The role of histones H3 and H1 in the formation of thymine-lysine cross-links during UV-irradiation of deoxyribonucleoprotein

The effect of UV light (lambda = 254 nm) on calf thymus DNP at low ionic strengths was studied. It was found that at the irradiation doses used the protein in the DNA-protein complex increases as the irradiation dose rises. Thermal treatment and acid hydrolysis resulted in a predominant release of histones H3 and H1 from the complex. Data from liquid high performance chromatography, amino acid analysis, thin-layer chromatography point to the induction by UV-light of a thymine-lysine bond, whose formation involves DNA thymines and histone lysine residues, predominantly H3 and H1 fractions.     

Isolation of modified histone H3 from ultraviolet-irradiated deoxyribonucleoprotein by reversed-phase high-performance liquid chromatography

A rapid reversed-phase high-performance liquid chromatography procedure for the isolation of histone H3 and/or of thymine modified at the lysine residue histone H3 from uv-irradiated deoxyribonucleoprotein and DNA-protein complex is reported. The system utilizes a C8 Ultrasphere macroporous column and an acetonitrile "inverse or negative gradient."     

Calculation of a single and of subsequent extraction-reextraction cycles

Estimation of the equilibrium distribution in the organic solvent-water system provided analysis of efficiency and optimal arrangement of subsequent extraction-reextraction cycles in isolation of various compounds. The analysis was performed with respect to optimization of the total yield and required volumes of the intermediate phases. It was shown that the best arrangement of the subsequent extraction-reextraction cycles depended on the compound distribution coefficients at various stages.     

Structure and folding of bacteriophage T4 gene product 9 triggering infection. I. Production and properties of recombinant protein

Gene product 9 (gp9, 288 amino acid residues per monomer, molecular weight 30.7 kD) of bacteriophage T4 triggers the baseplate reorganization and the sheath contraction after interaction of the long tail fibers with the receptors of the bacterial cell. In this work we have produced the recombinant protein and determined that gp9 is a stable homotrimer and active in in vitro complementation assay completing the defective phage particles which lack gp9. According to CD-spectroscopy data, the gp9 polypeptide chain contains 65-73% beta-structure and 11-16% alpha-helical segments, this being in good agreement with secondary structure prediction results. Additionally, we have constructed a set of plasmid vectors for expression of gp9 deletion mutants. The fragments with consecutive truncations of the N-terminus of the molecule, as well as the full-length protein, are trimers resistant to SDS treatment and decrease infective phage particle formation in in vitro complementation assay with native gp9. The deletion of the molecule C-terminal region results in failure of trimerization and decreases the stability of the protein.     

Co-expression of gene 31 and 23 products of bacteriophage T4

Folding of the major capsid protein of bacteriophage T4 encoded by gene 23 is aided by Escherichia coli GroEL chaperonin and phage co-chaperonin gp31. In the absence of gene product (gp) 31, aggregates of recombinant gp23 accumulate in the cell similar to inclusion bodies. These aggregates can be solubilized with 6 M urea. However, the protein cannot form regular structures in solution. A system of co-expression of gp31 and gp23 under the control of phage T7 promoter in E. coli cells has been constructed. Folding of entire-length gp23 (534 amino acid residues) in this system results in the correctly folded recombinant gp23, which forms long regular structures (polyheads) in the cell.     

Copper resistance in Desulfovibrio strain R2

A sulfate-reducing bacterium, designated as strain R2, was isolated from wastewater of a ball-bearing manufacturing facility in Tomsk, Western Siberia. This isolate was resistant up to 800 mg Cu/l in the growth medium. By comparison, Cu-resistance of reference cultures of sulfate-reducing bacteria ranged from 50 to 75 mg Cu/l. Growth experiments with strain R2 showed that Cu was an essential trace element and, on one hand, enhanced growth at concentrations up to 10 mg/l but, on the other hand, the growth rate decreased and lag-period extended at copper concentrations of >50 mg/l. Phenotypic characteristics and a 1078 bp nucleotide sequence of the 16S rDNA placed strain R2 within the genus Desulfovibrio. Desulfovibrio R2 carried at least one plasmid of approximately of 23.1 kbp. A 636 bp fragment ot the pcoR gene of the pco operon that encodes Cu resistance was amplified by PCR from plasmid DNA of strain R2. The pco genes are involved in Cu-resistance in some enteric and aerobic soil bacteria. Desulfovibrio R2 is a prospective strain for bioremediation purposes and for developing a homologous system for transformation of Cu-resistance in sulfate-reducing bacteria. This revised version was published online in June 2006 with corrections to the Cover Date.     

