[The family 28 carbohydrate-binding module of the thermostable endo-1,4-beta-glucanase CelD Caldicellulosiruptor bescii maximizes the enzyme's activity and binds irreversibly to amorphous cellulose].

The nucleotide sequence of a chromosome fragment of the thermophilic anaerobic bacterium Caldicellulosiruptor bescii (syn. Anaerocellum thermophilum) has been determined. The fragment contains four open reading frames with the second one of 749 aa encoding a multimodular endo-1,4-beta-glucanase CelD (85019 Da). N-terminal region of the protein includes the signal peptide and the catalytic module of glycoside hydrolase family 5 (GH5), followed by the substrate-binding module of family 28 (CBM28). The C-terminal region bears three SLH modules. The recombinant endoglucanase and its two separate modules, the catalytic one and CBM28, were produced in E. coli cells and purified to homogeneity. Analysis of the catalytic properties showed CelD to be endo-1,4-beta-glucanase whose maximum activity was exhibited on beta-glucan of barley at pH 6.2 and 70 degrees C. The enzyme was stable at 50 degrees C for 30 days. Upon removal of the C-terminal CBM28, the activity of GH5 decreased on cellulose substrates, and its thermostability was dropped. Binding of CBM28 to amorphous cellulose was almost irreversible as it could not be removed from this substrate in a range of pH 4-11, temperatures--of 0-75 degrees C, and NaCl concentration--of 0-5 M. Only 100% formamide or 1% SDS were able to remove the protein.

[The properties of four C-terminal carbohydrate-binding modules (CBM4) of laminarinase Lic16A of Clostridium thermocellum].

At the C-terminus of multimodular laminarinase Lic16A Clostridium thermocellum four carbohydrate-binding modules (CBM), belonging to family 4, were found. The isolated CBM - CBM4_1, CBM4_2, CBM4_3, CBM4_4 and the tandem CBM4_(1-4) were obtained. None of the recombinant proteins did have the affinity to soluble beta-1,3-1,4-glucans--laminarin and lihenan--the main specific substrates of Licl6A. All modules, except CBM4_4, had the ability to bind bacterial crystalline cellulose, that was atypical for the family 4 CBMs. We found that all CBMs 4 of Licl6A had affinity for xylan, chitin, beta-glucan from yeast cell wall and Avicel, while CBM4_3 and CBM4_4 had additional affinity to chitosan. The tandem CBM4_(1-4) had the highest affinity to yeast cell wall beta-glucan, avicel and pustulan. The binding constants for these substrates were about 100 times higher than that of the individual modules, suggesting a synergy in the process of absorption to these polysaccharides. This finding helps to explain the evolutionary process of CBM multiplication.

[Substrate-binding properties of family 54 module of laminarinase Lic16A of Clostridium thermocelwnum].

Endo beta-1.3-1.4-glucanase Lic16A of the moderate thermophilic anaerobe Clostridium thermocellum has a complex multimodular structure. In addition to the catalytic module it contains 8 auxiliary modules, 5 of which are substrate binding modules. The new family 54 substrate binding module CBM54 (25.2 kDa), localized at the N-terminus of the enzyme, owns a cleavage site, in its N-terminal part manifested by the appearance of a shortened module CBM54C (17.2 kDa) in vivo and in vito. CBM54C was cloned in Escherichia coli cells and purified to electrophoretic homogeneity. The binding constants of CBM54C to xylan, chitin, insoluble B-glucan of yeast cell wall and bacterial crystalline cellulose were in the same order of magnitude as for CBM54. However CBM54C, unlike CBM54, did not bind pustulan, avicel, and chitosan. Nevertheless the presence of calcium ions restored the ability of CBM54C to bind the latter three carbohydrates. CBM54 substrate binding promiscuity permits to suggest the presence of multiple binding sites, some of them calcium dependent. The collected data allow to localize Ca2+ -independent sites for avicel, pustulan an d chitosan binding inthe spontaneously split-off CBM54 N-terminal area (8 kDa). In this report the localization scheme of Ca2+ -dependent and Ca2+ -independent binding sites for various substrates has been suggested.

[Expression of the genes CelA and XylA isolated from a fragment of metagenomic DNA in Escherichia coli].

