forms two heterocycles and installs a quaternary ammonium ion in a single synthetic operation.

  6. SwissProt search result: AK104779 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK104779 001-039-C04 (Q9SQ80) Gibberellin 2-beta-dioxygenase 1 (EC 1.14.11.13) (Gibberellin... 2-beta-hydroxylase 1) (Gibberellin 2-oxidase 1) (GA 2-oxidase 1) (SLENDER protein) G2OX1_PEA 4e-16 ...

  7. GenBank blastx search result: AK107236 [KOME

    Lifescience Database Archive (English)

    Full Text Available AK107236 002-125-E12 BC019406.1 Mus musculus butyrobetaine (gamma), 2-oxoglutarate ...dioxygenase 1 (gamma-butyrobetaine hydroxylase), mRNA (cDNA clone MGC:30364 IMAGE:5134018), complete cds.|ROD ROD 8e-32 +2 ...

  8. Proteomic characterization of plasmid pLA1 for biodegradation of polycyclic aromatic hydrocarbons in the marine bacterium, Novosphingobium pentaromativorans US6-1.

    Directory of Open Access Journals (Sweden)

    Sung Ho Yun

    Full Text Available Novosphingobium pentaromativorans US6-1 is a halophilic marine bacterium able to degrade polycyclic aromatic hydrocarbons (PAHs. Genome sequence analysis revealed that the large plasmid pLA1 present in N. pentaromativorans US6-1 consists of 199 ORFs and possess putative biodegradation genes that may be involved in PAH degradation. 1-DE/LC-MS/MS analysis of N. pentaromativorans US6-1 cultured in the presence of different PAHs and monocyclic aromatic hydrocarbons (MAHs identified approximately 1,000 and 1,400 proteins, respectively. Up-regulated biodegradation enzymes, including those belonging to pLA1, were quantitatively compared. Among the PAHs, phenanthrene induced the strongest up-regulation of extradiol cleavage pathway enzymes such as ring-hydroxylating dioxygenase, putative biphenyl-2,3-diol 1,2-dioxygenase, and catechol 2,3-dioxygenase in pLA1. These enzymes lead the initial step of the lower catabolic pathway of aromatic hydrocarbons through the extradiol cleavage pathway and participate in the attack of PAH ring cleavage, respectively. However, N. pentaromativorans US6-1 cultured with p-hydroxybenzoate induced activation of another extradiol cleavage pathway, the protocatechuate 4,5-dioxygenase pathway, that originated from chromosomal genes. These results suggest that N. pentaromativorans US6-1 utilizes two different extradiol pathways and plasmid pLA1 might play a key role in the biodegradation of PAH in N. pentaromativorans US6-1.

  9. Functional identification of gene cluster for the aniline metabolic pathway mediated by transposable element

    Institute of Scientific and Technical Information of China (English)

    LIANG Quanfeng; Takeo Masahiro; LIN Min; CHEN Ming; XU Yuquan; ZHANG Wei; PING Shuzhen; LU Wei; SONG Xianlong; WANG Weiwei; GENG Lizhao

    2005-01-01

    A convenient and widely applicable method has been developed to clone aniline metabolic gene cluster in this study. Three positive recombinant plasmids pDA1, pDB2 and pDB11 were cloned from genomic library of aniline degradation strain AD9. The result of aniline dioxygenase (AD) activity and catechol 2,3-oxygenase (C23O) activity assay showed that pDA1 and pDB11 contain aniline dioxygenase genes and catechol 2,3-dioxygenase genes, respectively. The sequence analysis of the total 24.7-kb region revealed that this region contains 25 ORFs, of which 17 genes involve metabolism of aniline. In the gene cluster, the first five genes (tadQTA1A2B) and the subsequent gene (tadR1) were predicted to encode a multi-component aniline dioxygenase and a LysR-type regulator, respectively, while the others (tadD1C1D2C2EFGIJKL) were expected to encode meta- cleavage pathway enzymes for catechol degradation. The gene cluster was surrounded by two IS1071 sequences.

  10. InterProScan Result: BY940643 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available GENASE 3.4e-53 T IPR005708 Homogentisate 1,2-dioxygenase Biological Process: L-phenylalanine catabolic proce...ss (GO:0006559)|Biological Process: tyrosine metabolic process (GO:0006570)|Biological Process: oxidation reduction (GO:0055114) ...

  11. InterProScan Result: FS863249 [KAIKOcDNA[Archive

    Lifescience Database Archive (English)

    Full Text Available GENASE 1.3e-139 T IPR005708 Homogentisate 1,2-dioxygenase Biological Process: L-phenylalanine catabolic proc...ess (GO:0006559)|Biological Process: tyrosine metabolic process (GO:0006570)|Biological Process: oxidation reduction (GO:0055114) ...

  12. A Relay Pathway between Arginine and Tryptophan Metabolism Confers Immunosuppressive Properties on Dendritic Cells

    NARCIS (Netherlands)

    G. Mondanelli (Giada); R. Bianchi (Roberta); M.T. Pallotta (Maria Teresa); C. Orabona (Ciriana); E. Albini (Elisa); A. Iacono (Alberta); M.L. Belladonna (Maria Laura); C. Vacca (Carmine); F. Fallarino (Francesca); A. Macchiarulo (Antonio); S. Ugel (Stefano); V. Bronte (Vincenzo); F. Gevi (Federica); L. Zolla (Lello); A.P. Verhaar (Auke); M.P. Peppelenbosch (Maikel); E.M.C. Mazza (Emilia Maria Cristina); S. Bicciato (Silvio); Y. Laouar (Yasmina); L. Santambrogio (Laura); P. Puccetti (Paolo); C. Volpi (Claudia); U. Grohmann (Ursula)

    2016-01-01

    textabstractArginase 1 (Arg1) and indoleamine 2,3-dioxygenase 1 (IDO1) are immunoregulatory enzymes catalyzing the degradation of l-arginine and l-tryptophan, respectively, resulting in local amino acid deprivation. In addition, unlike Arg1, IDO1 is also endowed with non-enzymatic signaling activity

  13. Main: 1TFZ [RPSD[Archive

    Lifescience Database Archive (English)

    Full Text Available 27 (4-Hydroxyphenylpyruvate Dioxygenase) C.Yang, J.W.Pflugrath, D.L.Camper, M.L.Foster, D.J.P...ernich, T.A.Walsh C.Yang, J.W.Pflugrath, D.L.Camper, M.L.Foster, D.J.Pernich, T.A.Walsh Structur

  14. Main: 1TG5 [RPSD[Archive

    Lifescience Database Archive (English)

    Full Text Available 7 (4-Hydroxyphenylpyruvate Dioxygenase) C.Yang, J.W.Pflugrath, D.L.Camper, M.L.Foster, D.J.P...ernich, T.A.Walsh C.Yang, J.W.Pflugrath, D.L.Camper, M.L.Foster, D.J.Pernich, T.A.Walsh Structura

  15. Exogenous Tryptophan Promotes Cutaneous Wound Healing of Chronically Stressed Mice through Inhibition of TNF-α and IDO Activation.

    Directory of Open Access Journals (Sweden)

    Luana Graziella Bandeira

    Full Text Available Stress prolongs the inflammatory response compromising the dermal reconstruction and wound closure. Acute stress-induced inflammation increases indoleamine 2, 3-dioxygenase-stimulated tryptophan catabolism. To investigate the role of indoleamine 2, 3-dioxygenase expression and tryptophan administration in adverse effects of stress on cutaneous wound healing, mice were submitted to chronic restraint stress and treated with tryptophan daily until euthanasia. Excisional lesions were created on each mouse and 5 or 7 days later, the lesions were analyzed. In addition, murine skin fibroblasts were exposed to elevated epinephrine levels plus tryptophan, and fibroblast activity was evaluated. Tryptophan administration reversed the reduction of the plasma tryptophan levels and the increase in the plasma normetanephrine levels induced by stress 5 and 7 days after wounding. Five days after wounding, stress-induced increase in the protein levels of tumor necrosis factor-α and indoleamine 2, 3-dioxygenase, and this was inhibited by tryptophan. Stress-induced increase in the lipid peroxidation and the amount of the neutrophils, macrophages and T cells number was reversed by tryptophan 5 days after wounding. Tryptophan administration inhibited the reduction of myofibroblast density, collagen deposition, re-epithelialization and wound contraction induced by stress 5 days after wounding. In dermal fibroblast culture, the tryptophan administration increased the cell migration and AKT phosphorylation in cells treated with high epinephrine levels. In conclusion, tryptophan-induced reduction of inflammatory response and indoleamine 2, 3-dioxygenase expression may have accelerated cutaneous wound healing of chronically stressed mice.

  16. Distinct Tryptophan Catabolism and Th17/Treg Balance in HIV Progressors and Elite Controllers

    NARCIS (Netherlands)

    Jenabian, Mohammad-Ali; Patel, Mital; Kema, Ido; Kanagaratham, Cynthia; Radzioch, Danuta; Thebault, Pamela; Lapointe, Rejean; Tremblay, Cecile; Gilmore, Norbert; Ancuta, Petronela; Routy, Jean-Pierre

    2013-01-01

    Tryptophan (Trp) catabolism into immunosuppressive kynurenine (Kyn) by indoleamine 2,3-dioxygenase (IDO) was previously linked to Th17/Treg differentiation and immune activation. Here we examined Trp catabolism and its impact on Th17/Treg balance in uninfected healthy subjects (HS) and a large cohor

  17. Oil biodegradation by Bacillus strains isolated from the rock of an oil reservoir located in a deep-water production basin in Brazil

    Energy Technology Data Exchange (ETDEWEB)

    Duarte da Cunha, C.; Rosado, A.S.; Seldin, L.; Weid, I. von der [Universidade Federal do Rio de Janeiro (Brazil). Dept. de Microbiologia Geral; Sebastian, G.V. [CENPES, Petrobras, Ilha do Fundao, Rio de Janeiro (Brazil)

    2006-12-15

    Sixteen spore forming Gram-positive bacteria were isolated from the rock of an oil reservoir located in a deep-water production basin in Brazil. These strains were identified as belonging to the genus Bacillus using classical biochemical techniques and API 50CH kits, and their identity was confirmed by sequencing of part of the 16S rRNA gene. All strains were tested for oil degradation ability in microplates using Arabian Light and Marlin oils and only seven strains showed positive results in both kinds of oils. They were also able to grow in the presence of carbazole, n-hexadecane and polyalphaolefin (PAO), but not in toluene, as the only carbon sources. The production of key enzymes involved with aromatic hydrocarbons biodegradation process by Bacillus strains (catechol 1,2-dioxygenase and catechol 2,3-dioxygenase) was verified spectrophotometrically by detection of cis,cis-muconic acid and 2-hydroxymuconic semialdehyde, and results indicated that the ortho ring cleavage pathway is preferential. Furthermore, polymerase chain reaction (PCR) products were obtained when the DNA of seven Bacillus strains were screened for the presence of catabolic genes encoding alkane monooxygenase, catechol 1,2-dioxygenase, and/or catechol 2,3-dioxygenase. This is the first study on Bacillus strains isolated from an oil reservoir in Brazil. (orig.)

  18. The Kinetics of Plasmacytoid Dendritic Cell Accumulation in the Pancreas of the NOD Mouse during the Early Phases of Insulitis

    NARCIS (Netherlands)

    J.M.C. Welzen-Coppens (Jojanneke); C.G. van Helden-Meeuwsen; P.J. Leenen (Pieter); H.A. Drexhage (Hemmo); M.A. Versnel (Marjan)

    2013-01-01

    textabstractIn non-obese diabetic (NOD) mice that spontaneously develop autoimmune diabetes, plasmacytoid dendritic cells (pDCs) have a diabetes-promoting role through IFN-α production on one hand, while a diabetes-inhibiting role through indoleamine 2,3-dioxygenase (IDO) production on the other. Li

  19. An iron–oxygen intermediate formed during the catalytic cycle of cysteine dioxygenase† †Electronic supplementary information (ESI) available: Experimental and computational details. See DOI: 10.1039/c6cc03904a Click here for additional data file.

    Science.gov (United States)

    Tchesnokov, E. P.; Faponle, A. S.; Davies, C. G.; Quesne, M. G.; Turner, R.; Fellner, M.; Souness, R. J.; Wilbanks, S. M.

    2016-01-01

    Cysteine dioxygenase is a key enzyme in the breakdown of cysteine, but its mechanism remains controversial. A combination of spectroscopic and computational studies provides the first evidence of a short-lived intermediate in the catalytic cycle. The intermediate decays within 20 ms and has absorption maxima at 500 and 640 nm. PMID:27297454

  20. Using "Pseudomonas Putida xylE" Gene to Teach Molecular Cloning Techniques for Undergraduates

    Science.gov (United States)

    Dong, Xu; Xin, Yi; Ye, Li; Ma, Yufang

    2009-01-01

    We have developed and implemented a serial experiment in molecular cloning laboratory course for undergraduate students majored in biotechnology. "Pseudomonas putida xylE" gene, encoding catechol 2, 3-dioxygenase, was manipulated to learn molecular biology techniques. The integration of cloning, expression, and enzyme assay gave students…

  1. Rice cytochrome P450 MAX1 homologs catalyze distinct steps in strigolactone biosynthesis

    NARCIS (Netherlands)

    Zhang, Y.; Dijk, van A.D.J.; Scaffidi, A.; Flematti, G.R.; Hofmann, M.; Charnikhova, T.; Verstappen, F.W.A.; Hepworth, J.; Krol, van der A.R.; Leyser, O.

    2014-01-01

    Strigolactones (SLs) are a class of phytohormones and rhizosphere signaling compounds with high structural diversity. Three enzymes, carotenoid isomerase DWARF27 and carotenoid cleavage dioxygenases CCD7 and CCD8, were previously shown to convert all-trans-¿-carotene to carlactone (CL), the SL precu

  2. Arabidopsis VARIEGATED 3 encodes a chloroplast-targeted, zinc-finger protein required for chloroplast and palisade cell development

    DEFF Research Database (Denmark)

    Næsted, Henrik; Holm, Agnethe; Jenkins, Tom

    2004-01-01

    protein containing novel repeats and zinc fingers described as protein interaction domains. VAR3 interacts specifically in yeast and in vitro with NCED4, a putative polyene chain or carotenoid dioxygenase, and both VAR3 and NCED4 accumulate in the chloroplast stroma. Metabolic profiling demonstrates...

  3. Arabidopsis VARIEGATED 3 encodes a chloroplasttargeted, zinc-finger protein required for chloroplast and palisade cell development

    DEFF Research Database (Denmark)

    Næsted, Henrik; Holm, A.; Jenkins, T.

