T. M. Grishaeva

Similarity of the domain structure of proteins as a basis for the conservation of meiosis.

Meiosis is conserved in all eucaryotic kingdoms, and homologous rows of variability are revealed for the cytological traits of meiosis. To find the nature of these phenomenons, we reviewed the most-studied meiosis-specific proteins and studied them with the methods of bioinformatics. We found that synaptonemal complex proteins have no homology of amino-acid sequence, but are similar in the domain organization and three-dimensional (3D) structure of functionally important domains in budding yeast, nematode, Drosophila, Arabidopsis, and human. Recombination proteins of Rad51/Dmc1 family are conserved to the extent which permits them to make filamentous single-strand deoxyribonucleic acid (ssDNA)-protein intermediates of meiotic recombination. The same structural principles are valid for conservation of the ultrastructure of kinetochores, cell gap contacts, and nuclear pore complexes, such as in the cases when ultrastructure 3D parameters are important for the function. We suggest that self-assembly of protein molecules plays a significant role in building-up of all biological structures mentioned.

Conservation and Variability of Synaptonemal Complex Proteins in Phylogenesis of Eukaryotes

The problems of the origin and evolution of meiosis include the enigmatic variability of the synaptonemal complexes (SCs) which, being morphology similar, consist of different proteins in different eukaryotic phyla. Using bioinformatics methods, we monitored all available eukaryotic proteomes to find proteins similar to known SC proteins of model organisms. We found proteins similar to SC lateral element (LE) proteins and possessing the HORMA domain in the majority of the eukaryotic taxa and assume them the most ancient among all SC proteins. Vertebrate LE proteins SYCP2, SYCP3, and SC65 proved to have related proteins in many invertebrate taxa. Proteins of SC central space are most evolutionarily variable. It means that different protein-protein interactions can exist to connect LEs. Proteins similar to the known SC proteins were not found in Euglenophyta, Chrysophyta, Charophyta, Xanthophyta, Dinoflagellata, and primitive Coelomata. We conclude that different proteins whose common feature is the presence of domains with a certain conformation are involved in the formation of the SC in different eukaryotic phyla. This permits a targeted search for orthologs of the SC proteins using phylogenetic trees. Here we consider example of phylogenetic trees for protozoans, fungi, algae, mosses, and flowering plants.

Comparative Genomics and Proteomics of Drosophila, Brenner's Nematode, and Arabidopsis: Identification of Functionally Similar Genes and Proteins of Meiotic Chromosome Synapsis

The published principles of computer analysis of genomes and protein sets in taxonomically distant eukaryotes are expounded. The authors developed a search strategy to identify in genomes of such organisms genes and proteins nonhomologous in primary structure but having similar functions in cells dividing by meiosis. This strategy based on the combined principles of genomics, proteomics, and morphometric analysis of subcellular structures was applied to a computer search for genes encoding the proteins of synaptonemal complexes in genomes of Drosophila melanogaster, the nematode Caenorhabditis elegans, and the plant Arabidopsis thaliana. These proteins proved to be functionally similar to their counterparts in yeast Saccharomyces cerevisiae (protein Zip1p) and mammals (protein SCP1).

Gene CG17604 of Drosophila melanogaster May Be a Functional Homolog of Yeast Gene ZIP1 and Mammal Gene SCP1 (SYCP1) Encoding Proteins of the Synaptonemal Complex

From data on the molecular organization of transverse filament proteins of the synaptonemal complex (SC)—Zip1 in yeast and SCP1 in mammals—and on the width of the SC central space in these organisms and in Drosophila, the putative molecular structure and size of a transverse filament protein of the SC in Drosophila has been inferred. Using genetic and molecular databases and software from the Internet, we carried out in silico screening for a candidate gene for the Drosophila transverse filament protein. As a most likely candidate, gene c(3)G was chosen. The search in the 250-kb region overlapping the locus of this gene (sections 88E-89B) and containing 78 predicted genes has revealed only one gene,CG17604, whose protein meets all requirements for the transverse filament protein of the SC. It was suggested that gene CG17604is gene c(3)G. In this case, genec(3)G must be localized in section 89A7-8 of the cytological map of Drosophila melanogaster.

[In silico identification and characterization of meiotic DNA: AluJb possibly participates in the attachment of chromatin loops to synaptonemal complex].

Earlier, using bioinformatic methods, we reported the identification of repeated DNA sequences (RSs), presumably responsible for the attachment of chromatin loops to the lateral elements of synaptonemal complex in meiotic chromosomes. In the present study, consensus sequences for this class of RS were identified. It was demonstrated that at least part of these sequences belonged to the AluJb subfamily of Alu sequences. The Alu copies distribution along the major human histocompatibility complex (MHC) and their spatial separation from the sites of meiotic recombination was examined. It was demonstrated that simple sequences, like (GT/CA)n, were flanking meiotic recombination sites. A model of the RS organization in meiotic chromosome, most efficiently linking experimental data on the meiotic recombination in MHC and the in silico data on the RS localization (the coefficient of multiple correlation, r = 0.92) is suggested.

