The chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus uncovers patterns of genome evolution in mosquitoes

BACKGROUND

Understanding genome organization and evolution is important for species involved in transmission of human diseases, such as mosquitoes. Anophelinae and Culicinae subfamilies of mosquitoes show striking differences in genome sizes, sex chromosome arrangements, behavior, and ability to transmit pathogens. However, the genomic basis of these differences is not fully understood.

METHODS

In this study, we used a combination of advanced genome technologies such as Oxford Nanopore Technology sequencing, Hi-C scaffolding, Bionano, and cytogenetic mapping to develop an improved chromosome-scale genome assembly for the West Nile vector Culex quinquefasciatus.

RESULTS

We then used this assembly to annotate odorant receptors, odorant binding proteins, and transposable elements. A genomic region containing male-specific sequences on chromosome 1 and a polymorphic inversion on chromosome 3 were identified in the Cx. quinquefasciatus genome. In addition, the genome of Cx. quinquefasciatus was compared with the genomes of other mosquitoes such as malaria vectors An. coluzzi and An. albimanus, and the vector of arboviruses Ae. aegypti. Our work confirms significant expansion of the two chemosensory gene families in Cx. quinquefasciatus, as well as a significant increase and relocation of the transposable elements in both Cx. quinquefasciatus and Ae. aegypti relative to the Anophelines. Phylogenetic analysis clarifies the divergence time between the mosquito species. Our study provides new insights into chromosomal evolution in mosquitoes and finds that the X chromosome of Anophelinae and the sex-determining chromosome 1 of Culicinae have a significantly higher rate of evolution than autosomes.

CONCLUSION

The improved Cx. quinquefasciatus genome assembly uncovered new details of mosquito genome evolution and has the potential to speed up the development of novel vector control strategies.

The misregulation of mitochondria-associated genes caused by GAGA-factor lack promotes autophagic germ cell death in Drosophila testes

The Drosophila GAGA-factor encoded by the Trithorax-like (Trl) gene is DNA-binding protein with unusually wide range of applications in diverse cell contexts. In Drosophila spermatogenesis, reduced GAGA expression caused by Trl mutations induces mass autophagy leading to germ cell death. In this work, we investigated the contribution of mitochondrial abnormalities to autophagic germ cell death in Trl gene mutants. Using a cytological approach, in combination with an analysis of high-throughput RNA sequencing (RNA-seq) data, we demonstrated that the GAGA deficiency led to considerable defects in mitochondrial ultrastructure, by causing misregulation of GAGA target genes encoding essential components of mitochondrial molecular machinery. Mitochondrial anomalies induced excessive production of reactive oxygen species and their release into the cytoplasm, thereby provoking oxidative stress. Changes in transcription levels of some GAGA-independent genes in the Trl mutants indicated that testis cells experience ATP deficiency and metabolic aberrations, that may trigger extensive autophagy progressing to cell death.

Patterns of genetic differentiation imply distinct phylogeographic history of the mosquito species Anopheles messeae and Anopheles daciae in Eurasia

Detailed knowledge of phylogeography is important for control of mosquito species involved in the transmission of human infectious diseases. Anopheles messeae is a geographically widespread and genetically diverse dominant vector of malaria in Eurasia. A closely related species, An. daciae, was originally distinguished from An. messeae based on five nucleotide substitutions in its ribosomal DNA (rDNA). However, the patterns of phylogeographic history of these species in Eurasia remain poorly understood. Here, using internal transcribed spacer 2 (ITS2) of rDNA and karyotyping for the species identification we determined the composition of five Anopheles species in 28 locations in Eurasia. Based on the frequencies of 11 polymorphic chromosomal inversions used as genetic markers, a large-scale population genetics analysis was performed of 1932 mosquitoes identified as An. messeae, An. daciae and their hybrids. The largest genetic differences between the species were detected in the X sex chromosome suggesting a potential involvement of this chromosome in speciation. The frequencies of autosomal inversions in the same locations differed by 13%-45% between the species demonstrating a restricted gene flow between the species. Overall, An. messeae was identified as a diverse species with a more complex population structure than An. daciae. The clinal gradients in frequencies of chromosomal inversions were determined in both species implicating their possible involvement in climate adaptations. The frequencies of hybrids were low ~1% in northern Europe but high up to 50% in south-eastern populations. Thus, our study revealed critical differences in patterns of phylogeographic history between An. messeae and An. daciae in Eurasia. This knowledge will help to predict the potential of the malaria transmission in the northern territories of the continent.

Phylogenomics revealed migration routes and adaptive radiation timing of Holarctic malaria mosquito species of the Maculipennis Group

BACKGROUND

Phylogenetic analyses of closely related species of mosquitoes are important for better understanding the evolution of traits contributing to transmission of vector-borne diseases. Six out of 41 dominant malaria vectors of the genus Anopheles in the world belong to the Maculipennis Group, which is subdivided into two Nearctic subgroups (Freeborni and Quadrimaculatus) and one Palearctic (Maculipennis) subgroup. Although previous studies considered the Nearctic subgroups as ancestral, details about their relationship with the Palearctic subgroup, and their migration times and routes from North America to Eurasia remain controversial. The Palearctic species An. beklemishevi is currently included in the Nearctic Quadrimaculatus subgroup adding to the uncertainties in mosquito systematics.

