Insight into the metabolism of 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) by biphenyl dioxygenases

In this work we have investigated the ability of the biphenyl dioxygenase of Burkholderia xenovorans LB400 (BphAE_LB400) and of Pandoraea pnomenusa B356 (BphAE_B356) to metabolize DDT. Data show BphAE_LB400 is unable to metabolize this substrate but BphAE_B356 metabolizes DDT to produce two stereoisomers. Structural analysis of DDT-docked BphAE_LB400 and BphAE_B356 identified residue Phe336 of BphAE_LB400 as critical to prevent productive binding of DDT to BphAE_LB400. Furthermore, the fact that residue Gly319 of BphAE_B356 is less constrained than Gly321 of BphAE_LB400 most likely contributes to the ability of BphAE_B356 to bind DDT productively. This was confirmed by examining the ability of BphAE chimeras obtained by shuffling bphA genes from strain B356 and LB400. Chimeras where residues Thr335 (which modulates the constraints on Gly321) and Phe336 (which contacts the substrate) of BphAE_LB400 were replaced by Gly and Ile respectively were able to metabolize DDT. However their stereospecificities varied depending on the presence of other segments or residues from BphAE_B356. Structural analysis suggests that either one or both of residue 267 and a segments comprised of residue 247–260 are likely involved in stereospecificity.     

Molecular analysis of <Emphasis Type="Italic">Agrobacterium</Emphasis> T-DNA integration in tomato reveals a role for left border sequence homology in most integration events

Studies in several plants have shown that Agrobacterium tumefaciens T-DNA can integrate into plant chromosomal DNA by different mechanisms involving single-stranded (ss) or double-stranded (ds) forms. One mechanism requires sequence homology between plant target and ssT-DNA border sequences and another double-strand-break repair in which preexisting chromosomal DSBs “capture” dsT-DNAs. To learn more about T-DNA integration in Solanum lycopersicum we characterised 98 T-DNA/plant DNA junction sequences and show that T-DNA left border (LB) and right border transfer is much more variable than previously reported in Arabidopsis thaliana and Populus tremula. The analysis of seven plant target sequences showed that regions of homology between the T-DNA LB and plant chromosomal DNA plays an important role in T-DNA integration. One T-DNA insertion generated a target sequence duplication that resulted from nucleolytic processing of a LB/plant DNA heteroduplex that generated a DSB in plant chromosomal DNA. One broken end contained a captured T-DNA that served as a template for DNA repair synthesis. We propose that most T-DNA integrations in tomato require sequence homology between the ssT-DNA LB and plant target DNA which results in the generation of DSBs in plant chromosomal DNA.     

Biocontrol of tomato late blight with the combination of epiphytic antagonists and rhizobacteria

Control of tomato late blight (LB) in Brazil is heavily based on chemicals. However, reduction in fungicide usage is required in both conventional and organic production systems. Assuming that biological control is an alternative for LB management, 208 epiphytic microorganisms and 23 rhizobacteria (RB) were isolated from conventional and organically grown tomato plants and tested for antagonistic activity against Phytophthora infestans. Based on in vitro inhibition of sporangia germination and detached leaflet bioassays, four EP microorganisms (Aspergillus sp., Cellulomonas flavigena, Candida sp., and Cryptococcus sp.) were selected. These microorganisms were applied either singly or combined on tomato plants treated or not with the RB Bacillus cereus. On control plants, LB progress rate (r), area under disease progress curve, and final disease severity were high. Lowest values of final severity were recorded on plants colonized by B. cereus and treated with C. flavigena, Candida sp. and Cryptococcus sp. There was no reduction on disease severity in plants treated only with RB. Biological control of LB resulted in low values of r and final severity. Integration of biological control with fungicides, cultural practices, and other measures can contribute to manage LB on tomato production systems.     

