Biochemistry (Moscow) (v.81, #4)

Plant phenols and autophagy by N. K. Zenkov; A. V. Chechushkov; P. M. Kozhin; N. V. Kandalintseva; G. G. Martinovich; E. B. Menshchikova (297-314).
Many plant phenols (stilbenes, curcumins, catechins, flavonoids, etc.) are effective antioxidants and protect cells during oxidative stress. Extensive clinical studies on the potential of phenolic compounds for treatment of cardiovascular, neurodegenerative, oncological, and inflammatory diseases are now being conducted. In addition to direct antioxidant effect, plant phenols may provide a protective effect via activation of the Keap1/Nrf2/ARE redox-sensitive signaling system and regulation of autophagy. In this review, mechanisms of effects of the most common plant phenols on autophagy are presented.
Keywords: phenolic antioxidants; autophagy; Keap1/Nrf2/ARE signaling system; regulation

Molecular mechanisms and microRNAs in osteosarcoma pathogenesis by N. E. Kushlinskii; M. V. Fridman; E. A. Braga (315-328).
This review summarizes data on microRNA (miRNA) genomic organization, biogenesis, and functions in carcinogenesis. The roles of key genes and regulatory miRNAs in molecular mechanisms and signaling pathways involved in the development of osteosarcoma, the most aggressive type of bone tumor striking mainly in adolescence and early adulthood, are discussed in detail. The most critical pathways in osteosarcoma pathogenesis are the Notch, Wnt, NF-κB, p53, PI3K/Akt, and MAPK pathways. The balance between cell survival and apoptosis is determined by the Wnt and NF-κB pathways, as well as by the ratio between the activities of the MAPK and PI3K/Akt pathways. Several miRNAs (miR-21, -34a, -143, -148a, -195a, -199a-3p, -382) regulate multiple target genes, pathways, and processes essential for osteosarcoma pathogenesis. Data on the key genes and regulatory miRNAs involved in metastasis and tumor cell response to drug treatment are presented. Possible applications of miRNA in osteosarcoma diagnostics and treatment are discussed.
Keywords: regulatory miRNAs; key genes; oncogenesis; signaling pathways; osteosarcoma; metastasis

Mitochondria as a signaling Hub and target for phenoptosis shutdown by P. V. Zolotukhin; A. A. Belanova; E. V. Prazdnova; M. S. Mazanko; M. M. Batiushin; V. K. Chmyhalo; V. A. Chistyakov (329-337).
Mitochondria have long been studied as the main energy source and one of the most important generators of reactive oxygen species in the eukaryotic cell. Yet, new data suggest mitochondria serve as a powerful cellular regulator, pathway trigger, and signal hub. Some of these crucial mitochondrial functions appear to be associated with RNP-granules. Deep and versatile involvement of mitochondria in general cellular regulation may be the legacy of parasitic behavior of the ancestors of mitochondria in the host cells. In this regard, we also discuss here the perspectives of using mitochondria-targeted compounds for systemic correction of phenoptotic shifts.
Keywords: mitochondria; regulation; systems biology; mitochondrial targeting; Skulachev ions; phenoptosis

Activation of the constitutive androstane receptor (CAR) in hepatocytes occurs as a body adaptation in response to a number of external influences, and its functional activity is primarily related to induction of enzymes detoxifying xenobiotics. However, special attention was recently given to CAR due to the fact that its key role becomes unveiled in various physiological and pathophysiological processes occurring in the liver: gluconeogenesis, metabolism of fatty acids and bilirubin, hormonal regulation, proliferation of hepatocytes, and hepatocarcinogenesis. Here we review the main pathways and mechanisms that elevate hepatocyte proliferative activity related to CAR and whose disturbance may be a pivotal factor in hepatocarcinogenesis.
Keywords: CAR; activation of gene expression; ligands; proliferation; hepatocarcinogenesis

Autophagy is an efficient way of degradation and removal of unwanted or damaged intracellular components in plant cells. It plays an important role in recycling of intracellular structures (during starvation, removal of cell components formed during plant development or damaged by various stress factors) and in programmed cell death. Morphologically, autophagy is characterized by the formation of double-membrane vesicles called autophagosomes, which are essential for the isolation and degradation of cytoplasmic components. Among autophagic (ATG) proteins, ATG8 from the ubiquitinlike protein family plays a key role in autophagosome formation. ATG8 is also involved in selective autophagy, fusion of autophagosome with the vacuole, and some other intracellular processes not associated with autophagy. In contrast to yeasts that carry a single ATG8 gene, plants have multigene ATG8 families. The reason for such great ATG8 diversity in plants remains unclear. It is also unknown whether all members of the ATG8 family are involved in the formation and functioning of autophagosomes. To answer these questions, the identification of the structure and the possible functions of plant proteins from ATG8 family is required. In this review, we analyze the structures of ATG8 proteins from plants and their homologs from yeast and animal cells, interactions of ATG8 proteins with functional ligands, and involvement of ATG8 proteins in different metabolic processes in eukaryotes.
Keywords: autophagy; autophagosome; ATG8; plants; stress

