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https://www.readbyqxmd.com/read/29184004/a-global-view-of-structure-function-relationships-in-the-tautomerase-superfamily
#1
Rebecca Davidson, Bert-Jan Baas, Eyal Akiva, Gemma L Holliday, Benjamin J Polacco, Jake A LeVieux, Collin R Pullara, Yan Jessie Zhang, Christian P Whitman, Patricia C Babbitt
The tautomerase superfamily (TSF) consists of more than 11,000 non-redundant sequences present throughout the biosphere. Characterized members have attracted much attention because of the unusual and key catalytic role of an N-terminal proline. These few characterized members catalyze a diverse range of chemical reactions, but the full scale of their chemical capabilities and biological functions remains unknown. To gain new insight into TSF structure-function relationships, we performed a global analysis of similarities across the entire superfamily and computed a sequence-similarity network to guide classification into distinct subgroups...
November 28, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29182315/determinants-and-prediction-of-esterase-substrate-promiscuity-patterns
#2
Monica Martínez-Martínez, Cristina Coscolín, Gerard Santiago, Jennifer Chow, Peter J Stogios, Rafael Bargiela, Christoph Gertler, José Navarro-Fernández, Alexander Bollinger, Stephan Thies, Celia Méndez-García, Ana Popovic, Greg Brown, Tatyana N Chernikova, Antonio García-Moyano, Gro Ek Bjergah, Pablo Pérez-García, Tran Hai, Mercedes V Del Pozo, Runar Stokke, Ida H Steen, Hong Cui, Xiaohui Xu, Boguslaw P Nocek, María Alcaide, Marco Distaso, Victoria Mesa, Ana I Pelaez, Jesús Sánchez, Patrick C F Buchholz, Juergen Pleiss, Antonio Fernández-Guerra, Frank O Glöckner, Olga V Golyshina, Michail M Yakimov, Alexei Savchenko, Karl-Erich Jaeger, Alexander F Yakunin, Wolfgang R Streit, Peter N Golyshin, Victor Guallar, Manuel Ferrer
Esterases receive special attention because their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases substrate promiscuity level from sequence data and the molecular reasons why certain such enzymes are more promiscuous than others, remain to be elucidated. This limits the surveillance of the sequence space for esterases potentially leading to new versatile biocatalysts and new insights into their role in cellular function...
November 28, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29176711/exploration-of-protein-unfolding-by-modelling-calorimetry-data-from-reheating
#3
Stanislav Mazurenko, Antonin Kunka, Koen Beerens, Christopher M Johnson, Jiri Damborsky, Zbynek Prokop
Studies of protein unfolding mechanisms are critical for understanding protein functions inside cells, de novo protein design as well as defining the role of protein misfolding in neurodegenerative disorders. Calorimetry has proven indispensable in this regard for recording full energetic profiles of protein unfolding and permitting data fitting based on unfolding pathway models. While both kinetic and thermodynamic protein stability are analysed by varying scan rates and reheating, the latter is rarely used in curve-fitting, leading to a significant loss of information from experiments...
November 24, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29124958/streptomyces-sp-is-a-powerful-biotechnological-tool-for-the-biodegradation-of-hch-isomers-biochemical-and-molecular-basis
#4
S A Cuozzo, P E Sineli, J Davila Costa, G Tortella
Actinobacteria are well-known degraders of toxic materials that have the ability to tolerate and remove organochloride pesticides; thus, they are used for bioremediation. The biodegradation of organochlorines by actinobacteria has been demonstrated in pure and mixed cultures with the concomitant production of metabolic intermediates including γ-pentachlorocyclohexene (γ-PCCH); 1,3,4,6-tetrachloro-1,4-cyclohexadiene (1,4-TCDN); 1,2-dichlorobenzene (1,2-DCB), 1,3-dichlorobenzene (1,3-DCB), or 1,4-dichlorobenzene (1,4-DCB); 1,2,3-trichlorobenzene (1,2,3-TCB), 1,2,4-trichlorobenzene (1,2,4-TCB), or 1,3,5-trichlorobenzene (1,3,5-TCB); 1,3-DCB; and 1,2-DCB...
