Biodegradation of chlorpyrifos and its hydrolyzing metabolite 3,5,6-trichloro-2-pyridinol by Sphingobacterium sp. JAS3

Biodegradation of chlorpyrifos and its metabolite 3,5,6-trichloro-2-pyridinol (TCP) were studied in aqueous medium and in soil with a novel bacterial strain JAS3. The molecular characterization based on 16S rRNA sequence analysis revealed the strain JAS3 as Sphingobacterium sp. The strain JAS3 was able to grow in minimal salt medium (MSM) supplemented with 300 mg l^?1 of chlorpyrifos as sole carbon source. The degradation of chlorpyrifos and its primary metabolite TCP were examined by HPLC. After 5 d, Sphingobacterium sp. JAS3 degraded chlorpyrifos and its metabolite TCP to benzene, 1,3-bis(1,1-dimethylethyl) was analyzed by GCMS. Degradation of chlorpyrifos and TCP in soil with and without addition of nutrients was also studied. The ability to degrade chlorpyrifos makes this strain a useful candidate for remediation of pesticide contaminated sites.     

微生物降解3,5,6-三氯-2-吡啶醇的研究进展

随着高毒性有机磷杀虫剂的限制和禁止使用,近年来以毒死蜱为代表的低毒性有机磷杀虫剂的市场份额有所增加。然而,毒死蜱的使用也导致了环境中3,5,6-三氯-2-吡啶醇(TCP)的产生,因为TCP是毒死蜱和甲基毒死蜱在环境中降解的主要中间代谢产物。它具有较高的水溶性和迁移性,容易进入深层土壤及水体环境,从而引起广泛的污染。释放到环境中的TCP不仅可以抑制TCP及其母体化合物毒死蜱和甲基毒死蜱的生物降解,而且也能抑制其他有机污染物的生物降解,从而进一步加重环境中TCP以及其他有机污染物的累积残留,影响环境系统的自我修复功能。本文概述了TCP及其母体化合物的结构、TCP的生态毒性、TCP降解菌的多样性及其微生物降解的最新研究进展,为毒死蜱和TCP污染地区进行经济可行的生物修复提供参考。     

Computational studies of H5N1 hemagglutinin binding with SA-alpha-2, 3-Gal and SA-alpha-2, 6-Gal

For influenza H5N1 hemagglutinin, a switch from SA-alpha-2, 3-Gal to SA-alpha-2, 6-Gal receptor specificity is a critical step leading to the conversion from avian-to-human to human-to-human infection. Therefore, the understanding of the binding modes of SA-alpha-2, 3-Gal and SA-alpha-2, 6-Gal to H5N1 hemagglutinin will be very important for the examination of possible mutations needed for going from an avian to a human flu virus. Based on the available H5N1 hemagglutinin crystal structure, the binding profiles between H5N1 hemagglutinin and two saccharide ligands, SA-alpha-2, 3-Gal and SA-alpha-2, 6-Gal, were investigated by ab initio quantum mechanics, molecular docking, molecular mechanics, and molecular dynamics simulations. It was found that SA-alpha-2, 3-Gal has strong multiple hydrophobic and hydrogen bond interactions in its trans conformation with H5N1 hemagglutinin, whereas the SA-alpha-2, 6-Gal only shows weak interactions in a different conformation (cis type).     

Identification and characterization of chlorpyrifos-methyl and 3,5,6-trichloro-2-pyridinol degrading Burkholderia sp. strain KR100

A chlorpyrifos-methyl (CM) degrading bacterium (designated strain KR100) was isolated from a Korean rice paddy soil and was further tested for its sensitivity against eight commercial antibiotics. Based on morphological, biochemical, and molecular characteristics, this bacterium showed greatest similarity to members of the order Burkholderiales and was shown to be most closely related to members of the Burkholderia cepacia group. Strain KR100 hydrolyzed CM to 3,5,6-trichloro-2-pyridinol (TCP) and utilized TCP as the sole source of carbon for its growth. The isolate was also able to degrade chlorpyrifos, dimethoate, fenitrothion, malathion, and monocrotophos at 300 μg/ml but diazinon, dicrotophos, parathion, and parathion-methyl at 100 μg/ml. The ability to degrade CM was found to be encoded on a single plasmid of ~50 kb, pKR1. Genes encoding resistance to amphotericin B, polymixin B sulfate, and tetracycline were also located on the plasmid. This bacterium merits further study as a potential biological agent for the remediation of soil, water, or crop contaminated with organophosphorus compounds because of its greater biodegradation activity and its broad specificity against a range of organophosphorus insecticides.     

