Extraction of plasmid DNA from Escherichia coli cell lysate in a thermoseparating aqueous two-phase system

The primary purification of a 6.1 kilo base pair (kbp) plasmid from a desalted alkaline lysate has been accomplished by a thermoseparating aqueous two-phase system [(50% ethylene oxide-50% propylene oxide)-Dextran T 500]. The partitioning of the different nucleic acids (plasmid DNA, RNA, genomic DNA) in the thermoseparating aqueous two-phase system was followed both qualitatively by agarose gel electrophoresis and quantitatively by analytical chromatography (size exclusion- and anion-exchange mode) and PicoGreen fluorescence analysis. The experimental results showed a complete recovery of the plasmid DNA to the top phase, while 80% of total RNA and 58% of total protein was discarded to the bottom phase. Moreover, a 3.8-fold volume reduction of the plasmid DNA solution was achieved. By using a final thermoseparating step, the EO50PO50 polymer could be efficiently recycled, resulting in plasmid solution containing less than 1% polymer. The developed thermoseparating aqueous two-phase system shows great potential for the large-scale processing of plasmid DNA.     

Excision-repair capacity of UV-irradiated strains of Escherichia coli and Streptococcus pneumoniae, estimated by plasmid recovery

Although the biological role of many bacterial repair genes is known, there is still an interest in evaluating the capacity of repair pyrimidine dimers in some strains. For this purpose, we have developed a rapid assay. Cells bearing a plasmid are UV irradiated and incubated to allow recovery. The plasmid DNA is extracted, purified and treated with UV endonuclease from Micrococcus luteus that specifically produces single strand breaks at the site of pyrimidine dimers. The amount of open circular and covalently closed circular forms of the plasmid DNA after treatment and post-incubation provides an estimate of the repair capability of the host strain. The wild type strain and the uvrA mutant of Escherichia coli were used to adjust the assay. The lexA mutant of E. coli has been tested and its repair capability is equivalent to that of wild-type strain. The assay has been extended to Streptococcus pneumoniae, which is naturally deficient in photoreactivation and SOS-like functions. This strain is efficient in the repair of pyrimidine dimers, formed after UV irradiation.     

Immobilised metal affinity chromatography of beta-galactosidase from unclarified Escherichia coli homogenates using expanded bed adsorption

The development of an expanded bed process for the direct extraction and partial purification of beta-galactosidase from unclarified Escherichia coli homogenates using its natural affinity for metal loaded STREAMLINE Chelating is described. Small packed beds were used to determine the effect of chelated metal ion (Cu2+, Ni2+, Co2+ or Zn2+), loading pH and ionic strength on the selective binding capacity, and recovery of beta-galactosidase from clarified homogenates. An elution protocol was developed using the competitive displacer, imidazole, to recover beta-galactosidase in 87% yield and 3.4-fold purification. These results were then used to develop a separation for the recovery of beta-galactosidase from unclarified homogenates in a 2.5-cm diameter expanded bed. Although Ni2+ loaded STREAMLINE Chelating had a 5% dynamic capacity for beta-galactosidase of just 118 U ml(-1) (0.39 mg ml(-1)), the low capacity was thought to be due to the large size of the target (464,000) relative to the exclusion limit of the macroporous adsorbent. Despite this low capacity, Ni2 STREAMLINE Chelating was used successfully to recover beta-galactosidase from an unclarified homogenate in 86.4% yield and at 5.95-fold purification. The degree of purification relative to a commercial standard, as assessed using the purification factor and sodium dodecyl sulphate-polyacrylamide gel electrophoresis was high suggesting that this pseudo-affinity procedure compared favourably with alternative methods.     

