Biochemistry (Moscow) (v.80, #4)

Prospects for using self-assembled nucleic acid structures by M. N. Rudchenko; A. A. Zamyatnin Jr. (391-399).
According to the central dogma in molecular biology, nucleic acids are assigned with key functions on storing and executing genetic information in any living cell. However, features of nucleic acids are not limited only with properties providing template-dependent biosynthetic processes. Studies of DNA and RNA unveiled unique features of these polymers able to make various self-assembled three-dimensional structures that, among other things, use the complementarity principle. Here, we review various self-assembled nucleic acid structures as well as application of DNA and RNA to develop nanomaterials, molecular automata, and nanodevices. It can be expected that in the near future results of these developments will allow designing novel next-generation diagnostic systems and medicinal drugs.
Keywords: DNA; RNA; complementarity; aptamers; ribozyme; deoxyribozyme; molecular computing; molecular automata

Physiological role of alternative oxidase (from yeasts to plants) by A. G. Rogov; R. A. Zvyagilskaya (400-407).
Mitochondria of all so far studied organisms, with the exception of Archaea, mammals, some yeasts, and protists, contain, along with the classical phosphorylating cytochrome pathway, a so-called cyanide-insensitive alternative oxidase (AOX) localized on the matrix side of the mitochondrial inner membrane, and electron transport through which is not coupled with ATP synthesis and energy accumulation. Mechanisms underlying plentiful functions of AOX in organisms at various levels of organization ranging from yeasts to plants are considered. First and foremost, AOX provides a chance of cell survival after inhibiting the terminal components of the main respiratory chain or losing the ability to synthesize these components. The vitally important role of AOX is obvious in thermogenesis of thermogenic plant organs where it becomes the only terminal oxidase with a very high activity, and the energy of substrate oxidation by this respiratory pathway is converted into heat, thus promoting evaporation of volatile substances attracting pollinating insects. AOX plays a fundamentally significant role in alleviating or preventing oxidative stress, thus ensuring the defense against a wide range of stresses and adverse environmental conditions, such as changes in temperature and light intensities, osmotic stress, drought, and attack by incompatible strains of bacterial pathogens, phytopathogens, or their elicitors. Participation of AOX in pathogen survival during its existence inside the host, in antivirus defense, as well as in metabolic rearrangements in plants during embryogenesis and cell differentiation is described. Examples are given to demonstrate that AOX might be an important tool to overcome the adverse aftereffects of restricted activity of the main respiratory chain in cells and whole animals.
Keywords: alternative oxidase; reactive oxygen species; pathogen attack; fungi; yeasts; protists; plants; oxidative stress

Recombinant horseradish peroxidase: Production and analytical applications by V. G. Grigorenko; I. P. Andreeva; M. Yu. Rubtsova; A. M. Egorov (408-416).
Horseradish peroxidase is a key enzyme in bio- and immunochemical analysis. New approaches in functional expression of the peroxidase gene in E. coli cells and the subsequent refolding of the resulting protein yield a recombinant enzyme that is comparable in its spectral and catalytic characteristics to the native plant peroxidase. Genetic engineering approaches allow production of recombinant peroxidase conjugates with both protein antigens and Fab antibody fragments. The present article reviews the use of recombinant horseradish peroxidase as the marker enzyme in ELISA procedures as well as in amperometric sensors based on direct electron transfer.
Keywords: horseradish peroxidase; recombinant conjugate; amperometric biosensor

Plastoquinone bound with decyltriphenylphosphonium cation (SkQ1) penetrating through the membrane in nanomolar concentrations inhibited H2O2 generation in cells of epidermis of pea seedling leaves that was detected by the fluorescence of 2′,7′-dichlorofluorescein. Photosynthetic electron transfer in chloroplasts isolated from pea leaves is suppressed by SkQ1 at micromolar concentrations: the electron transfer in chloroplasts under the action of photosystem II or I (with silicomolybdate or methyl viologen as electron acceptors, respectively) is more sensitive to SkQ1 than under the action of photosystem II + I (with ferricyanide or p-benzoquinone as electron acceptors). SkQ1 reduced by borohydride is oxidized by ferricyanide, p-benzoquinone, and, to a lesser extent, by silicomolybdate, but not by methyl viologen. SkQ1 is not effective as an electron acceptor supporting O2 evolution from water in illuminated chloroplasts. The data on suppression of photosynthetic O2 evolution or consumption show that SkQ1, similarly to phenazine methosulfate, causes conversion of the chloroplast redox-chain from non-cyclic electron transfer mode to the cyclic mode without O2 evolution. Oxidation of NADH or succinate in mitochondria isolated from pea roots is stimulated by SkQ1.
Keywords: programmed cell death; mitochondria-targeted quinones; SkQ1; electron transfer; retardation in chloroplasts; stimulation in mitochondria

