Vavilovskii Zhurnal Genetiki i Selektsii最新文献

DNA oxidation is one of the main types of damage to the genetic material of living organisms. Of the many dozens of oxidative lesions, the most abundant is 8-oxoguanine (8-oxoG), a premutagenic base that leads to G→T transversions during replication. Double-stranded DNA can conduct holes through the π system of stacked nucleobases. Such electron vacancies are ultimately localized at the 5'-terminal nucleotides of polyguanine runs (G-runs), making these positions characteristic sites of 8-oxoG formation. While such properties of G-runs have been studied in vitro at the level of chemical reactivity, the extent to which they can influence mutagenesis spectra in vivo remains unclear. Here, we have analyzed the nucleotide context of G-runs in a representative set of 62 high-quality prokaryotic genomes and in the human telomere-to-telomere genome. G-runs were, on average, shorter than polyadenine runs (A- runs), and the probability of a G-run being elongated by one nucleotide is lower than in the case of A-runs. The representation of T in the position 5'-flanking G-runs is increased, especially in organisms with aerobic metabolism, which is consistent with the model of preferential G→T substitutions at the 5'-position with 8-oxoG as a precursor. Conversely, the frequency of G and C is increased and the frequency of T is decreased in the position 5'-flanking A- runs. A biphasic pattern of G-run expansion is observed in the human genome: the probability of sequences longer than 8-9 nucleotides being elongated by one nucleotide increases significantly. An increased representation of C in the 5'-flanking position to long G-runs was found, together with an elevated frequency of 5'-G→A substitutions in telomere repeats. This may indicate the existence of mutagenic processes whose mechanism has not yet been characterized but may be associated with DNA polymerase errors during replication of the products of further oxidation of 8-oxoG.

In the last few decades, yeasts have been successfully engineered to be an excellent microbial cell factory for producing recombinant proteins with desired properties. This was due to their cost-effective characteristics and the successful application of genomic modification technologies. In addition, yeasts have a conserved post-translational modification pathway among eukaryotic organisms, which ensures the correct folding of recombinant proteins. However, the folding machinery cannot always cope with the load caused by the overexpression of recombinant genes, leading to the accumulation of misfolded proteins, the formation of aggregates and low production. Therefore, the protein-folding capacity of the endoplasmic reticulum (ER) remains one of the main limitations for heterologous protein production in yeast host organisms. However, thanks to many years of effective research of the fundamental mechanisms of protein folding, these limitations have been largely overcome. The study of folding in both model organisms and bioproducers has allowed to identify the molecular factors and cellular mechanisms that determine how a nascent polypeptide chain acquires its three-dimensional functional structure. This knowledge has become the basis for developing new effective techniques for engineering highly productive yeast strains. In this review, we examined the main cellular mechanisms associated with protein folding, such as ER transition, chaperone binding, oxidative folding, glycosylation, protein quality control. We discuss the effectiveness of applying this knowledge to the development of various engineering techniques aimed at overcoming bottlenecks in the protein folding system. In particular, selection of optimal signal peptides, co-expression with chaperones and foldases, modification of protein quality control, inhibition of proteolysis, and other techniques have allowed to enhance the ability of yeast bioproducers to effectively secrete heterologous proteins.

Endophytic bacteria play a key role in agricultural ecosystems, as they can affect the availability of various compounds, crop yield and growth, and provide resistance to diseases and pests. Therefore, the study of endophytes of agriculturally important crop plants is a promising task in the field of biological plant protection. Understanding the mechanisms of interaction between endophytic bacteria and plants will allow the use of these microorganisms as bioagents in the future and thus reduce dependence on chemical pesticides. In this paper, samples obtained from the leaves and/or roots of wheat, rapeseed and soybean are considered. Whole-genome sequencing of the isolates was performed. Using an analytical pipeline, the genomes of 15 strains of endophyte bacteria of cultivated plants were assembled and characterized. Their insecticidal and fungicidal potential was analyzed. Gene repertoire analysis performed with GenAPI showed a high degree of correspondence between the gene repertoires of strain BZR 585 against Alcaligenes phenolicus, BZR 762 and BZR 278 against Alcaligenes sp., BZR 588 and BZR 201P against Paenochrobactrum pullorum. All strains, with the exception of BZR 162, BZR 588 and BZR 201P, were found to contain genes encoding proteins with fungicidal activity, such as iturins, fengycins and surfactins. All strains also contained genes encoding proteins with insecticidal activity, namely GroEL, Spp1Aa1, Spp1Aa2, Vpb1Ab1, Vpb4Ca1, HldE, mycosubtilin, fengycin and bacillomycin. The obtained genomic data are confirmed by the results of previous experimental studies: high insecticidal activity of a number of strains (BZR 1159, BZR 936, BZR 920, etc.) against Galleria mellonella, Tenebrio molitor and Cydia pomonella, as well as fungicidal properties against Fusarium, Alternaria, Trichothecium, was demonstrated. This shows the practical significance of the identified genetic determinants for the creation of new biocontrol agents.

