Biochemistry (Moscow) (v.74, #9)

Fundamental taboos of biology by E. D. Sverdlov (939-944).
This paper formulates some taboos relating to living systems and cognition of these systems: in nature, there exist no two identical living complex multicellular organisms; there is no way to create an exact copy of a multicellular organism; there is no way to obtain two identical clones of a unicellular organism if they contain a sufficiently large number of cells; based on comparing present-day organisms, it is impossible to restore the structure of the first living cell and the processes that have led to its emergence; it is impossible to create a living cell from its separate simple constituents; the mechanisms determining cell vitality are essentially incognizable.
Keywords: biology; general laws; taboos; prohibitions

The detection of catalytic activity of antibodies is the earliest indicator of development of autoimmune diseases (AID). In early stages of AID, the repertoire of abzymes with various properties is relatively small, but it is greatly increased during their development. Catalytic diversity of the abzymes includes DNase, RNase, ATPase, and oxidoreductase activities; there are antibodies phosphorylating proteins, lipids, and polysaccharides. This review summarizes new data on abzyme heterogeneity and possible reasons for this phenomenon. A possible role of abzymes and their exceptional multiplicity in the pathogenesis of different AID is discussed.
Keywords: natural abzymes; healthy donors; autoimmune diseases

The high frequency of mitochondrial DNA (mtDNA) mutations in somatic mammalian cells, which is more than two orders of magnitude higher than the mutation frequency of nuclear DNA (nDNA), significantly correlates with development of a variety of mitochondrial diseases (neurodegenerative diseases, cardiomyopathies, type II diabetes mellitus, cancer, etc.). A direct cause—consequence relationship has been established between mtDNA mutations and aging phenotypes in mammals. However, the unclear nature of the high frequency of mtDNA mutations requires a comprehensive consideration of factors that contribute to this phenomenon: oxidative stress, features of structural organization and repair of the mitochondrial genome, ribonucleotide reductase activity, replication errors, mutations of nuclear genes encoding mitochondrial proteins.
Keywords: oxidative stress; frequency of mtDNA mutations; structural features; repair mechanisms; ribonucleotide reductase activity

Structural-functional characteristics of a new bioregulator isolated from bovine pigmented epithelium tissue by V. P. Yamskova; V. S. Skripnikova; A. A. Molyavka; A. P. Il’ina; M. S. Krasnov; D. V. Margasyuk; A. V. Borisenko; B. B. Berezin; E. S. Kuznetsova; A. K. Buryak; I. A. Yamskov (971-978).
A new bioregulator operating in ultralow doses corresponding to 10−17 mg/ml has been isolated from tissue of pigmented epithelium of bovine eyes. It has been established that the functional basis of this bioregulator is a complex of a low molecular weight regulatory peptide (4372 Da) and a modulator consisting of a mixture of proteins with molecular weights of 14.980–66.283 kDa. It has been shown that the regulatory peptide is responsible for membranotropic activity of the bioregulator, and the modulator proteins are responsible for biological action in ultralow doses. The data demonstrate an interrelation between nanocondition of the bioregulator and its ability to show activity in ultralow doses.
Keywords: bioregulators; regulatory proteins; nanoparticles; ultralow doses

Dermatopontin is expressed in human liver and is downregulated in hepatocellular carcinoma by Xirong Li; Ping Feng; Jianfeng Ou; Zhijuan Luo; Ping Dai; Dapeng Wei; Chongjie Zhang (979-985).
Dermatopontin (DPT) was recently found as a downstream target of vitamin D receptor, which is a key molecule in the 1,25-dihydroxy-vitamin D3 anti-hepatoma proliferation pathway. MCTx-1 from Millepora, a homolog of DPT, is identified as a cytotoxin towards leukemia cells. The aim of this study was to analyze DPT expression in hepatocellular carcinoma (HCC) based on the analysis for DPT gene in normal tissues in order to estimate its function in the progression of HCC. DPT mRNA expression was analyzed in normal tissues and HCC cell lines by RT-PCR, and in HCC tissue by RT-PCR and real-time PCR. Its protein was examined in HCC tissues by Western blot and immunohistochemistry assays. Meanwhile, transforming growth factor-β1 (TGF-β1) that is closely associated with HCC and DPT was observed by immunohistochemistry in HCC tissues. The results showed that DPT mRNA was strongly expressed in human fetal and adult liver, kidney, and spleen, weakly in ovary and heart, and absent in other tissues and HCC cell lines examined. Its mRNA was significantly downregulated in HCC tissues, while its protein was weakly expressed in tumor compared with non-tumor. DPT is located mainly in the cytoplasm of several cell types in the liver; it has been identified also in the extra-cellular matrix of the skin. TGF-β1 was observed in extensive tumor tissue of HCC. This fact suggests that DPT can play various roles in different tissues and might be a molecule related to carcinogenesis and the progression of HCC via possible interaction with TGF-β1 and other potential mechanisms.
Keywords: liver; hepatocellular carcinoma; dermatopontin; transforming growth factor-β1