Chlorobenzoate inhibits growth and induces stress proteins in the PCB-degrading bacterium <Emphasis Type="Italic">Burkholderia xenovorans</Emphasis> LB400

Aerobic bacteria, such as Burkholderia xenovorans LB400, are able to degrade a wide range of polychlorobiphenyls (PCBs). Generally, these bacteria are not able to transform chlorobenzoates (CBAs), which accumulate during PCB degradation. In this study, the effects of CBAs on the growth, the morphology and the proteome of Burkholderia xenovorans LB400 were analysed. 4-CBA and 2-CBA were observed to inhibit the growth of strain LB400 on glucose. Strain LB400 exposed to 4-CBA exhibited increased number and size of electron-dense granules in the cytoplasm, which could be polyphosphates. Two-dimensional (2-D) polyacrylamide gel electrophoresis was used to characterise the molecular response of strain LB400 to 4-CBA. This compound induced the enzymes BenD and CatA of benzoate and catechol catabolic pathways. The induction of molecular chaperones DnaK and HtpG by 4-CBA indicated that the exposure to this compound constitutes a stressful condition for this bacterium. Additionally, the induction of some Krebs cycle enzymes was observed, probably as response to cellular energy requirements. This study contributes to the knowledge on the effects of CBA on the PCB-degrader Burkholderia xenovorans LB400.     

Investigation of substrate specificity of wildtype and mutant BphK (a glutathione S-transferase) from Burkholderia LB400

The bphK gene located in the bph operon of Burkholderia LB400 encodes a protein, BphK^LB400, with significant sequence similarity to glutathione-S-transferases (GST), a group of enzymes involved in the detoxification of many endobiotic and xenobiotic substances. Comparison of the amino acid sequence of BphK^LB400 with GST from other polychlorinated biphenyl (PCB)-degrading bacteria identified a number of highly conserved amino acids in the C-terminal region of the protein that may be associated with substrate specificity. In this study, two of these conserved amino acids in BphK^LB400 (amino acids 152 and 180) were selected for mutation, using site-directed mutagenesis, and substrate specificity assays. BphK^LB400 (wildtype and mutant) was over-expressed in Escherichia coli where the bphK gene (wildtype and mutant) is under the expression of a lac promoter and is induced by isopropyl thiogalactoside, and bacterial cell extracts were prepared for GST activity assays. Mutations at amino acids 152 and 180 were shown to affect GST activity of BphK^LB400 using 1-chloro-2,4-dinitrobenzene, the model substrate for GST activity assays; 4-chlorobenzoate and 3-chlorobenzoate, intermediates in the polychlorinated biphenyl (PCB) degradation pathway, and 2,4-dichlorophenoxyacetate and atrazine, commonly used herbicides; as substrates. A BphK^LB400 mutant (Ala180Pro) is identified in this study as having increased activity towards all substrates tested. This mutant may have potential in bioremediation.     

Introduction of Resistance to Herbicide Basta® in Savoy Cabbage

Resistance to herbicide Basta® was introduced into pure inbred lines of Savoy cabbage (Brassica oleracea L. var. sabauda) by cocultivation of cotyledon and hypocotyl explants with Agrobacterium tumefaciens strains AGL1/pDM805 and LBA4404/pGKB5 (LB5-1). Shoot regeneration occurred on Murashige and Skoog medium supplemented with 1 mg dm^–3 6-benzyladenine and 0.5 mg dm^–3 indole-3-butyric acid at 42.3 % and 71.4 % of hypocotyl explants treated with AGL1/pDM805 and LB5-1, respectively. Putative transformants that survived selection on 10 mg dm^–3 phosphinothricin (L-PPT) supplemented medium were confirmed by GUS assay and PCR analysis. The transformation rate was 58 % with AGL1/ pDM805 and 25 % with LB5-1. Rooted plantlets were acclimated and then again screened for Basta®-resistance by spraying with 15 – 60 mg dm^–3 L-PPT. Surviving plants were selfed and Basta®-resistance was demonstrated in T₁ progeny.     