RESULTS

To reconstruct historic relationships in the Maculipennis Group, we conducted a phylogenomic analysis of 11 Palearctic and 2 Nearctic species based on sequences of 1271 orthologous genes. The analysis indicated that the Palearctic species An. beklemishevi clusters together with other Eurasian species and represents a basal lineage among them. Also, An. beklemishevi is related more closely to An. freeborni, which inhabits the Western United States, rather than to An. quadrimaculatus, a species from the Eastern United States. The time-calibrated tree suggests a migration of mosquitoes in the Maculipennis Group from North America to Eurasia about 20-25 million years ago through the Bering Land Bridge. A Hybridcheck analysis demonstrated highly significant signatures of introgression events between allopatric species An. labranchiae and An. beklemishevi. The analysis also identified ancestral introgression events between An. sacharovi and its Nearctic relative An. freeborni despite their current geographic isolation. The reconstructed phylogeny suggests that vector competence and the ability to enter complete diapause during winter evolved independently in different lineages of the Maculipennis Group.

CONCLUSIONS

Our phylogenomic analyses reveal migration routes and adaptive radiation timing of Holarctic malaria vectors and strongly support the inclusion of An. beklemishevi into the Maculipennis Subgroup. Detailed knowledge of the evolutionary history of the Maculipennis Subgroup provides a framework for examining the genomic changes related to ecological adaptation and susceptibility to human pathogens. These genomic variations may inform researchers about similar changes in the future providing insights into the patterns of disease transmission in Eurasia.

The complex role of transcription factor GAGA in germline death during Drosophila spermatogenesis: transcriptomic and bioinformatic analyses

The GAGA protein (also known as GAF) is a transcription factor encoded by the Trl gene in D. melanogaster. GAGA is involved in the regulation of transcription of many genes at all stages of fly development and life. Recently, we investigated the participation of GAGA in spermatogenesis and discovered that Trl mutants experience massive degradation of germline cells in the testes. Trl underexpression induces autophagic death of spermatocytes, thereby leading to reduced testis size. Here, we aimed to determine the role of the transcription factor GAGA in the regulation of ectopic germline cell death. We investigated how Trl underexpression affects gene expression in the testes. We identified 15,993 genes in three biological replicates of our RNA-seq analysis and compared transcript levels between hypomorphic Trl ^R85/Trl ³⁶² and Oregon testes. A total of 2,437 differentially expressed genes were found, including 1,686 upregulated and 751 downregulated genes. At the transcriptional level, we detected the development of cellular stress in the Trl-mutant testes: downregulation of the genes normally expressed in the testes (indicating slowed or abrogated spermatocyte differentiation) and increased expression of metabolic and proteolysis-related genes, including stress response long noncoding RNAs. Nonetheless, in the Flybase Gene Ontology lists of genes related to cell death, autophagy, or stress, there was no enrichment with GAGA-binding sites. Furthermore, we did not identify any specific GAGA-dependent cell death pathway that could regulate spermatocyte death. Thus, our data suggest that GAGA deficiency in male germline cells leads to an imbalance of metabolic processes, impaired mitochondrial function, and cell death due to cellular stress.

New Cytogenetic Photomap and Molecular Diagnostics for the Cryptic Species of the Malaria Mosquitoes Anopheles messeae and Anopheles daciae from Eurasia

The Eurasian malaria vector Anopheles messeae is a widely spread and genetically diverse species. Five widespread polymorphic chromosomal inversions were found in natural populations of this mosquito. A cryptic species, Anopheles daciae, was differentiated from An. messeae by the presence of several nucleotide substitutions in the Internal Transcribed Spacer 2 (ITS2) region of ribosomal DNA. However, because of the absence of a high-quality reference cytogenetic map, the inversion polymorphisms in An. daciae and An. messeae remain poorly understood. Moreover, a recently determined heterogeneity in ITS2 in An. daciae questioned the accuracy of the previously used Restriction Fragment Length Polymorphism (RFLP) assay for species diagnostics. In this study, a standard-universal cytogenetic map was constructed based on orcein stained images of chromosomes from salivary glands for population studies of the chromosomal inversions that can be used for both An. messeae and An. daciae. In addition, a new ITS2-RFLP approach for species diagnostics was developed. Both methods were applied to characterize inversion polymorphism in populations of An. messeae and An. daciae from a single location in Western Siberia in Russia. The analysis demonstrates that cryptic species are remarkably different in their frequencies of chromosomal inversion variants. Our study supports previous observations that An. messeae has higher inversion polymorphism in all autosomes than the cryptic species An. daciae.

Loss of Drosophila E3 Ubiquitin Ligase Hyd Promotes Extra Mitosis in Germline Cysts and Massive Cell Death During Oogenesis

The Drosophila hyperplastic disc (hyd) gene is the ortholog of mammalian tumor suppressor EDD, which is implicated in a wide variety of cellular processes, and its regulation is impaired in various tumors. It is a member of the highly conserved HECT family of E3 ubiquitin ligases, which directly attach ubiquitin to targeted substrates. In early works, it was shown that Drosophila Hyd may be a tumor suppressor because it is involved in the control of imaginal-disc cell proliferation and growth. In this study, we demonstrated that Hyd is also important for the regulation of female germ cell proliferation and that its depletion leads to additional germline cell mitoses. Furthermore, we revealed a previously unknown Hyd function associated with the maintenance of germ cells' viability. A reduction in hyd expression by either mutations or RNA interference resulted in large-scale germ cell death at different stages of oogenesis. Thus, the analysis of phenotypes arising from the hyd deficiency points to Hyd's role in the regulation of germline metabolic processes during oogenesis.