Glutathione reductase gene expression depends on chloroplast signals in Arabidopsis thaliana by E. Yu. Garnik; V. I. Belkov; V. I. Tarasenko; M. A. Korzun; Yu. M. Konstantinov (364-372).
Glutathione reductase (EC is one of the main antioxidant enzymes of the plant cell. In Arabidopsis thaliana, glutathione reductase is encoded by two genes: the gr1 gene encodes the cytosolic-peroxisomal form, and the gr2 gene encodes the chloroplast-mitochondrial form. Little is known about the regulation of expression of plant glutathione reductase genes. In the present work, we have demonstrated that gr2 (but not gr1) gene expression in Arabidopsis leaves changes depending on changes in redox state of the photosynthetic electron transport chain. Expression of both the gr1 and gr2 genes was induced by reactive oxygen species. In heterotrophic suspension cell culture of Arabidopsis, expression of both studied genes did not depend on H2O2 level or on changes in the redox state of the mitochondrial electron transport chain. Our data indicate that chloroplasts are involved in the regulation of the glutathione reductase gene expression in Arabidopsis.
Keywords: reactive oxygen species; hydrogen peroxide; glutathione reductase; redox-regulation; chloroplast-nuclear regulation of gene expression; Arabidopsis thaliana

Investigation of the mesenchymal stem cell compartment by means of a lentiviral barcode library by A. E. Bigildeev; K. Cornils; T. Aranyossy; N. V. Sats; N. A. Petinati; I. N. Shipounova; V. L. Surin; O. S. Pshenichnikova; K. Riecken; B. Fehse; N. I. Drize (373-381).
The hematopoietic bone marrow microenvironment is formed by proliferation and differentiation of mesenchymal stem cells (MSCs). The MSC compartment has been less studied than the hematopoietic stem cell compartment. To characterize the structure of the MSC compartment, it is necessary to trace the fate of distinct mesenchymal cells. To do so, mesenchymal progenitors need to be marked at the single-cell level. A method for individual marking of normal and cancer stem cells based on genetic “barcodes” has been developed for the last 10 years. Such approach has not yet been applied to MSCs. The aim of this study was to evaluate the possibility of using such barcoding strategy to mark MSCs and their descendants, colony-forming units of fibroblasts (CFU-Fs). Adherent cell layers (ACLs) of murine long-term bone marrow cultures (LTBMCs) were transduced with a lentiviral library with barcodes consisting of 32 + 3 degenerate nucleotides. Infected ACLs were suspended, and CFU-F-derived clones were obtained. DNA was isolated from each individual colony, and barcodes were analyzed in marked CFU-F-derived colonies by means of conventional polymerase chain reaction and Sanger sequencing. Barcodes were identified in 154 marked colonies. All barcodes appeared to be unique: there were no two distinct colonies bearing the same barcode. It was shown that ACLs included CFU-Fs with different proliferative potential. MSCs are located higher in the hierarchy of mesenchymal progenitors than CFU-Fs, so the presented data indicate that MSCs proliferate rarely in LTBMCs. A method of stable individual marking and comparing the markers in mesenchymal progenitor cells has been developed in this work. We show for the first time that a barcoded library of lentiviruses is an effective tool for studying stromal progenitor cells.
Keywords: mesenchymal stem cell; MSC; colony-forming units of fibroblasts; CFU-Fs; long-term bone marrow culture; LTBMC; barcode; barcoded lentiviral library; LeGO vectors

