[The Involvement of the Gagr Gene, a Domesticated gag Retrovirus Gene, in the Stress-Response Pathway in Different Drosophila Species].

The Gagr gene is a domesticated gag retroelement gene in Drosophila melanogaster, whose function is associated with the stress response. The protein products of the Gagr gene and its homologues in different Drosophila species have a highly conserved structure; however, they demonstrate variability in the promoter region of the gene, which is apparently associated with the gradual acquisition of a new function and involvement in new signaling pathways. In this work, we studied the effect of oxidative stress induced by ammonium persulfate on the survival of various species of the genus Drosophila (D. melanogaster, D. mauritiana, D. simulans, D. yakuba, D. teissieri, and D. pseudoobscura), analyzed the correlation between the structure of promoter regions and stress-induced changes in the expression of the Gagr gene and its homologues in different Drosophila species, and compared the stress-induced changes in the expression of oxidative stress markers: the Jak-STAT signaling pathway activator gene upd3, Jak-STAT pathway effector vir-1, and IMD signaling pathway target Rel. It was found that in D. simulans and D. mauritiana sensitivity to ammonium persulfate is significantly increased, which correlates with a reduced level of transcription of vir-1 gene orthologues. The latter is due to a decrease in the number of binding sites for the transcription factor STAT92E, a component of the Jak-STAT signaling pathway, in the vir-1 promoter region. Consistent changes in the expression of the Gagr, upd3, and vir-1 genes are observed in all species of the melanogaster subgroup, except for D. pseudoobscura, which indicates an increase in the role of Gagr in the regulation of stress response pathways during the phylogenesis of the genus Drosophila.

[A Study of the Fertility of a Drosophila melanogaster MS Strain with Impaired Transposition Control of the gypsy Mobile Element].

The flamenco locus is one of the main components of the piRNA pathway of regulation of mobile genetic elements (MGEs) in Drosophila melanogaster. Mutations at this locus lead to an increase in the transposition activity of MGEs and, as a result, to genetic instability. In this paper, the fertility of a genetically unstable MS strain obtained more than 25 years ago and characterized by a mutation in the flamenco locus and the presence of a functionally active copy of gypsy retrotransposon was investigated. Complex violations of the ovarian morphology were revealed in the MS strain in females: defects in the follicular layer and ring channels, as well as degradation of trophocytes, which in turn led to a decrease in reproductive abilities. Analysis of the MS strain transcriptome showed a decrease in the expression level of 40 genes encoding chorionic proteins and expression specificity at different stages of follicle development. In the F1 and F2 hybrid females from the crosses of MS females with wild type males, restoration of reproductive abilities was observed, despite the fact that half of the F2 females had the flamenco genotype and genetic instability caused by transposition of gypsy (according to the ovo^(D) test). Moreover, the frequency of gypsy transposition in the hybrid F2 females with the flamenco genotype doubled in comparison with the MS strain females. Thus, the MS strain had acquired partial suppression of the flamenco phenotype and accumulated several recessive mutations in the genes that control oogenesis after cultivation for over 25 years.

[On the problem of female infertility: A search for genetic markers].

In every one case out often, the reason behind female infertility turns out to be an orphan disease called 'hypogonadotropic hypogonadism', the single symptom of which is the reduced level of gonadotropins and, as a consequence, amenorrhea in females. Most often, hypogonadotropic hypogonadism is caused by disorder in secretion of gonadoliberin, the product of gene GNRH1. However, the disease is heterogeneous one, so it may origin from either genetic or non-genetic causes. To study the genetic component of the disease pathogenesis, we conducted molecular-genetic analysis of 11 gene-candidates controlling synthesis and secretion of gonadoliberin as well as several gene-candidates functioning as neurodevelopmental and neuroendocrine regulators. In the study participated a group of patients afflicted by hypogonadotropic hypogonadism of an isolated form (n = 10), and a control group of healthy women (n = 20). All women were of reproductive age, with no detected mutations in gene-candidates that could cause any pathological effect. The data on gene-candidates expression in white blood cells are indicative of an increased expression of gene GNRH1 in the sampled patients as compared to the control group (p < 0.05). Other genes demonstrate heterogeneous expression both in the patients group and the control group. Thus, increased expression of gene GNRH1 in blood cells appears to be associated with the isolated form of hypogonadotropic hypogonadism and, in prospect, may be used as one of the disease markers.

