Vol 16, No 2 (2018)

Genetic basis of ecosystems evolution
Proteome dynamics of antibiotic resistant Staphylococcus aureus strains exposed to sub-inhibitory concentrations of beta-lactams
Sopova J.V., Gostev V.V., Kalinogorskaya O.S., Lykholay A.N., Sidorenko S.V.

Background. Ceftaroline is one of the first cephalosporins with activity against methicillin-resistant Staphylococcus aureus (MRSA), it effectively binds to and inhibits penicillin-binding protein 2a (PBP2a). However, isolates with decreased susceptibility to ceftaroline were reported before the commercial release of the antibiotic.

The aim of this study was to provide an overview of the proteome changes occurring in MRSA isolates resistant to ceftaroline in response to sub-inhibitory concentrations of cell-wall active antibiotics.

Materials and methods. Ceftaroline-resistant mutants were generated from two MRSA SA0077 and SA0422 isolates belonging to ST8-t008-SCCmec IV genetic lineage (sequence type 8, spa type t008, staphylococcal chromosomal cassette mec type IV) and one MRSA isolate SA0085 belonging to ST239-t631-SCCmec III genetic lineage (sequence type 239, spa type t631, staphylococcal chromosomal cassette mec type III). Proteome response of parental and mutant strains to sub-inhibitory concentration of beta-lactams and vancomycin was analyzed.

Results. The protein patterns revealed significant increase of 30 кDа band in mutant strains under induction by meropenem, no changes were observed in parental strains or under induction with other antibiotics. According to MS analysis, three proteins represented the band of the mutant strain in absence of meropenem induction. However, under meropenem induction additional protein was detected (BlaZ).

Conclusion. The cross talk between two systems with overlapping functions involved in transcription control of PBP2a and BlaZ ensure ceftaroline resistant phenotype.

Ecological genetics. 2018;16(2):4-10
Molecular genetic identification of arbuscular mycorrhizal fungi
Yurkov A.P., Kryukov A.A., Gorbunova A.O., Kojemyakov A.P., Stepanova G.V., Machs E.M., Rodionov A.V., Shishova M.F.

Arbuscular mycorrhiza (AM) is a widespread symbiosis formed by most land plants with fungi from Glomeromycotina subdivision. The main problem in study of AM fungi is the complication in identification, associated with high intra- and interspecific genetic polymorphism, as well as obligate status of AM fungi in relation to host plant. The methodology for AM fungi identification is constantly undergoing major changes. In the review the selection of optimal methods of molecular genetic identification for AM fungi is carried out. The sample preparation, selection of species-specific marker DNA fragments and primers design, amplification including nested PCR are considered. The prospects for cloning and next generation sequencing for AM fungi identification are analyzed and substantiated.

Ecological genetics. 2018;16(2):11-23
Genetic toxicology
Polymorphisms of 5’-UTR of rad51 gene in prostate cancer
Al-Zoubi M.S., Al-Batayneh K., Al Trad B., Alorjani M., Al Bashir S., Al-Zoubi R., Al-Zoubi R., Al-Khatib S.M., Al Hamad M., Abd Al-Razaq M., Muhaidat R., Matalka I.

Background. Notwithstanding that prostate cancer is largely studied all over the world for many decades, its etiology is not known and there is an intensive work to elucidate the cause and molecular markers for the development of this male cancer. Polymorphisms in DNA repairing genes may affect the DNA repairing capacity that in turn contributes to cancer development. This study aims to explore the polymorphisms of homologous recombination (HR) RAD51 gene (rs1801320 and rs1801321) as a possible risk factor for developing prostate cancer. Sequencing of 5'-UTR of RAD51 gene (rs1801320 and rs1801321) was studied in 80 DNA samples of prostate cancer and 50 DNA samples from a control group. Our results revealed a significant correlation between rs1801320 G>C polymorphism and the presence of prostate cancer in the Jordanian population (p = 0.041, X2 = 6.377). On the other hand, the rs1801321 G>T polymorphism was not associated with the presence of prostate cancer in the study population (p = 0.27, X2 = 2.6). In conclusion, our results shed a light on the possible role of RAD51 gene polymorphisms in the development of prostate cancer; however, a larger representative study is needed to elucidate a possible role of RAD51 gene polymorphisms in development and prognosis of prostate cancer.

