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Vol 83, No 12-13 (2018)

Article

Juri Markovich Vasiliev – My Mentor and Friend

Margolis L.B.

Abstract

This is an overview of the biography and scientific accomplishments of Dr. Juri Vasiliev, an outstanding Russian cell biologist. Ju. M. Vasiliev published seminal papers on carcinogenesis and cytoskeleton of normal and cancer cells. He founded a scientific school and mentored many students that are now occupying leading positions in different laboratories throughout the world.

Biochemistry (Moscow). 2018;83(12-13):1433-1436
pages 1433-1436 views

Can Aging Develop as an Adaptation to Optimize Natural Selection? (Application of Computer Modeling for Searching Conditions When the “Fable of Hares” Can Explain the Evolution of Aging)

Markov A.V., Barg M.A., Yakovleva E.Y.

Abstract

There are two points of view on the evolution of aging. The classical theory of aging suggests that natural selection does not efficiently eliminate mutations or alleles that are harmful to organisms at later age. Another hypothesis is that the genetic program of aging has evolved as an adaptation that contributes to the optimization of the evolutionary process. Academician V. P. Skulachev advocates the latter hypothesis, which he has illustrated with the “Fable of hares”. In this paper, we have used computer simulation to search for conditions when, according to the “Fable”, aging develops as an adaptation required for the evolution of useful traits. The simulation has shown that the evolutionary mechanism presented in the “Fable of hares” is only partially functional. We have found that under certain conditions, programmed deterioration of some organismal functions makes it possible to increase the efficiency of natural selection of other functions. However, we have not identified mechanisms that would ensure the distribution and support of genes of aging within the population.

Biochemistry (Moscow). 2018;83(12-13):1504-1516
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An Incipient Revolution in the Testing of Anti-aging Strategies

Mitteldorf J.

Abstract

Recent advances in the technology of “aging clocks” based on DNA methylation suggest that it may soon be possible to measure changes in the rate of human aging over periods as short as a year or two. If this potential is realized, the testing of putative anti–aging interventions will become radically cheaper and faster. This should prompt a re–appraisal of the entire spectrum of methods for evaluating anti–aging technologies in humans and in model systems. In the body of this article, I will argue that (1) testing, not development, is the bottleneck in the flow of knowledge about human anti–aging; (2) single interventions are unlikely to afford major increments in life expectancy in humans; (3) interactions among combinations of known anti–aging interventions are the most important unknown in the field; (4) the daunting number of combinations may be tamed by enrolling large numbers of early adopters who are already using diverse combinations of strategies; (5) the newest methylation clock, called “DNAm PhenoAge” (Levine, M., et al. (2018) Aging (Albany), 10, 573–591) has the potential to tell us which of these people are best succeeding in their quest to slow the aging clock; (6) further optimization of this clock, specialized to the proposed application, is feasible; and (7) multivariate statistics can be used to efficiently identify the best combinations of known interventions that are already being deployed by members of the community which actively seeks to enhance their long–term health. The integration of these ideas leads to a proposal for a human trial crowd–funded largely by the subjects, organized around a web site, as well as standardization of individual record–keeping and an open–source database of methylation results before and after.

Biochemistry (Moscow). 2018;83(12-13):1517-1523
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Potential Markers of Autoimmune Diseases, Alleles rs115662534(T) and rs548231435(C), Disrupt the Binding of Transcription Factors STAT1 and EBF1 to the Regulatory Elements of Human CD40 Gene

Putlyaeva L.V., Demin D.E., Korneev K.V., Kasyanov A.S., Tatosyan K.A., Kulakovskiy I.V., Kuprash D.V., Schwartz A.M.

Abstract

CD40 receptor is expressed on B lymphocytes and other professional antigen–presenting cells. The binding of CD40 to its ligand CD154 on the surface of T helper cells plays an important role in the activation of B lymphocytes required for production of antibodies, in particular, against autoantigens. Association of several single nucleotide polymorphisms (SNPs) located in the non–coding areas of human CD40 locus with the elevated risk of autoimmune diseases has been demonstrated. The most studied of these SNPs is rs4810485 located in the first intron of the CD40 gene. Expression of the CD40 gene in B lymphocytes of donors homozygous for the common allelic variant of this polymorphism (G) is higher than in B cells from donors carrying the minor (T) variant. We investigated the enhancer activity of this fragment of the CD40 locus in human B cell lines and showed that it is independent on the rs4810485 alleles. However, the minor allelic variants of the rs4810485–linked SNPs rs548231435 and rs115662534 were associated with a significant decrease in the activity of the CD40 promoter due to the impairments in the binding of EBF1 and STAT1 transcription factors, respectively.