GAGA Regulates Border Cell Migration in Drosophila

Collective cell migration is a complex process that happens during normal development of many multicellular organisms, as well as during oncological transformations. In Drosophila oogenesis, a small set of follicle cells originally located at the anterior tip of each egg chamber become motile and migrate as a cluster through nurse cells toward the oocyte. These specialized cells are referred to as border cells (BCs) and provide a simple and convenient model system to study collective cell migration. The process is known to be complexly regulated at different levels and the product of the slow border cells (slbo) gene, the C/EBP transcription factor, is one of the key elements in this process. However, little is known about the regulation of slbo expression. On the other hand, the ubiquitously expressed transcription factor GAGA, which is encoded by the Trithorax-like (Trl) gene was previously demonstrated to be important for Drosophila oogenesis. Here, we found that Trl mutations cause substantial defects in BC migration. Partially, these defects are explained by the reduced level of slbo expression in BCs. Additionally, a strong genetic interaction between Trl and slbo mutants, along with the presence of putative GAGA binding sites within the slbo promoter and enhancer, suggests the direct regulation of this gene by GAGA. This idea is supported by the reduction in the slbo-Gal4-driven GFP expression within BC clusters in Trl mutant background. However, the inability of slbo overexpression to compensate defects in BC migration caused by Trl mutations suggests that there are other GAGA target genes contributing to this process. Taken together, the results define GAGA as another important regulator of BC migration in Drosophila oogenesis.

Chromosome and Genome Divergence between the Cryptic Eurasian Malaria Vector-Species Anopheles messeae and Anopheles daciae

Chromosomal inversions are important drivers of genome evolution. The Eurasian malaria vector Anophelesmesseae has five polymorphic inversions. A cryptic species, An. daciae, has been discriminated from An. messeae based on five fixed nucleotide substitutions in the internal transcribed spacer 2 (ITS2) of ribosomal DNA. However, the inversion polymorphism in An. daciae and the genome divergence between these species remain unexplored. In this study, we sequenced the ITS2 region and analyzed the inversion frequencies of 289 Anopheles larvae specimens collected from three locations in the Moscow region. Five individual genomes for each of the two species were sequenced. We determined that An. messeae and An. daciae differ from each other by the frequency of polymorphic inversions. Inversion X1 was fixed in An. messeae but polymorphic in An. daciae populations. The genome sequence comparison demonstrated genome-wide divergence between the species, especially pronounced on the inversion-rich X chromosome (mean Fst = 0.331). The frequency of polymorphic autosomal inversions was higher in An. messeae than in An. daciae. We conclude that the X chromosome inversions play an important role in the genomic differentiation between the species. Our study determined that An. messeae and An. daciae are closely related species with incomplete reproductive isolation.

Estimated resistance of the malaria mosquito Anopheles messeae s.l. to the insecticide malathion

Resistance to agricultural pesticides is an important and insufficiently studied concern for pest and disease vector research. We determined the malathion resistance of species in the Anopheles maculipennis mosquito group in a habitat near Novosibirsk, Russia. Most of the 851 individuals we measured were members of the Anopheles messeae s.l. complex (An. messeae and An. daciae species). The LC₅₀ value for malathion was 0.052 mg/L for the mixed specimens, and we failed to find any differences between species. The LC₅₀ value was within the range of values for malathion resistance of Anopheles stephensi and Culex quinquefasciatus. As the main resistance mechanism to organophosphate and carbamate insecticides is a single mononucleotide substitution in the ace-1 gene, we searched for this mutation in An. messeae s.l. and An. beklemishevi by restriction analysis. This mutation was not found in 347 of the specimens. We sequenced the ace-1 gene fragment for 24 specimens from four species of the Anopheles maculipennis group, including An. messeae, An. daciae, An. atroparvus, and An. beklemishevi. These specimens harbored a nucleotide substitution in the triplet where a mutation can lead to insecticide resistance, but this substitution would make it difficult for the resistance to develop. Since the studied specimens belong to branches of the Palearctic portion of the Anopheles maculipennis group, we suspect that all other Palearctic species of this group would have difficulties harboring the ace-1 mutation that would lead to organophosphate and carbamate resistance.

The reasons of Trithorax-like expression disturbance in Trl 3609 allele of Drosophila melanogaster

The regulatory region of the Trl gene was analyzed using the mutation Trl ³⁶⁰⁹ , resulting from the insertion of the P-element into the promoter region of the gene as well as mutations obtained on its basis. It is shown that two last transcription start sites, which are most often used in vitro in S2 cells, are almost not used in vivo. Experimental data indicate that transcription terminators in transposons play an important role in the decrease in the transcription level of the recipient gene.

[Role of GAGA Factor in Drosophila Primordial Germ Cell Migration and Gonad Development]

The GAGA protein of drosophila is a factor involved in epigenetic transcription regulation of a large gene group controlling developmental processes. In this paper, the role of GAGA factor in germ cell migration is demonstrated as well as its effect on the gonad development in drosophila embryogenesis. Mutations in the Trl gene, encoding GAGA factor, prematurely induces the active migration program and relocation of the primordial cells inward the embryo before the beginning of gastrulation. The germ cells that prematurely separated from the main group migrate ectopically, lose orientation, and stay out of gonad development. Expression pattern of the Trl gene suggests its activity in epithelial cells of the embryonic blastoderm, part of which contact primordial cells. Thus, GAGA factor influences migration of these cells in an indirect manner via their somatic environment.

A standard photomap of ovarian nurse cell chromosomes in the European malaria vector Anopheles atroparvus

Anopheles atroparvus (Diptera: Culicidae) is one of the main malaria vectors of the Maculipennis group in Europe. Cytogenetic analysis based on salivary gland chromosomes has been used in taxonomic and population genetic studies of mosquitoes from this group. However, a high-resolution cytogenetic map that could be used in physical genome mapping in An. atroparvus is still lacking. In the present study, a high-quality photomap of the polytene chromosomes from ovarian nurse cells of An. atroparvus was developed. Using fluorescent in situ hybridization, 10 genes from the five largest genomic supercontigs on the polytene chromosome were localized and 28% of the genome was anchored to the cytogenetic map. The study established chromosome arm homology between An. atroparvus and the major African malaria vector Anopheles gambiae, suggesting a whole-arm translocation between autosomes of these two species. The standard photomap constructed for ovarian nurse cell chromosomes of An. atroparvus will be useful for routine physical mapping. This map will assist in the development of a fine-scale chromosome-based genome assembly for this species and will also facilitate comparative and evolutionary genomics studies in the genus Anopheles.