[Functional analysis of Grp and Iris, the gag and env domesticated errantivirus genes, in the Drosophila melanogaster genome].

Drosophila melanogaster is the only invertebrate that contains endogenous retroviruses, which are called errantiviruses. Two domesticated genes, Grp and Iris, which originate from errantivirus gag and env, respectively, have been found in the D. melanogaster genome. The functions performed by the genes in Drosophila are still unclear. To identify the functions of domesticated gag and env in the D. melanogaster genome, expression of Iris and Grp was studied in strains differing by the presence or absence of the functional gypsy errantivirus. In addition, the expression levels were measured after injection of gram-positive and gram-negative bacteria, which activate different immune response pathways, and exposure to various abiotic stress factors. The presence of functional D. melanogaster retrovirus gypsy was found to increase the Grp expression level in somatic tissues of the carcass, while exerting no effect on the Iris expression level. Activation of the immune response in D. melanogaster by bacteria Bacillus cereus increased the Grp expression level and did not affect Iris expression. As for the effects of abiotic stress factors (oxidative stress, starvation, and heat and cold stress), the Grp expression level increased in response to starvation in D. melanogaster females, and the Iris expression level was downregulated in heat shock and oxidative stress. Based on the findings, Grp was assumed to play a direct role in the immune response in D. melanogaster; Iris is not involved in immune responses, but and apparently performs a cell function that is inhibited in stress.

Expression of hp1 family genes and their plausible role in formation of flamenco phenotype in D. melanogaster.

Results of expression analysis of transcription of the flamenco locus that controls transposition of the mobile genetic element gypsy, RNA interference system genes ago3, zuc, aub, and HP1 heterochromatin protein family genes hp1a, hp1b, hp1c, hp1d (rhino), and hp1e in D. melanogaster SS strain mutant on the flamenco gene are presented. We show that the number of transcripts in the SS strain that are formed in the flamenco locus is unchanged in some freely chosen points, and this is different from the wild-type strain where a decreased number of transcripts is observed, which clearly is a result of processing of the flamenco locus primary transcript, a predecessor of piRNA. At the same time, expression of genes of the RNA interference system is not affected, but there is a reduced level of hp1d gene expression in ovary tissue. We suggest that the hp1d gene product is directly or indirectly involved in the flamenco locus primary transcript processing.

Domesticated retroviral GAG gene in Drosophila: new functions for an old gene.

The domestication of foreign genes is a powerful mechanism for new gene formation and genome evolution. It is known that domesticated retroviral gag genes in mammals not only take part in protecting against viral infection but also control cell division, apoptosis, function of the placenta, and other biological processes. In this study, we focused on the domesticated retroviral gag gene homolog (Grp) in the Drosophila melanogaster genome. According to the results of a bioinformatic analysis, the Grp gene product is primarily under purifying selection in Drosophilidae family. The Grp protein has been shown to be transmembrane. The Grp gene is expressed at the adult stage of D. melanogaster in gender-specific and tissue-specific manner. Also the Grp gene expression is increased in response to the gypsy retrovirus. A function of the protein as a component of the endosomic membrane is considered.

[Study of the transcriptional and transpositional activities of the Tirant retrotransposon in Drosophila melanogaster strains mutant for the flamenco locus].

Transpositions of the gypsy retrotransposon in the Drosophila melanogaster genome are controlled by the flamenco locus, which is represented as an accumulation of defective copies of transposable elements. In the present work, genetic control by the flamenco locus of the transcriptional and transpositional activities of the Tirant retrotransposon from the gypsy group was studied. Tissue-specific expression of Tirant was detected in the tissues of ovaries in a strain mutant for the flamenco locus. Tirant was found to be transpositionally active in isogenic D. melanogaster strains mutant for the flamenco locus. The sites of two new insertions have been localized by the method of subtractive hybridization. It has been concluded from the results obtained that the flamenco locus is involved in the genetic control of Tirant transpositions.

[Translational analysis of the Grp gene, a genomic homologue of the Gag gene of the gypsy retrotransposon of Drosophila melanogaster].

