Mechanistic DNA damage simulations in Geant4-DNA Part 2: Electron and proton damage in a bacterial cell

We extended a generic Geant4 application for mechanistic DNA damage simulations to an Escherichia coli cell geometry, finding electron damage yields and proton damage yields largely in line with experimental results. Depending on the simulation of radical scavenging, electrons double strand breaks (DSBs) yields range from 0.004 to 0.010 DSB Gy⁻¹ Mbp⁻¹, while protons have yields ranging from 0.004 DSB Gy⁻¹ Mbp⁻¹ at low LETs and with strict assumptions concerning scavenging, up to 0.020 DSB Gy⁻¹ Mbp⁻¹ at high LETs and when scavenging is weakest. Mechanistic DNA damage simulations can provide important limits on the extent to which physical processes can impact biology in low background experiments. We demonstrate the utility of these studies for low dose radiation biology calculating that in E. coli, the median rate at which the radiation background induces double strand breaks is 2.8 × 10⁻⁸ DSB day⁻¹, significantly less than the mutation rate per generation measured in E. coli, which is on the order of 10⁻³.     

Ligation of EcoRI endonuclease-generated DNA fragments into linear and circular structures.

Double-stranded DNA fragments terminated at their 5′-ends by the singlestranded sequence pA-A-T-T-, generated by digestion of DNA with EcoRI restriction endonuclease, were ligated with Escherichia coli polynucleotide ligase under various conditions of temperature, concentration and time. The linear and circular products of ligation were separated by electrophoresis in agarose gel and quantitated by densitometry. The rate of ligation of (EcoRI-cleaved) simian virus (SV40) DNA at a concentration of 100 μg/ml increased from 0 °C to 5 °C to 10 °C (6-fold increase overall); raising the temperature to 15 °C did not further increase the rate of ligation. At the appropriate DNA concentrations, the predominant products of ligation are either linear concatemers that are integral multimers of the starting DNA fragment, or covalently closed circular structures of the monomeric DNA fragment. Ligating a mixture of two different length DNA fragments gives rise to all of the possible expected recombinant molecules.Linear or circular products of ligation were predicted by consideration of the total concentration of DNA termini, i, and the local concentration of one terminus in the neighborhood of the other on the same DNA molecule, j. The parameter j is a function of the length of a DNA molecule, providing this length is greater than the random coil segment of DNA. Experimentally it was found that circular structures are formed in significant amounts only under conditions when the value of j is several times greater than that of i. When j = i, equal amounts of linear and circular products would be expected, but most of the molecules were ligated into linear concatemers. No circular structure of a DNA fragment whose contour length l (6 × 10⁻² μm) is smaller than the random coil segment value b (7·17 × 10⁻² μm) was observed, while circular structures of the dimer of the same molecule (12 × 10⁻² μm) were detected.     

Inhibition of membrane transport ATPases by halenaquinol,a natural cardioactive pentacyclic hydroquinone from the sponge Petrosia seriata

Halenaquinol, a natural cardioactive pentacyclic hydroquinone from the sponge Petrosia seriata, was found to be a powerful inhibitor of the rat brainstem and of the rat brain cortex Na⁺, K⁺-ATPases and the rabbit muscle sarcoplasmic reticulum Ca²⁺-ATPase with I₅₀ values of 7.0×10⁻⁷, 1.3×10⁻⁶ and 2.5×10⁻⁶ M, respectively. Halenaquinol also inhibited K⁺-phosphatase activity of the rat brain cortex Na⁺, K⁺-ATPase with an I₅₀ value of 3×10⁻⁶ M. Ouabain-insensitive Mg²⁺-ATPase activity of the microsomal fraction of the rat brain cortex was weakly inhibited by halenaquinol. Inhibition was irreversible, dose- and time-dependent. Naphthohydroquinone fragment in structures of halenaquinol, related natural and model compounds was very important for an inhibiting effect.     