GAGA protein is essential for male germ cell development in Drosophila

The Drosophila Trithorax-like (Trl) gene encodes a GAGA factor which regulates a number of developmentally important genes. In this study, we identify a new function for Drosophila GAGA factor in male germ cell development. Trl mutants carrying strong hypomorphic alleles display loss of primordial germ cells during their migration in embryogenesis and severe disruption in mitochondria structure during early spermatogenesis. The mutation resulted in small testes formation, a deficit of germ cells, abnormal mitochondrial morphogenesis, spermatocyte death through autophagy, and partial or complete male sterility. Pleiotropic mutation effects can be explained by the misexpression of GAGA factor target genes, the products of which are required for germ cell progression into mature sperm.

Capping protein beta is required for actin cytoskeleton organisation and cell migration during Drosophila oogenesis

Capping protein (CP) is a well-characterised actin-binding protein important for regulation of actin filament (AF) assembly. CP caps the barbed end of AFs, inhibiting the addition and loss of actin monomers. In Drosophila melanogaster, the gene encoding CP β-subunit is named capping protein beta (cpb; see Hopmann et al. [1996] J Cell Biol 133: 1293-305). The cpb level is reduced in the Drosophila bristle actin cytoskeleton and becomes disorganised with abnormal morphology. A reduced level of the CP protein in ovary results in disruption of oocyte determination, and disturbance of nurse cell (NC) cortical integrity and dumping. We describe novel defects appearing in cpb mutants during oogenesis, in which cpb plays an important role in border and centripetal follicle cell migration, ring canal development and cytoplasmic AF formation. The number of long cytoplasmic AFs was dramatically reduced in cpb hypomorphs and abnormal actin aggregates was seen on the inner side of NC membranes. A hypothesis to explain the formation of abnormal short-cut cytoplasmic AFs and actin aggregates in the cpb mutant NCs was proffered, along with a discussion of the reasons for 'dumpless' phenotype formation in the mutants.

Identification of functionally significant elements in the second intron of the Drosophila melanogaster Trithorax-like gene

It is known that a lot of genes having a distinct expression pattern require the complex system of transcription regulation. The regulatory regions of such genes can include not only the 5'-flanking regions, but also other regions, particularly their intron sequences. The Drosophila melanogaster Trithorax-like (Trl) gene, encoding the GAGA protein, is one of the genes with complex expression pattern. GAGA is one of a few transcription factors that can regulate gene expression at multiple levels. The GAGA-mediated modulation of expression seems to be linked with modifications of the chromatin structure. Nowadays, the regulatory potential of the Trl 5'-flanking region that contains multiple GAGA binding sites has been analyzed, but the presence of the functionally significant elements in other Trl regions has not been examined. We found DNase I hypersensitive sites, evolutionary-conserved sequences and numerous GAGA binding sites in the second intron of the Trl gene. Interestingly, these sequences localize in two main regions of the intron in immediate proximity to preferred regions of transposon insertions. Additionally, we revealed that deletion of the intron fragment in the Trl(1-72) mutants caused an alteration of the Trl expression pattern. These results allow us to conclude that the second intron of the Trl gene contains functionally significant elements.

[Main components of gene network controlling development of dorsal appendages of egg chorion in Drosophila melanogaster]

The development of dorsal appendages of the chorion (specialized structures in the D. melanogaster egg which look like elastic tubes and ensure the breathing of the developing embryo) is an attractive model for the study of genetic mechanisms of the development of organs and tissues, whose generation is based on transformation of the epithelial tissue in the tubular structures. In the present review, we present information on genes and proteins that control the development of dorsal appendages of the chorion. We demonstrated that three signal pathways (EGFR, DPP, and NOTCH), which are combined together in a single gene network through a number of components, play a major role in the development of dorsal appendages of the chorion.

Analysis and recognition of the GAGA transcription factor binding sites in Drosophila genes

The transcription factor GAGA, encoded by the gene Trl, controls expression of many Drosophila melanogaster genes. We have compiled the presently largest sample (120 sites) of published nucleotide sequences with experimentally confirmed binding to GAGA protein. Analysis of the sample has demonstrated that despite an apparent structural diversity of the GAGA sites, they fall into four distinct groups, namely, (1) the sites containing two GAG trinucleotides with no more than one nucleotide substitution in each and separated by spacers with a length of 1 or 3 nucleotides (GAGnGAG and GAGnnnGAG); (2) the sites containing a single GAGAG motif; (3) (GA)(3-9) microsatellite repeats; and (4) the sites corresponding to three and more direct repeats of GAG trinucleotide homolog and its inverted repeats separated by spacers of various lengths. Using the software package SITECON, the methods were elaborated for recognizing the sites of GAGnGAG (method 1) and GAGnnnGAG (method 2) types in DNA sequences. Experimental verification confirmed the ability to interact with the GAGA factor for 72% of the sites predicted using method 1 and 94.5% of the sites predicted by method 2. Application of the experimentally verified methods to analyzing the localization of potential GAGA binding sites in the target genes of this transcription factor has demonstrated that the 5'-untranslated regions (5'UTRs) and first introns are enriched for these sites (two-threefold relative to the average occurrence frequency in the D. melanogaster genome) as compared with a moderate enrichment (not exceeding 1.5-fold) of promoter regions (-4000/+200 bp or -1000/+100 bp).