<Emphasis Type="Italic">Prays oleae</Emphasis> Midgut Putative Receptor of <Emphasis Type="Italic">Bacillus thuringiensis</Emphasis> Vegetative Insecticidal Protein Vip3LB Differs from that of Cry1Ac Toxin

Vegetative insecticidal protein (Vip) is a class of insecticidal proteins produced by many Bacillus thuringiensis strains during their vegetative growth stage. The vip3LB gene of B. thuringiensis strain BUPM95, which encodes a protein active against the Lepidoptera olive tree pathogenic insect Prays oleae, was cloned into pET-14b vector and overexpressed in Escherichia coli. The expressed Vip3LB protein, found in the E. coli cytoplasmic fraction, was purified and used to produce anti-Vip3LB antibodies. Using the midgut extract of P. oleae, the purified Vip3LB bound to a 65-kDa protein, whereas Cry1Ac toxin bound to a 210-kDa midgut putative receptor. This result justifies the importance of the biological pest control agent Vip3LB that could be used as another alternative particularly in case of resistance to Cry toxins.     

Lake optics and depth limits for photogenesis and photosynthesis in charophyte meadows

Two series of lakes with increasing attenuation were examined for trends in spectral composition. They became the basis for an evaluation of the light environment at the lower boundary (LB) of Nitella meadows in three other series of lakes. Increased attenuation (K _d PAR) was marked by progressive erosion of the blue window and caused primarily by humic substances. An increase in K _d PAR from 0.06 to 0.81 produced, at the floor of the euphotic zone, a shift in K _d min from 440 to 580 nm. Regressions of boundary depths of Nitella meadows on water clarity produced similar slope coefficients for the three series of lakes. Several trends became evident: 1, PAR irradiance at the LB increases with depth of the LB; 2, red light (E _d 660) declines from richness at shallow LB to near extinction in deep water LB in clear lakes; while 3, blue light (K _d 450) increases to an asymptote. Blue light appears to substitute, although less effectively, for red light irradiance in the growth regulation of charophytes. These data support an hypothesis that spectral quality is involved in the determination of lower boundary depths for benthic macro-algae.     

Molecular genetics and evolutionary relationship of PCB-degrading bacteria

Biphenyl-utilizing soil bacteria are ubiquitously distributed in the natural environment. They cometabolize a variety of polychlorinated biphenyl (PCB) congeners to chlorobenzoic acids through a 2,3-dioxygenase pathway, or alternatively through a 3,4-dioxygenase system. Thebph genes coding for the metabolism of biphenyl have been cloned from several pseudomonads. The biochemistry and molecular genetics of PCB degradation are reviewed and discussed from the viewpoint of an evolutionary relationship.Abbreviations BP biphenyl - bph BP/PCB-degradative gene - 23DHBP 2,3-dihydroxybiphenyl - HPDA 2-hydroxy-6-oxo-6-phenylhexa 2,4-dienoic acid - KF707 P. pseudoalcaligenes strain KF707 - LB400 Pseudomonas sp. strain LB400 - PCB polychlorinated biphenyls - Q1 P. paucimobilis strain Q1tod; toluene catabolic gene     

Chromate resistance and reduction in Pseudomonas fluorescens strain LB300

Pseudomonas fluorescens LB300 is a chromateresistant strain isolated from chromium-contaminated river sediment. Chromate resistance is conferred by the plasmid pLHB1. Strain LB300 grew in minimal salts medium with as much as 1000 g of K₂CrO₄ ml^–1, and actively reduced chromate to Cr(III) while growing aerobically on a variety of substrates. Chromate was also reduced during anaerobic growth on acetate, the chromate serving as terminal electron acceptor. P. fluorescens LB303, a plasmidless, chromatesensitive variant of P. fluorescens LB300, did not grow in minimal salts medium with more than 10 g of K₂CrO₄ ml^–1. However, resting cells of strain LB303 grown without chromate reduced chromate as well as strain LB300 cells grown under the same conditions. Furthermore, resting cells of chromate-sensitive Pseudomonas putida strain AC10, also catalyzed chromate reduction. Evidently chromate resistance and chromate reduction in these organisms are unrelated. Comparison of the rates of chromate reduction by chromate grown cells and cells grown without chromate indicated that the chromate reductase activity is constitutive. Studies with cell-free extracts show that the reductase is membrane-associated and can mediate the transfer of electrons from NADH to chromate.     