Biochemistry (Moscow). 2018;83(12-13):1534-1542
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Non-structural Functions of Hordeivirus Capsid Protein Identified in Plants Infected by a Chimeric Tobamovirus

Makarova S.S., Makhotenko A.V., Khromov A.V., Skurat E.V., Solovyev A.G., Makarov V.V., Kalinina N.O.

Abstract

Capsid proteins (CPs) of (+)RNA–containing plant viruses are multifunctional proteins involved in many stages of viral infection cycle, in addition to their main function of virus capsid formation. For example, the tobamoviral CP ensures virus systemic transport in plants and defines the virus–host interactions, thereby influencing the virus host range, virus infectivity, pathogenicity, and manifestation of infection symptoms. Hordeiviruses and tobamoviruses belong to the Virgaviridae family and have rod–shaped virions with a helical symmetry; their CPs are similar in structure. However, no non–structural functions of hordeiviral CPs have been described so far. In this study, we assayed possible non–structural functions of CP from the barley stripe mosaic virus (BSMV) (hordeivirus). To do this, the genome of turnip vein clearing virus (TVCV) (tobamovirus) was modified by substituting the TVCV CP gene with the BSMV CP gene or its mutants. We found that BSMV CP efficiently replaced TVCV CP at all stages of viral infection. In particular, BSMV CP performed the role of tobamoviral CP in the long–distance transport of the chimeric virus, acted as a hypersensitive response elicitor, and served as a pathogenicity determinant that influenced the symptoms of the viral infection. The chimeric tobamovirus coding for the C–terminally truncated BSMV CP displayed an increased infectivity and was transported in plants in a form of atypical virions (ribonucleoprotein complexes).

Biochemistry (Moscow). 2018;83(12-13):1543-1551
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Mobile Loop in the Active Site of Metallocarboxypeptidases as an Underestimated Determinant of Substrate Specificity

Akparov V.K., Timofeev V.I., Khaliullin I.G., Konstantinova E.G., Kuranova I.P., Rakitina T.V., Švedas V.K.

Abstract

It is generally accepted that the primary specificity of metallocarboxypeptidases is mainly determined by the structure of the so–called primary specificity pocket. However, the G215S/A251G/T257A/D260G/T262D mutant of carboxypeptidase T from Thermoactinomyces vulgaris (CPT) with the primary specificity pocket fully reproducing the one in pancreatic carboxypeptidase B (CPB) retained the broad, mainly hydrophobic substrate specificity of the wild–type enzyme. In order to elucidate factors affecting substrate specificity of metallocarboxypeptidases and the reasons for the discrepancy with the established views, we have solved the structure of the complex of the CPT G215S/A251G/T257A/D260G/T262D mutant with the transition state analogue N–sulfamoyl–L–phenylalanine at a resolution of 1.35 Å and compared it with the structure of similar complex formed by CPB. The comparative study revealed a previously underestimated structural determinant of the substrate specificity of metallocarboxypeptidases and showed that even if substitution of five amino acid residues in the primary specificity pocket results in its almost complete structural correspondence to the analogous pocket in CPB, this does not lead to fundamental changes in the substrate specificity of the mutant enzyme due to the differences in the structure of the mobile loop located at the active site entrance that affects the substrate–induced conformational rearrangements of the active site.

Biochemistry (Moscow). 2018;83(12-13):1594-1602
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Review

Cytomegalovirus Infection in Cardiovascular Diseases

Lebedeva A.M., Shpektor A.V., Vasilieva E.Y., Margolis L.B.

Abstract

Atherosclerosis underlies the development of many cardiovascular diseases that continue to hold a leading place among the causes of death in developed countries. The role of activated immune cells in atherosclerosis progression has been convincingly demonstrated, but the mechanism of their action remains poorly investigated. Since atherosclerosis is associated with chronic inflammatory response, involvement of viral and bacterial infections in atherogenesis has been examined. A special place among the infectious agents is held by human herpesviruses as the most common persistent viruses in human population coupled to chronic inflammation during atherosclerosis. We found that activation of cytomegalovirus (CMV, human herpesvirus 5) infection is associated with the emergence of acute coronary syndrome, which is in a good agreement with the data on productive CMV infection published elsewhere. In this review, we discuss the data obtained by us and other researchers regarding the role of cytomegalovirus infection and related potential mechanisms resulting in the expansion of atherosclerotic plaques during ischemic heart disease and stroke, including virus transfer to immune and endothelial cells via extracellular vesicles. In particular, the data presented in the review demonstrate that virus spreading in the vascular wall triggers immune system activation in atherosclerotic plaques and causes endothelial dysfunction. Moreover, productive CMV infection in patients with acute myocardial infarction correlates with the extent of endothelial dysfunction. The mechanisms described by us and other researchers may explain the role of CMV infection in atherosclerosis and development of ischemic heart disease.