Evolutionary conservation of recombination proteins and variability of meiosis-specific proteins of chromosomes

A comparison of amino acid sequences is performed for orthologs to the meiosis-specific proteins in humans and seven other species, including animals, fungi, and plants that serve as models for the study of molecular mechanisms of meiosis. It is demonstrated that the RAD51 recombination mediator protein is the most conserved of the studied proteins. Its meiotic homolog DMC1 is less conserved, like the MHL1 mismatch-repair protein. The meiosis-specific SPO11 endonuclease is the least conserved among the studied meiotic enzymes. Structural proteins of meiotic chromosomes are poorly conserved. REC8 meiotic cohesin has 6 times lower similarity in the organisms from different kingdoms than its somatic homolog RAD21. The intermediate conservation level is characteristic of the synaptonemal complex proteins containing HORMA domain. Two functional domains of SPO11 endonuclease and MutL Trans_MLH1 domain of MLH1 enzyme are equally or even less conserved than the whole proteins. HORMA functional domain of a number of synaptonemal complex proteins is only 2–3 times more conserved than the whole molecule. Thus, among the key meiotic proteins, the most conserved are proteins responsible for the accuracy of meiotic recombination. Cohesins, synaptonemal complex proteins, and meiosis-specific SPO11 endonuclease are less conserved even within their functional domains. Obviously, the meiosis-specific proteins have undergone independent evolution in different phylogenetic lineages of eukaryotes.

Characteristic Features of Induced Mutagenesis in Hybrid Dysgenesis Systems of Drosophila melanogaster

The mutagenic effect of low-dose gamma-irradiation was studied inDrosophila melanogaster systems of hybrid dysgenesis by estimating polytene chromosome rearrangements, recombination frequency, and viability at the embryonic and postembryonic developmental stages. A dose of gamma-irradiation which had no effect detectable by routine interstrain cross proved to significantly reduce the number of recombinants in the H–E and P–M systems and mortality at postembryonic stages. However, this combined effect was obtained if irradiation followed trasposition, i.e., it depended on the application sequence of the mutagenic factors. The reverse order of the mutagenic treatment led to summation of the effects: as compared to either control, the frequencies of the dominant lethal mutations as well as the larval and pupal mortality in F2 increased significantly (at the level of 99.9%). This allowed us to estimate the contribution of extremely low-dose gamma-irradiation into the mutagenic effect, which was impossible under routine conditions.

Bioinformatical analysis of eukaryotic shugoshins reveals meiosis-specific features of vertebrate shugoshins

Background Shugoshins (SGOs) are proteins that protect cohesins located at the centromeres of sister chromatids from their early cleavage during mitosis and meiosis in plants, fungi, and animals. Their function is to prevent premature sister-chromatid disjunction and segregation. The study focused on the structural differences among SGOs acting during mitosis and meiosis that cause differences in chromosome behavior in these two types of cell division in different organisms. Methods A bioinformatical analysis of protein domains, conserved amino acid motifs, and physicochemical properties of 32 proteins from 25 species of plants, fungi, and animals was performed. Results We identified a C-terminal amino acid motif that is highly evolutionarily conserved among the SGOs protecting centromere cohesion of sister chromatids in meiotic anaphase I, but not among mitotic SGOs. This meiotic motif is arginine-rich in vertebrates. SGOs differ in different eukaryotic kingdoms by the sets and locations of amino acid motifs and the number of α-helical regions in the protein molecule. Discussion These structural differences between meiotic and mitotic SGOs probably could be responsible for the prolonged SGOs resistance to degradation during meiotic metaphase I and anaphase I. We suggest that the “arginine comb” in C-end meiotic motifs is capable of interaction by hydrogen bonds with guanine bases in the minor groove of DNA helix, thus protecting SGOs from hydrolysis. Our findings support independent evolution of meiosis in different lineages of multicellular organisms.

On the origin of synaptonemal complex proteins. Search for related proteins in proteomes of algae, lower fungi, mosses, and protozoa

A search for proteins similar to known synaptonemal complex (SC) proteins of seven higher eukaryote species, from budding yeast to mice (which are widely used as models for the study of meiosis), was conducted in the proteomes of algae, mosses, lower fungi, and Protozoa, using bioinformatics methods. It was established that proteins containing the HORMA domain have the largest similarity with the SC proteins of model organisms in proteomes of green and brown algae, mosses, and a number of lower fungi, as well as Euglenozoa, Sporozoa, and some other unicellular eukaryotes. They are close to the proteins of the lateral elements of the SC of higher eukaryotes that also carry the HORMA domain. This domain recognizes the state of chromatin and recruits other proteins for SC construction.

Identification and Characterization in silico of Meiotic DNA

A method of in silico search for specific repetitive DNA sequences related to the synaptonemal complex (meiDNA) in mammalian genomes was developed. A study of the distribution of these repeats over chromosomes revealed their scarcity on the Y chromosome and a decrease in recombination frequency in regions enriched in meiDNA. The results are discussed in context of the model of the looplike meiotic chromosome organization during the formation of the synaptonemal complex.