Biodegradation of chlorpyrifos and 3,5,6-trichloro-2-pyridinol by a newly isolated Paracoccus sp. strain TRP

A bacterium, isolated from activated sludge and named strain TRP, could biodegrade chlorpyrifos and 3,5,6-trichloro-2-pyridinol. Phenotypic features, physiological and chemotaxonomic characteristics, and phylogenetic analysis of 16S rRNA sequence revealed that the isolate belongs to the genus of Paracoccus. Strain TRP could also degrade pyridine, methyl parathion and carbonfuran when provided as sole carbon and energy sources. Native-PAGE and enzymatic degradation assay of the cell-free extracts indicated that an alternative degradation mechanism might involve an inducible enzyme. Degradation study of chlorpyrifos by strain TRP was examined by GC–MS and HPLC; no persistent accumulated metabolite was observed. To the best of our knowledge, this is the first report of a bacterium that could completely mineralize chlorpyrifos. This isolate will be potentially useful in biotreatment of wastewaters and bioremediation of contaminated soils.     

Isolation of a novel gene encoding a 3,5,6-trichloro-2-pyridinol degrading enzyme from a cow rumen metagenomic library

3,5,6-trichloro-2-pyridinol (TCP) is a major metabolite of the insecticide chlorpyrifos and is hazardous to human and animal health. A gene encoding a TCP degrading enzyme was cloned from a metagenomic library prepared from cow rumen. The gene (tcp3A) is 2.5 kb in length, encoding a protein (Tcp3A) of 599 amino acid residues. Tcp3A has a potential signal sequence, as well as a putative ATP/GTP binding site, and a likely amidation site. The molecular weight of the enzyme is 62 kDa by SDS–PAGE. Comparison of Tcp3A with the NCBI database using BLASTP revealed homology to amidohydrolase proteins. Recombinant Escherichia coli harboring the tcp3A gene could utilize TCP as the sole source of carbon. TLC and HPLC revealed that TCP was degraded by recombinant E. coli harboring tcp3A. This is the first report of a gene encoding a TCP degrading enzyme.     

Nse5/6 inhibits the Smc5/6 ATPase and modulates DNA substrate binding

Eukaryotic cells employ three SMC (structural maintenance of chromosomes) complexes to control DNA folding and topology. The Smc5/6 complex plays roles in DNA repair and in preventing the accumulation of deleterious DNA junctions. To elucidate how specific features of Smc5/6 govern these functions, we reconstituted the yeast holo‐complex. We found that the Nse5/6 sub‐complex strongly inhibited the Smc5/6 ATPase by preventing productive ATP binding. This inhibition was relieved by plasmid DNA binding but not by short linear DNA, while opposing effects were observed without Nse5/6. We uncovered two binding sites for Nse5/6 on Smc5/6, based on an Nse5/6 crystal structure and cross‐linking mass spectrometry data. One binding site is located at the Smc5/6 arms and one at the heads, the latter likely exerting inhibitory effects on ATP hydrolysis. Cysteine cross‐linking demonstrated that the interaction with Nse5/6 anchored the ATPase domains in a non‐productive state, which was destabilized by ATP and DNA. Under similar conditions, the Nse4/3/1 module detached from the ATPase. Altogether, we show how DNA substrate selection is modulated by direct inhibition of the Smc5/6 ATPase by Nse5/6.     

In vitro selection of DNA aptamers binding pesticide fluoroacetamide

Fluoroacetamide (Mw = 77.06) is a lethal rodenticide to humans and animals which is still frequently abused in food storage somewhere in China. The production of antibodies for fluoroacetamide is difficult due to its high toxicity to animals, which limits the application of immunoassay method in poison detection. In this work, aptamers targeting N-fluoroacetyl glycine as an analog of fluoroacetamide were selected by a specific systematic evolution of ligands by exponential enrichment (SELEX) strategy. The binding ability of the selected aptamers to fluoroacetamide was identified using surface plasmon resonance (SPR)-based assay. The estimated K_D values in the low micromolar range showed a good affinity of these aptamers to the target. Our work verified that the SELEX strategy has the potential for developing aptamers targeted to small molecular toxicants and aptamers can be employed as new recognition elements instead of antibodies for poison detection.     

Synthesis, DNA binding, and cleavage studies of novel PNA binding cyclen complexes

A novel coumarin‐appended PNA binding cyclen derivative ligand, C1 , and its copper(II) complex, C2 , have been synthesized and characterized. The interaction of these compounds with DNA was systematically investigated by absorption, fluorescence, and viscometric titration, and DNA‐melting and gel‐electrophoresis experiments. DNA Melting and viscometric titration experiments indicate that the binding mode of C1 is a groove binding, and C2 is a multiple binding mode that involves groove binding and electrostatic binding. From the absorption‐titration data, we can state that the primary interaction between CT DNA and the two compounds may be H‐bonds between nucleobases. Fluorescence studies indicate that the binding ability of C1 to d(A)₉ is as twice or thrice as that of other oligodeoxynucleotides. Agarose gel‐electrophoresis experiments demonstrate that C2 is an excellent chemical nuclease, which can cleave plasmid DNA completely within 24 h.     

Partners apart: Smc6-independent DNA binding activity of Smc5 on single-strand DNA

Comment on: Roy MA, et al. Cell Cycle 2011; 10:690-700.     