Biochemistry (Moscow). 2018;83(12-13):1437-1447
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Alterations in WNT Signaling in Leukemias

Fetisov T.I., Lesovaya E.A., Yakubovskaya M.G., Kirsanov K.I., Belitsky G.A.

Abstract

The WNT/β–catenin signaling pathway plays an important role in the differentiation and proliferation of hematopoietic cells. In recent years, special attention has been paid to the role of impairments in the WNT signaling path–way in pathogenesis of malignant neoplasms of the hematopoietic system. Disorders in the WNT/β–catenin signaling in leukemias identified to date include hypersensitivity to the WNT ligands, epigenetic repression of WNT antagonists, over–expression of WNT ligands, impaired β–catenin degradation in the cytoplasm, and changes in the activity of the TCF/Lef transcription factors. At the molecular level, these impairments involve overexpression of the FZD protein, hypermethylation of the SFRP, DKK, WiF, Sox, and CXXC gene promoters, overexpression of Lef1 and plakoglobin, mutations in GSK3β, and β–catenin phosphorylation by the BCR–ABL kinase. This review is devoted to the systematization of these data.

Biochemistry (Moscow). 2018;83(12-13):1448-1458
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Common and Specific Functions of Nonmuscle Myosin II Paralogs in Cells

Shutova M.S., Svitkina T.M.

Abstract

Various forms of cell motility critically depend on pushing, pulling, and resistance forces generated by the actin cytoskeleton. Whereas pushing forces largely depend on actin polymerization, pulling forces responsible for cell contractility and resistance forces maintaining the cell shape require interaction of actin filaments with the multivalent molecular motor myosin II. In contrast to muscle–specific myosin II paralogs, nonmuscle myosin II (NMII) functions in virtually all mammalian cells, where it executes numerous mechanical tasks. NMII is expressed in mammalian cells as a tissue–specific combination of three paralogs, NMIIA, NMIIB, and NMIIC. Despite overall similarity, these paralogs differ in their molecular properties, which allow them to play both unique and common roles. Importantly, the three paralogs can also cooperate with each other by mixing and matching their unique capabilities. Through specialization and cooperation, NMII paralogs together execute a great variety of tasks in many different cell types. Here, we focus on mammalian NMII paralogs and review novel aspects of their kinetics, regulation, and functions in cells from the perspective of how distinct features of the three myosin II paralogs adapt them to perform specialized and joint tasks in the cells.

Biochemistry (Moscow). 2018;83(12-13):1459-1468
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Role of Epithelial-Mesenchymal Transition in Tumor Progression

Gloushankova N.A., Zhitnyak I.Y., Rubtsova S.N.

Abstract

Epithelial–mesenchymal transition (EMT) is a fundamental process of morphogenesis whereby epithelial cells acquire the mesenchymal phenotype. Multiple data suggest a critical role of EMT in tumor progression. In carcinomas, EMT can be initiated and promoted by many oncogenic signaling pathways, hypoxia, and signals of tumor microenvironment resulting in epithelial cells losing their cell polarity and cell–cell adhesion and gaining the migratory and invasive properties. Downregulation of expression of the cell adhesion protein E–cadherin is considered a poor prognostic factor in cancer. Many tumors are characterized by incomplete EMT, where tumor cells acquire mesenchymal characteristics but retain their epithelial markers, in particular, E–cadherin. In cells with the hybrid epithelial–mesenchymal phenotype, E–cadherin is accumulated in adherens junctions which are less stable than adherens junctions in normal epithelial cells. E–cadherin–based adherens junctions are essential for efficient collective migration and invasion of carcinoma cells, and their survival in metastases. The plasticity of the hybrid epithelial–mesenchymal phenotype improves adaptive capabilities of cancer cells. By undergoing EMT, carcinoma cells become resistant to chemotherapy and acquire the ability to suppress immune response. Emergence of cancer stem cells after EMT activation has been observed in many types of carcinoma.