    2004-01-01

    protein containing novel repeats and zinc fingers described as protein interaction domains. VAR3 interacts specifically in yeast and in vitro with NCED4, a putative polyene chain or carotenoid dioxygenase, and both VAR3 and NCED4 accumulate in the chloroplast stroma. Metabolic profiling demonstrates...

  4. End-on and side-on peroxo derivatives of non-heme iron complexes with pentadentate ligands : Models for putative intermediates in biological iron/dioxygen chemistry

    NARCIS (Netherlands)

    Roelfes, G; Vrajmasu, [No Value; Ho, RYN; Rohde, JU; Zondervan, C; la Crois, RM; Schudde, EP; Lutz, M; Spek, AL; Hage, R; Feringa, BL; Munck, E; Que, L; Vrajmasu, Vladislav; Ho, Raymond Y.N.; Rohde, Jan-Uwe; Crois, Rene M. la; Spek, Anthony L.; Que, Jr.; Feringa, Bernard

    2003-01-01

    Mononuclear iron(III) species with end-on and side-on peroxide have been proposed or identified in the catalytic cycles of the antitumor drug bleomycin and a variety of enzymes, such as cytochrome P450 and Rieske dioxygenases, Only recently have biomimetic analogues of such reactive species been, ge

  5. OXIDATION OF BIPHENYL BY A MULTICOMPONENT ENZYME SYSTEM FROM PSEUDOMONAS SP. STRAIN LB400

    Science.gov (United States)

    Pseudomonas sp. strain LB400 grows on biphenyl as the sole carbon and energy source. This organism also cooxidizes several chlorinated biphenyl congeners. Biphenyl dioxygenase activity in cell extract required addition of NAD(P)H as an electron donor for the conversion of bipheny...

  6. Biological degradation of 4-chlorobenzoic acid by a PCB-metabolizing bacterium through a pathway not involving (chloro)catechol.

    Science.gov (United States)

    Adebusoye, Sunday A

    2017-02-01

    Cupriavidus sp. strain SK-3, previously isolated on polychlorinated biphenyl mixtures, was found to aerobically utilize a wide spectrum of substituted aromatic compounds including 4-fluoro-, 4-chloro- and 4-bromobenzoic acids as a sole carbon and energy source. Other chlorobenzoic acid (CBA) congeners such as 2-, 3-, 2,3-, 2,5-, 3,4- and 3,5-CBA were all rapidly transformed to respective chlorocatechols (CCs). Under aerobic conditions, strain SK-3 grew readily on 4-CBA to a maximum concentration of 5 mM above which growth became impaired and yielded no biomass. Growth lagged significantly at concentrations above 3 mM, however chloride elimination was stoichiometric and generally mirrored growth and substrate consumption in all incubations. Experiments with resting cells, cell-free extracts and analysis of metabolite pools suggest that 4-CBA was metabolized in a reaction exclusively involving an initial hydrolytic dehalogenation yielding 4-hydroxybenzoic acid, which was then hydroxylated to protocatechuic acid (PCA) and subsequently metabolized via the β-ketoadipate pathway. When strain SK-3 was grown on 4-CBA, there was gratuitous induction of the catechol-1,2-dioxygenase and gentisate-1,2-dioxygenase pathways, even if both were not involved in the metabolism of the acid. While activities of the modified ortho- and meta-cleavage pathways were not detectable in all extracts, activity of PCA-3,4-dioxygenase was over ten-times higher than those of catechol-1,2- and gentisate-1,2-dioxygenases. Therefore, the only reason other congeners were not utilized for growth was the accumulation of CCs, suggesting a narrow spectrum of the activity of enzymes downstream of benzoate-1,2-dioxygenase, which exhibited affinity for a number of substituted analogs, and that the metabolic bottlenecks are either CCs or catabolites of the modified ortho-cleavage metabolic route.

  7. 组蛋白去甲基化酶PHD锌指蛋白8与神经发育%The Histone Demethylase PHF8 and Neural Development

    Institute of Scientific and Technical Information of China (English)

    郭晓强; 沈永青; 刘贝; 常彦忠; 段相林

    2011-01-01

    PHF8 (PHD finger protein 8) is a Fe2+ and 2-oxoglutarate dependent histone lysine demethylase and belongs to a family of JmjC domain-containing proteins. PHF8 also contains a plant homeodomain (PHD) finger motif in its N-terminus, which involves in transcriptional regulation. PHF8 can demethylate H3K9me2/1,H4K20mel and H3K27me2 with JmjC domain, and also act as a transcriptional coactivator through binding to H3K4me3 via PHI) finger. PHF8 regulates expression of rRNA and many protein-coding genes involved in neural development such as JARID 1C. Mutations in human PHF8 which are defective in histone demethylase activity can cause inherited X-linked mental retardation (XLMR) and cleft lip/cleft palate. These researches suggested that PHF8 is an important regulator of neural development, which deepens the understanding of historne methylation with gene expression and provides novel clues to understanding of XLMR.%PHD锌指蛋白8(PHF8)是一种Fe2+和α-酮戊二酸依赖的组蛋白赖氨酸去甲基化酶.PHF8属于包含Jmjc结构域蛋白家族,在N端还含有一个PHD(plant homeadomain)锌指结构域.人的PHF8基因突变往往破坏组蛋白去甲基化酶活性,从而引发遗传性X-连锁智力迟滞(XLMR)并伴发唇裂的发生.PHF8一方面可催化H3K9me2/1、H4K20me1和H3K27me2的去甲基化,另一方面还通过N端PHD锌指结构域与H3K4me3结合而发挥转录共激活作用.PHF8可调节rRNA和多个涉及神经发育的蛋白质编码基因如JARID1C的表达.这些研究显示,PHF8是一种重要的神经发育调节因子,从而拓宽了对组蛋白甲基化与基因表达关联的理解,同时为XLMR疾病的理解提供了新的线索.

  8. The role of PHD2 mutations in the pathogenesis of erythrocytosis

    Directory of Open Access Journals (Sweden)

    Gardie B

    2014-07-01

    of EPO transcription. The α subunits of the hypoxia-inducible transcription factor are hydroxylated by three prolyl hydroxylase domain (PHD enzymes, which belong to the iron and 2-oxoglutarate-dependent oxygenase superfamily. Sequence analysis of the genes encoding the PHDs in patients with erythrocytosis has revealed heterozygous germline mutations only occurring in Egl nine homolog 1 (EGLN1, also known as PHD2, the gene that encodes PHD2. To date, 24 different EGLN1 mutations comprising missense, frameshift, and nonsense mutations have been described. The phenotypes associated with the patients carrying these mutations are fairly homogeneous and typically limited to erythrocytosis with normal to elevated EPO. However, exceptions exist; for example, there is one case with development of concurrent paraganglioma (PHD2-H374R. Analysis of the erythrocytosis-associated PHD2 missense mutations has shown heterogeneous results. Structural studies reveal that mutations can affect different domains of PHD2. Some are close to the hypoxia-inducible transcription factor α/2-oxoglutarate or the iron binding sites for PHD2. In silico studies demonstrate that the mutations do not always affect fully conserved residues. In vitro and in cellulo studies showed varying effects of the mutations, ranging from mild effects to severe loss of function. The exact mechanism of a potential tumor-suppressor role for PHD2 still needs to be elucidated. A knockin mouse model expressing the first reported PHD2-P317R mutation recapitulates the phenotype observed in humans (erythrocytosis with inappropriately normal serum EPO levels and demonstrates that haploinsufficiency and partial deregulation of PHD2 is sufficient to cause erythrocytosis. Keywords: PHD2, EGLN1, HIF, hypoxia, erythropoietin, erythrocytosis

  9. 极端耐盐放线菌白色普氏菌YIM90005T四氢嘧啶及5-羟基四氢嘧啶合成相关基因的克隆%Cloning and characterization of gene cluster for biosynthesis of ectoine and 5 -hydroxyectoine from extreme halotolerant actinomycete strain Prauserella alba YIM 90005T

    Institute of Scientific and Technical Information of China (English)

    李岩; 董雷; 王磊; 方福瑾; 何敏; 曹中莹; 梁媛; 唐蜀昆; 李文均

    2011-01-01

    [Objective]To study adaptive mechanism in hypersaline environments of extreme halotolerant filamentous actinomycetes.[Methods]Using HPLC we analyzed compatible solutes from extreme halotolerant filamentous actinomycete strain Prauserella alba YIM 90005 that was cultivated at different NaCl concentrations.[Results]Ectoine and 5-hydroxyectoine were two major compatible solutes for strain Prauserella alba YIM 90005.Ectoine accumulated to the maximum content of 18.77 μg/mg dry cell weight after being inoculated in 10% NaCl ( w/v).And 5-hydroxyectoine reached 22.98 μg/mg dry cell weight after being inoculated in 24% NaCl (w/v).The ectA ( acyltransferase) , ectB (aminotransferase) , ectC (ectoine synthase) and ectD ( ectoine hydroxylase) genes cluster encoding genes on ectoine and hydroxyectoine synthesis were further cloned by designing the degenerate primer and genome walking methods.The sequence analysis indicated that ectABCD was an operon.Furthermore, the expression of ectB and ectD inoculated at different salt concentrations was quantified by real-time PCR, and the results indicated that the expression of the gene cluster would be increasing as the salt concentration increased.[Conclusion]5-hydroxyectoine was the major compatible solute for osmotic regulation of strain Prauserella alba YIM 90005 to adapt high salt concentration.%[目的]为了研究耐盐放线菌对高盐环境的适应机理.[方法]用HPLC定量检测了极端耐盐、丝状产孢放线菌--白色普氏菌(Prauserella alba)YIM 90005T在不同盐浓度下胞内相容性溶质的种类和含量.[结果]结果发现,四氢嘧啶和5-羟基四氢嘧啶是其主要的相容性溶质.在培养基NaCI浓度为10%时,四氢嘧啶在胞内累积浓度最大,为18.77μg/mg干菌体重.之后随NaCl浓度的升高,胞内的四氢嘧啶含量逐渐减少,而5-羟基四氢嘧啶的含量逐渐增加,在该菌耐受的最高NaCl浓度下(24% w/v),胞内5-羟基四氢嘧啶含量达到最大值,为22

  10. Impact of clay mineral, wood sawdust or root organic matter on the bacterial and fungal community structures in two aged PAH-contaminated soils.

    Science.gov (United States)

    Cébron, Aurélie; Beguiristain, Thierry; Bongoua-Devisme, Jeanne; Denonfoux, Jérémie; Faure, Pierre; Lorgeoux, Catherine; Ouvrard, Stéphanie; Parisot, Nicolas; Peyret, Pierre; Leyval, Corinne

    2015-09-01

    The high organic pollutant concentration of aged polycyclic aromatic hydrocarbon (PAH)-contaminated wasteland soils is highly recalcitrant to biodegradation due to its very low bioavailability. In such soils, the microbial community is well adapted to the pollution, but the microbial activity is limited by nutrient availability. Management strategies could be applied to modify the soil microbial functioning as well as the PAH contamination through various amendment types. The impact of amendment with clay minerals (montmorillonite), wood sawdust and organic matter plant roots on microbial community structure was investigated on two aged PAH-contaminated soils both in laboratory and 1-year on-site pot experiments. Total PAH content (sum of 16 PAHs of the US-EPA list) and polar polycyclic aromatic compounds (pPAC) were monitored as well as the available PAH fraction using the Tenax method. The bacterial and fungal community structures were monitored using fingerprinting thermal gradient gel electrophoresis (TTGE) method. The abundance of bacteria (16S rRNA genes), fungi (18S rRNA genes) and PAH degraders (PAH-ring hydroxylating dioxygenase and catechol dioxygenase genes) was followed through qPCR assays. Although the treatments did not modify the total and available PAH content, the microbial community density, structure and the PAH degradation potential changed when fresh organic matter was provided as sawdust and under rhizosphere influence, while the clay mineral only increased the percentage of catechol-1,2-dioxygenase genes. The abundance of bacteria and fungi and the percentage of fungi relative to bacteria were enhanced in soil samples supplemented with wood sawdust and in the plant rhizospheric soils. Two distinct fungal populations developed in the two soils supplemented with sawdust, i.e. fungi related to Chaetomium and Neurospora genera and Brachyconidiellopsis and Pseudallescheria genera, in H and NM soils respectively. Wood sawdust amendment favoured the

  11. Biodegradation of pyrene and catabolic genes in contaminated soils cultivated with Lolium multiflorum L

    Energy Technology Data Exchange (ETDEWEB)

    Khan, Sardar [Dept. of Environmental Sciences, Univ. of Preshawar (Pakistan); Hesham, Abd El-Latif [Genetics Dept., Faculty of Agriculture, Assiut Univ. (Egypt); Qing Gu; Shuang Liu; He Jizheng [Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences (China)

    2009-10-15

    Background, aim, and scope In the soil environment, polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs) are of great environmental and human health concerns due to their widespread occurrence, persistence, and carcinogenic properties. Bioremediation of contaminated soil is a cost-effective, environmentally friendly, and publicly acceptable approach to address the removal of environmental contaminants. However, biore-mediation of contaminants depends on plant-microbe interactions in the rhizosphere. The microorganisms that can mineralize various PAHs have PAH dioxygenase genes like nahAc, phnAc, and pdol. To understand the fate of pyrene in rhizospheric and non-rhizospheric soils in the presence or absence of Pb, pyrene biodegradation, bacterial community structure, and dioxygenase genes were investigated in a pot experiment. (orig.)

  12. Biochemistry and occurrence of O-demethylation in plant metabolism

    Directory of Open Access Journals (Sweden)

    Jillian Hagel

    2010-07-01

    Full Text Available Demethylases play a pivitol role in numerous biological processes from covalent histone modification and DNA repair to specialized metabolism in plants and microorganisms. Enzymes that catalyze O- and N-demethylation include 2-oxoglutarate (2OG/Fe(II-dependent dioxygenases, cytochromes P450, Rieske-domain proteins and flavin adenine dinucleotide (FAD-dependent oxidases. Proposed mechanisms for demethylation by 2OG/Fe(II-dependent enzymes involve hydroxylation at the O- or N-linked methyl group followed by formaldehyde elimination. Members of this enzyme family catalyze a wide variety of reactions in diverse plant metabolic pathways. Recently, we showed that 2OG/Fe(II-dependent dioxygenases catalyze the unique O-demethylation steps of morphine biosynthesis in opium poppy, which provides a rational basis for the widespread occurrence of demethylases in benzylisoquinoline alkaloid metabolism.