The only open reading frame (ORF) (CG4680) encoding the Gag related protein (Grp) gene, a homologue of gag retrotransposons with long terminal repeats (LTR retrotransposons) of the gypsy group, has been found in the Drosophila melanogaster genome. Earlier, it was shown that the gene was expressed at the transcriptional level only in adult D. melanogaster. The Grp gene has been demonstrated to be a functional gene in the D. melanogaster genome, bit its function is yet to be determined.

[Transcriptional analysis of the Grp gene, a genomic homolog of the retrotransposon gypsy gag gene, in Drosophila melanogaster].

In the present work, we studied the Grp gene (CG4680, Gag related protein) expression at the transcriptional level. It was found that at the embryonic and larval stages of D. melanogaster development the Grp expression proceeds at a low level, but it significantly increases at the adult stage. Adult individuals display a tissue-specific expression: an eleveated level of transcription is observed in the gut tissues, but not in the chitin carcass, head, and gonads. Since the gut may potentially be a primary barrier for the penetration of a viral infection, we conducted a comparative analysis of Grp gene transcription in D. melanogaster strains differing in the presence of active copies of the gypsy errantivirus and in the status of the flamenco gene controlling sensitivity to errantiviral infections. No noticeable differences in the level of Grp gene transcription were revealed. Thus, the Grp gene is not a pseudogene, but it is a functional gene of the D. melanogaster genome whose role remains to be elucidated.

Integration specificity of LTR-retrotransposons and retroviruses in the Drosophila melanogaster genome.

Integration of DNA copies in a host genome is a necessary stage in the life cycle of retroviruses and LTR-retrotransposons. There is still no clear understanding of integration specificity of retroelements into a target site. The selection of the target DNA is believed to potentially affect a number of factors such as transcriptional status, association with histones and other DNA-binding proteins, and DNA bending. The authors performed a comprehensive computer analysis of the integration specificity of Drosophila melanogaster LTR-retrotransposons and retroviruses including an analysis of the nucleotide composition of targets, terminal sequences of LTRs, and integrase sequences. A classification of LTR-retrotransposons based on the integration specificity was developed. All the LTR-retrotransposons of the gypsy group with three open frames (errantiviruses) and their derivatives with two open frames demonstrate strict specificity to a target DNA selection. Such specificity correlates with the structural features of the target DNA: bendability, A-philicity, or protein-induced deformability. The remaining LTR-retrotransposons (copia and BEL groups, blastopia and 412 subgroups of the gypsy group) do not show specificity of integration. Chromodomain is present in the integrase structures of blastopia and 412 subgroup LTR-retrotransposons and may facilitate the process of non-specific integration.

[Analysis of the structure and expression of the cluster of Drosophila melanogaster genes DIP1, CG32500, CG32819, and CG14476 in the flamenco gene region].

The flamenco gene controlling transpositions of the gypsy retrovirus is localized in the 20A1-3 region, in which eight open reading frames organized in a cluster were discovered: DIP1, three repeats of CG32500 and CG32819, and CG14476. Analysis of the genes composing the cluster indicates that their transcription in Drosophila melanogaster is a stage-specific process. Comparison of the expression of these genes in the strains OreR, SS, and MS having the flamenco phenotype and in the strain 413 having the flamenco+ phenotype revealed differences only for the DIP1 gene, transcription of this gene being altered only in the OreR strain. Thus, mutant flamenco alleles are differently expressed in different strains. The structural organization of the flamenco gene region was studied in different Drosophila species: D. sechellia, D. simulans, D. mauritiana, D. yakuba, D. erecta, D. virilis, D. ananassae, D. grimshawi, and D. pseudoobscura. The genes of the cluster were found to be highly conserved in genomes of different species, but in none of them, except D. sechellia, the structural organization of the region repeats the structure of the D. melanogaster cluster.

[Molecular phylogeny and systematics of Drosophila retrotransposons and retroviruses].

