Vol 15, No 4 (2017)

Genetic basis of ecosystems evolution
Studying the biochemical function of the pea receptor-like kinases sym10, sym37 and k1, required for the legume-rhizobia symbiosis development
Dolgikh E.A., Kirienko A.N., Kovaleva O.D., Tikhonovich I.A.
Abstract

Background. Rhizobial Nod factors (NFs), the key regulators of legume-rhizobia symbiosis, act in low concentrations and their biological activity depends on structural features, that suggests the presence of specific receptors in plants. Putative receptors, LysM-receptor-like kinases (LysM-RLKs), were found in model legumes L. japonicus and M. truncatula. However, binding capacity with NFs was only studied for L. japonicus LysM-RLKs. In pea a few candidates for NF receptors like Sym10, Sym37 and K1 were found. Analysis of mutants revealed the importance of these proteins for symbiosis development. However, the biochemical function of these receptors has not been studied.

Materials and methods. Sequences encoding extracellular domains (ECDs) of LysM-RLKs Sym10, Sym37, and K1 were cloned in the pRSETa vector. Constructs were introduced in E. coli strain C41 to produce proteins with His6 residues on either the amino or carboxyl terminus. Protein purification was carried out using metal chelate affinity chromatography. The binding capacity with ligand was evaluated using ProteonXPR36 biosensor.

Results. To study binding capacity with NFs, we have developed approaches for the synthesis of LysM-RLK Sym10, Sym37 and K1 in soluble form in heterologous system. The high level of protein synthesis was achieved at +28 °C using 0,5 mM IPTG in 2-16 hours. Analysis of binding capacity of ECDs with NFs revealed the low affinity using the surface plasmon resonance.

Conclusion. The possibility of recombinant receptor synthesis in soluble state in E. coli at high level was demonstrated. Analysis of binding capacity with NFs showed the potential interaction, but with low affinity.

Ecological genetics. 2017;15(4):4-12
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Human ecological genetics
Polymorphism of the genes encoding for the carnitine acyltransferases in native populations of Siberia
Malyarchuk B.A., Derenko M.v.
Abstract

Background. Exome polymorphism is a rich source of information on the structure and function of proteins and metabolic pathways. The traditional diet of native populations of Northeast Asia (Eskimos, Chukchi and Koryaks) is enriched with fatty acids, which presupposes the existence of adaptive rearrangements of the lipid metabolism system among northern aborigines. Carnitine acyltransferases are the most important group of enzymes that metabolize fatty acids.

Materials and methods. To study adaptive changes in the genes encoding for the carnitine acyltransferases, we performed a screening of polymorphisms in the exons of CPT1A, CPT1B, CPT1C, CPT2, CRAT, and CROT genes in various populations of native inhabitants of Siberia.

Results. In exons of five genes (with the exception of CROT), 16 non-synonymous substitutions were identified. Of these, three substitutions were detected at high frequencies in populations of Northeast Asia (in Eskimos, Chukchi and Koryaks): at the loci rs80356779 of the CPT1A gene (replacement of P479L) and rs763273578 of the CPT1C gene (T740A), as well as a new polymorphism at position 131866581 of chromosome 9 at the CRAT gene (S99F). Exome analysis showed that among native populations of Northeast Asia, new non-synonymous substitutions with high pathogenicity indices appeared in the genes of energy metabolism and lipid exchange (genes GK2, ABHD6, NCOA2, OSPL3, LRP10, TTN, and PTTG2).

Conclusion. It is assumed that new variants of non-synonymous polymorphism arose as a result of genetic adaptation of native peoples to the extremely cold climate and a specific “Arctic” diet of aborigines of the Far North.

Ecological genetics. 2017;15(4):13-18
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Gene-environment interactions as the basis of health formation
Kucher A.N.
Abstract

The review discusses issues related to the importance of interaction between genetic and environmental factors for the implementation of the genetic program of individuals and determining the level of health. Data on the importance of some nutrients (vitamins, bio-elements) for formation of health, about a role of genetic factors in maintenance of a homeostasis of biologically active substances, about associations of the genes involved in a metabolism of nutrients with various pathologies, and examples of modification of effects of genetic polymorphic variants on risk of development of common diseases by various factors (bio-elements and other components of a diet, adverse factors of environment, drugs, etc.) are presented.

