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Dehalogenase

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https://www.readbyqxmd.com/read/29040506/high-throughput-sequencing-revealed-novel-dehalococcoidia-in-dechlorinating-microbial-enrichments-from-pcb-contaminated-marine-sediments
#1
B Matturro, E Frascadore, S Rossetti
In this study six PCE-to-ethene dechlorinating cultures, fed with a fermentable substrate (lactate) or hydrogen as electron donor, were obtained from PCB and PCE dechlorinating microcosms constructed with PCB contaminated marine sediments.A novel Chloroflexi member (OTU-DIS1) affiliated to Dehalococcoidales Incertae Sedis, only distantly related to known dechlorinating bacteria, dominated the enrichment cultures (up to 86% of total OTUs). Sulfate-, thiosulfate- and sulfur-reducing bacteria affiliated to genera Desulfobacter, Dethiosulfatibacter and Desulfuromusa were also found to lesser extent...
October 11, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29040502/comparative-genomics-of-the-genus-desulfitobacterium
#2
Thomas Kruse, Tobias Goris, Julien Maillard, Tanja Woyke, Ute Lechner, Willem de Vos, Hauke Smidt
The Desulfitobacterium genus comprises anaerobic Gram-positive bacteria, of which the majority are facultative organohalide-respirers. We here present the genomes of eight strains of Desulfitobacterium spp., including five strains of D. hafniense, one strain each from D. dichloroeliminans and D. metallireducens, and one strain that had not been assigned to any species prior to this study. The newly sequenced genomes were compared with four previously published desulfitobacterial genomes. The average genome sizes are 5...
October 11, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29040474/co-occurrence-of-genes-for-aerobic-and-anaerobic-biodegradation-of-dichloroethane-in-organochlorine-contaminated-groundwater
#3
Jacob E Munro, Önder Kimyon, Deborah J Rich, Joanna Koenig, Sihui Tang, Adrian Low, Matthew Lee, Mike Manefield, Nicholas V Coleman
1,2-dichloroethane (DCA) is a problematic groundwater pollutant. Factors influencing the distribution and activities of DCA-degrading bacteria are not well-understood, which has hampered their application for bioremediation. Here, we used quantitative PCR (qPCR) to investigate the distribution of putative DCA-dehalogenating bacteria at a DCA-impacted site in Sydney (Australia). The dehalogenase genes dhlA, tceA and bvcA were detected in all groundwater samples (n = 15), while vcrA was found in 11/15 samples...
October 12, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29031631/most-probable-number-with-visual-based-lamp-for-the-quantification-of-reductive-dehalogenase-genes-in-groundwater-samples
#4
Yogendra H Kanitkar, Robert D Stedtfeld, Paul B Hatzinger, Syed A Hashsham, Alison M Cupples
The remediation of chlorinated solvent contaminated sites frequently involves bioaugmentation with mixed cultures containing Dehalococcoides mccartyi. Their activity is then examined by quantifying reductive dehalogenase (RDase) genes. Recently, we described a rapid, low cost approach, based on loop mediated isothermal amplification (LAMP), which allowed for the visual detection of RDase genes from groundwater. In that study, samples were concentrated (without DNA extraction), incubated in a water bath (avoiding the use of a thermal cycler) and amplification was visualized by the addition of SYBR green (post incubation)...
October 12, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29021488/aerobic-dechlorination-of-dichloromethane-using-biostimulation-agent-bd-c-in-continuous-and-batch-cultures-of-xanthobacter-autotrophicus-gj10
#5
Akifumi Hosoda, Yuta Isomura, Syungo Takeo, Takuho Onai, Kazutaka Takeuchi, Minoru Toda, Hiroto Tamura
It is important to construct microbiological treatment systems for organic solvent-contaminated water. We developed a continuous culture supplemented with a biostimulation agent named BD-C, which is formulated from canola oil, and Xanthobacter autotrophicus strain GJ10 for an aerobic dichloromethane (DCM)-dechlorinating microorganism. The continuous culture was a chemostat constructed using a 1 L screw-capped bottle containing artificial wastewater medium with 2.0 mM DCM and 1.0% (v/v) BD-C. The expression of genes for DCM metabolism in the dechlorinating aerobe was monitored and analyzed by reverse transcription-quantitative PCR...