Optimization of a protective medium for enhancing the viability of freeze-dried Lactobacillus delbrueckii subsp. bulgaricus based on response surface methodology

Response surface methodology (RSM) was used to optimize a protective medium for enhancing the cell viability of Lactobacillus delbrueckii subsp. bulgaricus LB14 during freeze-drying. Using a previous Plackett–Burman design, it was found that sucrose, glycerol, sorbitol and skim milk were the most effective freeze-drying protective agents for L. bulgaricus LB14. A full factorial central composite design was applied to determine the optimum levels of these four protective agents. The experimental data allowed the development of an empirical model (P<0.0001) describing the inter-relationships between the independent and dependent variables. By solving the regression equation, and analyzing the response surface contour and surface plots, the optimal concentrations of the agents were determined as: sucrose 66.40 g/L, glycerol 101.20 g/L, sorbitol 113.00 g/L, and skim milk 130.00 g/L. L. bulgaricus LB14 freeze-dried in this medium obtained a cell viability of up to 86.53%.     

Degradation of PCB congeners by bacterial strains

Biological in situ methods are options for the remediation of contaminated sites. An approach to quantify biodegradation by soil bacteria was developed, combining experiment with mathematical modelling. We performed in vitro assays to investigate the potential and kinetics of the wild-type degrader, Burkholderia sp. strain LB400 (expressing bph) and the genetically modified Pseudomonas fluorescens strains F113pcb and F113L::1180 (expressing bph under different promoters) to metabolise individual congeners of polychlorinated biphenyls (PCBs). Kinetics of metabolism was analysed using the Monod model. Results revealed similar patterns of degradable PCB congeners for LB400 and F113L::1180. The degree of PCB degradation was comparable for LB400 and F113L::1180 but was much lower for F113rifpcb. In additional mesocosm experiments with PCB-contaminated soil, the F113 derivatives demonstrated a good survival ability in willow (Salix sp.) rhizosphere. Strain F113L::1180 in combination with willow plants is expected to degrade a large spectrum of PCB congeners in soil. The data from the experiments were used to calculate the time scale of the degradation process in a PCB-contaminated soil. The uncertainty of the model predictions due to the uncertainties of experimental removal velocities and bacterial cell density in soil was quantified.     

Soil nutrient status after bamboo flowering and death in a seasonal tropical forest in western Thailand

We have examined the surface (0–10 cm) soil characteristics of sites after bamboo (Cephalostachyum pergracile) mass flowering and death (DB sites) in comparison with sites with living bamboo (Bambusa tulda) (LB sites) in a seasonal tropical forest in Thailand. One year after bamboo flowering the DB sites were acidic with lower concentrations of exchangeable Ca and Mg and soil nitrogen than the LB sites. Therefore, although leaf and root litter of the dead bamboo was deposited in the DB sites after bamboo flowering, soil nutrient status decreased.     

Deposition behavior and photoelectrochemical characteristics of chlorophylla Langmuir-Blodgett films

The deposition behavior and photoelectric response characteristics of chlorophylla (Chla) monolayers and multilayers were investigated under various film fabrication conditions. Chla LB films were deposited onto quartz and pretreated ITO glass substrates under several fabrication conditions, including surface pressure and number of layers. The absorption spectra of Chla in a solution state and solid-like state (LB films) were fairly consistent with each other, and two absorption peaks were found at 678 and 438 nm, respectively. The prepared Chla LB films were set into an electrochemistry cell equipped with a Pt plate as the counter electrode, and the photoelectric response characteristics were obtained and analyzed relative to the light illumination. By considering the resulting photocurrents, the optimal fabrication conditions for Chla LB films were determined as 20 mN/m of surface pressure and 20 layers. The action spectrum of the Chla LB films was obtained in the visible region, and was found to be in good agreement with the absorption spectrum. The possible application of the proposed system as a constituent of an artificial color recognition device was suggested based on combining with the photoelectric conversion property of another lightsensitive biological pigment.     