Ecological genetics. 2017;15(4):19-32
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Genetic toxicology
Cytogenetic effects of excessive radon exposure depending on the individual dosage of active ribosomal genes
Timofeeva A.A., Minina V.I., Druzhinin V.G., Golovina T.A., Tolochko T.A., Larionov A.V.
Abstract

Background. Maintaining radon safety is one of the most critical challenges in modern ecology and genetic toxicology. Radon (222Rn) and its decay daughter products (218Po, 214Po, 214Pb and 214Bi) can interact with biological tissues and induce DNA damage. Because transcribed copies rDNA are necessary for DNA damage repair, we examined whether genomic dosages of active ribosomal genes modulate the genotoxic effects of exposure to high doses of radon.

Materials and methods. Chromosome aberration assay in peripheral blood lymphocytes was performed in pupils of the boarding school of Tashtagol (Kemerovo region, Russia) with long-term resident exposure to radon (n = 345) and in childrenof the Kemerovo Region living in radiation-safe conditions (n = 233). The dose of active (transcription-capable) ribosomal gene (AcRG) in the studied groups has been analyzed using Ag-NORS staining regions of chromosomes and cytogenetic semi-quantitative evaluation method.

Results. A statistically significant increase in the level of chromosome aberrations in exposure group has been revealed compared with the children of the Kemerovo Region living in radiation-safe conditions (p = 0.00001). It was found that the level of chromosomal abnormalities in Tashtagol’s children was higher in medium-dose carriers of AcRG compared to owners of a low dose (4.27 ± 0.22% vs. 3.24 ± 0.29%, p = 0.003). Perhaps the low level of chromosomal aberrations in children with low-dose AcRG is associated with an increase in cell death from damaged DNA under genotoxic exposure to radon.

Conclusion. The obtained results testify to the significant contribution of the individual characteristics of ribosomal genes in the formation of genotoxic effects of exposure to high doses of radon.

Ecological genetics. 2017;15(4):33-40
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5. Genetic education
Modern methods of assessing the taxonomic affiliation of honeybee colonies
Ilyasov R.A., Poskryakov A.V., Nikolenko A.G.
Abstract

At least 30 subspecies of the honeybee Apis mellifera L. were formed allopatrically during the evolution, which spreaded throughout all Africa, Europe and West Asia. The dark forest bee Apis mellifera mellifera is the only and most valuable subspecies for the Northern and Western Europe countries, adapted to productive living in the hard-continental climate of Eurasia. In the past 100 years, natural geographical isolation of subspecies has been disrupted as a result of a human activities. Mass transportations of honeybee colonies beyond the boundaries of their area have been threatened of loss the identity of gene pool of subspecies as a result of hybridization. Preservation of the gene pool of subspecies is possible only when controlling the transportation of honeybee colonies using the methods of identification of taxonomic affiliation of honeybee colonies. Now, dozens of methods have been developed to identify the taxonomic affiliation of honeybee's colony, which are based on the variability of body parts, allozyme loci, mitochondrial DNA loci, microsatellite nuclear loci, sites of single nucleotide polymorphism (SNP). The variability of microsatellite loci and the single nucleotide polymorphism sites have shown the greatest informativeness in identification of the taxonomic affiliation of honeybee's colony.

Ecological genetics. 2017;15(4):41-51
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The role of archaea in the origin of eukaryotes
Shestakov S.V.
Abstract

A key role of particular evolutionary branch of archaea in the emergence of eukaryotic cell is considered on the basis of phylogenomics. Genomes of recently discovered uncultivated proteoarchaea belonging to Lokiarchaea and Asgard-group contain a large sets of eukaryotic-like genes. This allows to suggest that ancient forms of such archaean could participate in symbiotic fusion with bacteria serving as a mitochondrial progenitor. The open questions concerning properties of LECA (so-called last eukaryotic common ancestor) are discussed in the frame of endosymbiotic hypothesis of eukaryogenesis.

Ecological genetics. 2017;15(4):52-59
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4. Systems biology in ecological genetics
Influence of oil pollution on the microbiocenosis of soils adjacent to the oil storage
Zhuravleva A.S., Labutova N.M., Andronov E.E.
Abstract

The aim of the work was an investigation of the effect of hydrocarbons on bacterial and fungal cenoses of sod-podzolic soils on the territory adjacent to the oil storage in the village Malye Kolpany, Leningrad Region. NGS methods were used to analyze the taxonomic composition and structure of the bacteriocenosis and the method of direct microscopy by Demkina-Mirchink to determine the length of the fungal mycelium and the number of spores. Taxonomic and structural changes in the bacterial community led to the dominance of genera containing numerous species-oil destructors. It is established that the main role in the decomposition of oil in the investigated territorybelongs to prokaryotes related to the genera Pseudoxanthomonas, Methylobacterium and Nocardioides. Mycocenosis showed high sensitivity and low adaptability to oil contamination.

Ecological genetics. 2017;15(4):60-68
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