High-sensitivity express immunochromatographic method for detection of plant infection by tobacco mosaic virus by Yu. F. Drygin; A. N. Blintsov; A. P. Osipov; V. G. Grigorenko; I. P. Andreeva; A. I. Uskov; Yu. A. Varitsev; B. V. Anisimov; V. K. Novikov; J. G. Atabekov (986-993).
A highly sensitive express immunochromatography method for molecular diagnosis of plant virus infections was elaborated on the example of a model object — tobacco mosaic virus (TMV). The analysis time does not exceed 5 min, and the lower limit of TMV detection in non-clarified leaf extract (2–4 ng/ml) is comparable with the sensitivity of the enzyme-linked immunosorbent assay of the virus. A single measurement requires 0.1–0.2 ml tested solution (extract from 10–20 mg of leaf material). The sensitivity of TMV determination in the leaf tissue extract was increased by more than one order of magnitude using signal enhancement by silver and is 0.1 ng/ml. In this case, analysis time did not exceed 25 min. The simplicity of this method makes it especially convenient in express diagnosis of numerous analyzed specimens. The prototype of a diagnostic kit for serial analyses of plant viral infections both in laboratory and field conditions was elaborated.
Keywords: tobacco mosaic virus; immunochromatography analysis; colloidal gold; lateral flow immune analysis

Methylcatechol 1,2-dioxygenase of Rhodococcus opacus 6a is a new type of the catechol-cleaving enzyme by I. P. Solyanikova; E. I. Konovalova; L. A. Golovleva (994-1001).
The strains Rhodococcus sp. 400, R. rhodochrous 172, and R. opacus 6a utilize 4-methylbenzoate as the only carbon and energy source. 4-Methylcatechol is a key intermediate of biodegradation. Its further conversion by all the strains proceeds via ortho-cleavage. The specific activity of catechol 1,2-dioxygenase assayed in crude extracts of Rhodococcus sp. 400 and R. rhodochrous 172 with 3- and 4-methylcatechols does not exceed the enzyme activity assayed with catechol. Two catechol 1,2-dioxygenases have been purified from the biomass of R. opacus strain 6a grown with 4-methylbenzoate. These enzymes differed in molecular mass and physicochemical and catalytic properties. One of these enzymes belongs to the type of enzymes cleaving the catechol ring and known as methylcatechol 1,2-dioxygenases. In bacteria of the Rhodococcus genus, such an enzyme is described here for the first time.
Keywords: para-toluate; degradation; methylcatechol 1,2-dioxygenase; Rhodococcus opacus 6a

Isolation and properties of extracellular β-xylosidases from fungi Aspergillus japonicus and Trichoderma reesei by M. V. Semenova; M. I. Drachevskaya; O. A. Sinitsyna; A. V. Gusakov; A. P. Sinitsyn (1002-1008).
Homogeneous β-xylosidases with molecular mass values 120 and 80 kDa (as shown by SDS-PAGE), belonging to the third family of glycosyl hydrolases, were isolated by anion-exchange, hydrophobic, and gel-penetrating chromatography from enzyme preparations based on the fungi Aspergillus japonicus and Trichoderma reesei, respectively. The enzymes exhibit maximal activity in acidic media (pH 3.5–4.0), and temperature activity optimum was 70°C for the β-xylosidase of A. japonicus and 60°C for the β-xylosidase of T. reesei. Kinetic parameters of p-nitrophenyl β-xylopyranoside and xylooligosaccharide hydrolysis by the purified enzymes were determined, which showed that β-xylosidase of A. japonicus was more specific towards low molecular weight substrates, while β-xylosidase of T. reesei preferred high molecular weight substrates. The competitive type of inhibition by reaction product (xylose) was found for both enzymes. The interaction of the enzymes of different specificity upon hydrolysis of glucurono- and arabinoxylans was found. The β-xylosidases exhibit synergism with endoxylanase upon hydrolysis of glucuronoxylan as well as with α-L-arabinofuranosidase and endoxylanase upon hydrolysis of arabinoxylan. Addition of β-xylosidases increased efficiency of hydrolysis of plant raw materials with high hemicellulose content (maize cobs) by the enzymic preparation Celloviridine G20x depleted of its own β-xylosidase.
Keywords: xylanases; β-xylosidase; xylooligosaccharides; xylans; hydrolysis

