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Stanislav Mazurenko, Sarka Bidmanova, Marketa Kotlanova, Jiri Damborsky, Zbynek Prokop
Analytical devices that combine sensitive biological component with a physicochemical detector hold a great potential for various applications, e.g., environmental monitoring, food analysis or medical diagnostics. Continuous efforts to develop inexpensive sensitive biodevices for detecting target substances typically focus on the design of biorecognition elements and their physical implementation, while the methods for processing signals generated by such devices have received far less attention. Here, we present fundamental considerations related to signal processing in biosensor design and investigate how undemanding signal treatment facilitates calibration and operation of enzyme-based biodevices...
2018: PloS One
Jonathan R Chekan, Bradley S Moore
While halogenases have been studied for decades, the first natural product dehalogenase was only recently described. This bacterial enzyme, Bmp8, catalyzes the reductive debromination of 2,3,4,5-tetrabromopyrrole to form 2,3,4-tribromopyrrole as part of the biosynthesis of pentabromopseudilin, a marine natural product. Bmp8 is hypothesized to utilize a catalytic mechanism analogous to the important human thyroid hormone deiodinase enzyme family, potentially enabling Bmp8 to serve as model system to study this conserved mechanism...
2018: Methods in Enzymology
Antonin Kunka, Jiri Damborsky, Zbynek Prokop
Haloalkane dehalogenases degrade halogenated compounds to corresponding alcohols by a hydrolytic mechanism. These enzymes are being intensively investigated as model systems in experimental and in silico studies of enzyme mechanism and evolution, but also hold importance as useful biocatalysts for a number of biotechnological applications. Haloalkane dehalogenases originate from various organisms including bacteria (degraders, symbionts, or pathogens), eukaryotes, and archaea. Several members of this enzyme family have been found in marine organisms...
2018: Methods in Enzymology
L Hermon, J Denonfoux, J Hellal, C Joulian, S Ferreira, S Vuilleumier, G Imfeld
Dichloromethane (DCM) is a widespread and toxic industrial solvent which often co-occurs with chlorinated ethenes at polluted sites. Biodegradation of DCM occurs under both oxic and anoxic conditions in soils and aquifers. Here we investigated in situ and ex situ biodegradation of DCM in groundwater sampled from the industrial site of Themeroil (France), where DCM occurs as a major co-contaminant of chloroethenes. Carbon isotopic fractionation (εC ) for DCM ranging from -46 to -22‰ were obtained under oxic or denitrifying conditions, in mineral medium or contaminated groundwater, and for laboratory cultures of Hyphomicrobium sp...
May 31, 2018: Water Research
Dominique Türkowsky, Patrick Lohmann, Marie Mühlenbrink, Torsten Schubert, Lorenz Adrian, Tobias Goris, Nico Jehmlich, Martin von Bergen
Thermal proteome profiling (TPP) is increasingly applied in eukaryotes to investigate protein-ligand binding through protein melting curve shifts induced by the presence of a ligand. In anaerobic bacteria, identification of protein-substrate interactions is a major challenge. We applied TPP to Sulfurospirillum multivorans, which is able to use trichloroethene as electron acceptor for growth, to investigate the interaction of its tetrachloroethene reductive dehalogenase PceA with trichloroethene. Several modifications in the protocol (e...
June 4, 2018: Journal of Proteomics
Alfredo Pérez-de-Mora, Anna Lacourt, Michaye L McMaster, Xiaoming Liang, Sandra M Dworatzek, Elizabeth A Edwards
Dehalococcoides mccartyi ( D. mccartyi ) strains differ primarily from one another by the number and identity of the reductive dehalogenase homologous catalytic subunit A ( rdhA ) genes within their respective genomes. While multiple rdhA genes have been sequenced, the activity of the corresponding proteins has been identified in only a few cases. Examples include the enzymes whose substrates are groundwater contaminants such as trichloroethene (TCE), cis -dichloroethene (cDCE) and vinyl chloride (VC). The associated rdhA genes, namely tceA, bvcA , and vcrA , along with the D...
2018: Frontiers in Microbiology
Piia Kokkonen, David Bednar, Veronika Dockalova, Zbynek Prokop, Jiri Damborsky
Haloalkane dehalogenases catalyze the hydrolysis of halogen-carbon bonds in organic halogenated compounds and as such are of great utility as biocatalysts. The crystal structures of the haloalkane dehalogenase DhlA from the bacterium from Xanthobacter autotrophicus GJ10, specifically adapted for the conversion of the small 1,2-dichloroethane (DCE) molecule, display the smallest catalytic site (110 Å3) within this enzyme family. However, during a substrate-specificity screening, we noted that DhlA can catalyze the conversion of far bulkier substrates, such as the 4-(bromomethyl)-6,7-dimethoxy-coumarin (220 Å3)...