  13. Transcriptional regulation of lycopene metabolism mediated by rootstock during the ripening of grafted watermelons.

    Science.gov (United States)

    Kong, Qiusheng; Yuan, Jingxian; Gao, Lingyun; Liu, Peng; Cao, Lei; Huang, Yuan; Zhao, Liqiang; Lv, Huifang; Bie, Zhilong

    2017-01-01

    Rootstocks have comprehensive effects on lycopene accumulation in grafted watermelon fruits. However, little is known about lycopene metabolic regulation in grafted watermelon. To address this problem, parallel changes in lycopene contents and the expression of its metabolic genes were analyzed during the fruit ripening of nongrafted watermelon and watermelon grafted onto bottle gourd, pumpkin, and wild watermelon. Results showed that rootstocks mediated the transcriptional regulations of lycopene accumulation in different ways. Bottle gourd and wild watermelon promoted lycopene accumulation in grafted watermelon fruits by upregulating the biosynthetic genes phytoene synthase (PSY) and ζ-carotene desaturase (ZDS), and downregulating the catabolic genes β-carotene hydroxylase (CHYB), zeaxanthin epoxidase (ZEP), 9-cis-epoxycarotenoid dioxygenase (NCED), and carotenoid cleavage dioxygenase (CCD). However, pumpkin did not affect lycopene accumulation by upregulating both biosynthetic and catabolic genes. The rootstock-dependent characteristic of lycopene accumulation in grafted watermelon fruits provided an alternative model for investigating lycopene metabolic regulation.

  14. Isolation and characteristics of a novel biphenyl-degrading bacterial strain, Dyella ginsengisoli LA-4

    Institute of Scientific and Technical Information of China (English)

    LI Ang; QU Yuanyuan; ZHOU Jiti; GOU Min

    2009-01-01

    A novel biphenyl-degrading bacterial strain LA-4 was isolated from activated sludge. It was identified as Dyella ginsengisoli according to phylogenetic similarity of 16S rRNA gene sequence. This isolate could utilize biphenyl as sole source of carbon and energy, which degraded over 95 mg/L biphenyl within 36 h. The major metabolites formed from biphenyl, such as 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid (HOPDA) and benzoic acid, were identified by LC-MS. The crude cell extract of strain LA-4 exhibited the activity of 2,3-dihydroxybiphenyl 1,2-dioxygenase (2,3-DHBD) and the kinetic parameters were Km= 26.48 μmol/L and Vmax= 8.12 μmol/mg protein. A conserved region of the biphenyl dioxygenase gene bphA1 of strain LA-4 was amplified by PCR and confirmed by DNA sequencing.

  15. Knee osteoarthrosis secondary to ochronosis – clinical case☆☆☆

    OpenAIRE

    Andreia Maria da Silva Martins Ferreira; Filipe Lima Santos; André Miguel Castro Costa; Bruno Miguel Pereira Barbosa; Rui Miguel Reis Rocha; Joaquim Fernando Fontes Lebre

    2014-01-01

    Alkaptonuria is a rare metabolic disease in which a deficiency of the enzyme homogentisate dioxygenase causes an accumulation of homogentisic acid. Ochronosis consists of excessive deposition of homogentisic acid in the connective tissue and presents as a chestnut brown or black pigmentation. With aging, the accumulation of pigments from homogentisic acid in the joints causes osteoarthrosis. There is no specific treatment for the disease and the approach is symptomatic. Arthroplasty is the so...

  16. Microbial community development of biofilm in Amaranth decolourization technology analysed by FISH

    Science.gov (United States)

    Belouhova, Mihaela; Schneider, Irina; Chakarov, Stoyan; Ivanova, Iliana; Topalova, Yana

    2014-01-01

    The aim of this study was to elucidate the role, the space distribution and the relationships of the bacteria from the genus Pseudomonas in a biofilm community during semi-continuous Amaranth decolourization process in model sand biofilters. The examined parameters of the process were as follows: technological parameters; key enzyme activities (azoreductase, succinate dehydrogenase, catechol-1,2-dioxygenase, catechol-2,3-dioxygenase); the number of azo-degrading bacteria and the bacteria from genus Pseudomonas (plate count technique); the amount and the location of Pseudomonas sp. using fluorescent in situ hybridization (FISH). The results showed that the increase of the Amaranth removal rate with 120% was accompanied with increase of the enzyme activities of the biofilm (azoreductase activity – with 25.90% and succinate dehydrogenase – with 10.61%). The enzyme assays showed absence of activity for сatechol-1,2-dioxygenase and catechol-2,3-dioxygenase at the early phase and high activities of the same oxygenases at the late phase (2.76 and 1.74 μmol/min mg protein, respectively). In the beginning of the process (0–191 h), the number of the culturable microorganisms from genus Pseudomonas was increased with 48.76% but at the late phase (191–455 h) they were decreased with 15.25% while the quantity of the non-culturable bacteria from this genus with synergetic relationships was increased with 23.26%. The dominant microbial factors were identified in the structure of the biofilm during the azo-degradation process by using FISH analysis. Furthermore, the inner mechanisms for increase of the rate and the range of the detoxification were revealed during the complex wastewater treatment processes. PMID:26019551

  17. Matériaux pour la dépollution basés sur le modèle des dioxygénases à manganèse

    OpenAIRE

    Chaignon, Jérémy

    2013-01-01

    The objective of this work is the synthesis of model material for manganese dioxygenase which is an enzyme that oxidizes catechol-like substrates with dioxygen. Our strategy comprises three main steps that form the different chapters of this thesis: - Synthesis and characterization of manganese(II) complexes with tridentate ligands. - Optimization of a microwave-assisted synthesis of a mesoporous silica. - Functionalization of these materials and complex grafting, as well as preliminary catal...

  18. Combined treatment with oral metronidazole and N-acetylcysteine is effective in ethylmalonic encephalopathy.

    Science.gov (United States)

    Viscomi, Carlo; Burlina, Alberto B; Dweikat, Imad; Savoiardo, Mario; Lamperti, Costanza; Hildebrandt, Tatjana; Tiranti, Valeria; Zeviani, Massimo

    2010-08-01

    Ethylmalonic encephalopathy is caused by mutations in ETHE1, a mitochondrial matrix sulfur dioxygenase, leading to failure to detoxify sulfide, a product of intestinal anaerobes and, in trace amounts, tissues. Metronidazole, a bactericide, or N-acetylcysteine, a precursor of sulfide-buffering glutathione, substantially prolonged the lifespan of Ethe1-deficient mice, with the combined treatment being additive. The same dual treatment caused marked clinical improvement in five affected children, with hardly any adverse or side effects.

  19. Employing a Recombinant Strain of Advenella mimigardefordensis for Biotechnical Production of Homopolythioesters from 3,3′-Dithiodipropionic Acid

    OpenAIRE

    Xia, Yongzhen; Wübbeler, Jan Hendrik; Qi, Qingsheng; Steinbüchel, Alexander

    2012-01-01

    Advenella mimigardefordensis strain DPN7T was genetically modified to produce poly(3-mercaptopropionic acid) (PMP) homopolymer by exploiting the recently unraveled process of 3,3′-dithiodipropionic acid (DTDP) catabolism. Production was achieved by systematically engineering the metabolism of this strain as follows: (i) deletion of its inherent 3MP dioxygenase-encoding gene (mdo), (ii) introduction of the buk-ptb operon (genes encoding the butyrate kinase, Buk, and the phosphotransbutyrylase,...

  20. Identification of a conserved protein involved in anaerobic unsaturated fatty acid synthesis in Neiserria gonorrhoeae: implications for facultative and obligate anaerobes that lack FabA

    OpenAIRE

    Isabella, Vincent M.; Clark, Virginia L.

    2011-01-01

    Transcriptome analysis of the facultative anaerobe, Neisseria gonorrhoeae, revealed that many genes of unknown function were induced under anaerobic conditions. Mutation of one such gene, NGO1024, encoding a protein belonging to the 2-nitropropane dioxygenase-like superfamiliy of proteins, was found to result in an inability of gonococci to grow anaerobically. Anaerobic growth of an NG1024 mutant was restored upon supplementation with unsaturated fatty acids (UFA), but not with the saturated ...

  1. Molecular perspectives and recent advances in microbial remediation of persistent organic pollutants.

    Science.gov (United States)

    Chakraborty, Jaya; Das, Surajit

    2016-09-01

    Nutrition and pollution stress stimulate genetic adaptation in microorganisms and assist in evolution of diverse metabolic pathways for their survival on several complex organic compounds. Persistent organic pollutants (POPs) are highly lipophilic in nature and cause adverse effects to the environment and human health by biomagnification through the food chain. Diverse microorganisms, harboring numerous plasmids and catabolic genes, acclimatize to these environmentally unfavorable conditions by gene duplication, mutational drift, hypermutation, and recombination. Genetic aspects of some major POP catabolic genes such as biphenyl dioxygenase (bph), DDT 2,3-dioxygenase, and angular dioxygenase assist in degradation of biphenyl, organochlorine pesticides, and dioxins/furans, respectively. Microbial metagenome constitutes the largest genetic reservoir with miscellaneous enzymatic activities implicated in degradation. To tap the metabolic potential of microorganisms, recent techniques like sequence and function-based screening and substrate-induced gene expression are proficient in tracing out novel catabolic genes from the entire metagenome for utilization in enhanced biodegradation. The major endeavor of today's scientific world is to characterize the exact genetic mechanisms of microbes for bioremediation of these toxic compounds by excavating into the uncultured plethora. This review entails the effect of POPs on the environment and involvement of microbial catabolic genes for their removal with the advanced techniques of bioremediation.

  2. Nonantibiotic Effects of Fluoroquinolones in Mammalian Cells.

    Science.gov (United States)

    Badal, Sujan; Her, Yeng F; Maher, L James

    2015-09-04

    Fluoroquinolones (FQ) are powerful broad-spectrum antibiotics whose side effects include renal damage and, strangely, tendinopathies. The pathological mechanisms underlying these toxicities are poorly understood. Here, we show that the FQ drugs norfloxacin, ciprofloxacin, and enrofloxacin are powerful iron chelators comparable with deferoxamine, a clinically useful iron-chelating agent. We show that iron chelation by FQ leads to epigenetic effects through inhibition of α-ketoglutarate-dependent dioxygenases that require iron as a co-factor. Three dioxygenases were examined in HEK293 cells treated with FQ. At sub-millimolar concentrations, these antibiotics inhibited jumonji domain histone demethylases, TET DNA demethylases, and collagen prolyl 4-hydroxylases, leading to accumulation of methylated histones and DNA and inhibition of proline hydroxylation in collagen, respectively. These effects may explain FQ-induced nephrotoxicity and tendinopathy. By the same reasoning, dioxygenase inhibition by FQ was predicted to stabilize transcription factor HIF-1α by inhibition of the oxygen-dependent hypoxia-inducible transcription factor prolyl hydroxylation. In dramatic contrast to this prediction, HIF-1α protein was eliminated by FQ treatment. We explored possible mechanisms for this unexpected effect and show that FQ inhibit HIF-1α mRNA translation. Thus, FQ antibiotics induce global epigenetic changes, inhibit collagen maturation, and block HIF-1α accumulation. We suggest that these mechanisms explain the classic renal toxicities and peculiar tendinopathies associated with FQ antibiotics.

  3. Peripheral distribution of kynurenine metabolites and activity of kynurenine pathway enzymes in renal failure.

    Science.gov (United States)

    Pawlak, D; Tankiewicz, A; Matys, T; Buczko, W

    2003-06-01

    We investigated L-kynurenine distribution and metabolism in rats with experimental chronic renal failure of various severity, induced by unilateral nephrectomy and partial removal of contralateral kidney cortex. In animals with renal insufficiency the plasma concentration and the content of L-tryptophan in homogenates of kidney, liver, lung, intestine and spleen were significantly decreased. These changes were accompanied by increase activity of liver tryptophan 2,3-dioxygenase, the rate-limiting enzyme of kynurenine pathway in rats, while indoleamine 2,3-dioxygenase activity was unchanged. Conversely, the plasma concentration and tissue content of L-kynurenine, 3-hydroxykynurenine, and anthranilic, kynurenic, xanthurenic and quinolinic acids in the kidney, liver, lung, intestine, spleen and muscles were increased. The accumulation of L-kynurenine and the products of its degradation was proportional to the severity of renal failure and correlated with the concentration of renal insufficiency marker, creatinine. Kynurenine aminotransferase, kynureninase and 3-hydroxyanthranilate-3,4-dioxygenase activity was diminished or unchanged, while the activity of kynurenine 3-hydroxylase was significantly increased. We conclude that chronic renal failure is associated with the accumulation of L-kynurenine metabolites, which may be involved in the pathogenesis of certain uremic syndromes.

  4. Biotransformation of eugenol via protocatechuic acid by thermophilic Geobacillus sp. AY 946034 strain.

    Science.gov (United States)

    Giedraityte, Gražina; Kalėdienė, Lilija

    2014-04-01

    The metabolic pathway of eugenol degradation by thermophilic Geobacillus sp. AY 946034 strain was analyzed based on the lack of data about eugenol degradation by thermophiles. TLC, GC-MS, and biotransformation with resting cells showed that eugenol was oxidized through coniferyl alcohol, and ferulic and vanillic acids to protocatechuic acid before the aromatic ring was cleaved. The cell-free extract of Geobacillus sp. AY 946034 strain grown on eugenol showed a high activity of eugenol hydroxylase, feruloyl-CoA synthetase, vanillate-O-demethylase, and protocatechuate 3,4-dioxygenase. The key enzyme, protocatechuate 3,4- dioxygenase, which plays a crucial role in the degradation of various aromatic compounds, was purified 135-fold to homogeneity with a 34% overall recovery from Geobacillus sp. AY 946034. The relative molecular mass of the native enzyme was about 450 ± 10 kDa and was composed of the non-identical subunits. The pH and temperature optima for enzyme activity were 8 and 60°C, respectively. The half-life of protocatechuate 3,4-dioxygenase at the optimum temperature was 50 min.

  5. 10th NTES Conference: Nickel and Arsenic Compounds Alter the Epigenome of Peripheral Blood Mononuclear Cells.

