Biochemistry (Moscow) (v.77, #13)

Domains of α- and β-globin genes in the context of the structural-functional organization of the eukaryotic genome by S. V. Razin; S. V. Ulianov; E. S. Ioudinkova; E. S. Gushchanskaya; A. A. Gavrilov; O. V. Iarovaia (1409-1423).
The eukaryotic cell genome has a multilevel regulatory system of gene expression that includes stages of preliminary activation of genes or of extended genomic regions (switching them to potentially active states) and stages of final activation of promoters and maintaining their active status in cells of a certain lineage. Current views on the regulatory systems of transcription in eukaryotes have been formed based on results of systematic studies on a limited number of model systems, in particular, on the α- and β-globin gene domains of vertebrates. Unexpectedly, these genomic domains harboring genes responsible for the synthesis of different subunits of the same protein were found to have a fundamentally different organization inside chromatin. In this review, we analyze specific features of the organization of the α- and β-globin gene domains in vertebrates, as well as principles of activities of the regulatory systems in these domains. In the final part of the review, we attempt to answer the question how the evolution of α- and β-globin genes has led to segregation of these genes into two distinct types of chromatin domains situated on different chromosomes.
Keywords: α- and β-globin genes; genomic domains; transcription regulation; globin gene evolution

Diversity of mitochondrial genome organization by A. A. Kolesnikov; E. S. Gerasimov (1424-1435).
In this review, we discuss types of mitochondrial genome structural organization (architecture), which includes the following characteristic features: size and the shape of DNA molecule, number of encoded genes, presence of cryptogenes, and editing of primary transcripts.
Keywords: mitochondrial genome; structural organization; mt-encoded genes; editing

Endonucleases and apoptosis in animals by N. I. Aleksandrushkina; B. F. Vanyushin (1436-1451).
Endonucleases are the main instruments of obligatory DNA degradation in apoptosis. Many endonucleases have marked processive action; initially they split DNA in chromatin into very large domains, and then they perform in it internucleosomal fragmentation of DNA followed by its hydrolysis to small fragments (oligonucleotides). During apoptosis, DNA of chromatin is attacked by many nucleases that are different in activity, specificity, and order of action. The activity of every endonuclease is regulated in the cell through its own regulatory mechanism (metal ions and other effectors, possibly also S-adenosylmethionine). Apoptosis is impossible without endonucleases as far as it leads to accumulation of unnecessary (defective) DNA, disorders in cell differentiation, embryogenesis, the organism’s development, and is accompanied by various severe diseases. The interpretation of the structure and functions of endonucleases and of the nature and action of their modulating effectors is important not only for elucidation of mechanisms of apoptosis, but also for regulation and control of programmed cell death, cell differentiation, and development of organisms.
Keywords: programmed cell death; apoptosis; DNases; endonucleases

Programmed cell death in plants by A. S. Fomicheva; A. I. Tuzhikov; R. E. Beloshistov; S. V. Trusova; R. A. Galiullina; L. V. Mochalova; N. V. Chichkova; A. B. Vartapetian (1452-1464).
The modern concepts of programmed cell death (PCD) in plants are reviewed as compared to PCD (apoptosis) in animals. Special attention is focused on considering the potential mechanisms of implementation of this fundamental biological process and its participants. In particular, the proteolytic enzymes involved in PCD in animals (caspases) and plants (phytaspases) are compared. Emphasis is put on elucidation of both common features and substantial differences of PCD implementation in plants and animals.
Keywords: apoptosis; caspase; programmed cell death; phytaspase

Translation initiation in eukaryotes: Versatility of the scanning model by O. M. Alekhina; K. S. Vassilenko (1465-1477).
It is generally accepted that the initiation of translation in eukaryotes involves the binding of the 40S ribosomal subunit to the capped 5′ end of an mRNA and subsequent scanning of 5′ UTR in search of an initiation codon. However, until recently this has remained a mere hypothesis. This review describes the novel experimental evidence in support of this classical model. Data on the participation of various factors in the eukaryotic initiation process are summarized. The sequence of initiation events is described in light of the latest experimental data. The existing physical models of scanning are presented. Special attention is paid to discussion of alternative models of eukaryotic initiation of translation. It is demonstrated that the canonical mechanism of initiation is more versatile than previously thought.
Keywords: eukaryotes; initiation of translation; scanning; 5′ UTR; initiation factor

More than 20 years ago we showed that some types of cells are capable of secreting RNAs. It was suggested that these secreted RNAs could serve as molecular envoys in intercellular communication, for example, these RNAs being complementary to specific sites of the gene in another cell (e.g. to the variable region of immunoglobulin gene) could regulate the expression of genes that contain sites in coding regions complementary to antisense RNA. It has since been proven that eukaryotic cells contain antisense RNAs (particularly microRNAs and small interfering RNAs), which can regulate the expression of genes at the posttranscriptional level (the so-called regulatory pathway of RNA interference). Here I provide a short review of advances in the field of intracellular regulation of gene expression by different types of RNAs. In addition, an overview of recent data on the secretion of RNA molecules by different cell types and possible involvement of these secreted antisense RNAs in intercellular regulation of gene expression in target cells is given.
Keywords: antisense RNA; circulating nucleic acids; RNA interference; gene regulation; suppressor T cells; secretion; intercellular communication