The glycosyl hydrolase genes cel5A and xyl3A previously isolated by ourselves within a fragment of DNA from the methagenomic library of cow rumen microflora DNA were sub-cloned and expressed in E. coli. The recombinant proteins Cel5A and Xyl3A were purified and characterized. Cellulase Cel5A belongs to the Family 5 glycosyl hydrolases and is a one-module 38.2 kDa enzyme that hydrolyses the 1,4-glycoside bonds of soluble cellulose substrates and amorphous cellulose, showing its maximal activity (31200 u/mg) on lichenan, a soluble substrate with mixed (beta-1,3-1,4) bonds. The end product of the amorphous cellulose hydrolysis is cellobiose. Cel5A is inactive toward the crystal forms of cellulose. Cel5A is an endoglucanase capable of exohydrolysis. The molecular mass of beta-xylosidase Xyl3A belonging to the Family 3 glycosyl hydrolases is 83.7 kDa. The enzyme is active only on xylooligosaccharides, with the maximal activity shown on xylobiose, the end product of the reaction being xylose. No activity on xylane was hitherto observed. Recombinant Cel5A and Xyl3A are stable over a wide range of pH and temperatures, their maximal activity being observed at pH 6.5 and at 55 degrees C.

[Cloning and characterization of a large metagenomic DNA fragment containing glycosyl-hydrolase genes].

The problem of search for and characterization of enzymes synthesized by non-cultivated microorganisms is presently being settled by creating metagenomic libraries. A 6000-clone library with the average size of its inserts amounting to 15 bp has been constructed on the basis of total DNA isolated from cow rumen microorganisms. As the result of the screening of the library on plates with different substrates, a clone was selected that efficiently hydrolyzed lichenan and carboxymethylcellulose. The clone contained the recombinant plasmid pBlue-13 bearing a 12071 bp.-long metagenomic fragment carrying ten open reading frames, two of them being identified as glycosyl hydrolase genes. No homology of the metagenomic DNA with any known microorganism genomes was revealed. The amino acid sequence, deduced on the basis of frame 4 and denoted by Xyl3A, bears resemblance with beta-xylosidases of glycosyl hydrolase Family 3. Frame 6 encodes polypeptide Cel5A homologous to cellulases of glycosyl hydrolase Family 5. The amino acid sequences deduced on the basis of seven out of ten open reading frames were homologous to proteins of microorganisms belonging to the Bacteroides sp. family, the bacteria inhabiting mammalian intestines.

[Research into the immunogenic properties of the recombinant cellulose-binding domain of Anaerocellum thermophilum in vivo].

Development of new technology allows different antigens of a necessary degree of cleanliness to be obtained. This development is a major problem of modern medical biotechnology. A promising approach to this problem includes use of the affinity domains (tags) incorporated in structure of a recombinant antigen and capable to bind to corresponding sorbents. The method of preparation of ready-for-use injections containing complexes formed by soluble antigens on insoluble cellulose immunosorbent (not chemical conjugates) in one stage is based on the fusion protein technology. This approach includes preparation of two-component recombinant proteins containing an antigen of interest and the cellulose-binding domain (CBD), which spontaneously binds to cellulose containing sorbents with high binding constant. Research into the immunogenic properties of the CBD in the complex with cellulose and in the preparation of recombinant CBD in a rat model was performed. The titers of specific antibodies in rat serum induced by recombinant CBD and CBD in the complex with cellulose was evaluated. The CBD in the complex with cellulose was more immunogenic in comparison with CBD alone. The spectrum and levels of cytokines in collected rat serum induced by developed preparations was also measured using the microsphere-based Luminex Flowmetrix system (BioPlex). It was found that the amorphous cellulose was not an immunotolerant sorbent, because it induced the expression of the proinfammatory cytokines in vivo.

[Extracellular glycosyl hydrolase activity of the clostridia producing acetone, butanol, and ethanol].

Production of acetone, butanol, ethanol, acetic acid, and butyric acid by three strains of anaerobic bacteria, which we identified as Clostridium acetobutylicum, was studied. The yield of acetone and alcohols in 6% flour medium amounted to 12.7-15 g/l with butanol constituting 51.0-55.6%. Activities of these strains towards xylan, beta-glucan, carboxymethylcellulose, and crystalline and amorphous celluloses were studied. C. acertobutylicum 6, C. acetoburylicum 7, and C. acertobutylicum VKPM B-4786 produced larger amounts of acetone and alcohols and displayed higher cellulase and hemicellulase activities than the type strain C. acetobutylicum ATCC 824. It was demonstrated that starch in the medium could be partially substituted with plant biomass.