    Science.gov (United States)

    Brocato, Jason; Costa, Max

    2015-01-01

    The mechanisms that underlie metal carcinogenesis are the subject of intense investigation; however, data from in vitro and in vivo studies are starting to piece together a story that implicates epigenetics as a key player. Data from our lab has shown that nickel compounds inhibit dioxygenase enzymes by displacing iron in the active site. Arsenic is hypothesized to inhibit these enzymes by diminishing ascorbate levels--an important co-factor for dioxygenases. Inhibition of histone demethylase dioxygenases can increase histone methylation levels, which also may affect gene expression. Recently, our lab conducted a series of investigations in human subjects exposed to high levels of nickel or arsenic compounds. Global levels of histone modifications in peripheral blood mononuclear cells (PBMCs) from exposed subjects were compared to low environmentally exposed controls. Results showed that nickel increased H3K4me3 and decreased H3K9me2 globally. Arsenic increased H3K9me2 and decreased H3K9ac globally. Other histone modifications affected by arsenic were sex-dependent. Nickel affected the expression of 2756 genes in human PBMCs and many of the genes were involved in immune and carcinogenic pathways. This review will describe data from our lab that demonstrates for the first time that nickel and arsenic compounds affect global levels of histone modifications and gene expression in exposed human populations.

  6. Biodegradation of phenanthrene by fungi screened from nature.

    Science.gov (United States)

    Hadibarata, Tony; Tachibana, Sanro; Itoh, Kazutaka

    2007-08-01

    Microbial degradation of Phenanthrene with several fungi screened from nature was conducted to select fungi for the bioremediation ofPhenanthrene. Thrichoderma sp. S019, a fungus collected from soil, had the highest rate of degradation on the agar medium containing Phenanthrene. Maximal degradation (72%) was obtained when Trichoderma sp. S019 was incubated for 30 days after the addition of 0.1 mM of Phenanthrene to the liquid medium. Furthermore, the degradation of Phenanthrene was affected by the addition of a carbon source, the addition of a nitrogen source and agitation. Also, 1,2-Dioxygenase and 2,3-Dioxygenase were produced by Trichoderma sp. S019 in a liquid medium. These enzymes play an important role in the metabolism of substrates, revealing a high stereoselectivity for initial dioxygenase and enzymatic hydration since the K-region of phenanthrene was the major site of metabolism. Phenanthrene was indeed degraded by Trichoderma sp. S019 because 1-Hydroxy-2-naphthoic acid, Salicyaldehyde, Salicylic acid and Catechol, considered to be the intermediates in the bioremediation of Phenanthrene, were detected among the reaction products.

  7. Biotransformation of various substituted aromatic compounds to chiral dihydrodihydroxy derivatives.

    Science.gov (United States)

    Raschke, H; Meier, M; Burken, J G; Hany, R; Müller, M D; Van Der Meer, J R; Kohler, H P

    2001-08-01

    The biotransformation of four different classes of aromatic compounds by the Escherichia coli strain DH5alpha(pTCB 144), which contained the chlorobenzene dioxygenase (CDO) from Pseudomonas sp. strain P51, was examined. CDO oxidized biphenyl as well as monochlorobiphenyls to the corresponding cis-2,3-dihydro-2,3-dihydroxy derivatives, whereby oxidation occurred on the unsubstituted ring. No higher substituted biphenyls were oxidized. The absolute configurations of several monosubstituted cis-benzene dihydrodiols formed by CDO were determined. All had an S configuration at the carbon atom in meta position to the substituent on the benzene nucleus. With one exception, the enantiomeric excess of several 1,4-disubstituted cis-benzene dihydrodiols formed by CDO was higher than that of the products formed by two toluene dioxygenases. Naphthalene was oxidized to enantiomerically pure (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene. All absolute configurations were identical to those of the products formed by toluene dioxygenases of Pseudomonas putida UV4 and P. putida F39/D. The formation rate of (+)-cis-(1R,2S)-dihydroxy-1,2-dihydronaphthalene was significantly higher (about 45 to 200%) than those of several monosubstituted cis-benzene dihydrodiols and more than four times higher than the formation rate of cis-benzene dihydrodiol. A new gas chromatographic method was developed to determine the enantiomeric excess of the oxidation products.

  8. Functional diversity of bacterial genes associated with aromatic hydrocarbon degradation in anthropogenic dark earth of Amazonia

    Directory of Open Access Journals (Sweden)

    Mariana Gomes Germano

    2012-05-01

    Full Text Available The objective of this work was to evaluate the catabolic gene diversity for the bacterial degradation of aromatic hydrocarbons in anthropogenic dark earth of Amazonia (ADE and their biochar (BC. Functional diversity analyses in ADE soils can provide information on how adaptive microorganisms may influence the fertility of soils and what is their involvement in biogeochemical cycles. For this, clone libraries containing the gene encoding for the alpha subunit of aromatic ring-hydroxylating dioxygenases (α-ARHD bacterial gene were constructed, totaling 800 clones. These libraries were prepared from samples of an ADE soil under two different land uses, located at the Caldeirão Experimental Station - secondary forest (SF and agriculture (AG -, and the biochar (SF_BC and AG_BC, respectively. Heterogeneity estimates indicated greater diversity in BC libraries; and Venn diagrams showed more unique operational protein clusters (OPC in the SF_BC library than the ADE soil, which indicates that specific metabolic processes may occur in biochar. Phylogenetic analysis showed unidentified dioxygenases in ADE soils. Libraries containing functional gene encoding for the alpha subunit of the aromatic ring-hydroxylating dioxygenases (ARHD gene from biochar show higher diversity indices than those of ADE under secondary forest and agriculture.

  9. Elucidation of fluoranthene degradative characteristics in a newly isolated Achromobacter xylosoxidans DN002.

    Science.gov (United States)

    Ma, Yan-Ling; Lu, Wei; Wan, Li-Li; Luo, Na

    2015-02-01

    Strain DN002 isolated from petroleum-contaminated soil was identified as Achromobacter xylosoxidans based on morphological and biochemical properties and 16S rRNA phylogeny, and investigated for its potential to utilize numerous polycyclic aromatic hydrocarbons (PAHs) such as fluoranthene and pyrene as sole carbon and energy resource. Biodegradation studies showed that 500 mg(·)l(-1)fluranthene was degraded to 35.6 ± 0.3 mg(·)l(-1) by DN002 after 14 days incubation. During fluoranthene biodegradation, catechol 2,3 dioxygenase (C23O) activity was augmented 1.5 times more than catechol 1,2 dioxygenase (C12O), which indicated that C23O played a major role in fluoranthene degradation by DN002. Protein profiles were examined by sodium dodecyl sulfate polyacrylamide gel electrophoresis and two-dimensional electrophoresis then analyzed by mass spectrometry induced by fluoranthene; a molecular mass range of 18 ∼ 66 kDa proteins were found upregulated compared with the uninduced control sample, including multiple isoenzymes of β-oxidation and dehydrogenases as well as dioxygenases. Besides, some new proteins, i.e., dihydrolipoamide succinyltransferase and aldehyde dehydrogenase family proteins and isocitrate lyase were also synthesized.

  10. Application of real-time PCR, DGGE fingerprinting, and culture-based method to evaluate the effectiveness of intrinsic bioremediation on the control of petroleum-hydrocarbon plume.

    Science.gov (United States)

    Kao, Chih-Ming; Chen, Colin S; Tsa, Fu-Yu; Yang, Kai-Hsing; Chien, Chih-Ching; Liang, Shih-Hsiung; Yang, Chin-an; Chen, Ssu Ching

    2010-06-15

    Real-time polymerase chain reaction (PCR), denaturing gradient gel electrophoresis (DGGE), and the culture-based method were applied in the intrinsic bioremediation study at a petroleum-hydrocarbon contaminated site. The genes of phenol hydroxylase (PHE), ring-hydroxylating toluene monooxygenase (RMO), naphthalene dioxygenase (NAH), toluene monooxygenase (TOL), toluene dioxygenase (TOD), and biphenyl dioxygenase (BPH4) were quantified by real-time PCR. Results show that PHE gene was detected in groundwater contaminated with benzene, toluene, ethylbenzene, xylene isomers (BTEX) and methyl tert-butyl ether (MTBE), and this indicates that intrinsic bioremediation occurred at this contaminated site. Results from DGGE analyses reveal that the petroleum-hydrocarbon plume caused the variation in microbial communities. In this study, MTBE degraders including Pseudomonas sp. NKNU01, Bacillus sp. NKNU01, Klebsiella sp. NKNU01, Enterobacter sp. NKNU01, and Enterobacter sp. NKNU02 were isolated from the contaminated groundwater using the cultured-based method. Results from MTBE biodegradation experiment show that the isolated bacteria were affected by propane. This indicates that propane may influence the metabolic pathway of MTBE by these bacteria. Knowledge and comprehension obtained from this study will be helpful in evaluating the occurrence and effectiveness of intrinsic bioremediation on the remediation of petroleum-hydrocarbon contaminated groundwater.

  11. Microbial community structure and biodegradation activity of particle-associated bacteria in a coal tar contaminated creek.

    Science.gov (United States)

    Debruyn, Jennifer M; Sayler, Gary S

    2009-05-01

    The Chattanooga Creek Superfund site (Chattanooga, TN) is one of the most polluted waterways in the southeastern U.S. with high polycyclic aromatic hydrocarbon (PAH) concentrations in the sediments. PAHs associate with suspended solids in the water column, and may be redeposited onto the floodplain. These suspended particles represent an interesting but understudied environment for PAH-degrading microbial communities. This study tested the hypotheses that particle-associated bacterial (PAB) communities have genotypic potential (PAH-dioxygenase genes) and activity (naphthalene and pyrene mineralization), and can contribute to natural attenuation of PAHs in Chattanooga Creek. Upstream of the Superfund site, mineralization ranged from 0.2 to 2.0% of added 14C-naphthalene and 0 to 0.1% 14C-pyrene (after 40 h), with first order biodegradation rate constants (k1) ranging from 1.09 to 9.18 x 10(-5) h(-1) and 0 to 1.13 x 10(-6) h(-1), respectively. Mineralization was significantly greater in PAB communities within the contaminated zone, with 11.8 to 31.2% 14C-naphthalene (k1 5.34 to 14.2 x 10(-4) h(-1)) and 1.3 to 6.6% 14C-pyrene mineralized (k1 2.89 to 15.0 x 10(-5) h(-1)). Abundances of nagAc (naphthalene dioxygenase) and nidA (pyrene dioxygenase) genes indicated that PAB communities harbored populations with genetic potential for both low- and high-molecularweight PAH degradation, and quantification of Mycobacterium 16S rDNA genes indicated that PAH-degrading mycobacteria are also prevalent in this environment. Phylogenetic comparisons (T-RFLPs) between PAB and sediments indicated these microbial communities were taxonomically distinct, but shared some functional similarities, namely PAH catabolic genotypes, mineralization capabilities, and community structuring along a contamination gradient

  12. Simultaneous biodegradation of nitrogen-containing aromatic compounds in a sequencing batch bioreactor

    Institute of Scientific and Technical Information of China (English)

    LIU Xing-yu; WANG Bao-jun; JIANG Cheng-ying; ZHAO Ke-xin; Harold L.Drake; LIU Shuang-Jiang

    2007-01-01

    Many nitrogen-containing aromatic compounds (NACs), such as nitrobenzene (NB), 4-nitrophenol (4-NP), aniline (AN), and 2,4-dinitrophenol (2,4-DNP), are environmentally hazardous, and their removal from contaminated water is one of the main challenges facing wastewater treatment plants. In this study, synthetic wastewater containing NB, 4-NP, 2,4-DNP, and AN at concentrations ranging from 50 to 180 mg/L was fed into a sequencing batch reactor (SBR). Analyses of the SBR system indicated that it simultaneously removed more than 99% of the NACs at loading rates of 0.36 kg NB/(m3·d), 0.3 kg 4-NP/(m3·d), 0.25 kg AN/(m3·d), and 0.1 kg 2,4-DNP/(m3·d). Bacterial groups of Bacteriodetes, Candidate division TM7, α-Proteobacteria, and β-Proteobacteria were dominant in the clone libraries of 16S rRNA genes retrieved from the microbial communities in the SBR system. "Cycle tests" designed to alter feeding and aeration parameters of the SBR system demonstrated that the resident microbial biome of the SBR system responded rapidly to changing conditions. Consumption of O2 was concomitant with the apparent mineralization of NACs. Aromatic ring-cleaving dioxygenase activities suggested that (1) AN and NB were degraded via catechol 2,3-dioxygenase; (2) 4-NP was degraded via 1,2,4-benzentriol 1,2-dioxygenase; and (3) 2,4-DNP was degraded via an unresolved pathway.

  13. Abundance and diversity of functional genes involved in the degradation of aromatic hydrocarbons in Antarctic soils and sediments around Syowa Station.

    Science.gov (United States)

    Muangchinda, C; Chavanich, S; Viyakarn, V; Watanabe, K; Imura, S; Vangnai, A S; Pinyakong, O

    2015-03-01

    Hydrocarbon catabolic genes were investigated in soils and sediments in nine different locations around Syowa Station, Antarctica, using conventional PCR, real-time PCR, cloning, and sequencing analysis. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase (PAH-RHD)-coding genes from both Gram-positive and Gram-negative bacteria were observed. Clone libraries of Gram-positive RHD genes were related to (i) nidA3 of Mycobacterium sp. py146, (ii) pdoA of Terrabacter sp. HH4, (iii) nidA of Diaphorobacter sp. KOTLB, and (iv) pdoA2 of Mycobacterium sp. CH-2, with 95-99% similarity. Clone libraries of Gram-negative RHD genes were related to the following: (i) naphthalene dioxygenase of Burkholderia glathei, (ii) phnAc of Burkholderia sartisoli, and (iii) RHD alpha subunit of uncultured bacterium, with 41-46% similarity. Interestingly, the diversity of the Gram-positive RHD genes found around this area was higher than those of the Gram-negative RHD genes. Real-time PCR showed different abundance of dioxygenase genes between locations. Moreover, the PCR-denaturing gradient gel electrophoresis (DGGE) profile demonstrated diverse bacterial populations, according to their location. Forty dominant fragments in the DGGE profiles were excised and sequenced. All of the sequences belonged to ten bacterial phyla: Proteobacteria, Actinobacteria, Verrucomicrobia, Bacteroidetes, Firmicutes, Chloroflexi, Gemmatimonadetes, Cyanobacteria, Chlorobium, and Acidobacteria. In addition, the bacterial genus Sphingomonas, which has been suggested to be one of the major PAH degraders in the environment, was observed in some locations. The results demonstrated that indigenous bacteria have the potential ability to degrade PAHs and provided information to support the conclusion that bioremediation processes can occur in the Antarctic soils and sediments studied here.