Loops and repeats in proteins as footprints of molecular evolution by E. I. Deryusheva; O. M. Selivanova; I. N. Serdyuk (1487-1499).
This review is devoted to substantiation of new characteristics for classification of living organisms. The novel view of a role of flexible regions in protein functioning and evolution is suggested. It is based on the newly revealed correlation between the number of loops in elongation factors and the complexity of organisms. This correlation allowed us to formulate a hypothesis of evolution of this protein family. In addition, the study of the ribosomal protein S1 family made it possible to consider the number of structural domains as a reliable indicator of a microorganism’s affiliation with a particular division and to judge about “direction” of their evolution. The findings allow us to consider the loops and repeats in these proteins as unique imprints of molecular evolution.
Keywords: predicted loops; complexity of organisms; number of structural domains; reductive evolution

Mutations of small heat shock proteins and human congenital diseases by P. N. Datskevich; V. V. Nefedova; M. V. Sudnitsyna; N. B. Gusev (1500-1514).
The structure and properties of different members of a large family of small heat shock proteins (sHsp) playing an important role in cell homeostasis are described. Participation of the N-terminal domain in formation of large oligomers and chaperone activity of sHsp is analyzed. The structure of the α-crystallin domain of sHsp is characterized and the role of this domain in sHsp dimerization and chaperone activity is discussed. The properties of the C-terminal region of sHsp are described, and its participation in formation of large oligomers and chaperone activity are analyzed. The data from the literature on HspB1 and HspB3 mutations are presented, and involvement of these mutations in development of certain neurodegenerative diseases is discussed. Mutations of HspB4 are described and data on involvement of these mutations in development of cataract are presented. Multiple effects of HspB5 mutations are analyzed, and data are presented indicating that mutations of this protein are accompanied by development of different congenital diseases, such as cataract and different types of myopathies. The data on HspB6 and HspB8 mutations are presented, and feasible effects of these mutations on proteins structure are analyzed. Probable mechanisms underlying sHsp mutation-induced development of different congenital diseases are discussed.
Keywords: small heat shock proteins; mutation; human congenital diseases; phosphorylation

This review summarizes results of our studies on titin isoform composition in vertebrate striated muscles under normal conditions, during hibernation, real and simulated microgravity, and under pathological conditions (stiff-person syndrome, post-apoplectic spasticity, dilated cardiomyopathy, cardiac hypertrophy). Experimental evidence for the existence in mammalian striated muscles of higher molecular weight isoforms of titin (NT-isoforms) in addition to the known N2A-, N2BA-, and N2B-titin isoforms was obtained. Comparative studies of changes in titin isoform composition and structure-functional properties of human and animal striated muscles during adaptive and pathological processes led to a conclusion about the key role of NT-isoforms of titin in maintenance of sarcomere structure and contractile function of these muscles.
Keywords: skeletal and cardiac muscles; NT-; N2A-; N2BA- and N2B-isoforms of titin; T2-fragment; hibernation; microgravity; stiff-person syndrome; post-apoplectic spasticity; dilated cardiomyopathy; cardiac hypertrophy; spontaneously hypertensive rats (SHR)

Application of atomic force microscopy for characteristics of single intermolecular interactions by I. V. Safenkova; A. V. Zherdev; B. B. Dzantiev (1536-1552).
Atomic force microscopy (AFM) can be used to make measurements in vacuum, air, and water. The method is able to gather information about intermolecular interaction forces at the level of single molecules. This review encompasses experimental and theoretical data on the characterization of ligand-receptor interactions by AFM. The advantage of AFM in comparison with other methods developed for the characterization of single molecular interactions is its ability to estimate not only rupture forces, but also thermodynamic and kinetic parameters of the rupture of a complex. The specific features of force spectroscopy applied to ligand-receptor interactions are examined in this review from the stage of the modification of the substrate and the cantilever up to the processing and interpretation of the data. We show the specificities of the statistical analysis of the array of data based on the results of AFM measurements, and we discuss transformation of data into thermodynamic and kinetic parameters (kinetic dissociation constant, Gibbs free energy, enthalpy, and entropy). Particular attention is paid to the study of polyvalent interactions, where the definition of the constants is hampered due to the complex stoichiometry of the reactions.
Keywords: atomic force microscopy; single-molecule force spectroscopy; rupture force; intermolecular interactions; multi-valent interactions

This review describes key directions in the development of different probes based on complex compounds of lanthanides for in vitro and in vivo researches. The role of microsecond fluorescence of lanthanides for overcoming problems of background fluorescence is considered. The basic classes of synthetic and genetically encoded complex compounds of lanthanides are summarized. Main principles of designing lanthanide-based molecular sensors, including FRET sensors based on lanthanides and colored fluorescent proteins are described. Their applications in bioanalytical research and cellular bioimaging are described. The main principles of cellular bioimaging using lanthanides are formulated, questions of their delivery into cells are considered, and the problem of their potential toxicity for living organisms is discussed. A technique using multiphoton excitation of lanthanides is described.
Keywords: lanthanide fluorescence assay; time-resolved fluorescence resonance energy transfer (TR-FRET); lanthanide-binding peptides (LBPs); fluorescent proteins (FPs); multiphoton excitation; bioimaging; molecular sensors