Bridged oligonucleotides as molecular probes for investigation of enzyme-substrate interaction and allele-specific analysis of DNA by I. A. Pyshnaya; O. A. Vinogradova; M. R. Kabilov; E. M. Ivanova; D. V. Pyshnyi (1009-1020).
The efficiency of enzymatic conversion of DNA complexes containing non-nucleotide inserts has been studied. T4 DNA ligase and Taq DNA polymerase have been included in the study as examples of widely used DNA-dependent enzymes. A series of substrate DNA complexes have been formed using native oligonucleotides and bridged ones bearing non-nucleotide inserts based on phosphodiesters of di-, tetra-, or hexaethylene glycol, 1,5-pentanediol, 1,10-decanediol, and 3-hydroxy-2(hydroxymethyl)-tetrahydrofuran. The perturbation in DNA located far from the site of the enzyme action had almost no influence on the substrate properties of the complex, while insertion near this site significantly deteriorated them. The use of a series of modified duplexes allows one to locate the position of the enzyme-binding site on DNA substrate with the accuracy of 1–2 nucleotides. The presence of a non-nucleotide insert in the complex has been also shown to enhance the efficiency of single mismatch discrimination upon both template-directed ligation and extension of oligonucleotides.
Keywords: bridged oligonucleotides; non-nucleotide insert; modified DNA complexes; footprinting; binding site; selectivity; T4 DNA ligase; Taq DNA polymerase

Interaction of tetrasubstituted cationic aluminum phthalocyanine with artificial and natural membranes by A. A. Pashkovskaya; I. V. Perevoshchikova; V. E. Maizlish; G. P. Shaposhnikov; E. A. Kotova; Yu. N. Antonenko (1021-1026).
A study of the properties of water-soluble tetrasubstituted cationic aluminum phthalocyanine (AlPcN4) revealed efficient binding of this photosensitizer to phospholipid membranes as compared with tetrasulfonated aluminum and zinc phthalocyanine complexes. This also manifested itself in enhanced photodynamic activity of AlPcN4 as measured by the photosensitized damage of gramicidin channels in a planar bilayer lipid membrane. The largest difference in the photodynamic activity of cationic and anionic phthalocyanines was observed in a membrane containing negatively charged lipids, thereby pointing to significant contribution of electrostatic interactions to the binding of photosensitizers to a membrane. Fluoride anions suppressed the photodynamic activity and binding to membrane of both tetraanionic and tetracationic aluminum phthalocyanines, which supports our hypothesis that interaction of charged metallophthalocyanines with phospholipid membranes is mostly determined by coordination of the central metal atom with the phosphate group of lipid.
Keywords: planar bilayer lipid membrane; photosensitizer; phthalocyanine; singlet oxygen; ion channels; gramicidin A; liposomes; mitochondria

A homogenous enzyme with both bilirubin oxidase and laccase activities was isolated from a submerged culture of the basidiomycete Pleurotus ostreatus mycelium and characterized. The yield of the enzyme was 127 μg/g dry biomass of the mycelium. The specific activity of the enzyme was 21 and 261 U/mg to bilirubin and to a laccase substrate ABTS, respectively. The intracellular phenol oxidase from the P. ostreatus mycelium was identified as bilirubin oxidase with the amino acid sequence highly homologous to that of the pox2 gene-encoded product. The enzyme displayed the maximal laccase activity at 50–55°C to all substrates examined, whereas the pH optimum was substrate-dependent and changed from 3.0 for ABTS to 7.0 for syringaldazine and guaiacol. The enzyme maintained catalytic activity within a broad pH range but was inactivated at pH 4.0. The enzyme was thermostable but very sensitive to metal chelating inhibitors. Trypan Blue (5 mg/liter) was completely decolorizated upon 3 h of incubation with the bilirubin oxidase (20 mU/ml) at room temperature.
Keywords: mycelium; Pleurotus ostreatus ; oxidoreductase; bilirubin oxidase; laccase