  14. OxDBase: a database of oxygenases involved in biodegradation

    Directory of Open Access Journals (Sweden)

    Raghava Gajendra PS

    2009-04-01

    Full Text Available Abstract Background Oxygenases belong to the oxidoreductive group of enzymes (E.C. Class 1, which oxidize the substrates by transferring oxygen from molecular oxygen (O2 and utilize FAD/NADH/NADPH as the co-substrate. Oxygenases can further be grouped into two categories i.e. monooxygenases and dioxygenases on the basis of number of oxygen atoms used for oxidation. They play a key role in the metabolism of organic compounds by increasing their reactivity or water solubility or bringing about cleavage of the aromatic ring. Findings We compiled a database of biodegradative oxygenases (OxDBase which provides a compilation of the oxygenase data as sourced from primary literature in the form of web accessible database. There are two separate search engines for searching into the database i.e. mono and dioxygenases database respectively. Each enzyme entry contains its common name and synonym, reaction in which enzyme is involved, family and subfamily, structure and gene link and literature citation. The entries are also linked to several external database including BRENDA, KEGG, ENZYME and UM-BBD providing wide background information. At present the database contains information of over 235 oxygenases including both dioxygenases and monooxygenases. This database is freely available online at http://www.imtech.res.in/raghava/oxdbase/. Conclusion OxDBase is the first database that is dedicated only to oxygenases and provides comprehensive information about them. Due to the importance of the oxygenases in chemical synthesis of drug intermediates and oxidation of xenobiotic compounds, OxDBase database would be very useful tool in the field of synthetic chemistry as well as bioremediation.

  15. Bacterial community dynamics during in-situ bioremediation of petroleum waste sludge in landfarming sites.

    Science.gov (United States)

    Katsivela, E; Moore, E R B; Maroukli, D; Strömpl, C; Pieper, D; Kalogerakis, N

    2005-03-01

    In-situ bioremediation of petroleum waste sludge in landfarming sites of Motor Oil Hellas (petroleum refinery) was studied by monitoring the changes of the petroleum composition of the waste sludge, as well as the changes in the structure of the microbial community, for a time period of 14 months. The analyses indicated an enhanced degradation of the petroleum hydrocarbons in the landfarming areas. A depletion of n-alkanes of approximately 75-100% was obtained. Marked changes of the microbial communities of the landfarms occurred concomitantly with the degradation of the petroleum hydrocarbons. The results obtained from terminal restriction fragment length polymorphism (T-RFLP) analysis of polymerase chain reaction (PCR) amplified 16S rRNA genes demonstrated that bacteria originating from the refinery waste sludge and newly selected bacteria dominated the soil bacterial community during the period of the highest degradation activity. However, the diversity of the microbial community was decreased with increased degradation of the petroleum hydrocarbons contained in the landfarms. T-RFLP fingerprints of bacteria of the genera Enterobacter and Ochrobactrum were detected in the landfarmed soil over the entire treatment period of 14 months. In contrast, the genus Alcaligenes appeared in significant numbers only within the 10 month old landfarmed soil. Genes encoding catechol 2,3-dioxygenase (subfamily I.2.A) were detected only in DNA of the untreated refinery waste sludge. However, none of the genes known to encode the enzymes alkane hydroxylase AlkB, catechol 2,3-dioxygenase (subfamily I.2.A) and naphthalene dioxygenase nahAc could be detected in DNA of the landfarmed soils.

  16. Involvement of the kynurenine pathway in human glioma pathophysiology.

    Directory of Open Access Journals (Sweden)

    Seray Adams

    Full Text Available The kynurenine pathway (KP is the principal route of L-tryptophan (TRP catabolism leading to the production of kynurenine (KYN, the neuroprotectants, kynurenic acid (KYNA and picolinic acid (PIC, the excitotoxin, quinolinic acid (QUIN and the essential pyridine nucleotide, nicotinamide adenine dinucleotide (NAD(+. The enzymes indoleamine 2,3-dioxygenase-1 (IDO-1, indoleamine 2,3-dioxygenase-2 (IDO-2 and tryptophan 2,3-dioxygenase (TDO-2 initiate the first step of the KP. IDO-1 and TDO-2 induction in tumors are crucial mechanisms implicated to play pivotal roles in suppressing anti-tumor immunity. Here, we report the first comprehensive characterisation of the KP in 1 cultured human glioma cells and 2 plasma from patients with glioblastoma (GBM. Our data revealed that interferon-gamma (IFN-γ stimulation significantly potentiated the expression of the KP enzymes, IDO-1 IDO-2, kynureninase (KYNU, kynurenine hydroxylase (KMO and significantly down-regulated 2-amino-3-carboxymuconate semialdehyde decarboxylase (ACMSD and kynurenine aminotransferase-I (KAT-I expression in cultured human glioma cells. This significantly increased KP activity but significantly lowered the KYNA/KYN neuroprotective ratio in human cultured glioma cells. KP activation (KYN/TRP was significantly higher, whereas the concentrations of the neuroreactive KP metabolites TRP, KYNA, QUIN and PIC and the KYNA/KYN ratio were significantly lower in GBM patient plasma (n = 18 compared to controls. These results provide further evidence for the involvement of the KP in glioma pathophysiology and highlight a potential role of KP products as novel and highly attractive therapeutic targets to evaluate for the treatment of brain tumors, aimed at restoring anti-tumor immunity and reducing the capacity for malignant cells to produce NAD(+, which is necessary for energy production and DNA repair.

  17. Assay Methods for H2S Biogenesis and Catabolism Enzymes

    Science.gov (United States)

    Banerjee, Ruma; Chiku, Taurai; Kabil, Omer; Libiad, Marouane; Motl, Nicole; Yadav, Pramod K.

    2015-01-01

    H2S is produced from sulfur-containing amino acids, cysteine and homocysteine, or a catabolite, 3-mercaptopyruvate, by three known enzymes: cystathionine β-synthase, γ-cystathionase, and 3-mercaptopyruvate sulfurtransferase. Of these, the first two enzymes reside in the cytoplasm and comprise the transsulfuration pathway, while the third enzyme is found both in the cytoplasm and in the mitochondrion. The following mitochondrial enzymes oxidize H2S: sulfide quinone oxidoreductase, sulfur dioxygenase, rhodanese, and sulfite oxidase. The products of the sulfide oxidation pathway are thiosulfate and sulfate. Assays for enzymes involved in the production and oxidative clearance of sulfide to thiosulfate are described in this chapter. PMID:25725523

  18. Oxygen-dependent catabolism of indole-3-acetic acid in Bradyrhizobium japonicum

    DEFF Research Database (Denmark)

    Egebo, L A; Nielsen, S V; Jochimsen, B U

    1991-01-01

    addition of the substrates for induction and is oxygen dependent. The highest activity is obtained when the concentration of inducer is 0.2 mM. Spectrophotometric data are consistent with the suggestion that the indole ring is broken during degradation of IAA. We hypothesize that the enzyme catalyzes...... an oxygen-consuming opening of the indole ring analogous to the one catalyzed by tryptophan 2,3-dioxygenase. The pattern of metabolite usage by known tryptophan-auxotrophic mutants and studies of metabolites by high-performance liquid chromatography indicate that anthranilic acid is a terminal degradation...

  19. Natural polyamines inhibit soybean (Glycine max) lipoxygenase-1, but not the lipoxygenase-2 isozyme.

    Science.gov (United States)

    Maccarrone, M; Baroni, A; Finazzi-Agrò, A

    1998-08-01

    Natural polyamines are shown to inhibit dioxygenase activity of soybean lipoxygenase-1, but they were ineffective toward the lipoxygenase-2 isozyme. The inhibitory power was dependent on the number of basic groups in the molecule, in the order spermine > spermidine > cadaverine >/= putrescine. Both spermidine and spermine acted as uncompetitive inhibitors of lipoxygenase-1 with respect to linoleic acid, the inhibition constants being 2.70 and 0.80 mM, respectively. The inhibitory power apparently correlated with the radical-trapping ability of the polyamines. Spermidine and spermine also inhibited the co-oxidase and peroxidase activities of lipoxygenase-1 and were effective inhibitors of lipoxygenase activity in lentil root protoplasts.

  20. Oxidation of indole-3-acetic acid to oxindole-3-acetic acid by an enzyme preparation from Zea mays

    Science.gov (United States)

    Reinecke, D. M.; Bandurski, R. S.

    1988-01-01

    Indole-3-acetic acid is oxidized to oxindole-3-acetic acid by Zea mays tissue extracts. Shoot, root, and endosperm tissues have enzyme activities of 1 to 10 picomoles per hour per milligram protein. The enzyme is heat labile, is soluble, and requires oxygen for activity. Cofactors of mixed function oxygenase, peroxidase, and intermolecular dioxygenase are not stimulatory to enzymic activity. A heat-stable, detergent-extractable component from corn enhances enzyme activity 6- to 10-fold. This is the first demonstration of the in vitro enzymic oxidation of indole-3-acetic acid to oxindole-3-acetic acid in higher plants.

  1. Main: 1FGR [RPSD[Archive

    Lifescience Database Archive (English)

    Full Text Available 1FGR 大豆 Soybean Glycine max (L.) Merrill Seed Lipoxygenase-1 Name=Lox1.1; Synonyms=Lox1; Glycin...e Max Molecule: Seed Lipoxygenase-1; Chain: A; Synonym: L-1; Engineered: Yes; Mutation: Yes Oxid...oreductase 1.13.11.12 (Seed Lipoxygenase-1) D.R.Tomchick, W.Minor, T.Holman D.R.Tomchick, P.Phan, C.Cymborowski, W.Min...or, T.R.Holman Structural And Functional Characterization Of Second-Coordin...ation Sphere Mutants Of Soybean Lipoxygenase-1 Biochemistry V. 40 7509 2001 Dioxygenase, Lipoxygenase, Metalloprotein

  2. In Silico/In Vivo Insights into the Functional and Evolutionary Pathway of Pseudomonas aeruginosa Oleate-Diol Synthase. Discovery of a New Bacterial Di-Heme Cytochrome C Peroxidase Subfamily

    OpenAIRE

    Mónica Estupiñán; Daniel Álvarez-García; Xavier Barril; Pilar Diaz; Angeles Manresa

    2015-01-01

    As previously reported, P. aeruginosa genes PA2077 and PA2078 code for 10S-DOX (10S-Dioxygenase) and 7,10-DS (7,10-Diol Synthase) enzymes involved in long-chain fatty acid oxygenation through the recently described oleate-diol synthase pathway. Analysis of the amino acid sequence of both enzymes revealed the presence of two heme-binding motifs (CXXCH) on each protein. Phylogenetic analysis showed the relation of both proteins to bacterial di-heme cytochrome c peroxidases (Ccps), similar to Xa...

  3. Function and Regulation of Vibrio campbellii Proteorhodopsin: Acquired Phototrophy in a Classical Organoheterotroph

    Science.gov (United States)

    2012-06-01

    synthase (CrtE), phytoene desaturase (CrtI), phytoene synthase (CrtB), lycopene cyclase (CrtY) and 15,159-ß-carotene dioxygenase (Blh) necessary for ß...16109 cells were resuspended in 1 ml PBS and stored in the dark at room temperature for 90 min. Both sets of cells were then illuminated for 10 min...Systems, Mentor, OH, USA) and resuspended to 16102 cells/ml in a final volume of 50 ml of room temperature ASW or ASW + 300 mM sodium azide. Cell

  4. RNA Regulation by Estrogen

    Science.gov (United States)

    2011-08-01

    protein P22 9.19 215578_at GPHN gephyrin 9.19 214932_at KIDINS220 kinase D-interacting substrate, 220kDa 9.19 205719_s_at pah phenylalanine hydroxylase ...oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase ) 1 10.56 211555_s_at gucy1b3 guanylate cyclase 1, soluble, beta 3 10.56 207267_s_at DSCR6 Down...benzimidazoles 1 homolog (yeast) 4.92 206932_at CH25H cholesterol 25- hydroxylase 4.92 217515_s_at CACNA1S calcium channel, voltage-dependent, L type

  5. RNA Regulation of Estrogen

    Science.gov (United States)

    2010-08-01

    kinase D-interacting substrate, 220kDa 9.19 205719_s_at pah phenylalanine hydroxylase 9.19 211906_s_at serpinb4 serpin peptidase inhibitor, clade B...polyphosphate-5-phosphatase, 145kDa 10.56 205363_at BBOX1 butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase ) 1 10.56...25- hydroxylase 4.92 217515_s_at CACNA1S calcium channel, voltage-dependent, L type, alpha 1S subunit 4.92 14 Appendix 1; Table 1 212524_x_at H2afx H2A

  6. Biotechnical approach to studies on the biodegradation of chlorobenzenes and trichloroethylene. Final report, 1 September 1988-31 May 1992

    Energy Technology Data Exchange (ETDEWEB)

    Gibson, D.T.

    1992-10-01

    The absolute stereochemistry of the chiral dihydrodiols formed from ortho- and meta-dichlorobenzene were determined. Both diols were found to be enantiomerically pure with 1S,2S absolute configuration. Toluene-grown cells of Pseudomonas putida F1 and Pseudomonas sp. JS150 were found to oxidize 2- and 3-nitrotoluene to benzyl alcohols. These results represent the first demonstration of the oxidation of a methyl substituent by toluene dioxygenase. Both organisms oxidized 4-nitrotoluene to 2-methyl-5-nitrophenol and 3-methyl-6-nitrocatechol. The significance of these unexpected results was evaluated.

  7. Tyrosinemia Type III detected via neonatal screening: management and outcome.

    Science.gov (United States)

    Heylen, Evelyne; Scherer, Gerd; Vincent, Marie-Françoise; Marie, Sandrine; Fischer, Judith; Nassogne, Marie-Cécile

    2012-11-01

    Tyrosinemia Type III is caused by the deficiency of 4-hydroxyphenylpyruvate dioxygenase (4-HPPD), an enzyme involved in the catabolic pathway of tyrosine. To our knowledge, only a few patients presenting with this disease have been described in the literature, and the clinical phenotype remains variable and unclear. We report the case of a boy with tyrosinemia Type III detected using neonatal screening, who is homozygous for the splice donor mutation IVS11+1G>A in intron 11 of the HPD gene. At the age of 30 months, the boy's outcome under mild protein restriction was characterized by normal growth and psychomotor development.

  8. A Comprehensive Review of Aliphatic Hydrocarbon Biodegradation by Bacteria.

    Science.gov (United States)

    Abbasian, Firouz; Lockington, Robin; Mallavarapu, Megharaj; Naidu, Ravi

    2015-06-01

    Hydrocarbons are relatively recalcitrant compounds and are classified as high-priority pollutants. However, these compounds are slowly degraded by a large variety of microorganisms. Bacteria are able to degrade aliphatic saturated and unsaturated hydrocarbons via both aerobic and anaerobic pathways. Branched hydrocarbons and cyclic hydrocarbons are also degraded by bacteria. The aerobic bacteria use different types of oxygenases, including monooxygenase, cytochrome-dependent oxygenase and dioxygenase, to insert one or two atoms of oxygen into their targets. Anaerobic bacteria, on the other hand, employ a variety of simple organic and inorganic molecules, including sulphate, nitrate, carbonate and metals, for hydrocarbon oxidation.