[Thermoanaerobacter ethanolicus gene cluster containing the alpha- and beta-galactosidases genes melA and lacA, and properties of recombinant lacA].

The nucleotide sequence of a 4936 bp Thermoanaerobacter ethanolicus genomic DNA fragment containing the thermostable beta-galactosidase gene lacA and two incomplete open reading frames has been determined. The product of the first frame is highly homologous to alpha-galactosidases (melibiases), the product of the third frame is homologous to the alpha-D-mannosidases. The terminal area of the lacA, immediately following the stop-codon, harbors presumably a transcription termination site. Based on the location of the putative alpha-galactosidase gene melA and of the beta-galactosidase gene lacA on the T. ethanolicus chromosome, their combined transcription could be presumed. The calculated molecular mass of LacA is 86 kDa. LacA belongs to GH family 2 (GH2). Maximal activity of the purified recombinant enzyme was observed between pH values of 5.7 and 6.0 and temperatures of 75-80 degrees C. The highest activity, 480 units mg(-1), was found on lactose (Km 30 mM), the activities on pNPhGal and oNPhGal amounting to 330 and 420 units mg(-1), respectively. Immobilization on aldehyde silochrome increases the thermostability of the enzyme and keeps its high activity.

[Prospects for practical application of substrate-binding modules of glycosyl hydrolases (A review)]. / Perspektivy prakticheskogo primeneniia substratsviazyvaiushchikh modulei glikozilgidrolaz (Obzor).

The properties of substrate-binding modules of glycosyl hydrolases have been reviewed. Variation of the properties of these modules makes them promising as components of chimeric proteins, which is a rapidly developing field of biotechnology. Examples of applying substrate-binding modules of glycosyl hydrolases to immobilization of proteins and whole cells on polysaccharides and purification of proteins are described. Promising methods for (1) detecting various compounds using hybrids of substrate-binding modules with antibodies and (2) locating polysaccharides in live tissues are reviewed as well.

[Phytase activity in some groups of bacteria. Search for and cloning of genes for bacterial phytases]. / Fitaznaia aktivnost' u nekotorykh grupp bakterii. Poisk i klonirovanie genov bakterial'nykh fitaz.

A search for phytase genes in 9 Bacillus strains from the collection of IMGAN was implemented. The growth optimum of strains IX-22, IX-12B, K17-2, K18, IMG I, IMG II, M4 and M8 was 50-60 degrees C; the optimal growth temperature for Bacillus sp. 790 was 45-47 degrees C. According to the sequence data of 16S RNA genes, Bacillus sp. 790 belongs to the B. subtilis/amyloliquefaciens group. The other 8 strains were identified as B. licheniformis. Selection of Bacillus strains, potentially containing the phytase genes, was performed via PCR with primers designed on the basis of the conserved sequence regions of the phyA gene from B. amyloliquefaciens FZB45 with chromosomal DNA being used as the template. The nucleotide sequences of all PCR fragments showed a high level of homology to the known Bacillus phytase genes. The gene libraries of B. licheniformis M8 and B. amyloliquefaciens 790 in E. coli were constructed and phytase-containing clones were selected from them. Twenty-four Pseudomonas strains of different species, 5 Xanthomonas maltophilia strains and 1 Xanthomonas malvacearum (all from the mentioned collection) were tested for phytase activity. Such activity was found in 13 Pseudomonas strains and in 6 Xanthomonas strains. The accumulation of phytase in Pseudomonas was shown to take place at later (over 2 days') growth stages. The optimum pH for phytase from 3 Pseudomonas strains were established. The enzymes were found to be most active at pH 5.5.

[Thermotoga neopolitina gene cluster, participating in degradation of starch and maltodextrins: expression of aglB and aglA gene in Escherichia coli, properties of recombinant enzymes]. / Klaster genov Thermotoga neapolitana, uchastvuiushchikh v degradatsii krakhmala i mal'todekstrinov: éksptressiia genov aglB i aglA v Escherichia coli, svoistva rekombinantykh fermentov.

