Vol 17, No 3 (2019)

Genetic basis of ecosystems evolution

Analysis of epitope distribution of arabinogalactan protein-extensins in pea (Pisum Sativum) nodules of wild-type and mutants impaired in infection thread growth

Tsyganova A.V., Brewin N., Tsyganov V.E.

Abstract

Background. During the colonization of root and nodule tissues of legumes by rhizobia, bacterial cells are immersed in a plant extracellular matrix which includes arabinogalactan protein-extensins (AGPE).

Materials and methods. Immunogold electron microscopy with monoclonal antibodies MAC204 and MAC236 was used to analyse the distribution and abundance of epitopes of AGPE in wild-type and symbiotically defective pea mutants.

Results. In the nodules of the wild-type line SGE, both AGPE epitopes were detected to the same extent in the matrix of infection threads and infection droplets. In the nodules of the mutant line SGEFix−-1 (sym40), the level of labelling by MAC204 was significantly higher than with SGE in both infection threads and infection droplets, but the level of labelling by MAC236 was only increased in the infection droplets. In the mutant line SGEFix−-2 (sym33-3), a relatively high level of both epitopes was observed among all analysed genotypes. The double mutant line RBT3 (sym33-3, sym40) showed an intermediate level of labelling for both epitopes in infection threads compared with the parental mutants. In SGEFix−-1, an abnormal distribution of both epitopes was observed in the intercellular space matrix. The MAC204 epitope was found in the cell walls of SGEFix−-1 and in the infection thread walls of SGEFix−-2, whereas in RBT3 this epitope was detected in both types of walls.

Conclusions. The sym33-3 and sym40 mutations have different effects on the accumulation of AGPE epitopes recognised by MAC204 and MAC236. This indicates that both the Sym33 and the Sym40 genes affect the composition of AGPE in the matrix of infection threads and infection droplets.

Ecological genetics. 2019;17(3):5-12
pages 5-12 views

Diversity of the gene of benzoate dioxygenase in bacterial associations isolated from long term organochlorine-contaminated soils

Nazarova E.A., Kiryanova T.D., Egorova D.O.

Abstract

Background. Communities of bacteria with specific enzymes are formed in the soil with long-term organochlorine contamination.

The aim of this study was to analyze the diversity of the benA gene encoding the α-subunit of the benzoate 1,2-dioxygenase in aerobic bacterial associations isolated from the soils of the Chapayevsk-city (Samara region, Russia).

Materials and methods. The soil samples were taken on the territory, contaminated with organochlorine compounds for a long time. As a selection factor in the enrichment cultures were used 4-chlorobenzoic acid and chlorobenzene, in the pure cultures – benzoic acid. The isolation of total DNA from bacterial associations was performed using a commercial FastDNA Spin Kit for Soil kit (USA). Amplification was performed on a MyCycler instrument (USA). Determination of the nucleotide sequence was performed on an automatic sequencer Genetic Analyzer 3500XL (USA). The search and analysis for benA gene homologs was carried out using international GenBank databases and BLAST system (http://www.ncbi.nlm.nih.gov).

Results. As a result of selection, 12 associations of aerobic bacteria were obtained. Fragments of the benA gene (α-subunit of benzoate dioxygenase) were obtained with the total DNA of six bacterial associations selected on chlorobenzene and with the total DNA of three bacterial associations selected on 4-chlorobenzoate. Pure cultures of aerobic bacterial strains using benzoic acid as a carbon source were isolated from benA-positive associations. It was established that the amplified fragments with the DNA of the A1, A4, A5, B1, B2, B3, B4 and B6 association strains form a single phylogenetic cluster with the α-subunit gene of the benzoate dioxygenase of the Pseudomonas putida strain KT2440 (level of similarity is 96–98%). The amplified fragment with the DNA of strain B5-170 (association B5) forms a cluster with the gene of the α-subunit of the benzoate dioxygenase of the strain Pseudomonas sp. VLB120 (93% similarity).

Ecological genetics. 2019;17(3):13-22
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Sinorhizobium meliloti: chromosomal types and genomic islands

Cherkasova M.E., Muntyan V.S., Saksaganskaia A.S., Simarov B.V., Roumiantseva M.L.