[Maintenance of the patterns of expression of homeotic genes in the development of Drosophila melanogaster by proteins of the polycomb, trithorax, and ETP groups]

Proteins encoded by genes of the groups Polycomb (PcG), trithorax (trxG), and the Enhancer of Trithorax and Polycomb Group (ETP) are important regulators of expression of most developmental genes. Data concerning all currently described genes assigned to these groups are summarized in the review. Genetic interactions of these genes and phenotypical manifestation of their mutations are described. Data on the PcG, trxG, and ETP proteins are systemized. Questions are considered concerning the formation of multimeric complexes containing proteins of these groups, recruitment of these complexes to regulatory elements of target genes, and the mechanisms of activation/repression of gene expression.

[Influence of Drosophila melanogaster genotype on biological effects of endocymbiont Wolbachia (stamm wMelPop)]

Comparative analyses of symbiotic bacteria Wolbachia (stamm wMelPop reducing lifespan of flies) morphology in normal and mutant strains of Drosophila melanogaster as well as the influence of Wolbachia on the host cell ultrastructure have been done. Wolbachia infected D. melanogaster mutation strains Trithorax-like -- Trl362/TM3, Sb1 Ser y+ and Trlen82/TM3, Sb1 Ser y+ have been received by special flies crossing. Uninfected strain D. melanogaster white-1118 (w1118) have been obtained by antibiotic treatment of initially infected strain D. melanogaster [w]w1118. Complex of different methods and approaches let to investigate for the first time the morphology of cell structure before and after bacterial infection of insects and to value the bacterial presence effect on flies viability and reproduction of normal and mutant flies. Morphology af cytoplasmic compartments in early embryos and eggs layed by infected and uninfecyed females Trl362/TM3, Sb1 Ser y+ and Trlen82/TM3, Sb1 Ser y+ have been analyzed. Electron microscopy has shown that D. melanogaster embryos contain typical Wolbachia contacting with different host organelles that verify preservation of their functional activity. Atificial mitochondria and Wolbachia (wMelPop) of unusual morphology with defective bacterial membranes have been visualised in D. melanogaster [w]Trl362/TM3, Sb1 Ser y+. Wolbachia presence in ovarium cells from strains [w]Trl362/TM3, Sb1 Ser y+ and [w]Trlen82/TM3, Sb1 Ser y+ did not influence on eggs quantity layed by females. We have demonstrated for the first time that lifespan of infected and uninfected strains: D. melanogaster Trl362/TM3, Sb1 Ser y+ and Trlen82/TM3, Sb1 Ser y+ were similar. However the lifespan of imago from strain [w]w1118 was lower in comparison to those from strains Trl362/TM3, Sb1 Ser y+ and Trlen82/TM3, Sb1 Ser y+. It suggests that either chromosomal balancer TM3 or Trl mutation play an importance role in host-symbiotic relationship. Next experiments have revealed that lifespan of homozygotic flies decreased essentially and was close to lifespan of strain [w]w1118. Data obtained confirm that chromosomal balancer TM3 can affect on symbiont-host relationship.

[Systemic regulation of genetic and cytogenetic processes by a signal cascade of actin remodeling: locus agnostic in Drosophila]

The concept on systemic regulation of genetic and cytogenetic processes has acquired a new perspective after the completion of the Human Genome project, when the view on systemic realization of genetic activity in the dynamic spatial organization of the genome is the nucleus was generally accepted. This organization underlies plasticity of complex biological systems. Chromosome position within the nucleus determined both processes of normal development and the development of genomic diseases, i.e., changes according to the environmental requirements, current needs of the organism, and its individual experience. Nuclear actin has been envisioned as a main factor bridging three levels of the genome organization (nucleotide, structural, and spatial), due to its capability of (1) regulating transcription by activating all three classes of RNA polymerase; (2) participating in chromatin remodeling by interacting with numerous proteins; and (3) lining the nuclear membrane, determining the chromosome attachment points and regulating export from the nucleus. In view of this, the role of actin remodeling factors (LIMK1, cofilin, actin) in the development of neurodegenerative diseases, including prionic ones, and in the mechanisms of generation of genomic diseases, syndromes resulting from unequal recombination, has been intensely studied. Drosophila is a helpful model organism to determine the sequence of events in this system of hierarchical relationships. Using spontaneous and mutant variants of the agnostic locus, we have designed a model of the Williams syndrome, which also reproduces main diagnostic traits of neurodegenerative diseases.

[Molecular and genetic description of a new hypomorphic mutation of Trithorax-like gene and analysis of its effect on Drosophila melanogaster oogenesis]

The Trithorax-like (Trl) gene of Drosophila melanogaster encodes the multifunctional protein GAGA involved in many cellular processes. We have isolated and described a new hypomorphic mutation of the Trl gene--Trl(en82). The mutation is the insertion of a 1.4 kb P-element into the 5' untranslated region. Trl expression decreased in the ovaries of mutant flies by about 30%; however, it caused abnormalities. The Trl(en82) mutation combined with the null allele of Trl caused female sterility: the females laid a few small eggs with abnormal shape. Many egg chambers demonstrated abnormalities in the Trl(en82) mutants: the oocyte had a regular shape and intruded into the egg chamber region with nurse cells; the rapid transport of nurse cell cytoplasm into the oocyte was disturbed, which resulted in the "dumpless" phenotype of the chambers in mutants; follicular cells often did not completely cover the oocyte and concentrated on its posterior end; and the migration of centripetal cells was affected. We propose that the sterility of the Trl(en82) females is due to the abnormal functioning of follicular cells resulting from low Trl expression. This proposal is confirmed by normalizing the mutant phenotype of Trl(en82) females after the transfection of Trl cDNA. Note that even an insignificant decrease in Trl expression in such females seriously affected the somatic cell functioning, while a significant decrease in its expression in strong hypomorphic mutants affected both somatic and germline cells in the egg chambers.

