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V V Sukhodolets

Publications and source records attributed to V V Sukhodolets.

At least 19 recordsLinked to original sources
PubMed2006

[Speciation in bacteria: comparison of the 16S rRNA gene for closely related Enterococcus species].

Sequencing of the 16S rRNA genes from enterococcal strains used as starters suggested the existence of specialized taxa of lactic acid enterococci within the species Enterococcus durans and E. faecium and a new species, E. lactis. Comparisons showed that the 16S rRNA genes of closely related species have the same sets of variable positions with different combinations of nucleotides. The presence of identical combinations of nucleotide substitutions in different species was assumed to result from a transfer of genetic information via gene conversion between different rRNA operons. Such events were presumably associated with speciation in bacteria.

Enterococcus↗
PubMed2006

[Recombinations occurring in the process of DNA replication in Escherichia coli].

In a number of works dealing with the relationship between replication and recombination in bacteria, it is assumed that recombinations permit the replication forks to resume moving after having stopped at the damage sites of the template DNA. As an evidence for recombination occurring during DNA replication, the involvement in this process of proteins RuvABC and RecG, providing processing of the Holliday junctions after recombination, is considered. However, it has been shown that these proteins are not essential for resuming DNA synthesis after an exposure of bacteria to UV light. These data cast doubt on the necessity of recombination for reactivation of replication initiated in the oriC region. Studying recombination in tandem duplications in Escherichia coli showed that during replication, unequal crossing over occurs between direct DNA repeats of sister chromosomes. In wild strains, this crossing over results in tandem duplications, thereby enhancing the expression of certain genes. Thus, recombination of two types occurs during DNA replication: unequal crossing over leading to duplications and homologous exchange, responsible for post-replication DNA repair. The unequal exchange constitutes a component of SOS response of the cell to deterioration of the environment.

Chromosomes, Bacterial↗
PubMed2006

[Unequal crossing-over in Escherichia coli].

Unequal crossing-over between sister chromosomes in the process of DNA replication in Escherichia coli leads to the formation of tandem duplications, thus enhancing the activity of certain genes. In conjugational matings between genetically marked E. coli strains, unequal crossing-over leads to the formation of heterozygous tandem duplications. Studying these duplications as model systems allowed the conclusion that unequal crossing-over between direct DNA repeats of sister chromosomes is the main pathway of the formation of selected recombinants in E. coli strains carrying duplications. This was inferred from the data on the segregation of homozygous diploid recombinants by heterozygous duplications. Unequal crossing-over between sister chromosomes occurs as adaptive exchange providing the survival of the greater part of bacterial cells on a selective medium. The known phenomenon of adaptive mutagenesis may also be a consequence of unequal exchanges at the level of DNA mononucleotide repeats.

Adaptation, Biological↗
PubMed2005

[Unequal genetic exchange in Escherichia coli tandem duplications may represent a special pathway of homologous recombination].

Heterozygous tandem duplications that appear in Escherichia coli conjugation matings segregate different types of haploid and diploid recombinants because of unequal crossing over between sister chromosomes. As shown previously, the frequency of segregants in the extended duplication D104 (approximately 150 kb or more than 3 min of the genetic map) heterozygous for E. coli deo-operon genes (deoA deoB::Tn5/deoC deoD) is not decreased in strains with defective RecBCD and RecF recombination pathways. Analysis of a shorter duplication of this type (approximately 46 kb) showed that the frequency of segregants in the strain recBC sbcBC recF was similar to that in a strain with undamaged system of recombination. Thus, genetic exchange between direct DNA repeats in tandem duplications may follow a special pathway of homologous recombination, which is independent of the recBC and recF genes.

Crossing Over, Genetic↗
PubMed2005

[Unequal crossing over is the principal pathway of homologous recombination in tandem duplications of Escherichia coli].

Homologous recombination between direct DNA repeats in tandem duplications usually leads to their dissociation. An even number of crossovers between two copies of a duplication should lead to the formation of diploid segregants, i.e., to the preservation of the duplication. However, in studies of the genotype of diploid segregants in heterozygous tandem duplications of Escherichia coli, it was shown that they arise by unequal exchanges between sister chromosomes rather than by intrachromosomal exchanges. Generally, these exchanges lead to the establishment of the homozygous state of (heterozygous) duplications. Since the available data suggest that the exchange between sister chromosomes may be coupled with DNA replication, it is supposed that unequal exchanges between direct DNA repeats occur in the process of DNA replication.