Analysis of extracellular vesicles using magnetic nanoparticles in blood of patients with acute coronary syndrome by M. S. Vagida; A. Arakelyan; A. M. Lebedeva; J. Ch. Grivel; A. V. Shpektor; E. Yu. Vasilieva; L. B. Margolis (382-391).
Extracellular vesicles (EVs) are released from various cell types and play an important role in intercellular interactions. In our study, we investigated abundance of individual EVs in patients with acute forms of ischemic heart disease. Previously, we developed an approach for individual analysis of EVs conjugated with magnetic nanoparticles (MNPs), which was applied in the current study for analyzing phenotypic composition of EVs (by staining for markers CD31, CD41a, and CD63). EVs were isolated using fluorescently labeled MNPs containing anti-CD31, CD41a, or CD63 antibodies and analyzed by combining fluorescently labeled anti-CD41a and CD63, CD31 and CD63, or CD41a and CD31 antibodies, respectively. EVs were analyzed in 30 individuals: 17 healthy volunteers and 13 patients with acute coronary syndrome (ACS). Six and seven ACS patients were with acute myocardial infarction and unstable angina, respectively. It was found that patients with ACS and healthy volunteers contained a dominant subset of EVs expressing surface CD41a antigen, suggesting that they originated from platelets. In addition, the total number of EVs isolated using either of the surface markers examined in our study was higher in patients with ACS compared to healthy volunteers. The subgroup of patients with acute myocardial infarction was found to contain significantly higher number of blood EVs compared to the control group. Moreover, increased number of EVs in patients with ACS is mainly due to the increased number of EVs in the subset of EVs bearing CD41a. By analyzing individual EVs, we found that plasma of patients with ACS, particularly upon developing of myocardial infarction, contained dominant platelet-derived EVs fraction, which may reflect activation of platelets in such patients.
Keywords: extracellular vesicles; platelets; acute coronary syndrome; flow cytometry

Interaction of chloramphenicol tripeptide analogs with ribosomes by A. G. Tereshchenkov; A. V. Shishkina; V. N. Tashlitsky; G. A. Korshunova; A. A. Bogdanov; N. V. Sumbatyan (392-400).
Chloramphenicol amine peptide derivatives containing tripeptide fragments of regulatory “stop peptides”–MRL, IRA, IWP–were synthesized. The ability of the compounds to form ribosomal complexes was studied by displacement of the fluorescent erythromycin analog from its complex with E. coli ribosomes. It was found that peptide chloramphenicol analogs are able to bind to bacterial ribosomes. The dissociation constants were 4.3-10 μM, which is 100-fold lower than the corresponding values for chloramphenicol amine–ribosome complex. Interaction of the chloramphenicol peptide analogs with ribosomes was simulated by molecular docking, and the most probable contacts of “stop peptide” motifs with the elements of nascent peptide exit tunnel were identified.
Keywords: ribosome; “stop peptides”; chloramphenicol; peptide derivatives; nascent peptide exit tunnel

Structure and biosynthesis gene cluster of the O-antigen of Escherichia coli O12 by S. N. Senchenkova; Yuanyuan Zhang; A. V. Perepelov; Xi Guo; A. S. Shashkov; Bin Liu; Yu. A. Knirel (401-406).
Two polysaccharides were isolated from Escherichia coli O12, the major being identified as the O12-antigen and the minor as the K5-antigen. The polysaccharides were studied by sugar analysis, Smith degradation, and one- and twodimensional 1H and 13C NMR spectroscopy. As a result, the following structure of the O12-polysaccharide was elucidated, which, to our knowledge, has not been hitherto found in bacterial carbohydrates: →2)-β-D-Glcp-(1→6)-α-D-GlcpNAc(1→3)-α-L-FucpNAc-(1→3)-β-D-GlcpNAc-(1→. The →4)-β-D-GlcpA-(1→4)-α-D-GlcpNAc-(1→ structure established for the K5-polysaccharide (heparosan) is previously known. Functions of genes in the O-antigen biosynthesis gene cluster of E. coli O12 were assigned by comparison with sequences in the available databases and found to be consistent with the O12-polysaccharide structure.
Keywords: Escherichia coli ; O-polysaccharide structure; O-antigen gene cluster; glycosyltransferase

The amino acid sequence of protein Gln3 in yeast Saccharomyces cerevisiae has a region enriched with Gln (Q) and Asn (N) residues. In this study, we analyzed the effects of overexpression of Gln3 and its Q/N-rich fragment fused with yellow fluorescent protein (YFP). Being overexpressed, full-length Gln3-YFP does not form aggregates, inhibits vegetative growth, and demonstrates nuclear localization, while the Q/N-rich fragment (Gln3QN) fused with YFP forms aggregates that do not colocalize with the nucleus and do not affect growth of the cells. Although detergent-resistant aggregates of Gln3QN are formed in the absence of yeast prions, the aggregation of Gln3QN significantly increases in the presence of [PIN +] prion, while in the presence of two prions, [PSI +] and [PIN +], the percentage of cells with Gln3QN aggregates is significantly lower than in the strain bearing only [PIN +]. Data on colocalization demonstrate that this effect is mediated by interaction between Gln3QN aggregates and [PSI +] and [PIN +] prions.
Keywords: amyloid; prion; Gln3; Rnq1; Sup35; yeast; S. cerevisiae