November 10, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/29112726/reconstructed-genomes-of-novel-dehalococcoides-mccartyi-strains-from-1-2-3-4-tetrachlorodibenzo-p-dioxin-dechlorinating-enrichment-cultures-reveal-divergent-reductive-dehalogenase-gene-profiles
#5
Hang T Dam, John Vollmers, Anne-Kristin Kaster, Max M Häggblom
Polychlorinated dibenzo-p-dioxin (PCDD) contaminated sites are widespread and associated with a variety of anthropogenic sources. PCDDs and other organohalide pollutants can serve as terminal electron acceptors for anaerobic respiration by specialized bacteria containing reductive dehalogenases (RdhA). These microorganisms, therefore, play an important role in bioremediation of PCDD contaminated sites. Two anaerobic enrichment cultures established using sediments collected from the PCDD polluted Hackensack (USA) and Kymijoki (Finland) rivers showed robust reductive dechlorination of 1,2,3,4-tetrachlorodibenzo-p-dioxin (1,2,3,4-TeCDD)...
November 3, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29111295/kinetic-and-structural-characterization-of-a-cis-3-chloroacrylic-acid-dehalogenase-homologue-in-pseudomonas-sp-uw4-a-potential-step-between-subgroups-in-the-tautomerase-superfamily
#6
Jake A LeVieux, Bert-Jan Baas, Tamer S Kaoud, Rebecca Davidson, Patricia C Babbitt, Yan Jessie Zhang, Christian P Whitman
A Pseudomonas sp. UW4 protein (UniProt K9NIA5) of unknown function was identified as similar to 4-oxalocrotonate tautomerase (4-OT)-like and cis-3-chloroacrylic acid dehalogenase (cis-CaaD)-like subgroups of the tautomerase superfamily (TSF). This protein lacks only Tyr-103 of the amino acids critical for cis-CaaD activity (Pro-1, His-28, Arg-70, Arg-73, Tyr-103, Glu-114). As it may represent an important variant of these enzymes, its kinetic and structural properties have been determined. The protein shows tautomerase activity with phenylenolpyruvate, but lacks native 4-OT activity and dehalogenase activity with the isomers of 3-chloroacrylic acid...
October 27, 2017: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/29106396/purinyl-cobamide-is-a-native-prosthetic-group-of-reductive-dehalogenases
#7
Jun Yan, Meng Bi, Allen K Bourdon, Abigail T Farmer, Po-Hsiang Wang, Olivia Molenda, Andrew T Quaile, Nannan Jiang, Yi Yang, Yongchao Yin, Burcu Şimşir, Shawn R Campagna, Elizabeth A Edwards, Frank E Löffler
Cobamides such as vitamin B12 are structurally conserved, cobalt-containing tetrapyrrole biomolecules that have essential biochemical functions in all domains of life. In organohalide respiration, a vital biological process for the global cycling of natural and anthropogenic organohalogens, cobamides are the requisite prosthetic groups for carbon-halogen bond-cleaving reductive dehalogenases. This study reports the biosynthesis of a new cobamide with unsubstituted purine as the lower base and assigns unsubstituted purine a biological function by demonstrating that Coα-purinyl-cobamide (purinyl-Cba) is the native prosthetic group in catalytically active tetrachloroethene reductive dehalogenases of Desulfitobacterium hafniense...
November 6, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/29101190/a-haloalkane-dehalogenase-from-a-marine-microbial-consortium-possessing-exceptionally-broad-substrate-specificity
#8
T Buryska, P Babkova, O Vavra, J Damborsky, Z Prokop
The haloalkane dehalogenase enzyme DmmA was identified by marine metagenomic screening. Determination of its crystal structure revealed an unusually large active site compared to previously characterized haloalkane dehalogenases. Here we present a biochemical characterization of this interesting enzyme with emphasis on its structure-function relationships. DmmA exhibited an exceptionally broad substrate specificity and degraded several halogenated environmental pollutants that are resistant to other members of this enzyme family...
November 3, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29040506/high-throughput-sequencing-revealed-novel-dehalococcoidia-in-dechlorinating-microbial-enrichments-from-pcb-contaminated-marine-sediments
#9
Bruna Matturro, Emanuela Frascadore, Simona 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...
November 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/29040502/comparative-genomics-of-the-genus-desulfitobacterium
#10
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
#11
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 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. The 16S rRNA gene sequences specific to the dehalogenating genera Dehalobacter, Desulfitobacterium and Dehalogenimonas were detected in 15/15, 13/15 and 13/15 samples, respectively, while Dehalococcoides sequences were found in 9/15 samples...
November 1, 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
#12
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
#13
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
#14
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...
November 7, 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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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