  9. Immobilized Native Bacteria as a Tool for Bioremediation of Soils and Waters: Implementation and Modeling

    Directory of Open Access Journals (Sweden)

    C. Lobo

    2002-01-01

    Full Text Available Based on 3,4-dihydroxyphenylacetate (3,4-DHPA dioxygenase amino acid sequence and DNA sequence data for homologous genes, two different oligonucleotides were designed. These were assayed to detect 3,4-DHPA related aromatic compound—degrading bacteria in soil samples by using the FISH method. Also, amplification by PCR using a set of ERIC primers was assayed for the detection of Pseudomonas GCH1 strain, which used in the soil bioremediation process. A model was developed to understand and predict the behavior of bacteria and pollutants in a bioremediation system, taking into account fluid dynamics, molecular/cellular scale processes, and biofilm formation.

  10. Disease: H00165 [KEGG MEDICUS

    Lifescience Database Archive (English)

    Full Text Available osition of tyrosine crystals within the cornea. Type III is a rare disorder cause...ardation. Inherited metabolic disease; Nervous system disease hsa00350(2184+6898+3242+C00082) Tyrosine metab...II) HPD; 4-hydroxyphenylpyruvate dioxygenase [HSA:3242] [KO:K00457] (Type I) Increased fumarylacetoacetic ac...id [CPD:C01061] and succinylacetone (Type II) Increased tyrosine [CPD:C00082] (Type III) Increased 4-hydroxy...emin Med Genet 142C:121-6 (2006) PMID:15531838 Karnik D, Thomas N, Eapen CE, Jana AK, Oommen A Tyrosinemia type I: a clinico-laboratory case report. Indian J Pediatr 71:929-32 (2004) ...

  11. EL ENZIMA INDOLEAMINA 2,3 DIOXIGENASA (IDO Y LA TOLERANCIA INMUNE

    Directory of Open Access Journals (Sweden)

    Coma-del-Corral MJ

    2013-09-01

    Full Text Available Indoleamine 2,3-dioxygenase (IDO is an intracellular and extrahepatic enzyme predominantly found in many cells, especially macrophages. Tryptophan degradation generates kynurenine, and this pathway of tryptophan metabolism is an effective mechanism for modulating the immune response. The IDO facilitates immune tolerance and is one of the main actors involved in the inhibition of cell proliferation, including activated T cells. IDO induces production of reactive oxygen species (ROS and nitric oxide (NO radicals. Several pathways involved in the regulation of immune response are regulated by redox mechanisms. Reactive oxygen and nitrogen species (ROS-RNS and other redox active molecules play key roles in immunity.

  12. 1-MT Enhances Potency of Tumor Cell Lysate-pulsed Dendritic Cells against Pancreatic Adenocarcinoma by Downregulating the Percentage of Tregs

    Institute of Scientific and Technical Information of China (English)

    李元栋; 徐钧; 邹浩军; 王春友

    2010-01-01

    This study examined whether 1-methyl-tryptophan [1-MT,an indoleamine 2,3-dioxygenase(IDO) inhibitor] could reduce CD4+CD25+ regulatory T cells(Tregs) proliferation and improve the anti-tumor efficacy of dendritic cells(DCs) pulsed with tumor cell lysate in the mice bearing pancreatic adenocarcinoma.The models of pancreatic adenocarcinoma were established in C57BL/6 mice by subcutaneous injection of Pan02 cells.Eight mice which were subcutaneously injected with PBS served as control.The expression of IDO was...

  13. Biodegradation of polycyclic aromatic hydrocarbons by Novosphingobium pentaromativorans US6-1.

    Directory of Open Access Journals (Sweden)

    Yihua Lyu

    Full Text Available Novosphingobium pentaromativorans US6-1, a marine bacterium isolated from muddy sediments of Ulsan Bay, Republic of Korea, was previously shown to be capable of degrading multiple polycyclic aromatic hydrocarbons (PAHs. In order to gain insight into the characteristics of PAHs degradation, a proteome analysis of N. pentaromativorans US6-1 exposed to phenanthrene, pyrene, and benzo[a]pyrene was conducted. Several enzymes associated with PAHs degradation were identified, including 4-hydroxybenzoate 3-monooxygenase, salicylaldehyde dehydrogenase, and PAH ring-hydroxylating dioxygenase alpha subunit. Reverse transcription and real-time quantitative PCR was used to compare RHDα and 4-hydroxybenzoate 3-monooxygenase gene expression, and showed that the genes involved in the production of these two enzymes were upregulated to varying degrees after exposing the bacterium to PAHs. These results suggested that N. pentaromativorans US6-1 degraded PAHs via the metabolic route initiated by ring-hydroxylating dioxygenase, and further degradation occurred via the o-phthalate pathway or salicylate pathway. Both pathways subsequently entered the tricarboxylic acid (TCA cycle, and were mineralized to CO2.

  14. Biodegradation of polycyclic aromatic hydrocarbons by Novosphingobium pentaromativorans US6-1.

    Science.gov (United States)

    Lyu, Yihua; Zheng, Wei; Zheng, Tianling; Tian, Yun

    2014-01-01

    Novosphingobium pentaromativorans US6-1, a marine bacterium isolated from muddy sediments of Ulsan Bay, Republic of Korea, was previously shown to be capable of degrading multiple polycyclic aromatic hydrocarbons (PAHs). In order to gain insight into the characteristics of PAHs degradation, a proteome analysis of N. pentaromativorans US6-1 exposed to phenanthrene, pyrene, and benzo[a]pyrene was conducted. Several enzymes associated with PAHs degradation were identified, including 4-hydroxybenzoate 3-monooxygenase, salicylaldehyde dehydrogenase, and PAH ring-hydroxylating dioxygenase alpha subunit. Reverse transcription and real-time quantitative PCR was used to compare RHDα and 4-hydroxybenzoate 3-monooxygenase gene expression, and showed that the genes involved in the production of these two enzymes were upregulated to varying degrees after exposing the bacterium to PAHs. These results suggested that N. pentaromativorans US6-1 degraded PAHs via the metabolic route initiated by ring-hydroxylating dioxygenase, and further degradation occurred via the o-phthalate pathway or salicylate pathway. Both pathways subsequently entered the tricarboxylic acid (TCA) cycle, and were mineralized to CO2.

  15. Identification of naphthalene metabolism by white rot fungus Armillaria sp.F022

    Institute of Scientific and Technical Information of China (English)

    Tony Hadibarata; Abdull Rahim Mohd Yusoff; Azmi Aris; Risky Ayu Kristanti

    2012-01-01

    Armillaria sp.F022,a white rot fungus isolated from tropical rain forest (Samarinda,Indonesia) was used to biodegrade naphthalene in cultured medium.Transformation of naphthalene by Armillaria sp.F022 which is able to use naphthalene,a two ring-polycyclic aromatic hydrocarbon (PAH) as a source of carbon and energy was investigated.The metabolic pathway was elucidated by identifying metabolites,biotransformation studies and monitoring enzyme activities in cell-free extracts.The identification of metabolites suggests that Armillaria sp.F022 initiates its attack on naphthalene by dioxygenation at its C-1 and C-4 positions to give 1,4-naphthoquinone.The intermediate 2-hydroxybenzaldehyde and salicylic acid,and the characteristic of the meta-cleavage of the resulting diol were identified in the long-term incubation.A part from typical metabolites of naphthalene degradation known from mesophiles,benzoic acid was identified as the next intermediate for the naphthalene pathway of this Armillaria sp.F022.Neither phthalic acid,catechol and cis,cis-muconic acid metabolites were detected in culture extracts.Several enzymes (manganese peroxidase,lignin peroxidase,laccase,1,2-dioxygenase and 2,3-dioxygenase) produced by Armillaria sp.F022 were detected during the incubation.

  16. Abilities and genes for PAH biodegradation of bacteria isolated from mangrove sediments from the central of Thailand.

    Science.gov (United States)

    Wongwongsee, Wanwasan; Chareanpat, Promchat; Pinyakong, Onruthai

    2013-09-15

    PAH-degrading bacteria, including Novosphingobium sp. PCY, Microbacterium sp. BPW, Ralstonia sp. BPH, Alcaligenes sp. SSK1B, and Achromobacter sp. SSK4, were isolated from mangrove sediments. These isolates degraded 50-76% of 100 mg/l phenanthrene within 2 weeks. Strains PCY and BPW also degraded pyrene at 98% and 71%, respectively. Furthermore, all of them probably produced biosurfactants in the presence of hydrocarbons. Interestingly, PCY has a versatility to degrade various PAHs. Molecular techniques and plasmid curing remarkably revealed the presence of the alpha subunit of pyrene dioxygenase gene (nidA), involving in its pyrene/phenanthrene degrading ability, located on megaplasmid of PCY which has never before been reported in sphingomonads. Moreover, genes encoding ferredoxin, reductase, extradiol dioxygenase (bphA3A4C) and exopolysaccharide biosynthetase, which may be involved in PAH degradation and biosurfactant production, were also found in PCY. Therefore, we conclude that these isolates, especially PCY, can be the candidates for use as inoculums in the bioremediation.

  17. Use of bromodeoxyuridine immunocapture to identify psychrotolerant phenanthrene-degrading bacteria in phenanthrene-enriched polluted Baltic Sea sediments

    Energy Technology Data Exchange (ETDEWEB)

    Edlund, A.; Jansson, J.

    2008-05-01

    The aim of this study was to enrich and identify psychrotolerant phenanthrenedegrading bacteria from polluted Baltic Sea sediments. Polyaromatic hydrocarbon (PAH)-contaminated sediments were spiked with phenanthrene and incubated for 2 months in the presence of bromodeoxyuridine that is incorporated into the DNA of replicating cells. The bromodeoxyuridine-incorporated DNA was extracted by immunocapture and analyzed by terminal-restriction fragment length polymorphism and 16S rRNA gene cloning and sequencing to identify bacterial populations that were growing. In addition, degradation genes were quantified in the bromodeoxyuridine-incorporated DNA by real-time PCR. Phenanthrene concentrations decreased after 2 months of incubation in the phenanthrene-enriched sediments and this reduction correlated to increases in copy numbers of xylE and phnAc dioxygenase genes. Representatives of Exiguobacterium, Schewanella,Methylomonas, Pseudomonas, Bacteroides and an uncultured Deltaproteobacterium and a Gammaproteobacterium dominated the growing community in the phenanthrene spiked sediments. Isolates that were closely related to three of these bacteria (two pseudomonads and an Exiguobacterium sp.) could reduce phenanthrene concentrations in pure cultures and they all harbored phnAc dioxygenase genes. These results confirm that this combination of culture-based and molecular approaches was useful for identification of actively growing bacterial species with a high potential for phenanthrene degradation.

  18. Effects of a block in cysteine catabolism on energy balance and fat metabolism in mice.

    Science.gov (United States)

    Niewiadomski, Julie; Zhou, James Q; Roman, Heather B; Liu, Xiaojing; Hirschberger, Lawrence L; Locasale, Jason W; Stipanuk, Martha H

    2016-01-01

    To gain further insights into the effects of elevated cysteine levels on energy metabolism and the possible mechanisms underlying these effects, we conducted studies in cysteine dioxygenase (Cdo1)-null mice. Cysteine dioxygenase (CDO) catalyzes the first step of the major pathway for cysteine catabolism. When CDO is absent, tissue and plasma cysteine levels are elevated, resulting in enhanced flux of cysteine through desulfhydration reactions. When Cdo1-null mice were fed a high-fat diet, they gained more weight than their wild-type controls, regardless of whether the diet was supplemented with taurine. Cdo1-null mice had markedly lower leptin levels, higher feed intakes, and markedly higher abundance of hepatic stearoyl-CoA desaturase 1 (SCD1) compared to wild-type control mice, and these differences were not affected by the fat or taurine content of the diet. Thus, reported associations of elevated cysteine levels with greater weight gain and with elevated hepatic Scd1 expression are also seen in the Cdo1-null mouse model. Hepatic accumulation of acylcarnitines suggests impaired mitochondrial β-oxidation of fatty acids in Cdo1-null mice. The strong associations of elevated cysteine levels with excess H2 S production and impairments in energy metabolism suggest that H2 S signaling could be involved.

  19. Vitamin C down-regulate apo(a) expression via Tet2-dependent DNA demethylation in HepG2 cells.

    Science.gov (United States)

    Qu, Kai; Ma, Xiao-Feng; Li, Guo-Hua; Zhang, Hai; Liu, Ya-Mi; Zhang, Kai; Zeng, Jun-Fa; Lei, Jian-Jun; Wei, Dang-Heng; Wang, Zuo

    2017-05-01

    Lipoprotein(a)[Lp(a)] is a risk factor for coronary heart diseases. However, the metabolism of this protein remains poorly understood. Efficient and specific drugs that can decrease high plasma levels of Lp(a) have not been developed yet. Vitamin C is responsible for maintaining the catalytic activity of a group of iron and 2-oxoglutarate (2OG)-dependent dioxygenases and induces the generation of 5-hydroxymethylcytosine (5hmC) via Ten-eleven translocation (Tet) dioxygenases. In addition, It has been reported vitamin C deficiency induces atherosclerosis and increases Lp(a) and apo(a) plasma levels in Lp(a)+ mice. However, the mechanism is still unclear. In this study, we investigated the effects of vitamin C on apo(a) expression and the possible molecular mechanism of vitamin C that influences apolipoprotein(a) [apo(a)] biosynthesis in HepG2 cells. Results showed that vitamin C significantly inhibited the expression and secretion levels of apo(a). Vitamin C can also increase ELK1 expression and hydroxymethylation of ELK1 promoter and the globle DNA in HepG2 cells. In addition, the effects of vitamin C inhibiting the apo(a) expression were attenuated by ELK1siRNA and Tet2siRNA. These results suggested vitamin C down-regulate apo(a) expression via Tet2-dependent DNA demethylation in HepG2 cells.

