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Lomakin Y.A.,RAS Shemyakin Ovchinnikov Institute of Bioorganic Chemistry | Zakharova M.Y.,RAS Shemyakin Ovchinnikov Institute of Bioorganic Chemistry | Stepanov A.V.,RAS Shemyakin Ovchinnikov Institute of Bioorganic Chemistry | Dronina M.A.,RAS Shemyakin Ovchinnikov Institute of Bioorganic Chemistry | And 21 more authors.
Molecular Immunology | Year: 2014

The mechanisms triggering most of autoimmune diseases are still obscure. Autoreactive B cells play a crucial role in the development of such pathologies and, in particular, production of autoantibodies of different specificities. The combination of deep-sequencing technology with functional studies of antibodies selected from highly representative immunoglobulin combinatorial libraries may provide unique information on specific features in the repertoires of autoreactive B cells. Here, we have analyzed cross-combinations of the variable regions of human immunoglobulins against the myelin basic protein (MBP) previously selected from a multiple sclerosis (MS)-related scFv phage-display library. On the other hand, we have performed deep sequencing of the sublibraries of scFvs against MBP, Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1), and myelin oligodendrocyte glycoprotein (MOG). Bioinformatics analysis of sequencing data and surface plasmon resonance (SPR) studies have shown that it is the variable fragments of antibody heavy chains that mainly determine both the affinity of antibodies to the parent autoantigen and their cross-reactivity. It is suggested that LMP1-cross-reactive anti-myelin autoantibodies contain heavy chains encoded by certain germline gene segments, which may be a hallmark of the EBV-specific B cell subpopulation involved in MS triggering. © 2014 The Authors.


Yuzbashev T.V.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika | Bondarenko P.Y.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika | Sobolevskaya T.I.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika | Yuzbasheva E.Y.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika | And 6 more authors.
Biotechnology and Bioengineering | Year: 2016

Bio-based succinic acid production can redirect industrial chemistry processes from using limited hydrocarbons to renewable carbohydrates. A fermentation process that does not require pH-titrating agents will be advantageous to the industry. Previously, a Yarrowia lipolytica strain that was defective for succinate dehydrogenase was constructed and was found to accumulate up to 17.5 g L−1 of succinic acid when grown on glycerol without buffering. Here, a derivative mutant was isolated that produced 40.5 g L−1 of succinic acid in 36 h with a yield of 0.32 g g−1 glycerol. A combination approach of induced mutagenesis and metabolic evolution allowed isolation of another derivative that could utilize glucose efficiently and accumulated 50.2 g L−1 succinic acid in 54 h with a yield of 0.43 g g−1. The parent strain of these isolated mutants was used for [1,6-13C2]glucose assimilation analysis. At least 35% glucose was estimated to be utilized through the pentose phosphate pathway, while ≥84% succinic acid was formed through the oxidative branch of the tricarboxylic acid cycle. Biotechnol. Bioeng. 2016;113: 2425–2432. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.


PubMed | RAS N. D. Zelinsky Institute of Organic Chemistry and State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika
Type: Journal Article | Journal: Biotechnology and bioengineering | Year: 2016

Bio-based succinic acid production can redirect industrial chemistry processes from using limited hydrocarbons to renewable carbohydrates. A fermentation process that does not require pH-titrating agents will be advantageous to the industry. Previously, a Yarrowia lipolytica strain that was defective for succinate dehydrogenase was constructed and was found to accumulate up to 17.5gL(-1) of succinic acid when grown on glycerol without buffering. Here, a derivative mutant was isolated that produced 40.5gL(-1) of succinic acid in 36h with a yield of 0.32gg(-1) glycerol. A combination approach of induced mutagenesis and metabolic evolution allowed isolation of another derivative that could utilize glucose efficiently and accumulated 50.2gL(-1) succinic acid in 54h with a yield of 0.43gg(-1) . The parent strain of these isolated mutants was used for [1,6-(13) C2 ]glucose assimilation analysis. At least 35% glucose was estimated to be utilized through the pentose phosphate pathway, while 84% succinic acid was formed through the oxidative branch of the tricarboxylic acid cycle. Biotechnol. Bioeng. 2016;113: 2425-2432. 2016 Wiley Periodicals, Inc.


Yuzbashev T.V.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika | Larina A.S.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika | Vybornaya T.V.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika | Yuzbasheva E.Y.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika | And 2 more authors.
Fungal Biology | Year: 2015

The vast number of repetitive genomic elements was identified in the genome of Rhizopus oryzae. Such genomic repeats can be used as homologous regions for integration of plasmids. Here, we evaluated the use of two different repeats: the short (575bp) rptZ, widely distributed (about 34 copies per genome) and the long (2053 bp) rptH, less prevalent (about 15 copies). The plasmid carrying rptZ integrated, but did so through a 2256-bp region of homology to the pyrG locus, a unique genomic sequence. Thus, the length of rptZ was below the minimal requirements for homologous strand exchange in this fungus. In contrast, rptH was used efficiently for homologous integration. The plasmid bearing this repeat integrated in multicopy fashion, with up to 25 copies arranged in tandem. The latter vector, pPyrG-H, could be a valuable tool for integration at homologous sequences, for such purposes as high-level expression of proteins. © 2015 The British Mycological Society.


