Skryabin Institute of Biochemistry and Physiology of Microorganisms

Pushchino, Russia

Skryabin Institute of Biochemistry and Physiology of Microorganisms

Pushchino, Russia
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Myasoedova N.M.,Skryabin Institute of Biochemistry and Physiology of Microorganisms | Gasanov N.B.,Pushchino State Institute of Natural science | Chernykh A.M.,Skryabin Institute of Biochemistry and Physiology of Microorganisms | Kolomytseva M.P.,Skryabin Institute of Biochemistry and Physiology of Microorganisms | Golovleva L.A.,Skryabin Institute of Biochemistry and Physiology of Microorganisms
Applied Biochemistry and Microbiology | Year: 2015

The effects of a number of culture medium components, such as peptone, yeast extract, mono- and disaccharides, copper ions, 2,6-dimethylphenol, and polycaproamide fiber, on the laccase activity dynamics in the culture liquid and laccase isoform production by the Lentinus strigosus 1566 fungus were studied. It was demonstrated that some saccharides selectively induced or inhibited the synthesis of different laccase isoforms. Similar action was exerted by copper ions, 2,6-dimethylphenol, and polycaproamide fiber, as well as by their combination. Selective in vivo regulation of the production of certain laccase isoforms by basidial fungi by means of altering the culturing medium composition can be utilised for various biotechnological purposes. © Pleiades Publishing, Inc., 2015.


Rozova O.N.,Skryabin Institute of Biochemistry and Physiology of Microorganisms | Khmelenina V.N.,Skryabin Institute of Biochemistry and Physiology of Microorganisms | Vuilleumier S.,University of Strasbourg | Trotsenko Y.A.,Skryabin Institute of Biochemistry and Physiology of Microorganisms
Research in Microbiology | Year: 2010

Pyrophosphate-dependent 6-phosphofructokinase (PPi-PFK) was obtained as His6-tagged protein by cloning of the pfp gene from the aerobic obligate methanotroph Methylomicrobium alcaliphilum 20Z and characterized. The recombinant PPi-PFK (4×45kDa) was highly active, non-allosteric and stringently specific to pyrophosphate as the phosphoryl donor. The enzyme was more specific for the reverse reaction substrate fructose-1,6-bisphosphate (Km 0.095mM, Vmax 805U/mg of protein) than for the forward reaction substrate fructose-6-phosphate (Km 0.64mM, Vmax 577U/mg of protein). It also phosphorylated sedoheptulose-7-phosphate with much lower efficiency (Km 1.01mM, Vmax 0.118U/mg of protein). The kinetic properties of the M. alcaliphilum PPi-PFK were analyzed and compared with those of PPi-PFKs from other methanotrophs. The PPi-PFK from M. alcaliphilum shows highest sequence identity to PPi-PFK from obligate mesophilic methanotroph Methylomonas methanica (89%), and only low identity to the enzyme from thermotolerant Methylococcus capsulatus Bath (16%). This extensive sequence divergence of PPi-PFKs correlated with differential ability to phosphorylate sedoheptulose-7-phosphate and with the metabolic patterns of these bacteria assimilating C1 substrate either via the ribulose monophoshate (RuMP) cycle or simultaneously via the RuMP and the Calvin cycles. Based on enzymic and genomic data, the involvement of PPi-PFK in pyrophosphate-dependent glycolysis in M. alcaliphilum 20Z was fist proposed. © 2010 Institut Pasteur.


Volkov P.V.,RAS A.N. Bach Institute of Biochemistry | Rozhkova A.M.,RAS A.N. Bach Institute of Biochemistry | Pravilnikov A.G.,RAS A.N. Bach Institute of Biochemistry | Andrianov R.M.,RAS A.N. Bach Institute of Biochemistry | And 6 more authors.
Applied Biochemistry and Microbiology | Year: 2012

An enzyme preparation has been produced on the basis of Penicillium canescens strains with the activity of cellibiohydrolase I, II; endo-1,4-β-gluconase of Penicillium verruculosum; and β-glucosidase of Aspergillus niger. It was shown that for the most effective hydrolysis of aspen wood pulp the optimal ratio of cellobiohydrolase and endo-1,4-β-gluconase in enzyme preparations was 8: 2 (by protein). It was also established that the homologous xylanase secreted by the Penicillium canescens fungus is a required component for the enzyme complex for hydrolysis of the hemicellulose matrix of aspen wood. © 2012 Pleiades Publishing, Ltd.