Suppression of transfer of non-T-DNA ‘vector backbone’ sequences by multiple left border repeats in vectors for transformation of higher plants mediated by Agrobacterium tumefaciens

Vectors for transformation of higher plants mediated by Agrobacterium tumefaciens were modified so that one, two or three additional copies of the left border (LB) sequences were inserted close to the original LB of the T-DNA. A gene for -glucuronidase (gusA) was placed outside the T-DNA to monitor the transfer to plants of 'vector backbone' sequences. The expression of GUS in immature embryos of rice that had been co-cultivated with A. tumefaciens carrying these constructs was around one tenth of that with A. tumefaciens carrying an unmodified control vector. Between 88 and 127 of independent transformants were regenerated from rice tissues infected with A. tumefaciens carrying each of these vectors. The GUS expressors among the rice transformed with the modified vectors were much less frequent than ones among the control transformants, and rate of reduction in the ratio of transgenic plants that expressed GUS was higher than 93%. Detection of a fragment across the LB region by the polymerase chain reaction and the gusA gene by Southern hybridization correlated well with GUS expression. These results indicate that transfer of the 'vector backbone' from the control vectors resulted mainly from inefficient termination of formation of the transfer intermediate of the T-DNA and additional LB sequences effectively suppressed such transfer. This approach is simpler than the strategy to place a 'lethal gene' outside the T-DNA and will likely help produce 'clean' transformants efficiently.     

植物根际益生细菌代表性菌株贝莱斯芽孢杆菌FZB42对松材线虫的抑杀性

[目的]由松材线虫导致的松树萎蔫病是松树的毁灭性病害,也是我国最主要的林业病害之一.本研究测评了在农业上广泛使用的、我国微生物肥料行业主要菌种资源之一——贝莱斯芽孢杆菌,对松材线虫的潜在抑杀性能.[方法]选用贝莱斯芽孢杆菌的代表性菌株FZB42为材料,测定对不同条件下的菌液上清、不同菌株的菌液上清、细菌素plantaz...     

Characterisation and expression of the paired box protein 7 (Pax7) gene in polymorphic Arctic charr (Salvelinus alpinus)

Arctic charr (Salvelinus alpinus L.) from Lake Thingvallavatn, Iceland occur as four distinct morphs: large benthivorous (LB), dwarf benthivorous (DB), piscivorous (PI) and planktonivorous (PL). The morphs differ with respect to body size, head morphology, growth rate, and life history. The aim of this study was to investigate the paired box protein 7 (Pax7) gene as a candidate for such polymorphisms due to its importance in cranio-facial, skeletal muscle, and central nervous system development. No variation in coding and intronic sequences was found between morphs. We identified 10 alternate Pax7 isoforms with insertions/deletions: a four-residue (GNRT) deletion, a GEASS insertion truncated by the first serine residue (GEAS), and a thirteen-residue insertion (GQYA/TGPEYVYCGT). The latter insertion with a threonine (T) contains a putative casein kinase II (CK-2) phosphorylation site. Pax7 spatial expression patterns were identical in embryos of DB-, LB-, and PL-morphs, and were similar to those described for zebrafish Pax7c, but a difference in temporal expression for segmentation was observed between DB and LB morphs. At the end of segmentation, novel expression was observed in the mandibular region as two bilateral domains. The potential role of multiple alternative splicing of the Pax7 gene for the generation of different Arctic charr morphs is briefly discussed.     

Insights into recognition of the T-DNA border repeats as termination sites for T-strand synthesis by Agrobacterium tumefaciens

The recognition of the T-DNA left border (LB) repeat is affected by its surrounding sequences. Here, the LB regions were further characterized by molecular analysis of transgenic plants, obtained after Agrobacterium tumefaciens-mediated transformation with T-DNA vectors that had been modified in this LB region. At least the 24-bp LB repeat by itself was insufficient to terminate the T-strand synthesis. Addition of the natural inner and/or outer border regions to at least the LB repeat, even when present at a distance, enhanced the correct recognition of the LB repeat, reducing the number of plants containing vector backbone sequences. In tandem occurrence of both the octopine and nopaline LB regions with their repeats terminated the T-strand synthesis most efficiently at the LB, yielding a reproducibly high number of plants containing only the T-DNA. Furthermore, T-strand synthesis did not terminate efficiently at the right border (RB) repeat, which might indicate that signals in the outer RB region inhibit the termination of T-strand synthesis at the RB repeat.     