This review focuses on cellulases, a subclass of hydrolases that catalyse the breakdown of the polysaccharide cellulose. Cellulases are of immense practical significance, given that cellulose-containing materials are utilised across a multitude of industrial sectors. An overview of the fundamental properties and structure of cellulases is provided. However, primary attention is paid to the industrial application of these enzymes, with other aspects discussed within this context. The most practically significant bacterial and fungal cellulases are analysed, with their key benefits and differences being emphasised. Particular attention is paid to extremophilic (specifically thermo-, psychro-, and halophilic) cellulases, as they possess properties essential for modern technological processes. Given that practical application necessitates mass production and an optimal combination of enzymatic characteristics, the creation of effective producers and the modification of cellulase properties are also assessed. Finally, key trends in cellulase production approaches and their future application potential are summarised.

Rhesus macaques (Macaca mulatta) are the most common non-human primates living in captivity. The use of rhesus macaques as model objects is determined, first of all, by their phylogenetic and physiological closeness to humans, and, as a consequence, the possibility of extrapolating the obtained results to humans. Currently, it is known that a number of biochemical changes occur under various physiological conditions, including at the transcriptomic level. The real-time polymerase chain reaction is a widely used universal method for gene expression analysis. Carrying out such studies always requires a preliminary selection of "housekeeping genes" (HKGs) - genes necessary for the implementation of basic functions in the cell and stably expressed in different cell types and under different conditions. At present, there are only two systematic studies on the search for HKGs in the rhesus macaque brain, and therefore in this work a search and systematization of HKGs for this species were carried out. As a result, two panels of promising HKGs for M. mulatta were formed: an extended panel, consisting of 56 genes, and a small panel, consisting of 8 genes: ARHGDIA, CYB5R1, NDUFA7, RRAGA, TTC1, UBA6, VPS72, and YWHAH. Both panels of potential HKGs do not have pseudogenes in macaques or humans, are characterized by stable and sufficient expression in the brain of rhesus macaques and can be used to analyze expression not only in the brain but also in peripheral blood. However, it should be noted that the data have not been experimentally verified and require verification in laboratory conditions.

The ABH2 enzyme belongs to the AlkB-like family of Fe(II)/α-ketoglutarate-dependent dioxygenases. Various non-heme dioxygenases act on a wide range of substrates and have a complex catalytic mechanism involving α-ketoglutarate and an Fe(II) ion as a cofactor. Representatives of the AlkB family catalyze the direct oxidation of alkyl substituents in the nitrogenous bases of DNA and RNA, providing protection against the mutagenic effects of endogenous and exogenous alkylating agents, and also participate in the regulation of the methylation level of some RNAs. DNA dioxygenase ABH2, localized predominantly in the cell nucleus, is specific for double-stranded DNA substrates and, unlike most other human AlkB-like enzymes, has a fairly broad spectrum of substrate specificity, oxidizing alkyl groups of such modified nitrogenous bases as, for example, N 1-methyladenosine, N 3-methylcytidine, 1,N 6-ethenoadenosine and 3,N 4-ethenocytidine. To analyze the mechanism underlying the enzyme's substrate specificity and to clarify the functional role of key active-site amino acid residues, we performed molecular dynamics simulations of complexes of the wild-type ABH2 enzyme and its mutant forms containing amino acid substitutions V99A, F124A and S125A with two types of DNA substrates carrying methylated bases N 1-methyladenine and N 3-methylcytosine, respectively. It was found that the V99A substitution leads to an increase in the mobility of protein loops L1 and L2 involved in binding the DNA substrate and changes the distribution of π-π contacts between the side chain of residue F102 and nitrogenous bases located near the damaged nucleotide. The F124A substitution leads to the loss of π-π stacking with the damaged base, which in turn destabilizes the architecture of the active site, disrupts the interaction with the iron ion and prevents optimal catalytic positioning of α-ketoglutarate in the active site. The S125A substitution leads to the loss of direct interaction of the L2 loop with the 5'-phosphate group of the damaged nucleotide, weakening the binding of the enzyme to the DNA substrate. Thus, the obtained data revealed the functional role of three amino acid residues of the active site and contributed to the understanding of the structural-functional relationships in the recognition of a damaged nucleotide and the formation of a catalytic complex by the human ABH2 enzyme.