Screen-printed electrochemical hybridization biosensor for the detection of DNA sequences from the Escherichia coli pathogen

An electrochemical biosensor for the specific detection of short DNA sequences from the E. coli pathogen is described. This hybridization device relies on the immobilization of a 25-mer oligonucleotide probe, from the E. coli lacZ gene, onto a screen-printed carbon electrode. Chronopotentiometric detection of the Co(bpy)₃⁺³ indicator is used for monitoring the hybridization event. Numerous variables of the assay protocol, including those of the probe immobilization step, the hybridization event, and the indicator association/detection, are characterized and optimized. Hybridization times of 2- and 30-min are sufficient for detecting 300- and 50 ng/mL, respectively, of the E. coli DNA target. Applicability to analysis of untreated environmental water samples is illustrated. Such single-use electrochemical sensors hold great promise for decentralized environmental and food testing for the E. coli pathogen.     

N-acyl derivatives of arginine and tryptophan isolated from environmental DNA expressed in Escherichia coli

Heterologous expression of microbial DNA extracted directly from environmental samples (environmental DNA, eDNA) in easily cultured hosts can provide access to natural products produced by previously uncultured bacteria. This report describes the characterization of antibacterially active long-chain N-acyl derivatives of tryptophan and arginine that are produced by eDNA clones hosted in Escherichia coli. The sequencing and subcloning of the proposed N-acyl amino acid synthases (NASs) for each family of natural products are also described. [reaction: see text]     

Effect of ecological factors on conjugal transfer of chromium-resistant plasmid in Escherichia coli isolated from tannery effluent

The influence of total organic carbon (TOC), pH, and mating temperature on transfer of chromium-resistant plasmid between Escherichia coli strains in terms of variation in the number of transconjugants formed and variation in transfer frequency was investigated. In vitro transfer was studied in five chromate-tolerant E. coli strains isolated from tannery effluent using E. coli K12 J62 (Nal^r Lac⁻) as a recipient. Conjugal transfer of different selection markers was observed in three strains. The study was carried out in sterile wastewater. A gradual decrease was observed both in the number of transconjugants and in transfer frequencies as the concentration of TOC in the mating medium descended from 10,095 to 1.2 mg of C/L, obtaining the maximum values with a TOC concentration of 10,095 mg of C/L. The number of transconjugants and the transfer frequency were maximum at 30°C. However, neither the transfer frequency nor the transconjugant number varied significantly in the range of pHs assayed. The strains were also found resistant to different heavy metals and antibiotics. Curing of these strains resulted in loss of one or more resistance markers indicating the plasmid-borne resistance. It is inferred that plasmid transfer by conjugation occurs in wastewater bodies within a wide range of conditions.     

Inorganic adsorbent containing polymeric membrane reservoir for the recovery of lithium from seawater

Polymeric membrane reservoir system which contains inorganic ion-exchange adsorbent inside is suggested for the recovery of lithium from natural seawater. Manganese oxide particles having high selectivity toward lithium adsorption was used as inorganic ion-exchange adsorbent. Polymeric membrane reservoir was prepared from non-woven fabric, polysulfone (PSf) membrane, PSf/non-woven fabric composite membrane, and Kimtex^®. Leakage of the inorganic particles and morphology of the membrane were investigated and availability as membrane reservoir for the lithium recovery was evaluated by the lithium desorption from Li_1.33Mn_1.67O₄ in the membrane reservoir. From this study, ease of water diffusion to the reservoir was the most important factor for the reservoir system to be applied to lithium recovery from seawater and membrane reservoir prepared by Kimtex^® showed the best result. The proposed system has the advantage of direct application in the sea without using pressurized flow system.     

