[Comparison of genotypic and biochemical characteristics of Streptococcus thermophilus strains isolated from sour milk products].

Overall, 72 strains of lactic acid thermophilic streptococci isolated from sour milk products manufactured in various regions of Russia and European countries were analyzed using classical microbiological and molecular biological methods. Physiological and biochemical properties and genetic diversity of these Streptococcus thermophilus strains were studied, and a comparative analysis of the nucleotide sequences of the 16S rRNA gene was conducted. It has been demonstrated that the homology of proximal parts of the 16S rRNA gene of all the strains studied towards one another and towards the reference strain ATCC19258 amounts to 100%.

[Comparative analysis of genome sizes in Streptococcus thermophilus strains].

Twenty-five Streptococcus thermophilus isolates were analyzed using pulse-field gel electrophoresis (PFGE) and gene restriction profile analysis techniques. 16S rRNA gene sequences of the isolates were almost 100% homologous. However, genomic fingerprinting analysis has shown variability in both genome size and restriction fragments length.

[The main postulate of the vertical evolution theory].

In the series of previous publications by the author (2000, 2002, 2005), a genetic model explaining the phenomenon of evolutionary progress was presented. In the present paper, this model is described in general terms. The model is based on views on regular changes of ecological potential of organisms on a macroevolutionary time scale.

[Genetic diversity of the natural strains of Streptococcus thermophilus].

The method of RAPD-PCR and comparative analysis of the PCR fingerprinting profiles similarity was used to characterize interspecific diversity of natural isolates of the lactic acid bacteria Streptococcus thermophilus. The strain genetic diversity was demonstrated using three primer variants, designed for different bacterial genome regions. The resolution of RAPD-PCR technique with different primers for identification at the species level and for certification at the strain level, was examined relative to the commercially important cultures of S.

[Studying recombination in heterozygous tandem duplications in Escherichia coli].

Our previous data showed that the principal pathway of the formation of selected recombinants in Escherichia coli strains carrying heterozygous tandem duplications is unequal crossing over between sister chromosomes. Data presented in this work showed that when DNA homology is not disturbed (due to transposon insertion), intragenic recombinants can occur directly in the region of recombination through intrachromomal exchange as well.

[Identification of industrial strains of lactic acid bacteria by methods of molecular genetic typing].

Various methods currently used in microbiology for determining taxonomic state of bacteria are discussed. The main focus is aimed at identifying and gene typing of lactic acid bacteria, used as starter cultures for industrial process of production of sour milk products, meat products, and probiotics.

[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.

[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.

[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.

[The importance of recombinations occuring in the process of DNA replication].

In the process of DNA replication in Escherichia coli, the unequal crossing over occurs between DNA direct repeats in sister chromosomes. Such exchanges lead to the formation of tandem duplications and, therefore, to an increase of gene expression. It is proposed that non-homologous cohesion of sister chromosomes and unequal crossing over occur if the movement of replication fork is stopped.

[The lactic acid enterococci Enterococcus faecium and Enterococcus durans: nucleotide sequence diversity in 16S rRNA genes].

Among the strains used as starters for making sour milk products on the territory of the CIS, the bacteria Enterococcus faecium and Enterococcus durans are frequently found. In this work, we studied a new collection of lactic acid enterococci and also obtained more complete data on the nucleotide sequences of 16S rRNA genes in some strains studied earlier and found that most strains had certain distinctions in their 16S rRNA genes as compared with the E. durans and E.

[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.

[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.

[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.

[Adaptation and ecological resistance].

The notion fitness, widely used in genetics usually serves to measure a relative rate of organism reproduction. Another important character of an organism is its ecological resistance which is basically the product of macroevolution. It can be determined as a probability of an organism survival and participation in reproduction of the species.

[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.

[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.

[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.

[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.

[Divergence in the level of DNA hybridization and formation of sibling species in the lactic acid bacteria Streptococcus thermophilus].

Previously, five distinct groups with 80-90% intragroup DNA homology values were revealed among 19 lactic acid-producing bacterial strains. The study of 39 new strains of thermophilic streptococci in the present work allowed us to reveal the sixth DNA homology group. The nine strains of this group are similar, at 55-70% DNA homology levels, to the type strain S.

[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.

[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.