The aglB and aglA genes from the starch/maltodextrin utilization gene cluster of Thermotoga neapolitana were subcloned into pQE vectors for expression in Escherichia coli. The recombinant proteins AglB and AglA were purified to homogeneity and characterized. Both enzymes are hyperthermostable, the highest activity was observed at 85 degrees C. AglB is an oligomer of identical 55-kDa subunits capable of aggregation. This protein hydrolyses cyclodextrins and linear maltodextrins to glucose and maltose by liberating glucose from the reducing end of the molecules, and it is a cyclodextrinase with alpha-glucosidase activity. The pseudo-tetrasaccharide acarbose, a potent alpha-amylase and alpha-glucosidase inhibitor, does not inhibit AglB but, on the contrary, acarbose is degraded quantitatively by AglB. Recombinant AglB is activated in the presence of CaCl2, KCl, and EDTA, as well as after heating of the enzyme. AglA is a dimer of two identical 54-kDa subunits, and it hydrolyses the alpha-glycoside bonds of disaccharides and short maltooligosaccharides, acting on the substrate from the non-reducing end of the chain. It is a cofactor-dependent alpha-glucosidase with a wide action range, hydrolysing both oligoglucosides and galactosides with alpha-link. Thereby, the enzyme is not specific with respect to the configuration at the C4 position of its substrate. For the enzyme to be active, the presence of NAD+, DTT, and Mn2+ is required. Enzymes AglB and AglA supplement one another in substrate specificity and ensure complete hydrolysis to glucose for the intermediate products of starch degradation.

[Thermotoga neapolitana gene clusters participating in degradation of starch and maltodextins: molecular structure of the locus]. / Klaster genov Thermotoga neapolitana, uchastvuiushchikh v degradatsii krakhmala i mal'todekstrinov: molekuliarnaia struktura lokusa.

A 5451-bp genome fragment of the hyperthermophilic anaerobic eubacterium Thermotoga neapolitana has been cloned and sequenced. The fragment contains one truncated and three complete open reading frames highly homologous to the starch/maltodextrin utilization gene cluster from Thermotoga maritima whose genome sequence is known. The incomplete product of the first frame is highly homologous to MalG, the E. coli protein of starch and maltodextrin transport. The product of the second frame, AglB, is highly homologous to cyclomaltodextrinase with the alpha-glucosidase activity TMG belonging to family 13 of glycosyl hydrolases (GH13). The product of the third frame, AglA, is homologous to the Thermotoga maritima cofactor-dependent alpha-glucosidase from the GH4 family. The two enzymes form a separate branch on the phylogenetic tree of the family. The AglA and AglB proteins supplement each other in substrate specificity and can ensure complete hydrolysis to glucose of cyclic and linear maltodextrins, the intermediate products of starch degradation. The product of the fourth reading frame has sequence similarity with the riboflavin-specific deaminase RibD from T. maritima. The homologous locus of this bacterium, between the aglA and ribD genes, has five open reading frames missing in T. neapolitana. The nucleotide sequences of two frames are homologous to transposase genes. The deletion size is 2.9 kb.

[Cloning and expression of the gene for thermostable beta-galactosidase from Thermoanaerobacter ethanolicus in Escherichia coli: purification and properties of the product]. / Klonirovanie i ékspressiia gena termostabil'noi beta-galaktozidazy Thermoanaerobacter ethanolicus v kletkakh Escherichia coli, ochistka i svoistva produkta.

An anaerobic thermophilic bacterium Thermoanaerobacter ethanolicus 39E (Clostridium thermohydrosulfuricum 39E) gene library was constructed in E. coli. Recombinant plasmid (pUT50) containing the thermostable beta-galactosidase was isolated by direct selection of clones for enzyme activity using 5-bromo-4-chloro-3-indolyl-D-galactopyranoside (X-gal) and mapping procedures were carried out. The beta-galactosidase was purified from cell extracts of E. coli. Physicochemical characteristics of the recombinant beta-galactosidase were determined. The enzyme has two optimum pH values: 5.3 and 6.0, the temperature optimum is 75-80 degrees C. The molecular weight of beta-galactosidase was determined by PAG electrophoresis: about 83 kDa.

The solid-state catalytic synthesis of tritium labeled amino acids, peptides and proteins.