In vivo dopamine receptor binding studies with a non-radioactively labeled agonist,dipropyl-5, 6-ADTN

Evidence is presented that a low dose of peripherally administered N, N-dipropylamino-5, 6-dihydroxytetralin (DiPr-5, 6-ADTN) specifically labels dopamine (DA) receptors in rat brain.Concentrations of this potent DA receptor agonist were determined by a highly selective method using reversed phase liquid chromatography and amperometric detection. The binding characteristics satisfy all criteria regarding saturability, stereospecificity, regional distribution and relation with pharmacological effects that are associated with DA receptor interactions. A rough estimation of the density of binding sites in the striatum resulted in values of 60–70 pmol/g. Lesioning the nigrostriatal pathway does not significantly alter the amount of ligand bound, nor do pretreatments with serotonergic, α-adrenergic or β-adrenergic antagonists. DiPr-5, 6-ADTN has thus been shown to be a useful ligand for labeling central DA receptors and a powerful tool in the study of DA-ergic mechanisms.     

dabPNA: design, synthesis, and DNA binding studies

In continuing our research efforts for developing new oligodeoxynucleotide (ODN)-like drugs and diagnostics, we designed diaminobutyric peptide nucleic acids (dabPNAs), nucleopeptides characterized by a diaminobutyric-based building block that is an isomer of the aminoethylglycyl PNA (aegPNA) unit and the acyclic modification of the aminoprolyl PNA (ampPNA) monomer. In this work we present the solid phase synthesis of a dabPNA oligomer and of two aegPNAs containing a single dabPNA unit. A study relative to their binding ability towards DNA is also reported even in comparison with the well known aegPNAs.     

Preparation and properties of N6-monobutyryl adenosine 5'-monophosphate. A major hepatic metabolite of N6,O2'-dibutyryl cyclic adenosine 3':5'-monophosphate.

The synthesis and properties of N6-monobutyryl adenosine 5'-monophosphate are described. The properties of synthesized monobutyryl nucleotide have been compared to those of a metabolite recognized in previous studies (Castagna, M. C., Palmer, W.K., and Walsh, D.A. (1977) Arch. Biochem. Biophys. 181, 46-60) as the major radioactive product produced in the liver upon perfusion with N6,O2'-dibutyryl cyclic [3H]adenosine 3':5'-monophosphate. By the criteria of cochromatography on DEAE-cellulose and in three thin layer chromatographic systems and from equivalent rates of alkaline hydrolysis, N6-monobutyryl adenosine 5'-monophosphate has been identified as a major hepatic metabolite of N6,O2'-dibutyryl cyclic adenosine 3':5'-monophosphate.     

Mutagenicity studies with N6, O2'-dibutyryl cyclic adenosine 3',5'-monophosphate (DBcAMP)

N6,O2'-Dibutyryl cyclic adenosine 3,5-monophosphate (DBcAMP) was studied for mutagenicity using the rec assay, the Ames method, and in vitro cytogenetics. DBcAMP had no mutagenic effect on B. subtilis in the rec assay, or on S. typhimurium (TA1535, TA1537, TA1538, TA98 and TA100) or E. coli (WP2 uvrA). In the cytogenetic study, a significant increase in chromosomal aberrations was observed at a concentration of 50,000 micrograms/ml, but it was considered that this effect could be attributed to the secondary effect of the high osmotic pressure in the culture medium. These results suggest that DBcAMP has no mutagenic potential.     

Fluorescence and photoelectron studies of the intercalative binding of benz(a)anthracene metabolite models to DNA

An analog of the peptidyl transferase inhibitor sparsomycin was a competitive inhibitor (Ki = 1.8 microM) of peptidyl-puromycin synthesis on E. coli polysomes. Preincubation of polysomes with the compound enhanced the degree of inhibition of peptide bond formation. A model for the involvement of a histidine residue in peptidyl transferase activity is presented as a result of our observations which include direct association of [3H] labelled analog with 70S ribosomes. The correct oxidation state of sulfur in the compound was necessary for the "preincubation effect" and entry of the compound into bacterial cells.     

Synthesis,antiproliferative and antitrypanosomal activities,and DNA binding of novel 6-amidino-2-arylbenzothiazoles

A series of 6-amidinobenzothiazoles, linked via phenoxymethylene or directly to the 1,2,3-triazole ring with a p-substituted phenyl or benzyl moiety, were synthesised and evaluated in vitro against four human tumour cell lines and the protozoan parasite Trypanosoma brucei. The influence of the type of amidino substituent and phenoxymethylene linker on antiproliferative and antitrypanosomal activities was observed, showing that the imidazoline moiety had a major impact on both activities. Benzothiazole imidazoline 14a, which was directly connected to N-1-phenyl-1,2,3-triazole, had the most potent growth-inhibitory effect (IC₅₀ = 0.25 µM) on colorectal adenocarcinoma (SW620), while benzothiazole imidazoline 11b, containing a phenoxymethylene linker, exhibited the best antitrypanosomal potency (IC₉₀ = 0.12 µM). DNA binding assays showed a non-covalent interaction of 6-amidinobenzothiazole ligands, indicating both minor groove binding and intercalation modes of DNA interaction. Our findings encourage further development of novel structurally related 6-amidino-2-arylbenzothiazoles to obtain more selective anticancer and anti-HAT agents.