Joining of bacteriophage T4D heads and tails: A kinetic study by inelastic light scattering

We have used inelastic laser light scattering to study the kinetics of the spontaneous assembly of heads and tails of bacteriophage T4D to form noninfectious tail fiberless particles. For interpretation of the kinetics, it was first necessary to determine the physical properties of the strongly scattering phage parts. For heads, these are D_{20,w = 3.60 × 10⁻⁸cm²/s, 820,w = 1025 S, M = 1.76 × 10⁸}. For tail fiberless particles, D_20,w = 3.14 × 10⁻⁸cm²/s, 8_20,w = 968 S, and M = 1.95 × 10⁸. The kinetics of the head-tail joining process was followed by measuring the time variation of the homodyne scattering autocorrelation function. This was interpreted as a sum of exponentials whose decay constants were known from the scattering angle and the diffusion coefficients, and whose amplitudes were related to the concentrations of reactants and products. Scattering experiments at 22 °C gave a bimolecular rate constant of 1.02 × 10⁷m⁻¹ s⁻¹, while infectivity assays at 30 °C gave a rate constant of 1.28 × 10⁷. Adjustment of both rate constants to 20 °C, assuming diffusion controlled reaction, gave 0.97 × 10⁷ and 0.98 × 10⁷m⁻¹ s⁻¹, respectively. This rate is about $\text{1}\text{500}$ that predicted by Smoluchowski theory for a diffusion controlled reaction between two spherical particles; the discrepancy is largely explicable from orientational factors.     

Improvement of a synthetic medium for Dictyostelium discoideum

Dictyostelium discoideum is of considerable interest as an expression system for the production of proteins of high value. The cultivation of this social amoeba is not as easy as that of other common microbial expression systems. Wildtype strains grow on bacteria. Mutant strains growing on axenic media reach cell densities of 1–2×10⁷ ml⁻¹ when cultivated in commonly used complex media. A totally synthetic medium formulated by Franke and Kessin (Proc. Natl. Acad. Sci. USA 74 (1977) 2157) has become popular and allows cell densities of about 3×10⁷ ml⁻¹ to be obtained. This medium (FM) is being improved mainly on the basis of the analysis of limitations with respect to amino acids. With this improved synthetic medium (SIH) cell densities in the order of 5–6×10⁷ ml⁻¹ have been achieved.     

Susceptibility ofParacoccidioides brasiliensis conidia to products of oxidative metabolism

The toxic effect of components of the peroxide-peroxidase-halide system onParacoccidioides brasiliensis conidia was investigated. By itself, hydrogen peroxide was lethal at a concentration of 0.5M. The addition of peroxidase (14 U/ml) and KI (5 × 10⁻⁴M) markedly reduced the amount of hydrogen peroxide (from 5 × 10⁻¹ to 5 × 10⁻⁶M) required to kill 99% of the conidia. The lethal effect of the system suggested that it may play a role in host defense againstP. brasiliensis.     

Characterization and optimization of a new immobilized system of κ-carrageenan through interaction with carob bean gum and polyols

The optimum relationships of κ-carrageenan and carob bean gum were investigated in order to obtain an immobilization system with better compression resistance, trapping capacity, and storage stability, and less syneresis phenomenon, when compared to κ-carrageenan itself. With that objective, different concentrations of polyols (glycerol and propylene glycol) were added, because of their water-retention characterization in the containing system. In this way, an improved system with good compression resistance was obtained: 15 × 10⁻⁴ N/m² in modified κ-carrageenan gel without E. coli cells and 11 × 10⁻⁴ N/m² with Escherichia coli cells. In the modified κ-carrageenan gel, the syneresis phenomenon decreased. The enzymatic activity in the system was 18 U/g, which did not present a change over a storage period of six months.     

A spontaneous Escherichia coli K12 mutant which inhibits the excision-reintegration process of Mu gem2ts

Escherichia coli K12 strains lysogenic for Mu gem2ts with the prophage inserted in a target gene (i.e., lacZ::Mu gem2ts lysogenic strains) revert to Lac⁺ by prophage precise excision with a relatively high frequency (about 1×10⁻⁶). The revertants obtained are still lysogens with the prophage inserted elsewhere in the bacterial chromosome. We have observed that, with the time of storage in stabs, bacterial cultures lysogenic for Mu gem2ts lose the ability to excise the prophage. The mutation responsible for this effect was co-transducible with the gyrB gene. After the removal of the prophage by P1 vir transduction from these strains, one randomly chosen clone, R3538, was further analyzed. It shows an increment of DNA supercoiling of plasmid pAT153, used as a reporter, and a reduced β-galactosidase activity. On the other hand, R3538 is totally permissive to both lytic and lysogenic cycles of bacteriophage Mu.     