  20. The effect of cyclic anaerobic-aerobic conditions on biodegradation of azo dyes.

    Science.gov (United States)

    Yaşar, Semra; Cirik, Kevser; Cinar, Ozer

    2012-03-01

    The effect of cyclic anaerobic-aerobic conditions on the biodegradative capability of the mixed microbial culture for the azo dye Remazol Brilliant Violet 5R (RBV-5R) was investigated in the sequencing batch reactor (SBR) fed with a synthetic textile wastewater. The SBR had a 12-h cycle time with anaerobic-aerobic periods of 3/9, 6/6 and 9/3 h. General SBR performance was assessed by measurement of catabolic enzymes (catechol 2,3-dioxygenase, azo reductase), chemical oxygen demand (COD), color and amount of aromatic amines. In this study, under steady-state conditions, the anaerobic period of the cyclic SBR was found to allow the reductive decolorization of azo dye. Longer anaerobic periods resulted in higher color removal efficiencies, approximately 71% for the 3-h, 87% for 6-h and 92% for the 9-h duration. Total COD removal efficiencies were over 84% under each of the cyclic conditions and increased as the length of the anaerobic period was increased; however, the highest color removal rate was attained for the cycle with the shortest anaerobic period of 3 h. During the decolorization of RBV-5R, two sulfonated aromatic amines (benzene based and naphthalene based) were formed. Additionally, anaerobic azo reductase enzyme was found to be positively affected with the increasing duration of the anaerobic period; however; it was vice versa for the aerobic catechol 2,3-dioxygenase (C23DO) enzyme.

  1. Stringency of the 2-His-1-Asp active-site motif in prolyl 4-hydroxylase.

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    Kelly L Gorres

    Full Text Available The non-heme iron(II dioxygenase family of enzymes contain a common 2-His-1-carboxylate iron-binding motif. These enzymes catalyze a wide variety of oxidative reactions, such as the hydroxylation of aliphatic C-H bonds. Prolyl 4-hydroxylase (P4H is an alpha-ketoglutarate-dependent iron(II dioxygenase that catalyzes the post-translational hydroxylation of proline residues in protocollagen strands, stabilizing the ensuing triple helix. Human P4H residues His412, Asp414, and His483 have been identified as an iron-coordinating 2-His-1-carboxylate motif. Enzymes that catalyze oxidative halogenation do so by a mechanism similar to that of P4H. These halogenases retain the active-site histidine residues, but the carboxylate ligand is replaced with a halide ion. We replaced Asp414 of P4H with alanine (to mimic the active site of a halogenase and with glycine. These substitutions do not, however, convert P4H into a halogenase. Moreover, the hydroxylase activity of D414A P4H cannot be rescued with small molecules. In addition, rearranging the two His and one Asp residues in the active site eliminates hydroxylase activity. Our results demonstrate a high stringency for the iron-binding residues in the P4H active site. We conclude that P4H, which catalyzes an especially demanding chemical transformation, is recalcitrant to change.

  2. Recent advances in understanding resin acid biodegradation: microbial diversity and metabolism.

    Science.gov (United States)

    Martin, V J; Yu, Z; Mohn, W W

    1999-09-01

    Resin acids are tricyclic diterpenoids that are found in the oleoresin of coniferous trees. Resin-acid-degrading microorganisms are ubiquitous in the environment. The bacterial isolates that grow on resin acids as sole organic substrates are physiologically and phylogenetically diverse, and include psychrotolerant, mesophilic, and thermophilic bacteria. Recent studies of the biodegradation of resin acids by these organisms have demonstrated that in gram-negative bacteria, distinct biochemical pathways exist for the degradation of abietane- and pimerane-type resin acids. One of these organisms, Pseudomonas abietaniphila BKME-9, harbors a convergent pathway that channels the nonaromatic abietanes and dehydroabietic acid into 7-oxodehydroabietic acid. This dioxygenolytic pathway is encoded by the recently cloned and sequenced dit gene cluster. The dit cluster encodes the ferredoxin and the alpha- and beta-subunits of a new class of ring-hydroxylating dioxygenases as well as an extradiol ring-cleavage dioxygenase. Although it was previously thought that resin acids are very recalcitrant under anoxic conditions, recent investigations have demonstrated that they are partially metabolized under anoxic conditions by undefined microorganisms. The anaerobic degradation of resin acids principally generates aromatized and decarboxylated products (such as retene) that are thought to persist in the environment.

  3. Biochemical, transcriptional and translational evidences of the phenol-meta-degradation pathway by the hyperthermophilic Sulfolobus solfataricus 98/2.

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    Alexia Comte

    Full Text Available Phenol is a widespread pollutant and a model molecule to study the biodegradation of monoaromatic compounds. After a first oxidation step leading to catechol in mesophilic and thermophilic microorganisms, two main routes have been identified depending on the cleavage of the aromatic ring: ortho involving a catechol 1,2 dioxygenase (C12D and meta involving a catechol 2,3 dioxygenase (C23D. Our work aimed at elucidating the phenol-degradation pathway in the hyperthermophilic archaea Sulfolobus solfataricus 98/2. For this purpose, the strain was cultivated in a fermentor under different substrate and oxygenation conditions. Indeed, reducing dissolved-oxygen concentration allowed slowing down phenol catabolism (specific growth and phenol-consumption rates dropped 55% and 39%, respectively and thus, evidencing intermediate accumulations in the broth. HPLC/Diode Array Detector and LC-MS analyses on culture samples at low dissolved-oxygen concentration (DOC  =  0.06 mg x L(-1 suggested, apart for catechol, the presence of 2-hydroxymuconic acid, 4-oxalocrotonate and 4-hydroxy-2-oxovalerate, three intermediates of the meta route. RT-PCR analysis on oxygenase-coding genes of S. solfataricus 98/2 showed that the gene coding for the C23D was expressed only on phenol. In 2D-DIGE/MALDI-TOF analysis, the C23D was found and identified only on phenol. This set of results allowed us concluding that S. solfataricus 98/2 degrade phenol through the meta route.

  4. Evaluating the biodegradation of aromatic hydrocarbons by monitoring of several functional genes.

    Science.gov (United States)

    Piskonen, Reetta; Nyyssönen, Mari; Itävaara, Merja

    2008-11-01

    Various microbial activities determine the effectiveness of bioremediation processes. In this work, we evaluated the feasibility of gene array hybridization for monitoring the efficiency of biodegradation processes. Biodegradation of 14C-labelled naphthalene and toluene by the aromatic hydrocarbon-degrading Pseudomonas putida F1, P. putida mt-2 and P. putida G7 was followed in mixed liquid culture microcosm by a preliminary, nylon membrane-based gene array. In the beginning of the study, toluene was degraded rapidly and increased amount of toluene degradation genes was detected by the preliminary gene array developed for the study. After toluene was degraded, naphthalene mineralization started and the amount of naphthalene degradation genes increased as biodegradation proceeded. The amount of toluene degradation genes decreased towards the end of the study. The hybridization signal intensities determined by preliminary gene array were in good agreement with mineralization of naphthalene and toluene and with the amount of naphthalene dioxygenase and toluene dioxygenase genes quantified by dot blot hybridization. The clear correlation between the results obtained by the preliminary array and the biodegradation process suggests that gene array methods can be considered as a promising tool for monitoring the efficiency of biodegradation processes.

  5. Overlaps between the various biodegradation pathways in Sphingomonas subarctica SA1.

    Science.gov (United States)

    Magony, Mónika; Kákonyi, Ildikó; Gara, Anna; Rapali, P; Perei, Katalin; Kovács, K L; Rákhely, G

    2007-01-01

    A bacterium capable to grow on sulfanilic acid as sole carbon, nitrogen and sulfur source has been isolated. A unique feature of this strain is that it contains the full set of enzymes necessary for the biodegradation of sulfanilic acid. Taxonomical analysis identified our isolate as Sphingomonas subaretica SA1 sp. The biodegradation pathway of sulfanilic acid was investigated at the molecular level. Screening the substrate specificity of the strain disclosed its capacity to degrade six analogous aromatic compounds including p-aminobenzoic acid. Moreover, the strain was successfully used for removal of oil contaminations. S. subarctica SA1 seemed to use distinct enzyme cascades for decomposition of these molecules, since alternative enzymes were induced in cells grown on various substrates. However, the protein patterns appearing upon induction by sulfanilic acid and sulfocatechol were very similar to each other indicating common pathways for the degradation of these substrates. Cells grown on sulfanilic acid could convert p-aminobenzoic acid to some extent and vice versa. Two types of ring cleaving dioxygenases were detected in the cells grown on various substrates: one preferred protocatechol, while the other had higher activity with sulfocatechol. This latter enzyme, named as sulfocatechol dioxygenase was partially purified and characterized.

  6. Biochemical and molecular mechanisms involved in simultaneous phenol and Cr(VI) removal by Acinetobacter guillouiae SFC 500-1A.

    Science.gov (United States)

    Ontañon, Ornella M; González, Paola S; Agostini, Elizabeth

    2015-09-01

    Bioremediation has emerged as an environmental friendly strategy to deal with environmental pollution. Since the majority of polluted sites contain complex mixtures of inorganic and organic pollutants, it is important to find bacterial strains that can cope with multiple contaminants. In this work, a bacterial strain isolated from tannery sediments was identified as Acinetobacter guillouiae SFC 500-1A. This strain was able to simultaneously remove high phenol and Cr(VI) concentrations, and the mechanisms involved in such process were evaluated. The phenol biodegradation was catalized by a phenol-induced catechol 1,2-dioxygenase through an ortho-cleavage pathway. Also, NADH-dependent chromate reductase activity was measured in the cytosolic fraction. The ability of this strain to reduce Cr(VI) to Cr(III) was corroborated by detection of Cr(III) in cellular biomass after the removal process. While phenol did not affect significantly the chromate reductase activity, Cr(VI) was a major disruptor of catechol dioxygenase activity. Nevertheless, this activity was high even in presence of high Cr(VI) concentrations. Our results suggest the potential application of A. guillouiae SFC 500-1A for wastewaters treatment, and the obtained data provide the insights into the removal mechanisms, dynamics, and possible limitations of the bioremediation.

  7. Exploring the Nitric Oxide Detoxification Mechanism of Mycobacterium tuberculosis Truncated Haemoglobin N

    Science.gov (United States)

    Bidon-Chanal, A.; Martí, M. A.; Estrín, D. A.; Luque, F. J.

    Mycobacterium tuberculosis, the causative agent of human tuberculosis, encodes a haemoprotein named Truncated Haemoglobin N (trHbN), which in its active site transforms nitric oxide (NO) to nitrate anion.left( {{text{NO}}_3^ - } right). The NO-dioxygenase activity of trHbN seems to be crucial for the bacillus, which can survive under the nitrosative stress conditions that occur upon infection of the host. As a defense mechanism against the copious amounts of NO produced by macrophages upon infection, the protein must achieve a high level of NO-dioxygenase activity to eliminate NO, but this is modulated by its efficiency in capturing O2 and NO. Migration of small diatomic ligands through the protein matrix is related to the presence of a doubly branched tunnel system connecting the surface and the haem cavity site. In this work, we have studied the mechanism that controls ligand diffusion and product egression with state-of-the-art molecular dynamics simulations. The results support a dual path mechanism for migration of O2 and NO through distinct branches of the tunnel, where migration of NO is facilitated upon binding of O2 to the haem group. Finally, egression of left( {{text{NO}}_3^ - } right) is preceded by the entrance of water to the haem cavity and occurs through a different pathway. Overall, the results highlight the intimate relationship between structure, dynamical behavior and biological function of trHbN.

  8. [Degradation and biosynthesis of L-phenylalanine by chloridazon-degrading bacteria].

    Science.gov (United States)

    Buck, R; Eberspächer, J; Lingens, F

    1979-07-01

    Incubating chloridazon-degrading bacteria with L-phenylalanine leads to the accumulation of L-2,3-dihydroxyphenylalanine, o-tyrosine and m-tyrosine in the medium. Incubating the bacteria with N-acetyl-L-phenylalanine leads to N-acetyl-(2,3-dihydroxyphenyl)alanine. Using phenylacetic acid as substrate leads to the accumulation of malonic acid. The products are isolated by gel chromatography and high performance liquid chromatography. 2,3-Dihydroxy-L-phenylalanine is attacked by a catechol 2,3-dioxygenase in the presence of Fe2. An unstable yellow compound is formed in this reaction. This meta-cleavage-product is again cleaved by a hydrolase, leading to aspartic acid and 4-hydroxy-2-oxovaleric acid. Both products were isolated fromthe reaction buffer by amino acid analysis and high performance liquid chromatography. The dioxygenase and hydrolase were partially purified and characterized. A new degradation pathway for phenylalanine is discussed and compared with known pathways. The enzymes chorismate mutase, prephenate dehydratase and prephenate dehydrogenase are characterized and inhibition as well as repression are investigated. Only prephenate dehydrogenase is inhibited by phenylalanine, tyrosine and tryptophane. Chorismate mutase is repressed by phenylalanine, prephenate dehydrogenase by phenylalanine and tyrosine. Prephenate dehydratase is not repressed by aromatic amino acids. Regulation of aromatic amino acid biosynthesis in connection with phenylalanine degradation is discussed.

  9. Tryptophan catabolizing enzymes – party of three

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    Helen J Ball

    2014-10-01

    Full Text Available Indoleamine 2,3-dioxygenase (IDO and tryptophan 2,3-dioxygenase (TDO are tryptophan-degrading enzymes that have independently evolved to catalyze the first step in tryptophan catabolism via the kynurenine pathway. The depletion of tryptophan and formation of kynurenine pathway metabolites modulates the activity of the mammalian immune, reproductive and central nervous systems. IDO and TDO enzymes can have overlapping or distinct functions depending on their expression patterns. The expression of TDO and IDO enzymes in mammals differs not only by tissue/cellular localization but also by their induction by distinct stimuli. To add to the complexity, these genes also have undergone duplications in some organisms leading to multiple isoforms of IDO or TDO. For example, many vertebrates, including all mammals, have acquired two IDO genes via gene duplication, although the IDO1-like gene has been lost in some lower vertebrate lineages. Gene duplications can allow the homologs to diverge and acquire different properties to the original gene. There is evidence for IDO enzymes having differing enzymatic characteristics, signaling properties and biological functions. This review analyses the evolutionary convergence of IDO and TDO enzymes as tryptophan-catabolizing enzymes and the divergent evolution of IDO homologs to generate an enzyme family with diverse characteristics not possessed by TDO enzymes, with an emphasis on the immune system.