Abstract

Background. Polymorphism analysis was done for the core genome sequences of nodule bacteria of S. meliloti species in order to identify chromosomal types and to evaluate the occurrence of accessory elements (genomic islands) in them.

Materials and methods. Chromosomal studied loci were: betBC (marker M-I) and SMc04407-SMc04881 (marker M-II) both are related to metabolic processes and stress tolerance, and 16S-23S intergenic sequences (marker M-III) to search phylogenetical distance at intraspecies level.

Results. Significant differences between the occurrence of alleles of gene-markers M-I/M-II and MIII were determined between strains related to tested the 5 typical groups and 9 subgroups of strains differing by geographical region/source (nodule, soil) of isolation, as well as by salt tolerance. Four chromosomal types were identified among tested S. meliloti native isolates and a preference occurence of one of the three islands Rm1021 in links with particular chromosomal type was shown. The significant prevalence of strains with particular chromosomal type was shown for S. meliloti populations native to centers of alfalfa diversity at the NE of Caucasus, as well as at NE of Kazakhstan (Aral sea related region), as well as in agrocenoses. Conclusion. It was predicted that strains inherited altered markers M-I/M-II may belong to divergent clonal lines occured in both centers of alfalfa diversity, while strains with altered sequences of all three markers could be a representatives of a new S. meliloti biovar(s), the formation of which is occurred much more intensively at the modern center of the introgressive hybridization of alfalfa at NE of Kazakhstan.

Ecological genetics. 2019;17(3):23-38
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Identification of sequences encoding for ncr-peptides and defensins in the ‘meta-assembly’ of transcriptome of pea (pisum sativum l.) Nitrogen-fixing nodules

Zorin E.A., Kliukova M.S., Kulaeva O.A., Afonin A.M., Tikhonovich I.A., Zhukov V.A.

Abstract

Background. The active and careless applying of antibiotics in medicine and agriculture leads to the emergence of resistance to the existing antimicrobial drugs, which reduces the effectiveness of their use. One of the ways to solve this problem is the development of new antibiotics based on plant peptides with antimicrobial activity, for example plant defensins (which identified in all plants) and NCR peptides that are specifically synthesized in nodules of some leguminous plants.

Materials and methods. In the present study, a meta-assembly of a transcriptome was constructed based on publicly available RNA-sequencing transcriptomes of pea nodules (Pisum sativum L.). This meta-assembly was used to search for sequences encoding antimicrobial peptides.

Results. As a result, 55 and 908 unique sequences encoding defensins and NCR peptides, respectively, were identified. The recognition site for the signal peptidase was predicted and sequences were divided into the signal and mature part of the peptide. Among mature defensins, 22 peptides possess in silico predicted antimicrobial activity, and for the NCR peptides family their number was 422.

Conclusion. Sequences encoding defensins and NCR peptides expressed in nitrogen-fixing pea nodules were identified. They are candidates for testing their antimicrobial activity in vitro.

Ecological genetics. 2019;17(3):39-46
pages 39-46 views

Transcription factor genes involved in plant response to abiotic stress factors

Zaikina E.A., Rumyantsev S.D., Sarvarova E.R., Kuluev B.R.

Abstract

Hypothermia, drought, salinity and heavy metals are the most widespread stress factors negatively affecting plant growth and development. Plants respond to these stress factors on molecular, cellular, and physiological levels through the complicated mechanisms of signal perception and transduction, subsequently inducing various defense mechanisms. Transcription factors controlling the expression of numerous defense proteins are the most significant abiotic stress reaction regulators. Mainly, the negative environmental influence activates the AP2/ERF, WRKY, MYB, NAC, bZIP transcription factors. The numerous transcription factors genes can be used in genetic engineering of agricultural crops resistant to abiotic stress. These genes are also of great interest in marker assisted selection of cultivated plants. This review is dedicated to description of transcription factors and their genes, involved in plant response to hypothermia, drought, salinity and heavy metals.

Ecological genetics. 2019;17(3):47-58
pages 47-58 views

Saccharomyces cerevisiae killer toxins: synthesis, mechanisms of action and practical use

Sambuk E.V., Muzaev D.M., Rumyantsev A.M., Padkina M.V.

