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Dehalogenase

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https://www.readbyqxmd.com/read/28809851/grape-pomace-compost-harbors-organohalide-respiring-dehalogenimonas-species-with-novel-reductive-dehalogenase-genes
#1
Yi Yang, Steven A Higgins, Jun Yan, Burcu Şimşir, Karuna Chourey, Ramsunder Iyer, Robert L Hettich, Brett Baldwin, Dora M Ogles, Frank E Löffler
Organohalide-respiring bacteria have key roles in the natural chlorine cycle; however, most of the current knowledge is based on cultures from contaminated environments. We demonstrate that grape pomace compost without prior exposure to chlorinated solvents harbors a Dehalogenimonas (Dhgm) species capable of using chlorinated ethenes, including the human carcinogen and common groundwater pollutant vinyl chloride (VC) as electron acceptors. Grape pomace microcosms and derived solid-free enrichment cultures were able to dechlorinate trichloroethene (TCE) to less chlorinated daughter products including ethene...
August 15, 2017: ISME Journal
https://www.readbyqxmd.com/read/28807839/characterization-of-fm2382-from-fulvimarina-manganoxydans-sp-nov-8047-with-potential-enzymatic-decontamination-of-sulfur-mustard
#2
Yuan-Zhong Zhao, Xuan Guo, Jin-Yi Zhong, Nan Guo, Lin-Cai Chen, Zhi-Yang Dong
Sulfur mustard (SM) can be hydrolyzed by haloalkane dehalogenases such as DhaA, LinB and DmbA. However, the low resistance to the elevated temperatures limited the practical application of haloalkane dehalogenases. Here we reported a new thermotolerant dehalogenase FM2382 from Fulvimarina manganoxydans sp. nov. 8047. The specific activity of FM2382 to SM is 0.6 U/mg. FM2382 possessed high heat stability (45 °C) in slight alkali environment (pH 7.5) and retained approximately 50% activity after incubation at 70 °C for 40 min...
August 11, 2017: Protein Expression and Purification
https://www.readbyqxmd.com/read/28803405/pcb-dechlorination-hotspots-and-reductive-dehalogenase-genes-in-sediments-from-a-contaminated-wastewater-lagoon
#3
Timothy E Mattes, Jessica M Ewald, Yi Liang, Andres Martinez, Andrew Awad, Patrick Richards, Keri C Hornbuckle, Jerald L Schnoor
Polychlorinated biphenyls (PCBs) are a class of persistent organic pollutants that are distributed worldwide. Although industrial PCB production has stopped, legacy contamination can be traced to several different commercial mixtures (e.g., Aroclors in the USA). Despite their persistence, PCBs are subject to naturally occurring biodegradation processes, although the microbes and enzymes involved are poorly understood. The biodegradation potential of PCB-contaminated sediments in a wastewater lagoon located in Virginia (USA) was studied...
August 12, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28765600/combinatorial-metabolic-engineering-of-pseudomonas-putida-kt2440-for-efficient-mineralization-of-1-2-3-trichloropropane
#4
Ting Gong, Xiaoqing Xu, You Che, Ruihua Liu, Weixia Gao, Fengjie Zhao, Huilei Yu, Jingnan Liang, Ping Xu, Cunjiang Song, Chao Yang
An industrial waste, 1,2,3-trichloropropane (TCP), is toxic and extremely recalcitrant to biodegradation. To date, no natural TCP degraders able to mineralize TCP aerobically have been isolated. In this work, we engineered a biosafety Pseudomonas putida strain KT2440 for aerobic mineralization of TCP by implantation of a synthetic biodegradation pathway into the chromosome and further improved TCP mineralization using combinatorial engineering strategies. Initially, a synthetic pathway composed of haloalkane dehalogenase, haloalcohol dehalogenase and epoxide hydrolase was functionally assembled for the conversion of TCP into glycerol in P...
August 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28741946/investigating-substrate-scope-and-enantioselectivity-of-a-defluorinase-by-a-stereochemical-probe
#5
Jian-Bo Wang, Adriana Ilie, Shuguang Yuan, Manfred T Reetz
The possibility of a double Walden inversion mechanism of the fluoracetate dehalogenase FAcD (RPA1163) has been studied by subjecting rac-2-fluoro-2-phenyl acetic acid to the defluorination process. This stereochemical probe led to inversion of configuration in a kinetic resolution with an extremely high selectivity factor (E > 500), showing that the classical mechanism involving SN2 reaction by Asp110 pertains. The high preference for the (S)-substrate is of synthetic value. Wide substrate scope of RPA1163 in such hydrolytic kinetic resolutions can be expected because the reaction of the even more sterically demanding rac-2-fluoro-2-benzyl acetic acid proceeded similarly...