Burkholderia xenovorans LB400联苯双加氧酶及突变体对DDTs的降解

DDTs（dichlorodiphenyltrichloroethane,1,1,1-三氯-2,2-双氯苯基乙烷）是一种典型的持久性有机污染物,曾在疟疾防治和农业除虫方面被广泛应用。虽然包括我国在内的很多国家已经禁止使用DDTs,但目前对环境中DDTs的检测发现它仍然广泛存在且具有新的输入源。DDTs的持续存在对近海生态系统和人类健康具有一定危害,因此它所造成的环境污染问题仍然值得关注。由于Rieske型芳香羟化双加氧酶能够起始多种持久性污染物的降解,过去的几十年里一直是芳香化合物降解领域的焦点。[目的] 为探讨联苯双加氧酶对DDTs的降解特性及机制,本研究选取了食异生素伯克霍尔德氏菌LB400（Burkholderia xenovorans）联苯双加氧酶及突变体对p,p''-DDT和o,p''-DDT的降解过程进行研究。[方法] 以BphAE_LB400为亲本,通过两步定点突变将283位的丝氨酸突变为蛋氨酸,获得突变体BphAE_S283M。通过比较亲本酶与突变体对DDTs的催化性能,模拟突变蛋白结构和分子对接等方法,探究其降解特性及机制。[结果] BphAE_LB400和突变体BphAE_S283M都无法降解对位的p,p''-DDT,但突变体BphAE_S283M可以代谢o,p''-DDT并产生2个立体异构体。对接p,p''-DDT的BphAE_LB400和BphAE_S283M的结构分析表明,BphAE_LB400和BphAE_S283M中p,p''-DDT的反应环均不与原晶体结构中的联苯反应环重合。而对接o,p''-DDT的BphAE_S283M的结构分析表明o,p''-DDT的反应环与晶体结构中的联苯反应环距离很近,且2、3位的碳原子与单核铁原子催化中心的距离在0.5 nm以内,此外,BphAE_S283M的催化腔表面积和体积比BphAE_LB400更大,这很可能有助于BphAE_S283M与o,p''-DDT的结合。[结论] 283位氨基酸是影响BphAE_LB400对DDTs的催化代谢能力的关键氨基酸残基,它可以通过调节反应碳原子与催化中心的距离以及催化腔的大小来影响底物特异性。本次研究进一步阐明了283位氨基酸残基的影响机理,为更有效修复DDTs污染提供理论依据和技术支持。     

Identification of four genomic groups ofBorrelia burgdorferi sensu lato inIxodes ricinus ticks collected in a Lyme borreliosis endemic region of northern Croatia

We investigated the presence ofBorrelia burgdorferi sensu lato inIxodes ricinus ticks collected in a Lyme borreliosis (LB) endemic region of northern Croatia. Ticks (n=124) were collected at five locations and analysed by the polymerase chain reaction (PCR). A DNA fragment from the internal transcribed spacer (ITS2) ofI. ricinus was detected in all tick lysates, indicating that PCR inhibitors were not present.Borrelia burgdorferi sensu lato DNA was detected in 56 out of 124 ticks (45%). Four genomic groups were identified:Borrelia afzelii (n=26),Borrelia garinii (n=5), group VS116 (n=5) andB. burgdorferi sensu stricto (n=1). Mixed infections ofB. afzelii with group VS116 (n=10) andB. afzelii withB. burgdorferi sensu stricto (n=1) were also detected. Eight ticks containedB. burgdorferi sensu lato, which could not be typed. The detection ofB. afzelii andB. garinii in ticks was in agreement with manifestations of LB found locally. The occurrence of group VS116 in northern Croatia and in an earlier study in The Netherlands, infers that this genomic group may be well established in EuropeanI. ricinus.