Human Sin3B (hSin3B), a transcription regulator, is a scaffold protein that binds to different transcription factors and regulates transcription. It consists of six conserved domains that include four paired amphipathic helices (PAH 1–4), histone deacetylase interaction domain (HID), and highly conserved region (HCR). Interestingly, the PAH domains of hSin3B are significantly homologous to each other, yet each one interacts with a specific set of unique transcription factors. Though various partners interacting with hSin3B PAH domains have been characterized, there is no structural information available on the individual PAH domains of hSin3B. Here we characterize the structure and stability of different PAH domains of hSin3B at both nuclear and physiological pH values by using different optical probes. We found that the native state structure and stability of different PAH domains are different at nuclear pH where hSin3B performs its biological function. We also found that PAH2 and PAH3 behave differently at both nuclear and physiological pH in terms of native state structure and thermodynamic stability, while the structural identity of PAH1 remains unaltered at both pH values. The study indicates that the structural heterogeneity of different PAH domains might be responsible for having a unique set of interacting transcription factors.
Keywords: protein structure; thermodynamic stability; circular dichroism; transcription regulator; scaffold protein

Identification and biochemical characterization of a new antibacterial and antifungal peptide derived from the insect Sphodromantis viridis by Hadi Zare-Zardini; Asghar Taheri-Kafrani; Mahtab Ordooei; Leila Ebrahimi; Behnaz Tolueinia; Mojgan Soleimanizadeh (433-440).
Antimicrobial peptides are members of the immune system that protect the host from infection. In this study, a potent and structurally novel antimicrobial peptide was isolated and characterized from praying mantis Sphodromantis viridis. This 14-amino acid peptide was purified by RP-HPLC. Tandem mass spectrometry was used for sequencing this peptide, and the results showed that the peptide belongs to the Mastoparan family. The peptide was named Mastoparan-S. Mastoparan-S demonstrated that it has antimicrobial activities against a broad spectrum of microorganisms (Gram-positive and Gram-negative bacteria and fungi), and it was found to be more potent than common antibiotics such as kanamycin. Mastoparan-S showed higher antimicrobial activity against Gram-negative bacteria compared to Gram-positive ones and fungi. The minimum inhibitory concentration (MIC) values of Mastoparan-S are 15.1–28.3 μg/ml for bacterial and 19.3–24.6 μg/ml for fungal pathogens. In addition, this newly described peptide showed low hemolytic activity against human red blood cells. The in vitro cytotoxicity of Mastoparan-S was also evaluated on monolayer of normal human cells (HeLa) by MTT assay, and the results illustrated that Mastoparan-S had significant cytotoxicity at concentrations higher than 40 μg/ml and had no any cytotoxicity at the MIC (−30 μg/ml). The findings of the present study reveal that this newly described peptide can be introduced as an appropriate candidate for treatment of topical infection.
Keywords: antimicrobial peptides; cytotoxicity; Sphodromantis viridis ; immune system; hemolytic activity