Solyanikova I.P.,Skryabin Institute of Biochemistry and Physiology of Microorganisms | Baskunov B.P.,Skryabin Institute of Biochemistry and Physiology of Microorganisms | Baboshin M.A.,Skryabin Institute of Biochemistry and Physiology of Microorganisms | Saralov A.I.,Russian Academy of Sciences | Golovleva L.A.,Skryabin Institute of Biochemistry and Physiology of Microorganisms
Applied Biochemistry and Microbiology | Year: 2012

The ability of the strains-destructors of various aromatic compounds to utilize trinitrotoluene (TNT) up to concentration of 70 mg/l was shown. An increase in the TNT concentration from 100 to 150 mg/l did not inhibit its conversion rate by the Kocuria palustris RS32 strain. The Acinetobacter sp. VT11 strain utilized TNT as a sole substrate for growth; 3,5-dinitro-4-methyl anilide acetate and 2,6-dinitro-4-aminotoluene were identified as intermediates of TNT degradation by active strains of Pseudomonas sp. VT-7W and Kocuria rosea RS51. At the same time, 4-methyl-3,5-dinitroformamide was discovered for the first time upon the TNT destruction by the bacteria strains of Rhdococcus opacus 1G and Rhdococcus sp. VT-7. The active bacterial strains achieved an 82-90% destruction of TNT when they were introduced into the soil. © 2012 Pleiades Publishing, Ltd.


Puchkov E.O.,Skryabin Institute of Biochemistry and Physiology of Microorganisms
BIOINFORMATICS 2011 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms | Year: 2011

For Saccharomyces cerevisiae yeast studies, three approaches have been developed. They are based on the image analysis (ImageJ software) application for the fluorescence microscopy data treatment. The first is a computer-aided fluorescence microscopy procedure for quantifying of the damaged cells in the ethanol-producing yeast culture. It was shown to be applicable for the assessment of the culture viability. The second is a means of characterizing Brownian motion of the insoluble polyphosphate complexes in the vacuoles. Using this approach, the apparent viscosity in the vacuoles was measured. The third is a method for locating intracellular sites/targets of the nucleic acid intercalators. This method may be of help in designing of new DNA-targeted drugs and in preliminary studies of their interaction with eukaryotic cells.


Burenina O.Y.,Moscow State University | Fedotova E.A.,Moscow State University | Ryazanova A.Y.,Moscow State University | Protsenko A.S.,Skryabin Institute of Biochemistry and Physiology of Microorganisms | And 5 more authors.
Acta Naturae | Year: 2013

Transcription regulation in bacterial restriction-modification (R-M) systems is an important process, which provides coordinated expression levels of tandem enzymes, DNA methyltransferase (MTase) and restriction endonuclease (RE) protecting cells against penetration of alien DNA. The present study focuses on (cytosine-5)-DNA methyltransferase Ecl18kI (M. Ecl18kI), which is almost identical to DNA methyltransferase SsoII (M. SsoII) in terms of its structure and properties. Each of these enzymes inhibits expression of the intrinsic gene and activates expression of the corresponding RE gene via binding to the regulatory site in the promoter region of these genes. In the present work, complex formation of M. Ecl18kI and RNA polymerase from Escherichia s{cyrillic}oli with the promoter regions of the MTase and RE genes is studied. The mechanism of regulation of gene expression in the Ecl18kI R-M system is thoroughly investigated. M. Ecl18kI and RNA polymerase are shown to compete for binding to the promoter region. However, no direct contacts between M. Ecl18kI and RNA polymerase are detected. The properties of M. Ecl18kI and M. SsoII mutants are studied. Amino acid substitutions in the N-terminal region of M. Ecl18kI, which performs the regulatory function, are shown to influence not only M. Ecl18kI capability to interact with the regulatory site and to act as a transcription factor, but also its ability to bind and methylate the substrate DNA. The loss of methylation activity does not prevent MTase from performing its regulatory function and even increases its affinity to the regulatory site. However, the presence of the domain responsible for methylation in the M. Ecl18kI molecule is necessary for M. Ecl18kI to perform its regulatory function. © 2013 Park-media.


Zyakun A.M.,Skryabin Institute of Biochemistry and Physiology of Microorganisms
Journal of Analytical Chemistry | Year: 2011

Metabolic products of biological systems in most cases are polyatomic molecular structures containing polyisotopic elements (hydrogen, carbon, nitrogen, oxygen, sulfur, chorine, etc.) that are different in genesis and biosynthetic pathways. In the molecules carrying two and more atoms of polyisotopic element in different positions (sites), the probability of detection of isotopes by sites in the pool (array) of analyzed molecules may be different, i.e.; there is intramolecular isotopic heterogeneity by the specified element. Detection and quantitative estimation of isotopic heterogeneity of polyisotopic elements in molecules by the methods of isotopic mass spectrometry is a novel source of information about the processes involving the respective polyisotopic element. An isotopic equation has been proposed, the coefficients of which are normalized peak intensities of isotopically different molecular ions in the mass spectrum of the analyte. Solutions of this equation reflect the abundance ratios of isotopic atoms of polyisotopic element by its positions in molecules comprising the analyzed pool. During homogenous (equally probable) distribution of isotopic atoms of the element by all of its sites in molecules of the analyzed pool, solutions of the isotopic equation are equal to each other. In the case of non-homogenous isotope distribution of the polyisotopic element in the pool of molecules, solutions of the isotopic equation take on different values and may be presented by both real and complex numbers. Solutions of the isotopic equation reflect the peculiarities of distribution of element isotopes in a molecule and possible pathways of formation of a pool of analyzed molecules under laboratory and natural conditions. © 2011 Pleiades Publishing, Ltd.

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