Read by QxMD icon Read


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
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
Manaki Mimura, Rémi Zallot, Thomas Daniel Niehaus, Ghulam Hasnain, Satinder K Gidda, Thuy Nd Nguyen, Erin M Anderson, Robert T Mullen, Greg Brown, Alexander F Yakunin, Valerié 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 was shown to reduce ThDP levels by half and to increase ThMP levels five-fold, implying that the THIAMIN REQUIRING 2 (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...
September 27, 2016: Plant Cell
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
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 get a first insight into the regulation of rdh operons, the control of gene expression of rdhA1453/rdhB1452 and rdhA1455/rdhB1454 by a MarR-type regulator RdhR1456 encoded directly upstream was studied using heterologous expression and in vitro studies...
September 12, 2016: Journal of Bacteriology
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...
August 29, 2016: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
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...
2016: International Journal of Molecular Sciences
Rui-Juan Niu, Qing-Chuan Zheng, Hong-Xing Zhang
The haloalkaloic acid dehalogenase (HAD) phosphatase from Thermococcus onnurineus NA1 (TON_0338), has phosphatase activity the flavin mono-nucleotide (FMN). The molecular origin and structural motifs for the activity deficiency of double-tryptophan mutant have not been rationalized at atomic resolution. Molecular dynamics (MD) simulations and the molecular mechanics/Generalized-Born surface area (MM/GBSA) free energy calculations were used to explore the effects of mutations on the changes in both structural flexibility and conformational dynamics...
September 2016: Journal of Molecular Graphics & Modelling
Samuel H Schneider, Steven G Boxer
IR and Raman frequency shifts have been reported for numerous probes of enzyme transition states, leading to diverse interpretations. In the case of the model enzyme ketosteroid isomerase (KSI), we have argued that IR spectral shifts for a carbonyl probe at the active site can provide a connection between the active site electric field and the activation free energy (Fried et al. Science 2014, 346, 1510-1514). Here we generalize this approach to a much broader set of carbonyl probes (e.g., oxoesters, thioesters, and amides), first establishing the sensitivity of each probe to an electric field using vibrational Stark spectroscopy, vibrational solvatochromism, and MD simulations, and then applying these results to reinterpret data already in the literature for enzymes such as 4-chlorobenzoyl-CoA dehalogenase and serine proteases...
September 15, 2016: Journal of Physical Chemistry. B
Iren Wang, Szu-Yu Chen, Shang-Te Danny Hsu
DehI is a homodimeric haloacid dehalogenase from Pseudomonas putida that contains the most complex 61 Stevedore's protein knot within its folding topology. To examine how DehI attains such an intricate knotted topology we combined far-UV circular dichroism (CD), intrinsic fluorescence spectroscopy and small angle X-ray scattering (SAXS) to investigate its folding mechanism. Equilibrium unfolding of DehI by chemical denaturation indicated the presence of two highly populated folding intermediates, I and I'. While the two intermediates vary in secondary structure contents and tertiary packing according to CD and intrinsic fluorescence, respectively, their overall dimension and compactness are similar according to SAXS...
2016: Scientific Reports
Anett Schallmey, Marcus Schallmey
Halohydrin dehalogenases are industrially relevant enzymes that catalyze the reversible dehalogenation of vicinal haloalcohols with formation of the corresponding epoxides. In the reverse reaction, also other negatively charged nucleophiles such as azide, cyanide, or nitrite are accepted besides halides to open the epoxide ring. Thus, novel C-N, C-C, or C-O bonds can be formed by halohydrin dehalogenases, which makes them attractive biocatalysts for the production of various β-substituted alcohols. Despite the fact that only five individual halohydrin dehalogenase enzyme sequences have been known until recently enabling their heterologous production, a large number of different biocatalytic applications have been reported using these enzymes...
September 2016: Applied Microbiology and Biotechnology
Na Sa, Renu Rawat, Chelsea Thornburg, Kevin D Walker, Sanja Roje
Despite the importance of riboflavin as the direct precursor of the cofactors flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN), the physiologically relevant catalyst dephosphorylating the riboflavin biosynthesis pathway intermediate 5-amino-6-ribitylamino-2,4(1H,3H) pyrimidinedione 5'-phosphate (ARPP) has not been characterized from any organism. By using as the query sequence a previously identified plastidial FMN hydrolase AtcpFHy1 (At1g79790), belonging to the haloacid dehalogenase (HAD) superfamily, seven candidates for the missing ARPP phosphatase were found, cloned, recombinantly expressed, and purified...
August 4, 2016: Plant Journal: for Cell and Molecular Biology
Rong-Zhen Liao, Shi-Lu Chen, Per E M Siegbahn
PceA is a cobalamin-dependent reductive dehalogenase that catalyzes the dechlorination of perchloroethylene to trichloroethylene and then to cis-dichloroethylene as the sole final product. The reaction mechanism and the regioselectivity of this enzyme are investigated by using density functional calculations. Four different substrates, namely, perchloroethylene, trichloroethylene, cis-dichloroethylene, and chlorotheylene, have been considered and were found to follow the same reaction mechanism pattern. The reaction starts with the reduction of Co(II) to Co(I) through a proton-coupled electron transfer process, with the proton delivered to a Tyr246 anion...