Reevaluation of the rate constants for the reaction of hypochlorous acid (HOCl) with cysteine,methionine, and peptide derivatives using a new competition kinetic approach

Activated white cells use oxidants generated by the heme enzyme myeloperoxidase to kill invading pathogens. This enzyme utilizes H₂O₂ and Cl⁻, Br⁻, or SCN⁻ to generate the oxidants HOCl, HOBr, and HOSCN, respectively. Whereas controlled production of these species is vital in maintaining good health, their uncontrolled or inappropriate formation (as occurs at sites of inflammation) can cause host tissue damage that has been associated with multiple inflammatory pathologies including cardiovascular diseases and cancer. Previous studies have reported that sulfur-containing species are major targets for HOCl but as the reactions are fast the only physiologically relevant kinetic data available have been extrapolated from data measured at high pH (>10). In this study these values have been determined at pH 7.4 using a newly developed competition kinetic approach that employs a fluorescently tagged methionine derivative as the competitive substrate (k(HOCl + Fmoc-Met), 1.5×10⁸ M⁻¹ s⁻¹). This assay was validated using the known k(HOCl + NADH) value and has allowed revised k values for the reactions of HOCl with Cys, N-acetylcysteine, and glutathione to be determined as 3.6×10⁸, 2.9×10⁷, and 1.24×10⁸ M⁻¹ s⁻¹, respectively. Similar experiments with methionine derivatives yielded k values of 3.4×10⁷ M⁻¹ s⁻¹ for Met and 1.7×10⁸ M⁻¹ s⁻¹ for N-acetylmethionine. The k values determined here for the reaction of HOCl with thiols are up to 10-fold higher than those previously determined and further emphasize the critical importance of reactions of HOCl with thiol targets in biological systems.     

Cloning,expression and some properties of α-carbonic anhydrase from Helicobacter pylori

The α-carbonic anhydrase gene from Helicobacter pylori strain 26695 has been cloned and sequenced. The full-length protein appears to be toxic to Escherichia coli, so we prepared a modified form of the gene lacking a part that presumably encodes a cleavable signal peptide. This truncated gene could be expressed in E. coli yielding an active enzyme comprising 229 amino acid residues. The amino acid sequence shows 36% identity with that of the enzyme from Neisseria gonorrhoeae and 28% with that of human carbonic anhydrase II. The H. pylori enzyme was purified by sulfonamide affinity chromatography and its circular dichroism spectrum and denaturation profile in guanidine hydrochloride have been measured. Kinetic parameters for CO₂ hydration catalyzed by the H. pylori enzyme at pH 8.9 and 25°C are k_cat=2.4×10⁵ s⁻¹, K_M=17 mM and k_cat/K_M=1.4×10⁷ M⁻¹ s⁻¹. The pH dependence of k_cat/K_M fits with a simple titration curve with pK_a=7.5. Thiocyanate yields an uncompetitive inhibition pattern at pH 9 indicating that the maximal rate of CO₂ hydration is limited by proton transfer between a zinc-bound water molecule and the reaction medium in analogy to other forms of the enzyme. The 4-nitrophenyl acetate hydrolase activity of the H. pylori enzyme is quite low with an apparent catalytic second-order rate constant, k_enz, of 24 M⁻¹ s⁻¹ at pH 8.8 and 25°C. However, with 2-nitrophenyl acetate as substrate a k_enz value of 665 M⁻¹ s⁻¹ was obtained under similar conditions.     