Impact of SiC particle size upon the microstructure and characteristics of Ni-SiC nanocomposites

In order to deposit the Ni–SiC nanocomposites on Q235A steel substrates, magnetic pulse electrodeposition was employed in this article. Scanning electron microscopy (SEM), triboindenter in-situ nanomechanical testing, scanning probe microscopy (SPM), and X-ray diffraction (XRD) were used to assess the composites in terms of their compositions, microstructures, and microhardness. There were three specimens in total, with SiC particle sizes of 30, 80, and 200 nm, referred to as SN-30, SN-80, and SN-200 composites. With fine nickel grains and nanoparticles of SiC, SN-30 nanocomposites have fine, compact, and homogeneous architectures. There is a substantial impact of the size of SiC particles on the spectra of XRD for the nanocomposites. For SN-200 nanocomposite, the peaks of diffraction for SiC and Ni seemed to be high and sharp. SiC nanoparticle and Ni grain sizes in SN-30 nanocomposite were measured to be 34.4 and 381.3 nm, respectively. SN-30 and SN-200 composites have final depths of roughly 15.2 μm and 24.6 μm, accordingly. Following a subsequent investigation of the corrosion and wear characteristics of Ni-SiC nano-composites, the weight loss values of SN-30, SN-80, and SN-200 composites were calculated to be 1.01, 1.48, and 1.69 g, respectively, after corrosion testing for 24 h. During wear testing, however, just a few small pits were discovered on the SN-30 nanocomposite surface, indicating optimum wear resistance.     

Analysis of plasmid DNA synthesis by double tracer method--differential effects of rifampicin and chloramphenicol on the replication of pSC101 and ColEl-amp in Escherichia coli K-12

An Escherichia coli strain, CR34 , harboring both pSC101 and ColEl -amp plasmids was exposed to media containing rifampicin (100 micrograms/ml) and/or chloramphenicol (180 micrograms/ml) and the cells were labeled for 20 min with 3H-thymine at 3, 25 and 50 min after exposure to drug(s). The plasmid DNA synthesis was assayed by DNA-DNA hybridization with 14C-labeled pSC 134 DNA as internal marker. In the presence of rifampicin, the replication of pSC 101 was from 57 to 104% that in its absence, and that of ColEl -amp was from 17 to 26%. The DNA replication of pSC 101 after addition of chloramphenicol was reduced to 35 to 75%, and that of ColEl -amp was reduced to 39% and then restored to 92%. This restoration was not observed in the presence of rifampicin.     

DNA polymerase I-mediated repair of 365 nm-induced single-strand breaks in the DNA of Escherichia coli.

Abstract. Irradiation of closed circular phage Λ DNA in vivo at 365 nm results in the induction of single-strand breaks and alkali-labile lesions at rates of 1.1 × 10^-14, and 0.2 × 10^-14/dalton/J/m², respectively. The sum of the induction rates is similar to the rate of induction of single-strand breaks plus alkali-labile lesions (1 × 10^-14/dalton/J/m²) observed in the E. coli genome. Postirradiation incubation of wild-type cells in buffer results in rapid repair of the breaks (up to 80% repaired in 10 min). No repair was observed in a DNA polymerase I-deficient mutant of E. coli.     

Preparation and characterization of the native iron(II)-containing DNA repair AlkB protein directly from Escherichia coli

The Escherichia coli AlkB protein was recently found to repair cytotoxic DNA lesions 1-methyladenine and 3-methylcytosine by using a novel iron-catalyzed oxidative demethylation mechanism. This protein belongs to a family of 2-ketoglutarate-Fe(II)-dependent dioxygenase proteins that utilize iron and 2-ketoglutarate to activate dioxygen for oxidation reactions. We report here the overexpression and isolation of the native Fe(II)-AlkB with a bound cofactor, 2-ketoglutarate, directly from E. coli. UV-vis measurements showed an absorption peak at 560 nm, which is characteristic of a bidentate 2-ketoglutarate bound to an iron(II) ion. Addition of excess amounts of single-stranded DNA to this isolated Fe(II)-AlkB protein caused a 9 nm shift of the 560 nm band to a higher energy, indicating a DNA-binding-induced geometry change of the active site. X-ray absorption spectra of the active site iron(II) in AlkB suggest a five-coordinate iron(II) center in the protein itself and a centrosymmetric six-coordinate iron(II) site upon addition of single-stranded DNA. This geometry change may play important roles in the DNA damage-searching and damage-repair functions of AlkB. These results provide direct evidence for DNA binding to AlkB which modulates the active site iron(II) geometry. The isolation of the native Fe(II)-AlkB also allows for further investigation of the iron(II) center and detailed mechanistic studies of the dioxygen-activation and damage-repair reactions performed by AlkB.     