[Basic aspects of ovarian development in Drosophila melanogaster]

Modern views of the development and structural organization of the female reproductive system in Drosophila melanogaster are reviewed. Special emphasis is placed on the generation and development of follicles in the germarium and the interactions of germline and somatic cells in the egg chamber. Detailed consideration is given to the main events that ensure and regulate the transport of mRNA, proteins, and organelles from nurse cells to the oocyte in the germarium and at later stages of egg chamber development.

[Effect of hypomorphic mutation in Trithorax-like gene on Drosophila melanogaster oogenesis]

We generated and characterized a new hypomorphic mutation of Drosophila melanogaster Trithorax-like (Trl) gene named Trl362. The Trl362 homozygous females are sterile and lay a small number of eggs; most embryos die at the early developmental stages. The transcriptional Trl level of adult Trl362 females was markedly lowered. Little or no GAGA protein, encoded by Trl@, was detected in the nurse cell nuclei. The ovaries of Trl362 females showed impairments, such considerable changes in the structure of both ovarioles and individual egg chambers. We believe that the observed ovarian defects in Trl362 mutants are mostly due to a decreased amount of GAGA protein in the germline cells. An increase of GAGA-519 protein caused by introduction of hsp83:GAGA-519 transgene against Trl362 background rescued partially the female fertility. It may well be that a decrease of GAGA protein in Trl362 germline cells leads to a defective expression of the genes regulated by transcription factor GAGA, whose products are essential for normal Drosophila oogenesis.

[Generation and analysis of novel mutations of the trithorax-like gene in Drosophila melanogaster]

The Trithorax-like (Trl) gene of Drosophila melanogaster encodes the multifunctional GAGA factor. The expression of Trl is known to depend on numerous factors, such as the organ, the tissue, the ontogenetic stage, and the ambient temperature. Apparently, this expression is controlled by a complex system of regulatory elements, which so far has been scarcely studied. Our preliminary results indicate that the second intron of the Trl gene bears functionally significant elements. To test this assumption, we generated 23 novel alleles of the gene via P-induced male recombination and analyzed them cytogenetically. Of these mutations, 13 (recessive lethals) are deletions, disrupting the coding gene region. Ten mutations (seven deletions and three duplications) remove parts of the second Trl intron only. Some of these mutant stocks exhibit lower viability at different temperatures. These results suggest that the second intron region harbors functionally significant elements. The deletion mapping results verified the localization of the Trl gene in the 70F1-2 region.

[Specific DNA sequences are associated with nuclear envelopes of pseudonurse cells in Drosophila melanogaster otu 11]

Nuclei of ovarian pseudonurse cells from the mutant strain of Drosophila melanogaster otu 11 are suitable for mapping the attachment of chromosomes to the nuclear envelope (NE). Loci in contact with the NE included region 20CD of the X chromosome, region 41 of chromosome 2, the proximal end of region 81 of chromosome 3, and region 101 of chromosome 4. In situ hybridization revealed that all 4 regions contained sequences homologous to clone lambda20p1.4. DNA of clone lambda20p1.4 was previously found to bind specifically to purified D. melanogaster lamins. These results suggest that specific DNA sequences are involved in attachment of chromosomes to NE in vivo.

[Architecture of the X chromosome, expression of LIM kinase 1, and recombination in the agnostic mutants of Drosophila: a model of human Williams syndrome]

As the Human Genome and Drosophila Genome Projects were completed, it became clear that functions of human disease-associated genes may be elucidated by studying the phenotypic expression of mutations affecting their structural or functional homologs in Drosophila. Genomic diseases were identified as a new class of human disorders. Their cause is recombination, which takes place at gene-flanking duplicons to generate chromosome aberrations such as deletions, duplications, inversions, and translocations. The resulting imbalance of the dosage of developmentally important genes arises at a frequency of 10(-3) (higher than the mutation rate of individual genes) and leads to syndromes with multiple manifestations, including cognitive defects. Genomic DNA fragments were cloned from the Drosophila melanogaster agnostic locus, whose mutations impair learning ability and memory. As a result, the locus was exactly localized in X-chromosome region 11A containing the LIM kinase 1 (LIMK1) gene (CG1848), which is conserved among many species. Hemizygosity for the LIMK1 gene, which is caused by recombination at neighboring extended repeats, underlies cognitive disorders in human Williams syndrome. LIMK1 is a component of the integrin signaling cascade, which regulates the functions of the actin cytoskeleton, synaptogenesis, and morphogenesis in the developing brain. Immunofluorescence analysis revealed LIMK1 in all subdomains of the central complex and the visual system of Drosophila melanogaster. Like in the human genome, the D. melanogaster region is flanked by numerous repeats, which were detected by molecular genetic methods and analysis of ectopic chromosome pairing. The repeats determined a higher rate of spontaneous and induced recombination. including unequal crossing over, in the agnostic gene region. Hence, the agnostic locus was considered as the first D. melanogaster model suitable for studying the genetic defect associated with Williams syndrome in human.