Factors affecting the synthesis of the n-terminal methionine-free molecule of recombinant human interleukin-2 by Escherichia coli

Escherichia coli harboring the gene encoding human interleukin-2 (IL-2) produces a mixture of two recombinant IL-2 species: one with the amino-terminal alanine (rIL-2) and the other having an additional methionine residue at the amino terminus (Met-rIL-2). Ways to increase the amount of rIL-2 and its proportion to the total IL-2 were tried. Among E. coli K-12 derivatives, N4830 was an effective producer of recombinant IL-2. The production of the mixture was greatly increased by optimizing the medium ingredients or culture conditions. However, the percentage of rIL-2 in the product decreased almost linearly with an increase of the total production of recombinant IL-2 and was less than 10% under optimal culture conditions. By adding 4.1 × 10⁻⁵ M maganese and 7.4 × 10⁻⁵ M ferric ions to the medium, we succeeded in raising the percentage of rIL-2 to 50% without any decrease of the total production.     

Agrobacterium tumefaciens-mediated genetic transformation of mungbean (Vigna radiata L. Wilczek) — a recalcitrant grain legume

Agrobacterium-mediated transformation of Vigna radiata L. Wilczek has been achieved. Hypocotyl and primary leaves excised from 2-day-old in-vitro grown seedlings produced transgenic calli on B₅ basal medium supplemented with 5×10⁻⁶ M BAP, 2.5×10⁻⁶ M each of 2,4-D and NAA and 50 mg l⁻¹ kanamycin after co-cultivation with Agrobacterium tumefaciens strains, LBA4404 (pTOK233), EHA105 (pBin9GusInt) and C58C1 (pIG121Hm) all containing β-glucuronidase (gusA) and neomycin phosphotransferase II (nptII) marker genes. Transformed calli were found resistant to kanamycin up to 1000 mg^.l⁻¹. Gene expression of kanamycin resistance (nptII) and gusA in transformed calli was demonstrated by nptII assay and GUS histochemical analysis, respectively. Stable integration of T-DNA into the genome of transformed calli of mungbean was confirmed by Southern blot analysis. Transgenic calli could not regenerate shoots on B₅ or B₅ containing different cytokinins or auxins alone or in combination. However, for the first time, transformed green shoots showing strong GUS activity were regenerated directly from cotyledonary node explants cultured after co-cultivation with LBA4404 (pTOK233) on B₅ medium containing 6-benzylaminopurine (5×10⁻⁷ M) and 75 mg l⁻¹ kanamycin. The putative transformed shoots were rooted on B₅+indole-3-butyric acid (5×10⁻⁶ M) within 10–14 days and resulted plantlets subsequently developed flowers and pods with viable seeds in vitro after 20 days of root induction. The stamens, pollen grains and T₀ seeds showed GUS activity. Molecular analysis of putative transformed plants revealed the integration and expression of transgenes in T₀ plants and their seeds.     

The use of glucose to regulate pH values of culture media and increase the production of baculovirus (BmNPV) and foreign protein (HBsAg)

When BmN-4 and M-BmN cells were grown in shake flasks, the pH initially dropped and later increased. The increase in pH signaled a ‘metabolic switch’ that was used here as an indicator for initiating a supplemental glucose and glutamine feed. Using the pH-based fed-batch culture method described, the maximum cell densities of BmN-4 cells and M-BmN cells were increased from 30×10⁵ cells ml⁻¹ to 43×10⁵ and 52×10⁵ cells ml⁻¹, respectively. Correspondingly, the production of polyhedra (4·5×10⁵ OBs ml⁻¹) and HBsAg (574 ng ml⁻¹), from the infection of BmN-4 and M-BmN by wild-type and recombinant BmNPV viruses, respectively, were both significantly enhanced 50% and 100%, respectively. This feeding strategy was implemented with no advanced instrumentation yet facilitated significantly increased yield in shake flasks. The technique should benefit those in research laboratories employing the baculovirus expression system as a rapid and efficient production system.     

Electron microscopic studies of the binding of Escherichia coli RNA polymerase to DNA. I. Characterization of the non-specific interactions of holoenzyme with a restriction fragment of bacteriophage T7 DNA

Non-specific interactions between a 3800 base-pair restriction fragment of bacteriophage T7 DNA (MboI-C) and Escherichia coli RNA polymerase holoenzyme have been examined by electron microscopy. Holoenzyme displays a relatively weak and rapidly reversible binding to DNA that is only slightly reduced at elevated salt concentrations. As the concentration of NaCl is increased from 50 mm to 200 mm, the binding constant decreases from 2 × 10⁴m^?1to 4 × 10³m^?1. It is concluded that only 1 to 2 sodium ions are released from the DNA when holoenzyme binds non-specifically.The validity of the electron microscopic technique for determining binding constants has been investigated by varying aspects of the grid surface and by examining the non-specific interactions of lac repressor with DNA.     