August 22, 2016: Chemistry: a European Journal
Bat-Erdene Jugder, Haluk Ertan, Yie Kuan Wong, Nady Braidy, Michael Manefield, Christopher P Marquis, Matthew Lee
Organohalide respiring bacteria (ORB) are capable of utilising organohalides as electron acceptors for the generation of cellular energy and consequently play an important role in the turnover of natural and anthropogenically-derived organohalides. In this study, the response of a Dehalobacter sp. strain UNSWDHB to the addition of trichloromethane (TCM) after a 50 h period of its absence (suffocation) was evaluated from a transcriptomic and proteomic perspective. The up-regulation of TCM reductive dehalogenase genes (tmrABC) and their gene products (TmrABC) was confirmed at both transcriptional and proteomic levels...
July 25, 2016: Environmental Microbiology Reports
Hui Jian, Yingwu Wang, Yan Bai, Rong Li, Renjun Gao
Formylglycine-generating enzymes can selectively recognize and oxidize cysteine residues within the sulfatase sub motif at the terminus of proteins to form aldehyde-bearing formylglycine (FGly) residues, and are normally used in protein labeling. In this study, an aldehyde tag was introduced to proteins using formylglycine-generating enzymes encoded by a reconstructed set of the pET28a plasmid system for enzyme immobilization. The haloacid dehalogenase ST2570 from Sulfolobus tokodaii was used as a model enzyme...
2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Pascal Weigold, Mohamed El-Hadidi, Alexander Ruecker, Daniel H Huson, Thomas Scholten, Maik Jochmann, Andreas Kappler, Sebastian Behrens
In soils halogens (fluorine, chlorine, bromine, iodine) are cycled through the transformation of inorganic halides into organohalogen compounds and vice versa. There is evidence that these reactions are microbially driven but the key enzymes and groups of microorganisms involved are largely unknown. Our aim was to uncover the diversity, abundance and distribution of genes encoding for halogenating and dehalogenating enzymes in a German forest soil by shotgun metagenomic sequencing. Metagenomic libraries of three soil horizons revealed the presence of genera known to be involved in halogenation and dehalogenation processes such as Bradyrhizobium or Pseudomonas...
2016: Scientific Reports
Aliyu Adamu, Roswanira Abdul Wahab, Fahrul Huyop
l-2-Haloacid dehalogenase (DehL) from Rhizobium sp. RC1 is a stereospecific enzyme that acts exclusively on l-isomers of 2-chloropropionate and dichloroacetate. The amino acid sequence of this enzyme is substantially different from those of other l-specific dehalogenases produced by other organisms. DehL has not been crystallised, and hence its three-dimensional structure is unavailable. Herein, we review what is known concerning DehL and tentatively identify the amino acid residues important for catalysis based on a comparative structural and sequence analysis with well-characterised l-specific dehalogenases...
2016: SpringerPlus
Mohamed Faraj Edbeib, Roswanira Abdul Wahab, Fahrul Huyop
The unique cellular enzymatic machinery of halophilic microbes allows them to thrive in extreme saline environments. That these microorganisms can prosper in hypersaline environments has been correlated with the elevated acidic amino acid content in their proteins, which increase the negative protein surface potential. Because these microorganisms effectively use hydrocarbons as their sole carbon and energy sources, they may prove to be valuable bioremediation agents for the treatment of saline effluents and hypersaline waters contaminated with toxic compounds that are resistant to degradation...
August 2016: World Journal of Microbiology & Biotechnology
Jacob E Munro, Elissa F Liew, Mai-Anh Ly, Nicholas V Coleman
UNLABELLED: 1,2-Dichloroethane (DCA) is a problematic xenobiotic groundwater pollutant. Bacteria are capable of biodegrading DCA, but the evolution of such bacteria is not well understood. In particular, the mechanisms by which bacteria acquire the key dehalogenase genes dhlA and dhlB have not been well defined. In this study, the genomic context of dhlA and dhlB was determined in three aerobic DCA-degrading bacteria (Starkeya novella strain EL1, Xanthobacter autotrophicus strain EL4, and Xanthobacter flavus strain EL8) isolated from a groundwater treatment plant (GTP)...
September 1, 2016: Applied and Environmental Microbiology
Trent A Key, Dray P Richmond, Kimberly S Bowman, Yong-Joon Cho, Jongsik Chun, Milton S da Costa, Fred A Rainey, William M Moe
Dehalogenimonas alkenigignens IP3-3(T) is a strictly anaerobic, mesophilic, Gram negative staining bacterium that grows by organohalide respiration, coupling the oxidation of H2 to the reductive dehalogenation of polychlorinated alkanes. Growth has not been observed with any non-polyhalogenated alkane electron acceptors. Here we describe the features of strain IP3-3(T) together with genome sequence information and its annotation. The 1,849,792 bp high-quality-draft genome contains 1936 predicted protein coding genes, 47 tRNA genes, a single large subunit rRNA (23S-5S) locus, and a single, orphan, small unit rRNA (16S) locus...
2016: Standards in Genomic Sciences
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"