Na+-translocating rhodopsin from Dokdonia sp. PRO95 does not contain carotenoid antenna by Y. V. Bertsova; A. M. Arutyunyan; A. V. Bogachev (414-419).
Carotenoid-binding properties of Na+-translocating rhodopsin (NaR) from Dokdonia sp. PRO95 were studied. Carotenoids were extracted from Dokdonia sp. PRO95 cells. It was found that zeaxanthin is the predominant carotenoid of this bacterium. Incubation of recombinant NaR purified from Escherichia coli cells with carotenoids from Dokdonia sp. PRO95 did not result in any changes in optical absorption or circular dichroism spectra, indicating the absence of binding of the carotenoids by NaR. The same results were obtained using salinixanthin as the carotenoid. These data along with genome analysis of Dokdonia sp. PRO95 and other flavobacteria indicate that NaR from Dokdonia sp. PRO95 and possibly the other flavobacterial Na+-translocating rhodopsins do not contain a carotenoid antenna.
Keywords: Na+-translocating rhodopsin; xanthorhodopsin; carotenoid antenna; zeaxanthin; salinixanthin; flavobacteria

Construction of a fusion enzyme exhibiting superoxide dismutase and peroxidase activity by M. G. Sharapov; V. I. Novoselov; V. K. Ravin (420-427).
A chimeric gene construct encoding human peroxiredoxin 6 and Mn-superoxide dismutase from Escherichia coli was developed. Conditions for expression of the fusion protein in E. coli cell were optimized. Fusing of the enzymes into a single polypeptide chain with peroxiredoxin 6 at the N-terminus (PSH) did not affect their activities. On the contrary, the chimeric protein with reverse order of enzymes (SPH) was not obtained in a water-soluble active form. The active chimeric protein (PSH) exhibiting both peroxidase and superoxide dismutase activities was prepared and its physicochemical properties were characterized.
Keywords: superoxide dismutase; peroxiredoxin 6; chimeric protein; oxidative stress

A new program for detecting the geometrical core of a set of structures of macromolecular complexes by Yu. A. Vakulenko; B. E. Nagaev; A. V. Alexeevski; A. S. Karyagina; S. A. Spirin (428-431).
Comparison of structures of homological proteins often helps to understand functionally significant features of these structures. This concerns not only structures of separate protein chains, but also structures of macromolecular complexes. In particular, a comparison of complexes of homologous proteins with DNA is significant for analysis of the recognition of DNA by proteins. We present program LCore for detecting geometrical cores of a family of structures; a geometrical core is a set of amino acid residues and nucleotides that disposed similarly in all structures of the family. We describe the algorithm of the program, its web interface, and an example of its application to analysis of complexes of homeodomains with DNA.
Keywords: structural bioinformatics; structures of macromolecules; macromolecular complexes; web interface

More about interactions of rhodamine 19 butyl ester with rat liver mitochondria by A. G. Rogov; T. A. Trendeleva; D. A. Aliverdieva; R. A. Zvyagilskaya (432-438).
Oxidative stress is one of the major factors underlying mitochondrial dysfunctions. One of the most promising approaches for alleviating or preventing oxidative stress is the use of cationic uncouplers that accumulate in mitochondria in accordance to the level of the membrane potential, producing “mild” uncoupling. Based on this theoretical background, cationic rhodamine 19 butyl ester (C4R1) was synthesized and tested within the framework of the research project guided by V. P. Skulachev. The results of these tests were presented (Khailova et al. (2014) Biochim. Biophys. Acta, 1837, 1739-1747), but one publication could not accommodate all data on interactions of C4R1 with isolated mitochondria. In addition to previously presented data, we found that the effect of C4R1 on the rate of oxygen uptake is subject to temporal variations, which probably reflects variable rates of C4R1 entry into the mitochondria. Consequently, transient stimulation of respiration can be followed by inhibition. C4R1 was found not to shunt electron flow from complex I of the respiratory chain; it largely acted as an inhibitor of complex I in the respiratory chain and showed antioxidant activity. C4R1 taken at low, non-uncoupling concentrations enhanced the uncoupling activity of fatty acids (e.g. palmitate). Relatively low C4R1 concentrations stimulated opening of a nonspecific Ca2+/Pi-dependent pore. ATP synthesis and hydrolysis were substantially inhibited by C4R1 at low concentrations that had no appreciable effects on respiration in states 4 and 3 and only slightly decreased the membrane potential. Besides, conditions were revealed allowing correct evaluation of the membrane potential generated at the inner mitochondrial membrane with safranin O upon oxidation of both succinate and NAD-dependent substrates in the presence of C4R1.
Keywords: rat liver mitochondria; C4R1; mild uncoupling; respiration; membrane potential; ATP synthesis; ATP hydrolysis; Ca2+/Pi-dependent pore; swelling