August 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28696117/catalytic-cycle-of-haloalkane-dehalogenases-toward-unnatural-substrates-explored-by-computational-modeling
#6
Sérgio M Marques, Zuzana Dunajova, Zbynek Prokop, Radka Chaloupkova, Jan Brezovsky, Jiri Damborsky
The anthropogenic toxic compound 1,2,3-trichloropropane is poorly degradable by natural enzymes. We have previously constructed the haloalkane dehalogenase DhaA31 by focused directed evolution ( Pavlova, M. et al. Nat. Chem. Biol. 2009 , 5 , 727 - 733 ), which is 32 times more active than the wild-type enzyme and is currently the most active variant known against that substrate. Recent evidence has shown that the structural basis responsible for the higher activity of DhaA31 was poorly understood. Here we have undertaken a comprehensive computational study of the main steps involved in the biocatalytic hydrolysis of 1,2,3-trichloropropane to decipher the structural basis for such enhancements...
July 28, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28690604/phenol-is-the-initial-product-formed-during-growth-and-degradation-of-bromobenzene-by-tropical-marine-yeast-yarrowia-lipolytica-ncim-3589-via-an-early-dehalogenation-step
#7
Aakanksha A Vatsal, Smita S Zinjarde, Ameeta RaviKumar
Bromobenzene (BrB), a hydrophobic, recalcitrant organic compound, is listed by the environmental protection agencies as an environmental and marine pollutant having hepatotoxic, mutagenic, teratogenic, and carcinogenic effects. The tropical marine yeast Yarrowia lipolytica 3589 was seen to grow aerobically on BrB and displayed a maximum growth rate (μmax) of 0.04 h(-1). Furthermore, we also observed an increase in cell size and sedimentation velocity for the cells grown on BrB as compared to the glucose grown cells...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28674849/metagenome-derived-haloalkane-dehalogenases-with-novel-catalytic-properties
#8
Michael Kotik, Pavel Vanacek, Antonin Kunka, Zbynek Prokop, Jiri Damborsky
Haloalkane dehalogenases (HLDs) are environmentally relevant enzymes cleaving a carbon-halogen bond in a wide range of halogenated pollutants. PCR with degenerate primers and genome-walking was used for the retrieval of four HLD-encoding genes from groundwater-derived environmental DNA. Using specific primers and the environmental DNA as a template, we succeeded in generating additional amplicons, resulting altogether in three clusters of sequences with each cluster comprising 8-13 closely related putative HLD-encoding genes...
July 3, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28671181/cobamide-mediated-enzymatic-reductive-dehalogenation-via-long-range-electron-transfer
#9
Cindy Kunze, Martin Bommer, Wilfred R Hagen, Marie Uksa, Holger Dobbek, Torsten Schubert, Gabriele Diekert
The capacity of metal-containing porphyrinoids to mediate reductive dehalogenation is implemented in cobamide-containing reductive dehalogenases (RDases), which serve as terminal reductases in organohalide-respiring microbes. RDases allow for the exploitation of halogenated compounds as electron acceptors. Their reaction mechanism is under debate. Here we report on substrate-enzyme interactions in a tetrachloroethene RDase (PceA) that also converts aryl halides. The shape of PceA's highly apolar active site directs binding of bromophenols at some distance from the cobalt and with the hydroxyl substituent towards the metal...
July 3, 2017: Nature Communications
https://www.readbyqxmd.com/read/28666054/conversion-of-a-dehalogenase-to-a-nitroreductase-by-swapping-its-flavin-cofactor-with-a-5-deazaflavin-analog
#10
Qi Su, Petrina A Boucher, Steve Rokita
Natural and engineered nitroreductases have rarely supported full reduction of nitroaromatics to their amine products and more typically transformations are limited to formation of the hydroxylamine intermediates. Efficient use of these enzymes also requires a regenerating system for NAD(P)H to avoid the costs associated with this natural reductant. Iodotyrosine deiodinase is a member of the same structural superfamily of many nitroreductases but does not directly consume reducing equivalents from NAD(P)H nor demonstrates a nitroreductase activity...