Full classification of Drosophila melanogaster retrotransposons with long terminal repeats (LTR-retrotransposons) has been recomposed, and their evolutional analysis in sequenced genomes of different species of drosophila and other arthropods has been carried out. D. melanogaster LTR-retrotransposons are divided in three groups: gypsy (one, two or three open reading frames - ORFs), copia (one ORF), BEL (one ORF). Gypsy group is divided into three subgroups. Subgroup I is underrepresented by retrotransposons-retroviruses with three ORFs and their derivatives which have lost the env gene (ORF3). Subgroup II is underrepresented by retrotransposons with two ORFs, subgroup III - by retrotransposons with one ORF. Comparative analysis of homologs of gypsy group LTR-retrotransposons evidences that subgroups I and II are only in genomes of Lepidoptera and Diptera. Gypsy group of LTR-retrotransposons with one and two ORFs are found in almost all genomes of arthropods. Most of the families of D. melanogaster gypsy group LTR-retrotransposons have close homologs in genomes of other species of drosophila. A degree of identity of retrotransposons sequences is correlated with a degree of relation between species of drosophila; it's evidences about vertical transmission of retrotransposons. Obvious cases of horizontal transfer of some mobile elements have been detected including retrotransposons without the env gene. Homologs of distinct ORFs of retrotransposons - genes gag and env - have been found. Gene-homolog of the gag gene - Grp (CG4680) - is under purifying selection; so it has an important function in drosophila genome.

[Analysis of the structure and expression of the DIP1 gene in Drosophila melanogaster strains mutant for the flamenco gene].

DIP1 gene transcription was analyzed with the use of RT-PCR in three Drosophila melanogaster strains with the flamenco- phenotype (flam(SS), flam(MS), and flam(Ore)) and in one flamenco+ strain at the stages of embryos (0-24 h), third-instar larvae, and adult flies. The mutant strains flam(SS) and flam(Ore) lack an active copy of transposon gypsy. Theflam(MS) strain was obtained by introducing an active copy of gypsy in flies of theflam(SS) strain and is characterized by a high rate of gypsy transpositions. The experiments showed that at least five forms of DIP1 gene transcripts are produced. The form of cDNA corresponding to CDS DIP1-d was discovered only in embryos. It was found that DIP1 gene transcription depends on the age of flies: at the larval stage the level of transcription is significantly reduced. However, no reduction of gene transcription is observed in theflam(Ore) strain. These results suggest that the flamenco- phenotype may be associated with an alteration of DIP1 gene transcription, as in differentflamenco- strains the DIP1 gene expression is changed differently.

[Molecular evolution of mobile elements of the gypsy group: a homolog of the gag gene in Drosophila].

Retrotransposons of the gypsy group of Drosophila melanogaster that are structurally similar to retroviruses of vertebrates occupy an important place among retroelements of eukaryotes. The infectious abilities of some retrotransposons of this group (gypsy, ZAM, and Idefix) have been demonstrated experimentally, and therefore they are true retroviruses. It is supposed that retrotransposons can evolve acquiring new components, the sources of which remain to be elucidated. In this work, the CG4680 gene (Gag related protein, Grp) homologous to gag of retrotransposons of the gypsy group has been identified in the genome of D. melanogaster and characterized. The Grp gene product has a highly conserved structure in different species of the Drosophilidae family and is under of stabilizing selection, which suggests its important genomic function in Drosophila. In view of the earlier data, it can be concluded that homologous genes of all components of gypsy retrotransposons are present in the Drosophila genome. These genes can be both precursors and products of domestication of retrovirus genes.

[Inversion of phototaxis in cells of Synechocystis sp. PCC 6803 determined by a mutation in the regulatory gene prqR].

Phototaxis, positive (movement toward the light source) or negative (from the light source) mediates the adaptation of cyanobacteria to varying wave lengths and illumination intensity. The transcription regulator PrqR of the family TetR is known as a repressor of the prqRA operon controlling resistance to the oxidative stress inducer methyl viologen in the cyanobacterium Synechocystis sp. PCC6803. However, it was shown in this work that mutation prqRL17Q affecting the DNA-binding domain of the PrqR protein, which causes derepression of the prqRA operon and enhances cell resistance to methyl viologen, additionally determines negative phototaxis induced with daylight and red light of low intensity. The inactivation of gene prqA did not affect cell motility in mutant PqR carrying mutation prqRL17Q and in the wild-type strain characterized by positive phototaxis appearing in response to the light of low intensity. Moreover, a mutant with deletion prqR did not differ from the wild-type strain with respect to phototaxis type suggesting that the specificity of the regulator protein was changed in cells carrying prqRL17Q mutation. Note that changes in transcription of pilA genes that control biogenesis of pili providing for cell motility were not detected in mutant PqR, and, in agreement with data of atomic force microscopy, the type of pili formation is identical in prqR mutants and the wild-type strain. Meanwhile, mutant PqR manifested a decrease in transcription of gene taxD1 encoding the photoreceptor of red light that is required for the positive phototaxis of cyanobacteria. These data imply that mutation prqRL17Q changes the specificity of the PrqR repressor protein and thereby affects the regulation of phototaxis at the level of photoperception and signal transduction in cells.