  10. Assessing environmental drivers of microbial communities in estuarine soils of the Aconcagua River in Central Chile.

    Science.gov (United States)

    Fuentes, Sebastián; Ding, Guo-Chun; Cárdenas, Franco; Smalla, Kornelia; Seeger, Michael

    2015-10-01

    Aconcagua River basin (Central Chile) harbors diverse economic activities such as agriculture, mining and a crude oil refinery. The aim of this study was to assess environmental drivers of microbial communities in Aconcagua River estuarine soils, which may be influenced by anthropogenic activities taking place upstream and by natural processes such as tides and flood runoffs. Physicochemical parameters were measured in floodplain soils along the estuary. Bacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, Pseudomonas, Bacillus and Fungi were studied by DGGE fingerprinting of 16S rRNA gene and ribosomal ITS-1 amplified from community DNA. Correlations between environment and communities were assessed by distance-based redundancy analysis. Mainly hydrocarbons, pH and the composed variable copper/arsenic/calcium but in less extent nitrogen and organic matter/phosphorous/magnesium correlated with community structures at different taxonomic levels. Aromatic hydrocarbons degradation potential by bacterial community was studied. Polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenases genes were detected only at upstream sites. Naphthalene dioxygenase ndo genes were heterogeneously distributed along estuary, and related to Pseudomonas, Delftia, Comamonas and Ralstonia. IncP-1 plasmids were mainly present at downstream sites, whereas IncP-7 and IncP-9 plasmids showed a heterogeneous distribution. This study strongly suggests that pH, copper, arsenic and hydrocarbons are main drivers of microbial communities in Aconcagua River estuarine soils.

  11. Changes in mouse liver and chicken embryo yolk sac membrane soluble proteins due to an organophosphorous insecticide (OPI) diazinon linked to several noncholinergic OPI effects in mice and chicken embryos.

    Science.gov (United States)

    Seifert, Josef

    2014-11-01

    The objective of this study was to identify proteins in mouse livers and chicken embryo yolk sac membranes whose quantities were altered by an organophosphorous insecticide (OPI) treatment and which might be linked, based on their functionality, to the recognized noncholinergic effects of OPI. Mice and fertile chicken eggs were treated with an OPI representative diazinon. The quantitative changes in mouse liver and chicken embryo yolk sac membrane soluble proteins caused by diazinon were determined by two-dimensional electrophoresis. Proteins whose quantity was affected by diazinon were identified by the mass spectrometry. In mouse livers, the altered levels of several enzymes of glucose metabolism were considered with regards to amelioration of hyperglycemia due to diazinon; the reduced levels of 3-hydroxyanthranilate 3,4-dioxygenase to the changes in the l-tryptophan to NAD metabolism caused by pyrimidinyl and crotonamide OPI; the reduced levels of catalase, peroxiredoxin and superoxide dismutase to OPI-increased lipid and/or kynurenine oxidation, the latter effect resulting also in increased urinary excretion of xanthurenic and kynurenic acids; and an increase in glutathione S-methyltransferase to OPI detoxification. In chicken embryo yolk sac membranes, the reduced availability of procollagen-proline dioxygenase may be the factor in micromelia caused by OPI in chicken embryos.

  12. Crystal Structure of the Non-heme Iron Dixoygenase PtlH in Pentalenolactone Biosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    You,Z.; Omura, S.; Ikeda, H.; Cane, D.; Jogl, G.

    2007-01-01

    The non-heme iron dioxygenase PtlH from the soil organism Streptomyces avermitilis is a member of the iron(II)/{alpha}-ketoglutarate-dependent dioxygenase superfamily and catalyzes an essential reaction in the biosynthesis of the sesquiterpenoid antibiotic pentalenolactone. To investigate the structural basis for substrate recognition and catalysis, we have determined the x-ray crystal structure of PtlH in several complexes with the cofactors iron, a-ketoglutarate, and the non-reactive enantiomer of the substrate, ent-1-deoxypentalenic acid, in four different crystal forms to up to 1.31 Angstroms resolution. The overall structure of PtlH forms a double-stranded barrel helix fold, and the cofactor-binding site for iron and a-ketoglutarate is similar to other double-stranded barrel helix fold enzymes. Additional secondary structure elements that contribute to the substrate-binding site in PtlH are not conserved in other double-stranded barrel helix fold enzymes. Binding of the substrate enantiomer induces a reorganization of the monoclinic crystal lattice leading to a disorder-order transition of a C-terminal {alpha}-helix. The newly formed helix blocks the major access to the active site and effectively traps the bound substrate. Kinetic analysis of wild type and site-directed mutant proteins confirms a critical function of two arginine residues in substrate binding, while simulated docking of the enzymatic reaction product reveals the likely orientation of bound substrate.

  13. Tryptophan oxygenation: mechanistic considerations.

    Science.gov (United States)

    Naismith, James H

    2012-06-01

    From a protein structural viewpoint, tryptophan is often considered an inert structural amino acid, playing a role as a hydrophobic anchor in membrane proteins or as part of the hydrophobic core of soluble proteins. However, tryptophan is the only polyaromatic amino acid and, from a chemical viewpoint, possesses unique reactivity owing to the electron-richness of the indole system. This reactivity is seen in the area of natural products and metabolites which have exquisite modifications of the indole ring system. Enzymes have evolved multiple strategies to break or modify the indole ring; one particular class is the IDO/TDO (indoleamine/tryptophan dioxygenase) superfamily. A new member of this family, PrnB, on the surface catalyses a very different reaction, but actually shares much of the early chemistry with the tryptophan dioxygenases. Studies on PrnB have contributed to our understanding of the wider superfamily. In the present mini-review, recent developments in our understanding of how the TDO class of enzymes use activated molecular oxygen to break the indole ring are discussed.

  14. 新筛选菌种Delftia sp.XYJ5生物降解苯胺的途径%Biodegradation of Aniline by a Newly Isolated Delftia sp. XYJ6

    Institute of Scientific and Technical Information of China (English)

    肖诚斌; 宁君; 闫海; 孙旭东; 胡继业

    2009-01-01

    A promising gram-negative bacterial strain for the biodegradation of aniline as the sole carbon, nitrogen and energy sources was successfully isolated and identified as Delftia sp. XYJ6. The optimal temperature and pH for both the growth of Delftia sp. XYJ6 and the biodegradation of aniline were 30℃ and 7.0, respectively. Initial aniline of 2000 mg·L1 could be completely removed by the strain at 22 h, which showed that Delftia sp. XYJ6 had a strong ability in the biodegradation of aniline. It indicated that aniline was firstly converted to catechol catalyzed by aniline dioxygenase as a first product, which was then further biodegraded to cis,cis-muconic acid catalyzed by the catechol 1,2-dioxygenase of Delftia sp. XYJ6 as a second product. Cis,.cid-muconic acid could also be further biodegraded to other small compound again. The pathway for the biodegradation of aniline by Delftia sp. XYJ6 was not previously reported.

  15. Development of microbial engineered whole-cell systems for environmental benzene determination.

    Science.gov (United States)

    Di Gennaro, P; Bruzzese, N; Anderlini, D; Aiossa, M; Papacchini, M; Campanella, L; Bestetti, G

    2011-03-01

    This paper reports the development of two recombinant bacterial systems that can be used to monitor environmental benzene contamination based on Escherichia coli, which carry genes coding for benzene dioxygenase and benzene dihydrodiol dehydrogenase from Pseudomonas putida MST. E. coli strains express these two enzymes under the control of the Ptac promoter or without any induction. These activities can be detected electrochemically or colorimetrically and used to monitor benzene pollution in environmental air samples collected from an oil refinery assessing benzene by different laboratory experimental procedures. The procedures involving whole-cell bioassays determine the concentration of benzene through benzene dioxygenase activity, which allows for direct correlation of oxygen consumption, and through the benzene dihydrodiol dehydrogenase that causes catechol accumulation and restores NADH necessary for the activity of the first enzyme. Oxygen consumption and catechol production deriving from both enzymatic activities are related to benzene concentration and their measurements determined the sensitivity of the system. The results indicated that the sensitivity was enough to detect the benzene vapor at a lower concentration level of 0.01 mM in about 30 min. The possibility for on-line monitoring of benzene concentration by our new recombinant cells results from the fact that no particular treatment of environmental samples is required. This is a major advantage over other biosensors or assays. Moreover, the development of microbial cells that did not require any addition or effectors for the transcription of the specific enzymes, allowed these systems to be more versatile in automated environmental benzene monitoring.

  16. Overlapping Requirements for Tet2 and Tet3 in Normal Development and Hematopoietic Stem Cell Emergence

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    Cheng Li

    2015-08-01

    Full Text Available The Tet family of methylcytosine dioxygenases (Tet1, Tet2, and Tet3 convert 5-methylcytosine to 5-hydroxymethylcytosine. To date, functional overlap among Tet family members has not been examined systematically in the context of embryonic development. To clarify the potential for overlap among Tet enzymes during development, we mutated the zebrafish orthologs of Tet1, Tet2, and Tet3 and examined single-, double-, and triple-mutant genotypes. Here, we identify Tet2 and Tet3 as the major 5-methylcytosine dioxygenases in the zebrafish embryo and uncover a combined requirement for Tet2 and Tet3 in hematopoietic stem cell (HSC emergence. We demonstrate that Notch signaling in the hemogenic endothelium is regulated by Tet2/3 prior to HSC emergence and show that restoring expression of the downstream gata2b/scl/runx1 transcriptional network can rescue HSCs in tet2/3 double mutant larvae. Our results reveal essential, overlapping functions for tet genes during embryonic development and uncover a requirement for 5hmC in regulating HSC production.

  17. Mycobacterium tuberculosis Rv3406 is a type II alkyl sulfatase capable of sulfate scavenging.

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    Kimberly M Sogi

    Full Text Available The genome of Mycobacterium tuberculosis (Mtb encodes nine putative sulfatases, none of which have a known function or substrate. Here, we characterize Mtb's single putative type II sulfatase, Rv3406, as a non-heme iron (II and α-ketoglutarate-dependent dioxygenase that catalyzes the oxidation and subsequent cleavage of alkyl sulfate esters. Rv3406 was identified based on its homology to the alkyl sulfatase AtsK from Pseudomonas putida. Using an in vitro biochemical assay, we confirmed that Rv3406 is a sulfatase with a preference for alkyl sulfate substrates similar to those processed by AtsK. We determined the crystal structure of the apo Rv3406 sulfatase at 2.5 Å. The active site residues of Rv3406 and AtsK are essentially superimposable, suggesting that the two sulfatases share the same catalytic mechanism. Finally, we generated an Rv3406 mutant (Δrv3406 in Mtb to study the sulfatase's role in sulfate scavenging. The Δrv3406 strain did not replicate in minimal media with 2-ethyl hexyl sulfate as the sole sulfur source, in contrast to wild type Mtb or the complemented strain. We conclude that Rv3406 is an iron and α-ketoglutarate-dependent sulfate ester dioxygenase that has unique substrate specificity that is likely distinct from other Mtb sulfatases.

  18. Identification of PAHX, a Refsum disease gene.

    Science.gov (United States)

    Mihalik, S J; Morrell, J C; Kim, D; Sacksteder, K A; Watkins, P A; Gould, S J

    1997-10-01

    Refsum disease is an autosomal recessive disorder characterized by retinitis pigmentosa, peripheral polyneuropathy, cerebellar ataxia and increased cerebrospinal fluid protein. Biochemically, the disorder is defined by two related properties: pronounced accumulation of phytanic acid and selective loss of the peroxisomal dioxygenase required for alpha-hydroxylation of phytanoyl-CoA2. Decreased phytanic-acid oxidation is also observed in human cells lacking PEX7, the receptor for the type-2 peroxisomal targetting signal (PTS2; refs 3,4), suggesting that the enzyme defective in Refsum disease is targetted to peroxisomes by a PTS2. We initially identified the human PAHX and mouse Pahx genes as expressed sequence tags (ESTs) capable of encoding PTS2 proteins. Human PAHX is targetted to peroxisomes, requires the PTS2 receptor for peroxisomal localization, interacts with the PTS2 receptor in the yeast two-hybrid assay and has intrinsic phytanoyl-CoA alpha-hydroxylase activity that requires the dioxygenase cofactor iron and cosubstrate 2-oxoglutarate. Radiation hybrid data place PAHX on chromosome 10 between the markers D10S249 and D10S466, a region previously implicated in Refsum disease by homozygosity mapping. We find that both Refsum disease patients examined are homozygous for inactivating mutations in PAHX, demonstrating that mutations in PAHX can cause Refsum disease.

  19. 2-Oxoglutarate: linking TCA cycle function with amino acid, glucosinolate, flavonoid, alkaloid and gibberellin biosynthesis

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    Wagner L. Araújo

    2014-10-01

    Full Text Available The tricarboxylic acid (TCA cycle intermediate 2-oxoglutarate (2-OG is used as an obligatory substrate in a range of oxidative reactions catalyzed by 2-OG-dependent dioxygenases. These enzymes are widespread in nature being involved in several important biochemical processes. We have recently demonstrated that tomato plants in which the TCA cycle enzyme 2-OG dehydrogenase (2-ODD was antisense inhibited were characterized by early senescence and modified fruit ripening associated with differences in the levels of bioactive gibberellin (GA. Accordingly, there is now compelling evidence that the TCA cycle plays an important role in modulating the rate of flux from 2-OG to amino acid metabolism. Here we discuss recent advances in the biochemistry and molecular biology of 2-OG metabolism occurring in different biological systems indicating the importance of 2-OG and 2-OG dependent dioxygenases not only in glucosinolate, flavonoid and alkaloid metabolism but also in GA and amino acid metabolism. We additionally summarize recent findings regarding the impact of modification of 2-OG metabolism on biosynthetic pathways involving 2-ODDs.

  20. New metabolic pathway for degradation of 2-nitrobenzoate by Arthrobacter sp. SPG

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    Pankaj Kumar Arora

    2015-06-01

    Full Text Available Arthrobacter sp. SPG utilized 2-nitrobenzoate as its sole source of carbon and energy and degraded it with accumulation of stoichiometric amounts of nitrite ions. Salicylate and catechol were detected as metabolites of the 2-nitrobenzoate degradation using high performance liquid chromatography and gas chromatography-mass spectrometry. Enzyme activities for 2-nitrobenzoate-2-monooxygenase, salicylate hydroxylase, and catechol-1,2-dioxygenase were detected in the crude extracts of the 2-nitrobenzoate-induced cells of strain SPG. The 2-nitrobenzoate-monooxygenase activity resulted in formation of salicylate and nitrite from 2-nitrobenzoate whereas salicylate hydroxylase catalyzed the conversion of salicylate to catechol. The ring-cleaving enzyme, catechol-1,2-dioxygenase cleaved catechol to cis, cis-muconic acid. Cells of strain SPG were able to degrade 2-nitrobenzoate in sterile as well as non-sterile soil microcosms. The results of microcosm studies showed that strain SPG degraded more than 90% of 2-nitrobenzoate within 10-12 days. This study clearly shows that Arthrobacter sp. SPG degraded 2-nitrobenzoate via a new pathway with formation of salicylate and catechol as metabolites. Arthrobacter sp. SPG may be used for bioremediation of 2-nitrobenzoate-contaminated sites due to its ability to degrade 2-nitrobenzoate in soil.