[The effect of some mutations in the Trl gene on mitosis in embryonal and larval tissues and egg chamber morphology in Drosophila melanogaster]

A study was made of three insertional mutations (Trl13C, Trls2325, and TrlEP(3)3184) located in the second intron of the Trithorax-like (Trl) gene for the GAGA transcription factor (GAF). Their cytological effects were analyzed in oogenesis, early embryonic development, and in larval development (96-108 h) in cells of nervous ganglia and imaginal disks. Notwithstanding an interallelic difference in expression, all three P-element insertions proved to be dominant as far as the examined parameters were concerned. The most substantial defects were the formation of "granular" chromatin during the interphase and mitosis and high proportions of cells with hypercondensed chromatin (which were arrested at the G2/M boundary) and cells with abnormal chromosome segregation. A higher frequency of egg chambers with trophocytes defective in number and in chromatin condensation was observed in females carrying the mutant Trl gene. The defects were assumed to result from poor coordination of the chromosome and cell cycles and, including, the nuclear and centrosomal cycles in embryonic development and the cycles of chromosome condensation and spindle formation in cells of larval imaginal disks and nervous ganglia.

[Molecular genetic analysis of Thrithorax-like gene encoded transcriptional factor GAGA in Drosophila melanogaster]

The Drosophila melanogaster Trithorax-like (Trl) gene is classed with the trx-G genes and codes for several isoforms of the GAGA transcription factor (GAF) which regulates expression of homeotic and numerous other genes. GAF acts as a transcriptional antirepressor, i.e., its interaction with nucleosomal DNA results in the open chromatin conformation in promoter gene regions. The regions thereby become accessible to other transcription factors. As mutations of the Trl gene enhance position effect variegation and disturb chromosome segregation in mitosis and meiosis, GAF is thought to play another, more significant role in determining the chromatin structure. To study the molecular basis of its pleiotropic effect, the Trl gene was subjected to a structural analysis. The genomic Trl gene was sequenced, the sizes of its exons and introns was established, and a complex structure of the 5' and 3' gene regions was demonstrated. The Trl13C, Trl62, DfTrlR67, and DfTrlR85 mutations were exactly mapped. In addition, four insertions of the P element were identified as Trl alleles (Trll(3)s2325, TrlEP(3)3184, TrlEP(3)3191, and TrlEP(3)3609). The viability at various developmental stages was studied in homozygotes for the Trl mutations and in interallelic compounds. The following lethality stages were established: hatching, (Trl13C, DfTrlR85, TrlEP(3)3609), larval molts (Trll(3)s2325), pupation, metamorphosis (DfTrlR67, Trl62), and eclosion (several compounds).

Expression of Drosophila melanogaster gene encoding transcription factor GAGA is tissue-specific and temperature-dependent

The GAGA factor (GAF) of Drosophila melanogaster encoded by the Trithorax-like gene is known to maintain expression of many Drosophila genes including homeotic ones, through configuration remodeling of local chromatin. The complicated transcript pattern of the GAF gene has been revealed at all stages of development. The study of GAF gene expression in whole flies and in salivary glands and in the brains with adjacent imaginal disks of the third instar larvae showed tissue-specific variations in transcript patterns and dependence of these patterns on the temperature of development (14-37 degrees C).

A molecular and cytogenetic analysis of lambda 20p7 fragment DNA from the proximal beta-heterochromatin of Drosophila melanogaster

A DNA fragment from the Drosophila melanogaster genome, cloned in lambda 20p7, was derived independently from clones lambda 20 and lambda L [Baiborodin et al., Genetika 29 (1993) 403-416; Sharakhov et al., Genetika 29 (1993) 392-402]. In situ hybridization of lambda 20p7 DNA to the chromosomes of D. melanogaster demonstrated preferential hybridization of the fragment to the chromocenter of polytene chromosomes and to pericentric heterochromatin of chromosomes II, IV and X at the metaphase plate. Copy number per haploid genome for lambda 20p7 was estimated as approximately 200. Based on Southern blotting, the major portion of this moderate repeat was localized in the region of a 5.5-kb HindIII digest. In situ hybridization to polytene chromosomes from strain fs(2)B trophocytes revealed that repeats homologous to lambda 20p7 are located in the proximal heterochromatin which undergoes structural reorganization during tissue differentiation. The nucleotide sequence of two segments of the clone lambda 20p7, Dm0.9 and Dm270, was determined. Sequence analysis of the 300-bp Dm0.9 clone revealed that it contains 21-bp and 30-bp d(GT/CA) sequences, a 12-bp AT box, recognition sites for nuclear factors NFI and SpI, and a set of inverted repeats. Clone Dm270 contains an open reading frame (ORF). The deduced amino acid (aa) sequence shares homology with the gag-like gene from type-I (R1) ribosomal DNA insertion and may code for a polypeptide of 10 kDa. The Dm270 sequence was found to contain two direct repeats showing homology to the human CENP-B box.

[The evolutionarily conserved gene Nc70F, expressed in nerve tissue of Drosophila melanogaster, encodes a protein homologous to the mouse delta transcription factor]

A cDNA copy of the Nc70F gene which is specifically expressed in Drosophila neural tissue was cloned and characterized. The gene has an open reading frame for the protein of 384 amino acids. The protein contains dimerization, DNA binding, activation and repression domains which are common for the eucaryotic transcription factors. However, the domain organization of the Nc70F protein has some peculiarities. The primary structure of the Nc70F product and other transcription factors were compared. High level of homology of Nc70F protein with the mouse delta transcription factor was found. The in situ hybridization on tissue section showed that the Nc70F gene expression is restricted to the central nerve system at all stages of Drosophila ontogenesis. By using Drosophila genomic and cDNA clones of Nc70F genes as probes, homologous transcripts were identified in the human poly(A) +RNA. The evolutionary conservative portion of this gene was localized in the 5-exons.

