卷 57, 编号 2 (2023)

Non-ribosomal peptides play an important role in the vital activity of bacteria and have an extremely broad field of biological activity. In particular, they act as antibiotics, toxins, surfactants, siderophores, and also perform a number of other specific functions. Biosynthesis of these molecules does not occur on ribosomes but by special enzymes that form gene clusters in bacterial genomes. We hypothesized that the presence of non-ribosomal peptide synthesis pathways is a specific feature of bacterial metabolism, which may affect other vital processes of the cell, including translational ones. This work was the first to show the relationship between the translation regulation mechanism of protein-coding genes in bacteria, which is largely determined by the efficiency of translation elongation, and the presence of gene clusters in the genomes for the biosynthesis of non-ribosomal peptides. Bioinformatic analysis of the translation elongation efficiency of protein-coding genes was performed in 11679 bacterial genomes, some of which contained gene clusters of non-ribosomal peptide biosynthesis and some of which did not. The analysis showed that bacteria whose genomes contained clusters of non-ribosomal peptide biosynthetic genes and those without such gene clusters differ significantly in the molecular mechanisms that ensure translation efficiency. Thus, among microorganisms whose genomes contain gene clusters of non-ribosomal peptide synthetases, a significantly smaller part of them is characterized by optimized regulation of the number of local inverted repeats, while most of them have genomes optimized by the averaged energy of inverted repeats studs in mRNA and additionally by codon composition. Our results suggest that the presence of non-ribosomal peptide biosynthetic pathways in bacteria may influence the structure of the overall bacterial metabolism, which is also expressed in the specific mechanisms of ribosomal protein biosynthesis.

Currently, the search for manifestations of selection under the influence of the environment in molecular sequences is usually carried out within closely related species or at the intraspecific level. It is believed that at high taxonomic levels this is unpromising due to phylogenetic relationship. Cytochrome b amino acid sequences of 67 rodent and lagomorph species with known geographic coordinates were digitized using the AAindex database. Based on more than 200 thousand features, the main components were obtained. A well-known statistical method, which has not previously been used for such problems, was used, which makes it possible to orthogonally decompose multidimensional variability into intra- and intertaxon variability and analyze them separately. Subfamily level selected. For the second principal component (17.05% of intertaxon variability), a correlation with latitude was found (r = 0.561; n = 67; p < E–5). The clear division into two groups revealed by the first principal component (39.48% of intertaxon variability), which does not coincide with the taxonomic one, indicates a possible physicochemical underlying reason for the differences between them. This requires further research.

DNA-polymerases catalyze DNA synthesis during DNA replication, repair, and recombination. A number of DNA-polymerases, such as the Taq enzyme from Thermus aquaticus, are used in various applications of molecular biology and biotechnology, in particular as DNA amplification tools. However, the efficiency of these enzymes depends on factors such as DNA origin, primer composition, template length, GC-content, and the ability to form stable secondary structures. Such limitations in the use of currently known DNA-polymerases leave the problem of searching for new enzymes with improved properties. This review summarizes the main structural and molecular-kinetic features of the functioning of DNA-polymerases belonging to the structural family A, including Taq polymerase. A phylogenetic analysis of these enzymes was carried out, which made it possible to establish a highly conserved consensus sequence containing 62 amino acid residues distributed over the structure of the enzyme. A comparative analysis of these amino acid residues among poorly studied DNA-polymerases revealed 7 enzymes that potentially have the properties necessary for their use for DNA amplification.

Adenine-DNA-glycosylase MutY is a monofunctional enzyme and catalyzes the hydrolysis of N-glycosidic bonds with adenine residues located opposite 8-oxonuanine residues in DNA. A rational design of mutant forms of the enzyme with altered catalytic activity was carried out. An analysis of the structures of mutant forms of MutY calculated by the molecular dynamics method led to the conclusion that some mutant forms of MutY, in addition to hydrolysis of the N-glycosidic bond, may have AP-lyase activity, as in the case of bifunctional DNA glycosylases. Mutant forms of MutY containing substitutions A120K or S124K were obtained by site-directed mutagenesis, and their catalytic activity was determined. It was shown that the S120K substitution leads to the appearance of additional AP-lyase activity, while the A124K substitution completely inactivates the enzyme.

Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a DNA repair enzyme that removes various adducts from the 3'‑end of DNA. Such damage is formed, for example, under the action of enzymes that introduce single-strand breaks in DNA during catalysis (for example, topoisomerase 1), as well as a number of anticancer drugs with different mechanisms of action. Poly(ADP-ribose) polymerase 1 (PARP1) is an enzyme that catalyzes the post-translational modification of various targets (PARylation), and with its help controls many processes in the cell, including DNA repair. The target of PARP1 is also Tdp1, whose PARylation attracts Tdp1 to the site of DNA damage. Olaparib is a PARP1 inhibitor used in clinical practice to treat homologous recombination deficient tumors. The main mechanism of action of olaparib is to obstruction of PARylation and thus DNA repair. In this study, we used the Tdp1 inhibitor OL7-43 in combination with olaparib to increase the antitumor effect of the latter. Despite the increase in cytotoxicity of olaparib in the presence of OL7-43 in vitro, we did not find a sensitizing effect of this compound in the Lewis and Krebs-2 carcinoma models, but it showed its own antitumor and antimetastatic effects.

Autism spectrum disorder (ASD) is a developmental disorder characterized by the early onset of communication, learning, and behavioral problems. The syndromic form of ASD is caused by monogenic mutations, in the case when it is not possible to find genetic or other known mechanisms, the term “idiopathic autism” is used. A significant part of both syndromic and idiopathic autism is associated with translational deregulation dependent on the mechanistic target of rapamycin (mTOR). In this review, we present both bioinformatic and experimental data that link the mTOR signaling pathway to maternal autoantibody-induced autism and childhood autoimmune neuropsychiatric disorders such as Sydenham’s chorea and pediatric autoimmune neuropsychiatric disorder associated with streptococcal infections (PANDAS). The need for ASD subtyping and the possibility of mechanism-based therapy with inhibitors of the mTOR signaling pathway are also discussed.

Poly(ADP-ribose) (PAR) is a negatively charged polymer, linear and branched, consisting of ADP-ribose monomers. This polymer is synthesized by poly(ADP-ribose)polymerase (PARP) enzymes which are activated on DNA damage and use nicotinamide adenine dinucleotide (NAD⁺) as a substrate. The most studied members of the PARP family, PARP1 and PARP2, are the most important nuclear proteins involved in many cellular processes, including the regulation of DNA repair. PARP1 and PARP2 catalyze both the synthesis and transfer of poly(ADP-ribose) to amino acid residues of target proteins, including autoPARylation. In view of the key role in the regulation of the DNA repair process, PARP1 and PARP2 are promising targets for chemotherapy. Recently, a novel histone PARylation factor (HPF1) has been discovered to modulate PARP1/2 activity by forming a transient joint active site with PARP1/2. In the presence of HPF1, histone modification occurs at serine residues. The general mechanism of interaction between HPF1 and PARP1/2 is only beginning to be elucidated. In this review, we consider the discovery and classical mechanism of this important process in higher eukaryotes, as well as the role of a new histone PARylation factor in this HPF1 process.

The base excision repair (BER) system is aimed at repair of the largest group of DNA lesions, namely of damaged bases. The main steps in BER are: recognition and removal of the aberrant base, cutting the DNA sugar-phosphate backbone, gap processing (including dNMP insertion), and DNA ligation. The precise functioning of BER depends on the regulation of each step of the process by regulatory/accessory proteins, the most important of which is poly(ADP-ribose)polymerase 1 (PARP1). PARP1 plays an important role in various processes of DNA repair, maintenance of genome integrity, and regulation of mRNA stability and decay. In this regard, PARP1 can affect BER both at the level of proteins involved in the process and at the level of expression of the mRNAs encoding them. There are no systematic data on the effect of various amounts of PARP1 on the activity of key BER proteins and the levels of mRNAs encoding them in human cells. In our work, using whole-cell extracts and RNA preparations obtained from the parental HEK293T cell line and its derivative HEK293T/P1-KD cell line with reduced PARP1 expression (shPARP1-expressing cells, PARP1 knockdown), we assessed the levels of mRNA encoding BER proteins: PARP1, PARP2, uracil DNA glycosylase (UNG2), AP endonuclease 1 (APE1), DNA polymerase β (POLβ), DNA ligase III (LIG3), and XRCC1. In parallel, the catalytic activity of these enzymes was evaluated. No significant effect of the PARP1 amount of on the mRNA levels of UNG2, APE1, POLβ, LIG3, and XRCC1 was found. At the same time, in HEK293T/P1-KD cells, the amount of PARP2 mRNA was reduced by 2 times. The activities of these enzymes in whole-cell extracts of HEK293T and HEK293T/P1-KD cells also did not differ significantly. Under the conditions of poly(ADP-ribose) synthesis, the efficiency of the reactions catalyzed by UNG2, APE1, POLβ, and LIG3 also did not change significantly. In addition, it was shown that a reduced amount of PARP1 in the extract of HEK293T/P1-KD cells does not cause fundamental changes in the nature of DNA PARylation compared to the extract of the parental HEK293T cell line.