Supramolecular organization of Hfq-like proteins by V. N. Murina; O. M. Selivanova; A. O. Mikhaylina; A. S. Kazakov; E. Yu. Nikonova; N. V. Lekontseva; S. V. Tishchenko; A. D. Nikulin (441-448).
Bacterial Hfq proteins are structural homologs of archaeal and eukaryotic Sm/Lsm proteins, which are characterized by a 5-stranded β-sheet and an N-terminal α-helix. Previously, it was shown that archaeal Lsm proteins (SmAP) could produce long fibrils spontaneously, in contrast to the Hfq from Escherichia coli that could form similar fibrils only after special treatment. The organization of these fibrils is significantly different, but the reason for the dissimilarity has not been found. In the present work, we studied the process of fibril formation by bacterial protein Hfq from Pseudomonas aeruginosa and archaeal protein SmAP from Methanococcus jannaschii. Both proteins have high homology with E. coli Hfq. We found that Hfq from P. aeruginosa could form fibrils after substitutions in the conserved Sm2 motif only. SmAP from M. jannaschii, like other archaeal Lsm proteins, form fibrils spontaneously. Despite differences in the fibril formation conditions, the architecture of both was similar to that described for E. coli Hfq. Therefore, universal nature of fibril architecture formed by Hfq proteins is suggested.
Keywords: Sm-like proteins; Hfq; quaternary structure of proteins; fibrils

Proteorhodopsin from Dokdonia sp. PRO95 is a light-driven Na+-pump by Y. V. Bertsova; A. V. Bogachev; V. P. Skulachev (449-454).
The gene encoding proteorhodopsin AEX55013 from Dokdonia sp. PRO95 was cloned and expressed in Escherichia coli cells. Illumination of the proteorhodopsin-producing E. coli cells in Na+-containing media resulted in alkalinization of the media. This response was accelerated by uncoupler CCCP and inhibited by penetrating anion SCN. Illumination of the cells in a sodium-free medium (made by substituting Na+ with K+) resulted in SCN-stimulated and CCCP-sensitive acidification of the medium. Illumination of the proteorhodopsin-containing E. coli cells caused CCCP-resistant transmembrane sodium export from these cells. We conclude that the proteorhodopsin from the marine flavobacterium Dokdonia sp. PRO95 is a primary light-driven Na+-pump. A high level of the heterologous production in E. coli cells as well as stability and purity of the isolated protein makes this proteorhodopsin an attractive model for studying the mechanism of active sodium transmembrane translocation.
Keywords: Na+-translocating proteorhodopsin; transmembrane sodium transport; flavobacteria

Coxsackievirus B3 induces viral myocarditis by upregulating toll-like receptor 4 expression by Zhao Zhao; Tian-Zhi Cai; Yan Lu; Wen-Jun Liu; Man-Li Cheng; Yu-Qiang Ji (455-462).
In the present study, we investigated the potential pathogenesis of coxsackievirus B3 (CVB3)-induced viral myocarditis and the promising protective effect of silencing RNA (small interfering RNA, siRNA). One hundred and twenty mice were included in the study, and 30 mice were intraperitoneally inoculated with CVB3 to establish an acute viral myocarditis model. The survival rate was observed for the CVB3-infected mouse model (MOD), and myocardial injury was examined by HE (hematoxylin and eosin) staining assay. Real-time PCR (RT-PCR) and Western blot assay were selected to detect the toll-like receptor 4 (TLR4) expression in myocardial tissues. The TLR4 gene was silenced for the MOD mice, and the effects of this treatment were observed. The results indicate that the expression of TLR4 mRNA and the protein significantly and persistently increased during the progression of CVB3-induced myocarditis. The activities of cardiac enzymes including CK, LDH, AST, and CK-MB were also enhanced in CVB3-induced myocardial tissues. Interestingly, when the TLR4 gene was silenced, the CVB3-induced TLR4 production was significantly decreased and the severity of myocarditis was significantly lessened. In conclusion, CVB3 may induce viral myocarditis by upregulating toll-like receptor 4 expression. The viral myocarditis can be ameliorated by silencing the TLR4 gene in the CVB3 viral myocarditis model, which may be a feasible therapeutic method for treatment of viral myocarditis.
Keywords: viral myocarditis; coxsackievirus B3; toll-like receptor 4; cardiac enzymes