Ecological genetics. 2018;16(2):24-29
Human ecological genetics
Long-term gene-environment interactions and genetics of metabolic disorders in aboriginal populations of Northeast Asia
Malyarchuk B.A.

A review of features of polymorphism of lipid and carbohydrate metabolism genes in aboriginal populations of Siberia is presented. The most significant genetic changes in aboriginal populations of Northeast Asia (Eskimos, Chukchi and Koryaks) are described, related to long-term adaptation to extreme conditions of the natural environment and dietary characteristics. Part of the genetic variability of aboriginal populations of this region is represented by polymorphisms associated with metabolic disorders (deficiency of carnitine palmitoyltransferase 1A, pancreatic amylase, sucrase-isomaltase, trehalase) caused by the change of the traditional protein-lipid diet to “European” carbohydrate one. In modern conditions, it is extremely important to perform large-scale genetic testing of aboriginal populations of the Far North.

Ecological genetics. 2018;16(2):30-35
Sensitive periods in development of endometriosis
Baranov V.

The hypothesis of three sensitive periods (SP) in development of common gynecological disease – external endometriosis (EM) is suggested: I – prenatal female genital system development from the stem cells (SC) of Mullerian ducts; II – uterine endometrial cells transition into mesenchymal meSC; III – endometriotic lesions implantation and growth within pelvic lining. Genetic and epigenetic drivers operative at each SP of EM are outlined and their implication for understanding EM origin and development are briefly discussed.

Ecological genetics. 2018;16(2):36-39
6. History, personalities, information
Peterhof collection of rye and its use in genetic studies
Voylokov A.V., Sosnikhina S.P., Tikhenko N.D., Tsvetkova N.V., Mikhailova E.I., Smirnov V.G.

The article provides information about the history and methods of development of “Peterhof” rye genetic collection, founded by V.S. Fedorov, Associate Professor of the Leningrad University. Isolation of self-compatible mutants, their crosses with self-incompatible rye plants, and subsequent self-pollination of hybrids allowed to reveal the allele diversity in heterogeneous and heterozygous rye varieties. In the course of genetic collection assembly the study of inheritance of qualitative and quantitative morphological traits, genetic control of self-compatibility, genetics of meiosis, genetics of interspecific incompatibility was performed. The corresponding genes were identified and, in most cases, mapped using isozymes and molecular markers. Fundamental research was introduced into practical breeding. Under the direction of V. S. Fedorov, and V. G. Smirnov the first in Russia tetraploid rye variety Leningradskaja Tetra was produced. Currently, based on the study of the genetics of self-fertility, the initial material is being obtained and used for improving rye population varieties. The possibility of using the genetic collection of rye to solve the fundamental problems of plant genetics is discussed.

Ecological genetics. 2018;16(2):40-49
Methodology in ecological genetics
Cloning of PpKAR2 and PpPDI1 genes promoters from yeast Pichia pastoris, an evaluation of their activity and efficacy for the heterologous genes expression
Tsygankov M.A., Padkina M.V.

Background. Yeast Pichia pastoris is successfully used in biotechnology, with their help synthesized various compounds. Promoters are a key factor in the productivity of an expression system, since they determine the expression level of a heterologous gene.

The aim of our work was to study the promoter regions of the PpKAR2 and PpPDI1 genes and to evaluate their use for effective expression of heterologous genes.

Materials and Methods. To evaluate the activity of promoters, we used a reporter system based on the structural gene of acid phosphatase of yeast Saccharomyces cerevisiae – PHO5. To determine the effect of overproduction of native and heterologous protein on the activity of the promoters under study, we used the producer strains of P. pastoris protein disulfide isomerase and maize delta-zein. To evaluate the effectiveness of the use of the promoters under study for the expression of heterologous genes, we have expressed under their control a gene encoding human interferon-alpha16.

Results. The promoters of the yeast genes – PpKAR2 and PpPDI1 were cloned. Their activity was compared with the promoter of the PpAOX1 gene in the native strains, as well as in strains with overproduction of native and heterologous proteins. Under the control of these promoters, the gene encoding human interferon-alpha 16 is expressed.

Conclusion. The promoters studied were weaker than the promoter of the AOX1 gene, but increase their activity in response to the production of heterologous proteins and can be used to express hete­rologous genes.

Ecological genetics. 2018;16(2):50-59

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