Chitosan-induced programmed cell death in plants by L. A. Vasil’ev; E. V. Dzyubinskaya; R. A. Zinovkin; D. B. Kiselevsky; N. V. Lobysheva; V. D. Samuilov (1035-1043).
Chitosan, CN, or H2O2 caused the death of epidermal cells (EC) in the epidermis of pea leaves that was detected by monitoring the destruction of cell nuclei; chitosan induced chromatin condensation and marginalization followed by the destruction of EC nuclei and subsequent internucleosomal DNA fragmentation. Chitosan did not affect stoma guard cells (GC). Anaerobic conditions prevented the chitosan-induced destruction of EC nuclei. The antioxidants nitroblue tetrazolium or mannitol suppressed the effects of chitosan, H2O2, or chitosan + H2O2 on EC. H2O2 formation in EC and GC mitochondria that was determined from 2′,7′-dichlorofluorescein fluorescence was inhibited by CN and the protonophoric uncoupler carbonyl cyanide m-chlorophenylhydrazone but was stimulated by these agents in GC chloroplasts. The alternative oxidase inhibitors propyl gallate and salicylhydroxamate prevented chitosan- but not CN-induced destruction of EC nuclei; the plasma membrane NADPH oxidase inhibitors diphenylene iodonium and quinacrine abolished chitosan- but not CN-induced destruction of EC nuclei. The mitochondrial protein synthesis inhibitor lincomycin removed the destructive effect of chitosan or H2O2 on EC nuclei. The effect of cycloheximide, an inhibitor of protein synthesis in the cytoplasm, was insignificant; however, it was enhanced if cycloheximide was added in combination with lincomycin. The autophagy inhibitor 3-methyladenine removed the chitosan effect but exerted no influence on the effect of H2O2 as an inducer of EC death. The internucleosome DNA fragmentation in conjunction with the data on the 3-methyladenine effect provides evidence that chitosan induces programmed cell death that follows a combined scenario including apoptosis and autophagy. Based on the results of an inhibitor assay, chitosan-induced EC death involves reactive oxygen species generated by the NADPH oxidase of the plasma membrane.
Keywords: programmed cell death; apoptosis; autophagy; chitosan; plants; epidermal cells

Simulated 18O kinetic isotope effects in enzymatic hydrolysis of guanosine triphosphate by A. V. Nemukhin; M. S. Shadrina; B. L. Grigorenko; X. Du (1044-1048).
We compare the computed on the base of quantum mechanical-molecular mechanical (QM/MM) modeling kinetic isotope effects (KIEs) for a series of the 18O-labeled substrates in enzymatic hydrolysis of guanosine triphosphate (GTP) with those measured experimentally. Following the quantitative structure-activity relationship concept, we introduce the correlation between KIEs and structure of substrates with the help of a labeling index, which also aids better imaging of presentation of both experimental and theoretical data. An evident correlation of the computed and measured KIEs provides support to the predominantly dissociative-type reaction mechanism of enzymatic GTP hydrolysis predicted in QM/MM simulations.
Keywords: kinetic isotope effect; GTP hydrolysis; p21Ras; Ras-GAP; EF-Tu

In silico analysis of pectin lyase and pectinase sequences by P. K. Yadav; V. K. Singh; S. Yadav; K. D. S. Yadav; D. Yadav (1049-1055).
A total of 48 full-length protein sequences of pectin lyases from different source organisms available in NCBI were subjected to multiple sequence alignment, domain analysis, and phylogenetic tree construction. A phylogenetic tree constructed on the basis of the protein sequences revealed two distinct clusters representing pectin lyases from bacterial and fungal sources. Similarly, the multiple accessions of different source organisms representing bacterial and fungal pectin lyases also formed distinct clusters, showing sequence level homology. The sequence level similarities among different groups of pectinase enzymes, viz. pectin lyase, pectate lyase, polygalacturonase, and pectin esterase, were also analyzed by subjecting a single protein sequence from each group with common source organism to tree construction. Four distinct clusters representing different groups of pectinases with common source organisms were observed, indicating the existing sequence level similarity among them. Multiple sequence alignment of pectin lyase protein sequence of different source organisms along with pectinases with common source organisms revealed a conserved region, indicating homology at sequence level. A conserved domain Pec_Lyase_C was frequently observed in the protein sequences of pectin lyases and pectate lyases, while Glyco_hydro_28 domains and Pectate lyase-like β-helix clan domain are frequently observed in polygalacturonases and pectin esterases, respectively. The signature amino acid sequence of 41 amino acids, i.e. TYDNAGVLPITVN-SNKSLIGEGSKGVIKGKGLRIVSGAKNI, related with the Pec_Lyase_C is frequently observed in pectin lyase protein sequences and might be related with the structure and enzymatic function.
Keywords: pectin lyase; pectate lyase; polygalacturonase; pectin esterase; domain analysis

Essentials of glycobiology by G. Ya. Wiederschain (1056-1056).

Molecular biomethods handbook by G. Ya. Wiederschain (1057-1057).

The ELISA guidebook by G. Ya. Wiederschain (1058-1058).