Denaturation properties and folding transition states of leghemoglobin and other heme proteins by Pijush Basak; Niloy Kundu; Rudradip Pattanayak; Maitree Bhattacharyya (463-472).
This work reports unfolding transitions of monomeric heme proteins leghemoglobin (Lb), myoglobin (Mb), and cytochrome c (Cyt c) utilizing UV-Vis spectra, steady-state and time-resolved fluorescence methods. Conformational stabilities of the native “folded” state of the proteins and their “unfolded” states were investigated in the light of a two-state transition model. Two-state transition values for ΔGD (298K) were obtained by denaturation with the chaotropic agents urea and guanidium hydrochloride (GdnHCl). The free energy value of Lb is the lowest compared to Cyt c and Mb along the denaturation pathway. The m value is also the lowest for Lb compared to Cyt c and Mb. The m value (a measure of dependence of ΔGD on denaturant concentration) for Cyt c and Mb is lower when it is denatured with urea compared to GdnHCl. The UV-Vis absorbance maximum and steady state fluorescence emission maximum were drastically red shifted in the presence of a certain denaturant concentration both in cases of Mb and Lb, but the scenario is different for Cyt c. The results are analyzed using a two-state transition model. The lifetime data clearly indicate the presence of an intermediate state during denaturation. The unfolding transition can modulate the conformation, stability, and surface exposure of these biologically important proteins.
Keywords: chaotropic agent; denaturation; heme protein; Gibbs free energy; two-state transition

Properties of enzyme preparations and homogeneous enzymes — Endoglucanases EG2 Penicillium verruculosum and LAM Myceliophthora thermophila by D. A. Merzlov; I. N. Zorov; G. S. Dotsenko; Yu. A. Denisenko; A. M. Rozhkova; A. D. Satrutdinov; E. A. Rubtsova; E. G. Kondratieva; A. P. Sinitsyn (473-482).
The genes of endoglucanases EG2 (36.2 kDa) Penicillium verruculosum and LAM (30.8 kDa) Myceliophthora thermophila were cloned in P. verruculosum recombinant strain. New enzyme preparations with highly stable activity against β-glucan and laminarin were obtained and investigated, homogeneous enzymes EG2 (EC 3.2.1.4) and LAM (EC 3.2.1.6) being purified and characterized. For β-glucan, the EG2 K m value was found to be 10 times higher than that for LAM; however, EG2 demonstrated greater processivity due to its higher k cat. The pH and temperature optima of EG2 and LAM activity against barley β-glucan overlapped and were 4.3–4.9 and 61–67°C, respectively, and EG2 appeared to be more stable than LAM. Oligosaccharides with degree of polymerization 2–10 were formed by hydrolysis of β-glucan and laminarin by the studied enzymes. The recombinant enzyme preparations were faster and more effective in decreasing the reduced viscosity of wholegrain barley extract than some commercial enzyme preparations. Thus, the new enzyme preparations seem to be rather perspective as feed additives for degradation of non-starch polysaccharides in grain animal feed.
Keywords: endoglucanase; β-glucan; β-glucan endodepolymerases; enzyme preparations; Penicillium verruculosum ; Myceliophthora thermophila

Upregulation of RHOA and NKIRAS1 genes in lung tumors is associated with loss of their methylation as well as with methylation of regulatory miRNA genes by E. A. Braga; V. I. Loginov; I. V. Pronina; D. S. Khodyrev; S. V. Rykov; A. M. Burdennyy; M. V. Friedman; T. P. Kazubskaya; A. A. Kubatiev; N. E. Kushlinskii (483-494).
Methylation of CpG-islands in promoter regions as well as interaction of miRNAs with messenger RNAs of target genes are related to multilayer mechanisms regulating gene expression. The goal of this study was to assess a possibility for miRNA gene methylation to influence indirectly activation of their target genes in lung tumors. By using a unified collection of samples of non-small cell lung cancer, it was demonstrated that elevated levels of mRNA for RHOA and NKIRAS1 genes were significantly (Spearman rank correlation, P < 10−11) associated both with loss of methylation in their CpG-islands and methylation in a number of miRNA genes, which, according to the miRWalk database, were predicted to possess regulatory functions. Novel potential regulatory miRNAs for RHOA (miR-9-1/-3, -34b/c, -129-2, -125b-1, -375, -1258) and NKIRAS1 (miR-34b/c, -129-2, -125b-1, -193a, -124a-1/-2/-3, -212, -132) genes in lung cancer were identified.
Keywords: CpG-islands; methylation; miRNA; target genes; RHOA ; NKIRAS1 ; mRNA; lung cancer