Key Achievements

1. Using our developed supercomputer model of chordate evolution, we predicted that gene ENSXETG00000033176 is responsible for the loss of regenerative potential and development of the telencephalon in warm-blooded vertebrates compared to cold-blooded ones. Experimental studies of this gene at the IBCh RAS laboratory confirmed the prediction.
2. Applying the same model to rodents and primates, we identified genes absent in long-lived species but present in short-lived ones. We hypothesize these genes are associated with lifespan, which aligns well with physiological, anatomical, cancer-resistant, and other characteristics.
3. Through big data analysis, we statistically demonstrated that bacterial, archaeal, and algal plastid adaptation to environmental conditions (particularly temperature) correlates with specific changes in intergenic distances. For instance, high temperatures correspond to relatively small intergenic distances, while low temperatures correspond to larger ones.
4. We achieved clustering of proteins encoded in rhodophyte plastids, resulting in a refined classification within protein families. This revealed genes specific to red algal plastids. We predicted transcription regulation of the moeB gene by transcription factor Ycf28, encoded in red algal plastids.
5. We developed an efficient algorithm and software implementation for predicting ancestral chromosomal structures and their evolutionary scenarios. The program was used to reconstruct evolutionary pathways of plastid, mitochondrial, and eukaryotic nuclear gene chromosomal structures.
6. We classified and discovered new types of attenuator regulation at transcription and translation initiation levels, particularly in actinobacteria and alpha-proteobacteria. We were first to predict T-box-mediated translation initiation regulation and identified a novel attenuator type characterized by short distances (10-13 bp) between structural and leader genes, which we hypothesize relates to ribosome reinitialization during leader peptide translation. We conducted large-scale screening of all regulatory systems in actinobacteria and alpha-proteobacteria, predicting regulation of genes encoding proteins with PF00480 or PF14340 domains and hypothesizing their important role in sulfur metabolism.
7. We advanced the attenuator regulation model by incorporating DNA/RNA secondary structure dynamics, RNA triplexes, bacterial habitat temperature, and G-quadruplexes. The model was implemented as an efficient parallel computing program and validated experimentally.
8. We predicted co-regulation of all genes encoded in Toxoplasma gondii apicoplasts. Comparative analysis of apicoplast-targeted nuclear-encoded protein extensions revealed that T. gondii N-termini are on average 1.5 times longer than Neospora caninum and twice as long as Plasmodium falciparum. We proposed a hypothesis about coccidian apicoplast activity regulation through post-translational modification of excessively long N-termini in apicoplast-targeted proteins, playing a key role in coccidian reactivation via apicoplast reactivation. This hypothesis was recently confirmed experimentally.
9. We analyzed the complete mitochondrial genome of orthonectid Intoshia linei, placing it within the annelid crown group. Orthonectid position within annelids was further supported by synapomorphies shared between I. linei and annelid crown groups in mitochondrial proteins cox1, cytb, nad6, atp6, and by trnN-cox2 gene order. Orthonectids were previously considered a separate phylum. We substantiated our hypothesis that orthonectids are deviant annelids and studied the phylogenetic position of Dicyema sp.
10. We developed a mathematical model and efficient algorithm for reconstructing joint evolution of genomic elements and species considering diverse evolutionary events. The model comprises three modules: reconciliation of gene/protein and species phylogenetic trees, reconstruction of chromosomal rearrangement evolution, and joint scenarios of regulatory system, gene, and species evolution. The model was implemented as a supercomputing program.
11. We constructed evolutionary trees of eubacteria, plastids, and cyanobacteria (the latter aligned with species trees, enabling identification of species groups with plastids of common origin), trees of mitochondrial chromosomal structures in sporozoans and rhodophyte plastids, and seed plant plastid trees with minimal polytomy.
12. We predicted NtcA and NtcB regulons in cyanobacteria and studied direct repeat insertions in microevolution of seed plant mitochondria and plastids.
13. We developed a computational model of RNA polymerase competition in plastids and mitochondria, validated by known experiments on RNA polymerase competition in barley and Arabidopsis plastids. We predicted transcriptional regulation of plastid genes involved in sulfate transport in Viridiplantae. Applying the model to chordates, we proposed mechanisms for MELAS syndrome and thyroid hormone deficiency effects on phenotype.
14. We found an efficient algorithm reducing the NP-complete problem of weighted set partition into two equal-sum subsets to finding a special point on a hypersurface defined by a low-rank cubic form, yielding an efficient heuristic for the original problem.
15. We identified a pair of parallel hyperplanes in 30-dimensional space uniquely determined by unit cube vertices lying on each, without cube vertices but with integer points strictly between them. We also found a triple of such hyperplanes in 37-dimensional space.
16. We obtained recursive solutions to several descriptive set theory problems, including an explicit description of a simple uncountable number set containing no numbers that can be explicitly described or effectively defined.
17. We developed an efficient probabilistic algorithm reducing systems of linear equations to a single linear equation with relatively small integer coefficients having the same Boolean solutions as the original system, provided the first equation has few redundant Boolean solutions not satisfying the entire system.