Biochemistry (Moscow). 2018;83(12-13):1469-1476
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Elimination of Senescent Cells: Prospects According to the Subtelomere-Telomere Theory

Libertini G., Ferrara N., Rengo G., Corbi G.

Abstract

Cell senescence is an artificially reversible condition activated by various factors and characterized by replicative senescence and typical general alteration of cell functions, including extra–cellular secretion. The number of senescent cells increases with age and contributes strongly to the manifestations of aging. For these reasons, research is under way to obtain “senolytic” compounds, defined as drugs that eliminate senescent cells and therefore reduce aging–associated decay, as already shown in some experiments on animal models. This objective is analyzed in the context of the programmed aging paradigm, as described by the mechanisms of the subtelomere–telomere theory. In this regard, positive effects of the elimination of senescent cells and limits of this method are discussed. For comparison, positive effects and limits of telomerase activation are also analyzed, as well of the combined action of the two methods and the possible association of opportune gene modifications. Ethical issues associated with the use of these methods are outlined.

Biochemistry (Moscow). 2018;83(12-13):1477-1488
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Ants as Object of Gerontological Research

Shilovsky G.A., Putyatina T.S., Ashapkin V.V., Rozina A.A., Lyubetsky V.A., Minina E.P., Bychkovskaia I.B., Markov A.V., Skulachev V.P.

Abstract

Social insects with identical genotype that form castes with radically different lifespans are a promising model system for studying the mechanisms underlying longevity. The main direction of progressive evolution of social insects, in particular, ants, is the development of the social way of life inextricably linked with the increase in the colony size. Only in a large colony, it is possible to have a developed polyethism, create large food reserves, and actively regulate the nest micro–climate. The lifespan of ants hugely varies among genetically similar queens, workers (unproductive females), and males. The main advantage of studies on insects is the determinism of ontogenetic processes, with a single genome leading to completely different lifespans in different castes. This high degree of determinacy is precisely the reason why some researchers (incorrectly) call a colony of ants the “superorganism”, emphasizing the fact that during the development, depending on the community needs, ants can switch their ontogenetic programs, which influences their social roles, ability to learn (i.e., the brain [mushroom–like body] plasticity), and, respectively, the spectrum of tasks performed by a given individual. It has been shown that in many types of food behavior, older ants surpass young ones in both performing the tasks and transferring the experience. The balance between the need to reduce the “cost” of non–breeding individuals (short lifespan and small size of workers) and the benefit from experienced long–lived workers possessing useful skills (large size and “non–aging”) apparently determines the differences in the lifespan and aging rate of workers in different species of ants. A large spectrum of rigidly determined ontogenetic trajectories in different castes with identical genomes and the possibility of comparison between “evolutionarily advanced” and “primitive” subfamilies (e.g., Formicinae and Ponerinae) make ants an attractive object in the studies of both normal aging and effects of anti–aging drugs.

Biochemistry (Moscow). 2018;83(12-13):1489-1503
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Can Aging Be Programmed?

Mitteldorf J.

Abstract

Aging diminishes individual fitness, and aging could never evolve as an adaptive program according to the most prevalent model of evolutionary theory. On the other hand, some mechanisms of aging have been found to be conserved since the Cambrian explosion, and the physiology of aging sometimes looks like programmed self–destruction. Biostatisticians find evidence of an epigenetic aging clock, extending the clock that controls the growth and development into a realm of inexorably increasing mortality. These and other observations have suggested to some biologists that our understanding of aging is being constrained by restrictive evolutionary paradigms. Several computational models have been proposed; but evolution of an aging program requires group selection on a scale that goes beyond the theory of multilevel selection, a perspective that is already controversial. So, the question whether plausible models exist that can account for aging as a group–selected adaptation is central to our understanding of what aging is, where it comes from and, importantly, how anti–aging medicine might most propitiously be pursued. In a 2016 Aging Cell article, Kowald and Kirkwood reviewed computational models that evolve aging as an adaptation. They find fault with each of these models in turn, based on theory alone, and on this basis, they endorse the standing convention that aging must be understood in terms of trade–off models. But consideration of the corpus of experimental evidence creates a picture that stands in counterpoint to the conclusions of that review. Presented herein is a broad summary of that evidence, together with a description of one model that Kowald and Kirkwood omitted, the demographic theory of aging, which may be the most conservative, and therefore most plausible of the alternative evolutionary theories, and which is the subject of a book by the present author, published contemporaneously with Kowald and Kirkwood.

