Biochemistry (Moscow) (v.73, #13)

Nanocolonies: Detection, cloning, and analysis of individual molecules by H. V. Chetverina; A. B. Chetverin (1361-1387).
Nanocolonies (other names molecular colonies or polonies) are formed upon template nanomolecule (DNA or RNA) amplification in immobilized medium with efficient pore size in the nanometer range. This work deals with the principle, invention, development, and diverse nanocolony applications based on their unique abilities to compartmentalize amplification and expression of individual DNA and RNA molecules, including studying reactions between single molecules, digital molecular diagnostics, in vitro gene cloning and expression, as well as identification of the molecular cis-elements including DNA sequencing, analysis of single-nucleotide polymorphism, and alternative splicing investigation.
Keywords: molecular colonies; polonies; RNA recombination; RNA self-recombination; molecular cloning; gene expression; molecular diagnostics; DNA sequencing; single-nucleotide polymorphism; alternative splicing; fluorescence detection; detection in real time

This review deals with analysis of mechanisms involved in coordination of DNA replication and repair by SSB proteins; characteristics of eukaryotic, prokaryotic, and archaeal SSB proteins are considered, which made it possible to distinguish general mechanisms specific for functioning of proteins from organisms of different life domains. Mechanisms of SSB protein interactions with DNA during metabolism of the latter are studied; structural organization of the SSB protein complexes with DNA, as well as structural and functional peculiarities of different SSB proteins are analyzed.
Keywords: SSB proteins; replication protein A; protein-DNA complexes; DNA replication; DNA repair

Bacterial 5S rRNA-binding proteins of the CTC family by G. M. Gongadze; A. P. Korepanov; A. V. Korobeinikova; M. B. Garber (1405-1417).
The presence of CTC family proteins is a unique feature of bacterial cells. In the CTC family, there are true ribosomal proteins (found in ribosomes of exponentially growing cells), and at the same time there are also proteins temporarily associated with the ribosome (they are produced by the cells under stress only and incorporate into the ribosome). One feature is common for these proteins — they specifically bind to 5S rRNA. In this review, the history of investigations of the best known representatives of this family is described briefly. Structural organization of the CTC family proteins and their occurrence among known taxonomic bacterial groups are discussed. Structural features of 5S rRNA and CTC protein are described that predetermine their specific interaction. Taking into account the position of a CTC protein and its intermolecular contacts in the ribosome, a possible role of its complex with 5S rRNA in ribosome functioning is discussed.
Keywords: 5S rRNA-binding proteins; CTC proteins; ribosome; translation; Bacteria

Specific features of 5S rRNA structure — Its interactions with macromolecules and possible functions by A. V. Smirnov; N. S. Entelis; I. A. Krasheninnikov; R. Martin; I. A. Tarassov (1418-1437).
Small non-coding RNAs are today a topic of great interest for molecular biologists because they can be regarded as relicts of a hypothetical “RNA world” which, apparently, preceded the modern stage of organic evolution on Earth. The small molecule of 5S rRNA (∼120 nucleotides) is a component of large ribosomal subunits of all living beings (5S rRNAs are not found only in mitoribosomes of fungi and metazoans). This molecule interacts with various protein factors and 23S (28S) rRNA. This review contains the accumulated data to date concerning 5S rRNA structure, interactions with other biological macromolecules, intracellular traffic, and functions in the cell.
Keywords: 5S rRNA; structure; RNA-protein interaction; ribosome; intracellular transport

During the last two decades molecular genetic and cell mechanisms of proliferation and differentiation of mammalian stem cells have been intensively studied in leading laboratories all over the world. Studies in this field are very important both for basic science and for the development of promising cell therapy technologies. Embryonic stem cells represent a unique experimental model for the investigation of basic principles of mammalian cell differentiation and development. Using this model, important data on similarity in genetic programs during embryonic development and embryonic stem cells differentiation have been obtained. These include basically similar consequent expression of transcription factors, cell receptors, tissue specific proteins, and ion channels. Lines of embryonic stem cells are widely used for the investigation of gene functions in ontogenesis as well as in adult organisms (using gene-knockout strategy). This review deals with different pathways of mammalian (including human) embryonic stem cells differentiation. It considers the main approaches to directed differentiation of these cells in vitro: use of feeder cells, growth factors, and other chemical compounds and also genetic modification. Some examples of application of embryonic stem cells derivatives for cell therapy of some pathological conditions are discussed.
Keywords: embryonic stem cells; embryoid bodies; differentiation; pluripotency; transplantation; cell therapy; transfection; genetic modifications

Intermediate filaments (IF) represent one of three main cytoskeletal structures in most animal cells. The human IF protein family includes about 70 members divided into five main groups. The characteristic feature of IF is that in various cells and tissues they are formed by proteins of different groups. Structures of all IF proteins follow a unique scheme: a central α-helical part is flanked at the N and C ends by positively charged polypeptide chains devoid of a clear secondary structure. The central part is highly conserved for all proteins in all animals, whereas the N and C termini strongly differ both in size and amino acid composition. This review covers the broad spectrum of recent investigations of IF structure and diverse functions. Special attention is paid to the regulatory mechanisms of IF functions, mainly to phosphorylation by different protein kinases whose role is well studied. The review gives examples of hereditary diseases associated with mutations of some IF proteins, which point to an important physiological role of these cytoskeletal structures.
Keywords: intermediate filaments; vimentin; keratins; cytoskeleton