Abstract

Yeast Saccharomyces cerevisiae is a unique model for studying the molecular mechanisms of exotoxin-mediated antagonistic relationships between coexisting microorganisms. The synthesis of yeast toxins can be considered as an example of allelopathy and environmental competition. The elucidation of the role of allelopathy in the formation of microbial communities is of great interest for modern ecology. Yeast toxins are widely used in medicine, the food industry and biotechnology. The review examines the nature of exotoxins, the mechanisms of inheritance and interaction of the virus and yeast cells, as well as the prospects for their practical application.

Ecological genetics. 2019;17(3):59-73
pages 59-73 views

Darkening of the color as а marker sign of reduced reproductive ability of female sable (martes zibellina) and mink (neovison vison)

Beketov S.V., Chernova I.E., Rozhkov Y.I., Toporova L.V., Karpov K.S.

Abstract

Based on the materials of 23 fur-bearing animal farms of the Russia for different periods of years, a comparative assessment of the reproductive capacity of sable and mink females of standard breeds (wild type) has been carried out. It was established that during intrabreeding differentiation according to the overall color of the hair coat (almost black, black-brown, dark brown and chestnut), the lowest reproduction level is characterized by darker females of sable, which are a significant increase in the number of them, mated with male, but not given offspring (barren females). According to the results of interbreed comparisons of sables and minks, parallelism was found in the variability of the reproductive capacity of females, which is manifested in the fact that, in contrast to relatively light animals, animals that are dark in color are characterized by a greater number of barren females and low fecundity.

Ecological genetics. 2019;17(3):75-86
pages 75-86 views

Genetic toxicology

Bisphenol a and human diseases. Mechanisms of action

Dergacheva N.I., Patkin E.L., Suchkova I.O., Sofronov H.A.

Abstract

The review describes the molecular mechanisms and biological effects of bisphenol A exposure, which is a chemical (ecotoxicant) that destroys the endocrine system and has epigenetic toxicity.

Ecological genetics. 2019;17(3):87-98
pages 87-98 views

Human ecological genetics

Sensitive to the effects of environmental factors miR-638 and common diseases

Kucher A.N.

Abstract

The review provides information on environmental factors affecting the level of miR-638 in humans, potential target genes of this micro-RNA (according to “TargetScanHuman”), diseases and metabolic pathways which potentially regulated miR-638, as well as clinical and experimental data confirming the involvement of miR-638 in the developing a wide range of multifactorial diseases. The data presented in the review expand the understanding of the pathogenesis of various diseases of a multifactorial nature and determine new strategies for studying gene-environment interactions that are important for the formation of health.

Ecological genetics. 2019;17(3):99-110
pages 99-110 views

Study of acetylated histone h3k9 – an active chromatin mark – in chromosomes from adult and fetal human lymphocytes

Efimova O.A., Pendina A.A., Lezhnina Y.G., Tikhonov A.V., Chiryaeva O.G., Petrova L.I., Dudkina V.S., Koltsova A.S., Krapivin M.I., Petrovskaia-Kaminskaia A.V., Talantova O.E., Kuznetzova T.V., Baranov V.S.

Abstract

Background: Incorrect epigenetic modifications of the human genome may result in epigenetic disorders, thus, highlighting the necessity of studying chromosome epigenetic patterns in human development.

Aim of the study: A comparative analysis of acetylated histone H3K9 (AcH3K9) patterns in human metaphase chromosomes from the lymphocytes of adults and fetuses.

            Materials and methods: The immunocytochemical detection of AcH3K9 in the metaphase chromosomes from PHA-stimulated peripheral lymphocytes of 13 adults and cord blood lymphocytes of 10 fetuses at 20-22 weeks of gestation.

Results: Both in the chromosomes of the adults and the fetuses, AcH3K9 accumulated in the R- and T-, but not G-bands and avoided the regions of pericentromeric heterochromatin of the chromosomes 1, 9 and 16. When comparing the adult and the fetal chromosomes, different levels of AcH3K9 were revealed in a few bands: 2q31, 5p13, 5p15 and 16p13 had higher level of Н3К9 acetylation in adults, in contrast to 9q13 which was hyperacetylated in fetuses.

Conclusion: The АсН3К9 distribution in metaphase chromosomes is band-specific and is similar between the adults and the fetuses, excluding a few bands with different acetylation levels.

Ecological genetics. 2019;17(3):111-117
pages 111-117 views


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