Chromosomes, Bacterial↗
PubMed2005

[The uncertainty of "fitness:" what prevents understanding of the role of genetic exchange].

The evolutionary development of highly organized species is attained through an increase in average survival of individuals, whereas the evolution of primitive species involves only an increase in fecundity (Zavadsky, 1958, 1961). However, in population genetics, survival (or ecological resistance) and fecundity are regarded as components of a single character, fitness. Employment of the notion of fitness, which lacks a strict definition, hinders understanding of the mechanism of progressive evolution as the process that enhances ecological resistance of organisms. The notion of fitness also exacerbates understanding the role of genetic exchange, since the primary advantage of genetic recombination and sexual reproduction apparently is producing of progeny with high ecological resistance rather than with high genetic diversity as such. Thus, the regular genetic exchange ensures restoration of the level of ecological resistance characteristic for the species, and on the macroevolutionary scale leads to the formation of new genomes and new species with high ecological resistance.

Adaptation, Physiological↗
PubMed2004

[Unequal crossing over as the pathway of adaptive homologous recombination between the direct DNA repeats in tandem duplications of Escherichia coli].

Homologous recombination between direct DNA repeats within the extended tandem duplications in E. coli results from unequal sister-chromosome exchanges. This conclusion follows from the observations on the segregation of completely or partly homozygous diploid segregants by heterozygous duplications. The formation of diploid segregants with preserved heterozygosity for the unselected markers could also result from "symmetrical" intrachromosomal recombination. Analysis of the segregant genotypes, however, confirmed their formation via unequal crossing over. The data obtained indicated that in tandem duplications segregation of diploid recombinants of different types was preceded by the formation of triplications as the products of unequal sister-chromosome exchanges. In heterozygous duplications, unequal crossing over is manifested as a highly frequent adaptive exchange, providing the survival of the most part of the duplication-carrying cells on selective medium. It is suggested that adaptive mutagenesis can be the consequence of unequal sister crossing over.

Crossing Over, Genetic↗
PubMed2002

[Study of RecA-independent homologous recombination and a chromosomal rearrangement in the Escherichia coli strain carrying an extended tandem duplication].

A heterozygous tandem duplication in the Escherichia coli deo operon region deoA deoB::Tn5/deoC deoD thr::Tn9 with the total length approximately 150 kb, which was obtained in the conjugational mating in the HfrH strain, was examined. By means of digestion with the NotI enzyme, pulsed-field gel electrophoresis, and the conjugational transfer of the duplication in the F- strain, the chromosomal rearrangement, which occurred in the duplication region upon its stabilization in the bacterial genome, was studied. In a more stable strain, two new NotI sites were shown to appear in the chromosomal region located close to the duplication, which might have resulted from the transposition of the IS50 sequence from Tn5. The data were also obtained indicating the possibility of secondary transposition of the chromosomal segment between the two new NotI sites (approximately 30 kb) in the region located near the duplication. With the use of rec+ and recA strains, two types of haploid and diploid segregants generated by the duplication were studied: DeoD+ (the DeoD+ allele is not expressed in the original duplication due to the polar effect of the deoB::Tn5 insertion) and DeoC DeoD. The segregation of DeoD+ clones was shown to be RecA-dependent, whereas the DeoC DeoD segregants selected on the medium that contained thymine at a low concentration (i.e., under conditions of thymine starvation) appeared at a rather high frequency. However, the relative frequency of haploid clones, which have lost the duplication, strongly decreased in the recA genome among segregants of both types.

Chromosomes, Bacterial↗
PubMed2002

[Effect of mutations for the ruvABC genes on recombination between direct DNA repairs in Escherichia coli strains carrying extended tandem duplication].

The formation of haploid and diploid segregants was studied in Escherichia coli strains carrying heterozygous tandem duplications deoA deoB::Tn5/deoC deoD in the deoCABD operon region, in the genome of mutants for ruvABC genes. Homologous recombination in duplications of rec+ strains and in recBC sbcB, recQ and recF mutants, including those with blocks of both the RecBCD and RecF pathway, was shown in our previous work to be similar to adaptive mutagenesis: in this case, practically each cell forms a recombinant on a selective medium. In this work, mutants for ruv genes were found to differ in this respect, forming segregants at a frequency that was decreased by several orders of magnitude. These data confirm the conclusion that the genetic exchange in duplications proceeds through a special pathway of adaptive (or replicative) recombination connected with DNA replication. Upon selection of recombinants under conditions of thymine starvation, recombination cannot also be induced in ruv mutants. The recombinogenic effect of thymine starvation seems to occur at late stages of recombination, which are controlled by ruvABC genes.