June 30, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28654328/biochemistry-of-catabolic-reductive-dehalogenation
#11
REVIEW
Maeva Fincker, Alfred M Spormann
A wide range of phylogenetically diverse microorganisms couple the reductive dehalogenation of organohalides to energy conservation. Key enzymes of such anaerobic catabolic pathways are corrinoid and Fe-S cluster-containing, membrane-associated reductive dehalogenases. These enzymes catalyze the reductive elimination of a halide and constitute the terminal reductases of a short electron transfer chain. Enzymatic and physiological studies revealed the existence of quinone-dependent and quinone-independent reductive dehalogenases that are distinguishable at the amino acid sequence level, implying different modes of energy conservation in the respective microorganisms...
June 20, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28648508/iodide-handling-disorders-nis-tpo-tg-iyd
#12
REVIEW
Héctor M Targovnik, Cintia E Citterio, Carina M Rivolta
Iodide Handling Disorders lead to defects of the biosynthesis of thyroid hormones (thyroid dyshormonogenesis, TD) and thereafter congenital hypothyroidism (CH), the most common endocrine disease characterized by low levels of circulating thyroid hormones. The prevalence of CH is 1 in 2000-3000 live births. Prevention of CH is based on prenatal diagnosis, carrier identification, and genetic counseling. In neonates a complete diagnosis of TD should include clinical examination, biochemical thyroid tests, thyroid ultrasound, radioiodine or technetium scintigraphy and perchlorate discharge test (PDT)...
March 2017: Best Practice & Research. Clinical Endocrinology & Metabolism
https://www.readbyqxmd.com/read/28648395/the-complete-genome-of-the-tetrachloroethene-respiring-epsilonproteobacterium-sulfurospirillum-halorespirans
#13
Tobias Goris, Benjamin Schenz, Johannes Zimmermann, Mikael Lemos, Jörg Hackermüller, Torsten Schubert, Gabriele Diekert
Sulfurospirillum halorespirans is a bacterium that couples the reductive dehalogenation of chlorinated ethenes to growth. This process is called organohalide respiration (OHR), which can be of importance for bioremediation. Here, we report the complete genome of S. halorespirans, the second one of an organohalide-respiring Epsilonproteobacterium after that of Sulfurospirillum multivorans. With both genomes at hand, we were able to ascertain that the genomic region encoding OHR proteins in Epsilonproteobacteria differs from that found in organohalide-respiring bacteria (OHRB) affiliated to other phyla and that the production of a unique cobamide, norpseudo-B12, might not be limited to the model organism S...
June 22, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28641560/functional-and-catalytic-characterization-of-the-detoxifying-enzyme-haloalkane-dehalogenase-from-rhizobium-leguminosarum
#14
Nikolaos Georgakis, Evangelia Chronopoulou, Maria Anna Gad, Dimitrios Skliros, Rodica Efrose, Emmanouil Flemetakis, Nikolaos E Labrou
Haloalkanes are acutely toxic to animals and humans and their toxic effects are mainly observed in the liver, kidneys and central nervous system. In the present work, the haloalkane dehalogenase from Rhizobium leguminosarum bv. trifolii (DrlA) was characterized. Reverse transcription polymerase chain reaction analysis and enzyme activity assays revealed that the DrlA gene expression in R. leguminosarum bv. trifolii is induced by 1,2-dibromoethane (1,2-DBE) during the early exponential phase. The gene of the enzyme was isolated, cloned and expressed in E...
June 20, 2017: Protein and Peptide Letters
https://www.readbyqxmd.com/read/28637831/oshad1-a-haloacid-dehalogenase-like-apase-enhances-phosphate-accumulation
#15
Bipin K Pandey, Poonam Mehra, Lokesh Verma, Jyoti Bhadouria, Jitender Giri
Phosphorus (P) deficiency limits plant growth and yield. Since plants can absorb only the inorganic form of P (Pi), a large portion of soil P (organic and inorganic P complexes) remains unused. Here, we identified and characterized a PHR2-regulated, novel low-Pi-responsive haloacid dehalogenase (HAD)-like hydrolase, OsHAD1 While OsHAD1 is a functional HAD protein having both acid phosphatase and phytase activities, it showed little homology with other known low-Pi-responsive HAD superfamily members. Recombinant OsHAD1 is active at acidic pH and dephosphorylates a broad range of organic and inorganic P-containing substrates, including phosphorylated serine and sodium phytate...
August 2017: Plant Physiology
https://www.readbyqxmd.com/read/28631300/a-bacterial-chloroform-reductive-dehalogenase-purification-and-biochemical-characterization
#16
Bat-Erdene Jugder, Susanne Bohl, Helene Lebhar, Robert D Healey, Mike Manefield, Christopher P Marquis, Matthew Lee
We report herein the purification of a chloroform (CF)-reducing enzyme, TmrA, from the membrane fraction of a strict anaerobe Dehalobacter sp. strain UNSWDHB to apparent homogeneity with an approximate 23-fold increase in relative purity compared to crude lysate. The membrane fraction obtained by ultracentrifugation was solubilized in Triton X-100 in the presence of glycerol, followed by purification by anion exchange chromatography. The molecular mass of the purified TmrA was determined to be 44.5 kDa by SDS-PAGE and MALDI-TOF/TOF...