October 11, 2017: Journal of Oleo Science
https://www.readbyqxmd.com/read/28981261/relationships-between-the-abundance-and-expression-of-functional-genes-from-vinyl-chloride-vc-degrading-bacteria-and-geochemical-parameters-at-vc-contaminated-sites
#6
Yi Liang, Xikun Liu, Michael A Singletary, Kai Wang, Timothy E Mattes
Bioremediation of vinyl chloride (VC) contamination in groundwater could be mediated by three major bacterial guilds: anaerobic VC-dechlorinators, methanotrophs, and ethene-oxidizing bacteria (etheneotrophs) via metabolic or cometabolic pathways. We collected 95 groundwater samples across 6 chlorinated ethene-contaminated sites and searched for relationships among VC biodegradation gene abundance and expression and site geochemical parameters (e.g., VC concentrations). Functional genes from the three major VC-degrading bacterial guilds were present in 99% and expressed in 59% of the samples...
October 19, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28968436/identifying-and-sequencing-a-mycobacterium-sp-strain-f4-as-a-potential-bioremediation-agent-for-quinclorac
#7
Yingying Li, Wu Chen, Yunsheng Wang, Kun Luo, Yue Li, Lianyang Bai, Feng Luo
Quinclorac is a widely used herbicide in rice filed. Unfortunately, quinclorac residues are phytotoxic to many crops/vegetables. The degradation of quinclorac in nature is very slow. On the other hand, degradation of quinclorac using bacteria can be an effective and efficient method to reduce its contamination. In this study, we isolated a quinclorac bioremediation bacterium strain F4 from quinclorac contaminated soils. Based on morphological characteristics and 16S rRNA gene sequence analysis, we identified strain F4 as Mycobacterium sp...
2017: PloS One
https://www.readbyqxmd.com/read/28928379/ylehd-an-epoxide-hydrolase-with-promiscuous-haloalkane-dehalogenase-activity-from-tropical-marine-yeast-yarrowia-lipolytica-is-induced-upon-xenobiotic-stress
#8
Chandrika Bendigiri, Smita Zinjarde, Ameeta RaviKumar
Recalcitrant environmental pollutants, like bromoorganics and epoxides are hydrolysed with limited substrate specificities by microbial oxygenases, reductases, hydrolases and dehalogenases. Here, we report the identification and characterisation of a protein (XP_504164) from the tropical marine yeast Yarrowia lipolytica NCIM 3589, known to degrade bromoorganics and epoxides. Multiple sequence alignment suggests it belongs to α/β superfamily with conservation of catalytic triad and oxyanion hole motifs. The corresponding gene cloned and protein (Ylehd) expressed in E...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28927104/antisense-rna-transcripts-in-the-blood-may-be-novel-diagnostic-markers-for-colorectal-cancer
#9
Tomohiro Kurokawa, Keisuke Kohno, Kentaro Nagai, Mitsuru Chiba, Sugiru Pak, Soichiro Murata, Kiyoshi Fukunaga, Hiroshi Yasue, Nobuhiro Ohkohchi
Numerous genetic studies have been conducted regarding the occurrence of colorectal cancer (CRC) and the prognosis using microarrays. However, adequate investigations into the diagnostic application of microarrays have yet to be performed. The simplicity and accuracy of diagnosis and prognosis tracking are important requirements for its processes, and the use of blood cells for diagnosis is considered to be suitable to meet these requirements. The patients involved in the study were 28 preoperative patients with CRC and 6 healthy individuals who served as controls...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28919881/genomic-and-transcriptomic-analysis-of-growth-supporting-dehalogenation-of-chlorinated-methanes-in-methylobacterium
#10
Pauline Chaignaud, Bruno Maucourt, Marion Weiman, Adriana Alberti, Steffen Kolb, Stéphane Cruveiller, Stéphane Vuilleumier, Françoise Bringel
Bacterial adaptation to growth with toxic halogenated chemicals was explored in the context of methylotrophic metabolism of Methylobacterium extorquens, by comparing strains CM4 and DM4, which show robust growth with chloromethane and dichloromethane, respectively. Dehalogenation of chlorinated methanes initiates growth-supporting degradation, with intracellular release of protons and chloride ions in both cases. The core, variable and strain-specific genomes of strains CM4 and DM4 were defined by comparison with genomes of non-dechlorinating strains...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28894752/identification-of-multiple-dehalogenase-genes-involved-in-tetrachloroethene-to-ethene-dechlorination-in-a-dehalococcoides-dominated-enrichment-culture
#11
Mohamed Ismaeil, Naoko Yoshida, Arata Katayama