Adenosine Triphosphatases↗
PubMed2001

[Genetic explanation for vertical evolution].

The genetic theory of natural selection proposed by Fisher takes into account differential reproduction success of organisms, which may be estimated by using the Malthusian parameter as fitness. However, the minimum possible value of this parameter depends on ecological stability of an organism, which determines the probability of the survival and participation in reproduction for each viable offspring. In the course of vertical evolution, leading to an increase in the level of biological organization, ecological stability of organisms increases, and this might be accompanied by a decrease in their fitness. In the macroevolutionary process, alterations in ecological stability of organisms, including those responsible for an increase in the level of biological organization, are basic and primary changes whereas alterations in fitness are additional and secondary.

Adaptation, Physiological↗
PubMed2001

[Homologous recombination and chromosomal rearrangements in Escherichia coli strains carrying a heterozygous tandem duplication].

Heterozygous tandem duplications formed in conjugational matings in Escherichia coli provides a convenient model system for studying the evolution of bacterial chromosome. Heterozygous duplications segregate various classes of haploid and diploid recombinants that appear as a result of unequal crossing over between sister chromosomes. In this work, an extended tandem duplication in the deo operon of E. coli carrying deoA deoB::Tn5/deoC deoD thr::Tn9 alleles was examined. Recombination between homologous DNA repeats in the duplication was studied in strains carrying different combinations of recBC, sbcBC, recB::Tn10, recQ::Tn3 mutations. The frequency of recombination between homologous DNA repeats was very high in all strains and did not decrease when the RecBCD and RecF recombinational pathways were simultaneously damaged in strains with the recB sbcBC recQ (or recF) genotype. It is assumed that unequal crossing over between direct DNA repeats in duplications may proceed through a particular pathway of "adaptive" recombination.

Alleles↗
PubMed2000

[Adaptation, ecological stability and the evolution of diploid organisms].

The possibility of the existence of an organism under different environmental conditions is determined by its ecological stability. This parameter can be expressed as the product of the average life span corresponding species and the probability of an organism's participation in reproduction. If ecological conditions are not substantially altered, regulatory selection provides an increase in fitness of an organism in a certain direction of adaptation. It is supposed that the process of regulatory selection is accompanied by the accumulation of mutations occurring in regulatory genes and mutations in regulatory regions of structural genes which correct the effect of the former mutations. An alteration in ecological stability occurs when the conditions of population existence are changed and is usually accompanied by a decrease in the fitness level earlier achieved. Thus, an increase in organisms' ecological stability is achieved by hybridization between populations of different origin and is accompanied by a decrease in fitness due to outbreeding depression. Under conditions of inbreeding, ecological stability is decreased due to the segregation, in the homozygous state, of recessive alleles of adaptive genes that have not yet reached the stage of evolutionary fixation. Diploidy is a factor allowing organisms to improve their ecological stability in every new generation.

Adaptation, Biological↗
PubMed2000

[Homologous recombination between direct repeats of chromosomal segments comprising heterozygotic duplications in Escherichia coli].

In conjugational matings between double mutants for the deo operon of Escherichia coli, haploid recombinants and extended tandem duplications deoC deoD/deoA deoB::Tn5 with the DeoC+DeoA+DeoB+DeoD- phenotype are formed (the deoD+ allele is not expressed due to the polar effect of the Tn5 insertion). Selection for the expression of the recessive deoC deoD alleles (in the thyA genome) leads to the segregation of haploid clones by duplications and also of clones that retain the diploidy but that are homozygous for deoC deoD. In addition to haploids, diploid clones retaining the duplications have also been found among the DeoD+ segregants. The phenotype of segregants retaining the duplication shows that they were formed by an unequal exchange between sister chromosomes. A comparison of segregation frequency of haploid and diploid DeoD+ clones in rec+ and recBC sbcB sbcC strains shows that duplications in the rec+ genome are more stable. On this basis, it is assumed that the RecBCD pathway possibly makes a greater contribution than the RecF pathway to the preservation of heterozygous duplications playing an important role in the evolution of prokaryotes.

Chromosomes, Bacterial↗
PubMed1999

[Formation of the heterozygous tandem duplication in the process of conjugation recombination in Escherichia coli: study of the effect of mutations for the recQ, uvrD, and recJ genes].