Actin filaments are polar; their barbed (fast-growing) and pointed (slow-growing) ends differ in structure and dynamic properties. The slow-growing end is regulated by tropomodulins, a family of capping proteins that require tropomyosins for optimal function. There are four tropomodulin isoforms; their distributions vary depending on tissue type and change during development. The C-terminal half of tropomodulin contains one compact domain represented by alternating α-helices and β-structures. The tropomyosin-independent actin-capping site is located at the C-terminus. The N-terminal half has no regular structure; however, it contains a tropomyosin-dependent actin-capping site and two tropomyosin-binding sites. One tropomodulin molecule can bind two tropomyosin molecules. Effectiveness of tropomodulin binding to tropomyosin depends on the tropomyosin isoform. Regulation of tropomodulin binding at the pointed end as well as capping effectiveness in the presence of specific tropomyosins may affect formation of local cytoskeleton and dynamics of actin filaments in cells.
Keywords: actin filament; capping; tropomodulin; tropomyosin; protein-protein interactions

Pore-forming proteins and adaptation of living organisms to environmental conditions by Zh. I. Andreeva-Kovalevskaya; A. S. Solonin; E. V. Sineva; V. I. Ternovsky (1473-1492).
Pore-forming proteins are powerful “tools” for adaptation of living organisms to environmental conditions. A wide range of these proteins isolated from various sources, from viruses to mammals, has been used for the analysis of their role in the processes of intra- and inter-species competition, defense, attack, and signaling. Here we review a large number of pore-forming proteins from the perspective of their functions, structures, and mechanisms of membrane penetration. Various mechanisms of cell damage, executed by these proteins in the course of formation of a pore and after its passing to conducting state, have been considered: endo- and exocytosis, lysis, necrosis, apoptosis, etc. The role of pore-forming proteins in evolution is discussed. The relevance of practical application of pore formers has been shown, including application in nanotechnological constructions.
Keywords: pore-forming proteins; adaptation; pore structure; apoptosis; nanotechnology

Involvement of thio-, peroxi-, and glutaredoxins in cellular redox-dependent processes by E. V. Kalinina; N. N. Chernov; A. N. Saprin (1493-1510).
Among the key antioxidant enzymes, thioredoxin and glutaredoxin systems play an important role in cell defense against oxidative stress and maintenance of redox homeostasis owing to the regulation of thiol—disulfide exchange. The thioredoxin isoforms Trx1 (cytoplasmic form) and Trx2 (mitochondrial form) can reduce inter- and intramolecular disulfide bonds in proteins, in particular, in oxidized peroxiredoxins, which disrupt organic hydroperoxides, H2O2, and peroxynitrite. NADPH-dependent thioredoxin reductase, which reduces a broad range of substrates including oxidized form of thioredoxin, can also directly reduce lipid hydroperoxides, H2O2, and dehydroascorbic and lipoic acids. Glutaredoxin, whose major isoforms in mammals are Grx1, Grx2, and Grx5, as well as thioredoxin, catalyzes S-glutathionylation and deglutathionylation of proteins to protect SH-groups from oxidation and restore functionally active thiols. However, in contrast to thioredoxin, glutaredoxin reduces GSH-mixed disulfides and catalyzes the reaction not only via a dithiol mechanism but also via monothiol reduction. In addition to the role in cellular antioxidant defense, all of the reviewed redox proteins (thioredoxin, thioredoxin reductase, peroxiredoxin, and glutaredoxin) have a number of significant functions required for cell viability: they regulate transcription factor activities, play the role of growth factors, serve as enzyme cofactors, take part in regulation of cell cycle, and are involved in antiapoptotic mechanisms.
Keywords: oxidative stress; thioredoxin; thioredoxin reductase; peroxiredoxin; glutaredoxin; redox-dependent processes

D-Amino acid oxidase: Physiological role and applications by S. V. Khoronenkova; V. I. Tishkov (1511-1518).
D-Amino acids play a key role in regulation of many processes in living cells. FAD-dependent D-amino acid oxidase (DAAO) is one of the most important enzymes responsible for maintenance proper level of D-amino acids. The most interesting and important data for regulation of the nervous system, hormone secretion, and other processes by D-amino acids as well as development of different diseases under changed DAAO activity are presented. The mechanism of regulation is complex and multi-parametric because the same enzyme simultaneously influences the level of different D-amino acids, which can result in opposing effects. Use of DAAO for diagnostic and therapeutic purposes is also considered.
Keywords: D-amino acid oxidase; physiological role; practical application

The problem of the eukaryotic genome size by L. I. Patrushev; I. G. Minkevich (1519-1552).
The current state of knowledge concerning the unsolved problem of the huge interspecific eukaryotic genome size variations not correlating with the species phenotypic complexity (C-value enigma also known as C-value paradox) is reviewed. Characteristic features of eukaryotic genome structure and molecular mechanisms that are the basis of genome size changes are examined in connection with the C-value enigma. It is emphasized that endogenous mutagens, including reactive oxygen species, create a constant nuclear environment where any genome evolves. An original quantitative model and general conception are proposed to explain the C-value enigma. In accordance with the theory, the noncoding sequences of the eukaryotic genome provide genes with global and differential protection against chemical mutagens and (in addition to the anti-mutagenesis and DNA repair systems) form a new, third system that protects eukaryotic genetic information. The joint action of these systems controls the spontaneous mutation rate in coding sequences of the eukaryotic genome. It is hypothesized that the genome size is inversely proportional to functional efficiency of the anti-mutagenesis and/or DNA repair systems in a particular biological species. In this connection, a model of eukaryotic genome evolution is proposed.
Keywords: C-value paradox; genome size; genome evolution; coding sequences; non-coding sequences; gene protection