Comparative Study of the M.BstF5I-1 and M.BstF5I-3 DNA Methyltransferases from the Bacillus stearothermophilus F5 Restriction–Modification System

The BstF5I restriction–modification system from Bacillus stearothermophilus F5, unlike all known restriction–modification systems, contains three genes encoding DNA methyltransferases. In addition to revealing two DNA methylases responsible for modification of adenine in different DNA strands, it has been first shown that one bacterial cell has two DNA methylases, M.BstF5I-1 and M.BstF5I-3, with similar substrate specificity. The boundaries of the gene for DNA methyltransferase M.BstF5I-1 have been verified. The bstF5IM-1 gene was cloned in pJW and expressed in Escherichia coli. Homogeneous samples of M.BstF5I-1 and M.BstF5I-3 were obtained by chromatography with different sorbents. The main kinetic parameters have been determined for M.BstF5I-1 and M.BstF5I-3, both modifying adenine in the recognition site 5"-GGATG-3".     

Sorption of plasma components on the surface of particles of fluorocarbon emulsions stabilized by proxanol 268

It was found in the experiments in vivo and in vitro that the contact of perfluorocarbon emulsion stabilized with proxanol 268 with blood plasma leads to the sorption of various plasma proteins on the surface of emulsion particles. The profile of the proteins sorbed is complex and includes proteins with molecular weights ranging from 14 to 94 kDa. Among proteins sorbed on the emulsion particles circulating in blood, IgG was identified. Incubation of the emulsion stabilized with proxanol 268 with human blood plasma in vitro was shown to result in the sorption of IgG and IgA the perfluorocarbon particles. The sorbtion of serum proteins and immune complexes circulating in blood on the surface of perfluorocarbon particles stabilized with proxanol 268 was revealed to activate the complement system.     

Tobacco etch virus proteinase: crystal structure of the active enzyme and its inactive mutant

Tobacco Etch Virus Protease (TEV protease) is widely used as a tool for separation of recombinant target proteins from their fusion partners. The crystal structures of two mutants of TEV protease, active autolysis-resistant mutant TEV-S219D in complex with the proteolysis product, and inactive mutant TEV-C151A in complex with a substrate, have been determined at 1.8 and 2.2 A resolution, respectively. The active sites of both mutants, including their oxyanion holes, have identical structures. The C-terminal residues 217-221 of the enzyme are involved in formation of the binding pockets S3-S6. This indicates that the autolysis of the peptide bond Met218-Ser219 exerts a strong effect on the fine-tuning of the substrate in the enzyme active site, which results in considerable decrease in the enzymatic activity.     

Biotin-ubiquitin tagging of mammalian proteins in Escherichia coli

Ubiquitin has been used in protein expression for enhancing yields and biological activities of recombinant proteins. Biotin binds tightly and specifically to avidin and has been widely utilized as a tag for protein purification and monitoring. Here, we report a versatile system that takes the advantages of both biotin and ubiquitin for protein expression, purification, and monitoring. The tripartite system contained coding sequences for a leader biotinylation peptide, ubiquitin, and biotin holoenzyme synthetase in two reading frames under the control of T7 promoter. The expression and purification of several large mammalian enzymes as biotin-ubiquitin fusions were accomplished including human ubiquitin activating enzyme, SUMO activating enzymes, and aspartyl-tRNA synthetase. Expressed proteins were purified by one-step affinity column chromatography on monomeric avidin columns and purified proteins exhibited active function. Additionally, the ubiquitin protein hydrolase UBP41, expressed and purified as biotin-UBP41, efficiently and specifically cleaved off the biotin-ubiquitin tag from biotin-ubiquitin fusions to produce unmodified proteins. The present expression system should be useful for the expression, purification, and functional characterization of mammalian proteins and the construction of protein microarrays.     

The thermodynamic stability of nanoconstructions based on the double-stranded DNA molecules

The temperature stability of nanoconstructions formed by double-stranded DNA molecules fixed in the structure of their liquid crystalline dispersions and cross-linked by nanobridges was determined. It was shown that the heating of nanoconstructions is accompanied by a decrease in the amplitude of the negative bands in the CD spectrum both at lambda approximately 310 and lambda approximately 505 nm. Temperature "melting curves" were derived and characterzed by T(M) values. The T(M) values at lambda approximately 310 and lambda approximately 505 nm coincided with each other but differed from the T(M) value characteristic of the DNA cholesteric liquid crystalline dispersion.     

Bacteriophage T4Dam DNA-(adenine-N(6))-methyltransferase. Comparison of pre-steady state and single turnover methylation of 40-mer duplexes containing two (un)modified target sites