大肠杆菌MinCD蛋白复合物纯化方法和结晶筛选

大肠杆菌在细胞分裂时,细胞中部潜在分裂位点的选择受到Min系统(Min C、Min D和Min E蛋白)的精确调控,其中Min C与Min D可以形成复合物以抑制Z分裂环在错误的位置形成。本研究采用基因克隆方法获得min C、min D基因的克隆,并表达得到Min C和Min D的重组蛋白,用亲和层析与凝胶过滤层析对所得蛋白进行纯化,通过min C、min D分别单独转化、表达纯化后混合和min C、min D共转化法两种方法得到Min CD蛋白复合物,并分别对其进行晶体筛选。结果表明,共转化法得到的Min CD复合物纯度较好,且比例约为2∶1,通过晶体筛选初步获得针状蛋白晶体,为Min CD复合物的结构解析提供了实验基础。     

Effect of the cyclobutane cytidine dimer on the properties of Escherichia coli DNA photolyase

Cyclobutane pyrimidine dimer (CPD) photolyases are structure specific DNA-repair enzymes that specialize in the repair of CPDs, the major photoproducts that are formed upon irradiation of DNA with ultraviolet light. The purified enzyme binds a flavin adenine dinucleotide (FAD), which is in the neutral radical semiquinone (FADH(*)) form. The CPDs are repaired by a light-driven, electron transfer from the anionic hydroquinone (FADH(-)) singlet excited state to the CPD, which is followed by reductive cleavage of the cyclobutane ring and subsequent monomerization of the pyrimidine bases. CPDs formed between two adjacent thymidine bases (T< >T) are repaired with greater efficiency than those formed between two adjacent cytidine bases (C< >C). In this paper, we investigate the changes in Escherichia coli photolyase that are induced upon binding to DNA containing C< >C lesions using resonance Raman, UV-vis absorption, and transient absorption spectroscopies, spectroelectrochemistry, and computational chemistry. The binding of photolyase to a C< >C lesion modifies the energy levels of FADH(*), the rate of charge recombination between FADH(-) and Trp(306)(*), and protein-FADH(*) interactions differently than binding to a T< >T lesion. However, the reduction potential of the FADH(-)/FADH(*) couple is modified in the same way with both substrates. Our calculations show that the permanent electric dipole moment of C< >C is stronger (12.1 D) and oriented differently than that of T< >T (8.7 D). The possible role of the electric dipole moment of the CPD in modifying the physicochemical properties of photolyase as well as in affecting CPD repair will be discussed.     

Enhancing the sensitivity of DNA detection and recovery from agarose gels

By inserting nitrocellulose strips into agarose gels alongside the electrophoresed lanes and passing an electric current perpendicularly in the direction of the strips, highly efficient transfer of DNA bands onto the membrane in the form of concentrated dots is achieved. DNA detection limits by this technique are enhanced, at least three times as visualized by ethidium bromide fluorescence and at least twice more by radiolabeling.     

Optimization of simulated moving bed and column chromatography for a plasmid DNA purification step and for a chiral separation

This work analyzes the performance of the SMB and the column chromatography processes for two different case studies: the first stage of the plasmid DNA (pDNA) polishing, and the Tr?ger's base enantiomer separation, in which the adsorption isotherms are linear and non-linear, respectively. Simulation tools are used together with an optimization routine (Non-Sorting Genetic Algorithm (NSGA)) in order to find the optimum operating conditions leading to maximum productivity and minimum solvent consumption; the optimum solution for each of the processes is a curve on the productivity-solvent consumption plane, the so-called Pareto set. The comparison between the column and the SMB processes is based on the relative position of the two Pareto sets calculated at equal conditions and for the same final purity and recovery of the target species. The results show that SMB is superior to column chromatography in the two case studies investigated, i.e. in the case of the linear isotherm (pDNA), the productivity gain is up to a factor two for a given value of the solvent consumption. Furthermore, the flexibility of the SMB operation is larger, since the Pareto sets are flatter and they prolong into regions of the productivity-solvent consumption plane that are not accessible with the column chromatography process.     

