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Dehalogenase

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https://www.readbyqxmd.com/read/28075122/acetylene-fuels-tce-reductive-dechlorination-by-defined-dehalococcoides-pelobacter-consortia
#1
Xinwei Mao, Ronald S Oremland, Tong Liu, Sara Gushgari, Abigail Amanda Landers, Shaun M Baesman, Lisa Alvarez-Cohen
Acetylene (C2H2) can be generated in contaminated groundwater sites as a consequence of chemical degradation of trichloroethene (TCE) by in situ minerals, and C2H2 is known to inhibit bacterial dechlorination. In this study, we show that while high C2H2 (1.3 mM) concentrations reversibly inhibit reductive dechlorination of TCE by Dehalococcoides mccartyi isolates as well as enrichment cultures containing D. mccartyi sp., low C2H2 (0.4 mM) concentrations do not inhibit growth or metabolism of D. mccartyi. Co-cultures of Pelobacter SFB93, a C2H2-fermenting bacterium, with D...
January 11, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28074221/exploring-the-thermostable-properties-of-halohydrin-dehalogenase-from-agrobacterium-radiobacter-ad1-by-a-combinatorial-directed-evolution-strategy
#2
Zhiyun Wu, Wenfeng Deng, Yapei Tong, Qian Liao, Dongmin Xin, Huashun Yu, Juan Feng, Lixia Tang
As a crucial factor for biocatalysts, protein thermostability often arises from a combination of factors that are often difficult to rationalize. In this work, the thermostable nature of halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC) was systematically explored using a combinatorial directed evolution approach. For this, a mutagenesis library of HheC mutants was first constructed using error-prone PCR with low mutagenesis frequency. After screening approximately 2000 colonies, six mutants with eight mutation sites were obtained...
January 10, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28063652/molecular-and-carbon-isotopic-characterization-of-an-anaerobic-stable-enrichment-culture-containing-dehalobacterium-sp-during-dichloromethane-fermentation
#3
Alba Trueba-Santiso, Eloi Parladé, Mònica Rosell, Marc Lliros, Siti Hatijah Mortan, Maira Martínez-Alonso, Nuria Gaju, Lucía Martín-González, Teresa Vicent, Ernest Marco-Urrea
: Biodegradation of dichloromethane (DCM) under reducing conditions is of major concern due to its widespread detection in contaminated groundwaters. Here, we report an anaerobic enrichment culture derived from a membrane bioreactor operating in an industrial wastewater treatment plant, capable of fermenting DCM and the brominated analogue dibromomethane (DBM). Comparative analysis of bacterial 16S rDNA-DGGE profiles from fresh liquid medium inoculated with single colonies picked from serial dilution-to-extinction agar vials showed that cultures degrading DCM contained a predominant band belonging to Dehalobacterium, however this band was absent in cultures unable to degrade DCM...
January 4, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28002948/survival-of-vinyl-chloride-respiring-dehalococcoides-mccartyi-under-long-term-electron-donor-limitation
#4
Koshlan Mayer-Blackwell, Mohammad F Azizian, Jennifer K Green, Alfred M Spormann, Lewis Semprini
In anoxic groundwater aquifers, the long-term survival of Dehalococcoides mccartyi populations expressing the gene vcrA (or bvcA) encoding reductive vinyl chloride dehalogenases are important for complete dechlorination of tetrachloroethene (PCE) and trichloroethene (TCE) to non-chlorinated ethene. The absence or inactivity of vcrA-containing Dehalococcoides results in the accumulation of the harmful chlorinated intermediates dichloroethene (DCE) and vinyl chloride (VC). While vcrA-containing Dehalococcoides subpopulations depend on synergistic interaction with other organohalide-respiring populations generating their metabolic electron acceptors (DCE and VC), their survival requires successful competition for electron donor within the entire organohalide-respiring microbial community...
December 21, 2016: Environmental Science & Technology
https://www.readbyqxmd.com/read/27999093/a-robust-cosolvent-compatible-halohydrin-dehalogenase-by-computational-library-design
#5
Hesam Arabnejad, Marco Dal Lago, Peter A Jekel, Robert J Floor, Andy-Mark W H Thunnissen, Anke C Terwisscha van Scheltinga, Hein J Wijma, Dick B Janssen
To improve the applicability of halohydrin dehalogenase as a catalyst for reactions in the presence of organic cosolvents, we explored a computational library design strategy (Framework for Rapid Enzyme Stabilization by Computational libraries) that involves discovery and in silico evaluation of stabilizing mutations. Energy calculations, disulfide bond predictions and molecular dynamics simulations identified 218 point mutations and 35 disulfide bonds with predicted stabilizing effects. Experiments confirmed 29 stabilizing point mutations, most of which were located in two distinct regions, whereas introduction of disulfide bonds was not effective...