Novel beta-lactam structures: design problems]

The methology of the development of new biologically active betalactams is proposed. One of the two ways proposed is specific modification which is peculiar to certain betalactam structure and involves introduction of substitutes changing particular physico-chemical properties of the natural or synthetic analogous. General guidelines for modification of the biologically active compounds are given. The space and depth of the necessary physico-chemical investigation are determined. The alternative way of the new biologically active compounds development is the principle of similarity. The distinctive feature of this approach is the use as building blocks of the substitutes already used in the well-known betalactam antibiotics and "implantation" of this substitutes into other (new) betalactam structures. The ways of the new betalactams synthesis including the methods of enzyme engineering are considered. The possibility to use enzyme engineering processes for production of not only new individual betalactams--hits, but also for synthesis of the groups of betalactams--leads, is shown. More than 6000 new betalactam structures were constructed on the base of the principle of similarity. At least 700 of this compounds demonstrates not only antimicrobial activity but other types of biological activity due to the implementation of additional pharmaceutical units other than betalactams. The constructed compounds are summarized in the tables, the request for the electronic version of the tables can be sent by the address: valan@orc.ru.     

Phenogenetic Characterization of a Group of Giant φKZ-like Bacteriophages of Pseudomonas aeruginosa

A comparative study was made of a group ofPseudomonas aeruginosa virulent giant DNA bacteriophages similar to phage KZ in several genetic and phenotypic properties (particle size, particle morphology, genome size, appearance of negative colonies, high productivity, broad spectrum of lytic activity, ability to overcome the suppressing effect of plasmids, absence of several DNA restriction sites, capability of general transduction, pseudolysogeny). We have recently sequenced the phage KZ genome (288 334 bp) [J. Mol. Biol., 2002, vol. 317, pp. 1–19]. By DNA homology, the phages were assigned to three species (represented by phages KZ, Lin68, and EL, respectively) and two new genera (KZ and EL). Restriction enzyme analysis revealed the mosaic genome structure in four phages of the KZ species (KZ, Lin21, NN, and PTB80) and two phages of the EL species (EL and RU). Comparisons with respect to phage particle size, number of structural proteins, and the N-terminal sequences of the major capsid protein confirmed the phylogenetic relatedness of the phages belonging to the KZ genus. The origin and evolution of the KZ-like phages are discussed. Analysis of protein sequences encoded by the phage KZ genome made it possible to assume wide migration of the KZ-like phages (wandering phages) among various prokaryotes and possibly eukaryotes. Since the phage KZ genome codes for potentially toxic proteins, caution must be exercised in the employment of large bacteriophages in phage therapy.     

Growth of sulfate-reducing bacteria with solid-phase electron acceptors

Hannebachite (CaSO3 x 0.5H2O), gypsum (CaSO4 x 2H2O), anglesite (PbSO4), and barite (BaSO4) were tested as electron acceptors for sulfate-reducing bacteria with lactate as the electron donor. Hannebachite and gypsum are commonly associated with flue gas desulfurization products, and anglesite is a weathering product found in lead mines. Barite was included as the most insoluble sulfate. Growth of sulfate-reducing bacteria was monitored by protein and sulfide (dissolved H2S and HS-) measurements. Biogenic sulfide formation occurred with all four solid phases, and protein data confirmed that bacteria grew under these electron acceptor conditions. Sulfide formation from gypsum was almost comparable in rate and quantity to that produced from soluble sulfate salt (Na2SO4); hannebachite reduction to sulfide was not as fast. Anglesite as the electron acceptor was also reduced to sulfide in the solution phase and galena (PbS) was detected in solids retrieved from spent cultures. Barite as the electron acceptor supported the least amount of growth and H2S formation. The results demonstrate that low-solubility crystalline phases can be biologically reactive under reducing conditions. Furthermore, the results demonstrate that galena precipitation through sulfide production by sulfate-reducing bacteria serves as a lead enrichment mechanism, thereby also alleviating the potential toxicity of lead. In view of the role of acidophilic thiobacilli in the oxidation of sulfides, the present work accentuates the role of anaerobic and aerobic microbes in the biogeochemical cycling of solid-phase sulfates and sulfides.     

A three-dimensional cryo-electron microscopy structure of the bacteriophage phiKZ head

The three-dimensional structure of the Pseudomonas aeruginosa bacteriophage phiKZ head has been determined by cryo-electron microscopy and image reconstruction to 18A resolution. The head has icosahedral symmetry measuring 1455 A in diameter along 5-fold axes and a unique portal vertex to which is attached an approximately 1800 A-long contractile tail. The 65 kDa major capsid protein, gp120, is organized into a surface lattice of hexamers, with T = 27 triangulation. The shape and size of the hexamers is similar to the hexameric building blocks of the bacteriophages T4, phi29, P22, and HK97. Pentameric vertices of the capsid are occupied by complexes composed of several special vertex proteins. The double-stranded genomic DNA is packaged into a highly condensed series of layers, separated by 24 A, that follow the contour of the inner wall of the capsid.