[Evolution of errantiviruses of Drosophila melanogaster. Strategy 2: from retroviruses to retrotransposons].

Drosophila melanogaster retrotransposons of the gypsy group are considered to be potential errantiviruses. Their infectivity is caused by the functional activity of the third open reading frame (ORF3) encoding the Env protein, which was probably captured from baculoviruses. Mobile genetic elements (MGEs) of the gypsy group can be conventionally divided into three subgroups: with three ORFs, with a defective ORF3, and without the ORF3. To establish the patterns of evolution of gypsy retrotransposons in D. melanogaster, the members of the three subgroups were examined. Structural analysis of retrotransposons opus and rover, which carry a defective ORF3, as well as retrotransposons Burdock, McClintock, qbert, and HMS-Beagle, which lack the ORF3, suggests that the evolution of these MGEs followed the pattern of loosing the ORF3. At the same time, an MGE of the same subgroup, Transpac, may be an ancestral form, which had acquired the env gene and gave rise to the first errantiviruses. The capture of the ORF3 by retrotransposons provided their conversion to a fundamentally new state. However, the ORF3 in the genome is not subjected to strong selective pressure, because it is not essential for intragenomic transpositions. Because of this, the process of its gradual loss seems quite natural.

[HB mobile element in the Drosophila melanogaster genome: structural and functional analyses].

The structure was analyzed for 60 annotated copies of the mobile genetic element (MGE) HB from the Drosophila melanogaster genome. The genomic distribution of HB copies was studied, and preferential insertion sites (hot spots) were identified, which presumably amount to several kilobases. Structural analysis of the open reading frame (ORF) and terminal repeats of HB was performed. All 26 HB copies retaining the ORF sequence have a stop codon in the same position. Consequently, the HB ORF proved indeed to code for an enzyme of 148 amino acid residues, relatively small for Tc1-family transposases. The ORF consensus sequence was established. HB{}1185 was identified as the only HB copy potentially coding for a functional protein. All 37 repeat-containing HB copies were analyzed. Of these, only four had functional terminal sequences, lacking, however, a functional transposase gene. A new 7762-bp copy of MGE roo was found in the D. melanogaster genome; the copy was earlier unavailable from databases and represents an insert in the HB{}1605 sequence.

[Characteristics of the structural organization of the DIP1 gene in Drosophila melanogaster strains mutant for the flamenco gene].

Molecular cloning of the DIP1 gene located in the 20A4-5 region has been performed from the following strains with the flamenco phenotype: flamSS (SS) and flamMS (MS) characterized by a high transposition rate of retrotransposon gypsy (mdg4), flampy + (P) carrying the insertion of a construction based on the P element into the region of the flamenco gene, and flamenco+. The results of restriction analysis and sequencing cloned DNA fragments has shown that strains flamSS, flamMS, flampy +(P), and flamenco+ considerably differ from one another in the structure of DIP1. Strains flamss and flamMS have no Dral restriction site at position 1765 in the coding region of the gene, specifically, in the domain determining the signal of the nuclear localization of the DIP1 protein. This mutation has been found to consist in a nucleotide substitution in the recognition site of DraI restriction endonuclease, which is transformed from TTTAAA into TTTAAG and, hence, is not recognized by the enzyme. This substitution changes codon AAA into AAG and is translationally insignificant, because both triplets encode the same amino acid, lysine. The Dral gene of strainsflamSS andflamMS has been found to contain a 182-bp insertion denoted IdSS (insertion in DIP1 strain SS); it is located in the second intron of the gene. The IdSS sequence is part of the open reading frame encoding the putative transposase of the mobile genetic element HB1 belonging to the Tcl/mariner family. This insertion is presumed to disturb the conformations of DNA and the chromosome, in particular, by forming loops, which alters the expression of DIPI and, probably, neighboring genes. In strains flamenco+ and flampy + (P), the IdSS insertion within the HB1 sequence is deleted. The deletion encompasses five C-terminal amino acid residues of the conserved domain and the entire C-terminal region of the putative HB1 transposase. The obtained data suggest that DIP1 is involved in the control of gypsy transpositions either directly or through interaction with other elements of the genome.