June 20, 2017: Microbial Biotechnology
https://www.readbyqxmd.com/read/28631290/a-h2-oxidizing-1-2-3-trichlorobenzene-reducing-multienzyme-complex-isolated-from-the-obligately-organohalide-respiring-bacterium-dehalococcoides-mccartyi-strain-cbdb1
#17
Stefanie Hartwig, Nadya Dragomirova, Anja Kublik, Dominique Türkowsky, Martin von Bergen, Ute Lechner, Lorenz Adrian, R Gary Sawers
Dehalococcoides mccartyi is a small, slow-growing bacterium of the phylum Chloroflexi that conserves energy using aliphatic and aromatic organohalides as electron acceptors, and hydrogen as sole electron donor. A recent study identified a protein complex in the membrane of strain CBDB1 comprising a Hup hydrogenase, a complex iron-sulphur molybdoprotein and a reductive dehalogenase (RdhA) that catalyses reduction of 1,2,3,4-tetrachlorobenzene. Using a combination of size-exclusion chromatography, in-gel hydrogenase activity-staining, immunological analysis and mass spectrometry, we identified here a large molecular mass protein complex solubilized from the cytoplasmic membrane of D...
June 19, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28618195/novel-reductive-dehalogenases-from-the-marine-sponge-associated-bacterium-desulfoluna-spongiiphila
#18
Jie Liu, Nora Lopez, Young-Beom Ahn, Tatyana Goldberg, Yana Bromberg, Lee J Kerkhof, Max M Häggblom
Desulfoluna spongiiphila strain AA1 is an organohalide respiring bacterium, isolated from the marine sponge Aplysina aerophoba, that can use brominated and iodinated phenols, in addition to sulfate and thiosulfate as terminal electron acceptors. The genome of Desulfoluna spongiiphila strain AA1 is approximately 6.5 Mb. Three putative reductive dehalogenase (rdhA) genes involved in respiratory metabolism of organohalides were identified within the sequence. Conserved motifs found in respiratory reductive dehalogenases (a twin arginine translocation signal sequence and two iron-sulfur clusters) were present in all three putative AA1 rdhA genes...
June 15, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28618081/loss-of-the-ssra-genome-island-led-to-partial-debromination-in-the-pbde-respiring-dehalococcoides-mccartyi-strain-gy50
#19
Chang Ding, Matthew J Rogers, Kun-Lin Yang, Jianzhong He
Polybrominated diphenyl ethers (PBDEs), chemicals commonly used as flame-retardants in consumer products, are emerging persistent organic pollutants that are ubiquitous in the environment. In this study, we report a PBDE-respiring isolate - Dehalococcoides mccartyi strain GY50, which debrominates the most toxic tetra- and penta-BDE congeners (∼1.4 µM) to diphenyl ether within 12 days with hydrogen as the electron donor. The complete genome sequence revealed 26 reductive dehalogenase homologous genes (rdhAs), among which three genes (pbrA1, pbrA2 and pbrA3) were highly expressed during PBDE debromination...
June 15, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28593475/functional-metagenomics-of-oil-impacted-mangrove-sediments-reveals-high-abundance-of-hydrolases-of-biotechnological-interest
#20
Júlia Ronzella Ottoni, Lucélia Cabral, Sanderson Tarciso Pereira de Sousa, Gileno Vieira Lacerda Júnior, Daniela Ferreira Domingos, Fábio Lino Soares Junior, Mylenne Calciolari Pinheiro da Silva, Joelma Marcon, Armando Cavalcante Franco Dias, Itamar Soares de Melo, Anete Pereira de Souza, Fernando Dini Andreote, Valéria Maia de Oliveira
Mangroves are located in coastal wetlands and are susceptible to the consequences of oil spills, what may threaten the diversity of microorganisms responsible for the nutrient cycling and the consequent ecosystem functioning. Previous reports show that high concentration of oil favors the incidence of epoxide hydrolases and haloalkane dehalogenases in mangroves. This finding has guided the goals of this study in an attempt to broaden the analysis to other hydrolases and thereby verify whether oil contamination interferes with the prevalence of particular hydrolases and their assigned microorganisms...
July 2017: World Journal of Microbiology & Biotechnology
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