June 1, 2018: Journal of Biological Chemistry
Norbert V Heeb, Manuel Mazenauer, Simon Wyss, Birgit Geueke, Hans-Peter E Kohler, Peter Lienemann
LinB is a haloalkane dehalogenase found in Sphingobium indicum B90A, an aerobic bacterium isolated from contaminated soils of hexachlorocyclohexane (HCH) dumpsites. We showed that this enzyme also converts hexabromocyclododecanes (HBCDs). Here we give new insights in the kinetics and stereochemistry of the enzymatic transformation of δ-HBCD, which resulted in the formation of two pentabromocyclododecanols (PBCDols) as first- (P1δ , P2δ ) and two tetrabromocyclododecadiols (TBCDdiols) as second-generation products (T1δ , T2δ )...
May 12, 2018: Chemosphere
Xiao-Jian Zhang, Ping-Xiu Shi, Han-Zhong Deng, Xin-Xin Wang, Zhi-Qiang Liu, Yu-Guo Zheng
Asymmetric synthesis of chiral epichlorohydrin (ECH) from 1,3-dichloro-2-propanol (1,3-DCP) using halohydrin dehalogenase (HHDH) is of great value due to the 100% theoretical yield and high enantioselectivity. In this study, HheC (P175S/W249P) was immobilized on an A502Ps resin and used for the preparation of (S)-ECH. In aqueous system, the immobilized HheC catalyzed the biosynthesis of (S)-ECH with 83.78% yield and 92.53% enantiomeric excess (ee) at 1,3-DCP concentration of 20 mM. The non-aqueous system was further developed using water saturated ethyl acetate as solvent and reaction phase...
May 8, 2018: Bioresource Technology
Abhishek Phatarphekar, Qi Su, Suk Ho Eun, Xin Chen, Steven E Rokita
The ability of iodotyrosine deiodinase to salvage iodide from iodotyrosine has long been recognized as critical for iodide homeostasis and proper thyroid function in vertebrates. The significance of its additional ability to dehalogenate bromo- and chlorotyrosine is less apparent and none of these functions could have been anticipated in invertebrates until recently. Drosophila , as most arthropods, contains a deiodinase homolog encoded by CG6279 , now named condet ( cdt ), with a similar catalytic specificity...
May 15, 2018: Journal of Biological Chemistry
Taejun Chin, Masahiko Ikeuchi
Sorbitol-6-phosphatase (EC catalyzes sorbitol production from sorbitol-6-phosphate in certain organisms, but has not been identified unequivocally. We screened the activity of the haloacid dehalogenase-like hydrolases (HAD) superfamily and identified four HAD proteins from Escherichia coli as sorbitol-6-phosphatase. Of these proteins, HAD2 (YfbT) exhibited catalytic activity (kcat /Km ) that was better than that of the previously reported "preferred" substrate. HAD1 (YniC) and HAD2 exhibited higher sorbitol-6-phosphatase activity than that of HAD12 (YbiV) and HAD13 (YidA)...
May 8, 2018: Journal of General and Applied Microbiology
Géraldine F Buttet, Mathilde S Willemin, Romain Hamelin, Aamani Rupakula, Julien Maillard
Organohalide respiration (OHR) is the energy metabolism of anaerobic bacteria able to use halogenated organic compounds as terminal electron acceptors. While the terminal enzymes in OHR, so-called reductive dehalogenases, are well-characterized, the identity of proteins potentially involved in electron transfer to the terminal enzymes remains elusive. Among the accessory genes identified in OHR gene clusters, the C subunit ( rdhC ) could well code for the missing redox protein between the quinol pool and the reductive dehalogenase, although it was initially proposed to act as transcriptional regulator...
2018: Frontiers in Microbiology
Thiau-Fu Ang, Jonathan Maiangwa, Abu Bakar Salleh, Yahaya M Normi, Thean Chor Leow
The variety of halogenated substances and their derivatives widely used as pesticides, herbicides and other industrial products is of great concern due to the hazardous nature of these compounds owing to their toxicity, and persistent environmental pollution. Therefore, from the viewpoint of environmental technology, the need for environmentally relevant enzymes involved in biodegradation of these pollutants has received a great boost. One result of this great deal of attention has been the identification of environmentally relevant bacteria that produce hydrolytic dehalogenases—key enzymes which are considered cost-effective and eco-friendly in the removal and detoxification of these pollutants...
May 7, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Torsten Schubert, Lorenz Adrian, R Gary Sawers, Gabriele Diekert
The utilization of halogenated organic compounds as terminal electron acceptors separates the phylogenetically diverse organohalide-respiring bacteria from other respiratory anaerobes that predominantly use nitrate, fumarate, sulfate or oxidized metals. Organohalide respiration is unique in recruiting a cobamide-containing iron-sulfur protein, the extracellular membrane-bound reductive dehalogenase, as terminal reductase in the electron transfer chain. In recent years substantial contributions have been made to the understanding of how electron transfer paths couple mechanistically to chemiosmosis in the organohalide-respiring bacteria...