Wild emmer Triticum dicoccoides samples have a high content of protein and microelements in their grain, but when crossed with common wheat varieties, undesirable properties of a wild relative (low yield, spike fragility and difficult threshing) can be transmitted to the hybrid along with valuable traits. The possibility of improving economically useful traits of modern common wheat varieties using a wheat line with wild emmer genetic material (l29), combining high cytological stability with improved nutritional value and productivity, was studied. The F4- F5 hybrids obtained as a result of crossing in the forward and reverse directions of four common spring wheat varieties with l29 were studied. A C-banding technique and genotyping with SSR markers were used to determine the introgression fragments of T. dicoccoides genetic material. Cytological stability was assessed based on the study of chromosome behavior in microsporogenesis. The grain content of macro- (K, P, Ca and Mg) and microelements (Zn, Fe, Cu and Mn) was established by atomic emission spectrometry with inductively coupled plasma; the grain quality indices were measured on an Infra LUM FT-12 analyzer. The C-banding and microsatellite analysis data indicate a high frequency of alien genetic material introgression in the genome of hybrid forms. All variants of the l29 introgression of wild emmer material (1BL, 2BS, 3B, 5B and 6AL) were identified among the progeny of eight crossing combinations. The recombinant chromosome 3B was found in all hybrid combinations. The hybrids were characterized by a high level of cytological stability (the meiotic index was 90.0-98.0 %). The effectiveness of using a wheat line with T. dicoccoides genetic material to enhance modern varieties in terms of the content of protein, gluten and mineral composition of grain without reducing productivity was shown. Secondary introgression hybrids, exceeding the initial varieties by a set of grain quality characteristics and not inferior to them in terms of basic productivity indicators, were obtained.

Fungicide resistance is a global problem that reduces the effectiveness and duration of action of these compounds due to changes in the racial composition and virulence of phytopathogen populations. Currently, resistance to 100 active substances has been registered in more than 230 fungal plant pathogens. Leaf rust of barley (Puccinia hordei Otth.) is one of the most widespread and harmful pathogens in the barley pathocomplex; it is recorded in southern Russia every year. There are very few studies on the effect of fungicides on the characteristics of rust fungi populations, and none have been carried out on P. hordei in Russia. This research aimed to analyze the effect of fungicides belonging to the chemical classes of triazoles and strobilurins on intrapopulation changes in P. hordei in terms of pathogenicity (virulence and aggressiveness) under the conditions of the North Caucasus region of Russia. Two-component fungicides approved for use in the Russian Federation were selected for the study: Delaro, SC; Amistar Extra, SC; Amistar Gold, SC. Plants were treated using several application rates: 50, 100, 150 and 200 % (the recommended application rate was determined to be 100 %). Treatment of winter barley plants with fungicides with different application rates revealed intrapopulation changes in the virulence structure of P. hordei. In all treatment variants, the frequency of isolates virulent to the Rph4, Rph5, Rph6+2, Rph12 genes decreased with increasing fungicide application rate and the frequency of isolates virulent to Rph14 increased. No isolates virulent to Rph7 were found in either the original population or the experimental variants. The average virulence of the fungal populations treated with the fungicides in all experimental variants was lower compared to the original population (no treatment (48.5 %)) and depending on the application rate varied from 33.8 % (Amistar Gold, 50 %) to 28.5 % (Amistar Gold, 200 %). Under the influence of the increased application rates of the fungicides, an increase in the duration of the latent period was observed: from 168 h (original population) to 216 h (Delaro, Amistar Gold, 200 %). A decrease in sporulation ability (spore mass per pustule ranged from 0.013 mg (original population) to 0.002 mg (Delaro, Amistar Gold, 200 %)) and in the viability of P. hordei (from 100 % for the original population to 22.5 % in Amistar Gold, 200 % treatment) was found under the action of the fungicides. Thus, a fungicide-treated P. hordei population is characterized by intrapopulation changes in aggressiveness and virulence, which can significantly increase barley yield losses due to a decrease in the effectiveness of chemical protection, as well as an increase in the harmfulness of the pathogen.

Accumulated evidence links dysregulated cytokine signaling to the pathogenesis of autism spectrum disorder (ASD), implicating genes, proteins, and their intermolecular networks. This paper systematizes these findings using bioinformatics analysis and machine learning methods. The primary tool employed in the study was the ANDSystem cognitive platform, developed at the Institute of Cytology and Genetics, which utilizes artificial intelligence techniques for automated knowledge extraction from biomedical databases and scientific publications. Using ANDSystem, we reconstructed a gene network of cytokine-mediated regulation of autism spectrum disorder (ASD)-associated genes and proteins. The analysis identified 110 cytokines that regulate the activity, degradation, and transport of 58 proteins involved in ASD pathogenesis, as well as the expression of 91 ASD-associated genes. Gene Ontology (GO) enrichment analysis revealed statistically significant associations of these genes with biological processes related to the development and function of the central nervous system. Furthermore, topological network analysis and functional significance assessment based on association with ASD-related GO biological processes allowed us to identify 21 cytokines exerting the strongest influence on the regulatory network. Among these, eight cytokines (IL-4, TGF-β1, BMP4, VEGFA, BMP2, IL-10, IFN-γ, TNF-α) had the highest priority, ranking at the top across all employed metrics. Notably, eight of the 21 prioritized cytokines (TNF-α, IL-6, IL-4, VEGFA, IL-2, IL-1β, IFN-γ, IL-17) are known targets of drugs currently used as immunosuppressants and antitumor agents. The pivotal role of these cytokines in ASD pathogenesis provides a rationale for potentially repurposing such inhibitory drugs for the treatment of autism spectrum disorders.