New insights into the transition pathway from nonspecific to specific complex of DNA with Escherichia coli integration host factor

To elucidate the nature of the transition-state ensemble along the reaction pathway from a nonspecific protein-DNA complex to the specific complex, we have carried out measurements of DNA bending/unbending dynamics on a cognate DNA substrate in complex with integration host factor (IHF), an architectural protein from E. coli that bends its cognate site by approximately 180 degrees . We use a laser temperature jump to perturb the IHF-DNA complex and monitor the relaxation kinetics with time-resolved FRET measurements on DNA substrates end-labeled with a FRET pair. Previously, we showed that spontaneous bending/kinking of DNA, from thermal disruption of base-pairing/-stacking interactions, may be the rate-limiting step in the formation of the specific complex (Kuznetsov, S. V.; Sugimura, S.; Vivas, P.; Crothers, D. M.; Ansari, A. Proc. Natl. Acad. Sci. USA 2006, 103, 18515). Here, we probe the effect of varying [KCl], which affects the stability of the complex, on this rate-limiting step. We find that below approximately 250 mM KCl, the observed relaxation kinetics are from the unimolecular bending/unbending of DNA, and the relaxation rate kr is independent of [KCl]. Above approximately 300 mM KCl, dissociation of the IHF-DNA complex becomes significant, and the observed relaxation process includes contributions from the association/dissociation step, with kr decreasing with increasing [KCl]. The DNA bending step occurs with a positive activation enthalpy, despite the large negative enthalpy change reported for the specific IHF-DNA complex (Holbrook, J. A.; Tsodikov, O. V.; Saecker, R. M.; Record, M. T., Jr. J. Mol. Biol. 2001, 310, 379). Our conclusion from these studies is that in the uphill climb to the transition state, the DNA is kinked, but with no release of ions, as indicated by the salt-independent behavior of k(r) at low [KCl]. Any release of ions in the unimolecular process, together with conformational changes in the protein-DNA complex that facilitate favorable interactions and that contribute to the negative enthalpy change, must occur as the system leaves the transition state, downhill to the final complex.     

Direct purification of recombinant hepatitis B core antigen from two different pre-conditioned unclarified Escherichia coli feedstocks via expanded bed adsorption chromatography

Direct recovery of hepatitis B core antigen (HBcAg) from unclarified Escherichia coli homogenates via expanded bed adsorption chromatography (EBA) has been explored in this study. Streamline DEAE was selected as the anion exchanger to recover HBcAg from heat-treated and non-heat-treated unclarified feedstocks. The use of anion-exchanger for direct extraction of proteins from unclarified feedstock is not preferred due to lack of specificity of its ligand. In this study, thermal treatment of the unclarified feedstock at 60 degrees C has resulted in 1.2- and 1.8-fold increases in yield and purity of HBcAg, respectively, compared with that purified from non-heat-treated feedstock. Heating the crude feedstock has resulted in denaturation and precipitation of contaminants in the feedstock, hence reducing non-specific interactions between the cell debris and adsorbent. The selectivity of the anion-exchanger has also been increased as shown in the breakthrough curve obtained. Enzyme-linked immunosorbent assay showed that the antigenicity of the HBcAg from heat-treated unclarified feedstock is still preserved.     

Probing the structure and function of the Escherichia coli DNA alkylation repair AlkB protein through chemical cross-linking

Engineering chemical cross-linking groups at the protein/DNA interface provide a powerful method for probing the putative active site and a damage searching mechanism of the Escherichia coli alkylation DNA repair protein AlkB.