Conjugative transfer of plasmid pTO1 from Escherichia coli to Rhodococcus spp.

Summary We demonstrated the conjugative transfer of plasmid pTO1 from Escherichia coli S17-1 to different Rhodococcus spp. The plasmid contains the oriT fragment from RK2 and a fragment of Streptomyces C31 actinophage with the attachment site and the integration genes. Experiments on hybridization showed that plasmid pTO1 is chromosomally integrated into the Rhodococcus cells.     

New antibiotic-producing Streptomyces TT-strain,generated by electrical fusion of protoplasts

Interspecific electrofusion between protoplasts of multhiomycin-producing Streptomyces antibioticus aAL Ala⁻Leu⁻ and neomycin-producing S. fradiae fHL His⁻Leu⁻ was done. When the concentration of both protoplasts increased to 1 × 10⁹ protoplasts/ml, the frequency of fusion attained was 18.6%. The addition of multithiomycin and neomycin to the regeneration medium was very effective for screening for fusants able to produce new antibiotics. The ability to produce new antibiotics was very unstable in the fusants. After several subcultures, fusants selected as new antibiotic producers (10 strains) lost this ability with one exception (TT-strain). The antibiotic produced by the stable TT-strain clone was purified and characterized to some extent. It was active on a range of Gram-positive bacteria and distinguished from multhiomycin and neomycin by bioautographic analysis.     

Transition state stabilization by deaminases: Rates of nonenzymatic hydrolysis of adenosine and cytidine

Nonenzymatic rates of hydrolytic deamination of adenosine and cytidine by acids and bases analogous to side chains of naturally occurring amino acids are compared with the rates of uncatalyzed deamination in water and with the rates of the hydroxide- and hydrogen ion-catalyzed reactions. For adenosine, hydroxide ion is an effective catalyst, with a second-order rate constant of 7.5 × 10⁻⁶ m⁻¹ s⁻¹ at 85°C and an energy of activation of 19.9 kcal/mol. Acid-catalyzed deamination of adenine proceeds with a second-order rate constant of 1.5 × 10⁻⁶ m⁻¹ s⁻¹ at 85°C. At concentrations of 1 m and at pH values corresponding to their respective pK_a values, dimethylamine, acetate, selenide, imidazole, phosphate, and zinc(II) do not enhance the rate of deamination of adenosine beyond that observed in water, and 2-mercaptoethanol produces only a modest rate enhancement. The uncatalyzed rate of adenosine deamination in water is 8.6 × 10⁻⁹ s⁻¹ at 85°C: extrapolation to 37°C and comparison with k_cat for rat hepatoma adenosine deaminase yield a rate enhancement by the enzyme of approximately 2 × 10¹²-fold. 1,6-Dimethyladenosine, the conjugate acid of which has a pK_a value much higher than that of adenosine, is not readily deaminated, suggesting that the uncatalyzed deamination of adenosine does not proceed by hydroxide ion attack on the rare protonated form of adenosine, but rather by attack on the neutral species. Deamination of cytidine is catalyzed most effectively by hydroxide ion, with a second-order rate constant of 4.5 × 10⁻⁴ m⁻¹ s⁻¹ at 85°C and an energy of activation of 28.5 kcal/mol. The uncatalyzed rate of deamination of cytidine in water, which also exhibits an energy of activation of 28.5 kcal/mol, is 8.8 × 10⁻⁸ s⁻¹ at 85°C. Comparison of the rate extrapolated to 25°C with k_cat for bacterial cytidine deaminase gives a rate enhancement for the enzyme of 4 × 10¹¹-fold. The C-5 proton of the pyrimidine ring of cytidine does not exchange with solvent during alkaline hydrolysis, suggesting that deamination under these conditions does not involve prior addition of water across the 5,6 double bond.