December 19, 2016: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/27907199/identification-heterologous-expression-and-functional-characterization-of-bacillus-subtilis-yutf-a-had-superfamily-5-nucleotidase-with-broad-substrate-specificity
#6
Natalia P Zakataeva, Dmitriy V Romanenkov, Yuliya R Yusupova, Victoria S Skripnikova, Takayuki Asahara, Sergey V Gronskiy
5'-nucleotidases (EC 3.1.3.5) catalyze the hydrolytic dephosphorylation of 5'-ribonucleotides and 5'-deoxyribonucleotides as well as complex nucleotides, such as uridine 5'-diphosphoglucose (UDP-glucose), nicotinamide adenine dinucleotide and flavin adenine dinucleotide, to their corresponding nucleosides plus phosphate. These enzymes have been found in diverse species in intracellular and membrane-bound, surface-localized forms. Soluble forms of 5'-nucleotidases belong to the ubiquitous haloacid dehalogenase superfamily (HADSF) and have been shown to be involved in the regulation of nucleotide, nucleoside and nicotinamide adenine dinucleotide (NAD+) pools...
2016: PloS One
https://www.readbyqxmd.com/read/27863020/kinetics-of-binding-of-fluorescent-ligands-to-enzymes-with-engineered-access-tunnels
#7
Shubhangi Kaushik, Zbynek Prokop, Jiri Damborsky, Radka Chaloupkova
Molecular recognition mechanisms and kinetics of binding of ligands to buried active sites via access tunnels are not well understood. Fluorescence polarization enables rapid and non-destructive real-time quantification of the association between small fluorescent ligands and large biomolecules. In this study, we describe analysis of binding kinetics of fluorescent ligands resembling linear halogenated alkanes to haloalkane dehalogenases. Dehalogenases possess buried active sites connected to the surrounding solvent by access tunnels...
November 9, 2016: FEBS Journal
https://www.readbyqxmd.com/read/27856620/genomic-characterization-of-dehalococcoides-mccartyi-strain-11a5-reveals-a-circular-extrachromosomal-genetic-element-and-a-new-tetrachloroethene-reductive-dehalogenase-gene
#8
Siyan Zhao, Chang Ding, Jianzhong He
Dehalococcoides mccartyi exhibits versatile capabilities to respire halogenated compounds under anaerobic conditions. In this study, we report the assembly and annotation of the complete genome of a chloroethene dechlorinating D. mccartyi strain 11a5. Bearing a 1,461,973 base-pair chromosome, strain 11a5 distinguishes itself from other D. mccartyi strains by possessing a 5,940 base-pair circular extrachromosomal genetic element which contains a reductive dehalogenase homolog. The whole genome of strain 11a5 harbors 31 putative reductive dehalogenase genes...
November 16, 2016: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/27836849/identification-of-a-new-phosphatase-enzyme-potentially-involved-in-the-sugar-phosphate-stress-response-in-pseudomonas-fluorescens
#9
Susan Maleki, Radka Hrudikova, Sergey B Zotchev, Helga Ertesvåg
: The alginate-producing bacterium Pseudomonas fluorescens utilizes the Entner-Doudoroff (ED) and pentose phosphate (PP) pathways to metabolize fructose, since the upper part of its Embden-Meyerhof-Parnas pathway is defective. Our previous study indicated that perturbation of the central carbon metabolism by diminishing glucose-6-phosphate dehydrogenase activity could lead to sugar phosphate stress when P. fluorescens was cultivated on fructose. In the present study, we demonstrate that PFLU2693, annotated as a haloacid dehalogenase-like enzyme, is a new sugar phosphate phosphatase, now designated Spp, which is able to dephosphorylate a range of phosphate substrates, including glucose 6-phosphate and fructose 6-phosphate, in vitro The effect of spp overexpression on growth and alginate production was investigated using both the wild type and several mutant strains...
January 15, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27829029/inferring-gene-networks-for-strains-of-dehalococcoides-highlights-conserved-relationships-between-genes-encoding-core-catabolic-and-cell-wall-structural-proteins
#10
Cresten B Mansfeldt, Gretchen W Heavner, Annette R Rowe, Boris Hayete, Bruce W Church, Ruth E Richardson
The interpretation of high-throughput gene expression data for non-model microorganisms remains obscured because of the high fraction of hypothetical genes and the limited number of methods for the robust inference of gene networks. Therefore, to elucidate gene-gene and gene-condition linkages in the bioremediation-important genus Dehalococcoides, we applied a Bayesian inference strategy called Reverse Engineering/Forward Simulation (REFS™) on transcriptomic data collected from two organohalide-respiring communities containing different Dehalococcoides mccartyi strains: the Cornell University mixed community D2 and the commercially available KB-1® bioaugmentation culture...