April 1, 2018: FEMS Microbiology Ecology
Linlin Yang, Xu Jing, Bowen An, Cheng He, Yang Yang, Chunying Duan
By synergistic combination of multicomponent self-assembly and template-directed approaches, triply interlocked metal organic catenanes that consist of two isolated chirally identical tetrahedrons were constructed and stabilized as thermodynamic minima. In the presence of suitable template anions, the structural conversion from the isolated tetrahedral conformers into locked catenanes occurred via the cleavage of an intrinsically reversible coordination bond in each of the tetrahedrons, followed by the reengineering and interlocking of two fragments with the regeneration of the broken coordination bonds...
January 28, 2018: Chemical Science
Kaizhu Zeng, Qian Li, Jing Wang, Guowei Yin, Yajun Zhang, Chaoni Xiao, Taiping Fan, Xinfeng Zhao, Xiaohui Zheng
Protein immobilization techniques play an important role in the development of assays for disease diagnosis and drug discovery. However, many of these approaches are not applicable to transmembrane proteins. G protein-coupled receptors (GPCRs) are the largest protein superfamily encoded by the human genome and are targeted by a quarter of all prescription drugs. GPCRs are highly dynamic and sensitive to changes in the ambient environment, and current immobilization methodologies are not suitable for GPCRs. We used haloalkane dehalogenase (Halo) as an immobilization tag fused to the β2 -adrenoceptor (β2 -AR), angiotensin II type 1 (AT1 ) and angiotensin II type 2 (AT2 ) receptors...
January 14, 2018: Chemical Science
Mohsen Behbahani, Boren Lin, Tamara L Phares, Youngwoo Seo
The objective of this study is to evaluate the influence of water distribution system conditions (pH, total organic carbon, residual chlorine, and phosphate) on haloacetic acids (HAAs) biodegradation. A series of batch microcosm tests were conducted to determine biodegradation kinetics and collected biomass was used for real time quantitative reverse transcription polymerase chain reaction analyses to monitor how these drinking water distribution system conditions affect the relative expression of bacterial dehalogenase genes...
June 5, 2018: Journal of Hazardous Materials
Lingdi Zhang, Hengbo Zhou, Xueni Li, Rebecca L Vartuli, Michael Rowse, Yongna Xing, Pratyaydipta Rudra, Debashis Ghosh, Rui Zhao, Heide L Ford
Eya genes encode a unique family of multifunctional proteins that serve as transcriptional co-activators and as haloacid dehalogenase-family Tyr phosphatases. Intriguingly, the N-terminal domain of Eyas, which does not share sequence similarity to any known phosphatases, contains a separable Ser/Thr phosphatase activity. Here, we demonstrate that the Ser/Thr phosphatase activity of Eya is not intrinsic, but arises from its direct interaction with the protein phosphatase 2A (PP2A)-B55α holoenzyme. Importantly, Eya3 alters the regulation of c-Myc by PP2A, increasing c-Myc stability by enabling PP2A-B55α to dephosphorylate pT58, in direct contrast to the previously described PP2A-B56α-mediated dephosphorylation of pS62 and c-Myc destabilization...
March 13, 2018: Nature Communications
Géraldine Florence Buttet, Alexandra Marie Murray, Tobias Goris, Mélissa Burion, Biao Jin, Massimo Rolle, Christof Holliger, Julien Maillard
Two anaerobic bacterial consortia, each harboring a distinct Sulfurospirillum population, were derived from a 10 year old consortium, SL2, previously characterized for the stepwise dechlorination of tetrachloroethene (PCE) to cis-dichloroethene (cis-DCE) via accumulation of trichloroethene (TCE). Population SL2-1 dechlorinated PCE to TCE exclusively, while SL2-2 produced cis-DCE from PCE without substantial TCE accumulation. The reasons explaining the long-term coexistence of the populations were investigated...
May 1, 2018: FEMS Microbiology Ecology
Shubhangi Kaushik, Sérgio M Marques, Prashant Khirsariya, Kamil Paruch, Lenka Libichova, Jan Brezovsky, Zbynek Prokop, Radka Chaloupkova, Jiri Damborsky
The traditional way of rationally engineering enzymes to change their biocatalytic properties utilizes the modifications of their active sites. Another emerging approach is the engineering of structural features involved in the exchange of ligands between buried active sites and the surrounding solvent. However, surprisingly little is known about the effects of mutations that alter the access tunnels on the enzymes' catalytic properties, and how these tunnels should be redesigned to allow fast passage of cognate substrates and products...
April 2018: FEBS Journal
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