[Evolution from retrotransposons to retroviruses: origin of the env gene].

In genome of Drosophila melanogaster, various families of retrotransposons with different combination of functional domens and mechanisms of transposition are present. However only retrotransposons of gypsy family are retroviruses related to errantiviruses. Other families seemingly appeared as intermediate forms of retroviruses evolution. Despite the fact that the question on origin of retroviruses remains unclear, now the hypothesis of their origin from retrotransoposons can be considered the most consistent. Infectious properties of errantiviruses are linked to the presence of the third open reading frame (the env gene). Acquisition of the env gene conversed retrotransposons into retroviruses. So, origin of this gene is of special interest. Homologues of the env gene of errantiviruses are discovered in genomes of D. melanogaster, as well as in baculoviruses and in bacteria Wolbachia pipientis, the endosymbiont of Drosophila. It was shown that homologue of the env gene come to Wolbachia genome from Drosophila genome by horizontal transfer of the gypsy group retrotransposon. Thus, Wolbachia was not a donor of the env gene for errantiviruses. Seemingly, errantiviruses captured the baculoviral homologue of the env gene (f). However origin of the f gene is not clear. At the same time the env gene homologue in D. melanogaster genome exist (Iris). It must not be ruled out that the Iris gene was the source of the env gene of errantiviruses and baculoviruses.

[Precise excision of long terminal repeats of the gypsy (mdg4) retrotransposon of Drosophila melanogaster detected in Escherichia coli cells is explained by its integrase function].

An Escherichia coli model system was developed to estimate the capacity of the integrase of the Drosophila melanogaster retrotransposon gypsy (mdg4) for precise excision of the long terminal repeat (LTR) and, hence, the entire gypsy. The gypsy retrotransposon was cloned in the form of a PCR fragment in the pBlueScript II KS+ (pBSLTR) vector, and the region of the second open reading frame (INT ORF2) of this element encoding integrase was cloned under the lacZ promoter in the pUC19 vector and then recloned in pACYC184 compatible with pBSLTR. The LTR was cloned in such a manner that its precise excision from the recombinant plasmid led to the restoration of the nucleotide sequence and the function of the ORF of the lacZ gene contained in the vector; therefore, it was detected by the appearance of blue colonies on a medium containing X-gal upon IPTG induction. Upon IPTG induction of E. coli XL-1 Blue cells obtained by cotransformation with plasmids pACCint and pBSLTR on an X-gal-containing medium, blue clones appeared with a frequency of 1 x 10(-3) to 1 x 10(-4), the frequency of spontaneously appearing blue colonies not exceeding 10(-9) to 10(-8). The presence of blue colonies indicated that that the integrase encoded by the INT ORF2 (pACYC 184) fragment was active. After the expression of the integrase, it recognized and excised the gypsy LTR from pBSLTR, precisely restoring the nucleotide sequence and the function of the lacZ gene, which led to the expression of the beta-galactosidase enzymatic activity. PCR analysis confirmed that the LTR was excised precisely. Thus, the resultant biplasmid model system allowed precise excisions of the gypsy LTR from the target site to be detected. Apparently, the gypsy integrase affected not only the LTR of this mobile element, but also the host genome nucleotide sequences. The system is likely to have detected only some of the events occurring in E. coli cells. Thus, the integrase of gypsy is actually capable of not only transposing this element by inserting DNA copies of the gypsy retrotransposon to chromosomes of Drosophila, but also excising them, gypsy is excised via a precise mechanism, with the original nucleotide sequence of the target site being completely restored. The obtained data demonstrate the existence of alternative ways of the transposition of retrotransposons and, possibly, retroviruses, including gypsy (mdg4).