Khrul'nova S.A.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIGenetika | Maryshev I.V.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIGenetika | Kulikovsky A.D.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIGenetika | Manukhov I.V.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIGenetika | Zavilgelsky G.B.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIGenetika
Biologicheskie Membrany | Year: 2012

Structural features of lux operon of the psychrophilic marine luminescent bacteria Aliivibrio logei(strains KChl and BM1) isolated from the intestine of goby fish(White Sea and Sea of Okhotsk) are characterized. Bioluminescent characteristics of the strains are determined and compared with lux operon of the mesophilic marine luminescent bacteria A. fischeri. We conclude that in spite of differences in structure of lux operons of A. fischeri and A. logei they have similar sensitivities to autoinducer.


Mordkovich N.N.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika | Manuvera V.A.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika | Veiko V.P.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika | Debabov V.G.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika
Applied Biochemistry and Microbiology | Year: 2012

A DNA fragment containing a promoter-operator and structural parts of the uridine phosphorylase gene from Shewanella oneidensis MR-1 was cloned. Cross-heterological expression of the udp genes from Sh. oneidensis MR-1 and Escherichia coli under the control of authentic regulatory regions is shown. The UDP protein accumulates in an active form in the cytoplasmic fraction of cells. The recombinant UDP protein from Sh. oneidensis MR-1 obtained by heterological expression was isolated and characterized. E. coli udp gene promoter activity was observed during heterological expression in Sh. oneidensis MR-1 cells under both aerobic and anaerobic conditions. © 2012 Pleiades Publishing, Ltd.


Kurochkina V.B.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika | Sklyarenko A.V.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika | Satarova J.E.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika | Yarotsky S.V.,State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika
Bioprocess and Biosystems Engineering | Year: 2011

The article deals with experimental determination of ionization constants and solubility for the compounds (target products, initial β-lactams, acylating agents and by-products) involved in enzymatic synthesis of some therapeutically used aminopenicillins and aminocephalosporins, namely ampicillin, amoxicillin, cephalexin, cephadroxil, cephaloglycin, cefaclor, cefprozil, cefatrizine. Methodology of investigations and the evaluation of experimental data for the determination of ionization constants and solubility of the different type electrolytes are presented. Applications of the methods based on acid-base potentiometric titration and on determination of solubility-pH dependence of assayed substances are discussed. The original data on ionization constants and solubility of amoxicillin, cefprozil, cefatrizine, cephadroxil and initial β-lactams for production of cefaclor, cefprozil and cefatrizine, as well as solubility of by-product d-(-)-p-hydroxyphenylglycine are presented. Experimentally determined parameters and constants available in the literature for all abovementioned aminopenicillins and aminocephalosporins are collected. These data might be used for choice of the conditions of both processes: the enzymatic synthesis and the isolation of the product from reaction mixture. © 2011 Springer-Verlag.


PubMed | State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika
Type: Journal Article | Journal: Bioprocess and biosystems engineering | Year: 2011

The article deals with experimental determination of ionization constants and solubility for the compounds (target products, initial -lactams, acylating agents and by-products) involved in enzymatic synthesis of some therapeutically used aminopenicillins and aminocephalosporins, namely ampicillin, amoxicillin, cephalexin, cephadroxil, cephaloglycin, cefaclor, cefprozil, cefatrizine. Methodology of investigations and the evaluation of experimental data for the determination of ionization constants and solubility of the different type electrolytes are presented. Applications of the methods based on acid-base potentiometric titration and on determination of solubility-pH dependence of assayed substances are discussed. The original data on ionization constants and solubility of amoxicillin, cefprozil, cefatrizine, cephadroxil and initial -lactams for production of cefaclor, cefprozil and cefatrizine, as well as solubility of by-product D-(-)-p-hydroxyphenylglycine are presented. Experimentally determined parameters and constants available in the literature for all abovementioned aminopenicillins and aminocephalosporins are collected. These data might be used for choice of the conditions of both processes: the enzymatic synthesis and the isolation of the product from reaction mixture.


PubMed | State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika
Type: Journal Article | Journal: FEMS microbiology letters | Year: 2012

The mercury-resistance transposon Tn5053 inhibits restriction activity of the type I restriction-modification endonuclease EcoKI in Escherichia coli K12 cells. This is the first report of antirestriction activity of a non-conjugative transposon. The gene (ardD) coding for the antirestriction protein has been cloned. The ardD gene is located within the tniA gene, coding for transposase, on the complementary strand. The direction of transcription is opposite to transcription of the tniA gene.


PubMed | Moscow Institute of Physics and Technology and State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIgenetika
Type: | Journal: Microbiological research | Year: 2016

The antirestriction proteins ArdA ColIb-P9, Arn T4 and Ocr T7 specifically inhibit type I and type IV restriction enzymes and belong to the family of DNA-mimic proteins because their three-dimensional structure is similar to the double-helical B-form DNA. It is proposed that the DNA-mimic proteins are able to bind nucleoid protein H-NS and alleviate H-NS-silencing of the transcription of bacterial genes. Escherichia coli lux biosensors were constructed by inserting H-NS-dependent promoters into a vector, thereby placing each fragment upstream of the promoterless Photorhabdus luminescens luxCDABE operon. It was demonstrated that the DNA-mimic proteins ArdA, Arn and Ocr activate the transcription of H-NS-dependent promoters of the lux operon of marine luminescent bacteria (mesophilic Aliivibrio fischeri and psychrophilic Aliivibrio logei), and the dps gene from E. coli. It was also demonstrated that the ArdA antirestriction protein, the genes of which are located on transmissive plasmids ColIb-P9, R64, PK101, decreases levels of H-NS silencing of the PluxC promoter during conjugation in the recipient bacteria.

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