2016: PloS One
https://www.readbyqxmd.com/read/27809491/1-2-dichloroethane-exposure-alters-the-population-structure-metabolism-and-kinetics-of-a-trichloroethene-dechlorinating-dehalococcoides-mccartyi-consortium
#11
Koshlan Mayer-Blackwell, Maeva Fincker, Olivia Molenda, Benjamin Callahan, Holly Sewell, Susan Holmes, Elizabeth A Edwards, Alfred M Spormann
Bioremediation of groundwater contaminated with chlorinated aliphatic hydrocarbons such as perchloroethene and trichloroethene can result in the accumulation of the undesirable intermediate vinyl chloride. Such accumulation can either be due to the absence of specific vinyl chloride respiring Dehalococcoides mccartyi or to the inhibition of such strains by the metabolism of other microorganisms. The fitness of vinyl chloride respiring Dehalococcoides mccartyi subpopulations is particularly uncertain in the presence of chloroethene/chloroethane cocontaminant mixtures, which are commonly found in contaminated groundwater...
November 15, 2016: Environmental Science & Technology
https://www.readbyqxmd.com/read/27800712/multi-template-homology-based-structural-model-of-l-2-haloacid-dehalogenase-dehl-from-rhizobium-sp-rc1
#12
Aliyu Adamu, Mohd Shahir Shamsir, Roswanira Abdul Wahab, Sepideh Parvizpour, Fahrul Huyop
Dehalogenases are of high interest due to their potential applications in bioremediation and in synthesis of various industrial products. DehL is an L-2-haloacid dehalogenase (EC 3.8.1.2) that catalyses the cleavage of halide ion from L-2-halocarboxylic acid to produce D-2-hydroxycarboxylic acid. Although DehL utilises the same substrates as the other L-2-haloacid dehalogenases, its deduced amino acid sequence is substantially different (<25%) from those of the rest L-2-haloacid dehalogenases. To date, the 3D structure of DehL is not available...
November 21, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27795300/eya1-s-conformation-specificity-in-dephosphorylating-phosphothreonine-in-myc-and-its-activity-on-myc-stabilization-in-breast-cancer
#13
Jun Li, Yoel Rodriguez, Chunming Cheng, Lei Zeng, Elaine Y M Wong, Chelsea Y Xu, Ming-Ming Zhou, Pin-Xian Xu
EYA1 is known to be overexpressed in human breast cancer, in which the Myc protein is also accumulated in association with decreased phospho-T58 (pT58) levels. We have recently reported that EYA1 functions as a unique protein phosphatase to dephosphorylate Myc at pT58 to regulate Myc levels. However, it remains unclear whether EYA1-mediated Myc dephosphorylation on T58 is a critical function in regulating Myc protein stability in breast cancer. Furthermore, EYA1's substrate specificity has remained elusive...
January 1, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/27718236/production-of-chlorothalonil-hydrolytic-dehalogenase-from-agro-industrial-wastewater-and-its-application-in-raw-food-cleaning
#14
Xi-Hui Xu Qin He, Fan Zhang, Yu-Kai Tai, Yan-Fei Luo, Jian He, Qing Hong, Jian-Dong Jiang, Xin Yan
BACKGROUND: To reduce the fermentation cost for industrialization of chlorothalonil hydrolytic dehalogenase (Chd), agro-industrial wastewater including molasses, corn steep liquor (CSL) and fermentation wastewater were used to substitute the expensive carbon and nitrogen sources and fresh water for lab preparation. RESULTS: The results showed that molasses and CSL could replace 5% carbon source and 100% organic nitrogen source to maintain the same fermentation level...