New catalytic reaction between a solid bioorganic compound and activated spillover tritium (ST), based on High-temperature Solid-state Catalytic Isotopic Exchange (HSCIE) was examined. The HSCIE mechanism and determination of the reactivity of hydrogen atoms in amino acids, peptides and proteins was investigated. Quantum mechanical calculations of the reactivity of hydrogen atoms in amino acids in the HSCIE reaction were done. The carbon atom with a greater proton affinity undergoes a greater exchange of hydrogen for tritium in HSCIE. The electrofilic nature of spillover hydrogen in the reaction of HSCIE was revealed. The isotope exchange between ST and the hydrogen of the solid organic compound proceeds with a high degree of configuration retention at the carbon atoms. The HSCIE reaction enables to synthesize tritium labeled proteins with a specific activity of 20-30 mCi/mg and kept biological activity.

[Purification and some properties of Clostridium thermocellum endoglucanase, formed by a recombinant Escherichia coli strain]. / Ochistka i nekotorye svoistva éndogliukanazy Clostridium thermocellum, obrazuemoi rekombinantnym shtammom Escherichia coli.

The endoglucanase (EG5) has been isolated from the recombinant strain of E. coli TG1 carrying a plasmid with C. thermocellum F7 chromosomal DNA insertion. Using high performance ion-exchange chromatography and chromatofocusing, the enzyme was 98-fold purified with a 27% yield. The enzyme has a molecular mass of 35 kDa (SDS-PAGE data) and is represented by three isoforms with pI 4.4-4.8 (isoelectrofocusing data). The activity of EG5 was determined by chromatography on carboxymethylcellulose, amorphous cellulose, xylan, lichenan and avicel. The optimal conditions for these substrates hydrolysis are: pH 6.0-6.5, 80 degrees C (60 degrees C for avicel).

[Development of bacteriophage Mu in E. coli gyrBts mutant strain]. / Razvitie bakteriofaga Mu v kletkakh mutantnogo shtamma E. coli gyrBts.

The study deals with Mu growth in cells carrying a temperature-sensitive mutation in the gene of DNA gyrase B subunit. At a nonpermissive temperature the Mu growth is shown to be blocked in the host gyrB ts mutant both on infection and on prophage induction. Mu DNA does not get integrated in the host chromosome upon the infection of mutant cells, as demonstrated by DNA-DNA hybridization experiments. In the case of prophage induction in mutant cells, as opposed to the wild type cells early mRNA synthesis is practically fully inhibited while the total RNA synthesis is three times reduced after 20 min of induction. The transcription of phage DNA associated with the changed superhelicity of DNA in the cell.

[Transposition immunity in bacteriophage Mu. The effect of a mutation at the kil gene on the establishment of immunity]. / Immunnost' transpozitsii bakteriofaga Mu. Vliianie mutatsii po genu kil na ustanovlenie immunnosti.

Bacteriophage Mu is characterized by a phenomenon similar to the transposition immunity of TnA: the frequency of transposition of Mu or mini-Mu into plasmids containing certain phage sequences is reduced by two orders of magnitude. In order to lend transposition immunity to Mu, the recipient replicon must contain a sequence of phage DNA including a 5.1 kb early region from the c-end of Mu. The product of the kil (or cim) gene takes part in establishing the immunity. The transposition immunity of Mu is connected with the disturbance of cointegrate formation.

[Construction and characteristics of mini-Mu phages]. / Konstruirovanie i kharakteristika mini-Mu-fagov.

The paper reports on the principles of construction, physical characterization and results of preliminary genetic investigation of hybrid plasmids containing Mu DNA sequences or deletion derivatives of phage Mu, the so-called mini-Mu phages. The mini-Mu were obtained by joining both phage ends within one plasmid in a regular orientation. A collection obtained by in vitro manipulations included 14 recombinant plasmids containing different DNA fragments of the Mu genome. Seven plasmids have both ends of phage Mu, three plasmids containing regularly oriented ends, i.e. mini-phages of different size: the mini-Mu5 (11 kb) within pRM8 plasmid, the mini-Mu4 Ap (18 kb) within pRM6 and the mini-mini-Mu (4.4 kb) within pRM5. The collection comprises mini-Mu phages with the gene kil inactivated after treatment with hydroxylamine. Biological properties of the hybrid plasmids have been preliminary studied.