We analyzed pre-steady state and single turnover kinetics of bacteriophage T4Dam DNA-(adenine-N(6))-methyltransferase-mediated methyl group transfer from S-adenosyl-l-methionine (AdoMet) to 40-mer duplexes containing native recognition sites (5'-GATC/5'-GATC) or some modified variant(s). The results extend a model from studies with single-site 20-mer duplexes. Under pre-steady state conditions, monomeric T4Dam methyltransferase-AdoMet complexes were capable of rapid methylation of adenine residues in 40-mer duplexes containing two sites. During processive movement of T4Dam to the next site, the rate-limiting step was the exchange of the product S-adenosyl-l-homocysteine (AdoHcy) for AdoMet without T4Dam dissociating from the duplex. Consequently, instead of a single exponential rate dependence, complex methylation curves were obtained with at least two pre-steady state steps. With 40-mer duplexes containing a single target site, the kinetics were simpler, fitting a single exponential followed by a linear steady state phase. Single turnover methylation of 40-mer duplexes also proceeded in two stages. First, two dimeric T4Dam-AdoMet molecules bound, and each catalyzed a two-step methylation. Instead of processive movement of T4Dam, a conformational adaptation occurred. We propose that following methyl transfer to one strand, dimeric (T4Dam-AdoMet)-(T4Dam-AdoHcy) was capable of rapidly reorienting itself and catalyzing methyl transfer to the target adenine on the complementary, unmethylated strand. This second stage methyl transfer occurred at a rate about 25-fold slower than in the first step; it was rate-limited by Dam-AdoHcy dissociation or its clearance from the methylated complementary strand. Under single turnover conditions, there was complete methylation of all target adenine residues with each of the two-site 40-mer duplexes.     

Molecular enzymology of phage T4 Dam DNA-methyltransferase

The review reflects results of studies on the molecular mechanism of phage T4 Dam DNA-methyltransferase action. The enzyme (T4Dam) catalyzes methyl group transfer from S-adenosyl-l-methionine (AdoMet) to N6-adenine position in the palindromic recognition sequence GATC (EC 2.1.1.72). The enzyme subunit structure, substrate-binding and kinetic parameters for a wide range of native and modified oligonucleotide duplexes, as well as steady-state reaction kinetic scheme, included T4Dam isomerization to catalytically active form, are considered. The found mechanisms of DNA induced T4Dam dimerization, target base flipping, enzyme reorientation in an asymmetrically modified recognition sequence, effector action of reaction substrates and processive methylation of DNA substrates, containing more than one specific site, are discussed. The results obtained with T4Dam may be useful for understanding mechanisms of action of other homologous enzymes, most of all for specimens of numerous family of Dam DNA-methyltransferases.     

Neurotoxic Effect of Dexamethasone: Weakening upon the Action of Antidepressants

Dose-dependent neurotoxic effects (decrease in the amplitude of field potentials generated by neurons of the СА1 area, dentate gyrus, and dorsal striatum, but not by neurons of layers ІІ and ІІІ of the parietal cortex, recorded in slices of the rat brain) were observed 24 h after i.p. injection оf dexamethasone in doses of 7 and 20 mg/kg. Dexamethasone-induced decreases in the reactivity of glutamatergic synapses in the studied cerebral structures were weakened by a noncompetitive blocker of NMDA receptors, ketamine (30 mg/kg), and an inhibitor of tyrosine protein phosphatases, sodium vanadate (15 mg/kg), if the latter agent was injected 6 h after dexamethasone administration. The neurotoxic effect of dexamethasone was intensified by a coagonist of NMDA receptors, glycine (50 mg/kg), as well as in the case where injections of dexamethasone were combined with single injections of the antidepressant fluoxetine (20 mg/kg) but not when another antidepressant, pyrazidol, was injected in the same dose. Chronic (two weeks) injections of fluoxetine and pyrazidol weakened manifestations of dexamethasone neurotoxicity. On-regulation of NMDA receptors and suppression of expression of neurotrophins are considered probable mechanisms underlying neurotoxicity of this hormone. The effect of chronic injections of antidepressants on the respective processes is discussed. Neirofiziologiya/Neurophysiology, Vol. 40, No. 4, pp. 312–231, July–August, 2008.     

The pituitary-thyroid axis and oxygen consumption parameters under the conditions of chronic cold exposure in the North

The functional state of the pituitary-thyroid axis (PTA) and oxygen consumption were studied monthly during one year in a group of soldiers from northern European Russia daily staying outdoors for 6–10 h. It was shown that the chronic exposure to low temperatures on the human body was accompanied by activation of metabolism of thyroid hormones, which was evident from accumulation of their free forms. The irritant caused no tension of the central link of the endocrine system, and although the levels of thyroid hormones in the blood were reduced, the mechanism of negative feedback was not activated, which was evidenced by a stably low level of thyrotrophic hormone of the pituitary gland. At the same time, the rapid change in the duration of daytime influencing the central links of the neuroendocrine system resulted in unbalance of feedback mechanisms. The illumination factor under the conditions of chronic hypothermia proved to be a stronger irritant for the central link of the endocrine system than the signals transmitted by feedback mechanisms from the peripheral parts of the PTA.     

Kinetic aspects of inhibition of the phytopathogenic fungi growth by rhizosphere bacteria

Kinetics of growth inhibition of fungi Fusarium and Bipolaris caused by bacteria Pseudomonas sp. V-6798 and Azotobacter chroococum V-2272 D on dense nutrient media, both in single-crop system and by coinoculation, was demonstrated. The speed of fungal colonies growth as a function of bacteria concentration in inoculate was shown to be in accordance with the Ierysalimskii modified equation. The degree of antagonistic activity was suggested to be assessed by the constant of inhibition (K _i ) and residual rate of fungi growth. Constant of inhibition of fungal growth by bacteria varied within 10–100 cells/ml for observed species. More effective fungistatic influence of bacterial strains in combined culture was observed. Parameters reported in the present study allow comparing the degree of bacteria antifungal activity in vitro. Suggested screening method could be used for selection of bacteria as activity biofungicide and while selecting biomedication for defined plant pathogen disruption.