The study provides an overview of scientific results on the feasibility of using type III interferons against SARS-CoV-2. We have analyzed data obtained from the PubMed electronic database for the period 2020‒2022. The results of our own studies of pharmacological substances based on recombinant IFN-λ1 and its pegylated form are also presented. Completed and ongoing investigations allow us to position IFN-λ as an effective therapeutic agent against SARS-CoV-2.

To prevent erroneous incorporation of dUMP into DNA from the dUTP metabolic pool, all living cells contain 2′-deoxyuridine-5′-triphosphate nucleotide hydrolase (Dut), an enzyme that hydrolyzes dUTP to dUMP and pyrophosphate. Dut is considered a promising pharmacological target for antimetabolite therapy. Enzymatically active Dut is a trimer that binds the substrate at the interface between the subunits. Here we use high-speed nanoscale differential scanning fluorometry (nanoDSF) to study how various physicochemical factors affect the stability of the E. coli Dut trimer. Unlike for monomeric proteins, thermal denaturation of Dut occurred in two stages, the first of which corresponds to the dissociation of the trimer to monomeric subunits. Hydrophobic interactions and hydrogen bonds at the interfaces between subunits contributed most to trimer stabilization. The Dut trimer was partially stabilized upon binding of nucleotide ligands. In general, nanoDSF is a convenient assay for screening low molecular weight compounds for their ability to destabilize the active Dut trimer.

The study of immune response and inflammation gene polymorphism in a genogeographic context is a relevant direction in the study of human populations. Here, in the indigenous populations of Siberia the frequencies of polymorphic variants ‒174G/C (rs1800795) и ‒572C/G (rs1800796) of the IL6 gene encoding the proinflammatory cytokine IL-6 were determined. For the first time, it was shown that the frequencies of ‒174G and ‒572C alleles, which determine increased inflammatory response and also associated with several diseases were statistically significantly higher in ethnic groups of Buryats, Teleuts, Yakuts, Dolgans and Tuvinians than in Russians living in Siberia. These values were in the intermediate position between those in European and East-Asian groups. We suppose the adaptive role of these IL6 genetic variants in the human settlement from Africa to the Eurasian continent. However, due to the departure from the traditional way of life and increasing anthropogenic environmental pollution, the risk of diseases whose pathogenesis is based on inflammation in indigenous Siberian populations is probably increased.

ISIAH rats with inherited stress-induced arterial hypertension are characterized by increased stress reactivity of the hypothalamic-pituitary-adrenal and sympathoadrenal systems. The aim of this work was to study the genetic basis of increased susceptibility to stress in hypertensive ISIAH rats. Sequencing of the adrenal transcriptomes of hypertensive ISIAH and normotensive WAG rats revealed 9 differentially expressed genes (DEGs) in the X chromosome locus, which was previously associated with an increase in blood pressure and plasma corticosterone concentrations under mild emotional stress, and also with increased adrenal weight in ISIAH rats. An analysis of the functions of the proteins encoded by these DEGs suggested that the Sms gene encoding spermine synthase is the most likely candidate gene in the X chromosome locus associated with an increased level of stress susceptibility in ISIAH rats.

Cases of horizontal transfer of transposable elements (TEs) between species are known for the Drosophilidae family. In the middle of the last century, the case of horizontal transfer of the P-element from the Drosophila willistoni to the D. melanogaster was described. A novel P-element invasion into the D. simulans genome from D. melanogaster occurred approximately 10 years ago. Currently, the P-element has spread across all D. melanogaster population and 30% of D. simulans populations in Europe, Africa and America. In this paper, we investigated the presence of the P-element in D. simulans lines caught in different years in three Asian populations (Tashkent, Nalchik and Sakhalin Island). We also examined the physiological characteristics (cytotype, lifespan, fecundity and locomotor activity) of D. simulans lines with and without the P-element to determine the significance of this new mobile element in the genome. The P-element was found in lines isolated from nature after 2012. The number of P-element copies per genome (two-to-three dozen according to fluorescence in situ hybridization data) was greater than in the American and comparable to the African populations. There were signs of intraspecific hybrid dysgenesis for some pairs of lines. However, in general the presence of the P-element did not adversely affect the physiological characteristics. Either adaptation to the new TE occurs very quickly, or the rate of movement of the P-element is so insignificant that its appearance in the genome remains unnoticed.