Chloroethenes (CEs) are widespread groundwater toxicants that are reductively dechlorinated to nontoxic ethene (ETH) by members of Dehalococcoides. This study established a Dehalococcoides-dominated enrichment culture (designated "YN3") that dechlorinates tetrachloroethene (PCE) to ETH with high dechlorination activity, that is, complete dechlorination of 800 μM PCE to ETH within 14 days in the presence of Dehalococcoides species at 5.7 ± 1.9 × 10(7) copies of 16S rRNA gene/mL. The metagenome of YN3 harbored 18 rdhA genes (designated YN3rdhA1-18) encoding the catalytic subunit of reductive dehalogenase (RdhA), four of which were suggested to be involved in PCE-to-ETH dechlorination based on significant increases in their transcription in response to CE addition...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28873365/deciphering-the-catalytic-amino-acid-residues-of-l-2-haloacid-dehalogenase-dehl-from-rhizobium-sp-rc1-an-in-silico-analysis
#12
Aliyu Adamu, Roswanira Abdul Wahab, Mohd Shahir Shamsir, Firdausi Aliyu, Fahrul Huyop
The l-2-haloacid dehalogenases (EC 3.8.1.2) specifically cleave carbon-halogen bonds in the L-isomers of halogenated organic acids. These enzymes have potential applications for the bioremediation and synthesis of various industrial products. One such enzyme is DehL, the l-2-haloacid dehalogenase from Rhizobium sp. RC1, which converts the L-isomers of 2-halocarboxylic acids into the corresponding D-hydroxycarboxylic acids. However, its catalytic mechanism has not been delineated, and to enhance its efficiency and utility for environmental and industrial applications, knowledge of its catalytic mechanism, which includes identification of its catalytic residues, is required...
August 14, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28872321/oleb-from-bacterial-hydrocarbon-biosynthesis-is-a-%C3%AE-lactone-decarboxylase-that-shares-key-features-with-haloalkane-dehalogenases
#13
James K Christenson, Serina L Robinson, Tiffany A Engel, Jack E Richman, An N Kim, Larry P Wackett
OleB is an α/β-hydrolase found in bacteria that biosynthesize long-chain olefinic hydrocarbons, but its function has remained obscure. We report that OleB from the Gram-negative bacterium Xanthomonas campestris performs an unprecedented β-lactone decarboxylation reaction, to complete cis-olefin biosynthesis. OleB reactions monitored by (1)H nuclear magnetic resonance spectroscopy revealed a selectivity for decarboxylating cis-β-lactones and no discernible activity with trans-β-lactones, consistent with the known configuration of pathway intermediates...
October 10, 2017: Biochemistry
https://www.readbyqxmd.com/read/28869789/subtle-changes-in-the-active-site-architecture-untangled-overlapping-substrate-ranges-and-mechanistic-differences-of-two-reductive-dehalogenases
#14
Cindy Kunze, Gabriele Diekert, Torsten Schubert
Reductive dehalogenases (RDases) of organohalide-respiring bacteria are cobamide-containing iron-sulfur proteins that catalyze different reductive dehalogenation reactions. Here, we report a functional analysis of two recombinant RDases, the tetrachloroethene (PCE) reductive dehalogenase (PceA) of Desulfitobacterium hafniense Y51 and the 1,2-dichloroethane (1,2-DCA) reductive dehalogenase (DcaA) of Desulfitobacterium dichloroeliminans DCA1. Both enzymes share 88% protein sequence identity, but appeared to have divergent mechanisms...
September 4, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28826615/glycerol-3-phosphate-phosphatase-pgp-role-in-intermediate-metabolism-and-target-for-cardiometabolic-diseases
#15
REVIEW
Elite Possik, S R Murthy Madiraju, Marc Prentki
Metabolic diseases, including obesity, type 2 diabetes, and metabolic syndrome arise because of disturbances in glucose and fat metabolism, which impact associated physiological events such as insulin secretion and action, fat storage and oxidation. Even though, decades of research has contributed to our current understanding of the components involved in glucose and fat metabolism and their regulation, that led to the development of many therapeutics, there are still many unanswered questions. Glycerol-3-phosphate (Gro3P), which is formed during glycolysis, is at the intersection of glucose and fat metabolism, and the availability of this metabolite can regulate energy and intermediary metabolism in mammalian cells...
August 4, 2017: Biochimie
https://www.readbyqxmd.com/read/28809851/grape-pomace-compost-harbors-organohalide-respiring-dehalogenimonas-species-with-novel-reductive-dehalogenase-genes
#16
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
#17
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...
January 2018: Protein Expression and Purification
https://www.readbyqxmd.com/read/28803405/pcb-dechlorination-hotspots-and-reductive-dehalogenase-genes-in-sediments-from-a-contaminated-wastewater-lagoon
#18
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
#19
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
#20
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
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