Biochemistry (Moscow). 2018;83(12-13):1524-1533
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Application of the CRISPR/Cas System for Generation of Pathogen-Resistant Plants

Makarova S.S., Khromov A.V., Spechenkova N.A., Taliansky M.E., Kalinina N.O.

Abstract

The use of the CRISPR/Cas9 prokaryotic adaptive immune system has led to a breakthrough in targeted genome editing in eukaryotes. The CRISPR/Cas technology allows to generate organisms with desirable characteristics by introducing deletions/insertions into selected genome loci resulting in the knockout or modification of target genes. This review focuses on the current state of the CRISPR/Cas use for the generation of plants resistant to viruses, bacteria, and parasitic fungi. Resistance to DNA–and RNA–containing viruses is usually provided by expression in transgenic plants of the Cas endonuclease gene and short guide RNAs (sgRNAs) targeting certain sites in the viral or the host plant genomes to ensure either direct cleavage of the viral genome or modification of the plant host genome in order to decrease the efficiency of virus replication. Editing of plant genes involved in the defense response to pathogens increases plants resistance to bacteria and pathogenic fungi. The review explores strategies and prospects of the development of pathogen–resistant plants with a focus on the generation of non–transgenic (non–genetically modified) organisms, in particular, by using plasmid (DNA)–free systems for delivery of the Cas/sgRNA editing complex into plant cells.

Biochemistry (Moscow). 2018;83(12-13):1552-1562
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Iatrogenic Damage of Eye Tissues: Current Problems and Possible Solutions

Baksheeva V.E., Gancharova O.S., Tiulina V.V., Iomdina E.N., Zamyatnin A.A., Philippov P.P., Zernii E.Y., Senin I.I.

Abstract

Visual system is at high risk of iatrogenic damage. Laser ocular surgery, the use of powerful illumination devices in diagnostics and surgical treatment of eye diseases, as well as long surgeries under general anesthesia provoke the development of chronic degenerative changes in eye tissues, primarily in the cornea and the retina. Despite the existence of approaches for prevention and treatment of these complications, the efficacy of these approaches is often limited. Here, we review the mechanisms of iatrogenic damage to eye tissues at the cellular and biochemical levels. It is well recognized that oxidative stress is one of the main factors hindering regeneration of eye tissues after injuries and, thereby, aggravating iatrogenic eye disorders. It is accompanied by the downregulation of low–molecular–weight antioxidants and antioxidant enzymes, as well as changes in the expression and redox status of proteins in the damaged tissue. In this regard, antioxidant therapy, in particular, the use of highly effective mitochondria–targeted antioxidants such as SkQ1, is considered as a promising approach to the prevention of iatrogenesis. Recent findings indicate that the most efficient protection of eye tissues from the iatrogenic injury is achieved by preventive use of these antioxidants. In addition to preventing corneal and retinal cell death induced by oxidative stress, SkQ1 contributes to the restoration of innate antioxidant defense of these tissues and suppresses local inflammatory response. Since the timing of routine medical manipulations is usually known in advance, iatrogenic damage to the ocular tissues can be successfully prevented using mitochondria–targeted therapy.

Biochemistry (Moscow). 2018;83(12-13):1563-1574
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Alternate and Additional Functions of Erythrocyte Hemoglobin

Kosmachevskaya O.V., Topunov A.F.

Abstract

The review discusses pleiotropic effects of erythrocytic hemoglobin (Hb) and their significance for human health. Hemoglobin is mostly known as an oxygen carrier, but its biochemical functions are not limited to this. The following aspects of Hb functioning are examined: (i) catalytic functions of the heme component (nitrite reductase, NO dioxygenase, monooxygenase, alkylhydroperoxidase) and of the apoprotein (esterase, lipoxygenase); (ii) participation in nitric oxide metabolism; (iii) formation of membrane–bound Hb and its role in the regulation of erythrocyte metabolism; (iv) physiological functions of Hb catabolic products (iron, CO, bilirubin, peptides). Special attention is given to Hb participation in signal transduction in erythrocytes. The relationships between various erythrocyte metabolic parameters, such as oxygen status, ATP formation, pH regulation, redox balance, and state of the cytoskeleton are discussed with regard to Hb. Hb polyfunctionality can be considered as a manifestation of the principle of biochemical economy.

Biochemistry (Moscow). 2018;83(12-13):1575-1593
pages 1575-1593 views

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