[Drosophila beta-heterochromatin: molecular organization and function. Characteristics of the DNA sequences from proximal beta-heterochromatin, associated with the nuclear envelope of Drosophila melanogaster]

To study the nucleotide sequence from the pericentric heterochromatin associated with the nuclear envelope, a residual DNA was extracted from the DNAse-treated nuclear lamins of Drosophila melanogaster tissue culture cell line Kc. The isolated DNA was cloned in lambda vector. The DNA library obtained was screened for the clones homologous to the pericentric heterochromatin. The experiments on in situ hybridization to the polytene chromosome of the nurse cell nuclei of the strain fs(2) B assigned the reiterated sequence, homologous to the lamin DNA clone, to the nuclear envelope associated regions of the proximal beta-heterochromatin which is known to undergo structural reorganization during cell differentiation. The nucleotide analysis of 300 bp from this sequence has established the presence of 21 bp and 300 bp d(GT/CA), 12 bp AT-box, the regions of recognition of the nuclear factor and the inverted repeats.

[Drosophila beta-heterochromatin: molecular organization and function. Cloning and molecular biological analysis of the lambda 20 DNA fragment from Drosophila melanogaster beta-heterochromatin]

To isolate the DNA sequences specific for the pericentric heterochromatin of Drosophila we used two CREST-autoimmune sera which bind in the Western-blot analysis the nuclear antigens of 30 kDa, 43 kDa and 45 kDa molecular weight. Cloning of the DNA fragments associated with these CREST-specific proteins of Drosophila resulted in obtaining 8 clones. One of them, lambda 20, hybridized mainly to the chromomcenter of polytene chromosomes. The further analysis indicated that the lambda 20 DNA might belong to the proximal beta-heterochromatin of the polytene chromosomes of D. melanogaster.

Cytogenetic and molecular aspects of position effect variegation in Drosophila melanogaster. IV. Underreplication of chromosomal material as a result of gene inactivation

A chromosomal region subjected to position effect variegation was analysed for possible DNA under-replication. DNA clones from the vicinity of the euheterochromatin junction and from a distance of hundreds of kilobase pairs were used as probes. Formation of compact blocks of chromatin is regarded as a characteristic feature of position effect variegation. It was shown that in T (1;2) dorvar7 males undergoing position effect variegation clones representing the DNA nearest to the breakpoint in 2B7 hybridized normally in situ to the compact blocks, providing evidence against DNA underreplication. In females the same clones did not hybridize to the compact blocks. These variations in hybridization may be related to different degrees of compaction of chromosome regions in males and females. A correlation between the degree of underreplication and the level of cell polyteny was shown by Southern-blot hybridization of a DNA probe from the 2B region to DNA from an X/O strain carrying Dp (1;1)pn2b displaying position effect variegation and compaction in 94% of salivary gland cells. Almost complete underreplication of the DNA of this region was found in salivary gland cells (with a maximal degree of polyteny), intermediate underreplication was found in fat body cells (with an intermediate degree of polyteny), and replication was not disturbed in diploid cells of the larval cephalic complex.

Cytogenetic and molecular aspects of position effect variegation in Drosophila melanogaster. II. Peculiarities of morphology and genetic activity of the 2B region in the T(1;2)dorvar7 chromosome in males

The peculiarities of compact blocks appearing as a consequence of position effect variegation were studied in male polytene chromosomes. In T(1;2)dorvar7/Y males the frequency of nuclei with a block in the 2B region was lower at all temperature and the chromosome region involved in compaction was shorter than in T(1;2)dorvar7/FM6 females. The fraction of nuclei with blocks was considerably increased in dorvar7/0 males, especially at 18 degrees C when the viability of these males is sharply reduced. The following features distinguish the blocks in males from those in females: (i) compaction of the 2B region in the males results in genetic inactivation only to a very small extent; (ii) the structure of the blocks in males is diffuse; and (iii) the male blocks still maintain some transcriptional activity as indicated by 3H-uridine incorporation. The temperature-sensitive period of both block formation and genetic inactivation was found to be during the first 3 h of embryonic development.

Electron microscopical analysis of Drosophila polytene chromosomes. III. Mapping of puffs developing from one band

Mapping of 16 regions of polytene chromosomes in which 18 one-band puffs develop was carried out with the use of electron microscopy (EM). In most cases a uniform decondensation of the whole band was observed. However, there were examples in which only a part of the band was activated (three puffs) or its right and left parts decondensed simultaneously (three puffs). Splitting of the band into two parts with their further decondensation was also found (one puff). This suggests structural and functional complexity of the bands. On the basis of the data obtained here and those published earlier, a classification of 52 puffs by the number of bands participating in their formation is given. Four classes numbering 22, 21, 7, 2 puffs, developing from 1, 2, 3 and 4 bands, respectively, are revealed. The data show that active chromosome regions are rather diverse in both the pattern of decondensation and expansion of the decondensed region, thus providing evidence of the informational complexity of the majority of active regions.

Electron microscopical analysis of Drosophila polytene chromosomes. II. Development of complex puffs

Data are presented of electron microscopic (EM) analysis of consecutive developmental stages of Drosophila melanogaster complex puffs, formed as a result of simultaneous decondensation of several bands. EM mapping principles proposed by us permitted more exact determination of the banding patterns of 19 regions in which 31 puffs develop. It is shown that 20 of them develop as a result of synchronous decondensation of two bands, 7 of three and 4 of one band. Three cases of two-band puff formation when one or both bands undergo partial decondensation are described. In the 50CF, 62CE, 63F and 71CF regions puffing zones are located closely adjacent to each other but the decondensation of separate band groups occurs at different puff stages (PS). These data are interpreted as activation of independently regulated DNA sequences. The decondensation of two or three adjacent bands during formation of the majority of the puffs occurs simultaneously in the very first stages of their development. It demonstrates synchronous activation of the material of several bands presumably affected by a common inductor. Bands adjacent to puffing centres also lose their clarity as the puff develops, probably due to "passive" decondensation connected with puff growth. The morphological data obtained suggest a complex genetic organisation of many puffs.