October 8, 2016: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/27708637/microbiome-dynamics-of-a-polychlorobiphenyl-pcb-historically-contaminated-marine-sediment-under-conditions-promoting-reductive-dechlorination
#15
Bruna Matturro, Carla Ubaldi, Simona Rossetti
The toxicity of polychlorinated biphenyls (PCB) can be efficiently reduced in contaminated marine sediments through the reductive dechlorination (RD) process lead by anaerobic organohalide bacteria. Although the process has been extensively investigated on PCB-spiked sediments, the knowledge on the identity and metabolic potential of PCB-dechlorinating microorganisms in real contaminated matrix is still limited. Aim of this study was to explore the composition and the dynamics of the microbial communities of the marine sediment collected from one of the largest Sites of National Interest (SIN) in Italy (Mar Piccolo, Taranto) under conditions promoting the PCBs RD...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27677881/arabidopsis-th2-encodes-the-orphan-enzyme-thiamin-monophosphate-phosphatase
#16
Manaki Mimura, Rémi Zallot, Thomas D Niehaus, Ghulam Hasnain, Satinder K Gidda, Thuy N D Nguyen, Erin M Anderson, Robert T Mullen, Greg Brown, Alexander F Yakunin, Valérie de Crécy-Lagard, Jesse F Gregory, Donald R McCarty, Andrew D Hanson
To synthesize the cofactor thiamin diphosphate (ThDP), plants must first hydrolyze thiamin monophosphate (ThMP) to thiamin, but dedicated enzymes for this hydrolysis step were unknown and widely doubted to exist. The classical thiamin-requiring th2-1 mutation in Arabidopsis thaliana was shown to reduce ThDP levels by half and to increase ThMP levels 5-fold, implying that the THIAMIN REQUIRING2 (TH2) gene product could be a dedicated ThMP phosphatase. Genomic and transcriptomic data indicated that TH2 corresponds to At5g32470, encoding a HAD (haloacid dehalogenase) family phosphatase fused to a TenA (thiamin salvage) family protein...
October 2016: Plant Cell
https://www.readbyqxmd.com/read/27628599/identification-of-a-novel-sesquiterpene-biosynthetic-machinery-involved-in-astellolide-biosynthesis
#17
Yasutomo Shinohara, Shunji Takahashi, Hiroyuki Osada, Yasuji Koyama
Esterified drimane-type sesquiterpene lactones such as astellolides display various biological activities and are widely produced by plants and fungi. Given their low homology to known sesquiterpene cyclases, the genes responsible for their biosynthesis have not been uncovered yet. Here, we identified the astellolide gene cluster from Aspergillus oryzae and discovered a novel sesquiterpene biosynthetic machinery consisting of AstC, AstI, and AstK. All these enzymes are annotated as haloacid dehalogenase-like hydrolases, whereas AstC also contains a DxDTT motif conserved in class II diterpene cyclases...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27621279/the-marr-type-regulator-rdh2r-regulates-rdh-gene-transcription-in-dehalococcoides-mccartyi-strain-cbdb1
#18
Lydia Krasper, Hauke Lilie, Anja Kublik, Lorenz Adrian, Ralph Golbik, Ute Lechner
: Reductive dehalogenases are essential enzymes in organohalide respiration and consist of a catalytic subunit A and a membrane protein B, encoded by rdhAB genes. Thirty-two rdhAB genes exist in the genome of Dehalococcoides mccartyi strain CBDB1. To gain a first insight into the regulation of rdh operons, the control of gene expression of two rdhAB genes (cbdbA1453/cbdbA1452 and cbdbA1455/cbdbA1454) by the MarR-type regulator Rdh2R (cbdbA1456) encoded directly upstream was studied using heterologous expression and in vitro studies...
December 1, 2016: Journal of Bacteriology
https://www.readbyqxmd.com/read/27572957/structural-insight-into-dephosphorylation-by-trehalose-6-phosphate-phosphatase-otsb2-from-mycobacterium-tuberculosis
#19
Shan Shan, Haowei Min, Ting Liu, Dunquan Jiang, Zihe Rao
Trehalose serves as a key structural component in the cell wall of Mycobacterium tuberculosis. M. tuberculosis trehalose-6-phosphate phosphatase (MtbTPP), an essential enzyme in the trehalose biosynthesis OtsAB pathway, catalyzes the dephosphorylation of trehalose-6-phosphate (trehalose-6-P) to generate trehalose, and plays a critical role in M. tuberculosis survival-associated cell wall formation and permeability. Therefore, MtbTPP (OtsB2) is considered a promising potential target for discovery of antimicrobial drugs...
December 2016: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/27556449/how-many-conformations-of-enzymes-should-be-sampled-for-dft-mm-calculations-a-case-study-of-fluoroacetate-dehalogenase
#20
Yanwei Li, Ruiming Zhang, Likai Du, Qingzhu Zhang, Wenxing Wang
The quantum mechanics/molecular mechanics (QM/MM) method (e.g., density functional theory (DFT)/MM) is important in elucidating enzymatic mechanisms. It is indispensable to study "multiple" conformations of enzymes to get unbiased energetic and structural results. One challenging problem, however, is to determine the minimum number of conformations for DFT/MM calculations. Here, we propose two convergence criteria, namely the Boltzmann-weighted average barrier and the disproportionate effect, to tentatively address this issue...
August 20, 2016: International Journal of Molecular Sciences
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