Stable tandem duplications were shown to originate from conjugational recombination between Escherichia coli HfrH strains carrying mutations for the deo operon. The duplications deoC deoD/deoA deoB::Tn5 usually constitute approximately 5% of the Deo+ offspring. The effect of mutations for the recQ, uvrD, and recJ genes on the frequency of duplications was studied. The CM1563 strain carrying the recQ mutation was shown to give, as a recipient, 20% of duplications in the Deo+ offspring. However, this property of CM1563 seems to depend on the presence of a spontaneous mutation of unknown nature, which also increased UV sensitivity of bacteria. The recQ mutation itself increased the frequency of duplications by less than 50%. The recJ mutation did not virtually affect the frequency of duplications. The uvrD mutation possessing the recombinogenic effect was shown to increase the frequency of deo+ recombinants and simultaneously decrease the frequency of duplications. Tandem duplications are assumed to be normal intermediates of multi-stage conjugational recombination initiated by the integration of the proximal region of the Hfr chromosome into different nonhomologous regions of the recipient chromosome.

Conjugation, Genetic↗
PubMed1998

Isolation and analysis of UV and radio-resistant bacteria from Chernobyl.

The accident at the Chernobyl nuclear power station in 1986 led to the dispersal of large amounts of a variety of radioactive materials, most importantly uranium, plutonium, 137Cs, 131I and 90Sr, over very large distances estimated to reach as far as Sweden, Norway, Turkey and possibly the USA. As a consequence, the soil on which the radioactive materials fell was contaminated and the degree of contamination varied with distance from the station, the direction and strength of the wind and the amount of atmospheric scavenging by rainfall at that time. Some of the radioactive materials have left a significant impact on mankind in the form of chromosomal aberrations including trisomy, various forms of cancers and death, whilst others are still in the ground where they will remain for a prolonged period to continue to exert their effects. Likewise, microbes living in the soil and exposed to radioactive materials may have been affected in a number of ways; some perished, and others survived due to the acquisition of advantageous mutation. Six years after the accident, soil samples contaminated with different levels of radioactivity were obtained from five regions within a 30 km radius of the nuclear power plant. From these soil samples spore-forming bacilli were isolated, quantified, identified and tested for resistance to X-rays, UVC and 4-nitroquinoline 1-oxide (4NQO). As a control, spore-forming bacilli were obtained from 'Zeleny mys' (an area 50 km south-east of the power station and emitting basal levels of radioactivity). A mutant of Escherichia coli hyper-resistant to a variety of DNA-damaging agents and its parent strain were also included in the study. Analysis of results reveals that a proportion of isolates of the same species from near the power station and the E. coli mutant SA236 were more resistant to X-rays, UVC and 4NQO compared with isolates from the control site and the E. coli parent strain, KL14, respectively.

4-Nitroquinoline-1-oxide↗
PubMed1998

[The nature of adaptive evolutionary changes: fitness and potential].

Ecological potential of an individual can be defined as its viability in the broad sense including the ability to reproduce in various environments. From the biological viewpoint, ecological potential as a fundamental property of an organism is more important than fitness in the genetic sense, which is estimated as the relative rate of reproduction. In essence, fitness reflects the level of implementation of the biological potential. In the process of evolution, regulatory selection results in an increase of fitness: selected forms reproduce more successfully as the population size increases. By contrast, individuals with high ecological potential are more advantageous when the population size decreases, because the probability of their survival in adverse environments is high. Thus, high levels of fitness and ecological potential are achieved via operation of different types of selection.

Adaptation, Physiological↗
PubMed1998

[Possible function and origin of crossing over].

Crossing over to repair genetic material via exchange probably emerged at the initial stages of organic evolution, earlier than the appearance of the DNA molecule in its present form. In that period, nitrous bases existed as free molecules, although, like in double-helical DNA, they formed aggregates. The electrochemical characteristics of pyrimidines differ from one another to a greater extent than those of purines, which are almost electrically neutral. Therefore, it is possible that the DNA electrostatic balance is accounted for by nonspecific interaction between pyrimidine bases. The data obtained by Nussinov et al. indicate that, in homooligomers, the arrangement of pyrimidine bases in opposite DNA strands exhibits some restrictions with respect to their mutual positions. In functioning DNA, the electrostatic balance of pyrimidine arrangement in complementary strands may favor rapid transitions of the molecule between an open helix and the original state. It is supposed that crossing over restores the electrostatically balanced spatial arrangement of pyrimidine homooligomers and, hence, the functional activity of the entire DNA molecule.

Crossing Over, Genetic↗